Note: This page contains sample records for the topic showed high genetic from Science.gov.
While these samples are representative of the content of Science.gov,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of Science.gov
to obtain the most current and comprehensive results.
Last update: November 12, 2013.
1

Batrachochytrium dendrobatidis shows high genetic diversity and ecological niche specificity among haplotypes in the Maya Mountains of Belize.  

PubMed

The amphibian pathogen Batrachochytrium dendrobatidis (Bd) has been implicated in amphibian declines around the globe. Although it has been found in most countries in Central America, its presence has never been assessed in Belize. We set out to determine the range, prevalence, and diversity of Bd using quantitative PCR (qPCR) and sequencing of a portion of the 5.8 s and ITS1-2 regions. Swabs were collected from 524 amphibians of at least 26 species in the protected areas of the Maya Mountains of Belize. We sequenced a subset of 72 samples that had tested positive for Bd by qPCR at least once; 30 samples were verified as Bd. Eight unique Bd haplotypes were identified in the Maya Mountains, five of which were previously undescribed. We identified unique ecological niches for the two most broadly distributed haplotypes. Combined with data showing differing virulence shown in different strains in other studies, the 5.8 s - ITS1-2 region diversity found in this study suggests that there may be substantial differences among populations or haplotypes. Future work should focus on whether specific haplotypes for other genomic regions and possibly pathogenicity can be associated with haplotypes at this locus, as well as the integration of molecular tools with other ecological tools to elucidate the ecology and pathogenicity of Bd. PMID:22389681

Kaiser, Kristine; Pollinger, John

2012-02-28

2

Plasmodium vivax isolates from Cambodia and Thailand show high genetic complexity and distinct patterns of P. vivax multidrug resistance gene 1 (pvmdr1) polymorphisms.  

PubMed

Plasmodium vivax accounts for an increasing fraction of malaria infections in Thailand and Cambodia. We compared P. vivax genetic complexity and antimalarial resistance patterns in the two countries. Use of a heteroduplex tracking assay targeting the merozoite surface protein 1 gene revealed that vivax infections in both countries are frequently polyclonal (84%), with parasites that are highly diverse (HE = 0.86) but closely related (GST = 0.18). Following a history of different drug policies in Thailand and Cambodia, distinct patterns of antimalarial resistance have emerged: most Cambodian isolates harbor the P. vivax multidrug resistance gene 1 (pvmdr1) 976F mutation associated with chloroquine resistance (89% versus 8%, P < 0.001), whereas Thai isolates more often display increased pvmdr1 copy number (39% versus 4%, P < 0.001). Finally, genotyping of paired isolates from individuals suspected of suffering relapse supports a complex scheme of relapse whereby recurrence of multiple identical variants is sometimes accompanied by the appearance of novel variants. PMID:23509126

Lin, Jessica T; Patel, Jaymin C; Kharabora, Oksana; Sattabongkot, Jetsumon; Muth, Sinuon; Ubalee, Ratawan; Schuster, Anthony L; Rogers, William O; Wongsrichanalai, Chansuda; Juliano, Jonathan J

2013-03-18

3

Intracortical bone remodeling variation shows strong genetic effects.  

PubMed

Intracortical microstructure influences crack propagation and arrest within bone cortex. Genetic variation in intracortical remodeling may contribute to mechanical integrity and, therefore, fracture risk. Our aim was to determine the degree to which normal population-level variation in intracortical microstructure is due to genetic variation. We examined right femurs from 101 baboons (74 females, 27 males; aged 7-33 years) from a single, extended pedigree to determine osteon number, osteon area (On.Ar), haversian canal area, osteon population density, percent osteonal bone (%On.B), wall thickness (W.Th), and cortical porosity (Ct.Po). Through evaluation of the covariance in intracortical properties between pairs of relatives, we quantified the contribution of additive genetic effects (heritability [h (2)]) to variation in these traits using a variance decomposition approach. Significant age and sex effects account for 9 % (Ct.Po) to 21 % (W.Th) of intracortical microstructural variation. After accounting for age and sex, significant genetic effects are evident for On.Ar (h (2) = 0.79, p = 0.002), %On.B (h (2) = 0.82, p = 0.003), and W.Th (h (2) = 0.61, p = 0.013), indicating that 61-82 % of the residual variation (after accounting for age and sex effects) is due to additive genetic effects. This corresponds to 48-75 % of the total phenotypic variance. Our results demonstrate that normal, population-level variation in cortical microstructure is significantly influenced by genes. As a critical mediator of crack behavior in bone cortex, intracortical microstructural variation provides another mechanism through which genetic variation may affect fracture risk. PMID:23979114

Havill, L M; Allen, M R; Harris, J A K; Levine, S M; Coan, H B; Mahaney, M C; Nicolella, D P

2013-08-27

4

High Points of Human Genetics  

ERIC Educational Resources Information Center

Discusses such high points of human genetics as the study of chromosomes, somatic cell hybrids, the population formula: the Hardy-Weinberg Law, biochemical genetics, the single-active X Theory, behavioral genetics and finally how genetics can serve humanity. (BR)

Stern, Curt

1975-01-01

5

High Points of Human Genetics  

ERIC Educational Resources Information Center

|Discusses such high points of human genetics as the study of chromosomes, somatic cell hybrids, the population formula: the Hardy-Weinberg Law, biochemical genetics, the single-active X Theory, behavioral genetics and finally how genetics can serve humanity. (BR)|

Stern, Curt

1975-01-01

6

Genetics and high cognitive ability.  

PubMed

More is known about the genetics of general cognitive ability (g) than any other trait in psychology. Recent findings on the genetics of g include the following three examples: (1) heritability increases throughout the lifespan; (2) heritabilities of performance in cognitive tests are strongly correlated with the tests' loadings on a g factor; and (3) genetic effects on scholastic achievement largely overlap with genetic effects on cognitive ability. This body of genetic research addresses the aetiology of individual differences in the normal range. Much less is known about the genetics of the high end of the distribution. Finding heritability in the normal range of cognitive ability does not imply that high ability is also genetic in origin. However, the first twin study of high IQ children, which uses a new technique that analyses the average difference between extreme groups and the rest of the population, suggests that high IQ is as heritable as individual differences in the normal range. We are currently engaged in a molecular genetic study that attempts to identify specific genes that contribute to high ability. PMID:8168371

Plomin, R; Thompson, L A

1993-01-01

7

Multilocus Phylogenetics Show High Intraspecific Variability within Fusarium avenaceum  

PubMed Central

Fusarium avenaceum is a common soil saprophyte and plant pathogen of a variety of hosts worldwide. This pathogen is often involved in the crown rot and head blight of cereals that affects grain yield and quality. F. avenaceum contaminates grain with enniatins more than any species, and they are often detected at the highest prevalence among fusarial toxins in certain geographic areas. We studied intraspecific variability of F. avenaceum based on partial sequences of elongation factor-1 alpha, enniatin synthase, intergenic spacer of rDNA, arylamine N-acetyltransferase and RNA polymerase II data sets. The phylogenetic analyses incorporated a collection of 63 F. avenaceum isolates of various origin among which 41 were associated with wheat. Analyses of the multilocus sequence (MLS) data indicated a high level of genetic variation within the isolates studied with no significant linkage disequilibrium. Correspondingly, maximum parsimony analyses of both MLS and individual data sets showed lack of clear phylogenetic structure within F. avenaceum in relation to host (wheat) and geographic origin. Lack of host specialization indicates no host selective pressure in driving F. avenaceum evolution, while no geographic lineage structure indicates widespread distribution of genotypes that resulted in nullifying the effects of geographic isolation on the evolution of this species. Moreover, significant incongruence between all individual tree topologies and little clonality is consistent with frequent recombination within F. avenaceum.

Kulik, Tomasz; Pszczolkowska, Agnieszka; Lojko, Maciej

2011-01-01

8

5. View showing Crooked River High Bridge in background and ...  

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

5. View showing Crooked River High Bridge in background and Ralph Modjeski railroad bridge in foreground - Crooked River High Bridge, Spanning Crooked River Gorge at Dalles-California Highway, Terrebonne, Deschutes County, OR

9

20. SOUTH ELEVATION, SHOWING ORIGINAL HIGH VOLTAGE GETAWAYS. SCE negative ...  

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

20. SOUTH ELEVATION, SHOWING ORIGINAL HIGH VOLTAGE GETAWAYS. SCE negative no. 10340, November 1, 1923. Photograph by G. Haven Bishop. - Santa Ana River Hydroelectric System, SAR-3 Powerhouse, San Bernardino National Forest, Redlands, San Bernardino County, CA

10

Added Value Measures in Education Show Genetic as Well as Environmental Influence  

PubMed Central

Does achievement independent of ability or previous attainment provide a purer measure of the added value of school? In a study of 4000 pairs of 12-year-old twins in the UK, we measured achievement with year-long teacher assessments as well as tests. Raw achievement shows moderate heritability (about 50%) and modest shared environmental influences (25%). Unexpectedly, we show that for indices of the added value of school, genetic influences remain moderate (around 50%), and the shared (school) environment is less important (about 12%). The pervasiveness of genetic influence in how and how much children learn is compatible with an active view of learning in which children create their own educational experiences in part on the basis of their genetic propensities.

Haworth, Claire M. A.; Asbury, Kathryn; Dale, Philip S.; Plomin, Robert

2011-01-01

11

The neonicotinoid imidacloprid shows high chronic toxicity to mayfly nymphs.  

PubMed

The present study evaluated the acute and chronic toxicity of imidacloprid to a range of freshwater arthropods. Mayfly and caddisfly species were most sensitive to short-term imidacloprid exposures (10 tests), whereas the mayflies showed by far the most sensitive response to long-term exposure of all seven arthropod species tested (28-d EC10 values of approximately 0.03?µg/L). The results indicated a high aquatic risk of chronic exposure of imidacloprid to mayflies. PMID:23444274

Roessink, Ivo; Merga, Lemessa B; Zweers, Hans J; Van den Brink, Paul J

2013-04-03

12

Human genetic affinities for Y-chromosome P49a,f/TaqI haplotypes show strong correspondence with linguistics.  

PubMed Central

Numerous population samples from around the world have been tested for Y chromosome-specific p49a,f/TaqI restriction polymorphisms. Here we review the literature as well as unpublished data on Y-chromosome p49a,f/TaqI haplotypes and provide a new nomenclature unifying the notations used by different laboratories. We use this large data set to study worldwide genetic variability of human populations for this paternally transmitted chromosome segment. We observe, for the Y chromosome, an important level of population genetics structure among human populations (FST = .230, P < .001), mainly due to genetic differences among distinct linguistic groups of populations (FCT = .246, P < .001). A multivariate analysis based on genetic distances between populations shows that human population structure inferred from the Y chromosome corresponds broadly to language families (r = .567, P < .001), in agreement with autosomal and mitochondrial data. Times of divergence of linguistic families, estimated from their internal level of genetic differentiation, are fairly concordant with current archaeological and linguistic hypotheses. Variability of the p49a,f/TaqI polymorphic marker is also significantly correlated with the geographic location of the populations (r = .613, P < .001), reflecting the fact that distinct linguistic groups generally also occupy distinct geographic areas. Comparison of Y-chromosome and mtDNA RFLPs in a restricted set of populations shows a globally high level of congruence, but it also allows identification of unequal maternal and paternal contributions to the gene pool of several populations.

Poloni, E S; Semino, O; Passarino, G; Santachiara-Benerecetti, A S; Dupanloup, I; Langaney, A; Excoffier, L

1997-01-01

13

Genetic correlations between horse show jumping competition traits in five European countries  

Microsoft Academic Search

Genetic correlations were computed for show jumping competition traits from national estimated breeding values (EBV) of stallions of five countries: Belgium, Denmark, France, Ireland and Sweden. Data involved 24,390 horses, i.e. 8993 stallions with EBV and their ancestors. There were 617 stallions with several EBVs in more than one country. Method involved MACE (Multi-Trait Across Country Evaluation) methodology based on

C. Ruhlmann; S. Janssens; J. Philipsson; E. Thorén-Hellsten; H. Crolly; K. Quinn; E. Manfredi; A. Ricard

2009-01-01

14

Genetically obese mice do not show increased gut permeability or faecal bile acid hydrophobicity.  

PubMed

Gut barrier dysfunction may lead to metabolic endotoxaemia and low-grade inflammation. Recent publications have demonstrated gut barrier dysfunction in obesity induced by a diet high in fat, and a pathogenetic role for luminal bile acids has been proposed. We aimed to investigate whether genetically obese mice develop increased gut permeability and alterations in luminal bile acids on a diet with a regular fat content. We used seven obese male ob/ob mice of C57BL/6J background and ten male wild-type (WT) mice of the same strain. Faeces were collected for bile acid analysis. Intestinal permeability was measured in an Ussing chamber upon euthanasia, using 4 kDa fluorescein isothiocyanate dextran, as per mille (‰, 1/1000) of translocated dextran. We analysed the liver expression of lipopolysaccharide-binding protein (LBP), as well as serum LBP (ELISA). Intestinal permeability was not affected by genetic obesity (jejunum: 0·234 (sem 0·04) ‰ for obese v. 0·225 (sem 0·03) ‰ for WT, P= 0·93; colon: 0·222 (sem 0·06) ‰ for obese v. 0·184 (sem 0·03) ‰ for WT, P= 0·86), nor was liver LBP expression (relative expression: 0·55 (sem 0·08) for obese v. 0·55 (sem 0·13) for WT, P= 0·70). Serum LBP was 2·5-fold higher in obese than in WT mice (P= 0·001). Obese mice had increased daily excretion of total bile acids, but their faecal bile acid hydrophobicity was unchanged. In conclusion, genetic obesity did not impair gut barrier function in mice on a regular chow diet, nor was faecal bile acid hydrophobicity affected. PMID:23442231

Stenman, Lotta K; Holma, Reetta; Gylling, Helena; Korpela, Riitta

2013-02-26

15

Introducing High School Students to Human Genetics.  

ERIC Educational Resources Information Center

Considers six key concepts in human genetics in a question-and-answer format designed to help guide students to an understanding of the concept. Lists eight workshops in human genetics for high school biology teachers and four curriculum material packages on human genetics. (CW)

Haddow, Paula K.; And Others

1988-01-01

16

Introducing High School Students to Human Genetics.  

ERIC Educational Resources Information Center

|Considers six key concepts in human genetics in a question-and-answer format designed to help guide students to an understanding of the concept. Lists eight workshops in human genetics for high school biology teachers and four curriculum material packages on human genetics. (CW)|

Haddow, Paula K.; And Others

1988-01-01

17

Genetic marking of Lactococcus lactis shows its survival in the human gastrointestinal tract.  

PubMed Central

A human feeding study was performed with Lactococcus lactis TC165.5, which is genetically marked by insertion of the sucrose-nisin conjugative transposon Tn5276 and chromosomal resistance to rifampin and streptomycin. The fate of strain TC165.5 and its nucleic acids was monitored by conventional plating methods and by molecular detection techniques based on specific PCR amplification of the nisin (nisA) gene from DNA extracted from human feces. A method was developed for the efficient extraction of microbial DNA from human feces. The results show that a fraction of viable cells of L. lactis TC165.5 survived passage through the human gastrointestinal tract. Only cells that passed within 3 days of ingestion could be recovered from the feces of the volunteers, and they accounted for approximately 1% of the total number of cells consumed. The presence of nisA in DNA extracted from feces could be detected up to 4 days, when viable cells were no longer present.

Klijn, N; Weerkamp, A H; de Vos, W M

1995-01-01

18

Natural Selection and Evolution: Using Multimedia Slide Shows to Emphasize the Role of Genetic Variation  

ERIC Educational Resources Information Center

|Most middle school students comprehend that organisms have adaptations that enable their survival and that successful adaptations prevail in a population over time. Yet they often miss that those bird beaks, moth-wing colors, or whatever traits are the result of random, normal genetic variations that just happen to confer a negative, neutral, or…

Malone, Molly

2012-01-01

19

Genetic and morphological patterns show variation in frequency of hybrids between Ipomopsis (Polemoniaceae) zones of sympatry  

Microsoft Academic Search

Variation in rates of hybridization among zones of sympatry between a pair of species provides a useful window into the effect of local conditions on the evolution of reproductive isolation. We employed floral morphological traits and neutral genetic markers to quantify the frequency of individuals intermediate to the two parental species in two zones of sympatry between Ipomopsis aggregata and

G Aldridge; D R Campbell

2009-01-01

20

Genetic Marking ofLactococcus lactisShows Its Survival in the Human Gastrointestinal Tract  

Microsoft Academic Search

A human feeding study was performed with Lactococcus lactis TC165.5, which is genetically marked by insertion of the sucrose-nisin conjugative transposon Tn5276 and chromosomal resistance to rifampin and streptomycin. The fate of strain TC165.5 and its nucleic acids was monitored by conventional plating methods and by molecular detection techniques based on specific PCR amplification of the nisin (nisA) gene from

NICOLETTE KLIJN; ANTON H. WEERKAMP; ANDWILLEM M. DEVOS

1995-01-01

21

Genetic erosion in habitat specialist shows need to protect large peat bogs  

Microsoft Academic Search

The specialized fauna of peat bogs declines strongly both in species numbers and population density and becomes fragmented\\u000a because of anthropogenic land use changes. We investigated 15 populations of the stenotopic ground beetle species Agonum ericeti in south Sweden to address the question of reduced genetic variability in populations inhabiting smaller habitat patches.\\u000a Our results reveal a generally low differentiation

Claudia Drees; Pascale Zumstein; Thorsten Buck-Dobrick; Werner Härdtle; Andrea Matern; Hartmut Meyer; Goddert von Oheimb; Thorsten Assmann

22

Genetic analysis of an isolated red deer ( Cervus elaphus ) population showing signs of inbreeding depression  

Microsoft Academic Search

In the present study, we analysed 18 red deer specimens from a small (N?=?50) and isolated population in Schleswig-Holstein, northern Germany, with respect to variability at nine polymorphic microsatellite\\u000a loci and 439 bp of the mitochondrial DNA control region. Several cases of brachygnathy (shortened lower jaw), commonly associated\\u000a with inbreeding depression, have been recorded in the population. Genetic variability was very

F. E. Zachos; C. Althoff; Y. v. Steynitz; I. Eckert; G. B. Hartl

2007-01-01

23

Primary tumour genetic alterations and intra-tumoral heterogeneity are maintained in xenografts of human colon cancers showing chromosome instability.  

PubMed

Evaluation of the role of clonal heterogeneity in colon tumour sensitivity/resistance to drugs and/or in conferring metastatic potential requires an adequate experimental model in which the tumour cells maintain the initial genetic alterations and intra-tumoral heterogeneity through maintenance of the genetic clones present in the initial tumour. Therefore, we xenografted subcutaneously into nude mice seven human colonic tumours (from stages B1 to D) that showed chromosome instability and transplanted them sequentially for up to 14 passages. Maintenance after xenografting of the genetic alterations present in the initial tumours was scored by allelotype studies targeting 45 loci localized on 18 chromosomes. We show that xenografting does not alter the genetic or the histological profiles of the tumours even after 14 passages. Screening of the entire genome of one tumour by comparative genome hybridization also showed overall stability of the alterations between the initial and the xenografted tumour. In addition, intra-tumoral heterogeneity was maintained over time, suggesting that no clonal selection occurred in the nude mice. The observation that some loci showed partial allelic imbalance in the initial tumour but loss of heterozygosity after the first passage in nude mice when all the normal cells were lost may allow identification of interesting genetic defects that could be involved in tumour expansion. Thus, sequential xenografts of colon tumours will provide a powerful model for further study of tumour clonality and for the identification of genetic profiles responsible for differential resistance to therapeutic treatments. Our data also suggest that tumour expansion can result from alterations in several distinct genetic pathways. PMID:16450341

Guenot, D; Guérin, E; Aguillon-Romain, S; Pencreach, E; Schneider, A; Neuville, A; Chenard, M-P; Duluc, I; Du Manoir, S; Brigand, C; Oudet, P; Kedinger, M; Gaub, M-P

2006-04-01

24

Engineered plant phosphorylase showing extraordinarily high affinity for various alpha-glucan molecules.  

PubMed Central

alpha-Glucan phosphorylases are characterized by considerable difference in substrate specificities, even though the primary structures are well conserved among the enzymes from microorganisms, plants, and animals. The higher plant phosphorylase isozyme designated as type L exhibits low affinity for a large, highly branched glucan (glycogen), presumably due to steric hindrance caused by a unique 78-residue insertion located beside the mouth of the active-site cleft, whereas another isozyme without the insertion (designated as type H) shows very high affinity for both linear and branched glucans. Using the recombinant type L isozyme from potato tuber as a starting framework and aiming at altering its substrate specificity, we have genetically engineered the 78-residue insertion and its flanking regions. Firstly, removal of the insertion and connection of the newly formed C- and N-terminals yielded a totally inactive enzyme, although the protein was produced in Escherichia coli cells in a soluble form. Secondly, a chimeric phosphorylase, in which the 78-residue insertion and its flanking regions are replaced by the corresponding region of the type H isozyme, has been shown to exhibit high affinity for branched glucans (Mori, H., Tanizawa, K., & Fukui, T., 1993, J. Biol. Chem. 268, 5574-5581), but when two and four unconserved residues in the N-terminal flanking region of the chimeric phosphorylase were mutated back to those of the type L isozyme, the resulting mutants showed significantly lowered affinity for substrates.(ABSTRACT TRUNCATED AT 250 WORDS)

Mori, H.; Tanizawa, K.; Fukui, T.

1993-01-01

25

Eubacteria show their true colors: genetics of carotenoid pigment biosynthesis from microbes to plants.  

PubMed Central

The opportunities to understand eubacterial carotenoid biosynthesis and apply the lessons learned in this field to eukaryotes have improved dramatically in the last several years. On the other hand, many questions remain. Although the pigments illustrated in Fig. 2 represent only a small fraction of the carotenoids found in nature, the characterization of eubacterial genes required for their biosynthesis has not yet been completed. Identifying those eukaryotic carotenoid biosynthetic mutants, genes, and enzymes that have no eubacterial counterparts will also prove essential for a full description of the biochemical pathways (81). Eubacterial crt gene regulation has not been studied in detail, with the notable exceptions of M. xanthus and R. capsulatus (5, 33, 39, 45, 46, 84). Determination of the rate-limiting reaction(s) in carotenoid biosynthesis has thus far yielded species-specific results (12, 27, 47, 69), and the mechanisms of many of the biochemical conversions remain obscure. Predicted characteristics of some carotenoid biosynthesis gene products await confirmation by studying the purified proteins. Despite these challenges, (over)expression of eubacterial or eukaryotic carotenoid genes in heterologous hosts has already created exciting possibilities for the directed manipulation of carotenoid levels and content. Such efforts could, for example, enhance the nutritional value of crop plants or yield microbial production of novel and desirable pigments. In the future, the functional compatibility of enzymes from different organisms will form a central theme in the genetic engineering of carotenoid pigment biosynthetic pathways.

Armstrong, G A

1994-01-01

26

Added Value Measures in Education Show Genetic as Well as Environmental Influence  

Microsoft Academic Search

Does achievement independent of ability or previous attainment provide a purer measure of the added value of school? In a study of 4000 pairs of 12-year-old twins in the UK, we measured achievement with year-long teacher assessments as well as tests. Raw achievement shows moderate heritability (about 50%) and modest shared environmental influences (25%). Unexpectedly, we show that for indices

Claire M. A. Haworth; Kathryn Asbury; Philip S. Dale; Robert Plomin; Dorothy Bishop

2011-01-01

27

Genetic structure and demographic history should inform conservation: Chinese cobras currently treated as homogenous show population divergence.  

PubMed

An understanding of population structure and genetic diversity is crucial for wildlife conservation and for determining the integrity of wildlife populations. The vulnerable Chinese cobra (Naja atra) has a distribution from the mouth of the Yangtze River down to northern Vietnam and Laos, within which several large mountain ranges and water bodies may influence population structure. We combined 12 microsatellite loci and 1117 bp of the mitochondrial cytochrome b gene to explore genetic structure and demographic history in this species, using 269 individuals from various localities in Mainland China and Vietnam. High levels of genetic variation were identified for both mtDNA and microsatellites. mtDNA data revealed two main (Vietnam + southern China + southwestern China; eastern + southeastern China) and one minor (comprising only two individuals from the westernmost site) clades. Microsatellite data divided the eastern + southeastern China clade further into two genetic clusters, which include individuals from the eastern and southeastern regions, respectively. The Luoxiao and Nanling Mountains may be important barriers affecting the diversification of lineages. In the haplotype network of cytchrome b, many haplotypes were represented within a "star" cluster and this and other tests suggest recent expansion. However, microsatellite analyses did not yield strong evidence for a recent bottleneck for any population or genetic cluster. The three main clusters identified here should be considered as independent management units for conservation purposes. The release of Chinese cobras into the wild should cease unless their origin can be determined, and this will avoid problems arising from unnatural homogenization. PMID:22558439

Lin, Long-Hui; Qu, Yan-Fu; Li, Hong; Zhou, Kai-Ya; Ji, Xiang

2012-04-27

28

Genetic mapping of expressed sequences in onion and in silico comparisons with rice show scant colinearity  

Microsoft Academic Search

The Poales (which include the grasses) and Asparagales [which include onion (Allium cepa L.) and other Allium species] are the two most economically important monocot orders. Enormous genomic resources have been developed for the grasses;\\u000a however, their applicability to other major monocot groups, such as the Asparagales, is unclear. Expressed sequence tags (ESTs)\\u000a from onion that showed significant similarities (80%

William J. Martin; John McCallum; Masayoshi Shigyo; Jernej Jakse; Joseph C. Kuhl; Naoko Yamane; Meeghan Pither-Joyce; Ali Fuat Gokce; Kenneth C. Sink; Christopher D. Town; Michael J. Havey

2005-01-01

29

Genetic polymorphisms in monoamine neurotransmitter systems show only weak association with acute post-surgical pain in humans  

PubMed Central

Background Candidate gene studies on the basis of biological hypotheses have been a practical approach to identify relevant genetic variation in complex traits. Based on previous reports and the roles in pain pathways, we have examined the effects of variations of loci in the genes of monoamine neurotransmitter systems including metabolizing enzymes, receptors and transporters on acute clinical pain responses in humans. Results Variations in the catecholamine metabolizing enzyme genes (MAOA and COMT) showed significant associations with the maximum post-operative pain rating while the serotonin transporter gene (SLC6A4) showed association with the onset time of post-operative pain. Analgesic onset time after medication was significantly associated with the norepinephrine transporter gene (SLC6A2). However, the association between COMT genetic variation and pain sensitivity in our study differ from previous studies with small sample sizes, population stratification and pain phenotype derived from combining different types of pain stimuli. Correcting for multiple comparisons did not sustain these genetic associations between monoamine neurotransmitter systems and pain sensitivity even in this large and homogeneous sample. Conclusion These results suggest that the previously reported associations between genetic polymorphisms in the monoamine neurotransmitter systems and the interindividual variability in pain responses cannot be replicated in a clinically relevant pain phenotype.

Kim, Hyungsuk; Lee, Hyewon; Rowan, Janet; Brahim, Jaime; Dionne, Raymond A

2006-01-01

30

Anatomical and genetic study of an ancient animal tooth showing brachyodont and hypsodont mixed taxonomical characteristics.  

PubMed

A non-human dental piece was found in a Roman Empire tomb dated the 3rd century A.C. in Zaragoza (Spain). The morphology of this piece showed mixed brachyodont (carnivores) and hypsodont (herbivores) characteristics. As a result, the taxonomical assignation of the piece was impossible. Therefore, a protocolbased on the DNA sequence of the cytochrome c oxidase subunit 1 mitochondrial region (COI) was applied. For this purpose, a pair of primers able to amplify thisregion in a large variety of animals was designed. The results point to a species of the Genus Bos (Family Bovidae). This assignation was later confirmed by these quencing of a short fragment of the mitochondrial D-loop region. A complete morphological description of the tooth is presented together with the DNA sequence study and comparison protocol. PMID:23740506

Monteagudo, L V; Obón, J A; Whyte, A; Tejedor, M T; Whyte, J; Cisneros, A

2013-01-01

31

The X chromosome shows less genetic variation at restriction sites than the autosomes.  

PubMed Central

Using a standard technique, 122 single-copy probes were screened for their ability to detect restriction fragment length polymorphisms (RFLPs) in the human genome. The use of a standardized RFLP screening enables the introduction of statistical methods in the analysis of differences in RFLP content between chromosomes and enzymes. RFLPs were detected from panels containing at least 17 unrelated chromosomes, digested with TaqI, MspI, BglII, HindIII, EcoRI, and PstI. Forty autosomal probes, representing a sample of 2,710 base pairs (bp) per haploid genome, were tested, and 24 RFLPs were found. With 82 X-chromosomal probes, 17 RFLPs were found in 6,228 bp per haploid genome. The frequency of X-chromosomal RFLPs is three times less than that of the autosomes; this difference is highly significant (P = less than .001). The frequency of RFLPs revealed by various restriction enzymes and the possibility that the X chromosome is a "low mutation" niche in the human genome are discussed.

Hofker, M H; Skraastad, M I; Bergen, A A; Wapenaar, M C; Bakker, E; Millington-Ward, A; van Ommen, G J; Pearson, P L

1986-01-01

32

NPHS2 mutation analysis shows genetic heterogeneityof steroid-resistant nephrotic syndrome and lowpost-transplant recurrence  

Microsoft Academic Search

NPHS2 mutation analysis shows genetic heterogeneity of steroid-resistant nephrotic syndrome and low post-transplant recurrence.BackgroundMutations of NPHS2 are causative in familial autosomal-recessive (AR) and sporadic steroid-resistant nephrotic syndrome (SRNS). This study aimed to determine the spectrum of NPHS2 mutations and to establish genotype-phenotype correlations.MethodsNPHS2 mutation analysis was performed in 338 patients from 272 families with SRNS: 81 families with AR SRNS,

STEFANIE WEBER; OLIVIER GRIBOUVAL; ERNIE L ESQUIVEL; VINCENT MORINIÈRE; MARIE-JOSÈPHE TÊTE; CHRISTOPHE LEGENDRE; PATRICK NIAUDET; CORINNE ANTIGNAC

2004-01-01

33

Quantitative study on guinea pig spermatogenesis shows a relative high percentage of early meiotic prophase stages.  

PubMed

Meiosis is the special double cellular division characterized by the reduction of chromosome number of the final products and recombination of genetic information present in maternal and paternal homologous chromosomes. Early stages of meiotic prophase, leptotene and zygotene (L/Z), are functionally important since homologous chromosomes recognize, align, and pair during them. They are poorly represented in the seminiferous tubules of mammalian species, and this fact turns studies focused on these stages difficult to perform. As a consequence, the molecular bases of these important events are so far poorly known and understood in higher eukaryotes. The purpose of this work was to provide an advantageous experimental mammalian model (with a reasonable number of cells) for biochemical and molecular analysis of early meiotic prophase stages. Here, we present the results of our quantitative study on testes material of both immature and adult guinea pig specimens (Cavia porcellus). We show that their seminiferous tubules contain a comparatively high percentage of L/Z spermatocytes, as well as a very conspicuous chromosome bouquet at the L/Z transition, which points out this species as a well-suited one to address studies on such stages in mammals. PMID:15103745

Rodríguez, Rosana E; Wettstein, Rodolfo M

2004-05-01

34

Modes of Gene Duplication Contribute Differently to Genetic Novelty and Redundancy, but Show Parallels across Divergent Angiosperms  

PubMed Central

Background Both single gene and whole genome duplications (WGD) have recurred in angiosperm evolution. However, the evolutionary effects of different modes of gene duplication, especially regarding their contributions to genetic novelty or redundancy, have been inadequately explored. Results In Arabidopsis thaliana and Oryza sativa (rice), species that deeply sample botanical diversity and for which expression data are available from a wide range of tissues and physiological conditions, we have compared expression divergence between genes duplicated by six different mechanisms (WGD, tandem, proximal, DNA based transposed, retrotransposed and dispersed), and between positional orthologs. Both neo-functionalization and genetic redundancy appear to contribute to retention of duplicate genes. Genes resulting from WGD and tandem duplications diverge slowest in both coding sequences and gene expression, and contribute most to genetic redundancy, while other duplication modes contribute more to evolutionary novelty. WGD duplicates may more frequently be retained due to dosage amplification, while inferred transposon mediated gene duplications tend to reduce gene expression levels. The extent of expression divergence between duplicates is discernibly related to duplication modes, different WGD events, amino acid divergence, and putatively neutral divergence (time), but the contribution of each factor is heterogeneous among duplication modes. Gene loss may retard inter-species expression divergence. Members of different gene families may have non-random patterns of origin that are similar in Arabidopsis and rice, suggesting the action of pan-taxon principles of molecular evolution. Conclusion Gene duplication modes differ in contribution to genetic novelty and redundancy, but show some parallels in taxa separated by hundreds of millions of years of evolution.

Wang, Yupeng; Wang, Xiyin; Tang, Haibao; Tan, Xu; Ficklin, Stephen P.; Feltus, F. Alex; Paterson, Andrew H.

2011-01-01

35

Molecular Epidemiology of Aspergillus fumigatus Isolates Recovered from Water, Air, and Patients Shows Two Clusters of Genetically Distinct Strains  

PubMed Central

There has been an increase in data suggesting that besides air, hospital water is a potential source of transmission of filamentous fungi, and in particular Aspergillus fumigatus. Molecular characterization of environmental and clinical A. fumigatus isolates, collected prospectively during an 18-month period, was performed to establish if waterborne fungi play a role in the pathogenesis of invasive aspergillosis. Isolates recovered from water (n = 54) and air (n = 21) at various locations inside and outside the hospital and from 15 patients (n = 21) with proven, probable, or possible invasive aspergillosis were genotyped by amplified fragment length polymorphism analysis. Based on genomic fingerprints, the environmental A. fumigatus isolates could be grouped into two major clusters primarily containing isolates recovered from either air or water. The genotypic relatedness between clinical and environmental isolates suggests that patients with invasive aspergillosis can be infected by strains originating from water or from air. In addition, 12 clusters with genetically indistinguishable or highly related strains were differentiated, each containing two to three isolates. In two clusters, clinical isolates recovered from patients matched those recovered from water sources, while in another cluster the clinical isolate was indistinguishable from one cultured from air. This observation might open new perspectives in the development of infection control measures to prevent invasive aspergillosis in high-risk patients. The genetic variability found between airborne and waterborne A. fumigatus strains might prove to be a powerful tool in understanding the transmission of invasive aspergillosis and in outbreak control.

Warris, Adilia; Klaassen, Corne H. W.; Meis, Jacques F. G. M.; de Ruiter, Maaike T.; de Valk, Hanneke A.; Abrahamsen, Tore G.; Gaustad, Peter; Verweij, Paul E.

2003-01-01

36

Genome-Wide Association Scan Shows Genetic Variants in the FTO Gene Are Associated with Obesity-Related Traits  

PubMed Central

The obesity epidemic is responsible for a substantial economic burden in developed countries and is a major risk factor for type 2 diabetes and cardiovascular disease. The disease is the result not only of several environmental risk factors, but also of genetic predisposition. To take advantage of recent advances in gene-mapping technology, we executed a genome-wide association scan to identify genetic variants associated with obesity-related quantitative traits in the genetically isolated population of Sardinia. Initial analysis suggested that several SNPs in the FTO and PFKP genes were associated with increased BMI, hip circumference, and weight. Within the FTO gene, rs9930506 showed the strongest association with BMI (p = 8.6 ×10?7), hip circumference (p = 3.4 × 10?8), and weight (p = 9.1 × 10?7). In Sardinia, homozygotes for the rare “G” allele of this SNP (minor allele frequency = 0.46) were 1.3 BMI units heavier than homozygotes for the common “A” allele. Within the PFKP gene, rs6602024 showed very strong association with BMI (p = 4.9 × 10?6). Homozygotes for the rare “A” allele of this SNP (minor allele frequency = 0.12) were 1.8 BMI units heavier than homozygotes for the common “G” allele. To replicate our findings, we genotyped these two SNPs in the GenNet study. In European Americans (N = 1,496) and in Hispanic Americans (N = 839), we replicated significant association between rs9930506 in the FTO gene and BMI (p-value for meta-analysis of European American and Hispanic American follow-up samples, p = 0.001), weight (p = 0.001), and hip circumference (p = 0.0005). We did not replicate association between rs6602024 and obesity-related traits in the GenNet sample, although we found that in European Americans, Hispanic Americans, and African Americans, homozygotes for the rare “A” allele were, on average, 1.0–3.0 BMI units heavier than homozygotes for the more common “G” allele. In summary, we have completed a whole genome–association scan for three obesity-related quantitative traits and report that common genetic variants in the FTO gene are associated with substantial changes in BMI, hip circumference, and body weight. These changes could have a significant impact on the risk of obesity-related morbidity in the general population.

Chen, Wei-Min; Uda, Manuela; Albai, Giuseppe; Strait, James; Najjar, Samer; Nagaraja, Ramaiah; Orru, Marco; Usala, Gianluca; Dei, Mariano; Lai, Sandra; Maschio, Andrea; Busonero, Fabio; Mulas, Antonella; Ehret, Georg B; Fink, Ashley A; Weder, Alan B; Cooper, Richard S; Galan, Pilar; Chakravarti, Aravinda; Schlessinger, David; Cao, Antonio; Lakatta, Edward; Abecasis, Goncalo R

2007-01-01

37

High-throughput olfactory conditioning and memory retention test show variation in Nasonia parasitic wasps  

PubMed Central

Most of our knowledge on learning and memory formation results from extensive studies on a small number of animal species. Although features and cellular pathways of learning and memory are highly similar in this diverse group of species, there are also subtle differences. Closely related species of parasitic wasps display substantial variation in memory dynamics and can be instrumental to understanding both the adaptive benefit of and mechanisms underlying this variation. Parasitic wasps of the genus Nasonia offer excellent opportunities for multidisciplinary research on this topic. Genetic and genomic resources available for Nasonia are unrivaled among parasitic wasps, providing tools for genetic dissection of mechanisms that cause differences in learning. This study presents a robust, high-throughput method for olfactory conditioning of Nasonia using a host encounter as reward. A T-maze olfactometer facilitates high-throughput memory retention testing and employs standardized odors of equal detectability, as quantified by electroantennogram recordings. Using this setup, differences in memory retention between Nasonia species were shown. In both Nasonia vitripennis and Nasonia longicornis, memory was observed up to at least 5 days after a single conditioning trial, whereas Nasonia giraulti lost its memory after 2 days. This difference in learning may be an adaptation to species-specific differences in ecological factors, for example, host preference. The high-throughput methods for conditioning and memory retention testing are essential tools to study both ultimate and proximate factors that cause variation in learning and memory formation in Nasonia and other parasitic wasp species.

Hoedjes, K M; Steidle, J L M; Werren, J H; Vet, L E M; Smid, H M

2012-01-01

38

Landscape genetics of high mountain frog metapopulations.  

PubMed

Explaining functional connectivity among occupied habitats is crucial for understanding metapopulation dynamics and species ecology. Landscape genetics has primarily focused on elucidating how ecological features between observations influence gene flow. Functional connectivity, however, may be the result of both these between-site (landscape resistance) landscape characteristics and at-site (patch quality) landscape processes that can be captured using network based models. We test hypotheses of functional connectivity that include both between-site and at-site landscape processes in metapopulations of Columbia spotted frogs (Rana luteiventris) by employing a novel justification of gravity models for landscape genetics (eight microsatellite loci, 37 sites, n = 441). Primarily used in transportation and economic geography, gravity models are a unique approach as flow (e.g. gene flow) is explained as a function of three basic components: distance between sites, production/attraction (e.g. at-site landscape process) and resistance (e.g. between-site landscape process). The study system contains a network of nutrient poor high mountain lakes where we hypothesized a short growing season and complex topography between sites limit R. luteiventris gene flow. In addition, we hypothesized production of offspring is limited by breeding site characteristics such as the introduction of predatory fish and inherent site productivity. We found that R. luteiventris connectivity was negatively correlated with distance between sites, presence of predatory fish (at-site) and topographic complexity (between-site). Conversely, site productivity (as measured by heat load index, at-site) and growing season (as measured by frost-free period between-sites) were positively correlated with gene flow. The negative effect of predation and positive effect of site productivity, in concert with bottleneck tests, support the presence of source-sink dynamics. In conclusion, gravity models provide a powerful new modelling approach for examining a wide range of both basic and applied questions in landscape genetics. PMID:20723055

Murphy, Melanie A; Dezzani, R; Pilliod, D S; Storfer, A

2010-08-13

39

Molecular Characterization of Chinese Hamster Cells Mutants Affected in Adenosine Kinase and Showing Novel Genetic and Biochemical Characteristics  

PubMed Central

Background Two isoforms of the enzyme adenosine kinase (AdK), which differ at their N-terminal ends, are found in mammalian cells. However, there is no information available regarding the unique functional aspects or regulation of these isoforms. Results We show that the two AdK isoforms differ only in their first exons and the promoter regions; hence they arise via differential splicing of their first exons with the other exons common to both isoforms. The expression of these isoforms also varied greatly in different rat tissues and cell lines with some tissues expressing both isoforms and others expressing only one of the isoforms. To gain insights into cellular functions of these isoforms, mutants resistant to toxic adenosine analogs formycin A and tubercidin were selected from Chinese hamster (CH) cell lines expressing either one or both isoforms. The AdK activity in most of these mutants was reduced to <5% of wild-type cells and they also showed large differences in the expression of the two isoforms. Thus, the genetic alterations in these mutants likely affected both regulatory and structural regions of AdK. We have characterized the molecular alterations in a number of these mutants. One of these mutants lacking AdK activity was affected in the conserved NxxE motif thereby providing evidence that this motif involved in the binding of Mg2+ and phosphate ions is essential for AdK function. Another mutant, FomR-4, exhibiting increased resistance to only C-adenosine analogs and whose resistance was expressed dominantly in cell-hybrids contained a single mutation leading to Ser191Phe alteration in AdK. We demonstrate that this mutation in AdK is sufficient to confer the novel genetic and biochemical characteristics of this mutant. The unusual genetic and biochemical characteristics of the FomR-4 mutant suggest that AdK in this mutant might be complexed with the enzyme AMP-kinase. Several other AdK mutants were altered in surface residues that likely affect its binding to the adenosine analogs and its interaction with other cellular proteins. Conclusions These AdK mutants provide important insights as well as novel tools for understanding the cellular functions of the two isoforms and their regulation in mammalian cells.

2011-01-01

40

Short communication: Carora cattle show high variability in alpha(s1)-casein.  

PubMed

The objective of this study was to analyze the genetic variability of milk proteins of the Carora, a shorthorned Bos taurus cattle breed in Venezuela and in other Southern American countries that is primarily used for milk production. A total of 184 individual milk samples were collected from Carora cattle in 5 herds in Venezuela. The milk protein genes alpha(s1)-casein (CN) (CSN1S1), beta-CN (CSN2), kappa-CN (CSN3), and beta-lactoglobulin (LGB) were typed at the protein level by isoelectrofocusing. It was necessary to further analyze CSN1S1 at the DNA level by a PCR-based method to distinguish CSN1S1*G from B. Increased variation was found in particular at the CSN1S1 gene, where 4 variants were identified. The predominant variant was CSN1S1*B (frequency = 0.8). The second most common CSN1S1 variant was CSN1S1*G (0.101), followed by CSN1S1*C (0.082). Moreover, a new isoelectrofocusing pattern was identified, which may result from a novel CSN1S1 variant, named CSN1S1*I, migrating at an intermediate position between CSN1S1*B and CSN1S1*C. Six cows carried the variant at the heterozygous condition. For the other loci, predominance of CSN2*A2 (0.764), CSN3*B (0.609), and LGB*B (0.592) was observed. Haplotype frequencies (AF) at the CSN1S1-CSN2-CSN3 complex were also estimated by taking association into account. Only 7 haplotypes showed AF values >0.05, accounting for a cumulative frequency of 0.944. The predominant haplotype was B-A2-B (frequency = 0.418), followed by B-A2-A (0.213). The occurrence of the G variant is at a rather high frequency, which is of interest for selection within the Carora breed because of the negative association of this variant with the synthesis of the specific protein. From a cheese-making point of view, this variant is associated with improved milk-clotting parameters but is negatively associated with cheese ripening. Thus, milk protein typing should be routinely carried out in the breed, with particular emphasis on using a DNA test to detect the CSN1S*G variant. The CSN1S*G allele is likely to have descended from the Brown Swiss, which contributed to the Carora breed and also carries this allele. PMID:18096958

Caroli, A; Chessa, S; Chiatti, F; Rignanese, D; Meléndez, B; Rizzi, R; Ceriotti, G

2008-01-01

41

Stem and progenitor cells in myelodysplastic syndromes show aberrant stage-specific expansion and harbor genetic and epigenetic alterations  

PubMed Central

Even though hematopoietic stem cell (HSC) dysfunction is presumed in myelodysplastic syndrome (MDS), the exact nature of quantitative and qualitative alterations is unknown. We conducted a study of phenotypic and molecular alterations in highly fractionated stem and progenitor populations in a variety of MDS subtypes. We observed an expansion of the phenotypically primitive long-term HSCs (lineage?/CD34+/CD38?/CD90+) in MDS, which was most pronounced in higher-risk cases. These MDS HSCs demonstrated dysplastic clonogenic activity. Examination of progenitors revealed that lower-risk MDS is characterized by expansion of phenotypic common myeloid progenitors, whereas higher-risk cases revealed expansion of granulocyte-monocyte progenitors. Genome-wide analysis of sorted MDS HSCs revealed widespread methylomic and transcriptomic alterations. STAT3 was an aberrantly hypomethylated and overexpressed target that was validated in an independent cohort and found to be functionally relevant in MDS HSCs. FISH analysis demonstrated that a very high percentage of MDS HSC (92% ± 4%) carry cytogenetic abnormalities. Longitudinal analysis in a patient treated with 5-azacytidine revealed that karyotypically abnormal HSCs persist even during complete morphologic remission and that expansion of clonotypic HSCs precedes clinical relapse. This study demonstrates that stem and progenitor cells in MDS are characterized by stage-specific expansions and contain epigenetic and genetic alterations.

Will, Britta; Zhou, Li; Vogler, Thomas O.; Ben-Neriah, Susanna; Schinke, Carolina; Tamari, Roni; Yu, Yiting; Bhagat, Tushar D.; Bhattacharyya, Sanchari; Barreyro, Laura; Heuck, Christoph; Mo, Yonkai; Parekh, Samir; McMahon, Christine; Pellagatti, Andrea; Boultwood, Jacqueline; Montagna, Cristina; Silverman, Lewis; Maciejewski, Jaroslaw; Greally, John M.; Ye, B. Hilda; List, Alan F.; Steidl, Christian

2012-01-01

42

Stem and progenitor cells in myelodysplastic syndromes show aberrant stage-specific expansion and harbor genetic and epigenetic alterations.  

PubMed

Even though hematopoietic stem cell (HSC) dysfunction is presumed in myelodysplastic syndrome (MDS), the exact nature of quantitative and qualitative alterations is unknown. We conducted a study of phenotypic and molecular alterations in highly fractionated stem and progenitor populations in a variety of MDS subtypes. We observed an expansion of the phenotypically primitive long-term HSCs (lineage(-)/CD34(+)/CD38(-)/CD90(+)) in MDS, which was most pronounced in higher-risk cases. These MDS HSCs demonstrated dysplastic clonogenic activity. Examination of progenitors revealed that lower-risk MDS is characterized by expansion of phenotypic common myeloid progenitors, whereas higher-risk cases revealed expansion of granulocyte-monocyte progenitors. Genome-wide analysis of sorted MDS HSCs revealed widespread methylomic and transcriptomic alterations. STAT3 was an aberrantly hypomethylated and overexpressed target that was validated in an independent cohort and found to be functionally relevant in MDS HSCs. FISH analysis demonstrated that a very high percentage of MDS HSC (92% ± 4%) carry cytogenetic abnormalities. Longitudinal analysis in a patient treated with 5-azacytidine revealed that karyotypically abnormal HSCs persist even during complete morphologic remission and that expansion of clonotypic HSCs precedes clinical relapse. This study demonstrates that stem and progenitor cells in MDS are characterized by stage-specific expansions and contain epigenetic and genetic alterations. PMID:22753872

Will, Britta; Zhou, Li; Vogler, Thomas O; Ben-Neriah, Susanna; Schinke, Carolina; Tamari, Roni; Yu, Yiting; Bhagat, Tushar D; Bhattacharyya, Sanchari; Barreyro, Laura; Heuck, Christoph; Mo, Yonkai; Parekh, Samir; McMahon, Christine; Pellagatti, Andrea; Boultwood, Jacqueline; Montagna, Cristina; Silverman, Lewis; Maciejewski, Jaroslaw; Greally, John M; Ye, B Hilda; List, Alan F; Steidl, Christian; Steidl, Ulrich; Verma, Amit

2012-07-02

43

A New BSCS Project: Human Genetics Education for High School.  

ERIC Educational Resources Information Center

Described is the BSCS Center for Education in Human and Medical Genetics, established to design, develop, and evaluate an instructional module in human genetics for high school students. This module will be a self-contained curricular program and will provide individualized open-ended experiences which present basic genetics content in the context…

Biological Sciences Curriculum Study Journal, 1980

1980-01-01

44

Human Genetics Education in the High School: A Pilot Program.  

ERIC Educational Resources Information Center

Describes and evaluates a two-day workshop on human genetics for high school biology teachers which involved: (1) a series of lectures by professionals in medical genetics, ethics, and genetic counseling; (2) demonstrations; (3) question-and-answer sessions; (4) a curriculum packet; and (5) a follow-up bimonthly newsletter. (DC)

Haddow, Paula K.

1982-01-01

45

Familial\\/Bilateral and Sporadic Testicular Germ Cell Tumors Show Frequent Genetic Changes at Loci with Suggestive Linkage Evidence1  

Microsoft Academic Search

Testicular germ cell tumor (TGCT) is the most common tumor type among adolescent and young adult males. Familial clustering and bilateral disease are suggestive of a genetic predisposition among a subgroup of these patients, but susceptibility genes for testicular cancer have not yet been identified. However, suggestive linkage between disease and genetic markers has been reported at loci on chromosome

Rolf I. Skotheim; Sigrid M. Kraggerud; Sophie D. Fossaz; Anna E. Stenwig; Tobias Gedde-Dahl; Havard E. Danielsen; Kjetill S. Jakobsen; Ragnhild A. Lothe

2001-01-01

46

Genetic influence on brain catecholamines: high brain norepinephrine in salt-sensitive rats  

SciTech Connect

Rats genetically sensitive to salt-induced hypertension evinced higher levels of plasma norepinephrine and epinephrine than rats genetically resistant to hypertension. The hypertension-sensitive rats showed higher hypothalamic norepinephrine and lower epinephrine than resistant rats. In response to a high salt diet, brain stem norepinephrine increased in sensitive rats while resistant rats exhibited a decrease on the same diet.

Iwai, J; Friedman, R; Tassinari, L

1980-01-01

47

Use of residual feed intake in Holsteins during early lactation shows potential to improve feed efficiency through genetic selection.  

PubMed

Improved feed efficiency is a primary goal in dairy production to reduce feed costs and negative impacts of production on the environment. Estimates for efficiency of feed conversion to milk production based on residual feed intake (RFI) in dairy cattle are limited, primarily due to a lack of individual feed intake measurements for lactating cows. Feed intake was measured in Holstein cows during the first 90 d of lactation to estimate the heritability and repeatability of RFI, minimum test duration for evaluating RFI in early lactation, and its association with other production traits. Data were obtained from 453 lactations (214 heifers and 239 multiparous cows) from 292 individual cows from September 2007 to December 2011. Cows were housed in a free-stall barn and monitored for individual daily feed consumption using the GrowSafe 4000 System (GrowSafe Systems, Ltd., Airdrie, AB, Canada). Animals were fed a total mixed ration 3 times daily, milked twice daily, and weighed every 10 to 14 d. Milk yield was measured at each milking. Feed DM percentage was measured daily, and nutrient composition was analyzed from a weekly composite. Milk composition was analyzed weekly, alternating between morning and evening milking periods. Estimates of RFI were determined as the difference between actual energy intake and predicted intake based on a linear model with fixed effects of parity (1, 2, ? 3) and regressions on metabolic BW, ADG, and energy-corrected milk yield. Heritability was estimated to be moderate (0.36 ± 0.06), and repeatability was estimated at 0.56 across lactations. A test period through 53 d in milk (DIM) explained 81% of the variation provided by a test through 90 DIM. Multiple regression analysis indicated that high efficiency was associated with less time feeding per day and slower feeding rate, which may contribute to differences in RFI among cows. The heritability and repeatability of RFI suggest an opportunity to improve feed efficiency through genetic selection, which could reduce feed costs, manure output, and greenhouse gas emissions associated with dairy production. PMID:23658326

Connor, E E; Hutchison, J L; Norman, H D; Olson, K M; Van Tassell, C P; Leith, J M; Baldwin, R L

2013-05-08

48

Analysis of Single Nucleotide Polymorphisms in Three Genes Shows Evidence for Genetic Isolation of Certain Aspergillus flavus Vegetative Compatibility Groups  

Technology Transfer Automated Retrieval System (TEKTRAN)

Genetic exchange among populations of asexual filamentous fungi is presumed to be limited to isolates in the same vegetative compatibility group (VCG). To test this hypothesis, we compared the distribution of single nucleotide polymorphisms (SNP's) in Aspergills flavus isolates from six different V...

49

Genome-Wide Association Scan Shows Genetic Variants in the FTO Gene Are Associated with Obesity-Related Traits  

Microsoft Academic Search

The obesity epidemic is responsible for a substantial economic burden in developed countries and is a major risk factor for type 2 diabetes and cardiovascular disease. The disease is the result not only of several environmental risk factors, but also of genetic predisposition. To take advantage of recent advances in gene-mapping technology, we executed a genome-wide association scan to identify

Angelo Scuteri; Serena Sanna; Wei-Min Chen; Manuela Uda; Giuseppe Albai; James Strait; Samer Najjar; Ramaiah Nagaraja; Marco Orrú; Gianluca Usala; Mariano Dei; Sandra Lai; Andrea Maschio; Fabio Busonero; Antonella Mulas; Georg B. Ehret; Ashley A. Fink; Alan B. Weder; Richard S. Cooper; Pilar Galan; Aravinda Chakravarti; David Schlessinger; Antonio Cao; Edward Lakatta; Gonçalo R. Abecasis

2007-01-01

50

RFLP Markers Show Genetic Recombination in Botryotinia fuckeliana (Botrytis cinerea) and Transposable Elements Reveal Two Sympatric Species  

Microsoft Academic Search

Molecular markers revealed that Botryotinia jiickeliana (the teleomorph of Botrytis cinerea), a haploid, filamentous, heterothallic ascomycete, contained a large amount of intrapopulation genetic variation. The markers were used to determine the mode of reproduction and the population structure of this fungus. We did not detect any differentiation between isolates from different organs, collection dates, varieties of grape, or locations in

Tatiana Giraud; Dominique Fortini; Caroline Levis; Pierre Leroux; Yves Brygoo

51

Childhood hyperactivity scores are highly heritable and show sibling competition effects: Twin study evidence  

Microsoft Academic Search

Hyperactivity has consistently been shown to be familial. Until recently however, due to a lack of systematic twin evidence,\\u000a it has remained uncertain to what extent familial transmission can be explained by genetic factors. We used a systematically\\u000a ascertained population-based sample of twin pairs aged between 8 and 16 years old to explore the role of genetic influences\\u000a on maternally

Anita Thapar; Amaia Hervas; Peter McGuffin I

1995-01-01

52

Modes of Gene Duplication Contribute Differently to Genetic Novelty and Redundancy, but Show Parallels across Divergent Angiosperms  

Microsoft Academic Search

BackgroundBoth single gene and whole genome duplications (WGD) have recurred in angiosperm evolution. However, the evolutionary effects of different modes of gene duplication, especially regarding their contributions to genetic novelty or redundancy, have been inadequately explored.ResultsIn Arabidopsis thaliana and Oryza sativa (rice), species that deeply sample botanical diversity and for which expression data are available from a wide range of

Yupeng Wang; Xiyin Wang; Haibao Tang; Xu Tan; Stephen P. Ficklin; F. Alex Feltus; Andrew H. Paterson

2011-01-01

53

Genetic susceptibility to childhood acute lymphoblastic leukemia shows protection in Malay boys: Results from the Malaysia-Singapore ALL Study Group  

Microsoft Academic Search

To study genetic epidemiology of childhood acute lymphoblastic leukemia (ALL) in the Chinese and Malays, we investigated 10 polymorphisms encoding carcinogen- or folate-metabolism and transport. Sex-adjusted analysis showed NQO1 609CT significantly protects against ALL, whilst MTHFR 677CT confers marginal protection. Interestingly, we observed that NQO1 609CT and MTHFR 1298 C-allele have greater genetic impact in boys than in girls. The

Allen Eng-Juh Yeoh; Yi Lu; Jason Yong-Sheng Chan; Yiong Huak Chan; Hany Ariffin; Shirley Kow-Yin Kham; Thuan Chong Quah

2010-01-01

54

Georgian and kurd mtDNA sequence analysis shows a lack of correlation between languages and female genetic lineages.  

PubMed

Mitochondrial DNA sequences from Georgians and Kurds were analyzed in order to test the possible correlation between female lineages and languages in these two neighboring West Eurasian groups. Mitochondrial sequence pools in both populations are very similar despite their different linguistic and prehistoric backgrounds. Both populations present mtDNA lineages that clearly belong to the European gene pool, as shown by 1) similar nucleotide and sequence diversities; 2) a large number of sequences shared with the rest of European samples; 3) nonsignificant genetic distances; and 4) classification of the present lineages into the major European mtDNA haplogroups already described. The outlier position of the populations from the Caucasus according to classical genetic markers is not recognized in the present Georgian mtDNA sequence pool. This result suggests that the differentiation of mtDNA sequences in West Eurasia and the outlier features of Caucasian populations should be attributed to different processes. Moreover, the putative linguistic relationship between Caucasian groups and the Basques, another outlier population within Europe for classical genetic markers, is not detected by the analysis of mtDNA sequences. PMID:10766939

Comas, D; Calafell, F; Bendukidze, N; Fañanás, L; Bertranpetit, J

2000-05-01

55

High nuclearity nickel compounds with three, four or five metal atoms showing antibacterial activity  

Microsoft Academic Search

The effect on DNA and the antibacterial activity of a series of high nuclearity nickel compounds with three, four and five metal atoms were examined. The compounds have a mixed ligand composition with salicylhydroxamic acid and di-2-pyridyl-ketonoxime as chelate agents. In the trinuclear compound Ni3(shi)2(Hpko)2(py)2(1), two metal ions show a square planar geometry while the third one is in an

Maria Alexiou; Ioannis Tsivikas; Catherine Dendrinou-Samara; Anastasia A. Pantazaki; Pantelis Trikalitis; Nikolia Lalioti; Dimitris A. Kyriakidis; Dimitris P. Kessissoglou

2003-01-01

56

High-speed atomic force microscopy shows dynamic molecular processes in photoactivated bacteriorhodopsin  

NASA Astrophysics Data System (ADS)

Dynamic changes in protein conformation in response to external stimuli are important in biological processes, but it has proved difficult to directly visualize such structural changes under physiological conditions. Here, we show that high-speed atomic force microscopy can be used to visualize dynamic changes in stimulated proteins. High-resolution movies of a light-driven proton pump, bacteriorhodopsin, reveal that, upon illumination, a cytoplasmic portion of each bacteriorhodopsin monomer is brought into contact with adjacent trimers. The bacteriorhodopsin-bacteriorhodopsin interaction in the transiently formed assembly engenders both positive and negative cooperative effects in the decay kinetics as the initial bacteriorhodopsin recovers and, as a consequence, the turnover rate of the photocycle is maintained constant, on average, irrespective of the light intensity. These results confirm that high-resolution visualization is a powerful approach for studying elaborate biomolecular processes under realistic conditions.

Shibata, Mikihiro; Yamashita, Hayato; Uchihashi, Takayuki; Kandori, Hideki; Ando, Toshio

2010-03-01

57

A Twin Study of ADHD Symptoms in Early Adolescence: Hyperactivity-Impulsivity and Inattentiveness Show Substantial Genetic Overlap but Also Genetic Specificity  

ERIC Educational Resources Information Center

|A previous paper in this journal revealed substantial genetic overlap between the ADHD dimensions of hyperactivity-impulsivity and inattentiveness in a sample of 8-year old twins drawn from a UK-representative population sample. Four years later, when the twins were 12 years old, more than 5,500 pairs drawn from the same sample were rated again…

Greven, Corina U.; Rijsdijk, Fruhling V.; Plomin, Robert

2011-01-01

58

Lung cancer with loss of BRG1/BRM, shows epithelial mesenchymal transition phenotype and distinct histologic and genetic features.  

PubMed

BRG1 and BRM, two core catalytic subunits in SWI/SNF chromatin remodeling complexes, have been suggested as tumor suppressors, yet their roles in carcinogenesis are unclear. Here, we present evidence that loss of BRG1 and BRM is involved in the progression of lung adenocarcinomas. Analysis of 15 lung cancer cell lines indicated that BRG1 mutations correlated with loss of BRG1 expression and that loss of BRG1 and BRM expression was frequent in E-cadherin-low and vimentin-high cell lines. Immunohistochemical analysis of 93 primary lung adenocarcinomas showed loss of BRG1 and BRM in 11 (12%) and 16 (17%) cases, respectively. Loss of expression of BRG1 and BRM was frequent in solid predominant adenocarcinomas and tumors with low thyroid transcription factor-1 (TTF-1, master regulator of lung) and low cytokeratin7 and E-cadherin (two markers for bronchial epithelial differentiation). Loss of BRG1 was correlated with the absence of lepidic growth patterns and was mutually exclusive of epidermal growth factor receptor (EGFR) mutations. In contrast, loss of BRM was found concomitant with lepidic growth patterns and EGFR mutations. Finally, we analyzed the publicly available dataset of 442 cases and found that loss of BRG1 and BRM was frequent in E-cadherin-low, TTF-1-low, and vimentin-high cases and correlated with poor prognosis. We conclude that loss of either or both BRG1 and BRM is involved in the progression of lung adenocarcinoma into solid predominant tumors with features of epithelial mesenchymal transition and loss of the bronchial epithelial phenotype. BRG1 loss was specifically involved in the progression of EGFR wild-type, but not EGFR-mutant tumors. PMID:23163725

Matsubara, Daisuke; Kishaba, Yuka; Ishikawa, Shumpei; Sakatani, Takashi; Oguni, Sachiko; Tamura, Tomoko; Hoshino, Hiroko; Sugiyama, Yukihiko; Endo, Shunsuke; Murakami, Yoshinori; Aburatani, Hiroyuki; Fukayama, Masashi; Niki, Toshiro

2013-01-04

59

Hybrid Mice as Genetic Models of High Alcohol Consumption  

PubMed Central

We showed that F1 hybrid genotypes may provide a broader variety of ethanol drinking phenotypes than the inbred progenitor strains used to create the hybrids (Blednov et al. in Alcohol Clin Exp Res 29:1949–1958–2005). To extend this work, we characterized alcohol consumption as well as intake of other tastants (saccharin, quinine and sodium chloride) in five inbred strains of mice (FVB, SJL, B6, BUB, NZB) and in their reciprocal F1 hybrids with B6 (FVBxB6; B6xFVB; NZBxB6; B6xNZB; BUBxB6; B6xBUB; SJLxB6; B6xSJL). We also compared ethanol intake in these mice for several concentrations before and after two periods of abstinence. F1 hybrid mice derived from the crosses of B6 and FVB and also B6 and SJL drank higher levels of ethanol than their progenitor strains, demonstrating overdominance for two-bottle choice drinking test. The B6 and NZB hybrid showed additivity in two-bottle choice drinking, whereas the hybrid of B6 and BUB demonstrated full or complete dominance. Genealogical origin, as well as non-alcohol taste preferences (sodium chloride), predicted ethanol consumption. Mice derived from the crosses of B6 and FVB showed high sustained alcohol preference and the B6 and NZB hybrids showed reduced alcohol preference after periods of abstinence. These new genetic models offer some advantages over inbred strains because they provide high, sustained, alcohol intake, and should allow mapping of loci important for the genetic architecture of these traits.

Ozburn, A. R.; Walker, D.; Ahmed, S.; Belknap, J. K.; Harris, R. A.

2011-01-01

60

Genetic and Biochemical Analysis of High Iron Toxicity in Yeast  

PubMed Central

Iron storage in yeast requires the activity of the vacuolar iron transporter Ccc1. Yeast with an intact CCC1 are resistant to iron toxicity, but deletion of CCC1 renders yeast susceptible to iron toxicity. We used genetic and biochemical analysis to identify suppressors of high iron toxicity in ?ccc1 cells to probe the mechanism of high iron toxicity. All genes identified as suppressors of high iron toxicity in aerobically grown ?ccc1 cells encode organelle iron transporters including mitochondrial iron transporters MRS3, MRS4, and RIM2. Overexpression of MRS3 suppressed high iron toxicity by decreasing cytosolic iron through mitochondrial iron accumulation. Under anaerobic conditions, ?ccc1 cells were still sensitive to high iron toxicity, but overexpression of MRS3 did not suppress iron toxicity and did not result in mitochondrial iron accumulation. We conclude that Mrs3/Mrs4 can sequester iron within mitochondria under aerobic conditions but not anaerobic conditions. We show that iron toxicity in ?ccc1 cells occurred under both aerobic and anaerobic conditions. Microarray analysis showed no evidence of oxidative damage under anaerobic conditions, suggesting that iron toxicity may not be solely due to oxidative damage. Deletion of TSA1, which encodes a peroxiredoxin, exacerbated iron toxicity in ?ccc1 cells under both aerobic and anaerobic conditions, suggesting a unique role for Tsa1 in iron toxicity.

Lin, Huilan; Li, Liangtao; Jia, Xuan; Ward, Diane McVey; Kaplan, Jerry

2011-01-01

61

Molecular genetics in the high-school science curriculum  

SciTech Connect

The development of a curriculum at the high school level for genetics with experimental methods from molecular biology is described. The laboratory work includes protocols involving nucleic acids and proteins.

Ehrman, P.G.; Fritz, L.K.

1987-11-01

62

A Twin Study of ADHD Symptoms in Early Adolescence: Hyperactivity-impulsivity and Inattentiveness Show Substantial Genetic Overlap but Also Genetic Specificity  

Microsoft Academic Search

A previous paper in this journal revealed substantial genetic overlap between the ADHD dimensions of hyperactivity-impulsivity\\u000a and inattentiveness in a sample of 8-year old twins drawn from a UK-representative population sample. Four years later, when\\u000a the twins were 12 years old, more than 5,500 pairs drawn from the same sample were rated again on the DSM-IV based Revised\\u000a Conners’ Parent Rating

Corina U. Greven; Frühling V. Rijsdijk; Robert Plomin

2011-01-01

63

Pinus pinaster seedlings and their fungal symbionts show high plasticity in phosphorus acquisition in acidic soils.  

PubMed

Young seedlings of maritime pine (Pinus pinaster Soland in Aït.) were grown in rhizoboxes using intact spodosol soil samples from the southwest of France, in Landes of Gascogne, presenting a large variation of phosphorus (P) availability. Soils were collected from a 93-year-old unfertilized stand and a 13-year-old P. pinaster stand with regular annual fertilization of either only P or P and nitrogen (N). After 6 months of culture in controlled conditions, different morphotypes of ectomycorrhiza (ECM) were used for the measurements of acid phosphatase activity and molecular identification of fungal species using amplification of the ITS region. Total biomass, N and P contents were measured in roots and shoots of plants. Bicarbonate- and NaOH-available inorganic P (Pi), organic P (Po) and ergosterol concentrations were measured in bulk and rhizosphere soil. The results showed that bulk soil from the 93-year-old forest stand presented the highest Po levels, but relatively higher bicarbonate-extractable Pi levels compared to 13-year-old unfertilized stand. Fertilizers significantly increased the concentrations of inorganic P fractions in bulk soil. Ergosterol contents in rhizosphere soil were increased by fertilizer application. The dominant fungal species was Rhizopogon luteolus forming 66.6% of analysed ECM tips. Acid phosphatase activity was highly variable and varied inversely with bicarbonate-extractable Pi levels in the rhizosphere soil. Total P or total N in plants was linearly correlated with total plant biomass, but the slope was steep only between total P and biomass in fertilized soil samples. In spite of high phosphatase activity in ECM tips, P availability remained a limiting nutrient in soil samples from unfertilized stands. Nevertheless young P. pinaster seedlings showed a high plasticity for biomass production at low P availability in soils. PMID:19840995

Ali, M A; Louche, J; Legname, E; Duchemin, M; Plassard, C

2009-10-19

64

Genetic Variants of Coagulation Factor XI Show Association with Ischemic Stroke Up to 70 Years of Age  

PubMed Central

Background and Purpose Coagulation factor XI (FXI) has an important role in the propagation and stabilization of a thrombus upon vessel injury. High FXI levels have been implicated in thrombotic diseases including ischemic stroke. The aim of our study was to investigate whether FXI gene (F11) variants are associated with ischemic stroke. Methods The discovery sample, the Sahlgrenska Academy Study on Ischemic Stroke (SAHLSIS), included 844 patients with ischemic stroke and 668 controls, all aged 18-70 years. Replication was performed in the Lund Stroke Register (LSR) and Malmö Diet and Cancer study (MDC), together including 1213 patients and 788 controls up to 70 years of age, and in total 3145 patients and 1793 controls (18-102 years). Seven F11 single-nucleotide polymorphisms (SNPs) were selected using a tagging approach. Results The SNPs rs3733403, rs925451, and rs1593 showed independent associations with overall ischemic stroke in SAHLSIS, ORs of 0.74 (95% CI 0.59-0.94), 1.24 (95% CI 1.06-1.46), and 0.70 (95% CI 0.55-0.90), respectively. The association for rs925451 was replicated in the LSR and MDC sample in a pre-specified analysis of subjects aged 70 years or younger, OR of 1.16 (95% CI 1.00-1.34), whereas no SNP was replicated when all ages were included. In line with this, one F11 haplotype was associated with overall ischemic stroke in the discovery sample and in the replication sample ?70 years. Conclusions We found significant associations between F11 variation and overall ischemic stroke up to 70 years of age. These findings motivate further studies on the role of F11 in ischemic stroke, especially in younger individuals.

Hanson, Ellen; Nilsson, Staffan; Jood, Katarina; Norrving, Bo; Engstrom, Gunnar; Blomstrand, Christian; Lindgren, Arne; Melander, Olle; Jern, Christina

2013-01-01

65

Genetic diversity on the Comoros Islands shows early seafaring as major determinant of human biocultural evolution in the Western Indian Ocean.  

PubMed

The Comoros Islands are situated off the coast of East Africa, at the northern entrance of the channel of Mozambique. Contemporary Comoros society displays linguistic, cultural and religious features that are indicators of interactions between African, Middle Eastern and Southeast Asian (SEA) populations. Influences came from the north, brought by the Arab and Persian traders whose maritime routes extended to Madagascar by 700-900 AD. Influences also came from the Far East, with the long-distance colonisation by Austronesian seafarers that reached Madagascar 1500 years ago. Indeed, strong genetic evidence for a SEA, but not a Middle Eastern, contribution has been found on Madagascar, but no genetic trace of either migration has been shown to exist in mainland Africa. Studying genetic diversity on the Comoros Islands could therefore provide new insights into human movement in the Indian Ocean. Here, we describe Y chromosomal and mitochondrial genetic variation in 577 Comorian islanders. We have defined 28 Y chromosomal and 9 mitochondrial lineages. We show the Comoros population to be a genetic mosaic, the result of tripartite gene flow from Africa, the Middle East and Southeast Asia. A distinctive profile of African haplogroups, shared with Madagascar, may be characteristic of coastal sub-Saharan East Africa. Finally, the absence of any maternal contribution from Western Eurasia strongly implicates male-dominated trade and religion as the drivers of gene flow from the North. The Comoros provides a first view of the genetic makeup of coastal East Africa. PMID:20700146

Msaidie, Said; Ducourneau, Axel; Boetsch, Gilles; Longepied, Guy; Papa, Kassim; Allibert, Claude; Yahaya, Ali Ahmed; Chiaroni, Jacques; Mitchell, Michael J

2010-08-11

66

High volume molecular genetic identification of single nucleotide polymorphisms using Genetic Bit Analysis Application to human genetic diagnosis  

SciTech Connect

The most common type of genetic disease-associated mutation is the single nucleotide polymorphism (SNP). Because most genetic diseases can be caused by multiple SNPs in the same gene, effective routine diagnosis of complex genetic diseases is dependent on a simple and reliable method of interrogating SNP sites. Molecular Tool`s solid phase assay capable of direct genotyping (single base sequencing) of SNP sites, Genetic Bit Analysis (GBA), involves hybridization-capture of a single-stranded PCR product to a sequence-specific, microtiter plate-bound oligonucleotide primer. The captured PCR product then acts as template for single-base extension of the capture primer across the polymorphic site, enabling direct determination of the base composition of the polymorphism through a simple colormetric assay. Genotyping in a high volume, semi-automated, processing system with a current capacity of 100 SNP interrogations per technician per day enables the screening of candidate mutations rapidly and cost-effectively, critically important to comprehensive genetic diagnosis. Using this gel-free technology, we have developed prototype diagnostic tests for CFTR and ApoE polymorphisms which enable direct sequencing of the polymorphic base at each site of interest. Routine clinical diagnosis of genetically complex diseases such as cystic fibrosis is dependent on this combination of robust biochemistry and simple format. Additionally, the ability to transfer the format and biochemistry to any disease gene of interest enables the broad application of this technology to clinical diagnostics, especially for genetically complex diseases.

Boyce-Jacino, M.T.; Reynolds, J.; Nikiforov, T. [Molecular Tool, Inc., Baltimore, MD (United States)] [and others

1994-09-01

67

High and low sensation seeking adolescents show distinct patterns of brain activity during reward processing.  

PubMed

Previous research has shown that personality characteristics, such as sensation seeking (SS), are strong predictors of risk-taking behavior during adolescence. However, the relationship between levels of SS and brain response has not been studied during this time period. Given the prevalence of risky behavior during adolescence, it is important to understand neurobiological differences in reward sensitivity between youth with high and low SS personalities. To this end, we used functional magnetic resonance imaging (fMRI) to examine differences in brain activity in an adolescent sample that included 27 high (HSS) and 27 low sensation seekers (LSS), defined by the Impulsive Sensation Seeking scale of the Zuckerman-Kuhlman Personality Questionnaire (Zuckerman et al., 1993). In the scanner, participants played a modified Wheel of Fortune decision-making task (Cservenka and Nagel, 2012) that resulted in trials with monetary Wins or No Wins. We compared age- and sex-matched adolescent HSS and LSS (mean age=13.94±1.05) on brain activity by contrasting Win vs. No Win trials. Our findings indicate that HSS show greater bilateral insular and prefrontal cortex (PFC) brain response on Win vs. No Win compared to LSS. Analysis of simple effects showed that while LSS showed comparable brain activity in these areas during Wins and No Wins, HSS showed significant differences in brain response to winning (activation) vs. not winning (deactivation), with between-group comparison suggesting significant differences in brain response, largely to reward absence. Group differences in insular activation between reward receipt and absence may suggest weak autonomic arousal to negative outcomes in HSS compared with LSS. Additionally, since the PFC is important for goal-directed behavior and attention, the current results may reflect that HSS allocate fewer attentional resources to negative outcomes than LSS. This insensitivity to reward absence in HSS may lead to a greater likelihood of maladaptive choices when negative consequences are not considered, and may be an early neural marker of decreased loss sensitivity that has been seen in addiction. This neurobiological information may ultimately be helpful in establishing prevention strategies aimed at reducing youth risk-taking and suggests value in further examination of neural associations with personality characteristics during adolescence. PMID:23142276

Cservenka, Anita; Herting, Megan M; Seghete, Kristen L Mackiewicz; Hudson, Karen A; Nagel, Bonnie J

2012-11-01

68

High-resolution ?13C measurements of oak show a previously unobserved spring depletion  

NASA Astrophysics Data System (ADS)

We have subdivided single tree rings into between 24 and 35 contiguous samples and measured the ?13C value for each. These high-resolution measurements show a previously unobserved spring depletion as part of a pattern of enrichment-depletion-enrichment-depletion through a single growing season as opposed to the depletion-enrichment-depletion cycle previously thought to exist. The earlywood/latewood transition does not coincide with identifiable isotopic boundaries and therefore is not a suitable demarcation point for sampling as part of palaeoclimatic study. Latewood and post spring depletion values of ?13C were separately correlated with geophysical parameters. Post spring depletion wood yielded better correlations and is therefore more suitable for palaeoclimatic study.

Ogle, Neil; McCormac, F. G.

1994-11-01

69

Environmental toxicology: population modeling of cod larvae shows high sensitivity to loss of zooplankton prey.  

PubMed

Two factors determine whether pollution is likely to affect a population indirectly through loss of prey: firstly, the sensitivity of the prey to the pollutants, and secondly, the sensitivity of the predator population to loss of prey at the given life stage. We here apply a statistical recruitment model for Northeast Arctic cod to evaluate the sensitivity of cod cohorts to loss of zooplankton prey, for example following an oil spill. The calculations show that cod cohorts are highly sensitive to possible zooplankton biomass reductions in the distribution area of the cod larvae, and point to a need for more knowledge about oil-effects on zooplankton. Our study illustrates how knowledge about population dynamics may guide which indirect effects to consider in environmental impact studies. PMID:21194716

Stige, Leif Christian; Ottersen, Geir; Hjermann, Dag Ø; Dalpadado, Padmini; Jensen, Louise K; Stenseth, Nils Chr

2010-12-30

70

Pyrimidine based highly sensitive fluorescent receptor for Al3+ showing dual signalling mechanism.  

PubMed

A new fluorescent probe (5-[(4-diethylamino-2-hydroxy-benzylidene)-amino]-1H-pyrimidine-2, 4-dione) (Receptor 1) has been synthesized by the Schiff base condensation of 5-aminouracil with 4-(diethylamino)salicylaldehyde. The receptor 1 exhibits high selectively for Al(3+) in DMSO as well as in aqueous solution even in the presence of biologically relevant cations such as Na(+), K(+), Ca(2+), Mg(2+), Pb(2+) and several transition metal ions. The lowest detection limit for the receptor 1 was found to be 1.62 × 10(-10) M with its linear response towards Al(3+) in the concentration range of 1.75 × 10(-9) to 3.3 × 10(-8) M in DMSO. Receptor 1 is the first ever example where a single molecular probe is able to show imine (C=N) isomerization inhibition along with twisted intramolecular charge transfer (TICT) in combinatorial fashion. PMID:20820652

Upadhyay, K K; Kumar, Ajit

2010-08-31

71

Children with High Functioning Autism show increased prefrontal and temporal cortex activity during error monitoring  

PubMed Central

Evidence exists for deficits in error monitoring in autism. These deficits may be particularly important because they may contribute to excessive perseveration and repetitive behavior in autism. We examined the neural correlates of error monitoring using fMRI in 8–12-year-old children with high-functioning autism (HFA, n=11) and typically developing children (TD, n=15) during performance of a Go/No-Go task by comparing the neural correlates of commission errors versus correct response inhibition trials. Compared to TD children, children with HFA showed increased BOLD fMRI signal in the anterior medial prefrontal cortex (amPFC) and the left superior temporal gyrus (STempG) during commission error (versus correct inhibition) trials. A follow-up region-of-interest analysis also showed increased BOLD signal in the right insula in HFA compared to TD controls. Our findings of increased amPFC and STempG activity in HFA, together with the increased activity in the insula, suggest a greater attention towards the internally-driven emotional state associated with making an error in children with HFA. Since error monitoring occurs across different cognitive tasks throughout daily life, an increased emotional reaction to errors may have important consequences for early learning processes.

Goldberg, Melissa C.; Spinelli, Simona; Joel, Suresh; Pekar, James J.; Denckla, Martha B.; Mostofsky, Stewart H.

2010-01-01

72

Role of TNF-? in renal damage in mice showing hepatic steatosis induced by high fat diet.  

PubMed

The present study was designed to investigate the role of TNF-? in renal damage observed in mice with hepatic steatosis. We induced hepatic steatosis in mice using high fat diet and treated mice with ectanercept at the dose sufficient to block TNF-? receptors or vehicle for 1 month. Plasma TNF-?, total cholesterol (TC), triglyceride (TG), LDL-cholesterol (LDL-C), and HDL-cholesterol (HDL-C) were determined at the end of this treatment. Renal damage was identified by histologic observation and the higher of serum blood urea nitrogen (BUN) and creatinine. Also, changes of PPAR-? in kidney and renal mesangial cell (RMC) were analyzed using Western blot. Plasma TNF-? was markedly raised in mice showing hepatic steatosis. However, the levels of blood lipids (TC, TG, HDL-C, and LDL-C) and TNF-? were not modified by the treatment of etanercept although the hepatic steatosis has been improved. Etanercept shows renal protection from histological identification and recovery of serum BUN and creatinine levels. Moreover, restoration of PPAR-? expression by etanercept was observed in mice kidney. Direct effect of TNF-? on PPAR-? expression was also characterized in RMC cell. We suggest that renal damage in mice with hepatic steatosis is mainly induced by increase of TNF-? through the decrease of renal PPAR-?. Etanercept could block TNF-? receptors to restore PPAR-? and improve renal function in mice with hepatic steatosis. PMID:22956307

Lai, Y H; Chen, L J; Cheng, J T

2012-09-06

73

? sulphate PNA (PNA S): Highly Selective DNA Binding Molecule Showing Promising Antigene Activity  

PubMed Central

Peptide Nucleic Acids (PNAs), nucleic acid analogues showing high stability to enzyme degradation and strong affinity and specificity of binding toward DNA and RNA are widely investigated as tools to interfere in gene expression. Several studies have been focused on PNA analogues with modifications on the backbone and bases in the attempt to overcome solubility, uptake and aggregation issues. ? PNAs, PNA derivatives having a substituent in the ? position of the backbone show interesting properties in terms of secondary structure and affinity of binding toward complementary nucleic acids. In this paper we illustrate our results obtained on new analogues, bearing a sulphate in the ? position of the backbone, developed to be more DNA-like in terms of polarity and charge. The synthesis of monomers and oligomers is described. NMR studies on the conformational properties of monomers and studies on the secondary structure of single strands and triplexes are reported. Furthermore the hybrid stability and the effect of mismatches on the stability have also been investigated. Finally, the ability of the new analogue to work as antigene, interfering with the transcription of the ErbB2 gene on a human cell line overexpressing ErbB2 (SKBR3), assessed by FACS and qPCR, is described.

Avitabile, Concetta; Moggio, Loredana; Malgieri, Gaetano; Capasso, Domenica; Di Gaetano, Sonia; Saviano, Michele; Pedone, Carlo; Romanelli, Alessandra

2012-01-01

74

Antagonists show GTP-sensitive high-affinity binding to the sigma-1 receptor  

PubMed Central

BACKGROUND AND PURPOSE Sigma-1 receptors are atypical receptors with potentially two transmembrane domains. Antagonists require doses significantly higher than their published affinities to have biological effects. We have reassessed the binding characteristics of these ligands and found antagonists bind to high- and low-affinity states not distinguished by agonists. EXPERIMENTAL APPROACH The affinities of sigma-1 receptor ligands was assessed using radioligand saturation and competition binding of [3H]-(+)-pentazocine to permeabilized MDA-MB-468 cells. This was compared with the effect of ligands on metabolic activity using an MTS-based assay and calcium signalling using cells loaded with the calcium dye, Fura-2. KEY RESULTS Sigma-1 receptor antagonists, but not agonists, show GTP- and suramin-sensitive high-affinity binding. Functional responses (calcium signalling and metabolic activity), while associated with sigma-1 receptor binding, required binding to an unidentified, low-affinity target. CONCLUSIONS AND IMPLICATIONS Sigma-1 receptors are coupled to G proteins. This interaction is only observed when analysing antagonist binding. The identity of the G protein remains to be resolved. The concept of agonist and antagonist at the sigma-1 receptor needs to be revisited.

Brimson, JM; Brown, CA; Safrany, ST

2011-01-01

75

A novel lectin from Agrocybe aegerita shows high binding selectivity for terminal N-acetylglucosamine  

PubMed Central

A novel lectin was isolated from the mushroom Agrocybe aegerita (designated AAL-2) by affinity chromatography with GlcNAc (N-acetylglucosamine)-coupled Sepharose 6B after ammonium sulfate precipitation. The AAL-2 coding sequence (1224 bp) was identified by performing a homologous search of the five tryptic peptides identified by MS against the translated transcriptome of A. aegerita. The molecular mass of AAL-2 was calculated to be 43.175 kDa from MS, which was consistent with the data calculated from the amino acid sequence. To analyse the carbohydrate-binding properties of AAL-2, a glycan array composed of 465 glycan candidates was employed, and the result showed that AAL-2 bound with high selectivity to terminal non-reducing GlcNAc residues, and further analysis revealed that AAL-2 bound to terminal non-reducing GlcNAc residues with higher affinity than previously well-known GlcNAc-binding lectins such as WGA (wheatgerm agglutinin) and GSL-II (Griffonia simplicifolia lectin-II). ITC (isothermal titration calorimetry) showed further that GlcNAc bound to AAL-2 in a sequential manner with moderate affinity. In the present study, we also evaluated the anti-tumour activity of AAL-2. The results showed that AAL-2 could bind to the surface of hepatoma cells, leading to induced cell apoptosis in vitro. Furthermore, AAL-2 exerted an anti-hepatoma effect via inhibition of tumour growth and prolongation of survival time of tumour-bearing mice in vivo.

Jiang, Shuai; Chen, Yijie; Wang, Man; Yin, Yalin; Pan, Yongfu; Gu, Bianli; Yu, Guojun; Li, Yamu; Wong, Barry Hon Cheung; Liang, Yi; Sun, Hui

2012-01-01

76

Genetic toxicity of high-boiling petroleum substances.  

PubMed

There are several specific types of high-boiling petroleum substances (HBPS) having final boiling points >343°C, in which genetic toxicity can be related to the content of polycyclic aromatic compounds (PACs), specifically crude oils, gas oils, heavy fuel oils, lubricant base oils, waxes and aromatic extracts. Evaluation of optimized Salmonella tests covering over 250 samples from 43 types of HBPS revealed that gene mutation can be determined for these substances using a protocol optimized for the detection of mutagenic PAC. The outcomes of modified Salmonella assays can be predicted using HBPS compositional information as input to a newly developed statistical model. The general outcome of the optimized Salmonella assay can be predicted for an untested substance based on its Aromatic Ring Class (ARC) profile. Review of the results from numerous cytogenetic tests showed that although a few positive study results have been reported, most HBPS do not produce chromosomal effects when tested in rodent bone marrow assays or in in vitro chromosomal aberration assays. Results of both bacterial and cytogenetic studies can be used to satisfy genetic toxicity endpoints for the HBPS category substances. PMID:23685115

McKee, Richard H; Schreiner, Ceinwen A; Nicolich, Mark J; Gray, Thomas M

2013-05-14

77

Genetically resistant (Ityr) and susceptible (Itys) congenic mouse strains show similar cytokine responses following infection with Salmonella dublin.  

PubMed

IFN-gamma, TNF-alpha, IL-1, and granulocyte-macrophage CSF (GM-CSF) play an important role in host resistance to infection with nontyphoid Salmonella. In mice, resistance to Salmonella is determined by alleles of the susceptibility gene, Nramp, which maps to the Ity/Lsh/Bcg locus and is expressed in macrophages. In vitro studies suggested that macrophages from Salmonella-susceptible mice (Itys phenotype) are impaired functionally in their ability to produce, or stimulate the production of, cytokines such as TNF-alpha and IFN-gamma. BALB/c and BALB/c.DBA2 Idh-lb-Ityr-Pep-3b mice are congenic strains that differ at the Ity/Lsh/Bcg locus and in their susceptibility to Salmonella infection. These strains were used to question whether differences in the host cytokine response determine the outcome of Salmonella infection in genetically susceptible and resistant mice. As reported in this work, the in vivo response to Salmonella dublin infection in both Itys and Ityr mice was characterized by increased expression of IFN-gamma, TNF-alpha, GM-CSF, IL-1 alpha, IL-2, IL-6, IL-10, and IL-12 p40. In contrast, expression of IL-4, IL-5, and TGF-beta 1 was not altered, or decreased, during the course of infection. Moreover, the kinetics and magnitude of the cytokine response following S. dublin infection were similar in susceptible Itys and resistant Ityr mice, even though the former group died while the latter survived the infection. Thus, in vivo cytokine responses that are associated with survival of Ityr mice following S. dublin infection do not confer protection in mice of the Itys phenotype. PMID:8609409

Eckmann, L; Fierer, J; Kagnoff, M F

1996-04-15

78

Interdisciplinarity, Debate And Movie Clips As Highly Motivating Factors In Live Shows - Five Years Of Success  

NASA Astrophysics Data System (ADS)

A live show on any subject that includes experiments and continuous interaction with the audience is a well known approach for EPO activities that many are carrying out all over. We present such an initiative with some added ingredients such as interdisciplinarity, the use of movie clips, and especially the debate between the two presenters, a debate that is all the more attractive to the public if it not fully staged but closely represents their actual points of view. José Montesinos, from the "Orotava" Canarian Foundation for the History of Science, is and plays the role of the more mature math professor who has grown weary of the overrated value given in science to mathematics and its consequences. This poses a constant challenge to his colleague, Erik Stengler, from the Science Museum of Tenerife, the young down-to-earth hands-on scientist, who defends the usual view that science and technology are to be judged by their achievements, which have brought about the advancement of modern society. With this approach and as a collaboration between our institutions, we have produced and toured highly successful activities on: Einstein and Relativity (from 2005 to 2008, "Einstein Goes To School," including a theatre play); circularity, the number ?, forces of inertia and the Newtonian revolution (in 2008/2009, "The Tension Between Circularity and The Straight Line"); and the foundations of modern astronomy (in 2009/2010 "Kepler and Galileo, Messengers of the Stars"). Audiences were very varied - students, adult students, general public, prison inmates, teachers - and all appreciated the presentations as fun, thought-provoking and highly motivating, and valued especially the interdisciplinary character of the activity. Movie clips have shown to be especially useful to recover the attention of the young when they lose the thread due to the short attention spans they presently have.

Stengler, E.; Sirera, J. M.

2011-09-01

79

Indirect Genetic Effects for Survival in Domestic Chickens (Gallus gallus) Are Magnified in Crossbred Genotypes and Show a Parent-of-Origin Effect  

PubMed Central

Through social interactions, individuals can affect one another’s phenotype. The heritable effect of an individual on the phenotype of a conspecific is known as an indirect genetic effect (IGE). Although IGEs can have a substantial impact on heritable variation and response to selection, little is known about the genetic architecture of traits affected by IGEs. We studied IGEs for survival in domestic chickens (Gallus gallus), using data on two purebred lines and their reciprocal cross. Birds were kept in groups of four. Feather pecking and cannibalism caused mortality, as beaks were kept intact. Survival time was shorter in crossbreds than in purebreds, indicating outbreeding depression and the presence of nonadditive genetic effects. IGEs contributed the majority of heritable variation in crossbreds (87 and 72%) and around half of heritable variation in purebreds (65 and 44%). There was no evidence of dominance variance, neither direct nor indirect. Absence of dominance variance in combination with considerable outbreeding depression suggests that survival is affected by many loci. Direct–indirect genetic correlations were moderately to highly negative in crossbreds (?0.37 ± 0.17 and ?0.83 ± 0.10), but low and not significantly different from zero in purebreds (0.20 ± 0.21 and ?0.28 ± 0.18). Consequently, unlike purebreds, crossbreds would fail to respond positively to mass selection. The direct genetic correlation between both crosses was high (0.95 ± 0.23), whereas the indirect genetic correlation was moderate (0.41 ± 0.26). Thus, for IGEs, it mattered which parental line provided the sire and which provided the dam. This indirect parent-of-origin effect appeared to be paternally transmitted and is probably Z chromosome linked.

Peeters, K.; Eppink, T. T.; Ellen, E. D.; Visscher, J.; Bijma, P.

2012-01-01

80

Indirect genetic effects for survival in domestic chickens (Gallus gallus) are magnified in crossbred genotypes and show a parent-of-origin effect.  

PubMed

Through social interactions, individuals can affect one another's phenotype. The heritable effect of an individual on the phenotype of a conspecific is known as an indirect genetic effect (IGE). Although IGEs can have a substantial impact on heritable variation and response to selection, little is known about the genetic architecture of traits affected by IGEs. We studied IGEs for survival in domestic chickens (Gallus gallus), using data on two purebred lines and their reciprocal cross. Birds were kept in groups of four. Feather pecking and cannibalism caused mortality, as beaks were kept intact. Survival time was shorter in crossbreds than in purebreds, indicating outbreeding depression and the presence of nonadditive genetic effects. IGEs contributed the majority of heritable variation in crossbreds (87 and 72%) and around half of heritable variation in purebreds (65 and 44%). There was no evidence of dominance variance, neither direct nor indirect. Absence of dominance variance in combination with considerable outbreeding depression suggests that survival is affected by many loci. Direct-indirect genetic correlations were moderately to highly negative in crossbreds (-0.37 ± 0.17 and -0.83 ± 0.10), but low and not significantly different from zero in purebreds (0.20 ± 0.21 and -0.28 ± 0.18). Consequently, unlike purebreds, crossbreds would fail to respond positively to mass selection. The direct genetic correlation between both crosses was high (0.95 ± 0.23), whereas the indirect genetic correlation was moderate (0.41 ± 0.26). Thus, for IGEs, it mattered which parental line provided the sire and which provided the dam. This indirect parent-of-origin effect appeared to be paternally transmitted and is probably Z chromosome linked. PMID:22851648

Peeters, K; Eppink, T T; Ellen, E D; Visscher, J; Bijma, P

2012-07-30

81

[Comparative chromosome painting shows the red panda (Ailurus fulgens) has a highly conserved karyotype].  

PubMed

We have established a comparative chromosome map between red panda (Ailurus fulgens, 2n = 36) and dog by chromosome painting with biotin-labelled chromosome-specific probes of the dog. Dog probes specific for the 38 automates delineated 71 homologous segments in the metaphase chromosomes of red panda. Of the 38 autosomal paints, 18 probes each delineated one homologous segment in red panda genome, while the other 20 ones each detected two to five homologous segments. The dog X chromosome-specific paint delineated the whole X chromosome of the red panda. The results indicate that at least 28 fissions (breaks), 49 fusions and 4 inversions were needed to "convert" the dog karyotype to that of the red panda, suggesting that extensive chromosome rearrangements differentiate the karyotypes of red panda and dog. Based on the established comparative chromosome homologies of dog and domestic cat, we could infer that there were 26 segments of conserved synteny between red panda and domestic cat. Comparative analysis of the distribution patterns of conserved segments defined by dog paints in red panda and domestic cat genomes revealed at least 2 cryptic inversions in two large chromosomal regions of conserved synteny between red panda and domestic cat. The karyotype of red panda shows high degree of homology with that of domestic cat. PMID:11901994

Tian, Ying; Nie, Wen-Hui; Wang, Jin-Huan; Yang, Yun-Fei; Yang, Feng-Tang

2002-02-01

82

Genetic tagging shows increased frequency and longevity of antigen-presenting, skin-derived dendritic cells in vivo  

Microsoft Academic Search

Dendritic cells (DCs) are key regulators of immune responses that activate naive antigen-specific T lymphocytes. In draining lymph nodes, antigen-bearing DCs are reported to be rare and short-lived. How such small numbers of short-lived DCs can activate rare antigen-specific T cells is unclear. Here we show that after immunization of mouse skins by gene gun, the number of antigen-bearing DCs

Sanjay Garg; Alp Oran; Janine Wajchman; Shin Sasaki; Charles H Maris; Judith A Kapp; Joshy Jacob

2003-01-01

83

Molecular Characterization of Chinese Hamster Cells Mutants Affected in Adenosine Kinase and Showing Novel Genetic and Biochemical Characteristics  

Microsoft Academic Search

Background  Two isoforms of the enzyme adenosine kinase (AdK), which differ at their N-terminal ends, are found in mammalian cells. However,\\u000a there is no information available regarding the unique functional aspects or regulation of these isoforms.\\u000a \\u000a \\u000a \\u000a \\u000a Results  We show that the two AdK isoforms differ only in their first exons and the promoter regions; hence they arise via differential\\u000a splicing of their

Xianying A Cui; Tanvi Agarwal; Bhag Singh; Radhey S Gupta

2011-01-01

84

Relationships Among Molecular Genetic and Respiratory Properties of Parkinson's Disease Cybrid Cells Show Similarities to Parkinson's Brain Tissues  

PubMed Central

We have studied sporadic Parkinson’s disease (sPD) from expression of patient mitochondrial DNA (mtDNA) in neural cells devoid of their own mtDNA, the “cybrid” model. In spite of reproducing several properties of sPD brain, it remains unclear whether sPD cybrid cells reflect more complex sPD brain bioenergetic pathophysiology. We characterized and correlated respiration of intact sPD cybrid cells with electron transport chain (ETC) protein assembly, complex I ETC gene expression and ETC protein levels in sPD brain. We also assayed expression for multiple ETC genes coded by mtDNA and nuclear DNA (nDNA) in sPD cybrid cells and brain. sPD cybrid cells have reduced levels of mtDNA genes, variable compensatory normalization of mitochondrial gene expression and show robust correlations with mitochondrial ETC gene expression in sPD brains. Relationships among ETC protein levels predict impaired complex I-mediated respiration in sPD brain. That sPD cybrid cells and sPD brain samples show very correlated regulation of nDNA and mtDNA ETC transcriptomes suggests similar bioenergetic physiologies. We propose that further insights into sPD pathogenesis will follow elucidation of mechanisms leading to reduced mtDNA gene levels in spD cybrids. This will require characterization of the abnormalities and dynamics of mtDNA changes propagated through sPD cybrids over time.

Borland, M. Kathleen; Mohanakumar, K. P.; Rubinstein, Jeremy D.; Keeney, Paula M.; Xie, Jing; Capaldi, Roderick; Dunham, Lisa D.; Trimmer, Patricia A.; Bennett, James P.

2009-01-01

85

High genetic diversity and novelty in planktonic protists inhabiting inland and coastal high salinity water bodies.  

PubMed

We analyzed the genetic diversity (18S rRNA gene) of planktonic microbial eukaryotes in 34 different coastal and inland saline ponds. A wide range of environmental conditions was covered with up to 30-fold differences in salinity concentrations (12.5-384 g L(-1)), and in situ temperatures (1.3-37.5 °C), and three orders of magnitude in the trophic status (i.e. chlorophyll a < 0.1 to >50 mg L(-1)). Geographically distant sites were studied with contrasting salt origins, and different temporal patterns of wetting and drying. The genetic diversity was high, far beyond the few groups traditionally considered as high salinity-adapted, with sequences spread throughout eight high-rank taxonomic groups and 27 eukaryal classes. The novelty level was extremely high, with 10% of the whole dataset showing < 90% identity to any previously reported sequence in GenBank. Opisthokonta and Rhizaria contained the highest novelty and Chlorophyta and Alveolata the lowest. Low identity sequences were observed both in coastal and inland sites and at lower and at higher salinities, although the degree of novelty was higher in the hypersaline waters (> 6.5% salinity). Overall, this study shows important gaps in the current knowledge about protists inhabiting continental (hyper)saline water bodies, highlighting the need for future, more detailed investigations. PMID:23406313

Triadó-Margarit, Xavier; Casamayor, Emilio O

2013-03-11

86

X-ray survival characteristics and genetic analysis for nine saccharomyces deletion mutants that show altered radiation sensitivity  

SciTech Connect

The availability of a genome-wide set of Saccharomyces deletion mutants provides a chance to identify all the yeast genes involved in DNA repair. Using X-rays, we are screening these mutants to identify additional genes that show increased sensitivity to the lethal effects of ionizing radiation. For each mutant identified as sensitive, we are confirming that the sensitivity phenotype co-segregates with the deletion allele and are obtaining multipoint survival-versus-dose assays in at least two haploid and one homozygous diploid strains. We present data for deletion mutants involving the genes DOT1, MDM20, NAT3, SPT7, SPT20, GCN5, HFI1, DCC1 and VID21/EAF1, and discuss their potential roles in repair. Eight of these genes have a clear radiation-sensitive phenotype when deleted, but the ninth, GCN5, has at most a borderline phenotype. None of the deletions confer substantial sensitivity to ultra-violet radiation, although one or two may confer marginal sensitivity. The DOT1 gene is of interest because its only known function is to methylate one lysine residue in the core of the histone H3 protein. We find that histone H3 mutants (supplied by K. Struhl) in which this residue is replaced by other amino-acids are also X-ray sensitive, seeming to confirm that methylation of the lysine-79 residue is required for effective repair of radiation damage.

Game, John C.; Williamson, Marsha S.; Baccari, Clelia

2004-01-07

87

Microsatellite Typing of Clinical and Environmental Cryptococcus neoformans var. grubii Isolates from Cuba Shows Multiple Genetic Lineages  

PubMed Central

Background Human cryptococcal infections have been associated with bird droppings as a likely source of infection. Studies toward the local and global epidemiology of Cryptococcus spp. have been hampered by the lack of rapid, discriminatory, and exchangeable molecular typing methods. Methodology/Principal Findings We selected nine microsatellite markers for high-resolution fingerprinting from the genome of C. neoformans var. grubii. This panel of markers was applied to a collection of clinical (n?=?122) and environmental (n?=?68; from pigeon guano) C. neoformans var. grubii isolates from Cuba. All markers proved to be polymorphic. The average number of alleles per marker was 9 (range 5–51). A total of 104 genotypes could be distinguished. The discriminatory power of this panel of markers was 0.993. Multiple clusters of related genotypes could be discriminated that differed in only one or two microsatellite markers. These clusters were assigned as microsatellite complexes. The majority of environmental isolates (>70%) fell into 1 microsatellite complex containing only few clinical isolates (49 environmental versus 2 clinical). Clinical isolates were segregated over multiple microsatellite complexes. Conclusions/Significance A large genotypic variation exists in C. neoformans var. grubii. The genotypic segregation between clinical and environmental isolates from pigeon guano suggests additional source(s) of human cryptococcal infections. The selected panel of microsatellite markers is an excellent tool to study the epidemiology of C. neoformans var. grubii.

Illnait-Zaragozi, Maria-Teresa; Martinez-Machin, Gerardo F.; Fernandez-Andreu, Carlos M.; Boekhout, Teun; Meis, Jacques F.; Klaassen, Corne H. W.

2010-01-01

88

Amerindians show no association of PC-1 gene Gln121 allele and obesity: a thrifty gene population genetics.  

PubMed

PC-1 Gln121 gene is a risk factor for type 2 diabetes, obesity and insulin resistance in European/American Caucasoids and Orientals. We have aimed to correlate for the first time this gene in Amerindians with obesity and their corresponding individuals genotypes with obesity in order to establish preventive medicine programs for this population and also studying the evolution of gene frequencies in world populations. Central obesity was diagnosed by waist circumference perimeter and food intake independent HDL-cholesterol plasma levels were measured. HLA genes were determined in order to more objectively ascertain participants Amerindians origin. 321 Amerindian blood donors who were healthy according to the blood doning parameters were studied. No association was found between PC-1 Gln121 variant and obesity. Significant HDL-cholesterol lower values were found in the PC-1 Lys121 bearing gene individuals versus PC-1 Gln121 bearing gene ones (45.1 ± 12.7 vs. 48.7 ± 15.2 mg/dl, p < 0.05). Population analyses showed a world geographical gradient in the PC-1 Gln121 allele frequency: around 9% in Orientals, 15% in European Caucasoids and 76% in Negroids. The conclusions are: (1) No association of PC-1 Gln121 gene is found with obesity in Amerindians when association is well established in Europeans. (2) PC-1 Gln121 gene is associated to higher levels of HDL-cholesterol than the alternative PC-1 Lys121 allele. This may be specific for Amerindians. (3) Amerindians have an intermediate frequency of this possible PC-1 Gln121 thrifty gene when compared with Negroid African Americans (78.5%) or Han Chinese (7.5%, p < 0.0001). Historical details of African and other groups may support the hypothesis that PC-1 Gln121 is indeed a thrifty gene. PMID:22327785

Rey, Diego; Fernandez-Honrado, Mercedes; Areces, Cristina; Algora, Manuel; Abd-El-Fatah-Khalil, Sedeka; Enriquez-de-Salamanca, Mercedes; Coca, Carmen; Arribas, Ignacio; Arnaiz-Villena, Antonio

2012-02-12

89

Twenty Years Later: High School Students Who Showed Promise in Mathematics.  

ERIC Educational Resources Information Center

Data from longitudinal studies of high school students who took the Annual High School Mathematics Examination sponsored by the Mathematical Association of America (MAA) indicate that 56 percent of the top achievers pursued careers in mathematics or mathematically related fields. (MP)

Turner, Nura D.

1981-01-01

90

Molecular evaluation of foetuses with holoprosencephaly shows high incidence of microdeletions in the HPE genes.  

PubMed

Holoprosencephaly (HPE), the most common structural malformation of the forebrain in humans, can be detected early during pregnancy using prenatal ultrasonography . Among foetuses with a normal karyotype, 14% have mutations in the four main HPE genes (SHH, ZIC2, SIX3 and TGIF). Genomic rearrangements have now been implicated in many genetic diseases, so we hypothesized that microdeletions in the major HPE genes may also be common in HPE foetuses with severe phenotype or other associated malformations. We screened the DNA obtained from 94 HPE foetuses with a normal karyotype for the presence of microdeletions involving the four major HPE genes (SHH, ZIC2, SIX3 and TGIF). Thirteen of the foetuses had a point mutation in one of the 4 genes and 81 had no known mutations. Quantitative multiplex PCR of short fluorescent fragments (QMPSF) analysis was used for rapid determination of HPE genes copy numbers and the identified microdeletions were confirmed by real time quantitative PCR, or fluorescent in situ hybridization (FISH) (if a cell line was available). Microdeletions were detected in 8 of 94 foetuses (8.5%) (2 in SHH, 2 in SIX3, 3 in ZIC2 and 1 in TGIF genes), and only among the 81 foetuses with a normal karyotype and no point mutations. These data suggest that microdeletions in the four main HPE genes are a common cause of prenatal HPE, as well as point mutations, and increase the total diagnosis rate close to approximately 22.3% of foetuses with normal karyotype. Detection can be achieved by the QMPSF testing method that proved to be efficient for testing several genes in a single assay. PMID:16323008

Bendavid, Claude; Dubourg, Christèle; Gicquel, Isabelle; Pasquier, Laurent; Saugier-Veber, Pascale; Durou, Marie-Renée; Jaillard, Sylvie; Frébourg, Thierry; Haddad, Bassem R; Henry, Catherine; Odent, Sylvie; David, Véronique

2005-12-02

91

Study Shows Aspirin Reduces Colorectal Cancer in Those at High Risk  

Cancer.gov

Findings from the first large clinical trial of its kind indicate that taking high doses of aspirin daily for at least 2 years substantially reduces the risk of colorectal cancer among people at increased risk of the disease.

92

An advantage of magnetic index ? to show high local disturbances in ionosphere during quiet day conditions.  

NASA Astrophysics Data System (ADS)

We analysed data of ionospheric characteristics (foE, foEs, foF2, h'E, h'F2) during 30-day long quiet day conditions (Kp = 0-2) in 2004. We found correlations between high local disturbances in ionosphere during very quiet days and high values of magnetic index ?. The coexistence of E sporadic layer or high local disturbances of the foE during magnetically very quiet days with large values of magnetic index ? will be shown. The not large amount of analysed quiet days and area limited only to Europe and South Africa are not enough to prove thesis that ? index is perfect to predict existence of E sporadic layer.

Dziak-Jankowska, Beata; Stanislawska, Iwona; Buresova, Dalia; Ernst, Tomasz; Tomasik, Lukasz

2010-05-01

93

Principals of Religious and Religious-Affiliated High Schools: What the Data Show  

Microsoft Academic Search

The following data were developed as part of the National High School Principal Study conducted by NASSP. Because this aspect of the study was not treated as a separate analysis in the three-volume report1 it is considered here.

George A. Wanaski; Lloyd E. McCleary

1980-01-01

94

Modeling and Inquiry in a High School Genetics Class  

ERIC Educational Resources Information Center

In this article, the authors discuss their belief in organizing curricula around sets of causal models in order to provide students with opportunities not only to learn about the subject matter of particular disciplines, but also about how scientific knowledge is generated and justified. They describe a nine-week genetics course for high school…

Cartier, Jennifer L.; Stewart, Jim; Zoellner, Brian

2006-01-01

95

High speed frequency response masking filter design using genetic algorithm  

Microsoft Academic Search

This paper presents the design of high-speed, multiplier free, arbitrary bandwidth shape FIR filters based on frequency response masking technique (FRM). The FRM filter structure has been modified to improve the throughput by replacing long bandedge shaping filter with several cascaded short filters [Yong Lian, 2000]. Genetic algorithm (GA) is introduced to simultaneously optimize all subfilters in a cascaded connection.

Ling Cen; Yong Lian

2003-01-01

96

Genetic susceptibility to childhood acute lymphoblastic leukemia shows protection in Malay boys: results from the Malaysia-Singapore ALL Study Group.  

PubMed

To study genetic epidemiology of childhood acute lymphoblastic leukemia (ALL) in the Chinese and Malays, we investigated 10 polymorphisms encoding carcinogen- or folate-metabolism and transport. Sex-adjusted analysis showed NQO1 609CT significantly protects against ALL, whilst MTHFR 677CT confers marginal protection. Interestingly, we observed that NQO1 609CT and MTHFR 1298 C-allele have greater genetic impact in boys than in girls. The combination of SLC19A1 80GA heterozygosity and 3'-TYMS -6bp/-6bp homozygous deletion is associated with reduced ALL risk in Malay boys. Our study has suggested the importance of gender and race in modulating ALL susceptibility via the folate metabolic pathway. PMID:19651439

Yeoh, Allen Eng-Juh; Lu, Yi; Chan, Jason Yong-Sheng; Chan, Yiong Huak; Ariffin, Hany; Kham, Shirley Kow-Yin; Quah, Thuan Chong

2009-08-03

97

A cDNA clone highly expressed in ripe banana fruit shows homology to pectate lyases  

Microsoft Academic Search

A cDNA clone (Banl7), encoding a protein homologous to pec- tate lyase, has been isolated from a cDNA library from climacteric banana fruit by means of differential screening. Northern analysis showed that Banl7 mRNA is first detected in early climacteric fruit, reaches a steady-state maximum at the climacteric peak, and de- clines thereafter in overripe fruit. Accumulation of the Banl7

Eva Dominguez-Puigjaner; Miquel Vendrell; Salomé Prat

1997-01-01

98

The Caenorhabditis elegans intermediate-size transcriptome shows high degree of stage-specific expression  

PubMed Central

Earlier studies have revealed a substantial amount of transcriptional activity occurring outside annotated protein-coding genes of the Caenorhabditis elegans genome. One important fraction of this transcriptional activity relates to intermediate-size (70–500?nt) transcripts (is-ncRNAs) of mostly unknown function. Profiling the expression of this segment of the transcriptome on a tiling array through the C. elegans life cycle identified 5866 hitherto unannotated transcripts. The novel loci were distributed across intronic and intergenic space, with some enrichment toward protein-coding gene termini. The majority of the putative is-ncRNAs showed either stage-specific expression, or distinct developmental variation in their expression levels. More than 200 loci showed male-specific expression, and conserved loci were significantly enriched on the X chromosome, both observations strongly suggesting involvement of is-ncRNAs in sex-specific functions. Half of the novel loci were conserved in other nematodes, and numerous loci showed significant conservational correlations to nearby coding genes. Assuming functional roles for most of the novel loci, the data imply a nematode is-ncRNA tool kit of considerable size and variety.

Wang, Yunfei; Chen, Jingjing; Wei, Guifeng; He, Housheng; Zhu, Xiaopeng; Xiao, Tengfei; Yuan, Jiao; Dong, Bo; He, Shunmin; Skogerb?, Geir; Chen, Runsheng

2011-01-01

99

Patients treated with high-dose intravenous immunoglobulin show selective activation of regulatory T cells.  

PubMed

Intravenous immunoglobulin (IVIg) is used to treat autoimmune and systemic inflammatory diseases caused by derailment of humoral and cellular immunity. In this study we investigated whether IVIg treatment can modulate regulatory T cells (Tregs ) in humans in vivo. Blood was collected from IVIg-treated patients with immunodeficiency or autoimmune disease who were treated with low-dose (n = 12) or high-dose (n = 15) IVIg before, immediately after and at 7 days after treatment. Percentages and activation status of circulating CD4(+) CD25(+) forkhead box protein 3 (FoxP3(+)) Tregs and of conventional CD4(+) FoxP3(-) T-helper cells (Tconv) were measured. The suppressive capacity of Tregs purified from blood collected at the time-points indicated was determined in an ex-vivo assay. High-dose, but not low-dose, IVIg treatment enhanced the activation status of circulating Tregs , as shown by increased FoxP3 and human leucocyte antigen D-related (HLA-DR) expression, while numbers of circulating Tregs remained unchanged. The enhanced activation was sustained for at least 7 days after infusion, and the suppressive capacity of purified Tregs was increased from 41 to 70% at day 7 after IVIg treatment. The activation status of Tconv was not affected by IVIg. We conclude that high-dose IVIg treatment activates Tregs selectively and enhances their suppressive function in humans in vivo. This effect may be one of the mechanisms by which IVIg restores imbalanced immune homeostasis in patients with autoimmune and systemic inflammatory disorders. PMID:23607448

Tjon, A S W; Tha-In, T; Metselaar, H J; van Gent, R; van der Laan, L J W; Groothuismink, Z M A; te Boekhorst, P A W; van Hagen, P M; Kwekkeboom, J

2013-08-01

100

African elephants show high levels of interest in the skulls and ivory of their own species  

PubMed Central

An important area of biology involves investigating the origins in animals of traits that are thought of as uniquely human. One way that humans appear unique is in the importance they attach to the dead bodies of other humans, particularly those of their close kin, and the rituals that they have developed for burying them. In contrast, most animals appear to show only limited interest in the carcasses or associated remains of dead individuals of their own species. African elephants (Loxodonta africana) are unusual in that they not only give dramatic reactions to the dead bodies of other elephants, but are also reported to systematically investigate elephant bones and tusks that they encounter, and it has sometimes been suggested that they visit the bones of relatives. Here, we use systematic presentations of object arrays to demonstrate that African elephants show higher levels of interest in elephant skulls and ivory than in natural objects or the skulls of other large terrestrial mammals. However, they do not appear to specifically select the skulls of their own relatives for investigation so that visits to dead relatives probably result from a more general attraction to elephant remains.

McComb, Karen; Baker, Lucy; Moss, Cynthia

2005-01-01

101

High throughput genetic transformation mediated by Agrobacterium tumefaciens in maize  

Microsoft Academic Search

A high throughput genetic transformation system in maize has been developed with Agrobacterium tumefaciens mediated T-DNA delivery. With optimized conditions, stable callus transformation frequencies for Hi-II immature embryos averaged approximately 40%, with results in some experiments as high as 50%. The optimized conditions include N6 medium system for Agrobacterium inoculation, co-cultivation, resting and selection steps; no AgNo3 in the infection

Zuo-yu Zhao; Weining Gu; Tishu Cai; Laura Tagliani; David Hondred; Diane Bond; Sheryl Schroeder; Marjorie Rudert; Dottie Pierce

2002-01-01

102

Dysplastic cells in cytological cervical samples show a high incidence of chromosomal abnormalities.  

PubMed

Chromosomal abnormalities are frequent in most cervical cancers. Amplifications of both the 3q26 (TERC) and 8q24 (MYC) loci have been shown to be prevalent in both high-grade lesions and invasive cervical carcinoma. Most of these studies have looked at either the histological sample or at the entire cytological population of cells. We have developed a Papanicolaou (Pap) destaining method that allows for the accurate analysis of individual cells that were previously identified by cytopathology as dysplastic. The application of fluorescence in situ hybridization (FISH) was then implemented to determine the chromosomal status of the dysplastic cells in the samples and correlate the two events. Chromosomal abnormality is over a thousand times more frequent in dysplastic cells compared with their morphologically normal counterparts. PMID:19626623

Song, Minghao; Ruth, Adam; Policht, Frank A; Bubendorf, Lukas; Feichter, Georg; Kipp, Benjamin R; Halling, Kevin C; Sokolova, Irina A

2010-01-01

103

Two high-fertility mouse lines show differences in component fertility traits after long-term selection.  

PubMed

Two selected high-fertility mouse lines, namely FL1 and FL2, and a non-selected control (Fzt:DU), all derived from the same genetic pool, were analysed as an animal model for polytocous species to elucidate the effects of long-term selection and to identify relevant component traits that may be responsible for fertility performance. The index trait used for breeding selection was largely increased by 104% and 142% in the FL1 and FL2 lines, respectively, resulting in an average litter size of 17.3 pups and 18.7 pups per litter in the FL1 and FL2 lines, respectively, compared with a litter size of 11.0 pups per litter in the control (Fzt:DU). In addition, different component fertility traits were analysed in females of all three lines at different stages of the oestrous cycle and pregnancy. In conclusion: (1) early embryonic development was accelerated in the FL1 and FL2 lines compared with control; (2) plasma progesterone levels were not correlated with fertility performance; (3) a largely increased ovulation number (i.e. number of corpora lutea) was responsible for high prolificacy in both lines; however, (4) the number of ova shed, as well as the rate of loss of ova and pre- and postimplantation conceptuses, was very different in the FL1 and FL2 lines, suggesting that different genetic components may be responsible for the high prolificacy in both high-fertility lines. PMID:17897584

Spitschak, Marion; Langhammer, Martina; Schneider, Falk; Renne, Ulla; Vanselow, Jens

2007-01-01

104

Synchronized High-Resolution Lacustrine Records in Iceland show Non-Linear Response to Holocene Insolation  

NASA Astrophysics Data System (ADS)

Icelandic lakes commonly have sedimentation rates in excess of 1 m ka-1 through the Holocene, offering the potential for records of environmental change at decadal or better resolution. Icelandic lake sediment contains numerous volcanic tephra layers of known age, which together with high-resolution sediment paleomagnetic secular variations (PSV) allow synchronization of sediment cores from both lacustrine and marine archives. We present synchronized high-resolution paleoclimatic records from two Icelandic lakes with very different catchment characteristics. By combining PSV records and key tephra tie points we are able to synchronize the lacustrine records with each other and with a well-dated marine core from the shelf north of Iceland. The large PSV signal that characterizes the Icelandic Holocene records allows 40 to 60 secure tie points over the past 10 ka of sediment records. The high frequency of tie points allows the reconstruction of sediment accumulation rate changes in the lacustrine records that were not apparent from the tephrochonological controls. The first order trends in the lacustine climate proxies (BSi and TOC) are similar. BSi climbs to a maximum value shortly after 8 ka, then declines toward present, reflecting a relatively late Holocene thermal maximum, lagging the Greenland ice core record by ca. 2 ka. The peak of the HTM in Iceland was warm enough to melt glaciers completely with temperatures estimated to have been 3.5°C higher relative to 1960-1990 averages. Decreasing summer insolation is reflected not by gradual cooling after the HTM, but by incremental changes in state. TOC and BSi track each other during warm times, but diverge, and sedimentation rates increase, during perturbations and cold times at 8.4 ka, 5.5 ka, 4.3 to 4 ka, 3.1 ka to 2.8 ka. Following these departures, BSi usually exhibits a step-function change, re-equilibrating at a lower BSi value. Some of the departures may be related to Icelandic volcanism influencing catchment stability, but the lack of a full recovery to pre-existing values after the eruptions suggests a change in state occurred in the lake catchments indicating increased periglacial activity, decreased vegetation cover, and glacier growth in the highlands of Iceland. The strongest disturbance occurs during the last 2 ka with the transition into the Little Ice Age occurring in two-to-three steps. Initial summer cooling occurs 1250-1300 AD, followed by a more severe drop in summer temperatures between 1450 and 1500 AD, and the final and most severe step around 1800 AD. The LIA began earlier and apparently peaked later than reflected by many mainland European records. Independent proxies (BSi, TOC, C:N, sedimentation rate, IRD, alkenones, ice cap modeling) from glacial and non-glacial lakes and adjacent Icelandic shelves are self-consistent, providing robust support for our reconstructions.

Geirsdottir, A.; Miller, G. H.; Larsen, D. J.; Thordarson, T.; Ólafsdóttir, S.; Stoner, J. S.

2010-12-01

105

High-precision radiocarbon dating shows recent and rapid initial human colonization of East Polynesia.  

PubMed

The 15 archipelagos of East Polynesia, including New Zealand, Hawaii, and Rapa Nui, were the last habitable places on earth colonized by prehistoric humans. The timing and pattern of this colonization event has been poorly resolved, with chronologies varying by >1000 y, precluding understanding of cultural change and ecological impacts on these pristine ecosystems. In a meta-analysis of 1,434 radiocarbon dates from the region, reliable short-lived samples reveal that the colonization of East Polynesia occurred in two distinct phases: earliest in the Society Islands A.D. ?1025-1120, four centuries later than previously assumed; then after 70-265 y, dispersal continued in one major pulse to all remaining islands A.D. ?1190-1290. We show that previously supported longer chronologies have relied upon radiocarbon-dated materials with large sources of error, making them unsuitable for precise dating of recent events. Our empirically based and dramatically shortened chronology for the colonization of East Polynesia resolves longstanding paradoxes and offers a robust explanation for the remarkable uniformity of East Polynesian culture, human biology, and language. Models of human colonization, ecological change and historical linguistics for the region now require substantial revision. PMID:21187404

Wilmshurst, Janet M; Hunt, Terry L; Lipo, Carl P; Anderson, Atholl J

2010-12-27

106

High-precision radiocarbon dating shows recent and rapid initial human colonization of East Polynesia  

PubMed Central

The 15 archipelagos of East Polynesia, including New Zealand, Hawaii, and Rapa Nui, were the last habitable places on earth colonized by prehistoric humans. The timing and pattern of this colonization event has been poorly resolved, with chronologies varying by >1000 y, precluding understanding of cultural change and ecological impacts on these pristine ecosystems. In a meta-analysis of 1,434 radiocarbon dates from the region, reliable short-lived samples reveal that the colonization of East Polynesia occurred in two distinct phases: earliest in the Society Islands A.D. ?1025–1120, four centuries later than previously assumed; then after 70–265 y, dispersal continued in one major pulse to all remaining islands A.D. ?1190–1290. We show that previously supported longer chronologies have relied upon radiocarbon-dated materials with large sources of error, making them unsuitable for precise dating of recent events. Our empirically based and dramatically shortened chronology for the colonization of East Polynesia resolves longstanding paradoxes and offers a robust explanation for the remarkable uniformity of East Polynesian culture, human biology, and language. Models of human colonization, ecological change and historical linguistics for the region now require substantial revision.

Wilmshurst, Janet M.; Hunt, Terry L.; Lipo, Carl P.; Anderson, Atholl J.

2011-01-01

107

Ocean acidification shows negligible impacts on high-latitude bacterial community structure in coastal pelagic mesocosms  

NASA Astrophysics Data System (ADS)

The impact of ocean acidification and carbonation on microbial community structure was assessed during a large-scale in situ costal pelagic mesocosm study, included as part of the EPOCA 2010 Arctic campaign. The mesocosm experiment included ambient conditions (fjord) and nine mesocosms, with pCO2 range from ~145 to ~1420 ?atm. Samples collected at nine time points (t-1, t1, t5, t7, t12, t14, t22, t26 to t28) in seven treatments (ambient fjord (~145), 2×~185, ~270, ~685, ~820, ~1050 ?atm) were analysed for "free-living" and "particle associated" microbial community composition using 16S rRNA amplicon sequencing. This high-throughput sequencing analysis produced ~20 000 000 16S rRNA V4 reads, which comprised 7000 OTUs. The main variables structuring these communities were, sample origin (fjord or mesocosms) and the filter size fraction (free-living or particle associated). The community was significantly different between the fjord and both the control and elevated 2 mesocosms (which were not significant different) after nutrients were added to the mesocosms; suggesting that the addition of nutrients is the primary driver of the change in mesocosm community structure. The relative importance of each structuring variable depended greatly on the time at which the community was sampled in relation to the phytoplankton bloom. The size fraction was the second most important factor for community structure; separating free-living from particle-associated bacteria. When free-living and particle-associated bacteria were analysed separately at different time points, the only taxon pCO2 was found to significantly affect were the Gammaproteobacteria after nutrient addition. Finally, pCO2 treatment was found to be significantly correlated (non-linear) with 15 rare taxa, most of which increased in abundance with higher CO2.

Roy, A.-S.; Gibbons, S. M.; Schunck, H.; Owens, S.; Caporaso, J. G.; Sperling, M.; Nissimov, J. I.; Romac, S.; Bittner, L.; Riebesell, U.; LaRoche, J.; Gilbert, J. A.

2012-09-01

108

Ocean acidification shows negligible impacts on high-latitude bacterial community structure in coastal pelagic mesocosms  

NASA Astrophysics Data System (ADS)

The impact of ocean acidification and carbonation on microbial community structure was assessed during a large-scale in situ costal pelagic mesocosm study, included as part of the EPOCA 2010 Arctic campaign. The mesocosm experiment included ambient conditions (fjord) and nine mesocosms with pCO2 levels ranging from ~145 to ~1420 ?atm. Samples for the present study were collected at ten time points (t-1, t1, t5, t7, t12, t14, t18, t22, t26 to t28) in seven treatments (ambient fjord (~145), 2 × ~185, ~270, ~685, ~820, ~1050 ?atm) and were analysed for "small" and "large" size fraction microbial community composition using 16S RNA (ribosomal ribonucleic acid) amplicon sequencing. This high-throughput sequencing analysis produced ~20 000 000 16S rRNA V4 reads, which comprised 7000 OTUs. The main variables structuring these communities were sample origins (fjord or mesocosms) and the community size fraction (small or large size fraction). The community was significantly different between the unenclosed fjord water and enclosed mesocosms (both control and elevated CO2 treatments) after nutrients were added to the mesocosms, suggesting that the addition of nutrients is the primary driver of the change in mesocosm community structure. The relative importance of each structuring variable depended greatly on the time at which the community was sampled in relation to the phytoplankton bloom. The sampling strategy of separating the small and large size fraction was the second most important factor for community structure. When the small and large size fraction bacteria were analysed separately at different time points, the only taxon pCO2 was found to significantly affect were the Gammaproteobacteria after nutrient addition. Finally, pCO2 treatment was found to be significantly correlated (non-linear) with 15 rare taxa, most of which increased in abundance with higher CO2.

Roy, A.-S.; Gibbons, S. M.; Schunck, H.; Owens, S.; Caporaso, J. G.; Sperling, M.; Nissimov, J. I.; Romac, S.; Bittner, L.; Mühling, M.; Riebesell, U.; LaRoche, J.; Gilbert, J. A.

2013-01-01

109

Genetic causes of high and low serum HDL-cholesterol  

PubMed Central

Plasma levels of HDL cholesterol (HDL-C) have a strong inherited basis with heritability estimates of 40-60%. The well-established inverse relationship between plasma HDL-C levels and the risk of coronary artery disease (CAD) has led to an extensive search for genetic factors influencing HDL-C concentrations. Over the past 30 years, candidate gene, genome-wide linkage, and most recently genome-wide association (GWA) studies have identified several genetic variations for plasma HDL-C levels. However, the functional role of several of these variants remains unknown, and they do not always correlate with CAD. In this review, we will first summarize what is known about HDL metabolism, monogenic disorders associated with both low and high HDL-C levels, and candidate gene studies. Then we will focus this review on recent genetic findings from the GWA studies and future strategies to elucidate the remaining substantial proportion of HDL-C heritability. Comprehensive investigation of the genetic factors conferring to low and high HDL-C levels using integrative approaches is important to unravel novel pathways and their relations to CAD, so that more effective means of diagnosis, treatment, and prevention will be identified.

Weissglas-Volkov, Daphna; Pajukanta, Paivi

2010-01-01

110

Low levels of nestmate discrimination despite high genetic differentiation in the invasive pharaoh ant  

PubMed Central

Background Ants typically distinguish nestmates from non-nestmates based on the perception of colony-specific chemicals, particularly cuticular hydrocarbons present on the surface of the ants' exoskeleton. These recognition cues are believed to play an important role in the formation of vast so-called supercolonies that have been described for some invasive ant species, but general conclusions about the role of these cues are hampered by only few species being studied. Here we use data on cuticular hydrocarbons, aggression and microsatellite genetic markers to investigate the interdependence of chemical recognition cues, genetic distance and nestmate discrimination in the pharaoh ant (Monomorium pharaonis), a widespread pest species, and ask whether introduced populations of this species are genetically differentiated and exhibit intraspecific aggression. Results Microsatellite analyses of a total of 35 colonies from four continents revealed extremely high levels of genetic differentiation between almost all colonies (FST = 0.751 ± 0.006 SE) and very low within-colony diversity. This implies that at least 34 and likely hundreds more independent lineages of this ant have spread worldwide. Aggression tests involving workers from 14 different colonies showed only low levels of aggression, even between colonies that were geographically and/or genetically very distant. Chemical analyses of groups of worker ants showed that all colonies had the same cuticular compounds, which varied only quantitatively among colonies. There was a positive correlation between geographical and genetic distance, but no other significant relationships were detected between aggression, chemical profile, genetic distance and geographical distance. Conclusions The pharaoh ant has a global invasion history of numerous independent introductions resulting in genetically highly differentiated colonies typically displaying surprisingly low levels of intraspecific aggression, a behaviour that may have evolved in the native range or by lineage selection in the introduced range.

2010-01-01

111

Genetic Diversity and Population Structure of Mycobacterium tuberculosis in Casablanca, a Moroccan City with High Incidence of Tuberculosis  

PubMed Central

Although lower-resource countries have by far the highest burden of tuberculosis, knowledge of Mycobacterium tuberculosis population structure and genetic diversity in these regions remains almost nonexistent. In this paper, 150 Moroccan M. tuberculosis isolates circulating in Casablanca were genotyped by random amplified polymorphic DNA analysis using 10 different primers and by mycobacterial interspersed repetitive units-variable number of tandem repeats typing at 12 loci. The population genetic tests revealed a basically clonal structure for this population, without excluding rare genetic exchanges. Genetic analysis also showed a notable genetic polymorphism for the species M. tuberculosis, a weak cluster individualization, and an unexpected genetic diversity for a population in such a high-incidence community. Phylogenetic analyses of this Moroccan sample also supported that these isolates are genetically heterogeneous.

Tazi, Loubna; El Baghdadi, Jamila; Lesjean, Sarah; Locht, Camille; Supply, Philip; Tibayrenc, Michel; Banuls, Anne-Laure

2004-01-01

112

Genetic (co)variance components across age for Show Jumping performance as an estimation of phenotypic plasticity ability in Spanish horses.  

PubMed

The purpose of this study was to study phenotypic plasticity ability for Show Jumping performance in horses according to age differences. For this study, 11 352 participations, belonging to 1085 horses grouped by age (4-, 5- or 6-year olds), were analysed. repeatability animal models (RAM) and multiple trait animal models (MTAM) were compared. RAM assumed the same covariance components for all age groups, whereas MTAM considered the results of every animal at every age group as different (but correlated) traits. The age, sex, starting order and training level were included as fixed effects. The random effects were the animal, the individual permanent environment, the competition and the rider. Six models were compared, and the rider-horse interaction was added as a random effect; furthermore, heterogeneous residual variance was taken into consideration only for MTAM. The study of the genetic correlations between age groups highlighted the presence of an age-genotype interaction and, therefore, an underlying environmental effect. This study may allow us to select horses with a plastic response, which show either a gradual response or a precocious response and thus gain or lose genetic potential with age, respectively. PMID:23679944

Bartolomé, E; Menéndez-Buxadera, A; Valera, M; Cervantes, I; Molina, A

2012-09-18

113

Improving AFLP analysis of large-scale patterns of genetic variation--a case study with the Central African lianas Haumania spp (Marantaceae) showing interspecific gene flow.  

PubMed

AFLP markers are often used to study patterns of population genetic variation and gene flow because they offer a good coverage of the nuclear genome, but the reliability of AFLP scoring is critical. To assess interspecific gene flow in two African rainforest liana species (Haumania danckelmaniana, H. liebrechtsiana) where previous evidence of chloroplast captures questioned the importance of hybridization and species boundaries, we developed new AFLP markers and a novel approach to select reliable bands from their degree of reproducibility. The latter is based on the estimation of the broad-sense heritability of AFLP phenotypes, an improvement over classical scoring error rates, which showed that the polymorphism of most AFLP bands was affected by a substantial nongenetic component. Therefore, using a quantitative genetics framework, we also modified an existing estimator of pairwise kinship coefficient between individuals correcting for the limited heritability of markers. Bayesian clustering confirms the recognition of the two Haumania species. Nevertheless, the decay of the relatedness between individuals of distinct species with geographic distance demonstrates that hybridization affects the nuclear genome. In conclusion, although we showed that AFLP markers might be substantially affected by nongenetic factors, their analysis using the new methods developed considerably advanced our understanding of the pattern of gene flow in our model species. PMID:23398575

Ley, A C; Hardy, O J

2013-02-08

114

Pituitary Adenoma Showing Intermittent Secretion of High Molecular Weight Adrenocorticotropin without Evidence of Cushing’s Disease  

Microsoft Academic Search

A 29-year-old woman was admitted in March 1998 due to high plasma ACTH levels, amenorrhea and uncontrolled diabetes mellitus (DM) which had persisted since 1991. Plasma ACTH levels showed a wide range of changes: they were usually high (59–240 pg\\/ml), intermittently very high (336–942 pg\\/ml), and sometimes normal or low. Plasma cortisol levels were usually normal but were sometimes high

Kozo Hashimoto; Tadafumi Kaneda; Isao Nagano; Koichiro Asaba; Kyoko Takeda; Tosihiro Takao

1999-01-01

115

Dietary differentiation and the evolution of population genetic structure in a highly mobile carnivore.  

PubMed

Recent studies on highly mobile carnivores revealed cryptic population genetic structures correlated to transitions in habitat types and prey species composition. This led to the hypothesis that natal-habitat-biased dispersal may be responsible for generating population genetic structure. However, direct evidence for the concordant ecological and genetic differentiation between populations of highly mobile mammals is rare. To address this we analyzed stable isotope profiles (?(13)C and ?(15)N values) for Eastern European wolves (Canis lupus) as a quantifiable proxy measure of diet for individuals that had been genotyped in an earlier study (showing cryptic genetic structure), to provide a quantitative assessment of the relationship between individual foraging behavior and genotype. We found a significant correlation between genetic distances and dietary differentiation (explaining 46% of the variation) in both the marginal test and crucially, when geographic distance was accounted for as a co-variable. These results, interpreted in the context of other possible mechanisms such as allopatry and isolation by distance, reinforce earlier studies suggesting that diet and associated habitat choice are influencing the structuring of populations in highly mobile carnivores. PMID:22768075

Pilot, Ma?gorzata; J?drzejewski, W?odzimierz; Sidorovich, Vadim E; Meier-Augenstein, Wolfram; Hoelzel, A Rus

2012-06-29

116

High and distinct range-edge genetic diversity despite local bottlenecks.  

PubMed

The genetic consequences of living on the edge of distributional ranges have been the subject of a largely unresolved debate. Populations occurring along persistent low latitude ranges (rear-edge) are expected to retain high and unique genetic diversity. In contrast, currently less favourable environmental conditions limiting population size at such range-edges may have caused genetic erosion that prevails over past historical effects, with potential consequences on reducing future adaptive capacity. The present study provides an empirical test of whether population declines towards a peripheral range might be reflected on decreasing diversity and increasing population isolation and differentiation. We compare population genetic differentiation and diversity with trends in abundance along a latitudinal gradient towards the peripheral distribution range of Saccorhiza polyschides, a large brown seaweed that is the main structural species of kelp forests in SW Europe. Signatures of recent bottleneck events were also evaluated to determine whether the recently recorded distributional shifts had a negative influence on effective population size. Our findings show decreasing population density and increasing spatial fragmentation and local extinctions towards the southern edge. Genetic data revealed two well supported groups with a central contact zone. As predicted, higher differentiation and signs of bottlenecks were found at the southern edge region. However, a decrease in genetic diversity associated with this pattern was not verified. Surprisingly, genetic diversity increased towards the edge despite bottlenecks and much lower densities, suggesting that extinctions and recolonizations have not strongly reduced diversity or that diversity might have been even higher there in the past, a process of shifting genetic baselines. PMID:23967038

Assis, Jorge; Castilho Coelho, Nelson; Alberto, Filipe; Valero, Myriam; Raimondi, Pete; Reed, Dan; Serrão, Ester Alvares

2013-07-10

117

High and Distinct Range-Edge Genetic Diversity despite Local Bottlenecks  

PubMed Central

The genetic consequences of living on the edge of distributional ranges have been the subject of a largely unresolved debate. Populations occurring along persistent low latitude ranges (rear-edge) are expected to retain high and unique genetic diversity. In contrast, currently less favourable environmental conditions limiting population size at such range-edges may have caused genetic erosion that prevails over past historical effects, with potential consequences on reducing future adaptive capacity. The present study provides an empirical test of whether population declines towards a peripheral range might be reflected on decreasing diversity and increasing population isolation and differentiation. We compare population genetic differentiation and diversity with trends in abundance along a latitudinal gradient towards the peripheral distribution range of Saccorhizapolyschides, a large brown seaweed that is the main structural species of kelp forests in SW Europe. Signatures of recent bottleneck events were also evaluated to determine whether the recently recorded distributional shifts had a negative influence on effective population size. Our findings show decreasing population density and increasing spatial fragmentation and local extinctions towards the southern edge. Genetic data revealed two well supported groups with a central contact zone. As predicted, higher differentiation and signs of bottlenecks were found at the southern edge region. However, a decrease in genetic diversity associated with this pattern was not verified. Surprisingly, genetic diversity increased towards the edge despite bottlenecks and much lower densities, suggesting that extinctions and recolonizations have not strongly reduced diversity or that diversity might have been even higher there in the past, a process of shifting genetic baselines.

Assis, Jorge; Castilho Coelho, Nelson; Alberto, Filipe; Valero, Myriam; Raimondi, Pete; Reed, Dan; Alvares Serrao, Ester

2013-01-01

118

Development of new genomic microsatellite markers from robusta coffee ( Coffea canephora Pierre ex A. Froehner) showing broad cross-species transferability and utility in genetic studies  

Microsoft Academic Search

Background  Species-specific microsatellite markers are desirable for genetic studies and to harness the potential of MAS-based breeding\\u000a for genetic improvement. Limited availability of such markers for coffee, one of the most important beverage tree crops, warrants\\u000a newer efforts to develop additional microsatellite markers that can be effectively deployed in genetic analysis and coffee\\u000a improvement programs. The present study aimed to develop

Prasad Suresh Hendre; Regur Phanindranath; V Annapurna; Albert Lalremruata; Ramesh K Aggarwal

2008-01-01

119

Male Hatano high-avoidance rats show high avoidance and high anxiety-like behaviors as compared with male low-avoidance rats.  

PubMed

Our prime objective was to establish an optimal model animal for studying avoidance learning and memory in rodents. The two-way rat inbred strains of Hatano high- (HAA) and low-avoidance (LAA) animals were originally selected and bred in accordance with their high or low performance respectively in the shuttle-box active avoidance task. Previous studies demonstrated that they have clear strain differences in endocrine stress response, which is related to acquisition of aversive learning and emotional reactivity. To evaluate the effect of selection by the shuttle-box task on avoidance performance and emotional reactivity, male Hatano rats underwent passive avoidance, open field and elevated plus maze tests. The present results show that the avoidance performance in the passive task was significantly greater in HAA rats than in LAA rats. Furthermore, HAA rats showed high anxiety-like behaviors compared with LAA rats in open field and elevated plus maze tests. Taken together, this study demonstrated that 1) selection and breeding of Hatano HAA and LAA strain rats by shuttle-box task had been properly carried out with the criterion of high and low avoidance performance respectively and that 2) HAA rats were predisposed to high anxiety compared with LAA rats. These results indicated that Hatano HAA and LAA rats can be useful models for studying avoidance learning and memory. PMID:23095815

Horii, Yasuyuki; Kawaguchi, Maiko; Ohta, Ryo; Hirano, Akihiro; Watanabe, Gen; Kato, Nobumasa; Himi, Toshiyuki; Taya, Kazuyoshi

2012-01-01

120

Genetic Factors for Choroidal Neovascularization Associated with High Myopia  

PubMed Central

Purpose. Nonsyndromic high myopia, defined by a refractive error greater than ?6 diopters (D), is associated with an increased risk of macular choroidal neovascularization (CNV), a vision-threatening complication. The aim of this study was to investigate whether genetic factors associated with age-related macular degeneration (AMD) are related to myopic CNV. Methods. We conducted a case-control study, including 71 cases with myopic CNV and 196 myopic controls without CNV, from Creteil and Toulouse, France, and Boston, MA. Single nucleotide polymorphisms (SNPs) from 15 genes reported to be related to AMD were selected for association testing in this study. Results. In univariate analysis, the rs10033900 SNP located in CFI was associated with myopic CNV (P = 0.0011), and a SNP in APOE was also related (P = 0.041). After adjustment for age, sex, and degree of myopia, SNPs in three genes were significantly associated, including CFI (odds ratio [OR] 2.1, 95% confidence interval [CI] 1.3–3.37, P = 0.0023), COL8A1 (OR 1.88, 95% CI 1.18–2.98, P = 0.0076), and CFH (OR 1.65, 95% CI 1.02–2.66, P = 0.04). After correction for multiple testing, only CFI remained significantly related to high myopic CNV (P = 0.045). Conclusions. We report the first genetic associations with choroidal neovascularization (CNV) in a high myopic Caucasian population. One SNP (rs10033900) in the CFI gene, which encodes a protein involved in the inflammatory pathway, was significantly associated with myopic CNV in multivariate analysis after correction for multiple testing. This SNP is a plausible biological marker associated with CNV outgrowth among high myopic patients. Results generate hypotheses about potential loci related to CNV in high myopia, and larger studies are needed to expand on these findings.

Leveziel, Nicolas; Yu, Yi; Reynolds, Robyn; Tai, Albert; Meng, Weihua; Caillaux, Violaine; Calvas, Patrick; Rosner, Bernard; Malecaze, Francois; Souied, Eric H.; Seddon, Johanna M.

2012-01-01

121

High genetic load in the Pacific oyster Crassostrea gigas.  

PubMed Central

The causes of inbreeding depression and the converse phenomenon of heterosis or hybrid vigor remain poorly understood despite their scientific and agricultural importance. In bivalve molluscs, related phenomena, marker-associated heterosis and distortion of marker segregation ratios, have been widely reported over the past 25 years. A large load of deleterious recessive mutations could explain both phenomena, according to the dominance hypothesis of heterosis. Using inbred lines derived from a natural population of Pacific oysters and classical crossbreeding experiments, we compare the segregation ratios of microsatellite DNA markers at 6 hr and 2-3 months postfertilization in F(2) or F(3) hybrid families. We find evidence for strong and widespread selection against identical-by-descent marker homozygotes. The marker segregation data, when fit to models of selection against linked deleterious recessive mutations and extrapolated to the whole genome, suggest that the wild founders of inbred lines carried a minimum of 8-14 highly deleterious recessive mutations. This evidence for a high genetic load strongly supports the dominance theory of heterosis and inbreeding depression and establishes the oyster as an animal model for understanding the genetic and physiological causes of these economically important phenomena.

Launey, S; Hedgecock, D

2001-01-01

122

High-load resistors of doped titanate ceramics showing PTCR behavior in the entire temperature range of operation  

Microsoft Academic Search

Ceramic high-load resistors of donor-doped strontium titanate were manufactured and successfully tested. The samples do not only withstand short high-load pulses (10ms) with a power loss of ?1MW, but also show a PTCR behavior in the entire temperature range of operation. Compared to the common BaTiO3-PTCR devices, the samples do not exhibit a grain-boundary controlled resistance, that results in thermo-mechanical

Ralf Moos; Marco Fandel; Wolfgang Schäfer

1999-01-01

123

MHC ANTIGEN-BINDING LOCUS SHOWS STRONG SIGNAL OF SELECTION AND HIGH VARIABILITY IN FUNDULUS HETEROCLITUS POPULATIONS  

EPA Science Inventory

The major histocompatibility system provides a unique genetic locus in vertebrates to assess genetic diversity and to look for the effects of selecti.on on the immune system. Fish population studies using MHC are fairly new, and thus far they have focused on endangered population...

124

MHC ANTIGEN BINDING LOCUS DRB1 SHOWS STRONG SIGNAL OF SELECTION AND HIGH VARIABILITY IN FUNDULUS HETERCLITUS POPULATIONS  

EPA Science Inventory

The major histocompatibility system provides a unique complex of genetic loci in vertebrates to assess genetic diversity and to look for the effects of selection on the adaptive immune system. Studies using mammals and birds have demonstrated relationships between MHC genotyp...

125

A systems genetic analysis of high density lipoprotein metabolism and network preservation across mouse models  

Microsoft Academic Search

We report a systems genetic analysis of high density lipoprotein (HDL) levels in an F2 intercross between inbred strains CAST\\/EiJ and C57BL\\/6J. We previously showed that there are dramatic differences in HDL metabolism in a cross between these strains, and we now report co-expression network analysis of HDL that integrates global expression data from liver and adipose with relevant metabolic

Peter Langfelder; Lawrence W. Castellani; Zhiqiang Zhou; Eric Paul; Richard Davis; Eric E. Schadt; Aldons J. Lusis; Steve Horvath; Margarete Mehrabian

126

Microsatellite markers reveal high genetic diversity in date palm ( Phoenix dactylifera L.) germplasm from Sudan  

Microsoft Academic Search

Genetic diversity in date palm germplasm from Sudan representing 37 female and 23 male accessions was investigated using 16\\u000a loci of microsatellite (SSR) primers. Eight female accessions from Morocco were included as reference material. The tested\\u000a SSR markers showed a high level of polymorphism. A total of 343 alleles were detected at the 16 loci. The number of alleles\\u000a per

Sakina Elshibli; Helena Korpelainen

2008-01-01

127

The Yeast Hrs1 Gene Is Involved in Positive and Negative Regulation of Transcription and Shows Genetic Characteristics Similar to Sin4 and Gal11  

PubMed Central

We provide genetic evidence that HRS1/PGD1, a yeast gene previously identified as a suppressor of the hyper-recombination phenotype of hpr1, has positive and negative roles in transcriptional regulation. We have analyzed three differently regulated promoters, GAL1, PHO5 and HSP26, by ?-galactosidase assays of lacZ-fused promoters and by Northern analysis of the endogenous genes. Transcription of these promoters was derepressed in hrs1? mutants under conditions in which it is normally repressed in wild type. Under induced conditions it was either strongly reduced or significantly enhanced depending on the promoter system analyzed. Constitutive transcription was not affected, as determined in ADH1 and TEF2. In addition, Hrs1p was required for mating-factor expression, telomere-linked DNA silencing and DNA supercoiling of plasmids. Furthermore, hrs1? suppressed Ty-insertion mutations and conferred a Gal(-) phenotype. Many of these phenotypes also result from mutations in GAL11, SIN4 or RGR1, which encode proteins of the RNA polII mediator. We also show that gal11? and sin4? partially suppress the hyper-rec phenotype of hpr1 mutants, although to a lesser extent than hrs1?. Our results provide new evidence for the connection between hpr1?-induced deletions and transcription. We discuss the possibility that Hrs1p might be a component of the RNA polII transcription machinery.

Piruat, J. I.; Chavez, S.; Aguilera, A.

1997-01-01

128

Rats on a high-energy diet showing no weight gain present with ultrastructural changes associated with liver fibrosis.  

PubMed

Sibutramine is widely used as a weight-loss substance in the treatment of obesity and is a selective inhibitor of the neuronal reuptake of serotonin and noradrenaline. Although banned, it is often a hidden ingredient in herbal and dietary supplements that are widely used by the general public. Various weight loss products, including sibutramine, have successfully been tested in animal models of diet-induced obesity. In the female Sprague-Dawley rat model, fed a high-energy diet that did not produce a significant increase in BMI, the cellular structure of the liver was evaluated using transmission electron microscopy. Compared to controls showing no damage, the livers of rats fed a high-energy diet were found to have increased fibrosis without steatosis, while for rats fed high-energy diet with sibutramine, fibrosis was increased and steatosis had developed. In conclusion, in female rats fed a high-energy diet that does not result in weight gain hepatic fibrosis occurs without steatosis. In these rats the co-administration of sibutramine increases the degree of fibrosis and steatosis develops. Although it has been widely believed that sibutramine is not hepatotoxic, this study clearly shows that at an ultrastructural level, rats fed a high-energy diet treated with sibutramine show signs of hepatotoxicity. PMID:23672266

Oberholzer, Hester Magdalena; Bester, Megan Jean; van der Schoor, Ciska

2013-05-14

129

High Levels of Genetic Recombination during Nasopharyngeal Carriage and Biofilm Formation in Streptococcus pneumoniae  

PubMed Central

ABSTRACT Transformation of genetic material between bacteria was first observed in the 1920s using Streptococcus pneumoniae as a model organism. Since then, the mechanism of competence induction and transformation has been well characterized, mainly using planktonic bacteria or septic infection models. However, epidemiological evidence suggests that genetic exchange occurs primarily during pneumococcal nasopharyngeal carriage, which we have recently shown is associated with biofilm growth, and is associated with cocolonization with multiple strains. However, no studies to date have comprehensively investigated genetic exchange during cocolonization in vitro and in vivo or the role of the nasopharyngeal environment in these processes. In this study, we show that genetic exchange during dual-strain carriage in vivo is extremely efficient (10?2) and approximately 10,000,000-fold higher than that measured during septic infection (10?9). This high transformation efficiency was associated with environmental conditions exclusive to the nasopharynx, including the lower temperature of the nasopharynx (32 to 34°C), limited nutrient availability, and interactions with epithelial cells, which were modeled in a novel biofilm model in vitro that showed similarly high transformation efficiencies. The nasopharyngeal environmental factors, combined, were critical for biofilm formation and induced constitutive upregulation of competence genes and downregulation of capsule that promoted transformation. In addition, we show that dual-strain carriage in vivo and biofilms formed in vitro can be transformed during colonization to increase their pneumococcal fitness and also, importantly, that bacteria with lower colonization ability can be protected by strains with higher colonization efficiency, a process unrelated to genetic exchange.

Marks, Laura R.; Reddinger, Ryan M.; Hakansson, Anders P.

2012-01-01

130

Genetic control of obesity and gut microbiota composition in response to high-fat, high-sucrose diet in mice.  

PubMed

Obesity is a highly heritable disease driven by complex interactions between genetic and environmental factors. Human genome-wide association studies (GWAS) have identified a number of loci contributing to obesity; however, a major limitation of these studies is the inability to assess environmental interactions common to obesity. Using a systems genetics approach, we measured obesity traits, global gene expression, and gut microbiota composition in response to a high-fat/high-sucrose (HF/HS) diet of more than 100 inbred strains of mice. Here we show that HF/HS feeding promotes robust, strain-specific changes in obesity that are not accounted for by food intake and provide evidence for a genetically determined set point for obesity. GWAS analysis identified 11 genome-wide significant loci associated with obesity traits, several of which overlap with loci identified in human studies. We also show strong relationships between genotype and gut microbiota plasticity during HF/HS feeding and identify gut microbial phylotypes associated with obesity. PMID:23312289

Parks, Brian W; Nam, Elizabeth; Org, Elin; Kostem, Emrah; Norheim, Frode; Hui, Simon T; Pan, Calvin; Civelek, Mete; Rau, Christoph D; Bennett, Brian J; Mehrabian, Margarete; Ursell, Luke K; He, Aiqing; Castellani, Lawrence W; Zinker, Bradley; Kirby, Mark; Drake, Thomas A; Drevon, Christian A; Knight, Rob; Gargalovic, Peter; Kirchgessner, Todd; Eskin, Eleazar; Lusis, Aldons J

2013-01-01

131

High recombination rates and hotspots in a Plasmodium falciparum genetic cross  

PubMed Central

Background The human malaria parasite Plasmodium falciparum survives pressures from the host immune system and antimalarial drugs by modifying its genome. Genetic recombination and nucleotide substitution are the two major mechanisms that the parasite employs to generate genome diversity. A better understanding of these mechanisms may provide important information for studying parasite evolution, immune evasion and drug resistance. Results Here, we used a high-density tiling array to estimate the genetic recombination rate among 32 progeny of a P. falciparum genetic cross (7G8 × GB4). We detected 638 recombination events and constructed a high-resolution genetic map. Comparing genetic and physical maps, we obtained an overall recombination rate of 9.6 kb per centimorgan and identified 54 candidate recombination hotspots. Similar to centromeres in other organisms, the sequences of P. falciparum centromeres are found in chromosome regions largely devoid of recombination activity. Motifs enriched in hotspots were also identified, including a 12-bp G/C-rich motif with 3-bp periodicity that may interact with a protein containing 11 predicted zinc finger arrays. Conclusions These results show that the P. falciparum genome has a high recombination rate, although it also follows the overall rule of meiosis in eukaryotes with an average of approximately one crossover per chromosome per meiosis. GC-rich repetitive motifs identified in the hotspot sequences may play a role in the high recombination rate observed. The lack of recombination activity in centromeric regions is consistent with the observations of reduced recombination near the centromeres of other organisms.

2011-01-01

132

Pol III binding in six mammalian genomes shows high conservation among amino acid isotypes, despite divergence in tRNA gene usage  

PubMed Central

RNA polymerase III (pol III) transcription of transfer RNA (tRNA) genes is essential for generating the tRNA adapter molecules that link genetic sequence and protein translation. By mapping pol III occupancy genome-wide in the livers of mouse, rat, human, macaque, dog and opossum, we found that pol III binding to individual tRNA genes varies substantially in strength and location. However, taking into account tRNA redundancies by grouping pol III occupancy into 46 anticodon isoacceptor families or 21 amino acid-based isotype classes shows strong conservation. Similarly, pol III occupancy of amino-acid isotypes is almost invariant among transcriptionally and evolutionarily diverse tissues in mouse. Thus, synthesis of functional tRNA isotypes has been highly constrained, though the usage of individual tRNA genes has evolved rapidly.

Kutter, Claudia; Brown, Gordon D.; Goncalves, Angela; Wilson, Michael D.; Watt, Stephen; Brazma, Alvis; White, Robert J.; Odom, Duncan T.

2011-01-01

133

A tool-kit for high-throughput, quantitative analyses of genetic interactions in E. coli  

PubMed Central

Large-scale genetic interaction studies provide the basis for defining gene function and pathway architecture. Recent advances in the ability to generate double mutants en masse in S. cerevisiae have dramatically accelerated the acquisition of genetic interaction information and the biological inferences that follow. Here, we describe a method based on F-driven conjugation, which allows for high-throughput generation of double mutants in E. coli. This method, termed Genetic Interaction ANalysis Technology for E. coli (GIANT-coli), permits us to systematically generate and array double mutant cells on solid media, in high-density arrays. We show that colony size provides a robust and quantitative output of cellular fitness and that GIANT-coli can recapitulate known synthetic interactions and identify new negative (synthetic sickness/lethality) and positive (suppressive/epistatic) relationships. Finally, we describe a complementary strategy for suppressor mutant identification on a genome-wide level. Together, these methods permit rapid, large-scale genetic interaction studies in E. coli.

Typas, Athanasios; Nichols, Robert J.; Siegele, Deborah A.; Shales, Michael; Collins, Sean; Lim, Bentley; Braberg, Hannes; Yamamoto, Natsuko; Takeuchi, Rikiya; Wanner, Barry L.; Mori, Hirotada; Weissman, Jonathan S.; Krogan, Nevan J.; Gross, Carol A.

2009-01-01

134

"The Show"  

ERIC Educational Resources Information Center

|For the past 16 years, the blue-collar city of Huntington, West Virginia, has rolled out the red carpet to welcome young wrestlers and their families as old friends. They have come to town chasing the same dream for a spot in what many of them call "The Show". For three days, under the lights of an arena packed with 5,000 fans, the state's best…

Gehring, John

2004-01-01

135

Integrated DNA, cDNA, and protein studies in Becker muscular dystrophy show high exception to the reading frame rule.  

PubMed

Becker muscular dystrophy (BMD) is a milder form of X-linked Duchenne muscular dystrophy (DMD). Here, we report a study of 75 patients with immunoblot and/or immunostaining findings of muscle biopsy consistent with BMD (abnormal dystrophin). We utilized multiplex ligation dependent probe amplification (MLPA) on genomic DNA (gDNA) to screen all 79 exons for both deletions and duplications. A total of 19 patients testing negative for MLPA mutations were tested for mRNA splicing abnormalities using cDNA-MLPA on muscle biopsy. Complete cDNA sequencing was done on MLPA-negative patients. We identified disease-causing mutations in 66 (88%) of the patients. Of the mutation-positive patients, 42 (64%) showed deletions of one or more exons, 14 (21%) showed duplications, and 10 (15%) showed various mutations detected by cDNA-MLPA and sequencing studies. We found a high rate of "exceptions" to the reading frame rule in this BMD series (out-of-frame BMD; 17/56 deletions/duplications; 30%). This was partly explained by the high incidence of 5' gene deletions in BMD patients (a region known to be a hotspot for exceptions), and due to complex splicing patterns in which a subset of transcripts showed deletions larger than gDNA (exon-skipping). Comparing our findings in BMD to previously published DMD data, BMD patients have higher proportions of duplications, a different distribution of mutations, and higher exception to the reading frame rule. PMID:18348289

Kesari, Akanchha; Pirra, Laura N; Bremadesam, Lakshmi; McIntyre, Orinthal; Gordon, Erynn; Dubrovsky, Alberto L; Viswanathan, V; Hoffman, Eric P

2008-05-01

136

Development and characterization of highly polymorphic long TC repeat microsatellite markers for genetic analysis of peanut  

PubMed Central

Background Peanut (Arachis hypogaea L.) is a crop of economic and social importance, mainly in tropical areas, and developing countries. Its molecular breeding has been hindered by a shortage of polymorphic genetic markers due to a very narrow genetic base. Microsatellites (SSRs) are markers of choice in peanut because they are co-dominant, highly transferrable between species and easily applicable in the allotetraploid genome. In spite of substantial effort over the last few years by a number of research groups, the number of SSRs that are polymorphic for A. hypogaea is still limiting for routine application, creating the demand for the discovery of more markers polymorphic within cultivated germplasm. Findings A plasmid genomic library enriched for TC/AG repeats was constructed and 1401 clones sequenced. From the sequences obtained 146 primer pairs flanking mostly TC microsatellites were developed. The average number of repeat motifs amplified was 23. These 146 markers were characterized on 22 genotypes of cultivated peanut. In total 78 of the markers were polymorphic within cultivated germplasm. Most of those 78 markers were highly informative with an average of 5.4 alleles per locus being amplified. Average gene diversity index (GD) was 0.6, and 66 markers showed a GD of more than 0.5. Genetic relationship analysis was performed and corroborated the current taxonomical classification of A. hypogaea subspecies and varieties. Conclusions The microsatellite markers described here are a useful resource for genetics and genomics in Arachis. In particular, the 66 markers that are highly polymorphic in cultivated peanut are a significant step towards routine genetic mapping and marker-assisted selection for the crop.

2012-01-01

137

Is serum retinol binding protein-4: A predictor for diabetes in genetically high risk population?  

PubMed Central

Background: Retinol binding protein-4 (BP-4) a new adipocytokine, specifically binds to retinol, through experimental studies, reported its link between obesity and insulin resistance (IR). But till date no studies are available on influence of genetic predisposition of diabetes on RBP-4 expression. Hence, we aimed to study the influence of genetic predisposition of diabetes on the serum RBP-4 and its role in development of IR and diabetes in genetically high risk population. Materials and Methods: Healthy non diabetic individuals (age 18 to 22) were grouped into Group I: Control (n = 81), whose parents are non diabetic, non hypertensive and does not have any family history of coronary heart diseases. Group II: (n = 157) with one of their parents diabetic and Group III: (n = 47) with both parents diabetic. In all the participants, we estimated fasting serum RBP-4, insulin and glucose. Homeostasis model for assessment-insulin resistance (HOMA-IR) and homeostasis model for assessment-beta cell dysfunction (HOMA-B) were calculated from fasting serum insulin and glucose levels. Results: In this study, we observed significantly higher RBP-4 levels 12.71 ± 2.3 in Group-II and 13.25 ± 2 in Group-III, respectively when compared to Group-I 11.4 ± 1.8 (P < 0.01). RBP-4 showed a significantly strong positive correlation with plasma insulin, glucose and HOMA-IR in genetically high risk population (group II and III) P < 0.01. Linear regression analysis revealed a strong positive association of RBP-4 with parental diabetes even after adjusting for BMI, age and sex (OR 1.53, 95% CI 1.089-1.40). Conclusion: Higher serum RBP-4 and its positive correlation with Insulin, glucose, and HOMA-IR in healthy non diabetic participants of genetically high risk population, indicating its role as predictor for the onset of diabetes in coming future.

Bose, K. Subhash Chandra; Gupta, Shachin K.; Singh, Sandeep

2012-01-01

138

A Comprehensive Analysis of High School Genetics Standards: Are States Keeping Pace with Modern Genetics?  

PubMed Central

Science education in the United States will increasingly be driven by testing and accountability requirements, such as those mandated by the No Child Left Behind Act, which rely heavily on learning outcomes, or “standards,” that are currently developed on a state-by-state basis. Those standards, in turn, drive curriculum and instruction. Given the importance of standards to teaching and learning, we investigated the quality of life sciences/biology standards with respect to genetics for all 50 states and the District of Columbia, using core concepts developed by the American Society of Human Genetics as normative benchmarks. Our results indicate that the states’ genetics standards, in general, are poor, with more than 85% of the states receiving overall scores of Inadequate. In particular, the standards in virtually every state have failed to keep pace with changes in the discipline as it has become genomic in scope, omitting concepts related to genetic complexity, the importance of environment to phenotypic variation, differential gene expression, and the differences between inherited and somatic genetic disease. Clearer, more comprehensive genetics standards are likely to benefit genetics instruction and learning, help prepare future genetics researchers, and contribute to the genetic literacy of the U.S. citizenry.

Dougherty, M.J.; Pleasants, C.; Solow, L.; Wong, A.; Zhang, H.

2011-01-01

139

Awareness of Societal Issues among High School Biology Teachers Teaching Genetics  

ERIC Educational Resources Information Center

|The purpose of this study was to investigate how aware high school biology teachers are of societal issues (values, moral, ethic, and legal issues) while teaching genetics, genetics engineering, molecular genetics, human heredity, and evolution. The study includes a short historical review of World War II atrocities during the Holocaust when…

Lazarowitz, Reuven; Bloch, Ilit

2005-01-01

140

A mouse model of high trait anxiety shows reduced heart rate variability that can be reversed by anxiolytic drug treatment  

PubMed Central

Increasing evidence suggests that specific physiological measures may serve as biomarkers for successful treatment to alleviate symptoms of pathological anxiety. Studies of autonomic function investigating parameters such as heart rate (HR), HR variability and blood pressure (BP) indicated that HR variability is consistently reduced in anxious patients, whereas HR and BP data show inconsistent results. Therefore, HR and HR variability were measured under various emotionally challenging conditions in a mouse model of high innate anxiety (high anxiety behaviour; HAB) vs. control normal anxiety-like behaviour (NAB) mice. Baseline HR, HR variability and activity did not differ between mouse lines. However, after cued Pavlovian fear conditioning, both elevated tachycardia and increased fear responses were observed in HAB mice compared to NAB mice upon re-exposure to the conditioning stimulus serving as the emotional stressor. When retention of conditioned fear was tested in the home cage, HAB mice again displayed higher fear responses than NAB mice, while the HR responses were similar. Conversely, in both experimental settings HAB mice consistently exhibited reduced HR variability. Repeated administration of the anxiolytic NK1 receptor antagonist L-822429 lowered the conditioned fear response and shifted HR dynamics in HAB mice to a more regular pattern, similar to that in NAB mice. Additional receiver-operating characteristic (ROC) analysis demonstrated the high specificity and sensitivity of HR variability to distinguish between normal and high anxiety trait. These findings indicate that assessment of autonomic response in addition to freezing might be a useful indicator of the efficacy of novel anxiolytic treatments.

Gaburro, Stefano; Stiedl, Oliver; Giusti, Pietro; Sartori, Simone B.; Landgraf, Rainer; Singewald, Nicolas

2011-01-01

141

Copper tolerance and genetic diversity of Porcellionides sexfasciatus (ISOPODA) in a highly contaminated mine habitat.  

PubMed

Organisms inhabiting metal-contaminated areas may develop metal tolerance, with either phenotypic adjustments or genetic changes (adaptation) or with both. In the present study, three populations of the terrestrial isopod Porcellionides sexfasciatus, collected at an abandoned mine area, were compared to assess the effects of metal contamination on tolerance to lethal and sublethal levels of copper, through comparison of survival, avoidance, and feeding. The effects of metal contamination on genetic diversity were considered using random amplified polymorphic DNA (RAPD) markers. No evidence of increased metal tolerance of the population inhabiting the contaminated site was found. There was no correlation between metal exposure and within-population genetic variance, but the three populations were clearly separated from each other. In conclusion, the populations of P. sexfasciatus in the mine landscape live rather isolated from each other and show no differential tolerance to Cu or indications of genetic erosion. Their phenotypic plasticity provides a means to survive despite exposure to extremely high metal concentrations in the soil. PMID:23322508

Costa, Dalila; Bouchon, Didier; van Straalen, Nico M; Sousa, José Paulo; Ribeiro, Rui

2013-02-21

142

Discovering genetic associations with high-dimensional neuroimaging phenotypes: A sparse reduced-rank regression approach.  

PubMed

There is growing interest in performing genome-wide searches for associations between genetic variants and brain imaging phenotypes. While much work has focused on single scalar valued summaries of brain phenotype, accounting for the richness of imaging data requires a brain-wide, genome-wide search. In particular, the standard approach based on mass-univariate linear modelling (MULM) does not account for the structured patterns of correlations present in each domain. In this work, we propose sparse reduced rank regression (sRRR), a strategy for multivariate modelling of high-dimensional imaging responses (measurements taken over regions of interest or individual voxels) and genetic covariates (single nucleotide polymorphisms or copy number variations), which enforces sparsity in the regression coefficients. Such sparsity constraints ensure that the model performs simultaneous genotype and phenotype selection. Using simulation procedures that accurately reflect realistic human genetic variation and imaging correlations, we present detailed evaluations of the sRRR method in comparison with the more traditional MULM approach. In all settings considered, sRRR has better power to detect deleterious genetic variants compared to MULM. Important issues concerning model selection and connections to existing latent variable models are also discussed. This work shows that sRRR offers a promising alternative for detecting brain-wide, genome-wide associations. PMID:20624472

Vounou, Maria; Nichols, Thomas E; Montana, Giovanni

2010-07-17

143

HIGHLY PENETRANT GENETIC DISORDERS: AN ATLAS FOR CRITICAL ILLNESS INSURANCE  

Microsoft Academic Search

For estimates of critical illness (CI) insurance premiums in the presence of a known mutation leading to a genetic disorder, the key quantity is the penetrance, that is the probability qÖxÜ that the disease has developed by age x. This function is often estimated in the genetics literature, though typically with large confidence intervals. In this paper we suggest that

A. S. Macdonald; S. Y. Yang

2003-01-01

144

Low Genetic Variability in the Highly Endangered Mediterranean Monk Seal  

Microsoft Academic Search

Genetic variability is an important component in the ability of populations to adapt in the face of environmental change. Here we report the first description of nuclear genetic variability in the only remaining sizable colony of the Mediterranean monk seal (Monachus monachus), located at Cap Blanc (Western Sahara, Mauritania), whose estimated size during the study period (1994-May 1997) was about

T. Pastor; J. C. GARZA; P. ALLEN; W. AMOS; A. AGUILAR

2004-01-01

145

Accessing Genetic Information with High-Density DNA Arrays  

NASA Astrophysics Data System (ADS)

Rapid access to genetic information is central to the revolution taking place in molecular genetics. The simultaneous analysis of the entire human mitochondrial genome is described here. DNA arrays containing up to 135,000 probes complementary to the 16.6-kilobase human mitochondrial genome were generated by light-directed chemical synthesis. A two-color labeling scheme was developed that allows simultaneous comparison of a polymorphic target to a reference DNA or RNA. Complete hybridization patterns were revealed in a matter of minutes. Sequence polymorphisms were detected with single-base resolution and unprecedented efficiency. The methods described are generic and can be used to address a variety of questions in molecular genetics including gene expression, genetic linkage, and genetic variability.

Chee, Mark; Yang, Robert; Hubbell, Earl; Berno, Anthony; Huang, Xiaohua C.; Stern, David; Winkler, Jim; Lockhart, David J.; Morris, Macdonald S.; Fodor, Stephen P. A.

1996-10-01

146

High Quality Typhoon Cloud Image Restoration by Combining Genetic Algorithm with Contourlet Transform  

SciTech Connect

An efficient typhoon cloud image restoration algorithm is proposed. Having implemented contourlet transform to a typhoon cloud image, noise is reduced in the high sub-bands. Weight median value filter is used to reduce the noise in the contourlet domain. Inverse contourlet transform is done to obtain the de-noising image. In order to enhance the global contrast of the typhoon cloud image, in-complete Beta transform (IBT) is used to determine non-linear gray transform curve so as to enhance global contrast for the de-noising typhoon cloud image. Genetic algorithm is used to obtain the optimal gray transform curve. Information entropy is used as the fitness function of the genetic algorithm. Experimental results show that the new algorithm is able to well enhance the global for the typhoon cloud image while well reducing the noises in the typhoon cloud image.

Zhang Changjiang; Wang Xiaodong [College of Mathematics, Physics and Information Engineering, Zhejiang Normal University, Jinhua (China)

2008-11-06

147

GABA A receptor mediated transmission in the thalamic reticular nucleus of rats with genetic absence epilepsy shows regional differences: Functional implications  

Microsoft Academic Search

The aim of the present study was to investigate the effect of local injections of the GABAA receptor antagonist, bicuculline, into the rostral and caudal parts of the thalamic reticular nucleus (TRN), on the generation of spike-and-wave discharges in Genetic Absence Epilepsy Rats from Strasbourg (GAERS). Spike-and-wave discharges are important in the pathophysiology of absence epilepsy and generated by the

Rezzan Gülhan Aker; Hazan B. Özyurt; Hasan R. Yananli; Yusuf Özgür Çakmak; Aydan E. Özkaynakçi; Ümit Sehirli; Erdinç Saka; Safiye Çavdar; Filiz Y?lmaz Onat

2006-01-01

148

Transgenic rice as a system to study the stability of transgene expression: multiple heterologous transgenes show similar behaviour in diverse genetic backgrounds  

Microsoft Academic Search

The success of contemporary breeding programmes involving genetic engineering depends on the stability of transgene expression\\u000a over many generations. We studied the stability of transgene expression in 40 independent rice plant lines representing 11\\u000a diverse cultivated varieties. Each line contained three or four different transgenes delivered by particle bombardment, either\\u000a by cotransformation or in the form of a cointegrate vector.

D. Gahakwa; S. B. Maqbool; X. Fu; D. Sudhakar; P. Christou; A. Kohli

2000-01-01

149

A genetically encoded, high-signal-to-noise maltose sensor  

SciTech Connect

We describe the generation of a family of high-signal-to-noise single-wavelength genetically encoded indicators for maltose. This was achieved by insertion of circularly permuted fluorescent proteins into a bacterial periplasmic binding protein (PBP), Escherichia coli maltodextrin-binding protein, resulting in a four-color family of maltose indicators. The sensors were iteratively optimized to have sufficient brightness and maltose-dependent fluorescence increases for imaging, under both one- and two-photon illumination. We demonstrate that maltose affinity of the sensors can be tuned in a fashion largely independent of the fluorescent readout mechanism. Using literature mutations, the binding specificity could be altered to moderate sucrose preference, but with a significant loss of affinity. We use the soluble sensors in individual E. coli bacteria to observe rapid maltose transport across the plasma membrane, and membrane fusion versions of the sensors on mammalian cells to visualize the addition of maltose to extracellular media. The PBP superfamily includes scaffolds specific for a number of analytes whose visualization would be critical to the reverse engineering of complex systems such as neural networks, biosynthetic pathways, and signal transduction cascades. We expect the methodology outlined here to be useful in the development of indicators for many such analytes.

Marvin, Jonathan S.; Schreiter, Eric R.; Echevarría, Ileabett M.; Looger, Loren L. (Puerto Rico); (HHMI)

2012-10-23

150

A genetically encoded, high-signal-to-noise maltose sensor  

PubMed Central

We describe the generation of a family of high-signal-to-noise single-wavelength genetically encoded indicators for maltose. This was achieved by insertion of circularly permuted fluorescent proteins into a bacterial periplasmic binding protein (PBP), Escherichia coli maltodextrin-binding protein, resulting in a four-color family of maltose indicators. The sensors were iteratively optimized to have sufficient brightness and maltose-dependent fluorescence increases for imaging, under both one- and two-photon illumination. We demonstrate that maltose affinity of the sensors can be tuned in a fashion largely independent of the fluorescent readout mechanism. Using literature mutations, the binding specificity could be altered to moderate sucrose preference, but with a significant loss of affinity. We use the soluble sensors in individual E. coli bacteria to observe rapid maltose transport across the plasma membrane, and membrane fusion versions of the sensors on mammalian cells to visualize the addition of maltose to extracellular media. The PBP superfamily includes scaffolds specific for a number of analytes whose visualization would be critical to the reverse engineering of complex systems such as neural networks, biosynthetic pathways, and signal transduction cascades. We expect the methodology outlined here to be useful in the development of indicators for many such analytes.

Marvin, Jonathan S; Schreiter, Eric R; Echevarria, Ileabett M; Looger, Loren L

2011-01-01

151

Analysis of STR markers reveals high genetic structure in Portuguese native cattle.  

PubMed

Genetic structure and diversity of 13 Portuguese native and 3 imported cattle breeds were assessed with 39 microsatellites. Allelic richness per locus was high, with an overall average of 8.3 +/- 2.5. The mean observed and expected heterozygosities were 0.673 +/- 0.043 and 0.691 +/- 0.034, respectively. The mean number of alleles per breed ranged between 5.36 +/- 1.27 and 7.87 +/- 2.66. Brava de Lide and Mirandesa breeds had the lowest genetic diversity, whereas Minhota, Arouquesa, and Mertolenga had the highest. Significant (P < 0.05) heterozygote deficit was detected in all breeds except Garvonesa, Marinhoa, Minhota, and Limousin. Hardy-Weinberg deviations are most probably due to inbreeding, particularly in Alentejana, Brava de Lide, Mertolenga, and Ramo Grande (F(is) > 0, P < 0.0001). Based on the principal component and the Neighbor-Net analyses, Mirandesa was the most genetically distinct breed. Even though admixture was detected across all breeds (6.7%, q < 0.800), the molecular structure was consistent with original breed designations, with the exception of Cachena that had a clear influence of Barrosã (K = 15). Mertolenga showed substructure with independent clustering of red speckled animals. The percentage animals correctly assigned was >or=90 in all breeds except Cachena, Garvonesa, and Preta (q >or= 0.800). The results obtained here confirmed that high levels of genetic diversity exist within Portuguese native cattle and that the breeds are highly structured. Conservation measures should be implemented for all native breeds to minimize inbreeding. PMID:19965912

Ginja, Catarina; Telo Da Gama, Luís; Penedo, Maria Cecilia T

2009-12-04

152

Mn(II)-based porous metal-organic framework showing metamagnetic properties and high hydrogen adsorption at low pressure.  

PubMed

A Mn(II)-based homometallic porous metal-organic framework, Mn(5)(btac)(4)(?(3)-OH)(2)(EtOH)(2)·DMF·3EtOH·3H(2)O (1, btac = benzotriazole-5-carboxylate), has been solvothermally synthesized and structurally characterized by elemental analysis, thermogravimetric analysis, and X-ray crystallographic study. 1 is a 3D neutral framework featuring 1D porous channels constructed by {Mn-OH-Mn}(n) chains and btac linkers. Magnetic studies show that 1 is a 3D metamagnet containing 1D {Mn-OH-Mn}(n) ferrimagnetic chains. High-pressure H(2) adsorption measurement at 77 K reveals that activated 1 can absorb 0.99 wt % H(2) at 0.5 atm and reaches a maximum of 1.03 wt % at 5.5 atm. The steep H(2) absorption at lower pressure (98.2% of the storage capacity at 0.5 atm) is higher than the corresponding values of some MOFs (MIL-100 (16.1%), MOF-177 (57.1%), and MOF-5 (22.2%)). Furthermore, activated 1 can adsorb CO(2) at room temperature and 275 K. The adsorption enthalpy is 22.0 kJ mol(-1), which reveals the high binding ability for CO(2). Detailed gas sorption implies that the exposed Mn(II) coordination sites in the activated 1 play an important role to improve its adsorption capacities. PMID:22141338

Han, Zheng-Bo; Lu, Rui-Yun; Liang, Yan-Fang; Zhou, Yan-Ling; Chen, Qing; Zeng, Ming-Hua

2011-12-05

153

Genetic Screening and Counseling for High-Risk Populations  

Microsoft Academic Search

As we enter the 21st century, we are witnessing a historic transition in science that will reveal the genetic basis of common\\u000a medical conditions and have an enormous impact on biology, medicine, health care, and society. The role of genetics in understanding\\u000a and treating cancer has traditionally been limited to the observation of cytogenetic abnormalities in certain tumor types.\\u000a With

Mary B. Daly

154

High-density genetic mapping for coffee leaf rust resistance  

Microsoft Academic Search

Coffee leaf rust caused by the fungus Hemileia vastatrix causes considerable economic losses for coffee producers. Although agrochemical products can provide sufficient disease control,\\u000a the use of resistant cultivars is a safer alternative. This resistance may be constrained by one or a few genetic factors,\\u000a mainly those found in material originating from interspecific hybrids. In this study, the genetic analysis

Valdir Diola; Giovani Greigh de Brito; Eveline Teixeira Caixeta; Eunize Maciel-Zambolim; Ney Sussumu Sakiyama; Marcelo Ehlers Loureiro

155

Genetics.  

PubMed

The present state of knowledge on the genetics of anxiety disorders, in particular panic disorder, comprising clinical and molecular genetic studies, interaction analyses, as well as meta-analyses of single association studies will be presented in detail. A particular focus will be on the most robust findings in panic disorder to date in the serotonergic, noradrenergic, and dopaminergic system, such as the catechol-O-methyltransferase (COMT) gene. Additionally, findings on the adenosine receptor 2A (A2A) gene, which has been reported to be associated with panic disorder and also with anxiety levels after caffeine administration in a gene--environment interactional model, will be discussed. Furthermore, the first imaging genetic findings in panic disorder, social phobia, and anxiety-related traits using fMRI and PET techniques in combination with molecular genetic association analyses are reviewed, taking into account the present intermediate phenotype discussion in the investigation of complex genetic disorders. Finally, the first exemplary pharmacogenetic studies in panic disorder and generalized social phobia will be presented. The pathomechanism of anxiety disorders and in particular panic disorder is considered to be multifactorial with converging evidence for a pivotal role of genetic factors in particular, which will be presented in detail in this chapter. PMID:21309106

Domschke, Katharina; Deckert, Jürgen

2010-01-01

156

Cladodes, leaf-like organs in Asparagus, show the significance of co-option of pre-existing genetic regulatory circuit for morphological diversity of plants  

PubMed Central

Plants in the genus Asparagus have determinate leaf-like organs called cladodes in the position of leaf axils. Because of their leaf-like morphology, axillary position, and morphological variation, it has been unclear how this unusual organ has evolved and diversified. In the previous study, we have shown that cladodes in the genus Asparagus are modified axillary shoots and proposed a model that cladodes have arisen by co-option and deployment of genetic regulatory circuit (GRC) involved in leaf development. Moreover, we proposed that the alteration of the expression pattern of genes involved in establishment of adaxial/abaxial polarity has led to the morphological diversification from leaf-like to rod-like form of cladodes in the genus. Thus, these results indicated that the co-option and alteration of pre-existing GRC play an important role in acquisition and subsequent morphological diversification. Here, we present data of further expression analysis of A. asparagoides. The results suggested that only a part of the GRC involved in leaf development appears to have been co-opted into cladode development. Based on our study and several examples of the morphological diversification, we briefly discuss the importance of co-option of pre-existing GRC and its genetic modularity in the morphological diversity of plants during evolution.

Nakayama, Hokuto; Yamaguchi, Takahiro; Tsukaya, Hirokazu

2012-01-01

157

A comprehensive platform for highly multiplexed mammalian functional genetic screens  

PubMed Central

Background Genome-wide screening in human and mouse cells using RNA interference and open reading frame over-expression libraries is rapidly becoming a viable experimental approach for many research labs. There are a variety of gene expression modulation libraries commercially available, however, detailed and validated protocols as well as the reagents necessary for deconvolving genome-scale gene screens using these libraries are lacking. As a solution, we designed a comprehensive platform for highly multiplexed functional genetic screens in human, mouse and yeast cells using popular, commercially available gene modulation libraries. The Gene Modulation Array Platform (GMAP) is a single microarray-based detection solution for deconvolution of loss and gain-of-function pooled screens. Results Experiments with specially constructed lentiviral-based plasmid pools containing ~78,000 shRNAs demonstrated that the GMAP is capable of deconvolving genome-wide shRNA "dropout" screens. Further experiments with a larger, ~90,000 shRNA pool demonstrate that equivalent results are obtained from plasmid pools and from genomic DNA derived from lentivirus infected cells. Parallel testing of large shRNA pools using GMAP and next-generation sequencing methods revealed that the two methods provide valid and complementary approaches to deconvolution of genome-wide shRNA screens. Additional experiments demonstrated that GMAP is equivalent to similar microarray-based products when used for deconvolution of open reading frame over-expression screens. Conclusion Herein, we demonstrate four major applications for the GMAP resource, including deconvolution of pooled RNAi screens in cells with at least 90,000 distinct shRNAs. We also provide detailed methodologies for pooled shRNA screen readout using GMAP and compare next-generation sequencing to GMAP (i.e. microarray) based deconvolution methods.

2011-01-01

158

Getting a head start: the importance of personal genetics education in high schools.  

PubMed

With advances in sequencing technology, widespread and affordable genome sequencing will soon be a reality. However, studies suggest that "genetic literacy" of the general public is inadequate to prepare our society for this unprecedented access to our genetic information. As the current generation of high school students will come of age in an era when personal genetic information is increasingly utilized in health care, it is of vital importance to ensure these students understand the genetic concepts necessary to make informed medical decisions. These concepts include not only basic scientific knowledge, but also considerations of the ethical, legal, and social issues that will arise in the age of personal genomics. In this article, we review the current state of genetics education, highlight issues that we believe need to be addressed in a comprehensive genetics education curriculum, and describe our education efforts at the Harvard Medical School-based Personal Genetics Education Project. PMID:22461746

Kung, Johnny T; Gelbart, Marnie E

2012-03-29

159

Getting a Head Start: The Importance of Personal Genetics Education in High Schools  

PubMed Central

With advances in sequencing technology, widespread and affordable genome sequencing will soon be a reality. However, studies suggest that “genetic literacy” of the general public is inadequate to prepare our society for this unprecedented access to our genetic information. As the current generation of high school students will come of age in an era when personal genetic information is increasingly utilized in health care, it is of vital importance to ensure these students understand the genetic concepts necessary to make informed medical decisions. These concepts include not only basic scientific knowledge, but also considerations of the ethical, legal, and social issues that will arise in the age of personal genomics. In this article, we review the current state of genetics education, highlight issues that we believe need to be addressed in a comprehensive genetics education curriculum, and describe our education efforts at the Harvard Medical School-based Personal Genetics Education Project.

Kung, Johnny T.; Gelbart, Marnie E.

2012-01-01

160

Genealogical surveys show a high rate of non-paternal surname transmission with regional differences in Argentina.  

PubMed

Surnames are a vertically transmitted cultural trait that in Argentina follows the paternal line of descent when the paternity is known. There was a lack of empirical information regarding non-paternal surname transmissions among the general population, so we performed 2,550 genealogical interviews, which included 6,954 surname passes, in different regions of this country. We compared the proportion of non-paternal transmissions between the propositus and parental generation and found no significant difference between them (p<0.01). Inter-population comparisons allowed us to describe 4 regional groups. We also drew models and simulations to estimate how many generations it would take to find that only half of the population maintained the paternal transmission. The lowest proportion of non-paternal transmission was 7.3%, estimating 9 generations (between 225 and 315 years) to find that, at most, half its population keeps following the paternal transmission; the highest proportion was 23%, taking 3 generations (75-105 years). Our results show a high proportion of unrecognized paternities among the general population, a very quick loss of association between male lineages and surnames, and regional proportions with significant differences between each other. PMID:22305123

Muzzio, M; Motti, J M B; Chiarullo, S M; Bravi, C M; Bailliet, G

2012-02-01

161

High-Resolution Structural Analysis Shows How Tah1 Tethers Hsp90 to the R2TP Complex.  

PubMed

The ubiquitous Hsp90 chaperone participates in snoRNP and RNA polymerase assembly through interaction with the R2TP complex. This complex includes the proteins Tah1, Pih1, Rvb1, and Rvb2. Tah1 bridges Hsp90 to R2TP. Its minimal TPR domain includes two TPR motifs and a capping helix. We established the high-resolution solution structures of Tah1 free and in complex with the Hsp90 C-terminal peptide. The TPR fold is similar in the free and bound forms and we show experimentally that in addition to its solvating/stabilizing role, the capping helix is essential for the recognition of the Hsp90 (704)EMEEVD(709) motif. In addition to Lys79 and Arg83 from the carboxylate clamp, this helix bears Tyr82 forming a ?/S-CH3 interaction with Hsp90 M(705) from the peptide 310 helix. The Tah1 C-terminal region is unfolded, and we demonstrate that it is essential for the recruitment of the Pih1 C-terminal domain and folds upon binding. PMID:24012479

Back, Régis; Dominguez, Cyril; Rothé, Benjamin; Bobo, Claude; Beaufils, Chrystel; Moréra, Solange; Meyer, Philippe; Charpentier, Bruno; Branlant, Christiane; Allain, Frédéric H-T; Manival, Xavier

2013-09-05

162

Allozyme Evidence for Genetic Autopolyploidy and High Genetic Diversity in Tetraploid Cranberry, Vaccinium oxycoccos (Ericaceae)  

Microsoft Academic Search

Polyploidy has been important in the evolution of angiosperms and may significantly affect population genetic diversity and structure. Nineteen isoenzyme loci were studied in diploid and tetraploid populations of Vaccinium oxycoccos (Ericaceae), and the results are compared with data previously reported for the related V. macrocarpon. Diploid V. oxycoccos and V. macrocarpon were readily discriminated based on their allozymic variation.

Gregory Mahy; Leo P. Bruederle; Bridget Connors; Michael Van Hofwegen; Nicholi Vorsa

2000-01-01

163

Similarity in Recombination Rate Estimates Highly Correlates with Genetic Differentiation in Humans  

PubMed Central

Recombination varies greatly among species, as illustrated by the poor conservation of the recombination landscape between humans and chimpanzees. Thus, shorter evolutionary time frames are needed to understand the evolution of recombination. Here, we analyze its recent evolution in humans. We calculated the recombination rates between adjacent pairs of 636,933 common single-nucleotide polymorphism loci in 28 worldwide human populations and analyzed them in relation to genetic distances between populations. We found a strong and highly significant correlation between similarity in the recombination rates corrected for effective population size and genetic differentiation between populations. This correlation is observed at the genome-wide level, but also for each chromosome and when genetic distances and recombination similarities are calculated independently from different parts of the genome. Moreover, and more relevant, this relationship is robustly maintained when considering presence/absence of recombination hotspots. Simulations show that this correlation cannot be explained by biases in the inference of recombination rates caused by haplotype sharing among similar populations. This result indicates a rapid pace of evolution of recombination, within the time span of differentiation of modern humans.

Laayouni, Hafid; Montanucci, Ludovica; Sikora, Martin; Mele, Marta; Dall'Olio, Giovanni Marco; Lorente-Galdos, Belen; McGee, Kate M.; Graffelman, Jan; Awadalla, Philip; Bosch, Elena; Comas, David; Navarro, Arcadi; Calafell, Francesc; Casals, Ferran; Bertranpetit, Jaume

2011-01-01

164

Awareness of Societal Issues Among High School Biology Teachers Teaching Genetics  

Microsoft Academic Search

The purpose of this study was to investigate how aware high school biology teachers are of societal issues (values, moral,\\u000a ethic, and legal issues) while teaching genetics, genetics engineering, molecular genetics, human heredity, and evolution.\\u000a The study includes a short historical review of World War II atrocities during the Holocaust when scientists from all the\\u000a above-mentioned disciplines had been involved

Reuven Lazarowitz; Ilit Bloch

2005-01-01

165

Baculovirus expression system and method for high throughput expression of genetic material  

DOEpatents

The present invention provides novel recombinant baculovirus expression systems for expressing foreign genetic material in a host cell. Such expression systems are readily adapted to an automated method for expression foreign genetic material in a high throughput manner. In other aspects, the present invention features a novel automated method for determining the function of foreign genetic material by transfecting the same into a host by way of the recombinant baculovirus expression systems according to the present invention.

Clark, Robin (Benecia, CA); Davies, Anthony (Mill Valley, CA)

2001-01-01

166

Complete Genome Sequences from Three Genetically Distinct Strains Reveal High Intraspecies Genetic Diversity in the Microsporidian Encephalitozoon cuniculi  

PubMed Central

Microsporidia from the Encephalitozoonidae are obligate intracellular parasites with highly conserved and compacted nuclear genomes: they have few introns, short intergenic regions, and almost identical gene complements and chromosome arrangements. Comparative genomics of Encephalitozoon and microsporidia in general have focused largely on the genomic diversity between different species, and we know very little about the levels of genetic diversity within species. Polymorphism studies with Encephalitozoon are so far restricted to a small number of genes, and a few genetically distinct strains have been identified; most notably, three genotypes (ECI, ECII, and ECIII) of the model species E. cuniculi have been identified based on variable repeats in the rRNA internal transcribed spacer (ITS). To determine if E. cuniculi genotypes are genetically distinct lineages across the entire genome and at the same time to examine the question of intraspecies genetic diversity in microsporidia in general, we sequenced de novo genomes from each of the three genotypes and analyzed patterns of single nucleotide polymorphisms (SNPs) and insertions/deletions across the genomes. Although the strains have almost identical gene contents, they harbor large numbers of SNPs, including numerous nonsynonymous changes, indicating massive intraspecies variation within the Encephalitozoonidae. Based on this diversity, we conclude that the recognized genotypes are genetically distinct and propose new molecular markers for microsporidian genotyping.

Pombert, Jean-Francois; Xu, Jinshan; Smith, David R.; Heiman, David; Young, Sarah; Cuomo, Christina A.; Weiss, Louis M.

2013-01-01

167

A Hybrid Genetic Algorithm for Highly Constrained Timetabling Problems  

Microsoft Academic Search

In this paper, we present a powerful hybrid genetic algorithm based around a heuristic timetabling framework. This combines a direct representation of the timetable with heuristic crossover operators to ensure that the most fundamental constraints are never violated. We explain how the population is seeded so as to produce a solution which cannot be outperformed by the heuristic method alone.

Edmund K. Burke; Dave Elliman; Rupert F. Weare

1995-01-01

168

Genetic Variants on Chromosome 1q41 Influence Ocular Axial Length and High Myopia  

PubMed Central

As one of the leading causes of visual impairment and blindness, myopia poses a significant public health burden in Asia. The primary determinant of myopia is an elongated ocular axial length (AL). Here we report a meta-analysis of three genome-wide association studies on AL conducted in 1,860 Chinese adults, 929 Chinese children, and 2,155 Malay adults. We identified a genetic locus on chromosome 1q41 harboring the zinc-finger 11B pseudogene ZC3H11B showing genome-wide significant association with AL variation (rs4373767, ??=??0.16 mm per minor allele, Pmeta?=?2.69×10?10). The minor C allele of rs4373767 was also observed to significantly associate with decreased susceptibility to high myopia (per-allele odds ratio (OR)?=?0.75, 95% CI: 0.68–0.84, Pmeta?=?4.38×10?7) in 1,118 highly myopic cases and 5,433 controls. ZC3H11B and two neighboring genes SLC30A10 and LYPLAL1 were expressed in the human neural retina, retinal pigment epithelium, and sclera. In an experimental myopia mouse model, we observed significant alterations to gene and protein expression in the retina and sclera of the unilateral induced myopic eyes for the murine genes ZC3H11A, SLC30A10, and LYPLAL1. This supports the likely role of genetic variants at chromosome 1q41 in influencing AL variation and high myopia.

Fan, Qiao; Barathi, Veluchamy A.; Cheng, Ching-Yu; Zhou, Xin; Meguro, Akira; Nakata, Isao; Khor, Chiea-Chuen; Goh, Liang-Kee; Li, Yi-Ju; Lim, Wan'e; Ho, Candice E. H.; Hawthorne, Felicia; Zheng, Yingfeng; Chua, Daniel; Inoko, Hidetoshi; Yamashiro, Kenji; Ohno-Matsui, Kyoko; Matsuo, Keitaro; Matsuda, Fumihiko; Vithana, Eranga; Seielstad, Mark; Mizuki, Nobuhisa; Beuerman, Roger W.; Tai, E.-Shyong; Yoshimura, Nagahisa; Aung, Tin; Young, Terri L.; Wong, Tien-Yin

2012-01-01

169

High Genetic Variability of Herbivore-Induced Volatile Emission within a Broad Range of Maize Inbred Lines1  

PubMed Central

Maize plants (Zea mays) attacked by caterpillars release a mixture of odorous compounds that attract parasitic wasps, natural enemies of the herbivores. We assessed the genetic variability of these induced volatile emissions among 31 maize inbred lines representing a broad range of genetic diversity used by breeders in Europe and North America. Odors were collected from young plants that had been induced by injecting them with caterpillar regurgitant. Significant variation among lines was found for all 23 volatile compounds included in the analysis: the lines differed enormously in the total amount of volatiles emitted and showed highly variable odor profiles distinctive of each genotype. Principal component analysis performed on the relative quantities of particular compounds within the blend revealed clusters of highly correlated volatiles, which may share common metabolic pathways. European and American lines belonging to established heterotic groups were loosely separated from each other, with the most clear-cut difference in the typical release of (E)-?-caryophyllene by European lines. There was no correlation between the distances among the lines based on their odor profiles and their respective genetic distances previously assessed by neutral RFLP markers. This most comprehensive study to date on intraspecific variation in induced odor emission by maize plants provides a further example of the remarkably high genetic diversity conserved within this important crop plant. A better understanding of the genetic control of induced odor emissions may help in the development of maize varieties particularly attractive to parasitoids and other biological control agents and perhaps more repellent for herbivores.

Degen, Thomas; Dillmann, Christine; Marion-Poll, Frederic; Turlings, Ted C.J.

2004-01-01

170

Genetic structure in a fragmented Northern Hemisphere rainforest: large effective sizes and high connectivity among populations of the epiphytic lichen Lobaria pulmonaria.  

PubMed

An extraordinary diversity of epiphytic lichens is found in the boreal rainforest of central Norway, the highest-latitude rainforest in the world. These rainforest relicts are located in ravine systems, and clear cutting has increased the distance between remaining patches. We hypothesized that the relatively small lichen populations in the remaining forest stands have suffered a depletion of genetic diversity through bottlenecks and founder events. To test this hypothesis, we assessed genetic diversity and structure in the populations of the tripartite lichen Lobaria pulmonaria using eight SSR loci. We sampled thalli growing on Picea abies branches and propagules deposited in snow at three localities. Contrary to expectations, we found high genetic diversity in lichen and snow samples, and high effective sizes of the studied populations. Also, limited genetic differentiation between populations, high historical migration rates, and a high proportion of first generation immigrants were estimated, implying high connectivity across distances <30km. Almost all genetic variation was attributed to variation within sites; spatial genetic structures within populations were absent or appeared on small scales (5-10m). The high genetic diversity in the remaining old boreal rainforests shows that even relict forest patches might be suitable for conservation of genetic diversity. PMID:22571538

Hilmo, Olga; Lundemo, Sverre; Holien, Håkon; Stengrundet, Kirsti; Stenøien, Hans K

2012-05-09

171

High [ 18 F] 2-fluoro-2-deoxy- d -glucose (FDG) uptake of adrenocortical adenoma showing subclinical Cushing's syndrome  

Microsoft Academic Search

A 48-year-old woman with left adrenal tumor, which showed increased uptake of [18F] 2-fluoro-2-deoxy-d-glucose (FDG) was presented. Her adrenal tumor was incidentally discovered, although she had no remarkable illness, and her\\u000a blood pressure was normal. Hormonal examination including dexamethason suppression test and diurnal variation in serum cortisol\\u000a level confirmed preclinical Cushing's syndrome. CT, MRI and131I-adosterol scintigraphy showed findings consistent with

Akiko Shimizu; Noboru Oriuchi; Yoshito Tsushima; Tetsuya Higuchi; Jun Aoki; Keigo Endo

2003-01-01

172

Bottlenecked but long-lived: high genetic diversity retained in white-tailed eagles upon recovery from population decline  

PubMed Central

Most of the white-tailed eagle (Haliaeetus albicilla) populations in Europe experienced dramatic declines during the twentieth century. However, owing to intense conservation actions and the ban of DDT and other persistent pollutants, populations are currently recovering. We show that despite passing through demographic bottlenecks, white-tailed eagle populations have retained significant levels of genetic diversity. Both genetic and ringing data indicate that migration between populations has not been a major factor for the maintenance of genetic variability. We argue that the long generation time of eagles has acted as an intrinsic buffer against loss of genetic diversity, leading to a shorter effective time of the experienced bottleneck. Notably, conservation actions taken in several small sub-populations have ensured the preservation of a larger proportion of the total genetic diversity than if conservation had focused on the population stronghold in Norway. For conservation programmes targeting other endangered, long-lived species, our results highlight the possibility for local retention of high genetic diversity in isolated remnant populations.

Hailer, Frank; Helander, Bjorn; Folkestad, Alv O; Ganusevich, Sergei A; Garstad, Steinar; Hauff, Peter; Koren, Christian; Nygard, Torgeir; Volke, Veljo; Vila, Carles; Ellegren, Hans

2006-01-01

173

Regional genetic differentiation among northern high-latitude island populations of a broadcast-spawning coral  

NASA Astrophysics Data System (ADS)

Knowledge of genetic connectivity is useful for understanding of the recovery potential of coral populations after various disturbances, such as coral mass bleaching. Population genetic studies in corals are mostly restricted to Australian and Caribbean species; studies in the northern Pacific are relatively limited. Using microsatellite markers, the population genetics of Acropora sp. 1 was examined between two regions in Japan, the Okinawa-Aka and Bonin Islands, which are separated by approximately 1,500 km of open water in a high-latitude area. Statistically significant but small genetic differentiation in Acropora sp. 1 was detected between and within these regions. Genetic diversity was not obviously reduced in populations of the Bonin Islands, which are relatively isolated. Thus, some level of connectivity appears to be maintained between the two regions, likely because of the high dispersal ability of this broadcast spawner.

Nakajima, Y.; Nishikawa, A.; Iguchi, A.; Sakai, K.

2012-12-01

174

High genome heterozygosity and endemic genetic recombination in the wheat stripe rust fungus.  

PubMed

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases of wheat. Here we report a 110-Mb draft sequence of Pst isolate CY32, obtained using a 'fosmid-to-fosmid' strategy, to better understand its race evolution and pathogenesis. The Pst genome is highly heterozygous and contains 25,288 protein-coding genes. Compared with non-obligate fungal pathogens, Pst has a more diverse gene composition and more genes encoding secreted proteins. Re-sequencing analysis indicates significant genetic variation among six isolates collected from different continents. Approximately 35% of SNPs are in the coding sequence regions, and half of them are non-synonymous. High genetic diversity in Pst suggests that sexual reproduction has an important role in the origin of different regional races. Our results show the effectiveness of the 'fosmid-to-fosmid' strategy for sequencing dikaryotic genomes and the feasibility of genome analysis to understand race evolution in Pst and other obligate pathogens. PMID:24150273

Zheng, Wenming; Huang, Lili; Huang, Jinqun; Wang, Xiaojie; Chen, Xianming; Zhao, Jie; Guo, Jun; Zhuang, Hua; Qiu, Chuangzhao; Liu, Jie; Liu, Huiquan; Huang, Xueling; Pei, Guoliang; Zhan, Gangming; Tang, Chunlei; Cheng, Yulin; Liu, Minjie; Zhang, Jinshan; Zhao, Zhongtao; Zhang, Shijie; Han, Qingmei; Han, Dejun; Zhang, Hongchang; Zhao, Jing; Gao, Xiaoning; Wang, Jianfeng; Ni, Peixiang; Dong, Wei; Yang, Linfeng; Yang, Huanming; Xu, Jin-Rong; Zhang, Gengyun; Kang, Zhensheng

2013-10-23

175

Litter stoichiometric traits of plant species of high-latitude ecosystems show high responsiveness to global change without causing strong variation in litter decomposition.  

PubMed

High-latitude ecosystems are important carbon accumulators, mainly as a result of low decomposition rates of litter and soil organic matter. We investigated whether global change impacts on litter decomposition rates are constrained by litter stoichiometry. • Thereto, we investigated the interspecific natural variation in litter stoichiometric traits (LSTs) in high-latitude ecosystems, and compared it with climate change-induced LST variation measured in the Meeting of Litters (MOL) experiment. This experiment includes leaf litters originating from 33 circumpolar and high-altitude global change experiments. Two-year decomposition rates of litters from these experiments were measured earlier in two common litter beds in sub-Arctic Sweden. • Response ratios of LSTs in plants of high-latitude ecosystems in the global change treatments showed a three-fold variation, and this was in the same range as the natural variation among species. However, response ratios of decomposition were about an order of magnitude lower than those of litter carbon/nitrogen ratios. • This implies that litter stoichiometry does not constrain the response of plant litter decomposition to global change. We suggest that responsiveness is rather constrained by the less responsive traits of the Plant Economics Spectrum of litter decomposability, such as lignin and dry matter content and specific leaf area. PMID:22889103

Aerts, R; van Bodegom, P M; Cornelissen, J H C

2012-08-13

176

Field, Genetic, and Modeling Approaches Show Strong Positive Selection Acting upon an Insecticide Resistance Mutation in Anopheles gambiae s.s.  

PubMed Central

Alleles subject to strong, recent positive selection will be swept toward fixation together with contiguous sections of the genome. Whether the genomic signatures of such selection will be readily detectable in outbred wild populations is unclear. In this study, we employ haplotype diversity analysis to examine evidence for selective sweeps around knockdown resistance (kdr) mutations associated with resistance to dichlorodiphenyltrichloroethane and pyrethroid insecticides in the mosquito Anopheles gambiae. Both kdr mutations have significantly lower haplotype diversity than the wild-type (nonresistant) allele, with kdr L1014F showing the most pronounced footprint of selection. We complement these data with a time series of collections showing that the L1014F allele has increased in frequency from 0.05 to 0.54 in 5 years, consistent with a maximum likelihood–fitted selection coefficient of 0.16 and a dominance coefficient of 0.25. Our data show that strong, recent positive selective events, such as those caused by insecticide resistance, can be identified in wild insect populations.

Lynd, Amy; Weetman, David; Barbosa, Susana; Egyir Yawson, Alexander; Mitchell, Sara; Pinto, Joao; Hastings, Ian; Donnelly, Martin J.

2010-01-01

177

Genetic structure in striped skunks (Mephitis mephitis) on the southern high plains of Texas  

USGS Publications Warehouse

Genetic variation within populations reflects population-level social and demographic processes and influences how a population behaves as an evolutionary unit. We examined partitioning of genetic variation in striped skunks (Mephitis mephitis) from the Southern High Plains of Texas during 1994-1995. Sixty-nine male and 35 female skunks were sampled on four 12.8-km2 study plots. Plot centers ranged from 17.6 to 61.6 km apart. We used multi-locus DNA fingerprinting with 2 probes, pV47 and CTTxAGG, to test 3 hypotheses: (1) females are more genetically similar to other females than males are to other males on the same plot (indicating greater female philopatry than male philopatry), (2) genetic similarity is greater within plots than among plots (indicating partitioning of genetic variation in space), and (3) genetic similarity of males decreases as the distance separating males increases (indicating geographic distance affects rates of gene flow). In general, males on a plot had lower average genetic similarity than females. Genetic similarity within plots was not different from genetic similarity among plots for males or for females. Genetic similarity of males did not decrease with increasing distance among plots. The lack of geographical genetic structure in striped skunks suggests at the scale of this study (<60 km) that gene flow of biparentally inherited genes is not distance-mediated. However, the higher similarity values for females than for males on the same plot supports an effect of male-biased dispersal and female philopatry on partitioning of genetic variation between sexes.

Hansen, L. A.; Mathews, N. E.; Hansen, R. W.; Vander Lee, B. A.; Scott, Lutz, R.

2003-01-01

178

Population genetics of purple saxifrage (Saxifraga oppositifolia) in the high Arctic archipelago of Svalbard  

PubMed Central

We investigated patterns of genetic variability in Saxifraga oppositifolia in the isolated Arctic Svalbard archipelago. The genetic analysis included genotyping using nine polymorphic microsatellite markers and sequencing of the nuclear internal transcribed spacer region. Among populations, mean allele numbers per microsatellite locus ranged from 2.0 to 2.6, and 9 % of alleles were unique. Observed (HO) and expected (HE) heterozygosities averaged 0.522 and 0.445, respectively. Typically negative but non-significant FIS values (mean ?0.173) were found in S. oppositifolia populations. FST values were relatively low (mean 0.123). The Bayesian structure analysis provided additional information on population genetic structures. Seven out of 11 studied populations, including populations located both near each other and far apart (distances 5–210 km), showed relatively homogeneous clustering patterns, while one population located on a slope in the main settlement of Longyearbyen possessed a unique genetic structure. The Mantel test proved that there is no significant correlation between genetic and geographical distances. Different growth habits (compact, trailing and intermediate) did not possess distinct genetic compositions based on microsatellite variation. Internal transcribed spacer sequencing revealed 12 polymorphic sites. Among 24 sequenced Svalbard samples, eight haplotypes were detected, none shared by the mainland samples. Population genetic structures of S. oppositifolia in Svalbard show that both genetic variation and differentiation levels are modest, outcrossing is the main mating system, and dispersal and gene flow are important, probably attributable to strong winds and human and animal vectors.

Pietilainen, Maria; Korpelainen, Helena

2013-01-01

179

Population Genetic Screening for Alpha1Antitrypsin Deficiency in a High-Prevalence Area  

Microsoft Academic Search

Background: Current guidelines for ?1-antitrypsin deficiency (AATD) state that adult population screening should only be done in high-risk areas. Up-to-date genetic methods are always recommended. Objectives: To determine the prevalence of AATD in a suspected high-risk area by population screening, applying new genetic analyses and comparing the prevalence of liver and lung abnormalities in subjects with or without AATD. Methods:

Luciano Corda; Daniela Medicina; Giuseppe Emanuele La Piana; Enrica Bertella; Giovanni Moretti; Luca Bianchi; Valentina Pinelli; Gianfranco Savoldi; Paola Baiardi; Fabio Facchetti; Nuccia Gatta; Isabella Annesi-Maesano; Bruno Balbi

2011-01-01

180

HIV-1 low-level viraemia assessed with 3 commercial real-time PCR assays show high variability  

PubMed Central

Background Current real-time PCR-based HIV-1 viral load (VL) assays allow the detection of residual viraemia in antiretroviral-treated patients. The clinical outcome of HIV1 patients experiencing low-level replication (<50 cop/mL) in comparison with fully suppressed patients is currently debated. We analysed variability of 3 VL assays <50 cop/mL, and evaluated the reproducibility of viral blips <100 cop/mL. Methods Three commercial VL assays were tested: Versant HIV-1 RNA 1.0 kPCR (Siemens), Abbott Realtime HIV-1, and Cobas Ampliprep/Cobas Taqman HIV-1 v2.0 (Roche). Ten replicates of a reference sample at 4 low target dilutions were tested to evaluate assay variability. Prospective collection of 181 clinical samples with detectable VL <50 cop/mL was used to evaluate intra-and inter-assay variability by triplicate testing. Samples from 26 patients experiencing a viral blip were retested. Results All assays showed substantial variability at low VL level: the coefficient of variation at 100, 50, 25 and 12 cop/mL ranged respectively from 32 to 44%, 35 to 68%, 41 to 83% and 33 to 77%. In the intra-assay evaluation of repeatability, 52.5 to 57.5% of detectable VL <50 cop/mL tested in triplicate showed at least one fully undetected result. Variability was similar in the inter-assay arm. The VL blips could only be reproduced in 19% of cases. Conclusions The most recent versions of widespread commercial VL assays showed substantial variability at low levels and residual viraemia could not be consistently reproduced. Patient outcome studies comparing residual VL to full suppression are therefore biased when using commercial assays.

2012-01-01

181

Phenacetin O-deethylase: an activity of a cytochrome P-450 showing genetic linkage with that catalysing the 4-hydroxylation of debrisoquine?  

PubMed Central

Phenacetin O-deethylase activity was impaired, both in vivo and in vitro, in poor metabolisers of debrisoquine, consistent with the work of others. No impairment was observed in the oxidation of acetanilide, amylobarbitone or antipyrine in the PM phenotype. There was a good correlation (r = 0.804) between the high affinity component of phenacetin O-deethylase and debrisoquine 4-hydroxylase activities. No such correlation was observed with the low affinity component of phenacetin O-deethylase activity. Although debrisoquine was a competitive inhibitor of phenacetin O-deethylase activity, phenacetin was without effect on debrisoquine 4-hydroxylation. There was also marked differences in the effects of sparteine, guanoxan and alpha-naphthoflavone on the two activities. Cigarette smoking was associated with a significant, two-fold, increase in phenacetin O-deethylase activity whilst debrisoquine 4-hydroxylase activity was not affected. It is concluded that the high affinity component of phenacetin O-deethylase and debrisoquine 4-hydroxylase activities are catalysed by different isozymes of cytochrome P-450 but that these are most probably regulated by closely linked genes.

Kahn, G C; Boobis, A R; Brodie, M J; Toverud, E L; Murray, S; Davies, D S

1985-01-01

182

A simple topological identification method for highly (3,12)-connected 3D MOFs showing anion exchange and luminescent properties.  

PubMed

Reaction of a semi-rigid tripodal ligand 1,1',1''-(2,4,6-trimethylbenzene-1,3,5-triyl)tris(methylene)tripyridinium-4-olate) (TTP) with Ln(3+) (Ln = Eu, Gd) afforded rare (3,12)-connected metal-organic frameworks (MOFs). A topological simplification of such highly connected 3D MOFs on the basis of 2D CdI(2) (3,6)-nets is proposed. The luminescent and anion exchange properties of the compounds were determined. PMID:21359292

Yang, Qing-Yuan; Li, Kang; Luo, Jian; Pan, Mei; Su, Cheng-Yong

2011-02-25

183

Thermal nonlinearity and small-scale stratification in a magnetized plasma showing coulomb collisions in a high-frequency field  

SciTech Connect

A magnetized plasma having Coulomb collisions in a strong high-frequency field behaves as a nonlinear medium having a new thermal nonlinearity mechanism due to the transverse thermal driving force affecting the transport. This is due to thermal diffusion transverse to the magnetic field, so the charged-particle concentration in the field-heated region increases, not decreases, as is the case in other thermal-nonlinearity mechanisms. The quasistatic instability in such a plasma has been examined for the case where the electric-field vector is perpendicular to the external magnetic field. Threshold fields have been determined for instability, together with maximum increments and wave numbers for the most rapidly growing perturbations. A qualitative study is made on the stationary structures in the nonlinear plasma formations. This instability is used in a proposed mechanism for small-scale stratification in the ionospheric plasma in a strong radio wave.

Kostrov, A.V.; Kim, A.V.

1988-11-01

184

Essay Contest Reveals Misconceptions of High School Students in Genetics Content  

PubMed Central

National educational organizations have called upon scientists to become involved in K–12 education reform. From sporadic interaction with students to more sustained partnerships with teachers, the engagement of scientists takes many forms. In this case, scientists from the American Society of Human Genetics (ASHG), the Genetics Society of America (GSA), and the National Society of Genetic Counselors (NSGC) have partnered to organize an essay contest for high school students as part of the activities surrounding National DNA Day. We describe a systematic analysis of 500 of 2443 total essays submitted in response to this contest over 2 years. Our analysis reveals the nature of student misconceptions in genetics, the possible sources of these misconceptions, and potential ways to galvanize genetics education.

Mills Shaw, Kenna R.; Van Horne, Katie; Zhang, Hubert; Boughman, Joann

2008-01-01

185

Predicted HIV-1 coreceptor usage among Kenya patients shows a high tendency for subtype d to be cxcr4 tropic  

PubMed Central

Background CCR5 antagonists have clinically been approved for prevention or treatment of HIV/AIDS. Countries in Sub-Saharan Africa with the highest burden of HIV/AIDS are due to adopt these regimens. However, HIV-1 can also use CXCR4 as a co-receptor. There is hence an urgent need to map out cellular tropism of a country’s circulating HIV strains to guide the impending use of CCR5 antagonists. Objectives To determine HIV-1 coreceptor usage among patients attending a comprehensive care centre in Nairobi, Kenya. Methods Blood samples were obtained from HIV infected patients attending the comprehensive care centre, Kenyatta National Hospital in years 2008 and 2009. The samples were separated into plasma and peripheral blood mononuclear cells (PBMCs). Proviral DNA was extracted from PBMCs and Polymerase Chain reaction (PCR) done to amplify the HIV env fragment spanning the C2-V3 region. The resultant fragment was directly sequenced on an automated sequencer (ABI, 3100). Co-receptor prediction of the env sequences was done using Geno2pheno [co-receptor], and phylogenetic relationships determined using CLUSTALW and Neighbor Joining method. Results A total of 67 samples (46 treatment experienced and 21 treatment naive) were successfully amplified and sequenced. Forty nine (73%) sequences showed a prediction for R5 tropism while 18(27%) were X4 tropic. Phylogenetic analysis showed that 46(69%) were subtype A, 11(16%) subtype C, and 10(15%) subtype D. No statistical significant associations were observed between cell tropism and CD4+ status, patient gender, age, or treatment option. There was a tendency for more X4 tropic strains being in the treatment experienced group than the naive group: Of 46 treatment experiencing participants, 14(30%) harboured X4, compared with 4(19%) of 21 of the treatment-naïve participants, the association is however not statistically significant (p?=?0.31). However, a strong association was observed between subtype D and CXCR4 co- receptor usage (p?=?0.015) with 6(60%) of the 10 subtype D being X4 tropic and 4(40%) R5 tropic. Conclusion HIV-1 R5 tropic strains were the most prevalent in the study population and HIV infected patients in Kenya may benefit from CCR5 antagonists. However, there is need for caution where subtype D infection is suspected or where antiretroviral salvage therapy is indicated.

2012-01-01

186

Thermostable trypsin conjugates immobilized to biogenic magnetite show a high operational stability and remarkable reusability for protein digestion  

NASA Astrophysics Data System (ADS)

In this work, magnetosomes produced by microorganisms were chosen as a suitable magnetic carrier for covalent immobilization of thermostable trypsin conjugates with an expected applicability for efficient and rapid digestion of proteins at elevated temperatures. First, a biogenic magnetite was isolated from Magnetospirillum gryphiswaldense and its free surface was coated with the natural polysaccharide chitosan containing free amino and hydroxy groups. Prior to covalent immobilization, bovine trypsin was modified by conjugating with ?-, ?- and ?-cyclodextrin. Modified trypsin was bound to the magnetic carriers via amino groups using 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide and N-hydroxysulfosuccinimide as coupling reagents. The magnetic biomaterial was characterized by magnetometric analysis and electron microscopy. With regard to their biochemical properties, the immobilized trypsin conjugates showed an increased resistance to elevated temperatures, eliminated autolysis, had an unchanged pH optimum and a significant storage stability and reusability. Considering these parameters, the presented enzymatic system exhibits properties that are superior to those of trypsin forms obtained by other frequently used approaches. The proteolytic performance was demonstrated during in-solution digestion of model proteins (horseradish peroxidase, bovine serum albumin and hen egg white lysozyme) followed by mass spectrometry. It is shown that both magnetic immobilization and chemical modification enhance the characteristics of trypsin making it a promising tool for protein digestion.

Pe?ová, M.; Šebela, M.; Marková, Z.; Poláková, K.; ?uda, J.; Šafá?ová, K.; Zbo?il, R.

2013-03-01

187

Synthesis and structure of nanocrystalline TiO2 with lower band gap showing high photocatalytic activity.  

PubMed

Nanocrystalline TiO2 was synthesized by the solution combustion method using titanyl nitrate and various fuels such as glycine, hexamethylenetetramine, and oxalyldihydrazide. These catalysts are active under visible light, have optical absorption wavelengths below 600 nm, and show superior photocatalytic activity for the degradation of methylene blue and phenol under UV and solar conditions compared to commercial TiO2, Degussa P-25. The higher photocatalytic activity is attributed to the structure of the catalyst. Various studies such as X-ray diffraction, Raman spectroscopy, Brunauer-Emmett-Teller surface area, thermogravimetric-differential thermal analysis, FT-IR spectroscopy, NMR, UV-vis spectroscopy, and surface acidity measurements were conducted. It was concluded that the primary factor for the enhanced activity of combustion-synthesized catalyst is a larger amount of surface hydroxyl groups and a lowered band gap. The lower band gap can be attributed to the carbon inclusion into the TiO2 giving TiO(2-2x)C(x) VO2**. PMID:15835170

Nagaveni, K; Hegde, M S; Ravishankar, N; Subbanna, G N; Madras, Giridhar

2004-03-30

188

Comparative genomic hybridization in chronic B-cell leukemias shows a high incidence of chromosomal gains and losses.  

PubMed

In chronic B-cell leukemias, fluorescence in situ hybridization has greatly improved the ability to detect certain chromosomal aberrations, as cells in all phases of the cell cycle are analyzed. To obtain a comprehensive view of chromosomal gains and losses, we applied the recently developed technique of comparative genomic hybridization (CGH) to 28 patients with chronic B-cell leukemias. CGH results were compared with those obtained by chromosome banding analysis and interphase cytogenetics. In 19 of the 28 cases, chromosomal imbalances were detected, including amplified DNA sequences in three instances. The most common aberrations included gains of chromosomal material on 8q and 12 as well as losses of 6q, 11q, 13q, and 17p. In 13 cases, CGH revealed chromosomal gains and losses not detected by banding analysis. In 8 of these 13 cases, discrepancies were further investigated using other methods, and in all instances, the CGH findings were confirmed. A limitation of detecting small deleted regions by CGH was found in one example of 18p. In conclusion, our data show that the results of banding analysis in chronic B-cell leukemias often do not reflect the chromosomal changes in the predominant cell clone. This may be one explanation for the as yet poor correlation between cytogenetic findings and clinical course in this group of neoplasms. PMID:7780145

Bentz, M; Huck, K; du Manoir, S; Joos, S; Werner, C A; Fischer, K; Döhner, H; Lichter, P

1995-06-15

189

Thermostable trypsin conjugates immobilized to biogenic magnetite show a high operational stability and remarkable reusability for protein digestion.  

PubMed

In this work, magnetosomes produced by microorganisms were chosen as a suitable magnetic carrier for covalent immobilization of thermostable trypsin conjugates with an expected applicability for efficient and rapid digestion of proteins at elevated temperatures. First, a biogenic magnetite was isolated from Magnetospirillum gryphiswaldense and its free surface was coated with the natural polysaccharide chitosan containing free amino and hydroxy groups. Prior to covalent immobilization, bovine trypsin was modified by conjugating with ?-, ?- and ?-cyclodextrin. Modified trypsin was bound to the magnetic carriers via amino groups using 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide and N-hydroxysulfosuccinimide as coupling reagents. The magnetic biomaterial was characterized by magnetometric analysis and electron microscopy. With regard to their biochemical properties, the immobilized trypsin conjugates showed an increased resistance to elevated temperatures, eliminated autolysis, had an unchanged pH optimum and a significant storage stability and reusability. Considering these parameters, the presented enzymatic system exhibits properties that are superior to those of trypsin forms obtained by other frequently used approaches. The proteolytic performance was demonstrated during in-solution digestion of model proteins (horseradish peroxidase, bovine serum albumin and hen egg white lysozyme) followed by mass spectrometry. It is shown that both magnetic immobilization and chemical modification enhance the characteristics of trypsin making it a promising tool for protein digestion. PMID:23466477

Pe?ová, M; Šebela, M; Marková, Z; Poláková, K; ?uda, J; Šafá?ová, K; Zbo?il, R

2013-03-06

190

Taxonomic study of the Burmoniscus ocellatus complex (Crustacea, Isopoda, Oniscidea) in Japan shows genetic diversification in the southern Ryukyus, southwestern Japan.  

PubMed

To clarify the taxonomic status of the Burmoniscus ocellatus complex in Japan, we carried out morphological observations and phylogenetic analyses of specimens collected from Yonagunijima, Iriomotejima, Ishigakijima, and Miyakojima Islands of the southern Ryukyus and from Okinawajima Island of the central Ryukyus in southwestern Japan. Observations of the holotypes of Aphiloscia iriomotensis ( Nunomura, 1986 ), Ap. ishigakiensis ( Nunomura, 1986 ), and Ap. yonakuniensis ( Nunomura, 1986 ), in addition to the specimens newly collected from the five islands, indicated that these specimens belong to the genus Burmoniscus. Analyses of five morphological characters of 268 specimens collected from the five islands showed that the body size of Okinawajima specimens is distinctly smaller than those of the specimens from the southern Ryukyus. The ranges of the five morphological characters tended to overlap among the specimens from Yonagunijima, Iriomotejima, Ishigakijima and Miyakojima Islands; these morphological characters were congruent with those of 6. ocellatus (Verhoeff, 1928). The phylogenetic analyses were based on three regions of mitochondrial DNA-COI, 12S rRNA, and 16S rRNA-and indicated that the specimens collected from the southern Ryukyus constitute a monophyletic group, which is clearly distinct from the clade composed of the Okinawajima specimens. These results strongly suggest that Ap. iriomotensis, Ap. ishigakiensis, and Ap. yonakuniensis are synonymous with B. ocellatus, a species widely distributed in the southern Ryukyus. On the other hand, the species from Okinawajima Island in the central Ryukyus is considered to be an undescribed Burmoniscus species, which is closely related to but clearly distinct from S. ocellatus. PMID:22873811

Karasawa, Shigenori; Honda, Masanao

2012-08-01

191

Awareness of Societal Issues Among High School Biology Teachers Teaching Genetics  

NASA Astrophysics Data System (ADS)

The purpose of this study was to investigate how aware high school biology teachers are of societal issues (values, moral, ethic, and legal issues) while teaching genetics, genetics engineering, molecular genetics, human heredity, and evolution. The study includes a short historical review of World War II atrocities during the Holocaust when scientists from all the above-mentioned disciplines had been involved in trying to support and develop the eugenics theories. It investigates pre- and postwar theories of the eugenics movement in the United States which were implemented successfully in Germany and a literature survey of the studies of societal issues related to these subjects. The sample consisted of 30 male and female biology teachers. Enclosed are teachers' answers in favor or against including debates about societal issues in their classrooms while teaching the disciplines mentioned above. Teachers' answers were analyzed in relation to three variables: years of teaching experience, gender, and religion faith. Data were collected from questionnaires and personal interviews and analyzed according to qualitative and quantitative methods. The results show that amongst the teachers there is a medium to low level of awareness of societal issues, while mainly emphasizing scientific subjects in preparation of matriculation examinations. The majority of the teachers do not include societal issues in their teaching, but if students raise these issues, teachers claimed to address them. No differences in teachers' opinions to societal issues were found in relation to gender or religious faith. Teachers with more years of teaching experience tend to teach with a more Science, Technology, and Society (STS) approach than novice teachers. The results are discussed in relation to teachers' professional development and teaching strategies are suggested to be used in their classrooms based on a STS approach, which includes the societal issues as a main goal.

Lazarowitz, Reuven; Bloch, Ilit

2005-12-01

192

Remotely sensed forest cover loss shows high spatial and temporal variation across Sumatera and Kalimantan, Indonesia 2000-2008  

NASA Astrophysics Data System (ADS)

The Indonesian islands of Sumatera and Kalimantan (the Indonesian part of the island of Borneo) are a center of significant and rapid forest cover loss in the humid tropics with implications for carbon dynamics, biodiversity conservation, and local livelihoods. The aim of our research was to analyze and interpret annual trends of forest cover loss for different sub-regions of the study area. We mapped forest cover loss for 2000-2008 using multi-resolution remote sensing data from the Landsat enhanced thematic mapper plus (ETM +) and moderate resolution imaging spectroradiometer (MODIS) sensors and analyzed annual trends per island, province, and official land allocation zone. The total forest cover loss for Sumatera and Kalimantan 2000-2008 was 5.39 Mha, which represents 5.3% of the land area and 9.2% of the year 2000 forest cover of these two islands. At least 6.5% of all mapped forest cover loss occurred in land allocation zones prohibiting clearing. An additional 13.6% of forest cover loss occurred where clearing is legally restricted. The overall trend of forest cover loss increased until 2006 and decreased thereafter. The trends for Sumatera and Kalimantan were distinctly different, driven primarily by the trends of Riau and Central Kalimantan provinces, respectively. This analysis shows that annual mapping of forest cover change yields a clearer picture than a one-time overall national estimate. Monitoring forest dynamics is important for national policy makers, especially given the commitment of Indonesia to reducing greenhouse gas emissions as part of the reducing emissions from deforestation and forest degradation in developing countries initiative (REDD +). The improved spatio-temporal detail of forest change monitoring products will make it possible to target policies and projects in meeting this commitment. Accurate, annual forest cover loss maps will be integral to many REDD + objectives, including policy formulation, definition of baselines, detection of displacement, and the evaluation of the permanence of emission reduction.

Broich, Mark; Hansen, Matthew; Stolle, Fred; Potapov, Peter; Arunarwati Margono, Belinda; Adusei, Bernard

2011-01-01

193

Genome Characteristics of a Novel Phage from Bacillus thuringiensis Showing High Similarity with Phage from Bacillus cereus  

PubMed Central

Bacillus thuringiensis is an important entomopathogenic bacterium belongs to the Bacillus cereus group, which also includes B. anthracis and B. cereus. Several genomes of phages originating from this group had been sequenced, but no genome of Siphoviridae phage from B. thuringiensis has been reported. We recently sequenced and analyzed the genome of a novel phage, BtCS33, from a B. thuringiensis strain, subsp. kurstaki CS33, and compared the gneome of this phage to other phages of the B. cereus group. BtCS33 was the first Siphoviridae phage among the sequenced B. thuringiensis phages. It produced small, turbid plaques on bacterial plates and had a narrow host range. BtCS33 possessed a linear, double-stranded DNA genome of 41,992 bp with 57 putative open reading frames (ORFs). It had a typical genome structure consisting of three modules: the “late” region, the “lysogeny-lysis” region and the “early” region. BtCS33 exhibited high similarity with several phages, B. cereus phage W? and some variants of W?, in genome organization and the amino acid sequences of structural proteins. There were two ORFs, ORF22 and ORF35, in the genome of BtCS33 that were also found in the genomes of B. cereus phage W? and may be involved in regulating sporulation of the host cell. Based on these observations and analysis of phylogenetic trees, we deduced that B. thuringiensis phage BtCS33 and B. cereus phage W? may have a common distant ancestor.

Yuan, Yihui; Gao, Meiying; Wu, Dandan; Liu, Pengming; Wu, Yan

2012-01-01

194

High levels of genetic variation at MHC class II DBB loci in the tammar wallaby ( Macropus eugenii )  

Microsoft Academic Search

High levels of MHC diversity are crucial for immunological fitness of populations, with island populations particularly susceptible\\u000a to loss of genetic diversity. In this study, the level of MHC class II DBB diversity was examined in tammar wallabies (Macropus eugenii) from Kangaroo Island by genotyping class II-linked microsatellite loci and sequencing of DBB genes. Here we show that the\\u000a tammar

Yuanyuan Cheng; Hannah V. Siddle; Stephan Beck; Mark D. B. Eldridge; Katherine Belov

2009-01-01

195

High-resolution deep Northeast Pacific radiocarbon record shows little change in ventilation rate during the last deglaciation  

NASA Astrophysics Data System (ADS)

The rise in atmospheric carbon dioxide during the last deglaciation is thought to be driven by release of carbon sequestered in the abyssal ocean. This mechanism requires a poorly ventilated deep Pacific during the Last Glacial Maximum (LGM) and enhanced ventilation during the deglaciation. Here we evaluate the plausibility of this scenario using planktonic and benthic foraminiferal radiocarbon data from a high-sedimentation rate core (~25 cm/kyr) collected in the deep (2700 m) Northeast Pacific. We estimate that the mean benthic-planktonic (B-P) age was 1620±190 years during the LGM (n=10 pairs). This value is indistinguishable from the mean B-P difference for the deglaciation (1500±230; n=20 pairs) and the difference between surface and deep water 14C ages today (1560±70 years). Furthermore, our time series of benthic ?14C parallels atmospheric ?14C with an offset of 300±50‰ from 22 to 10 kyr BP. These data suggest the ventilation rate of the deep NE Pacific remained nearly constant during the deglaciation, consistent with lower resolution data from this region (Okazaki et al., 2010). Between 22 and 16 kyr BP, ?14C in the deep NE Pacific varied between 0 and 100‰, well above the -200‰ values estimated at intermediate depths off of Baja California during the Mystery Interval (Marchitto et al., 2007). The deep NE Pacific apparently did not contain water of adequate age to source deglacial ?14C anomalies shallower in the water column. Given that Antarctic Intermediate Water is also an unlikely source (de Pol-Holz et al., 2010; Rose et al., 2010), an alternative explanation is necessary for the extreme 14C depletions in the eastern tropical Pacific. De Pol-Holz, R. D., et al. 2010. No signature of abyssal carbon in intermediate waters off Chile during deglaciation. Nature Geoscience 3, 192-195. Marchitto, T., Lehman, S., Ortiz, J., Fluckiger, J. & van Geen, A. 2007. Marine radiocarbon evidence for the mechanism of deglacial atmospheric CO2 rise. Science 316, 1456-1459. Okazaki et al. 2010. Deepwater formation in the North Pacific during the Last Glacial Termination. Science 329, 200-204. Rose, K. A., et al. 2010. Upper-ocean-to-atmosphere offsets imply fast deglacial radiocarbon release, Nature 466, 1093-1097.

Lund, D. C.; Mix, A. C.

2010-12-01

196

Migration and dispersal may drive to high genetic variation and significant genetic mixing: the case of two agriculturally important, continental hoverflies (Episyrphus balteatus and Sphaerophoria scripta).  

PubMed

Population structure of pests and beneficial species is an important issue when designing management strategies to optimize ecosystem services. In this study, we investigated for the first time the population structure at a continental scale of two migratory species of hoverflies providing both pest regulation and pollination services [Episyrphus balteatus and Sphaerophoria scripta (Diptera: Syrphidae)]. To achieve this objective, we used two sets of 12 species-specific microsatellite markers on a large-scale sampling from all over Europe. Our findings showed a high level of genetic mixing resulting in a lack of genetic differentiation at a continental scale and a great genetic diversity in the two species. All the pairwise FST values between European localities were less 0.05 in the two species. These low values reflect a large-scale genetic mixing probably caused by the existence of frequent migratory movements in the two species. Mantel tests revealed isolation-by-distance pattern on the East-West axis, but not on the North-South axis. This isolation-by-distance pattern confirms the existence of North-South migratory movements in both directions and suggests an important step by step dispersal. Population features shown by this study are common in invasive species and pests, but are not often observed in beneficial species. They reflect great colonization abilities and a high adaptive potential when dealing with a changing environment. Our results highlight the two studied species as particularly interesting beneficial insects for pollination and pest predation in the current context of global change. PMID:24138027

Raymond, Lucie; Plantegenest, Manuel; Vialatte, Aude

2013-09-24

197

Genetic variants on chromosome 1q41 influence ocular axial length and high myopia.  

PubMed

As one of the leading causes of visual impairment and blindness, myopia poses a significant public health burden in Asia. The primary determinant of myopia is an elongated ocular axial length (AL). Here we report a meta-analysis of three genome-wide association studies on AL conducted in 1,860 Chinese adults, 929 Chinese children, and 2,155 Malay adults. We identified a genetic locus on chromosome 1q41 harboring the zinc-finger 11B pseudogene ZC3H11B showing genome-wide significant association with AL variation (rs4373767, ??=?-0.16 mm per minor allele, P(meta)?=2.69 × 10(-10)). The minor C allele of rs4373767 was also observed to significantly associate with decreased susceptibility to high myopia (per-allele odds ratio (OR)?=0.75, 95% CI: 0.68-0.84, P(meta)?=4.38 × 10(-7)) in 1,118 highly myopic cases and 5,433 controls. ZC3H11B and two neighboring genes SLC30A10 and LYPLAL1 were expressed in the human neural retina, retinal pigment epithelium, and sclera. In an experimental myopia mouse model, we observed significant alterations to gene and protein expression in the retina and sclera of the unilateral induced myopic eyes for the murine genes ZC3H11A, SLC30A10, and LYPLAL1. This supports the likely role of genetic variants at chromosome 1q41 in influencing AL variation and high myopia. PMID:22685421

Fan, Qiao; Barathi, Veluchamy A; Cheng, Ching-Yu; Zhou, Xin; Meguro, Akira; Nakata, Isao; Khor, Chiea-Chuen; Goh, Liang-Kee; Li, Yi-Ju; Lim, Wan'e; Ho, Candice E H; Hawthorne, Felicia; Zheng, Yingfeng; Chua, Daniel; Inoko, Hidetoshi; Yamashiro, Kenji; Ohno-Matsui, Kyoko; Matsuo, Keitaro; Matsuda, Fumihiko; Vithana, Eranga; Seielstad, Mark; Mizuki, Nobuhisa; Beuerman, Roger W; Tai, E-Shyong; Yoshimura, Nagahisa; Aung, Tin; Young, Terri L; Wong, Tien-Yin; Teo, Yik-Ying; Saw, Seang-Mei

2012-06-07

198

ARCING HIGH IMPEDANCE FAULT DETECTION USING REAL CODED GENETIC ALGORITHM  

Microsoft Academic Search

Safety and reliability are two of the most important aspects of electric power supply systems. Sensitivity and robustness to detect and isolate faults can influence the safety and reliability of such systems. Overcurrent relays are generally used to protect the high voltage feeders in distribution systems. Downed conductors, tree branches touching conductors, and failing insulators often cause high-impedance faults in

Naser Zamanan; Jan Sykulski; A. K. Al-Othman

199

Microsatellites and the genetics of highly selfing populations in the freshwater snail Bulinus truncatus.  

PubMed

Hermaphrodite tropical freshwater snails provide a good opportunity to study the effects of mating system and genetic drift on population genetic structure because they are self-fertile and they occupy transient patchily distributed habitats (ponds). Up to now the lack of detectable allozyme polymorphism prevented any intrapopulation studies. In this paper, we examine the consequences of selfing and bottlenecks on genetic polymorphism using microsatellite markers in 14 natural populations (under a hierarchical sampling design) of the hermaphrodite freshwater snail Bulinus truncatus. These population genetics data allowed us to discuss the currently available mutation models for microsatellite sequences. Microsatellite markers revealed an unexpectedly high levels of genetic variation with < or = 41 alleles for one locus and gene diversity of 0.20-0.75 among populations. The values of any estimator of Fis indicate high selfing rates in all populations. Linkage disequilibria observed at all loci for some populations may also indicate high levels of inbreeding. The large extent of genetic differentiation measured by Fst, Rst or by a test for homogeneity between genic distributions is explained by both selfing and bottlenecks. Despite a limited gene flow, migration events could be detected when comparing different populations within ponds. PMID:8846901

Viard, F; Bremond, P; Labbo, R; Justy, F; Delay, B; Jarne, P

1996-04-01

200

High-density genetic linkage maps of Phytophthora infestans reveal trisomic progeny and chromosomal rearrangements.  

PubMed Central

Detailed analysis of the inheritance of molecular markers was performed in the oomycete plant pathogen Phytophthora infestans. Linkage analysis in the sexual progeny of two Dutch field isolates (cross 71) resulted in a high-density map containing 508 markers on 13 major and 10 minor linkage groups. The map showed strong clustering of markers, particularly of markers originating from one parent, and dissimilarity between the parental isolates on linkage group III in the vicinity of the mating-type locus, indicating a chromosomal translocation. A second genetic map, constructed by linkage analysis in sexual progeny of two Mexican isolates (cross 68), contained 363 markers and is thus less dense than the cross 71 map. For some linkage groups the two independent linkage maps could be aligned, but sometimes markers appeared to be in a different order, or not linked at all, indicating chromosomal rearrangements between genotypes. Graphical genotyping showed that some progeny contained three copies of a homologous linkage group. This trisomy was found for several linkage groups in both crosses. Together, these analyses suggest a genome with a high degree of flexibility, which may have implications for evolution of new races and resistance development to crop protection agents.

van der Lee, Theo; Testa, Antonino; Robold, Andrea; van 't Klooster, John; Govers, Francine

2004-01-01

201

Genetic variation in tolerance to high concentrations of soil boron exists in lentil germplasm  

Microsoft Academic Search

Soils with high concentrations of boron are common in the grain belt of south-eastern Australia. The reduction of soil boron concentration is considered impractical and so the viable alternative is to develop boron tolerant crop cultivars. A glasshouse experiment was conducted with 310 lentil accessions to determine the genetic variation in response to high concentrations of soil boron. The collection

Kristy Hobson; Roger Armstrong; David Connor; Marc Nicolas; Michael Materne

2003-01-01

202

High-Voltage Electroporation of Bacteria: Genetic Transformation of Campylobacter jejuni with Plasmid DNA  

Microsoft Academic Search

Electroporation permits the uptake of DNA by mammalian cells and plant protoplasts because it induces transient permeability of the cell membrane. We investigated the utility of high-voltage electroporation as a method for genetic transformation of intact bacterial cells by using the enteric pathogen Campylobacter jejuni as a model system. This report demonstrates that the application of high-voltage discharges to bacterial

Jeff F. Miller; William J. Dower; Lucy S. Tompkins

1988-01-01

203

Plasmodium falciparum populations from northeastern Myanmar display high levels of genetic diversity at multiple antigenic loci.  

PubMed

Levels of genetic diversity of the malaria parasites and multiclonal infections are correlated with transmission intensity. In order to monitor the effect of strengthened malaria control efforts in recent years at the China-Myanmar border area, we followed the temporal dynamics of genetic diversity of three polymorphic antigenic markers msp1, msp2, and glurp in the Plasmodium falciparum populations. Despite reduced malaria prevalence in the region, parasite populations exhibited high levels of genetic diversity. Genotyping 258 clinical samples collected in four years detected a total of 22 PCR size alleles. Multiclonal infections were detected in 45.7% of the patient samples, giving a minimum multiplicity of infection of 1.41. The majority of alleles experienced significant temporal fluctuations through the years. Haplotype diversity based on the three-locus genotypes ranged from the lowest in 2009 at 0.33 to the highest in 2010 at 0.80. Sequencing of msp1 fragments from 36 random samples of five allele size groups detected 13 different sequences, revealing an additional layer of genetic complexity. This study suggests that despite reduced prevalence of malaria infections in this region, the parasite population size and transmission intensity remained high enough to allow effective genetic recombination of the parasites and continued maintenance of genetic diversity. PMID:23000544

Yuan, Lili; Zhao, Hui; Wu, Lanou; Li, Xiaomei; Parker, Daniel; Xu, Shuhui; Zhao, Yousheng; Feng, Guohua; Wang, Ying; Yan, Guiyun; Fan, Qi; Yang, Zhaoqing; Cui, Liwang

2012-09-20

204

Modeling the Genetic Control of HIV-1 Dynamics After Highly Active Antiretroviral Therapy  

PubMed Central

The progression of HIV disease has been markedly slowed by the use of highly active antiretroviral therapy (HAART). However, substantial genetic variation was observed to occur among different people in the decay rate of viral loads caused by HAART. The characterization of specific genes involved in HIV dynamics is central to design personalized drugs for the prevention of this disease, but usually cannot be addressed by experimental methods alone rather than require the help of mathematical and statistical methods. A novel statistical model has been recently developed to detect genetic variants that are responsible for the shape of HAART-induced viral decay curves. This model was employed to an HIV/AIDS trial, which led to the identification of a major genetic determinant that triggers an effect on HIV dynamics. This detected major genetic determinant also affects several clinically important parameters, such as half-lives of infected cells and HIV eradication times.

Ma, Chang-Xing; Li, Yao; Wu, Rongling

2008-01-01

205

Genetic basis of unstable expression of high gamma-tocopherol content in sunflower seeds  

PubMed Central

Background Tocopherols are natural antioxidants with both in vivo (vitamin E) and in vitro activity. Sunflower seeds contain predominantly alpha-tocopherol (>90% of total tocopherols), with maximum vitamin E effect but lower in vitro antioxidant action than other tocopherol forms such as gamma-tocopherol. Sunflower germplasm with stable high levels of gamma-tocopherol (>85%) has been developed. The trait is controlled by recessive alleles at a single locus Tph2 underlying a gamma-tocopherol methyltransferase (gamma-TMT). Additionally, unstable expression of increased gamma-tocopherol content in the range from 5 to 85% has been reported. The objective of this research was to determine the genetic basis of unstable expression of high gamma-tocopherol content in sunflower seeds. Results Male sterile plants of nuclear male sterile line nmsT2100, with stable high gamma-tocopherol content, were crossed with plants of line IAST-1, with stable high gamma-tocopherol content but derived from a population that exhibited unstable expression of the trait. F2 seeds showed continuous segregation for gamma-tocopherol content from 1.0 to 99.7%. Gamma-tocopherol content in F2 plants (average of 24 individual F3 seeds) segregated from 59.4 to 99.4%. A genetic linkage map comprising 17 linkage groups (LGs) was constructed from this population using 109 SSR and 20 INDEL marker loci, including INDEL markers for tocopherol biosynthesis genes. QTL analysis revealed a major QTL on LG 8 that corresponded to the gamma-TMT Tph2 locus, which suggested that high gamma-tocopherol lines nmsT2100 and IAST-1 possess different alleles at this locus. Modifying genes were identified at LGs 1, 9, 14 and 16, corresponding in most cases with gamma-TMT duplicated loci. Conclusions Unstable expression of high gamma-tocopherol content is produced by the effect of modifying genes on tph2a allele at the gamma-TMT Tph2 gene. This allele is present in line IAST-1 and is different to allele tph2 present in line nmsT2100, which is not affected by modifying genes. No sequence differences at the gamma-TMT gene were found associated to allelic unstability. Our results suggested that modifying genes are mostly epistatically interacting gamma-TMT duplicated loci.

2012-01-01

206

High Genetic Diversity vs. Low Genetic Differentiation in Nouelia insignis (Asteraceae), a Narrowly Distributed and Endemic Species in China, Revealed by ISSR Fingerprinting  

PubMed Central

• Background and Aims Nouelia insignis Franch., a monotypic genus of the Asteraceae, is an endangered species endemic in Yunnan and Sichuan Provinces of China. Most of the populations are seriously threatened. Some of them are even at the brink of extinction. In this study, the genetic diversity and differentiation between populations of this species were examined in two drainage areas. • Methods DNA fingerprinting based on inter-simple sequence repeat polymorphisms was employed to detect the genetic variation and population structure in the species. • Key Results Genetic diversity at species level was high with P = 65·05?% (percentage of polymorphic loci) and Ht = 0·2248 (total genetic diversity). The coefficient of genetic differentiation among populations, Gst, which was estimated by partitioning the total gene diversity, was 0·2529; whereas, the genetic differentiation between populations in the Jinsha and Nanpan drainage areas was unexpectedly low (Gst = 0·0702). • Conclusions Based on the genetic analyses of the DNA fingerprinting, recent habitat fragmentation may not have led to genetic differentiation or the loss of genetic diversity in the rare species. Spatial apportionment of fingerprinting polymorphisms provides a footprint of historical migration across geographical barriers. The high diversity detected in this study holds promise for conservation and restoration efforts to save the endangered species from extinction.

LUAN, SHANSHAN; CHIANG, TZEN-YUH; GONG, XUN

2006-01-01

207

The genetic basis of high-altitude pulmonary oedema  

Microsoft Academic Search

High-altitude pulmonary oedema (HAPE) is a potentially fatal condition affecting fit and previously well individuals at altitudes in excess of 3000 m. This article discusses the mechanisms of HAPE, considers the contribution of hypoxic pulmonary vasoconstriction and alterations in sodium transport to the pathological process. It discusses the various biochemical mediators such as nitric oxide (NO), endothelin-1 (ET-1), and the

Heather Mortimer; Sam Patel; Andrew J. Peacock

2004-01-01

208

Nutritional value of a genetically improved high-lysine, high-oil corn for young pigs1,2  

Microsoft Academic Search

Two experiments were conducted to compare the nutritional adequacy of a genetically im- proved high-lysine, high-oil corn (HLHOC; .408% ly- sine, 6.21% fat, as-fed basis) and a high-oil corn (HOC; .289% lysine, 5.97% fat, as-fed basis) for young growing pigs. Experiment 1 used four non-littermate barrows (initially 20.0 kg BW) fitted with ileal T-cannulas in a crossover-designed digestion study. The

P. R. O'Quinn; J. L. Nelssen; R. D. Goodband; D. A. Knabe; J. C. Woodworth; M. D. Tokach; T. T. Lohrmann

209

Hybrid Mice as Genetic Models of High Alcohol Consumption  

Microsoft Academic Search

We showed that F1 hybrid genotypes may provide a broader variety of ethanol drinking phenotypes than the inbred progenitor\\u000a strains used to create the hybrids (Blednov et al. in Alcohol Clin Exp Res 29:1949–1958, 2005). To extend this work, we characterized alcohol consumption as well as intake of other tastants (saccharin, quinine and sodium\\u000a chloride) in five inbred strains of

Y. A. BlednovA; A. R. Ozburn; D. Walker; S. Ahmed; J. K. Belknap; R. A. Harris

2010-01-01

210

COMPARATIVE GENOMIC AND POPULATION GENETIC ANALYSES INDICATE HIGHLY POROUS GENOMES AND HIGH LEVELS OF GENE FLOW BETWEEN DIVERGENT HELIANTHUS SPECIES  

PubMed Central

While speciation can be found in the presence of gene flow, it is not clear what impact this gene flow has on genome- and range-wide patterns of differentiation. Here we examine gene flow across the entire range of the common sunflower, H. annuus, its historically allopatric sister species H. argophyllus and a more distantly related, sympatric relative H. petiolaris. Analysis of genotypes at 26 microsatellite loci in 1015 individuals from across the range of the three species showed substantial introgression between geographically proximal populations of H. annuus and H. petiolaris, limited introgression between H. annuus and H. argophyllus, and essentially no gene flow between the allopatric pair, H. argophyllus and H. petiolaris. Analysis of sequence divergence levels among the three species in 1420 orthologs identified from EST databases identified a subset of loci showing extremely low divergence between H. annuus and H. petiolaris and extremely high divergence between the sister species H. annuus and H. argophyllus, consistent with introgression between H. annuus and H. petiolaris at these loci. Thus, at many loci, the allopatric sister species are more genetically divergent than the more distantly related sympatric species, which have exchanged genes across much of the genome while remaining morphologically and ecologically distinct.

Kane, Nolan C.; King, Matthew G.; Barker, Michael S.; Raduski, Andrew; Karrenberg, Sophie; Yatabe, Yoko; Knapp, Steven J.; Rieseberg, Loren H.

2009-01-01

211

High-throughput target discovery using cell-based genetics  

Microsoft Academic Search

High-throughput target discovery requires robust disease models and the ability to rapidly survey the genome for function. In the post-genomics era, there has been a strong emphasis placed upon ‘gene-to-function’ approaches that take advantage of the large amount of gene sequence information now available. Here, we advocate a return to ‘function-to-gene’ approaches as a first step in target discovery (and

P. David Jackson; John J. Harrington

2005-01-01

212

An Evolutionary Model for Identifying Genetic Adaptation to High Altitude  

Microsoft Academic Search

Coordinated maternal\\/fetal responses to pregnancy are required to ensure continuous O2 delivery to the developing organism. Mammals employ distinctive reproductive strategies that afford their young an improved\\u000a chance of survival through the completion or the reproductive period. Thus, mortality prior to the end of the reproductive\\u000a period is concentrated in the earliest phases of the lifecycle. At high altitude, fetal

Lorna G. Moore; Mark Shriver; Lynne Bemis; Enrique Vargas

213

A High-Throughput Arabidopsis Reverse Genetics System  

Microsoft Academic Search

A collection of Arabidopsis lines with T-DNA insertions in known sites was generated to increase the efficiency of func- tional genomics. A high-throughput modified thermal asymetric interlaced (TAIL)-PCR protocol was developed and used to amplify DNA fragments flanking the T-DNA left borders from ? 100,000 transformed lines. A total of 85,108 TAIL-PCR products from 52,964 T-DNA lines were sequenced and

Allen Sessions; Ellen Burke; Gernot Presting; John McElver; David Patton; Bob Dietrich; Patrick Ho; Johana Bacwaden; Cynthia Ko; Joseph D. Clarke; David Cotton; David Bullis; Jennifer Snell; Trini Miguel; Theresa Mitzel; Fumiaki Katagiri; Jane Glazebrook; Marc Law; Stephen A. Goff

2002-01-01

214

High-seas Biodiversity and Genetic Resources: Science and Policy Questions  

NSDL National Science Digital Library

Global efforts to protect marine genetic resources and high-seas biodiversity peak in 2010, a very eventful year for the conservation and study of high-seas biodiversity, with developments that put relevant policy and scientific directions at a significant crossroads. With these timely developments come important conservation, equity, and research questions: How do we protect deep-seas biodiversity against irresponsible exploitation in hard-to-monitor areas? How do we equitably govern the use of marine genetic resources while also fostering advanced scientific research?

Richard Blaustein (freelance writer;)

2010-06-01

215

Nuclear genetic diversity in human lice (Pediculus humanus) reveals continental differences and high inbreeding among worldwide populations.  

PubMed

Understanding the evolution of parasites is important to both basic and applied evolutionary biology. Knowledge of the genetic structure of parasite populations is critical for our ability to predict how an infection can spread through a host population and for the design of effective control methods. However, very little is known about the genetic structure of most human parasites, including the human louse (Pediculus humanus). This species is composed of two ecotypes: the head louse (Pediculus humanus capitis De Geer), and the clothing (body) louse (Pediculus humanus humanus Linnaeus). Hundreds of millions of head louse infestations affect children every year, and this number is on the rise, in part because of increased resistance to insecticides. Clothing lice affect mostly homeless and refugee-camp populations and although they are less prevalent than head lice, the medical consequences are more severe because they vector deadly bacterial pathogens. In this study we present the first assessment of the genetic structure of human louse populations by analyzing the nuclear genetic variation at 15 newly developed microsatellite loci in 93 human lice from 11 sites in four world regions. Both ecotypes showed heterozygote deficits relative to Hardy-Weinberg equilibrium and high inbreeding values, an expected pattern given their parasitic life history. Bayesian clustering analyses assigned lice to four distinct genetic clusters that were geographically structured. The low levels of gene flow among louse populations suggested that the evolution of insecticide resistance in lice would most likely be affected by local selection pressures, underscoring the importance of tailoring control strategies to population-specific genetic makeup and evolutionary history. Our panel of microsatellite markers provides powerful data to investigate not only ecological and evolutionary processes in lice, but also those in their human hosts because of the long-term coevolutionary association between lice and humans. PMID:23460886

Ascunce, Marina S; Toups, Melissa A; Kassu, Gebreyes; Fane, Jackie; Scholl, Katlyn; Reed, David L

2013-02-27

216

Pathways and barriers to genetic testing and screening: Molecular genetics meets the high-risk family. Final report.  

National Technical Information Service (NTIS)

The proliferation of genetic screening and testing is requiring increasing numbers of Americans to integrate genetic knowledge and interventions into their family life and personal experience. This study examines the social processes that occur as familie...

T. Duster

1998-01-01

217

Physical mapping evidence for a duplicated region on chromosome 10qter showing high homology with the facioscapulohumeral muscular dystrophy locus on chromosome 4qter.  

PubMed

p13E-11, a probe (D4F104S1 locus) derived from chromosome 4q35, detects EcoRI-rearranged fragments less than 28 kb in both sporadic and familial cases of facioscapulohumeral muscular dystrophy (FSHD). These fragments are smaller than those observed in healthy individuals. The interpretation of Southern blots is complicated by the fact that p13E-11 reveals two pairs of polymorphic alleles, one 4q35-specific and the other unlinked to 4q35, that sometimes overlap each other. We cloned a non-4q35 13-kb fragment not related to the disease from a sporadic FSHD patient of Italian origin. Haplotype analysis and in situ hybridization experiments showed that this fragment was located on the 10qter region. Restriction mapping of the 10qter clone, when compared with the 4q35 fragment, indicates a similar arrangement of KpnI tandemly repeated units and flanking sequences. However 4q35 and 10q26 EcoRI clones can be distinguished by restriction analysis with SfiI and StyI. This observation could be exploited for future applications in the field of molecular diagnosis and genetic counseling. In addition the isolation of two 10q26 cosmid clones (D10S1484 and D10S1485) from a human genomic library and the construction of a detailed physical map, spanning about 40 kb, showed that the structural homology extended upstream of the EcoRI sites, suggesting that a duplicated FSHD locus resided in the subtelomeric region of the long arm of chromosome 10. We cannot exclude the involvement of the duplicated locus in the molecular mechanism of the disease and in the genetic heterogeneity of FSHD syndromes. PMID:7583041

Deidda, G; Cacurri, S; Grisanti, P; Vigneti, E; Piazzo, N; Felicetti, L

1995-01-01

218

A Single Mother's Perspective of How High School Students Respond to her Interaction with the Science Road Show at Northeast Texas Community College  

Microsoft Academic Search

The use of SPS student participation during a science road show at local schools will be addressed. Specifically the author will address how she shared her story during a science road show and how her story relates to high school students staying focused on science, math, and school in general.

Ashley Hanson

2008-01-01

219

A Single Mother's Perspective of How High School Students Respond to her Interaction with the Science Road Show at Northeast Texas Community College  

NASA Astrophysics Data System (ADS)

The use of SPS student participation during a science road show at local schools will be addressed. Specifically the author will address how she shared her story during a science road show and how her story relates to high school students staying focused on science, math, and school in general.

Hanson, Ashley

2008-03-01

220

High altitude hypoxia environment changes of the content of RAAS and ACE2 Genetics polymorphisms  

Microsoft Academic Search

Objective To study the function of the rennin- angiotensin-aldoterone system(RAAS) under high altitude hypoxia environment and objective to investigate the effects of high altitude hypoxia on the angiotensin conversion enzyme 2(ACE2) Genetics polymorphisms. Methods Forty male adult Sprague Dawley( SD) rats, under high altitude hypoxia environment were divided randomly into 4 groups: the control group(D group, Xi'an area 5m above

Wenhua Li; Liu Zhong

2011-01-01

221

Confirmation of a genetic locus for X-linked recessive high myopia outside MYP1  

Microsoft Academic Search

High myopia is a severe ocular condition affecting ?100 million people throughout the world. It is a common cause of blindness,\\u000a and several studies have suggested it is transmitted through Mendelian traits. High myopia is clinically and genetically heterogeneous,\\u000a with eight loci assigned. Most loci have not been confirmed by additional studies, and genes responsible for high myopia have\\u000a not been

Qingjiong Zhang; Shiqiang Li; Xueshan Xiao; Xiaoyun Jia; Xiangming Guo

2007-01-01

222

Plasma membrane of Beta vulgaris storage root shows high water channel activity regulated by cytoplasmic pH and a dual range of calcium concentrations  

Microsoft Academic Search

Plasma membrane vesicles isolated by two-phase par- titioning from the storage root of Beta vulgaris show atypically high water permeability that is equivalent only to those reported for active aquaporins in tono- plast or animal red cells (Pf5542 l ms 21 ). The values were determined from the shrinking kinetics measured by stopped-flow light scattering. This high Pf was only

Karina Alleva; Christa M. Niemietz; Moira Sutka; Christophe Maurel; Mario Parisi; Stephen D. Tyerman; Gabriela Amodeo

2006-01-01

223

Quantitative high-throughput analysis of synthetic genetic interactions in Caenorhabditis elegans by RNA interference.  

PubMed

Biological processes are highly dynamic but the current representation of molecular networks is static and largely qualitative. To investigate the dynamic property of genetic networks, a novel quantitative high-throughput method based on RNA interference and capable of calculating the relevance of each interaction, was developed. With this approach, it will be possible to identify not only the components of a network, but also to investigate quantitatively how network and biological processes react to perturbations. As a first application of this method, the genetic interactions of a weak loss-of-function mutation in the gene efl-1/E2F with all the genes of chromosome III were investigated during embryonic development of Caenorhabditis elegans. Fifteen synthetic genetic interactions of efl-1/E2F with the genes of chromosome III were detected, measured and ranked by statistical relevance. PMID:19059334

Fortunato, Angelo

2008-12-23

224

A Systems Genetic Analysis of High Density Lipoprotein Metabolism and Network Preservation across Mouse Models  

PubMed Central

We report a systems genetics analysis of high density lipoproteins (HDL) levels in an F2 intercross between inbred strains CAST/EiJ and C57BL/6J. We previously showed that there are dramatic differences in HDL metabolism in a cross between these strains, and we now report co-expression network analysis of HDL that integrates global expression data from liver and adipose with relevant metabolic traits. Using data from a total of 293 F2 intercross mice, we constructed weighted gene co-expression networks and identified modules (subnetworks) associated with HDL and clinical traits. These were examined for genes implicated in HDL levels based on large human genome-wide associations studies (GWAS) and examined with respect to conservation between tissue and sexes in a total of 9 data sets. We identify genes that are consistently ranked high by association with HDL across the 9 data sets. We focus in particular on two genes, Wfdc2 and Hdac3, that are located in close proximity to HDL QTL peaks where causal testing indicates that they may affect HDL. Our results provide a rich resource for studies of complex metabolic interactions involving HDL.

Langfelder, Peter; Castellani, Lawrence W.; Zhou, Zhiqiang; Paul, Eric; Davis, Richard; Schadt, Eric E.; Lusis, Aldons J.; Horvath, Steve; Mehrabian, Margarete

2011-01-01

225

Genetic algorithm-support vector regression for high reliability SHM system based on FBG sensor network  

NASA Astrophysics Data System (ADS)

Structural Health Monitoring (SHM) based on fiber Bragg grating (FBG) sensor network has attracted considerable attention in recent years. However, FBG sensor network is embedded or glued in the structure simply with series or parallel. In this case, if optic fiber sensors or fiber nodes fail, the fiber sensors cannot be sensed behind the failure point. Therefore, for improving the survivability of the FBG-based sensor system in the SHM, it is necessary to build high reliability FBG sensor network for the SHM engineering application. In this study, a model reconstruction soft computing recognition algorithm based on genetic algorithm-support vector regression (GA-SVR) is proposed to achieve the reliability of the FBG-based sensor system. Furthermore, an 8-point FBG sensor system is experimented in an aircraft wing box. The external loading damage position prediction is an important subject for SHM system; as an example, different failure modes are selected to demonstrate the SHM system's survivability of the FBG-based sensor network. Simultaneously, the results are compared with the non-reconstruct model based on GA-SVR in each failure mode. Results show that the proposed model reconstruction algorithm based on GA-SVR can still keep the predicting precision when partial sensors failure in the SHM system; thus a highly reliable sensor network for the SHM system is facilitated without introducing extra component and noise.

Zhang, Xiaoli; Liang, Dakai; Zeng, Jie; Asundi, Anand

2012-02-01

226

The genetic landscape of high-risk neuroblastoma  

PubMed Central

Neuroblastoma is a malignancy of the developing sympathetic nervous system that often presents with widespread metastatic disease, resulting in survival rates of less than 50%1. To determine the spectrum of somatic mutation in high-risk neuroblastoma, we studied 240 cases using a combination of whole exome, genome and transcriptome sequencing as part of the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) initiative. Here we report a low median exonic mutation frequency of 0.60 per megabase (0.48 non-silent), and remarkably few recurrently mutated genes in these tumors. Genes with significant somatic mutation frequencies included ALK (9.2% of cases), PTPN11 (2.9%), ATRX (2.5%, an additional 7.1% had focal deletions), MYCN (1.7%, a recurrent p.Pro44Leu alteration), and NRAS (0.83%). Rare, potentially pathogenic germline variants were significantly enriched in ALK, CHEK2, PINK1, and BARD1. The relative paucity of recurrent somatic mutations in neuroblastoma challenges current therapeutic strategies reliant upon frequently altered oncogenic drivers.

Pugh, Trevor J.; Morozova, Olena; Attiyeh, Edward F.; Asgharzadeh, Shahab; Wei, Jun S.; Auclair, Daniel; Carter, Scott L.; Cibulskis, Kristian; Hanna, Megan; Kiezun, Adam; Kim, Jaegil; Lawrence, Michael S.; Lichenstein, Lee; McKenna, Aaron; Pedamallu, Chandra Sekhar; Ramos, Alex H.; Shefler, Erica; Sivachenko, Andrey; Sougnez, Carrie; Stewart, Chip; Ally, Adrian; Birol, Inanc; Chiu, Readman; Corbett, Richard D.; Hirst, Martin; Jackman, Shaun D.; Kamoh, Baljit; Khodabakshi, Alireza Hadj; Krzywinski, Martin; Lo, Allan; Moore, Richard A.; Mungall, Karen L.; Qian, Jenny; Tam, Angela; Thiessen, Nina; Zhao, Yongjun; Cole, Kristina A.; Diamond, Maura; Diskin, Sharon J.; Mosse, Yael P.; Wood, Andrew C.; Ji, Lingyun; Sposto, Richard; Badgett, Thomas; London, Wendy B.; Moyer, Yvonne; Gastier-Foster, Julie M.; Smith, Malcolm A.; Auvil, Jaime M. Guidry; Gerhard, Daniela S.; Hogarty, Michael D.; Jones, Steven J. M.; Lander, Eric S.; Gabriel, Stacey B.; Getz, Gad; Seeger, Robert C.; Khan, Javed; Marra, Marco A.; Meyerson, Matthew; Maris, John M.

2013-01-01

227

A Highly Sensitive Genetic Protocol to Detect NF1 Mutations  

PubMed Central

Neurofibromatosis type 1 (NF1) is a hereditary disorder caused by mutations in the NF1 gene. Detecting mutation in NF1 is hindered by the gene's large size, the lack of mutation hotspots, the presence of pseudogenes, and the wide variety of possible lesions. We developed a method for detecting germline mutations by combining an original RNA-based cDNA-PCR mutation detection method and denaturing high-performance liquid chromatography (DHPLC) with multiplex ligation-dependent probe amplification (MLPA). The protocol was validated in a cohort of 56 blood samples from NF1 patients who fulfilled NIH diagnostic criteria, identifying the germline mutation in 53 cases (95% sensitivity). The efficiency and reliability of this approach facilitated detection of different types of mutations, including single-base substitutions, deletions or insertions of one to several nucleotides, microdeletions, and changes in intragenic copy number. Because mutational screening for minor lesions was performed using cDNA and the characterization of mutated alleles was performed at both the RNA and genomic DNA level, the analysis provided insight into the nature of the different mutations and their effect on NF1 mRNA splicing. After validation, we implemented the protocol as a routine test. Here we present the overall unbiased spectrum of NF1 mutations identified in 93 patients in a cohort of 105. The results indicate that this protocol is a powerful new tool for the molecular diagnosis of NF1.

Carmen Valero, Maria; Martin, Yolanda; Hernandez-Imaz, Elisabete; Marina Hernandez, Alba; Melean, German; Maria Valero, Ana; Javier Rodriguez-Alvarez, Francisco; Telleria, Dolores; Hernandez-Chico, Concepcion

2011-01-01

228

High-gain nonlinear observer for simple genetic regulation process  

NASA Astrophysics Data System (ADS)

High-gain nonlinear observers occur in the nonlinear automatic control theory and are in standard usage in chemical engineering processes. We apply such a type of analysis in the context of a very simple one-gene regulation circuit. In general, an observer combines an analytical differential-equation-based model with partial measurement of the system in order to estimate the non-measured state variables. We use one of the simplest observers, that of Gauthier et al., which is a copy of the original system plus a correction term which is easy to calculate. For the illustration of this procedure, we employ a biological model, recently adapted from Goodwin's old book by De Jong, in which one plays with the dynamics of the concentrations of the messenger RNA coding for a given protein, the protein itself, and a single metabolite. Using the observer instead of the metabolite, it is possible to rebuild the non-measured concentrations of the mRNA and the protein.

Torres, L. A.; Ibarra-Junquera, V.; Escalante-Minakata, P.; Rosu, H. C.

2007-07-01

229

Long-term selection strategies for complex traits using high-density genetic markers.  

PubMed

Selection of animals for breeding ranked on estimated breeding value maximizes genetic gain in the next generation but does not necessarily maximize long-term response. An alternative method, as practiced by plant breeders, is to build a desired genotype by selection on specific loci. Maximal long-term response in animal breeding requires selection on estimated breeding values with constraints on coancestry. In this paper, we compared long-term genetic response using either a genotype building or a genomic estimated breeding value (GEBV) strategy for the Australian Selection Index (ASI), a measure of profit. First, we used real marker effects from the Australian Dairy Herd Improvement Scheme to estimate breeding values for chromosome segments (approximately 25 cM long) for 2,650 Holstein bulls. Second, we selected 16 animals to be founders for a simulated breeding program where, between them, founders contain the best possible combination of 2 segments from 2 animals at each position in the genome. Third, we mated founder animals and their descendants over 30 generations with 2 breeding objectives: (1) to create a population with the "ideal genotype," where the best 2 segments from the founders segregate at each position, or (2) obtain the highest possible response in ASI with coancestry lower than that achieved under breeding objective 1. Results show that genotype building achieved the ideal genotype for breeding objective 1 and obtained a large gain in ASI over the current population (+A$864.99). However, selection on overall GEBV had greater short-term response and almost as much long-term gain (+A$820.42). When coancestry was lowered under breeding objective 2, selection on overall GEBV achieved a higher response in ASI than the genotype building strategy. Selection on overall GEBV seems more flexible in its selection decisions and was therefore better able to precisely control coancestry while maximizing ASI. We conclude that selection on overall GEBV while minimizing average coancestry is the more practical strategy for dairy cattle where selection is for highly polygenic traits, the reproductive rate is relatively low, and there is low tolerance of coancestry. The outcome may be different for traits controlled by few loci of relatively large effects or for different species. In contrast to other simulations, our results indicate that response to selection on overall GEBV may continue for several generations. This is because long-term genetic change in complex traits requires favorable changes to allele frequencies for many loci located throughout the genome. PMID:22818479

Kemper, K E; Bowman, P J; Pryce, J E; Hayes, B J; Goddard, M E

2012-08-01

230

High-Pitched Notes during Vocal Contests Signal Genetic Diversity in Ocellated Antbirds  

PubMed Central

Animals use honest signals to assess the quality of competitors during aggressive interactions. Current theory predicts that honest signals should be costly to produce and thus reveal some aspects of the phenotypic or genetic quality of the sender. In songbirds, research indicates that biomechanical constraints make the production of some acoustic features costly. Furthermore, recent studies have found that vocal features are related to genetic diversity. We linked these two lines of research by evaluating if constrained acoustic features reveal male genetic diversity during aggressive interactions in ocellated antbirds (Phaenostictus mcleannani). We recorded the aggressive vocalizations of radiotagged males at La Selva Biological Station in Costa Rica, and found significant variation in the highest frequency produced among individuals. Moreover, we detected a negative relationship between the frequency of the highest pitched note and vocalization duration, suggesting that high pitched notes might constrain the duration of vocalizations through biomechanical and/or energetic limitations. When we experimentally exposed wild radiotagged males to simulated acoustic challenges, the birds increased the pitch of their vocalization. We also found that individuals with higher genetic diversity (as measured by zygosity across 9 microsatellite loci) produced notes of higher pitch during aggressive interactions. Overall, our results suggest that the ability to produce high pitched notes is an honest indicator of male genetic diversity in male-male aggressive interactions.

Araya-Ajoy, Yi-men; Chaves-Campos, Johel; Kalko, Elisabeth K. V.; DeWoody, J. Andrew

2009-01-01

231

Predictive genetic testing for the identification of high-risk groups: a simulation study on the impact of predictive ability  

PubMed Central

Background Genetic risk models could potentially be useful in identifying high-risk groups for the prevention of complex diseases. We investigated the performance of this risk stratification strategy by examining epidemiological parameters that impact the predictive ability of risk models. Methods We assessed sensitivity, specificity, and positive and negative predictive value for all possible risk thresholds that can define high-risk groups and investigated how these measures depend on the frequency of disease in the population, the frequency of the high-risk group, and the discriminative accuracy of the risk model, as assessed by the area under the receiver-operating characteristic curve (AUC). In a simulation study, we modeled genetic risk scores of 50 genes with equal odds ratios and genotype frequencies, and varied the odds ratios and the disease frequency across scenarios. We also performed a simulation of age-related macular degeneration risk prediction based on published odds ratios and frequencies for six genetic risk variants. Results We show that when the frequency of the high-risk group was lower than the disease frequency, positive predictive value increased with the AUC but sensitivity remained low. When the frequency of the high-risk group was higher than the disease frequency, sensitivity was high but positive predictive value remained low. When both frequencies were equal, both positive predictive value and sensitivity increased with increasing AUC, but higher AUC was needed to maximize both measures. Conclusions The performance of risk stratification is strongly determined by the frequency of the high-risk group relative to the frequency of disease in the population. The identification of high-risk groups with appreciable combinations of sensitivity and positive predictive value requires higher AUC.

2011-01-01

232

Oxidative and thermal stabilities of genetically modified high oleic sunflower oil  

Microsoft Academic Search

The oxidative and thermal stabilities of genetically modified high oleic sunflower oil (87% oleic acid) were compared with those of regular sunflower (17% oleic acid), soybean, corn, and peanut oils during storage at 55°C and simulated deep fat frying at 185°C. Oxidative stability was evaluated by measuring the oxygen content and volatile compounds in the sample bottle headspace and peroxide

Stephanie A. Smith; Robert E. King; David B. Min

2007-01-01

233

Bilateral cataract and high serum ferritin: a new dominant genetic disorder?  

Microsoft Academic Search

This paper reports the cosegregation in a three generation pedigree of dominantly inherited cataract with an abnormally high level of serum ferritin. In this family, circulating L ferritin was raised in all subjects affected by cataract independently of iron overload. We suggest that a disorder of ferritin metabolism could be a new genetic disorder leading to lens opacity. Cataract-hyperferritaemia syndrome

Dominique Bonneau; Isabelle Winter-Fuseau; Marie-Noëlle Loiseau; Patrizia Amati; Michel Berthier; Denis Oriot; Carole Beaumont

1995-01-01

234

A high-resolution neutron spectra unfolding method using the Genetic Algorithm technique  

Microsoft Academic Search

The Bonner sphere spectrometers (BSS) are commonly used to determine the neutron spectra within various nuclear facilities. Sophisticated mathematical tools are used to unfold the neutron energy distribution from the output data of the BSS. This paper highlights a novel high-resolution neutron spectra-unfolding method using the Genetic Algorithm (GA) technique. The GA imitates the biological evolution process prevailing in the

Bhaskar Mukherjee

2002-01-01

235

Hepatic lipase activity influences high density lipoprotein subclass distribution in normotriglyceridemic men: genetic and pharmacological evidence  

Microsoft Academic Search

Several studies have reported an inverse relation- ship between hepatic lipase activity and plasma high density lipoprotein (HDL) cholesterol concentrations. The purpose of the present study was to determine whether genetic and pharmacological variation in hepatic lipase activity alters the distribution of HDL subclasses. Two independent ana- lytical methods (nuclear magnetic resonance and gradient gel electrophoresis) were used to compare

Scott M. Grundy; Gloria L. Vega; James D. Otvos; David L. Rainwater

236

Estrogen receptor positive breast cancer identified by 95-gene classifier as at high risk for relapse shows better response to neoadjuvant chemotherapy.  

PubMed

A 95-gene classifier (95-GC) recently developed by us can predict the risk of relapse for ER-positive and node-negative breast cancer patients with high accuracy. This study investigated association of risk classification by 95-GC with response to neoadjuvant chemotherapy (NAC). Tumor biopsy samples obtained preoperatively from 72 patients with ER-positive breast cancer were classified by 95-GC into high-risk and low-risk for relapse. Pathological complete response (pCR) rate was numerically higher for high-risk (15.8%) than low-risk patients (8.8%) although the difference was not statistically significant. Pathological response evaluated in terms of the pathological partial response (pPR) rate (loss of tumor cells in more than two-thirds of the primary tumor) showed a significant association (P=0.005) between the high-risk patients and a high pPR rate. Besides, external validation study using the public data base (GSE25066) showed that the pCR rate (16.4%) for high-risk patients (n=128) was significantly (P=0.003) higher than for low-risk patients (5.7%) (n=159). These results demonstrate that the high-risk patients for relapse show a higher sensitivity to chemotherapy and thus are likely to benefit more from adjuvant chemotherapy. PMID:22546287

Tsunashima, Ryo; Naoi, Yasuto; Kishi, Kazuki; Baba, Yosuke; Shimomura, Atsushi; Maruyama, Naomi; Nakayama, Takahiro; Shimazu, Kenzo; Kim, Seung Jin; Tamaki, Yasuhiro; Noguchi, Shinzaburo

2012-04-27

237

High genetic diversity in a rare and endangered sunflower as compared to a common congener.  

PubMed

Determining the genetic structure of isolated or fragmented species is of critical importance when planning a suitable conservation strategy. In this study, we use nuclear and chloroplast SSRs (simple sequence repeats) to investigate the population genetics of an extremely rare sunflower, Helianthus verticillatus Small, which is known from only three locations in North America. We investigated levels of genetic diversity and population structure compared to a more common congener, Helianthus angustifolius L., using both nuclear and chloroplast SSRs. We also investigated its proposed hybrid origin from Helianthus grosseserratus Martens and H. angustifolius. Twenty-two nuclear SSRs originating from the cultivated sunflower (Helianthus annuus L.) expressed sequence tag (EST) database, and known to be transferable to H. verticillatus and its putative parental taxa, were used in this study thereby allowing for statistical control of locus-specific effects in population genetic analyses. Despite its rarity, H. verticillatus possessed significantly higher levels of genetic diversity than H. angustifolius at nuclear loci and equivalent levels of chloroplast diversity. Significant levels of population subdivision were observed in H. verticillatus but of a magnitude comparable to that of H. angustifolius. Inspection of multilocus genotypes also revealed that clonal spread is highly localized. Finally, we conclude that H. verticillatus is not of hybrid origin as it does not exhibit a mixture of parental alleles at nuclear loci, and it does not share a chloroplast DNA haplotype with either of its putative parents. PMID:16842410

Ellis, J R; Pashley, C H; Burke, J M; McCauley, D E

2006-08-01

238

High genetic differentiation and cross-shelf patterns of genetic diversity among Great Barrier Reef populations of Symbiodinium  

Microsoft Academic Search

The resilience of Symbiodinium harboured by corals is dependent on the genetic diversity and extent of connectivity among reef populations. This study presents\\u000a genetic analyses of Great Barrier Reef (GBR) populations of clade C Symbiodinium hosted by the alcyonacean coral, Sinularia flexibilis. Allelic variation at four newly developed microsatellite loci demonstrated that Symbiodinium populations are genetically differentiated at all spatial scales

E. J. Howells; M. J. H. van Oppen; B. L. Willis

2009-01-01

239

Genetic and phenotypic divergence between low- and high-altitude populations of two recently diverged cinnamon teal subspecies.  

PubMed

Spatial variation in the environment can lead to divergent selection between populations occupying different parts of a species' range, and ultimately lead to population divergence. The colonization of new areas can thus facilitate divergence in beneficial traits, yet with little differentiation at neutral genetic markers. We investigated genetic and phenotypic patterns of divergence between low- and high-altitude populations of cinnamon teal inhabiting normoxic and hypoxic regions in the Andes and adjacent lowlands of South America. Cinnamon teal showed strong divergence in body size (PC1; P(ST) = 0.56) and exhibited significant frequency differences in a single nonsynonymous ?-hemoglobin amino acid polymorphism (Asn/Ser-?9; F(ST) = 0.60) between environmental extremes, despite considerable admixture of mtDNA and intron loci (F(ST) = 0.004-0.168). Inferences of strong population segregation were further supported by the observation of few mismatched individuals in either environmental extreme. Coalescent analyses indicated that the highlands were most likely colonized from lowland regions but following divergence, gene flow has been asymmetric from the highlands into the lowlands. Multiple selection pressures associated with high-altitude habitats, including cold and hypoxia, have likely shaped morphological and genetic divergence within South American cinnamon teal populations. PMID:23289570

Wilson, Robert E; Peters, Jeffrey L; McCracken, Kevin G

2012-08-10

240

A High-Density Simple Sequence Repeat and Single Nucleotide Polymorphism Genetic Map of the Tetraploid Cotton Genome  

PubMed Central

Genetic linkage maps play fundamental roles in understanding genome structure, explaining genome formation events during evolution, and discovering the genetic bases of important traits. A high-density cotton (Gossypium spp.) genetic map was developed using representative sets of simple sequence repeat (SSR) and the first public set of single nucleotide polymorphism (SNP) markers to genotype 186 recombinant inbred lines (RILs) derived from an interspecific cross between Gossypium hirsutum L. (TM-1) and G. barbadense L. (3-79). The genetic map comprised 2072 loci (1825 SSRs and 247 SNPs) and covered 3380 centiMorgan (cM) of the cotton genome (AD) with an average marker interval of 1.63 cM. The allotetraploid cotton genome produced equivalent recombination frequencies in its two subgenomes (At and Dt). Of the 2072 loci, 1138 (54.9%) were mapped to 13 At-subgenome chromosomes, covering 1726.8 cM (51.1%), and 934 (45.1%) mapped to 13 Dt-subgenome chromosomes, covering 1653.1 cM (48.9%). The genetically smallest homeologous chromosome pair was Chr. 04 (A04) and 22 (D04), and the largest was Chr. 05 (A05) and 19 (D05). Duplicate loci between and within homeologous chromosomes were identified that facilitate investigations of chromosome translocations. The map augments evidence of reciprocal rearrangement between ancestral forms of Chr. 02 and 03 versus segmental homeologs 14 and 17 as centromeric regions show homeologous between Chr. 02 (A02) and 17 (D02), as well as between Chr. 03 (A03) and 14 (D03). This research represents an important foundation for studies on polyploid cottons, including germplasm characterization, gene discovery, and genome sequence assembly.

Yu, John Z.; Kohel, Russell J.; Fang, David D.; Cho, Jaemin; Van Deynze, Allen; Ulloa, Mauricio; Hoffman, Steven M.; Pepper, Alan E.; Stelly, David M.; Jenkins, Johnie N.; Saha, Sukumar; Kumpatla, Siva P.; Shah, Manali R.; Hugie, William V.; Percy, Richard G.

2012-01-01

241

A fully simultaneously optimizing genetic approach to the highly excited coupled-cluster factorization problem  

NASA Astrophysics Data System (ADS)

In this article we report on the coupled-cluster factorization problem. We describe the first implementation that optimizes (i) the contraction order for each term, (ii) the identification of reusable intermediates, (iii) the selection and factoring out of common factors simultaneously, considering all projection levels in a single step. The optimization is achieved by means of a genetic algorithm. Taking a one-term-at-a-time strategy as reference our factorization yields speedups of up to 4 (for intermediate excitation levels, smaller basis sets). We derive a theoretical lower bound for the highest order scaling cost and show that it is met by our implementation. Additionally, we report on the performance of the resulting highly excited coupled-cluster algorithms and find significant improvements with respect to the implementation of Kállay and Surján [J. Chem. Phys. 115, 2945 (2001)] and comparable performance with respect to MOLPRO's handwritten and dedicated open shell coupled cluster with singles and doubles substitutions implementation [P. J. Knowles, C. Hampel, and H.-J. Werner, J. Chem. Phys. 99, 5219 (1993)].

Engels-Putzka, Anna; Hanrath, Michael

2011-03-01

242

High-Throughput Automated Phenotyping of Two Genetic Mouse Models of Huntington's Disease.  

PubMed

Phenotyping with traditional behavioral assays constitutes a major bottleneck in the primary screening, characterization, and validation of genetic mouse models of disease, leading to downstream delays in drug discovery efforts. We present a novel and comprehensive one-stop approach to phenotyping, the PhenoCube™. This system simultaneously captures the cognitive performance, motor activity, and circadian patterns of group-housed mice by use of home-cage operant conditioning modules (IntelliCage) and custom-built computer vision software. We evaluated two different mouse models of Huntington's Disease (HD), the R6/2 and the BACHD in the PhenoCube™ system. Our results demonstrated that this system can efficiently capture and track alterations in both cognitive performance and locomotor activity patterns associated with these disease models. This work extends our prior demonstration that PhenoCube™ can characterize circadian dysfunction in BACHD mice and shows that this system, with the experimental protocols used, is a sensitive and efficient tool for a first pass high-throughput screening of mouse disease models in general and mouse models of neurodegeneration in particular. PMID:23863947

Balci, Fuat; Oakeshott, Stephen; Shamy, Jul Lea; El-Khodor, Bassem F; Filippov, Igor; Mushlin, Richard; Port, Russell; Connor, David; Paintdakhi, Ahmad; Menalled, Liliana; Ramboz, Sylvie; Howland, David; Kwak, Seung; Brunner, Dani

2013-07-11

243

High-Throughput Automated Phenotyping of Two Genetic Mouse Models of Huntington's Disease  

PubMed Central

Phenotyping with traditional behavioral assays constitutes a major bottleneck in the primary screening, characterization, and validation of genetic mouse models of disease, leading to downstream delays in drug discovery efforts. We present a novel and comprehensive one-stop approach to phenotyping, the PhenoCube™. This system simultaneously captures the cognitive performance, motor activity, and circadian patterns of group-housed mice by use of home-cage operant conditioning modules (IntelliCage) and custom-built computer vision software. We evaluated two different mouse models of Huntington’s Disease (HD), the R6/2 and the BACHD in the PhenoCube™ system. Our results demonstrated that this system can efficiently capture and track alterations in both cognitive performance and locomotor activity patterns associated with these disease models. This work extends our prior demonstration that PhenoCube™ can characterize circadian dysfunction in BACHD mice and shows that this system, with the experimental protocols used, is a sensitive and efficient tool for a first pass high-throughput screening of mouse disease models in general and mouse models of neurodegeneration in particular.

Balci, Fuat; Oakeshott, Stephen; Shamy, Jul Lea; El-Khodor, Bassem F.; Filippov, Igor; Mushlin, Richard; Port, Russell; Connor, David; Paintdakhi, Ahmad; Menalled, Liliana; Ramboz, Sylvie; Howland, David; Kwak, Seung; Brunner, Dani

2013-01-01

244

Spatial genetic analysis reveals high connectivity of tiger (Panthera tigris) populations in the Satpura-Maikal landscape of Central India.  

PubMed

We investigated the spatial genetic structure of the tiger meta-population in the Satpura-Maikal landscape of central India using population- and individual-based genetic clustering methods on multilocus genotypic data from 273 individuals. The Satpura-Maikal landscape is classified as a global-priority Tiger Conservation Landscape (TCL) due to its potential for providing sufficient habitat that will allow the long-term persistence of tigers. We found that the tiger meta-population in the Satpura-Maikal landscape has high genetic variation and very low genetic subdivision. Individual-based Bayesian clustering algorithms reveal two highly admixed genetic populations. We attribute this to forest connectivity and high gene flow in this landscape. However, deforestation, road widening, and mining may sever this connectivity, impede gene exchange, and further exacerbate the genetic division of tigers in central India. PMID:23403813

Sharma, Sandeep; Dutta, Trishna; Maldonado, Jesús E; Wood, Thomas C; Panwar, Hemendra Singh; Seidensticker, John

2012-11-29

245

High-resolution in-situ thermal imaging of microbial mats at El Tatio Geyser, Chile shows coupling between community color and temperature  

Microsoft Academic Search

Microbial mats have spatially heterogeneous structured communities that manifest visually through vibrant color zonation often associated with environmental gradients. We report the first use of high-resolution thermal infrared imaging to map temperature at four hot springs within the El Tatio Geyser Field, Chile. Thermal images with millimeter resolution show drastic variability and pronounced patterning in temperature, with changes on the

Anne E. Dunckel; M. Bayani Cardenas; Audrey H. Sawyer; Philip C. Bennett

2009-01-01

246

Dimensions of Peer Sexual Harassment in Swedish High Schools: What Factor Structures Show the Best Fit to Girls' and Boys' Self-Reports?  

Microsoft Academic Search

Dimensions of peer sexual harassment in schools were analyzed with confirmatory factor analyses of data from a questionnaire study of 980 Swedish high-school students. The factorial structures suggested in the literature on sexual harassment in the workplace showed a bad fit to the student data, especially for boys. A nested structure, with one general factor and two specific factors (closest

Eva Witkowska; Anders Kjellberg

2005-01-01

247

A High Resolution Genetic Map Anchoring Scaffolds of the Sequenced Watermelon Genome  

PubMed Central

As part of our ongoing efforts to sequence and map the watermelon (Citrullus spp.) genome, we have constructed a high density genetic linkage map. The map positioned 234 watermelon genome sequence scaffolds (an average size of 1.41 Mb) that cover about 330 Mb and account for 93.5% of the 353 Mb of the assembled genomic sequences of the elite Chinese watermelon line 97103 (Citrullus lanatus var. lanatus). The genetic map was constructed using an F8 population of 103 recombinant inbred lines (RILs). The RILs are derived from a cross between the line 97103 and the United States Plant Introduction (PI) 296341-FR (C. lanatus var. citroides) that contains resistance to fusarium wilt (races 0, 1, and 2). The genetic map consists of eleven linkage groups that include 698 simple sequence repeat (SSR), 219 insertion-deletion (InDel) and 36 structure variation (SV) markers and spans ?800 cM with a mean marker interval of 0.8 cM. Using fluorescent in situ hybridization (FISH) with 11 BACs that produced chromosome-specifc signals, we have depicted watermelon chromosomes that correspond to the eleven linkage groups constructed in this study. The high resolution genetic map developed here should be a useful platform for the assembly of the watermelon genome, for the development of sequence-based markers used in breeding programs, and for the identification of genes associated with important agricultural traits.

Kou, Qinghe; Jiang, Jiao; Guo, Shaogui; Zhang, Haiying; Hou, Wenju; Zou, Xiaohua; Sun, Honghe; Gong, Guoyi; Levi, Amnon; Xu, Yong

2012-01-01

248

High-dimensional variance partitioning reveals the modular genetic basis of adaptive divergence in gene expression during reproductive character displacement.  

PubMed

Although adaptive change is usually associated with complex changes in phenotype, few genetic investigations have been conducted on adaptations that involve sets of high-dimensional traits. Microarrays have supplied high-dimensional descriptions of gene expression, and phenotypic change resulting from adaptation often results in large-scale changes in gene expression. We demonstrate how genetic analysis of large-scale changes in gene expression generated during adaptation can be accomplished by determining high-dimensional variance partitioning within classical genetic experimental designs. A microarray experiment conducted on a panel of recombinant inbred lines (RILs) generated from two populations of Drosophila serrata that have diverged in response to natural selection, revealed genetic divergence in 10.6% of 3762 gene products examined. Over 97% of the genetic divergence in transcript abundance was explained by only 12 genetic modules. The two most important modules, explaining 50% of the genetic variance in transcript abundance, were genetically correlated with the morphological traits that are known to be under selection. The expression of three candidate genes from these two important genetic modules was assessed in an independent experiment using qRT-PCR on 430 individuals from the panel of RILs, and confirmed the genetic association between transcript abundance and morphological traits under selection. PMID:22023580

McGraw, Elizabeth A; Ye, Yixin H; Foley, Brad; Chenoweth, Stephen F; Higgie, Megan; Hine, Emma; Blows, Mark W

2011-06-27

249

Pathways and barriers to genetic testing and screening: Molecular genetics meets the high-risk family. Final report  

SciTech Connect

The proliferation of genetic screening and testing is requiring increasing numbers of Americans to integrate genetic knowledge and interventions into their family life and personal experience. This study examines the social processes that occur as families at risk for two of the most common autosomal recessive diseases, sickle cell disease (SC) and cystic fibrosis (CF), encounter genetic testing. Each of these diseases is found primarily in a different ethnic/racial group (CF in Americans of North European descent and SC in Americans of West African descent). This has permitted them to have a certain additional lens on the role of culture in integrating genetic testing into family life and reproductive planning. A third type of genetic disorder, the thalassemias was added to the sample in order to extent the comparative frame and to include other ethnic and racial groups.

Duster, T.

1998-11-01

250

Genetic patterns of habitat fragmentation and past climate-change effects in the Mediterranean high-mountain plant Armeria caespitosa (Plumbaginaceae).  

PubMed

• Premise of the Study: Mountain plants are among the species most vulnerable to global warming, because of their isolation, narrow geographic distribution, and limited geographic range shifts. Stochastic and selective processes can act on the genome, modulating genetic structure and diversity. Fragmentation and historical processes also have a great influence on current genetic patterns, but the spatial and temporal contexts of these processes are poorly known. We aimed to evaluate the microevolutionary processes that may have taken place in Mediterranean high-mountain plants in response to changing historical environmental conditions. • Methods: Genetic structure, diversity, and loci under selection were analyzed using AFLP markers in 17 populations distributed over the whole geographic range of Armeria caespitosa, an endemic plant that inhabits isolated mountains (Sierra de Guadarrama, Spain). Differences in altitude, geographic location, and climate conditions were considered in the analyses, because they may play an important role in selective and stochastic processes. • Key Results: Bayesian clustering approaches identified nine genetic groups, although some discrepancies in assignment were found between alternative analyses. Spatially explicit analyses showed a weak relationship between genetic parameters and spatial or environmental distances. However, a large proportion of outlier loci were detected, and some outliers were related to environmental variables. • Conclusions: A. caespitosa populations exhibit spatial patterns of genetic structure that cannot be explained by the isolation-by-distance model. Shifts along the altitude gradient in response to Pleistocene climatic oscillations and environmentally mediated selective forces might explain the resulting structure and genetic diversity values found. PMID:23857736

García-Fernández, Alfredo; Iriondo, Jose M; Escudero, Adrián; Aguilar, Javier Fuertes; Feliner, Gonzalo Nieto

2013-07-15

251

High-Performance Genetically Targetable Optical Neural Silencing via Light-Driven Proton Pumps  

PubMed Central

The ability to silence the activity of genetically specified neurons in a temporally precise fashion would open up the ability to investigate the causal role of specific cell classes in neural computations, behaviors, and pathologies. Here we show that members of the class of light-driven outward proton pumps can mediate very powerful, safe, multiple-color silencing of neural activity. The gene archaerhodopsin-31 (Arch) from Halorubrum sodomense enables near-100% silencing of neurons in the awake brain when virally expressed in mouse cortex and illuminated with yellow light. Arch mediates currents of several hundred picoamps at low light powers, and supports neural silencing currents approaching 900 pA at light powers easily achievable in vivo. In addition, Arch spontaneously recovers from light-dependent inactivation, unlike light-driven chloride pumps that enter long-lasting inactive states in response to light. These properties of Arch are appropriate to mediate the optical silencing of significant brain volumes over behaviourally-relevant timescales. Arch function in neurons is well tolerated because pH excursions created by Arch illumination are minimized by self-limiting mechanisms to levels comparable to those mediated by channelrhodopsins2,3 or natural spike firing. To highlight how proton pump ecological and genomic diversity may support new innovation, we show that the blue-green light-drivable proton pump from the fungus Leptosphaeria maculans4 (Mac) can, when expressed in neurons, enable neural silencing by blue light, thus enabling alongside other developed reagents the potential for independent silencing of two neural populations by blue vs. red light. Light-driven proton pumps thus represent a high-performance and extremely versatile class of “optogenetic” voltage and ion modulator, which will broadly empower new neuroscientific, biological, neurological, and psychiatric investigations.

Chow, Brian Y.; Han, Xue; Dobry, Allison S.; Qian, Xiaofeng; Chuong, Amy S.; Li, Mingjie; Henninger, Michael A.; Belfort, Gabriel M.; Lin, Yingxi; Monahan, Patrick E.; Boyden, Edward S.

2009-01-01

252

A high-capacity cell macroencapsulation system supporting the long-term survival of genetically engineered allogeneic cells.  

PubMed

The rapid increase in the number of approved therapeutic proteins, including recombinant antibodies, for diseases necessitating chronic treatments raises the question of the overall costs imposed on healthcare systems. It is therefore important to investigate alternative methods for recombinant protein administration. The implantation of genetically engineered cells is an attractive strategy for the chronic long-term delivery of recombinant proteins. Here, we have developed a high-capacity cell encapsulation system for the implantation of allogeneic myoblasts, which survive at high density for at least one year. This flat sheet device is based on permeable polypropylene membranes sealed to a mechanically resistant frame which confine cells seeded in a tailored biomimetic poly(ethylene glycol) (PEG)-based hydrogel matrix. In order to quantitate the number of cells surviving in the device and optimize initial conditions leading to high-density survival, we implant devices containing C2C12 mouse myoblasts expressing a luciferase reporter in the mouse subcutaneous tissue. We show that initial cell load, hydrogel stiffness and permeable membrane porosity are critical parameters to achieve long-term implant survival and efficacy. Optimization of these parameters leads to the survival of encapsulated myogenic cells at high density for several months, with minimal inflammatory response and dense neovascularization in the adjacent host tissue. Therefore, this encapsulation system is an effective platform for the implantation of genetically engineered cells in allogeneic conditions, which could be adapted to the chronic administration of recombinant proteins. PMID:24103654

Lathuilière, Aurélien; Cosson, Steffen; Lutolf, Matthias P; Schneider, Bernard L; Aebischer, Patrick

2013-10-05

253

On the Origin of Tibetans and Their Genetic Basis in Adapting High-Altitude Environments  

PubMed Central

Since their arrival in the Tibetan Plateau during the Neolithic Age, Tibetans have been well-adapted to extreme environmental conditions and possess genetic variation that reflect their living environment and migratory history. To investigate the origin of Tibetans and the genetic basis of adaptation in a rigorous environment, we genotyped 30 Tibetan individuals with more than one million SNP markers. Our findings suggested that Tibetans, together with the Yi people, were descendants of Tibeto-Burmans who diverged from ancient settlers of East Asia. The valleys of the Hengduan Mountain range may be a major migration route. We also identified a set of positively-selected genes that belong to functional classes of the embryonic, female gonad, and blood vessel developments, as well as response to hypoxia. Most of these genes were highly correlated with population-specific and beneficial phenotypes, such as high infant survival rate and the absence of chronic mountain sickness.

Zhang, Feng; Lin, Hongbin; Wang, Xumin; Wan, Ning; Ye, Zhenqing; Weng, Haiyu; Zhang, Lili; Li, Xin; Yan, Jiangwei; Wang, Panpan; Wu, Tingting; Cheng, Longfei; Wang, Jing; Wang, Duen-Mei; Ma, Xu; Yu, Jun

2011-01-01

254

Avian genetic stocks: the high and low points from an academia researcher.  

PubMed

Poultry genetic resources, which are valuable for research, span an impressive gamut from breeds to highly specialized inbred lines. The community of scientists utilizing specialized lines is broad, including researchers in medicine, basic biology, and agricultural science. The majority of specialized research lines used by such scientists are held at land grant universities. Over the prior 2 decades, hundreds of lines were eliminated. This pattern continues today with no evidence of abatement. Awareness and visibility of the causes and ongoing problems have been highlighted via a number of high-profile forums. Given the large community of scientists and the negative impact on future advances in biological, medical, and agricultural research as these genetic resources dwindle, the issue is of national interest and warrants federal funding to support a united network of avian and poultry stocks centers. PMID:16523617

Delany, M E

2006-02-01

255

Interpretation of Genetic Association Studies: Markers with Replicated Highly Significant Odds Ratios May Be Poor Classifiers  

PubMed Central

Recent successful discoveries of potentially causal single nucleotide polymorphisms (SNPs) for complex diseases hold great promise, and commercialization of genomics in personalized medicine has already begun. The hope is that genetic testing will benefit patients and their families, and encourage positive lifestyle changes and guide clinical decisions. However, for many complex diseases, it is arguable whether the era of genomics in personalized medicine is here yet. We focus on the clinical validity of genetic testing with an emphasis on two popular statistical methods for evaluating markers. The two methods, logistic regression and receiver operating characteristic (ROC) curve analysis, are applied to our age-related macular degeneration dataset. By using an additive model of the CFH, LOC387715, and C2 variants, the odds ratios are 2.9, 3.4, and 0.4, with p-values of 10?13, 10?13, and 10?3, respectively. The area under the ROC curve (AUC) is 0.79, but assuming prevalences of 15%, 5.5%, and 1.5% (which are realistic for age groups 80 y, 65 y, and 40 y and older, respectively), only 30%, 12%, and 3% of the group classified as high risk are cases. Additionally, we present examples for four other diseases for which strongly associated variants have been discovered. In type 2 diabetes, our classification model of 12 SNPs has an AUC of only 0.64, and two SNPs achieve an AUC of only 0.56 for prostate cancer. Nine SNPs were not sufficient to improve the discrimination power over that of nongenetic predictors for risk of cardiovascular events. Finally, in Crohn's disease, a model of five SNPs, one with a quite low odds ratio of 0.26, has an AUC of only 0.66. Our analyses and examples show that strong association, although very valuable for establishing etiological hypotheses, does not guarantee effective discrimination between cases and controls. The scientific community should be cautious to avoid overstating the value of association findings in terms of personalized medicine before their time.

Jakobsdottir, Johanna; Gorin, Michael B.; Conley, Yvette P.; Ferrell, Robert E.; Weeks, Daniel E.

2009-01-01

256

High-performance genetically targetable optical neural silencing by light-driven proton pumps  

Microsoft Academic Search

The ability to silence the activity of genetically specified neurons in a temporally precise fashion would provide the opportunity to investigate the causal role of specific cell classes in neural computations, behaviours and pathologies. Here we show that members of the class of light-driven outward proton pumps can mediate powerful, safe, multiple-colour silencing of neural activity. The gene archaerhodopsin-3 (Arch)

Brian Y. Chow; Xue Han; Allison S. Dobry; Xiaofeng Qian; Amy S. Chuong; Mingjie Li; Michael A. Henninger; Gabriel M. Belfort; Yingxi Lin; Patrick E. Monahan; Edward S. Boyden

2010-01-01

257

Characterization of unknown genetic modifications using high throughput sequencing and computational subtraction  

PubMed Central

Background When generating a genetically modified organism (GMO), the primary goal is to give a target organism one or several novel traits by using biotechnology techniques. A GMO will differ from its parental strain in that its pool of transcripts will be altered. Currently, there are no methods that are reliably able to determine if an organism has been genetically altered if the nature of the modification is unknown. Results We show that the concept of computational subtraction can be used to identify transgenic cDNA sequences from genetically modified plants. Our datasets include 454-type sequences from a transgenic line of Arabidopsis thaliana and published EST datasets from commercially relevant species (rice and papaya). Conclusion We believe that computational subtraction represents a powerful new strategy for determining if an organism has been genetically modified as well as to define the nature of the modification. Fewer assumptions have to be made compared to methods currently in use and this is an advantage particularly when working with unknown GMOs.

Tengs, Torstein; Zhang, Haibo; Holst-Jensen, Arne; Bohlin, Jon; Butenko, Melinka A; Kristoffersen, Anja Brathen; Sorteberg, Hilde-Gunn Opsahl; Berdal, Knut G

2009-01-01

258

Clinical and Genetic Description of a Family With a High Prevalence of Autosomal Dominant Restless Legs Syndrome  

PubMed Central

OBJECTIVE: To conduct clinical and molecular genetic analyses of the members of an extended family in Central Indiana with a high prevalence of restless legs syndrome (RLS). PARTICIPANTS AND METHODS: From February 1, 2006, through August 31, 2008, we collected data from members of this family, which is of English descent. Genealogical methods were used to expand the family tree, and family members were screened with an RLS questionnaire. Telephone interviews and personal examinations were performed at Mayo Clinic and during a field trip to Central Indiana. Blood samples were collected for molecular genetic analysis. A follow-up telephone interview was conducted 1 year later. RESULTS: The family tree spans 7 generations with 88 living members, 30 of whom meet the criteria for diagnosis of RLS established by the International Restless Legs Syndrome Study Group. Three affected family members also have Parkinson disease or essential tremor. The mode of RLS inheritance is compatible with an autosomal dominant pattern. The affected family members do not exhibit linkage to the 5 known RLS loci or mutations in the RLS susceptibility genes MEIS1 and BTBD9. CONCLUSION: Of 88 members of this single extended family in Central Indiana, 30 were diagnosed as having RLS. Because our analysis shows that the disease is not linked to any of the known RLS loci or risk-associated genes, we postulate that members of this family may carry a gene mutation in a novel genetic locus.

Young, Jessica E.; Vilarino-Guell, Carles; Lin, Siong-Chi; Wszolek, Zbigniew K.; Farrer, Matthew J.

2009-01-01

259

High-throughput genomic technology in research and clinical management of breast cancer. Evolving landscape of genetic epidemiological studies  

Microsoft Academic Search

Candidate polymorphism-based genetic epidemiological studies have yielded little success in the search for low-penetrance breast cancer susceptibility genes. The lack of progress is partially due to insufficient coverage of genomic regions with genetic markers, as well as economic constraints, limiting both the number of genetic targets and the number of individuals being studied. Recent rapid advances in high-throughput genotyping technology

Yen-Ling Low; Sara Wedrén; Jianjun Liu

2006-01-01

260

Genetic Requirements for High Constitutive SOS Expression in recA730 Mutants of Escherichia coli ?  

PubMed Central

The RecA protein in its functional state is in complex with single-stranded DNA, i.e., in the form of a RecA filament. In SOS induction, the RecA filament functions as a coprotease, enabling the autodigestion of the LexA repressor. The RecA filament can be formed by different mechanisms, but all of them require three enzymatic activities essential for the processing of DNA double-stranded ends. These are helicase, 5?–3? exonuclease, and RecA loading onto single-stranded DNA (ssDNA). In some mutants, the SOS response can be expressed constitutively during the process of normal DNA metabolism. The RecA730 mutant protein is able to form the RecA filament without the help of RecBCD and RecFOR mediators since it better competes with the single-strand binding (SSB) protein for ssDNA. As a consequence, the recA730 mutants show high constitutive SOS expression. In the study described in this paper, we studied the genetic requirements for constitutive SOS expression in recA730 mutants. Using a ?-galactosidase assay, we showed that the constitutive SOS response in recA730 mutants exhibits different requirements in different backgrounds. In a wild-type background, the constitutive SOS response is partially dependent on RecBCD function. In a recB1080 background (the recB1080 mutation retains only helicase), constitutive SOS expression is partially dependent on RecBCD helicase function and is strongly dependent on RecJ nuclease. Finally, in a recB-null background, the constitutive SOS expression of the recA730 mutant is dependent on the RecJ nuclease. Our results emphasize the importance of the 5?–3? exonuclease for high constitutive SOS expression in recA730 mutants and show that RecBCD function can further enhance the excellent intrinsic abilities of the RecA730 protein in vivo.

Vlasic, Ignacija; Simatovic, Ana; Brcic-Kostic, Krunoslav

2011-01-01

261

GENETICS Serotonergic Mediation of Aggression in High and Low Aggressive Chicken Strains  

Microsoft Academic Search

Serotonin (5-HT) regulates aggressive be- havior via binding to its receptors, such as 5-HT1A and 1B, in humans and rodents. Here we investigate the heri- table components of 5-HT regulation of aggressiveness in chickens, utilizing 3 distinct genetic strains. In this study, we used 2 divergently selected strains (high and low group productivity and survivability, respectively; HGPS and LGPS) and

R. L. Dennis; Z. Q. Chen; H. W. Cheng

262

Genetic selection for a highly functional cysteine-less membrane protein using site saturation mutagenesis  

Microsoft Academic Search

We describe an efficient method for generating highly functional membrane proteins with variant amino acids at defined positions that couples a modified site saturation strategy with functional genetic selection. We applied this method to the production of a cysteine-less variant of the Crithidia fasciculata inosine-guanosine permease CfNT2 to facilitate biochemical studies using thiol-specific modifying reagents. Of 10 endogenous cysteine residues

Cassandra S. Arendt; Keirei Ri; Phillip A. Yates; Buddy Ullman

2007-01-01

263

High genetic polymorphism of relapsing P. vivax isolates in northwest Colombia.  

PubMed

Genetic diversity of Plasmodium populations has been more extensively documented in Colombia for Plasmodium falciparum than for Plasmodium vivax. Recently, highly variable microsatellite markers have been described and used in population-level studies of genetic variation of P. vivax throughout the world. We applied this approach to understand the genetic structure of P. vivax populations and to identify recurrence-associated haplotypes. In this, three microsatellite markers of P. vivax were amplified and the combined size of the fragments was used to establish genotypes. Patients from an ongoing treatment efficacy trial who were kept either in endemic or non-endemic regions in the northwest of Colombia were included in the study. In total 58 paired clinical isolates, were amplified. A total of 54 haplotypes were observed among the two regions. Some haplotypes were exclusive to the endemic region where the highest degree of polymorphism was detected. In addition, we confirmed the different genotypes of recurrent-relapsing and primary infection isolates suggesting the activation of heterologous hypnozoite populations. We conclude that analysis of the three microsatellites is a valuable tool to establish the genetic characteristics of P. vivax populations in Colombia. PMID:21497586

Restrepo, Eliana; Imwong, Mallika; Rojas, Winston; Carmona-Fonseca, Jaime; Maestre, Amanda

2011-04-07

264

High Genetic Diversity and Low Differentiation of Michelia coriacea (Magnoliaceae), a Critically Endangered Endemic in Southeast Yunnan, China  

PubMed Central

Michelia coriacea, a critically endangered tree, has a restricted and fragmented distribution in Southeast Yunnan Province, China. The genetic diversity, genetic structure and gene flow in the three extant populations of this species were detected by 10 inter-simple sequence repeat (ISSR) markers and 11 simple sequence repeat (SSR) markers. Examination of genetic diversity revealed that the species maintained a relatively high level of genetic diversity at the species level (percentage of polymorphic bands) PPB = 96.36% from ISSRs; PPL (percentage of polymorphic loci) = 95.56% from SSRs, despite several fragmental populations. Low levels of genetic differentiation among the populations of M. coriacea were detected by Nei’s Gst = 0.187 for ISSR and Wright’s Fst = 0.090 for SSR markers, which is further confirmed by Bayesian model-based STRUCTURE and PCoA analysis that could not reveal a clear separation between populations, although YKP was differentiated to other two populations by ISSR markers. Meanwhile, AMOVA analysis also indicated that 22.84% and 13.90% of genetic variation existed among populations for ISSRs and SSRs, respectively. The high level of genetic diversity, low genetic differentiation, and the population, structure imply that the fragmented habitat and the isolated population of M. coriacea may be due to recent over-exploitation. Conservation and management of M. coriacea should concentrate on maintaining the high level of genetic variability through both in and ex-situ conservation actions.

Zhao, Xingfeng; Ma, Yongpeng; Sun, Weibang; Wen, Xiangying; Milne, Richard

2012-01-01

265

High Genetic Diversity and Low Differentiation of Michelia coriacea (Magnoliaceae), a Critically Endangered Endemic in Southeast Yunnan, China.  

PubMed

Michelia coriacea, a critically endangered tree, has a restricted and fragmented distribution in Southeast Yunnan Province, China. The genetic diversity, genetic structure and gene flow in the three extant populations of this species were detected by 10 inter-simple sequence repeat (ISSR) markers and 11 simple sequence repeat (SSR) markers. Examination of genetic diversity revealed that the species maintained a relatively high level of genetic diversity at the species level (percentage of polymorphic bands) PPB = 96.36% from ISSRs; PPL (percentage of polymorphic loci) = 95.56% from SSRs, despite several fragmental populations. Low levels of genetic differentiation among the populations of M. coriacea were detected by Nei's G(st) = 0.187 for ISSR and Wright's F(st) = 0.090 for SSR markers, which is further confirmed by Bayesian model-based STRUCTURE and PCoA analysis that could not reveal a clear separation between populations, although YKP was differentiated to other two populations by ISSR markers. Meanwhile, AMOVA analysis also indicated that 22.84% and 13.90% of genetic variation existed among populations for ISSRs and SSRs, respectively. The high level of genetic diversity, low genetic differentiation, and the population, structure imply that the fragmented habitat and the isolated population of M. coriacea may be due to recent over-exploitation. Conservation and management of M. coriacea should concentrate on maintaining the high level of genetic variability through both in and ex-situ conservation actions. PMID:22605985

Zhao, Xingfeng; Ma, Yongpeng; Sun, Weibang; Wen, Xiangying; Milne, Richard

2012-04-10

266

Genetic analyses of fertility and predictor traits in Holstein herds with low and high mean calving intervals and in Jersey herds.  

PubMed

Genetic parameters were estimated with the aim of identifying useful predictor traits for the genetic evaluation of fertility. For this study, data included calving interval (CI), days from calving to first service (CFS), pregnancy diagnosis, lactation length (LL), daily milk yield close to 90 d of lactation (milk yield), and survival to second lactation on Australian Holstein and Jersey cows. The effect of level of fertility, measured here as CI, on correlations among traits was investigated by dividing the Holstein herds into those that managed short CI (proxy for seasonal-calving herds) and long CI (proxy for herds that practice extended lactations). In all cases, genetic correlations of CI with CFS, pregnancy, and LL were high (>0.7). Genetic correlations between fertility and predictor traits were generally similar in the 2 Holstein herd groups and in Jerseys. However, some differences in both the direction and strength of correlations were observed. In Jerseys, the genetic correlation between CI and survival was positive, but in Holstein herds, this correlation was negative. Particularly in low mean CI herds, the correlation suggests that cows with a genetic potential for longer CI were more likely to be culled. The genetic correlation of CI with survival was intermediate in high mean CI Holstein herds. Furthermore, Jersey cows with a high genetic potential for milk yield had a higher chance of surviving than those with low genetic potential. In contrast, the genetic correlation between milk yield and survival in low mean CI Holstein herds was near zero. The high genetic correlation between CI and LL suggests that LL could be used as proxy for CI in cows that do not calve again. Although the phenotypic variance for CI in high mean CI herds was nearly twice that in Jerseys and low mean CI herds, we found no bull reranking for CI due to having daughters in low or high mean CI herds. However, the ranges in estimated breeding values (EBV) were narrower in low mean CI herds than in high mean CI herds. The genetic trend in cows and bulls showed that CI EBV were increasing by 0.3 to 0.8 d/yr in both Holstein and Jersey. Phenotypically, CI was increasing by 2 d/yr in high mean CI Holstein herds and by 1 d/yr in Jersey and low mean CI Holstein herds. However, in recent years, both phenotypic and genetic trends have stabilized. In summary, if the main trait for genetic evaluation of fertility is CI, predictor traits such as milk yield, survival, LL, and other fertility traits can be used in joint analyses to increase reliability of bull EBV. If the genetic evaluation is to be carried out simultaneously for Holstein and Jersey using the same variance-covariance matrix, survival should not be used as a predictor because its correlation with CI is different in Jersey than in Holstein. On the other hand, LL could be used instead of CI for cows that do not calve again in both breeds and herd groups. PMID:23127912

Haile-Mariam, M; Bowman, P J; Pryce, J E

2012-11-03

267

High-Resolution Analysis of Human Y-Chromosome Variation Shows a Sharp Discontinuity and Limited Gene Flow between Northwestern Africa and the Iberian Peninsula  

PubMed Central

In the present study we have analyzed 44 Y-chromosome biallelic polymorphisms in population samples from northwestern (NW) Africa and the Iberian Peninsula, which allowed us to place each chromosome unequivocally in a phylogenetic tree based on >150 polymorphisms. The most striking results are that contemporary NW African and Iberian populations were found to have originated from distinctly different patrilineages and that the Strait of Gibraltar seems to have acted as a strong (although not complete) barrier to gene flow. In NW African populations, an Upper Paleolithic colonization that probably had its origin in eastern Africa contributed 75% of the current gene pool. In comparison, ?78% of contemporary Iberian Y chromosomes originated in an Upper Paleolithic expansion from western Asia, along the northern rim of the Mediterranean basin. Smaller contributions to these gene pools (constituting 13% of Y chromosomes in NW Africa and 10% of Y chromosomes in Iberia) came from the Middle East during the Neolithic and, during subsequent gene flow, from Sub-Saharan to NW Africa. Finally, bidirectional gene flow across the Strait of Gibraltar has been detected: the genetic contribution of European Y chromosomes to the NW African gene pool is estimated at 4%, and NW African populations may have contributed 7% of Iberian Y chromosomes. The Islamic rule of Spain, which began in a.d. 711 and lasted almost 8 centuries, left only a minor contribution to the current Iberian Y-chromosome pool. The high-resolution analysis of the Y chromosome allows us to separate successive migratory components and to precisely quantify each historical layer.

Bosch, Elena; Calafell, Francesc; Comas, David; Oefner, Peter J.; Underhill, Peter A.; Bertranpetit, Jaume

2001-01-01

268

T-Cell Immune Responses Against Env from CRF12_BF and Subtype B HIV-1 Show High Clade-Specificity that Can Be Overridden by Multiclade Immunizations  

PubMed Central

Background The extreme genetic diversity of the human immunodeficiency virus type 1 (HIV-1) poses a daunting challenge to the generation of an effective AIDS vaccine. In Argentina, the epidemic is characterized by the high prevalence of infections caused by subtype B and BF variants. The aim of this study was to characterize in mice the immunogenic and antigenic properties of the Env protein from CRF12_BF in comparison with clade B, employing prime-boost schemes with the combination of recombinant DNA and vaccinia virus (VV) vectors. Methodology/Principal Findings As determined by ELISPOT from splenocytes of animals immunized with either EnvBF or EnvB antigens, the majority of the cellular responses to Env were found to be clade-specific. A detailed peptide mapping of the responses reveal that when there is cross-reactivity, there are no amino acid changes in the peptide sequence or were minimal and located at the peptide ends. In those cases, analysis of T cell polifunctionality and affinity indicated no differences with respect to the cellular responses found against the original homologous sequence. Significantly, application of a mixed immunization combining both clades (B and BF) induced a broader cellular response, in which the majority of the peptides targeted after the single clade vaccinations generated a positive response. In this group we could also find significant cellular and humoral responses against the whole gp120 protein from subtype B. Conclusions/Significance This work has characterized for the first time the immunogenic peptides of certain EnvBF regions, involved in T cell responses. It provides evidence that to improve immune responses to HIV there is a need to combine Env antigens from different clades, highlighting the convenience of the inclusion of BF antigens in future vaccines for geographic regions where these HIV variants circulate.

Monaco, Daniela C.; Rodriguez, Ana M.; Pascutti, Maria F.; Carobene, Mauricio; Falivene, Juliana; Gomez, Alejandro; Maeto, Cynthia; Turk, Gabriela; Najera, Jose L.; Esteban, Mariano; Gherardi, M. Magdalena

2011-01-01

269

Genetic analysis of bed bug populations reveals small propagule size within individual infestations but high genetic diversity across infestations from the eastern United States.  

PubMed

Bed bugs (Cimex lectularius L.) are a resurgent pest worldwide and infestations within the United States are increasing at a rapid rate. Because of the physical and psychological discomfort inflicted by their blood feeding habits, and allergies and secondary infections associated with bites, bed bugs are recognized as a significant public health problem. Although bed bug infestations are spreading and becoming more prevalent, we have a poor understanding of their dispersal patterns and sources of infestation. To help fill this gap, we conducted a genetic study of 21 bed bug infestations from the eastern United States, nearly all of which came from single rooms within residences. We genotyped samples comprised of 8-10 individuals per infestation at nine polymorphic microsatellite loci. Despite high genetic diversity across all infestations, with 5-17 alleles per locus (mean = 10.3 alleles per locus), we found low genetic diversity (1-4 alleles per locus) within all but one of the infestations. These results suggest that nearly all the studied infestations were started by a small propagule possibly consisting of a singly mated female and/or her progeny, or a female mated with multiple males that were highly related to her. All infestations were strongly genetically differentiated from each other (mean pairwise F(ST) between populations = 0.68) and we did not find strong evidence of a geographic pattern of genetic structure, indicating infestations located in closer proximity to each other were nearly as genetically differentiated as those located hundreds of kilometers away. The high level of genetic diversity across infestations from the eastern United States together with the lack of geographically organized structure is consistent with multiple introductions into the United States from foreign sources. PMID:22897047

Saenz, Virna L; Booth, Warren; Schal, Coby; Vargo, Edward L

2012-07-01

270

How Not to Be a BlackBox: Evolution and Genetic-Engineering of High-Level Behaviours  

Microsoft Academic Search

In spite of many success stories in various do- mains, Genetic Algorithm and Genetic Program- ming still suffer from some significant pitfalls. Those evolved programs often lack of some im- portant properties such as robustness, compre- hensibility, transparency, modifiability and us- ability of domain knowledge easily available. We attempt to resolve these problems, at least in evolving high-level behaviours, by

Ik Soo Lim; Daniel Thalmann

271

Construction of a high density integrated genetic map for cucumber (Cucumis sativus L.).  

PubMed

The high-density consensus map was constructed based on the GY14 × PI 183967 map from an inter-subspecific cross and the extended S94 × S06 map from an intra-subspecific cross. The consensus map was composed of 1,369 loci, including 1,152 SSR loci, 192 SRAP loci, 21 SCAR loci and one STS locus as well as three gene loci of fruit external quality traits in seven chromosomes, and spanned 700.5 cM, of which 682.7 cM (97.5%) were covered by SSR markers. The average genetic distance and physical interval between loci were 0.51 cM and ~268 kbp, respectively. Additionally, the physical position of the sequence-associated markers aligned along the assembled cucumber genome sequence established a relationship between genetic maps and cucumber genome sequence and to a great extent validated the order of markers in individual maps and consensus map. This consensus map with a high marker density and well-ordered markers is a saturated and reliable linkage map for genetic analysis of cucumber or the Cucurbitaceae family of plants. PMID:21971891

Zhang, Wei-Wei; Pan, Jun-Song; He, Huan-Le; Zhang, Chi; Li, Zheng; Zhao, Jun-Long; Yuan, Xiao-Jun; Zhu, Li-Huang; Huang, San-Wen; Cai, Run

2011-10-05

272

High resolution melting: improvements in the genetic diagnosis of hypertrophic cardiomyopathy in a Portuguese cohort  

PubMed Central

Background Hypertrophic Cardiomyopathy (HCM) is a complex myocardial disorder with a recognized genetic heterogeneity. The elevated number of genes and mutations involved in HCM limits a gene-based diagnosis that should be considered of most importance for basic research and clinical medicine. Methodology In this report, we evaluated High Resolution Melting (HRM) robustness, regarding HCM genetic testing, by means of analyzing 28 HCM-associated genes, including the most frequent 4 HCM-associated sarcomere genes, as well as 24 genes with lower reported HCM-phenotype association. We analyzed 80 Portuguese individuals with clinical phenotype of HCM allowing simultaneously a better characterization of this disease in the Portuguese population. Results HRM technology allowed us to identify 60 mutated alleles in 72 HCM patients: 49 missense mutations, 3 nonsense mutations, one 1-bp deletion, one 5-bp deletion, one in frame 3-bp deletion, one insertion/deletion, 3 splice mutations, one 5'UTR mutation in MYH7, MYBPC3, TNNT2, TNNI3, CSRP3, MYH6 and MYL2 genes. Significantly 22 are novel gene mutations. Conclusions HRM was proven to be a technique with high sensitivity and a low false positive ratio allowing a rapid, innovative and low cost genotyping of HCM. In a short return, HRM as a gene scanning technique could be a cost-effective gene-based diagnosis for an accurate HCM genetic diagnosis and hopefully providing new insights into genotype/phenotype correlations.

2012-01-01

273

X-ray photoelectron spectroscopy of negative electrodes from high-power lithium-ion cells showing various levels of power fade  

SciTech Connect

High-power lithium-ion cells for transportation applications are being developed and studied at Argonne National Laboratory. The current generation of cells containing LiNi{sub 0.8}Co{sub 0.15}Al{sub 0.05}O{sub 2}-based cathodes, graphite-based anodes, and LiPF6-based electrolytes show loss of capacity and power during accelerated testing at elevated temperatures. Negative electrode samples harvested from some cells that showed varying degrees of power and capacity fade were examined by X-ray photoelectron spectroscopy (XPS). The samples exhibited a surface film on the graphite, which was thicker on samples from cells that showed higher fade. Furthermore, solvent-based compounds were dominant on samples from low power fade cells, whereas LiPF{sub 6}-based products were dominant on samples from high power fade cells. The effect of sample rinsing and air exposure is discussed. Mechanisms are proposed to explain the formation of compounds suggested by the XPS data.

Herstedt, Marie; Abraham, Daniel P.; Kerr, John B.

2004-02-28

274

Rats perinatally exposed to food restriction and high-fat diet show differences in adipose tissue gene expression under chronic caloric restriction  

PubMed Central

The aim of this study is to analyze how maternal diet during the lactational period influences the adipose tissue response to chronic caloric restriction in offspring. Lactating dams were subjected to one of three treatments: 50% food restriction (FR), ad lib standard chow (AL), or ad lib high-fat diet (HF). Juveniles were first weaned onto standard chow, then in adulthood 50% calorically restricted and maintained at 90% of normal body weight for 60 d. HF animals showed increased percent body fat compared with AL and FR animals despite equivalent body weights. HF animals showed alterations in the balance of adipose tissue lipogenic (FAS, LPL) and lipolytic (HSL) gene expression that may underlie their propensity to maintain fat stores under caloric restriction.

MacKay, Harry; Khazall, Rim; Patterson, Zachary R; Wellman, Martin; Abizaid, Alfonso

2013-01-01

275

Correlated transport and high resolution transmission electron microscopy investigations on inorganic-filled single-walled carbon nanotubes showing negative differential resistance  

NASA Astrophysics Data System (ADS)

We describe a strategy for fabricating devices on perforated silicon nitride membranes that is ideal for systems with modulated structure, in particular for nanotubes with endohedral inorganic compounds or molecules, or nanotubes externally functionalized with soft materials. It uses dynamic nanostenciling and focussed ion beam while avoiding nanotubes' exposure to chemicals or beams. Physical properties and high resolution transmission electron microscopy are then correlated. Devices with individual single-walled carbon nanotubes partially filled with potassium iodide (KI) showed negative differential resistance (NDR). We attribute the NDR to electrostatic potential modulation on the nanotube due to permanent dipoles in the KI chain.

Ilie, Adelina; Egger, Stefan; Friedrichs, Steffi; Kang, Dae-Joon; Green, Malcolm L. H.

2007-12-01

276

Attitudes toward direct-to-consumer advertisements and online genetic testing among high-risk women participating in a hereditary cancer clinic.  

PubMed

Genetic testing for the breast cancer genes 1/2 (BRCA 1/2) has helped women determine their risk of developing breast and ovarian cancer. As interest in genetic testing has grown, companies have created strategies to disseminate information about testing, including direct-to-consumer advertising (DTCA) and online genetic testing. This study examined attitudes toward DTCA and online testing for BRCA among 84 women at a high-risk clinic as well as additional factors that may be associated with these attitudes, such as personal and familial cancer history, cancer worry and risk perception, and history with genetic testing/counseling. Results showed that the majority of the women held favorable attitudes toward DTCA for BRCA testing but did not support online testing. Factors such as familial ovarian cancer, cancer worry, and satisfaction with genetic counseling/testing were associated with positive attitudes toward DTCA, whereas personal breast cancer history was related to negative attitudes. The findings suggest that women may view DTCA as informational but rely on physicians for help in their decision to undergo testing, and also suggest that cancer history may affect women's acceptance of DTCA and genetic testing. PMID:21432710

Perez, Giselle K; Cruess, Dean G; Cruess, Stacy; Brewer, Molly; Stroop, Jennifer; Schwartz, Robin; Greenstein, Robert

2011-05-24

277

Microsatellites in the mitochondrial genome of phytophthora cinnamomi failed to provide highly polymorphic markers for population genetics.  

PubMed

Microsatellites were evaluated as genetic markers for the mitochondrial genome (mtDNA) of Phytophthora cinnamomi for population studies. Two (A)n microsatellite loci were cloned from the mtDNA of P. cinnamomi. Amplification products from these loci showed little polymorphism among Phytophthora isolates due to their location in coding regions of mtDNA. A further three (A)n microsatellite loci obtained from the complete mtDNA sequence of P. infestans were also not highly polymorphic, although located in non-coding mtDNA. The presence of the (A)n microsatellites was not conserved in the genus Phytophthora. Unlike those of the chloroplast genome of plants, (A)n microsatellite loci of mtDNA do not have potential as highly polymorphic markers in Phytophthora. PMID:9673029

Dobrowolski, M P; Tommerup, I C; O'Brien, P A

1998-06-15

278

Development of a Large SNP Genotyping Array and Generation of High-Density Genetic Maps in Tomato  

PubMed Central

The concurrent development of high-throughput genotyping platforms and next generation sequencing (NGS) has increased the number and density of genetic markers, the efficiency of constructing detailed linkage maps, and our ability to overlay recombination and physical maps of the genome. We developed an array for tomato with 8,784 Single Nucleotide Polymorphisms (SNPs) mainly discovered based on NGS-derived transcriptome sequences. Of the SNPs, 7,720 (88%) passed manufacturing quality control and could be scored in tomato germplasm. The array was used to generate high-density linkage maps for three interspecific F2 populations: EXPEN 2000 (Solanum lycopersicum LA0925 x S. pennellii LA0716, 79 individuals), EXPEN 2012 (S. lycopersicum Moneymaker x S. pennellii LA0716, 160 individuals), and EXPIM 2012 (S. lycopersicum Moneymaker x S. pimpinellifolium LA0121, 183 individuals). The EXPEN 2000-SNP and EXPEN 2012 maps consisted of 3,503 and 3,687 markers representing 1,076 and 1,229 unique map positions (genetic bins), respectively. The EXPEN 2000-SNP map had an average marker bin interval of 1.6 cM, while the EXPEN 2012 map had an average bin interval of 0.9 cM. The EXPIM 2012 map was constructed with 4,491 markers (1,358 bins) and an average bin interval of 0.8 cM. All three linkage maps revealed an uneven distribution of markers across the genome. The dense EXPEN 2012 and EXPIM 2012 maps showed high levels of colinearity across all 12 chromosomes, and also revealed evidence of small inversions between LA0716 and LA0121. Physical positions of 7,666 SNPs were identified relative to the tomato genome sequence. The genetic and physical positions were mostly consistent. Exceptions were observed for chromosomes 3, 10 and 12. Comparing genetic positions relative to physical positions revealed that genomic regions with high recombination rates were consistent with the known distribution of euchromatin across the 12 chromosomes, while very low recombination rates were observed in the heterochromatic regions.

Sim, Sung-Chur; Durstewitz, Gregor; Plieske, Jorg; Wieseke, Ralf; Ganal, Martin W.; Van Deynze, Allen; Hamilton, John P.; Buell, C. Robin; Causse, Mathilde; Wijeratne, Saranga; Francis, David M.

2012-01-01

279

NOTCH1 mutations identify a genetic subgroup of chronic lymphocytic leukemia patients with high risk of transformation and poor outcome.  

PubMed

NOTCH1 has been found recurrently mutated in a subset of patients with chronic lymphocytic leukemia (CLL). To analyze biological features and clinical impact of NOTCH1 mutations in CLL, we sequenced this gene in 565 patients. NOTCH1 mutations, found in 63 patients (11%), were associated with unmutated IGHV, high expression of CD38 and ZAP-70, trisomy 12, advanced stage and elevated lactate dehydrogenase. Sequential analysis in 200 patients demonstrated acquisition of mutation in one case (0.5%) and disappearance after treatment in two. Binet A and B patients with NOTCH1-mutated had a shorter time to treatment. NOTCH1-mutated patients were more frequently refractory to therapy and showed shorter progression-free and overall survival after complete remission. Overall survival was shorter in NOTCH1-mutated patients, although not independently from IGHV. NOTCH1 mutation increased the risk of transformation to diffuse large B-cell lymphoma independently from IGHV, with this being validated in resampling tests of replicability. In summary, NOTCH1 mutational status, that was rarely acquired during the course of the disease, identify a genetic subgroup with high risk of transformation and poor outcome. This recently identified genetic subgroup of CLL patients deserves prospective studies to define their best management. PMID:23295735

Villamor, N; Conde, L; Martínez-Trillos, A; Cazorla, M; Navarro, A; Beà, S; López, C; Colomer, D; Pinyol, M; Aymerich, M; Rozman, M; Abrisqueta, P; Baumann, T; Delgado, J; Giné, E; González-Díaz, M; Hernández, J M; Colado, E; Payer, A R; Rayon, C; Navarro, B; José Terol, M; Bosch, F; Quesada, V; Puente, X S; López-Otín, C; Jares, P; Pereira, A; Campo, E; López-Guillermo, A

2012-12-06

280

Performance enhancing genetic variants, oxygen uptake, heart rate, blood pressure and body mass index of elite high altitude mountaineers.  

PubMed

Aim: To analyse and compare the ACE (angiotensin-converting enzyme), ACTN3 (actinin-3) and AMPD1 (adenosine monophosphate deaminase 1) genetic variants, oxygen uptake (VO2max), heart rate (HR), blood pressure (BP) and body mass index (BMI) of elite high altitude mountaineers and average athletes. Methods: Elite Bulgarian alpinists (n = 5) and control group of athletes (n = 72) were recruited. VO2max was measured using a treadmill graded protocol. HR, BP and BMI were recorded. Genotyping was done by polymerase chain reaction (PCR) amplification followed by agarose gel electrophoresis. Chi2-test and Fisher's exact test were used for statistical analysis. Results: Alpinists showed significantly higher frequencies of 60% ACE I allele (p = 0.002), 50% ACTN3 X allele (p = 0.032) and 30% AMPD1 T allele (p = 0.003) compared to controls - 39%, 36%, 13%, respectively. ACE ID genotype prevalence and null DD genotype were observed in mountaineers. Higher absolute VO2max, but no differences in VO2max ml kg-1 min-1, HR, oxygen pulse, blood pressure and BMI were found. Conclusions: The ID genotype and higher frequencies of ACE I allele could contribute to successful high altitude ascents in mountaineers. The genetic make-up of the two mountaineers who made the summit of Mt Everest was distinctive, revealing ACE ID genotype, mutant ACTN3 XX and AMPD1 TT genotypes. PMID:24058088

Djarova, Trayana; Bardarev, D; Boyanov, D; Kaneva, R; Atanasov, P

2013-09-01

281

Combinatorial Genetic Regulatory Network Analysis Tools for High Throughput Transcriptomic Data  

SciTech Connect

Abstract. A series of genome-scale algorithms and high-performance implementations is described and shown to be useful in the genetic analysis of gene transcription. With them it is possible to address common questions such as: "are the sets of genes co-expressed under one type of conditions the same as those sets co-expressed under another?" A new noise-adaptive graph algorithm, dubbed "paraclique," is introduced and analyzed for use in biological hypotheses testing. A notion of vertex coverage is also devised, based on vertex-disjoint paths within correlation graphs, and used to determine the identity, proportion and number of transcripts connected to individual phenotypes and quantitative trait loci (QTL) regulatory models. A major goal is to identify which, among a set of candidate genes, are the most likely regulators of trait variation. These methods are applied in an effort to identify multiple-QTL regulatory models for large groups of genetically co-expressed genes, and to extrapolate the consequences of this genetic variation on phenotypes observed across levels of biological scale through the evaluation of vertex coverage. This approach is furthermore applied to definitions of homology-based gene sets, and the incorporation of categorical data such as known gene pathways. In all these tasks discrete mathematics and combinatorial algorithms form organizing principles upon which methods and implementations are based. Keywords: Microarray Analysis, Putative Co-Regulation, Quantitative Trait Loci, Regulatory Models.

Chesler, Elissa J [ORNL; Langston, Michael A [University of Tennessee, Knoxville (UTK)

2006-05-01

282

The Genetic Structure of Iceland  

Microsoft Academic Search

Gene frequencies and parent-offspring migration data from nine geographic subdivisions in Iceland are analyzed. Estimated values of FST show high genetic homogeneity. Genetic maps are studied and the results are interpreted in the light of social and historical patterns. Actual road distances between subdivisions provide a slightly better indication of geographic isolation by distance than do straight-line distances. A high

L. B. Jorde; A. w. Eriksson; K. Morgan; P. L. Workman

1982-01-01

283

Potential Vulnerability Markers within the Affective Domain in Subjects at Genetic and Clinical High Risk for Schizophrenia  

Microsoft Academic Search

Background: Relative to ample high-risk studies on neurocognitive function, only a few high-risk studies have examined affective functioning components as possible vulnerability markers. In this study, we comprehensively assessed baseline affective functioning in subjects at clinical high risk (CHR) and genetic high risk (GHR) for schizophrenia, and healthy controls (HC), and compared the results to elucidate possible vulnerability markers in

Seung Jae Lee; So Young Yoo; Do-Hyung Kang; Kyung Jin Lee; Tae Hyun Ha; Whee Wee; Ae-Ra Lee; Nam Sick Kim; Jun Soo Kwon

2008-01-01

284

High-precision genetic mapping of behavioral traits in the diversity outbred mouse population  

PubMed Central

Historically our ability to identify genetic variants underlying complex behavioral traits in mice has been limited by low mapping resolution of conventional mouse crosses. The newly developed Diversity Outbred (DO) population promises to deliver improved resolution that will circumvent costly fine-mapping studies. The DO is derived from the same founder strains as the Collaborative Cross (CC), including three wild-derived strains. Thus the DO provides more allelic diversity and greater potential for discovery compared to crosses involving standard mouse strains. We have characterized 283 male and female DO mice using open-field, light–dark box, tail-suspension and visual-cliff avoidance tests to generate 38 behavioral measures. We identified several quantitative trait loci (QTL) for these traits with support intervals ranging from 1 to 3 Mb in size. These intervals contain relatively few genes (ranging from 5 to 96). For a majority of QTL, using the founder allelic effects together with whole genome sequence data, we could further narrow the positional candidates. Several QTL replicate previously published loci. Novel loci were also identified for anxiety- and activity-related traits. Half of the QTLs are associated with wild-derived alleles, confirming the value to behavioral genetics of added genetic diversity in the DO. In the presence of wild-alleles we sometimes observe behaviors that are qualitatively different from the expected response. Our results demonstrate that high-precision mapping of behavioral traits can be achieved with moderate numbers of DO animals, representing a significant advance in our ability to leverage the mouse as a tool for behavioral genetics

Logan, R W; Robledo, R F; Recla, J M; Philip, V M; Bubier, J A; Jay, J J; Harwood, C; Wilcox, T; Gatti, D M; Bult, C J; Churchill, G A; Chesler, E J

2013-01-01

285

High-density SNP-based genetic map development and linkage disequilibrium assessment in Brassica napus L  

PubMed Central

Background High density genetic maps built with SNP markers that are polymorphic in various genetic backgrounds are very useful for studying the genetics of agronomical traits as well as genome organization and evolution. Simultaneous dense SNP genotyping of segregating populations and variety collections was applied to oilseed rape (Brassica napus L.) to obtain a high density genetic map for this species and to study the linkage disequilibrium pattern. Results We developed an integrated genetic map for oilseed rape by high throughput SNP genotyping of four segregating doubled haploid populations. A very high level of collinearity was observed between the four individual maps and a large number of markers (>59%) was common to more than two maps. The precise integrated map comprises 5764 SNP and 1603 PCR markers. With a total genetic length of 2250 cM, the integrated map contains a density of 3.27 markers (2.56 SNP) per cM. Genotyping of these mapped SNP markers in oilseed rape collections allowed polymorphism level and linkage disequilibrium (LD) to be studied across the different collections (winter vs spring, different seed quality types) and along the linkage groups. Overall, polymorphism level was higher and LD decayed faster in spring than in “00” winter oilseed rape types but this was shown to vary greatly along the linkage groups. Conclusions Our study provides a valuable resource for further genetic studies using linkage or association mapping, for marker assisted breeding and for Brassica napus sequence assembly and genome organization analyses.

2013-01-01

286

Second-generation high-throughput forward genetic screen in mice to isolate subtle behavioral mutants  

PubMed Central

Forward genetic screens have been highly successful in revealing roles of genes and pathways in complex biological events. Traditionally these screens have focused on isolating mutants with the greatest phenotypic deviance, with the hopes of discovering genes that are central to the biological event being investigated. Behavioral screens in mice typically use simple activity-based assays as endophenotypes for more complex emotional states of the animal. They generally set the selection threshold for a putative mutant at 3 SDs (z score of 3) from the average behavior of normal animals to minimize false-positive results. Behavioral screens using a high threshold for detection have generally had limited success, with high false-positive rates and subtle phenotypic differences that have made mapping and cloning difficult. In addition, targeted reverse genetic approaches have shown that when genes central to behaviors such as open field behavior, psychostimulant response, and learning and memory tasks are mutated, they produce subtle phenotypes that differ from wild-type animals by 1 to 2 SDs (z scores of 1 to 2). We have conducted a second-generation (G2) dominant N-ethyl-N-nitrosourea (ENU) screen especially designed to detect subtle behavioral mutants for open field activity and psychostimulant response behaviors. We successfully detect mutant lines with only 1 to 2 SD shifts in mean response compared with wild-type control animals and present a robust statistical and methodological framework for conducting such forward genetic screens. Using this methodology we have screened 229 ENU mutant lines and have identified 15 heritable mutant lines. We conclude that for screens in mice that use activity-based endophenotypic measurements for complex behavioral states, this G2 screening approach yields better results.

Kumar, Vivek; Kim, Kyungin; Joseph, Chryshanthi; Thomas, Lisa C.; Hong, Heekyung; Takahashi, Joseph S.

2011-01-01

287

Molecular Evidence For High Levels of Intrapopulation Genetic Diversity in Woodrats (Neotoma Micropus)  

PubMed Central

Nucleotide sequences from the mitochondrial control region and genotypes from 5 nuclear microsatellite loci were used to examine genetic structure and infer recent (within approximately the last 3,000 years) evolutionary history of a population (549 individuals) of the southern plains woodrat (Neotoma micropus). Observed heterozygosity values ranged from 0.61 to 0.89 across microsatellite loci and systematically were lower than expected heterozygosity values (0.66–0.95). Probability of unique identity using microsatellite data was high (1 individual in 66,005,424). Fifty-three mitochondrial haplotypes were obtained from 150 individuals. FST values estimated from sequence and microsatellite data were 0.061 and 0.011, respectively, and the RST for microsatellite data was 0.007. Within-group genetic variation ranged from 93.90% to 99.99% depending on whether sequence or microsatellite data were examined. Analyses of microsatellite data suggested that all sampled individuals belonged to a single population, albeit genetically diverse. However, combined data analyses suggested the presence of low levels of substructure attributable to maternal lineages within the population. Low nucleotide-diversity values (0.007–0.010) in addition to high haplotype-diversity values (0.915–0.933) indicate a high number of closely related haplotypes, and suggest that this population may have undergone a recent expansion. However, Fu's FS statistic did not fully support this finding, because it did not reveal a significant excess of recent mutations. A phylogenetic approach using the haplotype sequence data and a combined set including both haplotype and genotype data was used to test for evolutionary patterns and history.

Mendez-Harclerode, Francisca M.; Strauss, Richard E.; Fulhorst, Charles F.; Milazzo, Mary L.; Ruthven, Donald C.; Bradley, Robert D.

2009-01-01

288

High-Significance Averages of Event-Related Potential Via Genetic Programming  

NASA Astrophysics Data System (ADS)

In this paper we use register-based genetic programming with memory-with memory to discover probabilistic membership functions that are used to divide up data-sets of event-related potentials recorded via EEG in psycho-physiological experiments based on the corresponding response times. The objective is to evolve membership functions which lead to maximising the statistical significance with which true brain waves can be reconstructed when averaging the trials in each bin. Results show that GP can significantly improve the fidelity with which ERP components can be recovered.

Citi, Luca; Poli, Riccardo; Cinel, Caterina

289

Healthy working school teachers with high effort-reward-imbalance and overcommitment show increased pro-inflammatory immune activity and a dampened innate immune defence.  

PubMed

To test whether chronic work stress is accompanied by altered immune functioning, changes in lymphocyte subsets and in lymphocyte production of cytokines were examined in reaction to acute psychosocial stress. Work stress was measured according to Siegrist's effort-reward-imbalance (ERI) model. ERI reflects stress due to a lack of reciprocity between costs and gains at work. Overcommitment (OC) is conceptualized as a dysfunctional coping pattern mainly characterized by the inability to withdraw from work obligations. Fifty-five healthy teachers (34 women, 21 men, mean age 50.0 ± 8.47 years) were exposed to a standardized laboratory stressor (Trier Social Stress Test). Lymphocyte subset counts and lymphocyte production of tumor-necrosis-factor (TNF)-?, interferon (IFN)-?, interleukin (IL)-2, -4, -6 and -10 were measured before and after challenge. High levels of ERI and OC were associated with lower natural killer (NK) cell (CD16+/56+) numbers whereas high levels of OC were related to a lower increase in T-helper cells (CD4+) after stress. Furthermore, subjects with higher ERI showed an overall increased pro-inflammatory activity, with higher TNF-? production at both time points and elevated pre-stress IL-6 production. IL-10 production decreased with higher ERI after stress. The ratios of TNF-?/IL-10 and IL-6/IL-10 were significantly increased in subjects high on ERI. Finally, OC was associated with higher IL-2 production post-stress. The present findings suggest a dampened innate immune defence, reflected in lower NK cell numbers together with an increased pro-inflammatory activity in teachers high on ERI and OC. Such pathways could partly be responsible for the increased vulnerability for stress-related diseases in individuals suffering from chronic work stress. PMID:20599495

Bellingrath, Silja; Rohleder, Nicolas; Kudielka, Brigitte M

2010-07-03

290

An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce  

PubMed Central

We have generated an ultra-high-density genetic map for lettuce, an economically important member of the Compositae, consisting of 12,842 unigenes (13,943 markers) mapped in 3696 genetic bins distributed over nine chromosomal linkage groups. Genomic DNA was hybridized to a custom Affymetrix oligonucleotide array containing 6.4 million features representing 35,628 unigenes of Lactuca spp. Segregation of single-position polymorphisms was analyzed using 213 F7:8 recombinant inbred lines that had been generated by crossing cultivated Lactuca sativa cv. Salinas and L. serriola acc. US96UC23, the wild progenitor species of L. sativa. The high level of replication of each allele in the recombinant inbred lines was exploited to identify single-position polymorphisms that were assigned to parental haplotypes. Marker information has been made available using GBrowse to facilitate access to the map. This map has been anchored to the previously published integrated map of lettuce providing candidate genes for multiple phenotypes. The high density of markers achieved in this ultradense map allowed syntenic studies between lettuce and Vitis vinifera as well as other plant species.

Truco, Maria Jose; Ashrafi, Hamid; Kozik, Alexander; van Leeuwen, Hans; Bowers, John; Wo, Sebastian Reyes Chin; Stoffel, Kevin; Xu, Huaqin; Hill, Theresa; Van Deynze, Allen; Michelmore, Richard W.

2013-01-01

291

Genetic evidence suggests that homosporous ferns with high chromosome numbers are diploid  

PubMed Central

Homosporous ferns have usually been considered highly polyploid because they have high chromosome numbers (average n = 57.05). In angiosperms, species with chromosome numbers higher than n = 14 generally have more isozymes than those with lower numbers, consistent with their polyploidy. By extrapolation, homosporous ferns would be expected to have many isozymes. However, ongoing surveys indicate that within fern genera, species having the lowest chromosome numbers have the number of isozymes considered typical of diploid seed plants. Only species above these lowest numbers have additional isozymes. Therefore, homosporous ferns either have gone through repeated cycles of polyploidy and gene silencing or were initiated with relatively high chromosome numbers. The latter possibility represents a radical departure from currently advocated hypotheses of fern evolution and suggests that there may be fundamental differences between the genomes of homosporous ferns and those of higher plants. These hypotheses can be tested by genetic, karyological, and molecular techniques. Images

Haufler, Christopher H.; Soltis, Douglas E.

1986-01-01

292

Tissue-specific adherent Enterococcus faecalis strains that show highly efficient adhesion to human bladder carcinoma T24 cells also adhere to extracellular matrix proteins.  

PubMed

The ability of Enterococcus faecalis clinical isolates to adhere to immobilized extracellular matrixes (ECMs) coating the walls of microtiter plates was examined by microscopy. The ECMs consisted of fibronectin, laminin, collagen types I, II, IV, and V, fibrinogen, and lactoferrin. With the exception of fibrinogen, each isolate showed a different level of adherence to each of the ECMs. No significant level of adherence to fibrinogen was observed for any isolate. The tissue-specific adhesive strains AS11, AS12, AS14, AS15, HT11, and HT12, which showed highly efficient adherence to human bladder carcinoma T24 cells and human bladder epithelial cells, showed strong adherence to fibronectin, laminin, and collagen type I, II, IV, and V ECMs, and the levels were greater than 10(4) cells/mm2 of well surface coated by ECM. None of the isolates that showed little adherence to human bladder carcinoma T24 cells showed efficient adherence to all the ECMs. The levels of adherence of gelatinase-producing isolates to the collagens were lower than the levels of adherence of gelatinase-negative isolates. When tissue-specific adhesive strains that adhered strongly to each ECM were preincubated with fibronectin, the adherence of the strains to fibronectin was inhibited, but the adherence of the strains to collagen type IV was not inhibited. Likewise, preincubation with collagen type IV inhibited adherence to collagen type IV but not adherence to fibronectin. All of the E. faecalis isolates were shown to carry the ace gene by PCR analysis performed with specific primers for collagen binding domain A of ace. The ace gene encodes Ace (adhesin of collagen from enterococci). The prtF gene of group A streptococci, which encodes the fibronectin binding protein of group A streptococci, was not detected in the tissue-specific adhesive strains by Southern analysis performed with the prtF probe of the Streptococcus pyogenes JRS4 strain. Mutants with altered collagen binding were isolated by insertion of Tn916 into the chromosome of tissue-specific adhesive strain AS14. The number of mutant adhesive bacterial cells that adhered to collagen and also to laminin was 1 or 2 orders lower than the number observed for the wild-type strain, but the level of adherence to fibronectin remained the same as that of the wild-type strain. PMID:15385489

Tomita, Haruyoshi; Ike, Yasuyoshi

2004-10-01

293

Pyrogallol[4]arenes show highly variable amphiphilic behavior at the air-water interface dependent upon side chain length and branching.  

PubMed

The behavior of pyrogallol[4]arenes (Pgs) substituted with normal and branched alkyl side chains at the air-water interface was examined on a Langmuir trough. The amphiphilic systems studied form stable monolayers when the straight chains are as short as n-propyl. Remarkably, n-propylpyrogallol[4]arene shows a behavior at the air-water interface that is indistinguishable from that of pyrogallolarenes bearing n-hexyl, n-nonyl, and n-dodecyl side chains. There is no report of amphiphilic side-chain-length dependence or Langmuir trough behavior for families of branched alkyl chain calixarenes or resorcinarenes. In the Pg family reported here, Pgs with straight chains (except for methyl and ethyl) behave very similarly to each other and very differently from symmetrical branched chain analogues having the same total number of carbon atoms. For example, the shortest possible branched side chain of a Pg, isopropyl-Pg, forms stable monolayers by a unique molecular subduction mechanism. Isopropyl-Pg (dimethylmethyl side chain, iPrPg) and 3-pentyl-Pg (diethylmethyl side chain, 3-pentylPg) both show high levels of organization, albeit by quite different mechanisms, at the air-water interface. Both iPrPg and 3-pentylPg differ in behavior from 4-heptylPg. Brewster angle microscopy revealed differences in organization of the Pgs that supports the mechanistic suggestions offered herein. PMID:21688332

Daschbach, Megan M; Kulikov, Oleg V; Long, Elizabeth F; Gokel, George W

2011-06-17

294

Resistance to listeriosis in two lines of mice genetically selected for high and low antibody production.  

PubMed Central

Infection by the intracellular parasite Listeria monocytogenes was studied in two inbred lines of mice genetically selected for high and low antibody production against xenogeneic red blood cells. It was revealed that, during the early non-specific phase of infection, bacterial growth in tissues was significantly enhanced in high responder (HR) mice, as opposed to low responder (LR) mice. This is interpreted as the in vivo expression of a genetic impairment of the bactericidal activity of resident macrophages in this line of mice. After Day 2 of infection, the kinetics of bacterial growth in the spleen and the liver was almost identical in the two lines, indicating that mice from both lines generated efficient anti-Listeria immunity. This was confirmed by the fact that no interline difference could be detected in the expression of T-cell mediated immunity, as estimated by the production of protective T cells and delayed sensitivity T cells, and by the level of immunological memory. The genetic impairment in the bactericidal activity of resident macrophages resulted in a significant increase of anti-Listeria antibody production in HR mice and did not prevent T-dependent activation of effector macrophages mobilized in infectious sites. This explains that the overall resistance to listeriosis was similar in LR and HR mice, as shown by the LD50 values respectively estimated as 2.2 X 10(5) and 3.8 X 10(5) bacteria per mouse. This natural resistance was expressed at the same level as that of C57BL/6 mice.

Berche, P A

1985-01-01

295

Wavelets meet genetic imaging  

NASA Astrophysics Data System (ADS)

Genetic image analysis is an interdisciplinary area, which combines microscope image processing techniques with the use of biochemical probes for the detection of genetic aberrations responsible for cancers and genetic diseases. Recent years have witnessed parallel and significant progress in both image processing and genetics. On one hand, revolutionary multiscale wavelet techniques have been developed in signal processing and applied mathematics in the last decade, providing sophisticated tools for genetic image analysis. On the other hand, reaping the fruit of genome sequencing, high resolution genetic probes have been developed to facilitate accurate detection of subtle and cryptic genetic aberrations. In the meantime, however, they bring about computational challenges for image analysis. In this paper, we review the fruitful interaction between wavelets and genetic imaging. We show how wavelets offer a perfect tool to address a variety of chromosome image analysis problems. In fact, the same word "subband" has been used in the nomenclature of cytogenetics to describe the multiresolution banding structure of the chromosome, even before its appearance in the wavelet literature. The application of wavelets to chromosome analysis holds great promise in addressing several computational challenges in genetics. A variety of real world examples such as the chromosome image enhancement, compression, registration and classification will be demonstrated. These examples are drawn from fluorescence in situ hybridization (FISH) and microarray (gene chip) imaging experiments, which indicate the impact of wavelets on the diagnosis, treatments and prognosis of cancers and genetic diseases.

Wang, Yu-Ping

2005-08-01

296

Two Different High Throughput Sequencing Approaches Identify Thousands of De Novo Genomic Markers for the Genetically Depleted Bornean Elephant  

PubMed Central

High throughput sequencing technologies are being applied to an increasing number of model species with a high-quality reference genome. The application and analyses of whole-genome sequence data in non-model species with no prior genomic information are currently under way. Recent sequencing technologies provide new opportunities for gathering genomic data in natural populations, laying the empirical foundation for future research in the field of conservation and population genomics. Here we present the case study of the Bornean elephant, which is the most endangered subspecies of Asian elephant and exhibits very low genetic diversity. We used two different sequencing platforms, the Roche 454 FLX (shotgun) and Illumina, GAIIx (Restriction site associated DNA, RAD) to evaluate the feasibility of the two methodologies for the discovery of de novo markers (single nucleotide polymorphism, SNPs and microsatellites) using low coverage data. Approximately, 6,683 (shotgun) and 14,724 (RAD) SNPs were detected within our elephant sequence dataset. Genotyping of a representative sample of 194 SNPs resulted in a SNP validation rate of ? 83 to 94% and 17% of the loci were polymorphic with a low diversity (Ho?=?0.057). Different numbers of microsatellites were identified through shotgun (27,226) and RAD (868) techniques. Out of all di-, tri-, and tetra-microsatellite loci, 1,706 loci had sufficient flanking regions (shotgun) while only 7 were found with RAD. All microsatellites were monomorphic in the Bornean but polymorphic in another elephant subspecies. Despite using different sample sizes, and the well known differences in the two platforms used regarding sequence length and throughput, the two approaches showed high validation rate. The approaches used here for marker development in a threatened species demonstrate the utility of high throughput sequencing technologies as a starting point for the development of genomic tools in a non-model species and in particular for a species with low genetic diversity.

Sharma, Reeta; Goossens, Benoit; Kun-Rodrigues, Celia; Teixeira, Tatiana; Othman, Nurzhafarina; Boone, Jason Q.; Jue, Nathaniel K.; Obergfell, Craig; O'Neill, Rachel J.; Chikhi, Lounes

2012-01-01

297

Highly lytic and persistent lentiviruses naturally present in sheep with progressive pneumonia are genetically distinct.  

PubMed Central

Ovine and caprine lentiviruses share the capacity to induce slowly progressive and inflammatory diseases of the central nervous system (leukoencephalitis or visna), lungs (progressive pneumonia or maedi), and joints (arthritis) in their natural hosts. Studies on their replication indicated that ovine lentiviruses and caprine arthritis-encephalitis virus (CAEV) recently isolated in the United States establish persistent infection in ovine and caprine fibroblasts, whereas older prototype ovine lentiviruses such as Icelandic visna virus or American progressive pneumonia virus irreversibly lyse fibroblast cultures. Since all of the recent isolates were found to be persistent, Narayan et al. (J. Gen. Virol. 59:345-356, 1982) concluded that the highly lytic viruses were only tissue-culture-adapted strains. In the present report, we isolated new ovine lentiviruses from French sheep with naturally occurring progressive pneumonia which are either highly lytic (five isolates), as are the Icelandic strains of visna virus, or persistent (one isolate), as are CAEV or American persistent ovine lentiviruses. Protein and nucleic acid content analyses of these new highly lytic (type I) and persistent (type II) isolates indicated that type I and type II ovine lentiviruses were genetically distinct, type I and type II viruses being closely related to the Icelandic strains of visna virus and to CAEV, respectively. We conclude that (i) highly lytic ovine lentiviruses, such as the Icelandic prototype strains of visna virus and persistent lentiviruses more related to CAEV, are naturally present in the ovine species, and (ii) irreversible cell lysis induced by highly lytic viruses does not result from a tissue culture adaptation of field isolates that were originally persistent but is instead the consequence of a genetic content distinct from that of persistent viruses. Images

Querat, G; Barban, V; Sauze, N; Filippi, P; Vigne, R; Russo, P; Vitu, C

1984-01-01

298

An fMRI study of language processing in people at high genetic risk for schizophrenia  

PubMed Central

Background Abnormalities in language processing and the related brain structures have been reported in people with schizophrenia. It has been proposed that the brain pathways for language processing are anomalous in these individuals and form the underlying basis for the positive symptoms of the illness. If language pathway abnormalities can be detected early in people at high-risk for schizophrenia prior to the onset of symptoms, early treatment can ensue. Methods Fifteen young adults at high genetic risk for developing schizophrenia were compared with 15 of their siblings with schizophrenia or schizoaffective disorder and 15 age and sex matched individuals at low risk for schizophrenia using a visual lexical decision task during fMRI. The data were analyzed by contrasting activation obtained during a real word–pseudoword discrimination task to activation obtained during a nonlinguistic discrimination task, and the differential activations were examined. Results Patterns of brain activation while reading and discriminating between real and pseudowords differed across groups, with more bilateral activation in schizophrenia patients and their high-risk siblings than controls. In control subjects discrimination of words from psuedowords significantly activated Brodmann’s area 44 more strongly than when non-linguistic symbols were discriminated. However, high-risk subjects and their siblings with schizophrenia activated this region similarly for both language and non-language tasks. Conclusions Normal individuals can be distinguished from subjects at high genetic risk for schizophrenia and patients with schizophrenia by their more lateralized and stronger activation of Brodmann’s area 44 to word compared with symbol discrimination tasks. Thus, evaluation of language processing by fMRI may be a valuable tool for use in the prediction of individual risk for developing schizophrenia.

Li, Xiaobo; Branch, Craig A.; Bertisch, Hilary C.; Brown, Kyle; Szulc, Kamila U.; Ardekani, Babak A.; DeLisi, Lynn E.

2007-01-01

299

Evidence of high genetic variation among linguistically diverse populations on a micro-geographic scale: a case study of the Italian Alps.  

PubMed

Although essential for the fine-scale reconstruction of genetic structure, only a few micro-geographic studies have been carried out in European populations. This study analyzes mitochondrial variation (651 bp of the hypervariable region plus 17 single-nucleotide polymorphisms) in 393 samples from nine populations from Trentino (Eastern Italian Alps), a small area characterized by a complex geography and high linguistic diversity. A high level of genetic variation, comparable to geographically dispersed European groups, was observed. We found a difference in the intensity of peopling processes between two longitudinal areas, as populations from the west-central part of the region show stronger signatures of expansion, whereas those from the eastern area are closer to the expectations of a stationary demographic state. This may be explained by geomorphological factors and is also supported by archeological data. Finally, our results reveal a striking difference in the way in which the two linguistically isolated populations are genetically related to the neighboring groups. The Ladin speakers were found to be genetically close to the Italian-speaking populations and differentiated from the other Dolomitic Ladins, whereas the German-speaking Cimbri behave as an outlier, showing signatures of founder effects and low growth rate. PMID:22418692

Coia, Valentina; Boschi, Ilaria; Trombetta, Federica; Cavulli, Fabio; Montinaro, Francesco; Destro-Bisol, Giovanni; Grimaldi, Stefano; Pedrotti, Annaluisa

2012-03-15

300

An unusual BRCA mutation distribution in a high risk cancer genetics clinic.  

PubMed

The Database of Individuals at High Risk for Breast, Ovarian, or Other Hereditary Cancers at the Arizona Cancer Center in Tucson, Arizona assesses cancer risk factors and outcomes in patients with a family history of cancer or a known genetic mutation. We analyzed the subset of clinic probands who carry deleterious BRCA gene mutations to identify factors that could explain why mutations in BRCA2 outnumber those in BRCA1. Medical, family, social, ethnic and genetic mutation histories were collected from consenting patients' electronic medical records. Differences between BRCA1 and BRCA2 probands from this database were analyzed for statistical significance and compared to published analyses. A significantly higher proportion of our clinic probands carry mutations in BRCA2 than BRCA1, compared with previous reports of mutation prevalence. This also holds true for the Hispanic sub-group. Probands with BRCA2 mutations were significantly more likely than their BRCA1 counterparts to present to the high risk clinic without a diagnosis of cancer. Other differences between the groups were not significant. Six previously unreported BRCA2 mutations appear in our clinic population. The increased proportion of probands carrying deleterious BRCA2 mutations is likely multifactorial, but may reflect aspects of Southern Arizona's unique ethnic heritage. PMID:23179792

Nelson-Moseke, Anna C; Jeter, Joanne M; Cui, Haiyan; Roe, Denise J; Chambers, Setsuko K; Laukaitis, Christina M

2013-03-01

301

New disease gene location and high genetic heterogeneity in idiopathic scoliosis  

PubMed Central

Idiopathic scoliosis (IS) is a spine disorder of unknown origin with 1.5–3% prevalence in the general population. Besides the large multifactorial-form sample of IS, there is a good evidence for the existence of a monogenic subgroup in which the disease is inherited in a dominant manner. However, results from literature suggest a strong heterogeneity in the locations of the mutated genes. Using a high-resolution genome-wide scan, we performed linkage analyses in three large multigenerational IS families compatible with dominant inheritance including 9–12 affected members or obligate carriers. In two of these families, our results suggested intra-familial genetic heterogeneity, whereas, in the other, we observed a perfect marker disease co-segregation in two regions at 3q12.1 and 5q13.3. We can state that one of these two locations is a novel IS disease gene locus, as the probability of having this perfect co-segregation twice by chance in the genome is very low (P=0.001). Lastly, in all three families studied, linkage to the previously mapped dominant IS loci on chromosomes 19p13.3, 17p11.2, 9q34, 17q25 and 18q is unlikely, confirming that there is a high genetic heterogeneity within the subgroup of dominant forms of IS.

Edery, Patrick; Margaritte-Jeannin, Patricia; Biot, Bernard; Labalme, Audrey; Bernard, Jean-Claude; Chastang, Joelle; Kassai, Behrouz; Plais, Marie-Helene; Moldovan, Florina; Clerget-Darpoux, Francoise

2011-01-01

302

High prevalence of genetically diverse Borrelia bavariensis-like strains in Ixodes persulcatus from Selenge Aimag, Mongolia.  

PubMed

In Mongolia, Lyme borreliosis was first reported in 2003. To determine which Borrelia species may contribute to the occurrence of Lyme borreliosis in Mongolia, real-time PCR was conducted on 372 adult Ixodes persulcatus ticks collected in Selenge Aimag, the province with the highest incidence of human Lyme borreliosis. 24.5% of ticks were identified to be positive for Borrelia burgdorferi sensu lato DNA. Species differentiation using an SNP-based real-time PCR and multi-locus sequence analysis revealed that strains phylogenetically closely related to B. bavariensis (previously known as B. garinii OspA serotype 4) is the most prevalent species, showing an unexpectedly high genetic diversity. PMID:23084366

Scholz, Holger C; Margos, G; Derschum, H; Speck, S; Tserennorov, D; Erdenebat, N; Undraa, B; Enkhtuja, M; Battsetseg, J; Otgonchimeg, C; Otgonsuren, G; Nymadulam, B; Römer, A; Thomas, A; Essbauer, S; Wölfel, R; Kiefer, D; Zöller, L; Otgonbaatar, D; Fingerle, V

2012-10-16

303

Genetic variation within the HLA class III influences T1D susceptibility conferred by high risk HLA haplotypes  

PubMed Central

HLA class II DRB1 and DQB1 represent the major type 1 diabetes (T1D) genetic susceptibility loci; however, other genes in the HLA region are also involved in T1D risk. We analyzed 1411 pedigrees (2865 affected individuals) from the type 1 diabetes genetics consortium (T1DGC) genotyped for HLA classical loci and for 12 SNPs in the class III region previously shown to be associated with T1D in a subset of 886 pedigrees. Using the transmission disequilibrium test, we compared the proportion of SNP alleles transmitted from within the high risk DR3 and DR4 haplotypes to affected offspring. Markers rs4151659 (mapping to CFB) and rs7762619 (mapping 5? of LTA) were the most strongly associated with T1D on DR3 (p=1.2 × 10?9 and p=2 × 10?12 respectively) and DR4 (p=4 × 10?15 and p= 8 × 10?8 respectively) haplotypes. They remained significantly associated after stratifying individuals in analyses for B*1801, A*0101-B*0801, DPB1*0301, DPB1*0202, DPB1*0401 or DPB1*0402. Rs7762619 and rs4151659 are in strong linkage disequilibrium (LD) (r2=0.82) with each other, but a joint analysis showed that the association for each SNP was not solely due to LD. Our data support a role for more than one locus in the class III region contributing to risk of T1D.

Valdes, Ana M; Thomson, Glenys; Barcellos, Lisa F

2009-01-01

304

Advanced methods for high-throughput microscopy screening of genetically modified yeast libraries.  

PubMed

High-throughput methodologies have created new opportunities for studying biological phenomena in an unbiased manner. Using automated cell manipulations and microscopy platforms, it is now possible to easily screen entire genomes for genes that affect any cellular process that can be visualized. The onset of these methodologies promises that the near future will bring with it a more comprehensive and richly integrated understanding of complex and dynamic cellular structures and processes. In this review, we describe how to couple systematic genetic tools in the budding yeast Saccharomyces cerevisiae alongside robotic visualization systems to attack biological questions. The combination of high-throughput microscopy screens with the powerful, yet simple, yeast model system for studying the eukaryotic cell should pioneer new knowledge in all areas of cell biology. PMID:21877281

Cohen, Yifat; Schuldiner, Maya

2011-01-01

305

A High-Density Simple Sequence Repeat-Based Genetic Linkage Map of Switchgrass  

PubMed Central

Switchgrass (Panicum virgatum) has been identified as a promising cellulosic biofuel crop in the United States. Construction of a genetic linkage map is fundamental for switchgrass molecular breeding and the elucidation of its genetic mechanisms for economically important traits. In this study, a novel population consisting of 139 selfed progeny of a northern lowland genotype, NL 94 LYE 16X13, was used to construct a linkage map. A total of 2493 simple sequence repeat markers were screened for polymorphism. Of 506 polymorphic loci, 80.8% showed a goodness-of-fit of 1:2:1 segregation ratio. Among 469 linked loci on the framework map, 241 coupling vs. 228 repulsion phase linkages were detected that conformed to a 1:1 ratio, confirming disomic inheritance. A total of 499 loci were mapped to 18 linkage groups (LG), of which the cumulative length was 2085.2 cM, with an average marker interval of 4.2 cM. Nine homeologous LG pairs were identified based on multi-allele markers and comparative genomic analysis. Two clusters of segregation-distorted loci were identified on LG 5b and 9b, respectively. Comparative analysis indicated a one-to-one relationship between nine switchgrass homeologous groups and nine foxtail millet (Setaria italica) chromosomes, suggesting strong homology between the two species. The linkage map derived from selfing a heterozygous parent, instead of two separate maps usually constructed for a cross-fertilized species, provides a new genetic framework to facilitate genomics research, quantitative trait locus (QTL) mapping, and marker-assisted breeding.

Liu, Linglong; Wu, Yanqi; Wang, Yunwen; Samuels, Tim

2012-01-01

306

Genetic structure in four West African population groups  

Microsoft Academic Search

BACKGROUND: Africa contains the most genetically divergent group of continental populations and several studies have reported that African populations show a high degree of population stratification. In this regard, it is important to investigate the potential for population genetic structure or stratification in genetic epidemiology studies involving multiple African populations. The presences of genetic sub-structure, if not properly accounted for,

Adebowale A Adeyemo; Guanjie Chen; Yuanxiu Chen; Charles Rotimi

2005-01-01

307

Construction of a high-throughput rat genetic mapping system with 466 arbitrarily primed-representational difference analysis markers  

Microsoft Academic Search

.   Linkage mapping of quantitative trait loci (QTLs) requires genetic markers that can be efficiently genotyped for a large\\u000a number of individuals. To isolate genetic markers suitable for this purpose, we previously established the arbitrarily primed\\u000a RDA (AP-RDA) method. Dot-blotting AP-PCR products (AP-amplicons) onto filters at a high density and hybridization of the filters\\u000a with the AP-RDA markers made it

Satoshi Yamashita; Yukinari Yoshida; Ayako Kurahashi; Takashi Sugimura; Toshikazu Ushijima

2000-01-01

308

Characterization of genetic lesions in rhabdomyosarcoma using a high-density single nucleotide polymorphism array.  

PubMed

Rhabdomyosarcoma (RMS) is a common solid tumor in childhood divided into two histological subtypes, embryonal (ERMS) and alveolar (ARMS). The ARMS subtype shows aggressive clinical behavior with poor prognosis, while the ERMS subtype has a more favorable outcome. Because of the rarity, diagnostic diversity and heterogeneity of this tumor, its etiology remains to be completely elucidated. Thus, to identify genetic alterations associated with RMS development, we performed single nucleotide polymorphism array analyses of 55 RMS samples including eight RMS-derived cell lines. The ERMS subtype was characterized by hyperploidy, significantly associated with gains of chromosomes 2, 8 and 12, whereas the majority of ARMS cases exhibited near-diploid copy number profiles. Loss of heterozygosity of 15q was detected in 45.5% of ARMS that had been unrecognized in RMS to date. Novel amplifications were also detected, including IRS2 locus in two fusion-positive tumors, and KRAS or NRAS loci in three ERMS cases. Of note, gain of 13q was significantly associated with good patient outcome in ERMS. We also identified possible application of an ALK inhibitor to RMS, as ALK amplification and frequent expression of ALK were detected in our RMS cohort. These findings enhance our understanding of the genetic mechanisms underlying RMS pathogenesis and support further studies for therapeutic development of RMS. PMID:23578105

Nishimura, Riki; Takita, Junko; Sato-Otsubo, Aiko; Kato, Motohiro; Koh, Katsuyoshi; Hanada, Ryoji; Tanaka, Yukichi; Kato, Keisuke; Maeda, Daichi; Fukayama, Masashi; Sanada, Masashi; Hayashi, Yasuhide; Ogawa, Seishi

2013-05-23

309

Isolation of Bacillus subtilis (chungkookjang), a poly-gamma-glutamate producer with high genetic competence.  

PubMed

A bacterium with high poly-gamma-glutamate (PGA) productivity was isolated from the traditional Korean seasoning, Chung-Kook-Jang. This bacterium could be classified as a Bacillus subtilis, but sporulation in culture was infrequent in the absence of Mn2+. It was judged to be a variety of B. subtilis and designated B. subtilis (chungkookjang). L-Glutamate significantly induced PGA production, and highly elongated PGAs were synthesized. The volumetric yield reached 13.5 mg ml(-1) in the presence of 2% L-glutamate. The D-glutamate content was over 50% in every PGA produced under the conditions used. During PGA production, glutamate racemase activity was found in the cells, suggesting that the enzyme is involved in the D-glutamate supply. Molecular sizes of PGAs were changed by the salt concentration in the medium; PGAs with comparatively low molecular masses were produced in culture media containing high concentrations of NaCl. B. subtilis (chungkookjang) harbors no plasmid and is the first B. subtilis strain reported with both naturally high PGA productivity and high genetic competence. PMID:11778891

Ashiuchi, M; Kamei, T; Baek, D H; Shin, S Y; Sung, M H; Soda, K; Yagi, T; Misono, H

2001-12-01

310

Historical and biological determinants of genetic diversity in the highly endemic triploid sea lavender Limonium dufourii (Plumbaginaceae).  

PubMed

Microsatellite markers were used to evaluate the genetic diversity and population genetic structure in the critically endangered Limonium dufourii (Plumbaginaceae), a highly endemic triploid species from the coasts of eastern Spain. Sixty-five alleles from 13 microsatellite regions were amplified in a sample of 122 individuals collected from the six extant populations. Microsatellite patterns were consistent with the triploid nature of L. dufourii. Alleles were unambiguously assigned to two different parental subgenomes in this hybrid species and the greater contribution of the diploid parental subgenome was confirmed. Eleven, 25 and 26 multilocus genotypes were recorded from the haploid, diploid and from the combined information of both subgenomes, respectively. Genetic diversity was mostly distributed among populations (72.06% of the total genetic variation). Genotypes from Marjal del Moro populations grouped into two highly structured clusters (88.41% of the total variance). The observed patterns of distribution of genetic diversity are interpreted to result from multiple hybridization events and isolation between populations. Threats to this species are mainly anthropogenic (urbanization and tourism pressure), although stochastic risks cannot be ignored. Therefore, in order to preserve extant genetic variation of L. dufourii, in situ strategies such as the preservation of its habitat are a high priority. Several recommendations in order to assist ex situ measures to guarantee the success of conservation strategies and maintain the relationships between individuals and populations are proposed. PMID:17850548

Palop-Esteban, M; Segarra-Moragues, J G; González-Candelas, F

2007-09-01

311

Development of highly efficient genetic transformation protocols for table grape Sugraone and Crimson Seedless.  

PubMed

Genetic engineering of grapevine is a powerful tool to study gene function as well as to introduce new traits into existing Vitis cultivars without altering their essential characters and identity. Agrobacterium-mediated transformation is one of the most efficient methods for gene transfer, but the efficiency of the procedure depends on several parameters such as the grapevine genotype, the selection strategy, the Agrobacterium strain, and concentration used to infect as well as the culture method among others. This chapter describes highly efficient genetic transformation protocols for seedless table grapevine cultivars Sugraone and Crimson Seedless by co-culturing embryogenic calli with Agrobacterium tumefaciens. The procedures are specific for each cultivar by adjusting the kanamycin concentration used to select transformed cells (20 mg/L and 50 mg/L kanamycin for Crimson Seedless and Sugraone, respectively) and the low Agrobacterium density used to infect the embryogenic calli (0.06 OD(600) being more effective for the transformation of Crimson Seedless and 0.2 OD(600) for Sugraone). Other factors that affect the transformation efficiency are the initial amount of embryogenic calli used to co-culture with Agrobacterium and the culture method of calli. PMID:22351012

Dabauza, Mercedes; Velasco, Leonardo

2012-01-01

312

A highly therapy-resistant case of B-cell lymphoma, unclassifiable, with features intermediate between diffuse large B-cell lymphoma and Burkitt lymphoma showing strong BCL2 staining, otherwise indistinguishable from Burkitt lymphoma.  

PubMed

B-cell lymphoma, unclassifiable, with features intermediate between diffuse large B-cell lymphoma and Burkitt lymphoma (iDLBCL/BL) is a newly categorized lymphoma in the WHO Classification of Tumors of Haematopoietic and Lymphoid Tissues v4. This lymphoma has characteristics of both DLBCL and BL, morphologically and genetically. We report a case with therapy-resistant iDLBCL/BL, which used to be categorized as BL in the WHO Classification v3. This case showed strong BCL2 staining, otherwise exhibiting features of BL. The case was treated with intensive chemotherapy containing high-dose methotrexate, cyclophosphamide, and cytarabine. However, soon after the chemotherapy, the lymphoma relapsed in the central nervous system and was resistant to whole-brain radiation therapy and allogeneic stem cell transplantation. The patient died 37 days after the transplantation. The clinical course was different from that of typical BL in terms of resistance to intensive chemotherapy, in agreement with the characteristics of iDLBCL/BL. PMID:21628859

Kurita, Naoki; Nishikii, Hidekazu; Nakamoto, Rie; Nakamura, Naoya; Kondo, Yuzuru; Okoshi, Yasushi; Suzukawa, Kazumi; Hasegawa, Yuichi; Yokoyama, Yasuhisa; Noguchi, Masayuki; Chiba, Shigeru

2011-01-01

313

Partnership to engage St. Louis high school students in investigative genetics.  

PubMed

The authors describe the Modern Genetics Project, based on a successful hands-on science implementation model that was developed and field-tested in St. Louis area high schools between 1992 and 1998. The project, begun in 1991, features a curriculum enhancement unit, "Modern Genetics for All Students," that combines strong scientific content, hands-on investigations, and human health applications, with reference to developing national and state science-teaching standards for this topic. The unit provides a significantly higher level of hands-on involvement throughout the school year for students than is found in traditional biology classrooms. This project aims to enhance scientific literacy among St. Louis high school students (all grades) of all learning levels and all socioeconomic, racial, and ethnic backgrounds; many of the students using the curriculum are from underrepresented minorities. This long-term project is carried out by a strong partnership among scientists at Washington University, implementation specialists from the Mathematics and Science Education Center of the Cooperating School Districts of St. Louis, project evaluators from Southern Illinois University at Edwardsville, and biology teachers at local high schools. Funding was originally from the National Institutes of Health and is now from the Howard Hughes Medical Institute. In 1998, there were 31 teachers and approximately 3,200 students participating in the project. Both quantitative and qualitative evaluations of the project during the 1995-96 and 1996-97 school years indicate that there were significant gains in knowledge and attitudes among the students of all racial, ethnic, and socioeconomic groups represented, and among both boys and girls. PMID:10219205

Moore, C J; May, V L; Abusharbain, E

1999-04-01

314

High genetic diversity in a rare and endangered sunflower as compared to a common congener  

Microsoft Academic Search

Determining the genetic structure of isolated or fragmented species is of critical importance when planning a suitable conservation strategy. In this study, we use nuclear and chloroplast SSRs (simple sequence repeats) to investigate the population genetics of an extremely rare sunflower, Helianthus verticillatus Small, which is known from only three locations in North America. We investigated levels of genetic diversity

J. R. ELLIS; C. H. PASHLEY; J. M. BURKE; D. E. M C CAULEY

2006-01-01

315

Structured Parenting of Toddlers at High versus Low Genetic Risk: Two Pathways to Child Problems  

ERIC Educational Resources Information Center

|Objective: Little is known about how parenting might offset genetic risk to prevent the onset of child problems during toddlerhood. We used a prospective adoption design to separate genetic and environmental influences and test whether associations between structured parenting and toddler behavior problems were conditioned by genetic risk for…

Leve, Leslie D.; Harold, Gordon T.; Ge, Xiaojia; Neiderhiser, Jenae M.; Shaw, Daniel; Scaramella, Laura V.; Reiss, David

2009-01-01

316

How Do Geneticists and Genetic Counselors Counsel Women from High-Risk Breast Cancer Families?  

Microsoft Academic Search

This qualitative study asked Australian Genetic Counselors and Clinical Geneticists working in cancer genetics to describe their practice when a woman attends a consultation about her family history and her risk of developing breast cancer. Twenty-nine out of 36 Clinical Geneticists\\/Genetic Counselors returned the questionnaire (82%). Participants identified the key goals of the consultation as (a) identifying the individual needs

Elizabeth Lobb; Phyllis Butow; Bettina Meiser; Katherine Tucker; Alexandra Barratt

2001-01-01

317

Two-dimensional and three-dimensional imaging show ciclesonide has high lung deposition and peripheral distribution: a nonrandomized study in healthy volunteers.  

PubMed

Drug deposition is an important factor that contributes to safety and efficacy outcomes of inhaled steroid therapy. Ciclesonide is a nonhalogenated, inhaled corticosteroid under investigation for the treatment of asthma. Therefore, this study was performed to assess lung deposition of ciclesonide. Technetium-99m (99mTc)-labeled ciclesonide (where the 99mTc-label is physically dissolved in the ciclesonide-hydrofluoroalkane [HFA] solution aerosol) inhaled by healthy volunteers was analyzed by two-dimensional (2-D) and three-dimensional (3-D) imaging to determine lung deposition. Six healthy volunteers inhaled one puff of 40 microg (exactuator, equivalent to 50 microg ex-valve) ciclesonide for 2-D imaging, and two healthy volunteers inhaled 10 puffs of 40 microg ciclesonide for 2-D and 3-D imaging. The ciclesonide aerosol was administered via metered-dose inhaler (MDI) containing HFA-134a as propellant. The ex-actuator mean (+/- standard deviation) deposition of ciclesonide in the lungs was higher (52% +/- 11%) than in the mouth/pharynx (38% +/- 14%). Two-dimensional and 3-D imaging showed that ciclesonide reached all regions of the lung. Mean percent deposition in peripheral regions (47% and 34%) was higher than in lower central regions (17% and 30%), as revealed by 3-D and 2-D imaging, respectively. Inhalation of up to 400 microg of ciclesonide produced no drug-related side effects. In conclusion, ciclesonide administered via metered-dose inhaler using HFA-134a as a propellant provided high lung deposition (>50%), greater distribution throughout peripheral regions of the lungs, and relatively low oropharyngeal deposition. PMID:16796536

Leach, Chet L; Bethke, Thomas D; Boudreau, Robert J; Hasselquist, Bruce E; Drollmann, Anton; Davidson, Patricia; Wurst, Wilhelm

2006-01-01

318

Males with high genetic similarity to females sire more offspring in sperm competition in Peron's tree frog Litoria peronii.  

PubMed

Recent work has confirmed that genetic compatibility among mates can be an important determinant of siring success in sperm competition experiments and in free-ranging populations. Most of this work points towards mate choice of less related mates. However, there may also be the potential for mate choice for intermediate or even genetically similar mates to prevent outbreeding depression or hybridization with closely related taxa. We studied relatedness effects on post-copulatory gametic choice and/or sperm competition in an external fertilizer, Peron's tree frog (Litoria peronii), since external fertilizers offer exceptional control in order to test gametic interaction effects on probability of paternity and zygote viability. Sperm competition experiments were done blindly with respect to genetic relatedness among males and females. Thereafter, paternity of offspring was assigned using eight microsatellite loci. Three hybridization trials between L. peronii and a closely related sympatric species Litoria tyleri were also carried out. In the sperm competition trials, males that are more genetically similar to the female achieved higher siring success compared with less genetically similar males. The hybridization trials confirmed that the two species can interbreed and we suggest that the risk of hybridization may contribute to selection benefits for genetically more similar males at fertilization. To our knowledge, this study is the first to show evidence for post-copulatory selection of sperm from genetically more similar individuals within a natural population. PMID:18230591

Sherman, C D H; Wapstra, E; Uller, T; Olsson, M

2008-04-22

319

Phase II Study of Flavopiridol in Relapsed Chronic Lymphocytic Leukemia Demonstrating High Response Rates in Genetically High-Risk Disease  

PubMed Central

Purpose Patients with chronic lymphocytic leukemia (CLL) with high-risk genomic features achieve poor outcomes with traditional therapies. A phase I study of a pharmacokinetically derived schedule of flavopiridol suggested promising activity in CLL, irrespective of high-risk features. Given the relevance of these findings to treating genetically high-risk CLL, a prospective confirmatory study was initiated. Patients and Methods Patients with relapsed CLL were treated with single-agent flavopiridol, with subsequent addition of dexamethasone to suppress cytokine release syndrome (CRS). High-risk genomic features were prospectively assessed for response to therapy. Results Sixty-four patients were enrolled. Median age was 60 years, median number of prior therapies was four, and all patients had received prior purine analog therapy. If patients tolerated treatment during week 1, dose escalation occurred during week 2. Dose escalation did not occur in four patients, as a result of severe tumor lysis syndrome; three of these patients required hemodialysis. Thirty-four patients (53%) achieved response, including 30 partial responses (PRs; 47%), three nodular PRs (5%), and one complete response (1.6%). A majority of high-risk patients responded; 12 (57%) of 21 patients with del(17p13.1) and 14 (50%) of 28 patients with del(11q22.3) responded irrespective of lymph node size. Median progression-free survival among responders was 10 to 12 months across all cytogenetic risk groups. Reducing the number of weekly treatments per cycle from four to three and adding prophylactic dexamethasone, which abrogated interleukin-6 release and CRS (P ? .01), resulted in improved tolerability and treatment delivery. Conclusion Flavopiridol achieves significant clinical activity in patients with relapsed CLL, including those with high-risk genomic features and bulky lymphadenopathy. Subsequent clinical trials should use the amended treatment schedule developed herein and prophylactic corticosteroids.

Lin, Thomas S.; Ruppert, Amy S.; Johnson, Amy J.; Fischer, Beth; Heerema, Nyla A.; Andritsos, Leslie A.; Blum, Kristie A.; Flynn, Joseph M.; Jones, Jeffrey A.; Hu, Weihong; Moran, Mollie E.; Mitchell, Sarah M.; Smith, Lisa L.; Wagner, Amy J.; Raymond, Chelsey A.; Schaaf, Larry J.; Phelps, Mitch A.; Villalona-Calero, Miguel A.; Grever, Michael R.; Byrd, John C.

2009-01-01

320

Television Quiz Show Simulation  

ERIC Educational Resources Information Center

|This article explores the simulation of four television quiz shows for students in China studying English as a foreign language (EFL). It discusses the adaptation and implementation of television quiz shows and how the students reacted to them.|

Hill, Jonnie Lynn

2007-01-01

321

Genetic alterations activating kinase and cytokine receptor signaling in high-risk acute lymphoblastic leukemia  

PubMed Central

SUMMARY Genomic profiling has identified a subtype of high-risk B-progenitor acute lymphoblastic leukemia (B-ALL) with alteration of IKZF1, a gene expression profile similar to BCR-ABL1-positive ALL and poor outcome (Ph-like ALL). The genetic alterations that activate kinase signaling in Ph-like ALL are poorly understood. We performed transcriptome and whole genome sequencing on 15 cases of Ph-like ALL, and identified rearrangements involving ABL1, JAK2, PDGFRB, CRLF2 and EPOR, activating mutations of IL7R and FLT3, and deletion of SH2B3, which encodes the JAK2 negative regulator LNK. Importantly, several of these alterations induce transformation that is attenuated with tyrosine kinase inhibitors, suggesting the treatment outcome of these patients may be improved with targeted therapy.

Roberts, Kathryn G.; Morin, Ryan D.; Zhang, Jinghui; Hirst, Martin; Zhao, Yongjun; Su, Xiaoping; Chen, Shann-Ching; Payne-Turner, Debbie; Churchman, Michelle; Harvey, Richard C.; Chen, Xiang; Kasap, Corynn; Yan, Chunhua; Becksfort, Jared; Finney, Richard P.; Teachey, David T.; Maude, Shannon L.; Tse, Kane; Moore, Richard; Jones, Steven; Mungall, Karen; Birol, Inanc; Edmonson, Michael N.; Hu, Ying; Buetow, Kenneth E.; Chen, I-Ming; Carroll, William L.; Wei, Lei; Ma, Jing; Kleppe, Maria; Levine, Ross L.; Garcia-Manero, Guillermo; Larsen, Eric; Shah, Neil P.; Devidas, Meenakshi; Reaman, Gregory; Smith, Malcolm; Paugh, Steven W.; Evans, William E.; Grupp, Stephan A.; Jeha, Sima; Pui, Ching-Hon; Gerhard, Daniela S.; Downing, James R.; Willman, Cheryl L.; Loh, Mignon; Hunger, Stephen P.; Marra, Marco; Mullighan, Charles G.

2012-01-01

322

High-Throughput Genetic Identification of Functionally Important Regions of the Yeast DEAD-Box Protein Mss116p  

SciTech Connect

The Saccharomyces cerevisiae DEAD-box protein Mss116p is a general RNA chaperone that functions in splicing mitochondrial group I and group II introns. Recent X-ray crystal structures of Mss116p in complex with ATP analogs and single-stranded RNA show that the helicase core induces a bend in the bound RNA, as in other DEAD-box proteins, while a C-terminal extension (CTE) induces a second bend, resulting in RNA crimping. Here, we illuminate these structures by using high-throughput genetic selections, unigenic evolution, and analyses of in vivo splicing activity to comprehensively identify functionally important regions and permissible amino acid substitutions throughout Mss116p. The functionally important regions include those containing conserved sequence motifs involved in ATP and RNA binding or interdomain interactions, as well as previously unidentified regions, including surface loops that may function in protein-protein interactions. The genetic selections recapitulate major features of the conserved helicase motifs seen in other DEAD-box proteins but also show surprising variations, including multiple novel variants of motif III (SAT). Patterns of amino acid substitutions indicate that the RNA bend induced by the helicase core depends on ionic and hydrogen-bonding interactions with the bound RNA; identify a subset of critically interacting residues; and indicate that the bend induced by the CTE results primarily from a steric block. Finally, we identified two conserved regions - one the previously noted post II region in the helicase core and the other in the CTE - that may help displace or sequester the opposite RNA strand during RNA unwinding.

Mohr, Georg; Del Campo, Mark; Turner, Kathryn G.; Gilman, Benjamin; Wolf, Rachel Z.; Lambowitz, Alan M. (Texas)

2012-03-15

323

Adipocytokine Levels in Genetically High Risk for Type 2 Diabetes in the Indian Population: A Cross-Sectional Study  

PubMed Central

Introduction. In view of the noteworthy role of adipocytokines in the onset of insulin resistance and diabetes in gene-knockout-rat-model-cell-line studies we aimed to study the influence of genetic predisposition for diabetes on adipocytokine levels and their role in building insulin-resistance-like environment well before the onset of diabetes; thus a hypothesis can be drawn on their role in developing diabetes in high risk population. Methods. Ages between 18 and 22 years were selected and divided into three groups. Group I (n = 81): control group with no family history of diabetes. Group II (n = 157): with one of their parents with history of type 2 diabetes. Group III (n = 47): with both parents having history of type 2 diabetes. In all the groups we estimated fasting plasma glucose, insulin and adipocytokines like adiponectin, leptin, TNF-?, and IL-6. Results. Of all adipocytokines we observed significantly lower levels of adiponectin (8.7 ± 1??g/mL in group III and 9.5 ± 1.3??g/mL group II) when compared to control (11.0 ± 1.2??g/mL; P < 0.01) and it has strong correlation with family history of diabetes with Pearson's coefficient of ?0.502. Linear regression analysis showed significant negative association with HOMA-IR (P < 0.01) and logistic regression analysis showed highest association with parental diabetes (P < 0.01; OR .260, 95% CI .260–.468). Conclusion. Genetic predisposition for diabetes may influence adiponectin gene expression leading to decrease in its plasma concentration, which might play a key role in developing diabetes in near future.

Bose, K. Subhash Chandra; Gupta, Shachin K.; Vyas, Prerna

2012-01-01

324

Impact of Genetic Background on Allele Selection in a Highly Mutable Candida albicans Gene, PNG2  

PubMed Central

In many microbes rapid mutation of highly mutable contingency genes continually replenishes a pool of variant alleles from which the most suitable are selected, assisting in rapid adaptation and evasion of the immune response. In some contingency genes mutability is achieved through DNA repeats within the coding region. The fungal human pathogen Candida albicans has 2600 repeat-containing ORFs. For those investigated (ALS genes, HYR1, HYR2, CEK1, RLM1) many protein variants with differing amino acid repeat regions exist, as expected for contingency genes. However, specific alleles dominate in different clades, which is unexpected if allele variation is used for short-term adaptation. Generation of new alleles of repeat-containing C. albicans ORFs has never been observed directly. Here we present evidence for restrictions on the emergence of new alleles in a highly mutable C. albicans repeat-containing ORF, PNG2, encoding a putative secreted or cell surface glycoamidase. In laboratory cultures new PNG2 alleles arose at a rate of 2.8×10?5 (confidence interval 3.3×10?6?9. 9×10?5) per cell per division, comparable to rates measured for contingency genes. Among 80 clinical isolates 17 alleles of different length and 23 allele combinations were distinguishable; sequence differences between repeat regions of identical size suggest the existence of 36 protein variants. Specific allele combinations predominated in different genetic backgrounds, as defined by DNA fingerprinting and multilocus sequence typing. Given the PNG2 mutation rate, this is unexpected, unless in different genetic backgrounds selection favors different alleles. Specific alleles or allele combinations were not preferentially associated with C. albicans isolates from particular body sites or geographical regions. Our results suggest that the mutability of PNG2 is not used for short-term adaptation or evasion of the immune system. Nevertheless the large number of alleles observed indicates that mutability of PNG2 may assist C. albicans strains from different genetic backgrounds optimize their interaction with the host in the long term.

Zhang, Ningxin; Cannon, Richard D.; Holland, Barbara R.; Patchett, Mark L.; Schmid, Jan

2010-01-01

325

The Great Cometary Show  

NASA Astrophysics Data System (ADS)

The ESO Very Large Telescope Interferometer, which allows astronomers to scrutinise objects with a precision equivalent to that of a 130-m telescope, is proving itself an unequalled success every day. One of the latest instruments installed, AMBER, has led to a flurry of scientific results, an anthology of which is being published this week as special features in the research journal Astronomy & Astrophysics. ESO PR Photo 06a/07 ESO PR Photo 06a/07 The AMBER Instrument "With its unique capabilities, the VLT Interferometer (VLTI) has created itself a niche in which it provide answers to many astronomical questions, from the shape of stars, to discs around stars, to the surroundings of the supermassive black holes in active galaxies," says Jorge Melnick (ESO), the VLT Project Scientist. The VLTI has led to 55 scientific papers already and is in fact producing more than half of the interferometric results worldwide. "With the capability of AMBER to combine up to three of the 8.2-m VLT Unit Telescopes, we can really achieve what nobody else can do," added Fabien Malbet, from the LAOG (France) and the AMBER Project Scientist. Eleven articles will appear this week in Astronomy & Astrophysics' special AMBER section. Three of them describe the unique instrument, while the other eight reveal completely new results about the early and late stages in the life of stars. ESO PR Photo 06b/07 ESO PR Photo 06b/07 The Inner Winds of Eta Carinae The first results presented in this issue cover various fields of stellar and circumstellar physics. Two papers deal with very young solar-like stars, offering new information about the geometry of the surrounding discs and associated outflowing winds. Other articles are devoted to the study of hot active stars of particular interest: Alpha Arae, Kappa Canis Majoris, and CPD -57o2874. They provide new, precise information about their rotating gas envelopes. An important new result concerns the enigmatic object Eta Carinae. Using AMBER with its high spatial and spectral resolution, it was possible to zoom into the very heart of this very massive star. In this innermost region, the observations are dominated by the extremely dense stellar wind that totally obscures the underlying central star. The AMBER observations show that this dense stellar wind is not spherically symmetric, but exhibits a clearly elongated structure. Overall, the AMBER observations confirm that the extremely high mass loss of Eta Carinae's massive central star is non-spherical and much stronger along the poles than in the equatorial plane. This is in agreement with theoretical models that predict such an enhanced polar mass-loss in the case of rapidly rotating stars. ESO PR Photo 06c/07 ESO PR Photo 06c/07 RS Ophiuchi in Outburst Several papers from this special feature focus on the later stages in a star's life. One looks at the binary system Gamma 2 Velorum, which contains the closest example of a star known as a Wolf-Rayet. A single AMBER observation allowed the astronomers to separate the spectra of the two components, offering new insights in the modeling of Wolf-Rayet stars, but made it also possible to measure the separation between the two stars. This led to a new determination of the distance of the system, showing that previous estimates were incorrect. The observations also revealed information on the region where the winds from the two stars collide. The famous binary system RS Ophiuchi, an example of a recurrent nova, was observed just 5 days after it was discovered to be in outburst on 12 February 2006, an event that has been expected for 21 years. AMBER was able to detect the extension of the expanding nova emission. These observations show a complex geometry and kinematics, far from the simple interpretation of a spherical fireball in extension. AMBER has detected a high velocity jet probably perpendicular to the orbital plane of the binary system, and allowed a precise and careful study of the wind and the shockwave coming from the nova. The stream of results from the VLTI and AMBER

2007-01-01

326

Relative role of environmental and genetic factors in respiratory adaptation to high altitude  

Microsoft Academic Search

A VARIETY of adaptive mechanisms which aid in the physiological adjustment to the hypoxic environment of altitude have been reported in man1. Although visitors to high altitudes increase ventilation in response to environmental hypoxia, natives in the Andes and Himalayas show a blunted or absent ventilatory response to acute hypoxia both at rest and during exercise2-5. Adult high altitude natives

S. Lahiri; R. G. Delaney; J. S. BRODY; M. SIMPSER; T. VELASQUEZ; C. POLGAR

1976-01-01

327

Reduced genetic variance among high fitness individuals: inferring stabilizing selection on male sexual displays in Drosophila serrata.  

PubMed

Directional selection is prevalent in nature, yet phenotypes tend to remain relatively constant, suggesting a limit to trait evolution. However, the genetic basis of this limit is unresolved. Given widespread pleiotropy, opposing selection on a trait may arise from the effects of the underlying alleles on other traits under selection, generating net stabilizing selection on trait genetic variance. These pleiotropic costs of trait exaggeration may arise through any number of other traits, making them hard to detect in phenotypic analyses. Stabilizing selection can be inferred, however, if genetic variance is greater among low- compared to high-fitness individuals. We extend a recently suggested approach to provide a direct test of a difference in genetic variance for a suite of cuticular hydrocarbons (CHCs) in Drosophila serrata. Despite strong directional sexual selection on these traits, genetic variance differed between high- and low-fitness individuals and was greater among the low-fitness males for seven of eight CHCs, significantly more than expected by chance. Univariate tests of a difference in genetic variance were nonsignificant but likely have low power. Our results suggest that further CHC exaggeration in D. serrata in response to sexual selection is limited by pleiotropic costs mediated through other traits. PMID:23025601

Sztepanacz, Jacqueline L; Rundle, Howard D

2012-05-05

328

Antiviral resistance among highly pathogenic influenza A (H5N1) viruses isolated worldwide in 2002-2012 shows need for continued monitoring.  

PubMed

Highly pathogenic (HP) H5N1 influenza viruses are evolving pathogens with the potential to cause sustained human-to-human transmission and pandemic virus spread. Specific antiviral drugs can play an important role in the early stages of a pandemic, but the emergence of drug-resistant variants can limit control options. The available data on the susceptibility of HP H5N1 influenza viruses to neuraminidase (NA) inhibitors and adamantanes is scarce, and there is no extensive analysis. Here, we systematically examined the prevalence of NA inhibitor and adamantane resistance among HP H5N1 influenza viruses that circulated worldwide during 2002-2012. The phenotypic fluorescence-based assay showed that both human and avian HP H5N1 viruses are susceptible to NA inhibitors oseltamivir and zanamivir with little variability over time and ?5.5-fold less susceptibility to oseltamivir of viruses of hemagglutinin (HA) clade 2 than of clade 1. Analysis of available sequence data revealed a low incidence of NA inhibitor-resistant variants. The established markers of NA inhibitor resistance (E119A, H274Y, and N294S, N2 numbering) were found in 2.4% of human and 0.8% of avian isolates, and the markers of reduced susceptibility (I117V, K150N, I222V/T/K, and S246N) were found in 0.8% of human and 2.9% of avian isolates. The frequency of amantadine-resistant variants was higher among human (62.2%) than avian (31.6%) viruses with disproportionate distribution among different HA clades. As in human isolates, avian H5N1 viruses carry double L26I and S31N M2 mutations more often than a single S31N mutation. Overall, both human and avian HP H5N1 influenza viruses are susceptible to NA inhibitors; some proportion is still susceptible to amantadine in contrast to ?100% amantadine resistance among currently circulating seasonal human H1N1 and H3N2 viruses. Continued antiviral susceptibility monitoring of H5N1 viruses is needed to maintain therapeutic approaches for control of disease. PMID:23458714

Govorkova, Elena A; Baranovich, Tatiana; Seiler, Patrick; Armstrong, Jianling; Burnham, Andrew; Guan, Yi; Peiris, Malik; Webby, Richard J; Webster, Robert G

2013-02-28

329

“They Don’t Teach This in High School”: An Examination of the Portrayal of Teenage Pregnancy in the MTV Television Show 16 and Pregnant  

Microsoft Academic Search

This paper examines the depiction of teenage pregnancy on the MTV show 16 and Pregnant- a documentary style reality show. Using a qualitative textual analysis the author examines how he teen girls describe themselves, whether contraception was discussed and if it was how so, what options the teens discussed in regards to the pregnancy, the role of the father of

Elizabeth F. Smith

2012-01-01

330

Association between Genetic Subgroups of Pancreatic Ductal Adenocarcinoma Defined by High Density 500 K SNP-Arrays and Tumor Histopathology  

PubMed Central

The specific genes and genetic pathways associated with pancreatic ductal adenocarcinoma are still largely unknown partially due to the low resolution of the techniques applied so far to their study. Here we used high-density 500 K single nucleotide polymorphism (SNP)-arrays to define those chromosomal regions which most commonly harbour copy number (CN) alterations and loss of heterozygozity (LOH) in a series of 20 PDAC tumors and we correlated the corresponding genetic profiles with the most relevant clinical and histopathological features of the disease. Overall our results showed that primary PDAC frequently display (>70%) extensive gains of chromosomes 1q, 7q, 8q and 20q, together with losses of chromosomes 1p, 9p, 12q, 17p and 18q, such chromosomal regions harboring multiple cancer- and PDAC-associated genes. Interestingly, these alterations clustered into two distinct genetic profiles characterized by gains of the 2q14.2, 3q22.1, 5q32, 10q26.13, 10q26.3, 11q13.1, 11q13.3, 11q13.4, 16q24.1, 16q24.3, 22q13.1, 22q13.31 and 22q13.32 chromosomal regions (group 1; n?=?9) versus gains at 1q21.1 and losses of the 1p36.11, 6q25.2, 9p22.1, 9p24.3, 17p13.3 and Xp22.33 chromosomal regions (group 2; n?=?11). From the clinical and histopathological point of view, group 1 cases were associated with smaller and well/moderately-differentiated grade I/II PDAC tumors, whereas and group 2 PDAC displayed a larger size and they mainly consisted of poorly-differentiated grade III carcinomas. These findings confirm the cytogenetic complexity and heterogenity of PDAC and provide evidence for the association between tumor cytogenetics and its histopathological features. In addition, we also show that the altered regions identified harbor multiple cancer associate genes that deserve further investigation to determine their relevance in the pathogenesis of PDAC.

Gutierrez, Maria Laura; Munoz-Bellvis, Luis; Abad, Maria del Mar; Bengoechea, Oscar; Gonzalez-Gonzalez, Maria

2011-01-01

331

Exploring the genetic characteristics of two recombinant inbred line populations via high-density SNP markers in maize.  

PubMed

Understanding genetic characteristics can reveal the genetic diversity in maize and be used to explore evolutionary mechanisms and gene cloning. A high-density linkage map was constructed to determine recombination rates (RRs), segregation distortion regions (SDRs), and recombinant blocks (RBs) in two recombinant inbred line populations (RILs) (B73/By804 and Zong3/87-1) generated by the single seed descent method. Population B73/By804 containing 174 lines were genotyped with 198 simple sequence repeats (SSRs) markers while population Zong3/87-1 comprised of 175 lines, were genotyped with 210 SSR markers along with 1536 single nucleotide polymorphism (SNP) markers for each population, spanning 1526.7 cM and 1996.2 cM in the B73/By804 and Zong3/87-1 populations, respectively. The total variance of the RR in the whole genome was nearly 100 fold, and the maximum average was 10.43-11.50 cM/Mb while the minimum was 0.08-0.10 cM/Mb in the two populations. The average number of RB was 44 and 37 in the Zong3/87-1 and B73/By804 populations, respectively, whereas 28 SDRs were observed in both populations. We investigated 11 traits in Zong3/87-1 and 10 traits in B73/By804. Quantitative trait locus (QTLs) mapping of SNP+SSR with SNP and SSR marker sets were compared to showed the impact of different density markers on QTL mapping and resolution. The confidence interval of QTL Pa19 (FatB gene controlling palmitic acid content) was reduced from 3.5 Mb to 1.72 Mb, and the QTL Oil6 (DGAT1-2 gene controlling oil concentration) was significantly reduced from 10.8 Mb to 1.62 Mb. Thus, the use of high-density markers considerably improved QTL mapping resolution. The genetic information resulting from this study will support forthcoming efforts to understand recombination events, SDRs, and variations among different germplasm. Furthermore, this study will facilitate gene cloning and understanding of the fundamental sources of total variation and RR in maize, which is the most widely cultivated cereal crop. PMID:23300772

Pan, Qingchun; Ali, Farhan; Yang, Xiaohong; Li, Jiansheng; Yan, Jianbing

2012-12-27

332

Exploring the Genetic Characteristics of Two Recombinant Inbred Line Populations via High-Density SNP Markers in Maize  

PubMed Central

Understanding genetic characteristics can reveal the genetic diversity in maize and be used to explore evolutionary mechanisms and gene cloning. A high-density linkage map was constructed to determine recombination rates (RRs), segregation distortion regions (SDRs), and recombinant blocks (RBs) in two recombinant inbred line populations (RILs) (B73/By804 and Zong3/87-1) generated by the single seed descent method. Population B73/By804 containing 174 lines were genotyped with 198 simple sequence repeats (SSRs) markers while population Zong3/87-1 comprised of 175 lines, were genotyped with 210 SSR markers along with 1536 single nucleotide polymorphism (SNP) markers for each population, spanning 1526.7 cM and 1996.2 cM in the B73/By804 and Zong3/87-1 populations, respectively. The total variance of the RR in the whole genome was nearly 100 fold, and the maximum average was 10.43–11.50 cM/Mb while the minimum was 0.08–0.10 cM/Mb in the two populations. The average number of RB was 44 and 37 in the Zong3/87-1 and B73/By804 populations, respectively, whereas 28 SDRs were observed in both populations. We investigated 11 traits in Zong3/87-1 and 10 traits in B73/By804. Quantitative trait locus (QTLs) mapping of SNP+SSR with SNP and SSR marker sets were compared to showed the impact of different density markers on QTL mapping and resolution. The confidence interval of QTL Pa19 (FatB gene controlling palmitic acid content) was reduced from 3.5 Mb to 1.72 Mb, and the QTL Oil6 (DGAT1-2 gene controlling oil concentration) was significantly reduced from 10.8 Mb to 1.62 Mb. Thus, the use of high-density markers considerably improved QTL mapping resolution. The genetic information resulting from this study will support forthcoming efforts to understand recombination events, SDRs, and variations among different germplasm. Furthermore, this study will facilitate gene cloning and understanding of the fundamental sources of total variation and RR in maize, which is the most widely cultivated cereal crop.

Pan, Qingchun; Ali, Farhan; Yang, Xiaohong; Li, Jiansheng; Yan, Jianbing

2012-01-01

333

High-level DNA amplifications are common genetic aberrations in B-cell neoplasms.  

PubMed Central

Gene amplification is one of the molecular mechanisms resulting in the up-regulation of gene expression. In non-Hodgkin's lymphomas, such gene amplifications have been identified rarely. Using comparative genomic hybridization, a technique that has proven to be very sensitive for the detection of high-level DNA amplifications, we analyzed 108 cases of B-cell neoplasms (42 chronic B-cell leukemias, 5 mantle cell lymphomas, and 61 aggressive B-cell lymphomas). Twenty-four high-level amplifications were identified in 13% of the patients and mapped to 15 different genomic regions. Regions most frequently amplified were bands Xq26-28, 2p23-24, and 2p14-16 as well as 18q21 (three times each). Amplification of several proto-oncogenes and a cell cycle control gene (N-MYC (two cases), BCL2, CCND2, and GLI) located within the amplified regions was demonstrated by Southern blot analysis or fluorescence in situ hybridization to interphase nuclei of tumor cells. These data demonstrate that gene amplifications in B-cell neoplasms are much more frequent than previously assumed. The identification of highly amplified DNA regions and genes included in the amplicons provides important information for further analyses of genetic events involved in lymphomagenesis. Images Figure 2 Figure 3

Werner, C. A.; Dohner, H.; Joos, S.; Trumper, L. H.; Baudis, M.; Barth, T. F.; Ott, G.; Moller, P.; Lichter, P.; Bentz, M.

1997-01-01

334

High-throughput genetic analysis using microfabricated 96-sample capillary array electrophoresis microplates  

PubMed Central

Capillary array electrophoresis (CAE) microplates that can analyze 96 samples in less than 8 min have been produced by bonding 10-cm-diameter micromachined glass wafers to form a glass sandwich structure. The microplate has 96 sample wells and 48 separation channels with an injection unit that permits the serial analysis of two different samples on each capillary. An elastomer sheet with an 8 by 12 array of holes is placed on top of the glass sandwich structure to define the sample wells. Samples are addressed with an electrode array that makes up the third layer of the assembly. Detection of all lanes with high temporal resolution was achieved by using a laser-excited confocal fluorescence scanner. To demonstrate the functionality of these microplates, electrophoretic separation and fluorescence detection of a restriction fragment marker for the diagnosis of hereditary hemochromatosis were performed. CAE microplates will facilitate all types of high-throughput genetic analysis because their high assay speed provides a throughput that is 50 to 100 times greater than that of conventional slab gels.

Simpson, Peter C.; Roach, David; Woolley, Adam T.; Thorsen, Todd; Johnston, Rick; Sensabaugh, George F.; Mathies, Richard A.

1998-01-01

335

Examination of a genetic algorithm for the application in high-throughput downstream process development.  

PubMed

Compared to traditional strategies, application of high-throughput experiments combined with optimization methods can potentially speed up downstream process development and increase our understanding of processes. In contrast to the method of Design of Experiments in combination with response surface analysis (RSA), optimization approaches like genetic algorithms (GAs) can be applied to identify optimal parameter settings in multidimensional optimizations tasks. In this article the performance of a GA was investigated applying parameters applicable in high-throughput downstream process development. The influence of population size, the design of the initial generation and selection pressure on the optimization results was studied. To mimic typical experimental data, four mathematical functions were used for an in silico evaluation. The influence of GA parameters was minor on landscapes with only one optimum. On landscapes with several optima, parameters had a significant impact on GA performance and success in finding the global optimum. Premature convergence increased as the number of parameters and noise increased. RSA was shown to be comparable or superior for simple systems and low to moderate noise. For complex systems or high noise levels, RSA failed, while GA optimization represented a robust tool for process optimization. Finally, the effect of different objective functions is shown exemplarily for a refolding optimization of lysozyme. PMID:22700464

Treier, Katrin; Berg, Annette; Diederich, Patrick; Lang, Katharina; Osberghaus, Anna; Dismer, Florian; Hubbuch, Jürgen

2012-07-30

336

EGLN1 involvement in high-altitude adaptation revealed through genetic analysis of extreme constitution types defined in Ayurveda.  

PubMed

It is being realized that identification of subgroups within normal controls corresponding to contrasting disease susceptibility is likely to lead to more effective predictive marker discovery. We have previously used the Ayurvedic concept of Prakriti, which relates to phenotypic differences in normal individuals, including response to external environment as well as susceptibility to diseases, to explore molecular differences between three contrasting Prakriti types: Vata, Pitta, and Kapha. EGLN1 was one among 251 differentially expressed genes between the Prakriti types. In the present study, we report a link between high-altitude adaptation and common variations rs479200 (C/T) and rs480902 (T/C) in the EGLN1 gene. Furthermore, the TT genotype of rs479200, which was more frequent in Kapha types and correlated with higher expression of EGLN1, was associated with patients suffering from high-altitude pulmonary edema, whereas it was present at a significantly lower frequency in Pitta and nearly absent in natives of high altitude. Analysis of Human Genome Diversity Panel-Centre d'Etude du Polymorphisme Humain (HGDP-CEPH) and Indian Genome Variation Consortium panels showed that disparate genetic lineages at high altitudes share the same ancestral allele (T) of rs480902 that is overrepresented in Pitta and positively correlated with altitude globally (P < 0.001), including in India. Thus, EGLN1 polymorphisms are associated with high-altitude adaptation, and a genotype rare in highlanders but overrepresented in a subgroup of normal lowlanders discernable by Ayurveda may confer increased risk for high-altitude pulmonary edema. PMID:20956315

Aggarwal, Shilpi; Negi, Sapna; Jha, Pankaj; Singh, Prashant K; Stobdan, Tsering; Pasha, M A Qadar; Ghosh, Saurabh; Agrawal, Anurag; Prasher, Bhavana; Mukerji, Mitali

2010-10-18

337

Development of a high density integrated reference genetic linkage map for the multinational Brassica rapa Genome Sequencing Project.  

PubMed

We constructed a high-density Brassica rapa integrated linkage map by combining a reference genetic map of 78 doubled haploid lines derived from Chiifu-401-42 × Kenshin (CKDH) and a new map of 190 F2 lines derived from Chiifu-401-42 × rapid cycling B. rapa (CRF2). The integrated map contains 1017 markers and covers 1262.0 cM of the B. rapa genome, with an average interlocus distance of 1.24 cM. High similarity of marker order and position was observed among the linkage groups of the maps with few short-distance inversions. In total, 155 simple sequence repeat (SSR) markers, anchored to 102 new bacterial artificial chromosomes (BACs) and 146 intron polymorphic (IP) markers were mapped in the integrated map, which would be helpful to align the sequenced BACs in the ongoing multinational Brassica rapa Genome Sequencing Project (BrGSP). Further, comparison of the B. rapa consensus map with the 10 B. juncea A-genome linkage groups by using 98 common IP markers showed high-degree colinearity between the A-genome linkage groups, except for few markers showing inversion or translocation. Suggesting that chromosomes are highly conserved between these Brassica species, although they evolved independently after divergence. The sequence information coming out of BrGSP would be useful for B. juncea breeding. and the identified Arabidopsis chromosomal blocks and known quantitative trait loci (QTL) information of B. juncea could be applied to improve other Brassica crops including B. rapa. PMID:21076509

Li, Xiaonan; Ramchiary, Nirala; Choi, Su Ryun; Van Nguyen, Dan; Hossain, Md Jamil; Yang, Hyeon Kook; Lim, Yong Pyo

2010-11-01

338

Psychological impact of genetic testing in women from high-risk breast cancer families  

Microsoft Academic Search

Psychological adjustment in 90 women (30 carriers and 60 non-carriers) who had undergone genetic testing for mutations in BRCA1 and BRCA2 breast\\/ovarian cancer susceptibility genes was compared with that of 53 women who were not offered genetic testing. Women were assessed prior to genetic testing and 7–10 days, 4 and 12 months after carrier status disclosure using self-administered questionnaires. Compared

B Meiser; P Butow; M Friedlander; A Barratt; V Schnieden; M Watson; J Brown; K Tucker

2002-01-01

339

An experiment shows that a well-designed report on costs and quality can help consumers choose high-value health care.  

PubMed

Advocates of health reform continue to pursue policies and tools that will make information about comparative costs and resource use available to consumers. Reformers expect that consumers will use the data to choose high-value providers-those who offer higher quality and lower prices-and thus contribute to the broader goal of controlling national health care spending. However, communicating this information effectively is more challenging than it might first appear. For example, consumers are more interested in the quality of health care than in its cost, and many perceive a low-cost provider to be substandard. In this study of 1,421 employees, we examined how different presentations of information affect the likelihood that consumers will make high-value choices. We found that a substantial minority of the respondents shied away from low-cost providers, and even consumers who pay a larger share of their health care costs themselves were likely to equate high cost with high quality. At the same time, we found that presenting cost data alongside easy-to-interpret quality information and highlighting high-value options improved the likelihood that consumers would choose those options. Reporting strategies that follow such a format will help consumers understand that a doctor who provides higher-quality care than other doctors does not necessarily cost more. PMID:22392666

Hibbard, Judith H; Greene, Jessica; Sofaer, Shoshanna; Firminger, Kirsten; Hirsh, Judith

2012-03-01

340

A Holographic Road Show.  

ERIC Educational Resources Information Center

|Describes the viewing sessions and the holograms of a holographic road show. The traveling exhibits, believed to stimulate interest in physics, include a wide variety of holograms and demonstrate several physical principles. (GA)|

Kirkpatrick, Larry D.; Rugheimer, Mac

1979-01-01

341

The Diane Rehm Show  

NSDL National Science Digital Library

The Diane Rehm Show has its origins in a mid-day program at WAMU in Washington, D.C. Diane Rehm came on to host the program in 1979, and in 1984 it was renamed "The Diane Rehm Show". Over the past several decades, Rehm has played host to hundreds of guests, include Archbishop Desmond Tutu, Julie Andrews, and President Bill Clinton. This website contains an archive of her past programs, and visitors can use the interactive calendar to look through past shows. Those visitors looking for specific topics can use the "Topics" list on the left-hand side of the page, or also take advantage of the search engine. The show has a number of social networking links, including a Facebook page and a Twitter feed.

342

A Twin Study of the Genetics of High Cognitive Ability Selected from 11,000 Twin Pairs in Six Studies from Four Countries  

Microsoft Academic Search

Although much genetic research has addressed normal variation in intelligence, little is known about the etiology of high\\u000a cognitive abilities. Using data from 11,000 twin pairs (age range = 6–71 years) from the genetics of high cognitive abilities\\u000a consortium, we investigated the genetic and environmental etiologies of high general cognitive ability (g). Age-appropriate psychometric cognitive tests were administered to the twins and used

Claire M. A. Haworth; Margaret J. Wright; Nicolas W. Martin; Nicholas G. Martin; Dorret I. Boomsma; Meike Bartels; Danielle Posthuma; Oliver S. P. Davis; Angela M. Brant; Robin P. Corley; John K. Hewitt; William G. Iacono; Matthew McGue; Lee A. Thompson; Sara A. Hart; Stephen A. Petrill; David Lubinski; Robert Plomin

2009-01-01

343

High-Resolution Genetic Mapping Using the Mouse Diversity Outbred Population  

PubMed Central

The JAX Diversity Outbred population is a new mouse resource derived from partially inbred Collaborative Cross strains and maintained by randomized outcrossing. As such, it segregates the same allelic variants as the Collaborative Cross but embeds these in a distinct population architecture in which each animal has a high degree of heterozygosity and carries a unique combination of alleles. Phenotypic diversity is striking and often divergent from phenotypes seen in the founder strains of the Collaborative Cross. Allele frequencies and recombination density in early generations of Diversity Outbred mice are consistent with expectations based on simulations of the mating design. We describe analytical methods for genetic mapping using this resource and demonstrate the power and high mapping resolution achieved with this population by mapping a serum cholesterol trait to a 2-Mb region on chromosome 3 containing only 11 genes. Analysis of the estimated allele effects in conjunction with complete genome sequence data of the founder strains reduced the pool of candidate polymorphisms to seven SNPs, five of which are located in an intergenic region upstream of the Foxo1 gene.

Svenson, Karen L.; Gatti, Daniel M.; Valdar, William; Welsh, Catherine E.; Cheng, Riyan; Chesler, Elissa J.; Palmer, Abraham A.; McMillan, Leonard; Churchill, Gary A.

2012-01-01

344

A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map  

SciTech Connect

As part of a larger project to sequence the Populus genome and generate genomic resources for this emerging model tree, we constructed a physical map of the Populus genome, representing one of the few such maps of an undomesticated, highly heterozygous plant species. The physical map, consisting of 2802 contigs, was constructed from fingerprinted bacterial artificial chromosome (BAC) clones. The map represents approximately 9.4-fold coverage of the Populus genome, which has been estimated from the genome sequence assembly to be 485 {+-} 10 Mb in size. BAC ends were sequenced to assist long-range assembly of whole-genome shotgun sequence scaffolds and to anchor the physical map to the genome sequence. Simple sequence repeat-based markers were derived from the end sequences and used to initiate integration of the BAC and genetic maps. A total of 2411 physical map contigs, representing 97% of all clones assigned to contigs, were aligned to the sequence assembly (JGI Populus trichocarpa, version 1.0). These alignments represent a total coverage of 384 Mb (79%) of the entire poplar sequence assembly and 295 Mb (96%) of linkage group sequence assemblies. A striking result of the physical map contig alignments to the sequence assembly was the co-localization of multiple contigs across numerous regions of the 19 linkage groups. Targeted sequencing of BAC clones and genetic analysis in a small number of representative regions showed that these co-aligning contigs represent distinct haplotypes in the heterozygous individual sequenced, and revealed the nature of these haplotype sequence differences.

Kelleher, Colin [University of British Columbia, Vancouver; CHIU, Dr. R. [Genome Sciences Centre, Vancouver, BC, Canada; Shin, Dr. H. [Genome Sciences Centre, Vancouver, BC, Canada; Krywinski, Martin [Genome Sciences Centre, Vancouver, BC, Canada; Fjell, Chris [Genome Sciences Centre, Vancouver, BC, Canada; Wilkin, Jennifer [University of British Columbia, Vancouver; Yin, Tongming [ORNL; Difazio, Stephen P. [West Virginia University

2007-01-01

345

High-Level Genetic Diversity but No Population Structure Inferred from Nuclear and Mitochondrial Markers of the Peritrichous Ciliate Carchesium polypinum in the Grand River Basin (North America)? †  

PubMed Central

Studies that assess intraspecific genetic variation in ciliates are few and quite recent. Consequently, knowledge of the subject and understanding of the processes that underlie it are limited. We sought to assess the degree of intraspecific genetic variation in Carchesium polypinum (Ciliophora: Peritrichia), a cosmopolitan, freshwater ciliate. We isolated colonies of C. polypinum from locations in the Grand River basin in Southwestern Ontario, Canada. We then used the nuclear markers—ITS1, ITS2, and the hypervariable regions of the large subunit rRNA—and an 819-bp fragment of the mitochondrial cytochrome c oxidase I gene (cox-1) to investigate the intraspecific genetic variation of C. polypinum and the degree of resolution of the above-mentioned markers at the population level. We also sought to determine whether the organism demonstrated any population structure that mapped onto the geography of the region. Our study shows that there is a high degree of genetic diversity at the isolate level, revealed by the mitochondrial markers but not the nuclear markers. Furthermore, our results indicate that C. polypinum is likely not a single morphospecies as previously thought.

Gentekaki, E.; Lynn, D. H.

2009-01-01

346

Delineating the genetic heterogeneity of ALS using targeted high-throughput sequencing  

PubMed Central

Background Over 100 genes have been implicated in the aetiology of amyotrophic lateral sclerosis (ALS). A detailed understanding of their independent and cumulative contributions to disease burden may help guide various clinical and research efforts. Methods Using targeted high-throughput sequencing, we characterised the variation of 10 Mendelian and 23 low penetrance/tentative ALS genes within a population-based cohort of 444 Irish ALS cases (50 fALS, 394 sALS) and 311 age-matched and geographically matched controls. Results Known or potential high-penetrance ALS variants were identified within 17.1% of patients (38% of fALS, 14.5% of sALS). 12.8% carried variants of Mendelian disease genes (C9orf72 8.78%; SETX 2.48%; ALS2 1.58%; FUS 0.45%; TARDBP 0.45%; OPTN 0.23%; VCP 0.23%. ANG, SOD1, VAPB 0%), 4.7% carried variants of low penetrance/tentative ALS genes and 9.7% (30% of fALS, 7.1% of sALS) carried previously described ALS variants (C9orf72 8.78%; FUS 0.45%; TARDBP 0.45%). 1.6% of patients carried multiple known/potential disease variants, including all identified carriers of an established ALS variant (p<0.01); TARDBP:c.859G>A(p.[G287S]) (n=2/2 sALS). Comparison of our results with those from studies of other European populations revealed significant differences in the spectrum of disease variation (p=1.7×10?4). Conclusions Up to 17% of Irish ALS cases may carry high-penetrance variants within the investigated genes. However, the precise nature of genetic susceptibility differs significantly from that reported within other European populations. Certain variants may not cause disease in isolation and concomitant analysis of disease genes may prove highly important.

Kenna, Kevin P; McLaughlin, Russell L; Byrne, Susan; Elamin, Marwa; Heverin, Mark; Kenny, Elaine M; Cormican, Paul; Morris, Derek W; Donaghy, Colette G; Bradley, Daniel G; Hardiman, Orla

2013-01-01

347

Genome wide association studies reveal genetic variants in CTNND2 for high myopia in Singapore Chinese  

PubMed Central

Objective To determine susceptibility genes for high myopia in Singaporean Chinese. Design A meta-analysis of two genome wide association (GWA) datasets in Chinese and a follow-up replication cohort in Japanese. Participants and Controls Two independent datasets of Singaporean Chinese individuals aged 10–12 years (SCORM -- Singapore Cohort Study of the Risk factors for Myopia: cases=65, controls=238) and aged > 21 years (SP2 -- Singapore Prospective Study Program: cases=222, controls=435) for GWA studies, and a Japanese dataset aged >20 years (cases=959, controls=2128) for replication. Methods Genomic DNA samples from SCORM and SP2 were genotyped using various Illumina Beadarray platforms (> HumanHap 500). Single-locus association tests were conducted for each dataset with meta-analysis using pooled z-scores. The top-ranked genetic markers were examined for replication in Japanese dataset. Fisher’s P was calculated for the combined analysis of all three cohorts. Main outcome measures High myopia, defined by spherical equivalent (SE) ? ?6.00 diopters (D); controls defined by SE between ?0.50D and +1.00D. Results Two SNPs (rs12716080 and rs6885224) in the gene CTNND2 on chromosome 5p15 ranked top in the meta-analysis of our Chinese datasets (meta- P = 1.14×10?5 and meta- P = 1.51×10?5, respectively) with strong supporting evidence in each individual dataset analysis (Max P = 1.85.x10?4 in SCORM: Max P = 8.8×10?3 in SP2). Evidence of replication was observed in Japanese dataset for rs6885224 (P = 0.035, meta-P of three datasets: 7.84×10?6). Conclusion This study identified strong association of CTNND2 for high myopia in Asian datasets. The CTNND2 gene maps to a known high myopia linkage region on chromosome 5p15.

Li, Yi-Ju; Goh, Liang; Khor, Chiea-Chuen; Fan, Qiao; Yu, Miao; Han, Siyu; Sim, Xueling; Ong, Rick Twee-Hee; Wong, Tien-Yin; Vithana, Eranga Nishanthie; Yap, Eric; Nakanishi, Hideo; Matsuda, Fumihiko; Ohno-Matsui, Kyoko; Yoshimura, Nagahisa; Seielstad, Mark; Tai, E-Shyong; Young, Terri L.; Saw, Seang-Mei

2010-01-01

348

Sympatric populations of the highly cross-fertile coral species Acropora hyacinthus and Acropora cytherea are genetically distinct.  

PubMed Central

High cross-fertilization rates in vitro and non-monophyletic patterns in molecular phylogenies challenge the taxonomic status of species in the coral genus Acropora. We present data from eight polymorphic allozyme loci that indicate small, but significant, differentiation between sympatric populations of Acropora cytherea and Acropora hyacinthus (F(ST) = 0.025-0.068, p < 0.05), a pair of acroporid corals with very high interspecific fertilization rates in vitro. Although no fixed allelic differences were found between these species, the absence of genetic differentiation between widely allopatric populations suggests that allele frequency differences between A. cytherea and A. hyacinthus in sympatry are biologically significant. By contrast, populations of Acropora tenuis, a species which spawns 2-3 hours earlier and shows low cross-fertilization rates with congeners in vitro, were clearly distinct from A. cytherea and A. hyacinthus (F(ST) = 0.427-0.465, p < 0.05). Moreover, allopatric populations of A. tenuis differed significantly, possibly as a consequence of its relatively short period of larval competency. Our results effectively rule out the possibility that A. hyacinthus and A. cytherea are morphotypes within a single species, and indicate that hybridization occurs relatively infrequently between these taxa in nature.

Marquez, L M; van Oppen, M J H; Willis, B L; Miller, D J

2002-01-01

349

Design and Synthesis of Two Porous Metal-Organic Frameworks with nbo and agw Topologies Showing High CO2 Adsorption Capacity.  

PubMed

Two novel porous copper-based metal-organic frameworks with nbo and agw topologies have been designed and synthesized using tetracarboxylate and tricarboxylate ligands, respectively. They possess large surface areas and high CO2 adsorption capacities (up to 170 cm(3)/g or 7.59 mmol/g at 0 °C under ambient pressure). PMID:24041328

Liang, Zhiqiang; Du, Jingjing; Sun, Libo; Xu, Jin; Mu, Ying; Li, Yi; Yu, Jihong; Xu, Ruren

2013-09-16

350

A high-density genetic map of Arachis duranensis, a diploid ancestor of cultivated peanut  

PubMed Central

Background Cultivated peanut (Arachis hypogaea) is an allotetraploid species whose ancestral genomes are most likely derived from the A-genome species, A. duranensis, and the B-genome species, A. ipaensis. The very recent (several millennia) evolutionary origin of A. hypogaea has imposed a bottleneck for allelic and phenotypic diversity within the cultigen. However, wild diploid relatives are a rich source of alleles that could be used for crop improvement and their simpler genomes can be more easily analyzed while providing insight into the structure of the allotetraploid peanut genome. The objective of this research was to establish a high-density genetic map of the diploid species A. duranensis based on de novo generated EST databases. Arachis duranensis was chosen for mapping because it is the A-genome progenitor of cultivated peanut and also in order to circumvent the confounding effects of gene duplication associated with allopolyploidy in A. hypogaea. Results More than one million expressed sequence tag (EST) sequences generated from normalized cDNA libraries of A. duranensis were assembled into 81,116 unique transcripts. Mining this dataset, 1236 EST-SNP markers were developed between two A. duranensis accessions, PI 475887 and Grif 15036. An additional 300 SNP markers also were developed from genomic sequences representing conserved legume orthologs. Of the 1536 SNP markers, 1054 were placed on a genetic map. In addition, 598 EST-SSR markers identified in A. hypogaea assemblies were included in the map along with 37 disease resistance gene candidate (RGC) and 35 other previously published markers. In total, 1724 markers spanning 1081.3 cM over 10 linkage groups were mapped. Gene sequences that provided mapped markers were annotated using similarity searches in three different databases, and gene ontology descriptions were determined using the Medicago Gene Atlas and TAIR databases. Synteny analysis between A. duranensis, Medicago and Glycine revealed significant stretches of conserved gene clusters spread across the peanut genome. A higher level of colinearity was detected between A. duranensis and Glycine than with Medicago. Conclusions The first high-density, gene-based linkage map for A. duranensis was generated that can serve as a reference map for both wild and cultivated Arachis species. The markers developed here are valuable resources for the peanut, and more broadly, to the legume research community. The A-genome map will have utility for fine mapping in other peanut species and has already had application for mapping a nematode resistance gene that was introgressed into A. hypogaea from A. cardenasii.

2012-01-01

351

Characterization of unknown genetic modifications using high throughput sequencing and computational subtraction  

Microsoft Academic Search

BACKGROUND: When generating a genetically modified organism (GMO), the primary goal is to give a target organism one or several novel traits by using biotechnology techniques. A GMO will differ from its parental strain in that its pool of transcripts will be altered. Currently, there are no methods that are reliably able to determine if an organism has been genetically

Torstein Tengs; Haibo Zhang; Arne Holst-Jensen; Jon Bohlin; Melinka A Butenko; Anja Bråthen Kristoffersen; Hilde-Gunn Opsahl Sorteberg; Knut G Berdal

2009-01-01

352

GENETIC DIVERSITY OF CLETHRIONOMYS GLAREOLUS POPULATIONS FROM HIGHLY CONTAMINATED SITES IN THE CHORNOBYL REGION, UKRAINE  

Microsoft Academic Search

At radioactive sites, at least two mechanisms may affect the genetic diversity of populations of a given species. Increased mutation rates due to radiation exposure may increase the amount of genetic diversity in a population. Alternatively, population bottlenecks exacerbated by environmental degradation may lead to a reduction of diversity. The relationship between these two contradictory forces is complex. To explore

Cole W. Matson; Brenda E. Rodgers; Ronald K. Chesser; Robert J. Baker

2000-01-01

353

Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity  

Microsoft Academic Search

Cells respond to stimuli by changes in various processes, including signaling pathways and gene expression. Efforts to identify components of these responses increasingly depend on mRNA profiling and genetic library screens. By comparing the results of these two assays across various stimuli, we found that genetic screens tend to identify response regulators, whereas mRNA profiling frequently detects metabolic responses. We

Esti Yeger-Lotem; Laura Riva; Linhui Julie Su; Aaron D Gitler; Anil G Cashikar; Oliver D King; Pavan K Auluck; Melissa L Geddie; Julie S Valastyan; David R Karger; Susan Lindquist; Ernest Fraenkel

2009-01-01

354

High efficiency site-specific genetic engineering of the mosquito genome  

Microsoft Academic Search

Current techniques for the genetic engineering of insect genomes utilize transposable genetic elements, which are inefficient, have limited carrying capacity and give rise to position effects and insertional mutagenesis. As an alternative, we investigated two site-specific integration mechanisms in the yellow fever mosquito, Aedes aegypti . One was a modified CRE\\/ lox system from phage P1 and the other a

D. D. Nimmo; L. Alphey; J. M. Meredith; P. Eggleston

2006-01-01

355

Preliminary operational genetic management units of a highly fragmented forest tree species of southern South America  

Microsoft Academic Search

The management of the genetic resources of any wild species requires the definition of genetically homogeneous units about which practical decisions can be taken. To this end, a structure analysis was performed on the Patagonian cypress Austrocedrus chilensis (D.Don) Pic. Ser. et Bizzarri. A total of 746 seed trees corresponding to 27 natural populations sampled across its entire Argentinean range

Mario J. Pastorino; Leonardo A. Gallo

2009-01-01

356

In vivo localisation of the mitotic POLO kinase shows a highly dynamic association with the mitotic apparatus during early embryogenesis in Drosophila  

Microsoft Academic Search

The gene polo encodes a highly conserved serine\\/threonine protein kinase that has been implicated in several functions during cell division. Polo-like kinases are important positive regulators of cell cycle progression and have also been implicated in the exit from mitosis through the activation of the anaphase-promoting complex. Several data indicate that Plks are required for centrosome function, bipolar spindle organisation

Tatiana Moutinho-Santos; Paula Sampaio; Isabel Amorim; Madalena Costa; Claudio E Sunkel

1999-01-01

357

Do Elephants Show Empathy?  

Microsoft Academic Search

Elephants show a rich social organization and display a number of unusual traits. In this paper, we analyse reports collected over a thirty-five year period, describing behaviour that has the potential to reveal signs of empathic understanding. These include coalition formation, the offering of protection and comfort to others, retrieving and 'babysitting' calves, aiding individuals that would otherwise have difficulty

Lucy A. Bates; Phyllis C. Lee; Norah Njiraini; Joyce H. Poole; Katito Sayialel; Soila Sayialel; Cynthia J. Moss; Richard W. Byrne

2008-01-01

358

What Do Maps Show?  

ERIC Educational Resources Information Center

|This curriculum packet, appropriate for grades 4-8, features a teaching poster which shows different types of maps (different views of Salt Lake City, Utah), as well as three reproducible maps and reproducible activity sheets which complement the maps. The poster provides teacher background, including step-by-step lesson plans for four geography…

Geological Survey (Dept. of Interior), Reston, VA.

359

Shakespearean Slide Shows.  

ERIC Educational Resources Information Center

|Presents a condensed method for involving students in the kind of theatrical problem-solving that transforms a script to a play. Describes how to incorporate a "human slide show" into the class. Notes that students must read plays not just to understand events, but to make artistic choices about how to stage the action so that an audience…

Flynn, Rosalind M.

2002-01-01

360

Btu accounting: Showing results  

Microsoft Academic Search

In the preceding article in this series last month, the author showed how to calculate the energy consumed to make a pound of product. To realize a payoff, however, the results must be presented in graphs or tables that clearly display what has happened. They must call attention to plant performance and ultimately lead to more efficient use of energy.

1994-01-01

361

Stage a Water Show  

ERIC Educational Resources Information Center

In the author's book titled "The Incredible Water Show," the characters from "Miss Alaineus: A Vocabulary Disaster" used an ocean of information to stage an inventive performance about the water cycle. In this article, the author relates how she turned the story into hands-on science teaching for real-life fifth-grade students. The author also…

Frasier, Debra

2008-01-01

362

ISU Demonstration Road Show  

NSDL National Science Digital Library

The Idaho State University Department of Physics conducts science demonstration shows at SE Idaho schools. Four different presentations are currently available; "Forces and Motion", "States of Matter", "Electricity and Magnetism", and "Sound and Waves". Student activities and descriptions of the demonstrated material are also provided.

Shropshire, Steven

2004-04-06

363

Genetic diversity among selected ethnic subpopulations of Australia: evidence from three highly polymorphic DNA loci.  

PubMed

Immigration has been the principal source of population growth in Australia since European settlement began in 1788. As a result, the Australian gene pool has been constantly evolving, particularly over the last 50 years, during which peoples from many European and Asian countries have arrived in large numbers. Three highly polymorphic DNA loci (D1S80, HLA-DQA1, and human THO1) are used to assess the level of diversity among six immigrant subpopulations that compose significant elements in present-day Australia, namely, Asians, Italians, Greeks, Slavs, Middle Easterners, and a "general white" sample. Asian migrants are the most distinctive of the groups at all three loci, possessing the highest frequencies of alleles HLA-DQA1*3 and D1S80*27, *28, and *30, and an exceptionally high frequency of THO1*9. The European-derived groups cluster together separately from Asians, but Greeks are characterized by their frequencies of HLA-DQA1*2 and *4 and THO1*8. Middle Easterners lie on the fringe of the European cluster. When the results of the present study are combined with worldwide data for each of the three DNA markers, these hypervariable loci, especially D1S80 and THO1, are able to differentiate the major groups of humans. The level of population differentiation revealed by RST values for the three DNA markers is similar to or even less than the values recorded for the less polymorphic classical genetic markers. Therefore these three DNA markers are highly suitable for both forensic purposes and the investigation of population relationships. PMID:8754256

Robinson, S L; Gutowski, S J; van Oorschot, R A; Fripp, Y; Mitchell, J

1996-08-01

364

Genetic transformation of intact Lactococcus lactis subsp. lactis by high-voltage electroporation.  

PubMed Central

To apply recombinant DNA techniques for genetic manipulation of the industrially important lactococci, an efficient and reliable high-frequency transformation system must be available. High-voltage electric pulses have been demonstrated to enhance uptake of DNA into protoplasts and intact cells of numerous gram-negative and gram-positive microorganisms. The objective of this study was to develop a system for electroporating intact cells of Lactococcus lactis subsp. lactis LM0230 (previously designated Streptococcus lactis LM0230) with a commercially available electroporation unit (BTX Transfector 100; BTX, Inc., San Diego, Calif.). Parameters which influenced the efficiency of transformation included growth phase and final concentration of cells, ionic strength of the suspending medium, concentration of plasmid DNA, and the amplitude and duration of the pulse. Washed suspensions of intact cells suspended in deionized distilled water were subjected to one high-voltage electric pulse varying in voltage (300 to 900 V corresponding to field strengths of 5 to 17 kV/cm) and duration (100 microseconds to 1 s). Transformation efficiencies of 10(3) transformants per microgram of DNA were obtained when dense suspensions (final concentration, 5 x 10(10) CFU/ml) of stationary-phase cells were subjected to one pulse with a peak voltage of 900 V (field strength, 17 kV/cm) and a pulse duration of 5 ms in the presence of plasmid DNA. Dilution of porated cells in broth medium followed by an expression period of 2 h at 30 degrees C was beneficial in enhancing transformation efficiencies. Plasmids ranging in size from 9.8 to 30.0 kilobase pairs could be transformed by this procedure. Images

McIntyre, D A; Harlander, S K

1989-01-01

365

Single molecule analysis of the Arabidopsis FRA1 kinesin shows that it is a functional motor protein with unusually high processivity.  

PubMed

The Arabidopsis FRA1 kinesin contributes to the organization of cellulose microfibrils through an unknown mechanism. The cortical localization of this kinesin during interphase raises the possibility that it transports cell wall-related cargoes along cortical microtubules that either directly or indirectly influence cellulose microfibril patterning. To determine whether FRA1 is an authentic motor protein, we combined bulk biochemical assays and single molecule fluorescence imaging to analyze the motor properties of recombinant, GFP-tagged FRA1 containing the motor and coiled-coil domains (designated as FRA1(707)-GFP). We found that FRA1(707)-GFP binds to microtubules in an ATP-dependent manner and that its ATPase activity is dramatically stimulated by the presence of microtubules. Using single molecule studies, we found that FRA1(707)-GFP moves processively along microtubule tracks at a velocity of about 0.4? ?m?s(-1). In addition, we found that FRA1(707)-GFP is a microtubule plus-end-directed motor and that it moves along microtubules as a dimer. Interestingly, our single molecule analysis shows that the processivity of FRA1(707)-GFP is at least twice the processivity of conventional kinesin, making FRA1 the most processive kinesin to date. Together, our data show that FRA1 is a bona fide motor protein that has the potential to drive long-distance transport of cargo along cortical microtubules. PMID:21914648

Zhu, Chuanmei; Dixit, Ram

2011-09-13

366

Viewing television talk shows  

Microsoft Academic Search

We examined how motivation, audience activity, and attitudes influenced the likelihood of watching societal?issue and relational topics on television talk programs. Path analysis supported differences in ritualized and instrumental motives for watching talk shows. Information and exciting?entertainment motivation predicted greater’ realism of, affinity with, involvement with, and intent to watch talk television. Pass?time motivation predicted reduced affinity with and intent

Alan M. Rubin; Mary M. Step

1997-01-01

367

The Truman Show  

Microsoft Academic Search

The Truman Show is hardly a film you would automatically speak about as a game. At first glance, it is tempting to interpret the story of\\u000a Truman Burbank — his perpetual subjection to the artificial (televisual) world of Seahaven and its gargantuan reality TV project,\\u000a his eventual escape from the “OmniCam Ecosphere” building and the paternalistic surveillance of director Christof

Rolf F. Nohr

368

Capillary electrophoresis with electrochemiluminescent detection for highly sensitive assay of genetically modified organisms.  

PubMed

A capillary electrophoresis coupled with electrochemiluminescent detection system (CE-ECL) was developed for the detection of polymerase chain reaction (PCR) amplicons. The ECL luminophore, tris(1,10-phenanthroline) ruthenium(II) (Ru(phen)(3)(2+)), was labeled to the PCR primers before amplification. Ru(phen)(3)(2+) was then introduced to PCR amplicons by PCR amplification. Eventually, the PCR amplicons were separated and detected by the homemade CE-ECL system. The detection of a typical genetically modified organism (GMO), Roundup Ready Soy (RRS), was shown as an example to demonstrate the reliability of the proposed approach. Four pairs of primers were amplified by multiple PCR (MPCR) simultaneously, three of which were targeted on the specific sequence of exogenous genes of RRS, and another was targeted on the endogenous reference gene of soybean. Both the conditions for PCR amplification and CE-ECL separation and detection were investigated in detail. Results showed that, under the optimal conditions, the proposed method can accurately identifying RRS. The corresponding limit of detection (LOD) was below 0.01% with 35 PCR cycles. PMID:19902925

Guo, Longhua; Yang, Huanghao; Qiu, Bin; Xiao, Xueyang; Xue, Linlin; Kim, Donghwan; Chen, Guonan

2009-12-01

369

High Genetic Differentiation between the M and S Molecular Forms of Anopheles gambiae in Africa  

PubMed Central

Background Anopheles gambiae, a major vector of malaria, is widely distributed throughout sub-Saharan Africa. In an attempt to eliminate infective mosquitoes, researchers are trying to develop transgenic strains that are refractory to the Plasmodium parasite. Before any release of transgenic mosquitoes can be envisaged, we need an accurate picture of the differentiation between the two molecular forms of An. gambiae, termed M and S, which are of uncertain taxonomic status. Methodology/Principal Findings Insertion patterns of three transposable elements (TEs) were determined in populations from Benin, Burkina Faso, Cameroon, Ghana, Ivory Coast, Madagascar, Mali, Mozambique, Niger, and Tanzania, using Transposon Display, a TE-anchored strategy based on Amplified Fragment Length Polymorphism. The results reveal a clear differentiation between the M and S forms, whatever their geographical origin, suggesting an incipient speciation process. Conclusions/Significance Any attempt to control the transmission of malaria by An. gambiae using either conventional or novel technologies must take the M/S genetic differentiation into account. In addition, we localized three TE insertion sites that were present either in every individual or at a high frequency in the M molecular form. These sites were found to be located outside the chromosomal regions that are suspected of involvement in the speciation event between the two forms. This suggests that these chromosomal regions are either larger than previously thought, or there are additional differentiated genomic regions interspersed with undifferentiated regions.

Esnault, Caroline; Boulesteix, Matthieu; Duchemin, Jean Bernard; Koffi, Alphonsine A.; Chandre, Fabrice; Dabire, Roch; Robert, Vincent; Simard, Frederic; Tripet, Frederic; Donnelly, Martin J.; Fontenille, Didier; Biemont, Christian

2008-01-01

370

Exploring the genetic landscape in chronic lymphocytic leukemia using high-resolution technologies.  

PubMed

Abstract During recent years, microarray-based technologies and next-generation sequencing (NGS) have been applied in chronic lymphocytic leukemia (CLL) in order to identify novel genomic aberrations that may contribute to the pathogenesis of the disease. Even though high-resolution microarray studies have confirmed the importance of the known recurrent aberrations, i.e. del(11q), trisomy 12, del(13q) and del(17p), and have more precisely delineated the genomic borders of these aberrations, only a few novel aberrations, found at a low frequency, have been detected with these techniques. In contrast to this, the application of NGS technology of the coding genome (exome sequencing) or the entire genome (whole-genome sequencing) has unveiled a number of novel recurrent mutations in e.g. the NOTCH1, SF3B1 and BIRC3 genes. Importantly, mutations in these latter genes were reported to be associated with a particularly poor outcome, similar to TP53 aberrations, and may play key roles in tumor development, treatment resistance and prognosis. In this review, we not only summarize the latest achievements using array-based or NGS technologies, but also point to new directions for research aiming to unravel the complex genetic "map" in CLL and its prognostic subsets. PMID:23167608

Gunnarsson, Rebeqa; Mansouri, Larry; Rosenquist, Richard

2013-02-28

371

Heterogeneous T-cell response to MAGE-A10(254-262): high avidity-specific cytolytic T lymphocytes show superior antitumor activity.  

PubMed

MAGE-encoded antigens, which are expressed by tumors of many histological types but not in normal tissues, are suitable candidates for vaccine-based immunotherapy of cancers. Thus far, however, T-cell responses to MAGE antigens have been detected only occasionally in cancer patients. In contrast, by using HLA/peptide fluorescent tetramers, we have observed recently that CD8(+) T cells specific for peptide MAGE-A10(254-262) can be detected frequently in peptide-stimulated peripheral blood mononuclear cells from HLA-A2-expressing melanoma patients and healthy donors. On the basis of these results, antitumoral vaccination trials using peptide MAGE-A10(254-262) have been implemented recently. In the present study, we have characterized MAGE-A10(254-262)-specific CD8(+) T cells in polyclonal cultures and at the clonal level. The results indicate that the repertoire of MAGE-A10(254-262)-specific CD8(+) T cells is diverse both in terms of clonal composition, efficiency of peptide recognition, and tumor-specific lytic activity. Importantly, only CD8(+) T cells able to recognize the antigenic peptide with high efficiency are able to lyse MAGE-A10-expressing tumor cells. Under defined experimental conditions, the tetramer staining intensity exhibited by MAGE-A10(254-262)-specific CD8(+) T cells correlates with efficiency of peptide recognition so that "high" and "low" avidity cells can be separated by FACS. Altogether, the data reported here provide evidence for functional diversity of MAGE-A10(254-262)-specific T cells and will be instrumental for the monitoring of peptide MAGE-A10(254-262)-based clinical trials. PMID:11479225

Dutoit, V; Rubio-Godoy, V; Dietrich, P Y; Quiqueres, A L; Schnuriger, V; Rimoldi, D; Liénard, D; Speiser, D; Guillaume, P; Batard, P; Cerottini, J C; Romero, P; Valmori, D

2001-08-01

372

Imidazenil: a low efficacy agonist at alpha1- but high efficacy at alpha5-GABAA receptors fail to show anticonvulsant cross tolerance to diazepam or zolpidem.  

PubMed

Whereas advances in the molecular biology of GABA(A) receptor complex using knock-out and knock-in mice have been valuable in unveiling the structure, composition, receptor assembly, and several functions of different GABA(A) receptor subtypes, the mechanism(s) underlying benzodiazepine (BZ) tolerance and withdrawal remain poorly understood. Studies using specific GABA(A) receptor subunit knock-in mice suggest that tolerance to sedative action of diazepam requires long-term activation of alpha1 and alpha5 GABA(A) receptor subunits. We investigated the role of long-term activation of these GABA(A) receptor subunits during anticonvulsant tolerance using high affinity and high intrinsic efficacy ligands for GABA(A) receptors expressing the alpha5 subunit (imidazenil) or alpha1 subunit (zolpidem), and a non-selective BZ recognition site ligand (diazepam). We report here that long-term activation of GABA(A) receptors by zolpidem and diazepam but not by imidazenil elicits anticonvulsant tolerance. Although anticonvulsant cross-tolerance occurs between diazepam and zolpidem, there is no cross-tolerance between imidazenil and diazepam or zolpidem. Furthermore, diazepam or zolpidem long-term treatment decreased the expression of mRNA encoding the alpha1 GABA(A) receptor subunit in prefrontal cortex by 43% and 20% respectively. In addition, diazepam but not zolpidem long-term treatment produced a 30% increase in the expression of the alpha5 GABA(A) receptor subunit mRNA in prefrontal cortex. In contrast, imidazenil which is devoid of anticonvulsant tolerance does not elicit significant changes in the expression of alpha1 or alpha5 GABA(A) receptor subunit. These findings suggest that long-term activation of GABA(A) receptors containing the alpha1 or other subunits but not the alpha5 receptor subunit is essential for the induction of anticonvulsant tolerance. PMID:18555494

Auta, James; Impagnatiello, Francesco; Kadriu, Bashkim; Guidotti, Alessandro; Costa, Erminio

2008-05-09

373

Imidazenil: A Low Efficacy Agonist at ?1- but High Efficacy at ?5-GABAA Receptors Fail to Show Anticonvulsant Cross Tolerance to Diazepam or Zolpidem  

PubMed Central

SUMMARY Whereas advances in the molecular biology of GABAA receptor complex using knock-out and knock-in mice have been valuable in unveiling the structure, composition, receptor assembly, and several functions of different GABAA receptor subtypes, the mechanism(s) underlying benzodiazepine (BZ) tolerance and withdrawal remain poorly understood. Studies using specific GABAA receptor subunit knock-in mice suggest that tolerance to sedative action of diazepam requires long-term activation of ?1 and ?5 GABAA receptor subunits. We investigated the role of long-term activation of these GABAA receptor subunits during anticonvulsant tolerance using high affinity and high intrinsic efficacy ligands for GABAA receptors expressing the ?5 subunit (imidazenil) or ?1 subunit (Zolpidem), and a non-selective BZ recognition site ligand (diazepam). We report here that long-term activation of GABAA receptors by zolpidem and diazepam but not by imidazenil elicits anticonvulsant tolerance. Although anticonvulsant cross-tolerance occurs between diazepam and zolpidem, there is no cross-tolerance between imidazenil and diazepam or zolpidem. Furthermore, diazepam or zolpidem long-term treatment decreased the expression of mRNA encoding the ?1 GABAA receptor subunit in prefrontal cortex by 43% and 20% respectively. In addition, diazepam but not zolpidem long-term treatment produced a 30% increase in the expression of the ?5 GABAA receptor subunit mRNA in prefrontal cortex. In contrast, imidazenil which is devoid of anticonvulsant tolerance does not elicit significant changes in the expression of ?1 or ?5 GABAA receptor subunit. These findings suggest that long-term activation of GABAA receptors containing the ?1 or other subunits but not the ?5 receptor subunit is essential for the induction of anticonvulsant tolerance.

Auta, James; Impagnatiello, Francesco; Kadriu, Bashkim; Guidotti, Alessandro; Costa, Erminio

2008-01-01

374

Impact of a microRNA MIR137 susceptibility variant on brain function in people at high genetic risk of schizophrenia or bipolar disorder.  

PubMed

A recent 'mega-analysis' combining genome-wide association study data from over 40,000 individuals identified novel genetic loci associated with schizophrenia (SCZ) at genome-wide significance level. The strongest finding was a locus within an intron of a putative primary transcript for microRNA MIR137. In the current study, we examine the impact of variation at this locus (rs1625579, G/T; where T is the common and presumed risk allele) on brain activation during a sentence completion task that differentiates individuals with SCZ, bipolar disorder (BD), and their relatives from controls. We examined three groups of individuals performing a sentence completion paradigm: (i) individuals at high genetic risk of SCZ (n=44), (ii) individuals at high genetic risk of BD (n=90), and (iii) healthy controls (n=81) in order to test the hypothesis that genotype at rs1625579 would influence brain activation. Genotype groups were assigned as 'RISK-' for GT and GG individuals, and 'RISK+' for TT homozygotes. The main effect of genotype was significantly greater activation in the RISK- individuals in the posterior right medial frontal gyrus, BA 6. There was also a significant genotype(*)group interaction in the left amygdala and left pre/postcentral gyrus. This was due to differences between the controls (where individuals with the RISK- genotype showed greater activation than RISK+ subjects) and the SCZ high-risk group, where the opposite genotype effect was seen. These results suggest that the newly identified SCZ locus may influence brain activation in a manner that is partly dependent on the presence of existing genetic susceptibility for SCZ. PMID:22850735

Whalley, Heather C; Papmeyer, Martina; Romaniuk, Liana; Sprooten, Emma; Johnstone, Eve C; Hall, Jeremy; Lawrie, Stephen M; Evans, Kathryn L; Blumberg, Hilary P; Sussmann, Jessika E; McIntosh, Andrew M

2012-08-01

375

NPR: The Picture Show  

NSDL National Science Digital Library

National Public Radio's "The Picture Show" photo blog is a great way to avoid culling through the thousands of less interesting and engaging photographs on the web. With a dedicated team of professionals, this blog brings together different posts that profile various sets of photographs that cover 19th century war in Afghanistan, visual memories of WWII, unpublished photographs of JFK's presidential campaign, and abandoned buildings on the islands in Boston Harbor. Visitors can search through previous posts, use social media features to share the photo features with friends, and also sign up to receive new materials via their RSS feed. There's quite a nice mix of material here, and visitors can also comment on the photos and recommend the collection to friends and others.

376

Egg: the Arts Show  

NSDL National Science Digital Library

"Egg is a new TV show about people making art across America" from PBS. This accompanying Website presents excerpts from sixteen episodes of the series, with three more "hatching soon," such as Close to Home, profiling three photographers: Jeanine Pohlhaus, whose pictures document her father's struggle with mental illness; Gregory Crewdson's photos of Lee, Massachusetts; and Joseph Rodriguez's photos of Hispanics in New York City. Excerpts include video clips, gallery listings where the artists' work can be seen, and short interviews with artists. Some episodes also offer "peeps," glimpses of material not shown on TV, such as the Space episode's peep, Shooting Stars, that provides directions for astrophotography, taking photographs of star trails. Other sections of the site are airdates, for local listings; see and do usa, where vacationers can search for art events at their destinations; and egg on the arts, a discussion forum.

377

American History Picture Show  

NSDL National Science Digital Library

In class we read Katie's Picture Show, a book about a girl who discovers art first-hand one day at an art museum in London. She realizes she can climb into the paintings, explore her surroundings, and even solve problems for the subjects of the paintings. As part of our unit on American history, we are going to use art to further learn about some of the important events we have been discussing. Each of these works of art depicts an important event in American History. When you click on a picture, you will be able to see the name of the event as well as the artist who created it. You will be using all three pictures for this assignment.Use the websites ...

Bennion, Ms.

2009-11-23

378

Co5/Co8-cluster-based coordination polymers showing high-connected self-penetrating networks: syntheses, crystal structures, and magnetic properties.  

PubMed

Two novel Co(II)-cluster-based coordination polymers--namely, [Co5(?3-OH)2(1,4-ndc)4(bix)2]n (1) and {[Co8(?3-OH)4(1,4-ndc)6(btp)(H2O)6]·H2O}n (2)--were prepared by hydrothermal reactions of Co(II) perchlorate with 1,4-naphthalenedicarboxylic acid (1,4-H2ndc) and different N-donor coligands (bix = 1,4-bis(imidazol-1-ylmethyl)benzene and btp = 4,4'-bis(triazol-1-ylmethyl)biphenyl). In 1, 10-connected [Co5(?3-OH)2(COO)8] clusters are extended by the ?4-1,4-ndc(2-) and trans-bix ligands to construct a rare, self-penetrating ile framework that can interestingly be regarded as the cross-link of two interpenetrating 6-connected pcu networks. While for 2, [Co8(?3-OH)4(COO)12] clusters serve as the 8-connected nodes, which are bridged by the ?4/?5-1,4-ndc(2-) and trans-btp ligands to afford the highest-connected uninodal self-penetrating (4(20).6(8)) network based on octacobalt clusters. A synthetic and structural comparison of 1 and 2 demonstrates that the features of auxiliary N-donor ligands play a key role in governing the in situ formed clusters and the final 3-D coordination frameworks. Magnetic susceptibility measurements indicate that complex 1 shows an antiferromagnetic interaction between the adjacent Co(II) ions, whereas 2 displays the dominant antiferromagnetic exchanges in 300-50 K and a ferrimagnetic-like behavior at lower temperatures. PMID:23819571

Li, Dong-Sheng; Zhao, Jun; Wu, Ya-Pan; Liu, Bin; Bai, Liang; Zou, Kun; Du, Miao

2013-07-02

379

Randomised controlled trial shows that glyceryl trinitrate heals anal fissures, higher doses are not more effective, and there is a high recurrence rate  

PubMed Central

BACKGROUND—Topical application of glyceryl trinitrate (GTN) ointment heals chronic anal fissures, providing an alternative to the traditional first line treatment of surgical sphincterotomy. ?AIMS—To determine the most effective dose of topical GTN for treatment of chronic anal fissures and to assess long term results. ?METHODS—Seventy consecutive patients with chronic anal fissure, were randomly allocated to eight weeks treatment with placebo, 0.2% GTN three times daily, or GTN starting at 0.2% with weekly 0.1% increments to a maximum of 0.6%, in a double blind study. ?RESULTS—After eight weeks fissure had healed in 67% of patients treated with GTN compared with 32% with placebo (p=0.008). No significant difference was seen between the two active treatments. Headaches were reported by 72% of patients on GTN compared with 27% on placebo (p<0.001). Maximum anal sphincter pressure reduced significantly from baseline by GTN treatment (p=0.02), but not placebo (p=0.8). Mean pain scores were lower after treatment with GTN compared with placebo (NS). Of fissures healed with placebo 43% recurred, compared with 33% of those healed with 0.2% GTN and 25% healed with escalating dose GTN (p=0.7). ?CONCLUSIONS—GTN is a good first line treatment for two thirds of patients with anal fissure. An escalating dose of GTN does not result in earlier healing. Significant recurrence of symptomatic fissures and a high incidence of headaches are limitations of the treatment. ?? Keywords: glyceryl trinitrate; anal fissures

Carapeti, E; Kamm, M; McDonald, P; Chadwick, S; Melville, D; Phillips, R

1999-01-01

380

Genetic Determinants of Sindbis Virus Mosquito Infection Are Associated with a Highly Conserved Alphavirus and Flavivirus Envelope Sequence?  

PubMed Central

Wild-type Sindbis virus (SINV) strain MRE16 efficiently infects Aedes aegypti midgut epithelial cells (MEC), but laboratory-derived neurovirulent SINV strain TE/5?2J infects MEC poorly. SINV determinants for MEC infection have been localized to the E2 glycoprotein. The E2 amino acid sequences of MRE16 and TE/5?2J differ at 60 residue sites. To identify the genetic determinants of MEC infection of MRE16, the TE/5?2J virus genome was altered to contain either domain chimeras or more focused nucleotide substitutions of MRE16. The growth patterns of derived viruses in cell culture were determined, as were the midgut infection rates (MIR) in A. aegypti mosquitoes. The results showed that substitutions of MRE16 E2 aa 95 to 96 and 116 to 119 into the TE/5?2J virus increased MIR both independently and in combination with each other. In addition, a unique PPF/.GDS amino acid motif was located between these two sites that was found to be a highly conserved sequence among alphaviruses and flaviviruses but not other arboviruses.

Pierro, Dennis J.; Powers, Erik L.; Olson, Ken E.

2008-01-01

381

Genetic Affinities between Trans-Oceanic Populations of Non-Buoyant Macroalgae in the High Latitudes of the Southern Hemisphere  

PubMed Central

Marine biologists and biogeographers have long been puzzled by apparently non-dispersive coastal taxa that nonetheless have extensive transoceanic distributions. We here carried out a broad-scale phylogeographic study to test whether two widespread Southern Hemisphere species of non-buoyant littoral macroalgae are capable of long-distance dispersal. Samples were collected from along the coasts of southern Chile, New Zealand and several subAntarctic islands, with the focus on high latitude populations in the path of the Antarctic Circumpolar Current or West Wind Drift. We targeted two widespread littoral macroalgal species: the brown alga Adenocystisutricularis (Ectocarpales, Heterokontophyta) and the red alga Bostrychiaintricata (Ceramiales, Rhodophyta). Phylogenetic analyses were performed using partial mitochondrial (COI), chloroplast (rbcL) and ribosomal nuclear (LSU / 28S) DNA sequence data. Numerous deeply-divergent clades were resolved across all markers in each of the target species, but close phylogenetic relationships – even shared haplotypes – were observed among some populations separated by large oceanic distances. Despite not being particularly buoyant, both Adenocystisutricularis and Bostrychiaintricata thus show genetic signatures of recent dispersal across vast oceanic distances, presumably by attachment to floating substrata such as wood or buoyant macroalgae.

Fraser, Ceridwen I.; Zuccarello, Giuseppe C.; Spencer, Hamish G.; Salvatore, Laura C.; Garcia, Gabriella R.; Waters, Jonathan M.

2013-01-01

382

Postmenopausal women with osteoporosis and osteoarthritis show different microstructural characteristics of trabecular bone in proximal tibia using high-resolution magnetic resonance imaging at 3 tesla  

PubMed Central

Background Osteoporosis (OP) and osteoarthritis (OA) are two common musculoskeletal disorders that affect the quality of life in aged people. An inverse relationship between OP and OA was proposed four decades ago. However, the difference in microstructure of the trabecular bone of these two disorders by high-resolution MRI (HR-MRI) has not been compared. The primary objective of the study is to explain the actual relationship between OA and OP based on differences between bone microstructure of these two diseases. The secondary objectives are to find out the significance of Euler number and its relationship with other structural parameters, and important role of HR-MRI to reveal the microstructure of trabecular bone directly. Methods Totally, 30 women with OP and 30 women with OA (n?=?60) were included in this study. Primary OA of hip, knee, as well as spinal arthrosis were diagnosed according to plain X-ray film findings. Osteoporosis was defined based on the latest criteria of World Health Organization (WHO). Structural and textural parameters derived from HR-MRI images of proximal tibia were calculated and compared with special software. Results There were significant differences in apparent bone volume fraction, trabecular thickness, mean roundness, Euler number, entropy and inverse different moment between OP and OA patients. In OP group, apparent trabecular separation (Tb.Sp), inertia, absolute value and contrast were positively correlated with Euler number, whereas apparent trabecular number (Tb.N), mean trabecular area, inverse difference and inverse different moment were negatively correlated. Apparent trabecular bone volume fraction (BV/TV), mean trabecular area, mean trabecular perimeter and mean skeleton length negatively correlated with Euler number in OA group. Inverse different moment was the texture parameter, which influenced bone mineral density (BMD) of femoral neck, meanwhile contrast influenced BMD of both great trochanter and Ward’s triangle in OP group. While in OA group, Euler number was the exclusive parameter, which affected BMD of femoral neck and Ward’s triangle. Conclusions We found significant differences in microstructure parameters derived from HR-MRI images between postmenopausal women with OP and OA. It convincingly supports the hypothesis that there might be an inverse relationship between OP and OA.

2013-01-01

383

High-efficiency derivation of human embryonic stem cell lines following pre-implantation genetic diagnosis  

Microsoft Academic Search

Pre-implantation genetic diagnosis allows the characterisation of embryos that carry a gene responsible for a severe monogenic\\u000a disease and to transfer to the mother’s uterus only the unaffected one(s). The genetically affected embryos can be used to\\u000a establish human embryonic stem cell (hESC) lines. We are currently establishing a cell bank of ESC lines carrying specific\\u000a disease-causing mutant genes. These

Philippe Tropel; Johana Tournois; Julien Côme; Christine Varela; Céline Moutou; Pascal Fragner; Michel Cailleret; Yacine Laâbi; Marc Peschanski; Stéphane Viville

2010-01-01

384

Foraging segregation and genetic divergence between geographically proximate colonies of a highly mobile seabird  

Microsoft Academic Search

Foraging segregation may play an important role in the maintenance of animal diversity, and is a proposed mechanism for promoting\\u000a genetic divergence within seabird species. However, little information exists regarding its presence among seabird populations.\\u000a We investigated genetic and foraging divergence between two colonies of endangered Hawaiian petrels (Pterodroma sandwichensis) nesting on the islands of Hawaii and Kauai using the

Anne E. Wiley; Andreanna J. Welch; Peggy H. Ostrom; Helen F. James; Craig A. Stricker; Robert C. Fleischer; Hasand Gandhi; Josh Adams; David G. Ainley; Fern Duvall; Nick Holmes; Darcy Hu; Seth Judge; Jay Penniman; Keith A. Swindle

385

High sexual reproduction and limited contemporary dispersal in the ectomycorrhizal fungus Tricholoma scalpturatum: new insights from population genetics and spatial autocorrelation analysis.  

PubMed

Dispersal and establishment are fundamental processes influencing the response of species to environmental changes, and the long-term persistence of populations. A previous study on the symbiotic ectomycorrhizal fungus Tricholoma scalpturatum revealed strong genetic differentiations between populations in Western Europe, suggesting restricted dispersal for this wind-dispersed cosmopolitan fungus. Two distinct genetic groups (genetic groups 1 and 2), co-occurring in some locations, were also identified and could correspond to cryptic species. In the present work, we examine the reproductive strategy and dispersal biology of the two T. scalpturatum's genetic groups. Variable molecular markers (intersimple sequence repeats and intergenic spacer 2-restriction fragment length polymorphisms) and spatial autocorrelation analyses were used to examine fine-scale patterns (< 140 m) o