Development and Characterization of 18 Novel EST-SSRs from the Western Flower Thrips, Frankliniella occidentalis (Pergande)

PubMed Central

Yang, Xian-Ming; Sun, Jing-Tao; Xue, Xiao-Feng; Zhu, Wen-Chao; Hong, Xiao-Yue

2012-01-01

The western flower thrips, Frankliniella occidentalis (Pergande), is an invasive species and the most economically important pest within the insect order Thysanoptera. For a better understanding of the genetic makeup and migration patterns of F. occidentalis throughout the world, we characterized 18 novel polymorphic EST-derived microsatellites. The mutational mechanism of these EST-SSRs was also investigated to facilitate the selection of appropriate combinations of markers for population genetic studies. Genetic diversity of these novel markers was assessed in 96 individuals from three populations in China (Harbin, Dali, and Guiyang). The results showed that all these 18 loci were highly polymorphic; the number of alleles ranged from 2 to 15, with an average of 5.50 alleles per locus. The observed (HO) and expected (HE) heterozygosities ranged from 0.072 to 0.707 and 0.089 to 0.851, respectively. Furthermore, only two locus/population combinations (WFT144 in Dali and WFT50 in Guiyang) significantly deviated from Hardy–Weinberg equilibrium (HWE). Pairwise FST analysis showed a low but significant differentiation (0.026 < FST < 0.032) among all three pairwise population comparisons. Sequence analysis of alleles per locus revealed a complex mutational pattern of these EST-SSRs. Thus, these EST-SSRs are useful markers but greater attention should be paid to the mutational characteristics of these microsatellites when they are used in population genetic studies. PMID:22489130

Development and characterization of 18 novel EST-SSRs from the western flower Thrips, Frankliniella occidentalis (Pergande).

PubMed

Yang, Xian-Ming; Sun, Jing-Tao; Xue, Xiao-Feng; Zhu, Wen-Chao; Hong, Xiao-Yue

2012-01-01

The western flower thrips, Frankliniella occidentalis (Pergande), is an invasive species and the most economically important pest within the insect order Thysanoptera. For a better understanding of the genetic makeup and migration patterns of F. occidentalis throughout the world, we characterized 18 novel polymorphic EST-derived microsatellites. The mutational mechanism of these EST-SSRs was also investigated to facilitate the selection of appropriate combinations of markers for population genetic studies. Genetic diversity of these novel markers was assessed in 96 individuals from three populations in China (Harbin, Dali, and Guiyang). The results showed that all these 18 loci were highly polymorphic; the number of alleles ranged from 2 to 15, with an average of 5.50 alleles per locus. The observed (H(O)) and expected (H(E)) heterozygosities ranged from 0.072 to 0.707 and 0.089 to 0.851, respectively. Furthermore, only two locus/population combinations (WFT144 in Dali and WFT50 in Guiyang) significantly deviated from Hardy-Weinberg equilibrium (HWE). Pairwise F(ST) analysis showed a low but significant differentiation (0.026 < F(ST) < 0.032) among all three pairwise population comparisons. Sequence analysis of alleles per locus revealed a complex mutational pattern of these EST-SSRs. Thus, these EST-SSRs are useful markers but greater attention should be paid to the mutational characteristics of these microsatellites when they are used in population genetic studies.

Population genetics of the malaria vector Anopheles aconitus in China and Southeast Asia

PubMed Central

Chen, Bin; Harbach, Ralph E.; Walton, Catherine; He, Zhengbo; Zhong, Daibin; Yan, Guiyun; Butlin, Roger K.

2012-01-01

Anopheles aconitus is a well-known vector of malaria and is broadly distributed in the Oriental Region, yet there is no information on its population genetic characteristics. In this study, the genetic differentiation among populations was examined using 140 mtDNA COII sequences from 21 sites throughout southern China, Myanmar, Vietnam, Thailand, Laos and Sri Lanka. The population in Sri Lanka has characteristic rDNA D3 and ITS2, mtDNA COII and ND5 haplotypes, and may be considered a distinct subspecies. Clear genetic structure was observed with highly significant genetic variation present among population groups in Southeast Asia. The greatest genetic diversity exists in Yunnan and Myanmar population groups. All population groups are significantly different from one another in pairwise Fst values, except northern Thailand with central Thailand. Mismatch distributions and extremely significant Fs values suggest that the populations passed through a recent demographic expansion. These patterns are discussed in relation to the likely biogeographic history of the region and compared to other Anopheles species. PMID:22982161

Constructing STR multiplexes for individual identification of Hungarian red deer.

PubMed

Szabolcsi, Zoltan; Egyed, Balazs; Zenke, Petra; Padar, Zsolt; Borsy, Adrienn; Steger, Viktor; Pasztor, Erzsebet; Csanyi, Sandor; Buzas, Zsuzsanna; Orosz, Laszlo

2014-07-01

Red deer is the most valuable game of the fauna in Hungary, and there is a strong need for genetic identification of individuals. For this purpose, 10 tetranucleotide STR markers were developed and amplified in two 5-plex systems. The study presented here includes the flanking region sequence analysis and the allele nomenclature of the 10 loci as well as the PCR optimization of the DeerPlex I and II. LD pairwise tests and cross-species similarity analyses showed the 10 loci to be independently inherited. Considerable levels of genetic differences between two subpopulations were recorded, and F(ST) was 0.034 using AMOVA. The average probability of identity (PI(ave)) was at the value of 2.6736 × 10(-15). This low value for PI(ave) nearly eliminates false identification. An illegal hunting case solved by DeerPlex is described herein. The calculated likelihood ratio (LR) illustrates the potential of the 10 red deer microsatellite markers for forensic investigations. © 2014 American Academy of Forensic Sciences.

Follistatin is a metastasis suppressor in a mouse model of HER2-positive breast cancer.

PubMed

Seachrist, Darcie D; Sizemore, Steven T; Johnson, Emhonta; Abdul-Karim, Fadi W; Weber Bonk, Kristen L; Keri, Ruth A

2017-06-05

Follistatin (FST) is an intrinsic inhibitor of activin, a member of the transforming growth factor-β superfamily of ligands. The prognostic value of FST and its family members, the follistatin-like (FSTL) proteins, have been studied in various cancers. However, these studies, as well as limited functional analyses of the FSTL proteins, have yielded conflicting results on the role of these proteins in disease progression. Furthermore, very few have been focused on FST itself. We assessed whether FST may be a suppressor of tumorigenesis and/or metastatic progression in breast cancer. Using publicly available gene expression data, we examined the expression patterns of FST and INHBA, a subunit of activin, in normal and cancerous breast tissue and the prognostic value of FST in breast cancer metastases, recurrence-free survival, and overall survival. The functional effects of activin and FST on in vitro proliferation, migration, and invasion of breast cancer cells were also examined. FST overexpression in an autochthonous mouse model of breast cancer was then used to assess the in vivo impact of FST on metastatic progression. Examination of multiple breast cancer datasets revealed that FST expression is reduced in breast cancers compared with normal tissue and that low FST expression predicts increased metastasis and reduced overall survival. FST expression was also reduced in a mouse model of HER2/Neu-induced metastatic breast cancer. We found that FST blocks activin-induced breast epithelial cell migration in vitro, suggesting that its loss may promote breast cancer aggressiveness. To directly determine if FST restoration could inhibit metastatic progression, we transgenically expressed FST in the HER2/Neu model. Although FST had no impact on tumor initiation or growth, it completely blocked the formation of lung metastases. These data indicate that FST is a bona fide metastasis suppressor in this mouse model and support future efforts to develop an FST mimetic to suppress metastatic progression.

A genome-wide scan for signatures of selection in Chinese indigenous and commercial pig breeds.

PubMed

Yang, Songbai; Li, Xiuling; Li, Kui; Fan, Bin; Tang, Zhonglin

2014-01-15

Modern breeding and artificial selection play critical roles in pig domestication and shape the genetic variation of different breeds. China has many indigenous pig breeds with various characteristics in morphology and production performance that differ from those of foreign commercial pig breeds. However, the signatures of selection on genes implying for economic traits between Chinese indigenous and commercial pigs have been poorly understood. We identified footprints of positive selection at the whole genome level, comprising 44,652 SNPs genotyped in six Chinese indigenous pig breeds, one developed breed and two commercial breeds. An empirical genome-wide distribution of Fst (F-statistics) was constructed based on estimations of Fst for each SNP across these nine breeds. We detected selection at the genome level using the High-Fst outlier method and found that 81 candidate genes show high evidence of positive selection. Furthermore, the results of network analyses showed that the genes that displayed evidence of positive selection were mainly involved in the development of tissues and organs, and the immune response. In addition, we calculated the pairwise Fst between Chinese indigenous and commercial breeds (CHN VS EURO) and between Northern and Southern Chinese indigenous breeds (Northern VS Southern). The IGF1R and ESR1 genes showed evidence of positive selection in the CHN VS EURO and Northern VS Southern groups, respectively. In this study, we first identified the genomic regions that showed evidences of selection between Chinese indigenous and commercial pig breeds using the High-Fst outlier method. These regions were found to be involved in the development of tissues and organs, the immune response, growth and litter size. The results of this study provide new insights into understanding the genetic variation and domestication in pigs.

A genome-wide scan for signatures of selection in Chinese indigenous and commercial pig breeds

PubMed Central

2014-01-01

Background Modern breeding and artificial selection play critical roles in pig domestication and shape the genetic variation of different breeds. China has many indigenous pig breeds with various characteristics in morphology and production performance that differ from those of foreign commercial pig breeds. However, the signatures of selection on genes implying for economic traits between Chinese indigenous and commercial pigs have been poorly understood. Results We identified footprints of positive selection at the whole genome level, comprising 44,652 SNPs genotyped in six Chinese indigenous pig breeds, one developed breed and two commercial breeds. An empirical genome-wide distribution of Fst (F-statistics) was constructed based on estimations of Fst for each SNP across these nine breeds. We detected selection at the genome level using the High-Fst outlier method and found that 81 candidate genes show high evidence of positive selection. Furthermore, the results of network analyses showed that the genes that displayed evidence of positive selection were mainly involved in the development of tissues and organs, and the immune response. In addition, we calculated the pairwise Fst between Chinese indigenous and commercial breeds (CHN VS EURO) and between Northern and Southern Chinese indigenous breeds (Northern VS Southern). The IGF1R and ESR1 genes showed evidence of positive selection in the CHN VS EURO and Northern VS Southern groups, respectively. Conclusions In this study, we first identified the genomic regions that showed evidences of selection between Chinese indigenous and commercial pig breeds using the High-Fst outlier method. These regions were found to be involved in the development of tissues and organs, the immune response, growth and litter size. The results of this study provide new insights into understanding the genetic variation and domestication in pigs. PMID:24422716

Geographic differences in allele frequencies of susceptibility SNPs for cardiovascular disease

PubMed Central

2011-01-01

Background We hypothesized that the frequencies of risk alleles of SNPs mediating susceptibility to cardiovascular diseases differ among populations of varying geographic origin and that population-specific selection has operated on some of these variants. Methods From the database of genome-wide association studies (GWAS), we selected 36 cardiovascular phenotypes including coronary heart disease, hypertension, and stroke, as well as related quantitative traits (eg, body mass index and plasma lipid levels). We identified 292 SNPs in 270 genes associated with a disease or trait at P < 5 × 10-8. As part of the Human Genome-Diversity Project (HGDP), 158 (54.1%) of these SNPs have been genotyped in 938 individuals belonging to 52 populations from seven geographic areas. A measure of population differentiation, FST, was calculated to quantify differences in risk allele frequencies (RAFs) among populations and geographic areas. Results Large differences in RAFs were noted in populations of Africa, East Asia, America and Oceania, when compared with other geographic regions. The mean global FST (0.1042) for 158 SNPs among the populations was not significantly higher than the mean global FST of 158 autosomal SNPs randomly sampled from the HGDP database. Significantly higher global FST (P < 0.05) was noted in eight SNPs, based on an empirical distribution of global FST of 2036 putatively neutral SNPs. For four of these SNPs, additional evidence of selection was noted based on the integrated Haplotype Score. Conclusion Large differences in RAFs for a set of common SNPs that influence risk of cardiovascular disease were noted between the major world populations. Pairwise comparisons revealed RAF differences for at least eight SNPs that might be due to population-specific selection or demographic factors. These findings are relevant to a better understanding of geographic variation in the prevalence of cardiovascular disease. PMID:21507254

Microsatellite-based genetic diversity patterns in disjunct populations of a rare orchid.

PubMed

Pandey, Madhav; Richards, Matt; Sharma, Jyotsna

2015-12-01

We investigated the patterns of genetic diversity and structure in seven disjunct populations of a rare North American orchid, Cypripedium kentuckiense by including populations that represented the periphery and the center of the its range. Eight nuclear and two chloroplast microsatellites were used. Genetic diversity was low across the sampled populations of C. kentuckiense based on both nuclear (average An = 4.0, Ho = 0.436, He = 0.448) and cpDNA microsatellites (average An = 1.57, Nh = 1.57 and H = 0.133). The number of private alleles ranged from one to four per population with a total of 17 private alleles detected at five nuclear microsatellites. One private allele at one cpDNA microsatellite was also observed. Although the absolute values for nuclear microsatellite based population differentiation were low (Fst = 0.075; ϕPT = 0.24), they were statistically significant. Pairwise Fst values ranged from 0.038 to 0.123 and each comparison was significant. We also detected isolation by distance with nDNA microsatellites based on the Mantel test (r(2) = 0.209, P = 0.05). STRUCTURE analysis and the neighbor joining trees grouped the populations similarly whereby the geographically proximal populations were genetically similar. Our data indicate that the species is genetically depauperate but the diversity is distributed more or less equally across its range. Population differentiation and isolation by distance were detectable, which indicates that genetic isolation is beginning to manifest itself across the range in this rare species.

Genetic variability and differentiation among populations of the Azorean endemic gymnosperm Juniperus brevifolia: baseline information for a conservation and restoration perspective.

PubMed

Silva, Luís; Elias, Rui B; Moura, Mónica; Meimberg, Harald; Dias, Eduardo

2011-12-01

The Azorean endemic gymnosperm Juniperus brevifolia (Seub.) Antoine is a top priority species for conservation in Macaronesia, based on its ecological significance in natural plant communities. To evaluate genetic variability and differentiation among J. brevifolia populations from the Azorean archipelago, we studied 15 ISSR and 15 RAPD markers in 178 individuals from 18 populations. The average number of polymorphic bands per population was 65 for both ISSR and RAPD. The majority of genetic variability was found within populations and among populations within islands, and this partitioning of variability was confirmed by AMOVA. The large majority of population pairwise F(ST) values were above 0.3 and below 0.6. The degree of population genetic differentiation in J. brevifolia was relatively high compared with other species, including Juniperus spp. The genetic differentiation among populations suggests that provenance should be considered when formulating augmentation or reintroduction strategies.

Sex-biased gene flow among elk in the greater Yellowstone ecosystem

USGS Publications Warehouse

Hand, Brian K.; Chen, Shanyuan; Anderson, Neil; Beja-Pereira, Albano; Cross, Paul C.; Ebinger, Michael R.; Edwards, Hank; Garrott, Robert A.; Kardos, Marty D.; Kauffman, Matthew J.; Landguth, Erin L.; Middleton, Arthur; Scurlock, Brandon M.; White, P.J.; Zager, Pete; Schwartz, Michael K.; Luikart, Gordon

2014-01-01

We quantified patterns of population genetic structure to help understand gene flow among elk populations across the Greater Yellowstone Ecosystem. We sequenced 596 base pairs of the mitochondrial control region of 380 elk from eight populations. Analysis revealed high mitochondrial DNA variation within populations, averaging 13.0 haplotypes with high mean gene diversity (0.85). The genetic differentiation among populations for mitochondrial DNA was relatively high (FST  =  0.161; P  =  0.001) compared to genetic differentiation for nuclear microsatellite data (FST  =  0.002; P  =  0.332), which suggested relatively low female gene flow among populations. The estimated ratio of male to female gene flow (mm/mf  =  46) was among the highest we have seen reported for large mammals. Genetic distance (for mitochondrial DNA pairwise FST) was not significantly correlated with geographic (Euclidean) distance between populations (Mantel's r  =  0.274, P  =  0.168). Large mitochondrial DNA genetic distances (e.g., FST > 0.2) between some of the geographically closest populations (<65 km) suggested behavioral factors and/or landscape features might shape female gene flow patterns. Given the strong sex-biased gene flow, future research and conservation efforts should consider the sexes separately when modeling corridors of gene flow or predicting spread of maternally transmitted diseases. The growing availability of genetic data to compare male vs. female gene flow provides many exciting opportunities to explore the magnitude, causes, and implications of sex-biased gene flow likely to occur in many species.

Genetic variability of Echinococcus granulosus complex in various geographical populations of Iran inferred by mitochondrial DNA sequences.

PubMed

Spotin, Adel; Mahami-Oskouei, Mahmoud; Harandi, Majid Fasihi; Baratchian, Mehdi; Bordbar, Ali; Ahmadpour, Ehsan; Ebrahimi, Sahar

2017-01-01

To investigate the genetic variability and population structure of Echinococcus granulosus complex, 79 isolates were sequenced from different host species covering human, dog, camel, goat, sheep and cattle as of various geographical sub-populations of Iran (Northwestern, Northern, and Southeastern). In addition, 36 sequences of other geographical populations (Western, Southeastern and Central Iran), were directly retrieved from GenBank database for the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene. The confirmed isolates were grouped as G1 genotype (n=92), G6 genotype (n=14), G3 genotype (n=8) and G2 genotype (n=1). 50 unique haplotypes were identified based on the analyzed sequences of cox1. A parsimonious network of the sequence haplotypes displayed star-like features in the overall population containing IR23 (22: 19.1%) as the most common haplotype. According to the analysis of molecular variance (AMOVA) test, the high value of haplotype diversity of E. granulosus complex was shown the total genetic variability within populations while nucleotide diversity was low in all populations. Neutrality indices of the cox1 (Tajima's D and Fu's Fs tests) were shown negative values in Western-Northwestern, Northern and Southeastern populations which indicating significant divergence from neutrality and positive but not significant in Central isolates. A pairwise fixation index (Fst) as a degree of gene flow was generally low value for all populations (0.00647-0.15198). The statistically Fst values indicate that Echinococcus sensu stricto (genotype G1-G3) populations are not genetically well differentiated in various geographical regions of Iran. To appraise the hypothetical evolutionary scenario, further study is needed to analyze concatenated mitogenomes and as well a panel of single locus nuclear markers should be considered in wider areas of Iran and neighboring countries. Copyright © 2016 Elsevier B.V. All rights reserved.

Weak genetic differentiation in cobia, Rachycentron canadum from Indian waters as inferred from mitochondrial DNA ATPase 6 and 8 genes.

PubMed

Joy, Linu; Mohitha, C; Divya, P R; Gopalakrishnan, A; Basheer, V S; Jena, J K

2016-07-01

Cobia, Rachycentron canadum, is an economically important migratory fish distributed in tropical waters worldwide and is a candidate fish species for aquaculture practices. The genetic stock structure of R. canadum distributed along the Indian waters was identified using mitochondrial ATPase 6 and 8 genes. A total of 842 bp sequence of ATPase 6/8 genes obtained in this study revealed 15 haplotypes with mean low nucleotide diversity (π = 0.001) and high haplotype diversity (h = 0.785). AMOVA indicated the genetic differentiation of 90.47% for individuals within the population. This is well supported by co-efficient of genetic differentiation (FST) values obtained for pairwise populations that were low and non-significant with an overall value of 0.002. The parsimony network tree revealed star-like phylogeny and all the haplotypes were connected with each other by single mutational event. The findings of the present study indicated the panmixia nature of the species which can be managed as a unit stock in Indian waters.

Genomic variation among populations of threatened coral: Acropora cervicornis.

PubMed

Drury, C; Dale, K E; Panlilio, J M; Miller, S V; Lirman, D; Larson, E A; Bartels, E; Crawford, D L; Oleksiak, M F

2016-04-13

Acropora cervicornis, a threatened, keystone reef-building coral has undergone severe declines (>90 %) throughout the Caribbean. These declines could reduce genetic variation and thus hamper the species' ability to adapt. Active restoration strategies are a common conservation approach to mitigate species' declines and require genetic data on surviving populations to efficiently respond to declines while maintaining the genetic diversity needed to adapt to changing conditions. To evaluate active restoration strategies for the staghorn coral, the genetic diversity of A. cervicornis within and among populations was assessed in 77 individuals collected from 68 locations along the Florida Reef Tract (FRT) and in the Dominican Republic. Genotyping by Sequencing (GBS) identified 4,764 single nucleotide polymorphisms (SNPs). Pairwise nucleotide differences (π) within a population are large (~37 %) and similar to π across all individuals. This high level of genetic diversity along the FRT is similar to the diversity within a small, isolated reef. Much of the genetic diversity (>90 %) exists within a population, yet GBS analysis shows significant variation along the FRT, including 300 SNPs with significant FST values and significant divergence relative to distance. There are also significant differences in SNP allele frequencies over small spatial scales, exemplified by the large FST values among corals collected within Miami-Dade county. Large standing diversity was found within each population even after recent declines in abundance, including significant, potentially adaptive divergence over short distances. The data here inform conservation and management actions by uncovering population structure and high levels of diversity maintained within coral collections among sites previously shown to have little genetic divergence. More broadly, this approach demonstrates the power of GBS to resolve differences among individuals and identify subtle genetic structure, informing conservation goals with evolutionary implications.

Relative contributions of neutral and non-neutral processes to clinal variation in calyx lobe length in the series Sakawanum (Asarum: Aristolochiaceae).

PubMed

Takahashi, Daiki; Teramine, Tsutomu; Sakaguchi, Shota; Setoguchi, Hiroaki

2018-01-25

Clines, the gradual variation in measurable traits along a geographical axis, play a major role in evolution and can contribute to our understanding of the relative roles of selective and neutral process in trait variation. Using genetic and morphological analyses, the relative contributions of neutral and non-neutral processes were explored to infer the evolutionary history of species of the series Sakawanum (genus Asarum), which shows significant clinal variation in calyx lobe length. A total of 27 populations covering the natural geographical distribution of the series Sakawanum were sampled. Six nuclear microsatellite markers were used to investigate genetic structure and genetic diversity. The lengths of calyx lobes of multiple populations were measured to quantify their geographical and taxonomic differentiation. To detect the potential impact of selective pressure, morphological differentiation was compared with genetic differentiation (QCT-FST comparison). Average calyx lobe length of A. minamitanianum was 124.11 mm, while that of A. costatum was 13.80 mm. Though gradually changing along the geographical axis within series, calyx lobe lengths were significantly differentiated among the taxa. Genetic differentiation between taxa was low (FST = 0.099), but a significant geographical structure along the morphological cline was detected. Except for one taxon pair, pairwise QCT values were significantly higher than the neutral genetic measures of FST and G'ST. Divergent selection may have driven the calyx lobe length variation in series Sakawanum taxa, although the underlying mechanism is still not clear. The low genetic differentiation indicates recent divergence and/or gene flows between geographically close taxa. These neutral processes would also affect the clinal variation in calyx lobe lengths. Overall, this study implies the roles of population history and divergent selection in shaping the current cline of a flower trait in the series Sakawanum. © The Author(s) 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Genetic structuring of remnant forest patches in an endangered medicinal tree in North-western Ethiopia

PubMed Central

2014-01-01

Background Habitat loss and fragmentation may have detrimental impacts on genetic diversity, population structure and overall viability of tropical trees. The response of tropical trees to fragmentation processes may, however, be species, cohort or region-specific. Here we test the hypothesis that forest fragmentation is associated with lower genetic variability and higher genetic differentiation in adult and seedling populations of Prunus africana in North-western Ethiopia. This is a floristically impoverished region where all but a few remnant forest patches have been destroyed, mostly by anthropogenic means. Results Genetic diversity (based on allelic richness) was significantly greater in large and less-isolated forest patches as well as in adults than seedlings. Nearly all pairwise FST comparisons showed evidence for significant population genetic differentiation. Mean FST values were significantly greater in seedlings than adults, even after correction for within population diversity, but varied little with patch size or isolation. Conclusions Analysis of long-lived adult trees suggests the formerly contiguous forest in North-western Ethiopia probably exhibited strong spatial patterns of genetic structure. This means that protecting a range of patches including small and isolated ones is needed to conserve the extant genetic resources of the valuable forests in this region. However, given the high livelihood dependence of the local community and the high impact of foreign investors on forest resources of this region, in situ conservation efforts alone may not be helpful. Therefore, these efforts should be supported with ex situ gene conservation actions. PMID:24602239

Population structure and genetic diversity of black redhorse (Moxostoma duquesnei) in a highly fragmented watershed

USGS Publications Warehouse

Reid, S.M.; Wilson, C.C.; Mandrak, N.E.; Carl, L.M.

2008-01-01

Dams have the potential to affect population size and connectivity, reduce genetic diversity, and increase genetic differences among isolated riverine fish populations. Previous research has reported adverse effects on the distribution and demographics of black redhorse (Moxostoma duquesnei), a threatened fish species in Canada. However, effects on genetic diversity and population structure are unknown. We used microsatellite DNA markers to assess the number of genetic populations in the Grand River (Ontario) and to test whether dams have resulted in a loss of genetic diversity and increased genetic differentiation among populations. Three hundred and seventy-seven individuals from eight Grand River sites were genotyped at eight microsatellite loci. Measures of genetic diversity were moderately high and not significantly different among populations; strong evidence of recent population bottlenecks was not detected. Pairwise FST and exact tests identified weak (global FST = 0.011) but statistically significant population structure, although little population structuring was detected using either genetic distances or an individual-based clustering method. Neither geographic distance nor the number of intervening dams were correlated with pairwise differences among populations. Tests for regional equilibrium indicate that Grand River populations were either in equilibrium between gene flow and genetic drift or that gene flow is more influential than drift. While studies on other species have identified strong dam-related effects on genetic diversity and population structure, this study suggests that barrier permeability, river fragment length and the ecological characteristics of affected species can counterbalance dam-related effects. ?? 2007 Springer Science+Business Media B.V.

Climate variables explain neutral and adaptive variation within salmonid metapopulations: The importance of replication in landscape genetics

USGS Publications Warehouse

Hand, Brian K.; Muhlfeld, Clint C.; Wade, Alisa A.; Kovach, Ryan; Whited, Diane C.; Narum, Shawn R.; Matala, Andrew P.; Ackerman, Michael W.; Garner, B. A.; Kimball, John S; Stanford, Jack A.; Luikart, Gordon

2016-01-01

Understanding how environmental variation influences population genetic structure is important for conservation management because it can reveal how human stressors influence population connectivity, genetic diversity and persistence. We used riverscape genetics modelling to assess whether climatic and habitat variables were related to neutral and adaptive patterns of genetic differentiation (population-specific and pairwise FST) within five metapopulations (79 populations, 4583 individuals) of steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin, USA. Using 151 putatively neutral and 29 candidate adaptive SNP loci, we found that climate-related variables (winter precipitation, summer maximum temperature, winter highest 5% flow events and summer mean flow) best explained neutral and adaptive patterns of genetic differentiation within metapopulations, suggesting that climatic variation likely influences both demography (neutral variation) and local adaptation (adaptive variation). However, we did not observe consistent relationships between climate variables and FST across all metapopulations, underscoring the need for replication when extrapolating results from one scale to another (e.g. basin-wide to the metapopulation scale). Sensitivity analysis (leave-one-population-out) revealed consistent relationships between climate variables and FST within three metapopulations; however, these patterns were not consistent in two metapopulations likely due to small sample sizes (N = 10). These results provide correlative evidence that climatic variation has shaped the genetic structure of steelhead populations and highlight the need for replication and sensitivity analyses in land and riverscape genetics.

Phylogeographical structure in mitochondrial DNA of eggplant fruit and shoot borer, Leucinodes orbonalis Guenée (Lepidoptera: Crambidae) in South and Southeast Asia.

PubMed

Chang, Jian-Cheng; Ponnath, Daniel W; Ramasamy, Srinivasan

2016-01-01

Leucinodes orbonalis is the most detrimental South and Southeast Asian insect pest of eggplant. To help reduce the impact of this pest, population genetic diversity and structure of L. orbonalis were examined in eight populations from six countries using mitochondrial cytochrome c oxidase subunit I DNA sequences. No correlation between genetic diversity and geographic distance was detected among populations. Low levels of haplotype and nucleotide diversities were observed in the Philippines population, suggesting recent colonization. No significant gene flow was found among local populations in different countries. The Vietnam population is highly differentiated, indicated by significant pairwise FST values, and may be ascribed to a new subspecies or race. India was confirmed to be the source of genetic variation in L. orbonalis populations. Our study showed that L. orbonalis formed subpopulations for each local region, and the corresponding pest management technology should be developed at the country scale.

If F(ST) does not measure neutral genetic differentiation, then comparing it with Q(ST) is misleading. Or is it?

PubMed

Edelaar, Pim; Björklund, Mats

2011-05-01

The comparison between neutral genetic differentiation (F(ST) ) and quantitative genetic differentiation (Q(ST) ) is commonly used to test for signatures of selection in population divergence. However, there is an ongoing discussion about what F(ST) actually measures, even resulting in some alternative metrics to express neutral genetic differentiation. If there is a problem with F(ST) , this could have repercussions for its comparison with Q(ST) as well. We show that as the mutation rate of the neutral marker increases, F(ST) decreases: a higher within-population heterozygosity (He) yields a lower F(ST) value. However, the same is true for Q(ST) : a higher mutation rate for the underlying QTL also results in a lower Q(ST) estimate. The effect of mutation rate is equivalent in Q(ST) and F(ST) . Hence, the comparison between Q(ST) and F(ST) remains valid, if one uses neutral markers whose mutation rates are not too high compared to those of quantitative traits. Usage of highly variable neutral markers such as hypervariable microsatellites can lead to serious biases and the incorrect inference that divergent selection has acted on populations. Much of the discussion on F(ST) seems to stem from the misunderstanding that it measures the differentiation of populations, whereas it actually measures the fixation of alleles. In their capacity as measures of population differentiation, Hedrick's G'(ST) and Jost's D reach their maximum value of 1 when populations do not share alleles even when there remains variation within populations, which invalidates them for comparisons with Q(ST) . © 2011 Blackwell Publishing Ltd.

Genome-wide single nucleotide polymorphisms reveal population history and adaptive divergence in wild guppies.

PubMed

Willing, Eva-Maria; Bentzen, Paul; van Oosterhout, Cock; Hoffmann, Margarete; Cable, Joanne; Breden, Felix; Weigel, Detlef; Dreyer, Christine

2010-03-01

Adaptation of guppies (Poecilia reticulata) to contrasting upland and lowland habitats has been extensively studied with respect to behaviour, morphology and life history traits. Yet population history has not been studied at the whole-genome level. Although single nucleotide polymorphisms (SNPs) are the most abundant form of variation in many genomes and consequently very informative for a genome-wide picture of standing natural variation in populations, genome-wide SNP data are rarely available for wild vertebrates. Here we use genetically mapped SNP markers to comprehensively survey genetic variation within and among naturally occurring guppy populations from a wide geographic range in Trinidad and Venezuela. Results from three different clustering methods, Neighbor-net, principal component analysis (PCA) and Bayesian analysis show that the population substructure agrees with geographic separation and largely with previously hypothesized patterns of historical colonization. Within major drainages (Caroni, Oropouche and Northern), populations are genetically similar, but those in different geographic regions are highly divergent from one another, with some indications of ancient shared polymorphisms. Clear genomic signatures of a previous introduction experiment were seen, and we detected additional potential admixture events. Headwater populations were significantly less heterozygous than downstream populations. Pairwise F(ST) values revealed marked differences in allele frequencies among populations from different regions, and also among populations within the same region. F(ST) outlier methods indicated some regions of the genome as being under directional selection. Overall, this study demonstrates the power of a genome-wide SNP data set to inform for studies on natural variation, adaptation and evolution of wild populations.

Resurrecting an extinct salmon evolutionarily significant unit: archived scales, historical DNA and implications for restoration.

PubMed

Iwamoto, Eric M; Myers, James M; Gustafson, Richard G

2012-04-01

Archival scales from 603 sockeye salmon (Oncorhynchus nerka), sampled from May to July 1924 in the lower Columbia River, were analysed for genetic variability at 12 microsatellite loci and compared to 17 present-day O. nerka populations-exhibiting either anadromous (sockeye salmon) or nonanadromous (kokanee) life histories-from throughout the Columbia River Basin, including areas upstream of impassable dams built subsequent to 1924. Statistical analyses identified four major genetic assemblages of sockeye salmon in the 1924 samples. Two of these putative historical groupings were found to be genetically similar to extant evolutionarily significant units (ESUs) in the Okanogan and Wenatchee Rivers (pairwise F(ST)  = 0.004 and 0.002, respectively), and assignment tests were able to allocate 77% of the fish in these two historical groupings to the contemporary Okanogan River and Lake Wenatchee ESUs. A third historical genetic grouping was most closely aligned with contemporary sockeye salmon in Redfish Lake, Idaho, although the association was less robust (pairwise F(ST)  = 0.060). However, a fourth genetic grouping did not appear to be related to any contemporary sockeye salmon or kokanee population, assigned poorly to the O. nerka baseline, and had distinctive early return migration timing, suggesting that this group represents a historical ESU originating in headwater lakes in British Columbia that was probably extirpated sometime after 1924. The lack of a contemporary O. nerka population possessing the genetic legacy of this extinct ESU indicates that efforts to reestablish early-migrating sockeye salmon to the headwater lakes region of the Columbia River will be difficult. © 2012 Blackwell Publishing Ltd.

Population and forensic genetic analyses of mitochondrial DNA control region variation from six major provinces in the Korean population.

PubMed

Hong, Seung Beom; Kim, Ki Cheol; Kim, Wook

2015-07-01

We generated complete mitochondrial DNA (mtDNA) control region sequences from 704 unrelated individuals residing in six major provinces in Korea. In addition to our earlier survey of the distribution of mtDNA haplogroup variation, a total of 560 different haplotypes characterized by 271 polymorphic sites were identified, of which 473 haplotypes were unique. The gene diversity and random match probability were 0.9989 and 0.0025, respectively. According to the pairwise comparison of the 704 control region sequences, the mean number of pairwise differences between individuals was 13.47±6.06. Based on the result of mtDNA control region sequences, pairwise FST genetic distances revealed genetic homogeneity of the Korean provinces on a peninsular level, except in samples from Jeju Island. This result indicates there may be a need to formulate a local mtDNA database for Jeju Island, to avoid bias in forensic parameter estimates caused by genetic heterogeneity of the population. Thus, the present data may help not only in personal identification but also in determining maternal lineages to provide an expanded and reliable Korean mtDNA database. These data will be available on the EMPOP database via accession number EMP00661. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Genetic structure of lake whitefish (Coregonus clupeaformis) in Lake Michigan

USGS Publications Warehouse

VanDeHey, J.A.; Sloss, Brian L.; Peeters, Paul J.; Sutton, T.M.

2009-01-01

Genetic relationships among lake whitefish (Coregonus clupeaformis) spawning aggregates in Lake Michigan were assessed and used to predict a stock or management unit (MU) model for the resource. We hypothesized that distinct spawning aggregates represented potential MUs and that differences at molecular markers underlie population differentiation. Genetic stock identification using 11 microsatellite loci indicated the presence of six genetic MUs. Resolved MUs corresponded to geographically proximate spawning aggregates clustering into genetic groups. Within MUs, analyses suggested that all but one delineated MU was a stable grouping (i.e., no between-population differences), with the exception being the Hog Island - Traverse Bay grouping. Elk Rapids was the most genetically divergent population within Lake Michigan. However, low F st values suggested that moderate to high levels of gene flow occur or have occurred in the past between MUs. Significant tests of isolation by distance and low pairwise Fst values potentially led to conflicting results between traditional analyses and a Bayesian approach. This data set could provide baseline data from which a comprehensive mixed-stock analysis could be performed, allowing for more efficient and effective management of this economically and socially important resource.

Gene flow for Echinococcus granulosus metapopulations determined by mitochondrial sequences: A reliable approach for reflecting epidemiological drift of parasite among neighboring countries.

PubMed

Mahami-Oskouei, Mahmoud; Kaseb-Yazdanparast, Azam; Spotin, Adel; Shahbazi, Abbas; Adibpour, Mohammad; Ahmadpour, Ehsan; Ghabouli-Mehrabani, Nader

2016-12-01

In genetic diversity and population structure of Echinococcus granulosus, the gene flow can illustrate how the Echinococcus isolates have epidemiologically drifted among endemic neighboring countries. 51 isolates of hydatid cysts were collected from human, dog, cattle and sheep in northwest Iran, where placed co-border with Turkey. DNA samples were extracted, amplified and subjected to sequence analysis of NADH dehydrogenase subunit 1 (nad1) and cytochrome oxidase subunit 1 (cox1) genes. As well, sequences of Echinococcus at east to the southeast regions of Turkey were retrieved from GenBank database for the cox1 gene. The confirmed isolates were grouped as G1 (n = 74) and G3 (n = 6) genotypes. 31 unique haplotypes were identified inferred by the analyzed sequences of cox1 among two distinct populations. A parsimonious network of the sequence haplotypes displayed star-like features in the overall population containing TUR1, IR15 and IR22 as the most common haplotypes. According to AMOVA test, the high value of haplotype diversity (0.94758-0.98901) of E. granulosus was reflected the total genetic variability within populations while nucleotide diversity was low (0.00727-0.01046) in Iranian and Turkish metapopulations. Neutrality indices of the cox1 were shown negative values (-15.078 to -10.057) in Echinococcus populations which indicating a significant divergence from neutrality. A pairwise fixation index (Fst) as a degree of gene flow was partially high value for all populations (0.151). The statistically Fst value indicates that E. granulosus sensu stricto (G1-G3) are genetically moderate differentiated among Iranian and Turkish isolates. The occurrence of TUR1 and IR15 elucidate that there is possibly the dawn of domestication due to transfer of alleles between populations through the diffusion of stock raising or anthropogenic movements. To evaluate the hypothetical evolutionary scenario, further exploration is necessitated to analyze isolates from various host species in rest Middle East countries. Copyright © 2016 Elsevier Inc. All rights reserved.

Gene migration for re-emerging amebiasis in Iran's northwest-Iraq borders: a microevolutionary scale for reflecting epidemiological drift of Entamoeba histolytica metapopulations.

PubMed

Mohammadzadeh, Asad; Spotin, Adel; Mahami-Oskouei, Mahmoud; Haghighi, Ali; Zebardast, Nozhat; Kohansal, Kobra

2017-01-01

In the microevolutionary scales of Entamoeba isolates, the gene migration shows how Entamoeba spp. has epidemiologically drifted among border countries. Five hundred fecal samples were taken from patients suffering gastrointestinal disorders, abdominal pain, and diarrhea at Saggez, northwest Iran located within the border Iraq country. Following parasitological techniques, DNA samples were extracted and amplified by polymerase chain reaction (PCR) of 18S rRNA region to identify Entamoeba infections. To distinguish the Entamoeba spp., a multiplex PCR was conducted. Amplicons were sequenced to reconfirm their heterogeneity traits and phylogenetic analysis. Additionally, Entamoeba histolytica sequences of Iraq were retrieved from GenBank database. The suspected isolates were diagnosed as E. histolytica (2.2 %), Entamoeba moshkovskii (1 %), and Entamoeba dispar (0.4 %). Mixed Entamoeba infections did not detect among isolates. A parsimonious network of the sequence haplotypes displayed star-like features in the overall isolates containing E.h1, E.d2, and E.m3 as the most common haplotypes. According to analysis of molecular variance (AMOVA) test, high partial value of haplotype diversity (0.700 to 0.800) of E. histolytica was shown the total genetic variability within populations while nucleotide diversity was low among Iranian and Iraqi metapopulations. Neutrality indices of the 18S rRNA were shown negative values in E. histolytica populations which indicating significant deviations from neutrality. A pairwise fixation index (F-statistics [Fst]) as a degree of gene flow had a low value for all populations (0.001) while the number of migrants was 2.48. The statistically Fst value indicates that E. histolytica isolates are not genetically differentiated among shared isolates of Iran and Iraq. Occurrence of E.h1 between two regional populations indicates that there is dawn of Entamoeba flow due to transfer of alleles from one population to another population through host mobility and ecological alterations. To evaluate the hypothetical evolutionary scenario, further study is required to analyze Entamoeba spp. in the neighboring Middle East countries.

Worldwide F(ST) estimates relative to five continental-scale populations.

PubMed

Steele, Christopher D; Court, Denise Syndercombe; Balding, David J

2014-11-01

We estimate the population genetics parameter FST (also referred to as the fixation index) from short tandem repeat (STR) allele frequencies, comparing many worldwide human subpopulations at approximately the national level with continental-scale populations. FST is commonly used to measure population differentiation, and is important in forensic DNA analysis to account for remote shared ancestry between a suspect and an alternative source of the DNA. We estimate FST comparing subpopulations with a hypothetical ancestral population, which is the approach most widely used in population genetics, and also compare a subpopulation with a sampled reference population, which is more appropriate for forensic applications. Both estimation methods are likelihood-based, in which FST is related to the variance of the multinomial-Dirichlet distribution for allele counts. Overall, we find low FST values, with posterior 97.5 percentiles < 3% when comparing a subpopulation with the most appropriate population, and even for inter-population comparisons we find FST < 5%. These are much smaller than single nucleotide polymorphism-based inter-continental FST estimates, and are also about half the magnitude of STR-based estimates from population genetics surveys that focus on distinct ethnic groups rather than a general population. Our findings support the use of FST up to 3% in forensic calculations, which corresponds to some current practice.

Unravelling the effects of gene flow and selection in highly connected populations of the silver-lip pearl oyster (Pinctada maxima).

PubMed

Nayfa, Maria G; Zenger, Kyall R

2016-08-01

Many marine organisms often display weak levels of population genetic structuring as a result of both environmental characteristics (e.g., ocean currents) and life history traits (e.g., widely dispersed planktonic larval stages) maintaining high levels of gene flow. This can lead to the assumption that these organisms can be managed as a single stock based on high levels of population connectivity. However, this neglects to account for other micro-evolutionary forces such as selection, which also shape these populations. This study utilizes 1130 genome-wide SNP loci to unravel the effects of gene flow and selection shaping three highly connected populations of the silver-lip pearl oyster (Pinctada maxima) in the ecologically and economically important Indo-Pacific region (Aru, Bali, and West Papua). Twenty-two loci under directional selection were identified amongst the populations, providing further supporting evidence of strong local adaptation (i.e., G×E effects) among populations in this region. Global Fst values for directional outliers (0.348) were up to eight times greater than for neutral markers (0.043). Pairwise Fst comparisons between Aru and Bali revealed the largest directional differences (0.488), while Bali and West Papua had the least (0.062). Unrooted neighbour-joining (NJ) distance trees and genetic diversity indices of directional outliers revealed that individuals from Bali and West Papua had reduced allelic variation (MAFavg=0.144, Ho=0.238 and MAFavg=0.232, Ho=0.369, respectively) compared to Aru (MAFavg=0.292, Ho=0.412). This indicates that directional selection is most likely acting upon genetic variation within the Bali and West Papua populations. NJ distance trees, discriminant analysis of principal components, and Fst analyses of directional outliers revealed two divergent groups ("Bali/West Papua"; "Aru") that had previously gone unrecognized. This study not only illustrates that relatively strong local adaptive forces are occurring despite high gene flow, but identifies the populations that are most likely experiencing selection. Additionally, this study highlights the need to understand all micro-evolutionary forces acting on populations when resolving stock structure. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Geographic variation and genetic structure in Spotted Owls

USGS Publications Warehouse

Haig, Susan M.; Wagner, R.S.; Forsman, E.D.; Mullins, Thomas D.

2001-01-01

We examined genetic variation, population structure, and definition of conservation units in Spotted Owls (Strix occidentalis). Spotted Owls are mostly non-migratory, long-lived, socially monogamous birds that have decreased population viability due to their occupation of highly-fragmented late successional forests in western North America. To investigate potential effects of habitat fragmentation on population structure, we used random amplified polymorphic DNA (RAPD) to examine genetic variation hierarchically among local breeding areas, subregional groups, regional groups, and subspecies via sampling of 21 breeding areas (276 individuals) among the three subspecies of Spotted Owls. Data from 11 variable bands suggest a significant relationship between geographic distance among local breeding groups and genetic distance (Mantel r = 0.53, P < 0.02) although multi-dimensional scaling of three significant axes did not identify significant grouping at any hierarchical level. Similarly, neighbor-joining clustering of Manhattan distances indicated geographic structure at all levels and identified Mexican Spotted Owls as a distinct clade. RAPD analyses did not clearly differentiate Northern Spotted Owls from California Spotted Owls. Among Northern Spotted Owls, estimates of population differentiation (FST) ranged from 0.27 among breeding areas to 0.11 among regions. Concordantly, within-group agreement values estimated via multi-response permutation procedures of Jaccarda??s distances ranged from 0.22 among local sites to 0.11 among regions. Pairwise comparisons of FST and geographic distance within regions suggested only the Klamath region was in equilibrium with respect to gene flow and genetic drift. Merging nuclear data with recent mitochondrial data provides support for designation of an Evolutionary Significant Unit for Mexican Spotted Owls and two overlapping Management Units for Northern and California Spotted Owls.

Dispersal, mating events and fine-scale genetic structure in the lesser flat-headed bats.

PubMed

Hua, Panyu; Zhang, Libiao; Guo, Tingting; Flanders, Jon; Zhang, Shuyi

2013-01-01

Population genetic structure has important consequences in evolutionary processes and conservation genetics in animals. Fine-scale population genetic structure depends on the pattern of landscape, the permanent movement of individuals, and the dispersal of their genes during temporary mating events. The lesser flat-headed bat (Tylonycteris pachypus) is a nonmigratory Asian bat species that roosts in small groups within the internodes of bamboo stems and the habitats are fragmented. Our previous parentage analyses revealed considerable extra-group mating in this species. To assess the spatial limits and sex-biased nature of gene flow in the same population, we used 20 microsatellite loci and mtDNA sequencing of the ND2 gene to quantify genetic structure among 54 groups of adult flat-headed bats, at nine localities in South China. AMOVA and F(ST) estimates revealed significant genetic differentiation among localities. Alternatively, the pairwise F(ST) values among roosting groups appeared to be related to the incidence of associated extra-group breeding, suggesting the impact of mating events on fine-scale genetic structure. Global spatial autocorrelation analyses showed positive genetic correlation for up to 3 km, indicating the role of fragmented habitat and the specialized social organization as a barrier in the movement of individuals among bamboo forests. The male-biased dispersal pattern resulted in weaker spatial genetic structure between localities among males than among females, and fine-scale analyses supported that relatedness levels within internodes were higher among females than among males. Finally, only females were more related to their same sex roost mates than to individuals from neighbouring roosts, suggestive of natal philopatry in females.

Fine-scale population structure of Malays in Peninsular Malaysia and Singapore and implications for association studies.

PubMed

Hoh, Boon-Peng; Deng, Lian; Julia-Ashazila, Mat Jusoh; Zuraihan, Zakaria; Nur-Hasnah, Ma'amor; Nur-Shafawati, Ab Rajab; Hatin, Wan Isa; Endom, Ismail; Zilfalil, Bin Alwi; Khalid, Yusoff; Xu, Shuhua

2015-07-22

Fine scale population structure of Malays - the major population in Malaysia, has not been well studied. This may have important implications for both evolutionary and medical studies. Here, we investigated the population sub-structure of Malay involving 431 samples collected from all states from peninsular Malaysia and Singapore. We identified two major clusters of individuals corresponding to the north and south peninsular Malaysia. On an even finer scale, the genetic coordinates of the geographical Malay populations are in correlation with the latitudes (R(2) = 0.3925; P = 0.029). This finding is further supported by the pairwise FST of Malay sub-populations, of which the north and south regions showed the highest differentiation (FST [North-south] = 0.0011). The collective findings therefore suggest that population sub-structure of Malays are more heterogenous than previously expected even within a small geographical region, possibly due to factors like different genetic origins, geographical isolation, could result in spurious association as demonstrated in our analysis. We suggest that cautions should be taken during the stage of study design or interpreting the association signals in disease mapping studies which are expected to be conducted in Malay population in the near future.

Structure based alignment and clustering of proteins (STRALCP)

DOEpatents

Zemla, Adam T.; Zhou, Carol E.; Smith, Jason R.; Lam, Marisa W.

2013-06-18

Disclosed are computational methods of clustering a set of protein structures based on local and pair-wise global similarity values. Pair-wise local and global similarity values are generated based on pair-wise structural alignments for each protein in the set of protein structures. Initially, the protein structures are clustered based on pair-wise local similarity values. The protein structures are then clustered based on pair-wise global similarity values. For each given cluster both a representative structure and spans of conserved residues are identified. The representative protein structure is used to assign newly-solved protein structures to a group. The spans are used to characterize conservation and assign a "structural footprint" to the cluster.

Exon-Enriched Libraries Reveal Large Genic Differences Between Aedes aegypti from Senegal, West Africa, and Populations Outside Africa

PubMed Central

Dickson, Laura B.; Campbell, Corey L.; Juneja, Punita; Jiggins, Francis M.; Sylla, Massamba; Black, William C.

2016-01-01

Aedes aegypti is one of the most studied mosquito species, and the principal vector of several arboviruses pathogenic to humans. Recently failure to oviposit, low fecundity, and poor egg-to-adult survival were observed when Ae. aegypti from Senegal (SenAae) West Africa were crossed with Ae. aegypti (Aaa) from outside of Africa, and in SenAae intercrosses. Fluorescent in situ hybridization analyses indicated rearrangements on chromosome 1, and pericentric inversions on chromosomes 2 and 3. Herein, high throughput sequencing (HTS) of exon-enriched libraries was used to compare chromosome-wide genetic diversity among Aaa collections from rural Thailand and Mexico, a sylvatic collection from southeastern Senegal (PK10), and an urban collection from western Senegal (Kaolack). Sex-specific polymorphisms were analyzed in Thailand and PK10 to assess genetic differences between sexes. Expected heterozygosity was greatest in SenAae. FST distributions of 15,735 genes among all six pairwise comparisons of the four collections indicated that Mexican and Thailand collections are genetically similar, while FST distributions between PK10 and Kaolack were distinct. All four comparisons of SenAae with Aaa indicated extreme differentiation. FST was uniform between sexes across all chromosomes in Thailand, but were different, especially on the sex autosome 1, in PK10. These patterns correlate with the reproductive isolation noted earlier. We hypothesize that cryptic Ae. aegypti taxa may exist in West Africa, and the large genic differences between Aaa and SenAae detected in the present study have accumulated over a long period following the evolution of chromosome rearrangements in allopatric populations that subsequently cause reproductive isolation when these populations became sympatric. PMID:28007834

Genomic patterns of species diversity and divergence in Eucalyptus.

PubMed

Hudson, Corey J; Freeman, Jules S; Myburg, Alexander A; Potts, Brad M; Vaillancourt, René E

2015-06-01

We examined genome-wide patterns of DNA sequence diversity and divergence among six species of the important tree genus Eucalyptus and investigated their relationship with genomic architecture. Using c. 90 range-wide individuals of each Eucalyptus species (E. grandis, E. urophylla, E. globulus, E. nitens, E. dunnii and E. camaldulensis), genetic diversity and divergence were estimated from 2840 polymorphic diversity arrays technology markers covering the 11 chromosomes. Species differentiating markers (SDMs) identified in each of 15 pairwise species comparisons, along with species diversity (HHW ) and divergence (FST ), were projected onto the E. grandis reference genome. Across all species comparisons, SDMs totalled 1.1-5.3% of markers and were widely distributed throughout the genome. Marker divergence (FST and SDMs) and diversity differed among and within chromosomes. Patterns of diversity and divergence were broadly conserved across species and significantly associated with genomic features, including the proximity of markers to genes, the relative number of clusters of tandem duplications, and gene density within or among chromosomes. These results suggest that genomic architecture influences patterns of species diversity and divergence in the genus. This influence is evident across the six species, encompassing diverse phylogenetic lineages, geography and ecology. © 2015 University of Tasmania New Phytologist © 2015 New Phytologist Trust.

Population structure of elephant foot yams (Amorphophallus paeoniifolius (Dennst.) Nicolson) in Asia

PubMed Central

Misra, Raj Shekhar; Boonkorkaew, Patchareeya; Thanomchit, Kanokwan

2017-01-01

The corms and leaves of elephant foot yams (Amorphophallus paeoniifolius (Dennst.) Nicolson) are important foods in the local diet in many Asian regions. The crop has high productivity and wide agroecological adaptation and exhibits suitability for the agroforestry system. Although the plant is assumed to reproduce via panmixia, a comprehensive study on the genetic background across regions to enhance wider consumer palatability is still lacking. Here, ten informative microsatellites were analyzed in 29 populations across regions in India, Indonesia and Thailand to understand the genetic diversity, population structure and distribution to improve breeding and conservation programs. The genetic diversity was high among and within regions. Some populations exhibited excess heterozygosity and bottlenecking. Pairwise FST indicated very high genetic differentiation across regions (FST = 0.274), and the Asian population was unlikely to be panmictic. Phylogenetic tree construction grouped the populations according to country of origin with the exception of the Medan population from Indonesia. The current gene flow was apparent within the regions but was restricted among the regions. The present study revealed that Indonesia and Thailand populations could be alternative centers of the gene pool, together with India. Consequently, regional action should be incorporated in genetic conservation and breeding efforts to develop new varieties with global acceptance. PMID:28658282

Population data of six STR loci using hexaplex PCR amplification and typing system, "Midi-6" in four regional populations in Japan.

PubMed

Uchihi, Rieko; Yamamoto, Toshimichi; Yoshimoto, Takashi; Inoue, Chikako; Kishida, Tetsuko; Yoshioka, Naofumi; Katsumata, Yoshinao

2007-07-04

The genetic differences of the allele frequency distributions for six STR loci (D20S480, D6S2439, D6S1056, D9S1118, D4S2639, and D17S1290) among regions in Japan were examined using our recently designed hexaplex amplification and typing system, "Midi-6" newly named, to construct a database in the Japanese population. Genotypes at six loci were analyzed in 198, 200, 175, and 196 individuals from the area of Akita, Nagoya, Oita, and Okinawa, respectively, in Japan. The allele frequency distributions were significantly different (p<0.05) at from one to five loci among the four populations when compared pairwise. Significant differences were also observed at two or three loci between Oita- or Okinawa-Japanese and the "pooled" population (n=769), respectively. However, since F(ST) (theta) values were extremely low (<0.05), ranging from 0.0020 to 0.0118 for six loci, genetic differentiation within the pooled Japanese population was negligible. Therefore, it suggested that the data of the allele frequencies at six loci in the pooled population would be employed as the base of calculation for statistical probabilities.

Population genetic structure and conservation of marbled murrelets (Brachyramphus marmoratus)

USGS Publications Warehouse

Friesen, Vicki L.; Birt, T.P.; Piatt, John F.; Golightly, R.T.; Newman, S.H.; Hebert, P.N.; Congdon, B.C.; Gissing, G.

2005-01-01

Marbled murrelets (Brachyramphus marmoratus) are coastal seabirds that nest from California to the Aleutian Islands. They are declining and considered threatened in several regions. We compared variation in the mitochondrial control region, four nuclear introns and three microsatellite loci among 194 murrelets from throughout their range except Washington and Oregon. Significant population genetic structure was found: nine private control region haplotypes and three private intron alleles occurred at high frequency in the Aleutians and California; global estimates of FST or ??ST and most pairwise estimates involving the Aleutians and/or California were significant; and marked isolation-by-distance was found. Given the available samples, murrelets appear to comprise five genetic management units: (1) western Aleutian Islands, (2) central Aleutian Islands, (3) mainland Alaska and British Columbia, (4) northern California, and (5) central California.

An assessment of the portability of ancestry informative markers between human populations

PubMed Central

Myles, Sean; Stoneking, Mark; Timpson, Nic

2009-01-01

Background Recent work has shown that population stratification can have confounding effects on genetic association studies and statistical methods have been developed to correct for these effects. Subsets of markers that are highly-differentiated between populations, ancestry-informative markers (AIMs), have been used to correct for population stratification. Often AIMs are discovered in one set of populations and then employed in a different set of populations. The underlying assumption in these cases is that the population under study has the same substructure as the population in which the AIMs were discovered. The present study assesses this assumption and evaluates the portability between worldwide populations of 10 SNPs found to be highly-differentiated within Britain (BritAIMs). Methods We genotyped 10 BritAIMs in ~1000 individuals from 53 populations worldwide. We assessed the degree to which these 10 BritAIMs capture population stratification in other groups of populations by use of the Fst statistic. We used Fst values from 2750 random markers typed in the same set of individuals as an empirical distribution to which the Fst values of the 10 BritAIMs were compared. Results Allele frequency differences between continental groups for the BritAIMs are not unusually high. This is also the case for comparisons within continental groups distantly related to Britain. However, two BritAIMs show high Fst between European populations and two BritAIMs show high Fst between populations from the Middle East. Overall the median Fst across all BritAIMs is not unusually high compared to the empirical distribution. Conclusion We find that BritAIMs are generally not useful to distinguish between continental groups or within continental groups distantly related to Britain. Moreover, our analyses suggest that the portability of AIMs across geographical scales (e.g. between Europe and Britain) can be limited and should therefore be taken into consideration in the design and interpretation of genetic association studies. PMID:19619313

[Analysis of Alu-insertion polymorphism in three subethnic groups of Kalmyks].

PubMed

Khusainova, R I; Balinova, N V; Kutuev, I A; Spitsina, N Kh; Akhmetova, V L; Valiev, R R; Spitsyn, V A; Khusnutdinova, E K

2009-03-01

Eight Alu insertions at the NBC27, TPA25, NBC148, NBC123, ACE, APOA1, NBC51, and PV92 locus were examined in three subethnic groups of Kalmyks (Torgouds, Derbets, and Buzava). In general, the pattern of allele frequencies in Kalmyks was consistent with that in Asian populations of the world, and was similar to the Alu insertion frequencies pattern in Turkic populations of the Volga--Ural region and Central Asia. Pairwise comparisons of three subpopulations of Kalmyks with respect to the frequency distributions of eight Alu insertions revealed the differences between the groups examined. The coefficient of gene differentiation, F(st), constituted 1.37%, pointing to the common origin of the groups of interest, as well as to the uniformity of the gene pools of subethnic groups of Kalmyks examined.

Shallow Population Genetic Structures of Thread-sail Filefish (Stephanolepis cirrhifer) Populations from Korean Coastal Waters

PubMed Central

Yoon, M.; Park, W.; Nam, Y. K.; Kim, D. S.

2012-01-01

Genetic diversities, population genetic structures and demographic histories of the thread-sail filefish Stephanolepis cirrhifer were investigated by nucleotide sequencing of 336 base pairs of the mitochondrial DNA (mtDNA) control region in 111 individuals collected from six populations in Korean coastal waters. A total of 70 haplotypes were defined by 58 variable nucleotide sites. The neighbor-joining tree of the 70 haplotypes was shallow and did not provide evidence of geographical associations. Expansion of S. cirrhifer populations began approximate 51,000 to 102,000 years before present, correlating with the period of sea level rise since the late Pleistocene glacial maximum. High levels of haplotype diversities (0.974±0.029 to 1.000±0.076) and nucleotide diversities (0.014 to 0.019), and low levels of genetic differentiation among populations inferred from pairwise population FST values (−0.007 to 0.107), support an expansion of the S. cirrhifer population. Hierarchical analysis of molecular variance (AMOVA) revealed weak but significant genetic structures among three groups (FCT = 0.028, p<0.05), and no genetic variation within groups (0.53%; FSC = 0.005, p = 0.23). These results may help establish appropriate fishery management strategies for stocks of S. cirrhifer and related species. PMID:25049547

Genetic diversity based on SSR analysis of the cultured snakehead fish, Channa argus, (Channidae) in China.

PubMed

Zhu, S-R; Li, J-L; Xie, N; Zhu, L-M; Wang, Q; Yue, G-H

2014-02-13

The snakehead fish Channa argus is an important food fish in China. We identified six microsatellite loci for C. argus. These six microsatellite loci and four other microsatellite markers were used to analyze genetic diversity in four cultured populations of C. argus (SD, JX, HN, and ZJ) and determine their relationships. A total of 154 alleles were detected at the 10 microsatellite loci. The average expected and observed heterozygosities varied from 0.70-0.84 and 0.69-0.83, respectively, and polymorphism information content ranged between 0.66 and 0.82 in the four populations, indicating high genetic diversity. Population JX deviated from mutation-drift equilibrium and may have experienced a recent bottleneck. Analysis of pairwise genetic differentiation revealed FST values that ranged from 0.028 to 0.100, which indicates a moderate level of genetic differentiation. The largest distances were observed between populations HN and SD, whereas the smallest distances were obtained between populations HN and JX. Genetic clustering analysis demonstrated that the ZJ and HN populations probably share the same origin. This information about the genetic diversity within each of the four populations, and their genetic relationships will be useful for future genetic improvement of C. argus through selective breeding.

High genetic diversity and connectivity in Colossoma macropomum in the Amazon basin revealed by microsatellite markers.

PubMed

Fazzi-Gomes, Paola; Guerreiro, Sávio; Palheta, Glauber David Almeida; Melo, Nuno Filipe Alves Correa de; Santos, Sidney; Hamoy, Igor

2017-01-01

Colossoma macropomum is the second largest scaled fish of the Amazon. It is economically important for commercial fisheries and for aquaculture, but few studies have examined the diversity and genetic structure of natural populations of this species. The aim of this study was to investigate the levels of genetic variability and connectivity that exist between three natural populations of C. macropomum from the Amazon basin. In total, 247 samples were collected from the municipalities of Tefé, Manaus, and Santarém. The populations were genotyped using a panel of 12 multiplex microsatellite markers. The genetic diversity found in these populations was high and similar to other populations described in the literature. These populations showed a pattern of high gene flow associated with the lack of a genetic structure pattern, indicating that the number of migrants per generation and recent migration rates are high. The values of the FST, RST, and exact test of differentiation were not significant for pairwise comparisons between populations. The Bayesian population clustering analysis indicated a single population. Thus, the data provide evidence for high genetic diversity and high gene flow among C. macropomum populations in the investigated region of the Amazon basin. This information is important for programs aiming at the conservation of natural populations.

High genetic diversity and connectivity in Colossoma macropomum in the Amazon basin revealed by microsatellite markers

PubMed Central

Fazzi-Gomes, Paola; Guerreiro, Sávio; Palheta, Glauber David Almeida; de Melo, Nuno Filipe Alves Correa; Santos, Sidney; Hamoy, Igor

2017-01-01

Abstract Colossoma macropomum is the second largest scaled fish of the Amazon. It is economically important for commercial fisheries and for aquaculture, but few studies have examined the diversity and genetic structure of natural populations of this species. The aim of this study was to investigate the levels of genetic variability and connectivity that exist between three natural populations of C. macropomum from the Amazon basin. In total, 247 samples were collected from the municipalities of Tefé, Manaus, and Santarém. The populations were genotyped using a panel of 12 multiplex microsatellite markers. The genetic diversity found in these populations was high and similar to other populations described in the literature. These populations showed a pattern of high gene flow associated with the lack of a genetic structure pattern, indicating that the number of migrants per generation and recent migration rates are high. The values of the FST, RST, and exact test of differentiation were not significant for pairwise comparisons between populations. The Bayesian population clustering analysis indicated a single population. Thus, the data provide evidence for high genetic diversity and high gene flow among C. macropomum populations in the investigated region of the Amazon basin. This information is important for programs aiming at the conservation of natural populations. PMID:28170026

City-Dwellers and Country Folks: Lack of Population Differentiation Along an Urban-Rural Gradient in the Mosquito Culex pipiens (Diptera: Culicidae).

PubMed

Honnen, Ann-Christin; Monaghan, Michael T; Sharakhov, Igor

2017-09-01

Mosquitoes (Diptera, Culicidae) occur in natural, urban, and peri-urban areas throughout the globe. Although the characteristics of urban and peri-urban habitats differ from those of natural habitats in many ways (e.g., fragmentation, pollution, noise, and light), few studies have examined the population connectivity of mosquitoes in urban areas. To obtain an overview of the species composition, we sampled mosquitoes from 23 sites in and around the city of Berlin, Germany. Of 23 species, five occurred in urban, 10 in peri-urban, and 20 in rural areas. Culex pipiens Linnaeus (Diptera: Culicidae) was the most common species collected (75% of all individuals) and occurred in all habitats. Hence this species was selected to be analysed at 10 microsatellite markers. There was no significant differentiation (FST = 0.016, P = 0.9) or isolation by distance (P = 0.06) among Cx. pipiens populations along an urban-rural gradient. The only significant differences detected were between Cx. pipiens and a laboratory population of Cx. pipiens f. molestus (pairwise FST = 0.114-0.148, P ≤ 0.001 in all comparisons), suggesting that the markers chosen were suitable for the identification of population differentiation. Our results indicate that Cx. pipiens gene flow is widespread within and among urban, peri-urban, and rural areas and that urban habitat does not necessarily impede or enhance gene flow among these populations. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America.

[Genetic Variability and Structure of SNP Haplotypes in the DMPK Gene in Yakuts and Other Ethnic Groups of Northern Eurasia in Relation to Myotonic Dystrophy].

PubMed

Swarovskaya, M G; Stepanova, S K; Marussin, A V; Sukhomyasova, A L; Maximova, N R; Stepanov, V A

2015-06-01

The genetic variability of the DMPK locus has been studied in relation to six SNP markers (rs2070736, rs572634, rs1799894, rs527221, rs915915, and rs10415988) in Yakuts with myotonic dystrophy (MD) in the Yakut population and in populations of northern Eurasia. Significant differences were observed in the allele frequencies between patients and a population sample of Yakuts for three SNP loci (rs915915, rs1799894, and rs10415988) associated with a high chance of disease manifestation. The odds ratios (OR) of MD development in representatives of the Yakut population for these three loci were 2.59 (95% CI, p = 0,004), 4.99 (95% CI, p = 0.000), and 3.15 (95% CI, p = 0.01), respectively. Haplotype TTTCTC, which is associated with MD, and haplotype GTCCTT, which was observed only in Yakut MD patients (never in MD patients of non-Yakut origin), were revealed. A low level of variability in the locus of DMRK gene in Yakuts (H(e) = 0.283) compared with other examined populations was noted. An analysis of pairwise genetic relationships between populations revealed their significant differentiation for all the examined loci. In addition, a low level of differentiation in territorial groups of Yakut populations (F(ST) = 0.79%), which was related to the high subdivision of the northern Eurasian population (F(ST) = 11.83%), was observed.

Vascular Endothelial Growth Factor-A Is Associated with Chronic Mountain Sickness in the Andean Population

PubMed Central

Espinoza, Jose R.; Alvarez, Giancarlo; León-Velarde, Fabiola; Ju Preciado, Hugo F.; Macarlupu, Jose-Luis; Rivera-Ch, Maria; Rodriguez, Jorge; Favier, Judith; Gimenez-Roqueplo, Anne-Paule

2014-01-01

Abstract Espinoza, Jose R., Giancarlo Alvarez, Fabiola León-Velarde, Hugo F. Ju Preciado, Jose-Luis Macarlupu, Maria Rivera-Ch, Jorge Rodriguez, Judith Favier, Anne-Paule Gimenez-Roqueplo, and Jean-Paul Richalet. Vascular endothelial growth factor-A is associated with chronic mountain sickness in Andean population. High Alt Med Biol. 15:146–154, 2014.—A study of chronic mountain sickness (CMS) with a candidate gene—vascular endothelial growth factor A (VEGFA)—was carried out in a Peruvian population living at high altitude in Cerro de Pasco (4380 m). The study was performed by genotyping of 11 tag SNPs encompassing 2.2 kb of region of VEGFA gene in patients with a diagnosis of CMS (n=131; 49.1±12.7 years old) and unrelated healthy controls (n=84; 47.2±13.4 years old). The VEGFA tag SNP rs3025033 was found associated with CMS (p<0.05), individuals with AG genotype have 2.5 more risk of CMS compared to those with GG genotype (p<0.02; OR, 2.54; 95% CI: 1.10–5.88). Pairwise Fst and Nei's distance indicate genetic differentiation between Cerro de Pasco population and HapMap3 population (Fst>0.36, p<0.01), suggesting selection is operating on the VEGF gene. Our results suggest that VEGFA is associated with CMS in long-term residents at high altitude in the Peruvian Andes. PMID:24971768

Classification and conservation priority of five Deccani sheep ecotypes of Maharashtra, India

PubMed Central

Arora, Reena; Jain, Anand

2017-01-01

Characterization of Indian livestock breeds has mostly been limited to single breed/population focused on either physical description of traditionally recognized breeds/populations or to their genetic description. Usually, morphological and genetic characterization has taken place in isolation. A parallel morphological characterization of genetically identified breeds or genetic characterization of morphologically described breeds is mostly missing, and their conservation priorities have largely been based on solely considering degree of endangerment. This study uses parallel approach based on morphometric and genetic differentiation for classification of five sheep ecotypes of Maharashtra state, and sets their conservation priority using threat parameters, current utilities/merits and contribution to genetic diversity. A total of 1101 animals were described for 7 body measurements for morphometric characterization. From this sample set, 456 animals were genotyped for 25 microsatellite markers for genetic characterization. Conservation priorities were assessed combining genetic and non-genetic factors. All studied traits varied significantly among ecotypes (p<0.05). All morphometric traits exhibited substantial sexual dimorphism except ear length. Males were 42% heavier than females. Madgyal sheep were the largest amongst the five ecotypes. In the stepwise discriminant analysis, all measured traits were significant and were found to have potential discriminatory power. Tail length was the most discriminatory trait. The Mahalanobis distance of the morphological traits between Kolhapuri and Madgyal was maximum (12.07) while the least differentiation was observed between Madgyal and Solapuri (1.50). Discriminant analysis showed that 68.12% sheep were classified into their source population. The Sangamneri sheep showed least assignment error (22%) whilst Solapuri exhibited maximum error level (41%). A total of 407 alleles were observed, with an average of 16.28 alleles per locus. Sufficient levels of genetic diversity were observed in all the ecotypes with observed heterozygosity values exceeding 0.47 and gene diversity values exceeding 0.76. About 6% of the total genetic variation was explained by population differences (FST = 0.059). Pairwise FST values indicated least differentiation between Solapuri and Madgyal (0.025). In terms of genetic distances, Kolhapuri and Lonand were most closely related (Ds = 0.177). The most probable structure clustering of the five studied populations was at K = 5. The study showed a fair congruence between the dendrogram constructed on the basis of Mahalanobis distances and Nei’s as well as Reynolds genetic distances. The findings gave highest conservation priority to Lonand and least to Solapuri ecotype. PMID:28910329

Studies on free stream turbulence as related to gas turbine heat transfer. A review of authors' past work and future implications.

PubMed

Yavuzkurt, S; Iyer, G R

2001-05-01

A review of the past work done on free stream turbulence (FST) as applied to gas turbine heat transfer and its implications for future studies are presented. It is a comprehensive approach to the results of many individual studies in order to derive the general conclusions that could be inferred from all rather than discussing the results of each individual study. Three experimental and four modeling studies are reviewed. The first study was on prediction of heat transfer for film cooled gas turbine blades. An injection model was devised and used along with a 2-D low Reynolds number k-epsilon model of turbulence for the calculations. Reasonable predictions of heat transfer coefficients were obtained for turbulence intensity levels up to 7%. Following this modeling study a series of experimental studies were undertaken. The objective of these studies was to gain a fundamental understanding of mechanisms through which FST augments the surface heat transfer. Experiments were carried out in the boundary layer and in the free stream downstream of a gas turbine combustor simulator, which produced initial FST levels of 25.7% and large length scales (About 5-10 cm for a boundary layer 4-5 cm thick). This result showed that one possible mechanism through which FST caused an increase in heat transfer is by increasing the number of ejection events. In a number of modeling studies several well-known k-epsilon models were compared for their predictive capability of heat transfer and skin friction coefficients under moderate and high FST. Two data sets, one with moderate levels of FST (about 7%) and one with high levels of FST (about 25%) were used for this purpose. Although the models did fine in their predictions of cases with no FST (baseline cases) they failed one by one as FST levels were increased. Under high FST (25.7% initial intensity) predictions of Stanton number were between 35-100% in error compared to the measured values. Later a new additional production term indicating the interaction between the turbulent kinetic energy (TKE) and mean velocity gradients was introduced into the TKE equation. The predicted results of skin friction coefficient and Stanton number were excellent both in moderate and high FST cases. In fact these model also gave good predictions of TKE profiles whereas earlier unmodified models did not predict the correct TKE profiles even under moderate turbulence intensities. Although this new production term seems to achieve the purpose, it is the authors' belief that it is diffusion term of the TKE equation, which needs to be modified in order to fit the physical events in high FST boundary layer flows. The results of these studies are currently being used to come up with new diffusion model for the TKE equation.

Application of site and haplotype-frequency based approaches for detecting selection signatures in cattle

PubMed Central

2011-01-01

Background 'Selection signatures' delimit regions of the genome that are, or have been, functionally important and have therefore been under either natural or artificial selection. In this study, two different and complementary methods--integrated Haplotype Homozygosity Score (|iHS|) and population differentiation index (FST)--were applied to identify traces of decades of intensive artificial selection for traits of economic importance in modern cattle. Results We scanned the genome of a diverse set of dairy and beef breeds from Germany, Canada and Australia genotyped with a 50 K SNP panel. Across breeds, a total of 109 extreme |iHS| values exceeded the empirical threshold level of 5% with 19, 27, 9, 10 and 17 outliers in Holstein, Brown Swiss, Australian Angus, Hereford and Simmental, respectively. Annotating the regions harboring clustered |iHS| signals revealed a panel of interesting candidate genes like SPATA17, MGAT1, PGRMC2 and ACTC1, COL23A1, MATN2, respectively, in the context of reproduction and muscle formation. In a further step, a new Bayesian FST-based approach was applied with a set of geographically separated populations including Holstein, Brown Swiss, Simmental, North American Angus and Piedmontese for detecting differentiated loci. In total, 127 regions exceeding the 2.5 per cent threshold of the empirical posterior distribution were identified as extremely differentiated. In a substantial number (56 out of 127 cases) the extreme FST values were found to be positioned in poor gene content regions which deviated significantly (p < 0.05) from the expectation assuming a random distribution. However, significant FST values were found in regions of some relevant genes such as SMCP and FGF1. Conclusions Overall, 236 regions putatively subject to recent positive selection in the cattle genome were detected. Both |iHS| and FST suggested selection in the vicinity of the Sialic acid binding Ig-like lectin 5 gene on BTA18. This region was recently reported to be a major QTL with strong effects on productive life and fertility traits in Holstein cattle. We conclude that high-resolution genome scans of selection signatures can be used to identify genomic regions contributing to within- and inter-breed phenotypic variation. PMID:21679429

Is ITS-2 rDNA suitable marker for genetic characterization of Sarcoptes mites from different wild animals in different geographic areas?

PubMed

Alasaad, S; Soglia, D; Spalenza, V; Maione, S; Soriguer, R C; Pérez, J M; Rasero, R; Degiorgis, M P Ryser; Nimmervoll, H; Zhu, X Q; Rossi, L

2009-02-05

The present study examined the relationship among individual Sarcoptes scabiei mites from 13 wild mammalian populations belonging to nine species in four European countries using the second internal transcribed spacer (ITS-2) of nuclear ribosomal DNA (rDNA) as genetic marker. The ITS-2 plus primer flanking 5.8S and 28S rDNA (ITS-2+) was amplified from individual mites by polymerase chain reaction (PCR) and the amplicons were sequenced directly. A total of 148 ITS-2+ sequences of 404bp in length were obtained and 67 variable sites were identified (16.59%). UPGMA analyses did not show any geographical or host-specific clustering, and a similar outcome was obtained using population pairwise Fst statistics. These results demonstrated that ITS-2 rDNA does not appear to be suitable for examining genetic diversity among mite populations.

Multivariate Qst–Fst Comparisons: A Neutrality Test for the Evolution of the G Matrix in Structured Populations

PubMed Central

Martin, Guillaume; Chapuis, Elodie; Goudet, Jérôme

2008-01-01

Neutrality tests in quantitative genetics provide a statistical framework for the detection of selection on polygenic traits in wild populations. However, the existing method based on comparisons of divergence at neutral markers and quantitative traits (Qst–Fst) suffers from several limitations that hinder a clear interpretation of the results with typical empirical designs. In this article, we propose a multivariate extension of this neutrality test based on empirical estimates of the among-populations (D) and within-populations (G) covariance matrices by MANOVA. A simple pattern is expected under neutrality: D = 2Fst/(1 − Fst)G, so that neutrality implies both proportionality of the two matrices and a specific value of the proportionality coefficient. This pattern is tested using Flury's framework for matrix comparison [common principal-component (CPC) analysis], a well-known tool in G matrix evolution studies. We show the importance of using a Bartlett adjustment of the test for the small sample sizes typically found in empirical studies. We propose a dual test: (i) that the proportionality coefficient is not different from its neutral expectation [2Fst/(1 − Fst)] and (ii) that the MANOVA estimates of mean square matrices between and among populations are proportional. These two tests combined provide a more stringent test for neutrality than the classic Qst–Fst comparison and avoid several statistical problems. Extensive simulations of realistic empirical designs suggest that these tests correctly detect the expected pattern under neutrality and have enough power to efficiently detect mild to strong selection (homogeneous, heterogeneous, or mixed) when it is occurring on a set of traits. This method also provides a rigorous and quantitative framework for disentangling the effects of different selection regimes and of drift on the evolution of the G matrix. We discuss practical requirements for the proper application of our test in empirical studies and potential extensions. PMID:18245845

Genetic variability and discrimination of low doses of Toxocara spp. from public areas soil inferred by loop-mediated isothermal amplification assay as a field-friendly molecular tool

PubMed Central

Ozlati, Maryam; Spotin, Adel; Shahbazi, Abbas; Mahami-Oskouei, Mahmoud; Hazratian, Teimour; Adibpor, Mohammad; Ahmadpour, Ehsan; Dolatkhah, Afsaneh; Khoshakhlagh, Paria

2016-01-01

Abstract: Aim: One of the main diagnostic problems of conventional polymerase chain reaction (PCR) is indiscrimination of low parasitic loads in soil samples. The aim of this study is to determine the genetic diversity and identification of Toxocara spp. from public areas soil inferred by loop-mediated isothermal amplification (LAMP) assay. Materials and Methods: A total of 180 soil samples were collected from various streets and public parks of northwest Iran. The DNA of recovered Toxocara eggs were extracted and amplified by PCR and LAMP following ZnSO4 flotation technique. The amplicons of internal transcribed spacer-2 gene were sequenced to reveal the heterogeneity traits of Toxocara spp. In addition, Toxocara canis sequences of southwest Iran were directly retrieved to compare gene flow between two distinct populations. Results: Toxocara spp. eggs were found in 57, 14 and 77 of soil samples using the microscopy, PCR and LAMP (detection limit 1-3 eggs/200 g soil), respectively. 7.7% of isolates were identified as T. canis by PCR method, while LAMP was able to detect 27.2%, 15.5% and 12.2% as Toxocara cati, T. canis and mixed infections, respectively. The kappa coefficient between LAMP and microscopy indicated a strong agreement (0.765) but indicated a faint agreement among LAMP-PCR (0.203) and PCR-microscopy (0.308) methods. A pairwise fixation index (Fst) as a degree of gene flow was generally low (0.02156) among Toxocara populations of northwest and southwest Iran. Conclusions: The statistically significant Fst value indicates that the T. canis populations are not genetically well differentiated between northwest and southwest Iran. This shows that here is possibly an epidemiological drift due to the transfer of alleles. The LAMP assay because of its shorter reaction time, more sensitivity, and simultaneous detection of environmental contamination to be appears as valuable field diagnosis compared to PCR. Therefore, the detection of low Toxocara spp. loads from public area soils will help to expand epidemiological understanding of toxocariasis and establishing preventive strategies in resource-limited endemic of Iran. PMID:28096624

Expanded Croatian 12 X-STR loci database with an overview of anomalous profiles.

PubMed

Mršić, Gordan; Ozretić, Petar; Crnjac, Josip; Merkaš, Siniša; Sukser, Viktorija; Račić, Ivana; Rožić, Sara; Barbarić, Lucija; Popović, Maja; Korolija, Marina

2018-05-01

In order to implement X-chromosome short tandem repeat (X-STR) typing into routine forensic practice, reference database of a given population should be established. Therefore we extended already published data with additional 397 blood samples from unrelated Croatian citizens, and analyzed the total of 995 samples (549 male and 446 female) typed by Investigator ® Argus X-12 Kit. To test genetic homogeneity of consecutively processed five historic-cultural regions covering the entire national territory, we calculated pairwise Fst genetic distances between regions based on allele and full haplotype frequencies. Since the comparison did not yield any statistically significant difference, we integrated STR profile information from all regions and used the whole data set to calculate forensic parameters. The most informative marker is DXS10135 (polymorphism information content (PIC = 0.929) and the most informative linkage group (LG) is LG1 (PIC = 0.996). We confirmed linkage disequilibrium (LD) for seven marker pairs belonging to LG2, LG3 and LG4. By including LD information, we calculated cumulative power of discrimination that amounted to 0.999999999997 in females and 0.999999005 in males. We also compared Croatia with 13 European populations based on haplotype frequencies and detected no statistically significant Fst values after Bonferroni correction in any LG. Multi-dimensional scaling plot revealed tight grouping of four Croatian regions amongst populations of southern, central and northern Europe, with the exception of northern Croatia. In this study we gave the first extensive overview of aberrant profiles encountered during Investigator ® Argus X-12 typing. We found ten profiles consistent with single locus duplication followed by tetranucleotide tract length polymorphism. Locus DXS10079 is by far the most frequently affected one, presumably mutated in eight samples. We also found four profiles consistent with X-chromosome aneuploidy (three profiles with XXX pattern and one profile with XXY pattern). In conclusion, we established integral forensic Croatian X-chromosome database, proved forensic pertinence of Investigator ® Argus X-12 Kit for the entire Croatian population and identified locus DXS10079 as a potential duplication hotspot. Copyright © 2018 Elsevier B.V. All rights reserved.

Population-specific FST values for forensic STR markers: A worldwide survey.

PubMed

Buckleton, John; Curran, James; Goudet, Jérôme; Taylor, Duncan; Thiery, Alexandre; Weir, B S

2016-07-01

The interpretation of matching between DNA profiles of a person of interest and an item of evidence is undertaken using population genetic models to predict the probability of matching by chance. Calculation of matching probabilities is straightforward if allelic probabilities are known, or can be estimated, in the relevant population. It is more often the case, however, that the relevant population has not been sampled and allele frequencies are available only from a broader collection of populations as might be represented in a national or regional database. Variation of allele probabilities among the relevant populations is quantified by the population structure quantity FST and this quantity affects matching proportions. Matching within a population can be interpreted only with respect to matching between populations and we show here that FST, can be estimated from sample allelic matching proportions within and between populations. We report such estimates from data we extracted from 250 papers in the forensic literature, representing STR profiles at up to 24 loci from nearly 500,000 people in 446 different populations. The results suggest that theta values in current forensic use do not have the buffer of conservatism often thought. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Population-specific FST values for forensic STR markers: A worldwide survey

PubMed Central

Buckleton, John; Curran, James; Goudet, Jérôme; Taylor, Duncan; Thiery, Alexandre; Weir, B.S.

2016-01-01

The interpretation of matching between DNA profiles of a person of interest and an item of evidence is undertaken using population genetic models to predict the probability of matching by chance. Calculation of matching probabilities is straightforward if allelic probabilities are known, or can be estimated, in the relevant population. It is more often the case, however, that the relevant population has not been sampled and allele frequencies are available only from a broader collection of populations as might be represented in a national or regional database. Variation of allele probabilities among the relevant populations is quantified by the population structure quantity FST and this quanity affects matching propoptions. Matching within a population can be interpreted only with respect to matching between populations and we show here that FST, can be estimated from sample allelic matching proportions within and between populations. We report such estimates from data we extracted from 250 papers in the forensic literature, representing STR profiles at up to 24 loci from nearly 500,000 people in 446 different populations. The results suggest that theta values in current forensic use do not have the buffer of conservativism often thought. PMID:27082756

Matching genetics with oceanography: directional gene flow in a Mediterranean fish species.

PubMed

Schunter, C; Carreras-Carbonell, J; Macpherson, E; Tintoré, J; Vidal-Vijande, E; Pascual, A; Guidetti, P; Pascual, M

2011-12-01

Genetic connectivity and geographic fragmentation are two opposing mechanisms determining the population structure of species. While the first homogenizes the genetic background across populations the second one allows their differentiation. Therefore, knowledge of processes affecting dispersal of marine organisms is crucial to understand their genetic distribution patterns and for the effective management of their populations. In this study, we use genetic analyses of eleven microsatellites in combination with oceanographic satellite and dispersal simulation data to determine distribution patterns for Serranus cabrilla, a ubiquitous demersal broadcast spawner, in the Mediterranean Sea. Pairwise population F(ST) values ranged between -0.003 and 0.135. Two genetically distinct clusters were identified, with a clear division located between the oceanographic discontinuities at the Ibiza Channel (IC) and the Almeria-Oran Front (AOF), revealing an admixed population in between. The Balearic Front (BF) also appeared to dictate population structure. Directional gene flow on the Spanish coast was observed as S. cabrilla dispersed from west to east over the AOF, from north to south on the IC and from south of the IC towards the Balearic Islands. Correlations between genetic and oceanographic data were highly significant. Seasonal changes in current patterns and the relationship between ocean circulation patterns and spawning season may also play an important role in population structure around oceanographic fronts. © 2011 Blackwell Publishing Ltd.

Population-structure and genetic diversity in a haplochromine cichlid fish [corrected] of a satellite lake of Lake Victoria.

PubMed

Abila, Romulus; Barluenga, Marta; Engelken, Johannes; Meyer, Axel; Salzburger, Walter

2004-09-01

The approximately 500 species of the cichlid fish species flock of Lake Victoria, East Africa, have evolved in a record-setting 100,000 years and represent one of the largest adaptive radiations. We examined the population structure of the endangered cichlid species Xystichromis phytophagus from Lake Kanyaboli, a satellite lake to Lake Victoria in the Kenyan Yala wetlands. Two sets of molecular markers were analysed--sequences of the mitochondrial control region as well as six microsatellite loci--and revealed surprisingly high levels of genetic variability in this species. Mitochondrial DNA sequences failed to detect population structuring among the three sample populations. A model-based population assignment test based on microsatellite data revealed that the three populations most probably aggregate into a larger panmictic population. However, values of population pairwise FST indicated moderate levels of genetic differentiation for one population. Eleven distinct mitochondrial haplotypes were found among 205 specimens of X. phytophagus, a relatively high number compared to the total number of 54 haplotypes that were recovered from hundreds of specimens of the entire cichlid species flock of Lake Victoria. Most of the X. phytophagus mitochondrial DNA haplotypes were absent from the main Lake Victoria, corroborating the putative importance of satellite lakes as refugia for haplochromine cichlids that went extinct from the main lake in the last decades and possibly during the Late Pleistocene desiccation of Lake Victoria.

The Y-STR genetic diversity of an Idaho Basque population, with comparison to European Basques and US Caucasians.

PubMed

Zubizarreta, Josu; Davis, Michael C; Hampikian, Greg

2011-12-01

Fifty unrelated Basque males from southwest Idaho were typed for the 17 Y-STR loci in the Yfiler multiplex kit (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, YGATA H4.1 and DYS385a/b). In total, 42 haplotypes were identified, with no more than two individuals sharing a single haplotype. The haplotype diversity (HD) was 0.9935, and gene diversity (D) over loci was 0.457 ± 0.137. The Idaho Basque population was compared to the source population from the Basque autonomous region of Northern Spain and Southern France, as well as a United States Caucasian population. The haplotype diversity for the immigrant Basque sample is within 0.4% of the haplotype diversity of the European Basques (0.9903); thus the power of discrimination is similar for each population. The Idaho Basque population has less diversity in 9 out of 16 loci (considering DYS385a/b together) and 3% less diversity across all loci, compared to the European Basque population. A multidimensional scaling analysis (MDS) was created using pairwise R(ST) values to compare the Idaho Basques to other populations. Based upon R(ST) and F(ST) measures, no significant differentiation was found between the Idaho and source European Basque population.

Genetic Evaluation of Natural Populations of the Endangered Conifer Thuja koraiensis Using Microsatellite Markers by Restriction-Associated DNA Sequencing

PubMed Central

Hou, Lu; Cui, Yanhong; Li, Xiang; Chen, Wu; Zhang, Zhiyong; Pang, Xiaoming; Li, Yingyue

2018-01-01

Thuja koraiensis Nakai is an endangered conifer of high economic and ecological value in Jilin Province, China. However, studies on its population structure and conservation genetics have been limited by the lack of genomic data. Here, 37,761 microsatellites (simple sequence repeat, SSR) were detected based on 875,792 de novo-assembled contigs using a restriction-associated DNA (RAD) approach. Among these SSRs, 300 were randomly selected to test for polymorphisms and 96 obtained loci were able to amplify a fragment of expected size. Twelve polymorphic SSR markers were developed to analyze the genetic diversity and population structure of three natural populations. High genetic diversity (mean NA = 5.481, HE = 0.548) and moderate population differentiation (pairwise Fst = 0.048–0.078, Nm = 2.940–4.958) were found in this species. Molecular variance analysis suggested that most of the variation (83%) existed within populations. Combining the results of STRUCTURE, principal coordinate, and neighbor-joining analysis, the 232 individuals were divided into three genetic clusters that generally correlated with their geographical distributions. Finally, appropriate conservation strategies were proposed to protect this species. This study provides genetic information for the natural resource conservation and utilization of T. koraiensis and will facilitate further studies of the evolution and phylogeography of the species. PMID:29673217

Genetic variation in scaly hair-fin anchovy Setipinna tenuifilis (Engraulididae) based on the mitochondrial DNA control region.

PubMed

Xu, Shengyong; Song, Na; Lu, Zhichuang; Wang, Jun; Cai, Shanshan; Gao, Tianxiang

2014-06-01

Scaly hair-fin anchovy (Setipinna tenuifilis) is a small, pelagic and economical species and widely distributed in Chinese coastal water. However, resources of S. tenuifilis have been reduced due to overfishing. For better fishery management, it is necessary to understand the pattern of S. tenuifilis's biogeography. Genetic analyses were taken place to detect their population genetic variation. A total of 153 individuals from 7 locations (Dongying, Yantai, Qingdao, Nantong, Wenzhou, Xiamen and Beibu Bay) were sequenced at the 5' end of mtDNA control region. A 39-bp tandem repeated sequence was found at the 5' end of the segment and a polymorphism of tandem repeated sequence was detected among 7 populations. Both mismatch distribution analysis and neutrality tests showed S. tenuifilis had experienced a recent population expansion. The topology of neighbor-joining tree and Bayesian evolutionary tree showed no significant genealogical branches or clusters of samples corresponding to sampling locality. Hierarchical analysis of molecular variance and conventional pairwise population Fst value at group hierarchical level implied that there might have genetic divergence between southern group (population WZ, XM and BB) and northern group (population DY, YT, QD and NT). We concluded that there might have three different fishery management groups of S. tenuifilis and the late Pleistocene glacial event might have a crucial effect on present-day demography of S. tenuifilis in this region.

Psychophysical Measurement of Rod and Cone Thresholds in Stargardt Disease with Full-Field Stimuli

PubMed Central

Collison, Frederick T.; Fishman, Gerald A.; McAnany, J. Jason; Zernant, Jana; Allikmets, Rando

2014-01-01

Purpose To investigate psychophysical thresholds in Stargardt disease with the full-field stimulus test (FST). Methods Visual acuity (VA), spectral-domain optical coherence tomography (SD-OCT), full-field electroretinogram (ERG), and FST measurements were made in one eye of 24 patients with Stargardt disease. Dark-adapted rod FST thresholds were measured with short-wavelength stimuli, and cone FST thresholds were obtained from the cone plateau phase of dark adaptation using long-wavelength stimuli. Correlation coefficients were calculated for FST thresholds versus macular thickness, VA and ERG amplitudes. Results Stargardt patient FST cone thresholds correlated significantly with VA, macular thickness, and ERG cone-response amplitudes (all P<0.01). The patients’ FST rod thresholds correlated with ERG rod-response amplitudes (P<0.01), but not macular thickness (P=0.05). All Stargardt disease patients with flecks confined to the macula and most of the patients with flecks extending outside of the macula had normal FST thresholds. All patients with extramacular atrophic changes had elevated FST cone thresholds and most had elevated FST rod thresholds. Conclusion FST rod and cone threshold elevation in Stargardt disease patients correlated well with measures of structure and function, as well as ophthalmoscopic retinal appearance. FST appears to be a useful tool for assessing rod and cone function in Stargardt disease. PMID:24695063

Effects of integration time on in-water radiometric profiles.

PubMed

D'Alimonte, Davide; Zibordi, Giuseppe; Kajiyama, Tamito

2018-03-05

This work investigates the effects of integration time on in-water downward irradiance E d , upward irradiance E u and upwelling radiance L u profile data acquired with free-fall hyperspectral systems. Analyzed quantities are the subsurface value and the diffuse attenuation coefficient derived by applying linear and non-linear regression schemes. Case studies include oligotrophic waters (Case-1), as well as waters dominated by Colored Dissolved Organic Matter (CDOM) and Non-Algal Particles (NAP). Assuming a 24-bit digitization, measurements resulting from the accumulation of photons over integration times varying between 8 and 2048ms are evaluated at depths corresponding to: 1) the beginning of each integration interval (Fst); 2) the end of each integration interval (Lst); 3) the averages of Fst and Lst values (Avg); and finally 4) the values weighted accounting for the diffuse attenuation coefficient of water (Wgt). Statistical figures show that the effects of integration time can bias results well above 5% as a function of the depth definition. Results indicate the validity of the Wgt depth definition and the fair applicability of the Avg one. Instead, both the Fst and Lst depths should not be adopted since they may introduce pronounced biases in E u and L u regression products for highly absorbing waters. Finally, the study reconfirms the relevance of combining multiple radiometric casts into a single profile to increase precision of regression products.

Intra-specific genetic diversity in wild olives (Olea europaea ssp cuspidata) in Hormozgan Province, Iran.

PubMed

Noormohammadi, Z; Samadi-Molayousefi, H; Sheidai, M

2012-03-19

Wild olive (O. europaea ssp cuspidata) plants grow in various regions of Iran and are expected to have considerable genetic diversity due to adaptation to the various environmental conditions. We examined the genetic diversity of four populations of wild olive growing in Hormozgan Province located in southern Iran by using 30 RAPDs and 10 ISSR markers. The mean value of polymorphism for RAPD loci was 73.71%, while the value for ISSR loci was 81.74%. The Keshar population had the highest value of intra-population polymorphism for both RAPD and ISSR loci (66.86 and 62.71%, respectively), while the Tudar population had the lowest values (20.35 and 28.81%, respectively). Similarly, the highest and lowest number of effective alleles, Shannon index and Nei's genetic diversity were also found for these two populations. The highest value of H(pop)/H(sp) within population genetic diversity for RAPD and ISSR loci was found for the Keshar population (H(pop) = 0.85 and H(sp) = 0.90). OPA04-750, OPA13-650 and OPA02-350 RAPD bands were specific for Tudar, Bondon and Keshar populations, respectively, while no specific ISSR bands were observed. Analysis of molecular variance as well as the pairwise F(ST) test showed significant differences for RAPD and ISSR markers among the populations. The NJ and UPGMA trees also separated the wild olive populations from each other, indicating their genetic distinctness. UPGMA clustering of the four wild olive populations placed the Tudar population far from the other populations; Keshar and Bokhoon population samples revealed more similarity and were grouped together. We conclude that there is high genetic diversity among O. europaea ssp cuspidata populations located in southern Iran. We also found RAPD and ISSR markers to be useful molecular tools to discriminate and evaluate genetic variations in wild olive trees.

Molecular cloning, expression pattern of follistatin gene and association analysis with growth traits in bighead carp (Hypophthalmichthys nobilis).

PubMed

Pang, Meixia; Tong, Jingou; Yu, Xiaomu; Fu, Beide; Zhou, Ying

2018-04-01

Follistatin (FST) is a single-chain gonadal protein involving in various biological effects. FST plays important roles in not only ovary development but also body growth, whereas myostatin (MSTN) negatively regulates muscle growth. In this study, FST gene in bighead carp (HynFST) was cloned and characterized. A 5797 bp genomic sequence of HynFST, consisting six exons and five introns were cloned. The full-length cDNA of HynFST (2134 bp) has an open reading fragment encoding a polypeptide of 349 amino acids. Sequence comparison and phylogenetic analysis confirmed that FSTs are conserved throughout the vertebrates and HynFST belongs to FST-1 isoform. Nine single nucleotide polymorphisms (SNPs) of the HynFST were identified and three of them (g.2443 T > C, g.2852 T > C and g.5483A > G) were significantly associated with four growth-related traits. The average body weight of those fish with the combined genotype (CC CC GG) was 12.15-22.63% higher than that of triplotype (TT TT AA) in two bighead carp populations. HynFST was expressed in most of the development stages and various tissues with highest level in ovary. The co-expression results for FST and MSTN in brain and muscle of divergent weight groups showed that FST may inhibit MSTN expression, thus enhancing growth in bighead carp. Our results suggest that FST has significant genetic effects on the regulation of early growth in bighead carp. This study would facilitate the elucidation of multiple functions of FST gene in fish and exploration of the potentials as a gene marker in selective breeding programs for growth of bighead carp. Copyright © 2018 Elsevier Inc. All rights reserved.

Microsatellite and mtDNA analysis of lake trout, Salvelinus namaycush, from Great Bear Lake, Northwest Territories: impacts of historical and contemporary evolutionary forces on Arctic ecosystems

PubMed Central

Harris, Les N; Howland, Kimberly L; Kowalchuk, Matthew W; Bajno, Robert; Lindsay, Melissa M; Taylor, Eric B

2013-01-01

Resolving the genetic population structure of species inhabiting pristine, high latitude ecosystems can provide novel insights into the post-glacial, evolutionary processes shaping the distribution of contemporary genetic variation. In this study, we assayed genetic variation in lake trout (Salvelinus namaycush) from Great Bear Lake (GBL), NT and one population outside of this lake (Sandy Lake, NT) at 11 microsatellite loci and the mtDNA control region (d-loop). Overall, population subdivision was low, but significant (global FST θ = 0.025), and pairwise comparisons indicated that significance was heavily influenced by comparisons between GBL localities and Sandy Lake. Our data indicate that there is no obvious genetic structure among the various basins within GBL (global FST = 0.002) despite the large geographic distances between sampling areas. We found evidence of low levels of contemporary gene flow among arms within GBL, but not between Sandy Lake and GBL. Coalescent analyses suggested that some historical gene flow occurred among arms within GBL and between GBL and Sandy Lake. It appears, therefore, that contemporary (ongoing dispersal and gene flow) and historical (historical gene flow and large founding and present-day effective population sizes) factors contribute to the lack of neutral genetic structure in GBL. Overall, our results illustrate the importance of history (e.g., post-glacial colonization) and contemporary dispersal ecology in shaping genetic population structure of Arctic faunas and provide a better understanding of the evolutionary ecology of long-lived salmonids in pristine, interconnected habitats. PMID:23404390

Microsatellite and mtDNA analysis of lake trout, Salvelinus namaycush, from Great Bear Lake, Northwest Territories: impacts of historical and contemporary evolutionary forces on Arctic ecosystems.

PubMed

Harris, Les N; Howland, Kimberly L; Kowalchuk, Matthew W; Bajno, Robert; Lindsay, Melissa M; Taylor, Eric B

2012-01-01

Resolving the genetic population structure of species inhabiting pristine, high latitude ecosystems can provide novel insights into the post-glacial, evolutionary processes shaping the distribution of contemporary genetic variation. In this study, we assayed genetic variation in lake trout (Salvelinus namaycush) from Great Bear Lake (GBL), NT and one population outside of this lake (Sandy Lake, NT) at 11 microsatellite loci and the mtDNA control region (d-loop). Overall, population subdivision was low, but significant (global F(ST) θ = 0.025), and pairwise comparisons indicated that significance was heavily influenced by comparisons between GBL localities and Sandy Lake. Our data indicate that there is no obvious genetic structure among the various basins within GBL (global F(ST) = 0.002) despite the large geographic distances between sampling areas. We found evidence of low levels of contemporary gene flow among arms within GBL, but not between Sandy Lake and GBL. Coalescent analyses suggested that some historical gene flow occurred among arms within GBL and between GBL and Sandy Lake. It appears, therefore, that contemporary (ongoing dispersal and gene flow) and historical (historical gene flow and large founding and present-day effective population sizes) factors contribute to the lack of neutral genetic structure in GBL. Overall, our results illustrate the importance of history (e.g., post-glacial colonization) and contemporary dispersal ecology in shaping genetic population structure of Arctic faunas and provide a better understanding of the evolutionary ecology of long-lived salmonids in pristine, interconnected habitats.

Directional genetic selection by pulp mill effluent on multiple natural populations of three-spined stickleback (Gasterosteus aculeatus).

PubMed

Lind, Emma E; Grahn, Mats

2011-05-01

Contamination can cause a rapid environmental change which may require populations to respond with evolutionary changes. To evaluate the effects of pulp mill effluents on population genetics, we sampled three-spined sticklebacks (Gasterosteus aculeatus) near four pulp mills and four adjacent reference sites and analyzed Amplified Fragment Length Polymorphism (AFLP) to compare genetic variability. A fine scale genetic structure was detected and samples from polluted sites separated from reference sites in multidimensional scaling plots (P<0.005, 1000 permutations) and locus-by-locus Analysis of Molecular Variance (AMOVA) further confirmed that habitats are significantly separated (F(ST)=0.021, P<0.01, 1023 permutations). The amount of genetic variation between populations did not differ between habitats, and populations from both habitats had similar levels of heterozygosity (polluted sites Nei's Hs=0.11, reference sites Nei's Hs=0.11). Still, pairwise F(ST): s between three, out of four, pairs of polluted-reference sites were significant. A F(ST)-outlier analysis showed that 21 (8.4%) loci were statistically different from a neutral distribution at the P<0.05 level and therefore indicated to be under divergent selection. When removing 13 F(ST)-outlier loci, significant at the P<0.01 level, differentiation between habitats disappeared in a multidimensional scaling plot. In conclusion, pulp mill effluence has acted as a selective agent on natural populations of G. aculeatus, causing a convergence in genotype composition change at multiple sites in an open environment. © The Author(s) 2011. This article is published with open access at Springerlink.com

The roles of genetic drift and natural selection in quantitative trait divergence along an altitudinal gradient in Arabidopsis thaliana

PubMed Central

Luo, Y; Widmer, A; Karrenberg, S

2015-01-01

Understanding how natural selection and genetic drift shape biological variation is a central topic in biology, yet our understanding of the agents of natural selection and their target traits is limited. We investigated to what extent selection along an altitudinal gradient or genetic drift contributed to variation in ecologically relevant traits in Arabidopsis thaliana. We collected seeds from 8 to 14 individuals from each of 14 A. thaliana populations originating from sites between 800 and 2700 m above sea level in the Swiss Alps. Seed families were grown with and without vernalization, corresponding to winter-annual and summer-annual life histories, respectively. We analyzed putatively neutral genetic divergence between these populations using 24 simple sequence repeat markers. We measured seven traits related to growth, phenology and leaf morphology that are rarely reported in A. thaliana and performed analyses of altitudinal clines, as well as overall QST-FST comparisons and correlation analyses among pair-wise QST, FST and altitude of origin differences. Multivariate analyses suggested adaptive differentiation along altitude in the entire suite of traits, particularly when expressed in the summer-annual life history. Of the individual traits, a decrease in rosette leaf number in the vegetative state and an increase in leaf succulence with increasing altitude could be attributed to adaptive divergence. Interestingly, these patterns relate well to common within- and between-species trends of smaller plant size and thicker leaves at high altitude. Our results thus offer exciting possibilities to unravel the underlying mechanisms for these conspicuous trends using the model species A. thaliana. PMID:25293874

Unraveling Haplotype Diversity of the Apical Membrane Antigen-1 Gene in Plasmodium falciparum Populations in Thailand

PubMed Central

Lumkul, Lalita; Sawaswong, Vorthon; Simpalipan, Phumin; Kaewthamasorn, Morakot; Harnyuttanakorn, Pongchai; Pattaradilokrat, Sittiporn

2018-01-01

Development of an effective vaccine is critically needed for the prevention of malaria. One of the key antigens for malaria vaccines is the apical membrane antigen 1 (AMA-1) of the human malaria parasite Plasmodium falciparum, the surface protein for erythrocyte invasion of the parasite. The gene encoding AMA-1 has been sequenced from populations of P. falciparum worldwide, but the haplotype diversity of the gene in P. falciparum populations in the Greater Mekong Subregion (GMS), including Thailand, remains to be characterized. In the present study, the AMA-1 gene was PCR amplified and sequenced from the genomic DNA of 65 P. falciparum isolates from 5 endemic areas in Thailand. The nearly full-length 1,848 nucleotide sequence of AMA-1 was subjected to molecular analyses, including nucleotide sequence diversity, haplotype diversity and deduced amino acid sequence diversity and neutrality tests. Phylogenetic analysis and pairwise population differentiation (Fst indices) were performed to infer the population structure. The analyses identified 60 single nucleotide polymorphic loci, predominately located in domain I of AMA-1. A total of 31 unique AMA-1 haplotypes were identified, which included 11 novel ones. The phylogenetic tree of the AMA-1 haplotypes revealed multiple clades of AMA-1, each of which contained parasites of multiple geographical origins, consistent with the Fst indices indicating genetic homogeneity or gene flow among geographically distinct populations of P. falciparum in Thailand’s borders with Myanmar, Laos and Cambodia. In summary, the study revealed novel haplotypes and population structure needed for the further advancement of AMA-1-based malaria vaccines in the GMS. PMID:29742870

Effects of waterproof covering on hand immersion tests using water at 10 degrees C, 12 degrees C and 15 degrees C for diagnosis of hand-arm vibration syndrome.

PubMed

Suizu, K; Harada, N

2005-05-01

To compare effects of waterproof covering on finger skin temperature (FST) and subjective hand pain during immersion tests using cold water at 10 degrees C, 12 degrees C and 15 degrees C. In the (Draft International Standard) of the International Organization for Standardization (ISO/DIS 14835-1), a water temperature of 12 degrees C and use of water covering are proposed. Six healthy male subjects took part in the immersion tests and immersed both hands into water at 10 degrees C, 12 degrees C and 15 degrees C for 5 min, repeatedly, with waterproof covering (polyethylene gloves) or without (bare hands). The FST data from middle fingers and subjective pain scores for hand pain were analyzed. Furthermore, the test with water at 12 degrees C was repeated to assess the repeatability of the test. The glove and water temperature factors for FST were significant at every minute from 1 min during immersion up to 2 min after recovery, showing higher values for waterproof covering than for bare hands and showing lowest values for water temperature of 10 degrees C and highest for 15 degrees C. The glove and water temperature factors for subjective pain score were significant at the 1-min and 2-min points during immersion, showing lower scores for waterproof covering than for bare hands and showing highest scores for water temperature of 10 degrees C and lowest for 15 degrees C. The results of the first and second tests using water of 12 degrees C showed no systematic difference in FST and hand pain between the tests, with a few exceptions. Subjective pain during the cold immersion test with polyethylene gloves and water at 12 degrees C can be reduced, while the differences in FST between water temperatures of 10 degrees C and 12 degrees C were small or not apparent at some points during immersion and recovery. The test also seems to be suitable for repeatability. Further investigation on hand-arm vibration syndrome (HAVS) patients to validate the use of the immersion test with gloves to obtain sufficient data for diagnostic value is required.

Test-retest paradigm of the forced swimming test in female mice is not valid for predicting antidepressant-like activity: participation of acetylcholine and sigma-1 receptors.

PubMed

Su, Jing; Hato-Yamada, Noriko; Araki, Hiroaki; Yoshimura, Hiroyuki

2013-01-01

The forced swimming test (FST) in mice is widely used to predict the antidepressant activity of a drug, but information describing the immobility of female mice is limited. We investigated whether a prior swimming experience affects the immobility duration in a second FST in female mice and whether the test-retest paradigm is a valid screening tool for antidepressants. Female ICR mice were exposed to the FST using two experimental paradigms: a single FST and a double FST in which mice had experienced FST once 24 h prior to the second trail. The initial FST experience reliably prolonged immobility duration in the second FST. The antidepressants imipramine and paroxetine significantly reduced immobility duration in the single FST, but not in the double FST. Scopolamine and the sigma-1 (σ1) antagonist NE-100 administered before the second trial significantly prevented the prolongation of immobility. Neither a 5-HT1A nor a 5-HT2A receptor agonist affected immobility duration. We suggest that the test-retest paradigm in female mice is not adequate for predicting antidepressant-like activity of a drug; the prolongation of immobility in the double FST is modulated through acetylcholine and σ1 receptors.

The diagnostic value of finger systolic blood pressure and cold-provocation testing for the vascular component of hand-arm vibration syndrome in health surveillance.

PubMed

Poole, K; Elms, J; Mason, H J

2004-12-01

Hand-arm vibration syndrome (HAVS) is a complex condition with vascular, sensorineural and musculoskeletal components. A number of quantitative tests have been used for assisting in the diagnosis of HAVS and grading disease severity. To investigate and compare the diagnostic value of finger systolic blood pressure (FSBP) and rewarming of finger skin temperature (FST) following cold-provocation testing, in the assessment of vascular HAVS. Twenty-four individuals with vascular HAVS (Stockholm Workshop stage 2 or 3V) and 22 control subjects underwent FSBP measurements at 30, 15 and 10 degrees C and monitoring of FST following immersion of the hands in water at 15 degrees C for 5 min. There was a significant reduction in median FSBP% in the vascular HAVS group in the change in FSBP from 30 to 15 degrees C adjusted for brachial blood pressure (FSBPC%). There was no difference in the median time for FST to rewarm by 4 degrees C between HAVS cases and controls. The sensitivity and specificity of FSBP to discriminate between the groups varied between 44 and 61% and 91 and 95%, respectively. The sensitivity and specificity for the time for FST to rewarm by 4 degrees C were 71 and 77%. There is little evidence that the described form of finger rewarming after cold-provocation testing is a useful diagnostic test for vascular HAVS, although it may have some moderate influence in ruling out vascular problems. Based on our data, the FSBP may also have limited use in confirming a positive diagnosis of vibration-induced vascular problems. The higher specificity of the FSBP test suggests it may have some value in ruling out the vascular component of HAVS. The data from this study do not confirm the diagnostic power of FSBP for the vascular component of HAVS reported by a few other investigators.

Efficient photocatalytic degradation of organic pollutants by magnetically recoverable nitrogen-doped TiO2 nanocomposite photocatalysts under visible light irradiation.

PubMed

Hamzezadeh-Nakhjavani, Sahar; Tavakoli, Omid; Akhlaghi, Seyed Parham; Salehi, Zeinab; Esmailnejad-Ahranjani, Parvaneh; Arpanaei, Ayyoob

2015-12-01

Preparation of novel nanocomposite particles (NCPs) with high visible-light-driven photocatalytic activity and possessing recovery potential after advanced oxidation process (AOP) is much desired. In this study, pure anatase phase titania (TiO2) nanoparticles (NPs) as well as three types of NCPs including nitrogen-doped titania (TiO2-N), titania-coated magnetic silica (Fe3O4 cluster@SiO2@TiO2 (FST)), and a novel magnetically recoverable TiO2 nanocomposite photocatalyst containing nitrogen element (Fe3O4 cluster@SiO2@TiO2-N (FST-N)) were successfully synthesized via a sol-gel process. The photocatalysts were characterized by X-ray diffraction (XRD), Fourier transform infrared (FT-IR) spectroscopy, field emission scanning electron microscopy (FE-SEM) with an energy-dispersive X-ray (EDX) spectroscopy analysis, X-ray photoelectron spectroscopy (XPS), UV-vis diffuse reflectance spectroscopy (DRS), and vibrating sample magnetometer (VSM). The photocatalytic activity of as-prepared samples was further investigated and compared with each other by degradation of phenol, as a model for the organic pollutants, in deionized (DI) water under visible light irradiation. The TiO2-N (55 ± 1.5%) and FST-N (46 ± 1.5%) samples exhibited efficient photocatalytic activity in terms of phenol degradation under visible light irradiation, while undoped samples were almost inactive under same operating conditions. Moreover, the effects of key operational parameters, the optimum sample calcination temperature, and reusability of FST-N NCPs were evaluated. Under optimum conditions (calcination temperature of 400 °C and near-neutral reaction medium), the obtained results revealed efficient degradation of phenol for FST-N NCPs under visible light irradiation (46 ± 1.5%), high yield magnetic separation and efficient reusability of FST-N NCPs (88.88% of its initial value) over 10 times reuse.

Genetic Diversity and Population Structure of Theileria annulata in Oman

PubMed Central

Al-Hamidhi, Salama; H. Tageldin, Mohammed.; Weir, William; Al-Fahdi, Amira; Johnson, Eugene H.; Bobade, Patrick; Alqamashoui, Badar; Beja-Pereira, Albano; Thompson, Joanne; Kinnaird, Jane; Shiels, Brian; Tait, Andy; Babiker, Hamza

2015-01-01

Background Theileriosis, caused by a number of species within the genus Theileria, is a common disease of livestock in Oman. It is a major constraint to the development of the livestock industry due to a high rate of morbidity and mortality in both cattle and sheep. Since little is currently known about the genetic diversity of the parasites causing theileriosis in Oman, the present study was designed to address this issue with specific regard to T. annulata in cattle. Methods Blood samples were collected from cattle from four geographically distinct regions in Oman for genetic analysis of the Theileria annulata population. Ten genetic markers (micro- and mini-satellites) representing all four chromosomes of T. annulata were applied to these samples using a combination of PCR amplification and fragment analysis. The resultant genetic data was analysed to provide a first insight into the structure of the T. annulata population in Oman. Results We applied ten micro- and mini-satellite markers to a total of 310 samples obtained from different regions (174 [56%] from Dhofar, 68 [22%] from Dhira, 44 [14.5%] from Batinah and 24 [8%] from Sharqia). A high degree of allelic diversity was observed among the four parasite populations. Expected heterozygosity for each site ranged from 0.816 to 0.854. A high multiplicity of infection was observed in individual hosts, with an average of 3.3 to 3.4 alleles per locus, in samples derived from Batinah, Dhofar and Sharqia regions. In samples from Dhira region, an average of 2.9 alleles per locus was observed. Mild but statistically significant linkage disequilibrium between pairs of markers was observed in populations from three of the four regions. In contrast, when the analysis was performed at farm level, no significant linkage disequilibrium was observed. Finally, no significant genetic differentiation was seen between the four populations, with most pair-wise FST values being less than 0.03. Slightly higher FST values (GST’ = 0.075, θ = 0.07) were detected when the data for T. annulata parasites in Oman was compared with that previously generated for Turkey and Tunisia. Conclusion Genetic analyses of T. annulata samples representing four geographical regions in Oman revealed a high level of genetic diversity in the parasite population. There was little evidence of genetic differentiation between parasites from different regions, and a high level of genetic diversity was maintained within each sub-population. These findings are consistent with a high parasite transmission rate and frequent movement of animals between different regions in Oman. PMID:26469349

Genetic Diversity and Population Structure of Theileria annulata in Oman.

PubMed

Al-Hamidhi, Salama; H Tageldin, Mohammed; Weir, William; Al-Fahdi, Amira; Johnson, Eugene H; Bobade, Patrick; Alqamashoui, Badar; Beja-Pereira, Albano; Thompson, Joanne; Kinnaird, Jane; Shiels, Brian; Tait, Andy; Babiker, Hamza

2015-01-01

Theileriosis, caused by a number of species within the genus Theileria, is a common disease of livestock in Oman. It is a major constraint to the development of the livestock industry due to a high rate of morbidity and mortality in both cattle and sheep. Since little is currently known about the genetic diversity of the parasites causing theileriosis in Oman, the present study was designed to address this issue with specific regard to T. annulata in cattle. Blood samples were collected from cattle from four geographically distinct regions in Oman for genetic analysis of the Theileria annulata population. Ten genetic markers (micro- and mini-satellites) representing all four chromosomes of T. annulata were applied to these samples using a combination of PCR amplification and fragment analysis. The resultant genetic data was analysed to provide a first insight into the structure of the T. annulata population in Oman. We applied ten micro- and mini-satellite markers to a total of 310 samples obtained from different regions (174 [56%] from Dhofar, 68 [22%] from Dhira, 44 [14.5%] from Batinah and 24 [8%] from Sharqia). A high degree of allelic diversity was observed among the four parasite populations. Expected heterozygosity for each site ranged from 0.816 to 0.854. A high multiplicity of infection was observed in individual hosts, with an average of 3.3 to 3.4 alleles per locus, in samples derived from Batinah, Dhofar and Sharqia regions. In samples from Dhira region, an average of 2.9 alleles per locus was observed. Mild but statistically significant linkage disequilibrium between pairs of markers was observed in populations from three of the four regions. In contrast, when the analysis was performed at farm level, no significant linkage disequilibrium was observed. Finally, no significant genetic differentiation was seen between the four populations, with most pair-wise FST values being less than 0.03. Slightly higher FST values (GST' = 0.075, θ = 0.07) were detected when the data for T. annulata parasites in Oman was compared with that previously generated for Turkey and Tunisia. Genetic analyses of T. annulata samples representing four geographical regions in Oman revealed a high level of genetic diversity in the parasite population. There was little evidence of genetic differentiation between parasites from different regions, and a high level of genetic diversity was maintained within each sub-population. These findings are consistent with a high parasite transmission rate and frequent movement of animals between different regions in Oman.

Microsatellite variation in Donax trunculus from the Iberian Peninsula, with particular attention to Galician estuaries (NW Spain)

NASA Astrophysics Data System (ADS)

Nantón, A.; Arias-Pérez, A.; Freire, R.; Fernández-Pérez, J.; Nóvoa, S.; Méndez, J.

2017-10-01

Genetic variation and population structure information is essential for conservation and stock management policies. The wedge clam Donax trunculus is an important fishing resource in the Iberian Peninsula and in some areas, such as the northwestern Spain, wild stocks have decreased greatly. Despite this, information is mainly from the southwestern Atlantic to the northwestern Mediterranean of the Iberian Peninsula. In this study, fifteen microsatellite loci were examined at 17 localities along the Iberian Peninsula to characterize its genetic diversity and population structure. Particular attention was paid to the northwestern Atlantic area, and to test if the pattern previously described for this species is confirmed when localities distributed across the Atlantic coast are included and different microsatellite markers are used. All localities displayed similar allelic richness values and heterozygosity levels but when genetic diversity levels were compared among groups of localities, tests were significant and samples from the northwestern area (Galicia) showed the lowest values. The analysis of population structure indicated that localities from the Atlantic coast are genetically homogeneous although some samples showed significant pairwise Fst values. These values were low and Bayesian analysis of genetic differentiation did not show a consistent structure along the Atlantic coast of the Iberian Peninsula. However, Atlantic samples were genetically different from those located in Mediterranean coast, which may be explained by the existence of the Almeria-Oran front. Moreover, Fuengirola, locality situated in the Alboran Sea between the Strait of Gibraltar and Mediterranean Sea, showed significant differences from all remaining localities included in the study. Overall, the data showed the existence of genetic homogeneity along the Atlantic coast of the Iberian Peninsula and support the three management units (Atlantic Ocean, the Alboran Sea and the northwestern Mediterranean) previously described in this species. Reduced diversity in the northwestern Spain samples could be related to the exploitation of this resource.

Comparison of quantitative and qualitative tests for glucose-6-phosphate dehydrogenase deficiency in the neonatal period.

PubMed

Keihanian, F; Basirjafari, S; Darbandi, B; Saeidinia, A; Jafroodi, M; Sharafi, R; Shakiba, M

2017-06-01

Considering the high prevalence of glucose-6-phosphate dehydrogenase (G6PD) deficiency among newborns, different screening methods have been established in various countries. In this study, we aimed to assess the prevalence of G6PD deficiency among newborns in Rasht, Iran, and compare G6PD activity in cord blood samples, using quantitative and qualitative tests. This cross-sectional, prospective study was performed at five largest hospitals in Rasht, Guilan Province, Iran. The screening tests were performed for all the newborns, referred to these hospitals. Specimens were characterized in terms of G6PD activity under ultraviolet light, using the kinetic method and the qualitative fluorescent spot test (FST). We also determined the sensitivity, specificity, negative predictive value, and positive predictive value of the qualitative assay. Blood samples were collected from 1474 newborns. Overall, 757 (51.4%) subjects were male. As the findings revealed, 1376 (93.4%) newborns showed normal G6PD activity, while 98 (6.6%) had G6PD deficiency. There was a significant difference in the mean G6PD level between males and females (P = 0.0001). Also, a significant relationship was detected between FST results and the mean values obtained in the quantitative test (P < 0.0001). According to the present study, FST showed acceptable sensitivity and specificity for G6PD activity, although it appeared inefficient for diagnostic purposes in some cases. © 2017 John Wiley & Sons Ltd.

Psychophysical assessment of low visual function in patients with retinal degenerative diseases (RDDs) with the Diagnosys full-field stimulus threshold (D-FST).

PubMed

Klein, M; Birch, D G

2009-12-01

To determine whether the Diagnosys full-field stimulus threshold (D-FST) is a valid, sensitive and repeatable psychophysical method of measuring and following visual function in low-vision subjects. Fifty-three affected eyes of 42 subjects with severe retinal degenerative diseases (RDDs) were tested with achromatic stimuli on the D-FST. Included were subjects who were either unable to perform a static perimetric field or had non-detectable or sub-microvolt electroretinograms (ERGs). A subset of 21 eyes of 17 subjects was tested on both the D-FST and the FST2, a previous established full-field threshold test. Seven eyes of 7 normal control subjects were tested on both the D-FST and the FST2. Results for the two methods were compared with the Bland-Altman test. On the D-FST, a threshold could successfully be determined for 13 of 14 eyes with light perception (LP) only (median 0.9 +/- 1.4 log cd/m2), and all eyes determined to be counting fingers (CF; median 0.3 +/- 1.8 log cd/m2). The median full-field threshold for the normal controls was -4.3 +/- 0.6 log cd/m2 on the D-FST and -4.8 +/- 0.9 log cd/m2 on the FST2. The D-FST offers a commercially available method with a robust psychophysical algorithm and is a useful tool for following visual function in low vision subjects.

Concordance study and population frequencies for 16 autosomal STRs analyzed with PowerPlex® ESI 17 and AmpFℓSTR® NGM SElect™ in Somalis, Danes and Greenlanders.

PubMed

Tomas, C; Mogensen, H S; Friis, S L; Hallenberg, C; Stene, M C; Morling, N

2014-07-01

A concordance study of the results of PowerPlex(®) ESI 17 and AmpFℓSTR(®) NGM SElect™ kits obtained from 591 individuals from Somalia (N=198), Denmark (N=199) and Greenland (N=194) was performed. Among 9456 STR types, seven discordant results were found with the two kits: one observed in the D19S433 system in an individual from Denmark and six in the SE33 system in six individuals from Somalia. Sequencing of SE33 in the six samples with discordant results showed G>A transition 15bp downstream of the repeat unit in three of the individuals, and G>A transition 68bp downstream of the repeat unit in the other three individuals. Population data for 16 autosomal STR systems analyzed in 989 individuals from Somalia, Denmark and Greenland are also presented. The highest mean heterozygosity was observed in Danes (82.5%). With the exception of D8S1179 in Danes, no significant deviations from Hardy-Weinberg expectations were observed. Only one pair of systems (D12S391 and D18S51) showed significant allelic association in Greenlanders (after Holm-Šidák correction). A MDS plot drawn from pairwise FST values calculated between 21 populations showed a clear displacement of the Greenlandic population versus the other ones included in the analyses. The highest combined chance of exclusion and power of discrimination was observed for Danes reaching values of 99.9999987% and 1 in 1.8×10(21), respectively. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Effects of swim stress and fluoxetine on 5-HT1A receptor gene expression and monoamine metabolism in the rat brain regions.

PubMed

Shishkina, G T; Kalinina, T S; Dygalo, N N

2012-07-01

Changes in gene expression of the brain serotonin (5-HT) 1A receptors may be important for the development and ameliorating depression, however identification of specific stimuli that activate or reduce the receptor transcriptional activity is far from complete. In the present study, the forced swim test (FST) exposure, the first stress session of which is already sufficient to induce behavioral despair in rats, significantly increased 5-HT1A receptor mRNA levels in the brainstem, frontal cortex, and hippocampus at 24 h. In the brainstem and frontal cortex, the elevation in the receptor gene expression after the second forced swim session was not affected following chronic administration of fluoxetine, while in the cortex, both control and FST values were significantly reduced in fluoxetine-treated rats. In contrast to untreated rats, no increase in hippocampal 5-HT1A receptor mRNA was observed in response to FST in rats chronically treated with fluoxetine. Metabolism of 5-HT (5-HIAA/5-HT) in the brainstem was significantly decreased by fluoxetine and further reduced by swim stress, showing a certain degree of independence of these changes on 5-HT1A receptor gene expression that was increased in this brain region only after the FST, but not after fluoxetine. FST exposure also decreased the brainstem dopamine metabolism, which was unexpectedly positively correlated with 5-HT1A receptor mRNA levels in the frontal cortex. Together, these data suggest that the effects of the forced swim stress as well as fluoxetine involve brain region-dependent alterations in 5-HT1A receptor gene transcription, some of which may be interrelated with concomitant changes in catecholamine metabolism.

Re-evaluation of the fludrocortisone test: duration, NaCl supplementation and cut-off limits for aldosterone.

PubMed

Westerdahl, Christina; Bergenfelz, Anders; Larsson, Johanna; Nerbrand, Christina; Valdemarsson, Stig; Wihl, Anders; Isaksson, Anders

2009-01-01

Primary aldosteronism (PA) is the most common form of secondary hypertension. Thus, the aims of this study were: (1) to clarify whether the fludrocortisone suppression test (FST), which confirms autonomous aldosterone secretion, is reliable when carried out during a shorter period of time and (2) to confirm the importance of NaCl supplementation. The cut-off limits already obtained for aldosterone in healthy subjects during the FST were applied in hypertensive patients with a high aldosterone to renin ratio (ARR). The healthy subjects were allocated to three groups. Fludrocortisone was administered 4 times daily over 4 days and sodium chloride was supplemented in 3 different doses. The result was applied in 24 hypertensive patients, in 24 healthy subjects (10 women (23-38 years old) and 14 men (23-58 years old)) and in 24 patients with hypertension and high ARR (16 women (45-74 years old) and 8 men (56-73 years old)). Blood pressure, aldosterone, renin, potassium and sodium were measured. After three days of FST, there was a significant decrease in the serum level of aldosterone in the healthy subjects, regardless of high or low sodium chloride supplementation (p<0.001). The decrease in serum aldosterone was significantly less pronounced in patients with PA than in healthy subjects and hypertensive patients without PA (p<0.001). The 95th percentile of plasma aldosterone at the end of the test was 225 pmol/L. The FST can be shortened to 3 days and a daily 500 mg NaCl supplementation is sufficient. A cut-off value for aldosterone of 225 pmol/L after 4 days with FST is appropriate.

Analysis of genetic diversity in Bolivian llama populations using microsatellites.

PubMed

Barreta, J; Gutiérrez-Gil, B; Iñiguez, V; Romero, F; Saavedra, V; Chiri, R; Rodríguez, T; Arranz, J J

2013-08-01

South American camelids (SACs) have a major role in the maintenance and potential future of rural Andean human populations. More than 60% of the 3.7 million llamas living worldwide are found in Bolivia. Due to the lack of studies focusing on genetic diversity in Bolivian llamas, this analysis investigates both the genetic diversity and structure of 12 regional groups of llamas that span the greater part of the range of distribution for this species in Bolivia. The analysis of 42 microsatellite markers in the considered regional groups showed that, in general, there were high levels of polymorphism (a total of 506 detected alleles; average PIC across per marker: 0.66), which are comparable with those reported for other populations of domestic SACs. The estimated diversity parameters indicated that there was high intrapopulational genetic variation (average number of alleles and average expected heterozygosity per marker: 12.04 and 0.68, respectively) and weak genetic differentiation among populations (FST range: 0.003-0.052). In agreement with these estimates, Bolivian llamas showed a weak genetic structure and an intense gene flow between all the studied regional groups, which is due to the exchange of reproductive males between the different flocks. Interestingly, the groups for which the largest pairwise FST estimates were observed, Sud Lípez and Nor Lípez, showed a certain level of genetic differentiation that is probably due to the pattern of geographic isolation and limited communication infrastructures of these southern localities. Overall, the population parameters reported here may serve as a reference when establishing conservation policies that address Bolivian llama populations. © 2012 Blackwell Verlag GmbH.

Influence of habitat discontinuity, geographical distance, and oceanography on fine-scale population genetic structure of copper rockfish (Sebastes caurinus).

PubMed

Johansson, M L; Banks, M A; Glunt, K D; Hassel-Finnegan, H M; Buonaccorsi, V P

2008-07-01

The copper rockfish is a benthic, nonmigratory, temperate rocky reef marine species with pelagic larvae and juveniles. A previous range-wide study of the population-genetic structure of copper rockfish revealed a pattern consistent with isolation-by-distance. This could arise from an intrinsically limited dispersal capability in the species or from regularly-spaced extrinsic barriers that restrict gene flow (offshore jets that advect larvae offshore and/or habitat patchiness). Tissue samples were collected along the West Coast of the contiguous USA between Neah Bay, WA and San Diego, CA, with dense sampling along Oregon. At the whole-coast scale (approximately 2200 km), significant population subdivision (F(ST) = 0.0042), and a significant correlation between genetic and geographical distance were observed based on 11 microsatellite DNA loci. Population divergence was also significant among Oregon collections (approximately 450 km, F(ST) = 0.001). Hierarchical amova identified a weak but significant 130-km habitat break as a possible barrier to gene flow within Oregon, across which we estimated that dispersal (N(e)m) is half that of the coast-wide average. However, individual-based Bayesian analyses failed to identify more than a single population along the Oregon coast. In addition, no correlation between pairwise population genetic and geographical distances was detected at this scale. The offshore jet at Cape Blanco was not a significant barrier to gene flow in this species. These findings are consistent with low larval dispersal distances calculated in previous studies on this species, support a mesoscale dispersal model, and highlight the importance of continuity of habitat and adult population size in maintaining gene flow.

Determination of Genetic Structure and Signatures of Selection in Three Strains of Tanzania Shorthorn Zebu, Boran and Friesian Cattle by Genome-Wide SNP Analyses

PubMed Central

Msalya, George; Kim, Eui-Soo; Laisser, Emmanuel L. K.; Kipanyula, Maulilio J.; Karimuribo, Esron D.; Kusiluka, Lughano J. M.; Chenyambuga, Sebastian W.; Rothschild, Max F.

2017-01-01

Background More than 90 percent of cattle in Tanzania belong to the indigenous Tanzania Short Horn Zebu (TSZ) population which has been classified into 12 strains based on historical evidence, morphological characteristics, and geographic distribution. However, specific genetic information of each TSZ population has been lacking and has caused difficulties in designing programs such as selection, crossbreeding, breed improvement or conservation. This study was designed to evaluate the genetic structure, assess genetic relationships, and to identify signatures of selection among cattle of Tanzania with the main goal of understanding genetic relationship, variation and uniqueness among them. Methodology/Principal findings The Illumina Bos indicus SNP 80K BeadChip was used to genotype genome wide SNPs in 168 DNA samples obtained from three strains of TSZ cattle namely Maasai, Tarime and Sukuma as well as two comparative breeds; Boran and Friesian. Population structure and signatures of selection were examined using principal component analysis (PCA), admixture analysis, pairwise distances (FST), integrated haplotype score (iHS), identical by state (IBS) and runs of homozygosity (ROH). There was a low level of inbreeding (F~0.01) in the TSZ population compared to the Boran and Friesian breeds. The analyses of FST, IBS and admixture identified no considerable differentiation between TSZ trains. Importantly, common ancestry in Boran and TSZ were revealed based on admixture and IBD, implying gene flow between two populations. In addition, Friesian ancestry was found in Boran. A few common significant iHS were detected, which may reflect influence of recent selection in each breed or strain. Conclusions Population admixture and selection signatures could be applied to develop conservation plan of TSZ cattle as well as future breeding programs in East African cattle. PMID:28129396

Genetic and morphological divergence among Cooper's Hawk (Accipiter cooperii) populations breeding in north-central and western North America

USGS Publications Warehouse

Sonsthagen, Sarah A.; Rosenfield, Robert N.; Bielefeldt, John; Murphy, Robert K.; Stewart, Andrew C.; Stout, William C.; Driscoll, Timothy G.; Bozek, Michael A.; Sloss, Brian L.; Talbot, Sandra L.

2012-01-01

Cooper's Hawk (Accipiter cooperii) populations breeding in the northern portion of the species' range exhibit variation in morphological traits that conforms to predictions based on differences in prey size, tree stand density, and migratory behavior. We examined genetic structure and gene flow and compared divergence at morphological traits (PST) and genetic markers (FST) to elucidate mechanisms (selection or genetic drift) that promote morphological diversification among Cooper's Hawk populations. Cooper's Hawks appear to conform to the genetic pattern of an east-west divide. Populations in British Columbia are genetically differentiated from north-central populations (Wisconsin, Minnesota, and North Dakota; pairwise microsatellite FST= 0.031-0.050; mitochondrial DNA ΦST = 0.177-0.204), which suggests that Cooper's Hawks were restricted to at least two Pleistocene glacial refugia. The strength of the Rocky Mountains—Great Plains area as a barrier to dispersal is further supported by restricted gene-flow rates between British Columbia and other sampled breeding populations. Divergence in morphological traits (PST) was also observed across study areas, but with British Columbia and North Dakota differentiated from Wisconsin and Minnesota, a pattern not predicted on the basis of FST and ΦST interpopulation estimates. Comparison of PSTand FSTestimates suggests that heterogeneous selection may be acting on Cooper's Hawks in the northern portion of their distribution, which is consistent with hypotheses that variation in prey mass and migratory behavior among populations may be influencing overall body size and wing chord. We were unable to distinguish between the effects of genetic drift and selection on tail length in the study populations.

Multi-Gene Analysis Reveals a Lack of Genetic Divergence between Calanus agulhensis and C. sinicus (Copepoda; Calanoida)

PubMed Central

Kozol, Robert; Blanco-Bercial, Leocadio; Bucklin, Ann

2012-01-01

The discrimination and taxonomic identification of marine species continues to pose a challenge despite the growing number of diagnostic metrics and approaches. This study examined the genetic relationship between two sibling species of the genus Calanus (Crustacea; Copepoda; Calanidae), C. agulhensis and C. sinicus, using a multi-gene analysis. DNA sequences were determined for portions of the mitochondrial cytochrome c oxidase I (mtCOI); nuclear citrate synthase (CS), and large subunit (28S) rRNA genes for specimens collected from the Sea of Japan and North East (NE) Pacific Ocean for C. sinicus and from the Benguela Current and Agulhas Bank, off South Africa, for C. agulhensis. For mtCOI, C. sinicus and C. agulhensis showed similar levels of haplotype diversity (Hd = 0.695 and 0.660, respectively) and nucleotide diversity (π = 0.003 and 0.002, respectively). Pairwise FST distances for mtCOI were significant only between C. agulhensis collected from the Agulhas and two C. sinicus populations: the Sea of Japan (FST = 0.152, p<0.01) and NE Pacific (FST = 0.228, p<0.005). Between the species, FST distances were low for both mtCOI (FST = 0.083, p = 0.003) and CS (FST = 0.050, p = 0.021). Large subunit (28S) rRNA showed no variation between the species. Our results provide evidence of the lack of genetic distinction of C. sinicus and C. agulhensis, raise questions of whether C. agulhensis warrants status as a distinct species, and indicate the clear need for more intensive and extensive ecological and genetic analysis. PMID:23118849

Population structure of the NPGS Senegalese sorghum collection and its evaluation to identify new disease resistant genes.

PubMed

Cuevas, Hugo E; Prom, Louis K; Rosa-Valentin, Giseiry

2018-01-01

Sorghum germplasm from West and Central Africa is cultivated in rainy and high humidity regions and is an important source of resistance genes to fungal diseases. Mold and anthracnose are two important biotic constraints to sorghum production in wet areas worldwide. Here, 158 National Plant Germplasm System (NPGS) accessions from Senegal were evaluated for agronomic traits, anthracnose, and grain mold resistance at two locations, and genetically characterized according to 20 simple sequence repeat markers. A total of 221 alleles were amplified with an average of 11 alleles per locus. Each accession had a unique genetic profile (i.e., no duplicates), and the average genetic distance between accessions was 0.42. Population structure and cluster analysis separated the collection into four populations with pairwise FST values >0.15. Three of the populations were composed of Guinea-race sorghum germplasm, and one included multiple races. Anthracnose resistant accessions were present at high frequency and evenly distributed among the three Guinea-race populations. Fourteen accessions showed resistance to grain mold, and eight were resistant to both diseases. These results indicated that the NPGS of Senegal is a genetically diverse collection with a high frequency of disease resistant accessions. Nevertheless, its population structure suggests the presence of few sources of resistance to both grain mold and anthracnose, which are fixed in the germplasm. The phenotypic and genotypic information for these accessions provides a valuable resource for its correct use to broaden the genetic base of breeding programs.

Fast switching thyristor applied in nanosecond-pulse high-voltage generator with closed transformer core.

PubMed

Li, Lee; Bao, Chaobing; Feng, Xibo; Liu, Yunlong; Fochan, Lin

2013-02-01

For a compact and reliable nanosecond-pulse high-voltage generator (NPHVG), the specification parameter selection and potential usage of fast controllable state-solid switches have an important bearing on the optimal design. The NPHVG with closed transformer core and fast switching thyristor (FST) was studied in this paper. According to the analysis of T-type circuit, the expressions for the voltages and currents of the primary and secondary windings on the transformer core of NPHVG were deduced, and the theoretical maximum analysis was performed. For NPHVG, the rise-rate of turn-on current (di/dt) across a FST may exceed its transient rating. Both mean and maximum values of di/dt were determined by the leakage inductances of the transformer, and the difference is 1.57 times. The optimum winding ratio is helpful to getting higher voltage output with lower specification FST, especially when the primary and secondary capacitances have been established. The oscillation period analysis can be effectively used to estimate the equivalent leakage inductance. When the core saturation effect was considered, the maximum di/dt estimated from the oscillating period of the primary current is more accurate than one from the oscillating period of the secondary voltage. Although increasing the leakage inductance of NPHVG can decrease di/dt across FST, it may reduce the output peak voltage of the NPHVG.

[Genetic structure of people from the Volga-Ural region and Central Asia from data of Alu-polymorphism].

PubMed

Khusainova, R I; Akhmetova, V L; Kutuev, I A; Salimova, A Z; Korshunova, T Iu; Lebedev, Iu B; Khusnutdinova, E K

2004-04-01

Nine Alu loci (Ya5NBC5, Ya5NBC27, Ya5NBC148, Ya5NBC182, YA5NBC361, ACE, ApoA1, PV92, TPA25) were analyzed in six ethnic populations (Trans-Ural Bashkirs, Tatars-Mishars, Mordovians-Moksha, Mountain Maris, Udmurts, and Komi-Permyaks) of the Volga-Ural region and in three Central Asian populations (Uzbeks, Kazakhs, and Uigurs). All Alu insertions analyzed appeared to be polymorphic in all populations examined. The frequency of insertion varied from 0.110 in Mountain Maris at the Ya5NBC5 locus to 0.914 in Tatars at the ApoA1 locus. The data on the allele frequency distribution at nine loci point to the existence of substantial genetic diversity in the populations examined. The value of the observed heterozygosity averaged over nine Alu insertions varied from 0.326 in Mountain Maris to 0.445 in Kazakhs and Uigurs. The level of the interpopulation genetic differences for the Volga-Ural population (Fst = 0.061) was higher than for the populations of Central Asia (Fst = 0.024), Europe (Fst = 0.02), and Southeastern Asia (Fst = 0.018). The populations examined were highly differentiated both in respect of linguistic characteristics and the geographical position. The data obtained confirmed the effectiveness of the marker system used for the assessment of genetic differentiation and the relationships between the ethnic groups.

Reliability and convergent validity of the five-step test in people with chronic stroke.

PubMed

Ng, Shamay S M; Tse, Mimi M Y; Tam, Eric W C; Lai, Cynthia Y Y

2018-01-10

(i) To estimate the intra-rater, inter-rater and test-retest reliabilities of the Five-Step Test (FST), as well as the minimum detectable change in FST completion times in people with stroke. (ii) To estimate the convergent validity of the FST with other measures of stroke-specific impairments. (iii) To identify the best cut-off times for distinguishing FST performance in people with stroke from that of healthy older adults. A cross-sectional study. University-based rehabilitation centre. Forty-eight people with stroke and 39 healthy controls. None. The FST, along with (for the stroke survivors only) scores on the Fugl-Meyer Lower Extremity Assessment (FMA-LE), the Berg Balance Scale (BBS), Limits of Stability (LOS) tests, and Activities-specific Balance Confidence (ABC) scale were tested. The FST showed excellent intra-rater (intra-class correlation coefficient; ICC = 0.866-0.905), inter-rater (ICC = 0.998), and test-retest (ICC = 0.838-0.842) reliabilities. A minimum detectable change of 9.16 s was found for the FST in people with stroke. The FST correlated significantly with the FMA-LE, BBS, and LOS results in the forward and sideways directions (r = -0.411 to -0.716, p < 0.004). The FST completion time of 13.35 s was shown to discriminate reliably between people with stroke and healthy older adults. The FST is a reliable, easy-to-administer clinical test for assessing stroke survivors' ability to negotiate steps and stairs.

Current and future trends in fecal source tracking and deployment in the Lake Taihu Region of China

NASA Astrophysics Data System (ADS)

Hagedorn, Charles; Liang, Xinqiang

The emerging discipline of microbial and/or chemical source tracking (collectively termed fecal source tracking (FST)) is being used to identify origins of fecal contamination in polluted waters in many countries around the world. FST has developed rapidly because standard methods of measuring contamination in water by enumerating fecal indicator bacteria (FIB) such as fecal coliforms and enterococci do not identify the sources of the contamination. FST is an active area of research and development in both the academic and private sectors and includes: Developing and testing new microbial and chemical FST methods. Determining the geographic application and animal host ranges of existing and emerging FST techniques. Conducting experimental comparisons of FST techniques. Combining direct monitoring of human pathogens associated with waterborne outbreaks and zoonotic pathogens responsible for infections among people, wildlife, or domesticated animals with the use of FST techniques. Applying FST to watershed analysis and coastal environments. Designing appropriate statistical and probability analysis of FST data and developing models for mass loadings of host-specific fecal contamination. This paper includes a critical review of FST with emphasis on the extent to which methods have been tested (especially in comparison with other methods and/or with blind samples), which methods are applicable to different situations, their shortcomings, and their usefulness in predicting public health risk or pathogen occurrence. In addition, the paper addresses the broader question of whether FST and fecal indicator monitoring is the best approach to regulate water quality and protect human health. Many FST methods have only been tested against sewage or fecal samples or isolates in laboratory studies (proof of concept testing) and/or applied in field studies where the “real” answer is not known, so their comparative performance and accuracy cannot be assessed. For FST to be quantitative, stability of ratios between host-specific markers in the environment must be established. In addition, research is needed on the correlation between host-specific markers and pathogens, and survival of markers after waste treatments. As a result of the exclusive emphasis on FIB by regulatory agencies, monitoring and FST development has concentrated on FIB rather than the actual pathogens. A more rational approach to regulating water quality might be to use available epidemiological data to identify pathogens of concern in a particular water body, and then use targeted pathogen monitoring coupled with very specific FST approaches to control the pathogens. Baseline monitoring of FIB would be just one tool among many in this example.

Comparing population structure as inferred from genealogical versus genetic information.

PubMed

Colonna, Vincenza; Nutile, Teresa; Ferrucci, Ronald R; Fardella, Giulio; Aversano, Mario; Barbujani, Guido; Ciullo, Marina

2009-12-01

Algorithms for inferring population structure from genetic data (ie, population assignment methods) have shown to effectively recognize genetic clusters in human populations. However, their performance in identifying groups of genealogically related individuals, especially in scanty-differentiated populations, has not been tested empirically thus far. For this study, we had access to both genealogical and genetic data from two closely related, isolated villages in southern Italy. We found that nearly all living individuals were included in a single pedigree, with multiple inbreeding loops. Despite F(st) between villages being a low 0.008, genetic clustering analysis identified two clusters roughly corresponding to the two villages. Average kinship between individuals (estimated from genealogies) increased at increasing values of group membership (estimated from the genetic data), showing that the observed genetic clusters represent individuals who are more closely related to each other than to random members of the population. Further, average kinship within clusters and F(st) between clusters increases with increasingly stringent membership threshold requirements. We conclude that a limited number of genetic markers is sufficient to detect structuring, and that the results of genetic analyses faithfully mirror the structuring inferred from detailed analyses of population genealogies, even when F(st) values are low, as in the case of the two villages. We then estimate the impact of observed levels of population structure on association studies using simulated data.

Comparing population structure as inferred from genealogical versus genetic information

PubMed Central

Colonna, Vincenza; Nutile, Teresa; Ferrucci, Ronald R; Fardella, Giulio; Aversano, Mario; Barbujani, Guido; Ciullo, Marina

2009-01-01

Algorithms for inferring population structure from genetic data (ie, population assignment methods) have shown to effectively recognize genetic clusters in human populations. However, their performance in identifying groups of genealogically related individuals, especially in scanty-differentiated populations, has not been tested empirically thus far. For this study, we had access to both genealogical and genetic data from two closely related, isolated villages in southern Italy. We found that nearly all living individuals were included in a single pedigree, with multiple inbreeding loops. Despite Fst between villages being a low 0.008, genetic clustering analysis identified two clusters roughly corresponding to the two villages. Average kinship between individuals (estimated from genealogies) increased at increasing values of group membership (estimated from the genetic data), showing that the observed genetic clusters represent individuals who are more closely related to each other than to random members of the population. Further, average kinship within clusters and Fst between clusters increases with increasingly stringent membership threshold requirements. We conclude that a limited number of genetic markers is sufficient to detect structuring, and that the results of genetic analyses faithfully mirror the structuring inferred from detailed analyses of population genealogies, even when Fst values are low, as in the case of the two villages. We then estimate the impact of observed levels of population structure on association studies using simulated data. PMID:19550436

Isolation-by-distance in landscapes: considerations for landscape genetics

PubMed Central

van Strien, M J; Holderegger, R; Van Heck, H J

2015-01-01

In landscape genetics, isolation-by-distance (IBD) is regarded as a baseline pattern that is obtained without additional effects of landscape elements on gene flow. However, the configuration of suitable habitat patches determines deme topology, which in turn should affect rates of gene flow. IBD patterns can be characterized either by monotonically increasing pairwise genetic differentiation (for example, FST) with increasing interdeme geographic distance (case-I pattern) or by monotonically increasing pairwise genetic differentiation up to a certain geographical distance beyond which no correlation is detectable anymore (case-IV pattern). We investigated if landscape configuration influenced the rate at which a case-IV pattern changed to a case-I pattern. We also determined at what interdeme distance the highest correlation was measured between genetic differentiation and geographic distance and whether this distance corresponded to the maximum migration distance. We set up a population genetic simulation study and assessed the development of IBD patterns for several habitat configurations and maximum migration distances. We show that the rate and likelihood of the transition of case-IV to case-I FST–distance relationships was strongly influenced by habitat configuration and maximum migration distance. We also found that the maximum correlation between genetic differentiation and geographic distance was not related to the maximum migration distance and was measured across all deme pairs in a case-I pattern and, for a case-IV pattern, at the distance where the FST–distance curve flattens out. We argue that in landscape genetics, separate analyses should be performed to either assess IBD or the landscape effects on gene flow. PMID:25052412

Founding events influence genetic population structure of sockeye salmon (Oncorhynchus nerka) in Lake Clark, Alaska

USGS Publications Warehouse

Ramstad, K.M.; Woody, C.A.; Sage, G.K.; Allendorf, F.W.

2004-01-01

Bottlenecks can have lasting effects on genetic population structure that obscure patterns of contemporary gene flow and drift. Sockeye salmon are vulnerable to bottleneck effects because they are a highly structured species with excellent colonizing abilities and often occupy geologically young habitats. We describe genetic divergence among and genetic variation within spawning populations of sockeye salmon throughout the Lake Clark area of Alaska. Fin tissue was collected from sockeye salmon representing 15 spawning populations of Lake Clark, Six-mile Lake, and Lake Iliamna. Allele frequencies differed significantly at 11 microsatellite loci in 96 of 105 pairwise population comparisons. Pairwise estimates of FST ranged from zero to 0.089. Six-mile Lake and Lake Clark populations have historically been grouped together for management purposes and are geographically proximate. However, Six-mile Lake populations are genetically similar to Lake Iliamna populations and are divergent from Lake Clark populations. The reduced allelic diversity and strong divergence of Lake Clark populations relative to Six-mile Lake and Lake Iliamna populations suggest a bottleneck associated with the colonization of Lake Clark by sockeye salmon. Geographic distance and spawning habitat differences apparently do not contribute to isolation and divergence among populations. However, temporal isolation based on spawning time and founder effects associated with ongoing glacial retreat and colonization of new spawning habitats contribute to the genetic population structure of Lake Clark sock-eye salmon. Nonequilibrium conditions and the strong influence of genetic drift caution against using estimates of divergence to estimate gene flow among populations of Lake Clark sockeye salmon.

Spatial structure of morphological and neutral genetic variation in Brook Trout

USGS Publications Warehouse

Kazyak, David C.; Hilderbrand, Robert H.; Keller, Stephen R.; Colaw, Mark C.; Holloway, Amanda E.; Morgan, Raymond P.; King, Timothy L.

2015-01-01

Brook Trout Salvelinus fontinalis exhibit exceptional levels of life history variation, remarkable genetic variability, and fine-scale population structure. In many cases, neighboring populations may be highly differentiated from one another to an extent that is comparable with species-level distinctions in other taxa. Although genetic samples have been collected from hundreds of populations and tens of thousands of individuals, little is known about whether differentiation at neutral markers reflects phenotypic differences among Brook Trout populations. We compared differentiation in morphology and neutral molecular markers among populations from four geographically proximate locations (all within 24 km) to examine how genetic diversity covaries with morphology. We found significant differences among and/or within streams for all three morphological axes examined and identified the source stream of many individuals based on morphology (52.3% classification efficiency). Although molecular and morphological differentiation among streams ranged considerably (mean pairwise FST: 0.023–0.264; pairwise PST: 0.000–0.339), the two measures were not significantly correlated. While in some cases morphological characters appear to have diverged to a greater extent than expected by neutral genetic drift, many traits were conserved to a greater extent than were neutral genetic markers. Thus, while Brook Trout exhibit fine-scale spatial patterns in both morphology and neutral genetic diversity, these types of biological variabilities are being structured by different ecological and evolutionary processes. The relative influences of genetic drift versus selection and phenotypic plasticity in shaping morphology appear to vary among populations occupying nearby streams.

Lack of population genetic structure and host specificity in the bat fly, Cyclopodia horsfieldi, across species of Pteropus bats in Southeast Asia

PubMed Central

2013-01-01

Background Population-level studies of parasites have the potential to elucidate patterns of host movement and cross-species interactions that are not evident from host genealogy alone. Bat flies are obligate and generally host-specific blood-feeding parasites of bats. Old-World flies in the family Nycteribiidae are entirely wingless and depend on their hosts for long-distance dispersal; their population genetics has been unstudied to date. Methods We collected a total of 125 bat flies from three Pteropus species (Pteropus vampyrus, P. hypomelanus, and P. lylei) from eight localities in Malaysia, Cambodia, and Vietnam. We identified specimens morphologically and then sequenced three mitochondrial DNA gene fragments (CoI, CoII, cytB; 1744 basepairs total) from a subset of 45 bat flies. We measured genetic diversity, molecular variance, and population genetic subdivision (FST), and used phylogenetic and haplotype network analyses to quantify parasite genetic structure across host species and localities. Results All flies were identified as Cyclopodia horsfieldi with the exception of two individuals of Eucampsipoda sundaica. Low levels of population genetic structure were detected between populations of Cyclopodia horsfieldi from across a wide geographic range (~1000 km), and tests for isolation by distance were rejected. AMOVA results support a lack of geographic and host-specific population structure, with molecular variance primarily partitioned within populations. Pairwise FST values from flies collected from island populations of Pteropus hypomelanus in East and West Peninsular Malaysia supported predictions based on previous studies of host genetic structure. Conclusions The lack of population genetic structure and morphological variation observed in Cyclopodia horsfieldi is most likely due to frequent contact between flying fox species and subsequent high levels of parasite gene flow. Specifically, we suggest that Pteropus vampyrus may facilitate movement of bat flies between the three Pteropus species in the region. We demonstrate the utility of parasite genetics as an additional layer of information to measure host movement and interspecific host contact. These approaches may have wide implications for understanding zoonotic, epizootic, and enzootic disease dynamics. Bat flies may play a role as vectors of disease in bats, and their competence as vectors of bacterial and/or viral pathogens is in need of further investigation. PMID:23924629

Lack of population genetic structure and host specificity in the bat fly, Cyclopodia horsfieldi, across species of Pteropus bats in Southeast Asia.

PubMed

Olival, Kevin J; Dick, Carl W; Simmons, Nancy B; Morales, Juan Carlos; Melnick, Don J; Dittmar, Katharina; Perkins, Susan L; Daszak, Peter; Desalle, Rob

2013-08-08

Population-level studies of parasites have the potential to elucidate patterns of host movement and cross-species interactions that are not evident from host genealogy alone. Bat flies are obligate and generally host-specific blood-feeding parasites of bats. Old-World flies in the family Nycteribiidae are entirely wingless and depend on their hosts for long-distance dispersal; their population genetics has been unstudied to date. We collected a total of 125 bat flies from three Pteropus species (Pteropus vampyrus, P. hypomelanus, and P. lylei) from eight localities in Malaysia, Cambodia, and Vietnam. We identified specimens morphologically and then sequenced three mitochondrial DNA gene fragments (CoI, CoII, cytB; 1744 basepairs total) from a subset of 45 bat flies. We measured genetic diversity, molecular variance, and population genetic subdivision (FST), and used phylogenetic and haplotype network analyses to quantify parasite genetic structure across host species and localities. All flies were identified as Cyclopodia horsfieldi with the exception of two individuals of Eucampsipoda sundaica. Low levels of population genetic structure were detected between populations of Cyclopodia horsfieldi from across a wide geographic range (~1000 km), and tests for isolation by distance were rejected. AMOVA results support a lack of geographic and host-specific population structure, with molecular variance primarily partitioned within populations. Pairwise FST values from flies collected from island populations of Pteropus hypomelanus in East and West Peninsular Malaysia supported predictions based on previous studies of host genetic structure. The lack of population genetic structure and morphological variation observed in Cyclopodia horsfieldi is most likely due to frequent contact between flying fox species and subsequent high levels of parasite gene flow. Specifically, we suggest that Pteropus vampyrus may facilitate movement of bat flies between the three Pteropus species in the region. We demonstrate the utility of parasite genetics as an additional layer of information to measure host movement and interspecific host contact. These approaches may have wide implications for understanding zoonotic, epizootic, and enzootic disease dynamics. Bat flies may play a role as vectors of disease in bats, and their competence as vectors of bacterial and/or viral pathogens is in need of further investigation.

Allelic frequencies and statistical data obtained from 48 AIM INDEL loci in an admixed population from the Brazilian Amazon.

PubMed

Francez, Pablo Abdon da Costa; Ribeiro-Rodrigues, Elzemar Martins; dos Santos, Sidney Emanuel Batista

2012-01-01

Allelic frequencies of 48 informative insert-delete (INDEL) loci were obtained from a sample set of 130 unrelated individuals living in Macapá, a city located in the northern Amazon region, in Brazil. The values of heterozygosity (H), polymorphic information content (PIC), power of discrimination (PD), power of exclusion (PE), matching probability (MP) and typical paternity index (TPI) were calculated and showed the forensic efficiency of these genetic markers. Based on the allele frequency obtained for the population of Macapá, we estimated an interethnic admixture for the three parental groups (European, Native American and African) of, respectively, 50%, 21% and 29%. Comparing these allele frequencies with those of other Brazilian populations and the parental populations, statistically significant distances were found. The interpopulation genetic distance (F(ST) coefficients) to the present database ranged from F(ST)=0.0431 (p<0.00001) between Macapá and Belém to F(ST)=0.266 (p<0.00001) between Macapá and the Native American group. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Characterization of Culex pipiens Complex (Diptera: Culicidae) Populations in Colorado, USA Using Microsatellites

PubMed Central

Kothera, Linda; Godsey, Marvin S.; Doyle, Michael S.; Savage, Harry M.

2012-01-01

Mosquitoes such as those in the Culex pipiens complex are important vectors of disease. This study was conducted to genetically characterize Cx. pipiens complex populations in the state of Colorado, USA, and to determine the number of genetic clusters represented by the data. Thirteen populations located among four major river basins were sampled (n = 597 individuals) using a panel of 14 microsatellites. The lowest-elevation sites had the highest Expected Heterozygosity (HE) values (range 0.54–0.65). AMOVA results indicated the presence of statistically significant amounts of variation within each level when populations were analyzed as one group or when they were grouped either by river basin or by their position on the east or west side of the Rocky Mountains. Most pairwise FST values were significant via permutation test (range 0–0.10), with the highest values from comparisons with Lamar, in southeast CO. A neighbor joining tree based on Cavalli–Sforza and Edwards’s chord distances was consistent with the geographic locations of populations, as well as with the AMOVA results. There was a significant isolation by distance effect, and the cluster analysis resolved five groups. Individuals were also assayed with an additional microsatellite marker, Cxpq78, proposed to be monomorphic in Cx. pipiens but polymorphic in the closely related but biologically distinct species Cx. quinquefasciatus. Low frequencies (≤3%) of Cx. quinquefasciatus alleles for this marker were noted, and mostly confined to populations along the Interstate 25 corridor. Pueblo was distinct in that it had 10% Cx. quinquefasciatus alleles, mostly of one allele size. The degree of population genetic structure observed in this study is in contrast with that of Cx. tarsalis, the other major vector of WNV in the western U.S., and likely reflects the two species’ different dispersal strategies. PMID:23094068

Factors influencing behavior in the forced swim test

PubMed Central

Bogdanova, Olena V.; Kanekar, Shami; D’Anci, Kristen E.; Renshaw, Perry F.

2017-01-01

The forced swim test (FST) is a behavioral test in rodents which was developed in 1978 by Porsolt and colleagues as a model for predicting the clinical efficacy of antidepressant drugs. A modified version of the FST added the classification of active behaviors into swimming and climbing, in order to facilitate the differentiation between serotonergic and noradrenergic classes of antidepressant drugs. The FST is now widely used in basic research and the pharmaceutical screening of potential antidepressant treatments. It is also one of the most commonly used tests to assess depressive-like behavior in animal models. Despite the simplicity and sensitivity of the FST procedure, important differences even in baseline immobility rates have been reported between different groups, which complicate the comparison of results across studies. In spite of several methodological papers and reviews published on the FST, the need still exists for clarification of factors which can influence the procedure. While most recent reviews have focused on antidepressant effects observed with the FST, this one considers the methodological aspects of the procedure, aiming to summarize issues beyond antidepressant action in the FST. The previously published literature is analyzed for factors which are known to influence animal behavior in the FST. These include biological factors, such as strain, age, body weight, gender and individual differences between animals; influence of preconditioning before the FST: handling, social isolation or enriched environment, food manipulations, various kinds of stress, endocrine manipulations and surgery; schedule and routes of treatment, dosage and type of the drugs as well as experimental design and laboratory environmental effects. Consideration of these factors in planning experiments may result in more consistent FST results. PMID:23685235

Cloning and expression of follistatin gene in half-smooth tongue sole Cynoglossus semilaevis during the reproduction cycle

NASA Astrophysics Data System (ADS)

Wen, Haishen; Si, Yufeng; Zhang, Yuanqing; He, Feng; Li, Jifang

2015-03-01

Follistatin (FST) is a monomeric glycoprotein highly enriched in cysteines and belongs to TGF-β superfamily. FST can suppress the secretion of follicle-stimulating hormone and plays a vital role in the reproduction of vertebrates. We used rapid amplification of cDNA ends technology to clone the FST gene of half-smooth tongue sole, Cynoglossus semilaevis. We characterized its phylogenetic context and expression patterns to elucidate its function in the breeding season. The full-length sequence of FST is 1 455 bp and encodes a protein of 321 amino acids. We investigated the expression pattern of FST in C. semilaevis at different stages of reproduction using reverse transcription-polymerase chain reaction (RTPCR). FST mRNA was expressed in all 13 tissues analyzed, and was expressed at high levels in gonad and at slightly lower levels in gill and brain. During the reproductive cycle of C. semilaevis, the transcript level of FST was the highest in the perinucleolus stage, decreased in the primary yolk stage, slightly increased in the tertiary yolk stage, and then reduced to a minimal level in the atretic follicles stage of the ovary. We concluded that FST suppressed follicle-stimulating hormone, which stimulated oocyte development. However, no significant variation was observed across all stages of testis development, although the expression level in the spermatogenesis stage was relatively low, which may result from the regulation of FST by aromatase.

Population and forensic data for three sets of forensic genetic markers in four ethnic groups from Iran: Persians, Lurs, Kurds and Azeris.

PubMed

Poulsen, L; Farzad, M Sharafi; Børsting, C; Tomas, C; Pereira, V; Morling, N

2015-07-01

A total of 255 individuals (Persians, Lurs, Kurds and Azeris) from Iran were typed for three sets of forensic genetic markers with the NGM SElect™, DIPplex(®) and Argus X-12 kits. Statistically significant deviations (P≤0.002) from Hardy-Weinberg expectations were observed for the insertion-deletion markers HLD97 and HLD93 after Holm-Šidák correction. Statistically significant (P<0.05) levels of linkage disequilibrium were observed between markers within two of the four studied X-chromosomal linkage groups. AMOVA analyses of the three sets of markers did not show population structure when the individuals were grouped according to their ethnic group. The Iranian population grouped closely to populations living geographically near to Iran based on pairwise FST distances. The matching probabilities ranged from 1 in 3.2×10(7) males by using haplotype frequencies of four X-chromosomal haplogroups to 1 in 3.4×10(21) individuals for the 16 autosomal STRs. Copyright © 2015. Published by Elsevier Ireland Ltd.

Species traits influence the genetic consequences of river fragmentation on two co-occurring redhorse (Moxostoma) species

USGS Publications Warehouse

Reid, S.M.; Wilson, C.C.; Carl, L.M.; Zorn, T.G.

2008-01-01

We used microsatellite DNA markers to test whether fragmentation of the Trent River (Ontario, Canada) has reduced genetic diversity and increased genetic differentiation among populations of river redhorse (Moxostoma carinatum) and shorthead redhorse (Moxostoma macrolepidotum). Allelic richness of both species was significantly greater along the free-flowing Muskegon River (Michigan, USA) than along the fragmented Trent River. Contrary to expectations, there was no evidence of a fragment length effect on genetic diversity, recent population bottlenecks, or increased relatedness among individuals in fragmented populations. High levels of linkage disequilibrium indicate extinction-recolonization population dynamics along the Trent River. For both species, pairwise FST tests identified weak but statistically significant population differentiation. In the Trent River, differentiation was significantly greater for river redhorse than for shorthead redhorse and, for both species, greater than in the Muskegon River. Moderate fragmentation effects likely reflect the permeability of the dam-lock system to redhorse movement. Differences between species indicate that as a result of smaller effective population sizes, habitat specialists and species at the periphery of their geographic range are more sensitive to river fragmentation. ?? 2008 NRC.

Prenatal chronic mild stress induces depression-like behavior and sex-specific changes in regional glutamate receptor expression patterns in adult rats.

PubMed

Wang, Y; Ma, Y; Hu, J; Cheng, W; Jiang, H; Zhang, X; Li, M; Ren, J; Li, X

2015-08-20

Chronic stress during critical periods of human fetal brain development is associated with cognitive, behavioral, and mood disorders in later life. Altered glutamate receptor (GluR) expression has been implicated in the pathogenesis of stress-dependent disorders. To test whether prenatal chronic mild stress (PCMS) enhances offspring's vulnerability to stress-induced behavioral and neurobiological abnormalities and if this enhanced vulnerability is sex-dependent, we measured depression-like behavior in the forced swimming test (FST) and regional changes in GluR subunit expression in PCMS-exposed adult male and female rats. Both male and female PCMS-exposed rats exhibited stronger depression-like behavior than controls. Males and females exhibited unique regional changes in GluR expression in response to PCMS alone, FST alone (CON-FST), and PCMS with FST (PCMS-FST). In females, PCMS alone did not alter N-methyl-d-aspartate receptor (NMDAR) or metabotropic glutamate receptor (mGluR) expression, while in PCMS males, higher mGluR2/3, mGluR5, and NR1 expression levels were observed in the prefrontal cortex. In addition, PCMS altered the change in GluR expression induced by acute stress (the FST test), and this too was sex-specific. Male PCMS-FST rats expressed significantly lower mGluR5 levels in the hippocampus, lower mGluR5, NR1, postsynaptic density protein (PSD)95, and higher mGluR2/3 in the prefrontal cortex, and higher mGluR5 and PSD95 in the amygdala than male CON-FST rats. Female PCMS-FST rats expressed lower NR1 in the hippocampus, lower NR2B and PSD95 in the prefrontal cortex, lower mGluR2/3 in the amygdala, and higher PSD95 in the amygdala than female CON-FST rats. PCMS may increase the offspring's vulnerability to depression by altering sex-specific stress-induced changes in glutamatergic signaling. Copyright © 2015. Published by Elsevier Ltd.

Individual-based assessment of population structure and admixture in Austrian, Croatian and German draught horses.

PubMed

Druml, T; Curik, I; Baumung, R; Aberle, K; Distl, O; Sölkner, J

2007-02-01

All over Europe, the number of draught horses has decreased drastically during the last 50 years. As a prerequisite for efficient management decisions, we analysed the conservation status in Austrian (Noriker Carinthia - NC, Noriker Salzburg - NS), Croatian (Croatian Coldblood - C, Posavina horse - P) and German (Altmaerkisch Coldblood - A, Black Forest horse - BF, Mecklenburg Coldblood - M, Rhenish German Draught horse - R, Saxon Thuringa Coldblood - ST, Schleswig Draught horse - Sch, South German Coldblood - SG) draught horses (434) using multilocus genotypic information from 30 (effectively 27) microsatellite loci. Populations located in areas with less intensive agricultural production (C, NC, NS, P and SG) had greater diversity within the population and estimated effective population size than A, BF, Sch, M, R and ST populations. The PCA plots revealed that populations form five separate groups. The 'Noriker' group (NC, NS and SG) and the 'Rhenish' group (A, M, R and ST) were the most distinctive (pairwise F(ST) values ranged from 0.078 to 0.094). The 'Croatian' group (C and P) was in the centre, while the BF and Sch populations formed two out-groups. A posterior Bayesian analysis detected further differentiation, mainly caused by political and geographical factors. Thus, it was possible to separate the South German Coldblood from the Austrian Noriker population where no subpopulation structure was detected. The admixture analysis revealed imprecise classification between C and P populations. A small but notable separation of R from A, M and ST populations was detected, while Sch and BF populations remained as out-groups. The information obtained should aid in making efficient conservation decisions.

Low Genetic Diversity and Structuring of the Arapaima (Osteoglossiformes, Arapaimidae) Population of the Araguaia-Tocantins Basin

PubMed Central

Vitorino, Carla A.; Nogueira, Fabrícia; Souza, Issakar L.; Araripe, Juliana; Venere, Paulo C.

2017-01-01

The arapaima, Arapaima gigas, is a fish whose populations are threatened by both overfishing and the ongoing destruction of its natural habitats. In the Amazon basin, varying levels of population structure have been found in A. gigas, although no data are available on the genetic diversity or structure of the populations found in the Araguaia-Tocantins basin, which has a topographic profile, hydrological regime, and history of fishing quite distinct from those of the Amazon. In this context, microsatellite markers were used to assess the genetic diversity and connectivity of five wild A. gigas populations in the Araguaia-Tocantins basin. The results of the analysis indicated low levels of genetic diversity in comparison with other A. gigas populations, studied in the Amazon basin. The AMOVA revealed that the Arapaima populations of the Araguaia-Tocantins basin are structured significantly. No correlation was found between pairwise FST values and the geographical distance among populations. The low level of genetic variability and the evidence of restricted gene flow may both be accounted for by overfishing, as well as the other human impacts that these populations have been exposed to over the years. The genetic fragility of these populations demands attention, given that future environmental changes (natural or otherwise) may further reduce these indices and eventually endanger these populations. The results of this study emphasize the need to take the genetic differences among the study populations into account when planning management measures and conservation strategies for the arapaima stocks of the Araguaia-Tocantins basin. PMID:29114261

Mitochondrial DNA markers reveal high genetic diversity and strong genetic differentiation in populations of Dendrolimus kikuchii Matsumura (Lepidoptera: Lasiocampidae).

PubMed

Men, Qiulei; Xue, Guoxi; Mu, Dan; Hu, Qingling; Huang, Minyi

2017-01-01

Dendrolimus kikuchii Matsumura, 1927 is a serious forest pest causing great damage to coniferous trees in China. Despite its economic importance, the population genetics of this pest are poorly known. We used three mitochondrial genes (COI, COII and Cytb) to investigate the genetic diversity and genetic differentiation of 15 populations collected from the main distribution regions of D. kikuchii in China. Populations show high haplotype and nucleotide diversity. Haplotype network and phylogenetic analysis divides the populations into three major clades, the central and southeastern China (CC+SEC) clade, the eastern China (EC) clade, and the southwestern China (SWC) clade. Populations collected from adjacent localities share the same clade, which is consistent with the strong relationship of isolation by distance (r = 0.74824, P = 0.00001). AMOVA analysis indicated that the major portion of this molecular genetic variation is found among the three groups of CC+SEC, EC and SWC (61.26%). Of 105 pairwise FST comparisons, 93 show high genetic differentiation. Populations of Puer (PE), Yangshuo (YS) and Leishan (LS) are separated from other populations by a larger genetic distance. Distributions of pairwise differences obtained with single and combined gene data from the overall populations are multimodal, suggesting these populations had no prior population expansion in southern China. The nonsignificant neutral test on the basis of Tajima' D and Fu's Fs, and the lack of a star-shaped haplotype network together with the multiple haplotypes support this hypothesis. Pleistocene climatic fluctuations, combined with the host specificity to Pinus species, made these regions of south China into a refuge for D. kikuchii. The high level of population genetic structuring is related to their weak flight capacity, their variations of life history and the geographic distance among populations.

Environmental enrichment normalizes hippocampal timing coding in a malformed hippocampus.

PubMed

Hernan, Amanda E; Mahoney, J Matthew; Curry, Willie; Richard, Greg; Lucas, Marcella M; Massey, Andrew; Holmes, Gregory L; Scott, Rod C

2018-01-01

Neurodevelopmental insults leading to malformations of cortical development (MCD) are a common cause of psychiatric disorders, learning impairments and epilepsy. In the methylazoxymethanol (MAM) model of MCDs, animals have impairments in spatial cognition that, remarkably, are improved by post-weaning environmental enrichment (EE). To establish how EE impacts network-level mechanisms of spatial cognition, hippocampal in vivo single unit recordings were performed in freely moving animals in an open arena. We took a generalized linear modeling approach to extract fine spike timing (FST) characteristics and related these to place cell fidelity used as a surrogate of spatial cognition. We find that MAM disrupts FST and place-modulated rate coding in hippocampal CA1 and that EE improves many FST parameters towards normal. Moreover, FST parameters predict spatial coherence of neurons, suggesting that mechanisms determining altered FST are responsible for impaired cognition in MCDs. This suggests that FST parameters could represent a therapeutic target to improve cognition even in the context of a brain that develops with a structural abnormality.

Sustainment Study of Flipped Spherical Torus Plasmas on HIST

NASA Astrophysics Data System (ADS)

Takamiya, T.; Nagata, M.; Kawami, K.; Hasegawa, H.; Fukumoto, N.; Uyama, T.; Masamune, S.; Iida, M.; Katsurai, M.

2003-10-01

We have discovered that helicity-driven ST plasmas relax toward the flipped state by decreasing the external toroidal field and reversing its sign in time [1]. From the viewpoint of coaxial helicity injection (CHI) current drive, it is conceivable that the flipped ST (F-ST), which consists of only closed flux surfaces, compares favorably with the normal ST. We have investigated the sustainment mechanism of the F-ST plasma. The helicity-driven relaxed theory shows that there exist the mixed states of ST and F-ST in the flux conserver. Helicity is transferred to F-ST through the ST with coupling with gun electrodes. It has been found that magnetic reconnection between the toroidal magnetic field plays important role in the sustainment of the F-ST. The magnetic field in the outer edge region shows regular oscillations which have a large amplitude of the n=1 mode. The core region of the F-ST seems to be relatively stable. [1] M. Nagata, et al., Phys. Rev. Lett. 90, 225001 (2003)

The Face-Symbol Test and the Symbol-Digit Test are not reliable surrogates for the Paced Auditory Serial Addition Test in multiple sclerosis.

PubMed

Williams, J; O'Rourke, K; Hutchinson, M; Tubridy, N

2006-10-01

The Paced Auditory Serial Addition Test (PASAT) is the chosen task for cognitive assessment in the multiple sclerosis functional composite (MSFC) and a widely used task in neuropsychological studies of people with multiple sclerosis (MS), but is unpopular with patients. The Face-Symbol Test (FST) and Symbol-Digit Tests (SDT) are alternative methods of cognitive testing in MS, which are easily administered and patient-friendly. In order to evaluate the potential of the FST as a possible surrogate for the PASAT, we directly compared the FST to the PASAT and the SDT in a cohort of 50 MS patients with varying levels of disability. There was significant correlation between SDT and FST scores (Spearman's rho 0.80, 95% CI 0.66-0.88), R(2) 65%, with moderate inter-test agreement (k =0.52). In contrast, SDT and FST scores were less predictive of PASAT scores. We concluded that neither the FST nor SDT are reliable surrogates for the PASAT.

The Shrail: A Comparison of a Novel Attachable Rail System With the Current Deployment Operating Table.

PubMed

Dilday, Joshua; Sirkin, Maxwell R; Wertin, Thomas; Bradley, Frances; Hiles, Jason

The current forward surgical team (FST) operating table is heavy and burdensome and hinders essential movement flexibility. A novel attachable rail system, the Shrail, has been developed to overcome these obstacles. The Shrail turns a North Atlantic Treaty Organization litter into a functional operating table. A local FST compared the assembly of the FST operating table with assembling the Shrail. Device weight, storage space, and assembly space were directly measured and compared. The mean assembly time required for the Shrail was significantly less compared with the operating table (23.36 versus 151.6 seconds; p ≤ .01). The Shrail weighs less (6.80kg versus 73.03kg) and requires less storage space (0.019m3 versus 0.323m3) compared with the current FST operating table. The Shrail provides an FST with a faster, lighter surgical table assembly. For these reasons, it is better suited for the demands of an FST and the implementation of prolonged field care. 2018.

The influence of genetic drift and selection on quantitative traits in a plant pathogenic fungus.

PubMed

Stefansson, Tryggvi S; McDonald, Bruce A; Willi, Yvonne

2014-01-01

Genetic drift and selection are ubiquitous evolutionary forces acting to shape genetic variation in populations. While their relative importance has been well studied in plants and animals, less is known about their relative importance in fungal pathogens. Because agro-ecosystems are more homogeneous environments than natural ecosystems, stabilizing selection may play a stronger role than genetic drift or diversifying selection in shaping genetic variation among populations of fungal pathogens in agro-ecosystems. We tested this hypothesis by conducting a QST/FST analysis using agricultural populations of the barley pathogen Rhynchosporium commune. Population divergence for eight quantitative traits (QST) was compared with divergence at eight neutral microsatellite loci (FST) for 126 pathogen strains originating from nine globally distributed field populations to infer the effects of genetic drift and types of selection acting on each trait. Our analyses indicated that five of the eight traits had QST values significantly lower than FST, consistent with stabilizing selection, whereas one trait, growth under heat stress (22°C), showed evidence of diversifying selection and local adaptation (QST>FST). Estimates of heritability were high for all traits (means ranging between 0.55-0.84), and average heritability across traits was negatively correlated with microsatellite gene diversity. Some trait pairs were genetically correlated and there was significant evidence for a trade-off between spore size and spore number, and between melanization and growth under benign temperature. Our findings indicate that many ecologically and agriculturally important traits are under stabilizing selection in R. commune and that high within-population genetic variation is maintained for these traits.

Methylation Status of the Follistatin Gene at Different Development Stages of Japanese Flounder (Paralichthys olivaceus)

NASA Astrophysics Data System (ADS)

Huang, Yajuan; Hu, Nan; Si, Yufeng; Li, Siping; Wu, Shuxian; Zhang, Meizhao; Wen, Haishen; Li, Jifang; Li, Yun; He, Feng

2018-06-01

Follistatin (Fst) is a hyperplasia factor that plays a crucial role in muscle development. DNA methylation, a significant process, regulates gene expression. The aim of our study is to examine the DNA methylation and expression patterns of Fst gene at five different development stages of Japanese flounder (stage A, 7 dph; stage B, 90 dph; stage C, about 180 dph; stage D, about 24 months; stage E, about 36 months). The muscle tissue of Japanese flounder was obtained at different development stages in this experiment. DNA methylation levels in the promoter and exon 2 of Fst were determined by bisulfite sequencing, and the relative expression of the Fst gene at the five stages was measured by quantitative PCR. The results showed that the lowest methylation level was at stage A and the highest methylation level was at stage B. Moreover, the highest expression level of the Fst gene was observed at stage A. The mRNA abundance was negatively correlated with DNA methylation level. Three CpG islands in the promoter region and three CpG islands in exon 2 of Fst were found in the binding sequence of the putative transcription factor. These results offered a theoretical basis for the mechanism of Fst gene regulation to muscle development at different development stages.

Population structure and strong divergent selection shape phenotypic diversification in maize landraces.

PubMed

Pressoir, G; Berthaud, J

2004-02-01

To conserve the long-term selection potential of maize, it is necessary to investigate past and present evolutionary processes that have shaped quantitative trait variation. Understanding the dynamics of quantitative trait evolution is crucial to future crop breeding. We characterized population differentiation of maize landraces from the State of Oaxaca, Mexico for quantitative traits and molecular markers. Qst values were much higher than Fst values obtained for molecular markers. While low values of Fst (0.011 within-village and 0.003 among-villages) suggest that considerable gene flow occurred among the studied populations, high levels of population differentiation for quantitative traits were observed (ie an among-village Qst value of 0.535 for kernel weight). Our results suggest that although quantitative traits appear to be under strong divergent selection, a considerable amount of gene flow occurs among populations. Furthermore, we characterized nonproportional changes in the G matrix structure both within and among villages that are consequences of farmer selection. As a consequence of these differences in the G matrix structure, the response to multivariate selection will be different from one population to another. Large changes in the G matrix structure could indicate that farmers select for genes of major and pleiotropic effect. Farmers' decision and selection strategies have a great impact on phenotypic diversification in maize landraces.

Genomic ancestry of rural African-derived populations from Southeastern Brazil.

PubMed

Kimura, Lilian; Ribeiro-Rodrigues, Elzemar Martins; De Mello Auricchio, Maria Teresa Balester; Vicente, João Pedro; Batista Santos, Sidney Emanuel; Mingroni-Netto, Regina Célia

2013-01-01

xMany Africans were brought to Brazil as slaves. The runaway or abandoned slaves founded isolated communities named quilombos. There are many quilombo remnants in Vale do Ribeira region in the southern part of São Paulo State. The aim of our study was to contribute to understanding the origins of these populations, through admixture studies. We genotyped 307 unrelated DNA samples obtained from ten quilombo populations from Vale do Ribeira region, using a panel of 48 INDEL polymorphisms. We estimated genetic differentiation between populations (F(ST) ) and genomic ancestry from these populations. Our data were compared to a similar study performed in quilombo remnants from the Brazilian Amazon region. Population admixture estimates showed high degree of miscegenation in the quilombo remnants from Vale do Ribeira (average admixture estimates at 39.7% of African, 39.0% of European and 21.3% of Amerindian contribution). The proportions of ancestral genes varied greatly among individuals, ranging from 7.3 to 69.5%, 12.9 to 68.3%, and 7.3 to 58.5% (African, European, and Amerindian, respectively). Genetic differentiation between these populations was low (all F(ST) values <5%), indicating gene flow between them. Both groups of quilombos, from Vale do Ribeira and Amazon, presented similar patterns of admixture. INDEL markers were useful to evidence the triple interbreeding among African, European, and Amerindian in the formation of quilombo populations. The low F(ST) values suggested gene flow among quilombos from Vale do Ribeira. Our data highlight the important role of Amerindians in the formation of quilombo populations. Copyright © 2012 Wiley Periodicals, Inc.

Enhanced oral bioavailability and anticancer efficacy of fisetin by encapsulating as inclusion complex with HPβCD in polymeric nanoparticles.

PubMed

Kadari, Amrita; Gudem, Sagarika; Kulhari, Hitesh; Bhandi, Murali Mohan; Borkar, Roshan M; Kolapalli, Venkata Ramana Murthy; Sistla, Ramakrishna

2017-11-01

Fisetin (FST), a potent anticancer phytoconstituent, exhibits poor aqueous solubility and hence poor bioavailability. The aim of the present study is to improve the oral bioavailability of FST by encapsulating into PLGA NPs (poly-lactide-co-glycolic acid nanoparticles) as a complex of HPβCD (hydroxyl propyl beta cyclodextrin) and to assess its anti-cancer activity against breast cancer cells. FST-HPβCD inclusion complex (FHIC) was prepared and the supramolecular complex formation was characterized by FTIR, DSC, PXRD and 1 H NMR. FHIC encapsulated PLGA nanoparticles (FHIC-PNP) were prepared and were studied for in vitro anticancer activity, cellular uptake, apoptosis and reactive oxygen species generation in MCF-7 human breast cancer cells. Comparative bioavailability of FST was determined after oral administration in C57BL6 mice as pure FST and FHIC-PNP. The results revealed that FHIC-PNP not only enhanced the anti-cancer activity and apoptosis of FST against MCF-7 cells but also improved its oral bioavailability, as demonstrated by increased peak plasma concentration and total drug absorbed.

Brain activation patterns elicited by the 'Faces Symbol Test' -- a pilot fMRI study.

PubMed

Grabner, Rh; Popotnig, F; Ropele, S; Neuper, C; Gorani, F; Petrovic, K; Ebner, F; Strasser-Fuchs, S; Fazekas, F; Enzinger, C

2008-04-01

The Faces Symbol Test (FST) has recently been proposed as a brief and patient-friendly screening instrument for the assessment of cognitive dysfunction in patients with multiple sclerosis (MS). However, in contrast to well-established MS screening tests such as the Paced Auditory Serial Addition Test, the neural correlates of the FST have not been investigated so far. In the present study, we developed a functional MRI (fMRI) version of the FST to provide first data on brain regions and networks involved in this test. A sample of 19 healthy participants completed a version of the FST adapted for fMRI, requiring matching of faces and symbols in a multiple choice test and two further experimental conditions drawing on cognitive subcomponents (face matching and symbol matching). Imaging data showed a differential involvement of a fronto-parieto-occipital network in the three conditions. The most demanding FST condition elicited brain activation patterns related with sustained attention and executive control. These results suggest that the FST recruits brain networks critical for higher-order cognitive functions often impaired in MS patients.

High connectivity in the deepwater snapper Pristipomoides filamentosus (Lutjanidae) across the Indo-Pacific with isolation of the Hawaiian archipelago.

PubMed

Gaither, Michelle R; Jones, Shelley A; Kelley, Christopher; Newman, Stephen J; Sorenson, Laurie; Bowen, Brian W

2011-01-01

In the tropical Indo-Pacific, most phylogeographic studies have focused on the shallow-water taxa that inhabit reefs to approximately 30 m depth. Little is known about the large predatory fishes, primarily snappers (subfamily Etelinae) and groupers (subfamily Epinephelinae) that occur at 100-400 m. These long-lived, slow-growing species support fisheries across the Indo-Pacific, yet no comprehensive genetic surveys within this group have been conducted. Here we contribute the first range-wide survey of a deepwater Indo-Pacific snapper, Pristipomoides filamentosus, with special focus on Hawai'i. We applied mtDNA cytochrome b and 11 microsatellite loci to 26 samples (N=1,222) collected across 17,000 km from Hawai'i to the western Indian Ocean. Results indicate that P. filamentosus is a highly dispersive species with low but significant population structure (mtDNA Φ(ST)=0.029, microsatellite F(ST)=0.029) due entirely to the isolation of Hawai'i. No population structure was detected across 14,000 km of the Indo-Pacific from Tonga in the Central Pacific to the Seychelles in the western Indian Ocean, a pattern rarely observed in reef species. Despite a long pelagic phase (60-180 days), interisland dispersal as adults, and extensive gene flow across the Indo-Pacific, P. filamentosus is unable to maintain population connectivity with Hawai'i. Coalescent analyses indicate that P. filamentosus may have colonized Hawai'i 26 K-52 K y ago against prevailing currents, with dispersal away from Hawai'i dominating migration estimates. P. filamentosus harbors low genetic diversity in Hawai'i, a common pattern in marine fishes, and our data indicate a single archipelago-wide stock. However, like the Hawaiian Grouper, Hyporthodus quernus, this snapper had several significant pairwise comparisons (F(ST)) clustered around the middle of the archipelago (St. Rogatien, Brooks Banks, Gardner) indicating that this region may be isolated or (more likely) receives input from Johnston Atoll to the south. © 2011 Gaither et al.

High-performance FeSe0.5Te0.5 thin films fabricated on less-well-textured flexible coated conductor templates

NASA Astrophysics Data System (ADS)

Xu, Zhongtang; Yuan, Pusheng; Ma, Yanwei; Cai, Chuanbing

2017-03-01

We report on the transport properties of FeSe0.5Te0.5 (FST) thin films fabricated on less-well-textured flexible coated conductor templates with LaMnO3 (LMO) as buffer layers using pulsed laser deposition. The LMO buffer layers exhibit large in-plane misalignment of ˜7.72°, which is unfavorable for cuprate-coated conductors due to the high grain boundaries. The FST thin films show a superconducting transition temperature of 16.8 K, higher than that of bulk materials due to the compressive strain between LMO and FST. Atomic force microscopy observations reveal that island-like features appear at the surfaces of both LMO and FST, confirming the island growth mode. A self-field transport critical-current density of up to 0.43 MA cm-2 at 4.2 K has been observed in FST thin films, which is much higher than that in powder-in-tube processed FST tapes. The films are capable of carrying current densities of over 105 A cm-2 in the whole applied magnetic field up to 9 T, showing great potential for high-field applications. The results indicate that, for FST, highly textured metal tapes are not needed to produce coated conductors with high performance, which is of great advantage over cuprate-coated conductors.

The effects of dominance, regular inbreeding and sampling design on Q(ST), an estimator of population differentiation for quantitative traits.

PubMed

Goudet, Jérôme; Büchi, Lucie

2006-02-01

To test whether quantitative traits are under directional or homogenizing selection, it is common practice to compare population differentiation estimates at molecular markers (F(ST)) and quantitative traits (Q(ST)). If the trait is neutral and its determinism is additive, then theory predicts that Q(ST) = F(ST), while Q(ST) > F(ST) is predicted under directional selection for different local optima, and Q(ST) < F(ST) is predicted under homogenizing selection. However, nonadditive effects can alter these predictions. Here, we investigate the influence of dominance on the relation between Q(ST) and F(ST) for neutral traits. Using analytical results and computer simulations, we show that dominance generally deflates Q(ST) relative to F(ST). Under inbreeding, the effect of dominance vanishes, and we show that for selfing species, a better estimate of Q(ST) is obtained from selfed families than from half-sib families. We also compare several sampling designs and find that it is always best to sample many populations (>20) with few families (five) rather than few populations with many families. Provided that estimates of Q(ST) are derived from individuals originating from many populations, we conclude that the pattern Q(ST) > F(ST), and hence the inference of directional selection for different local optima, is robust to the effect of nonadditive gene actions.

Population connectivity and larval dispersal of the exploited mangrove crab Ucides cordatus along the Brazilian coast

PubMed Central

Schmidt, Anders J.; Carvalho, Adriana M.F.; Vasconcelos, Carolina C.M.P.; Farias, Antonia M.; Bentzen, Paul

2018-01-01

Background The mangrove crab Ucides cordatus is considered a key species for the ecological balance of mangrove forests and a major source of employment and income for traditional crab collectors in Brazil. Several studies evidenced weak genetic variation among populations due to an efficient larval transport. However, gene flow patterns of the species is poorly understood, with no information about migration rates. The influence of the two main Brazilian currents in larval dispersion is also not clear. In order to provide baseline information for conservation, planning and management of this important fishery resource, the present study aimed to estimate and evaluate spatial distribution of genetic diversity, migration rates and gene flow directivity among populations of U. cordatus in Brazil. Methods Nine microsatellites were used to resolve population structure of 319 crabs collected from six sites located along the Brazilian coast. The degree of geographical differentiation included estimates of genetic diversity, population structure and gene flow models, with spatial analysis of shared alleles (SAShA), isolation by distance tests, AMOVA, discriminant analysis of principal components (DAPC) and Bayesian clustering. We estimated the amount of ongoing gene flow between clusters using the coalescent-based method implemented in Migrate-N. Results Loci were highly polymorphic (average of 12.4 alleles per locus) evidencing high genetic variability. There was significant differentiation among localities, despite of the low value of FST (= 0.019; P < 0.001). FST and Jost’s D indexes were also estimated in pairwise comparisons and showed significant differences between most of the surveyed site pairs (P < 0.05). Structure evidenced a single genetic group among samples, however SAShA pointed to a non-panmictic condition (P = 0.011). AMOVA detected four statistical significant clusters with low level of differentiation (FCT = 0.037; P = 0.023). The gene flow model that best described the population connectivity was the island model, with ∼24 crabs being exchanged among localities per generation. Discussion The high migration rates found among localities seem to be the main force acting to sustain the distribution of the genetic diversity of U. cordatus. Despite the high gene flow and the weak population structure among samples, the significant genetic differences found suggest that gene flow alone does not bypass the effects of genetic drift, natural selection and/or human exploitation. These findings are vital for the establishment of a database to be used in the development of conservation programs. PMID:29736340

Population genetic structure of the acanthocephalan Acanthosentis cheni in anadromous, freshwater, and landlocked stocks of its fish host, Coilia nasus.

PubMed

Song, Rui; Li, Wen X; Wu, Shan G; Zou, Hong; Wang, Gui T

2014-04-01

The acanthocephalan Acanthosentis cheni was found in anadromous, freshwater, and landlocked stocks of its fish host, Coilia nasus. To examine the genetic variations of the acanthocephalan among the 3 populations with the adaptation of the host to the freshwater, the genetic structure of the helminth was investigated in anadromous (Zhoushan and Chongming islands, and Anqing), freshwater (Anqing, Ezhou, and Poyang Lake), and landlocked (Tian'ezhou Reserve) populations by sequencing intergenic transcribed spacers (ITS) of the ribosomal RNA coding genes. Low Fst values and high gene flow were found among the 7 populations (Fst = 0.0135, P = 0.2723; Nm = 36.48) and the 3 ecotypes of Acanthosentis cheni (Fst = 0.0178, P = 0.1044; Nm = 27.67). On the other hand, significant genetic differentiation of the C. nasus host populations was detected between the upstream and downstream areas of Xiaogu Mountain (Fst = 0.1961, P = 0.0030; Nm = 2.05), which is the farthest location of spawning migration for C. nasus . However, the migration break of the fish host appeared not to cause significant genetic differentiation of A. cheni populations between the upper and lower reaches of Xiaogu Mountain. Other factors might promote genetic exchange of A. cheni populations such as dispersal of the intermediate host by flooding or other fish species serving as the definitive or paratenic hosts. In Anqing, nucleotide diversity of the acanthocephalan was highest in the freshwater population (0.0038) and lower in the anadromous population (0.0026). This suggested that new mutations may have occurred in the freshwater A. cheni population in Anqing when adapting to a freshwater environment.

Effect of sociocultural cleavage on genetic differentiation: a study from North India.

PubMed

Khan, Faisal; Pandey, Atul Kumar; Borkar, Meenal; Tripathi, Manorma; Talwar, Sudha; Bisen, P S; Agrawal, Suraksha

2008-06-01

Indian populations possess an exclusive genetic profile primarily due to the many migratory events, which caused an extensive range of genetic diversity, and also due to stringent and austere sociocultural barriers that structure these populations into different endogamous groups. In the present study we attempt to explore the genetic relationships between various endogamous North Indian populations and to determine the effect of stringent social regulations on their gene pool. Twenty STR markers were genotyped in 1,800 random North Indians from 9 endogamous populations belonging to upper-caste and middle-caste Hindus and Muslims. All nine populations had high allelic diversity (176 alleles) and average observed heterozygosity (0.742 +/- 0.06), suggesting strong intrapopulation diversity. The average F(ST) value over all loci was as low as 0.0084. However, within-group F(ST) and genetic distance analysis showed that populations of the same group were genetically closer to each other. The genetic distance of Muslims from middle castes (F(ST) = 0.0090; DA = 0.0266) was significantly higher than that of Muslims from upper castes (F(ST) = 0.0050; DA = 0.0148). Phylogenetic trees (neighbor-joining and maximum-likelihood) show the basal cluster pattern of three clusters corresponding to Muslims, upper-caste, and middle-caste populations, with Muslims clustered with upper-caste populations. Based on the results, we conclude that the extensive gene flow through a series of migrations and invasions has created an enormous amount of genetic diversity. The interpopulation differences are minimal but have a definite pattern, in which populations of different socioreligious groups have more genetic similarity within the same group and are genetically more distant from populations of other groups. Finally, North Indian Muslims show a differential genetic relationship with upper- and middle-caste populations.

Age differences in the impact of forced swimming test on serotonin transporter levels in lateral septum and dorsal raphe

PubMed Central

2014-01-01

Background Forced swimming test (FST) is an animal model which evaluates behavioral despair and the effect of antidepressants such as the selective serotonin reuptake inhibitors; the FST modifies the expression of some receptors related to antidepressant response, but it is not known whether serotonin transporter (SERT), their main target, is affected by this test in animals of different ages. Antidepressant response has shown age-dependent variations which could be associated with SERT expression. The aim of the present study was to analyze changes in the SERT immunoreactivity (SERT-IR) in dorsal raphe and lateral septum of male rats from different age groups with or without behavioral despair induced by their exposure to the FST, since these two structures are related to the expression of this behavior. Methods Prepubertal (24 PN), pubertal (40 PN), young adult (3–5 months) and middle-aged (12 months) male rats were assigned to a control group (non-FST) or depressed group (FST, two sessions separated by 24 h). Changes in SERT-IR in dorsal raphe and lateral septum were determined with immunofluorescence. Results Pubertal and middle-aged rats showed higher levels of immobility behavior compared to prepubertal rats on the FST. SERT-IR showed an age-dependent increase followed by a moderate decrease in middle-aged rats in both structures; a decreased in SERT-IR in lateral septum and dorsal raphe of pubertal rats was observed after the FST. Conclusions Age differences were observed in the SERT-IR of structures related to behavioral despair; SERT expression was modified by the FST in lateral septum and dorsal raphe of pubertal rats. PMID:24490994

Clinical and Antiviral Efficacy of an Ophthalmic Formulation of Dexamethasone Povidone-Iodine in a Rabbit Model of Adenoviral Keratoconjunctivitis

PubMed Central

Clement, Christian; Capriotti, Joseph A.; Kumar, Manish; Hobden, Jeffery A.; Foster, Timothy P.; Bhattacharjee, Partha S.; Thompson, Hilary W.; Mahmud, Rashed; Liang, Bo

2011-01-01

Purpose. To determine the efficacy of a new formulation of topical dexamethasone 0.1%/povidone-iodine 0.4% (FST-100) in reducing clinical symptoms and infectious viral titers in a rabbit model of adenoviral keratoconjunctivitis. Methods. Rabbit corneas were inoculated bilaterally with 2 × 106 plaque-forming-units (PFU) of adenovirus type 5 (Ad5) after corneal scarification. Animals were randomized 1:1:1:1 (five rabbits per group) to FST-100, 0.5% cidofovir, tobramycin/dexamethasone (Tobradex; Alcon Laboratories, Fort Worth, TX) ophthalmic suspension, and balanced salt solution (BSS; Alcon Laboratories). Treatment began 12 hours after viral inoculation and continued for 7 consecutive days. The eyes were clinically scored daily for scleral inflammation (injection), ocular neovascularization, eyelid inflammation (redness), friability of vasculature, inflammatory discharge (pus), and epiphora (excessive tearing). Eye swabs were collected daily before treatment for the duration of the study. Virus was eluted from the swabs and PFU determined by titration on human A549 cells, according to standard procedures. Results. The FST-100 treatment resulted in significantly lower clinical scores (P < 0.05) than did the other treatments. The 0.5% cidofovir exhibited the most ocular toxicity compared with FST-100, tobramycin/dexamethasone, and balanced salt solution treatments. FST-100 and 0.5% cidofovir significantly (P < 0.05) reduced viral titers compared with tobramycin/dexamethasone or balanced salt solution. Conclusions. FST-100 was the most efficacious in minimizing the clinical symptoms of adenovirus infection in rabbit eyes. FST-100 and 0.5% cidofovir were both equally effective in reducing viral titers and decreasing the duration of viral shedding. By providing symptomatic relief in addition to reducing infectious virus titers, FST-100 should be a valuable addition to treatment of epidemic adenoviral keratoconjunctivitis. PMID:20702820

Preliminary characterization of a novel β-agarase from Thalassospira profundimonas.

PubMed

Zeng, Cheng; Zhang, Longtao; Miao, Song; Zhang, Yi; Zeng, Shaoxiao; Zheng, Baodong

2016-01-01

The objective of this study was to characterize the agarase from a newly isolated agarolytic bacterium Thalassospira profundimaris fst-13007. Agarase-fst was purified to homogeneity which apparent molecular weight was 66.2 kDa. Its activity was optimal at 45 °C and pH 8 and was stable at pH 5-9 or 30-50 °C. Agarase-fst required Mn(2+) for agarase activity and inhibition by Cu(2+), Fe(3+) and EDTA. Tests of hydrolysis pattern and substrate specificity, TLC analysis and mass spectrometry of the hydrolysis products revealed that it is an endo-type β-agarase hydrolyzing agarose into neoagarobiose, neoagarotetraose and neoagarohexaose. Results of MALDI-TOF-TOF/MS indicate that it lack of homology to previously identified proteins and present conserved domain of β-agarase. Agarase-fst from T. profundimaris fst-13007 was confirmed to be a novel endo-type β-agarase.

Hydrodynamic comparison of the Penumbra system and commonly available syringes in forced-suction thrombectomy.

PubMed

Simon, Scott Douglas; Grey, Casey Paul

2014-04-01

The Penumbra system uses a coaxial separator and continuous extracorporeal suction to remove a clot from a cerebral artery. Forced-suction thrombectomy (FST) involves aspirating clots through the same reperfusion catheter using only a syringe, decreasing the procedure time and supplies needed. To evaluate multiple combinations of catheters and syringes to determine the optimal pairing for use in FST. Tests were performed using both the Penumbra system and syringes to aspirate water through Penumbra 0.041 inch (041), 4Max, 0.054 inch (054) and 5Max reperfusion catheters and a shuttle sheath. Dynamic pressure and flow at the catheter tip were calculated from the fill times for each system. Static pressure and force for each aspiration source were determined with a vacuum gauge. All syringes provided significantly higher dynamic pressure at the catheter tip than the Penumbra system (p<0.001). Increasing syringe volume significantly increased static pressure (p<0.001). Both flow and aspiration force significantly increased with catheter size (p<0.001). Cases are presented to demonstrate the clinical value of the laboratory principles. Maximizing static and dynamic pressure when performing FST is achieved by aspirating with a syringe possessing both the largest volume and the largest inlet diameter available. Maximizing aspiration force and flow rate is achieved by using the largest catheter possible.

Empirical Selection of Informative Microsatellite Markers within Co-ancestry Pig Populations Is Required for Improving the Individual Assignment Efficiency

PubMed Central

Li, Y. H.; Chu, H. P.; Jiang, Y. N.; Lin, C. Y.; Li, S. H.; Li, K. T.; Weng, G. J.; Cheng, C. C.; Lu, D. J.; Ju, Y. T.

2014-01-01

The Lanyu is a miniature pig breed indigenous to Lanyu Island, Taiwan. It is distantly related to Asian and European pig breeds. It has been inbred to generate two breeds and crossed with Landrace and Duroc to produce two hybrids for laboratory use. Selecting sets of informative genetic markers to track the genetic qualities of laboratory animals and stud stock is an important function of genetic databases. For more than two decades, Lanyu derived breeds of common ancestry and crossbreeds have been used to examine the effectiveness of genetic marker selection and optimal approaches for individual assignment. In this paper, these pigs and the following breeds: Berkshire, Duroc, Landrace and Yorkshire, Meishan and Taoyuan, TLRI Black Pig No. 1, and Kaohsiung Animal Propagation Station Black pig are studied to build a genetic reference database. Nineteen microsatellite markers (loci) provide information on genetic variation and differentiation among studied breeds. High differentiation index (FST) and Cavalli-Sforza chord distances give genetic differentiation among breeds, including Lanyu’s inbred populations. Inbreeding values (FIS) show that Lanyu and its derived inbred breeds have significant loss of heterozygosity. Individual assignment testing of 352 animals was done with different numbers of microsatellite markers in this study. The testing assigned 99% of the animals successfully into their correct reference populations based on 9 to 14 markers ranking D-scores, allelic number, expected heterozygosity (HE) or FST, respectively. All miss-assigned individuals came from close lineage Lanyu breeds. To improve individual assignment among close lineage breeds, microsatellite markers selected from Lanyu populations with high polymorphic, heterozygosity, FST and D-scores were used. Only 6 to 8 markers ranking HE, FST or allelic number were required to obtain 99% assignment accuracy. This result suggests empirical examination of assignment-error rates is required if discernible levels of co-ancestry exist. In the reference group, optimum assignment accuracy was achievable achieved through a combination of different markers by ranking the heterozygosity, FST and allelic number of close lineage populations. PMID:25049996

Alteration in follistatin gene expression detected in prenatally androgenized rats.

PubMed

Salehi Jahromi, Marziyeh; Ramezani Tehrani, Fahimeh; Hill, Jennifer W; Noroozzadeh, Mahsa; Zarkesh, Maryam; Ghasemi, Asghar; Zadeh-Vakili, Azita

2017-06-01

Impaired ovarian follicle development, the hallmark of polycystic ovarian syndrome (PCOS), is believed to be due to the changes in expression of related genes such as follistatin (FST). Expression of FST gene and methylation level of its promoter in theca cells from adult female rats, prenatally exposed to androgen excess, during different phases of the estrus cycle was determined and compared with controls. Eight pregnant Wistar rats (experimental group) were treated by subcutaneous injection of 5 mg free testosterone on day 20 of pregnancy, while controls (n = 8) received 500 ml solvent. Based on observed vaginal smear, adult female offspring of mothers were divided into three groups. Levels of serum steroidogenic sexual hormones and gonadotropins, expression and promoter methylation of the FST gene were measured using ELISA, cyber-green real-time PCR and bisulfite sequence PCR (BSP), respectively. Compared to controls, the relative expression of FST gene in the treated group decreased overall by 0.85 fold; despite significant changes in different phases, but no significant differences in methylation of FST promoter. Our results reveal that manifestation of PCOS-like phenotype following prenatal exposure to excess androgen is associated with irregularity in expression of the FST gene during the estrus cycle.

Population Genomics of the Euryhaline Teleost Poecilia latipinna

PubMed Central

Hoover, D.; Travis, J.; Oleksiak, M. F.; Crawford, D. L.

2015-01-01

Global climate change and increases in sea levels will affect coastal marine communities. The conservation of these ecologically important areas will be a challenge because of their wide geographic distribution, ecological diversity and species richness. To address this problem, we need to better understand how the genetic variation of the species in these communities is distributed within local populations, among populations and between distant regions. In this study we apply genotyping by sequencing (GBS) and examine 955 SNPs to determine Sailfin molly (Poecilia latipinna) genetic diversity among three geographically close mangrove salt marsh flats in the Florida Keys compared to populations in southern and northern Florida. The questions we are asking are whether there is sufficient genetic variation among isolated estuarine fish within populations and whether there are significant divergences among populations. Additionally, we want to know if GBS approaches agree with previous studies using more traditional molecular approaches. We are able to identify large genetic diversity within each saltmarsh community (π ≈ 36%). Additionally, among the Florida Key populations and the mainland or between southern and northern Florida regions, there are significant differences in allele frequencies seen in population structure and evolutionary relationships among individuals. Surprisingly, even though the cumulative FST value using all 955 SNPs within the three Florida Key populations is small, there are 29 loci with significant FST values, and 11 of these were outliers suggestive of adaptive divergence. These data suggest that among the salt marsh flats surveyed here, there is significant genetic diversity within each population and small but significant differences among populations. Much of the genetic variation within and among populations found here with GBS is very similar to previous studies using allozymes and microsatellites. However, the meaningful difference between GBS and these previous measures of genetic diversity is the number of loci examined, which allows more precise delineations of population structure as well as facilitates identifying loci with excessive FST values that could indicate adaptive divergence. PMID:26335684

Population Genomics of the Euryhaline Teleost Poecilia latipinna.

PubMed

Nunez, J C B; Seale, T P; Fraser, M A; Burton, T L; Fortson, T N; Hoover, D; Travis, J; Oleksiak, M F; Crawford, D L

2015-01-01

Global climate change and increases in sea levels will affect coastal marine communities. The conservation of these ecologically important areas will be a challenge because of their wide geographic distribution, ecological diversity and species richness. To address this problem, we need to better understand how the genetic variation of the species in these communities is distributed within local populations, among populations and between distant regions. In this study we apply genotyping by sequencing (GBS) and examine 955 SNPs to determine Sailfin molly (Poecilia latipinna) genetic diversity among three geographically close mangrove salt marsh flats in the Florida Keys compared to populations in southern and northern Florida. The questions we are asking are whether there is sufficient genetic variation among isolated estuarine fish within populations and whether there are significant divergences among populations. Additionally, we want to know if GBS approaches agree with previous studies using more traditional molecular approaches. We are able to identify large genetic diversity within each saltmarsh community (π ≈ 36%). Additionally, among the Florida Key populations and the mainland or between southern and northern Florida regions, there are significant differences in allele frequencies seen in population structure and evolutionary relationships among individuals. Surprisingly, even though the cumulative FST value using all 955 SNPs within the three Florida Key populations is small, there are 29 loci with significant FST values, and 11 of these were outliers suggestive of adaptive divergence. These data suggest that among the salt marsh flats surveyed here, there is significant genetic diversity within each population and small but significant differences among populations. Much of the genetic variation within and among populations found here with GBS is very similar to previous studies using allozymes and microsatellites. However, the meaningful difference between GBS and these previous measures of genetic diversity is the number of loci examined, which allows more precise delineations of population structure as well as facilitates identifying loci with excessive FST values that could indicate adaptive divergence.

Effects of aspirin on immobile behavior and endocrine and immune changes in the forced swimming test: comparison to fluoxetine and imipramine.

PubMed

Guan, Xi-ting; Shao, Feng; Xie, Xi; Chen, Lin; Wang, Weiwen

2014-09-01

Aspirin (ASP) is the most commonly used non-steroidal anti-inflammatory drug in the world. Recent clinical and preclinical evidence suggests that ASP may also exert psychoactive effects. It remains unclear whether ASP has antidepressant-like activity, and any molecular mechanisms underlying such activity have yet to be elucidated. Using the forced swimming test (FST), a well-established animal model of depression widely used to screen potential antidepressants in rodents, we investigated the effects of subacute treatment with ASP (0, 6, 12, 25, and 50mg/kg, i.p.) on immobility in the FST, and on FST-induced changes in endocrine and immune parameters in rats, in comparison to the clinical antidepressants imipramine (IMI) and fluoxetine (FLU). Serum levels of corticosterone, pro-inflammatory cytokine interleukin-6 (IL-6), and tumor necrosis factor-α (TNF-α) were determined by enzyme-linked immunosorbent assay. ASP dose-dependently decreased immobility in the FST, without altering the locomotor activity in the open-field test. The inhibitory effects of higher doses (25 and 50mg/kg) of ASP on immobility were similar to that of FLU and IMI at a dose of 10mg/kg. In addition, the levels of corticosterone, IL-6, and TNF-α in peripheral blood were significantly increased after the FST exposure. IMI, but not FLU and ASP at any dose tested, significantly attenuated corticosterone responses in the FST. Both FLU and IMI treatment reduced the increase of IL-6 and TNF-α levels following the FST exposure. ASP dose-dependently decreased FST-induced increase of cytokine levels, as manifested by significantly stronger effects on IL-6 and TNF-α levels at higher doses (25 and 50mg/kg) than the lowest dose of ASP (6 mg/kg). In all, these results indicate that ASP treatment dose-dependently decreased the immobility time and the release of pro-inflammatory cytokines in the FST, suggesting that the anti-inflammatory effects of ASP might be involved in the antidepressant-like effect. Copyright © 2014 Elsevier Inc. All rights reserved.

Genetic origin of goat populations in Oman revealed by mitochondrial DNA analysis.

PubMed

Al-Araimi, Nasser Ali; Gaafar, Osman Mahgoub; Costa, Vânia; Neira, Agusto Luzuriaga; Al-Atiyat, Raed Mahmoud; Beja-Pereira, Albano

2017-01-01

The Sultanate of Oman has a complex mosaic of livestock species and production systems, but the genetic diversity, demographic history or origins of these Omani animals has not been expensively studied. Goats might constitute one of the most abundant and important domestic livestock species since the Neolithic transition. Here, we examined the genetic diversity, origin, population structure and demographic history of Omani goats. Specifically, we analyzed a 525-bp fragment of the first hypervariable region of the mitochondrial DNA (mtDNA) control region from 69 Omani individuals and compared this fragment with 17 mtDNA sequences from Somalia and Yemen as well as 18 wild goat species and 1,198 previously published goat sequences from neighboring countries. The studied goat breeds show substantial diversity. The haplotype and nucleotide diversities of Omani goats were found equal to 0.983 ± 0.006 and 0.0284 ± 0.014, respectively. The phylogenetic analyses allowed us to classify Omani goats into three mtDNA haplogroups (A, B and G): haplogroup A was found to be predominant and widely distributed and accounted for 80% of all samples, and haplogroups B and G exhibited low frequencies. Phylogenetic comparisons with wild goats revealed that five of the native Omani goat populations originate from Capra aegagrus. Furthermore, most comparisons of pairwise population FST values within and between these five Omani goat breeds as well as between Omani goats and nine populations from nearby countries were not significant. These results suggest strong gene flow among goat populations caused by the extensive transport of goats and the frequent movements of human populations in ancient Arabia. The findings improve our understanding of the migration routes of modern goats from their region of domestication into southeastern Arabia and thereby shed light on human migratory and commercial networks during historical times.

Molecular and phylogenetic analyses of the liver amphistome Explanatum explanatum (Creplin, 1847) Fukui, 1929 in ruminants from Bangladesh and Nepal based on nuclear ribosomal ITS2 and mitochondrial nad1 sequences.

PubMed

Mohanta, U K; Rana, H B; Devkota, B; Itagaki, T

2017-07-01

Explanatum explanatum flukes, liver amphistomes of ruminants, cause significant economic loss in the livestock industry by inducing severe liver damage. A total of 66 flukes from 26 buffaloes and 7 cattle in four different geographic areas of Bangladesh and 20 flukes from 10 buffaloes in the Chitwan district of Nepal were subjected for analysis. The sequences (442 bp) of the second internal transcribed spacer (ITS2) of ribosomal DNA and the variable fragments (657 bp) of mitochondrial nicotinamide dehydrogenase subunit 1 (nad1) of E. explanatum flukes from Bangladesh and Nepal were analysed. The aim of this study was molecular characterization of the flukes and to elucidate their origin and biogeography. In the ITS2 region, two genotypes were detected among the flukes from Bangladesh, while flukes from Nepal were of only one genotype. Phylogenetic analyses inferred from the nad1 gene revealed that at least four divergent populations (groups I-IV) are distributed in Bangladesh, whereas two divergent populations were found to be distributed in Nepal. Fst values (pairwise fixation index) suggest that Bangladeshi and Nepalese populations of group I to IV are significantly different from each other; but within groups III and IV, the populations from Bangladesh and Nepal were genetically close. This divergence in the nad1 gene indicates that each lineage of E. explanatum from diverse geography was co-adapted during the multiple domestication events of ruminants. This study, for the first time, provides molecular characterization of E. explanatum in Bangladesh and Nepal, and may provide useful information for elucidating its origin and dispersal route in Asia.

Multilocus sequence analysis of Thermoanaerobacter isolates reveals recombining, but differentiated, populations from geothermal springs of the Uzon Caldera, Kamchatka, Russia

PubMed Central

Wagner, Isaac D.; Varghese, Litty B.; Hemme, Christopher L.; Wiegel, Juergen

2013-01-01

Thermal environments have island-like characteristics and provide a unique opportunity to study population structure and diversity patterns of microbial taxa inhabiting these sites. Strains having ≥98% 16S rRNA gene sequence similarity to the obligately anaerobic Firmicutes Thermoanaerobacter uzonensis were isolated from seven geothermal springs, separated by up to 1600 m, within the Uzon Caldera (Kamchatka, Russian Far East). The intraspecies variation and spatial patterns of diversity for this taxon were assessed by multilocus sequence analysis (MLSA) of 106 strains. Analysis of eight protein-coding loci (gyrB, lepA, leuS, pyrG, recA, recG, rplB, and rpoB) revealed that all loci were polymorphic and that nucleotide substitutions were mostly synonymous. There were 148 variable nucleotide sites across 8003 bp concatenates of the protein-coding loci. While pairwise FST values indicated a small but significant level of genetic differentiation between most subpopulations, there was a negligible relationship between genetic divergence and spatial separation. Strains with the same allelic profile were only isolated from the same hot spring, occasionally from consecutive years, and single locus variant (SLV) sequence types were usually derived from the same spring. While recombination occurred, there was an “epidemic” population structure in which a particular T. uzonensis sequence type rose in frequency relative to the rest of the population. These results demonstrate spatial diversity patterns for an anaerobic bacterial species in a relative small geographic location and reinforce the view that terrestrial geothermal springs are excellent places to look for biogeographic diversity patterns regardless of the involved distances. PMID:23801987

Genotypic and phenotypic characterization of genetic differentiation and diversity in the USDA rice mini-core collection.

PubMed

Li, Xiaobai; Yan, Wengui; Agrama, Hesham; Hu, Biaolin; Jia, Limeng; Jia, Melissa; Jackson, Aaron; Moldenhauer, Karen; McClung, Anna; Wu, Dianxing

2010-12-01

A rice mini-core collection consisting of 217 accessions has been developed to represent the USDA core and whole collections that include 1,794 and 18,709 accessions, respectively. To improve the efficiency of mining valuable genes and broadening the genetic diversity in breeding, genetic structure and diversity were analyzed using both genotypic (128 molecular markers) and phenotypic (14 numerical traits) data. This mini-core had 13.5 alleles per locus, which is the most among the reported germplasm collections of rice. Similarly, polymorphic information content (PIC) value was 0.71 in the mini-core which is the highest with one exception. The high genetic diversity in the mini-core suggests there is a good possibility of mining genes of interest and selecting parents which will improve food production and quality. A model-based clustering analysis resulted in lowland rice including three groups, aus (39 accessions), indica (71) and their admixtures (5), upland rice including temperate japonica (32), tropical japonica (40), aromatic (6) and their admixtures (12) and wild rice (12) including glaberrima and four other species of Oryza. Group differentiation was analyzed using both genotypic distance Fst from 128 molecular markers and phenotypic (Mahalanobis) distance D(2) from 14 traits. Both dendrograms built by Fst and D(2) reached similar-differentiative relationship among these genetic groups, and the correlation coefficient showed high value 0.85 between Fst matrix and D(2) matrix. The information of genetic and phenotypic differentiation could be helpful for the association mapping of genes of interest. Analysis of genotypic and phenotypic diversity based on genetic structure would facilitate parent selection for broadening genetic base of modern rice cultivars via breeding effort.

Assessment of Point-of-Care Diagnostics for G6PD Deficiency in Malaria Endemic Rural Eastern Indonesia

PubMed Central

Satyagraha, Ari W.; Sadhewa, Arkasha; Elvira, Rosalie; Elyazar, Iqbal; Feriandika, Denny; Antonjaya, Ungke; Oyong, Damian; Subekti, Decy; Rozi, Ismail E.; Domingo, Gonzalo J.; Harahap, Alida R.; Baird, J. Kevin

2016-01-01

Background Patients infected by Plasmodium vivax or Plasmodium ovale suffer repeated clinical attacks without primaquine therapy against latent stages in liver. Primaquine causes seriously threatening acute hemolytic anemia in patients having inherited glucose-6-phosphate dehydrogenase (G6PD) deficiency. Access to safe primaquine therapy hinges upon the ability to confirm G6PD normal status. CareStart G6PD, a qualitative G6PD rapid diagnostic test (G6PD RDT) intended for use at point-of-care in impoverished rural settings where most malaria patients live, was evaluated. Methodology/Principal Findings This device and the standard qualitative fluorescent spot test (FST) were each compared against the quantitative spectrophotometric assay for G6PD activity as the diagnostic gold standard. The assessment occurred at meso-endemic Panenggo Ede in western Sumba Island in eastern Indonesia, where 610 residents provided venous blood. The G6PD RDT and FST qualitative assessments were performed in the field, whereas the quantitative assay was performed in a research laboratory at Jakarta. The median G6PD activity ≥5 U/gHb was 9.7 U/gHb and was considered 100% of normal activity. The prevalence of G6PD deficiency by quantitative assessment (<5 U/gHb) was 7.2%. Applying 30% of normal G6PD activity as the cut-off for qualitative testing, the sensitivity, specificity, positive predictive value, and negative predictive value for G6PD RDT versus FST among males were as follows: 100%, 98.7%, 89%, and 100% versus 91.7%, 92%, 55%, and 99%; P = 0.49, 0.001, 0.004, and 0.24, respectively. These values among females were: 83%, 92.7%, 17%, and 99.7% versus 100%, 92%, 18%, and 100%; P = 1.0, 0.89, 1.0 and 1.0, respectively. Conclusions/Significance The overall performance of G6PD RDT, especially 100% negative predictive value, demonstrates suitable safety for G6PD screening prior to administering hemolytic drugs like primaquine and many others. Relatively poor diagnostic performance among females due to mosaic G6PD phenotype is an inherent limitation of any current practical screening methodology. PMID:26894297

Assessment of Point-of-Care Diagnostics for G6PD Deficiency in Malaria Endemic Rural Eastern Indonesia.

PubMed

Satyagraha, Ari W; Sadhewa, Arkasha; Elvira, Rosalie; Elyazar, Iqbal; Feriandika, Denny; Antonjaya, Ungke; Oyong, Damian; Subekti, Decy; Rozi, Ismail E; Domingo, Gonzalo J; Harahap, Alida R; Baird, J Kevin

2016-02-01

Patients infected by Plasmodium vivax or Plasmodium ovale suffer repeated clinical attacks without primaquine therapy against latent stages in liver. Primaquine causes seriously threatening acute hemolytic anemia in patients having inherited glucose-6-phosphate dehydrogenase (G6PD) deficiency. Access to safe primaquine therapy hinges upon the ability to confirm G6PD normal status. CareStart G6PD, a qualitative G6PD rapid diagnostic test (G6PD RDT) intended for use at point-of-care in impoverished rural settings where most malaria patients live, was evaluated. This device and the standard qualitative fluorescent spot test (FST) were each compared against the quantitative spectrophotometric assay for G6PD activity as the diagnostic gold standard. The assessment occurred at meso-endemic Panenggo Ede in western Sumba Island in eastern Indonesia, where 610 residents provided venous blood. The G6PD RDT and FST qualitative assessments were performed in the field, whereas the quantitative assay was performed in a research laboratory at Jakarta. The median G6PD activity ≥ 5 U/gHb was 9.7 U/gHb and was considered 100% of normal activity. The prevalence of G6PD deficiency by quantitative assessment (<5 U/gHb) was 7.2%. Applying 30% of normal G6PD activity as the cut-off for qualitative testing, the sensitivity, specificity, positive predictive value, and negative predictive value for G6PD RDT versus FST among males were as follows: 100%, 98.7%, 89%, and 100% versus 91.7%, 92%, 55%, and 99%; P = 0.49, 0.001, 0.004, and 0.24, respectively. These values among females were: 83%, 92.7%, 17%, and 99.7% versus 100%, 92%, 18%, and 100%; P = 1.0, 0.89, 1.0 and 1.0, respectively. The overall performance of G6PD RDT, especially 100% negative predictive value, demonstrates suitable safety for G6PD screening prior to administering hemolytic drugs like primaquine and many others. Relatively poor diagnostic performance among females due to mosaic G6PD phenotype is an inherent limitation of any current practical screening methodology.

Evaluation of genetic diversity and population structure of West-Central Indian cattle breeds.

PubMed

Shah, Tejas M; Patel, Jaina S; Bhong, Chandrakant D; Doiphode, Aakash; Umrikar, Uday D; Parmar, Shivnandan S; Rank, Dharamshibhai N; Solanki, Jitendra V; Joshi, Chaitanya G

2013-08-01

Evaluations of genetic diversity in domestic livestock populations are necessary to implement region-specific conservation measures. We determined the genetic diversity and evolutionary relationships among eight geographically and phenotypically diverse cattle breeds indigenous to west-central India by genotyping these animals for 22 microsatellite loci. A total of 326 alleles were detected, and the expected heterozygosity ranged from 0.614 (Kenkatha) to 0.701 (Dangi). The mean number of alleles among the cattle breeds ranged from 7.182 (Khillar) to 9.409 (Gaolao). There were abundant genetic variations displayed within breeds, and the genetic differentiation was also high between the Indian cattle breeds, which displayed 15.9% of the total genetic differentiation among the different breeds. The genetic differentiation (pairwise FST ) among the eight Indian breeds varied from 0.0126 for the Kankrej-Malvi pair to 0.2667 for Khillar-Kenkatha pair. The phylogeny, principal components analysis, and structure analysis further supported close grouping of Kankrej, Malvi, Nimari and Gir; Gaolao and Kenkatha, whereas Dangi and Khillar remained at distance from other breeds. © 2012 The Authors, Animal Genetics © 2012 Stichting International Foundation for Animal Genetics.

Multi-Phase US Spread and Habitat Switching of a Post-Columbian Invasive, Sorghum halepense

PubMed Central

Barney, Jacob N.; Atwater, Daniel Z.; Pederson, Gary A.; Pederson, Jeffrey F.; Chandler, J. Mike; Cox, T. Stan; Cox, Sheila; Dotray, Peter; Kopec, David; Smith, Steven E.; Schroeder, Jill; Wright, Steven D.; Jiao, Yuannian; Kong, Wenqian; Goff, Valorie; Auckland, Susan; Rainville, Lisa K.; Pierce, Gary J.; Lemke, Cornelia; Compton, Rosana; Phillips, Christine; Kerr, Alexandra; Mettler, Matthew; Paterson, Andrew H.

2016-01-01

Johnsongrass (Sorghum halepense) is a striking example of a post-Columbian founder event. This natural experiment within ecological time-scales provides a unique opportunity for understanding patterns of continent-wide genetic diversity following range expansion. Microsatellite markers were used for population genetic analyses including leaf-optimized Neighbor-Joining tree, pairwise FST, mismatch analysis, principle coordinate analysis, Tajima’s D, Fu’s F and Bayesian clusterings of population structure. Evidence indicates two geographically distant introductions of divergent genotypes, which spread across much of the US in <200 years. Based on geophylogeny, gene flow patterns can be inferred to have involved five phases. Centers of genetic diversity have shifted from two introduction sites separated by ~2000 miles toward the middle of the range, consistent with admixture between genotypes from the respective introductions. Genotyping provides evidence for a ‘habitat switch’ from agricultural to non-agricultural systems and may contribute to both Johnsongrass ubiquity and aggressiveness. Despite lower and more structured diversity at the invasion front, Johnsongrass continues to advance northward into cooler and drier habitats. Association genetic approaches may permit identification of alleles contributing to the habitat switch or other traits important to weed/invasive management and/or crop improvement. PMID:27755565

A comparison of neutral and immune genetic variation in Atlantic salmon, Salmo salar L. in Chilean aquaculture facilities.

PubMed

Portnoy, David S; Hollenbeck, Christopher M; Vidal, R Rodrigo; Gold, John R

2014-01-01

Genetic diversity was assessed in samples of cultured Atlantic salmon, Salmo salar L., obtained from facilities in Chile between 2005 and 2010, a period of time during which the infectious pathogens Infectious Salmon Anemia (ISA) virus, Caligus rogercresseyi (sea lice), and Piscirickettsia salmonis (salmon rickettsial syndrome) were common. Two panels of microsatellite markers were utilized: one with microsatellites with no known gene associations (neutral) and one featuring microsatellites linked to putative immune-related genes (immune-related). Allelic richness and gene diversity across samples were significantly greater in neutral loci as compared to immune-related loci. Both diversity measures were homogeneous among samples for immune-related loci and heterogeneous among samples for neutral loci. Immune-related loci were identified as F(ST) outliers in pairwise comparisons of samples at a 10-fold higher frequency than neutral loci. These results indicate that neutral and immune-related portions of the Atlantic salmon genome may have differed in response to the gauntlet of pathogens and that monitoring of specific, well characterized immune-related loci as well as neutral loci in cultured species could be useful when disease control and prevention is a goal.

A Comparison of Neutral and Immune Genetic Variation in Atlantic Salmon, Salmo salar L. in Chilean Aquaculture Facilities

PubMed Central

Portnoy, David S.; Hollenbeck, Christopher M.; Vidal, R. Rodrigo; Gold, John R.

2014-01-01

Genetic diversity was assessed in samples of cultured Atlantic salmon, Salmo salar L., obtained from facilities in Chile between 2005 and 2010, a period of time during which the infectious pathogens Infectious Salmon Anemia (ISA) virus, Caligus rogercresseyi (sea lice), and Piscirickettsia salmonis (salmon rickettsial syndrome) were common. Two panels of microsatellite markers were utilized: one with microsatellites with no known gene associations (neutral) and one featuring microsatellites linked to putative immune-related genes (immune-related). Allelic richness and gene diversity across samples were significantly greater in neutral loci as compared to immune-related loci. Both diversity measures were homogeneous among samples for immune-related loci and heterogeneous among samples for neutral loci. Immune-related loci were identified as FST outliers in pairwise comparisons of samples at a 10-fold higher frequency than neutral loci. These results indicate that neutral and immune-related portions of the Atlantic salmon genome may have differed in response to the gauntlet of pathogens and that monitoring of specific, well characterized immune-related loci as well as neutral loci in cultured species could be useful when disease control and prevention is a goal. PMID:24918941

Rangewide Genetic Variation in Coast Redwood Populations at a Chloroplast Microsatellite Locus

Treesearch

Chris Brinegar

2012-01-01

Old growth and second growth populations of coast redwood (Sequoia sempervirens) were sampled at 10 locations throughout its range and analyzed at a highly variable chloroplast microsatellite locus. Very low FST values indicated that there was no significant genetic differentiation between adjacent old growth and second growth populations at each location. Genetic...

Differential Rearing Alters Forced Swim Test Behavior, Fluoxetine Efficacy, and Post-Test Weight Gain in Male Rats.

PubMed

Arndt, David L; Peterson, Christy J; Cain, Mary E

2015-01-01

Environmental factors play a key role in the etiology of depression. The rodent forced swim test (FST) is commonly used as a preclinical model of depression, with increases in escape-directed behavior reflecting antidepressant effects, and increases in immobility reflecting behavioral despair. Environmental enrichment leads to serotonergic alterations in rats, but it is unknown whether these alterations may influence the efficacy of common antidepressants. Male Sprague-Dawley rats were reared in enriched (EC), standard (SC), or isolated (IC) conditions. Following the rearing period, fluoxetine (10 or 20 mg/kg, i.p.) was administered 23.5 hrs, 5 hrs, and 1 hr before locomotor and FST measures. Following locomotor testing and FST exposure, rats were weighed to assess fluoxetine-, FST-, and environmental condition-induced moderations in weight gain. Results revealed an antidepressant effect of environmental enrichment and a depressant effect of isolation. Regardless of significant fluoxetine effects on locomotor activity, fluoxetine generally decreased swimming and increased immobility in all three environmental conditions, with IC-fluoxetine (10 mg/kg) rats and EC-fluoxetine (20 mg/kg) rats swimming less than vehicle counterparts. Subchronic 20 mg/kg fluoxetine also induced significant weight loss, and differential rearing appeared to moderate weight gain following FST stress. These results suggest that differential rearing has the ability to alter FST behaviors, fluoxetine efficacy, and post-stressor well-being. Moreover, 20 mg/kg fluoxetine, administered subchronically, may lead to atypical effects of those commonly observed in the FST, highlighting the importance and impact of both environmental condition and dosing regimen in common animal models of depression.

Corrosion inhibition of powder metallurgy Mg by fluoride treatments.

PubMed

Pereda, M D; Alonso, C; Burgos-Asperilla, L; del Valle, J A; Ruano, O A; Perez, P; Fernández Lorenzo de Mele, M A

2010-05-01

Pure Mg has been proposed as a potential degradable biomaterial to avoid both the disadvantages of non-degradable internal fixation implants and the use of alloying elements that may be toxic. However, it shows excessively high corrosion rate and insufficient yield strength. The effects of reinforcing Mg by a powder metallurgy (PM) route and the application of biocompatible corrosion inhibitors (immersion in 0.1 and 1M KF solution treatments, 0.1M FST and 1M FST, respectively) were analyzed in order to improve Mg mechanical and corrosion resistance, respectively. Open circuit potential measurements, polarization techniques (PT), scanning electrochemical microscopy (SECM) and electrochemical impedance spectroscopy (EIS) were performed to evaluate its corrosion behavior. SECM showed that the local current of attacked areas decreased during the F(-) treatments. The corrosion inhibitory action of 0.1M FST and 1M FST in phosphate buffered solution was assessed by PT and EIS. Under the experimental conditions assayed, 0.1M FST revealed better performance. X-ray photoelectron spectroscopy, energy dispersive X-ray and X-ray diffraction analyses of Mg(PM) with 0.1M FST showed the presence of KMgF(3) crystals on the surface while a MgF(2) film was detected for 1M FST. After fluoride inhibition treatments, promising results were observed for Mg(PM) as degradable metallic biomaterial due to its higher yield strength and lower initial corrosion rate than untreated Mg, as well as a progressive loss of the protective characteristics of the F(-)-containing film which ensures the gradual degradation process. Copyright (c) 2009 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Voluntary Exercise Produces Antidepressant and Anxiolytic Behavioral Effects in Mice

PubMed Central

Duman, Catharine H.; Schlesinger, Lee; Russell, David S.; Duman, Ronald S.

2008-01-01

Reports of beneficial effects of exercise on psychological health in humans are increasingly supported by basic research studies. Exercise is hypothesized to regulate antidepressant-related mechanisms and we therefore characterized the effects of chronic exercise in mouse behavioral paradigms relevant to antidepressant actions. Mice given free access to running wheels showed antidepressant-like behavior in learned helplessness, forced-swim (FST) and tail suspension paradigms. These responses were similar to responses of antidepressant drug-treated animals. When tested under conditions where locomotor activity was not altered, exercising mice also showed reduced anxiety compared to sedentary control mice. In situ hybridization analysis showed that BDNF mRNA was increased in specific subfields of hippocampus after wheel running. We chose one paradigm, the FST, in which to investigate a functional role for brain-derived neurotrophic factor (BDNF) in the behavioral response to exercise. We tested mice heterozygous for a deletion of the BDNF gene in the FST after wheel-running. Exercising wild-type mice showed the expected antidepressant-like behavioral response in the FST but exercise was ineffective in improving FST performance in heterozygous BDNF knockout mice. A possible functional contribution of a BDNF signaling pathway to FST performance in exercising mice was investigated using the specific MEK inhibitor PD184161 to block the MAPK signaling pathway. Subchronic administration of PD184161 to exercising mice blocked the antidepressant-like behavioral response seen in vehicle-treated exercising mice in the FST. In summary, chronic wheel-running exercise in mice results in antidepressant-like behavioral changes that may involve a BDNF related mechanism similar to that hypothesized for antidepressant drug treatment. PMID:18267317

Differential Rearing Alters Forced Swim Test Behavior, Fluoxetine Efficacy, and Post-Test Weight Gain in Male Rats

PubMed Central

Arndt, David L.; Peterson, Christy J.; Cain, Mary E.

2015-01-01

Environmental factors play a key role in the etiology of depression. The rodent forced swim test (FST) is commonly used as a preclinical model of depression, with increases in escape-directed behavior reflecting antidepressant effects, and increases in immobility reflecting behavioral despair. Environmental enrichment leads to serotonergic alterations in rats, but it is unknown whether these alterations may influence the efficacy of common antidepressants. Male Sprague-Dawley rats were reared in enriched (EC), standard (SC), or isolated (IC) conditions. Following the rearing period, fluoxetine (10 or 20 mg/kg, i.p.) was administered 23.5 hrs, 5 hrs, and 1 hr before locomotor and FST measures. Following locomotor testing and FST exposure, rats were weighed to assess fluoxetine-, FST-, and environmental condition-induced moderations in weight gain. Results revealed an antidepressant effect of environmental enrichment and a depressant effect of isolation. Regardless of significant fluoxetine effects on locomotor activity, fluoxetine generally decreased swimming and increased immobility in all three environmental conditions, with IC-fluoxetine (10 mg/kg) rats and EC-fluoxetine (20 mg/kg) rats swimming less than vehicle counterparts. Subchronic 20 mg/kg fluoxetine also induced significant weight loss, and differential rearing appeared to moderate weight gain following FST stress. These results suggest that differential rearing has the ability to alter FST behaviors, fluoxetine efficacy, and post-stressor well-being. Moreover, 20 mg/kg fluoxetine, administered subchronically, may lead to atypical effects of those commonly observed in the FST, highlighting the importance and impact of both environmental condition and dosing regimen in common animal models of depression. PMID:26154768

Diagnostic performances of the fluorescent spot test for G6PD deficiency in newborns along the Thailand-Myanmar border: A cohort study.

PubMed

Thielemans, Laurence; Gornsawun, Gornpan; Hanboonkunupakarn, Borimas; Paw, Moo Kho; Porn, Pen; Moo, Paw Khu; Van Overmeire, Bart; Proux, Stephane; Nosten, François; McGready, Rose; Carrara, Verena I; Bancone, Germana

2018-01-01

Background: Glucose-6-phosphate dehydrogenase (G6PD) deficiency is an inherited enzymatic disorder associated with severe neonatal hyperbilirubinemia and acute haemolysis after exposure to certain drugs or infections. The disorder can be diagnosed phenotypically with a fluorescent spot test (FST), which is a simple test that requires training and basic laboratory equipment. This study aimed to assess the diagnostic performances of the FST used on umbilical cord blood by locally-trained staff and to compare test results of the neonates at birth with the results after one month of age. Methods : We conducted a cohort study on newborns at the Shoklo Malaria Research Unit, along the Thai-Myanmar border between January 2015 and May 2016. The FST was performed at birth on the umbilical cord blood by locally-trained staff and quality controlled by specialised technicians at the central laboratory. The FST was repeated after one month of age. Genotyping for common local G6PD mutations was carried out for all discrepant results. Results: FST was performed on 1521 umbilical cord blood samples. Quality control and genotyping revealed 10 misdiagnoses. After quality control, 10.7% of the males (84/786) and 1.2% of the females (9/735) were phenotypically G6PD deficient at birth. The FST repeated at one month of age or later diagnosed 8 additional G6PD deficient infants who were phenotypically normal at birth. Conclusions : This study shows the short-comings of the G6PD FST in neonatal routine screening and highlights the importance of training and quality control. A more conservative interpretation of the FST in male newborns could increase the diagnostic performances. Quantitative point-of-care tests might show higher sensitivity and specificity for diagnosis of G6PD deficiency on umbilical cord blood and should be investigated.

Diagnostic performances of the fluorescent spot test for G6PD deficiency in newborns along the Thailand-Myanmar border: A cohort study

PubMed Central

Thielemans, Laurence; Gornsawun, Gornpan; Hanboonkunupakarn, Borimas; Paw, Moo Kho; Porn, Pen; Moo, Paw Khu; Van Overmeire, Bart; Proux, Stephane; Nosten, François; McGready, Rose; Carrara, Verena I.; Bancone, Germana

2018-01-01

Background: Glucose-6-phosphate dehydrogenase (G6PD) deficiency is an inherited enzymatic disorder associated with severe neonatal hyperbilirubinemia and acute haemolysis after exposure to certain drugs or infections. The disorder can be diagnosed phenotypically with a fluorescent spot test (FST), which is a simple test that requires training and basic laboratory equipment. This study aimed to assess the diagnostic performances of the FST used on umbilical cord blood by locally-trained staff and to compare test results of the neonates at birth with the results after one month of age. Methods: We conducted a cohort study on newborns at the Shoklo Malaria Research Unit, along the Thai-Myanmar border between January 2015 and May 2016. The FST was performed at birth on the umbilical cord blood by locally-trained staff and quality controlled by specialised technicians at the central laboratory. The FST was repeated after one month of age. Genotyping for common local G6PD mutations was carried out for all discrepant results. Results: FST was performed on 1521 umbilical cord blood samples. Quality control and genotyping revealed 10 misdiagnoses. After quality control, 10.7% of the males (84/786) and 1.2% of the females (9/735) were phenotypically G6PD deficient at birth. The FST repeated at one month of age or later diagnosed 8 additional G6PD deficient infants who were phenotypically normal at birth. Conclusions: This study shows the short-comings of the G6PD FST in neonatal routine screening and highlights the importance of training and quality control. A more conservative interpretation of the FST in male newborns could increase the diagnostic performances. Quantitative point-of-care tests might show higher sensitivity and specificity for diagnosis of G6PD deficiency on umbilical cord blood and should be investigated. PMID:29552643

Evidences for amelioration of reserpine-induced fibromyalgia in rat by low dose of gamma irradiation and duloxetine.

PubMed

Shibrya, Eman E; Radwan, Rasha R; Abd El Fattah, Mai A; Shabaan, Esmat A; Kenawy, Sanaa A

2017-05-01

Fibromyalgia is a prevalent disorder characterized by chronic widespread pain and complex symptoms. This study was conducted to investigate the potential therapeutic effect of low-dose irradiation (LDI) alone or in combination with duloxetine on the reserpine-induced fibromyalgia in rats. Fibromyalgia was induced by administration of reserpine (1 mg/kg/s.c) for 3 consecutive days. Duloxetine (30 mg/kg, p.o) was administered 60 min before a forced swimming test (FST), and rats were exposed to a single dose of γ-radiation (0.5 Gy) 1 day before the FST. Reserpine significantly increased immobility time in the FST, decreased the amount of 5-hydroxytryptamine, dopamine, and norepinephrine in cerebral cortex. It also increased malondialdehyde and nitric oxide and reduced glutathione contents in brain tissue. LDI alone or combined with duloxetine completely antagonized reserpine-induced fibromyalgia as assessed by the measured parameters. One of the most significant findings in this study was that the therapeutic effect of duloxetine was more pronounced by its combination with LDI. A possible mechanism of action of LDI and duloxetine responsible for their therapeutic effect was discussed. On the basis of the presented evidences, it could be concluded that LDI alone or combined with duloxetine could be of value in the management of fibromyalgia.

Neurodynamic responses to the femoral slump test in patients with anterior knee pain syndrome.

PubMed

Lin, Pei-Ling; Shih, Yi-Fen; Chen, Wen-Yin; Ma, Hsiao-Li

2014-05-01

Matched-control, cross-sectional study. The purpose of this study was to compare the responses to the femoral slump test (FST), including the change in hip range of motion and level of discomfort, between subjects with and without anterior knee pain. Anterior knee pain syndrome is a common problem among adults. The FST is the neurodynamic test used to assess the mechanosensitivity of the femoral component of the nervous system. However, as of yet, there is no literature discussing the use of the FST in patients with anterior knee pain. Thirty patients with anterior knee pain and 30 control participants, matched by gender, age, and dominant leg, were recruited. The subjects received the FST, during which the hip extension angle and the location and intensity of pain/discomfort were recorded. Reproduction of symptoms that were alleviated by neck extension was interpreted as a positive test. Differences in hip extension angle and pain intensity between groups were examined using a 2-way, repeated-measures analysis of variance and a Kruskal-Wallis analysis. The level of significance was set at α = .05. Subjects with anterior knee pain had a smaller hip extension angle than that of controls (-3.6° ± 5.3° versus 0.6° ± 6.1°; mean difference, 4.2°; 95% confidence interval [CI]: 1.24°, 7.15°; P = .006). Eight patients with anterior knee pain showed a positive FST, and those with a positive FST had a smaller hip extension angle (-5.7° ± 4.5°) than that of controls (mean difference, 6.3°; 95% CI: 0.8°, 11.8°; P = .007). There was no difference in the hip extension angle between the positive and negative FST groups (mean difference, 2.9°; 95% CI: -8.5°, 2.0°) or between the negative FST and control groups (mean difference, 3.4°; 95% CI: -0.4°, 7.3°). Results of this study suggest that altered mechanosensitivity of the femoral nerve occurred in the patients with anterior knee pain who presented with a positive FST. The role of increased mechanosensitivity in the development and management of anterior knee pain should be investigated in the future.

Follistatin in chondrocytes: the link between TRPV4 channelopathies and skeletal malformations

PubMed Central

Leddy, Holly A.; McNulty, Amy L.; Lee, Suk Hee; Rothfusz, Nicole E.; Gloss, Bernd; Kirby, Margaret L.; Hutson, Mary R.; Cohn, Daniel H.; Guilak, Farshid; Liedtke, Wolfgang

2014-01-01

Point mutations in the calcium-permeable TRPV4 ion channel have been identified as the cause of autosomal-dominant human motor neuropathies, arthropathies, and skeletal malformations of varying severity. The objective of this study was to determine the mechanism by which TRPV4 channelopathy mutations cause skeletal dysplasia. The human TRPV4V620I channelopathy mutation was transfected into primary porcine chondrocytes and caused significant (2.6-fold) up-regulation of follistatin (FST) expression levels. Pore altering mutations that prevent calcium influx through the channel prevented significant FST up-regulation (1.1-fold). We generated a mouse model of theTRPV4V620I mutation, and found significant skeletal deformities (e.g., shortening of tibiae and digits, similar to the human disease brachyolmia) and increases in Fst/TRPV4 mRNA levels (2.8-fold). FST was significantly up-regulated in primary chondrocytes transfected with 3 different dysplasia-causing TRPV4 mutations (2- to 2.3-fold), but was not affected by an arthropathy mutation (1.1-fold). Furthermore, FST-loaded microbeads decreased bone ossification in developing chick femora (6%) and tibiae (11%). FST gene and protein levels were also increased 4-fold in human chondrocytes from an individual natively expressing the TRPV4T89I mutation. Taken together, these data strongly support that up-regulation of FST in chondrocytes by skeletal dysplasia-inducing TRPV4 mutations contributes to disease pathogenesis.—Leddy, H. A., McNulty, A. L., Lee, S. H., Rothfusz, N. E., Gloss, B., Kirby, M. L., Hutson, M. R., Cohn, D. H., Guilak, F., Liedtke, W. Follistatin in chondrocytes: the link between TRPV4 channelopathies and skeletal malformations. PMID:24577120

Influence of enrichment on behavioral and neurogenic effects of antidepressants in Wistar rats submitted to repeated forced swim test.

PubMed

Possamai, Fernanda; dos Santos, Juliano; Walber, Thais; Marcon, Juliana C; dos Santos, Tiago Souza; Lino de Oliveira, Cilene

2015-04-03

Repeated forced swimming test (rFST) may detect gradual effects of antidepressants in adult rats. Antidepressants, as enrichment, affected behavior and neurogenesis in rats. However, the influence of enrichment on behavioral and neurogenic effects of antidepressants is unknown. Here, effects of antidepressants on rFST and hippocampal neurogenesis were investigated in rats under enriched conditions. Behaviors of male Wistar rats, housed from weaning in standard (SE) or enriched environment (EE), were registered during rFST. The rFST consisted of 15min of swimming (pretest) followed by 5min of swimming in the first (test), seventh (retest 1) and fourteenth (retest 2) days after pretest. One hour before the test, rats received an intraperitoneal injection of saline (1ml/kg), fluoxetine (2.5mg/kg) or imipramine (2.5 or 5mg/kg). These treatments were performed daily until the day of the retest 2. After retest 2, rats were euthanized for the identification of markers for neurogenesis in the hippocampus. Fluoxetine or imipramine decreased immobility in retests 1 and 2, as compared to saline. EE abolished these differences. In EE, fluoxetine or imipramine (5mg/kg) reduced immobility time in retest 2, as compared to the test. Independent of the housing conditions, fluoxetine and imipramine (5mg/kg) increased the ratio of immature neurons per progenitor cell in the hippocampus. In summary, antidepressants or enrichment counteracted the high immobility in rFST. Enrichment changed the effects of antidepressants in rFST depending on the type, and the dose of a substance but failed to change neurogenesis in control or antidepressant treated-rats. Effects of antidepressants and enrichment on rFST seemed neurogenesis-independent. Copyright © 2014 Elsevier Inc. All rights reserved.

Empirical distributions of F(ST) from large-scale human polymorphism data.

PubMed

Elhaik, Eran

2012-01-01

Studies of the apportionment of human genetic variation have long established that most human variation is within population groups and that the additional variation between population groups is small but greatest when comparing different continental populations. These studies often used Wright's F(ST) that apportions the standardized variance in allele frequencies within and between population groups. Because local adaptations increase population differentiation, high-F(ST) may be found at closely linked loci under selection and used to identify genes undergoing directional or heterotic selection. We re-examined these processes using HapMap data. We analyzed 3 million SNPs on 602 samples from eight worldwide populations and a consensus subset of 1 million SNPs found in all populations. We identified four major features of the data: First, a hierarchically F(ST) analysis showed that only a paucity (12%) of the total genetic variation is distributed between continental populations and even a lesser genetic variation (1%) is found between intra-continental populations. Second, the global F(ST) distribution closely follows an exponential distribution. Third, although the overall F(ST) distribution is similarly shaped (inverse J), F(ST) distributions varies markedly by allele frequency when divided into non-overlapping groups by allele frequency range. Because the mean allele frequency is a crude indicator of allele age, these distributions mark the time-dependent change in genetic differentiation. Finally, the change in mean-F(ST) of these groups is linear in allele frequency. These results suggest that investigating the extremes of the F(ST) distribution for each allele frequency group is more efficient for detecting selection. Consequently, we demonstrate that such extreme SNPs are more clustered along the chromosomes than expected from linkage disequilibrium for each allele frequency group. These genomic regions are therefore likely candidates for natural selection.

Structure of myostatin·follistatin-like 3: N-terminal domains of follistatin-type molecules exhibit alternate modes of binding.

PubMed

Cash, Jennifer N; Angerman, Elizabeth B; Kattamuri, Chandramohan; Nolan, Kristof; Zhao, Huaying; Sidis, Yisrael; Keutmann, Henry T; Thompson, Thomas B

2012-01-06

TGF-β family ligands are involved in a variety of critical physiological processes. For instance, the TGF-β ligand myostatin is a staunch negative regulator of muscle growth and a therapeutic target for muscle-wasting disorders. Therefore, it is important to understand the molecular mechanisms of TGF-β family regulation. One form of regulation is through inhibition by extracellular antagonists such as the follistatin (Fst)-type proteins. Myostatin is tightly controlled by Fst-like 3 (Fstl3), which is the only Fst-type molecule that has been identified in the serum bound to myostatin. Here, we present the crystal structure of myostatin in complex with Fstl3. The structure reveals that the N-terminal domain (ND) of Fstl3 interacts uniquely with myostatin as compared with activin A, because it utilizes different surfaces on the ligand. This results in conformational differences in the ND of Fstl3 that alter its position in the type I receptor-binding site of the ligand. We also show that single point mutations in the ND of Fstl3 are detrimental to ligand binding, whereas corresponding mutations in Fst have little effect. Overall, we have shown that the NDs of Fst-type molecules exhibit distinctive modes of ligand binding, which may affect overall affinity of ligand·Fst-type protein complexes.

Inactivating hepatic follistatin alleviates hyperglycemia.

PubMed

Tao, Rongya; Wang, Caixia; Stöhr, Oliver; Qiu, Wei; Hu, Yue; Miao, Ji; Dong, X Charlie; Leng, Sining; Stefater, Margaret; Stylopoulos, Nicholas; Lin, Lin; Copps, Kyle D; White, Morris F

2018-06-04

Unsuppressed hepatic glucose production (HGP) contributes substantially to glucose intolerance and diabetes, which can be modeled by the genetic inactivation of hepatic insulin receptor substrate 1 (Irs1) and Irs2 (LDKO mice). We previously showed that glucose intolerance in LDKO mice is resolved by hepatic inactivation of the transcription factor FoxO1 (that is, LTKO mice)-even though the liver remains insensitive to insulin. Here, we report that insulin sensitivity in the white adipose tissue of LDKO mice is also impaired but is restored in LTKO mice in conjunction with normal suppression of HGP by insulin. To establish the mechanism by which white adipose tissue insulin signaling and HGP was regulated by hepatic FoxO1, we identified putative hepatokines-including excess follistatin (Fst)-that were dysregulated in LDKO mice but normalized in LTKO mice. Knockdown of hepatic Fst in the LDKO mouse liver restored glucose tolerance, white adipose tissue insulin signaling and the suppression of HGP by insulin; however, the expression of Fst in the liver of healthy LTKO mice had the opposite effect. Of potential clinical significance, knockdown of Fst also improved glucose tolerance in high-fat-fed obese mice, and the level of serum Fst was reduced in parallel with glycated hemoglobin in obese individuals with diabetes who underwent therapeutic gastric bypass surgery. We conclude that Fst is a pathological hepatokine that might be targeted for diabetes therapy during hepatic insulin resistance.

Evidence for the involvement of extinction-associated inhibitory learning in the forced swimming test.

PubMed

Campus, P; Colelli, V; Orsini, C; Sarra, D; Cabib, S

2015-02-01

The forced swimming test (FST) remains one of the most used tools for screening antidepressants in rodent models. Nonetheless, the nature of immobility, its main behavioral measure, is still a matter of debate. The present study took advantage of our recent finding that mice of the inbred DBA/2J strain require a functioning left dorsolateral striatum (DLS) to consolidate long-term memory of FST to test whether immobility is the outcome of stress-related learning. Infusion of the GABA-A agonist muscimol in the left DLS immediately after a single experience of FST prevented and infusion in the left or the right amygdala impaired recall of the acquired levels of immobility in a probe test performed 24h later. Post-training left DLS infusion of muscimol, at a dose capable of preventing retention of FST-induced immobility, did not influence 24h retention of inhibitory avoidance training or of the escape response acquired in a water T-maze. However, this same treatment prevented 24h retention of the extinction training of the consolidated escape response. These results indicate that a left DLS-centered memory system selectively mediates memory consolidation of FST and of escape extinction and support the hypothesis that immobility is the result of extinction-like inhibitory learning involving all available escape responses due to the inescapable/unavoidable nature of FST experience. Copyright © 2014 Elsevier B.V. All rights reserved.

Pairwise-additive hydrophobic effect for alkanes in water

PubMed Central

Wu, Jianzhong; Prausnitz, John M.

2008-01-01

Pairwise additivity of the hydrophobic effect is indicated by reliable experimental Henry's constants for a large number of linear and branched low-molecular-weight alkanes in water. Pairwise additivity suggests that the hydrophobic effect is primarily a local phenomenon and that the hydrophobic interaction may be represented by a semiempirical force field. By representing the hydrophobic potential between two methane molecules as a linear function of the overlap volume of the hydration layers, we find that the contact value of the hydrophobic potential (−0.72 kcal/mol) is smaller than that from quantum mechanics simulations (−2.8 kcal/mol) but is close to that from classical molecular dynamics (−0.5∼−0.9 kcal/mol). PMID:18599448

The structure of myostatin:follistatin 288: insights into receptor utilization and heparin binding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cash, Jennifer N.; Rejon, Carlis A.; McPherron, Alexandra C.

2009-09-29

Myostatin is a member of the transforming growth factor-{beta} (TGF-{beta}) family and a strong negative regulator of muscle growth. Here, we present the crystal structure of myostatin in complex with the antagonist follistatin 288 (Fst288). We find that the prehelix region of myostatin very closely resembles that of TGF-{beta} class members and that this region alone can be swapped into activin A to confer signalling through the non-canonical type I receptor Alk5. Furthermore, the N-terminal domain of Fst288 undergoes conformational rearrangements to bind myostatin and likely acts as a site of specificity for the antagonist. In addition, a unique continuousmore » electropositive surface is created when myostatin binds Fst288, which significantly increases the affinity for heparin. This translates into stronger interactions with the cell surface and enhanced myostatin degradation in the presence of either Fst288 or Fst315. Overall, we have identified several characteristics unique to myostatin that will be paramount to the rational design of myostatin inhibitors that could be used in the treatment of muscle-wasting disorders.« less

Specificity of the femoral slump test for the assessment of experimentally induced anterior knee pain.

PubMed

Lai, Weng-Hang; Shih, Yi-Fen; Lin, Pei-Ling; Chen, Wen-Yin; Ma, Hsiao-Li

2012-12-01

To assess the specificity of the femoral slump test (FST) when assessing experimentally induced anterior knee pain. Cross-sectional, exploratory study. Research laboratory. Asymptomatic subjects (N=12; 6 men; 6 women) for the study. An experimental pain model was used to simulate anterior knee pain by injecting .25 mL of hypertonic saline solution (5% NaCl) into the medial infrapatellar fat pad. Not applicable. The changes in pain intensity and diameter after applying the structure differential maneuver (neck flexion/extension) during the FST were recorded and analyzed. Results revealed that the structure differential maneuver of the FST did not alter the pain intensity or diameter in 9 (neck extension) and 10 (neck flexion) out of 12 subjects, which meant that the FST provided appropriate testing responses in 75% to 83% cases when the anterior knee pain did not originate in neural tissues. The FST had a specificity of more than .75 when detecting nerve mechanosensitivity problems of anterior knee pain. Copyright © 2012 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Modeling Regular Replacement for String Constraint Solving

NASA Technical Reports Server (NTRS)

Fu, Xiang; Li, Chung-Chih

2010-01-01

Bugs in user input sanitation of software systems often lead to vulnerabilities. Among them many are caused by improper use of regular replacement. This paper presents a precise modeling of various semantics of regular substitution, such as the declarative, finite, greedy, and reluctant, using finite state transducers (FST). By projecting an FST to its input/output tapes, we are able to solve atomic string constraints, which can be applied to both the forward and backward image computation in model checking and symbolic execution of text processing programs. We report several interesting discoveries, e.g., certain fragments of the general problem can be handled using less expressive deterministic FST. A compact representation of FST is implemented in SUSHI, a string constraint solver. It is applied to detecting vulnerabilities in web applications

Working with Missing Values

ERIC Educational Resources Information Center

Acock, Alan C.

2005-01-01

Less than optimum strategies for missing values can produce biased estimates, distorted statistical power, and invalid conclusions. After reviewing traditional approaches (listwise, pairwise, and mean substitution), selected alternatives are covered including single imputation, multiple imputation, and full information maximum likelihood…

Platelet-rich plasma-induced feedback inhibition of activin A/follistatin signaling: A mechanism for tumor-low risk skin rejuvenation in irradiated rats.

PubMed

Omar, Nesreen Nabil; Rashed, Rasha R; El-Hazek, Rania M; El-Sabbagh, Walaa A; Rashed, Engy R; El-Ghazaly, Mona A

2018-03-01

Platelet-rich plasma (PRP) is a source of natural growth factors and is emerging as a treatment modality to mitigate radiotherapy- induced adverse effects. Activin A (ACTA) is a member of the transforming growth factor-β (TGF-β) superfamily, which has been shown to modulate the inflammatory response and macrophages polarization between different phenotypes. The aim of this study is to determine the value of PRP in preventing radiation-induced malignancies in light of the cross-talk between PRP and activin A type II receptors (ActR-IIA)/follistatin (FST) signaling pathways where the inflammatory responses at 2 different time points were evaluated. Male albino rats were exposed to radiation and given PRP over the course of 6 days. Rats were sacrificed on day 7 or day 28 post radiation. Quantitative real-time reverse transcriptase polymerase chain reaction (QRT-PCR) and western-blot showed that after 7 days of administrating of PRP, ActR-IIA/FST signaling was markedly induced and was associated with the expressions of inflammatory, natural killer and M1 macrophages markers, TNF-α, IL-1β, IFN-γ and IL-12. By contrast, on day 28 of PRP administration, ActR-IIA/FST signaling and the expressions of proinflammatory cytokines were downregulated in parallel with inducing M2 macrophages phenotype as indicated by arginase-1, IL-10 and dectin-1. The suppression of inflammation and induction of M2 macrophages phenotype in response to PRP administration were found significantly linked to ActR-IIA/FST signaling downregulation. Furthermore, the specific M2 macrophage subtype was found to express dectin-1 receptors which have high affinity for tumor cells thereby is expected to reduce the potential for developing tumors after radiotherapy. Copyright © 2018 Elsevier B.V. All rights reserved.

Genetic Variation in the Acorn Barnacle from Allozymes to Population Genomics

PubMed Central

Flight, Patrick A.; Rand, David M.

2012-01-01

Understanding the patterns of genetic variation within and among populations is a central problem in population and evolutionary genetics. We examine this question in the acorn barnacle, Semibalanus balanoides, in which the allozyme loci Mpi and Gpi have been implicated in balancing selection due to varying selective pressures at different spatial scales. We review the patterns of genetic variation at the Mpi locus, compare this to levels of population differentiation at mtDNA and microsatellites, and place these data in the context of genome-wide variation from high-throughput sequencing of population samples spanning the North Atlantic. Despite considerable geographic variation in the patterns of selection at the Mpi allozyme, this locus shows rather low levels of population differentiation at ecological and trans-oceanic scales (FST ∼ 5%). Pooled population sequencing was performed on samples from Rhode Island (RI), Maine (ME), and Southwold, England (UK). Analysis of more than 650 million reads identified approximately 335,000 high-quality SNPs in 19 million base pairs of the S. balanoides genome. Much variation is shared across the Atlantic, but there are significant examples of strong population differentiation among samples from RI, ME, and UK. An FST outlier screen of more than 22,000 contigs provided a genome-wide context for interpretation of earlier studies on allozymes, mtDNA, and microsatellites. FST values for allozymes, mtDNA and microsatellites are close to the genome-wide average for random SNPs, with the exception of the trans-Atlantic FST for mtDNA. The majority of FST outliers were unique between individual pairs of populations, but some genes show shared patterns of excess differentiation. These data indicate that gene flow is high, that selection is strong on a subset of genes, and that a variety of genes are experiencing diversifying selection at large spatial scales. This survey of polymorphism in S. balanoides provides a number of genomic tools that promise to make this a powerful model for ecological genomics of the rocky intertidal. PMID:22767487

An experimental and theoretical investigation of a fuel system tuner for the suppression of combustion driven oscillations

NASA Astrophysics Data System (ADS)

Scarborough, David E.

Manufacturers of commercial, power-generating, gas turbine engines continue to develop combustors that produce lower emissions of nitrogen oxides (NO x) in order to meet the environmental standards of governments around the world. Lean, premixed combustion technology is one technique used to reduce NOx emissions in many current power and energy generating systems. However, lean, premixed combustors are susceptible to thermo-acoustic oscillations, which are pressure and heat-release fluctuations that occur because of a coupling between the combustion process and the natural acoustic modes of the system. These pressure oscillations lead to premature failure of system components, resulting in very costly maintenance and downtime. Therefore, a great deal of work has gone into developing methods to prevent or eliminate these combustion instabilities. This dissertation presents the results of a theoretical and experimental investigation of a novel Fuel System Tuner (FST) used to damp detrimental combustion oscillations in a gas turbine combustor by changing the fuel supply system impedance, which controls the amplitude and phase of the fuel flowrate. When the FST is properly tuned, the heat release oscillations resulting from the fuel-air ratio oscillations damp, rather than drive, the combustor acoustic pressure oscillations. A feasibility study was conducted to prove the validity of the basic idea and to develop some basic guidelines for designing the FST. Acoustic models for the subcomponents of the FST were developed, and these models were experimentally verified using a two-microphone impedance tube. Models useful for designing, analyzing, and predicting the performance of the FST were developed and used to demonstrate the effectiveness of the FST. Experimental tests showed that the FST reduced the acoustic pressure amplitude of an unstable, model, gas-turbine combustor over a wide range of operating conditions and combustor configurations. Finally, combustor acoustic pressure amplitude measurements made in using the model combustor were used in conjunction with model predicted fuel system impedances to verify the developed design rules. The FST concept and design methodology presented in this dissertation can be used to design fuel system tuners for new and existing gas turbine combustors to reduce, or eliminate altogether, thermo-acoustic oscillations.

Anxiolytic effects of buspirone and MTEP in the Porsolt Forced Swim Test.

PubMed

Lee, Kaziya M; Coelho, Michal A; Sern, Kimberly R; Class, MacKayla A; Bocz, Mark D; Szumlinski, Karen K

2017-01-01

Traditionally, a reduction in floating behavior or immobility in the Porsolt forced swim test (FST) is employed as a predictor of antidepressant efficacy. However, over the past several years, our studies of alcohol withdrawal-induced negative affect consistently indicate the coincidence of increased anxiety-related behaviors on various behavioral tests with reduced immobility in the FST. Further, this behavioral profile correlates with increased mGlu5 protein expression within limbic brain regions. As the role for mGlu5 in anxiety is well established, we hypothesized that the reduced immobility exhibited by alcohol-withdrawn mice when tested in the FST might reflect anxiety, possibly a hyper-reactivity to the acute swim stressor. Herein, we evaluated whether or not the decreased FST immobility during alcohol withdrawal responds to systemic treatment with a behaviorally-effective dose of the prototypical anxiolytic, buspirone (5 mg/kg). We also determined the functional relevance of the withdrawal-induced increase in mGlu5 expression for FST behavior by comparing the effects of buspirone to a behaviorally effective dose of the mGlu5 negative allosteric modulator MTEP (3 mg/kg). Adult male C57BL/6J mice were subjected to a 14-day, multi-bottle, binge-drinking protocol that elicits hyper-anxiety and increases glutamate-related protein expression during early withdrawal. Control animals received only water. At 24hr withdrawal, animals from each drinking condition were subdivided into groups and treated with an IP injection of buspirone, MTEP, or vehicle, 30min prior to the FST. Drug effects on general locomotor activity were also assessed. As we reported previously, alcohol-withdrawn animals exhibited significantly reduced immobility in the FST compared to water controls. Both buspirone and MTEP significantly increased immobility in alcohol-withdrawn animals, with a modest increase also seen in water controls. No significant group differences were observed for locomotor activity, indicating that neither anxiolytic was sedating. These results provide predictive validity for increased swimming/reduced immobility in the FST as a model of anxiety and provide novel evidence in favor of mGlu5 inhibition as an effective therapeutic strategy for treating hyperanxiety during alcohol withdrawal.

Phylogeography, intraspecific structure and sex-biased dispersal of Dall's porpoise, Phocoenoides dalli, revealed by mitochondrial and microsatellite DNA analyses.

PubMed

Escorza-Treviño, S; Dizon, A E

2000-08-01

Mitochondrial DNA (mtDNA) control-region sequences and microsatellite loci length polymorphisms were used to estimate phylogeographical patterns (historical patterns underlying contemporary distribution), intraspecific population structure and gender-biased dispersal of Phocoenoides dalli dalli across its entire range. One-hundred and thirteen animals from several geographical strata were sequenced over 379 bp of mtDNA, resulting in 58 mtDNA haplotypes. Analysis using F(ST) values (based on haplotype frequencies) and phi(ST) values (based on frequencies and genetic distances between haplotypes) yielded statistically significant separation (bootstrap values P < 0.05) among most of the stocks currently used for management purposes. A minimum spanning network of haplotypes showed two very distinctive clusters, differentially occupied by western and eastern populations, with some common widespread haplotypes. This suggests some degree of phyletic radiation from west to east, superimposed on gene flow. Highly male-biased migration was detected for several population comparisons. Nuclear microsatellite DNA markers (119 individuals and six loci) provided additional support for population subdivision and gender-biased dispersal detected in the mtDNA sequences. Analysis using F(ST) values (based on allelic frequencies) yielded statistically significant separation between some, but not all, populations distinguished by mtDNA analysis. R(ST) values (based on frequencies of and genetic distance between alleles) showed no statistically significant subdivision. Again, highly male-biased dispersal was detected for all population comparisons, suggesting, together with morphological and reproductive data, the existence of sexual selection. Our molecular results argue for nine distinct dalli-type populations that should be treated as separate units for management purposes.

Emergency canine surgery in a deployed forward surgical team: a case report.

PubMed

Beitler, Alan L; Jeanette, Joseph P; McGraw, Andrew L; Butera, Jennifer R; Vanfosson, Christopher A; Seery, Jason M

2011-04-01

Forward surgical teams (FSTs) perform a variety of non-doctrinal functions. During their deployment to Afghanistan, the 541st FST (Airborne) performed emergency surgery on a German shepherd military working dog (MWD). Retrospective examination of a case of veterinary surgery in a deployed FST. A 5 1/2-year-old German shepherd MWD presented with extreme lethargy, tachycardia, excessive drooling, and a firm, distended abdomen. These conditions resulted from gastric dilatation with volvulus. Since evacuation to a veterinarian was untenable, emergency laparotomy was performed in the FST. The gastric dilatation with volvulus was treated by detorsion and gastropexy, and the canine patient fully recovered. Canine surgery can be safely performed in an FST. Based on the number of MWDs deployed throughout the theater, FSTs may be called upon to care for them in the absence of available veterinary care.

Population structure of four Thai indigenous chicken breeds.

PubMed

Mekchay, Supamit; Supakankul, Pantaporn; Assawamakin, Anunchai; Wilantho, Alisa; Chareanchim, Wanwisa; Tongsima, Sissades

2014-03-27

In recent years, Thai indigenous chickens have increasingly been bred as an alternative in Thailand poultry market. Due to their popularity, there is a clear need to improve the underlying quality and productivity of these chickens. Studying chicken genetic variation can improve the chicken meat quality as well as conserving rare chicken species. To begin with, a minimal set of molecular markers that can characterize the Thai indigenous chicken breeds is required. Using AFLP-PCR, 30 single nucleotide polymorphisms (SNPs) from Thai indigenous chickens were obtained by DNA sequencing. From these SNPs, we genotyped 465 chickens from 7 chicken breeds, comprising four Thai indigenous chicken breeds--Pradhuhangdum (PD), Luenghangkhao (LK), Dang (DA) and Chee (CH), one wild chicken--the red jungle fowls (RJF), and two commercial chicken breeds--the brown egg layer (BL) and commercial broiler (CB). The chicken genotypes reveal unique genetic structures of the four Thai indigenous chicken breeds. The average expected heterozygosities of PD=0.341, LK=0.357, DA=0.349 and CH=0.373, while the references RJF= 0.327, CB=0.324 and BL= 0.285. The F(ST) values among Thai indigenous chicken breeds vary from 0.051 to 0.096. The F(ST) values between the pairs of Thai indigenous chickens and RJF vary from 0.083 to 0.105 and the FST values between the Thai indigenous chickens and the two commercial chicken breeds vary from 0.116 to 0.221. A neighbour-joining tree of all individual chickens showed that the Thai indigenous chickens were clustered into four groups which were closely related to the wild RJF but far from the commercial breeds. Such commercial breeds were split into two closely groups. Using genetic admixture analysis, we observed that the Thai indigenous chicken breeds are likely to share common ancestors with the RJF, while both commercial chicken breeds share the same admixture pattern. These results indicated that the Thai indigenous chicken breeds may descend from the same ancestors. These indigenous chicken breeds were more closely related to red jungle fowls than those of the commercial breeds. These findings showed that the proposed SNP panel can effectively be used to characterize the four Thai indigenous chickens.

Matrix multiplication operations using pair-wise load and splat operations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eichenberger, Alexandre E.; Gschwind, Michael K.; Gunnels, John A.

Mechanisms for performing a matrix multiplication operation are provided. A vector load operation is performed to load a first vector operand of the matrix multiplication operation to a first target vector register. A pair-wise load and splat operation is performed to load a pair of scalar values of a second vector operand and replicate the pair of scalar values within a second target vector register. An operation is performed on elements of the first target vector register and elements of the second target vector register to generate a partial product of the matrix multiplication operation. The partial product is accumulatedmore » with other partial products and a resulting accumulated partial product is stored. This operation may be repeated for a second pair of scalar values of the second vector operand.« less

Effect of Elevated Free Stream Turbulence on the Hydrodynamic Performance of a Tidal Turbine Blade Section

NASA Astrophysics Data System (ADS)

Vinod, Ashwin; Lawrence, Angela; Banerjee, Arindam

2016-11-01

The effects of elevated freestream turbulence (FST) on the performance of a tidal turbine blade is studied using laboratory experiments. Of interest for the current investigation is elevated levels of FST in the range of 6-24% that is prevalent in deployment sites of tidal turbines. A constant chord, no twist blade section (SG6043) is tested at an operating Reynolds number of 1.5x105 and at angles of attack ranging from -90o to +90o. The parameter space encompasses the entire operational range of a tidal turbine that includes flow reversal. Multiple levels of controlled FST are achieved using an active grid type turbulence generator placed at the entrance to the water tunnel test section. The hydrodynamic loads experienced by the blade section are measured using a 3-axis load cell; a Stereo-PIV technique is used to analyze the flow field around the blade. The results indicate that elevated levels of FST cause a delay in flow separation when compared to the case of a laminar freestream. Furthermore, the lift to drag ratio of the blade is considerably altered depending on the level of FST and angle of attack tested.

Exact p-values for pairwise comparison of Friedman rank sums, with application to comparing classifiers.

PubMed

Eisinga, Rob; Heskes, Tom; Pelzer, Ben; Te Grotenhuis, Manfred

2017-01-25

The Friedman rank sum test is a widely-used nonparametric method in computational biology. In addition to examining the overall null hypothesis of no significant difference among any of the rank sums, it is typically of interest to conduct pairwise comparison tests. Current approaches to such tests rely on large-sample approximations, due to the numerical complexity of computing the exact distribution. These approximate methods lead to inaccurate estimates in the tail of the distribution, which is most relevant for p-value calculation. We propose an efficient, combinatorial exact approach for calculating the probability mass distribution of the rank sum difference statistic for pairwise comparison of Friedman rank sums, and compare exact results with recommended asymptotic approximations. Whereas the chi-squared approximation performs inferiorly to exact computation overall, others, particularly the normal, perform well, except for the extreme tail. Hence exact calculation offers an improvement when small p-values occur following multiple testing correction. Exact inference also enhances the identification of significant differences whenever the observed values are close to the approximate critical value. We illustrate the proposed method in the context of biological machine learning, were Friedman rank sum difference tests are commonly used for the comparison of classifiers over multiple datasets. We provide a computationally fast method to determine the exact p-value of the absolute rank sum difference of a pair of Friedman rank sums, making asymptotic tests obsolete. Calculation of exact p-values is easy to implement in statistical software and the implementation in R is provided in one of the Additional files and is also available at http://www.ru.nl/publish/pages/726696/friedmanrsd.zip .

Online Pairwise Learning Algorithms.

PubMed

Ying, Yiming; Zhou, Ding-Xuan

2016-04-01

Pairwise learning usually refers to a learning task that involves a loss function depending on pairs of examples, among which the most notable ones are bipartite ranking, metric learning, and AUC maximization. In this letter we study an online algorithm for pairwise learning with a least-square loss function in an unconstrained setting of a reproducing kernel Hilbert space (RKHS) that we refer to as the Online Pairwise lEaRning Algorithm (OPERA). In contrast to existing works (Kar, Sriperumbudur, Jain, & Karnick, 2013 ; Wang, Khardon, Pechyony, & Jones, 2012 ), which require that the iterates are restricted to a bounded domain or the loss function is strongly convex, OPERA is associated with a non-strongly convex objective function and learns the target function in an unconstrained RKHS. Specifically, we establish a general theorem that guarantees the almost sure convergence for the last iterate of OPERA without any assumptions on the underlying distribution. Explicit convergence rates are derived under the condition of polynomially decaying step sizes. We also establish an interesting property for a family of widely used kernels in the setting of pairwise learning and illustrate the convergence results using such kernels. Our methodology mainly depends on the characterization of RKHSs using its associated integral operators and probability inequalities for random variables with values in a Hilbert space.

Use of locally weighted scatterplot smoothing (LOWESS) regression to study selection signatures in Piedmontese and Italian Brown cattle breeds.

PubMed

Pintus, Elia; Sorbolini, Silvia; Albera, Andrea; Gaspa, Giustino; Dimauro, Corrado; Steri, Roberto; Marras, Gabriele; Macciotta, Nicolò P P

2014-02-01

Selection is the major force affecting local levels of genetic variation in species. The availability of dense marker maps offers new opportunities for a detailed understanding of genetic diversity distribution across the animal genome. Over the last 50 years, cattle breeds have been subjected to intense artificial selection. Consequently, regions controlling traits of economic importance are expected to exhibit selection signatures. The fixation index (Fst ) is an estimate of population differentiation, based on genetic polymorphism data, and it is calculated using the relationship between inbreeding and heterozygosity. In the present study, locally weighted scatterplot smoothing (LOWESS) regression and a control chart approach were used to investigate selection signatures in two cattle breeds with different production aptitudes (dairy and beef). Fst was calculated for 42 514 SNP marker loci distributed across the genome in 749 Italian Brown and 364 Piedmontese bulls. The statistical significance of Fst values was assessed using a control chart. The LOWESS technique was efficient in removing noise from the raw data and was able to highlight selection signatures in chromosomes known to harbour genes affecting dairy and beef traits. Examples include the peaks detected for BTA2 in the region where the myostatin gene is located and for BTA6 in the region harbouring the ABCG2 locus. Moreover, several loci not previously reported in cattle studies were detected. © 2013 The Authors, Animal Genetics © 2013 Stichting International Foundation for Animal Genetics.

Molecular Genetic Analysis and Evolution of Segment 7 in Rice Black-Streaked Dwarf Virus in China

PubMed Central

Chen, Yanping; Wu, Jirong; Meng, Qingchang; Han, Xiaohua; Hao, Zhuanfang; Li, Mingshun; Yong, Hongjun; Zhang, Degui; Zhang, Shihuang; Li, Xinhai

2015-01-01

Rice black-streaked dwarf virus (RBSDV) causes maize rough dwarf disease or rice black-streaked dwarf disease and can lead to severe yield losses in maize and rice. To analyse RBSDV evolution, codon usage bias and genetic structure were investigated in 111 maize and rice RBSDV isolates from eight geographic locations in 2013 and 2014. The linear dsRNA S7 is A+U rich, with overall codon usage biased toward codons ending with A (A3s, S7-1: 32.64%, S7-2: 29.95%) or U (U3s, S7-1: 44.18%, S7-2: 46.06%). Effective number of codons (Nc) values of 45.63 in S7-1 (the first open reading frame of S7) and 39.96 in S7-2 (the second open reading frame of S7) indicate low degrees of RBSDV-S7 codon usage bias, likely driven by mutational bias regardless of year, host, or geographical origin. Twelve optimal codons were detected in S7. The nucleotide diversity (π) of S7 sequences in 2013 isolates (0.0307) was significantly higher than in 2014 isolates (0.0244, P = 0.0226). The nucleotide diversity (π) of S7 sequences in isolates from Jinan (0.0391) was higher than that from the other seven locations (P < 0.01). Only one S7 recombinant was detected in Baoding. RBSDV isolates could be phylogenetically classified into two groups according to S7 sequences, and further classified into two subgroups. S7-1 and S7-2 were under negative and purifying selection, with respective Ka/Ks ratios of 0.0179 and 0.0537. These RBSDV populations were expanding (P < 0.01) as indicated by negative values for Tajima's D, Fu and Li's D, and Fu and Li's F. Genetic differentiation was detected in six RBSDV subpopulations (P < 0.05). Absolute Fst (0.0790) and Nm (65.12) between 2013 and 2014, absolute Fst (0.1720) and Nm (38.49) between maize and rice, and absolute Fst values of 0.0085-0.3069 and Nm values of 0.56-29.61 among these eight geographic locations revealed frequent gene flow between subpopulations. Gene flow between 2013 and 2014 was the most frequent. PMID:26121638

Characterization of bovine MHC DRB3 diversity in Latin American Creole cattle breeds.

PubMed

Giovambattista, Guillermo; Takeshima, Shin-nosuke; Ripoli, Maria Veronica; Matsumoto, Yuki; Franco, Luz Angela Alvarez; Saito, Hideki; Onuma, Misao; Aida, Yoko

2013-04-25

In cattle, bovine leukocyte antigens (BoLAs) have been extensively used as markers for diseases and immunological traits. However, none of the highly adapted Latin American Creole breeds have been characterized for BoLA gene polymorphism by high resolution typing methods. In this work, we sequenced exon 2 of the BoLA class II DRB3 gene from 179 cattle (113 Bolivian Yacumeño cattle and 66 Colombian Hartón del Valle cattle breeds) using a polymerase chain reaction sequence-based typing (PCR-SBT) method. We identified 36 previously reported alleles and three novel alleles. Thirty-five (32 reported and three new) and 24 alleles (22 reported and two new) were detected in Yacumeño and Hartón del Valle breeds, respectively. Interestingly, Latin American Creole cattle showed a high degree of gene diversity despite their small population sizes, and 10 alleles including three new alleles were found only in these two Creole breeds. We next compared the degree of genetic variability at the population and sequence levels and the genetic distance in the two breeds with those previously reported in five other breeds: Holstein, Japanese Shorthorn, Japanese Black, Jersey, and Hanwoo. Both Creole breeds presented gene diversity higher than 0.90, a nucleotide diversity higher than 0.07, and mean number of pairwise differences higher than 19, indicating that Creole cattle had similar genetic diversity at BoLA-DRB3 to the other breeds. A neutrality test showed that the high degree of genetic variability may be maintained by balancing selection. The FST index and the exact G test showed significant differences across all cattle populations (FST=0.0478; p<0.001). Results from the principal components analysis and the phylogenetic tree showed that Yacumeño and Hartón del Valle breeds were closely related to each other. Collectively, our results suggest that the high level of genetic diversity could be explained by the multiple origins of the Creole germplasm (European, African and Indicus), and this diversity might be maintained by balancing selection. Copyright © 2013 Elsevier B.V. All rights reserved.

Microsatellite data suggest significant population structure and differentiation within the malaria vector Anopheles darlingi in Central and South America.

PubMed

Mirabello, Lisa; Vineis, Joseph H; Yanoviak, Stephen P; Scarpassa, Vera M; Póvoa, Marinete M; Padilla, Norma; Achee, Nicole L; Conn, Jan E

2008-03-26

Anopheles darlingi is the most important malaria vector in the Neotropics. An understanding of A. darlingi's population structure and contemporary gene flow patterns is necessary if vector populations are to be successfully controlled. We assessed population genetic structure and levels of differentiation based on 1,376 samples from 31 localities throughout the Peruvian and Brazilian Amazon and Central America using 5-8 microsatellite loci. We found high levels of polymorphism for all of the Amazonian populations (mean RS = 7.62, mean HO = 0.742), and low levels for the Belize and Guatemalan populations (mean RS = 4.3, mean HO = 0.457). The Bayesian clustering analysis revealed five population clusters: northeastern Amazonian Brazil, southeastern and central Amazonian Brazil, western and central Amazonian Brazil, Peruvian Amazon, and the Central American populations. Within Central America there was low non-significant differentiation, except for between the populations separated by the Maya Mountains. Within Amazonia there was a moderate level of significant differentiation attributed to isolation by distance. Within Peru there was no significant population structure and low differentiation, and some evidence of a population expansion. The pairwise estimates of genetic differentiation between Central America and Amazonian populations were all very high and highly significant (FST = 0.1859 - 0.3901, P < 0.05). Both the DA and FST distance-based trees illustrated the main division to be between Central America and Amazonia. We detected a large amount of population structure in Amazonia, with three population clusters within Brazil and one including the Peru populations. The considerable differences in Ne among the populations may have contributed to the observed genetic differentiation. All of the data suggest that the primary division within A. darlingi corresponds to two white gene genotypes between Amazonia (genotype 1) and Central America, parts of Colombia and Venezuela (genotype 2), and are in agreement with previously published mitochondrial COI gene sequences interpreted as incipient species. Overall, it appears that two main factors have contributed to the genetic differentiation between the population clusters: physical distance between the populations and the differences in effective population sizes among the subpopulations.

Population genetics analysis during the elimination process of Plasmodium falciparum in Djibouti

PubMed Central

2013-01-01

Background Case management of imported malaria within the context of malaria pre-elimination is increasingly considered to be relevant because of the risk of resurgence. The assessment of malaria importation would provide key data i) to select countries with propitious conditions for pre-elimination phase and ii) to predict its feasibility. Recently, a sero-prevalence study in Djibouti indicated low malaria prevalence, which is propitious for the implementation of pre-elimination, but data on the extent of malaria importation remain unknown. Methods Djiboutian plasmodial populations were analysed over an eleven-year period (1998, 1999, 2002 and 2009). The risk of malaria importation was indirectly assessed by using plasmodial population parameters. Based on 5 microsatellite markers, expected heterozygosity (H.e.), multiplicity of infection, pairwise Fst index, multiple correspondence analysis and individual genetic relationship were determined. The prevalence of single nucleotide polymorphisms associated with pyrimethamine resistance was also determined. Results Data indicated a significant decline in genetic diversity (0.51, 0.59, 0.51 and 0 in 1998, 1999, 2002 and 2009, respectively) over the study period, which is inconsistent with the level of malaria importation described in a previous study. This suggested that Djiboutian malaria situation may have benefited from the decline of malaria prevalence that occurred in neighbouring countries, in particular in Ethiopia. The high Fst indices derived from plasmodial populations from one study period to another (0.12 between 1999 and 2002, and 0.43 between 2002 and 2009) suggested a random sampling of parasites, probably imported from neighbouring countries, leading to oligo-clonal expansion of few different strains during each transmission season. Nevertheless, similar genotypes observed during the study period suggested recurrent migrations and imported malaria. Conclusion In the present study, the extent of genetic diversity was used to assess the risk of malaria importation in the low malaria transmission setting of Djibouti. The molecular approach highlights i) the evolution of Djiboutian plasmodial population profiles that are consistent and compatible with Djiboutian pre-elimination goals and ii) the necessity to implement the monitoring of plasmodial populations and interventions at the regional scale in the Horn of Africa to ensure higher efficiency of malaria control and elimination. PMID:23758989

Population genetics analysis during the elimination process of Plasmodium falciparum in Djibouti.

PubMed

Khaireh, Bouh Abdi; Assefa, Ashenafi; Guessod, Hawa Hassan; Basco, Leonardo K; Khaireh, Mohamed Abdi; Pascual, Aurélie; Briolant, Sébastien; Bouh, Samatar Mohamed; Farah, Ismaïl Hassan; Ali, Habib Moussa; Abdi, Abdoul-Ilah Ahmed; Aden, Mouna Osman; Abdillahi, Zamzam; Ayeh, Souleiman Nour; Darar, Houssein Youssouf; Koeck, Jean-Louis; Rogier, Christophe; Pradines, Bruno; Bogreau, Hervé

2013-06-13

Case management of imported malaria within the context of malaria pre-elimination is increasingly considered to be relevant because of the risk of resurgence. The assessment of malaria importation would provide key data i) to select countries with propitious conditions for pre-elimination phase and ii) to predict its feasibility. Recently, a sero-prevalence study in Djibouti indicated low malaria prevalence, which is propitious for the implementation of pre-elimination, but data on the extent of malaria importation remain unknown. Djiboutian plasmodial populations were analysed over an eleven-year period (1998, 1999, 2002 and 2009). The risk of malaria importation was indirectly assessed by using plasmodial population parameters. Based on 5 microsatellite markers, expected heterozygosity (H.e.), multiplicity of infection, pairwise Fst index, multiple correspondence analysis and individual genetic relationship were determined. The prevalence of single nucleotide polymorphisms associated with pyrimethamine resistance was also determined. Data indicated a significant decline in genetic diversity (0.51, 0.59, 0.51 and 0 in 1998, 1999, 2002 and 2009, respectively) over the study period, which is inconsistent with the level of malaria importation described in a previous study. This suggested that Djiboutian malaria situation may have benefited from the decline of malaria prevalence that occurred in neighbouring countries, in particular in Ethiopia. The high Fst indices derived from plasmodial populations from one study period to another (0.12 between 1999 and 2002, and 0.43 between 2002 and 2009) suggested a random sampling of parasites, probably imported from neighbouring countries, leading to oligo-clonal expansion of few different strains during each transmission season. Nevertheless, similar genotypes observed during the study period suggested recurrent migrations and imported malaria. In the present study, the extent of genetic diversity was used to assess the risk of malaria importation in the low malaria transmission setting of Djibouti. The molecular approach highlights i) the evolution of Djiboutian plasmodial population profiles that are consistent and compatible with Djiboutian pre-elimination goals and ii) the necessity to implement the monitoring of plasmodial populations and interventions at the regional scale in the Horn of Africa to ensure higher efficiency of malaria control and elimination.

Metabolic network prediction through pairwise rational kernels.

PubMed

Roche-Lima, Abiel; Domaratzki, Michael; Fristensky, Brian

2014-09-26

Metabolic networks are represented by the set of metabolic pathways. Metabolic pathways are a series of biochemical reactions, in which the product (output) from one reaction serves as the substrate (input) to another reaction. Many pathways remain incompletely characterized. One of the major challenges of computational biology is to obtain better models of metabolic pathways. Existing models are dependent on the annotation of the genes. This propagates error accumulation when the pathways are predicted by incorrectly annotated genes. Pairwise classification methods are supervised learning methods used to classify new pair of entities. Some of these classification methods, e.g., Pairwise Support Vector Machines (SVMs), use pairwise kernels. Pairwise kernels describe similarity measures between two pairs of entities. Using pairwise kernels to handle sequence data requires long processing times and large storage. Rational kernels are kernels based on weighted finite-state transducers that represent similarity measures between sequences or automata. They have been effectively used in problems that handle large amount of sequence information such as protein essentiality, natural language processing and machine translations. We create a new family of pairwise kernels using weighted finite-state transducers (called Pairwise Rational Kernel (PRK)) to predict metabolic pathways from a variety of biological data. PRKs take advantage of the simpler representations and faster algorithms of transducers. Because raw sequence data can be used, the predictor model avoids the errors introduced by incorrect gene annotations. We then developed several experiments with PRKs and Pairwise SVM to validate our methods using the metabolic network of Saccharomyces cerevisiae. As a result, when PRKs are used, our method executes faster in comparison with other pairwise kernels. Also, when we use PRKs combined with other simple kernels that include evolutionary information, the accuracy values have been improved, while maintaining lower construction and execution times. The power of using kernels is that almost any sort of data can be represented using kernels. Therefore, completely disparate types of data can be combined to add power to kernel-based machine learning methods. When we compared our proposal using PRKs with other similar kernel, the execution times were decreased, with no compromise of accuracy. We also proved that by combining PRKs with other kernels that include evolutionary information, the accuracy can also also be improved. As our proposal can use any type of sequence data, genes do not need to be properly annotated, avoiding accumulation errors because of incorrect previous annotations.

Serotonergic mediation of the effects of fluoxetine, but not desipramine, in the rat forced swimming test.

PubMed

Page, M E; Detke, M J; Dalvi, A; Kirby, L G; Lucki, I

1999-11-01

The forced swimming test (FST) is a behavioral test in rodents that predicts the clinical efficacy of many types of antidepressant treatments. Recently, a behavior sampling technique was developed that scores individual response categories, including swimming, climbing and immobility. Although all antidepressant drugs reduce immobility in the FST, at least two distinct active behavioral patterns are produced by pharmacologically selective antidepressant drugs. Serotonin-selective reuptake inhibitors increase swimming behavior, while drugs acting primarily to increase extracellular levels of norepinephrine or dopamine increase climbing behavior. Distinct patterns of active behaviors in the FST may be mediated by distinct neurotransmitters, but this has not been shown directly. The present study examined the role of serotonin in mediating active behaviors in the forced swimming test after treatment with two antidepressant drugs, the selective serotonin reuptake inhibitor, fluoxetine and the selective norepinephrine reuptake inhibitor, desipramine. Endogenous serotonin was depleted by administering para-cholorophenylalanine (PCPA, 150 mg/kg, IP.) to rats 72 h and 48 h prior to the swim test. Fluoxetine (10 mg/kg, SC) or desipramine (10 mg/kg, SC) was given three times over a 24-h period prior to the FST. Behavioral responses, including immobility, swimming and climbing, were counted during the 5-min test. Pretreatment with PCPA blocked fluoxetine-induced reduction in immobility and increase in swimming behavior during the FST. In contrast, PCPA pretreatment did not interfere with the ability of desipramine to reduce immobility and increase climbing behavior. Depletion of serotonin prevented the behavioral effects of the selective serotonin reuptake inhibitor fluoxetine in the rat FST. Furthermore, depletion of serotonin had no impact on the behavioral effects induced by the selective norepinephrine reuptake inhibitor, desipramine. The effects of antidepressant drugs on FST-induced immobility may be exerted by distinguishable contributions from different neurotransmitter systems.

Short communication: Genetic variants of Sarcocystis cruzi in infected Malaysian cattle based on 18S rDNA.

PubMed

Ng, Yit Han; Fong, Mun Yik; Subramaniam, Vellayan; Shahari, Shahhaziq; Lau, Yee Ling

2015-12-01

Sarcocystis species are pathogenic parasites that infect a wide range of animals, including cattle. A high prevalence of cattle sarcocystosis has been reported worldwide, but its status is unknown in Malaysia. This study focused on utilizing 18S rDNA to identify Sarcocystis species in Malaysian cattle and to determine their genetic variants. In this study, only Sarcocystis cruzi was detected in Malaysian cattle. The intra-species S. cruzi phylogenetic tree analysis and principal coordinate analysis (PCoA), respectively displayed two minor groups among the parasite isolates. This finding was supported by high Wright FST value (FST=0.647). The definitive hosts (dogs) may play a fundamental role in the development of S. cruzi genetic variants. Additionally, the existence of microheterogeneity within the S. cruzi merozoites and/or distinct genetic variants arisen from independent merozoites in mature sarcocysts, possibly contributed to the existence of intra-species variations within the population. Copyright © 2015 Elsevier Ltd. All rights reserved.

Population genetic structure of the round stingray Urobatis halleri (Elasmobranchii: Rajiformes) in southern California and the Gulf of California

PubMed Central

Plank, S. M.; Lowe, C. G.; Feldheim, K. A.; Wilson, R. R.; Brusslan, J. A.

2017-01-01

The round stingray, Urobatis halleri, is a viviparous elasmobranch that inhabits inshore, benthic habitats ranging from the western U.S.A. to Panama. The population genetic structure of this species was inferred with seven polymorphic microsatellite loci in samples collected at three sites in coastal southern California, one near Santa Catalina Island, California and one in the eastern Gulf of California. Urobatis halleri is relatively common, but little is known of its movement patterns or population structure. Small FST values (−0·0017 to 0·0005) suggested little structure among coastal populations of southern and Baja California. The population sampled at Santa Catalina Island, which is separated by a deep-water channel from the coastal sites, however, was significantly divergent (large FST, 0·0251) from the other populations, suggesting low connectivity with coastal populations. The Santa Catalina Island population also had the lowest allele richness and lowest average heterozygosity, suggesting recent population bottlenecks in size. PMID:20646159

Hierarchical semi-numeric method for pairwise fuzzy group decision making.

PubMed

Marimin, M; Umano, M; Hatono, I; Tamura, H

2002-01-01

Gradual improvements to a single-level semi-numeric method, i.e., linguistic labels preference representation by fuzzy sets computation for pairwise fuzzy group decision making are summarized. The method is extended to solve multiple criteria hierarchical structure pairwise fuzzy group decision-making problems. The problems are hierarchically structured into focus, criteria, and alternatives. Decision makers express their evaluations of criteria and alternatives based on each criterion by using linguistic labels. The labels are converted into and processed in triangular fuzzy numbers (TFNs). Evaluations of criteria yield relative criteria weights. Evaluations of the alternatives, based on each criterion, yield a degree of preference for each alternative or a degree of satisfaction for each preference value. By using a neat ordered weighted average (OWA) or a fuzzy weighted average operator, solutions obtained based on each criterion are aggregated into final solutions. The hierarchical semi-numeric method is suitable for solving a larger and more complex pairwise fuzzy group decision-making problem. The proposed method has been verified and applied to solve some real cases and is compared to Saaty's (1996) analytic hierarchy process (AHP) method.

Individual differences in the forced swimming test and neurochemical kinetics in the rat brain.

PubMed

Sequeira-Cordero, Andrey; Mora-Gallegos, Andrea; Cuenca-Berger, Patricia; Fornaguera-Trías, Jaime

2014-04-10

Individual differences in the forced swimming test (FST) could be associated with differential temporal dynamics of gene expression and neurotransmitter activity. We tested juvenile male rats in the FST and classified the animals into those with low and high immobility according to the amount of immobility time recorded in FST. These groups and a control group which did not undergo the FST were sacrificed either 1, 6 or 24 h after the test. We analyzed the expression of the CRF, CRFR1, BDNF and TrkB in the prefrontal cortex, hippocampus and nucleus accumbens as well as norepinephrine, dopamine, serotonin, glutamate, GABA and glutamine in the hippocampus and nucleus accumbens. Animals with low immobility showed significant reductions of BDNF expression across time points in both the prefrontal cortex and the nucleus accumbens when compared with non-swim control. Moreover, rats with high immobility only showed a significant decrease of BDNF expression in the prefrontal cortex 6h after the FST. Regarding neurotransmitters, only accumbal dopamine turnover and hippocampal glutamate content showed an effect of individual differences (i.e. animals with low and high immobility), whereas nearly all parameters showed significant differences across time points. Correlational analyses suggest that immobility in the FST, probably reflecting despair, is related to prefrontal cortical BDNF and to the kinetics observed in several other neurochemical parameters. Taken together, our results suggest that individual differences observed in depression-like behavior can be associated not only with changes in the concentrations of key neurochemical factors but also with differential time courses of such factors. Copyright © 2014 Elsevier Inc. All rights reserved.

Spatial genetic structuring of baobab (Adansonia digitata, Malvaceae) in the traditional agroforestry systems of West Africa.

PubMed

Kyndt, Tina; Assogbadjo, Achille E; Hardy, Olivier J; Glele Kakaï, Romain; Sinsin, Brice; Van Damme, Patrick; Gheysen, Godelieve

2009-05-01

This study evaluates the spatial genetic structure of baobab (Adansonia digitata) populations from West African agroforestry systems at different geographical scales using AFLP fingerprints. Eleven populations from four countries (Benin, Ghana, Burkina Faso, and Senegal) had comparable levels of genetic diversity, although the two populations in the extreme west (Senegal) had less diversity. Pairwise F(ST) ranged from 0.02 to 0.28 and increased with geographic distance, even at a regional scale. Gene pools detected by Bayesian clustering seem to be a byproduct of the isolation-by-distance pattern rather than representing actual discrete entities. The organization of genetic diversity appears to result essentially from spatially restricted gene flow, with some influences of human seed exchange. Despite the potential for relatively long-distance pollen and seed dispersal by bats within populations, statistically significant spatial genetic structuring within populations (SGS) was detected and gave a mean indirect estimate of neighborhood size of ca. 45. This study demonstrated that relatively high levels of genetic structuring are present in baobab at both large and within-population level, which was unexpected in regard to its dispersal by bats and the influence of human exchange of seeds. Implications of these results for the conservation of baobab populations are discussed.

[Variation of CAG repeats in coding region of ATXN2 gene in different ethnic groups].

PubMed

Chen, Xiao-Chen; Sun, Hao; Mi, Dong-Qing; Huang, Xiao-Qin; Lin, Ke-Qin; Yi, Wen; Yu, Liang; Shi, Lei; Shi, Li; Yang, Zhao-Qing; Chu, Jia-You

2011-04-01

Toinvestigate CAG repeats variation of ATXN2 gene coding region in six ethnic groups that live in comparatively different environments, to evaluate whether these variations are under positive selection, and to find factors driving selection effects, 291 unrelated healthy individuals were collected from six ethnic groups and their STR geneotyping was performed. The frequencies of alleles and genotypes were counted and thereby Slatkin's linearized Fst values were calculated. The UPGMA tree against this gene was constructed. The MDS analysis among these groups was carried out as well. The results from the linearized Fst values indicated that there were significant evolutionary differences of the STR in ATXN2 gene between Hui and Yi groups, but not among the other 4 groups. Further analysis was performed by combining our data with published data obtained from other groups. These results indicated that there were significant differences between Japanese and other groups including Hui, Hani, Yunnan Mongolian, and Inner Mongolian. Both Hui and Mongolian from Inner Mongolia were significantly different from Han. In conclusion, the six ethnic groups had their own distribution characterizations of allelic frequencies of ATXN2 STR, and the potential cause of frequency changes in rare alleles could be the consequence of positive selection.

Mitochondrial genetic variability of Didelphis albiventris (Didelphimorphia, Didelphidae) in Brazilian localities

PubMed Central

Sousa, Luciene C.C.; Gontijo, Célia M.F.; Botelho, Helbert A.; Fonseca, Cleusa G.

2012-01-01

Didelphis albiventris is a well-known and common marsupial. Due to its high adaptability, this very widespread generalist species occurs under various environmental conditions, this even including protected regions and disturbed urban areas. We studied a 653 bp fragment of cytochrome oxidase c (COI) from 93 biological samples from seven Brazilian localities, with linear distances ranging between 58 and about 1800 km to analyze the effects of geographic distances on variability and genetic differentiation. The haplotype network presented nine haplotypes and two genetic clusters compatible with the two most distant geographic areas of the states of Minas Gerais, in the southeast, and Rio Grande do Sul, in the extreme south. As each cluster was characterized by low nucleotide and high haplotype diversities, their populations were obviously composed of closely related haplotypes. Surprisingly, moderate to high FST differentiation values and a very weak phylogeographic signal characterizes interpopulation comparisons within Minas Gerais interdemes, these being correlated with the presence of privative haplotypes. On a large rgeographic scale, a comparison between demes from Minas Gerais and Rio Grande do Sul presented high FST values and a robust phylogeographic pattern. This unexpected scenario implies that mtDNA gene flow was insufficient to maintain population cohesion, reflected by the observed high differentiation. PMID:22888303

Repeated forced-swimming test in intact female rats: behaviour, oestrous cycle and enriched environment.

PubMed

Domingues, Karolina; Spezia, Inaê; Theindl, Lais C; Suman, Patrick R; Lima, Fernanda B; Lino de Oliveira, Cilene

2018-03-27

Psychopharmacology used animal models to study the effects of drugs on brain and behaviour. The repeated forced-swimming test (rFST), which is used to assess the gradual effects of antidepressants on rat behaviour, was standardized only in males. Because of the known sex differences in rats, experimental conditions standardized for males may not apply to female rats. Therefore, the present work aimed to standardize experimental and housing conditions for the rFST in female rats. Young or adult Wistar female rats were housed in standard or enriched environments for different experimental periods. As assessed in tested and nontested females, all rats had reached sexual maturity by the time behavioural testing occurred. The rFST consisted of a 15-min session of forced swimming (pretest), followed by 5-min sessions at 1 (test), 7 (retest 1) and 14 days (retest 2) later. The oestrous cycle was registered immediately before every behavioural session. All sessions were videotaped for further analysis. The immobility time of female rats remained similar over the different sessions of rFST independent of the age, the phase of the oestrous cycle or the housing conditions. These data indicate that rFST in female Wistar rats may be reproducible in different experimental conditions.

The 274th Forward Surgical Team experience during Operation Enduring Freedom.

PubMed

Peoples, George E; Gerlinger, Tad; Craig, Robert; Burlingame, Brian

2005-06-01

The 274th Forward Surgical Team (FST) was deployed in support of Operation Enduring Freedom from October 14, 2001 to May 8, 2002. During this period, the FST was asked to perform many nondoctrinal missions. The FST was tasked with functioning as a mini-combat support hospital during the earlier phases of Operation Enduring Freedom, performing in-flight surgical procedures and resuscitation of combat wounded, conducting split operations with surgical coverage of both Karshi and Khanabad, Uzbekistan, and Bagram, Afghanistan, and leading the multinational medical coalition assembled for Operation Anaconda and other combat operations staged from Bagram. Overall, the 274th FST took care of approximately 90% of U.S. combat casualties during this period and treated a total of 221 combat casualties. The FST treated 103 total surgical cases, including 73 with combat wounds. At the time, this experience with combat casualties and the surgical care of combat wounds was the largest since the Persian Gulf War. More importantly, this account describes the flow, frequency, and type of combat casualties seen in a low-intensity conflict like that being waged currently in Afghanistan. It is hoped that this depiction will aid in the preparation, equipping, and overall utilization of surgical assets in similar future conflicts.

Seated saline suppression testing for the diagnosis of primary aldosteronism: a preliminary study.

PubMed

Ahmed, Ashraf H; Cowley, Diane; Wolley, Martin; Gordon, Richard D; Xu, Shengxin; Taylor, Paul J; Stowasser, Michael

2014-08-01

Failure of aldosterone suppression by sodium loading during fludrocortisone suppression testing (FST) or saline suppression testing (SST) confirms primary aldosteronism (PA). We previously found recumbent SST (RSST) to lack sensitivity. Aldosterone levels can be higher upright (e.g. seated) than recumbent in patients with PA and upright levels are used during FST. We therefore hypothesized that seated SST (SSST) is more sensitive than RSST, especially for posture-responsive PA. Of 66 patients who underwent FST (upright plasma aldosterone levels measured at 10am basally and after 4 days fludrocortisone 0.1 mg 6-hourly and oral salt loading), 31 underwent SST (aldosterone levels measured basally at 8am and after infusion of 2 L normal saline over 4h) both recumbent and seated in randomized order and at least 2 weeks apart. FST confirmed PA in 23 of 31 patients (day 4 upright aldosterone level >165 pmol/L), excluded PA in three and was originally "inconclusive" in five. However, one with "inconclusive" FST had PA confirmed by lateralizing AVS and was reclassified "unilateral PA". Of 24 with confirmed PA (eight unilateral, 11 bilateral, and five undetermined subtype), 23 (96%) tested positive by SSST (4-h aldosterone level >165 pmol/L) compared with 8 (33%) by RSST (4-h plasma aldosterone level >140 pmol/L) (P < .001). RSST missed one unilateral, all bilateral, and four with as-yet undetermined subtype. RSST was positive in 7 of 10 (70%) posture-unresponsive vs one of 14 (7.1%) posture-responsive patients (P < .005). These preliminary results suggest that seated SST may be superior to recumbent SST in terms of sensitivity for detecting PA, especially posture-responsive forms, and may represent a reliable alternative to FST.

Repeated rat-forced swim test: reducing the number of animals to evaluate gradual effects of antidepressants.

PubMed

Mezadri, T J; Batista, G M; Portes, A C; Marino-Neto, J; Lino-de-Oliveira, C

2011-02-15

The forced swim test (FST) is a pre-clinical test to short and long term treatment with antidepressant drugs (ADT), which requires between-subject designs. Herein a modified protocol of the FST using within-subject design (repeated rat-FST) was evaluated. Male Wistar rats were submitted to 15 min of swimming (Day 1: pretest) followed by three subsequent 5 min-swimming tests one week apart (Day 2: test, Day 7: retest 1, Day 14: retest 2). To determine the temporal and factorial characteristics of the variables scored in the repeated rat-FST, the protocol was carried out in untreated animals (E1). To validate the method, daily injections of Fluoxetine (FLX, 2.5mg/kg, i.p.) or saline were given over a 2-week period (E2). Tests and retests have been videotaped for further register of the latency, frequency and duration of behaviors. Over retesting the latency to immobility decreased whereas duration of immobility tended to increase. Factorial analysis revealed that the test, the retest 1 as well as the retest 2 have variables suitable to detection of antidepressant-like effects of ADT. Compared to saline, FLX chronically administrated reduced duration of immobility whereas increased duration of swimming in retest 2. The data suggest that repeated rat-FST detected the gradual increase in the efficacy of low doses of FLX over time. Therefore, repeated rat-FST seemed suitable to detect short and long term effects of selective serotonin reuptake inhibitors, or other ADT, thus reducing the number of animals used in the screenings of this type of compounds. © 2010 Elsevier B.V. All rights reserved.

Fear of needles in children with type 1 diabetes mellitus on multiple daily injections and continuous subcutaneous insulin infusion.

PubMed

Cemeroglu, Ayse Pinar; Can, Argun; Davis, Alan T; Cemeroglu, Ozlem; Kleis, Lora; Daniel, Maala S; Bustraan, Jessica; Koehler, Tracy J

2015-01-01

To assess the prevalence of fear of needles and its effect on glycemic control in children with type 1 diabetes mellitus (T1DM) on multiple daily injections (MDI) or continuous subcutaneous insulin infusion (CSII). Patients aged 6 to 17 years with T1DM on MDI or CSII (n = 150) were enrolled. All caregivers and patients aged ≥11 years completed a "Diabetes Fear of Injecting and Self-testing Questionnaire" (D-FISQ). Needle phobia was defined as a score ≥6 for fear of self-testing (FST), fear of injections (FI), and fear of infusion-site changes (FISC). Positive FST scores were noted in 10.0% and positive FI or FISC scores in 32.7% (caregivers' responses). Patients aged 6 to 10 years on CSII had greater fear (FISC) than those on MDI (FI) (P = .010). FST was inversely related to the number of daily blood sugar checks (P = .003). Patients with positive scores for FI/FISC or FST had significantly higher glycated hemoglobin (HbA1c) levels than those without. An inverse association was noted between positive FI/FISC scores and age of the patient (P = .029). Based on patient responses, FST severity was directly related to the age of the patient (P = .013). Needle phobia is common in children with T1DM. Although FI/FISC are more common in younger children, especially in those on CSII, FST is more often encountered in older patients. Patients with a more intense fear of needles have higher HbA1c levels and less frequent blood sugar monitoring. Identifying these patients may help improve glycemic control.

Alterations on the morphology, nitric oxide synthesis and activity of platelets reproduced in rats as possible biomarkers for depression are reversed by fluoxetine.

PubMed

González-Trujano, María Eva; Alvarado-Vásquez, Noé; Mendoza-Sotelo, José; López, Guadalupe; Estrada-Camarena, Erika; Martínez-Mota, Lucia; Moreno, Julia

2012-08-01

Biochemical markers associated with the prognosis of depression in humans are being described in the literature, whereas experimental studies in animal models in search for antidepressant strategies are lacking. The aim of this study was to evaluate platelet morphology, platelet activity and nitric oxide (NO) synthesis as possible biomarkers of depressive-like behavior by using FST alone and in the presence of fluoxetine. Naïve rats were compared to those receiving vehicle or fluoxetine at 10mg/kg i.p. in acute, subchronic and chronic administration in the FST. After behavioral assessment, platelets were isolated from blood samples and analyzed by flow cytometry to determine the platelet mitochondrial membrane potential and NO synthesis. In addition, HPLC and electron microscopy were used to examine 5-HT and tryptophan levels and morphology of platelets, respectively. Rats receiving vehicle and exposed to FST showed depressive-like behavior at all the times tested; after chronic FST rats showed a similar pattern of alteration in platelet morphology and in the studied as possible biochemical markers as those previously recognized in depressive humans. Depressive-like behavior in rats exposed to FST was prevented in the presence of fluoxetine administration at all the times tested and associated with the prevention of alterations in platelet morphology, platelet activity and NO synthesis, and/or in 5-HT concentrations. The results of the present study suggest that platelet function and morphology might be relevant markers for the prognosis of depression and the search for functional treatments. Besides, the relevance of FST as model to study this psychiatric illness is reinforced. Copyright © 2012 Elsevier Inc. All rights reserved.

Isolation and identification of cellulose-producing strain Komagataeibacter intermedius from fermented fruit juice.

PubMed

Lin, Shin-Ping; Huang, Yin-Hsuan; Hsu, Kai-Di; Lai, Ying-Jang; Chen, Yu-Kuo; Cheng, Kuan-Chen

2016-10-20

A bacterial cellulose (BC) producing strain isolated from fermented fruit juice was identified as Komagataeibacter intermedius (K. intermedius) FST213-1 by 16s rDNA sequencing analysis and biochemical characteristics test. K. intermedius FST213-1 can produce BC within pH 4-9 and exhibit maximum BC production (1.2g/L) at pH 8 in short-term (4-day) cultivation. Results of Fourier transform infrared spectroscopy, X-ray diffraction, water content, thermogravimetric analysis and mechanical property indicated that BC produced from K. intermedius FST213-1 exhibits higher water content ability (99.5%), lower thermostability (315°C), lower crystallinity (79.3%) and similar mechanical properties in comparison with the specimen from model BC producer, Gluconacetobacter xylinus 23769. Based on these analyses, the novel based-resistant strain K. intermedius FST213-1 can efficiently produce BC, which can be applied for industrial manufacturing with potential features. Copyright © 2016 Elsevier Ltd. All rights reserved.

HacDivSel: Two new methods (haplotype-based and outlier-based) for the detection of divergent selection in pairs of populations

PubMed Central

2017-01-01

The detection of genomic regions involved in local adaptation is an important topic in current population genetics. There are several detection strategies available depending on the kind of genetic and demographic information at hand. A common drawback is the high risk of false positives. In this study we introduce two complementary methods for the detection of divergent selection from populations connected by migration. Both methods have been developed with the aim of being robust to false positives. The first method combines haplotype information with inter-population differentiation (FST). Evidence of divergent selection is concluded only when both the haplotype pattern and the FST value support it. The second method is developed for independently segregating markers i.e. there is no haplotype information. In this case, the power to detect selection is attained by developing a new outlier test based on detecting a bimodal distribution. The test computes the FST outliers and then assumes that those of interest would have a different mode. We demonstrate the utility of the two methods through simulations and the analysis of real data. The simulation results showed power ranging from 60–95% in several of the scenarios whilst the false positive rate was controlled below the nominal level. The analysis of real samples consisted of phased data from the HapMap project and unphased data from intertidal marine snail ecotypes. The results illustrate that the proposed methods could be useful for detecting locally adapted polymorphisms. The software HacDivSel implements the methods explained in this manuscript. PMID:28423003

A Pathway-Centered Analysis of Pig Domestication and Breeding in Eurasia

PubMed Central

Leno-Colorado, Jordi; Hudson, Nick J.; Reverter, Antonio; Pérez-Enciso, Miguel

2017-01-01

Ascertaining the molecular and physiological basis of domestication and breeding is an active area of research. Due to the current wide distribution of its wild ancestor, the wild boar, the pig (Sus scrofa) is an excellent model to study these processes, which occurred independently in East Asia and Europe ca. 9000 yr ago. Analyzing genome variability patterns in terms of metabolic pathways is attractive since it considers the impact of interrelated functions of genes, in contrast to genome-wide scans that treat genes or genome windows in isolation. To that end, we studied 40 wild boars and 123 domestic pig genomes from Asia and Europe when metabolic pathway was the unit of analysis. We computed statistical significance for differentiation (Fst) and linkage disequilibrium (nSL) statistics at the pathway level. In terms of Fst, we found 21 and 12 pathways significantly differentiated at a q-value < 0.05 in Asia and Europe, respectively; five were shared across continents. In Asia, we found six significant pathways related to behavior, which involved essential neurotransmitters like dopamine and serotonin. Several significant pathways were interrelated and shared a variable percentage of genes. There were 12 genes present in >10 significant pathways (in terms of Fst), comprising genes involved in the transduction of a large number of signals, like phospholipase PCLB1, which is expressed in the brain, or ITPR3, which has an important role in taste transduction. In terms of nSL, significant pathways were mainly related to reproductive performance (ovarian steroidogenesis), a similarly important target trait during domestication and modern animal breeding. Different levels of recombination cannot explain these results, since we found no correlation between Fst and recombination rate. However, we did find an increased ratio of deleterious mutations in domestic vs. wild populations, suggesting a relaxed functional constraint associated with the domestication and breeding processes. Purifying selection was, nevertheless, stronger in significantly differentiated pathways than in random pathways, mainly in Europe. We conclude that pathway analysis facilitates the biological interpretation of genome-wide studies. Notably, in the case of pig, behavior played an important role, among other physiological and developmental processes. PMID:28500056

A Pathway-Centered Analysis of Pig Domestication and Breeding in Eurasia.

PubMed

Leno-Colorado, Jordi; Hudson, Nick J; Reverter, Antonio; Pérez-Enciso, Miguel

2017-07-05

Ascertaining the molecular and physiological basis of domestication and breeding is an active area of research. Due to the current wide distribution of its wild ancestor, the wild boar, the pig ( Sus scrofa ) is an excellent model to study these processes, which occurred independently in East Asia and Europe ca. 9000 yr ago. Analyzing genome variability patterns in terms of metabolic pathways is attractive since it considers the impact of interrelated functions of genes, in contrast to genome-wide scans that treat genes or genome windows in isolation. To that end, we studied 40 wild boars and 123 domestic pig genomes from Asia and Europe when metabolic pathway was the unit of analysis. We computed statistical significance for differentiation (Fst) and linkage disequilibrium (nSL) statistics at the pathway level. In terms of Fst, we found 21 and 12 pathways significantly differentiated at a q -value < 0.05 in Asia and Europe, respectively; five were shared across continents. In Asia, we found six significant pathways related to behavior, which involved essential neurotransmitters like dopamine and serotonin. Several significant pathways were interrelated and shared a variable percentage of genes. There were 12 genes present in >10 significant pathways (in terms of Fst), comprising genes involved in the transduction of a large number of signals, like phospholipase PCLB1, which is expressed in the brain, or ITPR3, which has an important role in taste transduction. In terms of nSL, significant pathways were mainly related to reproductive performance (ovarian steroidogenesis), a similarly important target trait during domestication and modern animal breeding. Different levels of recombination cannot explain these results, since we found no correlation between Fst and recombination rate. However, we did find an increased ratio of deleterious mutations in domestic vs. wild populations, suggesting a relaxed functional constraint associated with the domestication and breeding processes. Purifying selection was, nevertheless, stronger in significantly differentiated pathways than in random pathways, mainly in Europe. We conclude that pathway analysis facilitates the biological interpretation of genome-wide studies. Notably, in the case of pig, behavior played an important role, among other physiological and developmental processes. Copyright © 2017 Leno-Colorado et al.

The Faces Symbol Test, a newly developed screening instrument to assess cognitive decline related to multiple sclerosis: first results of the Berlin Multi-Centre FST Validation Study.

PubMed

Scherer, P; Penner, I K; Rohr, A; Boldt, H; Ringel, I; Wilke-Burger, H; Burger-Deinerth, E; Isakowitsch, K; Zimmermann, M; Zahrnt, S; Hauser, R; Hilbert, K; Tiel-Wilck, K; Anvari, K; Behringer, A; Peglau, I; Friedrich, H; Plenio, A; Benesch, G; Ehret, R; Nippert, I; Finke, G; Schulz, I; Bergtholdt, B; Breitkopf, S; Kaskel, P; Reischies, F; Kugler, J

2007-04-01

Reliable, language-independent, short screening instruments to test for cognitive function in patients with multiple sclerosis (MS) remain rare, despite the high number of patients affected by cognitive decline. We developed a new, short screening instrument, the Faces Symbol Test (FST), and compared its diagnostic test characteristics with a composite of the Digit Symbol Substitution Test (DSST) and the Paced Auditory Serial Addition Test (PASAT), in 108 MS patients and 33 healthy controls. An Informant-Report Questionnaire, a Self-Report Questionnaire, and a neurologist's estimation of the Every Day Life Cognitive Status were also applied to the MS patients. The statistical analyses comprised of a receiver operating characteristic analysis for test accuracy and for confounding variables. The PASAT and DSST composite score estimated that 36.5% of the MS patients had cognitive impairment. The FST estimated that 40.7% of the MS patients were cognitively impaired (sensitivity 84%; specificity 85%). The FST, DSST and PASAT results were significantly correlated with the patients' physical impairment, as measured by the Expanded Disability Status Scale (EDSS). The results suggest that the FST might be a culture-free, sensitive, and practical short screening instrument for the detection of cognitive decline in patients with MS, including those in the early stages.

Genetic rescue of an endangered domestic animal through outcrossing with closely related breeds: A case study of the Norwegian Lundehund.

PubMed

Stronen, Astrid V; Salmela, Elina; Baldursdóttir, Birna K; Berg, Peer; Espelien, Ingvild S; Järvi, Kirsi; Jensen, Henrik; Kristensen, Torsten N; Melis, Claudia; Manenti, Tommaso; Lohi, Hannes; Pertoldi, Cino

2017-01-01

Genetic rescue, outcrossing with individuals from a related population, is used to augment genetic diversity in populations threatened by severe inbreeding and extinction. The endangered Norwegian Lundehund dog underwent at least two severe bottlenecks in the 1940s and 1960s that each left only five inbred dogs, and the approximately 1500 dogs remaining world-wide today appear to descend from only two individuals. The Lundehund has a high prevalence of a gastrointestinal disease, to which all remaining dogs may be predisposed. Outcrossing is currently performed with three Nordic Spitz breeds: Norwegian Buhund, Icelandic Sheepdog, and Norrbottenspets. Examination of single nucleotide polymorphism (SNP) genotypes based on 165K loci in 48 dogs from the four breeds revealed substantially lower genetic diversity for the Lundehund (HE 0.035) than for other breeds (HE 0.209-0.284). Analyses of genetic structure with > 15K linkage disequilibrium-pruned SNPs showed four distinct genetic clusters. Pairwise FST values between Lundehund and the candidate breeds were highest for Icelandic Sheepdog, followed by Buhund and Norrbottenspets. We assessed the presence of outlier loci among candidate breeds and examined flanking genome regions (1 megabase) for genes under possible selection to identify potential adaptive differences among breeds; outliers were observed in flanking regions of genes associated with key functions including the immune system, metabolism, cognition and physical development. We suggest crossbreeding with multiple breeds as the best strategy to increase genetic diversity for the Lundehund and to reduce the incidence of health problems. For this project, the three candidate breeds were first selected based on phenotypes and then subjected to genetic investigation. Because phenotypes are often paramount for domestic breed owners, such a strategy could provide a helpful approach for genetic rescue and restoration of other domestic populations at risk, by ensuring the involvement of owners, breeders and managers at the start of the project.

Big mountains but small barriers: population genetic structure of the Chinese wood frog (Rana chensinensis) in the Tsinling and Daba Mountain region of northern China.

PubMed

Zhan, Aibin; Li, Cheng; Fu, Jinzhong

2009-04-09

Amphibians in general are poor dispersers and highly philopatric, and landscape features often have important impacts on their population genetic structure and dispersal patterns. Numerous studies have suggested that genetic differentiation among amphibian populations are particularly pronounced for populations separated by mountain ridges. The Tsinling Mountain range of northern China is a major mountain chain that forms the boundary between the Oriental and Palearctic zoogeographic realms. We studied the population structure of the Chinese wood frog (Rana chensinensis) to test whether the Tsinling Mountains and the nearby Daba Mountains impose major barriers to gene flow. Using 13 polymorphic microsatellite DNA loci, 523 individuals from 12 breeding sites with geographical distances ranging from 2.6 to 422.8 kilometers were examined. Substantial genetic diversity was detected at all sites with an average of 25.5 alleles per locus and an expected heterozygosity ranging from 0.504 to 0.855, and two peripheral populations revealed significantly lower genetic diversity than the central populations. In addition, the genetic differentiation among the central populations was statistically significant, with pairwise FST values ranging from 0.0175 to 0.1625 with an average of 0.0878. Furthermore, hierarchical AMOVA analysis attributed most genetic variation to the within-population component, and the between-population variation can largely be explained by isolation-by-distance. None of the putative barriers detected from genetic data coincided with the location of the Tsinling Mountains. The Tsinling and Daba Mountains revealed no significant impact on the population genetic structure of R. chensinensis. High population connectivity and extensive juvenile dispersal may account for the significant, but moderate differentiation between populations. Chinese wood frogs are able to use streams as breeding sites at high elevations, which may significantly contribute to the diminishing barrier effect of mountain ridges. Additionally, a significant decrease in genetic diversity in the peripheral populations supports Mayr's central-peripheral population hypothesis.

Genetic origin of goat populations in Oman revealed by mitochondrial DNA analysis

PubMed Central

Gaafar, Osman Mahgoub; Costa, Vânia; Neira, Agusto Luzuriaga; Al-Atiyat, Raed Mahmoud; Beja-Pereira, Albano

2017-01-01

The Sultanate of Oman has a complex mosaic of livestock species and production systems, but the genetic diversity, demographic history or origins of these Omani animals has not been expensively studied. Goats might constitute one of the most abundant and important domestic livestock species since the Neolithic transition. Here, we examined the genetic diversity, origin, population structure and demographic history of Omani goats. Specifically, we analyzed a 525-bp fragment of the first hypervariable region of the mitochondrial DNA (mtDNA) control region from 69 Omani individuals and compared this fragment with 17 mtDNA sequences from Somalia and Yemen as well as 18 wild goat species and 1,198 previously published goat sequences from neighboring countries. The studied goat breeds show substantial diversity. The haplotype and nucleotide diversities of Omani goats were found equal to 0.983 ± 0.006 and 0.0284 ± 0.014, respectively. The phylogenetic analyses allowed us to classify Omani goats into three mtDNA haplogroups (A, B and G): haplogroup A was found to be predominant and widely distributed and accounted for 80% of all samples, and haplogroups B and G exhibited low frequencies. Phylogenetic comparisons with wild goats revealed that five of the native Omani goat populations originate from Capra aegagrus. Furthermore, most comparisons of pairwise population FST values within and between these five Omani goat breeds as well as between Omani goats and nine populations from nearby countries were not significant. These results suggest strong gene flow among goat populations caused by the extensive transport of goats and the frequent movements of human populations in ancient Arabia. The findings improve our understanding of the migration routes of modern goats from their region of domestication into southeastern Arabia and thereby shed light on human migratory and commercial networks during historical times. PMID:29281717

Genome-wide diversity and differentiation in New World populations of the human malaria parasite Plasmodium vivax

PubMed Central

de Oliveira, Thais C.; Rodrigues, Priscila T.; Menezes, Maria José; Gonçalves-Lopes, Raquel M.; Bastos, Melissa S.; Lima, Nathália F.; Barbosa, Susana; Gerber, Alexandra L.; Loss de Morais, Guilherme; Berná, Luisa; Phelan, Jody; Robello, Carlos; de Vasconcelos, Ana Tereza R.

2017-01-01

Background The Americas were the last continent colonized by humans carrying malaria parasites. Plasmodium falciparum from the New World shows very little genetic diversity and greater linkage disequilibrium, compared with its African counterparts, and is clearly subdivided into local, highly divergent populations. However, limited available data have revealed extensive genetic diversity in American populations of another major human malaria parasite, P. vivax. Methods We used an improved sample preparation strategy and next-generation sequencing to characterize 9 high-quality P. vivax genome sequences from northwestern Brazil. These new data were compared with publicly available sequences from recently sampled clinical P. vivax isolates from Brazil (BRA, total n = 11 sequences), Peru (PER, n = 23), Colombia (COL, n = 31), and Mexico (MEX, n = 19). Principal findings/Conclusions We found that New World populations of P. vivax are as diverse (nucleotide diversity π between 5.2 × 10−4 and 6.2 × 10−4) as P. vivax populations from Southeast Asia, where malaria transmission is substantially more intense. They display several non-synonymous nucleotide substitutions (some of them previously undescribed) in genes known or suspected to be involved in antimalarial drug resistance, such as dhfr, dhps, mdr1, mrp1, and mrp-2, but not in the chloroquine resistance transporter ortholog (crt-o) gene. Moreover, P. vivax in the Americas is much less geographically substructured than local P. falciparum populations, with relatively little between-population genome-wide differentiation (pairwise FST values ranging between 0.025 and 0.092). Finally, P. vivax populations show a rapid decline in linkage disequilibrium with increasing distance between pairs of polymorphic sites, consistent with very frequent outcrossing. We hypothesize that the high diversity of present-day P. vivax lineages in the Americas originated from successive migratory waves and subsequent admixture between parasite lineages from geographically diverse sites. Further genome-wide analyses are required to test the demographic scenario suggested by our data. PMID:28759591

Population structure of four Thai indigenous chicken breeds

PubMed Central

2014-01-01

Background In recent years, Thai indigenous chickens have increasingly been bred as an alternative in Thailand poultry market. Due to their popularity, there is a clear need to improve the underlying quality and productivity of these chickens. Studying chicken genetic variation can improve the chicken meat quality as well as conserving rare chicken species. To begin with, a minimal set of molecular markers that can characterize the Thai indigenous chicken breeds is required. Results Using AFLP-PCR, 30 single nucleotide polymorphisms (SNPs) from Thai indigenous chickens were obtained by DNA sequencing. From these SNPs, we genotyped 465 chickens from 7 chicken breeds, comprising four Thai indigenous chicken breeds- Pradhuhangdum (PD), Luenghangkhao (LK), Dang (DA) and Chee (CH), one wild chicken - the red jungle fowls (RJF), and two commercial chicken breeds - the brown egg layer (BL) and commercial broiler (CB). The chicken genotypes reveal unique genetic structures of the four Thai indigenous chicken breeds. The average expected heterozygosities of PD= 0.341, LK= 0.357, DA=0.349 and CH= 0.373, while the references RJF= 0.327, CB=0.324 and BL= 0.285. The FST values among Thai indigenous chicken breeds vary from 0.051 to 0.096. The FST values between the pairs of Thai indigenous chickens and RJF vary from 0.083 to 0.105 and the FST values between the Thai indigenous chickens and the two commercial chicken breeds vary from 0.116 to 0.221. A neighbour-joining tree of all individual chickens showed that the Thai indigenous chickens were clustered into four groups which were closely related to the wild RJF but far from the commercial breeds. Such commercial breeds were split into two closely groups. Using genetic admixture analysis, we observed that the Thai indigenous chicken breeds are likely to share common ancestors with the RJF, while both commercial chicken breeds share the same admixture pattern. Conclusion These results indicated that the Thai indigenous chicken breeds may descend from the same ancestors. These indigenous chicken breeds were more closely related to red jungle fowls than those of the commercial breeds. These findings showed that the proposed SNP panel can effectively be used to characterize the four Thai indigenous chickens. PMID:24674423

Inbreeding and population structure of the potato cyst nematode (Globodera pallida) in its native area (Peru).

PubMed

Picard, D; Plantard, O; Scurrah, M; Mugniery, D

2004-10-01

The dispersal abilities and the population genetic structure of nematodes living in the soil are poorly known. In the present study, we have pursued these issues in the potato cyst nematode Globodera pallida, which parasitizes potato roots and is indigenous to South America. A hierarchical sampling regime was conducted in Peru to investigate gene flow on regional, field and plant scales. Multilocus genotypes of single individuals were obtained using eight polymorphic microsatellites markers. Large heterozygote deficiencies were observed at most loci. The limited active dispersal of larvae from their cyst, which favours mating between (half) siblings, could be responsible for this pattern. Within fields, as well as among fields within regions (even 35 km apart), low F(ST) values suggest extensive gene flow. Among fields within regions, only 1.5-4.4% genetic variability was observed. Passive dispersal of cysts by natural means (wind, running water, or wild animals) or by anthropogenic means (tillage, movement of infected seed tubers) is probably responsible for the results observed. Among regions, high F(ST) values were observed. Thus long-range dispersal (more than 320 km apart) is probably limited by major biogeographical barriers such as the mountains found in the Andean Cordillera. These results provide useful information for the management of resistant varieties, to slow down the emergence and spread of resistance-breaking pathotypes.

Area-Wide Management of the Formosan subterranean termite, Coptotermes formosanus, Shiraki (Isoptera: Rhinotermitidae) in the New Orleans French Quarter

USDA-ARS?s Scientific Manuscript database

The Formosan subterranean termite, Coptotermes formosanus Shiraki (FST) was first introduced to the continental US after WWII. New Orleans’ French Quarter (FQ) in particular has been severely impacted experiencing reoccurring cycles of damages and repairs since FST was introduced to the region 65 ye...

Antidepressant-like effect of fluoxetine may depend on translocator protein activity and pretest session duration in forced swimming test in mice.

PubMed

Kudryashov, Nikita V; Kalinina, Tatiana S; Shimshirt, Alexander A; Korolev, Anton O; Volkova, Anna V; Voronina, Tatiana A

2018-06-01

The antidepressant-like effect of fluoxetine (20 mg/kg i.p.) has been assessed using the forced swimming test (FST) in IRC (CD-1) mice exposed or not to a pretest session of different duration (5 or 20 min). The influence of the mitochondrial translocator protein (TSPO) activity on the antidepressant-like effect of fluoxetine (20 mg/kg i.p.) in the FST was also studied. The antidepressant-like effect of fluoxetine was observed only in mice subjected to a 5-min pretest session 24 h before the FST. The TSPO antagonist PK11195 [1-(2-chlorophenyl)-N-methyl-N-(1-methylpropyl)-3-isoquinolinecarboxamide; 1 or 3 mg/kg i.p.] inhibited the antidepressant activity of fluoxetine in the FST. In the present study, fluoxetine or PK11195 was administered for a short duration. We suppose that the functional activity of TSPO may depend on a pretest session and that using this procedure is necessary to detect antidepressant activity of fluoxetine-like drugs.

Population Structure With Localized Haplotype Clusters

PubMed Central

Browning, Sharon R.; Weir, Bruce S.

2010-01-01

We propose a multilocus version of FST and a measure of haplotype diversity using localized haplotype clusters. Specifically, we use haplotype clusters identified with BEAGLE, which is a program implementing a hidden Markov model for localized haplotype clustering and performing several functions including inference of haplotype phase. We apply this methodology to HapMap phase 3 data. With this haplotype-cluster approach, African populations have highest diversity and lowest divergence from the ancestral population, East Asian populations have lowest diversity and highest divergence, and other populations (European, Indian, and Mexican) have intermediate levels of diversity and divergence. These relationships accord with expectation based on other studies and accepted models of human history. In contrast, the population-specific FST estimates obtained directly from single-nucleotide polymorphisms (SNPs) do not reflect such expected relationships. We show that ascertainment bias of SNPs has less impact on the proposed haplotype-cluster-based FST than on the SNP-based version, which provides a potential explanation for these results. Thus, these new measures of FST and haplotype-cluster diversity provide an important new tool for population genetic analysis of high-density SNP data. PMID:20457877

Sex and age differences in the impact of the forced swimming test on the levels of steroid hormones.

PubMed

Martínez-Mota, Lucía; Ulloa, Rosa-Elena; Herrera-Pérez, Jaime; Chavira, Roberto; Fernández-Guasti, Alonso

2011-10-24

Compared with the adult disorder, depression in children exhibits differences in its neurobiology, particularly in the HPA axis regulation. The bases of such differences can be evaluated in animal models of depression. The objective of the present study was to determine age and sex differences of Wistar rats in the forced swimming test (FST). The influence of sex and age on corticosterone, estrogens and testosterone serum levels was also determined. Prepubertal rats showed immobility, swimming and climbing behaviors during the pre-test and test sessions. In addition, in the prepubertal animals, no sex differences were found during the pre-test and test sessions. Age comparisons indicated no differences in the female groups, however adult males exhibited more immobility and less swimming than young males, in both FST sessions. The young and female rats showed less immobility behavior and increased levels of estrogens after the FST. The present results indicate that the FST is an animal model suitable to evaluate depressive-like behaviors in prepubertal subjects and to explore behavioral changes related to neurodevelopment. Copyright © 2011 Elsevier Inc. All rights reserved.

Correlations and Functional Connections in a Population of Grid Cells

PubMed Central

Roudi, Yasser

2015-01-01

We study the statistics of spike trains of simultaneously recorded grid cells in freely behaving rats. We evaluate pairwise correlations between these cells and, using a maximum entropy kinetic pairwise model (kinetic Ising model), study their functional connectivity. Even when we account for the covariations in firing rates due to overlapping fields, both the pairwise correlations and functional connections decay as a function of the shortest distance between the vertices of the spatial firing pattern of pairs of grid cells, i.e. their phase difference. They take positive values between cells with nearby phases and approach zero or negative values for larger phase differences. We find similar results also when, in addition to correlations due to overlapping fields, we account for correlations due to theta oscillations and head directional inputs. The inferred connections between neurons in the same module and those from different modules can be both negative and positive, with a mean close to zero, but with the strongest inferred connections found between cells of the same module. Taken together, our results suggest that grid cells in the same module do indeed form a local network of interconnected neurons with a functional connectivity that supports a role for attractor dynamics in the generation of grid pattern. PMID:25714908

Chronic treatment with fluoxetine and sertraline prevents forced swimming test-induced hypercontractility of rat detrusor muscle.

PubMed

Bilge, Sirri; Bozkurt, Ayhan; Bas, Duygu B; Aksoz, Elif; Savli, Evren; Ilkaya, Fatih; Kesim, Yuksel

2008-01-01

Serotonin (5-hydroxytryptamine, 5-HT) reuptake inhibitors represent important targets for the development of new treatments for detrusor overactivity and urinary incontinence. The present study was undertaken to investigate the effects of the forced swimming test (FST) on the contractile response of isolated rat detrusor muscle and to examine the effects of in vivo treatments of fluoxetine and sertraline on altered detrusor muscle contractility. Fluoxetine (20 mg/kg ip) and sertraline (10 mg/kg ip) were administered once a day for 14 days. Rats were exposed to the FST on the 15th day. After the test, detrusor muscles were removed and placed in organ baths, and the contraction responses induced by carbachol, potassium chloride (KCl) and electrical field stimulation (EFS) were recorded. The contractile responses of detrusor muscle strips to carbachol and electrical field stimulation were found to be increased at all carbachol doses and frequencies, respectively. FST also increased the contractile responses to KCl, which is used to test the differences in postreceptor-mediated contractions. The hypercontractile responses of detrusor strips to carbachol, EFS and KCl were abolished by treatment with both fluoxetine and sertraline. These treatments also decreased the immobility duration in the FST consistent with an antidepressant-like effect in this test. The results of this study provide the first evidence that FST increases contractility of the rat detrusor muscle, and this hypercontractility was abolished by chronic treatments of fluoxetine and sertraline at antidepressant doses by decreasing the postreceptor-mediated events.

A proposal for refining the forced swim test in Swiss mice.

PubMed

Costa, Ana Paula Ramos; Vieira, Cintia; Bohner, Lauren O L; Silva, Cristiane Felisbino; Santos, Evelyn Cristina da Silva; De Lima, Thereza Christina Monteiro; Lino-de-Oliveira, Cilene

2013-08-01

The forced swim test (FST) is a preclinical test to the screening of antidepressants based on rats or mice behaviours, which is also sensitive to stimulants of motor activity. This work standardised and validated a method to register the active and passive behaviours of Swiss mice during the FST in order to strength the specificity of the test. Adult male Swiss mice were subjected to the FST for 6 min without any treatment or after intraperitoneal injection of saline (0.1 ml/10 g), antidepressants (imipramine, desipramine, or fluoxetine, 30 mg/kg) or stimulants (caffeine, 30 mg/kg or apomorphine, 10mg/kg). The latency, frequency and duration of behaviours (immobility, swimming, and climbing) were scored and summarised in bins of 6, 4, 2 or 1 min. Parameters were first analysed using Principal Components Analysis generating components putatively related to antidepressant (first and second) or to stimulant effects (third). Antidepressants and stimulants affected similarly the parameters grouped into all components. Effects of stimulants on climbing were better distinguished of antidepressants when analysed during the last 4 min of the FST. Surprisingly, the effects of antidepressants on immobility were better distinguished from saline when parameters were scored in the first 2 min. The method proposed here is able to distinguish antidepressants from stimulants of motor activity using Swiss mice in the FST. This refinement should reduce the number of mice used in preclinical evaluation of antidepressants. Copyright © 2013 Elsevier Inc. All rights reserved.

How would publication bias distort the estimated effect size of prototypic antidepressants in the forced swim test?

PubMed

Ramos-Hryb, Ana B; Harris, Cari; Aighewi, Omorose; Lino-de-Oliveira, Cilene

2018-06-07

This commentary aims to discuss the impact of publication bias on the estimated effect of prototypic antidepressants in the forced swim test (FST). A systematic review and meta-analysis (SRMA) recently reported by Kara et al. (2018) showed that selected prototypic antidepressants reduced immobility time of mice in the FST across a variety of experimental designs. Despite differences in the procedures for SRMA, these results resemble the interim data collected by our research group according to a protocol deposited in the Systematic Review Facility and Open Science Framework (osf.io/9kxm4). Both studies detected a high amount of publications reporting statistically significant results and agreement with the primary hypothesis raising the possibility of publication bias in the field of FST. In our preliminary analysis, no evidence for publication bias was observed. However, the present work was limited to the effects of imipramine (doses ranging from 4 to 64 mg/kg) in different strains of mice. Therefore, more comprehensive studies are required to evaluate the risk of publication bias in the field of basic antidepressant research. We see the need to expand the current preliminary studies to evaluate the risk of publication bias within the preclinical research using the FST. Appraisal of the risk of publication bias may avoid misestimated effects of drugs in the FST providing better bases for the discovery of new antidepressants. Copyright © 2018. Published by Elsevier Ltd.

Towards understanding the low prevalence of Helicobacter pylori in Malays: genetic variants among Helicobacter pylori-negative ethnic Malays in the north-eastern region of Peninsular Malaysia and Han Chinese and South Indians.

PubMed

Maran, Sathiya; Lee, Yeong Yeh; Xu, Shu Hua; Raj, Mahendra Sundramoorthy; Abdul Majid, Noorizan; Choo, Keng Ee; Zilfalil, Bin Alwi; Graham, David Y

2013-04-01

To identify gene polymorphisms that differ between Malays, Han Chinese and South Indians, and to identify candidate genes for the investigation of their role in protecting Malays from Helicobacter pylori (H. pylori) infection. Malay participants born and residing in Kelantan with a documented absence of H. pylori infection were studied. Venous blood was used for genotyping using the Affymetrix 50K Xba I kit. CEL files from 141 Han Chinese and 76 South Indians were analyzed to compare their allele frequency with that of the Malays using fixation index (FST ) calculation. The single nucleotide polymorphisms (SNPs) with the highest allele frequency (outliers) were then examined for their functional characteristics using F-SNP software and the Entrez Gene database. In all, 37 Malays were enrolled in the study; of whom 7 were excluded for low genotyping call rates. The average FST estimated from the genome-wide data were 0.038 (Malays in Kelantan vs the South Indians), 0.015 (Malays in Kelantan vs Han Chinese) and 0.066 (Han Chinese vs South Indians), respectively. The outlier gene variants present in Malays with functional characteristics were C7orf10 (FST  0.29988), TSTD2 (FST  0.43278), SMG7 (FST  0.29877) and XPA (FST  0.43393 and 0.43644). Genetic variants possibly related to protection against H. pylori infection in ethnic Malays from the north-eastern region of Peninsular Malaysia were identified for testing in subsequent trials among infected and uninfected Malays. © 2012 The Authors. Journal of Digestive Diseases © 2012 Chinese Medical Association Shanghai Branch, Chinese Society of Gastroenterology, Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine and Wiley Publishing Asia Pty Ltd.

Ethanol induced antidepressant-like effect in the mouse forced swimming test: modulation by serotonergic system.

PubMed

Jain, Nishant S; Kannamwar, Uday; Verma, Lokesh

2017-02-01

The present investigation explored the modulatory role of serotonergic transmission in the acute ethanol-induced effects on immobility time in the mouse forced swim test (FST). Acute i.p. administration of ethanol (20% w/v, 2 or 2.5 g/kg, i.p.) decreased the immobility time in FST of mice, indicating its antidepressant-like effect while lower doses of ethanol (1, 1.5 g/kg, i.p.) were devoid of any effect in the FST. The mice pre-treated with a sub-effective dose of 5-HT 2A agonist, DOI (10 μg/mouse, i.c.v.) or 5-HT 1A receptor antagonist, WAY 100635 (0.1 μg/mouse, i.c.v.) but not with the 5-HT 2A/2C antagonist, ketanserin (1.5 μg/mouse, i.c.v.) exhibited a synergistic reduction in the immobility time induced by sub-effective dose of ethanol (1.5 g/kg, i.p.). On the other hand, ethanol (2.5 g/kg, i.p.) failed to decrease the immobility time in mice, pre-treated with 5-HT 1A agonist, 8-OH-DPAT (0.1 μg/mouse, i.c.v.) or ketanserin (1.5 μg/mouse, i.c.v.). In addition, pre-treatment with a 5-HT neuronal synthesis inhibitor, p-CPA (300 mg/kg, i.p. × 3 days) attenuated the anti-immobility effect ethanol (2.5 g/kg, i.p.) in mouse FST. Thus, the results of the present study points towards the essentiality of the central 5-HT transmission at the synapse for the ethanol-induced antidepressant-like effect in the FST wherein the regulatory role of the 5-HT 1A receptor or contributory role of the 5-HT 2A/2C receptor-mediated mechanism is proposed in the anti-immobility effect of acute ethanol in mouse FST.

Antidepressant-like effect of atorvastatin in the forced swimming test in mice: the role of PPAR-gamma receptor and nitric oxide pathway.

PubMed

Shahsavarian, Arash; Javadi, Shiva; Jahanabadi, Samane; Khoshnoodi, Mina; Shamsaee, Javad; Shafaroodi, Hamed; Mehr, Shahram Ejtemaei; Dehpour, Ahmadreza

2014-12-15

Atorvastatin is a synthetic and lipophilic statin which has been reported to have a positive role in reducing depression. The potential antidepressant-like effects of atorvastatin and the possible involvement of peroxisome proliferator-activated receptor gamma (PPAR_γ) and nitric oxide system were determined using forced swimming test (FST) in mice was studied. Atorvastatin (0.01, 0.1 and 1 mg/kg, p.o.) was administered 1 h before FST. To assess the involvement of PPAR_γ in the possible antidepressant effect of atorvastatin, pioglitazone, a PPAR_γ agonist (5 mg/kg), and GW-9662, a specific PPAR_γ antagonist (2 mg/kg), was co-administered with atorvastatin (0.01 mg/kg, p.o.) and then FST was performed. The possible role of nitric oxide pathway was determined by using co-administration of a non-specific NOS inhibitor, N-nitro-L-arginine methyl ester (L-NAME, 10 mg/kg, i.p.), and a NO precursor, L-arginine (750 mg/kg, i.p.) with sub-effective doses of atorvastatin and pioglitazone. Immobility time was significantly decreased after atorvastatin administration (0.1 and 1 mg/kg, p.o.). Administration of pioglitazone or L-NAME in combination with the sub-effective dose of atorvastatin (0.01 mg/kg, p.o.) reduced the immobility time in the FST compared to drugs alone, showing the participation of these pathways; while co-administration of non-effective doses of atorvastatin and pioglitazone with GW9662 or L-arginine reversed antidepressant-like effect of atorvastatin in FST. Data from concurrent use of GW9662 and atorvastatin also demonstrated that the antidepressant effect of atorvastatin was significantly reversed by GW9662. The antidepressant-like effect of atorvastatin on mice in the FST is mediated at least in part through PPAR_γ receptors and NO pathway. Copyright © 2014 Elsevier B.V. All rights reserved.

Antidepressant- and Anxiolytic-Like Effects of New Dual 5-HT1A and 5-HT7 Antagonists in Animal Models

PubMed Central

Pytka, Karolina; Partyka, Anna; Jastrzębska-Więsek, Magdalena; Siwek, Agata; Głuch-Lutwin, Monika; Mordyl, Barbara; Kazek, Grzegorz; Rapacz, Anna; Olczyk, Adrian; Gałuszka, Adam; Błachuta, Marian; Waszkielewicz, Anna; Marona, Henryk; Sapa, Jacek; Filipek, Barbara; Wesołowska, Anna

2015-01-01

The aim of this study was to further characterize pharmacological properties of two phenylpiperazine derivatives: 1-{2-[2-(2,6-dimethlphenoxy)ethoxy]ethyl}-4-(2-methoxyphenyl)piperazynine hydrochloride (HBK-14) and 2-[2-(2-chloro-6-methylphenoxy)ethoxy]ethyl-4-(2- methoxyphenyl)piperazynine dihydrochloride (HBK-15) in radioligand binding and functional in vitro assays as well as in vivo models. Antidepressant-like properties were investigated in the forced swim test (FST) in mice and rats. Anxiolytic-like activity was evaluated in the four-plate test in mice and elevated plus maze test (EPM) in rats. Imipramine and escitalopram were used as reference drugs in the FST, and diazepam was used as a standard anxiolytic drug in animal models of anxiety. Our results indicate that HBK-14 and HBK-15 possess high or moderate affinity for serotonergic 5-HT2, adrenergic α1, and dopaminergic D2 receptors as well as being full 5-HT1A and 5-HT7 receptor antagonists. We also present their potent antidepressant-like activity (HBK-14—FST mice: 2.5 and 5 mg/kg; FST rats: 5 mg/kg) and (HBK-15—FST mice: 1.25, 2.5 and 5 mg/kg; FST rats: 1.25 and 2.5 mg/kg). We show that HBK-14 (four-plate test: 2.5 and 5 mg/kg; EPM: 2.5 mg/kg) and HBK-15 (four-plate test: 2.5 and 5 mg/kg; EPM: 5 mg/kg) possess anxiolytic-like properties. Among the two, HBK-15 has stronger antidepressant-like properties, and HBK-14 displays greater anxiolytic-like activity. Lastly, we demonstrate the involvement of serotonergic system, particularly 5-HT1A receptor, in the antidepressant- and anxiolytic-like actions of investigated compounds. PMID:26554929

Myostatin and follistatin polymorphisms interact with muscle phenotypes and ethnicity.

PubMed

Kostek, Matthew A; Angelopoulos, Theodore J; Clarkson, Priscilla M; Gordon, Paul M; Moyna, Niall M; Visich, Paul S; Zoeller, Robert F; Price, Thomas B; Seip, Richard L; Thompson, Paul D; Devaney, Joseph M; Gordish-Dressman, Heather; Hoffman, Eric P; Pescatello, Linda S

2009-05-01

We examined associations among myostatin (MSTN) 2379 A > G and 163 G > A and follistatin (FST) -5003 A > T and -833 G > T single nucleotide polymorphisms (SNP) on the muscle size and the strength response to resistance training (RT). Subjects (n = 645, age = 24.1 +/- 0.2 yr, body mass index [BMI] = 24.2 +/- 0.2 kg x m(-2)) self-disclosed themselves as Caucasian (78.9%), African American (3.6%), Asian (8.4%), Hispanic (5.0%), or Other (4.2%). They were genotyped for MSTN 2379 A > G (n = 645), MSTN 163 G > A (n = 639), FST -5003 A > T (n = 580), and FST -833 G > T (n = 603). We assessed dynamic (one repetition maximum [1RM]) and isometric (maximum voluntary contraction [MVC]) muscle strength and size (cross-sectional area [CSA]) of the elbow flexors before and after 12 wk of unilateral upper-arm RT. Repeated-measures ANCOVA tested associations among genetic variants and muscle phenotypes with age and BMI as covariates. Baseline MVC was greater among African Americans who were carriers of the MSTN G(2379) allele (AG/GG, n = 15) than the A2379A homozygotes (n = 8; 64.2 +/- 6.8 vs 49.8 +/- 8.7 kg). African Americans who were carriers of the FST T(-5003) allele (n = 12) had greater baseline 1RM (11.9 +/- 0.7 vs 8.8 +/- 0.5 kg) and CSA (24.4 +/- 1.3 vs 19.1 +/- 1.2 cm(2)) than African Americans with the A-5003A genotype (n = 14; P < 0.05). No MSTN or FST genotype and muscle phenotype associations were found among the other ethnic groups (P >or= 0.05). MSTN 2379 A > G and FST -5003 A > T were associated with baseline muscle strength and size among African Americans only. These ethnic-specific associations are hypothesis generating and should be confirmed in a larger sample of African Americans.

Possible involvement of ATP-sensitive potassium channels in the antidepressant-like effect of baclofen in mouse forced swimming test.

PubMed

Nazari, Seyedeh Khadijeh; Nikoui, Vahid; Ostadhadi, Sattar; Chegini, Zahra Hadi; Oryan, Shahrbanoo; Bakhtiarian, Azam

2016-12-01

Previous study confirmed that the acute treatment with baclofen by inhibition of the l-arginine-nitric oxide (NO) pathway diminished the immobility behavior in the forced swimming test (FST) of mice. Considering the involvement of NO in adenosine triphosphate (ATP)-sensitive potassium channels (K ATP ), in the present study we investigated the involvement of K ATP channels in antidepressant-like effect of baclofen in the forced swimming test (FST). After assessment of locomotor behavior in the open-field test (OFT), FST was applied for evaluation of the antidepressant-like activity of baclofen in mice. Baclofen at different doses (0.1, 0.3, and 1mg/kg) and fluoxetine (20mg/kg) were administrated by intraperitoneal (ip) route, 30min before the FST or OFT. To clarify the probable involvement of K ATP channels, after determination of sub-effective doses of glibenclamide as a K ATP channel blocker and cromakalim, as an opener of these channels, they were co-administrated with the sub-effective and effective doses of baclofen, respectively. Baclofen at dose 1mg/kg significantly decreased the immobility behavior of mice similar to fluoxetine (20mg/kg). Co-administration of gelibenclamide sub-effective dose (1mg/kg) with baclofen (0.1mg/kg) showed a synergistic antidepressant-like effect in the FST. Also, sub-effective dose of cromakalim (0.1mg/kg) inhibited the antidepressant-like effect of baclofen (1mg/kg) in the FST. All aforementioned treatments had not any impact on the locomotor movement of mice in OFT. Our study for the first time revealed that antidepressant-like effect of baclofen on mice is K ATP -dependent, and baclofen seems that exert this effect by blocking the K ATP channels. Copyright © 2016 Institute of Pharmacology, Polish Academy of Sciences. Published by Elsevier Urban & Partner Sp. z o.o. All rights reserved.

Steroidobacter denitrificans gen. nov., sp. nov., a steroidal hormone-degrading gammaproteobacterium.

PubMed

Fahrbach, Michael; Kuever, Jan; Remesch, Markko; Huber, Birgit E; Kämpfer, Peter; Dott, Wolfgang; Hollender, Juliane

2008-09-01

A denitrifying bacterium, designated strain FS(T), was isolated from anoxic digested sludge on oestradiol [17beta-oestra-1,3,5(10)-triene-3,17-diol] or testosterone (17beta-hydroxyandrost-4-en-3-one) as the sole source of carbon and energy with nitrate as the electron acceptor. Strain FS(T) represents the first known bacterium to grow anaerobically on both oestradiol (C-18) and testosterone (C-19). Steroidal hormones were degraded completely by nitrate reduction to dinitrogen monoxide, which was further reduced to dinitrogen in stationary-phase cultures. Gram-negative cells were slightly curved rods, 0.3-0.5 x 0.6-1.6 microm in size, motile, non-fermentative, non-spore-forming and catalase- and oxidase-positive, showing optimal growth at pH 7.0, 28 degrees C and 0.1% (w/v) NaCl. Beside steroidal hormones, the bacterium utilized only a narrow range of organic substrates with nitrate as the electron acceptor, including several fatty acids and glutamate. No aerobic or anaerobic growth occurred on liquid or solid complex media. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain FS(T) has no known close relatives and represents a distinct lineage within the Gammaproteobacteria. Together with the genera Nevskia, Hydrocarboniphaga, Solimonas and Sinobacter (less than 88% 16S rRNA gene sequence similarity to strain FS(T)), it forms a phylogenetic cluster separated from the families Chromatiaceae, Ectothiorhodospiraceae and Xanthomonadaceae. The quinone system of strain FS(T) consisted exclusively of ubiquinone Q-8. The dominant polar lipids were diphosphatidylglycerol and phosphatidylethanolamine. Spermidine in combination with putrescine and traces of sym-homospermidine were the basic polyamines. The major fatty acids detected in testosterone- or heptanoate-grown cells were C(15:0) and C(17:1)omega8c, minor hydroxylated fatty acids were C(11:0) 3-OH and C(12:0) 3-OH. The G+C content of the DNA was 61.9 mol%. Based on the high 16S rRNA gene sequence divergence and different phenotypic properties from previously described gammaproteobacteria in combination with chemotaxonomic data, strain FS(T) is considered to represent a new genus and species, for which the name Steroidobacter denitrificans gen. nov., sp. nov. is proposed. The type strain of Steroidobacter denitrificans is FS(T) (=DSM 18526(T) =JCM 14622(T)).

Maternal and genetic effects on broiler bone properties during incubation period.

PubMed

Yair, R; Cahaner, A; Uni, Z; Shahar, R

2017-07-01

In order to examine the differences in bone properties between fast-growing and slow-growing broiler embryos and to understand the effects of genotype and egg size on these differences, fast- and slow-growing hens and males were reciprocally crossed to create 4 egg groups: FST (laid by fast-growing hens, inseminated by fast-growing males), H-FST (fast-growing hens and slow-growing males), H-SLW (slow-growing hens and fast-growing males), and SLW (slow-growing hens and slow-growing males). Embryos (n = 8) from these 4 groups were sacrificed and weighed, and both tibiae were harvested on embryonic d (E) 17, 19, and 21. Left tibiae were tested for their whole-bone mechanical properties using a micromechanical device. Cortical bone structure and bone mineral density (BMD) were examined by micro-computed tomography of the left tibiae. Bone mineralization was evaluated by measuring BMD and ash content, while the rate and location of mineralization were evaluated by fluorochrome labeling. Osteoclastic activity and osteocyte density were evaluated by histological stains [TRAP (Tartrate resistant acid phosphatase) and H&E (Hematoxylin and Eosin), respectively]. Groups with larger eggs (FST and H-FST) had higher BW and tibia weight than groups with smaller eggs (SLW and H-SLW); however, they had a lower ratio of tibia weight to BW. Between groups with similar egg weight, stiffness, maximal load, and yield load of the bones were higher in the SLW than the H-SLW, while no differences were found between the FST and H-FST. Additionally, the tibiae of the SLW were stiffer and their osteocyte density higher than in the FST on E21 and their periosteal mineralization rate was higher between E19 and E21. No differences were found between the groups in cortical bone structure. This study demonstrates that faster growing hatchlings, especially those that hatch from relatively small eggs, have inferior bone mechanical properties in comparison to slower growing hatchlings, and suggests that fast-growing chicks hatching from small eggs are at a higher risk for developing bone pathologies. Accordingly, selection for increased egg size may lead to improved mechanical performance of the skeleton of fast-growing broilers. © 2017 Poultry Science Association Inc.

Reconciling patterns of inter-ocean molecular variance from four classes of molecular markers in blue marlin (Makaira nigricans).

PubMed

Buonaccorsi, V P; McDowell, J R; Graves, J E

2001-05-01

Different classes of molecular markers occasionally yield discordant views of population structure within a species. Here, we examine the distribution of molecular variance from 14 polymorphic loci comprising four classes of molecular markers within approximately 400 blue marlin individuals (Makaira nigricans). Samples were collected from the Atlantic and Pacific Oceans over 5 years. Data from five hypervariable tetranucleotide microsatellite loci and restriction fragment length polymorphism (RFLP) analysis of whole molecule mitochondrial DNA (mtDNA) were reported and compared with previous analyses of allozyme and single-copy nuclear DNA (scnDNA) loci. Temporal variance in allele frequencies was nonsignificant in nearly all cases. Mitochondrial and microsatellite loci revealed striking phylogeographic partitioning among Atlantic and Pacific Ocean samples. A large cluster of alleles was present almost exclusively in Atlantic individuals at one microsatellite locus and for mtDNA, suggesting that, if gene flow occurs, it is likely to be unidirectional from Pacific to Atlantic oceans. Mitochondrial DNA inter-ocean divergence (FST) was almost four times greater than microsatellite or combined nuclear divergences including allozyme and scnDNA markers. Estimates of Neu varied by five orders of magnitude among marker classes. Using mathematical and computer simulation approaches, we show that substantially different distributions of FST are expected from marker classes that differ in mode of inheritance and rate of mutation, without influence of natural selection or sex-biased dispersal. Furthermore, divergent FST values can be reconciled by quantifying the balance between genetic drift, mutation and migration. These results illustrate the usefulness of a mitochondrial analysis of population history, and relative precision of nuclear estimates of gene flow based on a mean of several loci.

Genetic structure of the threatened Hopea chinensis in the Quang Ninh Province, Vietnam.

PubMed

Trang, N T P; Triest, L

2016-04-29

Hopea chinensis Hand-Mazz (synonym H. hongayensis Tardieu), is a wind and insect pollinated species. It is a threatened species known only from two locations: Quang Ninh (Vietnam) and Guangxi (China). As an endemic species, it is worth preserving both for dipterocarp biodiversity, as well as for its medicinal use and economic importance as a fine wood. The genetic diversity and population genetic structure of H. chinensis was investigated, using natural populations distributed throughout the Ba Mun and Cai Lim islands, Quang Ninh Province, Vietnam. A total of 65 alleles were detected. The adult allelic richness was higher than that found in juveniles and seedlings in both populations. Inbreeding was found to be significant in Ba Mun adults (F(ST) = 0.139), as well as in Cai Lim juveniles and seedlings (F(ST) = 0.283 and 0.345, respectively). Evidence of a bottleneck could be detected in the juveniles and seedlings of the Cai Lim population. A Bayesian analysis and F(ST) values suggested high genetic differentiation among the age classes of the Ba Mun and Cai Lim populations. Whereas the adults of the Ba Mun population showed evidence of inbreeding, the next generations showed more potential heterozygotes. In contrast, the adults in the Cai Lim population showed no significant inbreeding, but the observed heterozygosity in the next generation was lower than expected, suggesting significant inbreeding. The H. chinensis populations on islands are developed well and showed re-generation under good condition. Thus, the forestry protector should conserve and protect the natural spatial structure of H. chinensis on each island as their natural habitats and keep them through natural regeneration.

Paradoxical Neurobehavioral Rescue by Memories of Early-Life Abuse: The Safety Signal Value of Odors Learned during Abusive Attachment

PubMed Central

Raineki, Charlis; Sarro, Emma; Rincón-Cortés, Millie; Perry, Rosemarie; Boggs, Joy; Holman, Colin J; Wilson, Donald A; Sullivan, Regina M

2015-01-01

Caregiver-associated cues, including those learned in abusive attachment, provide a sense of safety and security to the child. Here, we explore how cues associated with abusive attachment, such as maternal odor, can modify the enduring neurobehavioral effects of early-life abuse. Two early-life abuse models were used: a naturalistic paradigm, where rat pups were reared by an abusive mother; and a more controlled paradigm, where pups underwent peppermint odor-shock conditioning that produces an artificial maternal odor through engagement of the attachment circuit. Animals were tested for maternal odor preference in infancy, forced swim test (FST), social behavior, and sexual motivation in adulthood—in the presence or absence of maternal odors (natural or peppermint). Amygdala odor-evoked local field potentials (LFPs) via wireless electrodes were also examined in response to the maternal odors in adulthood. Both early-life abuse models induced preference for the maternal odors in infancy. In adulthood, these early-life abuse models produced FST deficits and decreased social behavior, but did not change sexual motivation. Presentation of the maternal odors rescued FST and social behavior deficits induced by early-life abuse and enhanced sexual motivation in all animals. In addition, amygdala LFPs from both abuse animal models showed unique activation within the gamma frequency (70–90 Hz) bands in response to the specific maternal odor present during early-life abuse. These results suggest that attachment-related cues learned during infancy have a profound ability to rescue neurobehavioral dysregulation caused by early-life abuse. Paradoxically, abuse-associated cues seem to acquire powerful and enduring antidepressive properties and alter amygdala modulation. PMID:25284320

Paradoxical neurobehavioral rescue by memories of early-life abuse: the safety signal value of odors learned during abusive attachment.

PubMed

Raineki, Charlis; Sarro, Emma; Rincón-Cortés, Millie; Perry, Rosemarie; Boggs, Joy; Holman, Colin J; Wilson, Donald A; Sullivan, Regina M

2015-03-01

Caregiver-associated cues, including those learned in abusive attachment, provide a sense of safety and security to the child. Here, we explore how cues associated with abusive attachment, such as maternal odor, can modify the enduring neurobehavioral effects of early-life abuse. Two early-life abuse models were used: a naturalistic paradigm, where rat pups were reared by an abusive mother; and a more controlled paradigm, where pups underwent peppermint odor-shock conditioning that produces an artificial maternal odor through engagement of the attachment circuit. Animals were tested for maternal odor preference in infancy, forced swim test (FST), social behavior, and sexual motivation in adulthood-in the presence or absence of maternal odors (natural or peppermint). Amygdala odor-evoked local field potentials (LFPs) via wireless electrodes were also examined in response to the maternal odors in adulthood. Both early-life abuse models induced preference for the maternal odors in infancy. In adulthood, these early-life abuse models produced FST deficits and decreased social behavior, but did not change sexual motivation. Presentation of the maternal odors rescued FST and social behavior deficits induced by early-life abuse and enhanced sexual motivation in all animals. In addition, amygdala LFPs from both abuse animal models showed unique activation within the gamma frequency (70-90 Hz) bands in response to the specific maternal odor present during early-life abuse. These results suggest that attachment-related cues learned during infancy have a profound ability to rescue neurobehavioral dysregulation caused by early-life abuse. Paradoxically, abuse-associated cues seem to acquire powerful and enduring antidepressive properties and alter amygdala modulation.

Tests of two convection theories for red giant and red supergiant envelopes

NASA Technical Reports Server (NTRS)

Stothers, Richard B.; Chin, Chao-Wen

1995-01-01

Two theories of stellar envelope convection are considered here in the context of red giants and red supergiants of intermediate to high mass: Boehm-Vitense's standard mixing-length theory (MLT) and Canuto & Mazzitelli's new theory incorporating the full spectrum of turbulence (FST). Both theories assume incompressible convection. Two formulations of the convective mixing length are also evaluated: l proportional to the local pressure scale height (H(sub P)) and l proportional to the distance from the upper boundary of the convection zone (z). Applications to test both theories are made by calculating stellar evolutionary sequences into the red zone (z). Applications to test both theories are made by calculating stellar evolutionary sequences into the red phase of core helium burning. Since the theoretically predicted effective temperatures for cool stars are known to be sensitive to the assigned value of the mixing length, this quantity has been individually calibrated for each evolutionary sequence. The calibration is done in a composite Hertzsprung-Russell diagram for the red giant and red supergiant members of well-observed Galactic open clusters. The MLT model requires the constant of proportionality for the convective mixing length to vary by a small but statistically significant amount with stellar mass, whereas the FST model succeeds in all cases with the mixing lenghth simply set equal to z. The structure of the deep stellar interior, however, remains very nearly unaffected by the choices of convection theory and mixing lenghth. Inside the convective envelope itself, a density inversion always occurs, but is somewhat smaller for the convectively more efficient MLT model. On physical grounds the FST model is preferable, and seems to alleviate the problem of finding the proper mixing length.

Molecular Genetic Diversity of Major Indian Rice Cultivars over Decadal Periods

PubMed Central

Deborah, Dondapati Annekitty; Vipparla, Abhilash; Anuradha, Ghanta; Siddiq, Ebrahimali Abubacker; Vemireddy, Lakshminarayana Reddy

2013-01-01

Genetic diversity in representative sets of high yielding varieties of rice released in India between 1970 and 2010 was studied at molecular level employing hypervariable microsatellite markers. Of 64 rice SSR primer pairs studied, 52 showed polymorphism, when screened in 100 rice genotypes. A total of 184 alleles was identified averaging 3.63 alleles per locus. Cluster analysis clearly grouped the 100 genotypes into their respective decadal periods i.e., 1970s, 1980s, 1990s and 2000s. The trend of diversity over the decadal periods estimated based on the number of alleles (Na), allelic richness (Rs), Nei’s genetic diversity index (He), observed heterozygosity (Ho) and polymorphism information content (PIC) revealed increase of diversity over the periods in year of releasewise and longevitywise classification of rice varieties. Analysis of molecular variance (AMOVA) suggested more variation in within the decadal periods than among the decades. Pairwise comparison of population differentiation (Fst) among decadal periods showed significant difference between all the pairs except a few. Analysis of trends of appearing and disappearing alleles over decadal periods showed an increase in the appearance of alleles and decrease in disappearance in both the categories of varieties. It was obvious from the present findings, that genetic diversity was progressively on the rise in the varieties released during the decadal periods, between 1970s and 2000s. PMID:23805204

East-west genetic differentiation in Musk Ducks (Biziura lobata) of Australia suggests late Pleistocene divergence at the Nullarbor Plain

USGS Publications Warehouse

Guay, P.-J.; Chesser, R.T.; Mulder, R.A.; Afton, A.D.; Paton, D.C.; McCracken, K.G.

2010-01-01

Musk Ducks (Biziura lobata) are endemic to Australia and occur as two geographically isolated populations separated by the Nullarbor Plain, a vast arid region in southern Australia. We studied genetic variation in Musk Duck populations at coarse (eastern versus western Australia) and fine scales (four sites within eastern Australia). We found significant genetic structure between eastern and western Australia in the mtDNA control region (??ST = 0. 747), one nuclear intron (??ST = 0.193) and eight microsatellite loci (FST = 0.035). In contrast, there was little genetic structure between Kangaroo Island and adjacent mainland regions within eastern Australia. One small population of Musk Ducks in Victoria (Lake Wendouree) differed from both Kangaroo Island and the remainder of mainland eastern Australia, possibly due to genetic drift exacerbated by inbreeding and small population size. The observed low pairwise distance between the eastern and western mtDNA lineages (0.36%) suggests that they diverged near the end of the Pleistocene, a period characterised by frequent shifts between wet and arid conditions in central Australia. Our genetic results corroborate the display call divergence and Mathews' (Austral Avian Record 2:83-107, 1914) subspecies classification, and confirm that eastern and western populations of Musk Duck are currently isolated from each other. ?? 2010 Springer Science+Business Media B.V.

Admixture and gene flow from Russia in the recovering Northern European brown bear (Ursus arctos).

PubMed

Kopatz, Alexander; Eiken, Hans Geir; Aspi, Jouni; Kojola, Ilpo; Tobiassen, Camilla; Tirronen, Konstantin F; Danilov, Pjotr I; Hagen, Snorre B

2014-01-01

Large carnivores were persecuted to near extinction during the last centuries, but have now recovered in some countries. It has been proposed earlier that the recovery of the Northern European brown bear is supported by migration from Russia. We tested this hypothesis by obtaining for the first time continuous sampling of the whole Finnish bear population, which is located centrally between the Russian and Scandinavian bear populations. The Finnish population is assumed to experience high gene flow from Russian Karelia. If so, no or a low degree of genetic differentiation between Finnish and Russian bears could be expected. We have genotyped bears extensively from all over Finland using 12 validated microsatellite markers and compared their genetic composition to bears from Russian Karelia, Sweden, and Norway. Our fine masked investigation identified two overlapping genetic clusters structured by isolation-by-distance in Finland (pairwise FST = 0.025). One cluster included Russian bears, and migration analyses showed a high number of migrants from Russia into Finland, providing evidence of eastern gene flow as an important driver during recovery. In comparison, both clusters excluded bears from Sweden and Norway, and we found no migrants from Finland in either country, indicating that eastern gene flow was probably not important for the population recovery in Scandinavia. Our analyses on different spatial scales suggest a continuous bear population in Finland and Russian Karelia, separated from Scandinavia.

Detecting signatures of selection in nine distinct lines of broiler chickens.

PubMed

Stainton, John J; Haley, Chris S; Charlesworth, Brain; Kranis, Andreas; Watson, Kellie; Wiener, Pamela

2015-02-01

Modern commercial chickens have been bred for one of two specific purposes: meat production (broilers) or egg production (layers). This has led to large phenotypic changes, so that the genomic signatures of selection may be detectable using statistical techniques. Genetic differentiation between nine distinct broiler lines was calculated using Weir and Cockerham's pairwise FST estimator for 11 003 genome-wide markers to identify regions showing evidence of differential selection across lines. Differentiation measures were averaged into overlapping sliding windows for each line, and a permutation approach was used to determine the significance of each window. A total of 51 regions were found to show significant differentiation between the lines. Several lines were consistently found to share significant regions, suggesting that the pattern of line divergence is related to selection for broiler traits. The majority of the 51 regions contain QTL relating to broiler traits, but only five of them were found to be significantly enriched for broiler QTL, including a region on chromosome 27 containing 39 broiler QTL and 114 genes. Additionally, a number of these regions have been identified by other selection mapping studies. This study has identified a large number of potential selection signatures, and further tests with higher-density marker data may narrow these regions down to individual genes. © 2014 Stichting International Foundation for Animal Genetics.

Improved mortality of the Formosan subterranean termite by fungi, when amended with cuticle-degrading enzymes or eicosanoid biosynthesis inhibitors

USDA-ARS?s Scientific Manuscript database

Formosan subterranean termites (FST) were exposed to spores of the fungus Beauveria pseudobassiana (Bpb) strain 8046 to determine virulence of the fungus. Once Bpb was determined to cause mortality of FST it was combined with enzymes capable of degrading the insect cuticle to measure the potential ...

Alphasatellitidae: a new family with two subfamilies for the classification of geminivirus- and nanovirus-associated alphasatellites.

PubMed

Briddon, Rob W; Martin, Darren P; Roumagnac, Philippe; Navas-Castillo, Jesús; Fiallo-Olivé, Elvira; Moriones, Enrique; Lett, Jean-Michel; Zerbini, F Murilo; Varsani, Arvind

2018-05-09

Nanoviruses and geminiviruses are circular, single stranded DNA viruses that infect many plant species around the world. Nanoviruses and certain geminiviruses that belong to the Begomovirus and Mastrevirus genera are associated with additional circular, single stranded DNA molecules (~ 1-1.4 kb) that encode a replication-associated protein (Rep). These Rep-encoding satellite molecules are commonly referred to as alphasatellites and here we communicate the establishment of the family Alphasatellitidae to which these have been assigned. Within the Alphasatellitidae family two subfamilies, Geminialphasatellitinae and Nanoalphasatellitinae, have been established to respectively accommodate the geminivirus- and nanovirus-associated alphasatellites. Whereas the pairwise nucleotide sequence identity distribution of all the known geminialphasatellites (n = 628) displayed a troughs at ~ 70% and 88% pairwise identity, that of the known nanoalphasatellites (n = 54) had a troughs at ~ 67% and ~ 80% pairwise identity. We use these pairwise identity values as thresholds together with phylogenetic analyses to establish four genera and 43 species of geminialphasatellites and seven genera and 19 species of nanoalphasatellites. Furthermore, a divergent alphasatellite associated with coconut foliar decay disease is assigned to a species but not a subfamily as it likely represents a new alphasatellite subfamily that could be established once other closely related molecules are discovered.

Ensemble survival tree models to reveal pairwise interactions of variables with time-to-events outcomes in low-dimensional setting

PubMed Central

Dazard, Jean-Eudes; Ishwaran, Hemant; Mehlotra, Rajeev; Weinberg, Aaron; Zimmerman, Peter

2018-01-01

Unraveling interactions among variables such as genetic, clinical, demographic and environmental factors is essential to understand the development of common and complex diseases. To increase the power to detect such variables interactions associated with clinical time-to-events outcomes, we borrowed established concepts from random survival forest (RSF) models. We introduce a novel RSF-based pairwise interaction estimator and derive a randomization method with bootstrap confidence intervals for inferring interaction significance. Using various linear and nonlinear time-to-events survival models in simulation studies, we first show the efficiency of our approach: true pairwise interaction-effects between variables are uncovered, while they may not be accompanied with their corresponding main-effects, and may not be detected by standard semi-parametric regression modeling and test statistics used in survival analysis. Moreover, using a RSF-based cross-validation scheme for generating prediction estimators, we show that informative predictors may be inferred. We applied our approach to an HIV cohort study recording key host gene polymorphisms and their association with HIV change of tropism or AIDS progression. Altogether, this shows how linear or nonlinear pairwise statistical interactions of variables may be efficiently detected with a predictive value in observational studies with time-to-event outcomes. PMID:29453930

Detection of the pairwise kinematic Sunyaev-Zel'dovich effect with BOSS DR11 and the Atacama Cosmology Telescope

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bernardis, F. De; Aiola, S.; Vavagiakis, E. M.

Here, we present a new measurement of the kinematic Sunyaev-Zel'dovich effect using data from the Atacama Cosmology Telescope (ACT) and the Baryon Oscillation Spectroscopic Survey (BOSS). Using 600 square degrees of overlapping sky area, we evaluate the mean pairwise baryon momentum associated with the positions of 50,000 bright galaxies in the BOSS DR11 Large Scale Structure catalog. A non-zero signal arises from the large-scale motions of halos containing the sample galaxies. The data fits an analytical signal model well, with the optical depth to microwave photon scattering as a free parameter determining the overall signal amplitude. We estimate the covariancemore » matrix of the mean pairwise momentum as a function of galaxy separation, using microwave sky simulations, jackknife evaluation, and bootstrap estimates. The most conservative simulation-based errors give signal-to-noise estimates between 3.6 and 4.1 for varying galaxy luminosity cuts. We discuss how the other error determinations can lead to higher signal-to-noise values, and consider the impact of several possible systematic errors. Estimates of the optical depth from the average thermal Sunyaev-Zel'dovich signal at the sample galaxy positions are broadly consistent with those obtained from the mean pairwise momentum signal.« less

Detection of the pairwise kinematic Sunyaev-Zel'dovich effect with BOSS DR11 and the Atacama Cosmology Telescope

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bernardis, F. De; Vavagiakis, E.M.; Niemack, M.D.

We present a new measurement of the kinematic Sunyaev-Zel'dovich effect using data from the Atacama Cosmology Telescope (ACT) and the Baryon Oscillation Spectroscopic Survey (BOSS). Using 600 square degrees of overlapping sky area, we evaluate the mean pairwise baryon momentum associated with the positions of 50,000 bright galaxies in the BOSS DR11 Large Scale Structure catalog. A non-zero signal arises from the large-scale motions of halos containing the sample galaxies. The data fits an analytical signal model well, with the optical depth to microwave photon scattering as a free parameter determining the overall signal amplitude. We estimate the covariance matrixmore » of the mean pairwise momentum as a function of galaxy separation, using microwave sky simulations, jackknife evaluation, and bootstrap estimates. The most conservative simulation-based errors give signal-to-noise estimates between 3.6 and 4.1 for varying galaxy luminosity cuts. We discuss how the other error determinations can lead to higher signal-to-noise values, and consider the impact of several possible systematic errors. Estimates of the optical depth from the average thermal Sunyaev-Zel'dovich signal at the sample galaxy positions are broadly consistent with those obtained from the mean pairwise momentum signal.« less

Detection of the Pairwise Kinematic Sunyaev-Zel'dovich Effect with BOSS DR11 and the Atacama Cosmology Telescope

NASA Technical Reports Server (NTRS)

De Bernardis, F.; Aiola, S.; Vavagiakis, E. M.; Battaglia, N.; Niemack, M. D.; Beall, J.; Becker, D. T.; Bond, J. R.; Calabrese, E.; Cho, H.;

Detection of the pairwise kinematic Sunyaev-Zel'dovich effect with BOSS DR11 and the Atacama Cosmology Telescope

NASA Astrophysics Data System (ADS)

De Bernardis, F.; Aiola, S.; Vavagiakis, E. M.; Battaglia, N.; Niemack, M. D.; Beall, J.; Becker, D. T.; Bond, J. R.; Calabrese, E.; Cho, H.; Coughlin, K.; Datta, R.; Devlin, M.; Dunkley, J.; Dunner, R.; Ferraro, S.; Fox, A.; Gallardo, P. A.; Halpern, M.; Hand, N.; Hasselfield, M.; Henderson, S. W.; Hill, J. C.; Hilton, G. C.; Hilton, M.; Hincks, A. D.; Hlozek, R.; Hubmayr, J.; Huffenberger, K.; Hughes, J. P.; Irwin, K. D.; Koopman, B. J.; Kosowsky, A.; Li, D.; Louis, T.; Lungu, M.; Madhavacheril, M. S.; Maurin, L.; McMahon, J.; Moodley, K.; Naess, S.; Nati, F.; Newburgh, L.; Nibarger, J. P.; Page, L. A.; Partridge, B.; Schaan, E.; Schmitt, B. L.; Sehgal, N.; Sievers, J.; Simon, S. M.; Spergel, D. N.; Staggs, S. T.; Stevens, J. R.; Thornton, R. J.; van Engelen, A.; Van Lanen, J.; Wollack, E. J.

2017-03-01

We present a new measurement of the kinematic Sunyaev-Zel'dovich effect using data from the Atacama Cosmology Telescope (ACT) and the Baryon Oscillation Spectroscopic Survey (BOSS). Using 600 square degrees of overlapping sky area, we evaluate the mean pairwise baryon momentum associated with the positions of 50,000 bright galaxies in the BOSS DR11 Large Scale Structure catalog. A non-zero signal arises from the large-scale motions of halos containing the sample galaxies. The data fits an analytical signal model well, with the optical depth to microwave photon scattering as a free parameter determining the overall signal amplitude. We estimate the covariance matrix of the mean pairwise momentum as a function of galaxy separation, using microwave sky simulations, jackknife evaluation, and bootstrap estimates. The most conservative simulation-based errors give signal-to-noise estimates between 3.6 and 4.1 for varying galaxy luminosity cuts. We discuss how the other error determinations can lead to higher signal-to-noise values, and consider the impact of several possible systematic errors. Estimates of the optical depth from the average thermal Sunyaev-Zel'dovich signal at the sample galaxy positions are broadly consistent with those obtained from the mean pairwise momentum signal.

Ensemble survival tree models to reveal pairwise interactions of variables with time-to-events outcomes in low-dimensional setting.

PubMed

Dazard, Jean-Eudes; Ishwaran, Hemant; Mehlotra, Rajeev; Weinberg, Aaron; Zimmerman, Peter

2018-02-17

Unraveling interactions among variables such as genetic, clinical, demographic and environmental factors is essential to understand the development of common and complex diseases. To increase the power to detect such variables interactions associated with clinical time-to-events outcomes, we borrowed established concepts from random survival forest (RSF) models. We introduce a novel RSF-based pairwise interaction estimator and derive a randomization method with bootstrap confidence intervals for inferring interaction significance. Using various linear and nonlinear time-to-events survival models in simulation studies, we first show the efficiency of our approach: true pairwise interaction-effects between variables are uncovered, while they may not be accompanied with their corresponding main-effects, and may not be detected by standard semi-parametric regression modeling and test statistics used in survival analysis. Moreover, using a RSF-based cross-validation scheme for generating prediction estimators, we show that informative predictors may be inferred. We applied our approach to an HIV cohort study recording key host gene polymorphisms and their association with HIV change of tropism or AIDS progression. Altogether, this shows how linear or nonlinear pairwise statistical interactions of variables may be efficiently detected with a predictive value in observational studies with time-to-event outcomes.

Detection of the pairwise kinematic Sunyaev-Zel'dovich effect with BOSS DR11 and the Atacama Cosmology Telescope

DOE PAGES

Bernardis, F. De; Aiola, S.; Vavagiakis, E. M.; ...

2017-03-07

Here, we present a new measurement of the kinematic Sunyaev-Zel'dovich effect using data from the Atacama Cosmology Telescope (ACT) and the Baryon Oscillation Spectroscopic Survey (BOSS). Using 600 square degrees of overlapping sky area, we evaluate the mean pairwise baryon momentum associated with the positions of 50,000 bright galaxies in the BOSS DR11 Large Scale Structure catalog. A non-zero signal arises from the large-scale motions of halos containing the sample galaxies. The data fits an analytical signal model well, with the optical depth to microwave photon scattering as a free parameter determining the overall signal amplitude. We estimate the covariancemore » matrix of the mean pairwise momentum as a function of galaxy separation, using microwave sky simulations, jackknife evaluation, and bootstrap estimates. The most conservative simulation-based errors give signal-to-noise estimates between 3.6 and 4.1 for varying galaxy luminosity cuts. We discuss how the other error determinations can lead to higher signal-to-noise values, and consider the impact of several possible systematic errors. Estimates of the optical depth from the average thermal Sunyaev-Zel'dovich signal at the sample galaxy positions are broadly consistent with those obtained from the mean pairwise momentum signal.« less

Scale dependence in species turnover reflects variance in species occupancy.

PubMed

McGlinn, Daniel J; Hurlbert, Allen H

2012-02-01

Patterns of species turnover may reflect the processes driving community dynamics across scales. While the majority of studies on species turnover have examined pairwise comparison metrics (e.g., the average Jaccard dissimilarity), it has been proposed that the species-area relationship (SAR) also offers insight into patterns of species turnover because these two patterns may be analytically linked. However, these previous links only apply in a special case where turnover is scale invariant, and we demonstrate across three different plant communities that over 90% of the pairwise turnover values are larger than expected based on scale-invariant predictions from the SAR. Furthermore, the degree of scale dependence in turnover was negatively related to the degree of variance in the occupancy frequency distribution (OFD). These findings suggest that species turnover diverges from scale invariance, and as such pairwise turnover and the slope of the SAR are not redundant. Furthermore, models developed to explain the OFD should be linked with those developed to explain species turnover to achieve a more unified understanding of community structure.

Population genomic structure and linkage disequilibrium analysis of South African goat breeds using genome-wide SNP data.

PubMed

Mdladla, K; Dzomba, E F; Huson, H J; Muchadeyi, F C

2016-08-01

The sustainability of goat farming in marginal areas of southern Africa depends on local breeds that are adapted to specific agro-ecological conditions. Unimproved non-descript goats are the main genetic resources used for the development of commercial meat-type breeds of South Africa. Little is known about genetic diversity and the genetics of adaptation of these indigenous goat populations. This study investigated the genetic diversity, population structure and breed relations, linkage disequilibrium, effective population size and persistence of gametic phase in goat populations of South Africa. Three locally developed meat-type breeds of the Boer (n = 33), Savanna (n = 31), Kalahari Red (n = 40), a feral breed of Tankwa (n = 25) and unimproved non-descript village ecotypes (n = 110) from four goat-producing provinces of the Eastern Cape, KwaZulu-Natal, Limpopo and North West were assessed using the Illumina Goat 50K SNP Bead Chip assay. The proportion of SNPs with minor allele frequencies >0.05 ranged from 84.22% in the Tankwa to 97.58% in the Xhosa ecotype, with a mean of 0.32 ± 0.13 across populations. Principal components analysis, admixture and pairwise FST identified Tankwa as a genetically distinct population and supported clustering of the populations according to their historical origins. Genome-wide FST identified 101 markers potentially under positive selection in the Tankwa. Average linkage disequilibrium was highest in the Tankwa (r(2)  = 0.25 ± 0.26) and lowest in the village ecotypes (r(2) range = 0.09 ± 0.12 to 0.11 ± 0.14). We observed an effective population size of <150 for all populations 13 generations ago. The estimated correlations for all breed pairs were lower than 0.80 at marker distances >100 kb with the exception of those in Savanna and Tswana populations. This study highlights the high level of genetic diversity in South African indigenous goats as well as the utility of the genome-wide SNP marker panels in genetic studies of these populations. © 2016 Stichting International Foundation for Animal Genetics.

Genomic single-nucleotide polymorphisms confirm that Gunnison and Greater sage-grouse are genetically well differentiated and that the Bi-State population is distinct

USGS Publications Warehouse

Oyler-McCance, Sara J.; Cornman, Robert S.; Jones, Kenneth L.; Fike, Jennifer

2015-01-01

Sage-grouse are iconic, declining inhabitants of sagebrush habitats in western North America, and their management depends on an understanding of genetic variation across the landscape. Two distinct species of sage-grouse have been recognized, Greater (Centrocercus urophasianus) and Gunnison sage-grouse (C. minimus), based on morphology, behavior, and variation at neutral genetic markers. A parapatric group of Greater Sage-Grouse along the border of California and Nevada ("Bi-State") is also genetically distinct at the same neutral genetic markers, yet not different in behavior or morphology. Because delineating taxonomic boundaries and defining conservation units is often difficult in recently diverged taxa and can be further complicated by highly skewed mating systems, we took advantage of new genomic methods that improve our ability to characterize genetic variation at a much finer resolution. We identified thousands of single-nucleotide polymorphisms (SNPs) among Gunnison, Greater, and Bi-State sage-grouse and used them to comprehensively examine levels of genetic diversity and differentiation among these groups. The pairwise multilocus fixation index (FST) was high (0.49) between Gunnison and Greater sage-grouse, and both principal coordinates analysis and model-based clustering grouped samples unequivocally by species. Standing genetic variation was lower within the Gunnison Sage-Grouse. The Bi-State population was also significantly differentiated from Greater Sage-Grouse, albeit more weakly (FST = 0.09), and genetic clustering results were consistent with reduced gene flow with Greater Sage-Grouse. No comparable genetic divisions were found within the Greater Sage-Grouse sample, which spanned the southern half of the range. Thus, we provide much stronger genetic evidence supporting the recognition of Gunnison Sage-Grouse as a distinct species with low genetic diversity. Further, our work confirms that the Bi-State population is differentiated from other Greater Sage-Grouse. The level of differentiation is much less than the divergence between Greater and Gunnison sage-grouse, supporting the idea that the Bi-State represents a unique population within the Greater Sage-Grouse. New genomic methods like the restriction-site-associated DNA (RAD-tag) method used here illustrate how increasing the number of markers and coverage of the genome can better characterize patterns of genetic variation, particularly among recently diverged taxa, providing vital information for conservation and management.

From micro-correlations to macro-correlations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eliazar, Iddo, E-mail: iddo.eliazar@intel.com

2016-11-15

Random vectors with a symmetric correlation structure share a common value of pair-wise correlation between their different components. The symmetric correlation structure appears in a multitude of settings, e.g. mixture models. In a mixture model the components of the random vector are drawn independently from a general probability distribution that is determined by an underlying parameter, and the parameter itself is randomized. In this paper we study the overall correlation of high-dimensional random vectors with a symmetric correlation structure. Considering such a random vector, and terming its pair-wise correlation “micro-correlation”, we use an asymptotic analysis to derive the random vector’smore » “macro-correlation” : a score that takes values in the unit interval, and that quantifies the random vector’s overall correlation. The method of obtaining macro-correlations from micro-correlations is then applied to a diverse collection of frameworks that demonstrate the method’s wide applicability.« less

Calibration of Smartphone-Based Weather Measurements Using Pairwise Gossip.

PubMed

Zamora, Jane Louie Fresco; Kashihara, Shigeru; Yamaguchi, Suguru

2015-01-01

Accurate and reliable daily global weather reports are necessary for weather forecasting and climate analysis. However, the availability of these reports continues to decline due to the lack of economic support and policies in maintaining ground weather measurement systems from where these reports are obtained. Thus, to mitigate data scarcity, it is required to utilize weather information from existing sensors and built-in smartphone sensors. However, as smartphone usage often varies according to human activity, it is difficult to obtain accurate measurement data. In this paper, we present a heuristic-based pairwise gossip algorithm that will calibrate smartphone-based pressure sensors with respect to fixed weather stations as our referential ground truth. Based on actual measurements, we have verified that smartphone-based readings are unstable when observed during movement. Using our calibration algorithm on actual smartphone-based pressure readings, the updated values were significantly closer to the ground truth values.

Calibration of Smartphone-Based Weather Measurements Using Pairwise Gossip

PubMed Central

Yamaguchi, Suguru

2015-01-01

Accurate and reliable daily global weather reports are necessary for weather forecasting and climate analysis. However, the availability of these reports continues to decline due to the lack of economic support and policies in maintaining ground weather measurement systems from where these reports are obtained. Thus, to mitigate data scarcity, it is required to utilize weather information from existing sensors and built-in smartphone sensors. However, as smartphone usage often varies according to human activity, it is difficult to obtain accurate measurement data. In this paper, we present a heuristic-based pairwise gossip algorithm that will calibrate smartphone-based pressure sensors with respect to fixed weather stations as our referential ground truth. Based on actual measurements, we have verified that smartphone-based readings are unstable when observed during movement. Using our calibration algorithm on actual smartphone-based pressure readings, the updated values were significantly closer to the ground truth values. PMID:26421312

Dynamical pairwise entanglement and two-point correlations in the three-ligand spin-star structure

NASA Astrophysics Data System (ADS)

Motamedifar, M.

2017-10-01

We consider the three-ligand spin-star structure through homogeneous Heisenberg interactions (XXX-3LSSS) in the framework of dynamical pairwise entanglement. It is shown that the time evolution of the central qubit ;one-particle; state (COPS) brings about the generation of quantum W states at periodical time instants. On the contrary, W states cannot be generated from the time evolution of a ligand ;one-particle; state (LOPS). We also investigate the dynamical behavior of two-point quantum correlations as well as the expectation values of the different spin-components for each element in the XXX-3LSSS. It is found that when a W state is generated, the same value of the concurrence between any two arbitrary qubits arises from the xx and yy two-point quantum correlations. On the opposite, zz quantum correlation between any two qubits vanishes at these time instants.

Reduction in the latency of action of antidepressants by 17 beta-estradiol in the forced swimming test.

PubMed

Estrada-Camarena, E; Rivera, N M Vega; Berlanga, C; Fernández-Guasti, A

2008-12-01

Antidepressants (ADs) are slow to produce their therapeutic effect. This long latency promotes the development of new strategies to short their onset of action. Previous reports indicated that 17beta-estradiol (E(2)) promotes the antidepressant-like activity of fluoxetine (FLX) and desipramine (DMI) in the forced swimming test (FST). The aim of the present work was to analyze if E(2) reduces the antidepressant-like onset of action of venlafaxine (VLX), FLX, and DMI. Independent groups of ovariectomized female Wistar rats were tested in the FST and in the open field after chronic (1 to 14 days) treatment with VLX (20 mg/kg/day), FLX (1.25 mg/kg/day), or DMI (1.25 mg/kg/day) alone or in combination with a single injection of E(2) (2.5 microg/rat sc, 8 h before FST). VLX, FLX, or DMI by themselves at these doses did not induce changes in the FST at short intervals after their injection (from 1 to 7 days). The addition of E(2) promoted the antidepressant-like effect of VLX and DMI as early as day 1. Such action was also evident after 3, for FLX, and 14 days for both FLX and DMI, but not for VLX. The behavioral actions of these ADs combined with E(2) were not accompanied by increases in general activity in the open-field test. E(2) clearly reduced the latency to the onset of action for these ADs in the FST. These results represent an interesting therapeutic strategy for the treatment of depression in perimenopausal women.

The effect of nitrazepam on depression and curiosity in behavioral tests in mice: The role of potassium channels.

PubMed

Nikoui, Vahid; Ostadhadi, Sattar; Azhand, Pardis; Zolfaghari, Samira; Amiri, Shayan; Foroohandeh, Mehrdad; Motevalian, Manijeh; Sharifi, Ali Mohammad; Bakhtiarian, Azam

2016-11-15

Evidence show that gamma-aminobutyric acid (GABA) receptors are involved in depression, so the aim of this study was to investigate the effect of nitrazepam as agonist of GABA A receptors on depression and curiosity in male mice and the role of potassium channel in antidepressant-like response. For this purpose, we studied the antidepressant-like properties of fluoxetine, nitrazepam, glibenclamide, and cromakalim by both forced swimming test (FST) and tail suspension test (TST). Animals were injected by various doses of nitrazepam (0.05, 0.1, and 0.5mg/kg). Nitrazepam at dose of 0.5mg/kg significantly decreased the immobility time compared to control group in both FST and TST. Fluoxetine also showed such a response. Co-administration of nitrazepam (0.05mg/kg) with glibenclamide in TST (1mg/kg) and in FST (0.3, 1mg/kg) also showed antidepressant-like response. Beside, cromakalim (0.1mg/kg) could reverse the antidepressant-like effect of nitrazepam (0.5mg/kg) in both FST and TST, while cromakalim and glibenclamide alone could not change the immobility time compared to control group (P>0.05). The hole-board test revealed that nitrazepam at doses of 0.5 and 0.1mg/kg could increase the activity of the animal's head-dipping and boost the curiosity and exploration behavior of mice. The results of this study revealed that nitrazepam may possess antidepressant-like properties and this effect is dependent to potassium channels in both FST and TST. Copyright © 2016 Elsevier B.V. All rights reserved.

Antidepressant-like behavioral effects of impaired cannabinoid receptor type 1 signaling coincide with exaggerated corticosterone secretion in mice

PubMed Central

Steiner, Michel A; Marsicano, Giovanni; Nestler, Eric J; Holsboer, Florian; Lutz, Beat; Wotjak, Carsten T

2008-01-01

Summary Hypothalamic-pituitary-adrenocortical (HPA) axis hyperactivity is associated with major depressive disorders, and treatment with classical antidepressants ameliorates not only psychopathological symptoms, but also the dysregulation of the HPA axis. Here, we further elucidated the role of impaired cannabinoid type 1 (CB1) receptor signaling for neuroendocrine and behavioral stress coping in the mouse forced swim test (FST). We demonstrate that the genetic inactivation of CB1 is accompanied by increased plasma corticosterone levels both under basal conditions and at different time points following exposure to the FST. The latter effect could be mimicked in C57BL/6N mice by acute, subchronic and chronic administration of the selective CB1 antagonist SR141716. Further experiments confirmed the specificity of corticosterone-elevating SR141716 actions for CB1 in CB1-deficient mice. Subchronic and chronic pharmacological blockade of CB1, but not its genetic deletion, induced antidepressant-like behavioral responses in the FST that were characterized by decreased floating and/or increased struggling behavior. The antidepressant-like behavioral effects of acute desipramine treatment in the FST were absent in CB1-deficient mice, but the dampening effects of desipramine on FST stress-induced corticosterone secretion were not compromised by CB1-deficiency. However, antidepressant-like behavioral desipramine effects were intact in C57BL/6N mice pre-treated with SR141716, indicating potential developmental deficits in CB1-deficient mice. We conclude that pharmacological blockade of CB1 signaling shares antidepressant-like behavioral effects with desipramine, but reveals opposite effects on HPA axis activity. PMID:17976922

Passive Response to Stress in Adolescent Female and Adult Male Mice after Intermittent Nicotine Exposure in Adolescence

PubMed Central

Thanos, Panayotis; Delis, Foteini; Rosko, Lauren; Volkow, Nora D

2013-01-01

Smoking is frequently co-morbid with depression. Although it is recognized that depression increases the risk for smoking, it is unclear if early smoking exposure may increase the risk for depression. To test this possibility we assessed the effects of adolescent nicotine exposure on the Forced Swim Test (FST), which is used as a measure of passive coping, and depressive-like behavior in rodents, and on the open field test (OFT), which is used as a measure of locomotion and exploratory behavior. Male and female mice received daily saline or nicotine (0.3 or 0.6 mg/kg) injections from postnatal day (PD) 30 to PD 44. FST and OFT were performed either 1 or 30 days after the last injection (PD 45 and PD 74, respectively). In females, treatment with 0.3 mg/kg nicotine lead to increased FST immobility (64%) and decreased OFT locomotor activity (12%) one day following the last nicotine injection (PD 45); while no effects were observed in adulthood (PD 74). In contrast, on PD45, nicotine treatment did not change the male FST immobility but lead to lower OFT locomotor activity (0.6 mg/kg, 10%). In adulthood (PD 74), both nicotine doses lead to higher FST immobility (87%) in males while 0.6 mg/kg nicotine to lower OFT locomotor activity (13%). The results (i) identify females as more vulnerable to the immediate withdrawal that follows nicotine discontinuation in adolescence and (ii) suggest that adolescent nicotine exposure may enhance the risk for passive response towards unavoidable stress in adult males. PMID:24619539

Mifepristone Decreases Depression-Like Behavior and Modulates Neuroendocrine and Central Hypothalamic-Pituitary-Adrenocortical Axis Responsiveness to Stress

PubMed Central

Wulsin, Aynara C.; Herman, James P.; Solomon, Matia B.

2010-01-01

Summary Glucocorticoid dyshomeostasis is observed in a proportion of depressed individuals. As a result, glucocorticoid receptor (GR) antagonists are currently being tested as potential anti-depressants. The current study was designed to test the efficacy of mifepristone, a GR antagonist, in mitigating behavioral, neuroendocrine and central nervous system (CNS) responses to an acute stressor. Adult male rats were treated for five days with mifepristone (10 mg/kg) and then exposed to the forced swim test (FST). Treatment with mifepristone decreased immobility and increased swimming (but not climbing) behavior in the FST, consistent with antidepressant action. In addition, mifepristone dampened the ACTH response to FST exposure. In the CNS, mifepristone increased c-Fos expression in all subdivisions of the medial prefrontal cortex (mPFC) and decreased neuronal activity in some subdivisions of the hippocampus including the CA2, CA3, and hilus region of the dentate gyrus in animals exposed to FST. In contrast, mifepristone increased neuronal activity in the ventral subiculum (output region of the hippocampus) and decreased c-Fos expression in the central amygdala (CeA) in animals exposed to FST. These data suggest that antidepressant efficacy and perhaps HPA dampening properties of RU486 are related to alterations in key limbic circuits mediating CNS stress responses, resulting in enhanced stress inhibition (via the mPFC and ventral subiculum) as well as decreased stress excitation (central amygdala). Overall the data suggest that drugs targeting the glucocorticoid receptor may ameliorate stress dysfunction associated with depressive illness. PMID:20149549

How Personal Constructs about "Professional Identity" Might Act as a Barrier to Multi-Agency Working

ERIC Educational Resources Information Center

Hymans, Michael

2008-01-01

This paper describes a research study that examines how professionals in a multi-agency Family Support Team (FST) construe their role and the role of the team. The team comprised social workers, assistant social workers, a family therapist, a clinical psychologist and an educational psychologist. The aims of the FST included promoting better…

Absence of population genetic structure in Heterakis gallinarum of chicken from Sichuan, inferred from mitochondrial cytochrome c oxidase subunit I gene.

PubMed

Gu, Xiaobin; Zhu, Jun-Yang; Jian, Ke-Ling; Wang, Bao-Jian; Peng, Xue-Rong; Yang, Guang-You; Wang, Tao; Zhong, Zhi-Jun; Peng, Ke-Yun

2016-09-01

Population genetics information provides a foundation for understanding the transmission and epidemiology of parasite and, therefore, may be used to assist in the control of parasitosis. However, limited available sequence information in Heterakis gallinarum has greatly impeded the study in this area. In this study, we first investigated the genetic variability and genetic structure of H. gallinarum. The 1325 bp fragments of the mitochondrial COX1 gene were amplified in 56 isolates of H. gallinarum from seven different geographical regions in Sichuan province, China. The 56 sequences were classified into 22 haplotypes (H1-H22). The values of haplotype diversity (0.712) and nucleotide diversity (0.00158) in Sichuan population indicate a rapid expansion occurred from a relatively small, short-term effective population in the past. The haplotype network formed a distribution around H1 in a star-like topology, and the haplotypes did not cluster according to their geographical location. Similar conclusions could be made from MP phylogenetic tree. The Fst value (Fst<0.16965) and AMOVA analysis revealed that no significant genetic differentiation was observed among the seven different geographical populations. Neutrality tests (Tajima's D and Fu's Fs) and mismatch analysis indicated that H. gallinarum experienced a population expansion in the past. Our results indicated that H. gallinarum experienced a rapid population expansion in the past, and there was a low genetic diversity and an absence of population structure across the population.

Comparison of Three Screening Test Kits for G6PD Enzyme Deficiency: Implications for Its Use in the Radical Cure of Vivax Malaria in Remote and Resource-Poor Areas in the Philippines.

PubMed

Espino, Fe Esperanza; Bibit, Jo-Anne; Sornillo, Johanna Beulah; Tan, Alvin; von Seidlein, Lorenz; Ley, Benedikt

2016-01-01

We evaluated a battery of Glucose-6-Phosphate Dehydrogenase diagnostic point-of-care tests (PoC) to assess the most suitable product in terms of performance and operational characteristics for remote areas. Samples were collected in Puerto Princesa City, Palawan, Philippines and tested for G6PD deficiency with a fluorescent spot test (FST; Procedure 203, Trinity Biotech, Ireland), the semiquantitative WST8/1-methoxy PMS (WST; Dojindo, Japan) and the Carestart G6PD Rapid Diagnostic Test (CSG; AccessBio, USA). Results were compared to spectrophotometry (Procedure 345, Trinity Biotech, Ireland). Sensitivity and specificity were calculated for each test with cut-off activities of 10%, 20%, 30% and 60% of the adjusted male median. The adjusted male median was 270.5 IU/10(12) RBC. FST and WST were tested on 621 capillary blood samples, the CSG was tested on venous and capillary blood on 302 samples. At 30% G6PD activity, sensitivity for the FST was between 87.7% (95%CI: 76.8% to 93.9%) and 96.5% (95%CI: 87.9% to 99.5%) depending on definition of intermediate results; the WST was 84.2% (95%CI: 72.1% to 92.5%); and the CSG was between 68.8% (95%CI: 41.3% to 89.0%) and 93.8% (95%CI: 69.8% to 99.8%) when the test was performed on capillary or venous blood respectively. Sensitivity of FST and CSG (tested with venous blood) were comparable (p>0.05). The analysis of venous blood samples by the CSG yielded significantly higher results than FST and CSG performed on capillary blood (p<0.05). Sensitivity of the CSG varied depending on source of blood used (p<0.05). The operational characteristics of the CSG were superior to all other test formats. Performance and operational characteristics of the CSG performed on venous blood suggest the test to be a good alternative to the FST.

Comparison of Three Screening Test Kits for G6PD Enzyme Deficiency: Implications for Its Use in the Radical Cure of Vivax Malaria in Remote and Resource-Poor Areas in the Philippines

PubMed Central

Espino, Fe Esperanza; Sornillo, Johanna Beulah; Tan, Alvin; von Seidlein, Lorenz

2016-01-01

Objective We evaluated a battery of Glucose-6-Phosphate Dehydrogenase diagnostic point-of-care tests (PoC) to assess the most suitable product in terms of performance and operational characteristics for remote areas. Methods Samples were collected in Puerto Princesa City, Palawan, Philippines and tested for G6PD deficiency with a fluorescent spot test (FST; Procedure 203, Trinity Biotech, Ireland), the semiquantitative WST8/1-methoxy PMS (WST; Dojindo, Japan) and the Carestart G6PD Rapid Diagnostic Test (CSG; AccessBio, USA). Results were compared to spectrophotometry (Procedure 345, Trinity Biotech, Ireland). Sensitivity and specificity were calculated for each test with cut-off activities of 10%, 20%, 30% and 60% of the adjusted male median. Results The adjusted male median was 270.5 IU/1012 RBC. FST and WST were tested on 621 capillary blood samples, the CSG was tested on venous and capillary blood on 302 samples. At 30% G6PD activity, sensitivity for the FST was between 87.7% (95%CI: 76.8% to 93.9%) and 96.5% (95%CI: 87.9% to 99.5%) depending on definition of intermediate results; the WST was 84.2% (95%CI: 72.1% to 92.5%); and the CSG was between 68.8% (95%CI: 41.3% to 89.0%) and 93.8% (95%CI: 69.8% to 99.8%) when the test was performed on capillary or venous blood respectively. Sensitivity of FST and CSG (tested with venous blood) were comparable (p>0.05). The analysis of venous blood samples by the CSG yielded significantly higher results than FST and CSG performed on capillary blood (p<0.05). Sensitivity of the CSG varied depending on source of blood used (p<0.05). Conclusion The operational characteristics of the CSG were superior to all other test formats. Performance and operational characteristics of the CSG performed on venous blood suggest the test to be a good alternative to the FST. PMID:26849445

The genetic structure of a relict population of wood frogs

USGS Publications Warehouse

Scherer, Rick; Muths, Erin; Noon, Barry; Oyler-McCance, Sara

2012-01-01

Habitat fragmentation and the associated reduction in connectivity between habitat patches are commonly cited causes of genetic differentiation and reduced genetic variation in animal populations. We used eight microsatellite markers to investigate genetic structure and levels of genetic diversity in a relict population of wood frogs (Lithobates sylvatica) in Rocky Mountain National Park, Colorado, where recent disturbances have altered hydrologic processes and fragmented amphibian habitat. We also estimated migration rates among subpopulations, tested for a pattern of isolation-by-distance, and looked for evidence of a recent population bottleneck. The results from the clustering algorithm in Program STRUCTURE indicated the population is partitioned into two genetic clusters (subpopulations), and this result was further supported by factorial component analysis. In addition, an estimate of FST (FST = 0.0675, P value \\0.0001) supported the genetic differentiation of the two clusters. Estimates of migration rates among the two subpopulations were low, as were estimates of genetic variability. Conservation of the population of wood frogs may be improved by increasing the spatial distribution of the population and improving gene flow between the subpopulations. Construction or restoration of wetlands in the landscape between the clusters has the potential to address each of these objectives.

Variable continental distribution of polymorphisms in the coding regions of DNA-repair genes.

PubMed

Mathonnet, Géraldine; Labuda, Damian; Meloche, Caroline; Wambach, Tina; Krajinovic, Maja; Sinnett, Daniel

2003-01-01

DNA-repair pathways are critical for maintaining the integrity of the genetic material by protecting against mutations due to exposure-induced damages or replication errors. Polymorphisms in the corresponding genes may be relevant in genetic epidemiology by modifying individual cancer susceptibility or therapeutic response. We report data on the population distribution of potentially functional variants in XRCC1, APEX1, ERCC2, ERCC4, hMLH1, and hMSH3 genes among groups representing individuals of European, Middle Eastern, African, Southeast Asian and North American descent. The data indicate little interpopulation differentiation in some of these polymorphisms and typical FST values ranging from 10 to 17% at others. Low FST was observed in APEX1 and hMSH3 exon 23 in spite of their relatively high minor allele frequencies, which could suggest the effect of balancing selection. In XRCC1, hMSH3 exon 21 and hMLH1 Africa clusters either with Middle East and Europe or with Southeast Asia, which could be related to the demographic history of human populations, whereby human migrations and genetic drift rather than selection would account for the observed differences.

Evaluation of antidepressant like activity of curcumin and its combination with fluoxetine and imipramine: an acute and chronic study.

PubMed

Sanmukhani, Jayesh; Anovadiya, Ashish; Tripathi, Chandrabhanu B

2011-01-01

Curcumin is the active ingredient of commonly used spice Curuma longa Linn. In the present study, the antidepressant like activity of curcumin and its combination with fluoxetine and imipramine was studied in acute model (three doses 24, 5 and 1 h before test) of forced swimming test (FST) in glass jar and tail suspension test (TST) in mice and in chronic model (14 day study) of FST with water wheel in rats. All the tests were carried out in the following seven groups (n = 6 in each group), drugs being given orally (doses for mice): Group 1 (vehicle), group 2 (curcumin 50 mg/kg), group 3 (curcumin 100 mg/kg), group 4 (fluoxetine 20 mg/kg), group 5 (imipramine 15 mg/kg), group 6 (curcumin 100 mg/kg plus fluoxetine 20 mg/kg) and group 7 (curcumin 100 mg/kg plus imipramine 15 mg/kg). Equivalent doses for rats were used. Both the acute model of FST and TST, and the chronic model of FST with water wheel showed significant antidepressant like activity of curcumin in 100 mg/kg dose as compared to vehicle control (p < 0.05). The effect of curcumin (100 mg/kg) was similar to that of fluoxetine and imipramine (p > 0.05) but its addition to fluoxetine and imipramine did not improve their antidepressant activity (p > 0.05). Curcumin increased both the swimming and climbing behavior in FST, thus its antidepressant like activity could be due to an increase in serotonin, norepinephrine and dopamine levels in the brain. Curcumin can be a useful antidepressant especially in cases which respond to drugs having mixed effects on serotonin and catecholamines levels in the brain.

Effect of sub-optimal doses of fluoxetine plus estradiol on antidepressant-like behavior and hippocampal neurogenesis in ovariectomized rats.

PubMed

Vega-Rivera, Nelly M; Fernández-Guasti, Alonso; Ramírez-Rodríguez, Gerardo; Estrada-Camarena, Erika

2015-07-01

Estrogens and antidepressants synergize to reduce depressive symptoms and stimulate neurogenesis and neuroplastic events. The aim of this study was to explore whether the antidepressant-like effect induced by the combination of low doses of estradiol (E2) and fluoxetine (FLX) involves changes in cell proliferation, early survival, morphology and dendrite complexity of hippocampal new-immature neurons. The antidepressant-like effects of E2 and/or FLX were evaluated by the forced swimming test (FST), cell proliferation was determined with the endogenous marker Ki67, survival of newborn cells was established with bromo-deoxiuridine (BrdU) and immature neurons were ascertained by doublecortin (DCX) labeling while their dendrite complexity was evaluated with Sholl analysis. Ovariectomized Wistar rats were randomly assigned to one of the following groups: Vehicle (saline/14 days+Oil/-8h before FST); E2 (saline/14 days + E2 2.5 or 10 μg/rat; -8 h before FST); FLX (1.25 or 10 mg/kg for 14 days + oil -8h before FST), and FLX plus E2 (FLX 1.25 mg/kg for 14 days + E2 2.5 μg/rat -8 h before FST). The combination of sub-threshold doses of FLX plus E2 produced antidepressant-like actions similar to those induced by FLX or E2 given independently at optimal doses. Only FLX at an optimal dose and the combination of FLX plus E2 increased cell proliferation, the number of DCX-labeled immature neurons and the complexity of their dendritic tree, suggesting that these events may be responsible for their antidepressant-like effect. Copyright © 2015 Elsevier Ltd. All rights reserved.

Effects of prolonged ethanol vapor exposure on forced swim behavior, and neuropeptide Y and corticotropin-releasing factor levels in rat brains.

PubMed

Walker, Brendan M; Drimmer, David A; Walker, Jennifer L; Liu, Tianmin; Mathé, Aleksander A; Ehlers, Cindy L

2010-09-01

Depressive symptoms in alcohol-dependent individuals are well-recognized and clinically relevant phenomena. The etiology has not been elucidated although it is clear that the depressive symptoms may be alcohol independent or alcohol induced. To contribute to the understanding of the neurobiology of chronic ethanol use, we investigated the effects of chronic intermittent ethanol vapor exposure on behaviors in the forced swim test (FST) and neuropeptide Y (NPY) and corticotropin-releasing factor (CRF) levels in specific brain regions. Adult male Wistar rats were subjected to intermittent ethanol vapor (14 h on/10 h off) or air exposure for 2 weeks and were then tested at three time points corresponding to acute withdrawal (8-12 h into withdrawal) and protracted withdrawal (30 and 60 days of withdrawal) in the FST. The behaviors that were measured in the five-min FST consisted of latency to immobility, swim time, immobility time, and climbing time. The FST results showed that the vapor-exposed animals displayed depressive-like behaviors; for instance, decreased latency to immobility in acute withdrawal and decreased latency to immobility, decreased swim time and increased immobility time in protracted withdrawal, with differences between air- and vapor-exposed animals becoming more pronounced over the 60-day withdrawal period. NPY levels in the frontal cortex of the vapor-exposed animals were decreased compared with the control animals, and CRF levels in the amygdala were correlated with increased immobility time. Thus, extended ethanol vapor exposure produced long-lasting changes in FST behavior and NPY levels in the brain. Copyright © 2010 Elsevier Inc. All rights reserved.

Effects of co-administration of fluoxetine and risperidone on properties of peritoneal and pleural macrophages in rats subjected to the forced swimming test.

PubMed

Roman, Adam; Kuśmierczyk, Justyna; Klimek, Ewa; Rogóż, Zofia; Nalepa, Irena

2012-01-01

Literature data show that administration of atypical antipsychotic drug, risperidone (RIS), enhances antidepressive action of fluoxetine (FLU). As antidepressive treatments also regulate immune functions, we examined whether combined administration of FLU and RIS to rats subsequently subjected to a forced swimming test (FST) modifies parameters of macrophage activity that are directly related to their immunomodulatory functions, i.e., arginase (ARG) activity and nitric oxide (NO) synthesis. Antidepressive action of the drugs was assessed with FST. Peritoneal and pleural cells were eluted and selected parameters of immunoreactivity were assessed colorimetrically. We found that the concomitant administration of FLU (10 mg/kg) and RIS (0.1 mg/kg) produced antidepressive-like effects in the FST,whereas the drugs were ineffective if administered separately. Stress related to the FST affected immune cell redistribution and changed some of the metabolic and immunomodulatory properties of macrophages. FLU administered to rats at a suboptimal dose for antidepressive action potently influenced macrophage immunomodulatory properties and redirected their activity toward anti-inflammatory M2 functional phenotype, as manifested by changes in the ARG/NO ratio. These effects resulted from a direct cellular influence of the drug, as well as its action via neuroendocrine pathways, as evidenced in peritoneal and pleural cells. Addition of RIS did not augment immunomodulatory action of FLU, though the combination showed antidepressant-like activity in the FST. Our results suggest that when the drugs were administered together, FLU was potent enough to redirect macrophages toward M2 activity. It is also postulated that drug-induced changes in the immune system are not so closely related to antidepressant-like effects or might be secondary to those produced in the neuroendocrine system.

Antidepressant effects of the water extract from Taraxacum officinale leaves and roots in mice.

PubMed

Li, Yu-Cheng; Shen, Ji-Duo; Li, Yang-Yang; Huang, Qi

2014-08-01

The leaves and roots of the Taraxacum officinale F. (Asteraceae) is widely used as traditional medicinal herb in Eastern Asian countries. In the present study, the antidepressant-like effects of the water extract of T. officinale (WETO) leaves and roots were investigated in mice using forced swimming test (FST), tail suspension test (TST) and open field test (OFT). Effects of acute (1-day) and chronic treatments (14-days) with WETO (50, 100 and 200 mg/kg) on the behavioral changes in FST, TST and OFT, and the serum corticotrophin releasing factor (CRF), adrenocorticotropic hormone (ACTH) and corticosterone concentration were assessed in mice. Chronic treatment (14-days) with WETO at the doses of 50, 100 and 200 mg/kg significantly decreased the immobility time in both FST (92.6, 85.1 and 77.4 s) and TST (84.8, 72.1 and 56.9 s). Acute treatment (1-day) with WETO at a dose of 200 mg/kg also markedly decreased the immobility time in both FST (81.7 s) and TST (73.2 s). However, all treatments did not affect the locomotor activity in the OFT. Moreover, FST induced a significant increase in serum CRF (5.8 ng/ml), ACTH (104.7 pg/ml) and corticosterone levels (37.3 ng/ml). Chronic treatment (14-days) with WETO decreased the serum CRF (200 mg/kg: 3.9 ng/ml) and corticosterone (50 mg/kg: 29.9 ng/ml; 100 mg/kg: 22.5 ng/ml; 200 mg/kg: 19.8 ng/ml) levels. These results clearly demonstrated the antidepressant effects of WETO in animal models of behavioral despair and suggested the mechanism involved in the neuroendocrine system.

Geographic and temporal genetic patterns of Aedes aegypti populations in Rio de Janeiro, Brazil.

PubMed

da Costa-Ribeiro, Magda C V; Lourenço-de-Oliveira, Ricardo; Failloux, Anna-Bella

2006-08-01

Rio de Janeiro is considered as the most important entry point for dengue viruses in Brazil. Using isoenzyme markers, we investigated the genetic structure of the mosquito vector Aedes aegypti sampled at three-month intervals in 14 districts in Rio de Janeiro from December 2002 to December 2003. We detected high levels of genetic differentiation (i.e. high F(ST) values and significant P values), which tended to persist throughout the year. The species does not take advantage of routes and railways to disperse. Genetic structuring was higher in the rainy season, suggesting low dispersion of Ae. aegypti at this time of year when all dengue epidemics have been reported in the city.

Allelic frequencies and statistical data obtained from 12 codis STR loci in an admixed population of the Brazilian Amazon

PubMed Central

da Costa Francez, Pablo Abdon; Rodrigues, Elzemar Martins Ribeiro; Frazão, Gleycianne Furtado; dos Reis Borges, Nathalia Danielly; dos Santos, Sidney Emanuel Batista

2011-01-01

The allelic frequencies of 12 short tandem repeat loci were obtained from a sample of 307 unrelated individuals living in Macapá, a city in the northern Amazon region, Brazil. These loci are the most commonly used in forensics and paternity testing. Based on the allele frequency obtained for the population of Macapá, we estimated an interethnic admixture for the three parental groups (European, Native American and African) of, respectively, 46%, 35% and 19%. Comparing these allele frequencies with those of other Brazilian populations and of the Iberian Peninsula population, no significant distances were observed. The interpopulation genetic distances (FST coefficients) to the present database ranged from FST = 0.0016 between Macapá and Belém to FST = 0.0036 between Macapá and the Iberian Peninsula. PMID:21637540

Allelic frequencies and statistical data obtained from 12 codis STR loci in an admixed population of the Brazilian Amazon.

PubMed

da Costa Francez, Pablo Abdon; Rodrigues, Elzemar Martins Ribeiro; Frazão, Gleycianne Furtado; Dos Reis Borges, Nathalia Danielly; Dos Santos, Sidney Emanuel Batista

2011-01-01

The allelic frequencies of 12 short tandem repeat loci were obtained from a sample of 307 unrelated individuals living in Macapá, a city in the northern Amazon region, Brazil. These loci are the most commonly used in forensics and paternity testing. Based on the allele frequency obtained for the population of Macapá, we estimated an interethnic admixture for the three parental groups (European, Native American and African) of, respectively, 46%, 35% and 19%. Comparing these allele frequencies with those of other Brazilian populations and of the Iberian Peninsula population, no significant distances were observed. The interpopulation genetic distances (F(ST) coefficients) to the present database ranged from F(ST) = 0.0016 between Macapá and Belém to F(ST) = 0.0036 between Macapá and the Iberian Peninsula.

Effects of food limitation and emigration on self-thinning in experimental minnow cohorts

USGS Publications Warehouse

Dunham, J.B.; Dickerson, B. R.; Beever, E.; Duncan, R. D.; Vinyard, G.L.

2000-01-01

5. Most of the support for FST in mobile animals comes from observational data on mean body mass and population density. Potentially important mechanisms, including the manner in which individuals are lost or retained in populations, are usually not investigated directly. Such tests of FST can only provide equivocal support. Detailed observational study and controlled experiments are needed to understand casual mechanisms.

Genetic characterization of 11 microsatellite loci in Egyptian pigeons (Columba livia domestica) and their cross-species amplification in other Columbidae populations

PubMed Central

Ramadan, Sherif; Dawod, Ahmed; El-Garhy, Osama; Nowier, Amira M.; Eltanany, Marwa; Inoue-Murayama, Miho

2018-01-01

Aim This study aimed to analyze the genetic diversity and relationships of 10 Egyptian pigeon populations belonging to Columba livia domestica speciesusing 11 microsatellite markers and to investigate the success of these markers amplification across another eight pigeon species. Methods Genomic DNA was isolated from feather samples of179 pigeon samples from 10 Egyptian breeds: Asfer Weraq (n=14), Austoraly (n=20), Reehani (n=21), Messawed (n=17), Nemssawy (n=27), Otatti (n=12), Morasla (n=17), Tumbler (n=22), Halaby Asfer (n=10), and Karakandy (n=19) in addition to Japanese feral pigeons (n=30). Genotyping was done using 11 specific polymorphic microsatellite makers. Moreover, 37 samples not belonging to C. livia domestica but belonging to another eight pigeon species were genotyped. The polymerase chain reaction (PCR) products were electrophoresed on an ABI 3130xl DNA Sequencer. The basic measures of genetic diversity and phylogenetic trees were computed using bioinformatics software. Results Across the 10 studied Egyptian populations, the number of alleles per locus ranged from 3 to 19 and the average number of alleles observed was 9.091. The lowest value of expected heterozygosity (0.373) was obtained for the Reehani breed, and the highest value (0.706) was found for Morasla breed. The overall expected heterozygosity of Egyptian pigeons was 0.548. The FST coefficient which indicates fixation coefficients of subpopulations within the total population for the 11 loci varied from 0.318 to 0.114 with a relatively high mean (0.226). In our study, the FIS showed a relatively high average(0.037). The pairwise Reynolds’s genetic distance between the11 studied pigeon populations recorded lower values between Otatti and Austoraly (0.025) and between Morasla and Japanese feral pigeons (0.054). These results are supported by clustering pattern either by the neighbor-joining phylogenetic tree or by a Bayesian clustering of STRUCTURE with the admixture method. Conclusions We confirm the applicability of the CliµD17, CliµT17, CliµD16, CliµD32, CliµT13, CliµD01, PG1, PG2, PG4, PG6, and PG7 microsatellite markers among Egyptian domestic pigeons and across other pigeon species using cross-species amplification method. The information from this study should be useful for genetic characterization and for developing conservation programs of this important species. PMID:29805216

Neuronal NOS inhibitor 1-(2-trifluoromethylphenyl)-imidazole augment the effects of antidepressants acting via serotonergic system in the forced swimming test in rats.

PubMed

Ulak, Güner; Mutlu, Oguz; Akar, Füruzan Yildiz; Komsuoğlu, F Ipek; Tanyeri, Pelin; Erden, B Faruk

2008-10-01

Treatment-resistant depression has necessitated new therapeutic strategies in augmenting the therapeutic actions of currently existing antidepressant drugs. The aim of this study was to investigate the possibility of synergistic interaction between 1-(2-trifluoromethylphenyl)-imidazole (TRIM), a novel neuronal nitric oxide synthase (nNOS) inhibitor and conventional antidepressants of different classes in the forced swimming test (FST) in rats. TRIM decreased the immobility time at 50 mg/kg doses in the FST in rats. Treatment with a behaviourally subeffective dose of TRIM (20 mg/kg) augmented the behavioural effect of tricyclic antidepressant imipramine, selective serotonin re-uptake inhibitor (SSRI) citalopram and fluoxetine or selective serotonin reuptake enhancer tianeptine but failed to augment the antidepressant effect of reboxetine, a noradrenaline re-uptake inhibitor, in this test. Therefore inhibition of NOS augments the effects of antidepressants acting on serotonergic system in the FST. Neither TRIM (10-50 mg/kg) nor other drug treatments affected the locomotor activity of animals. These findings are in agreement with the view that antidepressant effects or augmentation of these effects in the FST may be explained with inhibition of NOS activity and this may be a new approach in offering greater therapeutic efficacy of antidepressants acting via serotonergic system.

Acute hypoglycemia causes depressive-like behaviors in mice.

PubMed

Park, Min Jung; Yoo, Samuel W; Choe, Brian S; Dantzer, Robert; Freund, Gregory G

2012-02-01

Reports in humans advocate a link between hypoglycemia and altered mood. Such observations, however, have not been mechanistically explored. Here we examined depressive-like behaviors in mice resulting from acute hypoglycemia. Mice were fasted for 12 hours and then administered intraperitoneal insulin to induce a blood glucose nadir of 50 mg/dL at 0.75 hour after injection that by 2 hours postinjection had returned to normal. The behaviors of locomotion, forced swim, saccharin preference, and novel object recognition were subsequently examined. Mice made hypoglycemic showed depressive-like behaviors 24 hours after resolution of hypoglycemia as evidenced by increased immobility in the forced swim test (FST) and reduced saccharin preference. Movement and memory were not impacted by hypoglycemia 24 hours after its resolution. By 48 hours posthypoglycemia, depressive-like behaviors resolved. In contrast, neither peripheral insulin administration without resultant hypoglycemia nor intracerebroventricular insulin administration altered performance in the FST. The antidepressants fluoxetine and desipramine prevented hypoglycemia-induced immobility in the FST, as did the antiadrenergic agents phentolamine, metoprolol, and butoxamine. Epinephrine and norepinephrine administration caused increased immobility in the FST at 24 hours postadministration that subsequently resolved by 48 hours. These data indicate that, in mice, acute hypoglycemia through adrenergic pathways caused depressive-like behaviors that exist well beyond the resolution of hypoglycemia. Copyright © 2012 Elsevier Inc. All rights reserved.

Antidepressant-like activity of resveratrol treatment in the forced swim test and tail suspension test in mice: the HPA axis, BDNF expression and phosphorylation of ERK.

PubMed

Wang, Zhen; Gu, Jianhua; Wang, Xueer; Xie, Kai; Luan, Qinsong; Wan, Nianqing; Zhang, Qun; Jiang, Hong; Liu, Dexiang

2013-11-01

Resveratrol is a natural polyphenol enriched in Polygonum cuspidatum and has diverse biological activities. There is only limited information about the antidepressant-like effect of resveratrol. The present study assessed whether resveratrol treatment (20, 40 and 80mg/kg, i.p., 21days) has an antidepressant-like effect on the forced swim test (FST) and tail suspension test (TST) in mice and examined what its molecular targets might be. The results showed that resveratrol administration produced antidepressant-like effects in mice, evidenced by the reduced immobility time in the FST and TST, while it had no effect on the locomotor activity in the open field test. Resveratrol treatment significantly reduced serum corticosterone levels, which had been elevated by the FST and TST. Moreover, resveratrol increased brain-derived neurotrophic factor (BDNF) protein and extracellular signal-regulated kinase (ERK) phosphorylation levels in the prefrontal cortex and hippocampus. All of these antidepressant-like effects of resveratrol were essentially similar to those observed with the clinical antidepressant, fluoxetine. These results suggest that the antidepressant-like effects of resveratrol in the FST and TST are mediated, at least in part, by modulating hypothalamic-pituitary-adrenal axis, BDNF and ERK phosphorylation expression in the brain region of mice. © 2013.

A comparison of Frost expression among species and life stages of Drosophila.

PubMed

Bing, X; Zhang, J; Sinclair, Brent J

2012-02-01

Frost (Fst) is a gene associated with cold exposure in Drosophila melanogaster. We used real-time PCR to assess whether cold exposure induces expression of Fst in 10 different life stages of D. melanogaster, and adults of seven other Drosophila species. We exposed groups of individuals to 0 °C (2 h), followed by 1 h recovery (22 °C). Frost was significantly upregulated in response to cold in eggs, third instar larvae, and 2- and 5-day-old male and female adults in D. melanogaster. Life stages in which cold did not upregulate Fst had high constitutive expression. Frost is located on the opposite strand of an intron of Diuretic hormone (DH), but cold exposure did not upregulate DH. Frost orthologues were identified in six other species within the Melanogaster group (Drosophila sechellia, Drosophila simulans, Drosophila yakuba, Drosophila erecta, Drosophila ananassae and Drosophila mauritiana). Frost orthologues were upregulated in response to cold exposure in both sexes in adults of all of these species. The predicted structure of a putative Frost consensus protein shows highly conserved tandem repeats of motifs involved in cell signalling (PEST and TRAF2), suggesting that Fst might encode an adaptor protein involved in acute stress or apoptosis signalling in vivo. © 2011 The Authors. Insect Molecular Biology © 2011 The Royal Entomological Society.

Modelling particles moving in a potential field with pairwise interactions and an application

Treesearch

D. R. Brillinger; Haiganoush Preisler; M. J. Wisdom

2011-01-01

Motions of particles in fields characterized by real-valued potential functions, are considered. Three particular expressions for potential functions are studied. One, U, depends on the ith particle’s location, ri(t) at times t

Adaptive multi-view clustering based on nonnegative matrix factorization and pairwise co-regularization

NASA Astrophysics Data System (ADS)

Zhang, Tianzhen; Wang, Xiumei; Gao, Xinbo

2018-04-01

Nowadays, several datasets are demonstrated by multi-view, which usually include shared and complementary information. Multi-view clustering methods integrate the information of multi-view to obtain better clustering results. Nonnegative matrix factorization has become an essential and popular tool in clustering methods because of its interpretation. However, existing nonnegative matrix factorization based multi-view clustering algorithms do not consider the disagreement between views and neglects the fact that different views will have different contributions to the data distribution. In this paper, we propose a new multi-view clustering method, named adaptive multi-view clustering based on nonnegative matrix factorization and pairwise co-regularization. The proposed algorithm can obtain the parts-based representation of multi-view data by nonnegative matrix factorization. Then, pairwise co-regularization is used to measure the disagreement between views. There is only one parameter to auto learning the weight values according to the contribution of each view to data distribution. Experimental results show that the proposed algorithm outperforms several state-of-the-arts algorithms for multi-view clustering.

Evolutionary relationships can be more important than abiotic conditions in predicting the outcome of plant-plant interactions

PubMed Central

Soliveres, Santiago; Torices, Rubén; Maestre, Fernando T.

2015-01-01

Positive and negative plant-plant interactions are major processes shaping plant communities. They are affected by environmental conditions and evolutionary relationships among the interacting plants. However, the generality of these factors as drivers of pairwise plant interactions and their combined effects remain virtually unknown. We conducted an observational study to assess how environmental conditions (altitude, temperature, irradiance and rainfall), the dispersal mechanism of beneficiary species and evolutionary relationships affected the co-occurrence of pairwise interactions in 11 Stipa tenacissima steppes located along an environmental gradient in Spain. We studied 197 pairwise plant-plant interactions involving the two major nurse plants (the resprouting shrub Quercus coccifera and the tussock grass S. tenacissima) found in these communities. The relative importance of the studied factors varied with the nurse species considered. None of the factors studied were good predictors of the co-ocurrence between S. tenacissima and its neighbours. However, both the dispersal mechanism of the beneficiary species and the phylogenetic distance between interacting species were crucial factors affecting the co-occurrence between Q. coccifera and its neighbours, while climatic conditions (irradiance) played a secondary role. Values of phylogenetic distance between 207-272.8 Myr led to competition, while values outside this range or fleshy-fruitness in the beneficiary species led to positive interactions. The low importance of environmental conditions as a general driver of pairwise interactions was caused by the species-specific response to changes in either rainfall or radiation. This result suggests that factors other than climatic conditions must be included in theoretical models aimed to generally predict the outcome of plant-plant interactions. Our study helps to improve current theory on plant-plant interactions and to understand how these interactions can respond to expected modifications in species composition and climate associated to ongoing global environmental change. PMID:25914426

Antidepressant Activity of Brahmi in Albino Mice

PubMed Central

Kadali, SLDV Ramana Murty; M.C., Das; Rao A.S.R., Srinivasa; Sri G, Karuna

2014-01-01

Context: In traditional system of medicine brahmi has been used to enhance memory. Recently it has been reported to have action in psychiatric disorders. With these backgrounds the work has been undertaken to study antidepressant activity of brahmi in albino mice. Aim: To evaluate antidepressant activity of brahmi in experimental models. Materials and Methods: The antidepressant activity was studied in albino mice using forced swimming test (FST), tail suspension test (TST) and shock induced depression (SID). Imipramine (10mg/kg), fluoxetine (30mg/kg) were used as standard drugs and brahmi (10, 20, 30mg/kg) was used as test drug. Results: Brahmi exhibited significant decrease in duration of immobility in FST and reduced the shock induced decrease in activity in SID models. It didn’t show any activity in the TST model. Conclusion: Brahmi has shown antidepressant activity in FST and SID. PMID:24783074

Evaluation of Antidepressant-like Effect of Citrus Maxima Leaves in Animal Models of Depression.

PubMed

Potdar, Vikram H; Kibile, Swati J

2011-09-01

This study planned to assess antidepressant like activity of aqueous extract from leaves of Citrus maxima Merr. (Rutaceae). Boiling was used for aqueous extraction. Acute toxicity study was performed in mice. Antidepressant activity was studied using locomotor activity test, modified forced swimming test (FST) and tail suspension test (TST). Three doses 100, 200 and 300 mg/kg of aqueous extract of leaves were selected for testing. Fluoxetine (20 mg/kg, i.p.) and imipramine (30 mg/kg, i.p.) were used as the standard drugs. Aqueous extract of Citrus maxima leaves significantly reduced immobility time in both TST and FST. In locomotor activity testing it showed psychostimulant effect. Extract increased the climbing behavior in FST, which is similar to effect observed with imipramine. The results of this study suggest that antidepressant like effect of Citrus maxima seems to be mediated by an increase in norepinephrine level in synapses.

Functional classification of rice flanking sequence tagged genes using MapMan terms and global understanding on metabolic and regulatory pathways affected by dxr mutant having defects in light response.

PubMed

Chandran, Anil Kumar Nalini; Lee, Gang-Seob; Yoo, Yo-Han; Yoon, Ung-Han; Ahn, Byung-Ohg; Yun, Doh-Won; Kim, Jin-Hyun; Choi, Hong-Kyu; An, GynHeung; Kim, Tae-Ho; Jung, Ki-Hong

2016-12-01

Rice is one of the most important food crops for humans. To improve the agronomical traits of rice, the functions of more than 1,000 rice genes have been recently characterized and summarized. The completed, map-based sequence of the rice genome has significantly accelerated the functional characterization of rice genes, but progress remains limited in assigning functions to all predicted non-transposable element (non-TE) genes, estimated to number 37,000-41,000. The International Rice Functional Genomics Consortium (IRFGC) has generated a huge number of gene-indexed mutants by using mutagens such as T-DNA, Tos17 and Ds/dSpm. These mutants have been identified by 246,566 flanking sequence tags (FSTs) and cover 65 % (25,275 of 38,869) of the non-TE genes in rice, while the mutation ratio of TE genes is 25.7 %. In addition, almost 80 % of highly expressed non-TE genes have insertion mutations, indicating that highly expressed genes in rice chromosomes are more likely to have mutations by mutagens such as T-DNA, Ds, dSpm and Tos17. The functions of around 2.5 % of rice genes have been characterized, and studies have mainly focused on transcriptional and post-transcriptional regulation. Slow progress in characterizing the function of rice genes is mainly due to a lack of clues to guide functional studies or functional redundancy. These limitations can be partially solved by a well-categorized functional classification of FST genes. To create this classification, we used the diverse overviews installed in the MapMan toolkit. Gene Ontology (GO) assignment to FST genes supplemented the limitation of MapMan overviews. The functions of 863 of 1,022 known genes can be evaluated by current FST lines, indicating that FST genes are useful resources for functional genomic studies. We assigned 16,169 out of 29,624 FST genes to 34 MapMan classes, including major three categories such as DNA, RNA and protein. To demonstrate the MapMan application on FST genes, transcriptome analysis was done from a rice mutant of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) gene with FST. Mapping of 756 down-regulated genes in dxr mutants and their annotation in terms of various MapMan overviews revealed candidate genes downstream of DXR-mediating light signaling pathway in diverse functional classes such as the methyl-D-erythritol 4-phosphatepathway (MEP) pathway overview, photosynthesis, secondary metabolism and regulatory overview. This report provides a useful guide for systematic phenomics and further applications to enhance the key agronomic traits of rice.

Landscape genetics as a tool for conservation planning: predicting the effects of landscape change on gene flow.

PubMed

van Strien, Maarten J; Keller, Daniela; Holderegger, Rolf; Ghazoul, Jaboury; Kienast, Felix; Bolliger, Janine

2014-03-01

For conservation managers, it is important to know whether landscape changes lead to increasing or decreasing gene flow. Although the discipline of landscape genetics assesses the influence of landscape elements on gene flow, no studies have yet used landscape-genetic models to predict gene flow resulting from landscape change. A species that has already been severely affected by landscape change is the large marsh grasshopper (Stethophyma grossum), which inhabits moist areas in fragmented agricultural landscapes in Switzerland. From transects drawn between all population pairs within maximum dispersal distance (< 3 km), we calculated several measures of landscape composition as well as some measures of habitat configuration. Additionally, a complete sampling of all populations in our study area allowed incorporating measures of population topology. These measures together with the landscape metrics formed the predictor variables in linear models with gene flow as response variable (F(ST) and mean pairwise assignment probability). With a modified leave-one-out cross-validation approach, we selected the model with the highest predictive accuracy. With this model, we predicted gene flow under several landscape-change scenarios, which simulated construction, rezoning or restoration projects, and the establishment of a new population. For some landscape-change scenarios, significant increase or decrease in gene flow was predicted, while for others little change was forecast. Furthermore, we found that the measures of population topology strongly increase model fit in landscape genetic analysis. This study demonstrates the use of predictive landscape-genetic models in conservation and landscape planning.

Genetic analysis across different spatial scales reveals multiple dispersal mechanisms for the invasive hydrozoan Cordylophora in the Great Lakes.

PubMed

Darling, John A; Folino-Rorem, Nadine C

2009-12-01

Discerning patterns of post-establishment spread by invasive species is critically important for the design of effective management strategies and the development of appropriate theoretical models predicting spatial expansion of introduced populations. The globally invasive colonial hydrozoan Cordylophora produces propagules both sexually and vegetatively and is associated with multiple potential dispersal mechanisms, making it a promising system to investigate complex patterns of population structure generated throughout the course of rapid range expansion. Here, we explore genetic patterns associated with the spread of this taxon within the North American Great Lakes basin. We collected intensively from eight harbours in the Chicago area in order to conduct detailed investigation of local population expansion. In addition, we collected from Lakes Michigan, Erie, and Ontario, as well as Lake Cayuga in the Finger Lakes of upstate New York in order to assess genetic structure on a regional scale. Based on data from eight highly polymorphic microsatellite loci we examined the spatial extent of clonal genotypes, assessed levels of neutral genetic diversity, and explored patterns of migration and dispersal at multiple spatial scales through assessment of population level genetic differentiation (pairwise F(ST) and factorial correspondence analysis), Bayesian inference of population structure, and assignment tests on individual genotypes. Results of these analyses indicate that Cordylophora populations in this region spread predominantly through sexually produced propagules, and that while limited natural larval dispersal can drive expansion locally, regional expansion likely relies on anthropogenic dispersal vectors.

Molecular Systematics of the Cape Parrot (Poicephalus robustus): Implications for Taxonomy and Conservation

PubMed Central

Coetzer, Willem G.; Downs, Colleen T.; Perrin, Mike R.; Willows-Munro, Sandi

2015-01-01

The taxonomic position of the Cape Parrot (Poicephalus robustus robustus) has been the focus of much debate. A number of authors suggest that the Cape Parrot should be viewed as a distinct species separate from the other two P. robustus subspecies (P. r. fuscicollis and P. r. suahelicus). These recommendations were based on morphological, ecological, and behavioural assessments. In this study we investigated the validity of these recommendations using multilocus DNA analyses. We genotyped 138 specimens from five Poicephalus species (P. cryptoxanthus, P. gulielmi, P. meyeri, P. robustus, and P. rueppellii) using 11 microsatellite loci. Additionally, two mitochondrial (cytochrome oxidase I gene and 16S ribosomal RNA) and one nuclear intron (intron 7 of the β-fibrinogen gene) markers were amplified and sequenced. Bayesian clustering analysis and pairwise FST analysis of microsatellite data identified P. r. robustus as genetically distinct from the other P. robustus subspecies. Phylogenetic and molecular clock analyses on sequence data also supported the microsatellite analyses, placing P. r. robustus in a distinct clade separate from the other P. robustus subspecies. Molecular clock analysis places the most recent common ancestor between P. r. robustus and P. r. fuscicollis / P. r. suahelicus at 2.13 to 2.67 million years ago. Our results all support previous recommendations to elevate the Cape Parrot to species level. This will facilitate better planning and implementation of international and local conservation management strategies for the Cape Parrot. PMID:26267261

Male Lineages in Brazil: Intercontinental Admixture and Stratification of the European Background.

PubMed

Resque, Rafael; Gusmão, Leonor; Geppert, Maria; Roewer, Lutz; Palha, Teresinha; Alvarez, Luis; Ribeiro-dos-Santos, Ândrea; Santos, Sidney

2016-01-01

The non-recombining nature of the Y chromosome and the well-established phylogeny of Y-specific Single Nucleotide Polymorphisms (Y-SNPs) make them useful for defining haplogroups with high geographical specificity; therefore, they are more apt than the Y-STRs to detect population stratification in admixed populations from diverse continental origins. Different Y-SNP typing strategies have been described to address issues of population history and movements within geographic territories of interest. In this study, we investigated a set of 41 Y-SNPs in 1217 unrelated males from the five Brazilian geopolitical regions, aiming to disclose the genetic structure of male lineages in the country. A population comparison based on pairwise FST genetic distances did not reveal statistically significant differences in haplogroup frequency distributions among populations from the different regions. The genetic differences observed among regions were, however, consistent with the colonization history of the country. The sample from the Northern region presented the highest Native American ancestry (8.4%), whereas the more pronounced African contribution could be observed in the Northeastern population (15.1%). The Central-Western and Southern samples showed the higher European contributions (95.7% and 93.6%, respectively). The Southeastern region presented significant European (86.1%) and African (12.0%) contributions. The subtyping of the most frequent European lineage in Brazil (R1b1a-M269) allowed differences in the genetic European background of the five Brazilian regions to be investigated for the first time.

Male Lineages in Brazil: Intercontinental Admixture and Stratification of the European Background

PubMed Central

Geppert, Maria; Roewer, Lutz; Palha, Teresinha; Alvarez, Luis; Ribeiro-dos-Santos, Ândrea; Santos, Sidney

2016-01-01

The non-recombining nature of the Y chromosome and the well-established phylogeny of Y-specific Single Nucleotide Polymorphisms (Y-SNPs) make them useful for defining haplogroups with high geographical specificity; therefore, they are more apt than the Y-STRs to detect population stratification in admixed populations from diverse continental origins. Different Y-SNP typing strategies have been described to address issues of population history and movements within geographic territories of interest. In this study, we investigated a set of 41 Y-SNPs in 1217 unrelated males from the five Brazilian geopolitical regions, aiming to disclose the genetic structure of male lineages in the country. A population comparison based on pairwise FST genetic distances did not reveal statistically significant differences in haplogroup frequency distributions among populations from the different regions. The genetic differences observed among regions were, however, consistent with the colonization history of the country. The sample from the Northern region presented the highest Native American ancestry (8.4%), whereas the more pronounced African contribution could be observed in the Northeastern population (15.1%). The Central-Western and Southern samples showed the higher European contributions (95.7% and 93.6%, respectively). The Southeastern region presented significant European (86.1%) and African (12.0%) contributions. The subtyping of the most frequent European lineage in Brazil (R1b1a-M269) allowed differences in the genetic European background of the five Brazilian regions to be investigated for the first time. PMID:27046235

Microsatellite variation and genetic structure of brook trout (Salvelinus fontinalis) populations in Labrador and neighboring Atlantic Canada: evidence for ongoing gene flow and dual routes of post-Wisconsinan colonization

PubMed Central

Pilgrim, Brettney L; Perry, Robert C; Keefe, Donald G; Perry, Elizabeth A; Dawn Marshall, H

2012-01-01

In conservation genetics and management, it is important to understand the contribution of historical and contemporary processes to geographic patterns of genetic structure in order to characterize and preserve diversity. As part of a 10-year monitoring program by the Government of Newfoundland and Labrador, Canada, we measured the population genetic structure of the world's most northern native populations of brook trout (Salvelinus fontinalis) in Labrador to gather baseline data to facilitate monitoring of future impacts of the recently opened Trans-Labrador Highway. Six-locus microsatellite profiles were obtained from 1130 fish representing 32 populations from six local regions. Genetic diversity in brook trout populations in Labrador (average HE= 0.620) is within the spectrum of variability found in other brook trout across their northeastern range, with limited ongoing gene flow occurring between populations (average pairwise FST= 0.139). Evidence for some contribution of historical processes shaping genetic structure was inferred from an isolation-by-distance analysis, while dual routes of post-Wisconsinan recolonization were indicated by STRUCTURE analysis: K= 2 was the most likely number of genetic groups, revealing a separation between northern and west-central Labrador from all remaining populations. Our results represent the first data from the nuclear genome of brook trout in Labrador and emphasize the usefulness of microsatellite data for revealing the extent to which genetic structure is shaped by both historical and contemporary processes. PMID:22837834

Genome-Wide Analysis in Brazilian Xavante Indians Reveals Low Degree of Admixture

PubMed Central

Kuhn, Patricia C.; Horimoto, Andréa R. V. Russo.; Sanches, José Maurício; Vieira Filho, João Paulo B.; Franco, Luciana; Fabbro, Amaury Dal; Franco, Laercio Joel; Pereira, Alexandre C.; Moises, Regina S

2012-01-01

Characterization of population genetic variation and structure can be used as tools for research in human genetics and population isolates are of great interest. The aim of the present study was to characterize the genetic structure of Xavante Indians and compare it with other populations. The Xavante, an indigenous population living in Brazilian Central Plateau, is one of the largest native groups in Brazil. A subset of 53 unrelated subjects was selected from the initial sample of 300 Xavante Indians. Using 86,197 markers, Xavante were compared with all populations of HapMap Phase III and HGDP-CEPH projects and with a Southeast Brazilian population sample to establish its population structure. Principal Components Analysis showed that the Xavante Indians are concentrated in the Amerindian axis near other populations of known Amerindian ancestry such as Karitiana, Pima, Surui and Maya and a low degree of genetic admixture was observed. This is consistent with the historical records of bottlenecks experience and cultural isolation. By calculating pair-wise Fst statistics we characterized the genetic differentiation between Xavante Indians and representative populations of the HapMap and from HGDP-CEPH project. We found that the genetic differentiation between Xavante Indians and populations of Ameridian, Asian, European, and African ancestry increased progressively. Our results indicate that the Xavante is a population that remained genetically isolated over the past decades and can offer advantages for genome-wide mapping studies of inherited disorders. PMID:22900041

Genome-wide analysis in Brazilian Xavante Indians reveals low degree of admixture.

PubMed

Kuhn, Patricia C; Horimoto, Andréa R V Russo; Sanches, José Maurício; Vieira Filho, João Paulo B; Franco, Luciana; Fabbro, Amaury Dal; Franco, Laercio Joel; Pereira, Alexandre C; Moises, Regina S

2012-01-01

Characterization of population genetic variation and structure can be used as tools for research in human genetics and population isolates are of great interest. The aim of the present study was to characterize the genetic structure of Xavante Indians and compare it with other populations. The Xavante, an indigenous population living in Brazilian Central Plateau, is one of the largest native groups in Brazil. A subset of 53 unrelated subjects was selected from the initial sample of 300 Xavante Indians. Using 86,197 markers, Xavante were compared with all populations of HapMap Phase III and HGDP-CEPH projects and with a Southeast Brazilian population sample to establish its population structure. Principal Components Analysis showed that the Xavante Indians are concentrated in the Amerindian axis near other populations of known Amerindian ancestry such as Karitiana, Pima, Surui and Maya and a low degree of genetic admixture was observed. This is consistent with the historical records of bottlenecks experience and cultural isolation. By calculating pair-wise F(st) statistics we characterized the genetic differentiation between Xavante Indians and representative populations of the HapMap and from HGDP-CEPH project. We found that the genetic differentiation between Xavante Indians and populations of Ameridian, Asian, European, and African ancestry increased progressively. Our results indicate that the Xavante is a population that remained genetically isolated over the past decades and can offer advantages for genome-wide mapping studies of inherited disorders.

Comparison of microsatellite variations between Red Junglefowl and a commercial chicken gene pool.

PubMed

Tadano, R; Kinoshita, K; Mizutani, M; Tsudzuki, M

2014-02-01

It is assumed that Red Junglefowl (Gallus gallus) is one of the main ancestors of domestic chickens (Gallus gallus domesticus). Differences in microsatellite polymorphisms between Red Junglefowl and modern commercial chickens, which are used for egg and meat production, have not been fully reported. A total of 361 individuals from 1 Red Junglefowl population that has been maintained as a closed flock, 5 final cross-bred commercial layer populations (white-, tinted-, and brown-egg layers), and 2 final cross-bred commercial broiler populations were genotyped for 40 autosomal microsatellite loci. We compared microsatellite variations in Red Junglefowl with those in a commercial chicken gene pool. The contribution of each population to the genetic diversity was also estimated based on the molecular coancestry. In total, 302 distinct alleles were detected in 1 Red Junglefowl and 7 commercial chicken populations, of which 31 alleles (10.3%) were unique to Red Junglefowl, most of which occurred at a high frequency. The genetic differentiation between Red Junglefowl and commercial chickens (pairwise FST) ranged from 0.32 to 0.47. According to the neighbor-joining tree based on the modified Cavalli-Sforza chord distances and the Bayesian clustering analysis, Red Junglefowl was genetically distant from the commercial chicken gene pool tested. In all of the populations analyzed, Red Junglefowl made the highest contribution to genetic diversity. These results suggest that Red Junglefowl has a distinct distribution of microsatellite alleles and that there is a high level of genetic divergence between Red Junglefowl and commercial chickens.

Genetic variability and haplotypes of Echinococcus isolates from Tunisia.

PubMed

Boufana, Belgees; Lahmar, Samia; Rebaï, Waël; Ben Safta, Zoubeir; Jebabli, Leïla; Ammar, Adel; Kachti, Mahmoud; Aouadi, Soufia; Craig, Philip S

2014-11-01

The species/genotypes of Echinococcus infecting a range of intermediate, canid and human hosts were examined as well as the intraspecific variation and population structure of Echinococcus granulosus sensu lato (s.l.) within these hosts. A total of 174 Echinococcus isolates from humans and ungulate intermediate hosts and adult tapeworms from dogs and jackals were used. Genomic DNA was used to amplify a fragment within a mitochondrial gene and a nuclear gene, coding for cytochrome c oxidase subunit 1 (cox1; 828 bp) and elongation factor 1-alpha (ef1a; 656 bp), respectively. E. granulosus sensu stricto was identified from all host species examined, E. canadensis (G6) in a camel and, for the first time, fertile cysts of E. granulosus (s.s.) and E. equinus in equids (donkeys) and E. granulosus (s.s.) from wild boars and goats. Considerable genetic variation was seen only for the cox1 sequences of E. granulosus (s.s.). The pairwise fixation index (Fst) for cox1 E. granulosus (s.s.) sequences from donkeys was high and was statistically significant compared with that of E. granulosus populations from other intermediate hosts. A single haplotype (EqTu01) was identified for the cox1 nucleotide sequences of E. equinus. The role of donkeys in the epidemiology of echinococcosis in Tunisia requires further investigation. © The Author 2014. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Population genetic analysis of Enterocytozoon bieneusi in humans.

PubMed

Li, Wei; Cama, Vitaliano; Feng, Yaoyu; Gilman, Robert H; Bern, Caryn; Zhang, Xichen; Xiao, Lihua

2012-01-01

Genotyping based on sequence analysis of the ribosomal internal transcribed spacer has revealed significant genetic diversity in Enterocytozoonbieneusi. Thus far, the population genetics of E. bieneusi and its significance in the epidemiology of microsporidiosis have not been examined. In this study, a multilocus sequence typing of E. bieneusi in AIDS patients in Lima, Peru was conducted, using 72 specimens previously genotyped as A, D, IV, EbpC, WL11, Peru7, Peru8, Peru10 and Peru11 at the internal transcribed spacer locus. Altogether, 39 multilocus genotypes were identified among the 72 specimens. The observation of strong intragenic linkage disequilibria and limited genetic recombination among markers were indicative of an overall clonal population structure of E. bieneusi. Measures of pair-wise intergenic linkage disequilibria and a standardised index of association (IAS) based on allelic profile data further supported this conclusion. Both sequence-based and allelic profile-based phylogenetic analyses showed the presence of two genetically isolated groups in the study population, one (group 1) containing isolates of the anthroponotic internal transcribed spacer genotype A, and the other (group 2) containing isolates of multiple internal transcribed spacer genotypes (mainly genotypes D and IV) with zoonotic potential. The measurement of linkage disequilibria and recombination indicated group 2 had a clonal population structure, whereas group 1 had an epidemic population structure. The formation of the two sub-populations was confirmed by STRUCTURE and Wright's fixation index (FST) analyses. The data highlight the power of MLST in understanding the epidemiology of E. bieneusi. Published by Elsevier Ltd.

On the use of star-shaped genealogies in inference of coalescence times.

PubMed Central

Rosenberg, Noah A; Hirsh, Aaron E

2003-01-01

Genealogies from rapidly growing populations have approximate "star" shapes. We study the degree to which this approximation holds in the context of estimating the time to the most recent common ancestor (T(MRCA)) of a set of lineages. In an exponential growth scenario, we find that unless the product of population size (N) and growth rate (r) is at least approximately 10(5), the "pairwise comparison estimator" of T(MRCA) that derives from the star genealogy assumption has bias of 10-50%. Thus, the estimator is appropriate only for large populations that have grown very rapidly. The "tree-length estimator" of T(MRCA) is more biased than the pairwise comparison estimator, having low bias only for extremely large values of Nr. PMID:12930771

Memory-efficient dynamic programming backtrace and pairwise local sequence alignment.

PubMed

Newberg, Lee A

2008-08-15

A backtrace through a dynamic programming algorithm's intermediate results in search of an optimal path, or to sample paths according to an implied probability distribution, or as the second stage of a forward-backward algorithm, is a task of fundamental importance in computational biology. When there is insufficient space to store all intermediate results in high-speed memory (e.g. cache) existing approaches store selected stages of the computation, and recompute missing values from these checkpoints on an as-needed basis. Here we present an optimal checkpointing strategy, and demonstrate its utility with pairwise local sequence alignment of sequences of length 10,000. Sample C++-code for optimal backtrace is available in the Supplementary Materials. Supplementary data is available at Bioinformatics online.

Evaluation of Goal Programming for the Optimal Assignment of Inspectors to Construction Projects

DTIC Science & Technology

1988-09-01

Inputs ..... .............. 90 Equation Coefficients . ....... .. 90 Weights, Priorities and the AHP . . 91 Right-Hand Side Values ........ .. 91...the AHP Hierarchy with k Levels . . 36 3. Sample Matrix for Pairwise Comparison ........ .. 37 4. Assignment of I and p for Example Problem...Weights for Example Problem ... 61 3. AHP Weights and Coefficient ci, Values. ........ 63 vii AFIT/GEM/LSM/88S-16 Abstract The purpose of this study was

Clinical doses of citalopram or reboxetine differentially modulate passive and active behaviors of female Wistar rats with high or low immobility time in the forced swimming test.

PubMed

Flores-Serrano, Ana Gisela; Vila-Luna, María Leonor; Álvarez-Cervera, Fernando José; Heredia-López, Francisco José; Góngora-Alfaro, José Luis; Pineda, Juan Carlos

2013-09-01

The sensitivity of immobility time (IT) to antidepressant-drugs differs in rats expressing high or low motor activity during the forced swimming test (FST). However, whether this heterogeneity is expressed after the administration of the most selective serotonin and norepinephrine reuptake inhibitors (SSRIs and SNRIs, respectively) is unknown. We compared the influence of either the SSRI citalopram or the SNRI reboxetine with the tricyclic antidepressant amitriptyline on two subgroups of female Wistar rats expressing high IT (HI; at or above the mean value) or low IT (LI; below the mean) during the initial 5 min of the first session of the FST. None of the tested drugs increased motor activity in the open field test. When vehicle was applied to either HI or LI rats, IT increased in the second session of the FST. This increment concurred with a simultaneous climbing time (CT) decrement. When amitriptyline (15 mg/kg) was tested the CT increased for both HI and LI rats. This increment was accompanied by an IT decrement in HI and LI rats. Reboxetine (0.16 or 1 mg/kg) precluded IT and CT changes in both HI and LI rats and produced a swimming time reduction. Citalopram (0.4, 1, and 3 mg/kg) essentially mimicked the influence of reboxetine on the IT and CT in LI rats, as well as in HI rats, but in the latter case only at 3 mg/kg. Yet, at the dose of 10 mg/kg citalopram lacked this effect in both subgroups. No differences were detected when the IT of LI rats was evaluated with citalopram (3 mg/kg) during estrus or diestrus stage. These results show that clinical doses of citalopram produced an antidepressant-like effect selectively in LI rats, while amitriptyline or reboxetine produced this effect in both LI and HI animals. Copyright © 2013 Elsevier Inc. All rights reserved.

Choice of population database for forensic DNA profile analysis.

PubMed

Steele, Christopher D; Balding, David J

2014-12-01

When evaluating the weight of evidence (WoE) for an individual to be a contributor to a DNA sample, an allele frequency database is required. The allele frequencies are needed to inform about genotype probabilities for unknown contributors of DNA to the sample. Typically databases are available from several populations, and a common practice is to evaluate the WoE using each available database for each unknown contributor. Often the most conservative WoE (most favourable to the defence) is the one reported to the court. However the number of human populations that could be considered is essentially unlimited and the number of contributors to a sample can be large, making it impractical to perform every possible WoE calculation, particularly for complex crime scene profiles. We propose instead the use of only the database that best matches the ancestry of the queried contributor, together with a substantial FST adjustment. To investigate the degree of conservativeness of this approach, we performed extensive simulations of one- and two-contributor crime scene profiles, in the latter case with, and without, the profile of the second contributor available for the analysis. The genotypes were simulated using five population databases, which were also available for the analysis, and evaluations of WoE using our heuristic rule were compared with several alternative calculations using different databases. Using FST=0.03, we found that our heuristic gave WoE more favourable to the defence than alternative calculations in well over 99% of the comparisons we considered; on average the difference in WoE was just under 0.2 bans (orders of magnitude) per locus. The degree of conservativeness of the heuristic rule can be adjusted through the FST value. We propose the use of this heuristic for DNA profile WoE calculations, due to its ease of implementation, and efficient use of the evidence while allowing a flexible degree of conservativeness. Copyright © 2014. Published by Elsevier Ireland Ltd.

Design, Synthesis and Evaluation of the Antidepressant and Anticonvulsant Activities of Triazole-Containing Benzo[d]oxazoles.

PubMed

Song, Ming-Xia; Rao, Bao-Qi; Cheng, Bin-Bin; Wu, Yi; Zeng, Hong; Luo, You-Gen; Deng, Xian-Qing

2017-01-01

Epilepsy and depression are two of the common diseases seriously threatening life and health of human. A shared neurobiological substrate led to the bidirectional relationship and high comorbid occurrence of the two disorders. Recently, an increasing number of patients with epilepsy (PWE) require some form of antidepressant medication. However, most of the available antidepressants are inadequate for PWE for some reasons. So, the search for novel and increasingly effective drugs with anticonvulsant and antidepressant activities is necessary. A series of 2-substituted-6-(4H-1,2,4-triazol-4-yl)benzo[d]oxazoles (5a-p) were designed and synthesized. Their anticonvulsant activities were evaluated using maximal electroshock shock (MES) and subcutaneous pentylenetetrazole (scPTZ) seizure models in mice. Their antidepressant activities were screened with the forced swimming test (FST). All the compounds showed anti-MES activities in different degree, among which 5g and 5j were the most promising one with ED50 value of 31.7 and 12.7 mg/kg, respectively. What's more, 5g and 5j also exhibited nice anti-scPTZ activities and low neurotoxicity. Interestingly, these compounds also showed good antidepressant activities in FST. And the efficacy of 5g were also confirmed by a tail suspension test and a open field test. The pretreatment of thiosemicarbazide (an inhibitor of γ- aminobutyric acid synthesis enzyme) significantly increased the ED50 of 5g in MES and reversed the reductions in the immobility time of 5g in FST. Triazole-containing benzo[d]oxazole is a good skeleton to develop compounds with both anticonvulsant and antidepressant activities. We have got the compound 5g, which display remarkable antidepressant and anticonvulsant activities, and the GABAergic system was involved in the action mechanism of 5g. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Comparison of Genetic Variants in Cancer-Related Genes between Chinese Hui and Han Populations

PubMed Central

Tian, Chaoyong; Chen, Zhiqiang; Ma, Xixian; Yang, Ming; Wang, Zhizhong; Dong, Ying; Yang, Ting; Yang, Wenjun

2015-01-01

Background The Chinese Hui population, as the second largest minority ethnic group in China, may have a different genetic background from Han people because of its unique demographic history. In this study, we aimed to identify genetic differences between Han and Hui Chinese from the Ningxia region of China by comparing eighteen single nucleotide polymorphisms in cancer-related genes. Methods DNA samples were collected from 99 Hui and 145 Han people from the Ningxia Hui Autonomous Region in China, and SNPs were detected using an improved multiplex ligase detection reaction method. Genotyping data from six 1000 Genomes Project population samples (99 Utah residents with northern and western European ancestry (CEU), 107 Toscani in Italy (TSI), 108 Yoruba in Ibadan (YRI), 61 of African ancestry in the southwestern US (ASW), 103 Han Chinese in Beijing (CHB), and 104 Japanese in Tokyo (JPT)) were also included in this study. Differences in the distribution of alleles among the populations were assessed using χ2 tests, and FST was used to measure the degree of population differentiation. Results We found that the genetic diversity of many SNPs in cancer-related genes in the Hui Chinese in Ningxia was different from that in the Han Chinese in Ningxia. For example, the allele frequencies of four SNPs (rs13361707, rs2274223, rs465498, and rs753955) showed different genetic distributions (p<0.05) between Chinese Ningxia Han and Chinese Ningxia Hui. Five SNPs (rs730506, rs13361707, rs2274223, rs465498 and rs753955) had different FST values (FST >0.000) between the Hui and Han populations. Conclusions These results suggest that some SNPs associated with cancer-related genes vary among different Chinese ethnic groups. We suggest that population differences should be carefully considered in evaluating cancer risk and prognosis as well as the efficacy of cancer therapy. PMID:26683024

Comparison of Genetic Variants in Cancer-Related Genes between Chinese Hui and Han Populations.

PubMed

Tian, Chaoyong; Chen, Zhiqiang; Ma, Xixian; Yang, Ming; Wang, Zhizhong; Dong, Ying; Yang, Ting; Yang, Wenjun

2015-01-01

The Chinese Hui population, as the second largest minority ethnic group in China, may have a different genetic background from Han people because of its unique demographic history. In this study, we aimed to identify genetic differences between Han and Hui Chinese from the Ningxia region of China by comparing eighteen single nucleotide polymorphisms in cancer-related genes. DNA samples were collected from 99 Hui and 145 Han people from the Ningxia Hui Autonomous Region in China, and SNPs were detected using an improved multiplex ligase detection reaction method. Genotyping data from six 1000 Genomes Project population samples (99 Utah residents with northern and western European ancestry (CEU), 107 Toscani in Italy (TSI), 108 Yoruba in Ibadan (YRI), 61 of African ancestry in the southwestern US (ASW), 103 Han Chinese in Beijing (CHB), and 104 Japanese in Tokyo (JPT)) were also included in this study. Differences in the distribution of alleles among the populations were assessed using χ2 tests, and FST was used to measure the degree of population differentiation. We found that the genetic diversity of many SNPs in cancer-related genes in the Hui Chinese in Ningxia was different from that in the Han Chinese in Ningxia. For example, the allele frequencies of four SNPs (rs13361707, rs2274223, rs465498, and rs753955) showed different genetic distributions (p<0.05) between Chinese Ningxia Han and Chinese Ningxia Hui. Five SNPs (rs730506, rs13361707, rs2274223, rs465498 and rs753955) had different FST values (FST>0.000) between the Hui and Han populations. These results suggest that some SNPs associated with cancer-related genes vary among different Chinese ethnic groups. We suggest that population differences should be carefully considered in evaluating cancer risk and prognosis as well as the efficacy of cancer therapy.

Modeling apple surface temperature dynamics based on weather data.

PubMed

Li, Lei; Peters, Troy; Zhang, Qin; Zhang, Jingjin; Huang, Danfeng

2014-10-27

The exposure of fruit surfaces to direct sunlight during the summer months can result in sunburn damage. Losses due to sunburn damage are a major economic problem when marketing fresh apples. The objective of this study was to develop and validate a model for simulating fruit surface temperature (FST) dynamics based on energy balance and measured weather data. A series of weather data (air temperature, humidity, solar radiation, and wind speed) was recorded for seven hours between 11:00-18:00 for two months at fifteen minute intervals. To validate the model, the FSTs of "Fuji" apples were monitored using an infrared camera in a natural orchard environment. The FST dynamics were measured using a series of thermal images. For the apples that were completely exposed to the sun, the RMSE of the model for estimating FST was less than 2.0 °C. A sensitivity analysis of the emissivity of the apple surface and the conductance of the fruit surface to water vapour showed that accurate estimations of the apple surface emissivity were important for the model. The validation results showed that the model was capable of accurately describing the thermal performances of apples under different solar radiation intensities. Thus, this model could be used to more accurately estimate the FST relative to estimates that only consider the air temperature. In addition, this model provides useful information for sunburn protection management.

Evaluation of follistatin as a therapeutic in models of skeletal muscle atrophy associated with denervation and tenotomy

PubMed Central

Sepulveda, Patricio V.; Lamon, Séverine; Hagg, Adam; Thomson, Rachel E.; Winbanks, Catherine E.; Qian, Hongwei; Bruce, Clinton R.; Russell, Aaron P.; Gregorevic, Paul

2015-01-01

Follistatin is an inhibitor of TGF-β superfamily ligands that repress skeletal muscle growth and promote muscle wasting. Accordingly, follistatin has emerged as a potential therapeutic to ameliorate the deleterious effects of muscle atrophy. However, it remains unclear whether the anabolic effects of follistatin are conserved across different modes of non-degenerative muscle wasting. In this study, the delivery of a recombinant adeno-associated viral vector expressing follistatin (rAAV:Fst) to the hind-limb musculature of mice two weeks prior to denervation or tenotomy promoted muscle hypertrophy that was sufficient to preserve muscle mass comparable to that of untreated sham-operated muscles. However, administration of rAAV:Fst to muscles at the time of denervation or tenotomy did not prevent subsequent muscle wasting. Administration of rAAV:Fst to innervated or denervated muscles increased protein synthesis, but markedly reduced protein degradation only in innervated muscles. Phosphorylation of the signalling proteins mTOR and S6RP, which are associated with protein synthesis, was increased in innervated muscles administered rAAV:Fst, but not in treated denervated muscles. These results demonstrate that the anabolic effects of follistatin are influenced by the interaction between muscle fibres and motor nerves. These findings have important implications for understanding the potential efficacy of follistatin-based therapies for non-degenerative muscle wasting. PMID:26657343

Modeling Apple Surface Temperature Dynamics Based on Weather Data

PubMed Central

Li, Lei; Peters, Troy; Zhang, Qin; Zhang, Jingjin; Huang, Danfeng

2014-01-01

The exposure of fruit surfaces to direct sunlight during the summer months can result in sunburn damage. Losses due to sunburn damage are a major economic problem when marketing fresh apples. The objective of this study was to develop and validate a model for simulating fruit surface temperature (FST) dynamics based on energy balance and measured weather data. A series of weather data (air temperature, humidity, solar radiation, and wind speed) was recorded for seven hours between 11:00–18:00 for two months at fifteen minute intervals. To validate the model, the FSTs of “Fuji” apples were monitored using an infrared camera in a natural orchard environment. The FST dynamics were measured using a series of thermal images. For the apples that were completely exposed to the sun, the RMSE of the model for estimating FST was less than 2.0 °C. A sensitivity analysis of the emissivity of the apple surface and the conductance of the fruit surface to water vapour showed that accurate estimations of the apple surface emissivity were important for the model. The validation results showed that the model was capable of accurately describing the thermal performances of apples under different solar radiation intensities. Thus, this model could be used to more accurately estimate the FST relative to estimates that only consider the air temperature. In addition, this model provides useful information for sunburn protection management. PMID:25350507

Involvement of NMDA receptors in the antidepressant-like effect of tramadol in the mouse forced swimming test.

PubMed

Ostadhadi, Sattar; Norouzi-Javidan, Abbas; Chamanara, Mohsen; Akbarian, Reyhaneh; Imran-Khan, Muhammad; Ghasemi, Mehdi; Dehpour, Ahmad-Reza

2017-09-01

Tramadol is an analgesic agent that is mainly used to treat moderate to severe pain. There is evidence that tramadol may have antidepressant property. However, the mechanisms underlying the antidepressant effects of tramadol have not been elucidated yet. Considering that fact that N-methyl-d-aspartate (NMDA) receptor signaling may play an important role in the pathophysiology of depression, the aim of the present study was to investigate the role of NMDA receptor signaling in the possible antidepressant-like effects of tramadol in the mouse forced swimming test (mFST). We found that tramadol exerted antidepressant-like effects at high dose (40mg/kg, intraperitoneally [i.p.]) in the mFST. Co-administration of non-effective doses of NMDA receptor antagonists (ketamine [1mg/kg, i.p.], MK-801 [0.05mg/kg, i.p.], or magnesium sulfate [10mg/kg, i.p.]) with sub-effective dose of tramadol (20mg/kg, i.p.) exerted significant antidepressant-like effects in the mFST. The antidepressant-like effects of tramadol (40mg/kg) was also inhibited by pre-treatment with non-effective dose of the NMDA receptor agonist NMDA (75mg/kg, i.p.). Our data suggest a role for NMDA receptor signaling in the antidepressant-like effects of tramadol in the mFST. Copyright © 2017 Elsevier Inc. All rights reserved.

New Measurement for Correlation of Co-evolution Relationship of Subsequences in Protein.

PubMed

Gao, Hongyun; Yu, Xiaoqing; Dou, Yongchao; Wang, Jun

2015-12-01

Many computational tools have been developed to measure the protein residues co-evolution. Most of them only focus on co-evolution for pairwise residues in a protein sequence. However, number of residues participate in co-evolution might be multiple. And some co-evolved residues are clustered in several distinct regions in primary structure. Therefore, the co-evolution among the adjacent residues and the correlation between the distinct regions offer insights into function and evolution of the protein and residues. Subsequence is used to represent the adjacent multiple residues in one distinct region. In the paper, co-evolution relationship in each subsequence is represented by mutual information matrix (MIM). Then, Pearson's correlation coefficient: R value is developed to measure the similarity correlation of two MIMs. MSAs from Catalytic Data Base (Catalytic Site Atlas, CSA) are used for testing. R value characterizes a specific class of residues. In contrast to individual pairwise co-evolved residues, adjacent residues without high individual MI values are found since the co-evolved relationship among them is similar to that among another set of adjacent residues. These subsequences possess some flexibility in the composition of side chains, such as the catalyzed environment.

Neurons the decision makers, Part I: The firing function of a single neuron.

PubMed

Saaty, Thomas

2017-02-01

This paper is concerned with understanding synthesis of electric signals in the neural system based on making pairwise comparisons. Fundamentally, every person and every animal are born with the talent to compare stimuli from things that share properties in space or over time. Comparisons always need experience to distinguish among things. Pairwise comparisons are numerically reciprocal. If a value is assigned to the larger of two elements that have a given property when compared with the smaller one, then the smaller has the reciprocal of that value when compared with the larger. Because making comparisons requires the reciprocal property, we need mathematics that can cope with division. There are four division algebras that would allow us to use our reciprocals arising from comparisons: The real numbers, the complex numbers, the non-commutative quaternions and the non-associative octonions. Rather than inferring function as from electric flow in a network, in this paper we infer the flow from function. Neurons fire in response to stimuli and their firings vary relative to the intensities of the stimuli. We believe neurons use some kind of pairwise comparison mechanism to determine when to fire based on the stimuli they receive. The ideas we develop here about flows are used to deduce how a system based on this kind of firing determination works and can be described. Furthermore the firing of neurons requires continuous comparisons. To develop a formula describing the output of these pairwise comparisons requires solving Fredholm's equation of the second kind which is satisfied if and only if a simple functional equation has solutions. The Fourier transform of the real solution of this equation leads to inverse square laws like those that are common in physics. The Fourier transform applied to a complex valued solution leads to Dirac type of firings. Such firings are dense in the very general fields of functions known as Sobolev spaces and thus can be used to represent the very diverse phenomena in and around us. The non-commutative solution in quaternions can be interpreted as rotations in space. The also non-commutative and non-associative solution in octonions has yet to be adequately interpreted outside physics. Copyright © 2016 Elsevier Ltd. All rights reserved.

Lotka-Volterra pairwise modeling fails to capture diverse pairwise microbial interactions

PubMed Central

Momeni, Babak; Xie, Li; Shou, Wenying

2017-01-01

Pairwise models are commonly used to describe many-species communities. In these models, an individual receives additive fitness effects from pairwise interactions with each species in the community ('additivity assumption'). All pairwise interactions are typically represented by a single equation where parameters reflect signs and strengths of fitness effects ('universality assumption'). Here, we show that a single equation fails to qualitatively capture diverse pairwise microbial interactions. We build mechanistic reference models for two microbial species engaging in commonly-found chemical-mediated interactions, and attempt to derive pairwise models. Different equations are appropriate depending on whether a mediator is consumable or reusable, whether an interaction is mediated by one or more mediators, and sometimes even on quantitative details of the community (e.g. relative fitness of the two species, initial conditions). Our results, combined with potential violation of the additivity assumption in many-species communities, suggest that pairwise modeling will often fail to predict microbial dynamics. DOI: http://dx.doi.org/10.7554/eLife.25051.001 PMID:28350295

Involvement of NMDA receptors and L-arginine/nitric oxide/cyclic guanosine monophosphate pathway in the antidepressant-like effects of topiramate in mice forced swimming test.

PubMed

Ostadhadi, Sattar; Khan, Muhammad Imran; Norouzi-Javidan, Abbas; Chamanara, Mohsen; Jazaeri, Farahnaz; Zolfaghari, Samira; Dehpour, Ahmad-Reza

2016-04-01

Topiramate (TPM) is an agent primarily used in the treatment of epilepsy. Using mice model of forced swimming test (FST) the current study was basically aimed to investigate the influence of TPM on depression by inhibiting NMDA receptor and nitric oxide-cGMP production. When TPM was administered in a dose of 20 and 30 mg/kg by i.p. route it reduced the immobility time during FST. However this effect of TPM (30 mg/kg, i.p.) in the FST was abolished when the mice were pretreated either with NMDA (75 mg/kg, i.p.), or l-arginine (750 mg/kg, i.p. NO precursor), or sildenafil (5mg/kg, i.p. Phosphodiesterase 5 inhibitor). The immobility time in the FST was reduced after administration of L-NAME (10mg/kg, i.p, a non-specific NOS inhibitor), 7-nitoinidazol (30 mg/kg, i.p. a nNOS inhibitor) or MK-801 (0.05 mg/kg, i.p, a NMDA receptor antagonist) in combination with a subeffective dose of TPM (10mg/kg, i.p.) as compared with single use of either drug. Co-administrated of lower doses of MK-801 (0.01 mg/kg) or L-NAME (1mg/kg) failed to effect immobility time. However, simultaneous administration of these two agents in the same doses with subeffective dose of TPM (10mg/kg, i.p.), reduced the immobility time during FST. None of these drugs were found to have a profound effect on the locomotor activity per se during the open field test. Taken together, our data demonstrates that TPM exhibit antidepressant-like effect which is accomplished either due to inhibition of NMDA receptors or NO-cGMP production. Copyright © 2016 Elsevier Inc. All rights reserved.

Noninferiority of glucose-6-phosphate dehydrogenase deficiency diagnosis by a point-of-care rapid test vs the laboratory fluorescent spot test demonstrated by copper inhibition in normal human red blood cells.

PubMed

Baird, J Kevin; Dewi, Mewahyu; Subekti, Decy; Elyazar, Iqbal; Satyagraha, Ari W

2015-06-01

Tens of millions of patients diagnosed with vivax malaria cannot safely receive primaquine therapy against repeated attacks caused by activation of dormant liver stages called hypnozoites. Most of these patients lack access to screening for glucose-6-phosphate dehydrogenase (G6PD) deficiency, a highly prevalent disorder causing serious acute hemolytic anemia with primaquine therapy. We optimized CuCl inhibition of G6PD in normal red blood cells (RBCs) to assess G6PD diagnostic technologies suited to point of care in the impoverished rural tropics. The most widely applied technology for G6PD screening-the fluorescent spot test (FST)-is impractical in that setting. We evaluated a new point-of-care G6PD screening kit (CareStart G6PD, CSG) against FST using graded CuCl treatments to simulate variable hemizygous states, and varying proportions of CuCl-treated RBC suspensions to simulate variable heterozygous states of G6PD deficiency. In experiments double-blinded to CuCl treatment, technicians reading FST and CSG test (n = 269) classified results as positive or negative for deficiency. At G6PD activity ≤40% of normal (n = 112), CSG test was not inferior to FST in detecting G6PD deficiency (P = 0.003), with 96% vs 90% (P = 0.19) sensitivity and 75% and 87% (P = 0.01) specificity, respectively. The CSG test costs less, requires no specialized equipment, laboratory skills, or cold chain for successful application, and performs as well as the FST standard of care for G6PD screening. Such a device may vastly expand access to primaquine therapy and aid in mitigating the very substantial burden of morbidity and mortality imposed by the hypnozoite reservoir of vivax malaria. Copyright © 2015 Elsevier Inc. All rights reserved.

Involvement of N-methyl-d-aspartate receptors in the antidepressant-like effect of 5-hydroxytryptamine 3 antagonists in mouse forced swimming test and tail suspension test.

PubMed

Kordjazy, Nastaran; Haj-Mirzaian, Arya; Amiri, Shayan; Ostadhadi, Sattar; Amini-Khoei, Hossein; Dehpour, Ahmad Reza

2016-02-01

Recent evidence indicates that 5-hydroxytryptamine 3 (5-HT3) antagonists such as ondansetron and tropisetron exert positive behavioral effects in animal models of depression. Due to the ionotropic nature of 5-HT3 and N-methyl-d-aspartate (NMDA) receptors, plus their contribution to the pathophysiology of depression, we investigated the possible role of NMDA receptors in the antidepressant-like effect of 5-HT3 receptor antagonists in male mice. In order to evaluate the animals' behavior in response to different treatments, we performed open-field test (OFT), forced swimming test (FST), and tail-suspension test (TST), which are considered as valid tasks for measuring locomotor activity and depressive-like behaviors in mice. Our data revealed that intraperitoneal (i.p.) administration of tropisetron (5, 10, and 30mg/kg) and ondansetron (0.01, and 0.1μg/kg) significantly decreased the immobility time in FST and TST. Also, co-administration of subeffective doses of tropisetron (1mg/kg, i.p.) or ondansetron (0.001μg/kg, i.p.) with subeffective doses of NMDA receptor antagonists, ketamine (1mg/kg, i.p.), MK-801 (0.05mg/kg, i.p.) and magnesium sulfate (10mg/kg, i.p.) resulted in a reduced immobility time both in FST and TST. The subeffective dose of NMDA (NMDA receptor agonist, 75mg/kg, i.p.) abolished the effects of 5-HT3 antagonists in FST and TST, further supporting the presumed interaction between 5-HT3 and NMDA receptors. These treatments did not affect the locomotor behavior of animals in OFT. Finally, the results of our study suggest that the positive effects of 5-HT3 antagonists on the coping behavior of mice in FST and TST are at least partly mediated through NMDA receptors participation. Copyright © 2015 Elsevier Inc. All rights reserved.

Pharmacological evidence for the involvement of the NMDA receptor and nitric oxide pathway in the antidepressant-like effect of lamotrigine in the mouse forced swimming test.

PubMed

Ostadhadi, Sattar; Ahangari, Mohammad; Nikoui, Vahid; Norouzi-Javidan, Abbas; Zolfaghari, Samira; Jazaeri, Farahnaz; Chamanara, Mohsen; Akbarian, Reyhaneh; Dehpour, Ahmad-Reza

2016-08-01

Lamotrigine is an anticonvulsant agent that shows clinical antidepressant properties. The aim of the present study was to investigate the involvement of N-methyl-d-aspartate (NMDA) receptors and nitric oxide-cyclic guanosine monophosphate (NO-cGMP) synthesis in possible antidepressant-like effect of lamotrigine in forced swimming test (FST) in mice. Intraperitoneal administration of lamotrigine (10mg/kg) decreased the immobility time in the FST (P<0.01) without any effect on locomotor activity in the open-field test (OFT), while higher dose of lamotrigine (30mg/kg) reduced the immobility time in the FST (P<0.001) as well as the number of crossings in the OFT. Pretreatment of animals with NMDA (75mg/kg), l-arginine (750mg/kg, a substrate for nitric oxide synthase [NOS]) or sildenafil (5mg/kg, a phosphodiesterase [PDE] 5 inhibitor) reversed the antidepressant-like effect of lamotrigine (10mg/kg) in the FST. Injection of l-nitroarginine methyl ester (l-NAME, 10mg/kg, a non-specific NOS inhibitor), 7-nitroindazole (30mg/kg, a neuronal NOS inhibitor), methylene blue (20mg/kg, an inhibitor of both NOS and soluble guanylate cyclase [sGC]), or MK-801 (0.05mg/kg), ketamine (1mg/kg), and magnesium sulfate (10mg/kg) as NMDA receptor antagonists in combination with a sub-effective dose of lamotrigine (5mg/kg) diminished the immobility time of animals in the FST compared with either drug alone. None of the drugs produced significant effects on the locomotor activity in the OFT. Based on our findings, it is suggested that the antidepressant-like effect of lamotrigine might mediated through inhibition of either NMDA receptors or NO-cGMP synthesis. Copyright © 2016. Published by Elsevier Masson SAS.

Surnames in Honduras: A study of the population of Honduras through isonymy.

PubMed

Herrera Paz, Edwin Francisco; Scapoli, Chiara; Mamolini, Elisabetta; Sandri, Massimo; Carrieri, Alberto; Rodriguez-Larralde, Alvaro; Barrai, Italo

2014-05-01

In this work, we investigated surname distribution in 4,348,021 Honduran electors with the aim of detecting population structure through the study of isonymy in three administrative levels: the whole nation, the 18 departments, and the 298 municipalities. For each administrative level, we studied the surname effective number, α, the total inbreeding, FIT , the random inbreeding, FST , and the local inbreeding, FIS . Principal components analysis, multidimensional scaling, and cluster analysis were performed on Lasker's distance matrix to detect the direction of surname diffusion and for a graphic representation of the surname relationship between different locations. The values of FIT , FST , and FIS display a variation of random inbreeding between the administrative levels in the Honduras population, which is attributed to the "Prefecture effect." Multivariate analyses of department data identified two main clusters, one south-western and the second north-eastern, with the Bay Islands and the eastern Gracias a Dios out of the main clusters. The results suggest that currently the population structure of this country is the result of the joint action of short-range directional migration and drift, with drift dominating over migration, and that population diffusion may have taken place mainly in the NW-SE direction. © 2014 John Wiley & Sons Ltd/University College London.

Identifying Genetic Signatures of Natural Selection Using Pooled Population Sequencing in Picea abies

PubMed Central

Chen, Jun; Källman, Thomas; Ma, Xiao-Fei; Zaina, Giusi; Morgante, Michele; Lascoux, Martin

2016-01-01

The joint inference of selection and past demography remain a costly and demanding task. We used next generation sequencing of two pools of 48 Norway spruce mother trees, one corresponding to the Fennoscandian domain, and the other to the Alpine domain, to assess nucleotide polymorphism at 88 nuclear genes. These genes are candidate genes for phenological traits, and most belong to the photoperiod pathway. Estimates of population genetic summary statistics from the pooled data are similar to previous estimates, suggesting that pooled sequencing is reliable. The nonsynonymous SNPs tended to have both lower frequency differences and lower FST values between the two domains than silent ones. These results suggest the presence of purifying selection. The divergence between the two domains based on synonymous changes was around 5 million yr, a time similar to a recent phylogenetic estimate of 6 million yr, but much larger than earlier estimates based on isozymes. Two approaches, one of them novel and that considers both FST and difference in allele frequencies between the two domains, were used to identify SNPs potentially under diversifying selection. SNPs from around 20 genes were detected, including genes previously identified as main target for selection, such as PaPRR3 and PaGI. PMID:27172202

Identifying Genetic Signatures of Natural Selection Using Pooled Population Sequencing in Picea abies.

PubMed

Chen, Jun; Källman, Thomas; Ma, Xiao-Fei; Zaina, Giusi; Morgante, Michele; Lascoux, Martin

2016-07-07

The joint inference of selection and past demography remain a costly and demanding task. We used next generation sequencing of two pools of 48 Norway spruce mother trees, one corresponding to the Fennoscandian domain, and the other to the Alpine domain, to assess nucleotide polymorphism at 88 nuclear genes. These genes are candidate genes for phenological traits, and most belong to the photoperiod pathway. Estimates of population genetic summary statistics from the pooled data are similar to previous estimates, suggesting that pooled sequencing is reliable. The nonsynonymous SNPs tended to have both lower frequency differences and lower FST values between the two domains than silent ones. These results suggest the presence of purifying selection. The divergence between the two domains based on synonymous changes was around 5 million yr, a time similar to a recent phylogenetic estimate of 6 million yr, but much larger than earlier estimates based on isozymes. Two approaches, one of them novel and that considers both FST and difference in allele frequencies between the two domains, were used to identify SNPs potentially under diversifying selection. SNPs from around 20 genes were detected, including genes previously identified as main target for selection, such as PaPRR3 and PaGI. Copyright © 2016 Chen et al.

Genetic characterization of Russian honey bee stock selected for improved resistance to Varroa destructor.

PubMed

Bourgeois, A Lelania; Rinderer, Thomas E

2009-06-01

Maintenance of genetic diversity among breeding lines is important in selective breeding and stock management. The Russian Honey Bee Breeding Program has strived to maintain high levels of heterozygosity among its breeding lines since its inception in 1997. After numerous rounds of selection for resistance to tracheal and varroa mites and improved honey production, 18 lines were selected as the core of the program. These lines were grouped into three breeding blocks that were crossbred to improve overall heterozygosity levels of the population. Microsatellite DNA data demonstrated that the program has been successful. Heterozygosity and allelic richness values are high and there are no indications of inbreeding among the three blocks. There were significant levels of genetic structure measured among the three blocks. Block C was genetically distinct from both blocks A and B (F(ST) = 0.0238), whereas blocks A and B did not differ from each other (F(ST) = 0.0074). The same pattern was seen for genic (based on numbers of alleles) differentiation. Genetic distance, as measured by chord distance, indicates that all of the 18 lines are equally distant, with minimal clustering. The data indicate that the overall design of the breeding program has been successful in maintaining high levels of diversity and avoiding problems associated with inbreeding.

Synthesis and evaluation of novel marine bromopyrrole alkaloid-based derivatives as potential antidepressant agents.

PubMed

Rane, Rajesh A; Napahde, Shital; Bangalore, Pavan Kumar; Sahu, Niteshkumar U; Shah, Nishant; Kulkarni, Yogesh A; Barve, Kalyani; Lokare, Leena; Karpoormath, Rajshekhar

2014-11-01

Herein, we report synthesis and screening of a series of twenty derivatives of bromopyrrole alkaloids with aroyl hydrazone feature for antidepressant activity by forced swim test (FST), tail suspension test (TST), and actophotometer method. The molecules were further evaluated for in vitro human MAO's inhibitory activities. The tested compounds exhibited moderate to good antidepressant activity compared with standard fluoxetine. Among these, most promising antidepressant derivatives 5b (%DID = 60.48), 5e (%DID = 59), and 5j (%DID = 74.86) reduced immobility duration of 50-70% at 30 mg/kg dose levels in FST. Further, derivative 5b, 5e, and 5j displayed good antidepressant activity with %DID value of 47.50, 46.62, and 52.49, respectively, in TST compared with standard fluoxetine (66.56% DID). Compound 5b showed high in vitro MAO-A potency and selectivity (Ki MAO-A (μM) = 2.4 ± 0.99, SI = 0.06) with promising pharmacological activity recognizing its potential as antidepressant lead candidate for further drug development. Study revealed that the presence of halogen atoms such as chlorine and fluorine at ortho- and/or para-position of phenyl ring and N-alkylation of pyrrole core is favored features for antidepressant activity. © 2014 John Wiley & Sons A/S.

Phylogeography of the sandy beach amphipod Haustorioides japonicus along the Sea of Japan: Paleogeographical signatures of cryptic regional divergences

NASA Astrophysics Data System (ADS)

Takada, Yoshitake; Sakuma, Kay; Fujii, Tetsuo; Kojima, Shigeaki

2018-01-01

Recent findings of genetic breaks within apparently continuous marine populations challenge the traditional vicariance paradigm in population genetics. Such "invisible" boundaries are sometimes associated with potential geographic barriers that have forced divergence of an ancestral population, habitat discontinuities, biogeographic disjunctions due to environmental gradients, or a combination of these factors. To explore the factors that influence the genetic population structure of apparently continuous populations along the Sea of Japan, the sandy beach amphipod Haustorioides japonicus was examined. We sampled a total of 300 individuals of H. japonicus from the coast of Japan, and obtained partial sequences of the mitochondrial COI gene. The sequences from 19 local populations were clustered into five groups (Northwestern Pacific, Northern, Central, Southern Sea of Japan, and East China Sea) based on a spatial genetic mixture analysis and a minimum-spanning network. AMOVA and pairwise Fst tests further supported the significant divergence of the five groups. Phylogenetic analysis revealed the relationship among the haplotypes of H. japonicus and outgroups, which inferred the northward range expansion of the species. A relaxed molecular-clock Bayesian analysis inferred the early-to middle-Pleistocene divergence of the populations. Among the five clusters, the Central Sea of Japan showed the highest values for genetic diversity indices indicating the existence of a relatively stable and large population there. The hypothesis is also supported by Bayesian Skyline Plots that showed sudden population expansion for all the clusters except for Central Sea of Japan. The present study shows genetic boundaries between the Sea of Japan and the neighboring seas, probably due to geographic isolation during the Pleistocene glacial periods. We further found divergence between the populations along the apparently continuous coast of the Sea of Japan. Historical changes in the geographic range of H. japonicus in relation to sandy beach habitat availability, account for the genetic breaks among the three populations in the Sea of Japan. The present results infer that the past geographic events influenced the population formation of H. japonicus.

Proceedings of the Annual Conference of the Military Testing Association (23rd) held at Arlington, Virginia on 25-30 October 1981. Volume 2

DTIC Science & Technology

1981-10-01

differentiated the high from low performers on * the criterion. Once a total score based on the differentiating items was computed, this score was... high school or worked a certain number of hours while in school, perform better on the FST, receive higher ratings on training school criteria and...closets are not related to performance on the FST, even though they would have a high probability of correlating with job proficiency measures. From

N -term pairwise-correlation inequalities, steering, and joint measurability

NASA Astrophysics Data System (ADS)

Karthik, H. S.; Devi, A. R. Usha; Tej, J. Prabhu; Rajagopal, A. K.; Sudha, Narayanan, A.

2017-05-01

Chained inequalities involving pairwise correlations of qubit observables in the equatorial plane are constructed based on the positivity of a sequence of moment matrices. When a jointly measurable set of positive-operator-valued measures (POVMs) is employed in the first measurement of every pair of sequential measurements, the chained pairwise correlations do not violate the classical bound imposed by the moment matrix positivity. We find that incompatibility of the set of POVMs employed in first measurements is only necessary, but not sufficient, in general, for the violation of the inequality. On the other hand, there exists a one-to-one equivalence between the degree of incompatibility (which quantifies the joint measurability) of the equatorial qubit POVMs and the optimal violation of a nonlocal steering inequality, proposed by Jones and Wiseman [S. J. Jones and H. M. Wiseman, Phys. Rev. A 84, 012110 (2011), 10.1103/PhysRevA.84.012110]. To this end, we construct a local analog of this steering inequality in a single-qubit system and show that its violation is a mere reflection of measurement incompatibility of equatorial qubit POVMs, employed in first measurements in the sequential unsharp-sharp scheme.

A spreadsheet template compatible with Microsoft Excel and iWork Numbers that returns the simultaneous confidence intervals for all pairwise differences between multiple sample means.

PubMed

Brown, Angus M

2010-04-01

The objective of the method described in this paper is to develop a spreadsheet template for the purpose of comparing multiple sample means. An initial analysis of variance (ANOVA) test on the data returns F--the test statistic. If F is larger than the critical F value drawn from the F distribution at the appropriate degrees of freedom, convention dictates rejection of the null hypothesis and allows subsequent multiple comparison testing to determine where the inequalities between the sample means lie. A variety of multiple comparison methods are described that return the 95% confidence intervals for differences between means using an inclusive pairwise comparison of the sample means. 2009 Elsevier Ireland Ltd. All rights reserved.

Social relationships as a major determinant in the valuation of health states.

PubMed

Frick, Ulrich; Irving, Hyacinth; Rehm, Jürgen

2012-03-01

To empirically determine the impact of the capacity to sustain social relationships on valuing health states. 68 clinical experts conducted a health state valuation exercise in five sites using pairwise comparison, ranking, and person trade-off as elicitation methods. 23,840 pairwise comparisons of a total of 379 health states were analyzed by conditional logistic regression. Social relationships had a clear monotonic association with perceived disability: the more limited the capacity to sustain social relationships, the more disabling the resulting health state valuations. The highest level of limitations with respect to social relationships was associated with slightly lower impact on health state valuations compared to the highest level of limitations in physical functioning. Social relationships showed an independent contribution to health state valuations and should be included in health state measures.

Identification of multiple genetic loci in the mouse controlling immobility time in the tail suspension and forced swimming tests.

PubMed

Abou-Elnaga, Ahmed F; Torigoe, Daisuke; Fouda, Mohamed M; Darwish, Ragab A; Abou-Ismail, Usama A; Morimatsu, Masami; Agui, Takashi

2015-05-01

Depression is one of the most famous psychiatric disorders in humans in all over the countries and considered a complex neurobehavioral trait and difficult to identify causal genes. Tail suspension test (TST) and forced swimming test (FST) are widely used for assessing depression-like behavior and antidepressant activity in mice. A variety of antidepressant agents are known to reduce immobility time in both TST and FST. To identify genetic determinants of immobility duration in both tests, we analyzed 101 F2 mice from an intercross between C57BL/6 and DBA/2 strains. Quantitative trait locus (QTL) mapping using 106 microsatellite markers revealed three loci (two significant and one suggestive) and five suggestive loci controlling immobility time in the TST and FST, respectively. Results of QTL analysis suggest a broad description of the genetic architecture underlying depression, providing underpinnings for identifying novel molecular targets for antidepressants to clear the complex genetic mechanisms of depressive disorders.

LOSITAN: a workbench to detect molecular adaptation based on a Fst-outlier method.

PubMed

Antao, Tiago; Lopes, Ana; Lopes, Ricardo J; Beja-Pereira, Albano; Luikart, Gordon

2008-07-28

Testing for selection is becoming one of the most important steps in the analysis of multilocus population genetics data sets. Existing applications are difficult to use, leaving many non-trivial, error-prone tasks to the user. Here we present LOSITAN, a selection detection workbench based on a well evaluated Fst-outlier detection method. LOSITAN greatly facilitates correct approximation of model parameters (e.g., genome-wide average, neutral Fst), provides data import and export functions, iterative contour smoothing and generation of graphics in a easy to use graphical user interface. LOSITAN is able to use modern multi-core processor architectures by locally parallelizing fdist, reducing computation time by half in current dual core machines and with almost linear performance gains in machines with more cores. LOSITAN makes selection detection feasible to a much wider range of users, even for large population genomic datasets, by both providing an easy to use interface and essential functionality to complete the whole selection detection process.

11-β hydroxysteroid type 1 knockout mice display an antidepressant-like phenotype in the forced swim test.

PubMed

Slattery, David A; Uzunov, Doncho P; Cryan, John F

2016-02-01

11β-dehydroxysteroid dehydrogenase (HSD) types 1 and 2, enzymes are involved in the activation and inactivation of glucocorticoids in vivo, respectively. Indirect evidence implicates two enzymes in the aetiology of depression but no study has directly assessed the potential role of 11 β-HSD1 in animal tests. We assessed 11 β-HSD1 knockout mice in the forced swim test (FST), tail suspension test (TST) and for locomotor activity. Genetic ablation of the 11β-HSD1 gene results in an antidepressant-like phenotype in the FST; the most widely utilised animal test of antidepressant activity, but not in the related TST. This may be related to the different biological substrates underlying these tests. The decreased FST immobility was not due to alterations in general activity. Taken together these results suggest that 11β-HSD1 may play an important role in depression-related behaviours and further studies are necessary to fully characterise its role in such behaviour.

Augmentation of the behavioural effects of desipramine by repeated immobilization stress.

PubMed

Hadweh, Nicolás; Santibañez, Marcos; González, Marcela Paz; Forray, María Inés

2010-12-25

The present report provides evidence that repeated immobilization stress (RIS) induced a noradrenergic-dependent depressive-like behaviour and an augmented behavioural response to desipramine (DMI), a noradrenaline reuptake inhibitor (NRI), in the forced swimming test (FST). The present results show that RIS decreased the baseline of climbing behaviour in the FST. Whereas subchronic administration of DMI (10mg/kg, three times in a 24h period) induced a significantly higher increase in climbing behaviour on repeatedly stressed rats compared to controls. The results also show that the concomitant administration of the low dose of DMI (3mg/Kg) during the RIS fully prevented the decrease of climbing behaviour induced by RIS, without exerting behavioural effects in control rats, further supporting an augmented response to the DMI antidepressant effects in the repeatedly stressed rats. In conclusion, our data indicate that RIS not only changes the behavioural responses in the FST but also increases the antidepressant effects of DMI. Copyright (c) 2010 Elsevier B.V. All rights reserved.

Progesterone receptor antagonist CDB-4124 increases depression-like behavior in mice without affecting locomotor ability

PubMed Central

Beckley, Ethan H.; Scibelli, Angela C.; Finn, Deborah A.

2010-01-01

Progesterone withdrawal has been proposed as an underlying factor in premenstrual syndrome and postpartum depression. Progesterone withdrawal induces forced swim test (FST) immobility in mice, a depression-like behavior, but the contribution of specific receptors to this effect is unclear. The role of progesterone’s GABAA receptor-modulating metabolite allopregnanolone in depression- and anxiety-related behaviors has been extensively documented, but little attention has been paid to the role of progesterone receptors. We administered the classic progesterone receptor antagonist mifepristone (RU-38486) and the specific progesterone receptor antagonist CDB-4124 to mice that had been primed with progesterone for five days, and found that both compounds induced FST immobility reliably, robustly, and in a dose-dependent fashion. Although CDB-4124 increased FST immobility, it did not suppress initial activity in a locomotor test. These findings suggest that decreased progesterone receptor activity contributes to depression-like behavior in mice, consistent with the hypothesis that progesterone withdrawal may contribute to the symptoms of premenstrual syndrome or postpartum depression. PMID:21163582

Cryogenic hydrogen fuel for controlled inertial confinement fusion (formation of reactor-scale cryogenic targets)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aleksandrova, I. V.; Koresheva, E. R., E-mail: elena.koresheva@gmail.com; Krokhin, O. N.

2016-12-15

In inertial fusion energy research, considerable attention has recently been focused on low-cost fabrication of a large number of targets by developing a specialized layering module of repeatable operation. The targets must be free-standing, or unmounted. Therefore, the development of a target factory for inertial confinement fusion (ICF) is based on methods that can ensure a cost-effective target production with high repeatability. Minimization of the amount of tritium (i.e., minimization of time and space at all production stages) is a necessary condition as well. Additionally, the cryogenic hydrogen fuel inside the targets must have a structure (ultrafine layers—the grain sizemore » should be scaled back to the nanometer range) that supports the fuel layer survivability under target injection and transport through the reactor chamber. To meet the above requirements, significant progress has been made at the Lebedev Physical Institute (LPI) in the technology developed on the basis of rapid fuel layering inside moving free-standing targets (FST), also referred to as the FST layering method. Owing to the research carried out at LPI, unique experience has been gained in the development of the FST-layering module for target fabrication with an ultrafine fuel layer, including a reactor- scale target design. This experience can be used for the development of the next-generation FST-layering module for construction of a prototype of a target factory for power laser facilities and inertial fusion power plants.« less

Differential involvement of 5-HT(1A) and 5-HT(1B/1D) receptors in human interferon-alpha-induced immobility in the mouse forced swimming test.

PubMed

Zhang, Hongmei; Wang, Wei; Jiang, Zhenzhou; Shang, Jing; Zhang, Luyong

2010-01-01

Although Interferon-alpha (IFN-alpha, CAS 9008-11-1) is a powerful drug in treating several viral infections and certain tumors, a considerable amount of neuropsychiatric side-effects such as depression and anxiety are an unavoidable consequence. Combination with the selective serotonin (5-HT) reuptake inhibitor (SSRI) fluoxetine (CAS 56296-78-7) significantly improved the situation. However, the potential 5-HT(1A) receptor- and 5-HT(1B) receptor-signals involved in the antidepressant effects are still unclear. The effects of 5-HT(1A) receptor- and 5-HT(1B) receptor signals were analyzed by using the mouse forced swimming test (FST), a predictive test of antidepressant-like action. The present results indicated that (1) fluoxetine (administrated intragastrically, 30 mg/kg; not subactive dose: 15 mg/kg) significantly reduced IFN-alpha-induced increase of the immobility time in the forced swimming test; (2) 5-HT(1A) receptor- and 5-HT(1B) receptor ligands alone or in combination had no effects on IFN-alpha-induced increase of the immobility time in the FST; (3) surprisingly, WAY 100635 (5-HT(1A) receptor antagonist, 634908-75-1) and 8-OH-DPAT(5-HT(1A) receptor agonist, CAS 78950-78-4) markedly enhanced the antidepressant effect of fluoxetine at the subactive dose (15 mg/kg, i. g.) on the IFN-alpha-treated mice in the FST. Further investigations showed that fluoxetine combined with WAY 100635 and 8-OH-DPAT failed to produce antidepressant effects in the FST. (4) Co-application of CGS 12066A (5-HT(1B) receptor agonist, CAS 109028-09-3) or GR 127935 (5-HT(1B/1D) receptor antagonist, CAS 148642-42-6) with fluoxetine had no synergistic effects on the IFN-alpha-induced increase of immobility time in FST. (5) Interestingly, co-administration of GR 127935, WAY 100635 and fluoxetine significantly reduced the IFN-alpha-induced increase in immobility time of FST, being more effective than co-administration of WAY 100635 and fluoxetine. All results suggest that (1) compared to the 5-HT(1B) receptor, the 5-HT(1A) receptor signal plays the dominant role in improving the anti-immobility effect of fluoxetine in the IFN-alpha-induced depression; (2) combination of the 5-HT(1A) antagonist with subactive fluoxetine can be helpful in IFN-alpha-induced depression treatment.

Evolution of biological sequences implies an extreme value distribution of type I for both global and local pairwise alignment scores.

PubMed

Bastien, Olivier; Maréchal, Eric

2008-08-07

Confidence in pairwise alignments of biological sequences, obtained by various methods such as Blast or Smith-Waterman, is critical for automatic analyses of genomic data. Two statistical models have been proposed. In the asymptotic limit of long sequences, the Karlin-Altschul model is based on the computation of a P-value, assuming that the number of high scoring matching regions above a threshold is Poisson distributed. Alternatively, the Lipman-Pearson model is based on the computation of a Z-value from a random score distribution obtained by a Monte-Carlo simulation. Z-values allow the deduction of an upper bound of the P-value (1/Z-value2) following the TULIP theorem. Simulations of Z-value distribution is known to fit with a Gumbel law. This remarkable property was not demonstrated and had no obvious biological support. We built a model of evolution of sequences based on aging, as meant in Reliability Theory, using the fact that the amount of information shared between an initial sequence and the sequences in its lineage (i.e., mutual information in Information Theory) is a decreasing function of time. This quantity is simply measured by a sequence alignment score. In systems aging, the failure rate is related to the systems longevity. The system can be a machine with structured components, or a living entity or population. "Reliability" refers to the ability to operate properly according to a standard. Here, the "reliability" of a sequence refers to the ability to conserve a sufficient functional level at the folded and maturated protein level (positive selection pressure). Homologous sequences were considered as systems 1) having a high redundancy of information reflected by the magnitude of their alignment scores, 2) which components are the amino acids that can independently be damaged by random DNA mutations. From these assumptions, we deduced that information shared at each amino acid position evolved with a constant rate, corresponding to the information hazard rate, and that pairwise sequence alignment scores should follow a Gumbel distribution, which parameters could find some theoretical rationale. In particular, one parameter corresponds to the information hazard rate. Extreme value distribution of alignment scores, assessed from high scoring segments pairs following the Karlin-Altschul model, can also be deduced from the Reliability Theory applied to molecular sequences. It reflects the redundancy of information between homologous sequences, under functional conservative pressure. This model also provides a link between concepts of biological sequence analysis and of systems biology.

Genetic composition and connectivity of the Antillean manatee (Trichechus manatus manatus) in Panama

USGS Publications Warehouse

Díaz-Ferguson, Edgardo; Hunter, Margaret; Guzmán, Héctor M.

2017-01-01

Genetic diversity and haplotype composition of the West Indian manatee (Trichechus manatus) population from the San San Pond Sak wetland in Bocas del Toro, Panama was studied using a segment of mitochondrial DNA (D’loop). No genetic information has been published to date for Panamanian populations. Due to the secretive behavior and small population size of the species in the area, DNA extraction was conducted from opportunistically collected fecal (N=20), carcass tissue (N=4) and bone (N=4) samples. However, after DNA processing only 10 samples provided good quality DNA for sequencing (3 fecal, 4 tissue and 3 bone samples). We found three haplotypes in total; two of these haplotypes are reported for the first time, J02 (N=3) and J03 (N=4), and one J01 was previously published (N=3). Genetic diversity showed similar values to previous studies conducted in other Caribbean regions with moderate values of nucleotide diversity (π= 0.00152) and haplotipic diversity (Hd= 0.57). Connectivity assessment was based on sequence similarity, genetic distance and genetic differentiation between San San population and other manatee populations previously studied. The J01 haplotype found in the Panamanian population is shared with populations in the Caribbean mainland and the Gulf of Mexico showing a reduced differentiation corroborated with Fst value between HSSPS and this region of 0.0094. In contrast, comparisons between our sequences and populations in the Eastern Caribbean (South American populations) and North Western Caribbean showed fewer similarities (Fst =0.049 and 0.058, respectively). These results corroborate previous phylogeographic patterns already established for manatee populations and situate Panamanian populations into the Belize and Mexico cluster. In addition, these findings will be a baseline for future studies and comparisons with manatees in other areas of Panama and Central America. These results should be considered to inform management decisions regarding conservation of genetic diversity, future controlled introductions, connectivity and effective population size of the West Indian manatee along the Central American corridor.

Allozyme diversity and morphometrics of Melocactus paucispinus (Cactaceae) and evidence for hybridization with M. concinnus in the Chapada Diamantina, North-eastern Brazil.

PubMed

Lambert, Sabrina Mota; Borba, Eduardo Leite; Machado, Marlon Câmara; Da Silva Andrade, Sónia Cristina

2006-03-01

Melocacatus paucispinus (Cactaceae) is endemic to the state of Bahia, Brazil, and due to its rarity and desirability to collectors it has been considered threatened with extinction. This species is usually sympatric and inter-fertile with M. concinnus, and morphological evidence for hybridization between them is present in some populations. Levels of genetic and morphological variation and sub-structuring in populations of these species were assessed and an attempt was made to verify the occurrence of natural hybridization between them. Genetic variability was surveyed using allozymes (12 loci) and morphological variability using multivariate morphometric analyses (17 vegetative characters) in ten populations of M. paucispinus and three of M. concinnus occurring in the Chapada Diamantina, Bahia. Genetic variability was low in both species (P = 0.0-33.3, A = 1.0-1.6, H(e) = 0.000-0.123 in M. paucispinus; P = 0.0-25.0, A = 1.0-1.4, H(e) = 0.000-0.104 in M. concinnus). Deficit of heterozygotes within the populations was detected in both species, with high values of F(IS) (0.732 and 0.901 in M. paucispinus and M. concinnus, respectively). Evidence of hybridization was detected by the relative allele frequency in the two diaphorase loci. High levels of genetic (F(ST) = 0.504 in M. paucispinus and 0.349 in M. concinnus) and morphological (A = 0.20 in M. paucispinus and 0.17 in M. concinnus) structuring among populations were found. The Melocactus spp. displayed levels of genetic variability lower than the values reported for other cactus species. The evidence indicates the occurrence of introgression in both species at two sites. The high F(ST) values cannot be explained by geographical substructuring, but are consistent with hybridization. Conversely, morphological differentiation in M. paucispinus, but not in M. concinnus, is probably due to isolation by distance.

[Influence of estradiol on tryptophan hydroxylase and 5-hydroxytryptamine content in raphe nuclei of rats under forced swimming stress].

PubMed

Yang, Fu-zhong; Wu, Yan; Zhang, Wei-guo; Cai, Yi-yun; Shi, Shen-xun

2010-07-20

To investigate the effect of estradiol (E2) on tryptophan hydroxylase (TPH) and 5-hydroxytryptamine (5-HT) content in raphe nuclei of rats under forced swimming stress and explore the role of estrogen and stress in disease mechanism of depression in women. At Week 3 post-ovariectomy, 35 ovariectomized (OVX) female SD rats were randomly divided into 5 groups (n = 7): non-stress group, control group, estradiol (E2) group and fluoxetine (FLX) group and E2 plus FLX group. Animals were administered with different drugs for 2 weeks. At Day 14, animals except those in the non-stress group were subjected to the 15 min forced swimming test (FST). At 2 hours post-FST, all animals including those in the non-stress group were perfused with 4% paraformaldehyde and brains removed for TPH and 5-HT immunofluorescence staining. We compared the content of TPH and 5-HT by observing and calculating the integrated optical density (IOD) of immunofluorescent-positive signals in raphe nuclei. (1) The IOD value of TPH- and 5-HT-positive region in raphe nuclei of rats in the control group was significantly lower than that of the non-stress group (P < 0.01); (2) the IOD value of TPH- and 5-HT-positive region in raphe nuclei of rats in the E2, FLX and E2 plus FLX groups was significantly higher than that in the control group (P < 0.05). Forced swimming stress can decrease the TPH and 5-HT content in raphe nuclei. Such changes can be prevented by a pre-administration of estradiol. Similar results are observed with antidepressant fluoxetine. These effects may underlie the role of estradiol and stress in the disease mechanism of depression in women.

Differentiation in stag beetles, Neolucanus swinhoei complex (Coleoptera: Lucanidae): four major lineages caused by periodical Pleistocene glaciations and separation by a mountain range.

PubMed

Tsai, Cheng-Lung; Wan, Xia; Yeh, Wen-Bin

2014-09-01

Taxonomic debates on Neolucanus swinhoei complex consisting of N. swinhoei, N. doro doro, N. doro horaguchii, and N. euganiae, distributed exclusively in Taiwan, have been ongoing for several decades because of their overlapping morphological characters. To clarify their taxonomic status and phylogeographical history, we analyzed nine morphological characteristics and four molecular amplicons. Phylogenetic inferences based on COI+16S rDNA+wingless showed one eastern and three western lineages, with the latter consisting of one low-hill and two montane lineages. Intermingled DNA sequences from different populations within each lineage, many low FST values, and a high variance component between lineages indicate the possibility of gene flow among populations. However, positive relationships were observed between the genetic divergences of 16S rDNA and its FST values with geographic distance. A divergence estimation based on COI+16S revealed that these beetles might have originated from Asian mainland and differentiated into western and eastern lineages ca. 1Mya, with the differentiation of the western lineages occurring approximately 0.50-0.75Mya. Isolation by mountain ranges and limited flying capability of these beetles as well as populations retreat to and expansion from refugia in response to glaciation cycles have resulted in the current distribution of N. swinhoei complex. Although most morphological characters are variable and undistinguishable, multi-dimensional scaling analysis based on measurable characteristics could recognize hill N. swinhoei as a cluster distinct from the others. However, based on the realities of genetic admixture, shared phylogeographical history and overlapping characteristics, all of these stag beetles should be regarded as Neolucanus swinhoei Bates, 1866. Copyright © 2014 Elsevier Inc. All rights reserved.

Low genetic variation and evidence of limited dispersal in the regionally important Belize manatee

USGS Publications Warehouse

Hunter, M.E.; Auil-Gomez, N. E.; Tucker, K.P.; Bonde, R.K.; Powell, J.; McGuire, P.M.

2010-01-01

The Antillean subspecies of the West Indian manatee Trichechus manatus is found throughout Central and South America and the Caribbean. Because of severe hunting pressure during the 17th through 19th centuries, only small populations of the once widespread aquatic mammal remain. Fortunately, protections in Belize reduced hunting in the 1930s and allowed the country's manatee population to become the largest breeding population in the Wider Caribbean. However, increasing and emerging anthropogenic threats such as coastal development, pollution, watercraft collision and net entanglement represent challenges to this ecologically important population. To inform conservation and management decisions, a comprehensive molecular investigation of the genetic diversity, relatedness and population structure of the Belize manatee population was conducted using mitochondrial and microsatellite DNA. Compared with other mammal populations, a low degree of genetic diversity was detected (HE=0.455; NA=3.4), corresponding to the small population size and long-term exploitation. Manatees from the Belize City Cayes and Southern Lagoon system were genetically different, with microsatellite and mitochondrial FST values of 0.029 and 0.078, respectively (P≤0.05). This, along with the distinct habitats and threats, indicates that separate protection of these two groups would best preserve the region's diversity. The Belize population and Florida subspecies appear to be unrelated with microsatellite and mitochondrial FST values of 0.141 and 0.63, respectively (P≤0.001), supporting the subspecies designations and suggesting low vagility throughout the northern Caribbean habitat. Further monitoring and protection may allow an increase in the Belize manatee genetic diversity and population size. A large and expanding Belize population could potentially assist in the recovery of other threatened or functionally extinct Central American Antillean manatee populations.

Does technique matter; a pilot study exploring weighting techniques for a multi-criteria decision support framework.

PubMed

van Til, Janine; Groothuis-Oudshoorn, Catharina; Lieferink, Marijke; Dolan, James; Goetghebeur, Mireille

2014-01-01

There is an increased interest in the use of multi-criteria decision analysis (MCDA) to support regulatory and reimbursement decision making. The EVIDEM framework was developed to provide pragmatic multi-criteria decision support in health care, to estimate the value of healthcare interventions, and to aid in priority-setting. The objectives of this study were to test 1) the influence of different weighting techniques on the overall outcome of an MCDA exercise, 2) the discriminative power in weighting different criteria of such techniques, and 3) whether different techniques result in similar weights in weighting the criteria set proposed by the EVIDEM framework. A sample of 60 Dutch and Canadian students participated in the study. Each student used an online survey to provide weights for 14 criteria with two different techniques: a five-point rating scale and one of the following techniques selected randomly: ranking, point allocation, pairwise comparison and best worst scaling. The results of this study indicate that there is no effect of differences in weights on value estimates at the group level. On an individual level, considerable differences in criteria weights and rank order occur as a result of the weight elicitation method used, and the ability of different techniques to discriminate in criteria importance. Of the five techniques tested, the pair-wise comparison of criteria has the highest ability to discriminate in weights when fourteen criteria are compared. When weights are intended to support group decisions, the choice of elicitation technique has negligible impact on criteria weights and the overall value of an innovation. However, when weights are used to support individual decisions, the choice of elicitation technique influences outcome and studies that use dissimilar techniques cannot be easily compared. Weight elicitation through pairwise comparison of criteria is preferred when taking into account its superior ability to discriminate between criteria and respondents' preferences.

Kernel machine methods for integrative analysis of genome-wide methylation and genotyping studies.

PubMed

Zhao, Ni; Zhan, Xiang; Huang, Yen-Tsung; Almli, Lynn M; Smith, Alicia; Epstein, Michael P; Conneely, Karen; Wu, Michael C

2018-03-01

Many large GWAS consortia are expanding to simultaneously examine the joint role of DNA methylation in addition to genotype in the same subjects. However, integrating information from both data types is challenging. In this paper, we propose a composite kernel machine regression model to test the joint epigenetic and genetic effect. Our approach works at the gene level, which allows for a common unit of analysis across different data types. The model compares the pairwise similarities in the phenotype to the pairwise similarities in the genotype and methylation values; and high correspondence is suggestive of association. A composite kernel is constructed to measure the similarities in the genotype and methylation values between pairs of samples. We demonstrate through simulations and real data applications that the proposed approach can correctly control type I error, and is more robust and powerful than using only the genotype or methylation data in detecting trait-associated genes. We applied our method to investigate the genetic and epigenetic regulation of gene expression in response to stressful life events using data that are collected from the Grady Trauma Project. Within the kernel machine testing framework, our methods allow for heterogeneity in effect sizes, nonlinear, and interactive effects, as well as rapid P-value computation. © 2017 WILEY PERIODICALS, INC.

Comparative Performance of Reagents and Platforms for Quantitation of Cytomegalovirus DNA by Digital PCR

PubMed Central

Gu, Z.; Sam, S. S.; Sun, Y.; Tang, L.; Pounds, S.; Caliendo, A. M.

2016-01-01

A potential benefit of digital PCR is a reduction in result variability across assays and platforms. Three sets of PCR reagents were tested on two digital PCR systems (Bio-Rad and RainDance), using three different sets of PCR reagents for quantitation of cytomegalovirus (CMV). Both commercial quantitative viral standards and 16 patient samples (n = 16) were tested. Quantitative accuracy (compared to nominal values) and variability were determined based on viral standard testing results. Quantitative correlation and variability were assessed with pairwise comparisons across all reagent-platform combinations for clinical plasma sample results. The three reagent sets, when used to assay quantitative standards on the Bio-Rad system, all showed a high degree of accuracy, low variability, and close agreement with one another. When used on the RainDance system, one of the three reagent sets appeared to have a much better correlation to nominal values than did the other two. Quantitative results for patient samples showed good correlation in most pairwise comparisons, with some showing poorer correlations when testing samples with low viral loads. Digital PCR is a robust method for measuring CMV viral load. Some degree of result variation may be seen, depending on platform and reagents used; this variation appears to be greater in samples with low viral load values. PMID:27535685

Genetic diversity and structure of Megabalanus azoricus in the Azores: Implications for aquaculture management

NASA Astrophysics Data System (ADS)

De Girolamo, Mirko; Torboli, Valentina; Pallavicini, Alberto; Isidro, Eduardo

2017-11-01

Megabalanus azoricus giant barnacles are the most traditional seafood of the Azores archipelago (NE Atlantic). This valuable commercial species has been highly exploited in the past and it is considered one of the key species for the development of aquaculture in the region. Despite the importance for conservation and aquaculture there is still a lack of basic information about M. azoricus genetic diversity and population structure. Here we used seven microsatellites markers to analyse 300 samples collected at six out of nine islands of the Azores archipelago, including also different locations from a single island, to provide information on the scale of genetic diversity and population structure of this species. Parameters like heterozygosity, allelic richness and effective number of alleles indicated a high genetic diversity and variability among islands. Pairwise comparisons and PCoA analysis on FST and Jost's DEST showed significant and evident differentiation among sampling locations. Additionally, AMOVA allocates a small (6.02%) but statistically significant portion of the variance to the among Island level revealing also a weak resolution (1.87%) at finer scale. Additionally Monte Carlo resampling methods indicated the most likely sources of the recruits were the local or adjacent populations. Genetic risks associated with the giant barnacle potential production scheme should be taken into account in a future management plan delimiting, as precautionary measure, this culture at a single island or at groups of islands here identified. Moreover a monitoring strategy should be implemented with the aim to evaluate possible changes in genetic parameters of native populations.

The possible physical barrier and coastal dispersal strategy for Japanese grenadier anchovy, Coilia nasus in the East China Sea and Yellow Sea: evidence from AFLP markers.

PubMed

Han, Zhi-Qiang; Han, Gang; Wang, Zhi-Yong; Gao, Tian-Xiang

2015-02-03

In order to ascertain the taxonomic status of the Ariake Sea population of Japanese grenadier anchovy, Coilia nasus, and assess the contemporary possible genetic barrier between the west and east coastal waters of the East China Sea, we used amplified fragment length polymorphism (AFLP) markers to detect the genetic structure of C. nasus, in the East China Sea and Yellow Sea. Eighty-one individuals of C. nasus were collected from five locations and 12 individuals of Coilia mystus were sampled from the Yangtze River Estuary. A total of 371 loci were detected by five primer combinations, 310 of which were polymorphic (83.56%). Analysis of molecular variation (AMOVA) and pairwise fixation index (FST) revealed significant genetic differentiation among five samples, indicating limited gene flow among populations. The dendrogram for populations by neighbor-joining (NJ) cluster analysis provided evidence of a clear relationship between genetic and geographic patterns, supporting significant genetic differentiation between China coastal populations and Ariake Sea populations. Compared to the genetic divergence between C. nasus and C. mystus, the level of genetic differentiation between China and the Ariake Sea populations of C. nasus is obvious below the species level, indicating isolated populations of C. nasus in the Ariake Sea. Isolation by distance analysis revealed that direct ocean distance with deep-water at the continental slope and high salinity between west and east coastal waters of the East China Sea served as major physical barrier to C. nasus, supporting the coastal dispersal pattern in this estuarine species, and rejecting offshore dispersal strategy.

Commensal ecology, urban landscapes, and their influence on the genetic characteristics of city-dwelling Norway rats (Rattus norvegicus).

PubMed

Gardner-Santana, L C; Norris, D E; Fornadel, C M; Hinson, E R; Klein, S L; Glass, G E

2009-07-01

Movement of individuals promotes colonization of new areas, gene flow among local populations, and has implications for the spread of infectious agents and the control of pest species. Wild Norway rats (Rattus norvegicus) are common in highly urbanized areas but surprisingly little is known of their population structure. We sampled individuals from 11 locations within Baltimore, Maryland, to characterize the genetic structure and extent of gene flow between areas within the city. Clustering methods and a neighbour-joining tree based on pairwise genetic distances supported an east-west division in the inner city, and a third cluster comprised of historically more recent sites. Most individuals (approximately 95%) were assigned to their area of capture, indicating strong site fidelity. Moreover, the axial dispersal distance of rats (62 m) fell within typical alley length. Several rats were assigned to areas 2-11.5 km away, indicating some, albeit infrequent, long-distance movement within the city. Although individual movement appears to be limited (30-150 m), locations up to 1.7 km are comprised of relatives. Moderate F(ST), differentiation between identified clusters, and high allelic diversity indicate that regular gene flow, either via recruitment or migration, has prevented isolation. Therefore, ecology of commensal rodents in urban areas and life-history characteristics of Norway rats likely counteract many expected effects of isolation or founder events. An understanding of levels of connectivity of rat populations inhabiting urban areas provides information about the spatial scale at which populations of rats may spread disease, invade new areas, or be eradicated from an existing area without reinvasion.

Global and local genetic diversity at two microsatellite loci in Plasmodium vivax parasites from Asia, Africa and South America.

PubMed

Schousboe, Mette L; Ranjitkar, Samir; Rajakaruna, Rupika S; Amerasinghe, Priyanie H; Konradsen, Flemming; Morales, Francisco; Ord, Rosalynn; Pearce, Richard; Leslie, Toby; Rowland, Mark; Gadalla, Nahla; Bygbjerg, Ib C; Alifrangis, Michael; Roper, Cally

2014-10-02

Even though Plasmodium vivax has the widest worldwide distribution of the human malaria species and imposes a serious impact on global public health, the investigation of genetic diversity in this species has been limited in comparison to Plasmodium falciparum. Markers of genetic diversity are vital to the evaluation of drug and vaccine efficacy, tracking of P. vivax outbreaks, and assessing geographical differentiation between parasite populations. The genetic diversity of eight P. vivax populations (n=543) was investigated by using two microsatellites (MS), m1501 and m3502, chosen because of their seven and eight base-pair (bp) repeat lengths, respectively. These were compared with published data of the same loci from six other P. vivax populations. In total, 1,440 P. vivax samples from 14 countries on three continents were compared. There was highest heterozygosity within Asian populations, where expected heterozygosity (He) was 0.92-0.98, and alleles with a high repeat number were more common. Pairwise FST revealed significant differentiation between most P. vivax populations, with the highest divergence found between Asian and South American populations, yet the majority of the diversity (~89%) was found to exist within rather than between populations. The MS markers used were informative in both global and local P. vivax population comparisons and their seven and eight bp repeat length facilitated population comparison using data from independent studies. A complex spatial pattern of MS polymorphisms among global P. vivax populations was observed which has potential utility in future epidemiological studies of the P. vivax parasite.

Subsequent Chemotherapy and Treatment Patterns After Abiraterone Acetate in Patients with Metastatic Castration-resistant Prostate Cancer: Post Hoc Analysis of COU-AA-302.

PubMed

de Bono, Johann S; Smith, Matthew R; Saad, Fred; Rathkopf, Dana E; Mulders, Peter F A; Small, Eric J; Shore, Neal D; Fizazi, Karim; De Porre, Peter; Kheoh, Thian; Li, Jinhui; Todd, Mary B; Ryan, Charles J; Flaig, Thomas W

2017-04-01

Treatment patterns for metastatic castration-resistant prostate cancer (mCRPC) have changed substantially in the last few years. In trial COU-AA-302 (chemotherapy-naïve men with mCRPC), abiraterone acetate plus prednisone (AA) significantly improved radiographic progression-free survival and overall survival (OS) when compared to placebo plus prednisone (P). This post hoc analysis investigated clinical responses to docetaxel as first subsequent therapy (FST) among patients who progressed following protocol-specified treatment with AA, and characterized subsequent treatment patterns among older (≥75 yr) and younger (<75 yr) patient subgroups. Data were collected at the final OS analysis (96% of expected death events). Subsequent therapy data were prospectively collected, while response and discontinuation data were collected retrospectively following discontinuation of the study drug. At the discretion of the investigator, 67% (365/546) of patients from the AA arm received subsequent treatment with one or more agents approved for mCRPC. Efficacy analysis was performed for patients for whom baseline and at least one post-baseline prostate-specific antigen (PSA) values were available. Baseline and at least one post-baseline PSA values were available for 100 AA patients who received docetaxel as FST. While acknowledging the limitations of post hoc analyses, 40% (40/100) of these patients had an unconfirmed ≥50% PSA decline with first subsequent docetaxel therapy, and 27% (27/100) had a confirmed ≥50% PSA decline. The median docetaxel treatment duration among these 100 patients was 4.2 mo. Docetaxel was the most common FST among older and younger patients from each treatment arm. However, 43% (79/185) of older patients who progressed on AA received no subsequent therapy for mCRPC, compared with 17% (60/361) of younger patients. Patients with mCRPC who progress with AA treatment may still derive benefit from subsequent docetaxel therapy. These data support further assessment of treatment patterns following AA treatment for mCRPC, particularly among older patients. ClinicalTrials.gov NCT00887198. Treatment patterns for advanced prostate cancer have changed substantially in the last few years. This additional analysis provides evidence of clinical benefit for subsequent chemotherapy in men with advanced prostate cancer whose disease progressed after treatment with abiraterone acetate. Older patients were less likely to be treated with subsequent therapy. Copyright © 2016 European Association of Urology. Published by Elsevier B.V. All rights reserved.

Depressive-like behavior induced by tumor necrosis factor-α in mice.

PubMed

Kaster, Manuella P; Gadotti, Vinícius M; Calixto, João B; Santos, Adair R S; Rodrigues, Ana Lúcia S

2012-01-01

Pro-inflammatory cytokines are implicated in the pathogenesis of depression. However, few animal models of cytokine-induced depression well characterized regarding its response to antidepressants are available. Hence, the aim of this study was to propose a model of depressive-like behavior induced by the administration of tumor necrosis factor-α (TNF-α) responsive to antidepressant treatments. TNF-α administered by i.c.v. route produced a depressive-like behavior in the forced swimming test (FST) and tail suspension test (TST) (0.1-1 fg/site and 0.001 fg/site, respectively), without altering the locomotor activity in the open-field test. In addition, anti-TNF-α antibody (0.1-1 pg/site, i.c.v.), but not the inhibitor of TNF-α synthesis thalidomide (3-30 mg/kg, s.c.) produced an antidepressant-like response in the FST. Moreover, either anti-TNF-α antibody (0.01 pg/site, i.c.v) or thalidomide (30 mg/kg, s.c.) reversed the depressive-like behavior induced by TNF- (0.1 fg/site, i.c.v.) in the FST. TNF-α receptor 1 (TNFR1) knockout mice exhibited an antidepressant-like behavior in the FST and in the TST as compared with the wild type mice. Treatment with fluoxetine (32 mg/kg, i.p), imipramine (15 mg/kg, i.p.) and desipramine (16 mg/kg, i.p) prevented the depressant-like effect induced by TNF-α (0.1 fg/site, i.c.v.) in the FST. In addition, TNF-α (0.1 fg/site, i.c.v.) administration produced an anhedonic response in a sucrose intake test, which was prevented by anti-TNF-α antibody (0.01 pg/site, i.c.v) or fluoxetine (32 mg/kg, i.p). Taken together, these results indicate that TNF-α produces a depressive-like state in mice, reinforcing the notion that an inflammatory component may play an important role in the pathophysiology of depression and suggesting that the central administration of TNF-α may be a novel approach to study the inflammatory component of depressive disorder. This article is part of a Special Issue entitled 'Anxiety and Depression'. Copyright © 2011 Elsevier Ltd. All rights reserved.

Effects of functional stabilization training on pain, function, and lower extremity biomechanics in women with patellofemoral pain: a randomized clinical trial.

PubMed

Baldon, Rodrigo de Marche; Serrão, Fábio Viadanna; Scattone Silva, Rodrigo; Piva, Sara Regina

2014-04-01

Randomized clinical trial. To compare the effects of functional stabilization training (FST) versus standard training on knee pain and function, lower-limb and trunk kinematics, trunk muscle endurance, and eccentric hip and knee muscle strength in women with patellofemoral pain. A combination of hip- and knee-strengthening exercise may be more beneficial than quadriceps strengthening alone to improve pain and function in individuals with patellofemoral pain. However, there is limited evidence of the effectiveness of these exercise programs on the biomechanics of the lower extremity. Thirty-one women were randomized to either the FST group or standard-training group. Patients attended a baseline assessment session, followed by an 8-week intervention, and were reassessed at the end of the intervention and at 3 months after the intervention. Assessment measures were a 10-cm visual analog scale for pain, the Lower Extremity Functional Scale, and the single-leg triple-hop test. A global rating of change scale was used to measure perceived improvement. Kinematics were assessed during the single-leg squat. Outcome measures also included trunk endurance and eccentric hip and knee muscle strength assessment. The patients in the FST group had less pain at the 3-month follow-up and greater global improvement and physical function at the end of the intervention compared to those in the standard-training group. Lesser ipsilateral trunk inclination, pelvis contralateral depression, hip adduction, and knee abduction, along with greater pelvis anteversion and hip flexion movement excursions during the single-leg squat, were only observed in the FST group after the intervention. Only those in the FST group had greater eccentric hip abductor and knee flexor strength, as well as greater endurance of the anterior, posterior, and lateral trunk muscles, after training. An intervention program consisting of hip muscle strengthening and lower-limb and trunk movement control exercises was more beneficial in improving pain, physical function, kinematics, and muscle strength compared to a program of quadriceps-strengthening exercises alone.

Experimental characterization of pairwise correlations from triple quantum correlated beams generated by cascaded four-wave mixing processes

NASA Astrophysics Data System (ADS)

Wang, Wei; Cao, Leiming; Lou, Yanbo; Du, Jinjian; Jing, Jietai

2018-01-01

We theoretically and experimentally characterize the performance of the pairwise correlations from triple quantum correlated beams based on the cascaded four-wave mixing (FWM) processes. The pairwise correlations between any two of the beams are theoretically calculated and experimentally measured. The experimental and theoretical results are in good agreement. We find that two of the three pairwise correlations can be in the quantum regime. The other pairwise correlation is always in the classical regime. In addition, we also measure the triple-beam correlation which is always in the quantum regime. Such unbalanced and controllable pairwise correlation structures may be taken as advantages in practical quantum communications, for example, hierarchical quantum secret sharing. Our results also open the way for the classification and application of quantum states generated from the cascaded FWM processes.

Licofelone Attenuates LPS-induced Depressive-like Behavior in Mice: A Possible Role for Nitric Oxide.

PubMed

Mousavi, Seyyedeh Elaheh; Saberi, Pegah; Ghasemkhani, Naeemeh; Fakhraei, Nahid; Mokhtari, Rezvan; Dehpour, Ahmad Reza

2018-01-01

Licofelone, a dual cyclooxygenase/5-lipoxygenase inhibitor, possesses antioxidant, antiapoptotic, neuroprotective, and anti-inflammatory properties. The aim of the present study was to investigate the effect of licofelone on lipopolysaccharide (LPS)-induced depression in a mouse model and also a possible role for nitric oxide (NO). To elucidate the role of NO on this effect of licofelone (5 and 20 mg/kg, i.p.), L-NAME, a non-specific NO synthase (NOS) inhibitor; aminoguanidine (AG), a specific inducible NOS (iNOS) inhibitor; 7-nitroindazole (7-NI) a preferential neuronal NOS inhibitor (nNOS) and; L-arginine (L-Arg), as a NO donor, were used. The animal's behaviors were evaluated employing forced swimming test (FST), tail suspension test (TST) and open field test (OFT). LPS (0.83 mg/kg, i.p.) induced depressive-like behavior increasing immobility time in FST and TST. Conversely, licofelone (20 mg/kg i.p.) reversed the depressive effect of LPS and lowered the immobility time in FST and TST. On the other hand, pretreatment with L-Arg also reversed the antidepressant-like effect of licofelone (20 mg/kg) in FST and TST. On the other hand, L-NAME (10 and 30 mg/kg), AG (50 and 100 mg/kg) and 7-NI (60 mg/kg) could potentiate licofelone (5 mg/kg) and lowered the immobility duration. NO down-regulation possibly through iNOS and nNOS inhibition may involve in the antidepressant property of licofelone. This article is open to POST-PUBLICATION REVIEW. Registered readers (see "For Readers") may comment by clicking on ABSTRACT on the issue's contents page.

Hypobaric Hypoxia Induces Depression-like Behavior in Female Sprague-Dawley Rats, but not in Males

PubMed Central

Bogdanova, Olena V.; Olson, Paul R.; Sung, Young-Hoon; D'Anci, Kristen E.; Renshaw, Perry F.

2015-01-01

Abstract Kanekar, Shami, Olena V. Bogdanova, Paul R. Olson, Young-Hoon Sung, Kristen E. D'Anci, and Perry F. Renshaw. Hypobaric hypoxia induces depression-like behavior in female Sprague-Dawley rats, but not males. High Alt Med Biol 16:52–60, 2015—Rates of depression and suicide are higher in people living at altitude, and in those with chronic hypoxic disorders like asthma, chronic obstructive pulmonary disorder (COPD), and smoking. Living at altitude exposes people to hypobaric hypoxia, which can lower rat brain serotonin levels, and impair brain bioenergetics in both humans and rats. We therefore examined the effect of hypobaric hypoxia on depression-like behavior in rats. After a week of housing at simulated altitudes of 20,000 ft, 10,000 ft, or sea level, or at local conditions of 4500 ft (Salt Lake City, UT), Sprague Dawley rats were tested for depression-like behavior in the forced swim test (FST). Time spent swimming, climbing, or immobile, and latency to immobility were measured. Female rats housed at altitude display more depression-like behavior in the FST, with significantly more immobility, less swimming, and lower latency to immobility than those at sea level. In contrast, males in all four altitude groups were similar in their FST behavior. Locomotor behavior in the open field test did not change with altitude, thus validating immobility in the FST as depression-like behavior. Hypobaric hypoxia exposure therefore induces depression-like behavior in female rats, but not in males. PMID:25803141

Antidepressant-like effects of Perilla frutescens seed oil during a forced swimming test.

PubMed

Lee, Hsiu-Chuan; Ko, Hsiang-Kai; Huang, Brian E T-G; Chu, Yan-Hwa; Huang, Shih-Yi

2014-05-01

Unipolar depressive disorder may become one of the major leading causes of disease burden by 2030 according to the World Health Organization (WHO). Thus, the discovery of antidepressive foods is attractive and could have considerable impacts worldwide. We investigated the antidepressant-like effects of Perilla frutescens seed oil on adult male rats subjected to a forced swimming test (FST). Forty Sprague-Dawley rats were housed and fed various diets, including soybean oil-rich, eicosapentaenoic acid (EPA)-rich, and P. frutescens seed oil-rich diets for 6 weeks. After the dietary intervention, animals were tested using an FST and were sacrificed after the test. We analyzed the fatty acid profiles of red blood cells (RBCs) and the brain prefrontal cortex (PFC). Levels of brain-derived neurotrophic factor (BDNF), serotonin, and dopamine in the PFC were also determined. After the FST, the imipramine, EPA-rich, and P. frutescens seed oil-rich groups showed significant shorter immobility time and longer struggling time than the control group (p < 0.05). Levels of BDNF in the P. frutescens seed oil-rich group and levels of serotonin in the EPA-rich group were significantly (p < 0.05) higher than those of the control group. Moreover, the BDNF concentration in the PFC was significantly positively correlated with the struggling time. However, there were no significant differences in dopamine levels between the intervention groups and the control group. In conclusion, a P. frutescens seed oil-rich diet exhibited antidepressant-like properties through modulation of fatty acid profiles and BDNF expression in the brain during an FST.

Genome-Wide SNP Discovery, Genotyping and Their Preliminary Applications for Population Genetic Inference in Spotted Sea Bass (Lateolabrax maculatus)

PubMed Central

Wang, Juan; Xue, Dong-Xiu; Zhang, Bai-Dong; Li, Yu-Long; Liu, Bing-Jian; Liu, Jin-Xian

2016-01-01

Next-generation sequencing and the collection of genome-wide single-nucleotide polymorphisms (SNPs) allow identifying fine-scale population genetic structure and genomic regions under selection. The spotted sea bass (Lateolabrax maculatus) is a non-model species of ecological and commercial importance and widely distributed in northwestern Pacific. A total of 22 648 SNPs was discovered across the genome of L. maculatus by paired-end sequencing of restriction-site associated DNA (RAD-PE) for 30 individuals from two populations. The nucleotide diversity (π) for each population was 0.0028±0.0001 in Dandong and 0.0018±0.0001 in Beihai, respectively. Shallow but significant genetic differentiation was detected between the two populations analyzed by using both the whole data set (FST = 0.0550, P < 0.001) and the putatively neutral SNPs (FST = 0.0347, P < 0.001). However, the two populations were highly differentiated based on the putatively adaptive SNPs (FST = 0.6929, P < 0.001). Moreover, a total of 356 SNPs representing 298 unique loci were detected as outliers putatively under divergent selection by FST-based outlier tests as implemented in BAYESCAN and LOSITAN. Functional annotation of the contigs containing putatively adaptive SNPs yielded hits for 22 of 55 (40%) significant BLASTX matches. Candidate genes for local selection constituted a wide array of functions, including binding, catalytic and metabolic activities, etc. The analyses with the SNPs developed in the present study highlighted the importance of genome-wide genetic variation for inference of population structure and local adaptation in L. maculatus. PMID:27336696

Genome-Wide SNP Discovery, Genotyping and Their Preliminary Applications for Population Genetic Inference in Spotted Sea Bass (Lateolabrax maculatus).

PubMed

Wang, Juan; Xue, Dong-Xiu; Zhang, Bai-Dong; Li, Yu-Long; Liu, Bing-Jian; Liu, Jin-Xian

2016-01-01

Next-generation sequencing and the collection of genome-wide single-nucleotide polymorphisms (SNPs) allow identifying fine-scale population genetic structure and genomic regions under selection. The spotted sea bass (Lateolabrax maculatus) is a non-model species of ecological and commercial importance and widely distributed in northwestern Pacific. A total of 22 648 SNPs was discovered across the genome of L. maculatus by paired-end sequencing of restriction-site associated DNA (RAD-PE) for 30 individuals from two populations. The nucleotide diversity (π) for each population was 0.0028±0.0001 in Dandong and 0.0018±0.0001 in Beihai, respectively. Shallow but significant genetic differentiation was detected between the two populations analyzed by using both the whole data set (FST = 0.0550, P < 0.001) and the putatively neutral SNPs (FST = 0.0347, P < 0.001). However, the two populations were highly differentiated based on the putatively adaptive SNPs (FST = 0.6929, P < 0.001). Moreover, a total of 356 SNPs representing 298 unique loci were detected as outliers putatively under divergent selection by FST-based outlier tests as implemented in BAYESCAN and LOSITAN. Functional annotation of the contigs containing putatively adaptive SNPs yielded hits for 22 of 55 (40%) significant BLASTX matches. Candidate genes for local selection constituted a wide array of functions, including binding, catalytic and metabolic activities, etc. The analyses with the SNPs developed in the present study highlighted the importance of genome-wide genetic variation for inference of population structure and local adaptation in L. maculatus.

Phosphodiesterase-1b (Pde1b) knockout mice are resistant to forced swim and tail suspension induced immobility and show upregulation of Pde10a.

PubMed

Hufgard, Jillian R; Williams, Michael T; Skelton, Matthew R; Grubisha, Olivera; Ferreira, Filipa M; Sanger, Helen; Wright, Mary E; Reed-Kessler, Tracy M; Rasmussen, Kurt; Duman, Ronald S; Vorhees, Charles V

2017-06-01

Major depressive disorder is a leading cause of suicide and disability. Despite this, current antidepressants provide insufficient efficacy in more than 60% of patients. Most current antidepressants are presynaptic reuptake inhibitors; postsynaptic signal regulation has not received as much attention as potential treatment targets. We examined the effects of disruption of the postsynaptic cyclic nucleotide hydrolyzing enzyme, phosphodiesterase (PDE) 1b, on depressive-like behavior and the effects on PDE1B protein in wild-type (WT) mice following stress. Littermate knockout (KO) and WT mice were tested in locomotor activity, tail suspension (TST), and forced swim tests (FST). FST was also used to compare the effects of two antidepressants, fluoxetine and bupropion, in KO versus WT mice. Messenger RNA (mRNA) expression changes were also determined. WT mice underwent acute or chronic stress and markers of stress and PDE1B expression were examined. Pde1b KO mice exhibited decreased TST and FST immobility. When treated with antidepressants, both WT and KO mice showed decreased FST immobility and the effect was additive in KO mice. Mice lacking Pde1b had increased striatal Pde10a mRNA expression. In WT mice, acute and chronic stress upregulated PDE1B expression while PDE10A expression was downregulated after chronic but not acute stress. PDE1B is a potential therapeutic target for depression treatment because of the antidepressant-like phenotype seen in Pde1b KO mice.

NPY intraperitoneal injections produce antidepressant-like effects and downregulate BDNF in the rat hypothalamus.

PubMed

Gelfo, Francesca; Tirassa, Paola; De Bartolo, Paola; Croce, Nicoletta; Bernardini, Sergio; Caltagirone, Carlo; Petrosini, Laura; Angelucci, Francesco

2012-06-01

Several studies have documented an involvement of Neuropeptide Y (NPY) in stress-related disorders. Stress-related disorders are also characterized by changes in brain-derived neurotrophic factor (BDNF) and nerve growth factor (NGF), neurotrophins implicated in the survival and function of neurons. Thus the aim of this study was to investigate whether an NPY intraperitoneal treatment has antidepressant-like effects in rats subjected to a classical stress paradigm, the Forced Swim Test (FST), in association with changes in local brain neurotrophin production. Rats were intraperitoneally injected with either NPY (60 μg/kg) or a vehicle for three consecutive days between two FST sessions and then tested for time spent (or delay onset) in immobile posture. Moreover, we measured by enzyme-linked immunosorbent assay (ELISA) neurotrophin levels in the hypothalamus and corticosterone levels in plasma. The data showed that NPY induced a significant delay in the onset and a significant reduction in the duration of the immobility posture in FST. We also found that NPY decreased BDNF levels in the hypothalamus and corticosterone levels in plasma. Immobility posture in FST can be reduced by antidepressant drugs. Thus, our data show an antidepressant-like effect of NPY associated with changes in BDNF levels in the hypothalamus and reduced activity of hypothalamic-pituitary-adrenal (HPA) axis. These findings, while confirming the involvement of the NPY system in stress-related disorders, suggest that a less invasive route of administration, such as an intraperitoneal injection, may be instrumental in coping with stressful events in animal models and perhaps in humans. © 2012 Blackwell Publishing Ltd.

Effect of desipramine and citalopram treatment on forced swimming test-induced changes in cocaine- and amphetamine-regulated transcript (CART) immunoreactivity in mice.

PubMed

Chung, Sung; Kim, Hee Jeong; Kim, Hyun Ju; Choi, Sun Hye; Kim, Jin Wook; Kim, Jeong Min; Shin, Kyung Ho

2014-05-01

Recent study demonstrates antidepressant-like effect of cocaine- and amphetamine-regulated transcript (CART) in the forced swimming test (FST), but less is known about whether antidepressant treatments alter levels of CART immunoreactivity (CART-IR) in the FST. To explore this possibility, we assessed the treatment effects of desipramine and citalopram, which inhibit the reuptake of norepinephrine and serotonin into the presynaptic terminals, respectively, on changes in levels of CART-IR before and after the test swim in mouse brain. Levels of CART-IR in the nucleus accumbens shell (AcbSh), dorsal bed nucleus of the stria terminalis (dBNST), and hypothalamic paraventricular nucleus (PVN) were significantly increased before the test swim by desipramine and citalopram treatments. This increase in CART-IR in the AcbSh, dBNST, and PVN before the test swim remained elevated by desipramine treatment after the test swim, but this increase in these brain areas returned to near control levels after test swim by citalopram treatment. Citalopram, but not desipramine, treatment increased levels of CART-IR in the central nucleus of the amygdala (CeA) and the locus ceruleus (LC) before the test swim, and this increase was returned to control levels after the test swim in the CeA, but not in the LC. These results suggest common and distinct regulation of CART by desipramine and citalopram treatments in the FST and raise the possibility that CART in the AcbSh, dBNST, and CeA may be involved in antidepressant-like effect in the FST.

Mesolimbic effects of the antidepressant fluoxetine in Holtzman rats, a genetic strain with increased vulnerability to stress

PubMed Central

Padilla, Eimeira; Shumake, Jason; Barrett, Douglas W.; Sheridan, Eva C.; Gonzalez-Lima, F.

2011-01-01

This is the first metabolic mapping study of the effects of fluoxetine after learned helplessness training. Antidepressants are the most commonly prescribed medications, but the regions underlying treatment effects in affectively disordered brains are poorly understood. We hypothesized the antidepressant action of fluoxetine would produce adaptations in mesolimbic regions after two weeks of treatment. We used Holtzman rats, a genetic strain showing susceptibility to novelty-evoked hyperactivity and stress-evoked helplessness, to map regional brain metabolic effects caused by fluoxetine treatment. Animals underwent learned helplessness, and subsequently immobility time was scored in the forced swim test (FST). On the next day, animals began receiving two weeks of fluoxetine (5 mg/kg/day) or vehicle and were retested in the FST at the end of drug treatment. Antidepressant behavioral effects of fluoxetine were analyzed using a ratio of immobility during pre- and post-treatment FST sessions. Brains were analyzed for regional metabolic activity using quantitative cytochrome oxidase histochemistry as in our previous study using congenitally helpless rats. Fluoxetine exerted a protective effect against FST-induced immobility behavior in Holtzman rats. Fluoxetine also caused a significant reduction in the mean regional metabolism of the nucleus accumbens shell and the ventral hippocampus as compared to vehicle-treated subjects. Additional networks affected by fluoxetine treatment included the prefrontal-cingulate cortex and brainstem nuclei linked to depression (e.g. habenula, dorsal raphe and interpeduncular nucleus). We concluded that corticolimbic regions such as the prefrontal-cingulate cortex, nucleus accumbens, ventral hippocampus and key brainstem nuclei represent important contributors to the neural network mediating fluoxetine antidepressant action. PMID:21376019

fRMSDPred: Predicting Local RMSD Between Structural Fragments Using Sequence Information

DTIC Science & Technology

2007-04-04

machine learning approaches for estimating the RMSD value of a pair of protein fragments. These estimated fragment-level RMSD values can be used to construct the alignment, assess the quality of an alignment, and identify high-quality alignment segments. We present algorithms to solve this fragment-level RMSD prediction problem using a supervised learning framework based on support vector regression and classification that incorporates protein profiles, predicted secondary structure, effective information encoding schemes, and novel second-order pairwise exponential kernel

Phytochemical analysis, antioxidant, antistress, and nootropic activities of aqueous and methanolic seed extracts of ladies finger (Abelmoschus esculentus L.) in mice.

PubMed

Doreddula, Sathish Kumar; Bonam, Srinivasa Reddy; Gaddam, Durga Prasad; Desu, Brahma Srinivasa Rao; Ramarao, Nadendla; Pandy, Vijayapandi

2014-01-01

Abelmoschus esculentus L. (ladies finger, okra) is a well-known tropical vegetable, widely planted from Africa to Asia and from South Europe to America. In the present study, we investigated the in vitro antioxidant capacity and in vivo protective effect of the aqueous and methanolic seed extracts of Abelmoschus esculentus against scopolamine-induced cognitive impairment using passive avoidance task and acute restraining stress-induced behavioural and biochemical changes using elevated plus maze (EPM) and forced swimming test (FST) in mice. Our results demonstrated that the pretreatment of mice with aqueous and methanolic seed extracts of Abelmoschus esculentus (200 mg/kg, p.o.) for seven days significantly (P < 0.01) attenuated scopolamine-induced cognitive impairment in the passive avoidance test. In addition, these extracts significantly reduced the blood glucose, corticosterone, cholesterol, and triglyceride levels elevated by acute restraint stress and also significantly increased the time spent in open arm in EPM and decreased the immobility time in FST. It has also been revealed that these extracts showed a significant antioxidant activity and no signs of toxicity or death up to a dose of 2000 mg/kg, p.o. These results suggest that the seed extracts of Abelmoschus esculentus L. possess antioxidant, antistress, and nootropic activities which promisingly support the medicinal values of ladies finger as a vegetable.

Association between ovine protein polymorphisms and geographical variables in Europe and south-west Asia.

PubMed

Ordas, J G; Carriedo, J A

1997-01-12

The spatial distribution of six blood-protein polymorphisms in European and south-west Asian ovine breeds was analysed. Latitudinal clines were found for haemoglobin and transferrin loci. The respective F(ST) values are not significantly greater than those for protein-X, esterase, carbonic anhydrase, and albumin, where gene frequencies are not associated with latitude. The results suggest that historical processes of gene flow, rather than adaptation to different environments, have played a major role in determining the observed lives of gene frequencies. RESUMEN: Asociación entre polimorfismos proteicos ovinos y variables geográficas en Europa y sudoeste de Asia Se ha analizado la distribución espacial de seis polimorfismos proteicos sanguíneos en razas ovinas de Europa y del sudoeste de Asia. La hemoglobina y la transferrina muestran clinas latitudinales. Los valores de F(ST) para estos dos loci no son significativamente más grandes que los de la proteína-X, esterasa, anhidrasa carbónica y albúmina, cuyas frecuencias génicas no están asociadas con la latitud. Los resultados sugieren que la distribución de las frecuencias génicas de la hemoglobina y la transferrina se debe a procesos históricos de flujo génico y deriva genética. 1997 Blackwell Verlag GmbH.

Phytochemical Analysis, Antioxidant, Antistress, and Nootropic Activities of Aqueous and Methanolic Seed Extracts of Ladies Finger (Abelmoschus esculentus L.) in Mice

PubMed Central

Doreddula, Sathish Kumar; Bonam, Srinivasa Reddy; Gaddam, Durga Prasad; Desu, Brahma Srinivasa Rao; Ramarao, Nadendla; Pandy, Vijayapandi

2014-01-01

Abelmoschus esculentus L. (ladies finger, okra) is a well-known tropical vegetable, widely planted from Africa to Asia and from South Europe to America. In the present study, we investigated the in vitro antioxidant capacity and in vivo protective effect of the aqueous and methanolic seed extracts of Abelmoschus esculentus against scopolamine-induced cognitive impairment using passive avoidance task and acute restraining stress-induced behavioural and biochemical changes using elevated plus maze (EPM) and forced swimming test (FST) in mice. Our results demonstrated that the pretreatment of mice with aqueous and methanolic seed extracts of Abelmoschus esculentus (200 mg/kg, p.o.) for seven days significantly (P < 0.01) attenuated scopolamine-induced cognitive impairment in the passive avoidance test. In addition, these extracts significantly reduced the blood glucose, corticosterone, cholesterol, and triglyceride levels elevated by acute restraint stress and also significantly increased the time spent in open arm in EPM and decreased the immobility time in FST. It has also been revealed that these extracts showed a significant antioxidant activity and no signs of toxicity or death up to a dose of 2000 mg/kg, p.o. These results suggest that the seed extracts of Abelmoschus esculentus L. possess antioxidant, antistress, and nootropic activities which promisingly support the medicinal values of ladies finger as a vegetable. PMID:25401145

A comparison of hand-arm vibration syndrome between Malaysian and Japanese workers.

PubMed

Su, Anselm Ting; Fukumoto, Jin; Darus, Azlan; Hoe, Victor C W; Miyai, Nobuyuki; Isahak, Marzuki; Takemura, Shigeki; Bulgiba, Awang; Yoshimasu, Kouichi; Maeda, Setsuo; Miyashita, Kazuhisa

2013-01-01

The aim of this study was to investigate the clinical characteristics of HAVS in a tropical environment in comparison with a temperate environment. We conducted a series medical examinations among the forestry, construction and automobile industry workers in Malaysia adopting the compulsory medical examination procedure used by Wakayama Medical University for Japanese vibratory tools workers. We matched the duration of vibration exposure and compared our results against the Japanese workers. We also compared the results of the Malaysian tree fellers against a group of symptomatic Japanese tree fellers diagnosed with HAVS. Malaysian subjects reported a similar prevalence of finger tingling, numbness and dullness (Malaysian=25.0%, Japanese=21.5%, p=0.444) but had a lower finger skin temperature (FST) and higher vibrotactile perception threshold (VPT) values as compared with the Japanese workers. No white finger was reported in Malaysian subjects. The FST and VPT of the Malaysian tree fellers were at least as bad as the Japanese tree fellers despite a shorter duration (mean difference=20.12 years, 95%CI=14.50, 25.40) of vibration exposure. Although the vascular disorder does not manifest clinically in the tropical environment, the severity of HAVS can be as bad as in the temperate environment with predominantly neurological disorder. Hence, it is essential to formulate national legislation for the control of the occupational vibration exposure.

Progesterone receptor antagonist CDB-4124 increases depression-like behavior in mice without affecting locomotor ability.

PubMed

Beckley, Ethan H; Scibelli, Angela C; Finn, Deborah A

2011-07-01

Progesterone withdrawal has been proposed as an underlying factor in premenstrual syndrome and postpartum depression. Progesterone withdrawal induces forced swim test (FST) immobility in mice, a depression-like behavior, but the contribution of specific receptors to this effect is unclear. The role of progesterone's GABA(A) receptor-modulating metabolite allopregnanolone in depression- and anxiety-related behaviors has been extensively documented, but little attention has been paid to the role of progesterone receptors. We administered the classic progesterone receptor antagonist mifepristone (RU-38486) and the specific progesterone receptor antagonist CDB-4124 to mice that had been primed with progesterone for five days, and found that both compounds induced FST immobility reliably, robustly, and in a dose-dependent fashion. Although CDB-4124 increased FST immobility, it did not suppress initial activity in a locomotor test. These findings suggest that decreased progesterone receptor activity contributes to depression-like behavior in mice, consistent with the hypothesis that progesterone withdrawal may contribute to the symptoms of premenstrual syndrome or postpartum depression. Copyright © 2010 Elsevier Ltd. All rights reserved.

Exponential series approaches for nonparametric graphical models

NASA Astrophysics Data System (ADS)

Janofsky, Eric

Markov Random Fields (MRFs) or undirected graphical models are parsimonious representations of joint probability distributions. This thesis studies high-dimensional, continuous-valued pairwise Markov Random Fields. We are particularly interested in approximating pairwise densities whose logarithm belongs to a Sobolev space. For this problem we propose the method of exponential series which approximates the log density by a finite-dimensional exponential family with the number of sufficient statistics increasing with the sample size. We consider two approaches to estimating these models. The first is regularized maximum likelihood. This involves optimizing the sum of the log-likelihood of the data and a sparsity-inducing regularizer. We then propose a variational approximation to the likelihood based on tree-reweighted, nonparametric message passing. This approximation allows for upper bounds on risk estimates, leverages parallelization and is scalable to densities on hundreds of nodes. We show how the regularized variational MLE may be estimated using a proximal gradient algorithm. We then consider estimation using regularized score matching. This approach uses an alternative scoring rule to the log-likelihood, which obviates the need to compute the normalizing constant of the distribution. For general continuous-valued exponential families, we provide parameter and edge consistency results. As a special case we detail a new approach to sparse precision matrix estimation which has statistical performance competitive with the graphical lasso and computational performance competitive with the state-of-the-art glasso algorithm. We then describe results for model selection in the nonparametric pairwise model using exponential series. The regularized score matching problem is shown to be a convex program; we provide scalable algorithms based on consensus alternating direction method of multipliers (ADMM) and coordinate-wise descent. We use simulations to compare our method to others in the literature as well as the aforementioned TRW estimator.

Gene ontology analysis of pairwise genetic associations in two genome-wide studies of sporadic ALS.

PubMed

Kim, Nora Chung; Andrews, Peter C; Asselbergs, Folkert W; Frost, H Robert; Williams, Scott M; Harris, Brent T; Read, Cynthia; Askland, Kathleen D; Moore, Jason H

2012-07-28

It is increasingly clear that common human diseases have a complex genetic architecture characterized by both additive and nonadditive genetic effects. The goal of the present study was to determine whether patterns of both additive and nonadditive genetic associations aggregate in specific functional groups as defined by the Gene Ontology (GO). We first estimated all pairwise additive and nonadditive genetic effects using the multifactor dimensionality reduction (MDR) method that makes few assumptions about the underlying genetic model. Statistical significance was evaluated using permutation testing in two genome-wide association studies of ALS. The detection data consisted of 276 subjects with ALS and 271 healthy controls while the replication data consisted of 221 subjects with ALS and 211 healthy controls. Both studies included genotypes from approximately 550,000 single-nucleotide polymorphisms (SNPs). Each SNP was mapped to a gene if it was within 500 kb of the start or end. Each SNP was assigned a p-value based on its strongest joint effect with the other SNPs. We then used the Exploratory Visual Analysis (EVA) method and software to assign a p-value to each gene based on the overabundance of significant SNPs at the α = 0.05 level in the gene. We also used EVA to assign p-values to each GO group based on the overabundance of significant genes at the α = 0.05 level. A GO category was determined to replicate if that category was significant at the α = 0.05 level in both studies. We found two GO categories that replicated in both studies. The first, 'Regulation of Cellular Component Organization and Biogenesis', a GO Biological Process, had p-values of 0.010 and 0.014 in the detection and replication studies, respectively. The second, 'Actin Cytoskeleton', a GO Cellular Component, had p-values of 0.040 and 0.046 in the detection and replication studies, respectively. Pathway analysis of pairwise genetic associations in two GWAS of sporadic ALS revealed a set of genes involved in cellular component organization and actin cytoskeleton, more specifically, that were not reported by prior GWAS. However, prior biological studies have implicated actin cytoskeleton in ALS and other motor neuron diseases. This study supports the idea that pathway-level analysis of GWAS data may discover important associations not revealed using conventional one-SNP-at-a-time approaches.

Population Expansion and Genetic Structure in Carcharhinus brevipinna in the Southern Indo-Pacific

PubMed Central

Geraghty, Pascal T.; Williamson, Jane E.; Macbeth, William G.; Wintner, Sabine P.; Harry, Alastair V.; Ovenden, Jennifer R.; Gillings, Michael R.

2013-01-01

Background Quantifying genetic diversity and metapopulation structure provides insights into the evolutionary history of a species and helps develop appropriate management strategies. We provide the first assessment of genetic structure in spinner sharks (Carcharhinus brevipinna), a large cosmopolitan carcharhinid, sampled from eastern and northern Australia and South Africa. Methods and Findings Sequencing of the mitochondrial DNA NADH dehydrogenase subunit 4 gene for 430 individuals revealed 37 haplotypes and moderately high haplotype diversity (h = 0.6770 ±0.025). While two metrics of genetic divergence (ΦST and F ST) revealed somewhat different results, subdivision was detected between South Africa and all Australian locations (pairwise ΦST, range 0.02717–0.03508, p values ≤ 0.0013; pairwise F ST South Africa vs New South Wales = 0.04056, p = 0.0008). Evidence for fine-scale genetic structuring was also detected along Australia’s east coast (pairwise ΦST = 0.01328, p < 0.015), and between south-eastern and northern locations (pairwise ΦST = 0.00669, p < 0.04). Conclusions The Indian Ocean represents a robust barrier to contemporary gene flow in C. brevipinna between Australia and South Africa. Gene flow also appears restricted along a continuous continental margin in this species, with data tentatively suggesting the delineation of two management units within Australian waters. Further sampling, however, is required for a more robust evaluation of the latter finding. Evidence indicates that all sampled populations were shaped by a substantial demographic expansion event, with the resultant high genetic diversity being cause for optimism when considering conservation of this commercially-targeted species in the southern Indo-Pacific. PMID:24086462

Manipulation of Karyotype in Caenorhabditis elegans Reveals Multiple Inputs Driving Pairwise Chromosome Synapsis During Meiosis

PubMed Central

Roelens, Baptiste; Schvarzstein, Mara; Villeneuve, Anne M.

2015-01-01

Meiotic chromosome segregation requires pairwise association between homologs, stabilized by the synaptonemal complex (SC). Here, we investigate factors contributing to pairwise synapsis by investigating meiosis in polyploid worms. We devised a strategy, based on transient inhibition of cohesin function, to generate polyploid derivatives of virtually any Caenorhabditis elegans strain. We exploited this strategy to investigate the contribution of recombination to pairwise synapsis in tetraploid and triploid worms. In otherwise wild-type polyploids, chromosomes first sort into homolog groups, then multipartner interactions mature into exclusive pairwise associations. Pairwise synapsis associations still form in recombination-deficient tetraploids, confirming a propensity for synapsis to occur in a strictly pairwise manner. However, the transition from multipartner to pairwise association was perturbed in recombination-deficient triploids, implying a role for recombination in promoting this transition when three partners compete for synapsis. To evaluate the basis of synapsis partner preference, we generated polyploid worms heterozygous for normal sequence and rearranged chromosomes sharing the same pairing center (PC). Tetraploid worms had no detectable preference for identical partners, indicating that PC-adjacent homology drives partner choice in this context. In contrast, triploid worms exhibited a clear preference for identical partners, indicating that homology outside the PC region can influence partner choice. Together, our findings, suggest a two-phase model for C. elegans synapsis: an early phase, in which initial synapsis interactions are driven primarily by recombination-independent assessment of homology near PCs and by a propensity for pairwise SC assembly, and a later phase in which mature synaptic interactions are promoted by recombination. PMID:26500263

Harmane induces anxiolysis and antidepressant-like effects in rats.

PubMed

Aricioglu, Feyza; Altunbas, Hale

2003-12-01

A forced swim test (FST) and an elevated plus maze (EPM) were used to determine antidepressant and anxiolytic effects of harmane in rats in comparison with a known antidepressant, imipramine (30 mg/kg i.p.). Harmane (2.5, 5.0, or 10 mg/kg, i.p.), saline, or imipramine were given 30 minutes before the tests. Administration of harmane decreased the time of immobility in the FST dose-dependently and increased the time spent in open arms in the EPM, as compared with the saline group. As an endogenous substance, harmane therefore has anti-anxiety and antidepressant effects.

Combat casualties from two current conflicts with the Seventh French Forward Surgical Team in Mali and Central African Republic in 2014.

PubMed

Dubost, Clément; Goudard, Y; Soucanye de Landevoisin, E; Contargyris, C; Evans, D; Pauleau, G

2016-12-01

The Seventh Airborne Forward Surgical Team (FST) has been deployed in Gao, Mali, and in Bangui, Central African Republic (CAR), for two 3-month periods in 2014. The initial role of the FST was to provide emergent care to French and coalition soldiers but it was expanded to include humanitarian assistance. The aim of the present study was to describe and compare injuries and surgical activity of the Seventh Airborne FST during these two conflicts. All surgical patients treated by the FST between January and December 2014 have been included. Patient demographics, mechanisms of injury, surgical management including triage categories and types of surgery performed and evacuation modalities were recorded. During the 6-month deployment period in 2014, the FST performed 129 operations on 134 patients, 61 of which were trauma patients (45 battle injuries (BI)). The remaining 73 patients were treated as part of the humanitarian mission. Thirty of the BI were managed during the Malian conflict and 15 in CAR; 29 patients (64%) were military. The median Injury Severity Score (range) was 20 (10-34) in Mali and 8 (5-21) in CAR with median (range) evacuation time of 390 min (240-947) in Mali and 120 min (60-120) in CAR (p<0.0001). The most frequent mechanisms of injury were gunshot wounds in Mali (15/30) and road traffic accident in CAR (7/15). Extremity injuries were most common (58%) with head, face and neck injuries and thoracic injuries in 15% of cases each and 12% had suffered abdominopelvic injuries. Ten patients were categorised as T1 and underwent urgent surgery, five had damage control surgery and four received transfusion. The average length of stay was 2 days (1-2), with most patients being transferred to another hospital. Casualties from Mali and CAR presented with a wide variety of injury patterns, and there were some instances where damage control surgery and whole blood transfusion were necessary. Surgical equipment scales must allow treatment of a large variety of injuries including all body regions and extreme emergency procedures. These two conflicts differ in terms of scope, one being an urban guerrilla and the other an open conflict in a large desertic area. Long distances in the Malian desert increase significantly the evacuation time. It has to be taken into account in the FST location when coalition forces are deployed in such places. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Analysis of laser printer and photocopier toners by spectral properties and chemometrics

NASA Astrophysics Data System (ADS)

Verma, Neha; Kumar, Raj; Sharma, Vishal

2018-05-01

The use of printers to generate falsified documents has become a common practice in today's world. The examination and identification of the printed matter in the suspected documents (civil or criminal cases) may provide important information about the authenticity of the document. In the present study, a total number of 100 black toner samples both from laser printers and photocopiers were examined using diffuse reflectance UV-Vis Spectroscopy. The present research is divided into two parts; visual discrimination and discrimination by using multivariate analysis. A comparison between qualitative and quantitative analysis showed that multivariate analysis (Principal component analysis) provides 99.59%pair-wise discriminating power for laser printer toners while 99.84% pair-wise discriminating power for photocopier toners. The overall results obtained confirm the applicability of UV-Vis spectroscopy and chemometrics, in the nondestructive analysis of toner printed documents while enhancing their evidential value for forensic applications.

‘Candidatus Phytoplasma palmicola’, a novel taxon associated with a lethal yellowing-type disease (LYD) of coconut (Cocos nucifera L.) in Mozambique

USDA-ARS?s Scientific Manuscript database

In this study, the taxonomic position and group classification of the phytoplasma associated with a lethal yellowing-type disease (LYD) of coconut (Cocos nucifera L.) in Mozambique were addressed. Pairwise sequence similarity values based on alignment of near full-length 16SrRNA genes (1530 bp) reve...

The Bacterial Gene IfpA Influences the Potent Induction of Calcitonin Receptor and Osteoclast-Related Genes in Burkholderia Pseudomallei-Induced TRAP-Positive Multinucleated Giant Cells

DTIC Science & Technology

2006-06-13

with arithmetic mean ( UPGMA ) using random tie breaking and uncorrected pairwise distances in MacVector 7.0 (Oxford Molecular). Numbers on branches...denote the UPGMA bootstrap percentage using a highly stringent number (1000) of replications (Felsenstein, 1985). All bootstrap values are 50%, as shown

Mates but not sexes differ in migratory niche in a monogamous penguin species.

PubMed

Thiebot, Jean-Baptiste; Bost, Charles-André; Dehnhard, Nina; Demongin, Laurent; Eens, Marcel; Lepoint, Gilles; Cherel, Yves; Poisbleau, Maud

2015-09-01

Strong pair bonds generally increase fitness in monogamous organisms, but may also underlie the risk of hampering it when re-pairing fails after the winter season. We investigated whether partners would either maintain contact or offset this risk by exploiting sex-specific favourable niches during winter in a migratory monogamous seabird, the southern rockhopper penguin Eudyptes chrysocome. Using light-based geolocation, we show that although the spatial distribution of both sexes largely overlapped, pair-wise mates were located on average 595 ± 260 km (and up to 2500 km) apart during winter. Stable isotope data also indicated a marked overlap between sex-specific isotopic niches (δ¹³C and δ¹⁵N values) but a segregation of the feeding habitats (δ¹³C values) within pairs. Importantly, the tracked females remained longer (12 days) at sea than males, but all re-mated with their previous partners after winter. Our study provides multiple evidence that migratory species may well demonstrate pair-wise segregation even in the absence of sex-specific winter niches (spatial and isotopic). We suggest that dispersive migration patterns with sex-biased timings may be a sufficient proximal cause for generating such a situation in migratory animals.

Comparison of the ITS1 and ITS2 rDNA in Emeria callospermophili (Apicomplexa: Eimeriidae) from Sciurid Rodents

PubMed Central

Motriuk-Smith, Dagmara; Seville, R Scott; Quealy, Leah; Oliver, Clinton E.

2011-01-01

The taxonomy of the coccidia has historically been morphologically based. The purpose of this study was to establish if conspecificity of isolates of Eimeria callospermophili from 4 ground-dwelling squirrel hosts (Rodentia: Sciuridae) is supported by comparison of rDNA sequence data and to examine how this species relates to eimerian species from other sciurid hosts. Eimeria callospermophili was isolated from 4 wild caught hosts, i.e., Urocitellus elegans, Cynomys leucurus, Marmota flaviventris, and Cynomys ludovicianus. The ITS1 and ITS2 genomic rDNA sequences were PCR generated, sequenced, and analyzed. The highest intraspecific pairwise distance values of 6.0% in ITS1 and 7.1% in ITS2 were observed in C. leucurus. Interspecific pairwise distance values greater than 5% do not support E. callospermophili conspecificity. Generated E. callospermophili sequences were compared to Eimeria lancasterensis from Sciuris niger and Sciurus niger cinereus, and Eimeria ontarioensis from S. niger. A single well-supported clade was formed by E. callospermophili amplicons in Neighbor Joining and Maximum Parsimony analyses. However, within the clade there was little evidence of host or geographic structuring of the species. PMID:21506777

Vanishing Parotid Tumors on MR Imaging

PubMed Central

Matsusue, Eiji; Fujihara, Yoshio; Matsuda, Eiken; Tokuyasu, Yusuke; Nakamoto, Shu; Nakamura, Kazuhiko; Ogawa, Toshihide

2018-01-01

Background Of all parotid gland tumors, only oncocytoma has been reported to appear isointense to the parotid gland, namely vanishing, on fat-saturated T2 and T1 postcontrast gadolinium-enhanced magnetic resonance imaging (MRI). The purpose of this study was to evaluate vanishing of parotid tumors on conventional MRI with and/or without postcontrast gadolinium-enhancement and on diffusion weighted imaging (DWI). Methods In 8 of 51 patients, ten parotid gland tumors had homogeneously enhanced lesions and were retrospectively analysed. Comparisons of signal intensity between those parotid tumors and parotid glands and evaluations of vanishing were performed on T1-weighted imaging (T1WI), T2-weighted imaging (T2WI), fat-suppressed T2WI (FS-T2WI), postcontrast gadolinium-enhanced T1WI (CE-T1WI) and fat-suppressed CE-T1WI (FS-CE-T1WI), DWI as well as apparent diffusion coefficient (ADC). Results Ten parotid gland tumors consisted of five Warthin tumors, two pleomorphic adenomas, two parotid carcinomas (small cell carcinoma and adenoid cystic carcinoma) and one oncocytoma. All tumors showed hypointensity on T1WI and hyperintensity on DWI. Nine of ten tumors showed vanishing on the other MR sequences. All Warthin tumors showed vanishing on FS-T2WI, FS-CE-T1WI and the ADC map. One oncocytoma showed vanishing on FS-T2WI and the ADC map and hyperintensity on FS-CE-T1WI. All pleomorphic adenomas showed vanishing on T2WI and CE-T1WI. One adenoid cystic carcinoma showed vanishing only on CE-T1WI. Conclusion Vanishing of parotid tumors can be observed not only on FS-T2WI and FS-CE-T1WI but also on T2WI, CE-T1WI and ADC mapping. PMID:29599620

Active coping of prenatally stressed rats in the forced swimming test: involvement of the Nurr1 gene.

PubMed

Montes, Pedro; Ruiz-Sánchez, Elizabeth; Calvillo, Minerva; Rojas, Patricia

2016-09-01

Depending on genetic predisposition, prenatal stress may result in vulnerability or resilience to develop psychiatric disorders in adulthood. Nurr1 is an immediate early gene, important in the brain for the stress response. We tested the hypothesis that prenatal stress and the decrease of hippocampal Nurr1 alter offspring behavioral responses in the forced swimming test (FST). Pregnant Wistar rats were exposed to restraint stress (45 min, thrice daily) from gestation day 14. Prenatally stressed (PS) and non-prenatally stressed (NPS) male offspring were treated bilaterally with a Nurr1 antisense oligodeoxynucleotide (ODN; or control) into the hippocampus at 97 d of age. After 1 h, the rats were exposed to the FST (acute stressor) to analyze their behavioral responses. Thirty minutes after the FST, we analyzed the gene expression of Nurr1, Bdnf and Nr3c1 (genes for Nurr1, brain-derived neurotrophic factor (BDNF) and glucocorticoid receptor (GR), respectively) in the hippocampus, prefrontal cortex (PFC) and hypothalamus. Results showed that the decrease of hippocampal Nurr1 after the antisense ODN in adult NPS rats induces immobility (indicating depressive-like behavior). The PS adult rats, including the group with decreased hippocampal Nurr1, presented low immobility in the FST. This low immobility was concordant with maintenance of Nurr1 and Bdnf expression levels in the three analyzed brain regions; Nr3c1 gene expression was also maintained in the PFC and hypothalamus. These findings suggest that Nurr1 and associated genes could participate in the brain modifications induced by prenatal stress, allowing active coping (resilience) with acute stress in adulthood.

Inhibition of the L-arginine-nitric oxide pathway mediates the antidepressant effects of ketamine in rats in the forced swimming test.

PubMed

Zhang, Guang-Fen; Wang, Nan; Shi, Jin-Yun; Xu, Shi-Xia; Li, Xiao-Min; Ji, Mu-Huo; Zuo, Zhi-Yi; Zhou, Zhi-Qiang; Yang, Jian-Jun

2013-09-01

Converging evidence shows that the acute administration of a sub-anaesthetic dose ketamine produces fast-acting and robust antidepressant properties in patients suffering from major depressive disorder. However, the underlying mechanisms have not been fully elucidated. The present study aimed to investigate the role of the L-arginine-nitric oxide pathway in the antidepressant effects of ketamine in rats performing the forced swimming test (FST). Ketamine (10 mg/kg) significantly decreased immobility times in the FST and the activities of total nitric oxide synthases (T-NOS), inducible NOS (iNOS), and endothelial NOS (eNOS) in the rat hippocampus. Interestingly, the plasma activities of T-NOS, iNOS, and eNOS increased after administration of ketamine. Furthermore, the activities of neuronal NOS (nNOS) did not change significantly in either the hippocampus or plasma after ketamine administration. The antidepressant effects of ketamine were prevented by pre-treatment with l-arginine (750 mg/kg). Pre-treatment with the NOS inhibitor L-NG-nitroarginine methyl ester at a sub-antidepressant dose of 50 mg/kg and ketamine at a sub-antidepressant dose of 3 mg/kg reduced immobility time in the FST compared to treatment with either drug alone. None of the drugs affected crossing and rearing scores in the open field test. These results suggest that the L-arginine-nitric oxide pathway is involved in the antidepressant effects of ketamine observed in rats in the FST and this involvement is characterised by the inhibition of brain T-NOS, iNOS, and eNOS activities. Copyright © 2013 Elsevier Inc. All rights reserved.

Modeling bipolar disorder in mice by increasing acetylcholine or dopamine: Chronic lithium treats most, but not all features

PubMed Central

van Enkhuizen, Jordy; Milienne-Petiot, Morgane; Geyer, Mark A.; Young, Jared W.

2015-01-01

Rationale Bipolar disorder (BD) is a disabling and life-threatening disease characterized by states of depression and mania. New and efficacious treatments have not been forthcoming partly due to a lack of well-validated models representing both facets of BD. Objectives We hypothesized that cholinergic- and dopaminergic-pharmacological manipulations would model depression and mania respectively, each attenuated by lithium treatment. Methods C57BL/6J mice received the acetylcholinesterase inhibitor physostigmine or saline before testing for ‘behavioral despair’ (immobility) in the tail-suspension test (TST) and forced-swim test (FST). Physostigmine effects on exploration and sensorimotor gating were assessed using the cross-species behavioral pattern monitor (BPM) and prepulse inhibition (PPI) paradigms. Other C57BL/6J mice received chronic lithium drinking water (300, 600, or 1200 mg/l) before assessing their effects alone in the BPM or with physostigmine on FST performance. Another group was tested with acute GBR12909 (dopamine transporter inhibitor) and chronic lithium (1000 mg/l) in the BPM. Results Physostigmine (0.03 mg/kg) increased immobility in the TST and FST without affecting activity, exploration, or PPI. Lithium (600 mg/l) resulted in low therapeutic serum concentrations and normalized the physostigmine-increased immobility in the FST. GBR12909 induced mania-like behavior in the BPM of which hyper-exploration was attenuated, though not reversed, after chronic lithium (1000 mg/ml). Conclusions Increased cholinergic levels induced depression-like behavior and hyperdopaminergia induced mania-like behavior in mice, while chronic lithium treated some, but not all, facets of these effects. These data support a cholinergic-monoaminergic mechanism for modeling BD aspects and provide a way to assess novel therapeutics. PMID:26141192

Cryogenic Hydrogen Fuel for Controlled Inertial Confinement Fusion (Cryogenic Target Factory Concept Based on FST-Layering Method)

NASA Astrophysics Data System (ADS)

Aleksandrova, I. V.; Koresheva, E. R.; Koshelev, I. E.; Krokhin, O. N.; Nikitenko, A. I.; Osipov, I. E.

2017-12-01

A central element of a power plant based on inertial confinement fusion (ICF) is a target with cryogenic hydrogen fuel that should be delivered to the center of a reactor chamber with a high accuracy and repetition rate. Therefore, a cryogenic target factory (CTF) is an integral part of any ICF reactor. A promising way to solve this problem consists in the FST layering method developed at the Lebedev Physical Institute (LPI). This method (rapid fuel layering inside moving free-standing targets) is unique, having no analogs in the world. The further development of FST-layering technologies is implemented in the scope of the LPI program for the creation of a modular CTF and commercialization of the obtained results. In this report, we discuss our concept of CTF (CTF-LPI) that exhibits the following distinctive features: using a FST-layering technology for the elaboration of an in-line production of cryogenic targets, using an effect of quantum levitation of high-temperature superconductors (HTSCs) in magnetic field for noncontacting manipulation, transport, and positioning of the free-standing cryogenic targets, as well as in using a Fourier holography technique for an on-line characterization and tracking of the targets flying into the reactor chamber. The results of original experimental and theoretical investigations performed at LPI indicate that the existing and developing target fabrication capabilities and technologies can be applied to ICF target production. The unique scientific, engineering, and technological base developed in Russia at LPI allows one to make a CTFLPI prototype for mass production of targets and delivery thereof at the required velocity into the ICF reactor chamber.

Lactobacillus amylovorus DSM 19280 as a novel food-grade antifungal agent for bakery products.

PubMed

Ryan, Liam A M; Zannini, Emanuele; Dal Bello, Fabio; Pawlowska, Agata; Koehler, Peter; Arendt, Elke K

2011-04-29

Mould spoilage is the main cause of substantial economic loss in bakery industry and might also cause public health problems due to the production of mycotoxins. The reduction of mould growth in bakery products is thus of crucial importance and there is great interest to develop safe and efficient strategies for this purpose. In this study Lactobacillus amylovorus DSM19280 has been shown to produce a wide spectrum of antifungal compounds active against common bread spoilage fungi. Among the indicator moulds, Aspergillus fumigatus and Fusarium culmorum were the most sensitive organisms. Several antifungal compounds were found to be present in synthetic medium inoculated with L. amylovorus DSM19280 strain, some of them being reported here for the first time. Wheat doughs fermented with L. amylovorus DSM19280 had good rheological properties and the breads thereof were of high quality as shown by rheofermentometer and texture analyser measurements. The results were compared with those obtained with a control non-antifungal L. amylovorus DSM20531(T) strain, a non-acidified and a chemically acidified dough. The quality of sourdough and bread fermented with L. amylovorus DSM 19280 was comparable to that obtained by using L. amylovorus DSM20531 (T). Additionally, breads were evaluated for the ability to retard the growth of Fusarium culmorum FST 4.05, Aspergillus niger FST4.21, Penicillium expansum FST 4.22, Penicillium roqueforti FST 4.11 and fungal flora from the bakery environment. The biological preservation of bread with L. amylovorus DSM 19280 was also compared to the most commonly used antifungal agent Calcium propionate. Breads containing sourdough fermented with L. amylovorus DSM 19280 were more effective in extending the shelf life of bread than the calcium propionate. Copyright © 2011 Elsevier B.V. All rights reserved.

Nucleus accumbens deep-brain stimulation efficacy in ACTH-pretreated rats: alterations in mitochondrial function relate to antidepressant-like effects

PubMed Central

Kim, Y; McGee, S; Czeczor, J K; Walker, A J; Kale, R P; Kouzani, A Z; Walder, K; Berk, M; Tye, S J

2016-01-01

Mitochondrial dysfunction has a critical role in the pathophysiology of mood disorders and treatment response. To investigate this, we established an animal model exhibiting a state of antidepressant treatment resistance in male Wistar rats using 21 days of adrenocorticotropic hormone (ACTH) administration (100 μg per day). First, the effect of ACTH treatment on the efficacy of imipramine (10 mg kg−1) was investigated alongside its effect on the prefrontal cortex (PFC) mitochondrial function. Second, we examined the mood-regulatory actions of chronic (7 day) high-frequency nucleus accumbens (NAc) deep-brain stimulation (DBS; 130 Hz, 100 μA, 90 μS) and concomitant PFC mitochondrial function. Antidepressant-like responses were assessed in the open field test (OFT) and forced swim test (FST) for both conditions. ACTH pretreatment prevented imipramine-mediated improvement in mobility during the FST (P<0.05). NAc DBS effectively improved FST mobility in ACTH-treated animals (P<0.05). No improvement in mobility was observed for sham control animals (P>0.05). Analyses of PFC mitochondrial function revealed that ACTH-treated animals had decreased capacity for adenosine triphosphate production compared with controls. In contrast, ACTH animals following NAc DBS demonstrated greater mitochondrial function relative to controls. Interestingly, a proportion (30%) of the ACTH-treated animals exhibited heightened locomotor activity in the OFT and exaggerated escape behaviors during the FST, together with general hyperactivity in their home-cage settings. More importantly, the induction of this mania-like phenotype was accompanied by overcompensative increased mitochondrial respiration. Manifestation of a DBS-induced mania-like phenotype in imipramine-resistant animals highlights the potential use of this model in elucidating mechanisms of mood dysregulation. PMID:27327257

Evidence for the involvement of NMDA receptors in the antidepressant-like effect of nicotine in mouse forced swimming and tail suspension tests.

PubMed

Haj-Mirzaian, Arya; Kordjazy, Nastaran; Haj-Mirzaian, Arvin; Ostadhadi, Sattar; Ghasemi, Mehdi; Amiri, Shayan; Faizi, Mehrdad; Dehpour, AhmadReza

2015-10-01

The antidepressant action of acute nicotine administration in clinical and animal studies is well recognized. But the underlying mechanism for this effect has not been carefully discovered. We attempted to evaluate the possible role of N-Methyl-D-aspartate (NMDA) receptors in the antidepressant-like effect of nicotine. After the assessment of locomotor activity in the open-field test, forced swimming test (FST) and tail suspension test (TST) were used to evaluate the antidepressant-like effect of nicotine in mice. We performed intraperitoneal administration of nicotine at different doses and periods before the tests. To assess the possible involvement of NMDA receptors, non-effective doses of NMDA antagonists and an NMDA agonist were obtained and were administered simultaneously with the non-effective and effective doses of nicotine, respectively. Nicotine (0.2 mg/kg, 30 min before FST/TST) significantly reduced the immobility time of mice similar to fluoxetine (20 mg/kg). Nicotine did not affect the locomotor behavior of mice in open-field test. Co-administration of non-effective doses of NMDA receptor antagonists, ketamine (1 or 0.3 mg/kg), MK-801 (0.05 or 0.005 mg/kg), and magnesium sulfate (10 or 5 mg/kg) with nicotine (0.1 or 0.03 mg/kg) had remarkable synergistic antidepressant effect in both FST and TST. Also, non-effective NMDA (75 or 30 mg/kg) reversed the anti-immobility effect of nicotine (0.2 mg/kg) on mouse FST and TST. Our study has for the first time confirmed that the antidepressant-like effect of nicotine on mice is NMDA-mediated, and nicotine presumably exerts this effect by antagonizing the glutamatergic NMDA receptors.

The folic acid combined with 17-β estradiol produces antidepressant-like actions in ovariectomized rats forced to swim.

PubMed

Molina-Hernández, Miguel; Téllez-Alcántara, N Patricia; Olivera-López, Jorge I; Jaramillo, M Teresa

2011-01-15

Folic acid or 17-β estradiol produces antidepressant effects, either alone or combined with several antidepressants. However, the antidepressant-like actions of folic acid combined with 17-β estradiol in the forced swimming test (FST) have not been tested before. Thus, in the present study, ovariectomized female rats received folic acid (5.0 nmol/i.c.v., P<0.05; 10.0 nmol/ i.c.v., P<0.05; or 50mg/kg, P<0.05, p.o.; 75.0; mg/kg, P<0.05, p.o.), or fluoxetine (20.0mg/kg, P<0.05; 25.0mg/kg, P<0.05) or 17-β estradiol (10.0 μg/rat, P<0.05; 20.0 μg/rat, P<0.05) and they displayed reduced immobility by increasing swimming behavior when they were tested in the FST. Combination of subthreshold doses of folic acid (2.5 nmol/i.c.v.; or 25.0mg/kg, p.o.) with subthreshold doses of 17-β estradiol (5.0 μg/rat, P<0.05) or with subthreshold doses of fluoxetine (15.0mg/kg, P<0.05) produced antidepressant-like actions. Ketanserin was used to evaluate the participation of the drugs used in the serotonergic pathway; ketanserin cancelled the antidepressant-like actions of the several combinations used. In conclusion, folic acid alone or combined with estradiol or fluoxetine in the FST reduced immobility in the FST. These antidepressant-like actions probably were due to modifications of the serotonergic system since swimming behavior was increased and these effects were cancelled by ketanserin. Copyright © 2010 Elsevier Inc. All rights reserved.

Effect of co-administration of fluoxetine and amantadine on immunoendocrine parameters in rats subjected to a forced swimming test.

PubMed

Rogóz, Zofia; Kubera, Marta; Rogóz, Katarzyna; Basta-Kaim, Agnieszka; Budziszewska, Bogusława

2009-01-01

Considerable attention has been paid to a possible role of immunological dysregulation in the pathogenesis of depression. It has been reported that combined administration of antidepressant drugs and the non-competitive NMDA receptor antagonist amantadine reduces immobility time in the forced swimming test (FST). Moreover, preliminary clinical data show that such a combination of drugs has a beneficial effect on treatment-resistant depressed patients. Since immune activation and a pro-inflammatory response are clearly evident in treatment-resistant depression, the aim of the present study was to examine the effect of a combination of the antidepressant fluoxetine and amantadine on immunoendocrine parameters in rats subjected to the forced swimming test. The obtained results revealed synergistic antidepressant effects of the combined administration of fluoxetine (10 mg/kg) and amantadine (10 mg/kg) - drugs otherwise ineffective when given separately in the above doses. Antidepressant activity was accompanied with a significant decrease in the capacity of splenocytes to proliferate in response to concanavalin A. Moerover, fluoxetine and the combination of amantadine and fluoxetine reduced relative spleen weight in rats subjected to the FST, compared to rats treated with the vehicle. The combination of amantadine and fluoxetine enhanced the production of the negative immunoregulator interleukin-10 (but not interferon-gamma) in rats subjected to the FST. The exposure to the FST produced an increase in plasma corticosterone levels, which was significantly attenuated by pretreatment with fluoxetine and amantadine. In summary, the antidepressive efficacy of a combination of fluoxetine and amantadine given in suboptimal doses may be related to the negative immunoendocrine effects of these drugs.

Dopamine mediated antidepressant effect of Mucuna pruriens seeds in various experimental models of depression

PubMed Central

Rana, Digvijay G.; Galani, Varsha J.

2014-01-01

Background: The effects of antidepressant treatments have traditionally been discussed primarily in terms of effects on noradrenergic and serotonergic systems. Multiple lines of investigation have also explored the role of dopaminergic systems in mental depression. Seed of Mucuna pruriens Linn. (DC) (Leguminoseae) is well-known with dopaminergic action and has several therapeutic applications in folk medicine in curing or managing a wide range of diseases including Parkinsonism. Aim: To elucidate the anti-depressent profile and possible dopaminergic modulating action of M. pruriens seeds in various experimental models of depression. Materials and Methods: In the present study, antidepressant effect of the hydroalcoholic extract of the M. pruriens seeds (MPE) (100 and 200 mg/kg, p.o.) was investigated in the Forced Swimming Test (FST), Tail Suspension Test (TST), and Chronic Unpredictable Mild Stress (CUMS) test in mice. Further, dopaminergic interaction of same doses of MPE in the FST and TST were checked by the administration of a haloperidol (0.1 mg/kg, i.p.) and bromocriptine (2 mg/kg, i.p.) on the 7th day of MPE treatment. Effect of MPE on locomotor activity was also checked using actophotometer. Results: MPE produced a significant reduction of the immobility time in the FST and TST. Further, antidepressant action of MPE was significantly inhibited by haloperidol and potentiated by bromocriptine in the FST and TST. 21 days of MPE treatment produced protection in CUMS as indicated by a significant increase of sucrose intake of stressed mice. Locomotor activities of mice were not significantly changed after 1 h and 7th day of the MPE treatment. Conclusion: The results of this study indicate that hydroalcoholic extract of MPE have antidepressant action, which may be mediated by an interaction with the dopaminergic system. PMID:25364207

Dopamine mediated antidepressant effect of Mucuna pruriens seeds in various experimental models of depression.

PubMed

Rana, Digvijay G; Galani, Varsha J

2014-01-01

The effects of antidepressant treatments have traditionally been discussed primarily in terms of effects on noradrenergic and serotonergic systems. Multiple lines of investigation have also explored the role of dopaminergic systems in mental depression. Seed of Mucuna pruriens Linn. (DC) (Leguminoseae) is well-known with dopaminergic action and has several therapeutic applications in folk medicine in curing or managing a wide range of diseases including Parkinsonism. To elucidate the anti-depressent profile and possible dopaminergic modulating action of M. pruriens seeds in various experimental models of depression. In the present study, antidepressant effect of the hydroalcoholic extract of the M. pruriens seeds (MPE) (100 and 200 mg/kg, p.o.) was investigated in the Forced Swimming Test (FST), Tail Suspension Test (TST), and Chronic Unpredictable Mild Stress (CUMS) test in mice. Further, dopaminergic interaction of same doses of MPE in the FST and TST were checked by the administration of a haloperidol (0.1 mg/kg, i.p.) and bromocriptine (2 mg/kg, i.p.) on the 7(th) day of MPE treatment. Effect of MPE on locomotor activity was also checked using actophotometer. MPE produced a significant reduction of the immobility time in the FST and TST. Further, antidepressant action of MPE was significantly inhibited by haloperidol and potentiated by bromocriptine in the FST and TST. 21 days of MPE treatment produced protection in CUMS as indicated by a significant increase of sucrose intake of stressed mice. Locomotor activities of mice were not significantly changed after 1 h and 7(th) day of the MPE treatment. The results of this study indicate that hydroalcoholic extract of MPE have antidepressant action, which may be mediated by an interaction with the dopaminergic system.

Male aromatase-knockout mice exhibit normal levels of activity, anxiety and "depressive-like" symptomatology.

PubMed

Dalla, C; Antoniou, K; Papadopoulou-Daifoti, Z; Balthazart, J; Bakker, J

2005-09-08

It is well known that estradiol derived from neural aromatization of testosterone plays a crucial role in the development of the male brain and the display of sexual behaviors in adulthood. It was recently found that male aromatase knockout mice (ArKO) deficient in estradiol due to a mutation in the aromatase gene have general deficits in coital behavior and are sexually less motivated. We wondered whether these behavioral deficits of ArKO males could be related to changes in activity, exploration, anxiety and "depressive-like" symptomatology. ArKO and wild type (WT) males were subjected to open field (OF), elevated plus maze (EPM), and forced swim tests (FST), after being exposed or not to chronic mild stress (CMS). CMS was used to evaluate the impact of chronic stressful procedures and to unveil possible differences between genotypes. There was no effect of genotype on OF, EPM and FST behavioral parameters. WT and ArKO mice exposed to CMS or not exhibited the same behavioral profile during these three types of tests. However, all CMS-exposed mice (ArKO and WT) spent less time in the center of the EPM. Additionally, floating duration measured in the FST increased between two tests in both WT and ArKO mice, though that increase was less prominent in mice previously subjected to CMS than in controls. Therefore, both ArKO and WT males displayed the same behavior and had the same response to CMS however CMS exposure slightly modified the behavior displayed by mice of both genotypes in the FST and EPM paradigms. These results show that ArKO males display normal levels of activity, exploration, anxiety and "depressive-like" symptomatology and thus their deficits in sexual behavior are specific in nature and do not result indirectly from other behavioral changes.

Progression of behavioural despair in R6/2 and Hdh knock-in mouse models recapitulates depression in Huntington's disease.

PubMed

Ciamei, Alessandro; Detloff, Peter J; Morton, A Jennifer

2015-09-15

In Huntington's disease (HD) depression is observed before the disease is diagnosed, and is likely to be a component of the disease, rather than a consequence. Depression in HD patients does not progress in parallel with other symptoms; rather it peaks at early- to mid-stages of the disease and declines thereafter. In mice, depressive-like behaviours can be measured as an increase in behavioural despair (floating) observed in the forced swim test (FST). Floating in the FST is modulated differently by antidepressants with different mechanisms of action. Drugs that increase levels of serotonin inhibit floating by promoting horizontal swimming, whereas drugs that increase levels of noradrenaline inhibit floating by enhancing vertical swimming (climbing). We compared the FST behavioural profiles of two different allelic series of HD mice, a fragment model (R6/2 mice carrying 120, 250, or 350 CAG repeats), and a knock-in model (Hdh mice carrying 50, 150, or 250 CAG repeats). The FST behavioural profile was similar in both lines. It was characterized by an early-stage increase in floating, and then, as the mice aged, floating decreased, whereas active behaviours of swimming and climbing increased. Our results show that, as with depression in HD patients, floating in HD mice does not progress linearly, suggesting that, at the late stages of the disease, an increase in serotonergic and noradrenergic activity might contribute to lower floating levels in HD mice. If similar compensatory changes occur in humans, this should be taken into account when considering the treatment of depression in HD patients. Copyright © 2015 Elsevier B.V. All rights reserved.

A Genome-wide Analysis of Admixture in Uyghurs and a High-Density Admixture Map for Disease-Gene Discovery

PubMed Central

Xu, Shuhua; Jin, Li

2008-01-01

Following up on our previous study, we conducted a genome-wide analysis of admixture for two Uyghur population samples (HGDP-UG and PanAsia-UG), collected from the northern and southern regions of Xinjiang in China, respectively. Both HGDP-UG and PanAsia-UG showed a substantial admixture of East-Asian (EAS) and European (EUR) ancestries, with an empirical estimation of ancestry contribution of 53:47 (EAS:EUR) and 48:52 for HGDP-UG and PanAsia-UG, respectively. The effective admixture time under a model with a single pulse of admixture was estimated as 110 generations and 129 generations, or admixture events occurred about 2200 and 2580 years ago for HGDP-UG and PanAsia-UG, respectively, assuming an average of 20 yr per generation. Despite Uyghurs' earlier history compared to other admixture populations, admixture mapping, holds promise for this population, because of its large size and its mixture of ancestry from different continents. We screened multiple databases and identified a genome-wide single-nucleotide polymorphism panel that can distinguish EAS and EUR ancestry of chromosomal segments in Uyghurs. The panel contains 8150 ancestry-informative markers (AIMs) showing large frequency differences between EAS and EUR populations (FST > 0.25, mean FST = 0.43) but small frequency differences (7999 AIMs validated) within both populations (FST < 0.05, mean FST < 0.01). We evaluated the effectiveness of this admixture map for localizing disease genes in two Uyghur populations. To our knowledge, our map constitutes the first practical resource for admixture mapping in Uyghurs, and it will enable studies of diseases showing differences in genetic risk between EUR and EAS populations. PMID:18760393

Antidepressant-like effect of aqueous extract of Channa striatus fillet in mice models of depression.

PubMed

Saleem, A M; Taufik Hidayat, M; Mat Jais, A M; Fakurazi, S; Moklas, Mohamad; Sulaiman, M R; Amom, Z

2011-07-01

Channa (C.) striatus (Malay-Haruan), is a fresh water snakehead fish, consumed as a rejuvenating diet in post-parturition period in local Malay population. The aqueous extract of C. striatus fillet (AECSF) was reported to act through serotonergic receptor system in a previous study. There is no scientific report on neuropharmacological effects of C. striatus. Based on these data, the antidepressant-like effect of C. striatus was evaluated in mice models of depression. AECSF was prepared by steaming the fillets as described previously. Antidepressant activity was studied in male ICR mice using forced swimming test (FST) and tail suspension test (TST). Open-field test was used to evaluate any psychomotor stimulant activity. AECSF was administered intraperitoneally at the concentrations of 30%, 40% and 50% w/v at the dosage of 10 ml/kg. Amitriptyline (10 mg/kg) was used as positive control. All the three concentrations of AECSF (30%, 40% and 50% w/v) significantly reduced the immobility time (p < 0.001) in FST and TST. All the three concentrations of AECSF (30%, 40% and 50% w/v) significantly (p < 0.001) reduced locomotor activity in a dose-dependent manner in open-field test. AECSF produced significant reduction of immobility time in both FST and TST. Amitriptyline produced a significant reduction of immobility time in both FST and TST similar to previous findings. The AECSF produced a dose-dependent decrease in locomotor activity in the open-field test. This hypolocomotion effect indicated the absence of any psychomotor stimulant activity thereby supporting the antidepressant-like effect of the AECSF. The pharmacological mechanisms of the observed antidepressant-like effect and hypolocomotion effect are not understood from our study. Hence, further studies are required.

Antidepressant-like property of Jobelyn®, an African unique herbal formulation, in mice.

PubMed

Umukoro, S; Eduviere, A T; Aladeokin, A C; Olugbemide, A S

2014-03-01

The purpose of this investigation was to evaluate whether Jobelyn® (JB) possesses anti-depressant-like property in the mouse forced swimming test (FST), tail suspension test (TST) and yohimbine-induced lethality test (YLT) in aggregated mice. Mice were given JB (10-100 mg/kg, p.o.) daily for 7 days and then subjected to FST, TST, YLT and open field test. The parameters assessed in both FST and TST were the time (s) spent in active movement (struggling time), first occurrence of immobility (s) and the duration of immobility (s). In the YLT, the mortality rate was recorded 24 h after yohimbine (35 mg/kg, i.p.) administration. In the open field test, the number of line crosses and total distance travelled (m) were measured for 10 min in the open field chamber. JB significantly (p<0.05) decrease the duration of immobility both in the FST and TST, which suggests antidepressant-like property. JB significantly (p<0.05) prolonged the time spent in active swimming and delayed the first occurrence of immobility, indicating endurance promoting effect. It potentiated the toxic effect of yohimbine, which further suggests antidepressant-like activity and facilitation of both serotonergic and noradrenergic neurotransmissions. However, JB did not significantly increase the locomotor activity in the open-field test. Jobelyn® has antidepressant-like activity, which may be related to the stimulation of serotonergic and noradrenergic pathways. The ability of Jobelyn® to delay the onset of immobility and to prolong the struggling time support its use as energizer in general body weakness or exhaustion. © Georg Thieme Verlag KG Stuttgart · New York.

Analysis of East Asia Genetic Substructure Using Genome-Wide SNP Arrays

PubMed Central

Tian, Chao; Kosoy, Roman; Lee, Annette; Ransom, Michael; Belmont, John W.; Gregersen, Peter K.; Seldin, Michael F.

2008-01-01

Accounting for population genetic substructure is important in reducing type 1 errors in genetic studies of complex disease. As efforts to understand complex genetic disease are expanded to different continental populations the understanding of genetic substructure within these continents will be useful in design and execution of association tests. In this study, population differentiation (Fst) and Principal Components Analyses (PCA) are examined using >200 K genotypes from multiple populations of East Asian ancestry. The population groups included those from the Human Genome Diversity Panel [Cambodian, Yi, Daur, Mongolian, Lahu, Dai, Hezhen, Miaozu, Naxi, Oroqen, She, Tu, Tujia, Naxi, Xibo, and Yakut], HapMap [ Han Chinese (CHB) and Japanese (JPT)], and East Asian or East Asian American subjects of Vietnamese, Korean, Filipino and Chinese ancestry. Paired Fst (Wei and Cockerham) showed close relationships between CHB and several large East Asian population groups (CHB/Korean, 0.0019; CHB/JPT, 00651; CHB/Vietnamese, 0.0065) with larger separation with Filipino (CHB/Filipino, 0.014). Low levels of differentiation were also observed between Dai and Vietnamese (0.0045) and between Vietnamese and Cambodian (0.0062). Similarly, small Fst's were observed among different presumed Han Chinese populations originating in different regions of mainland of China and Taiwan (Fst's <0.0025 with CHB). For PCA, the first two PC's showed a pattern of relationships that closely followed the geographic distribution of the different East Asian populations. PCA showed substructure both between different East Asian groups and within the Han Chinese population. These studies have also identified a subset of East Asian substructure ancestry informative markers (EASTASAIMS) that may be useful for future complex genetic disease association studies in reducing type 1 errors and in identifying homogeneous groups that may increase the power of such studies. PMID:19057645

The association effect of insulin and clonazepam on oxidative stress in liver of an experimental animal model of diabetes and depression.

PubMed

Wayhs, Carlos Alberto Yasin; Tortato, Caroline; Mescka, Caroline Paula; Pasquali, Matheus Augusto; Schnorr, Carlos Eduardo; Nin, Maurício Schüler; Barros, Helena Maria Tannhauser; Moreira, José Claudio Fonseca; Vargas, Carmen Regla

2013-05-01

It is known that oxidative stress occurs in peripheral blood in an experimental animal model of diabetes and depression, and acute treatment with insulin and clonazepam (CNZ) has a protective effect on oxidative stress in this model. This study evaluated the effect of insulin plus CNZ on oxidative stress parameters in the liver of diabetic male rats induced with streptozotocin (STZ) and subjected to forced swimming test (FST). Diabetes was induced by a single intraperitoneal (i.p.) dose of STZ 60 mg/kg in male Wistar rats. Insulin (4 IU/kg) plus CNZ acute i.p. treatment (0.25 mg/kg) was administered 24, 5 and 1 h before the FST. Nondiabetic control rats received i.p. injections of saline (1 mL/kg). Protein oxidative damage was evaluated by carbonyl formation and the antioxidant redox parameters were analyzed by the measurements of enzymatic activities of the superoxide dismutase (SOD), catalase and glyoxalase I (GLO). Glycemia levels also were determined. Our present study has shown an increase in carbonyl content from diabetic rats subjected to FST (2.04 ± 0.55), while the activity of catalase (51.83 ± 19.02) and SOD (2.30 ± 1.23) were significantly decreased in liver from these animals, which were reverted by the treatment. Also, the activity of GLO (0.15 ± 0.02) in the liver of the animals was decreased. Our findings showed that insulin plus CNZ acute treatment ameliorate the antioxidant redox parameters and protect against protein oxidative damage in the liver of diabetic rats subjected to FST.

Evidence for the involvement of the opioid system in the antidepressant-like effect of folic acid in the mouse forced swimming test.

PubMed

Brocardo, Patrícia S; Budni, Josiane; Lobato, Kelly R; Santos, Adair Roberto S; Rodrigues, Ana Lúcia S

2009-06-08

The opioid system has been implicated in major depression and in the mechanism of action of antidepressants. This study investigated the involvement of the opioid system in the antidepressant-like effect of the water-soluble B-vitamin folic acid in the forced swimming test (FST). The effect of folic acid (10 nmol/site, i.c.v.) was prevented by the pretreatment of mice with naloxone (1 mg/kg, i.p., a nonselective opioid receptor antagonist), naltrindole (3 mg/kg, i.p., a selective delta-opioid receptor antagonist), naloxonazine (10 mg/kg, i.p., a selective mu(1)-opioid receptor antagonist, 24 h before), but not with naloxone methiodide (1 mg/kg, s.c., a peripherally acting opioid receptor antagonist). In addition, a sub-effective dose of folic acid (1 nmol/site, i.c.v.) produced a synergistic antidepressant-like effect in the FST with a sub-effective dose of morphine (1 mg/kg, s.c.). A further approach was designed to investigate the possible relationship between the opioid system and NMDA receptors in the mechanism of action of folic acid in the FST. Pretreatment of the animals with naloxone (1 mg/kg, i.p.) prevented the synergistic antidepressant-like effect of folic acid (1 nmol/site, i.c.v.) and MK-801 (0.001 mg/kg, i.p., a non-competitive NMDA receptor antagonist). Together the results firstly indicate that the anti-immobility effect of folic acid in the FST is mediated by an interaction with the opioid system (mu(1) and delta), likely dependent on the inhibition of NMDA receptors elicited by folic acid.

NMDA-NO signaling in the dorsal and ventral hippocampus time-dependently modulates the behavioral responses to forced swimming stress.

PubMed

Diniz, Cassiano R A F; Casarotto, Plínio C; Joca, Sâmia R L

2016-07-01

Hodological and genetic differences between dorsal (DH) and ventral (VH) hippocampus may convey distinct behavioral roles. DH is responsible for mediating cognitive process, such as learning and memory, while VH modulates neuroendocrine and emotional-motivational responses to stress. Manipulating glutamatergic NMDA receptors and nitric oxide (NO) systems of the hippocampus induces important changes in behavioral responses to stress. Nevertheless, there is no study concerning functional differences between DH and VH in the modulation of behavioral responses induced by stress models predictive of antidepressant effects. Thus, this study showed that reversible blockade of the DH or VH of animals submitted to the forced swimming test (FST), by using cobalt chloride (calcium-dependent synaptic neurotransmission blocker), was not able to change immobility time. Afterwards, the NMDA-NO system was evaluated in the FST by means of intra-DH or intra-VH administration of NMDA receptor antagonist (AP7), NOS1 and sGC inhibitors (N-PLA and ODQ, respectively). Bilateral intra-DH injections after pretest or before test were able to induce antidepressant-like effects in the FST. On the other hand, bilateral VH administration of AP-7, N-PLA and ODQ induced antidepressant-like effects only when injected before the test. Administration of NO scavenger (C-PTIO) intra-DH, after pretest and before test, or intra-VH before test induced similar results. Increased NOS1 levels was associated to stress exposure in the DH. These results suggest that the glutamatergic-NO system of the DH and VH are both able to modulate behavioral responses in the FST, albeit with differential participation along time after stress exposure. Copyright © 2016 Elsevier B.V. All rights reserved.

Immobility time during the forced swimming test predicts sensitivity to amitriptyline, whereas traveled distance in the circular corridor indicates resistance to treatment in female Wistar rats.

PubMed

Flores-Serrano, Ana G; Zaldívar-Rae, Jaime; Salgado, Humberto; Pineda, Juan C

2015-03-25

Among the main issues in the pharmacological treatment of depression are the wide variation in response to antidepressants among individual patients and the lack of indexes that allow prediction of which drug will be effective in a particular case. We evaluated whether differential sensitivity to amitriptyline is related to dichotomous categorization of individuals on the basis of their behavioral responses to two common paradigms used to evaluate the potential of tricyclic drugs as antidepressants. Hence, we categorized a cohort of 38 female rats on the basis of their immobility time in the conditioning phase of the forced swimming test [FST; high immobility (HI) vs. low immobility (LI) rats] and their locomotor behavior in the circular corridor test [high locomotor response (HR) vs. low locomotor response (LR) rats]. We subjected the rodents to the FST while under the influence of vehicle (n=20) or amitriptyline (15 mg/kg; n=18). We found no statistical evidence of dependence between categorizations of rats on the basis of their behavior in the FST and circular corridor test. Rats categorized as HI/LI and HR/LR significantly differed in their sensitivity/resistance to amitriptyline, as evidenced by changes (or lack thereof) in their immobility time, climbing time, and swimming time during the FST. These results confirm that different behavioral styles among rats are linked to differential sensitivity/resistance to antidepressants. However, we specifically found that categorizing rats as HI/LI better reflected sensitivity to amitriptyline, whereas categorizing them as HR/LR better revealed resistance to the drug. These differential responses should be considered in experimental approaches. Copyright © 2015 Wolters Kluwer Health, Inc. All rights reserved.

Redshift-space distortions of group and galaxy correlations in the Updated Zwicky Catalog

NASA Astrophysics Data System (ADS)

Padilla, N. D.; Merchán, M.; García Lambas, D.; Maia, M. G.

We calculate two-point correlation functions of galaxies and groups of galaxies selected in three dimensions from the Updated Zwicky Galaxy Catalog - (UZC). The redshift space distortion of the correlation function ξ(σ,π) in the directions parallel and perpendicular to the line of sight, induced by pairwise group peculiar velocities is evaluated. Two methods are used to characterize the pairwise velocity field. The first method consists in fitting the observed ξ(σ,π) with a distorted model with an exponential pairwise velocity distribution, in fixed σ bins. The second method compares the contours of constant predicted correlation function of this model with the data. The results are consistent with a one-dimensional pairwise rms velocity dispersion of groups 1/2=250 ± 110 km/s. We find that UZC galaxy pairwise velocity dispersion is 1/2 = 460 ± 35 km/s. Such findings point towards a smoothly varying peculiar velocity field from galaxies to systems of galaxies, a expected in a hierarchical scenario of structure formation. We estimate the real-space correlation function in the power-law approximation ξ(r)=(r/r0)γ for groups and galaxies in UZC. We obtain the correlation length, r0, from the projected correlation function W(σ)=∫- ∞∞ξ(σ,π)dπ= 2 ∫0∞ ξ(σ,π) dπ using the values of γ derived from the correlation function in projected separations ω(σ). The best fitting parameters are γ=-1.89 ± 0.17 and r0=9.7 ± 4.5 Mpc h-1 for groups, and γ=-2.00 ± 0.03, r0=5.29 ± 0.21 Mpc h-1 for galaxies. We carried out an estimate of the parameter β= Ω0.6/b for groups and galaxies using the linear approximation regime relating the real and the redshift-space correlation functions. We find βgalaxies=0.51 ± 0.15 for galaxies, in agreement with previous works, while for groups we obtain a noisy estimate β < 1.5. We have tested our methods on mock UZC catalogs taken from N-body simulations. The results of these tests show that the conclusions derived from the application of our methods to the observations are reliable and provide a suitable characterization of the spatial correlation and pairwise velocities of groups and galaxies. We also find that the second method, developed in this work, provides more stable and precise results.

Forced swimming test and fluoxetine treatment: in vivo evidence that peripheral 5-HT in rat platelet-rich plasma mirrors cerebral extracellular 5-HT levels, whilst 5-HT in isolated platelets mirrors neuronal 5-HT changes.

PubMed

Bianchi, M; Moser, C; Lazzarini, C; Vecchiato, E; Crespi, F

2002-03-01

Low levels of central serotonin (5-HT) have been related to the state of depression, and 5-HT is the major target of the newer antidepressant drugs such as selective serotonin reuptake inhibitors (SSRIs). Neurons and platelets display structural and functional similarities, so that the latter have been proposed as a peripheral model of central functions. In particular, in blood more than 99% of 5-HT is contained in platelets, so that one could consider changes in 5-HT levels in platelets as a mirror of changes in central 5-HT. Here, this hypothesis has been studied via the analysis of the influence of: (1) the forced swimming test (FST, which has been proved to be of utility to predict the clinical efficacy of antidepressants in rodents) and (2) treatment with the SSRI fluoxetine upon 5-HT levels monitored in brain regions and in peripheral platelets by means of electrochemical in vivo and ex vivo measurements. The results obtained confirm that the FST increases immobility; furthermore they show a parallel and significant decrease in cerebral (brain homogenate) and peripheral (in platelet-rich plasma, PRP) voltammetric 5-HT levels following the FST in naive rats. In addition, subchronic treatment with fluoxetine was followed by a significant increase in 5-HT levels in PRP, while the same SSRI treatment performed within the FST resulted in a decrease in the 5-HT levels in PRP. However, this decrease was inferior to that observed without SSRI treatment. These data suggest that there is an inverse relationship between immobility and the levels of 5-HT in PRP and that these peripheral 5-HT levels are sensitive to: (1) the FST, (2) the treatment with fluoxetine and (3) the combination of both treatments, i.e. SSRI + FST. It has been reported that SSRI treatment at first inhibits the 5-HT transporter in brain, resulting in increased extracellular 5-HT, while following sustained SSRI treatments decreased intracellular levels of central 5-HT were observed. Accordingly, the present data show that the initial block of 5-HT reuptake is revealed by the selective increase in 5-HT levels (extracellular content) measured in PRP (not in insulated platelets, IPs) the 1st day of fluoxetine treatment. The initial action of this SSRI upon the 5-HT transporter in brain has also been confirmed by in vivo voltammetric data showing selective increase in the serotonergic signal following local injection of fluoxetine into the brain region studied. Successively, the major effect monitored is a decrease in 5-HT levels, which is more evident in IPs than in PRP. However, it is known that following 2 weeks treatment with an SSRI, 5-HT autoreceptors are desensitized and the serotonin synthesis is restored, together with the intracellular 5-HT levels. The present data showing that the levels of 5-HT in IPs tend to return to control values 12 days after the beginning of chronic fluoxetine treatment suggest that 5-HT levels in IPs (intracellular environment) mirror the influence of SSRI treatment upon the central 5-HT system. On the other hand, at day 12 of the chronic fluoxetine treatment, 5-HT content remains low in PRP. Similarly, low levels of 5-HT have been monitored in brain homogenate of rats chronically treated with fluoxetine. This would support the similarity between PRP preparation and brain homogenate as in both cases cells are disrupted by sample preparation. In conclusion this work supports the literature in proposing platelets as a peripheral model of central functions. In particular, the present data support the idea that peripheral 5-HT platelet levels can reflect the state of the central 5-HT system in conditions of depression. Furthermore, the main outcome of this study is that PRP may mirror central extracellular 5-HT levels, whilst IPs mirror neuronal 5-HT changes.

Time-resolved x-ray scattering instrumentation

DOEpatents

Borso, C.S.

1985-11-21

An apparatus and method for increased speed and efficiency of data compilation and analysis in real time is presented in this disclosure. Data is sensed and grouped in combinations in accordance with predetermined logic. The combinations are grouped so that a simplified reduced signal results, such as pairwise summing of data values having offsetting algebraic signs, thereby reducing the magnitude of the net pair sum. Bit storage requirements are reduced and speed of data compilation and analysis is increased by manipulation of shorter bit length data values, making real time evaluation possible.

Development of aircraft lavatory compartments with improved fire resistance characteristics. Phase 2: Sandwich panel resin system development

NASA Technical Reports Server (NTRS)

Anderson, R. A.; Arnold, D. B.; Johnson, G. A.

1979-01-01

A NASA-funded program is described which aims to develop a resin system for use in the construction of lavatory wall panels, sidewall panels, and ceiling panels possessing flammability, smoke and gas emission, and toxicity (FS&T) characteristics superior to the existing epoxy resin. Candidate resins studied were phenolic, polyimide, and bismaleimide. Based on the results of a series of FS&T as well as mechanical and aesthetic property tests, a phenolic resin was chosen as the superior material. Material and process specifications covering the phenolic resin based materials were prepared and a method of rating sandwich panel performance was developed.

Antidepressant behavioral effects of duloxetine and fluoxetine in the rat forced swimming test.

PubMed

Ciulla, Leandro; Menezes, Honório Sampaio; Bueno, Bárbara Beatriz Moreira; Schuh, Alexandre; Alves, Rafael José Vargas; Abegg, Milena Pacheco

2007-01-01

To compare the effects of the antidepressant drugs duloxetine and fluoxetine on depressive behaviors in rodents. Eighteen male Wistar rats were given systemic injections of duloxetine, fluoxetine, or saline prior to a Forced Swimming Test (FST). Immobility and number of stops were measured. Rats given injections of fluoxetine displayed significantly less immobility (p = 0.02) and fewer stops than the control group (p = 0.003). Duloxetine significantly reduced the number of stops (p = 0.003), but did not effect immobility (p = 0.48). Duloxetine and fluoxetine reduced depressive behaviors in the Forced FST. However, our findings suggest that fluoxetine is more effective than duloxetine.

Effects of fluoxetine on the rat brain in the forced swimming test: a [F-18]FDG micro-PET imaging study.

PubMed

Jang, Dong-Pyo; Lee, So-Hee; Park, Chan-Woong; Lee, Sang-Yoon; Kim, Young-Bo; Cho, Zang-Hee

2009-02-13

We used the [F-18]FDG micro-PET neuroimaging to examine the effects of fluoxetine on brain activity in rats and on their behavioral response in the forced swimming test (FST). In the first experiment, the rats were administered doses of fluoxetine (10 or 20mg/kg) 24, 19 and 1h before the rat brains were scanned. Fluoxetine induced strong activation of the dorsal hippocampus and the deactivation of the inferior colliculus, medulla oblongata, and prelimbic cortex in a dose-dependent manner. These results seemed to be related with the changes in 5-HT (5-hydroxytryptamine, serotonin) levels after selective serotonin reuptake-inhibitor treatments. In the second experiment, the changes in glucose metabolism in the test session were measured after fluoxetine was given between pre-test and test sessions of the FST. Fluoxetine administration significantly decreased immobility behavior compared with saline administration. At the same time, the activity of the insular/piriform cortex decreased significantly. In contrast, the extent of cerebellar activation increased. The glucose metabolism of the dorsal hippocampus also increased, which suggests that post-stress changes in the facilitation of hippocampal serotonergic neurotransmission lead to decreased immobilization in the FST.

Antidepressant-like activity of Sonchus oleraceus in mouse models of immobility tests.

PubMed

Vilela, Fabiana Cardoso; Padilha, Marina de Mesquita; Alves-da-Silva, Geraldo; Soncini, Roseli; Giusti-Paiva, Alexandre

2010-02-01

The aim of the present work is to evaluate the putative antidepressant-like effects of hydroethanolic and dichloromethanic extracts from the aerial parts of Sonchus oleraceus (Family Asteraceae) on the performance of male mice in the forced swimming test (FST) and tail suspension test (TST) models predictive of depression. The hydroethanolic and dichloromethanic extracts, both in doses of 30, 100, and 300 mg/kg, were orally administered 1 hour before carrying out the FST or the TST. The immobility time in both the FST and the TST was significantly reduced by acute oral treatment with the extracts (dose range, 100-300 mg/kg), without accompanying changes in ambulation, as assessed in an open-field test. This excluded the possibility that the effect of the extracts is due to an activation of locomotion. The efficacy of the extracts was found to be comparable to that of amitriptyline (10 mg/kg, p.o.). The present study provides evidence for an antidepressant-like effect of the active principle(s) present in the extracts of S. oleraceus in mice. Therefore, a standardized S. oleraceus extract or its purified constituents could be of potential interest for the treatment of depressive disorders.

Pythagorean fuzzy analytic hierarchy process to multi-criteria decision making

NASA Astrophysics Data System (ADS)

Mohd, Wan Rosanisah Wan; Abdullah, Lazim

2017-11-01

A numerous approaches have been proposed in the literature to determine the criteria of weight. The weight of criteria is very significant in the process of decision making. One of the outstanding approaches that used to determine weight of criteria is analytic hierarchy process (AHP). This method involves decision makers (DMs) to evaluate the decision to form the pair-wise comparison between criteria and alternatives. In classical AHP, the linguistic variable of pairwise comparison is presented in terms of crisp value. However, this method is not appropriate to present the real situation of the problems because it involved the uncertainty in linguistic judgment. For this reason, AHP has been extended by incorporating the Pythagorean fuzzy sets. In addition, no one has found in the literature proposed how to determine the weight of criteria using AHP under Pythagorean fuzzy sets. In order to solve the MCDM problem, the Pythagorean fuzzy analytic hierarchy process is proposed to determine the criteria weight of the evaluation criteria. Using the linguistic variables, pairwise comparison for evaluation criteria are made to the weights of criteria using Pythagorean fuzzy numbers (PFNs). The proposed method is implemented in the evaluation problem in order to demonstrate its applicability. This study shows that the proposed method provides us with a useful way and a new direction in solving MCDM problems with Pythagorean fuzzy context.

Benchmarking Inverse Statistical Approaches for Protein Structure and Design with Exactly Solvable Models.

PubMed

Jacquin, Hugo; Gilson, Amy; Shakhnovich, Eugene; Cocco, Simona; Monasson, Rémi

2016-05-01

Inverse statistical approaches to determine protein structure and function from Multiple Sequence Alignments (MSA) are emerging as powerful tools in computational biology. However the underlying assumptions of the relationship between the inferred effective Potts Hamiltonian and real protein structure and energetics remain untested so far. Here we use lattice protein model (LP) to benchmark those inverse statistical approaches. We build MSA of highly stable sequences in target LP structures, and infer the effective pairwise Potts Hamiltonians from those MSA. We find that inferred Potts Hamiltonians reproduce many important aspects of 'true' LP structures and energetics. Careful analysis reveals that effective pairwise couplings in inferred Potts Hamiltonians depend not only on the energetics of the native structure but also on competing folds; in particular, the coupling values reflect both positive design (stabilization of native conformation) and negative design (destabilization of competing folds). In addition to providing detailed structural information, the inferred Potts models used as protein Hamiltonian for design of new sequences are able to generate with high probability completely new sequences with the desired folds, which is not possible using independent-site models. Those are remarkable results as the effective LP Hamiltonians used to generate MSA are not simple pairwise models due to the competition between the folds. Our findings elucidate the reasons for the success of inverse approaches to the modelling of proteins from sequence data, and their limitations.

Molecular markers for establishing distinctness in vegetatively propagated crops: a case study in grapevine.

PubMed

Ibáñez, Javier; Vélez, M Dolores; de Andrés, M Teresa; Borrego, Joaquín

2009-11-01

Distinctness, uniformity and stability (DUS) testing of varieties is usually required to apply for Plant Breeders' Rights. This exam is currently carried out using morphological traits, where the establishment of distinctness through a minimum distance is the key issue. In this study, the possibility of using microsatellite markers for establishing the minimum distance in a vegetatively propagated crop (grapevine) has been evaluated. A collection of 991 accessions have been studied with nine microsatellite markers and pair-wise compared, and the highest intra-variety distance and the lowest inter-variety distance determined. The collection included 489 different genotypes, and synonyms and sports. Average values for number of alleles per locus (19), Polymorphic Information Content (0.764) and heterozygosities observed (0.773) and expected (0.785) indicated the high level of polymorphism existing in grapevine. The maximum intra-variety variability found was one allele between two accessions of the same variety, of a total of 3,171 pair-wise comparisons. The minimum inter-variety variability found was two alleles between two pairs of varieties, of a total of 119,316 pair-wise comparisons. In base to these results, the minimum distance required to set distinctness in grapevine with the nine microsatellite markers used could be established in two alleles. General rules for the use of the system as a support for establishing distinctness in vegetatively propagated crops are discussed.

A water market simulator considering pair-wise trades between agents

NASA Astrophysics Data System (ADS)

Huskova, I.; Erfani, T.; Harou, J. J.

2012-04-01

In many basins in England no further water abstraction licences are available. Trading water between water rights holders has been recognized as a potentially effective and economically efficient strategy to mitigate increasing scarcity. A screening tool that could assess the potential for trade through realistic simulation of individual water rights holders would help assess the solution's potential contribution to local water management. We propose an optimisation-driven water market simulator that predicts pair-wise trade in a catchment and represents its interaction with natural hydrology and engineered infrastructure. A model is used to emulate licence-holders' willingness to engage in short-term trade transactions. In their simplest form agents are represented using an economic benefit function. The working hypothesis is that trading behaviour can be partially predicted based on differences in marginal values of water over space and time and estimates of transaction costs on pair-wise trades. We discuss the further possibility of embedding rules, norms and preferences of the different water user sectors to more realistically represent the behaviours, motives and constraints of individual licence holders. The potential benefits and limitations of such a social simulation (agent-based) approach is contrasted with our simulator where agents are driven by economic optimization. A case study based on the Dove River Basin (UK) demonstrates model inputs and outputs. The ability of the model to suggest impacts of water rights policy reforms on trading is discussed.

Genetic diversity of a large set of horse breeds raised in France assessed by microsatellite polymorphism

PubMed Central

2009-01-01

The genetic diversity and structure of horses raised in France were investigated using 11 microsatellite markers and 1679 animals belonging to 34 breeds. Between-breed differences explained about ten per cent of the total genetic diversity (Fst = 0.099). Values of expected heterozygosity ranged from 0.43 to 0.79 depending on the breed. According to genetic relationships, multivariate and structure analyses, breeds could be classified into four genetic differentiated groups: warm-blooded, draught, Nordic and pony breeds. Using complementary maximisation of diversity and aggregate diversity approaches, we conclude that particular efforts should be made to conserve five local breeds, namely the Boulonnais, Landais, Merens, Poitevin and Pottok breeds. PMID:19284689

Conservation priorities of Iberoamerican pig breeds and their ancestors based on microsatellite information.

PubMed

Cortés, O; Martinez, A M; Cañon, J; Sevane, N; Gama, L T; Ginja, C; Landi, V; Zaragoza, P; Carolino, N; Vicente, A; Sponenberg, P; Delgado, J V

2016-07-01

Criollo pig breeds are descendants from pigs brought to the American continent starting with Columbus second trip in 1493. Pigs currently play a key role in social economy and community cultural identity in Latin America. The aim of this study was to establish conservation priorities among a comprehensive group of Criollo pig breeds based on a set of 24 microsatellite markers and using different criteria. Spain and Portugal pig breeds, wild boar populations of different European geographic origins and commercial pig breeds were included in the analysis as potential genetic influences in the development of Criollo pig breeds. Different methods, differing in the weight given to within- and between-breed genetic variability, were used in order to estimate the contribution of each breed to global genetic diversity. As expected, the partial contribution to total heterozygosity gave high priority to Criollo pig breeds, whereas Weitzman procedures prioritized Iberian Peninsula breeds. With the combined within- and between-breed approaches, different conservation priorities were achieved. The Core Set methodologies highly prioritized Criollo pig breeds (Cr. Boliviano, Cr. Pacifico, Cr. Cubano and Cr. Guadalupe). However, weighing the between- and within-breed components with FST and 1-FST, respectively, resulted in higher contributions of Iberian breeds. In spite of the different conservation priorities according to the methodology used, other factors in addition to genetic information also need to be considered in conservation programmes, such as the economic, cultural or historical value of the breeds involved.

Conservation priorities of Iberoamerican pig breeds and their ancestors based on microsatellite information

PubMed Central

Cortés, O; Martinez, A M; Cañon, J; Sevane, N; Gama, L T; Ginja, C; Landi, V; Zaragoza, P; Carolino, N; Vicente, A; Sponenberg, P; Delgado, J V

2016-01-01

Criollo pig breeds are descendants from pigs brought to the American continent starting with Columbus second trip in 1493. Pigs currently play a key role in social economy and community cultural identity in Latin America. The aim of this study was to establish conservation priorities among a comprehensive group of Criollo pig breeds based on a set of 24 microsatellite markers and using different criteria. Spain and Portugal pig breeds, wild boar populations of different European geographic origins and commercial pig breeds were included in the analysis as potential genetic influences in the development of Criollo pig breeds. Different methods, differing in the weight given to within- and between-breed genetic variability, were used in order to estimate the contribution of each breed to global genetic diversity. As expected, the partial contribution to total heterozygosity gave high priority to Criollo pig breeds, whereas Weitzman procedures prioritized Iberian Peninsula breeds. With the combined within- and between-breed approaches, different conservation priorities were achieved. The Core Set methodologies highly prioritized Criollo pig breeds (Cr. Boliviano, Cr. Pacifico, Cr. Cubano and Cr. Guadalupe). However, weighing the between- and within-breed components with FST and 1-FST, respectively, resulted in higher contributions of Iberian breeds. In spite of the different conservation priorities according to the methodology used, other factors in addition to genetic information also need to be considered in conservation programmes, such as the economic, cultural or historical value of the breeds involved. PMID:27025169

How to improve x-ray scattering techniques to quantify bone mineral density using spectroscopy

PubMed Central

Krmar, M.; Ganezer, K.

2012-01-01

Purpose: The purpose of this study was to develop a new diagnostic technique for measuring bone mineral density (BMD) for the assessment of osteoporosis, which improves upon the coherent to Compton scattering ratio (CCSR) method, which was first developed in the 1980s. To help the authors achieve these goals, they have identified and studied two new indices for CCSR, the forward scattered to backward scattered (FS-BS) and the forward scattered to transmitted (FS-T) ratios. They believe that, at small angles, these two parameters can offer a practical in vivo determination of BMD that can be used to overcome the limitations of past CCSR systems, including high radiation dosages, costs, and examination durations. Methods: In previous CCSR studies, a high-activity radioactive source with a long half-live (usually 241Am) and an expensive and bulky cryogenic HPGe detector were applied to both in vivo and in vitro measurements. To make this technique more suitable for clinical applications, the possibility of using a standard diagnostic x-ray tube generating a continuous spectrum was investigated in this paper. Scattered radiation from trabecular bone-simulating phantoms containing various mineral densities that span the normal range of in vivo BMD was collected in this study using relatively inexpensive noncryogenic CdTe or NaI detectors. Results: The initial results demonstrate that a modified version of CCSR can be successfully applied to trabecular bone assessment using a diagnostic x-ray tube with a continuous spectrum in two variations, the FS-BS and the FS-T ratio. When FS-BS is measured, intensity spectra in the forward and backward directions must be collected while FS-T requires only the integral intensity of the scattered and transmitted (T) spectra in the energy region above 40 keV. For both of these methods, forward scattering angles less than or equal to 15° and backward scattering angles greater than or equal to (165°= 180° − 15°) are needed. Conclusions: The authors determined that FS-T is more sensitive to changes in BMD than transmission or absorption alone and that the FS-BS method can yield an absolute measurement of the mean atomic number of the scattering medium, after a correction for path-dependent attenuation. Since this study determined that the FS-T ratio is independent of the incident energy over a broad energy region, it will be possible to apply FS-T to bone densitometry using inexpensive integral photon detectors. The authors believe that, by replacing the radionuclide source with an x-ray tube and the cryogenically cooled HPGe detector with a single solid state CdTe, NaI, or silicon detector or an annular array of detectors, as suggested in this study, the past difficulties of CCSR concerning high radiation exposure, costs, and durations as well as lack of convenience can be overcome and that CCSR could eventually become popular in clinical settings. PMID:22482605

Genetic differentiation over a small spatial scale of the sand fly Lutzomyia vexator (Diptera: Psychodidae).

PubMed

Neal, Allison T; Ross, Max S; Schall, Jos J; Vardo-Zalik, Anne M

2016-10-18

The geographic scale and degree of genetic differentiation for arthropod vectors that transmit parasites play an important role in the distribution, prevalence and coevolution of pathogens of human and wildlife significance. We determined the genetic diversity and population structure of the sand fly Lutzomyia vexator over spatial scales from 0.56 to 3.79 km at a study region in northern California. The study was provoked by observations of differentiation at fine spatial scales of a lizard malaria parasite vectored by Lu. vexator. A microsatellite enrichment/next-generation sequencing protocol was used to identify variable microsatellite loci within the genome of Lu. vexator. Alleles present at these loci were examined in four populations of Lu. vexator in Hopland, CA. Population differentiation was assessed using Fst and D (of Cavalli-Sforza and Edwards), and the program Structure was used to determine the degree of subdivision present. The effective population size for the sand fly populations was also calculated. Eight microsatellite markers were characterized and revealed high genetic diversity (uHe = 0.79-0.92, Na = 12-24) and slight but significant differentiation across the fine spatial scale examined (average pairwise D = 0.327; F ST  = 0.0185 (95 % bootstrapped CI: 0.0102-0.0264). Even though the insects are difficult to capture using standard methods, the estimated population size was thousands per local site. The results argue that Lu. vexator at the study sites are abundant and not highly mobile, which may influence the overall transmission dynamics of the lizard malaria parasite, Plasmodium mexicanum, and other parasites transmitted by this species.

Multispecies genetic structure and hybridization in the Betula genus across Eurasia.

PubMed

Tsuda, Yoshiaki; Semerikov, Vladimir; Sebastiani, Federico; Vendramin, Giovanni Giuseppe; Lascoux, Martin

2017-01-01

Boreal and cool temperate forests are the major land cover of northern Eurasia, and information about continental-scale genetic structure and past demographic history of forest species is important from an evolutionary perspective and has conservation implications. However, although many population genetic studies of forest tree species have been conducted in Europe or Eastern Asia, continental-scale genetic structure and past demographic history remain poorly known. Here, we focus on the birch genus Betula, which is commonly distributed in boreal and cool temperate forests, and examine 129 populations of two tetraploid and four diploid species collected from Iceland to Japan. All individuals were genotyped at seven to 18 nuclear simple sequence repeats (nSSRs). Pairwise FST' among the six species ranged from 0.285 to 0.903, and genetic differentiation among them was clear. structure analysis suggested that Betula pubescens is an allotetraploid and one of the parental species was Betula pendula. In both species pairs of B. pendula and B. plathyphylla, and B. pubescens and B. ermanii, genetic diversity was highest in central Siberia. A hybrid zone was detected around Lake Baikal for eastern and western species pairs regardless of ploidy level. Approximate Bayesian computation suggested that the divergence of B. pendula and B. platyphylla occurred around the beginning of the last ice age (36 300 years BP, 95% CI: 15 330-92 700) and hybridization between them was inferred to have occurred after the last glacial maximum (1614 years BP, 95% CI: 561-4710), with B. pendula providing a higher contribution to hybrids. © 2016 John Wiley & Sons Ltd.

Balancing Selection on a Regulatory Region Exhibiting Ancient Variation That Predates Human–Neandertal Divergence

PubMed Central

Iskow, Rebecca C.; Austermann, Christian; Scharer, Christopher D.; Raj, Towfique; Boss, Jeremy M.; Sunyaev, Shamil; Price, Alkes; Stranger, Barbara; Simon, Viviana; Lee, Charles

2013-01-01

Ancient population structure shaping contemporary genetic variation has been recently appreciated and has important implications regarding our understanding of the structure of modern human genomes. We identified a ∼36-kb DNA segment in the human genome that displays an ancient substructure. The variation at this locus exists primarily as two highly divergent haplogroups. One of these haplogroups (the NE1 haplogroup) aligns with the Neandertal haplotype and contains a 4.6-kb deletion polymorphism in perfect linkage disequilibrium with 12 single nucleotide polymorphisms (SNPs) across diverse populations. The other haplogroup, which does not contain the 4.6-kb deletion, aligns with the chimpanzee haplotype and is likely ancestral. Africans have higher overall pairwise differences with the Neandertal haplotype than Eurasians do for this NE1 locus (p<10−15). Moreover, the nucleotide diversity at this locus is higher in Eurasians than in Africans. These results mimic signatures of recent Neandertal admixture contributing to this locus. However, an in-depth assessment of the variation in this region across multiple populations reveals that African NE1 haplotypes, albeit rare, harbor more sequence variation than NE1 haplotypes found in Europeans, indicating an ancient African origin of this haplogroup and refuting recent Neandertal admixture. Population genetic analyses of the SNPs within each of these haplogroups, along with genome-wide comparisons revealed significant FST (p = 0.00003) and positive Tajima's D (p = 0.00285) statistics, pointing to non-neutral evolution of this locus. The NE1 locus harbors no protein-coding genes, but contains transcribed sequences as well as sequences with putative regulatory function based on bioinformatic predictions and in vitro experiments. We postulate that the variation observed at this locus predates Human–Neandertal divergence and is evolving under balancing selection, especially among European populations. PMID:23593015

Rethinking the influence of hydroelectric development on gene flow in a long-lived fish, the Lake Sturgeon Acipenser fulvescens

PubMed Central

McDougall, Craig A.; Welsh, Amy B.; Gosselin, Thierry; Anderson, W. Gary; Nelson, Patrick A.

2017-01-01

Many hydroelectric dams have been in place for 50 - >100 years, which for most fish species means that enough generations have passed for fragmentation induced divergence to have accumulated. However, for long-lived species such as Lake Sturgeon, Acipenser fulvescens, it should be possible to discriminate between historical population structuring and contemporary gene flow and improve the broader understanding of anthropogenic influence. On the Winnipeg River, Manitoba, two hypotheses were tested: 1) Measureable quantities of former reservoir dwelling Lake Sturgeon now reside downstream of the Slave Falls Generating Station, and 2) genetically differentiated populations of Lake Sturgeon occur upstream and downstream, a result of historical structuring. Genetic methods based on ten microsatellite markers were employed, and simulations were conducted to provide context. With regards to contemporary upstream to downstream contributions, the inclusion of length-at-age data proved informative. Both pairwise relatedness and Bayesian clustering analysis substantiated that fast-growing outliers, apparently entrained after residing in the upstream reservoir for several years, accounted for ~15% of the Lake Sturgeon 525–750 mm fork length captured downstream. With regards to historical structuring, upstream and downstream populations were found to be differentiated (FST = 0.011, and 0.013–0.014 when fast-growing outliers were excluded), and heterozygosity metrics were higher for downstream versus upstream juveniles. Historical asymmetric (downstream) gene flow in the vicinity of the generating station was the most logical explanation for the observed genetic structuring. In this section of the Winnipeg River, construction of a major dam does not appear to have fragmented a previously panmictic Lake Sturgeon population, but alterations to habitat may be influencing upstream to downstream contributions in unexpected ways. PMID:28329005

Rethinking the influence of hydroelectric development on gene flow in a long-lived fish, the Lake Sturgeon Acipenser fulvescens.

PubMed

McDougall, Craig A; Welsh, Amy B; Gosselin, Thierry; Anderson, W Gary; Nelson, Patrick A

2017-01-01

Many hydroelectric dams have been in place for 50 - >100 years, which for most fish species means that enough generations have passed for fragmentation induced divergence to have accumulated. However, for long-lived species such as Lake Sturgeon, Acipenser fulvescens, it should be possible to discriminate between historical population structuring and contemporary gene flow and improve the broader understanding of anthropogenic influence. On the Winnipeg River, Manitoba, two hypotheses were tested: 1) Measureable quantities of former reservoir dwelling Lake Sturgeon now reside downstream of the Slave Falls Generating Station, and 2) genetically differentiated populations of Lake Sturgeon occur upstream and downstream, a result of historical structuring. Genetic methods based on ten microsatellite markers were employed, and simulations were conducted to provide context. With regards to contemporary upstream to downstream contributions, the inclusion of length-at-age data proved informative. Both pairwise relatedness and Bayesian clustering analysis substantiated that fast-growing outliers, apparently entrained after residing in the upstream reservoir for several years, accounted for ~15% of the Lake Sturgeon 525-750 mm fork length captured downstream. With regards to historical structuring, upstream and downstream populations were found to be differentiated (FST = 0.011, and 0.013-0.014 when fast-growing outliers were excluded), and heterozygosity metrics were higher for downstream versus upstream juveniles. Historical asymmetric (downstream) gene flow in the vicinity of the generating station was the most logical explanation for the observed genetic structuring. In this section of the Winnipeg River, construction of a major dam does not appear to have fragmented a previously panmictic Lake Sturgeon population, but alterations to habitat may be influencing upstream to downstream contributions in unexpected ways.

Associations between forest fragmentation patterns and geneticstructure in Pfrimer’s Parakeet (Pyrrhura pfrimeri), an endangered endemic to central Brazil’s dry forests

USGS Publications Warehouse

Haig, Susan M.; Miller, Leonard F.; Bianchi, Carlos; Mullins, Thomas D.

2012-01-01

When habitat becomes fragmented, populations of species may become increasingly isolated. In the absence of habitat corridors, genetic structure may develop and populations risk reductions in genetic diversity from increased genetic drift and inbreeding. Deforestation of the Cerrado biome of Brazil, particularly of the dry forests within the Parana˜ River Basin, has incrementally occurred since the 1970s and increased forest fragmentation within the region. We performed landscape genetic analyses of Pfrimer’s parakeet (Pyrrhura pfrimeri), a globally endangered endemic to the region, to determine if forest fragmentation patterns were associated with genetic structuring in this species. We used previously generated satellite imagery that identified the locations of Parana˜ River Basin forest fragments in 1977, 1993/94, and 2008. Behavioral data quantifying the affinity of Pfrimer’s parakeet for forest habitat was used to parameterize empirically derived landscape conductance surfaces. Though genetic structure was observed among Pfrimer’s parakeet populations, no association between genetic and geographic distance was detected. Likewise, least cost path lengths, circuit theorybased resistance distances, and a new measure of least cost path length complexity could not be conclusively associated with genetic structure patterns. Instead, a new quantity that encapsulated connection redundancy from the 1977 forest fragmentation data provided the clearest associations with pairwise genetic differentiation patterns (Jost’s D: r = 0.72, P = 0.006; FST: r = 0.741, P = 0.001). Our analyses suggest a 35-year or more lag between deforestation and its effect on genetic structure. Because 66 % of the Parana˜ River Basin has been deforested since 1977, we expect that genetic structure will increase substantially among Pfrimer’s Parakeet populations in the future, especially if fragmentation continues at its current pace.

Evaluation of genetic population structure of smallmouth bass in the Susquehanna River basin, Pennsylvania

USGS Publications Warehouse

Schall, Megan K.; Bartron, Meredith L.; Wertz, Timothy; Niles, Jonathan M.; Shaw, Cassidy H.; Wagner, Tyler

2017-01-01

The Smallmouth Bass Micropterus dolomieu was introduced into the Susquehanna River basin, Pennsylvania, nearly 150 years ago. Since introduction, it has become an economically and ecologically important species that supports popular recreational fisheries. It is also one of the most abundant top predators in the system. Currently, there is no information on the level of genetic diversity or genetic structuring that may have occurred since introduction. An understanding of genetic diversity is important for the delineation of management units and investigation of gene flow at various management scales. The goals of this research were to investigate population genetic structure of Smallmouth Bass at sites within the Susquehanna River basin and to assess genetic differentiation relative to Smallmouth Bass at an out-of-basin site (Allegheny River, Pennsylvania) located within the species’ native range. During spring 2015, fin clips (n = 1,034) were collected from adults at 11 river sites and 13 tributary sites in the Susquehanna River basin and at one site on the Allegheny River. Fin clips were genotyped at 12 polymorphic microsatellite loci. Based on our results, adults sampled throughout the Susquehanna River basin did not represent separate genetic populations. There were only subtle differences in genetic diversity among sites (mean pairwise genetic differentiation index FST = 0.012), and there was an overall lack of population differentiation (K = 3 admixed populations). The greatest genetic differentiation was observed between fish collected from the out-of-basin site and those from the Susquehanna River basin sites. Knowledge that separate genetic populations of Smallmouth Bass do not exist in the Susquehanna River basin is valuable information for fisheries management in addition to providing baseline genetic data on an introduced sport fish population.

First insights into the genetic diversity of Echinococcus granulosus sensu stricto (s.s.) in Serbia.

PubMed

Debeljak, Zoran; Boufana, Belgees; Interisano, Maria; Vidanovic, Dejan; Kulisic, Zoran; Casulli, Adriano

2016-06-15

Cystic echinococcosis (CE) caused by Echinococcus granulosus sensu stricto (s.s.) is a cosmopolitan zoonotic infection which is endemic in Serbia where it is subject to mandatory reporting. However, information on the incidence of the disease in humans and prevalence of hydatid infection in livestock remains limited. We used sequenced data of the cytochrome c oxidase subunit 1 (cox 1) mitochondrial gene to examine the genetic diversity and population structure of E. granulosus (s.s.) from intermediate hosts from Serbia. We also compared our generated nucleotide sequences with those reported for neighbouring European countries. Echinococcus canadensis was molecularly confirmed from pig and human hydatid isolates. E. granulosus (G1) was confirmed from sheep and cattle hydatid isolates as well as the first molecular confirmation in Serbia of E. granulosus G2 in sheep and E. granulosus G3 in sheep and cattle hydatid isolates. The Serbian E. granulosus (s.s.) parsimony network displayed 2 main haplotypes (SB02 and SB05) which together with the neutrality indices were suggestive of bottleneck and/or balancing selection. Haplotype analysis showed the presence of the common E. granulosus haplotype described from other worldwide regions. Investigation of the pairwise fixation (Fst) index suggested that Serbian populations of E. granulosus (s.s.) from sheep and cattle hosts showed moderate genetic differentiation. Six of the Serbian haplotypes (SB02-SB07) were shared with haplotypes from Bulgaria, Hungary and/or Romania. Further studies using a larger number of hydatid isolates from various locations across Serbia will provide more information on the genetic structure of E. granulosus (s.s.) within this region. Copyright © 2016 Elsevier B.V. All rights reserved.

Genetic variations of ND5 gene of mtDNA in populations of Anopheles sinensis (Diptera: Culicidae) malaria vector in China

PubMed Central

2013-01-01

Background Anopheles sinensis is a principal vector for Plasmodium vivax malaria in most parts of China. Understanding of genetic structure and genetic differentiation of the mosquito should contribute to the vector control and malaria elimination in China. Methods The present study investigated the genetic structure of An. sinensis populations using a 729 bp fragment of mtDNA ND5 among 10 populations collected from seven provinces in China. Results ND5 was polymorphic by single mutations within three groups of An. sinensis that were collected from 10 different geographic populations in China. Out of 140 specimens collected from 10 representative sites, 84 haplotypes and 71 variable positions were determined. The overall level of genetic differentiation of An. sinensis varied from low to moderate across China and with a FST range of 0.00065 – 0.341. Genealogy analysis clustered the populations of An. sinensis into three main clusters. Each cluster shared one main haplotype. Pairwise variations within populations were higher (68.68%) than among populations (31.32%) and with high fixation index (FST = 0.313). The results of the present study support population growth and expansion in the An. sinensis populations from China. Three clusters of An. sinensis populations were detected in this study with each displaying different proportion patterns over seven Chinese provinces. No correlation between genetic and geographic distance was detected in overall populations of An. sinensis (R2 = 0.058; P = 0.301). Conclusions The results indicate that the ND5 gene of mtDNA is highly polymorphic in An. sinensis and has moderate genetic variability in the populations of this mosquito in China. Demographic and spatial results support evidence of expansion in An. sinensis populations. PMID:24192424

Evidence for extensive genetic diversity and substructuring of the Babesia bovis metapopulation.

PubMed

Flores, D A; Minichiello, Y; Araujo, F R; Shkap, V; Benítez, D; Echaide, I; Rolls, P; Mosqueda, J; Pacheco, G M; Petterson, M; Florin-Christensen, M; Schnittger, L

2013-11-01

Babesia bovis is a tick-transmitted haemoprotozoan and a causative agent of bovine babesiosis, a cattle disease that causes significant economic loss in tropical and subtropical regions. A panel of nineteen micro- and minisatellite markers was used to estimate population genetic parameters of eighteen parasite isolates originating from different continents, countries and geographic regions including North America (Mexico, USA), South America (Argentina, Brazil), the Middle East (Israel) and Australia. For eleven of the eighteen isolates, a unique haplotype was inferred suggesting selection of a single genotype by either in vitro cultivation or amplification in splenectomized calves. Furthermore, a high genetic diversity (H = 0.780) over all marker loci was estimated. Linkage disequilibrium was observed in the total study group but also in sample subgroups from the Americas, Brazil, and Israel and Australia. In contrast, corresponding to their more confined geographic origin, samples from Israel and Argentina were each found to be in equilibrium suggestive of random mating and frequent genetic exchange. The genetic differentiation (F(ST)) of the total study group over all nineteen loci was estimated by analysis of variance (Θ) and Nei's estimation of heterozygosity (G(ST')) as 0.296 and 0.312, respectively. Thus, about 30% of the genetic diversity of the parasite population is associated with genetic differences between parasite isolates sampled from the different geographic regions. The pairwise similarity of multilocus genotypes (MLGs) was assessed and a neighbour-joining dendrogram generated. MLGs were found to cluster according to the country/continent of origin of isolates, but did not distinguish the attenuated from the pathogenic parasite state. The distant geographic origin of the isolates studied allows an initial glimpse into the large extent of genetic diversity and differentiation of the B. bovis population on a global scale. © 2013 Blackwell Verlag GmbH.

Genetic Diversity of Plasmodium falciparum in Haiti: Insights from Microsatellite Markers

PubMed Central

Carter, Tamar E.; Malloy, Halley; Existe, Alexandre; Memnon, Gladys; St. Victor, Yves; Okech, Bernard A.; Mulligan, Connie J.

2015-01-01

Hispaniola, comprising Haiti and the Dominican Republic, has been identified as a candidate for malaria elimination. However, incomplete surveillance data in Haiti hamper efforts to assess the impact of ongoing malaria control interventions. Characteristics of the genetic diversity of Plasmodium falciparum populations can be used to assess parasite transmission, which is information vital to evaluating malaria elimination efforts. Here we characterize the genetic diversity of P. falciparum samples collected from patients at seven sites in Haiti using 12 microsatellite markers previously employed in population genetic analyses of global P. falciparum populations. We measured multiplicity of infections, level of genetic diversity, degree of population geographic substructure, and linkage disequilibrium (defined as non-random association of alleles from different loci). For low transmission populations like Haiti, we expect to see few multiple infections, low levels of genetic diversity, high degree of population structure, and high linkage disequilibrium. In Haiti, we found low levels of multiple infections (12.9%), moderate to high levels of genetic diversity (mean number of alleles per locus = 4.9, heterozygosity = 0.61), low levels of population structure (highest pairwise Fst = 0.09 and no clustering in principal components analysis), and moderate linkage disequilibrium (ISA = 0.05, P<0.0001). In addition, population bottleneck analysis revealed no evidence for a reduction in the P. falciparum population size in Haiti. We conclude that the high level of genetic diversity and lack of evidence for a population bottleneck may suggest that Haiti’s P. falciparum population has been stable and discuss the implications of our results for understanding the impact of malaria control interventions. We also discuss the relevance of parasite population history and other host and vector factors when assessing transmission intensity from genetic diversity data. PMID:26462203

Ecological dispersal barrier across the equatorial Atlantic in a migratory planktonic copepod

NASA Astrophysics Data System (ADS)

Goetze, Erica; Hüdepohl, Patricia T.; Chang, Chantel; Van Woudenberg, Lauren; Iacchei, Matthew; Peijnenburg, Katja T. C. A.

2017-11-01

Resolving the large-scale genetic structure of plankton populations is important to understanding their responses to climate change. However, few studies have reported on the presence and geographic extent of genetically distinct populations of marine zooplankton at ocean-basin scales. Using mitochondrial sequence data (mtCOI, 718 animals) from 18 sites across a basin-scale Atlantic transect (39°N-40°S), we show that populations of the dominant migratory copepod, Pleuromamma xiphias, are genetically subdivided across subtropical and tropical waters (global FST = 0.15, global ΦST = 0.21, both P < 0.00001), with a major genetic break observed in the equatorial Atlantic (between gyre FCT and ΦCT = 0.23, P < 0.005). This equatorial region of strong genetic transition coincides with an area of low abundance for the species. Transitional regions between the subtropical gyres and the equatorial province also harbor a distinct mitochondrial clade (clade 2), have higher haplotype and nucleotide diversities relative to the northern and/or southern subtropical gyres (e.g., mean h = 0.831 EQ, 0.742 North, 0.594 South, F2,11 = 20.53, P < 0.001), and are genetically differentiated from the majority of sites in the central gyre and temperate zones of the same hemisphere (significant pairwise ΦST 0.038-0.267, 79% significant). Our observations support the hypothesis that regions of low abundance within species mark areas of suboptimal habitat that serve as dispersal barriers for marine plankton, and we suggest that this may be a dominant mechanism driving the large-scale genetic structure of zooplankton species. Our results also demonstrate the potential importance of the Atlantic equatorial province as a region of evolutionary novelty for the holoplankton.

Geographically weighted regression as a generalized Wombling to detect barriers to gene flow.

PubMed

Diniz-Filho, José Alexandre Felizola; Soares, Thannya Nascimento; de Campos Telles, Mariana Pires

2016-08-01

Barriers to gene flow play an important role in structuring populations, especially in human-modified landscapes, and several methods have been proposed to detect such barriers. However, most applications of these methods require a relative large number of individuals or populations distributed in space, connected by vertices from Delaunay or Gabriel networks. Here we show, using both simulated and empirical data, a new application of geographically weighted regression (GWR) to detect such barriers, modeling the genetic variation as a "local" linear function of geographic coordinates (latitude and longitude). In the GWR, standard regression statistics, such as R(2) and slopes, are estimated for each sampling unit and thus are mapped. Peaks in these local statistics are then expected close to the barriers if genetic discontinuities exist, capturing a higher rate of population differentiation among neighboring populations. Isolation-by-Distance simulations on a longitudinally warped lattice revealed that higher local slopes from GWR coincide with the barrier detected with Monmonier algorithm. Even with a relatively small effect of the barrier, the power of local GWR in detecting the east-west barriers was higher than 95 %. We also analyzed empirical data of genetic differentiation among tree populations of Dipteryx alata and Eugenia dysenterica Brazilian Cerrado. GWR was applied to the principal coordinate of the pairwise FST matrix based on microsatellite loci. In both simulated and empirical data, the GWR results were consistent with discontinuities detected by Monmonier algorithm, as well as with previous explanations for the spatial patterns of genetic differentiation for the two species. Our analyses reveal how this new application of GWR can viewed as a generalized Wombling in a continuous space and be a useful approach to detect barriers and discontinuities to gene flow.

Pairwise-Comparison Software

NASA Technical Reports Server (NTRS)

Ricks, Wendell R.

1995-01-01

Pairwise comparison (PWC) is computer program that collects data for psychometric scaling techniques now used in cognitive research. It applies technique of pairwise comparisons, which is one of many techniques commonly used to acquire the data necessary for analyses. PWC administers task, collects data from test subject, and formats data for analysis. Written in Turbo Pascal v6.0.

Allozyme Diversity and Morphometrics of Melocactus paucispinus (Cactaceae) and Evidence for Hybridization with M. concinnus in the Chapada Diamantina, North-eastern Brazil

PubMed Central

LAMBERT, SABRINA MOTA; BORBA, EDUARDO LEITE; MACHADO, MARLON CÂMARA; ANDRADE, SÓNIA CRISTINA DA SILVA

2006-01-01

• Background and Aims Melocacatus paucispinus (Cactaceae) is endemic to the state of Bahia, Brazil, and due to its rarity and desirability to collectors it has been considered threatened with extinction. This species is usually sympatric and inter-fertile with M. concinnus, and morphological evidence for hybridization between them is present in some populations. Levels of genetic and morphological variation and sub-structuring in populations of these species were assessed and an attempt was made to verify the occurrence of natural hybridization between them. • Methods Genetic variability was surveyed using allozymes (12 loci) and morphological variability using multivariate morphometric analyses (17 vegetative characters) in ten populations of M. paucispinus and three of M. concinnus occurring in the Chapada Diamantina, Bahia. • Key Results Genetic variability was low in both species (P = 0·0–33·3, A = 1·0–1·6, He = 0·000–0·123 in M. paucispinus; P = 0·0–25·0, A = 1·0–1·4, He = 0·000–0·104 in M. concinnus). Deficit of heterozygotes within the populations was detected in both species, with high values of FIS (0·732 and 0·901 in M. paucispinus and M. concinnus, respectively). Evidence of hybridization was detected by the relative allele frequency in the two diaphorase loci. High levels of genetic (FST = 0·504 in M. paucispinus and 0·349 in M. concinnus) and morphological (A = 0·20 in M. paucispinus and 0·17 in M. concinnus) structuring among populations were found. • Conclusions The Melocactus spp. displayed levels of genetic variability lower than the values reported for other cactus species. The evidence indicates the occurrence of introgression in both species at two sites. The high FST values cannot be explained by geographical substructuring, but are consistent with hybridization. Conversely, morphological differentiation in M. paucispinus, but not in M. concinnus, is probably due to isolation by distance. PMID:16423866

As the raven flies: using genetic data to infer the history of invasive common raven (Corvus corax) populations in the Mojave Desert.

PubMed

Fleischer, Robert C; Boarman, William I; Gonzalez, Elena G; Godinez, Alvaro; Omland, Kevin E; Young, Sarah; Helgen, Lauren; Syed, Gracia; McIntosh, Carl E

2008-01-01

Common raven (Corvus corax) populations in Mojave Desert regions of southern California and Nevada have increased dramatically over the past five decades. This growth has been attributed to increased human development in the region, as ravens have a commensal relationship with humans and feed extensively at landfills and on road-killed wildlife. Ravens, as a partially subsidized predator, also represent a problem for native desert wildlife, in particular threatened desert tortoises (Gopherus agassizii). However, it is unclear whether the more than 15-fold population increase is due to in situ population growth or to immigration from adjacent regions where ravens have been historically common. Ravens were sampled for genetic analysis at several local sites within five major areas: the West Mojave Desert (California), East Mojave Desert (southern Nevada), southern coastal California, northern coastal California (Bay Area), and northern Nevada (Great Basin). Analyses of mtDNA control region sequences reveal an increased frequency of raven 'Holarctic clade' haplotypes from south to north inland, with 'California clade' haplotypes nearly fixed in the California populations. There was significant structuring among regions for mtDNA, with high F(ST) values among sampling regions, especially between the Nevada and California samples. Analyses of eight microsatellite loci reveal a mostly similar pattern of regional population structure, with considerably smaller, but mostly significant, values. The greater mtDNA divergences may be due to lower female dispersal relative to males, lower N(e), or effects of high mutation rates on maximal values of F(ST). Analyses indicate recent population growth in the West Mojave Desert and a bottleneck in the northern California populations. While we cannot rule out in situ population growth as a factor, patterns of movement inferred from our data suggest that the increase in raven populations in the West Mojave Desert resulted from movements from southern California and the Central Valley. Ravens in the East Mojave Desert are more similar to ones from northern Nevada, indicating movement between those regions. If this interpretation of high gene flow into the Mojave Desert is correct, then efforts to manage raven numbers by local control may not be optimally effective.

Mitochondrial DNA Analyses Indicate High Diversity, Expansive Population Growth and High Genetic Connectivity of Vent Copepods (Dirivultidae) across Different Oceans

PubMed Central

Kihara, Terue C.; Laurent, Stefan; Kodami, Sahar; Martinez Arbizu, Pedro

2016-01-01

Communities in spatially fragmented deep-sea hydrothermal vents rich in polymetallic sulfides could soon face major disturbance events due to deep-sea mineral mining, such that unraveling patterns of gene flow between hydrothermal vent populations will be an important step in the development of conservation policies. Indeed, the time required by deep-sea populations to recover following habitat perturbations depends both on the direction of gene flow and the number of migrants available for re-colonization after disturbance. In this study we compare nine dirivultid copepod species across various geological settings. We analyze partial nucleotide sequences of the mtCOI gene and use divergence estimates (FST) and haplotype networks to infer intraspecific population connectivity between vent sites. Furthermore, we evaluate contrasting scenarios of demographic population expansion/decline versus constant population size (using, for example, Tajima’s D). Our results indicate high diversity, population expansion and high connectivity of all copepod populations in all oceans. For example, haplotype diversity values range from 0.89 to 1 and FST values range from 0.001 to 0.11 for Stygiopontius species from the Central Indian Ridge, Mid Atlantic Ridge, East Pacific Rise, and Eastern Lau Spreading Center. We suggest that great abundance and high site occupancy by these species favor high genetic diversity. Two scenarios both showed similarly high connectivity: fast spreading centers with little distance between vent fields and slow spreading centers with greater distance between fields. This unexpected result may be due to some distinct frequency of natural disturbance events, or to aspects of individual life histories that affect realized rates of dispersal. However, our statistical performance analyses showed that at least 100 genomic regions should be sequenced to ensure accurate estimates of migration rate. Our demography parameters demonstrate that dirivultid populations are generally large and continuously undergoing population growth. Benthic and pelagic species abundance data support these findings. PMID:27732624

Isolation by distance and vicariance drive genetic structure of a coral reef fish in the Pacific Ocean.

PubMed

Planes, S; Fauvelot, C

2002-02-01

We studied the genetic diversity of a coral reef fish species to investigate the origin of the differentiation. A total of 727 Acanthurus triostegus collected from 15 locations throughout the Pacific were analyzed for 20 polymorphic loci. The genetic structure showed limited internal disequilibrium within each population; 3.7% of the loci showed significant Hardy-Weinberg disequilibrium, mostly associated with Adh*, and we subsequently removed this locus from further analysis of geographic pattern. The genetic structure of A. triostegus throughout the tropical Pacific Ocean revealed a strong geographic pattern. Overall, there was significant population differentiation (multilocus F(ST) = 0.199), which was geographically structured according to bootstraps of neighbor-joining analysis on Nei's unbiased genetic distances and AMOVA analysis. The genetic structure revealed five geographic groups in the Pacific Ocean: western Pacific (Guam, Philippines, Palau, and Great Barrier Reef); central Pacific (Solomons, New Caledonia, and Fiji); and three groups made up of the eastern populations, namely Hawaiian Archipelago (north), Marquesas (equatorial), and southern French Polynesia (south) that incorporates Clipperton Island located in the northeastern Pacific. In addition, heterozygosity values were found to be geographically structured with higher values grouped within Polynesian and Clipperton populations, which exhibited lower population size. Finally, the genetic differentiation (F(ST)) was significantly correlated with geographic distance when populations from the Hawaiian and Marquesas archipelagos were separated from all the other locations. These results show that patterns of differentiation vary within the same species according to the spatial scale, with one group probably issued from vicariance, whereas the other followed a pattern of isolation by distance. The geographic pattern for A. triostegus emphasizes the diversity of the evolutionary processes that lead to the present genetic structure with some being more influential in certain areas or according to a particular spatial scale.

Multiparametric voxel-based analyses of standardized uptake values and apparent diffusion coefficients of soft-tissue tumours with a positron emission tomography/magnetic resonance system: Preliminary results.

PubMed

Sagiyama, Koji; Watanabe, Yuji; Kamei, Ryotaro; Hong, Sungtak; Kawanami, Satoshi; Matsumoto, Yoshihiro; Honda, Hiroshi

2017-12-01

To investigate the usefulness of voxel-based analysis of standardized uptake values (SUVs) and apparent diffusion coefficients (ADCs) for evaluating soft-tissue tumour malignancy with a PET/MR system. Thirty-five subjects with either ten low/intermediate-grade tumours or 25 high-grade tumours were prospectively enrolled. Zoomed diffusion-weighted and fluorodeoxyglucose ( 18 FDG)-PET images were acquired along with fat-suppressed T2-weighted images (FST2WIs). Regions of interest (ROIs) were drawn on FST2WIs including the tumour in all slices. ROIs were pasted onto PET and ADC-maps to measure SUVs and ADCs within tumour ROIs. Tumour volume, SUVmax, ADCminimum, the heterogeneity and the correlation coefficients of SUV and ADC were recorded. The parameters of high- and low/intermediate-grade groups were compared, and receiver operating characteristic (ROC) analysis was also performed. The mean correlation coefficient for SUV and ADC in high-grade sarcomas was lower than that of low/intermediate-grade tumours (-0.41 ± 0.25 vs. -0.08 ± 0.34, P < 0.01). Other parameters did not differ significantly. ROC analysis demonstrated that correlation coefficient showed the best diagnostic performance for differentiating the two groups (AUC 0.79, sensitivity 96.0%, specificity 60%, accuracy 85.7%). SUV and ADC determined via PET/MR may be useful for differentiating between high-grade and low/intermediate-grade soft tissue tumours. • PET/MR allows voxel-based comparison of SUVs and ADCs in soft-tissue tumours. • A comprehensive assessment of internal heterogeneity was performed with scatter plots. • SUVmax or ADCminimum could not differentiate high-grade sarcoma from low/intermediate-grade tumours. • Only the correlation coefficient between SUV and ADC differentiated the two groups. • The correlation coefficient showed the best diagnostic performance by ROC analysis.

Mitochondrial DNA Analyses Indicate High Diversity, Expansive Population Growth and High Genetic Connectivity of Vent Copepods (Dirivultidae) across Different Oceans.

PubMed

Gollner, Sabine; Stuckas, Heiko; Kihara, Terue C; Laurent, Stefan; Kodami, Sahar; Martinez Arbizu, Pedro

2016-01-01

Communities in spatially fragmented deep-sea hydrothermal vents rich in polymetallic sulfides could soon face major disturbance events due to deep-sea mineral mining, such that unraveling patterns of gene flow between hydrothermal vent populations will be an important step in the development of conservation policies. Indeed, the time required by deep-sea populations to recover following habitat perturbations depends both on the direction of gene flow and the number of migrants available for re-colonization after disturbance. In this study we compare nine dirivultid copepod species across various geological settings. We analyze partial nucleotide sequences of the mtCOI gene and use divergence estimates (FST) and haplotype networks to infer intraspecific population connectivity between vent sites. Furthermore, we evaluate contrasting scenarios of demographic population expansion/decline versus constant population size (using, for example, Tajima's D). Our results indicate high diversity, population expansion and high connectivity of all copepod populations in all oceans. For example, haplotype diversity values range from 0.89 to 1 and FST values range from 0.001 to 0.11 for Stygiopontius species from the Central Indian Ridge, Mid Atlantic Ridge, East Pacific Rise, and Eastern Lau Spreading Center. We suggest that great abundance and high site occupancy by these species favor high genetic diversity. Two scenarios both showed similarly high connectivity: fast spreading centers with little distance between vent fields and slow spreading centers with greater distance between fields. This unexpected result may be due to some distinct frequency of natural disturbance events, or to aspects of individual life histories that affect realized rates of dispersal. However, our statistical performance analyses showed that at least 100 genomic regions should be sequenced to ensure accurate estimates of migration rate. Our demography parameters demonstrate that dirivultid populations are generally large and continuously undergoing population growth. Benthic and pelagic species abundance data support these findings.

Differential Item Functioning Detection across Two Methods of Defining Group Comparisons: Pairwise and Composite Group Comparisons

ERIC Educational Resources Information Center

Sari, Halil Ibrahim; Huggins, Anne Corinne

2015-01-01

This study compares two methods of defining groups for the detection of differential item functioning (DIF): (a) pairwise comparisons and (b) composite group comparisons. We aim to emphasize and empirically support the notion that the choice of pairwise versus composite group definitions in DIF is a reflection of how one defines fairness in DIF…

β-Hydroxy-β-methylbutyrate (HMB) supplementation and resistance exercise significantly reduce abdominal adiposity in healthy elderly men.

PubMed

Stout, Jeffrey R; Fukuda, David H; Kendall, Kristina L; Smith-Ryan, Abbie E; Moon, Jordan R; Hoffman, Jay R

2015-04-01

The effects of 12-weeks of HMB ingestion and resistance training (RT) on abdominal adiposity were examined in 48 men (66-78 yrs). All participants were randomly assigned to 1 of 4 groups: no-training placebo (NT-PL), HMB only (NT-HMB), RT with PL (RT-PL), or HMB with RT (RT-HMB). DXA was used to estimate abdominal fat mass (AFM) by placing the region of interest over the L1-L4 region of the spine. Outcomes were assessed by ANCOVA, with Bonferroni-corrected pairwise comparisons. Baseline AFM values were used as the covariate. The ANCOVA indicated a significant difference (p = 0.013) between group means for the adjusted posttest AFM values (mean (kg) ± SE: NT-PL = 2.59 ± 0.06; NT-HMB = 2.59 ± 0.61; RT-PL = 2.59 ± 0.62; RT-HMB = 2.34 ± 0.61). The pairwise comparisons indicated that AFM following the intervention period in the RT-HMB group was significantly less than NT-PL (p = 0.013), NT-HMB (p = 0.011), and RT-PL (p = 0.010). These data suggested that HMB in combination with 12 weeks of RT decreased AFM in elderly men. Copyright © 2015. Published by Elsevier Inc.

Mobile learning module improves knowledge of medical shock for forward surgical team members.

PubMed

Schulman, Carl I; Garcia, George D; Wyckoff, Mary M; Duncan, Robert C; Withum, Kelly F; Graygo, Jill

2012-11-01

Acute trauma care is characterized by dynamic situations that require adequate preparation to ensure success for military health professionals. The use of mobile learning in this environment can provide a solution that standardizes education and replaces traditional didactic lectures. A comparative evaluation with a pre-post test design regarding medical shock was delivered via either a didactic lecture or a mobile learning video module to U.S. Army Forward Surgical Team (FST) members. Participants completed a pretest, were randomly assigned to treatment group by FST, and then completed the post-test and scenario assessment. One-hundred and thirteen FST members participated with 53 in the mobile learning group and 60 in the lecture group (control). The percent mean score for the mobile learning group increased from 43.6 to 70 from pretest to post-test, with a scenario mean score of M = 56.2. The percent mean score for the control group increased from 41.5 to 72.5, with a scenario mean score of M = 59.7. The two-way analysis of variance mean score difference was 26.4 for the mobile learning group and 31.0 for the control, F = 2.18, (p = 0.14). Mobile learning modules, coupled with a structured assessment, have the potential to improve educational experiences in civilian and military settings.

Challenges in economic modeling of anticancer therapies: an example of modeling the survival benefit of olaparib maintenance therapy for patients with BRCA-mutated platinum-sensitive relapsed ovarian cancer.

PubMed

Hettle, Robert; Posnett, John; Borrill, John

2015-01-01

The aim of this paper is to describe a four health-state, semi-Markov model structure with health states defined by initiation of subsequent treatment, designed to make best possible use of the data available from a phase 2 clinical trial. The approach is illustrated using data from a sub-group of patients enrolled in a phase 2 clinical trial of olaparib maintenance therapy in patients with platinum-sensitive relapsed ovarian cancer and a BRCA mutation (NCT00753545). A semi-Markov model was developed with four health states: progression-free survival (PFS), first subsequent treatment (FST), second subsequent treatment (SST), and death. Transition probabilities were estimated by fitting survival curves to trial data for time from randomization to FST, time from FST to SST, and time from SST to death. Survival projections generated by the model are broadly consistent with the outcomes observed in the clinical trial. However, limitations of the trial data (small sample size, immaturity of the PFS and overall survival [OS] end-points, and treatment switching) create uncertainty in estimates of survival. The model framework offers a promising approach to evaluating cost-effectiveness of a maintenance therapy for patients with cancer, which may be generalizable to other chronic diseases.

Swim stress exaggerates the hyperactive mesocortical dopamine system in a rodent model of autism.

PubMed

Nakasato, Akane; Nakatani, Yasushi; Seki, Yoshinari; Tsujino, Naohisa; Umino, Masahiro; Arita, Hideho

2008-02-08

Several clinical reports have suggested that there is a hyperactivation of the dopaminergic system in people with autism. Using rats exposed prenatally to valproic acid (VPA) as an animal model of autism, we measured dopamine (DA) levels in samples collected from the frontal cortex (FC) using in vivo microdialysis and HPLC. The basal DA level in FC was significantly higher in VPA-exposed rats relative to controls. Since the mesocortical DA system is known to be sensitive to physical and psychological stressors, we measured DA levels in FC before, during, and after a 60-min forced swim test (FST). There were further gradual increases in FC DA levels during the FST in the VPA-exposed rats, but not in the control rats. Behavioral analysis during the last 10 min of the FST revealed a significant decrease in active, escape-oriented behavior and an increase in immobility, which is thought to reflect the development of depressive behavior that disengages the animal from active forms of coping with stressful stimuli. These results suggest that this rodent model of autism exhibits a hyperactive mesocortical DA system, which is exaggerated by swim stress. This abnormality may be responsible for depressive and withdrawal behavior observed in autism.

De-individualized psychophysiological strain assessment during a flight simulation test—Validation of a space methodology

NASA Astrophysics Data System (ADS)

Johannes, Bernd; Salnitski, Vyacheslav; Soll, Henning; Rauch, Melina; Hoermann, Hans-Juergen

For the evaluation of an operator's skill reliability indicators of work quality as well as of psychophysiological states during the work have to be considered. The herein presented methodology and measurement equipment were developed and tested in numerous terrestrial and space experiments using a simulation of a spacecraft docking on a space station. However, in this study the method was applied to a comparable terrestrial task—the flight simulator test (FST) used in the DLR selection procedure for ab initio pilot applicants for passenger airlines. This provided a large amount of data for a statistical verification of the space methodology. For the evaluation of the strain level of applicants during the FST psychophysiological measurements were used to construct a "psychophysiological arousal vector" (PAV) which is sensitive to various individual reaction patterns of the autonomic nervous system to mental load. Its changes and increases will be interpreted as "strain". In the first evaluation study, 614 subjects were analyzed. The subjects first underwent a calibration procedure for the assessment of their autonomic outlet type (AOT) and on the following day they performed the FST, which included three tasks and was evaluated by instructors applying well-established and standardized rating scales. This new method will possibly promote a wide range of other future applications in aviation and space psychology.

Does a social/behavioural gradient in dental health exist among adults? A cross-sectional study

PubMed Central

Arrica, Mariantonietta; Carta, Giovanna; Cocco, Fabio; Grazia Cagetti, Maria; Sale, Silvana; Ierardo, Gaetano; Strohmenger, Laura; Ottolenghi, Livia

2017-01-01

Objective To explore the potential presence of a social/behavioural gradient in dental health among Italian adults using a cross-sectional study. Methods Caries indices were recorded among 480 subjects (52.9% men, 47.1% women) who also completed a structured self-administered social and behavioural questionnaire. A social/behavioural gradient was generated as the sum of the worst circumstances recorded on the questionnaire (cariogenic diet, smoking, lowest occupational profile, brushing teeth < twice daily, lowest educational level, uneven dental examination attendance). Results Caries figures (DMFT) and the number of filled sound teeth (FS-T) were statistically significantly linked to the social/behavioural gradient (DMFT: χ2(9) = 20.17 p = 0.02, Z = 0.02 p = 0.99; FS-T: χ2(9) = 25.68 p < 0.01, Z = −4.31 p < 0.01). DMFT was statistically significantly associated with gender and with social and behavioural variables. FS-T was higher in women (p = 0.03) and was linked to smoking (p < 0.01). Conclusions The proposed social/behavioural gradient demonstrated how subjects reporting the worst circumstances on the questionnaire exhibited the worst dental health. The use of the gradient demonstrates that health promotion and prevention cannot be compartmentalized. PMID:28345424

Coming out of the starting blocks: extended lag time rearranges genetic diversity in introduced marine fishes of Hawai‘i

PubMed Central

Gaither, Michelle R.; Toonen, Robert J.; Bowen, Brian W.

2012-01-01

Biological invasions with known histories are rare, especially in the sea, and empirical studies of the genetic consequences are even rarer. Fifty-five years ago, the state of Hawai‘i began a remarkable, if unintentional, ‘experiment’ with the introduction of three reef fishes, Lutjanus fulvus, Cephalopholis argus and Lutjanus kasmira. All have since expanded from the initial introduction of 2204 to 3163 individuals; however, historical records show that initially L. fulvus remained scarce, C. argus had modest population expansion and L. kasmira experienced rapid population growth. The consequences of differential population growth rates are apparent in F-statistics: Hawaiian L. fulvus demonstrate strong and significant haplotype frequency shifts from the founder location (FST = 0.449), C. argus shows low but significant differentiation (FST = 0.066) and L. kasmira is nearly identical to the founder location (FST = 0.008). All three species had higher mtDNA diversity in the introduced range, which can be explained by multiple sources for L. fulvus and L. kasmira, but not for C. argus. We conclude that lag time before population expansion, in conjunction with genetic drift, has defined the genetic architecture of these three species in the introduced range. PMID:22874747

Does a social/behavioural gradient in dental health exist among adults? A cross-sectional study.

PubMed

Arrica, Mariantonietta; Carta, Giovanna; Cocco, Fabio; Cagetti, Maria Grazia; Campus, Guglielmo; Ierardo, Gaetano; Ottolenghi, Livia; Sale, Silvana; Strohmenger, Laura

2017-04-01

Objective To explore the potential presence of a social/behavioural gradient in dental health among Italian adults using a cross-sectional study. Methods Caries indices were recorded among 480 subjects (52.9% men, 47.1% women) who also completed a structured self-administered social and behavioural questionnaire. A social/behavioural gradient was generated as the sum of the worst circumstances recorded on the questionnaire (cariogenic diet, smoking, lowest occupational profile, brushing teeth < twice daily, lowest educational level, uneven dental examination attendance). Results Caries figures (DMFT) and the number of filled sound teeth (FS-T) were statistically significantly linked to the social/behavioural gradient (DMFT: χ 2 (9)  = 20.17 p = 0.02, Z = 0.02 p = 0.99; FS-T: χ 2 (9)  = 25.68 p < 0.01, Z = -4.31 p < 0.01). DMFT was statistically significantly associated with gender and with social and behavioural variables. FS-T was higher in women (p = 0.03) and was linked to smoking ( p < 0.01). Conclusions The proposed social/behavioural gradient demonstrated how subjects reporting the worst circumstances on the questionnaire exhibited the worst dental health. The use of the gradient demonstrates that health promotion and prevention cannot be compartmentalized.

Gemfibrozil has antidepressant effects in mice: Involvement of the hippocampal brain-derived neurotrophic factor system.

PubMed

Ni, Yu-Fei; Wang, Hao; Gu, Qiu-Yan; Wang, Fei-Ying; Wang, Ying-Jie; Wang, Jin-Liang; Jiang, Bo

2018-04-01

Major depressive disorder has become one of the most serious neuropsychiatric disorders worldwide. However, currently available antidepressants used in clinical practice are ineffective for a substantial proportion of patients and always have side effects. Besides being a lipid-regulating agent, gemfibrozil is an agonist of peroxisome proliferator-activated receptor-α (PPAR-α). We investigated the antidepressant effects of gemfibrozil on C57BL/6J mice using the forced swim test (FST) and tail suspension test (TST), as well as the chronic unpredictable mild stress (CUMS) model of depression. The changes in brain-derived neurotrophic factor (BDNF) signaling cascade in the brain after CUMS and gemfibrozil treatment were further assessed. Pharmacological inhibitors and lentivirus-expressed short hairpin RNA (shRNA) were also used to clarify the antidepressant mechanisms of gemfibrozil. Gemfibrozil exhibited significant antidepressant actions in the FST and TST without affecting the locomotor activity of mice. Chronic gemfibrozil administration fully reversed CUMS-induced depressive-like behaviors in the FST, TST and sucrose preference test. Gemfibrozil treatment also restored CUMS-induced inhibition of the hippocampal BDNF signaling pathway. Blocking PPAR-α and BDNF but not the serotonergic system abolished the antidepressant effects of gemfibrozil on mice. Gemfibrozil produced antidepressant effects in mice by promoting the hippocampal BDNF system.

Adaptive semantic tag mining from heterogeneous clinical research texts.

PubMed

Hao, T; Weng, C

2015-01-01

To develop an adaptive approach to mine frequent semantic tags (FSTs) from heterogeneous clinical research texts. We develop a "plug-n-play" framework that integrates replaceable unsupervised kernel algorithms with formatting, functional, and utility wrappers for FST mining. Temporal information identification and semantic equivalence detection were two example functional wrappers. We first compared this approach's recall and efficiency for mining FSTs from ClinicalTrials.gov to that of a recently published tag-mining algorithm. Then we assessed this approach's adaptability to two other types of clinical research texts: clinical data requests and clinical trial protocols, by comparing the prevalence trends of FSTs across three texts. Our approach increased the average recall and speed by 12.8% and 47.02% respectively upon the baseline when mining FSTs from ClinicalTrials.gov, and maintained an overlap in relevant FSTs with the base- line ranging between 76.9% and 100% for varying FST frequency thresholds. The FSTs saturated when the data size reached 200 documents. Consistent trends in the prevalence of FST were observed across the three texts as the data size or frequency threshold changed. This paper contributes an adaptive tag-mining framework that is scalable and adaptable without sacrificing its recall. This component-based architectural design can be potentially generalizable to improve the adaptability of other clinical text mining methods.

Conservation genetics of the eastern yellow-bellied racer (Coluber constrictor flaviventris) and bullsnake (Pituophis catenifer sayi): River valleys are critical features for snakes at northern range limits.

PubMed

Somers, Christopher M; Graham, Carly F; Martino, Jessica A; Frasier, Timothy R; Lance, Stacey L; Gardiner, Laura E; Poulin, Ray G

2017-01-01

On the North American Great Plains, several snake species reach their northern range limit where they rely on sparsely distributed hibernacula located in major river valleys. Independent colonization histories for the river valleys and barriers to gene flow caused by the lack of suitable habitat between them may have produced genetically differentiated snake populations. To test this hypothesis, we used 10 microsatellite loci to examine the population structure of two species of conservation concern in Canada: the eastern yellow-bellied racer (Coluber constrictor flaviventris) and bullsnake (Pituophis catenifer sayi) in 3 major river valleys in southern Saskatchewan. Fixation indices (FST) showed that populations in river valleys were significantly differentiated for both species (racers, FST = 0.096, P = 0.001; bullsnakes FST = 0.045-0.157, P = 0.001). Bayesian assignment (STRUCTURE) and ordination (DAPC) strongly supported genetically differentiated groups in the geographically distinct river valleys. Finer-scale subdivision of populations within river valleys was not apparent based on our data, but is a topic that should be investigated further. Our findings highlight the importance of major river valleys for snakes at the northern extent of their ranges, and raise the possibility that populations in each river valley may warrant separate management strategies.

Oceanographic connectivity and environmental correlates of genetic structuring in Atlantic herring in the Baltic Sea

PubMed Central

Teacher, Amber GF; André, Carl; Jonsson, Per R; Merilä, Juha

2013-01-01

Marine fish often show little genetic structuring in neutral marker genes, and Atlantic herring (Clupea harengus) in the Baltic Sea are no exception; historically, very low levels of population differentiation (FST ≍ 0.002) have been found, despite a high degree of interpopulation environmental heterogeneity in salinity and temperature. Recent exome sequencing and SNP studies have however shown that many loci are under selection in this system. Here, we combined population genetic analyses of a large number of transcriptome-derived microsatellite markers with oceanographic modelling to investigate genetic differentiation and connectivity in Atlantic herring at a relatively fine scale within the Baltic Sea. We found evidence for weak but robust and significant genetic structuring (FST = 0.008) explainable by oceanographic connectivity. Genetic differentiation was also associated with site differences in temperature and salinity, with the result driven by the locus Her14 which appears to be under directional selection (FST = 0.08). The results show that Baltic herring are genetically structured within the Baltic Sea, and highlight the role of oceanography and environmental factors in explaining this structuring. The results also have implications for the management of herring fisheries, the most economically important fishery in the Baltic Sea, suggesting that the current fisheries management units may be in need of revision. PMID:23745145

Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA.

PubMed

Kelly, Brendan J; Gross, Robert; Bittinger, Kyle; Sherrill-Mix, Scott; Lewis, James D; Collman, Ronald G; Bushman, Frederic D; Li, Hongzhe

2015-08-01

The variation in community composition between microbiome samples, termed beta diversity, can be measured by pairwise distance based on either presence-absence or quantitative species abundance data. PERMANOVA, a permutation-based extension of multivariate analysis of variance to a matrix of pairwise distances, partitions within-group and between-group distances to permit assessment of the effect of an exposure or intervention (grouping factor) upon the sampled microbiome. Within-group distance and exposure/intervention effect size must be accurately modeled to estimate statistical power for a microbiome study that will be analyzed with pairwise distances and PERMANOVA. We present a framework for PERMANOVA power estimation tailored to marker-gene microbiome studies that will be analyzed by pairwise distances, which includes: (i) a novel method for distance matrix simulation that permits modeling of within-group pairwise distances according to pre-specified population parameters; (ii) a method to incorporate effects of different sizes within the simulated distance matrix; (iii) a simulation-based method for estimating PERMANOVA power from simulated distance matrices; and (iv) an R statistical software package that implements the above. Matrices of pairwise distances can be efficiently simulated to satisfy the triangle inequality and incorporate group-level effects, which are quantified by the adjusted coefficient of determination, omega-squared (ω2). From simulated distance matrices, available PERMANOVA power or necessary sample size can be estimated for a planned microbiome study. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Antidepressant-like effects induced by NMDA receptor blockade and NO synthesis inhibition in the ventral medial prefrontal cortex of rats exposed to the forced swim test.

PubMed

Pereira, Vitor Silva; Romano, Angélica; Wegener, Gregers; Joca, Sâmia R L

2015-07-01

Systemic treatment with NMDA receptor (NMDAR) antagonists, inhibitors of neuronal nitric oxide synthase (nNOS) or of soluble guanylyl cyclase (sGC), induce antidepressant-like effects in rats. Increased levels of glutamate and nitric oxide (NO) in the medial prefrontal cortex (MPFC) of stressed animals have been described in the literature. However, the role of the NMDAR-nNOS-sGC pathway of the MPFC in the mediation of forced swim-induced behaviors remains unclear. The aim of this work was to test the hypothesis that the inhibition of the NMDAR-nNOS-sGC pathway in the ventral MPFC (infralimbic (IL) or prelimbic (PL)) would elicit antidepressant-like effects in the forced swim test (FST). Rats implanted with cannulae aimed at the PL or the IL were exposed to the FST and injected with LY235959 (NMDAR antagonist), NPA (nNOS inhibitor), ODQ (sGC inhibitor), or carboxy-PTIO (NO scavenger). Additional groups received the AMPA antagonist, NBQX, before the effective doses of LY235959 or NPA. LY235959 administration into PL or IL before the FS pretest produced no effects. Administration of LY235959 (3 and 10 nmol/0.2 μL) after pretest was effective only when administered into the PL. However, the administration of NPA (0.01 nmol/0.2 μL), c-PTIO (1.0 nmol/0.2 μL), and ODQ (1.0 nmol/0.2 μL) into the PL or IL before the FST produced antidepressant-like effects. NBQX blocked the antidepressant-like effect of LY235959 but not of NPA. Blocking NMDAR or NO signaling in the vMPFC, either in the IL or the PL, induces antidepressant-like effects in the rat FST. These effects seemingly occur through independent mechanisms, since NBQX blocked the former effect but not the latter.

Effect of co-treatment with fluoxetine or mirtazapine and risperidone on the active behaviors and plasma corticosterone concentration in rats subjected to the forced swim test.

PubMed

Rogóż, Zofia; Kabziński, Marcin; Sadaj, Witold; Rachwalska, Paulina; Gądek-Michalska, Anna

2012-01-01

Several clinical reports have postulated a beneficial effect of the addition of a low dose of risperidone to the ongoing treatment with antidepressants in treatment-resistant depression. The present study aimed to examine the effect of treatment with fluoxetine or mirtazapine, given separately or jointly with risperidone, on active behavior and plasma corticosterone level in male Wistar rats subjected to the forced swim test (FST). The obtained results showed that fluoxetine (5 mg/kg), mirtazapine (5 and 10 mg/kg) or risperidone (0.05 and 0.1 mg/kg) did not change the active behavior of rats in the FST. However, co-treatment with fluoxetine (10 mg/kg) and risperidone (0.1 mg/kg) induced an antidepressant-like effect in that test because it significantly increased the swimming time and decreased the immobility time, while combined treatment with mirtazapine at 5 and 10 mg/kg and risperidone at 0.05 and 0.1 mg/kg evoked a significant increase in the swimming time and also climbing, and decreased the immobility time. WAY 100635 (a 5-HT(1A) receptor antagonist) at a dose of 0.1 mg/kg inhibited the antidepressant-like effect induced by co-administration of fluoxetine or mirtazapine and risperidone. Active behavior in that test did not reflect an increase in general activity, since combined treatment with fluoxetine or mirtazapine and risperidone failed to enhance the exploratory activity of rats. Co-treatment with fluoxetine or mirtazapine and risperidone did not reduce the stress-induced increase in plasma corticosterone concentration in animals subjected to the FST. The obtained results indicate that risperidone applied in a low dose enhances the antidepressant-like activity of fluoxetine and mirtazapine in the FST (but does not normalize the stress-induced increase in corticosterone level in these rats), and that 5-HT(1A) receptors may play some role in these effects.

Enhancement of cortical extracellular 5-HT by 5-HT1A and 5-HT2C receptor blockade restores the antidepressant-like effect of citalopram in non-responder mice.

PubMed

Calcagno, Eleonora; Guzzetti, Sara; Canetta, Alessandro; Fracasso, Claudia; Caccia, Silvio; Cervo, Luigi; Invernizzi, Roberto W

2009-07-01

We recently found that the response of DBA/2 mice to SSRIs in the forced swim test (FST) was impaired and they also had a smaller basal and citalopram-stimulated increase in brain extracellular serotonin (5-HT) than 'responder' strains. We employed intracerebral microdialysis, FST and selective antagonists of 5-HT1A and 5-HT2C receptors to investigate whether enhancing the increase in extracellular 5-HT reinstated the anti-immobility effect of citalopram in the FST. WAY 100635 (0.3 mg/kg s.c.) or SB 242084 (1 mg/kg s.c.), respectively a selective 5-HT1A and 5-HT2C receptor antagonist, raised the effect of citalopram (5 mg/kg) on extracellular 5-HT in the medial prefrontal cortex of DBA/2N mice (citalopram alone 5.2+/-0.3 fmol/20 microl, WAY 100635+citalopram 9.9+/-2.1 fmol/20 microl, SB 242084+ citalopram 7.6+/-1.0 fmol/20 microl) to the level reached in 'responder' mice given citalopram alone. The 5-HT receptor antagonists had no effect on the citalopram-induced increase in extracellular 5-HT in the dorsal hippocampus. The combination of citalopram with WAY 100635 or SB 242084 significantly reduced immobility time in DBA/2N mice that otherwise did not respond to either drug singly. Brain levels of citalopram in mice given citalopram alone or with 5-HT antagonists did not significantly differ. The results confirm that impaired 5-HT transmission accounts for the lack of effect of citalopram in the FST and suggest that enhancing the effect of SSRIs on extracellular 5-HT, through selective blockade of 5-HT1A and 5-HT2C receptors, could be a useful strategy to restore the response in treatment-resistant depression.

Antidepressant-like activity of the neuropeptide Y Y5 receptor antagonist Lu AA33810: behavioral, molecular, and immunohistochemical evidence.

PubMed

Domin, Helena; Szewczyk, Bernadeta; Pochwat, Bartłomiej; Woźniak, Monika; Śmiałowska, Maria

2017-02-01

It has recently been found that chronic treatment with the highly selective, brain-penetrating Y5 receptor antagonist, Lu AA33810 [N-[[trans-4-[(4,5-dihydro [1] benzothiepino[5,4-d] thiazol-2-yl) amino] cyclohexyl]methyl]-methanesulfonamide], produces antidepressant-like effects in the rat chronic mild stress model. In the present study, we investigated the possible antidepressant-like activity of Lu AA33810 in rats subjected to glial ablation in the prefrontal cortex (PFC) by the gliotoxin L-AAA, which is an astroglial degeneration model of depression. We observed that Lu AA33810 administered intraperitoneally at a single dose of 10 mg/kg both reversed depressive-like behavioral changes in the forced swim test (FST) and prevented degeneration of astrocytes in the mPFC. The mechanism of antidepressant and glioprotective effects of Lu AA33810 has not been studied, so far. We demonstrated the contribution of the noradrenergic rather than the serotonergic pathway to the antidepressant-like action of Lu AA33810 in the FST. Moreover, we found that antidepressant-like effect of Lu AA33810 was connected with the influence on brain-derived neurotrophic factor (BDNF) protein expression. We also demonstrated the antidepressant-like effect of Lu AA33810 in the FST in rats which did not receive the gliotoxin. We found that intracerebroventricular injection of the selective MAPK/ERK inhibitor U0126 (5 μg/2 μl) and the selective PI3K inhibitor LY294002 (10 nmol/2 μl) significantly inhibited the anti-immobility effect of Lu AA33810 in the FST in rats, suggesting that MAPK/ERK and PI3K signaling pathways could be involved in the antidepressant-like effect of Lu AA33810. Our results indicate that Lu AA33810 exerts an antidepressant-like effect and suggest the Y5 receptors as a promising target for antidepressant therapy.

Different effects of vitamin D hormone treatment on depression-like behavior in the adult ovariectomized female rats.

PubMed

Fedotova, Julia; Dudnichenko, Tatyana; Kruzliak, Peter; Puchavskaya, Zhanna

2016-12-01

Vitamine D (VD) has important functions in the human brain and may play a role in affective-related disorders. VD receptors are expressed in multiple brain regions associated with depressive disorders. The aim of the preclinical study was to examine the effects of chronic cholecalciferol administration (1.0, 2.5 or 5.0mg/kg/day,s.c., once daily, for 14days) on the depression-like behavior and corticosterone levels in the blood samples following ovariectomy in female rats. Cholecalciferol was administered to the ovariectomized (OVX) rats and OVX rats treated with 17β-estradiol (17β-E 2 , 0.5μg/rat,s.c., once daily, for 14days). Depression-like behavior and spontaneous locomotor activity were assessed in the forced swimming test (FST) and the open field test (OFT), respectively. The corticosterone levels in the blood serum before and after FST were measured in all experimental groups. Treatment with cholecalciferol in high dose (5.0mg/kg/day,s.c.) significantly decreased the immobility time of OVX rats in the FST. Co-administration of cholecalciferol in high dose with 17β-E 2 exerted a markedly synergistic antidepressant-like effect in the OVX rats on the same model of depression-like behavior testing. Cholecalciferol in high dose (5.0mg/kg/day,s.c.) administered alone or together with 17β-E 2 significantly enhanced frequency of grooming for the OVX rats in the OFT. Moreover, cholecalciferol in high dose administered alone or together with 17β-E 2 significantly decreased the elevated corticosterone levels in the blood serum of OVX rats following the FST. These results indicate that Cholecalciferol in high dose has a marked antidepressant-like effect in the adult female rats with low levels of estrogen. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Dependence of Halo Bias and Kinematics on Assembly Variables

NASA Astrophysics Data System (ADS)

Xu, Xiaoju; Zheng, Zheng

2018-06-01

Using dark matter haloes identified in a large N-body simulation, we study halo assembly bias, with halo formation time, peak maximum circular velocity, concentration, and spin as the assembly variables. Instead of grouping haloes at fixed mass into different percentiles of each assembly variable, we present the joint dependence of halo bias on the values of halo mass and each assembly variable. In the plane of halo mass and one assembly variable, the joint dependence can be largely described as halo bias increasing outward from a global minimum. We find it unlikely to have a combination of halo variables to absorb all assembly bias effects. We then present the joint dependence of halo bias on two assembly variables at fixed halo mass. The gradient of halo bias does not necessarily follow the correlation direction of the two assembly variables and it varies with halo mass. Therefore in general for two correlated assembly variables one cannot be used as a proxy for the other in predicting halo assembly bias trend. Finally, halo assembly is found to affect the kinematics of haloes. Low-mass haloes formed earlier can have much higher pairwise velocity dispersion than those of massive haloes. In general, halo assembly leads to a correlation between halo bias and halo pairwise velocity distribution, with more strongly clustered haloes having higher pairwise velocity and velocity dispersion. However, the correlation is not tight, and the kinematics of haloes at fixed halo bias still depends on halo mass and assembly variables.

Sample size and power considerations in network meta-analysis

PubMed Central

2012-01-01

Background Network meta-analysis is becoming increasingly popular for establishing comparative effectiveness among multiple interventions for the same disease. Network meta-analysis inherits all methodological challenges of standard pairwise meta-analysis, but with increased complexity due to the multitude of intervention comparisons. One issue that is now widely recognized in pairwise meta-analysis is the issue of sample size and statistical power. This issue, however, has so far only received little attention in network meta-analysis. To date, no approaches have been proposed for evaluating the adequacy of the sample size, and thus power, in a treatment network. Findings In this article, we develop easy-to-use flexible methods for estimating the ‘effective sample size’ in indirect comparison meta-analysis and network meta-analysis. The effective sample size for a particular treatment comparison can be interpreted as the number of patients in a pairwise meta-analysis that would provide the same degree and strength of evidence as that which is provided in the indirect comparison or network meta-analysis. We further develop methods for retrospectively estimating the statistical power for each comparison in a network meta-analysis. We illustrate the performance of the proposed methods for estimating effective sample size and statistical power using data from a network meta-analysis on interventions for smoking cessation including over 100 trials. Conclusion The proposed methods are easy to use and will be of high value to regulatory agencies and decision makers who must assess the strength of the evidence supporting comparative effectiveness estimates. PMID:22992327

Pair-Wise Trajectory Management-Oceanic (PTM-O) . [Concept of Operations—Version 3.9

NASA Technical Reports Server (NTRS)

Jones, Kenneth M.

2014-01-01

This document describes the Pair-wise Trajectory Management-Oceanic (PTM-O) Concept of Operations (ConOps). Pair-wise Trajectory Management (PTM) is a concept that includes airborne and ground-based capabilities designed to enable and to benefit from, airborne pair-wise distance-monitoring capability. PTM includes the capabilities needed for the controller to issue a PTM clearance that resolves a conflict for a specific pair of aircraft. PTM avionics include the capabilities needed for the flight crew to manage their trajectory relative to specific designated aircraft. Pair-wise Trajectory Management PTM-Oceanic (PTM-O) is a regional specific application of the PTM concept. PTM is sponsored by the National Aeronautics and Space Administration (NASA) Concept and Technology Development Project (part of NASA's Airspace Systems Program). The goal of PTM is to use enhanced and distributed communications and surveillance along with airborne tools to permit reduced separation standards for given aircraft pairs, thereby increasing the capacity and efficiency of aircraft operations at a given altitude or volume of airspace.

A pairwise maximum entropy model accurately describes resting-state human brain networks

PubMed Central

Watanabe, Takamitsu; Hirose, Satoshi; Wada, Hiroyuki; Imai, Yoshio; Machida, Toru; Shirouzu, Ichiro; Konishi, Seiki; Miyashita, Yasushi; Masuda, Naoki

2013-01-01

The resting-state human brain networks underlie fundamental cognitive functions and consist of complex interactions among brain regions. However, the level of complexity of the resting-state networks has not been quantified, which has prevented comprehensive descriptions of the brain activity as an integrative system. Here, we address this issue by demonstrating that a pairwise maximum entropy model, which takes into account region-specific activity rates and pairwise interactions, can be robustly and accurately fitted to resting-state human brain activities obtained by functional magnetic resonance imaging. Furthermore, to validate the approximation of the resting-state networks by the pairwise maximum entropy model, we show that the functional interactions estimated by the pairwise maximum entropy model reflect anatomical connexions more accurately than the conventional functional connectivity method. These findings indicate that a relatively simple statistical model not only captures the structure of the resting-state networks but also provides a possible method to derive physiological information about various large-scale brain networks. PMID:23340410

Selecting Soldiers and Civilians into the U.S. Army Officer Candidate School : Developing Empirical Selection Composites

DTIC Science & Technology

2014-07-01

a biographical instrument measuring personality ; (b) a Work Values instrument representing work preferences investigated in prior officer and...items used in SelectOCS Phase 2 (see Table 2.5). TAPAS uses multidimensional pairwise preference (MDPP) personality items scored using item response...presented respondents with a list of 30 traits and 30 skills (derived from leadership and personality literature) and instructed them to rate the

Why rate when you could compare? Using the "EloChoice" package to assess pairwise comparisons of perceived physical strength.

PubMed

Clark, Andrew P; Howard, Kate L; Woods, Andy T; Penton-Voak, Ian S; Neumann, Christof

2018-01-01

We introduce "EloChoice", a package for R which uses Elo rating to assess pairwise comparisons between stimuli in order to measure perceived stimulus characteristics. To demonstrate the package and compare results from forced choice pairwise comparisons to those from more standard single stimulus rating tasks using Likert (or Likert-type) items, we investigated perceptions of physical strength from images of male bodies. The stimulus set comprised images of 82 men standing on a raised platform with minimal clothing. Strength-related anthropometrics and grip strength measurements were available for each man in the set. UK laboratory participants (Study 1) and US online participants (Study 2) viewed all images in both a Likert rating task, to collect mean Likert scores, and a pairwise comparison task, to calculate Elo, mean Elo (mElo), and Bradley-Terry scores. Within both studies, Likert, Elo and Bradley-Terry scores were closely correlated to mElo scores (all rs > 0.95), and all measures were correlated with stimulus grip strength (all rs > 0.38) and body size (all rs > 0.59). However, mElo scores were less variable than Elo scores and were hundreds of times quicker to compute than Bradley-Terry scores. Responses in pairwise comparison trials were 2/3 quicker than in Likert tasks, indicating that participants found pairwise comparisons to be easier. In addition, mElo scores generated from a data set with half the participants randomly excluded produced very comparable results to those produced with Likert scores from the full participant set, indicating that researchers require fewer participants when using pairwise comparisons.

Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA

PubMed Central

Kelly, Brendan J.; Gross, Robert; Bittinger, Kyle; Sherrill-Mix, Scott; Lewis, James D.; Collman, Ronald G.; Bushman, Frederic D.; Li, Hongzhe

2015-01-01

Motivation: The variation in community composition between microbiome samples, termed beta diversity, can be measured by pairwise distance based on either presence–absence or quantitative species abundance data. PERMANOVA, a permutation-based extension of multivariate analysis of variance to a matrix of pairwise distances, partitions within-group and between-group distances to permit assessment of the effect of an exposure or intervention (grouping factor) upon the sampled microbiome. Within-group distance and exposure/intervention effect size must be accurately modeled to estimate statistical power for a microbiome study that will be analyzed with pairwise distances and PERMANOVA. Results: We present a framework for PERMANOVA power estimation tailored to marker-gene microbiome studies that will be analyzed by pairwise distances, which includes: (i) a novel method for distance matrix simulation that permits modeling of within-group pairwise distances according to pre-specified population parameters; (ii) a method to incorporate effects of different sizes within the simulated distance matrix; (iii) a simulation-based method for estimating PERMANOVA power from simulated distance matrices; and (iv) an R statistical software package that implements the above. Matrices of pairwise distances can be efficiently simulated to satisfy the triangle inequality and incorporate group-level effects, which are quantified by the adjusted coefficient of determination, omega-squared (ω2). From simulated distance matrices, available PERMANOVA power or necessary sample size can be estimated for a planned microbiome study. Availability and implementation: http://github.com/brendankelly/micropower. Contact: brendank@mail.med.upenn.edu or hongzhe@upenn.edu PMID:25819674

Characterization of bifunctional L-glutathione synthetases from Actinobacillus pleuropneumoniae and Actinobacillus succinogenes for efficient glutathione biosynthesis.

PubMed

Yang, Jianhua; Li, Wei; Wang, Dezheng; Wu, Hui; Li, Zhimin; Ye, Qin

2016-07-01

Glutathione (GSH), an important bioactive substance, is widely applied in pharmaceutical and food industries. In this work, two bifunctional L-glutathione synthetases (GshF) from Actinobacillus pleuropneumoniae (GshFAp) and Actinobacillus succinogenes (GshFAs) were successfully expressed in Escherichia coli BL-21(DE3). Similar to the GshF from Streptococcus thermophilus (GshFSt), GshFAp and GshFAs can be applied for high titer GSH production because they are less sensitive to end-product inhibition (Ki values 33 and 43 mM, respectively). The active catalytic forms of GshFAs and GshFAp are dimers, consistent with those of GshFPm (GshF from Pasteurella multocida) and GshFSa (GshF from Streptococcus agalactiae), but are different from GshFSt (GshF from S. thermophilus) which is an active monomer. The analysis of the protein sequences and three dimensional structures of GshFs suggested that the binding sites of GshFs for substrates, L-cysteine, L-glutamate, γ-glutamylcysteine, adenosine-triphosphate, and glycine are highly conserved with only very few differences. With sufficient supply of the precursors, the recombinant strains BL-21(DE3)/pET28a-gshFas and BL-21(DE3)/pET28a-gshFap were able to produce 36.6 and 34.1 mM GSH, with the molar yield of 0.92 and 0.85 mol/mol, respectively, based on the added L-cysteine. The results showed that GshFAp and GshFAs are potentially good candidates for industrial GSH production.

Azure B and a synthetic structural analogue of methylene blue, ethylthioninium chloride, present with antidepressant-like properties.

PubMed

Delport, Anzelle; Harvey, Brian H; Petzer, Anél; Petzer, Jacobus P

2014-11-11

The phenothiazinium compound, methylene blue (MB), possesses diverse pharmacological actions and is attracting attention for the treatment of bipolar disorder and Alzheimer's disease. MB acts on both monoamine oxidase (MAO) and the nitric oxide (NO)-cGMP pathway, and possesses antidepressant activity in rodents. The goal of this study was to synthesise a structural analogue of MB, ethylthioninium chloride (ETC), and to evaluate the effects of the structural changes on the MAO inhibitory and antidepressant properties of MB. This study also investigated the antidepressant properties of azure B, the major metabolite of MB, versus MB and imipramine as active comparators. ETC and azure B were firstly evaluated as inhibitors of human MAO, and secondly for antidepressant-like activity in the acute forced swim test (FST) in rats, and compared to saline, imipramine and MB. The results document that ETC is a reversible inhibitor of MAO-A and MAO-B with IC50 values of 0.510 μM and 0.592 μM, respectively, and that it is a weaker MAO-A inhibitor than MB and azure B. ETC and azure B were more effective than imipramine and MB in reversing immobility in the FST without inducing locomotor effects, with evidence supporting a serotonergic action. Of interest is the finding that ETC is more toxic for cultured cells than MB. Azure B may therefore be a contributor to the antidepressant effect of MB. Small structural changes made to MB retain its antidepressant effect, even though the resulting phenothiazinium compound possesses reduced MAO-A inhibitory potency.

Phylogeography of the dark fruit-eating bat Artibeus obscurus in the Brazilian Amazon.

PubMed

Ferreira, Wallax Augusto Silva; Borges, Bárbara do Nascimento; Rodrigues-Antunes, Symara; de Andrade, Fernanda Atanaena Gonçalves; Aguiar, Gilberto Ferreira de Souza; de Sousa e Silva-Junior, José; Marques-Aguiar, Suely Aparecida; Harada, Maria Lúcia

2014-01-01

Artibeus obscurus (Mammalia: Chiroptera) is endemic to South America, being found in at least 18 Brazilian states. Recent studies revealed that different populations of this genus present distinct phylogeographic patterns; however, very little is known on the population genetics structure of A. obscurus in the Amazon rainforest. Here, using a fragment (1010bp) of the mitochondrial gene cytochrome b from 87 samples, we investigated patterns of genetic divergence among populations of A. obscurus from different locations in the Brazilian Amazon rainforest and compared them with other Brazilian and South American regions. Analysis of molecular variance (AMOVA), fixation index (Fst) analysis, and phylogeographic patterns showed divergence between two major monophyletic groups, each one corresponding to a geographic region associated with the Atlantic and Amazon forest biomes. The Atlantic forest clusters formed a monophyletic group with a high bootstrap support and a fragmented distribution that follows the pattern predicted by the Refuge Theory. On the other hand, a different scenario was observed for the Amazon forest, where no fragmentation was identified. The AMOVA results revealed a significant geographic heterogeneity in the distribution of genetic variation, with 70% found within populations across the studied populations (Fst values ranging from 0.05864 to 0.09673; φST = 0.55). The intrapopulational analysis revealed that one population (Bragança) showed significant evidence of population expansion, with the formation of 2 distinct phylogroups, suggesting the occurrence of a subspecies or at least a different population in this region. These results also suggest considerable heterogeneity for A. obscurus in the Amazon region.

Neonatal handling prevents the effects of phencyclidine in an animal model of negative symptoms of schizophrenia.

PubMed

Tejedor-Real, Purificación; Sahagún, Mar; Biguet, Nicole Faucon; Mallet, Jacques

2007-04-01

Environmental factors during the neonatal period have long-lasting effects on the brain. Neonatal handling, an early mild stress, enhances the ability to cope with stress in adult rats. In humans, inappropriate stress responses increase the risk of schizophrenia in genetically predisposed individuals. We studied the effect of neonatal handling on the phencyclidine (PCP)-induced immobility time of rats in the forced swimming test (FST, an animal model of negative symptoms of schizophrenia) and on plasma adrenocorticotropic hormone (ACTH) as a measure of hypothalamic-pituitary-adrenal axis (HPA) reactivity. Pups were removed from their mothers 15 min/21 days after birth. Postnatal day 65: animals were submitted to restraint stress. Postnatal day 75: after PCP treatment (5 mg/kg/5 days) animals were submitted to the FST. Neonatal handling reduced HPA reactivity to passive stress (restraint) but not to active coping stress (forced swimming). Immobilization time was significantly lower in saline- and PCP-treated, handled animals than in non-handled ones. Handling prevented the ACTH increase induced by PCP that was observed in the non-handled rats after FST. First, neonatal handling protects animals from acquiring the schizophrenic-like behavior provoked by sub-chronic PCP treatment, which was associated with a reduced HPA activity. Second, the beneficial properties of handling in stress responses seem to depend on the type of stress.

Genetically distinct populations of northern shrimp, Pandalus borealis, in the North Atlantic: adaptation to different temperatures as an isolation factor.

PubMed

Jorde, Per Erik; Søvik, Guldborg; Westgaard, Jon-Ivar; Albretsen, Jon; André, Carl; Hvingel, Carsten; Johansen, Torild; Sandvik, Anne Dagrun; Kingsley, Michael; Jørstad, Knut Eirik

2015-04-01

The large-scale population genetic structure of northern shrimp, Pandalus borealis, was investigated over the species' range in the North Atlantic, identifying multiple genetically distinct groups. Genetic divergence among sample localities varied among 10 microsatellite loci (range: FST = -0.0002 to 0.0475) with a highly significant average (FST = 0.0149; P < 0.0001). In contrast, little or no genetic differences were observed among temporal replicates from the same localities (FST = 0.0004; P = 0.33). Spatial genetic patterns were compared to geographic distances, patterns of larval drift obtained through oceanographic modelling, and temperature differences, within a multiple linear regression framework. The best-fit model included all three factors and explained approximately 29% of all spatial genetic divergence. However, geographic distance and larval drift alone had only minor effects (2.5-4.7%) on large-scale genetic differentiation patterns, whereas bottom temperature differences explained most (26%). Larval drift was found to promote genetic homogeneity in parts of the study area with strong currents, but appeared ineffective across large temperature gradients. These findings highlight the breakdown of gene flow in a species with a long pelagic larval phase (up to 3 months) and indicate a role for local adaptation to temperature conditions in promoting evolutionary diversification and speciation in the marine environment. © 2015 John Wiley & Sons Ltd.

Effects of fisetin on hyperhomocysteinemia-induced experimental endothelial dysfunction and vascular dementia.

PubMed

Hemanth Kumar, Boyina; Arun Reddy, Ravula; Mahesh Kumar, Jerald; Dinesh Kumar, B; Diwan, Prakash V

2017-01-01

This study was designed to investigate the effects of fisetin (FST) on hyperhomocysteinemia (HHcy)-induced experimental endothelial dysfunction (ED) and vascular dementia (VaD) in rats. Wistar rats were randomly divided into 8 groups: control, vehicle control, l-methionine, FST (5, 10, and 25 mg/kg, p.o.), FST-per se (25 mg/kg, p.o.), and donepezil (0.1 mg/kg, p.o.). l-Methionine administration (1.7 g/kg, p.o.) for 32 days induced HHcy. ED and VaD induced by HHcy were determined by vascular reactivity measurements, behavioral analysis using Morris water maze and Y-maze, along with a biochemical and histological evaluation of thoracic aorta and brain tissues. Administration of l-methionine developed behavioral deficits; triggered brain lipid peroxidation (LPO); compromised brain acetylcholinesterase activity (AChE); and reduced the levels of brain superoxide dismutase (SOD), brain catalase (CAT), brain reduced glutathione (GSH), and serum nitrite; and increased serum homocysteine and cholesterol levels. These effects were accompanied by decreased vascular NO bioavailability, marked intimal thickening of the aorta, and multiple necrotic foci in brain cortex. HHcy-induced alterations in the activities of SOD, CAT, GSH, AChE, LPO, behavioral deficits, ED, and histological aberrations were significantly attenuated by treatment with fisetin in a dose-dependent manner. Collectively, our results indicate that fisetin exerts endothelial and neuroprotective effects against HHcy-induced ED and VaD.

Flow profile measurement with multi-Mach probes on the HIST spherical torus device

NASA Astrophysics Data System (ADS)

Hashimoto, S.; Nishioka, T.; Ando, K.; Kikuchi, Y.; Fukumoto, N.; Nagata, M.

2008-11-01

Role of plasma flow during MHD relaxation and magnetic reconnection processes is still underlying physics. The HIST spherical torus can generate various spherical torus (ST) configurations by changing the external toroidal magnetic field. Especially, the flipped ST (F-ST) configuration has been for the first time found in the HIST device [1]. In the present study, plasma flow measurements were performed by multi-Mach probes in the ST and the F-ST configurations. In addition, the measured plasma flow was compared with that evaluated by an ion Doppler spectrometer (IDS) system and plasma images measured by a high-speed camera. As the result, it was shown that the toroidal plasma flow (˜ 20 km/s) at the location far from the plasma gun was clearly reversed after the transition from the ST to the F-ST. However, the direction of the toroidal flow was not changed near the plasma gun. Therefore, it can be considered that there are flipped and non-reversal regions in the plasma. The result agrees well with a magnetic configuration predicted by magnetic field measurements. The plasma images measured by the high-speed camera also indicated that a helically twisted structure appeared from the gun region, and it localized at the edge region. [1] M. Nagata et al., Phys. Rev. Lett. 90, pp. 225001-225004 (2003).

The BDNF Val66Met polymorphism regulates glucocorticoid-induced corticohippocampal remodeling and behavioral despair

PubMed Central

Notaras, M; Du, X; Gogos, J; van den Buuse, M; Hill, R A

2017-01-01

The BDNF Val66Met polymorphism has been associated with sensitivity to stress and affective disorders. We therefore sought to model the inter-causality of these relationships under controlled laboratory conditions. We subjected humanized BDNF Val66Met (hBDNFVal66Met) transgenic mice to a history of stress, modeled by chronic late-adolescent corticosterone (CORT) exposure, before evaluating affective-related behavior using the forced-swim test (FST) in adulthood. While hBDNFMet/Met mice had a depression-like phenotype in the FST irrespective of CORT, hBDNFVal/Val wildtype mice had a resilient phenotype but developed an equally robust depressive-like phenotype following CORT. A range of stress-sensitive molecules were studied across the corticohippocampal axis, and where genotype differences occurred following CORT they tended to inversely coincide with the behavior of the hBDNFVal/Val group. Notably, tyrosine hydroxylase was markedly down-regulated in the mPFC of hBDNFVal/Val mice as a result of CORT treatment, which mimicked expression levels of hBDNFMet/Met mice and the FST behavior of both groups. The expression of calretinin, PSD-95, and truncated TrkB were also concomitantly reduced in the mPFC of hBDNFVal/Val mice by CORT. This work establishes BDNFVal66Met genotype as a regulator of behavioral despair, and identifies new biological targets of BDNF genetic variation relevant to stress-inducible disorders such as depression. PMID:28926000

Differential Natural Selection of Human Zinc Transporter Genes between African and Non-African Populations

PubMed Central

Zhang, Chao; Li, Jing; Tian, Lei; Lu, Dongsheng; Yuan, Kai; Yuan, Yuan; Xu, Shuhua

2015-01-01

Zinc transporters play important roles in all eukaryotes by maintaining the rational zinc concentration in cells. However, the diversity of zinc transporter genes (ZTGs) remains poorly studied. Here, we investigated the genetic diversity of 24 human ZTGs based on the 1000 Genomes data. Some ZTGs show small population differences, such as SLC30A6 with a weighted-average FST (WA-FST = 0.015), while other ZTGs exhibit considerably large population differences, such as SLC30A9 (WA-FST = 0.284). Overall, ZTGs harbor many more highly population-differentiated variants compared with random genes. Intriguingly, we found that SLC30A9 was underlying natural selection in both East Asians (EAS) and Africans (AFR) but in different directions. Notably, a non-synonymous variant (rs1047626) in SLC30A9 is almost fixed with 96.4% A in EAS and 92% G in AFR, respectively. Consequently, there are two different functional haplotypes exhibiting dominant abundance in AFR and EAS, respectively. Furthermore, a strong correlation was observed between the haplotype frequencies of SLC30A9 and distributions of zinc contents in soils or crops. We speculate that the genetic differentiation of ZTGs could directly contribute to population heterogeneity in zinc transporting capabilities and local adaptations of human populations in regard to the local zinc state or diets, which have both evolutionary and medical implications. PMID:25927708

Characterization of G6PD Genotypes and Phenotypes on the Northwestern Thailand-Myanmar Border

PubMed Central

Somsakchaicharoen, Raweewan; Chowwiwat, Nongnud; Parker, Daniel M.; Charunwatthana, Prakaykaew; White, Nicholas J.; Nosten, François H.

2014-01-01

Mutations in the glucose-6-phosphate dehydrogenase (G6PD) gene result in red blood cells with increased susceptibility to oxidative damage. Significant haemolysis can be caused by primaquine and other 8-aminoquinoline antimalarials used for the radical treatment of Plasmodium vivax malaria. The distribution and phenotypes of mutations causing G6PD deficiency in the male population of migrants and refugees in a malaria endemic region on the Thailand-Myanmar border were characterized. Blood samples for G6PD fluorescent spot test (FST), G6PD genotyping, and malaria testing were taken from 504 unrelated males of Karen and Burman ethnicities presenting to the outpatient clinics. The overall frequency of G6PD deficiency by the FST was 13.7%. Among the deficient subjects, almost 90% had the Mahidol variant (487G>A) genotype. The remaining subjects had Chinese-4 (392G>T), Viangchan (871G>A), Açores (595A>G), Seattle (844G>C) and Mediterranean (563C>T) variants. Quantification of G6PD activity was performed using a modification of the standard spectrophotometric assay on a subset of 24 samples with Mahidol, Viangchan, Seattle and Chinese-4 mutations; all samples showed a residual enzymatic activity below 10% of normal and were diagnosed correctly by the FST. Further studies are needed to characterise the haemolytic risk of using 8-aminoquinolines in patients with these genotypes. PMID:25536053

Pollination Mode and Mating System Explain Patterns in Genetic Differentiation in Neotropical Plants

PubMed Central

Ballesteros-Mejia, Liliana; Lima, Natácia E.; Lima-Ribeiro, Matheus S.

2016-01-01

We studied genetic diversity and differentiation patterns in Neotropical plants to address effects of life history traits (LHT) and ecological attributes based on an exhaustive literature survey. We used generalized linear mixed models (GLMMs) to test the effects as fixed and random factors of growth form, pollination and dispersal modes, mating and breeding systems, geographical range and habitat on patterns of genetic diversity (HS, HeS, π and h), inbreeding coefficient (FIS), allelic richness (AR) and differentiation among populations (FST) for both nuclear and chloroplast genomes. In addition, we used phylogenetic generalized least squares (pGLS) to account for phylogenetic independence on predictor variables and verify the robustness of the results from significant GLMMs. In general, GLMM revealed more significant relationships among LHTs and genetic patterns than pGLS. After accounting for phylogenetic independence (i.e., using pGLS), FST for nuclear microsatellites was significantly related to pollination mode, mating system and habitat. Plants specifically with outcrossing mating system had lower FST. Moreover, AR was significantly related to pollination mode and geographical range and HeS for nuclear dominant markers was significantly related to habitat. Our findings showed that different results might be retrieved when phylogenetic non-independence is taken into account and that LHTs and ecological attributes affect substantially the genetic pattern in Neotropical plants, hence may drive key evolutionary processes in plants. PMID:27472384

The role of pregnenolone sulphate in spatial orientation-acquisition and retention: an interplay between cognitive potentiation and mood regulation.

PubMed

Plescia, Fulvio; Marino, Rosa A M; Cannizzaro, Emanuele; Brancato, Anna; Cannizzaro, Carla

2013-10-01

Neurosteroids can alter neuronal excitability interacting with specific neurotransmitter receptors, thus affecting several functions such as cognition and emotionality. In this study, we investigated, in adult male rats, the effects of the acute administration of pregnenolone-sulfate (PREGS) (10 mg/Kg, s.c.) on cognitive processes using the Can test, a non aversive spatial/visual task which allows the assessment of spatial information-acquisition during the baseline training, and of memory retention in the longitudinal study. Furthermore, on the basis of PREGS pharmacological profile, the modulation of depressive-like behaviour was also evaluated in the forced swim test (FST). Our results indicate that acute PREGS induces: an improvement in spatial orientation-acquisition and in reference memory, during the baseline training; a strengthening effect on reference and working memory during the longitudinal study. A decrease in immobility time in the FST has also been recorded. In conclusion, PREGS exerts enhancing properties on acquisition, consolidation and retrieval of spatial information, probably due of improved hippocampal-dependent memory processes. The additional antidepressant effect observed in the FST can provide further evidence in support of the potential of PREGS as a therapeutic tool for the treatment of cognitive deficits associated with mood disorders. This article is part of a Special Issue entitled: insert SI title. Copyright © 2013 Elsevier B.V. All rights reserved.

Conservation genetics of the eastern yellow-bellied racer (Coluber constrictor flaviventris) and bullsnake (Pituophis catenifer sayi): River valleys are critical features for snakes at northern range limits

PubMed Central

Graham, Carly F.; Martino, Jessica A.; Frasier, Timothy R.; Lance, Stacey L.; Gardiner, Laura E.; Poulin, Ray G.

2017-01-01

On the North American Great Plains, several snake species reach their northern range limit where they rely on sparsely distributed hibernacula located in major river valleys. Independent colonization histories for the river valleys and barriers to gene flow caused by the lack of suitable habitat between them may have produced genetically differentiated snake populations. To test this hypothesis, we used 10 microsatellite loci to examine the population structure of two species of conservation concern in Canada: the eastern yellow-bellied racer (Coluber constrictor flaviventris) and bullsnake (Pituophis catenifer sayi) in 3 major river valleys in southern Saskatchewan. Fixation indices (FST) showed that populations in river valleys were significantly differentiated for both species (racers, FST = 0.096, P = 0.001; bullsnakes FST = 0.045–0.157, P = 0.001). Bayesian assignment (STRUCTURE) and ordination (DAPC) strongly supported genetically differentiated groups in the geographically distinct river valleys. Finer-scale subdivision of populations within river valleys was not apparent based on our data, but is a topic that should be investigated further. Our findings highlight the importance of major river valleys for snakes at the northern extent of their ranges, and raise the possibility that populations in each river valley may warrant separate management strategies. PMID:29095863

Antidepressant-Like Activity of the Ethanolic Extract from Uncaria lanosa Wallich var. appendiculata Ridsd in the Forced Swimming Test and in the Tail Suspension Test in Mice

PubMed Central

Hsu, Lieh-Ching; Ko, Yu-Jen; Cheng, Hao-Yuan; Chang, Ching-Wen; Lin, Yu-Chin; Cheng, Ying-Hui; Hsieh, Ming-Tsuen; Peng, Wen Huang

2012-01-01

This study investigated the antidepressant activity of ethanolic extract of U. lanosa Wallich var. appendiculata Ridsd (ULEtOH) for two-weeks administrations by using FST and TST on mice. In order to understand the probable mechanism of antidepressant-like activity of ULEtOH in FST and TST, the researchers measured the levels of monoamines and monoamine oxidase activities in mice brain, and combined the antidepressant drugs (fluoxetine, imipramine, maprotiline, clorgyline, bupropion and ketanserin). Lastly, the researchers analyzed the content of RHY in the ULEtOH. The results showed that ULEtOH exhibited antidepressant-like activity in FST and TST in mice. ULEtOH increased the levels of 5-HT and 5-HIAA in cortex, striatum, hippocampus, and hypothalamus, the levels of NE and MHPG in cortex and hippocampus, the level of NE in striatum, and the level of DOPAC in striatum. Two-week injection of IMI, CLO, FLU and KET enhanced the antidepressant-like activity of ULEtOH. ULEtOH inhibited the activity of MAO-A. The amount of RHY in ULEtOH was 17.12 mg/g extract. Our findings support the view that ULEtOH exerts antidepressant-like activity. The antidepressant-like mechanism of ULEtOH may be related to the increase in monoamines levels in the hippocampus, cortex, striatum, and hypothalamus of mice. PMID:22567032

Why rate when you could compare? Using the “EloChoice” package to assess pairwise comparisons of perceived physical strength

PubMed Central

Howard, Kate L.; Woods, Andy T.; Penton-Voak, Ian S.; Neumann, Christof

2018-01-01

We introduce “EloChoice”, a package for R which uses Elo rating to assess pairwise comparisons between stimuli in order to measure perceived stimulus characteristics. To demonstrate the package and compare results from forced choice pairwise comparisons to those from more standard single stimulus rating tasks using Likert (or Likert-type) items, we investigated perceptions of physical strength from images of male bodies. The stimulus set comprised images of 82 men standing on a raised platform with minimal clothing. Strength-related anthropometrics and grip strength measurements were available for each man in the set. UK laboratory participants (Study 1) and US online participants (Study 2) viewed all images in both a Likert rating task, to collect mean Likert scores, and a pairwise comparison task, to calculate Elo, mean Elo (mElo), and Bradley-Terry scores. Within both studies, Likert, Elo and Bradley-Terry scores were closely correlated to mElo scores (all rs > 0.95), and all measures were correlated with stimulus grip strength (all rs > 0.38) and body size (all rs > 0.59). However, mElo scores were less variable than Elo scores and were hundreds of times quicker to compute than Bradley-Terry scores. Responses in pairwise comparison trials were 2/3 quicker than in Likert tasks, indicating that participants found pairwise comparisons to be easier. In addition, mElo scores generated from a data set with half the participants randomly excluded produced very comparable results to those produced with Likert scores from the full participant set, indicating that researchers require fewer participants when using pairwise comparisons. PMID:29293615

Multicriteria analysis of product operational effectiveness at design stages

NASA Astrophysics Data System (ADS)

Irzaev, G. Kh

2018-03-01

The multicriteria rapid assessment method of techno-economic parameters of new products is developed. It avoids expensive engineering changes during the operational stages through the analysis of external and internal factors at an early stage in the design that affect the maintainability and manufacturability of the product. The expert selection of the initial multitude of indicators from the five enlarged criteria groups and their subsequent pairwise comparison allow one to distinguish the complex compliance criteria of product design with the average and optimum values of the operational effectiveness. The values comparison provides an opportunity to decide on the continuation of the process for designing and preparation of the product manufacture.

Acute and joint toxicity of three agrochemicals to Chinese tiger frog (Hoplobatrachus chinensis) tadpoles.

PubMed

Wei, Li; Shao, Wei-Wei; Ding, Guo-Hua; Fan, Xiao-Li; Yu, Miao-Ling; Lin, Zhi-Hua

2014-07-01

We studied acute and joint toxicity of three different agrochemicals (chlorantraniliprole, flubendiamide-abamectin and penoxsulam) to Chinese tiger frog (Hoplobatrachus chinensis) tadpoles with the method of stability water tests. Results showed that the three agrochemicals increased tadpole mortality. For acute toxicity, the LC50 values after 24, 48 and 72 h of chlorantraniliprole, flubendiamide-abamectin and penoxsulam exposure were 5.37, 4.90 and 4.68 mg/L; 0.035, 0.025 and 0.021 mg/L; 1.74, 1.45 and 1.29 mg/L, respectively. The safety concentrations (SC) of chlorantraniliprole, flubendiamide-abamectin and penoxsulam to the tadpoles were 1.23, 0.30 and 0.003 mg/L, respectively. Based on these findings, chlorantraniliprole and penoxsulam were moderately toxic, while flubendiamide-abamectin was highly toxic. All pairwise joint toxicity tests showed moderate toxicity. The LC50 values after 24, 48 and 72 h of exposure were 7.08, 6.61 and 6.03 mg/L for chlorantraniliprole+penoxsulam, with corresponding values of 2.455, 2.328 and 2.183 mg/L for chlorantraniliprole+flubendiamide-abamectin, and 1.132, 1.084 and 1.050 mg/L for penoxsulam+flubendiamide-abamectin, with safe concentrations of 1.73, 0.63 and 0.30 mg/L, respectively. For toxic evaluations of pairwise combinations of the three agrochemicals, only the joint toxicity of chlorantraniliprole and flubendiamide-abamectin after 24 h was found to be synergistic, whereas all other tests were antagonistic. Our findings provide valuable information on the toxic effects of agrochemicals on amphibians and how various types of agrochemicals can be reasonably used in agricultural areas.

A Comparative Study of Pairwise Learning Methods Based on Kernel Ridge Regression.

PubMed

Stock, Michiel; Pahikkala, Tapio; Airola, Antti; De Baets, Bernard; Waegeman, Willem

2018-06-12

Many machine learning problems can be formulated as predicting labels for a pair of objects. Problems of that kind are often referred to as pairwise learning, dyadic prediction, or network inference problems. During the past decade, kernel methods have played a dominant role in pairwise learning. They still obtain a state-of-the-art predictive performance, but a theoretical analysis of their behavior has been underexplored in the machine learning literature. In this work we review and unify kernel-based algorithms that are commonly used in different pairwise learning settings, ranging from matrix filtering to zero-shot learning. To this end, we focus on closed-form efficient instantiations of Kronecker kernel ridge regression. We show that independent task kernel ridge regression, two-step kernel ridge regression, and a linear matrix filter arise naturally as a special case of Kronecker kernel ridge regression, implying that all these methods implicitly minimize a squared loss. In addition, we analyze universality, consistency, and spectral filtering properties. Our theoretical results provide valuable insights into assessing the advantages and limitations of existing pairwise learning methods.

Computer-Based Readability Testing of Information Booklets for German Cancer Patients.

PubMed

Keinki, Christian; Zowalla, Richard; Pobiruchin, Monika; Huebner, Jutta; Wiesner, Martin

2018-04-12

Understandable health information is essential for treatment adherence and improved health outcomes. For readability testing, several instruments analyze the complexity of sentence structures, e.g., Flesch-Reading Ease (FRE) or Vienna-Formula (WSTF). Moreover, the vocabulary is of high relevance for readers. The aim of this study is to investigate the agreement of sentence structure and vocabulary-based (SVM) instruments. A total of 52 freely available German patient information booklets on cancer were collected from the Internet. The mean understandability level L was computed for 51 booklets. The resulting values of FRE, WSTF, and SVM were assessed pairwise for agreement with Bland-Altman plots and two-sided, paired t tests. For the pairwise comparison, the mean L values are L FRE  = 6.81, L WSTF  = 7.39, L SVM  = 5.09. The sentence structure-based metrics gave significantly different scores (P < 0.001) for all assessed booklets, confirmed by the Bland-Altman analysis. The study findings suggest that vocabulary-based instruments cannot be interchanged with FRE/WSTF. However, both analytical aspects should be considered and checked by authors to linguistically refine texts with respect to the individual target group. Authors of health information can be supported by automated readability analysis. Health professionals can benefit by direct booklet comparisons allowing for time-effective selection of suitable booklets for patients.

Synthesis of 2,4-dihydroxychalcone derivatives as potential antidepressant effect.

PubMed

Guan, L-P; Zhao, D-H; Chang, Y; Wen, Z-S; Tang, L-M; Huang, F-F

2013-01-01

In this study, twelve 2,4-dihydroxychalcone derivatives were synthesized and evaluated for antidepressant activities using the forced swimming test (FST). The pharmacological test showed that 6 compounds significantly reduced the immobility times in the FST at a dose of 10 mg/kg, indicative of antidepressant activity. Among the derivatives, compounds designated 3d and 3 h exhibited the best antidepressant activity, with reduced immobility time by 32.05% and 34.33%, respectively. In the 5-hydroxytryptophan-induced head-twitch test and yohimbine-induced mortality test, compounds 3d and 3 h increased head-twitch and increased the mortality rate. The mechanisms of the antidepressant effects of compounds 3d and 3 h may be related with the 5-HTP and NE nervous system. © Georg Thieme Verlag KG Stuttgart · New York.

Structural Features and Potent Antidepressant Effects of Total Sterols and β-sitosterol Extracted from Sargassum horneri

PubMed Central

Zhao, Donghai; Zheng, Lianwen; Qi, Ling; Wang, Shuran; Guan, Liping; Xia, Yanan; Cai, Jianhui

2016-01-01

The purified total sterols and β-sitosterol extracted from Sargassum horneri were evaluated for their antidepressant-like activity using the forced swim test (FST) and tail suspension test (TST) in mice. Total sterols and β-sitosterol significantly reduced the immobility time in the FST and TST. Total sterols were administered orally for 7 days at doses of 50, 100, and 200 mg/kg, and β-sitosterol was administered intraperitoneally at doses of 10, 20, and 30 mg/kg. β-sitosterol had no effect on locomotor activity in the open field test. In addition, total sterols and β-sitosterol significantly increased NE, 5-HT, and the metabolite 5-HIAA in the mouse brain, suggesting that the antidepressant-like activity may be mediated through these neurotransmitters. PMID:27367705

Structural Features and Potent Antidepressant Effects of Total Sterols and β-sitosterol Extracted from Sargassum horneri.

PubMed

Zhao, Donghai; Zheng, Lianwen; Qi, Ling; Wang, Shuran; Guan, Liping; Xia, Yanan; Cai, Jianhui

2016-06-28

The purified total sterols and β-sitosterol extracted from Sargassum horneri were evaluated for their antidepressant-like activity using the forced swim test (FST) and tail suspension test (TST) in mice. Total sterols and β-sitosterol significantly reduced the immobility time in the FST and TST. Total sterols were administered orally for 7 days at doses of 50, 100, and 200 mg/kg, and β-sitosterol was administered intraperitoneally at doses of 10, 20, and 30 mg/kg. β-sitosterol had no effect on locomotor activity in the open field test. In addition, total sterols and β-sitosterol significantly increased NE, 5-HT, and the metabolite 5-HIAA in the mouse brain, suggesting that the antidepressant-like activity may be mediated through these neurotransmitters.

Fast and accurate estimation of the covariance between pairwise maximum likelihood distances.

PubMed

Gil, Manuel

2014-01-01

Pairwise evolutionary distances are a model-based summary statistic for a set of molecular sequences. They represent the leaf-to-leaf path lengths of the underlying phylogenetic tree. Estimates of pairwise distances with overlapping paths covary because of shared mutation events. It is desirable to take these covariance structure into account to increase precision in any process that compares or combines distances. This paper introduces a fast estimator for the covariance of two pairwise maximum likelihood distances, estimated under general Markov models. The estimator is based on a conjecture (going back to Nei & Jin, 1989) which links the covariance to path lengths. It is proven here under a simple symmetric substitution model. A simulation shows that the estimator outperforms previously published ones in terms of the mean squared error.

Fast and accurate estimation of the covariance between pairwise maximum likelihood distances

PubMed Central

2014-01-01

Pairwise evolutionary distances are a model-based summary statistic for a set of molecular sequences. They represent the leaf-to-leaf path lengths of the underlying phylogenetic tree. Estimates of pairwise distances with overlapping paths covary because of shared mutation events. It is desirable to take these covariance structure into account to increase precision in any process that compares or combines distances. This paper introduces a fast estimator for the covariance of two pairwise maximum likelihood distances, estimated under general Markov models. The estimator is based on a conjecture (going back to Nei & Jin, 1989) which links the covariance to path lengths. It is proven here under a simple symmetric substitution model. A simulation shows that the estimator outperforms previously published ones in terms of the mean squared error. PMID:25279263

Detecting epistasis with the marginal epistasis test in genetic mapping studies of quantitative traits

PubMed Central

Zeng, Ping; Mukherjee, Sayan; Zhou, Xiang

2017-01-01

Epistasis, commonly defined as the interaction between multiple genes, is an important genetic component underlying phenotypic variation. Many statistical methods have been developed to model and identify epistatic interactions between genetic variants. However, because of the large combinatorial search space of interactions, most epistasis mapping methods face enormous computational challenges and often suffer from low statistical power due to multiple test correction. Here, we present a novel, alternative strategy for mapping epistasis: instead of directly identifying individual pairwise or higher-order interactions, we focus on mapping variants that have non-zero marginal epistatic effects—the combined pairwise interaction effects between a given variant and all other variants. By testing marginal epistatic effects, we can identify candidate variants that are involved in epistasis without the need to identify the exact partners with which the variants interact, thus potentially alleviating much of the statistical and computational burden associated with standard epistatic mapping procedures. Our method is based on a variance component model, and relies on a recently developed variance component estimation method for efficient parameter inference and p-value computation. We refer to our method as the “MArginal ePIstasis Test”, or MAPIT. With simulations, we show how MAPIT can be used to estimate and test marginal epistatic effects, produce calibrated test statistics under the null, and facilitate the detection of pairwise epistatic interactions. We further illustrate the benefits of MAPIT in a QTL mapping study by analyzing the gene expression data of over 400 individuals from the GEUVADIS consortium. PMID:28746338

The antidepressant-like effect of 7-fluoro-1,3-diphenylisoquinoline-1-amine in the mouse forced swimming test is mediated by serotonergic and dopaminergic systems.

PubMed

Pesarico, Ana Paula; Sampaio, Tuane Bazanella; Stangherlin, Eluza Curte; Mantovani, Anderson C; Zeni, Gilson; Nogueira, Cristina Wayne

2014-10-03

The aim of the present study was to investigate the role of monoaminergic system in the antidepressant-like action of 7-fluoro-1,3-diphenylisoquinoline-1-amine (FDPI), a derivative of isoquinoline class, in Swiss mice. The antidepressant-like effect of FDPI was characterized in the modified forced swimming test (FST) and the possible mechanism of action was investigated by using serotonergic, dopaminergic and noradrenergic antagonists. Monoamine oxidase (MAO) activity and [(3)H]serotonin (5-HT) uptake were determined in prefrontal cortices of mice. The results showed that FDPI (1, 10 and 20mg/kg, i.g.) reduced the immobility time and increased the swimming time but did not alter climbing time in the modified FST. These effects were similar to those of paroxetine (8mg/kg, i.p.), a positive control. Pretreatments with p-chlorophenylalanine (100mg/kg, i.p., an inhibitor of 5-HT synthesis), WAY100635 (0.1mg/kg, s.c., 5-HT1A antagonist), ondansetron (1mg/kg, i.p., a 5-HT3 receptor antagonist), haloperidol (0.2mg/kg, i.p., a non-selective D2 receptor antagonist) and SCH23390 (0.05mg/kg, s.c., a D1 receptor antagonist) were effective to block the antidepressant-like effect of FDPI at a dose of 1mg/kg in the FST. Ritanserin (1mg/kg, i.p., a 5-HT2A/2C receptor antagonist), sulpiride (50mg/kg, i.p., a D2 and D3 receptor antagonist), prazosin (1mg/kg, i.p., an α1 receptor antagonist), yohimbine (1mg/kg, i.p., an α2 receptor antagonist) and propranolol (2mg/kg, i.p., a β receptor antagonist) did not modify the effect of FDPI in the FST. FDPI did not change synaptosomal [(3)H]5-HT uptake. At doses of 10 and 20mg/kg FDPI inhibited MAO-A and MAO-B activities. These results suggest that antidepressant-like effect of FDPI is mediated mostly by serotonergic and dopaminergic systems. Copyright © 2014 Elsevier Inc. All rights reserved.

Effects of interaction of an early experience of reward through maternal contact or its denial with social stress during adolescence on the serotonergic system and the stress responsiveness of adult female rats.

PubMed

Raftogianni, A; Diamantopoulou, A; Alikaridis, F; Stamatakis, A; Stylianopoulou, F

2012-05-03

Experiences during critical periods, such as the neonatal and adolescence, play a critical role in determining adult stress-coping behavior. Based on the aforementioned we developed an experimental protocol, which included a neonatal experience and a social stress during adolescence. The serotonergic system is known as an important modulator of coping ability and, in general, emotional balance in both normal and pathological states, such as depression and anxiety, for which females are more vulnerable. Thus in the present work we used female rats and determined 5-HT, 5-hydroxyindoleacetic acid (5-HIAA), and 5-hydroxytryptamine receptor type 1A (5-HT(1A)) receptor levels in the prefrontal cortex (PFC) and the amygdala (AMY). During postnatal days 10-13 (PND 10-13) rat pups were exposed to a T-maze, one arm of which lead to the mother. One group of animals was allowed contact with the mother (rewarded-receiving expected reward (RER)), whereas the other was denied the expected reward (DER). High performance liquid chromatography (HPLC) analysis revealed that in both the PFC and in AMY, adult RER animals had higher basal 5-HT levels. Furthermore, in the AMY of this group of animals, higher levels of 5-HT(1A) receptors were detected by Western blot analysis. In adulthood rats were exposed to the Forced Swimming Test/Stress (FST/S). RER animals not exposed to the adolescent stress exhibited longer immobility time during both the first and second day of FST. Corticosterone levels following the FST fell faster in the DER animals. Adolescent stress affected the responses to the adult FSS only in the DER animals, which had decreased 5-HT in the AMY and increased immobility time on both days of the FST, compared with the DER, not stressed in adolescence. The phenotype of the DER animals is in line with the "match-mismatch" hypothesis, which states that if two events during critical periods of life "match" in being mildly stressful, their interaction can be adaptive. Copyright © 2012 IBRO. Published by Elsevier Ltd. All rights reserved.

Migratory culture, population structure and stock identity in North Pacific beluga whales (Delphinapterus leucas)

PubMed Central

Suydam, Robert; Quakenbush, Lori; Potgieter, Brooke; Harwood, Lois; Litovka, Dennis; Ferrer, Tatiana; Citta, John; Burkanov, Vladimir; Frost, Kathy; Mahoney, Barbara

2018-01-01

The annual return of beluga whales, Delphinapterus leucas, to traditional seasonal locations across the Arctic may involve migratory culture, while the convergence of discrete summering aggregations on common wintering grounds may facilitate outbreeding. Natal philopatry and cultural inheritance, however, has been difficult to assess as earlier studies were of too short a duration, while genetic analyses of breeding patterns, especially across the beluga’s Pacific range, have been hampered by inadequate sampling and sparse information on wintering areas. Using a much expanded sample and genetic marker set comprising 1,647 whales, spanning more than two decades and encompassing all major coastal summering aggregations in the Pacific Ocean, we found evolutionary-level divergence among three geographic regions: the Gulf of Alaska, the Bering-Chukchi-Beaufort Seas, and the Sea of Okhotsk (Φst = 0.11–0.32, Rst = 0.09–0.13), and likely demographic independence of (Fst-mtDNA = 0.02–0.66), and in many cases limited gene flow (Fst-nDNA = 0.0–0.02; K = 5–6) among, summering groups within regions. Assignment tests identified few immigrants within summering aggregations, linked migrating groups to specific summering areas, and found that some migratory corridors comprise whales from multiple subpopulations (PBAYES = 0.31:0.69). Further, dispersal is male-biased and substantial numbers of closely related whales congregate together at coastal summering areas. Stable patterns of heterogeneity between areas and consistently high proportions (~20%) of close kin (including parent-offspring) sampled up to 20 years apart within areas (G = 0.2–2.9, p>0.5) is the first direct evidence of natal philopatry to migration destinations in belugas. Using recent satellite telemetry findings on belugas we found that the spatial proximity of winter ranges has a greater influence on the degree of both individual and genetic exchange than summer ranges (rwinter-Fst-mtDNA = 0.9, rsummer-Fst-nDNA = 0.1). These findings indicate widespread natal philopatry to summering aggregation and entire migratory circuits, and provide compelling evidence that migratory culture and kinship helps maintain demographically discrete beluga stocks that can overlap in time and space. PMID:29566001

Two standardized fractions of Gardenia jasminoides Ellis with rapid antidepressant effects are differentially associated with BDNF up-regulation in the hippocampus.

PubMed

Ren, Li; Tao, Weiwei; Zhang, Hailou; Xue, Wenda; Tang, Juanjuan; Wu, Ruyan; Xia, Baomei; Wu, Haoxing; Chen, Gang

2016-07-01

Gardenia jasminoides Ellis (GJ) is one of the five constituents of Yueju pill, a Traditional Chinese Medicine for treatment of syndromes associated with mood disorders. Recently, preclinical and clinical studies suggest that Yueju pill confers rapid antidepressant effects. GJ is identified as the constituent primary for Yueju pill's rapid antidepressant effects. GJ's antidepressant action is temporally associated with up-regulated expression of brain-derived neurotrophic factor (BDNF) in the hippocampus. The present study aimed to identify chemical fractions responsible for the rapid antidepressant efficacy of GJ and its association with BDNF signaling. Four fractions of GJ were extracted using standardized procedure. The four fractions were screened for rapid antidepressant potential, using the behavioral paradigm of forced swimming test (FST) and tail suspension test (TST) assessed at 24h post a single administration. A single dose of the putatively effective fractions was further tested in mice exposed to chronic mild stress (CMS), followed with a comprehensive behavioral testing including TST, FST, sucrose preference test (SPT), and novelty suppressed-feeding (NSF). To test the association of BDNF signaling with rapid antidepressant effects of effective factions, the expressions of BDNF and its receptor tropomyosin receptor kinase B (TrkB) in the hippocampus were assessed at different times post a single administration of effective fractions. Both petroleum ether (GJ-PE) and n-butyl alcohol fraction (GJ-BO) fractions of GJ displayed rapid antidepressant potential in the FST. In the TST, the antidepressant effects of GJ-PE lasted for a longer time than GJ-BO. Acute administration of either GJ-PE or GJ-BO significantly reversed the behavioral deficits in the tests of TST, FST, SPT and NSF in chronically stressed mice, confirming both fractions conferred rapid antidepressant efficacy. Interestingly, GJ-PE, but not GJ-BO, increased the expression of BDNF and TrkB in the hippocampus post a single administration. Two standardized fractions GJ-PE and GJ-BO exhibited comparable rapid antidepressant-like effects on the CMS mice. However, only the effects of GJ-PE was associated with BDNF signaling. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.