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1

Isolated populations of a rare alpine plant show high genetic diversity and considerable population differentiation  

PubMed Central

Background and Aims Gene flow and genetic variability within and among alpine plant populations can be greatly influenced by the steep environmental gradients and heterogeneous topography of alpine landscapes. In this study, the effects are examined of natural isolation of alpine habitats on genetic diversity and geographic structure in populations of C. thyrsoides, a rare and isolated European Alpine monocarpic perennial with limited seed dispersal capacity. Methods Molecular diversity was analysed for 736 individuals from 32 populations in the Swiss Alps and adjacent Jura mountains using five polymorphic microsatellite loci. Pollen flow was estimated using pollen grain-sized fluorescent powder. In addition, individual-based Bayesian approaches were applied to examine population structure. Key Results High within-population genetic diversity (HE = 0·76) and a relatively low inbreeding coefficient (FIS = 0·022) were found. Genetic differentiation among populations measured with a standardized measure was considerable (G?ST = 0·53). A significant isolation-by-distance relationship was found (r = 0·62, P < 0·001) and a significant geographic sub-structure, coinciding with proposed postglacial migration patterns. Altitudinal location and size of populations did not influence molecular variation. Direct measures of pollen flow revealed that insect-mediated pollen dispersal was restricted to short distances within a population. Conclusions The natural isolation of suitable habitats for C. thyrsoides restricts gene flow among the populations as expected for a monocarpic species with very limited seed dispersal capacities. The observed high within-population genetic diversity in this rare monocarpic perennial is best explained by its outcrossing behaviour, long-lived individuals and overlapping generations. Despite the high within-population genetic diversity, the considerable genetic differentiation and the clear western–eastern differentiation in this species merits consideration in future conservation efforts. PMID:19797423

AEgisdottir, Hafdis Hanna; Kuss, Patrick; Stocklin, Jurg

2009-01-01

2

X-chromosome SNP analyses in 11 human Mediterranean populations show a high overall genetic homogeneity except in North-west Africans (Moroccans)  

PubMed Central

Background Due to its history, with a high number of migration events, the Mediterranean basin represents a challenging area for population genetic studies. A large number of genetic studies have been carried out in the Mediterranean area using different markers but no consensus has been reached on the genetic landscape of the Mediterranean populations. In order to further investigate the genetics of the human Mediterranean populations, we typed 894 individuals from 11 Mediterranean populations with 25 single-nucleotide polymorphisms (SNPs) located on the X-chromosome. Results A high overall homogeneity was found among the Mediterranean populations except for the population from Morocco, which seemed to differ genetically from the rest of the populations in the Mediterranean area. A very low genetic distance was found between populations in the Middle East and most of the western part of the Mediterranean Sea. A higher migration rate in females versus males was observed by comparing data from X-chromosome, mt-DNA and Y-chromosome SNPs both in the Mediterranean and a wider geographic area. Multilocus association was observed among the 25 SNPs on the X-chromosome in the populations from Ibiza and Cosenza. Conclusion Our results support both the hypothesis of (1) a reduced impact of the Neolithic Wave and more recent migration movements in NW-Africa, and (2) the importance of the Strait of Gibraltar as a geographic barrier. In contrast, the high genetic homogeneity observed in the Mediterranean area could be interpreted as the result of the Neolithic wave caused by a large demic diffusion and/or more recent migration events. A differentiated contribution of males and females to the genetic landscape of the Mediterranean area was observed with a higher migration rate in females than in males. A certain level of background linkage disequilibrium in populations in Ibiza and Cosenza could be attributed to their demographic background. PMID:18312628

2008-01-01

3

Spatial and temporal genetic analyses show high gene flow among European corn borer (Lepidoptera: Crambidae) populations across the central U.S. corn belt.  

PubMed

European corn borer, Ostrinia nubilalis (Hübner), adults were sampled at 13 sites along two perpendicular 720-km transects intersecting in central Iowa and for the following two generations at four of the same sites separated by 240 km in the cardinal directions. More than 50 moths from each sample location and time were genotyped at eight microsatellite loci. Spatial analyses indicated that there is no spatial genetic structuring between European corn borer populations sampled 720 km apart at the extremes of the transects and no pattern of genetic isolation by distance at that geographic scale. Although these results suggest high gene flow over the spatial scale tested, it is possible that populations have not had time to diverge since the central Corn Belt was invaded by this insect approximately 60 yr ago. However, temporal analyses of genetic changes in single locations over time suggest that the rate of migration is indeed very high. The results of this study suggest that the geographic dimensions of European corn borer populations are quite large, indicating that monitoring for resistance to transgenic Bt corn at widely separated distances is justified, at least in the central Corn Belt. High gene flow further implies that resistance to Bt corn may be slow to evolve, but once it does develop, it may spread geographically with such speed that mitigation strategies will have to be implemented quickly to be effective. PMID:19689914

Kim, Kyung Seok; Bagley, Mark J; Coates, Brad S; Hellmich, Richard L; Sappington, Thomas W

2009-08-01

4

Plasmodium vivax Isolates from Cambodia and Thailand Show High Genetic Complexity and Distinct Patterns of P. vivax Multidrug Resistance Gene 1 (pvmdr1) Polymorphisms  

PubMed Central

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.

2013-01-01

5

Northwestern song sparrow populations show genetic effects of sequential colonization.  

PubMed

Two genetic consequences are often considered evidence of a founder effect: substantial loss in genetic diversity and rapid divergence between source and founder populations. Single-step founder events have been studied for these effects, but with mixed results, causing continued controversy over the role of founder events in divergence. Experiments of serial bottlenecks have shown losses of diversity, increased divergence, and rapid behavioural changes possibly leading to reproductive isolation between source and final populations. The few studies conducted on natural, sequentially founded systems show some evidence of these effects. We examined a natural vertebrate system of sequential colonization among northwestern song sparrows (Melospiza melodia). This system has an effectively linear distribution, it was probably colonized within the last 10,000 years, there are morphological and behavioural differences among populations, and the westernmost populations occur in atypical habitats for the species. Eight microsatellite loci from eight populations in Alaska and British Columbia (n = 205) showed stepwise loss of genetic diversity, genetic evidence for strong population bottlenecks, and increased population divergence. The endpoint population on Attu Island has extremely low diversity (H(E) = 0.18). Our study shows that sequential bottlenecks or founder events can have powerful genetic effects in reducing diversity, possibly leading to rapid evolutionary divergence. PMID:15813781

Pruett, Christin L; Winker, Kevin

2005-04-01

6

Courtship and genetic quality: asymmetric males show their best side  

Microsoft Academic Search

Fluctuating asymmetry (FA), the small random deviations from perfect morphological symmetry that result during development, is ubiquitous throughout the animal kingdom. In many species, FA seems to play a role in mate choice, perhaps because it signals an individual's genetic quality and health. However, the relationship between an individual's FA and behaviour is generally unknown: what do more asymmetric individuals

Mart R. Gross; Ho Young Suk; Cory T. Robertson

2007-01-01

7

Molecular Markers Show How Pollen and Seed Dispersal Affect Population Genetic  

E-print Network

485 Molecular Markers Show How Pollen and Seed Dispersal Affect Population Genetic Structure of fragmentation and decreased population sizes is reduced genetic diversity as populations become increasingly. Earlier studies indicated biochemical differentiation of central coast populations from those of Northern

Standiford, Richard B.

8

Invading populations of an ornamental shrub show rapid life history evolution despite genetic  

E-print Network

highlight the potential for even genetically depauperate founding populations to adapt and evolve invasiveLETTER Invading populations of an ornamental shrub show rapid life history evolution despite genetic bottlenecks Katrina M. Dlugosch* and Ingrid M. Parker Ecology and Evolutionary Biology, University

Linder, Tamás

9

Genetic Variants Associated with Complex Human Diseases Show Wide Variation across Multiple Populations  

Microsoft Academic Search

Background: The wide use of genome wide association studies (GWAS) has led to the successful identification of multiple genetic susceptibility variants to several complex human diseases. Given the limited amount of data on genetic variation at these loci in populations of non-European origin, we investigated population variation among 11 population groups for loci showing strong and consistent association from GWAS

A. Adeyemo; C. Rotimi

2010-01-01

10

Genome-Wide Association Scan Shows Genetic Variants in the FTO Gene  

E-print Network

Genome-Wide Association Scan Shows Genetic Variants in the FTO Gene Are Associated with Obesity, Baltimore, Maryland, United States of America, 3 Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, United States of America, 4 Istituto di

Abecasis, Goncalo

11

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. PMID:22016614

Kulik, Tomasz; Pszczolkowska, Agnieszka; Lojko, Maciej

2011-01-01

12

Amphibian DNA shows marked genetic structure and tracks pleistocene climate change in northeastern Brazil.  

PubMed

The glacial refugia paradigm has been broadly applied to patterns of species dynamics and population diversification. However, recent geological studies have demonstrated striking Pleistocene climate changes in currently semiarid northeastern Brazil at time intervals much more frequent than the climatic oscillations associated with glacial and interglacial periods. These geomorphic data documented recurrent pulses of wet regimes in the past 210,000 years that correlate with climate anomalies affecting multiple continents. While analyzing DNA sequences of two mitochondrial genes (cytochrome b and NADH-dehydrogenase subunit 2) and one nuclear marker (cellular-myelocytomatosis proto-oncogene) in the forest-associated frogs Proceratophrys boiei and Ischnocnema gr. ramagii, we found evidence of biological responses consistent with these pluvial maxima events. Sampled areas included old, naturally isolated forest enclaves within the semiarid Caatinga, as well as recent man-made fragments of humid coastal Atlantic forest. Results show that mtDNA lineages in enclave populations are monophyletic or nearly so, whereas nonenclave populations are polyphyletic and more diverse. The studied taxa show evidence of demographic expansions at times that match phases of pluvial maxima inferred from geological data. Divergence times between several populations fall within comparatively drier intervals suggested by geomorphology. Mitochondrial and nuclear data show local populations to be genetically structured, with some high levels of differentiation that suggest the need of further taxonomic work. PMID:17941838

Carnaval, Ana Carolina; Bates, John M

2007-12-01

13

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. PMID:21311598

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

2011-01-01

14

16. Aerial view, high vertical view showing site in immediate ...  

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

16. Aerial view, high vertical view showing site in immediate context. Top of photo is East. Photo by Eastern Topographics, Wolfeboro, N. H., Jan. 1986. - Lawrence Machine Shop, Union & Canal Streets, Lawrence, Essex County, MA

15

13. VIEW, LOOKING WEST FROM LEFT TO RIGHT, SHOWING HIGH ...  

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

13. VIEW, LOOKING WEST FROM LEFT TO RIGHT, SHOWING HIGH PRESSURE AIR FLASK ROOM AND PUMP ROOM - U.S. Naval Submarine Base, New London Submarine Escape Training Tank, Albacore & Darter Roads, Groton, New London County, CT

16

A twin study of ADHD symptoms in early adolescence: hyperactivity-impulsivity and inattentiveness show substantial genetic overlap but also genetic specificity.  

PubMed

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 on the DSM-IV based Revised Conners' Parent Rating Scale to assess symptoms on both ADHD dimensions. Heritabilities were high (around 70%) for both hyperactivity-impulsivity and inattentiveness and evidence for etiological sex differences was absent. The critical finding was a genetic correlation of 0.55, indicating that hyperactivity-impulsivity and inattentiveness are substantially influenced by the same genes but that the two dimensions also show large and significant unique genetic effects. These results in early adolescence confirm our findings in middle childhood, providing evidence for substantial genetic overlap as well as genetic heterogeneity of the ADHD dimensions. Future genetic studies should investigate the ADHD dimensions separately. PMID:21336711

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

2011-02-01

17

26. VIEW OF PUMP ROOM, SHOWING PORTIONS OF HIGH PRESSURE ...  

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

26. VIEW OF PUMP ROOM, SHOWING PORTIONS OF HIGH PRESSURE AIR SYSTEM AT LEFT AND CENTER AND OVERFLOW STORAGE TANK AT RIGHT, LOOKING NORTHWEST - U.S. Naval Submarine Base, New London Submarine Escape Training Tank, Albacore & Darter Roads, Groton, New London County, CT

18

Two invasive populations of the dry rot fungus Serpula lacrymans show divergent population genetic structures.  

PubMed

The dry rot fungus Serpula lacrymans is a devastating basidiomycete occurring in wooden constructions in temperate regions worldwide. In this study, we compare the genetic structures of two invasive populations from Europe and Japan. Microsatellite data from 14 loci and DNA sequences from four loci demonstrated that the two populations were highly differentiated. Significant isolation by distance effect was observed in Europe and Japan. Higher genetic variation was observed within the Japanese population than within the European population, corresponding with the observed higher richness of vegetative compatibility types in Japan, indicating that there has been a higher level of gene flow from the Asian source populations to Japan than to Europe. The European population is genetically more homogenous with only six detected vegetative compatibility types. Various tests indicate that both the European and the Japanese populations have gone through population bottlenecks prior to population expansion. No identical multi-locus genotypes were observed within Japan and very few within Europe, indicating limited clonal dispersal. Deviations from Hardy Weinberg expectations were observed both in Europe and Japan and heterozygote excess were observed at several loci, especially in Europe. Possible explanations for this pattern are discussed. PMID:20089125

Engh, Ingeborg Bjorvand; Carlsen, Tor; Saetre, Glenn-Peter; Högberg, Nils; Doi, Shuichi; Kauserud, Håvard

2010-02-01

19

Mixtures of thermostable enzymes show high performance in biomass saccharification.  

PubMed

Optimal enzyme mixtures of six Trichoderma reesei enzymes and five thermostable enzyme components were developed for the hydrolysis of hydrothermally pretreated wheat straw, alkaline oxidised sugar cane bagasse and steam-exploded bagasse by statistically designed experiments. Preliminary studies to narrow down the optimization parameters showed that a cellobiohydrolase/endoglucanase (CBH/EG) ratio of 4:1 or higher of thermostable enzymes gave the maximal CBH-EG synergy in the hydrolysis of hydrothermally pretreated wheat straw. The composition of optimal enzyme mixtures depended clearly on the substrate and on the enzyme system studied. The optimal enzyme mixture of thermostable enzymes was dominated by Cel7A and required a relatively high amount of xylanase, whereas with T. reesei enzymes, the high proportion of Cel7B appeared to provide the required xylanase activity. The main effect of the pretreatment method was that the required proportion of xylanase was higher and the proportion of Cel7A lower in the optimized mixture for hydrolysis of alkaline oxidised bagasse than steam-exploded bagasse. In prolonged hydrolyses, less Cel7A was generally required in the optimal mixture. Five-component mixtures of thermostable enzymes showed comparable hydrolysis yields to those of commercial enzyme mixtures. PMID:24752938

Kallioinen, Anne; Puranen, Terhi; Siika-aho, Matti

2014-07-01

20

A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy  

PubMed Central

Background Miscanthus (subtribe Saccharinae, tribe Andropogoneae, family Poaceae) is a genus of temperate perennial C4 grasses whose high biomass production makes it, along with its close relatives sugarcane and sorghum, attractive as a biofuel feedstock. The base chromosome number of Miscanthus (x = 19) is different from that of other Saccharinae and approximately twice that of the related Sorghum bicolor (x = 10), suggesting large-scale duplications may have occurred in recent ancestors of Miscanthus. Owing to the complexity of the Miscanthus genome and the complications of self-incompatibility, a complete genetic map with a high density of markers has not yet been developed. Results We used deep transcriptome sequencing (RNAseq) from two M. sinensis accessions to define 1536 single nucleotide variants (SNVs) for a GoldenGate™ genotyping array, and found that simple sequence repeat (SSR) markers defined in sugarcane are often informative in M. sinensis. A total of 658 SNP and 210 SSR markers were validated via segregation in a full sibling F1 mapping population. Using 221 progeny from this mapping population, we constructed a genetic map for M. sinensis that resolves into 19 linkage groups, the haploid chromosome number expected from cytological evidence. Comparative genomic analysis documents a genome-wide duplication in Miscanthus relative to Sorghum bicolor, with subsequent insertional fusion of a pair of chromosomes. The utility of the map is confirmed by the identification of two paralogous C4-pyruvate, phosphate dikinase (C4-PPDK) loci in Miscanthus, at positions syntenic to the single orthologous gene in Sorghum. Conclusions The genus Miscanthus experienced an ancestral tetraploidy and chromosome fusion prior to its diversification, but after its divergence from the closely related sugarcane clade. The recent timing of this tetraploidy complicates discovery and mapping of genetic markers for Miscanthus species, since alleles and fixed differences between paralogs are comparable. These difficulties can be overcome by careful analysis of segregation patterns in a mapping population and genotyping of doubled haploids. The genetic map for Miscanthus will be useful in biological discovery and breeding efforts to improve this emerging biofuel crop, and also provide a valuable resource for understanding genomic responses to tetraploidy and chromosome fusion. PMID:22524439

2012-01-01

21

Inherited genetic variants in autism-related CNTNAP2 show perturbed trafficking and ATF6 activation  

PubMed Central

Although genetic variations in several genes encoding for synaptic adhesion proteins have been found to be associated with autism spectrum disorders, one of the most consistently replicated genes has been CNTNAP2, encoding for contactin-associated protein-like 2 (CASPR2), a multidomain transmembrane protein of the neurexin superfamily. Using immunofluorescence confocal microscopy and complementary biochemical techniques, we compared wild-type CASPR2 to 12 point mutations identified in individuals with autism. In contrast to the wild-type protein, localized to the cell surface, some of the mutants show altered cellular disposition. In particular, CASPR2-D1129H is largely retained in the endoplasmic reticulum (ER) in HEK-293 cells and in hippocampal neurons. BiP/Grp78, Calnexin and ERp57, key ER chaperones, appear to be responsible for retention of this mutant and activation of one signaling pathway of the unfolded protein response (UPR). The presence of this mutation also lowers expression and activates proteosomal degradation. A frame-shift mutation that causes a form of syndromic epilepsy (CASPR2-1253*), results in a secreted protein with seemingly normal folding and oligomerization. Taken together, these data indicate that CASPR2-D1129H has severe trafficking abnormalities and CASPR2-1253* is a secreted soluble protein, suggesting that the structural or signaling functions of the membrane tethered form are lost. Our data support a complex genetic architecture in which multiple distinct risk factors interact with others to shape autism risk and presentation. PMID:22872700

Falivelli, Giulia; De Jaco, Antonella; Favaloro, Flores Lietta; Kim, Hyuck; Wilson, Jennifer; Dubi, Noga; Ellisman, Mark H.; Abrahams, Brett S.; Taylor, Palmer; Comoletti, Davide

2012-01-01

22

Inherited genetic variants in autism-related CNTNAP2 show perturbed trafficking and ATF6 activation.  

PubMed

Although genetic variations in several genes encoding for synaptic adhesion proteins have been found to be associated with autism spectrum disorders, one of the most consistently replicated genes has been CNTNAP2, encoding for contactin-associated protein-like 2 (CASPR2), a multidomain transmembrane protein of the neurexin superfamily. Using immunofluorescence confocal microscopy and complementary biochemical techniques, we compared wild-type CASPR2 to 12 point mutations identified in individuals with autism. In contrast to the wild-type protein, localized to the cell surface, some of the mutants show altered cellular disposition. In particular, CASPR2-D1129H is largely retained in the endoplasmic reticulum (ER) in HEK-293 cells and in hippocampal neurons. BiP/Grp78, Calnexin and ERp57, key ER chaperones, appear to be responsible for retention of this mutant and activation of one signaling pathway of the unfolded protein response (UPR). The presence of this mutation also lowers expression and activates proteosomal degradation. A frame-shift mutation that causes a form of syndromic epilepsy (CASPR2-1253*), results in a secreted protein with seemingly normal folding and oligomerization. Taken together, these data indicate that CASPR2-D1129H has severe trafficking abnormalities and CASPR2-1253* is a secreted soluble protein, suggesting that the structural or signaling functions of the membrane tethered form are lost. Our data support a complex genetic architecture in which multiple distinct risk factors interact with others to shape autism risk and presentation. PMID:22872700

Falivelli, Giulia; De Jaco, Antonella; Favaloro, Flores Lietta; Kim, Hyuck; Wilson, Jennifer; Dubi, Noga; Ellisman, Mark H; Abrahams, Brett S; Taylor, Palmer; Comoletti, Davide

2012-11-01

23

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

24

Synchrony in local population dynamics of stream-dwelling Dolly Varden: do genetically similar groups show similar demography?  

Microsoft Academic Search

We investigated the relationship between genetic divergence and demographic dependence. Genetically related groups may consist\\u000a of the same demographic unit or a single “population,” because high levels of dispersal may synchronize population dynamics.\\u000a We examined this hypothesis by assessing the levels of synchrony in seven demographic parameters among locations supporting\\u000a stream-dwelling Dolly Varden. We analyzed synchrony using demographic data collected

Itsuro Koizumi; Shoichiro Yamamoto; Kazuhiro Nomoto; Koji Maekawa

2008-01-01

25

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

26

Genetic characterization of Okinawan black rats showing coat color polymorphisms of white spotting and melanism.  

PubMed

We examined pelage color variation in wild populations of black rats (the Rattus rattus species complex) in the Yambaru forest area, northern Okinawa Island, Ryukyu Archipelago, Japan. Our field study revealed that 8.7% (38/438) and 0.2% (4/2500) of rats exhibited two types of coat color: white spotting and melanism, respectively. Using 34 representative animals, the phylogeography of the population was inferred using a nuclear gene marker, i.e., sequences (954 bp) of the melanocortin-1 receptor (Mc1r) gene responsible for the melanistic form in black rats. Four sequences from Okinawa were characterized as R. tanezumi, the Asian strain of black rat. Notably, neither of the phenotypic characters of white spotting or melanism was associated with the Mc1r haplotypes. Analysis of mitochondrial cytochrome b (Cytb) sequences (1140 bp) revealed that four haplotypes recovered from Okinawa clustered with the clade of R. tanezumi and differed by one or more bases from haplotypes at other localities in Japan and Asian countries. Thus, both variants may have arisen in the native rat population of Okinawa without interaction with the lineage of R. rattus, which exhibits a worldwide distribution and displays such coat color variants. The Yambaru population of black rats has thus experienced its own evolutionary history in allopatry for a substantial period of time (e.g., 10,000 years), which has preserved valuable genetic polymorphisms and will be useful for assessing the ecological consequences of genetic variation in natural populations. PMID:22531792

Kambe, Yoshikazu; Nakata, Katsushi; Yasuda, Shumpei P; Suzuki, Hitoshi

2012-01-01

27

Bulinus globosus (Planorbidae; Gastropoda) populations in the Lake Victoria basin and coastal Kenya show extreme nuclear genetic differentiation.  

PubMed

Bulinus globosus, a key intermediate host for Schistosoma haematobium that causes urinary schistosomiasis, is a hermaphroditic freshwater Planorbid snail species that inhabits patchy and transient water bodies prone to large seasonal variations in water availability. Although capable of self-fertilizing, this species has been reported to be preferentially out crossing. In this study, we characterized the population genetic structure of 19 B. globosus populations sampled across the Lake Victoria basin and coastal Kenya using four polymorphic microsatellite loci. Population genetic structure was characterized and quantified using FST statistics and Bayesian clustering algorithms. The four loci used in this study contained sufficient statistical power to detect low levels of population genetic differentiation and were highly polymorphic with the number of alleles per locus across populations ranging from 16 to 22. Average observed and expected heterozygosities across loci in each population ranged from 0.13 to 0.69 and from 0.39 to 0.79, respectively. Twenty-five of the seventy-six possible population-locus comparisons significantly deviated from Hardy-Weinberg equilibrium proportions after Bonferroni corrections, mostly due to the deficiency of heterozygotes. Significant genetic differentiation was observed between populations and Bayesian inferences identified 15 genetic clusters. The excess homozygosity, significant inbreeding and population genetic differentiation observed in B. globosus populations are likely to be due to the habitat patchiness, mating system and the proneness to cyclic extinction and recolonization in transient habitats. PMID:23266524

Nyakaana, Silvester; Stothard, J Russell; Nalugwa, Allen; Webster, Bonnie L; Lange, Charles N; Jørgensen, Aslak; Rollinson, David; Kristensen, Thomas K

2013-11-01

28

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

PubMed

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 I. tenuituba, using clustering methods that make no a priori assumptions about population structure. The sites differed not only in the frequency of intermediate individuals, but also in climate, pollinator abundance and behavior and spatial structure of plant populations. Both floral traits, which are likely to be under natural selection and molecular markers, which are quasi-neutral, indicated more population structure at one site than the other, the pattern being more pronounced for floral morphology. One likely explanation for this difference between sites is that local ecological conditions, particularly pollinator choice of flowers, have promoted different rates of hybridization between these species. Hence, the evolution of reproductive isolation might depend in part on local conditions, and thus differ among populations of the same pair of species. PMID:18971956

Aldridge, G; Campbell, D R

2009-03-01

29

Genetic Structure and Demographic History Should Inform Conservation: Chinese Cobras Currently Treated as Homogenous Show Population Divergence  

PubMed Central

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

2012-01-01

30

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. PMID:16848906

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

2006-01-01

31

Young Adult Female Fragile X Premutation Carriers Show Age- and Genetically-Modulated Cognitive Impairments  

ERIC Educational Resources Information Center

The high frequency of the fragile X premutation in the general population and its emerging neurocognitive implications highlight the need to investigate the effects of the premutation on lifespan cognitive development. Until recently, cognitive function in fragile X premutation carriers (fXPCs) was presumed to be unaffected by the mutation. Here…

Goodrich-Hunsaker, Naomi J.; Wong, Ling M.; McLennan, Yingratana; Srivastava, Siddharth; Tassone, Flora; Harvey, Danielle; Rivera, Susan M.; Simon, Tony J.

2011-01-01

32

High genetic diversity is not essential for successful introduction  

PubMed Central

Some introduced populations thrive and evolve despite the presumed loss of diversity at introduction. We aimed to quantify the amount of genetic diversity retained at introduction in species that have shown evidence of adaptation to their introduced environments. Samples were taken from native and introduced ranges of Arctotheca populifolia and Petrorhagia nanteuilii. Using microsatellite data, we identified the source for each introduction, estimated genetic diversity in native and introduced populations, and calculated the amount of diversity retained in introduced populations. These values were compared to those from a literature review of diversity in native, confamilial populations and to estimates of genetic diversity retained at introduction. Gene diversity in the native range of both species was significantly lower than for confamilials. We found that, on average, introduced populations showing evidence of adaptation to their new environments retained 81% of the genetic diversity from the native range. Introduced populations of P. nanteuilii had higher genetic diversity than found in the native source populations, whereas introduced populations of A. populifolia retained only 14% of its native diversity in one introduction and 1% in another. Our literature review has shown that most introductions demonstrating adaptive ability have lost diversity upon introduction. The two species studied here had exceptionally low native range genetic diversity. Further, the two introductions of A. populifolia represent the largest percentage loss of genetic diversity in a species showing evidence of substantial morphological change in the introduced range. While high genetic diversity may increase the likelihood of invasion success, the species examined here adapted to their new environments with very little neutral genetic diversity. This finding suggests that even introductions founded by small numbers of individuals have the potential to become invasive. PMID:24340190

Rollins, Lee A; Moles, Angela T; Lam, Serena; Buitenwerf, Robert; Buswell, Joanna M; Brandenburger, Claire R; Flores-Moreno, Habacuc; Nielsen, Knud B; Couchman, Ellen; Brown, Gordon S; Thomson, Fiona J; Hemmings, Frank; Frankham, Richard; Sherwin, William B

2013-01-01

33

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 protocol based 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 this region 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

2013-05-01

34

Highly structured genetic diversity of the Mycobacterium tuberculosis population in  

E-print Network

Highly structured genetic diversity of the Mycobacterium tuberculosis population in Djibouti S, Djibouti Ville, Djibouti Abstract Djibouti is an East African country with a high tuberculosis incidence with pulmonary tuberculosis (TB) were included. Genetic characterization of Mycobacterium tuberculosis, using

Choisy, Marc

35

High altitude living: genetic and environmental adaptation.  

PubMed

High altitude (HA) living produces physiological changes for adaptation to chronic hypobaric-hypoxemic conditions. Although much is known about these physiologic adaptations, no clear separation has been made regarding what is "native" or "genetic" adaptation and what is "acquired." In this review, we describe the genetic vs. acquired adaptation and only include studies performed in a population native to HA and not in an acclimatized population or trekkers. The changes encountered in animals and humans living at HA in terms of hematology, muscular, respiratory, cerebral, cardiovascular, hormonal, fluid and electrolytes and reproduction, strongly suggest that genetics play a very important role in HA adaptation. Unfortunately, the characteristic physiology of HA natives has not been systematically defined to established specific measurable parameters of adaptation in comparison to the acquired ambient adaptation of the non-native population. Once the parameters are established, we can compare non-native populations exposed to HA that must emulate the HA physiology for a definite adaptation to be present. With measurable parameters, especially in the management of fluids and electrolytes, we can define how long it will take for a sea level native to adapt to an HA altitude. Until these studies are performed, speculation will continue and no rational medical intervention can be offered to HA newcomers who may experience HA difficulties. PMID:9895025

Ramirez, G; Bittle, P A; Rosen, R; Rabb, H; Pineda, D

1999-01-01

36

Ettlia sp. YC001 showing high growth rate and lipid content under high CO2.  

PubMed

Over 100 green-colored colonies were isolated from environmental samples when cultivating on a BG11 agar medium, and 4 strains showing different morphologies were selected based on light microscopic observation. Among these strains, the microalgal species with the highest growth rate under 10% CO(2) was identified as Ettlia sp. YC001 using an 18S rDNA-based phylogenetic analysis and morphological comparison. The highest cell density of 3.10 g/L (based on dry cell weight) and biomass productivity of 0.19 g/L/d were obtained under 5% CO(2) after 16 days. The lipid content and productivity were also up to 42% of the dry cell weight and 80.0mg/L/d, respectively. The color of the Ettlia sp. YC001 culture changed from green to red after a month due to the accumulation of certain carotenoids. Therefore, it would seem that Ettlia sp. YC001 is appropriate for mitigating CO(2) due to its high biomass productivity, and a suitable candidate for producing biodiesel and high-value products. PMID:23147124

Yoo, Chan; Choi, Gang-Guk; Kim, Sun-Chang; Oh, Hee-Mock

2013-01-01

37

Populations of weedy crop-wild hybrid beets show contrasting variation in mating system and population genetic structure  

PubMed Central

Reproductive traits are key parameters for the evolution of invasiveness in weedy crop–wild hybrids. In Beta vulgaris, cultivated beets hybridize with their wild relatives in the seed production areas, giving rise to crop–wild hybrid weed beets. We investigated the genetic structure, the variation in first-year flowering and the variation in mating system among weed beet populations occurring within sugar beet production fields. No spatial genetic structure was found for first-year populations composed of F1 crop–wild hybrid beets. In contrast, populations composed of backcrossed weed beets emerging from the seed bank showed a strong isolation-by-distance pattern. Whereas gametophytic self-incompatibility prevents selfing in wild beet populations, all studied weed beet populations had a mixed-mating system, plausibly because of the introgression of the crop-derived Sf gene that disrupts self-incompatibility. No significant relationship between outcrossing rate and local weed beet density was found, suggesting no trends for a shift in the mating system because of environmental effects. We further reveal that increased invasiveness of weed beets may stem from positive selection on first-year flowering induction depending on the B gene inherited from the wild. Finally, we discuss the practical and applied consequences of our findings for crop-weed management.

Arnaud, Jean-Francois; Fenart, Stephane; Cordellier, Mathilde; Cuguen, Joel

2010-01-01

38

Small RNAs encoded within genetic islands of Salmonella typhimurium show host-induced expression and role in virulence  

PubMed Central

The emergence of pathogenic strains of enteric bacteria and their adaptation to unique niches are associated with the acquisition of foreign DNA segments termed ‘genetic islands’. We explored these islands for the occurrence of small RNA (sRNA) encoding genes. Previous systematic screens for enteric bacteria sRNAs were mainly carried out using the laboratory strain Escherichia coli K12, leading to the discovery of ?80 new sRNA genes. These searches were based on conservation within closely related members of enteric bacteria and thus, sRNAs, unique to pathogenic strains were excluded. Here we describe the identification and characterization of 19 novel unique sRNA genes encoded within the ‘genetic islands’ of the virulent strain Salmonella typhimurium. We show that the expression of many of the island-encoded genes is associated with stress conditions and stationary phase. Several of these sRNA genes are induced when Salmonella resides within macrophages. One sRNA, IsrJ, was further examined and found to affect the translocation efficiency of virulence-associated effector proteins into nonphagocytic cells. In addition, we report that unlike the majority of the E. coli sRNAs that are trans regulators, many of the island-encoded sRNAs affect the expression of cis-encoded genes. Our study suggests that the island encoded sRNA genes play an important role within the network that regulates bacterial adaptation to environmental changes and stress conditions and thus controls virulence. PMID:18267966

Padalon-Brauch, Gilly; Hershberg, Ruth; Elgrably-Weiss, Maya; Baruch, Kobi; Rosenshine, Ilan; Margalit, Hanah; Altuvia, Shoshy

2008-01-01

39

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

2010-09-01

40

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  

PubMed Central

Background Species-specific microsatellite markers are desirable for genetic studies and to harness the potential of MAS-based breeding for genetic improvement. Limited availability of such markers for coffee, one of the most important beverage tree crops, warrants newer efforts to develop additional microsatellite markers that can be effectively deployed in genetic analysis and coffee improvement programs. The present study aimed to develop new coffee-specific SSR markers and validate their utility in analysis of genetic diversity, individualization, linkage mapping, and transferability for use in other related taxa. Results A small-insert partial genomic library of Coffea canephora, was probed for various SSR motifs following conventional approach of Southern hybridisation. Characterization of repeat positive clones revealed a very high abundance of DNRs (1/15 Kb) over TNRs (1/406 kb). The relative frequencies of different DNRs were found as AT >> AG > AC, whereas among TNRs, AGC was the most abundant repeat. The SSR positive sequences were used to design 58 primer pairs of which 44 pairs could be validated as single locus markers using a panel of arabica and robusta genotypes. The analysis revealed an average of 3.3 and 3.78 alleles and 0.49 and 0.62 PIC per marker for the tested arabicas and robustas, respectively. It also revealed a high cumulative PI over all the markers using both sib-based (10-6 and 10-12 for arabicas and robustas respectively) and unbiased corrected estimates (10-20 and 10-43 for arabicas and robustas respectively). The markers were tested for Hardy-Weinberg equilibrium, linkage dis-equilibrium, and were successfully used to ascertain generic diversity/affinities in the tested germplasm (cultivated as well as species). Nine markers could be mapped on robusta linkage map. Importantly, the markers showed ~92% transferability across related species/genera of coffee. Conclusion The conventional approach of genomic library was successfully employed although with low efficiency to develop a set of 44 new genomic microsatellite markers of coffee. The characterization/validation of new markers demonstrated them to be highly informative, and useful for genetic studies namely, genetic diversity in coffee germplasm, individualization/bar-coding for germplasm protection, linkage mapping, taxonomic studies, and use as conserved orthologous sets across secondary genepool of coffee. Further, the relative frequency and distribution of different SSR motifs in coffee genome indicated coffee genome to be relatively poor in microsatellites compared to other plant species. PMID:18447947

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

2008-01-01

41

Genetic control of acquired high temperature tolerance in winter wheat  

Microsoft Academic Search

Summary The development of high temperature-tolerant wheat (Triticum aestivum L.) germplasm is necessary to improve plant productivity under high-temperature stress environments. The quantification of high temperature tolerance and the characterization of its genetic control are necessary for germplasm enhancement efforts. This study was conducted to determine the genetic control of acquired high temperature tolerance in common bread wheat cultivars. Reduction

David R. Porter; Henry T. Nguyen; John J. Burke

1995-01-01

42

Geographically distant isolates of the crinivirus Cucurbit yellow stunting disorder virus show very low genetic diversity in the coat protein gene  

Microsoft Academic Search

The population structure and genetic variation of Cucurbit yellow stunting disorder virus (CYSDV) isolates were estimated by single-strand confor- mation polymorphism and nucleotide sequence analyses of the CYSDV coat protein gene. Analysis of 71 isolates collected from Spain, Jordan, Turkey, Lebanon, Saudi Arabia and North America showed that, from a genetic viewpoint, these isolates could be divided into two diverged

Luis Rubio; Yusuf Abou-Jawdah; Han-Xin Lin; Bryce W. Falk

2001-01-01

43

South Florida Sun-Sentinel.com Palm Beach County high schools show improvement in latest grades  

E-print Network

South Florida Sun-Sentinel.com Palm Beach County high schools show improvement in latest grades ratings awarded to the local high schools, these areas gained some of the bragging rights associated there." High schools across Florida on Tuesday received report cards for the 2009-10 school year, based

Belogay, Eugene A.

44

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

45

High HIV1 genetic diversity in Cuba  

Microsoft Academic Search

Background: HIV-1 subtype B is largely predominant in the Caribbean, although other subtypes have been recently identified in Cuba. Objectives: To examine HIV-1 genetic diversity in Cuba. Methods: The study enrolled 105 HIV-1-infected individuals, 93 of whom had acquired the infection in Cuba. DNA from peripheral blood mononuclear cells was used for polymerase chain reaction amplification and sequencing of pol

Mar?a Teresa Cuevas; Ignacio Ruibal; Mar?a Luisa Villahermosa; He Ctor D?az; Elena Delgado; Elena Va Zquez-de Parga; Luc? Ap Erez-a Lvarez; Madel?n Blanco De Armas; Laureano Cuevas; Leandro Medrano; Enrique Noa; Saladin Osmanov; Rafael Na Jera; Michael M. Thomson

2002-01-01

46

High-Throughput Sequencing and Rare Genetic Diseases  

PubMed Central

High-throughput sequencing has drastically changed the research of genes responsible for genetic disorders and is now gradually introduced as an additional genetic diagnostic testing in clinical practice. The current debates on the emerging technical, medical and ethical issues as well as the potential optimum use of the available technology are discussed. PMID:23293577

Makrythanasis, P.; Antonarakis, S.E.

2012-01-01

47

Genetic landscape of high hyperdiploid childhood acute lymphoblastic leukemia  

PubMed Central

High hyperdiploid acute lymphoblastic leukemia (ALL) is one of the most common malignancies in children. It is characterized by gain of chromosomes, typically +X, +4, +6, +10, +14, +17, +18, and +21,+21; little is known about additional genetic aberrations. Approximately 20% of the patients relapse; therefore it is clinically important to identify risk-stratifying markers. We used SNP array analysis to investigate a consecutive series of 74 cases of high hyperdiploid ALL. We show that the characteristic chromosomal gains are even more frequent than previously believed, indicating that karyotyping mistakes are common, and that almost 80% of the cases display additional abnormalities detectable by SNP array analysis. Subclonality analysis strongly implied that the numerical aberrations were primary and arose before structural events, suggesting that step-wise evolution of the leukemic clone is common. An association between duplication of 1q and +5 was seen (P = 0.003). Other frequent abnormalities included whole-chromosome uniparental isodisomies (wUPIDs) 9 and 11, gain of 17q not associated with isochromosome formation, extra gain of part of 21q, deletions of ETS variant 6 (ETV6), cyclin-dependent kinase inhibitor 2A (CKDN2A) and paired box 5 (PAX5), and PAN3 poly(A) specific ribonuclease subunit homolog (PAN3) microdeletions. Comparison of whole-chromosome and partial UPID9 suggested different pathogenetic outcomes, with the former not involving CDKN2A. Finally, two cases had partial deletions of AT rich interactive domain 5B (ARID5B), indicating that acquired as well as constitutional variants in this locus may be associated with pediatric ALL. Here we provide a comprehensive characterization of the genetic landscape of high hyperdiploid childhood ALL, including the heterogeneous pattern of secondary genetic events. PMID:21098271

Paulsson, Kajsa; Forestier, Erik; Lilljebjorn, Henrik; Heldrup, Jesper; Behrendtz, Mikael; Young, Bryan D.; Johansson, Bertil

2010-01-01

48

Chromosome painting shows that skunks (Mephitidae, Carnivora) have highly rearranged karyotypes  

E-print Network

Chromosome painting shows that skunks (Mephitidae, Carnivora) have highly rearranged karyotypes P of carnivores are not yet established. Here, multi-directional chromosome painting was used to revealn = 38) were studied. Chromosomal homology was mapped by hybridization of five sets of whole-chromosome

49

Admixture facilitates genetic adaptations to high altitude in Tibet.  

PubMed

Admixture is recognized as a widespread feature of human populations, renewing interest in the possibility that genetic exchange can facilitate adaptations to new environments. Studies of Tibetans revealed candidates for high-altitude adaptations in the EGLN1 and EPAS1 genes, associated with lower haemoglobin concentration. However, the history of these variants or that of Tibetans remains poorly understood. Here we analyse genotype data for the Nepalese Sherpa, and find that Tibetans are a mixture of ancestral populations related to the Sherpa and Han Chinese. EGLN1 and EPAS1 genes show a striking enrichment of high-altitude ancestry in the Tibetan genome, indicating that migrants from low altitude acquired adaptive alleles from the highlanders. Accordingly, the Sherpa and Tibetans share adaptive haemoglobin traits. This admixture-mediated adaptation shares important features with adaptive introgression. Therefore, we identify a novel mechanism, beyond selection on new mutations or on standing variation, through which populations can adapt to local environments. PMID:24513612

Jeong, Choongwon; Alkorta-Aranburu, Gorka; Basnyat, Buddha; Neupane, Maniraj; Witonsky, David B; Pritchard, Jonathan K; Beall, Cynthia M; Di Rienzo, Anna

2014-01-01

50

HLA genes and surnames show a similar genetic structure in Lombardy: does this reflect part of the history of the region?  

PubMed

Lombardy, in northern Italy, is the most populated and industrialized Italian region. We attempt to study its genetic structure with two independent sets of data: HLA allele frequencies and surnames. According to our results, it is plausible to deduce that ancient history, more than genetic isolation and drift, may have contributed to the present genetic structure of Lombardy. The hypothesis seems to be confirmed by the results of the cluster analysis of the 11 provinces of the region, which was performed using two different types of markers. Both genes and surnames show approximately the same structure. Not only Celts but also ancient Ligurians (and Etruscans) probably shaped the region into the present three clusters in which the 11 provinces appear to be genetically structured. In particular, an ancient historic, archaeological, and linguistic boundary, along the Adda River, seems to be preserved in present-day Lombardy's population structure. PMID:17421007

Lisa, Antonella; De Silvestri, Annalisa; Mascaretti, Luca; Degiuli, Alberto; Guglielmino, Carmela R

2007-01-01

51

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. PMID:21115478

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

2011-01-01

52

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

53

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

54

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

PubMed Central

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

2011-01-01

55

Copyright 2002 by the Genetics Society of America High-Resolution Genetic Mapping With Ordered Arrays of  

E-print Network

Copyright 2002 by the Genetics Society of America High-Resolution Genetic Mapping With Ordered Genetics and Microbiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Program in Molecular-resolution genetic mapping that takes advantage of the ordered set of viable gene deletion mutants, which form a set

Boone, Charlie

56

All reovirus subtypes show oncolytic potential in primary cells of human high-grade glioma.  

PubMed

Reoviridae are non-human pathogenic viruses. The family of reoviridae consists of 4 different subtypes. Many studies have proven that the Dearing subtype 3 has oncolytic potential. This potential is related to the RAS protein expression in tumour cells. The aim of this study, was to investigate whether all reovirus subtypes have oncolytic potential and whether there are differences in their efficacy, in particular for high-grade glioma. To evaluate the oncolytic potential, we performed an in vitro head-to-head study for all reovirus subtypes in 5 primary cell cultures of high-grade gliomas. The oncolytic activity was determined using end-point titration with observation of the cytopathogenic effect. For measurement of RAS activity, we performed an immunofluorescent detection stain on all cell cultures. For quantification of the virus, an RT-PCR measurement for all subtypes was performed. All reovirus subtypes showed oncolytic activity in the observed glioma biopsies. These observations correlated with RAS overexpression in the observed cells. All glioma biopsies overexpressed the RAS protein. The quantitative oncolytic potential differed in relation to the single observed cell culture and in relation to the chosen reovirus subtype. To our knowledge, this is the first study showing oncolytic activity for all reovirus subtypes. We show the relationship and correlation between RAS protein overexpression and vulnerability of cells to reovirus. Efficacy of the different subtypes is interindividually different and cannot be forecast. PMID:21637921

Alloussi, S H; Alkassar, M; Urbschat, S; Graf, N; Gärtner, B

2011-09-01

57

Pericyte-Like Progenitors Show High Immaturity and Engraftment Potential as Compared with Mesenchymal Stem Cells  

PubMed Central

Mesenchymal stem cells (MSCs) and pericyte progenitors (PPs) are both perivascular cells with similar multipotential properties regardless of tissue of origin. We compared the phenotype and function of the 2 cell types derived from the same bone-marrow samples but expanded in their respective media – pericyte conditions (endothelial cell growth medium 2 [EGM-2]) for PPs and standard medium (mesenchymal stem cell medium [MSM]) for MSCs. After 3 weeks of culture, whatever the expansion medium, all cells showed similar characteristics (MSC markers and adipo-osteo-chondroblastic differentiation potential), although neuronal potential was greater in EGM-2– than MSM-cultured cells. As compared with MSM-cultured MSCs, EGM-2–cultured PPs showed higher expression of the pericyte-specific antigen 3G5 than ?-smooth muscle actin. In addition, EGM-2–cultured PPs showed an immature phenotype, with upregulation of stemness OCT4 and SOX2 proteins and downregulation of markers of osteoblastic, chondroblastic, adipocytic and vascular smooth muscle lineages. Despite having less effective in vitro immunosuppression capacities than standard MSCs, EGM-2–cultured PPs had higher engraftment potentials when combined with biomaterials heterotopically-transplanted in Nude mice. Furthermore, these engrafted cells generated more collagen matrix and were preferentially perivascular or lined trabeculae as compared with MSM-cultured MSCs. In conclusion, EGM-2–cultured PPs are highly immature cells with increased plasticity and engraftment potential. PMID:23144918

Bouacida, Amina; Rosset, Philippe; Trichet, Valerie; Guilloton, Fabien; Espagnolle, Nicolas; Cordonier, Thomas; Heymann, Dominique; Layrolle, Pierre; Sensebe, Luc; Deschaseaux, Frederic

2012-01-01

58

A new two-phase dimeticone pediculicide shows high efficacy in a comparative bioassay  

PubMed Central

Background Dimeticones kill head lice by physical means. Here we assessed in a comparative bioassay the ex vivo efficacy of "NYDA® sensitiv", a new two-phase dimeticone-based pediculicide similar to a product established on the market, but without fragrances. Methods We compared efficacy of the new product to a positive dimeticone control group, a sample of four other insecticidal and natural head lice products marketed in Germany, and an untreated control. In a bioassay, lice were exposed ex vivo to products and examined for activity for up to 24 hours, following a standard protocol. Results After 6 and 24 hours, 13.7 and 88.5% of untreated control lice did not show major vital signs. In contrast, no lice showed major vital signs 5 minutes after treatment with the new product or the control dimeticone group (NYDA®). This effect persisted at all observation points (100% efficacy). Efficacy of 0.5% permethrin (Infectopedicul®) ranged between 76 and 96% in evaluations between 5 min and 6 hours. All lice treated with a coconut-based compound (mosquito® Läuseshampoo) did not show major vital signs after 5 min, but mortality was only 58% after one hour. Pyrethrum extract (Goldgeist® forte) showed an efficacy of 22 - 52% between 5 min and 3 hours after treatment; after 6 hours, 76% of lice were judged dead. An oxyphthirine®-based compound (Liberalice DUO LP-PRO®) killed 22 - 54% of lice in the first 6 hours. Conclusions The two-phase dimeticone compound NYDA® sensitiv is highly efficacious. The removal of fragrances as compared to an established dimeticone product did not affect in vitro efficacy. PMID:20003435

2009-01-01

59

High Genetic Diversity in a Potentially Vulnerable Tropical Tree Species Despite Extreme Habitat Loss  

PubMed Central

Over the last 150 years, Singapore’s primary forest has been reduced to less than 0.2% of its previous area, resulting in extinctions of native flora and fauna. Remaining species may be threatened by genetic erosion and inbreeding. We surveyed >95% of the remaining primary forest in Singapore and used eight highly polymorphic microsatellite loci to assess genetic diversity indices of 179 adults (>30 cm stem diameter), 193 saplings (>1 yr), and 1,822 seedlings (<1 yr) of the canopy tree Koompassia malaccensis (Fabaceae). We tested hypotheses relevant to the genetic consequences of habitat loss: (1) that the K. malaccensis population in Singapore experienced a genetic bottleneck and a reduction in effective population size, and (2) K. malaccensis recruits would exhibit genetic erosion and inbreeding compared to adults. Contrary to expectations, we detected neither a population bottleneck nor a reduction in effective population size, and high genetic diversity in all age classes. Genetic diversity indices among age classes were not significantly different: we detected overall high expected heterozygosity (He?=?0.843–0.854), high allelic richness (R?=?16.7–19.5), low inbreeding co-efficients (FIS?=?0.013–0.076), and a large proportion (30.1%) of rare alleles (i.e. frequency <1%). However, spatial genetic structure (SGS) analyses showed significant differences between the adults and the recruits. We detected significantly greater SGS intensity, as well as higher relatedness in the 0–10 m distance class, for seedlings and saplings compared to the adults. Demographic factors for this population (i.e. <200 adult trees) are a cause for concern, as rare alleles could be lost due to stochastic factors. The high outcrossing rate (tm?=?0.961), calculated from seedlings, may be instrumental in maintaining genetic diversity and suggests that pollination by highly mobile bee species in the genus Apis may provide resilience to acute habitat loss. PMID:24367531

Noreen, Annika M. E.; Webb, Edward L.

2013-01-01

60

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

2013-02-01

61

DNA Barcode Detects High Genetic Structure within Neotropical Bird Species  

PubMed Central

Background Towards lower latitudes the number of recognized species is not only higher, but also phylogeographic subdivision within species is more pronounced. Moreover, new genetically isolated populations are often described in recent phylogenies of Neotropical birds suggesting that the number of species in the region is underestimated. Previous COI barcoding of Argentinean bird species showed more complex patterns of regional divergence in the Neotropical than in the North American avifauna. Methods and Findings Here we analyzed 1,431 samples from 561 different species to extend the Neotropical bird barcode survey to lower latitudes, and detected even higher geographic structure within species than reported previously. About 93% (520) of the species were identified correctly from their DNA barcodes. The remaining 41 species were not monophyletic in their COI sequences because they shared barcode sequences with closely related species (N?=?21) or contained very divergent clusters suggestive of putative new species embedded within the gene tree (N?=?20). Deep intraspecific divergences overlapping with among-species differences were detected in 48 species, often with samples from large geographic areas and several including multiple subspecies. This strong population genetic structure often coincided with breaks between different ecoregions or areas of endemism. Conclusions The taxonomic uncertainty associated with the high incidence of non-monophyletic species and discovery of putative species obscures studies of historical patterns of species diversification in the Neotropical region. We showed that COI barcodes are a valuable tool to indicate which taxa would benefit from more extensive taxonomic revisions with multilocus approaches. Moreover, our results support hypotheses that the megadiversity of birds in the region is associated with multiple geographic processes starting well before the Quaternary and extending to more recent geological periods. PMID:22163311

Tavares, Erika Sendra; Goncalves, Priscila; Miyaki, Cristina Yumi; Baker, Allan J.

2011-01-01

62

Acinic cell carcinoma of minor salivary gland showing features of high-grade transformation  

PubMed Central

Introduction: Acinic cell carcinoma (AciCC) of salivary gland is a relatively infrequent tumor. Though known for its low-grade behavior, its unpredictable element of recurrence and malignancy should never be ignored. Case Report: A male patient with complaints of pain and swelling in the left jaw region since a year was operated based on the computed tomography (CT) and incisional biopsy report. Histopathology (routine staining, special staining, immunostaining and electron microscopy) of the excised specimen revealed it to be a variant of AciCC from minor salivary gland. Discussion: To the best of our knowledge, this is the first case of AciCC showing propensity for high-grade transformation (HGT), arising from minor salivary gland, being reported. The rarity of such variants and the importance of various investigative techniques in the diagnosis of such cases are discussed. PMID:24959046

Ilayaraja, Vadivel; Prasad, H; Anuthama, Krishnamurthy; Sruthi, Ranganath

2014-01-01

63

Protein-polymer functionalized aqueous ferrofluids showing high T2 relaxivity.  

PubMed

Controlled size, shape and dispersibility of superparamagnetic iron oxide nanoparticles (SPIONs), has been achieved in a protein-polymer colloidal dispersion. Stable ferrofluid (FF) is synthesized in an aqueous medium of collagen, bovine serum albumin and poly(vinyl) alcohol that equilibrates with time, at ambient conditions, into an organized matrix with iron oxide particles sterically caged at defined sites. It mimics a biomineralization system; hence the process is termed biomimetics. Though the exact mechanism is not understood at this stage, we have established, with serial dilution of the protein-polymer solution that the SPIONs are formed inside the self-contained clusters of the two proteins and the polymer, which show a tendency to self assemble. More than the interparticle dipolar attractions of magnetic particles, electrostatic interactions play a role in cluster formation and collagen is responsible for the overall stability, supported by systematic dynamic light scattering data. The basic aim of this study was to increase magnetization of a previously synthesized ferrofluid without hampering stability, by reducing the total macromolecular concentration. Thrice the magnetization was achieved and in addition, the synthesized FFs exhibited very high transverse relaxivity and showed good contrast in mice liver, in the in vivo studies. PMID:24734534

Bhattacharya, S; Sheikh, L; Tiwari, V; Ghosh, M; Patel, J N; Patel, A B; Nayar, S

2014-05-01

64

Chromosome painting shows that skunks (Mephitidae, Carnivora) have highly rearranged karyotypes.  

PubMed

The karyotypic relationships of skunks (Mephitidae) with other major clades of carnivores are not yet established. Here, multi-directional chromosome painting was used to reveal the karyological relationships among skunks and between Mephitidae (skunks) and Procyonidae (raccoons). Representative species from three genera of Mephitidae (Mephitis mephitis, 2n = 50; Mephitis macroura, 2n = 50; Conepatus leuconotus, 2n = 46; Spilogale gracilis, 2n = 60) and one species of Procyonidae (Procyon lotor, 2n = 38) were studied. Chromosomal homology was mapped by hybridization of five sets of whole-chromosome paints derived from stone marten (Martes foina, 2n = 38), cat, skunks (M. mephitis; M. macroura) and human. The karyotype of the raccoon is highly conserved and identical to the hypothetical ancestral musteloid karyotype, suggesting that procyonids have a particular importance for establishing the karyological evolution within the caniforms. Ten fission events and five fusion events are necessary to generate the ancestral skunk karyotype from the ancestral carnivore karyotype. Our results show that Mephitidae joins Canidae and Ursidae as the third family of carnivores that are characterized by a high rate of karyotype evolution. Shared derived chromosomal fusion of stone marten chromosomes 6 and 14 phylogenetically links the American hog-nosed skunk and eastern spotted skunk. PMID:19051045

Perelman, P L; Graphodatsky, A S; Dragoo, J W; Serdyukova, N A; Stone, G; Cavagna, P; Menotti, A; Nie, W; O'Brien, P C M; Wang, J; Burkett, S; Yuki, K; Roelke, M E; O'Brien, S J; Yang, F; Stanyon, R

2008-01-01

65

Nanoscale anatase TiO2 with dominant {1 1 1} facets shows high photocatalytic activity  

NASA Astrophysics Data System (ADS)

In this work, we report a novel synthesis of nanoscale anatase TiO2 with dominant highly active {1 1 1} facets by a simple one-step hydrothermal route with the assistance of NH4F and HF. In this progress, the exposed crystal facets of TiO2 can been directly tuned by controlling the mole ratio of NH4+ and F-. When the mole ratio of NH4+ and F-reach 1:2, nanoscale anatase TiO2 with dominant {1 1 1} facets can be obtained. Nanoscale anatase TiO2 with exposed {1 0 1} or {0 0 1} facets will be prepared when there is only ammonia or HF added respectively. Such nano-TiO2 with exposed highly active {1 1 1} facets has large specific surface area and shows excellent photocatalytic activity: as much as 2-3 times than that of TiO2 nanosheets with exposed {0 0 1} facets and commercial Degussa P25 which confirms the {1 1 1} facets have higher photocatalytic activity than {0 0 1} and {1 0 1} facets. The higher photocatalytic activity of {1 1 1} facets can be ascribed to the fact that all Ti and O atoms on the surface are unsaturated Ti5c, Ti3c and O2c modes which produces a higher adsorption and degradation ability. The present work demonstrates a explore of hydrothermal synthetic method for controlling preparation of nano-materials.

Zhang, Jun; Qian, Lisha; Yang, Lingxia; Tao, Xi; Su, Kunpeng; Wang, Hongbo; Xi, Junhua; Ji, Zhenguo

2014-08-01

66

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

67

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

68

High frequency of cephalic neural crest cells shows coexistence of neurogenic, melanogenic, and osteogenic differentiation capacities  

PubMed Central

The neural crest (NC) is a vertebrate innovation that distinguishes vertebrates from other chordates and was critical for the development and evolution of a “New Head and Brain.” In early vertebrates, the NC was the source of dermal armor of fossil jawless fish. In extant vertebrates, including mammals, the NC forms the peripheral nervous system, melanocytes, and the cartilage and bone of the face. Here, we show that in avian embryos, a large majority of cephalic NC cells (CNCCs) have the ability to differentiate into cell types as diverse as neurons, melanocytes, osteocytes, and chondrocytes. Moreover, we find that the morphogen Sonic hedgehog (Shh) acts on CNCCs to increase endochondral osteogenesis while having no effect on osteoblasts prone to membranous ossification. We have developed culture conditions that demonstrate that “neural–mesenchymal” differentiation abilities are present in more than 90% of CNCCs. A highly multipotent progenitor (able to yield neurons, glia, melanocytes, myofibroblasts, chondrocytes, and osteocytes) comprises 7–13% of the clonogenic cells in the absence and presence of Shh, respectively. This progenitor is a good candidate for a cephalic NC stem cell. PMID:19447928

Calloni, Giordano W.; Le Douarin, Nicole M.; Dupin, Elisabeth

2009-01-01

69

[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

70

Escherichia coli W shows fast, highly oxidative sucrose metabolism and low acetate formation.  

PubMed

Sugarcane is the most efficient large-scale crop capable of supplying sufficient carbon substrate, in the form of sucrose, needed during fermentative feedstock production. However, sucrose metabolism in Escherichia coli is not well understood because the two most common strains, E. coli K-12 and B, do not grow on sucrose. Here, using a sucrose utilizing strain, E. coli W, we undertake an in-depth comparison of sucrose and glucose metabolism including growth kinetics, metabolite profiling, microarray-based transcriptome analysis, labelling-based proteomic analysis and (13)C-fluxomics. While E. coli W grew comparably well on sucrose and glucose integration of the omics, datasets showed that during growth on each carbon source, metabolism was distinct. The metabolism was generally derepressed on sucrose, and significant flux rearrangements were observed in central carbon metabolism. These included a reduction in the flux of the oxidative pentose phosphate pathway branch, an increase in the tricarboxylic acid cycle flux and a reduction in the glyoxylate shunt flux due to the dephosphorylation of isocitrate dehydrogenase. But unlike growth on other sugars that induce cAMP-dependent Crp regulation, the phosphoenol-pyruvate-glyoxylate cycle was not active on sucrose. Lower acetate accumulation was also observed in sucrose compared to glucose cultures. This was linked to induction of the acetate catabolic genes actP and acs and independent of the glyoxylic shunt. Overall, the cells stayed highly oxidative. In summary, sucrose metabolism was fast, efficient and led to low acetate accumulation making it an ideal carbon source for industrial fermentation with E. coli W. PMID:25125039

Arifin, Yalun; Archer, Colin; Lim, SooA; Quek, Lake-Ee; Sugiarto, Haryadi; Marcellin, Esteban; Vickers, Claudia E; Krömer, Jens O; Nielsen, Lars K

2014-11-01

71

High levels of genetic variability in west African Dwarf Crocodiles  

E-print Network

High levels of genetic variability in west African Dwarf Crocodiles Osteolaemus tetraspis getraspis Crocodile (Osteolaemus) has been a long-standing problem for crocodilian systematists. Previously divided, to which the dwarf African crocodile belongs, is generally considered the sister taxon to the genus

Ray, David

72

Using Show Homes (and Sponsorships) to Persuade Commissioning Relevancy and Factory Crafted High Performance Modular Homes  

E-print Network

The International Builders' Show (IBS) sponsored by the National Association of Home Builders is a venue attracting over 100,000 builders and building related professionals every year. The increased attendances each year improves the educational...

Thomas-Rees, S.; Chasar, D.; Beal, D.; Chandra, S.

2007-01-01

73

Efficient screening of long terminal repeat retrotransposons that show high insertion polymorphism via high-throughput sequencing of the primer binding site.  

PubMed

Retrotransposons have been used frequently for the development of molecular markers by using their insertion polymorphisms among cultivars, because multiple copies of these elements are dispersed throughout the genome and inserted copies are inherited genetically. Although a large number of long terminal repeat (LTR) retrotransposon families exist in the higher eukaryotic genomes, the identification of families that show high insertion polymorphism has been challenging. Here, we performed an efficient screening of these retrotransposon families using an Illumina HiSeq2000 sequencing platform with comprehensive LTR library construction based on the primer binding site (PBS), which is located adjacent to the 5' LTR and has a motif that is universal and conserved among LTR retrotransposon families. The paired-end sequencing library of the fragments containing a large number of LTR sequences and their insertion sites was sequenced for seven strawberry (Fragaria × ananassa Duchesne) cultivars and one diploid wild species (Fragaria vesca L.). Among them, we screened 24 families with a "unique" insertion site that appeared only in one cultivar and not in any others, assuming that this type of insertion should have occurred quite recently. Finally, we confirmed experimentally the selected LTR families showed high insertion polymorphisms among closely related cultivars. PMID:25072847

Monden, Yuki; Fujii, Nobuyuki; Yamaguchi, Kentaro; Ikeo, Kazuho; Nakazawa, Yoshiko; Waki, Takamitsu; Hirashima, Keita; Uchimura, Yosuke; Tahara, Makoto

2014-05-01

74

A Low-Cost High-Impact Computer Science Show for Family Audiences  

Microsoft Academic Search

Science shows are commonly presented for the general pub- lic, and especially children, at science centers and festivals. Usually they use attention-grabbing experiments from the physical sciences, and the science of computing is absent from such presentations. This paper describes a series of demonstrations that present fundamental ideas from Com- puter Science in a manner that will be engaging to

Tim Bell

2000-01-01

75

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

Microsoft Academic Search

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

E. Stengler; J. M. Sirera

2011-01-01

76

Trial results show high remission rate in leukemia following immune cell therapy  

Cancer.gov

Children and young adults (age 1 to age 30) with chemotherapy-resistant B-cell acute lymphoblastic leukemia (ALL) experienced high remission rates following treatment with an experimental immunotherapy. Results demonstrated that the immunotherapy treatment had anti-leukemia effects in patients and that the treatment was feasible and safe.

77

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

78

Biochemical Characterization of a First Fungal Esterase from Rhizomucor miehei Showing High Efficiency of Ester Synthesis  

PubMed Central

Background Esterases with excellent merits suitable for commercial use in ester production field are still insufficient. The aim of this research is to advance our understanding by seeking for more unusual esterases and revealing their characterizations for ester synthesis. Methodology/Principal Findings A novel esterase-encoding gene from Rhizomucor miehei (RmEstA) was cloned and expressed in Escherichia coli. Sequence analysis revealed a 975-bp ORF encoding a 324-amino-acid polypeptide belonging to the hormone-sensitive lipase (HSL) family IV and showing highest similarity (44%) to the Paenibacillus mucilaginosus esterase/lipase. Recombinant RmEstA was purified to homogeneity: it was 34 kDa by SDS-PAGE and showed optimal pH and temperature of 6.5 and 45°C, respectively. The enzyme was stable to 50°C, under a broad pH range (5.0–10.6). RmEstA exhibited broad substrate specificity toward p-nitrophenol esters and short-acyl-chain triglycerols, with highest activities (1,480 U mg?1 and 228 U mg?1) for p-nitrophenyl hexanoate and tributyrin, respectively. RmEstA efficiently synthesized butyl butyrate (92% conversion yield) when immobilized on AOT-based organogel. Conclusion RmEstA has great potential for industrial applications. RmEstA is the first reported esterase from Rhizomucor miehei. PMID:24204998

Liu, Yu; Xu, Haibo; Yan, Qiaojuan; Yang, Shaoqing; Duan, Xiaojie; Jiang, Zhengqiang

2013-01-01

79

International web survey shows high prevalence of symptomatic testosterone deficiency in men  

PubMed Central

Introduction Though the clinical significance of testosterone deficiency is becoming increasingly apparent, its prevalence in the general population remains unrecognised. A large web-based survey was undertaken over 3 years to study the scale of this missed diagnosis. Methods An online questionnaire giving the symptoms characterising testosterone deficiency syndrome (Aging Male Symptoms – AMS – scale) was set up on three web sites, together with questions about possible contributory factors. Results. Of over 10,000 men, mainly from the UK and USA, who responded, 80% had moderate or severe scores likely to benefit from testosterone replacement therapy (TRT). The average age was 52, but with many in their 40s when the diagnosis of ‘late onset hypogonadism’ is not generally considered. Other possible contributory factors to the high testosterone deficiency scores reported were obesity (29%), alcohol (17.3%), testicular problems such as mumps orchitis (11.4%), prostate problems (5.6%), urinary infection (5.2%) and diabetes 5.7%. Conclusions In this self-selected large international sample of men, there was a very high prevalence of scores which if clinically relevant would warrant a therapeutic trial of testosterone treatment. This study suggests that there are large numbers of men in the community whose testosterone deficiency is neither being diagnosed nor treated. PMID:20828244

TRINICK, TOM R; FENELEY, MARK R; WELFORD, HUGH; CARRUTHERS, MALCOLM

2011-01-01

80

Updated clinical results show experimental agent ibrutinib as highly active in CLL patients  

Cancer.gov

Updated results from a Phase Ib/II clinical trial led by the Ohio State University Comprehensive Cancer Center – Arthur G. James Cancer Hospital and Richard J. Solove Research Institute indicates that a novel therapeutic agent for chronic lymphocytic leukemia (CLL) is highly active and well tolerated in patients who have relapsed and are resistant to other therapy. The agent, ibrutinib (PCI-32765), is the first drug designed to target Bruton's tyrosine kinase (BTK), a protein essential for CLL-cell survival and proliferation. CLL is the most common form of leukemia, with about 15,000 new cases annually in the U.S. About 4,400 Americans die of the disease each year.

81

Tetranuclear silver(I) clusters showing high ionic conductivity in a bicontinuous cubic mesophase.  

PubMed

The synthesis and characterization of tetranuclear silver triazole metallomesogens, [Ag4(L(4)-C(n))6][BF4]4 (L(4)-C(n) = 4-alkyl-1,2,4-triazoles where C(n) stands for C(n)H(2n+1) with n = 12, 14, 16, and 18), are reported. Upon heating, a phase transition sequence of Cr ? SmC ? Cub ? SmA ? isotropic liquid is observed for all of these compounds. Depending on the alkyl chain length, two types of cubic phases are found in this series of compounds. Those with shorter alkyl chains (n = 12 and 14) exhibit a micellar cubic phase, whereas long alkyl chains (n =16 and 18) show a bicontinuous cubic phase. Superior ionic conductivity at the bicontinuous cubic mesophase for [Ag4(L4-C16)6][BF4]4 is observed because of the presence of a three-dimensional ion-transporting channel. Doping a small amount of AgBF4 enhances the ionic conduction dramatically, presumably via promotion of the migration of Ag(I) ions in the channels. PMID:24893070

Su, Padi Y S; Tseng, Jing C W; Lee, Kwang-Ming; Wang, Ju-Chun; Lin, Ivan J B

2014-06-16

82

Comparative Transcriptomics of Eastern African Cichlid Fishes Shows Signs of Positive Selection and a Large Contribution of Untranslated Regions to Genetic Diversity  

PubMed Central

The hundreds of endemic species of cichlid fishes in the East African Great Lakes Tanganyika, Malawi, and Victoria are a prime model system in evolutionary biology. With five genomes currently being sequenced, eastern African cichlids also represent a forthcoming genomic model for evolutionary studies of genotype-to-phenotype processes in adaptive radiations. Here we report the functional annotation and comparative analyses of transcriptome data sets for two eastern African cichlid species, Astatotilapia burtoni and Ophthalmotilapia ventralis, representatives of the modern haplochromines and ectodines, respectively. Nearly 647,000 expressed sequence tags were assembled in more than 46,000 contigs for each species using the 454 sequencing technology, largely expanding the current sequence data set publicly available for these cichlids. Total predicted coverage of their proteome diversity is approximately 50% for both species. Comparative qualitative and quantitative analyses show very similar transcriptome data for the two species in terms of both functional annotation and relative abundance of gene ontology terms expressed. Average genetic distance between species is 1.75% when all transcript types are considered including nonannotated sequences, 1.33% for annotated sequences only including untranslated regions, and decreases to nearly half, 0.95%, for coding sequences only, suggesting a large contribution of noncoding regions to their genetic diversity. Comparative analyses across the two species, tilapia and the outgroup medaka based on an overlapping data set of 1,216 genes (?526 kb) demonstrate cichlid-specific signature of disruptive selection and provide a set of candidate genes that are putatively under positive selection. Overall, these data sets offer the genetic platform for future comparative analyses in light of the upcoming genomes for this taxonomic group. PMID:21617250

Baldo, Laura; Santos, M.Emilia; Salzburger, Walter

2011-01-01

83

Nitrogen-doped diamond electrode shows high performance for electrochemical reduction of nitrobenzene.  

PubMed

Effective electrode materials are critical to electrochemical reduction, which is a promising method to pre-treat anti-oxidative and bio-refractory wastewater. Herein, nitrogen-doped diamond (NDD) electrodes that possess superior electrocatalytic properties for reduction were fabricated by microwave-plasma-enhanced chemical vapor deposition technology. Nitrobenzene (NB) was chosen as the probe compound to investigate the material's electro-reduction activity. The effects of potential, electrolyte concentration and pH on NB reduction and aniline (AN) formation efficiencies were studied. NDD exhibited high electrocatalytic activity and selectivity for reduction of NB to AN. The NB removal efficiency and AN formation efficiency were 96.5% and 88.4% under optimal conditions, respectively; these values were 1.13 and 3.38 times higher than those of graphite electrodes. Coulombic efficiencies for NB removal and AN formation were 27.7% and 26.1%, respectively; these values were 4.70 and 16.6 times higher than those of graphite electrodes under identical conditions. LC-MS analysis revealed that the dominant reduction pathway on the NDD electrode was NB to phenylhydroxylamine (PHA) to AN. PMID:24361797

Zhang, Qing; Liu, Yanming; Chen, Shuo; Quan, Xie; Yu, Hongtao

2014-01-30

84

N-Chlorotaurine shows high in vitro activity against promastigotes and amastigotes of Leishmania species.  

PubMed

Protozoan parasites of the genus Leishmania are the causative agents of life-threatening visceral as well as cutaneous and mucocutaneous leishmaniasis. First-line drugs are antimonials, but toxicity and resistance in some endemic areas cause serious problems. In the current study, the antileishmanial activity of the weak oxidant N-chlorotaurine (NCT) was investigated. NCT is a derivative of the amino acid taurine produced by granulocytes and monocytes during oxidative burst, but can also be synthesized chemically and used topically as an antiseptic at a concentration of 1 % (55 mM) in vivo. NCT susceptibility tests were performed in vitro with promastigotes and amastigotes of Leishmania infantum and Leishmania donovani. As NH(4)Cl is known to increase the activity of NCT by the formation of monochloramine (NH(2)Cl), co-treatment assays were included in the study. Mean EC(50) values after 1 h of treatment were 5.94 mM for L. infantum and 9.8 mM for L. donovani promastigotes. Co-treatment with 5.5 mM NCT plus 19 mM NH(4)Cl led to complete killing of promastigotes of both strains within 15 min. Amastigotes were inactivated by treatment with 2 mM NCT alone. The results of this study indicate a high potential of NCT against Leishmania species. PMID:19541788

Fürnkranz, Ursula; Nagl, Markus; Gottardi, Waldemar; Matt, Ulrich; Aspöck, Horst; Walochnik, Julia

2009-10-01

85

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

86

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

87

Dietary Differentiation and the Evolution of Population Genetic Structure in a Highly Mobile Carnivore  

PubMed Central

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 (?13C and ?15N 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, Malgorzata; Jedrzejewski, Wlodzimierz; Sidorovich, Vadim E.; Meier-Augenstein, Wolfram; Hoelzel, A. Rus

2012-01-01

88

High genetic diversity in a remote island population system: sans Eric F. Karlin1  

E-print Network

words: allopolyploid, bryophyte, clone, genetic diversity, Hawaii, long-distance dispersal, SphagnumHigh genetic diversity in a remote island population system: sans sex Eric F. Karlin1 , Sara C genetic diversity to that found in populations of S. palustre in other regions. · The genetic diversity

Wisconsin at Madison, University of

89

High latitudes and high genetic diversity: phylogeography of a widespread boreal bird, the gray jay (Perisoreus canadensis).  

PubMed

We describe range-wide phylogeographic variation in gray jays (Perisoreus canadensis), a boreal Nearctic corvid that occurs today primarily in recently glaciated regions. Phylogenetic analysis of mitochondrial DNA (1041 base pairs ND2 gene; N=205, 50 localities) revealed four reciprocally monophyletic groups. One widespread clade occurs across the North American boreal zone, from Newfoundland to Alaska and southwest into Utah. Three other clades occur at lower latitudes in the montane West in Colorado, the northern Rocky Mountains, and the Pacific Northwest respectively. The geographic distribution of clades in gray jays corresponds with a general pattern that is emerging for boreal taxa, having one widespread northern clade and one or more geographically restricted southwestern clades. Population genetic analyses indicate that the larger boreal clade is genetically structured and harbors significantly more genetic diversity than those clades occurring at lower latitudes. Species distribution modeling (SDM) revealed multiple putative Pleistocene refugia including several occurring at higher latitudes. We suggest that multiple post-glacial colonization routes, some of which originate from these northern refugia, are responsible for the relatively high genetic diversity at high latitudes. Conversely, lower latitude clades show little variation, probably as a result of historical restriction to smaller geographical areas with smaller long-term population sizes. This 'upside-down' pattern of genetic diversity contrasts with the conventional view that populations of north-temperate species occupying previously glaciated habitats should possess lower levels of diversity than their southern counterparts. PMID:22321688

van Els, Paul; Cicero, Carla; Klicka, John

2012-05-01

90

A high-throughput SNP array in the amphidiploid species Brassica napus shows diversity in resistance genes.  

PubMed

Single-nucleotide polymorphisms (SNPs)are molecular markers based on nucleotide variation and can be used for genotyping assays across populations and to track genomic inheritance. SNPs offer a comprehensive genotyping alternative to whole-genome sequencing for both agricultural and research purposes including molecular breeding and diagnostics, genome evolution and genetic diversity analyses, genetic mapping, and trait association studies. Here genomic SNPs were discovered between four cultivars of the important amphidiploid oilseed species Brassica napus and used to develop a B. napus Infinium™ array containing 5,306 SNPs randomly dispersed across the genome. Assay success was high, with >94 % of these producing a reproducible, polymorphic genotype in the 1,070 samples screened. Although the assay was designed to B. napus, successful SNP amplification was achieved in the B. napus progenitor species, Brassica rapa and Brassica oleracea, and to a lesser extent in the related species Brassica nigra. Phylogenetic analysis was consistent with the expected relationships between B. napus individuals. This study presents an efficient custom SNP assay development pipeline in the complex polyploid Brassica genome and demonstrates the utility of the array for high-throughput genotyping in a number of related Brassica species. It also demonstrates the utility of this assay in genotyping resistance genes on chromosome A7, which segregate amongst the 1,070 samples. PMID:25147024

Dalton-Morgan, Jessica; Hayward, Alice; Alamery, Salman; Tollenaere, Reece; Mason, Annaliese S; Campbell, Emma; Patel, Dhwani; Lorenc, Micha? T; Yi, Bin; Long, Yan; Meng, Jinling; Raman, Rosy; Raman, Harsh; Lawley, Cindy; Edwards, David; Batley, Jacqueline

2014-12-01

91

X-linked Charcot-Marie-Tooth (CMT) neuropathies (CMTX1, CMTX2, CMTX3) show different clinical phenotype and molecular genetics  

SciTech Connect

The purpose of this study was to compare the X-linked dominant type CMTX1 (20 families) with X-linked recessive types CMTX2 and CMTX3 (2 families). The clinical phenotype was consistent with CMT peripheral neuropathy in all cases including distal weakness, atrophy and sensory loss, pes cavus and areflexia. Additional clinicial involvement of the central nervous system was present in one family with CMTX2 (mental retardation) and one family with CMTX3 (spastic paraparesis). Tight genetic linkage to Xq13.1 was present in 20 families with CMTX1 (Z=34.07 at {theta}=0) for the marker DXS453. Fifteen of the CMTX1 families showed point mutations of the connexin 32 coding region (5 nonsense mutations, 8 missense mutations, 2 deletions). Five CMTX1 neuropathy families showed no evidence of point mutations of the CX32 coding sequence. These findings suggest that the CMTX1 neuropathy genotype in these families may be the result of promoter mutations, 3{prime}-untranslated region mutations or exon/intron splice site mutations or a mutation with a different type of connexin but which has close structural similarities to CX32. No mutations of the CX32 coding region were found in the CMTX2 or CMTX3 families. Linkage to Xq13.1 was excluded in both families. Genetic linkage to Xp22.2 was present in the CMTX2 family (Z=3.54 at {theta}=0) for the markers DXS987 and DXS999. Suggestion of linkage to Xq26 (Z=1.81 at {theta}=0) for the marker DXS86 was present in the CMTX3 family.

Ionasescu, V.V.; Searby, C.C.; Ionasescu, R. [Univ. of Iowa Hospitals and Clinics, Iowa City, IA (United States)

1994-09-01

92

Genetic evidence for high-altitude adaptation in Tibet.  

PubMed

Tibetans have lived at very high altitudes for thousands of years, and they have a distinctive suite of physiological traits that enable them to tolerate environmental hypoxia. These phenotypes are clearly the result of adaptation to this environment, but their genetic basis remains unknown. We report genome-wide scans that reveal positive selection in several regions that contain genes whose products are likely involved in high-altitude adaptation. Positively selected haplotypes of EGLN1 and PPARA were significantly associated with the decreased hemoglobin phenotype that is unique to this highland population. Identification of these genes provides support for previously hypothesized mechanisms of high-altitude adaptation and illuminates the complexity of hypoxia-response pathways in humans. PMID:20466884

Simonson, Tatum S; Yang, Yingzhong; Huff, Chad D; Yun, Haixia; Qin, Ga; Witherspoon, David J; Bai, Zhenzhong; Lorenzo, Felipe R; Xing, Jinchuan; Jorde, Lynn B; Prchal, Josef T; Ge, RiLi

2010-07-01

93

High-throughput neuroimaging-genetics computational infrastructure  

PubMed Central

Many contemporary neuroscientific investigations face significant challenges in terms of data management, computational processing, data mining, and results interpretation. These four pillars define the core infrastructure necessary to plan, organize, orchestrate, validate, and disseminate novel scientific methods, computational resources, and translational healthcare findings. Data management includes protocols for data acquisition, archival, query, transfer, retrieval, and aggregation. Computational processing involves the necessary software, hardware, and networking infrastructure required to handle large amounts of heterogeneous neuroimaging, genetics, clinical, and phenotypic data and meta-data. Data mining refers to the process of automatically extracting data features, characteristics and associations, which are not readily visible by human exploration of the raw dataset. Result interpretation includes scientific visualization, community validation of findings and reproducible findings. In this manuscript we describe the novel high-throughput neuroimaging-genetics computational infrastructure available at the Institute for Neuroimaging and Informatics (INI) and the Laboratory of Neuro Imaging (LONI) at University of Southern California (USC). INI and LONI include ultra-high-field and standard-field MRI brain scanners along with an imaging-genetics database for storing the complete provenance of the raw and derived data and meta-data. In addition, the institute provides a large number of software tools for image and shape analysis, mathematical modeling, genomic sequence processing, and scientific visualization. A unique feature of this architecture is the Pipeline environment, which integrates the data management, processing, transfer, and visualization. Through its client-server architecture, the Pipeline environment provides a graphical user interface for designing, executing, monitoring validating, and disseminating of complex protocols that utilize diverse suites of software tools and web-services. These pipeline workflows are represented as portable XML objects which transfer the execution instructions and user specifications from the client user machine to remote pipeline servers for distributed computing. Using Alzheimer's and Parkinson's data, we provide several examples of translational applications using this infrastructure1. PMID:24795619

Dinov, Ivo D.; Petrosyan, Petros; Liu, Zhizhong; Eggert, Paul; Hobel, Sam; Vespa, Paul; Woo Moon, Seok; Van Horn, John D.; Franco, Joseph; Toga, Arthur W.

2014-01-01

94

High Levels of Genetic Differentiation between Ugandan Glossina fuscipes fuscipes Populations Separated by Lake Kyoga  

PubMed Central

Background Glossina fuscipes fuscipes is the major vector of human African trypanosomiasis, commonly referred to as sleeping sickness, in Uganda. In western and eastern Africa, the disease has distinct clinical manifestations and is caused by two different parasites: Trypanosoma brucei rhodesiense and T. b. gambiense. Uganda is exceptional in that it harbors both parasites, which are separated by a narrow 160-km belt. This separation is puzzling considering there are no restrictions on the movement of people and animals across this region. Methodology and Results We investigated whether genetic heterogeneity of G. f. fuscipes vector populations can provide an explanation for this disjunct distribution of the Trypanosoma parasites. Therefore, we examined genetic structuring of G. f. fuscipes populations across Uganda using newly developed microsatellite markers, as well as mtDNA. Our data show that G. f. fuscipes populations are highly structured, with two clearly defined clusters that are separated by Lake Kyoga, located in central Uganda. Interestingly, we did not find a correlation between genetic heterogeneity and the type of Trypanosoma parasite transmitted. Conclusions The lack of a correlation between genetic structuring of G. f. fuscipes populations and the distribution of T. b. gambiense and T. b. rhodesiense indicates that it is unlikely that genetic heterogeneity of G. f. fuscipes populations explains the disjunct distribution of the parasites. These results have important epidemiological implications, suggesting that a fusion of the two disease distributions is unlikely to be prevented by an incompatibility between vector populations and parasite. PMID:18509474

Robinson, Alan S.; Muwanika, Vincent B.; Enyaru, John C. K.; Lokedi, Loyce M.; Aksoy, Serap; Caccone, Adalgisa

2008-01-01

95

Cirsium species show disparity in patterns of genetic variation at their range-edge, despite similar patterns of reproduction and isolation  

Microsoft Academic Search

Summary • Genetic variation was assessed across the UK geographical range of Cirsium acaule and Cirsium heterophyllum . A decline in genetic diversity and increase in population divergence approaching the range edge of these species was predicted based on parallel declines in population density and seed production reported seperately. Patterns were compared with UK populations of the widespread Cirsium arvense

Alistair S. Jump; F. Ian Woodward; Terry Burke

2003-01-01

96

Genetic Connectivity of the Moth Pollinated Tree Glionnetia sericea in a Highly Fragmented Habitat  

PubMed Central

Long-distance gene flow is thought to be one prerequisite for the persistence of plant species in fragmented environments. Human influences have led to severe fragmentation of native habitats in the Seychelles islands, with many species surviving only in small and isolated populations. The endangered Seychelles endemic tree Glionnetia sericea is restricted to altitudes between 450 m and 900 m where the native forest vegetation has been largely lost and replaced with exotic invasives over the last 200 years. This study explores the genetic and ecological consequences of population fragmentation in this species by analysing patterns of genetic diversity in a sample of adults, juveniles and seeds, and by using controlled pollination experiments. Our results show no decrease in genetic diversity and no increase in genetic structuring from adult to juvenile cohorts. Despite significant inbreeding in some populations, there is no evidence of higher inbreeding in juvenile cohorts relative to adults. A Bayesian structure analysis and a tentative paternity analysis indicate extensive historical and contemporary gene flow among remnant populations. Pollination experiments and a paternity analysis show that Glionnetia sericea is self-compatible. Nevertheless, outcrossing is present with 7% of mating events resulting from pollen transfer between populations. Artificial pollination provided no evidence for pollen limitation in isolated populations. The highly mobile and specialized hawkmoth pollinators (Agrius convolvuli and Cenophodes tamsi; Sphingidae) appear to promote extensive gene flow, thus mitigating the potential negative ecological and genetic effects of habitat fragmentation in this species. We conclude that contemporary gene flow is sufficient to maintain genetic connectivity in this rare and restricted Seychelles endemic, in contrast to other island endemic tree species with limited contemporary gene flow. PMID:25347541

Finger, Aline; Valentin, Terence; Ghazoul, Jaboury

2014-01-01

97

Discovery in Genetic Skin Disease: The Impact of High Throughput Genetic Technologies  

PubMed Central

The last decade has seen considerable advances in our understanding of the genetic basis of skin disease, as a consequence of high throughput sequencing technologies including next generation sequencing and whole exome sequencing. We have now determined the genes underlying several monogenic diseases, such as harlequin ichthyosis, Olmsted syndrome, and exfoliative ichthyosis, which have provided unique insights into the structure and function of the skin. In addition, through genome wide association studies we now have an understanding of how low penetrance variants contribute to inflammatory skin diseases such as psoriasis vulgaris and atopic dermatitis, and how they contribute to underlying pathophysiological disease processes. In this review we discuss strategies used to unravel the genes underlying both monogenic and complex trait skin diseases in the last 10 years and the implications on mechanistic studies, diagnostics, and therapeutics. PMID:25093584

Maruthappu, Thiviyani; Scott, Claire A.; Kelsell, David P.

2014-01-01

98

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. PMID:9409823

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

1997-01-01

99

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. PMID:21463505

2011-01-01

100

Dendritic polyglycerols with oligoamine shells show low toxicity and high siRNA transfection efficiency in vitro.  

PubMed

RNA interference provides great opportunities for treating diseases from genetic disorders, infection, and cancer. The successful application of small interference RNA (siRNA) in cells with high transfection efficiency and low cytotoxicity is, however, a major challenge in gene-mediated therapy. Several pH-responsive core shell architectures have been designed that contain a nitrogen shell motif and a polyglycerol core, which has been prepared by a two-step protocol involving the activation of primary and secondary hydroxyl groups by phenyl chloroformate and amine substitution. Each polymer was analyzed by particle size and ? potential measurements, whereas the respective polyplex formation was determined by ethidium bromide displacement assay, atomic force microscopy (AFM), and surface charge analysis. The in vitro gene silencing properties of the different polymers were evaluated by using a human epithelial carcinoma cell (HeLaS3) line with different proteins (Lamin, CDC2, MAPK2). Polyplexes yielded similar knockdown efficiencies as HiPerFect controls, with comparably low cytotoxicity. Therefore, these efficient and highly biocompatible dendritic polyamines are promising candidates for siRNA delivery in vivo. PMID:20857928

Fischer, Wiebke; Calderón, Marcelo; Schulz, Andrea; Andreou, Ioanna; Weber, Martin; Haag, Rainer

2010-10-20

101

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...

102

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...

103

Genetic determinants of Tibetan high-altitude adaptation.  

PubMed

Some highland populations have genetic adaptations that enable their successful existence in a hypoxic environment. Tibetans are protected against many of the harmful responses exhibited by non-adapted populations upon exposure to severe hypoxia, including elevated hemoglobin concentration (i.e., polycythemia). Recent studies have highlighted several genes subject to natural selection in native high-altitude Tibetans. Three of these genes, EPAS1, EGLN1 and PPARA, regulate or are regulated by hypoxia inducible factor, a principal controller of erythropoiesis and other organismal functions. Uncovering the molecular basis of hypoxic adaptation should have implications for understanding hematological and other adaptations involved in hypoxia tolerance. Because the hypoxia response involves a variety of cardiovascular, pulmonary and metabolic functions, this knowledge would improve our understanding of disease mechanisms and could ultimately be translated into targeted therapies for oxygen deprivation, cardiopulmonary and cerebral pathologies, and metabolic disorders such as diabetes and obesity. PMID:22068265

Simonson, Tatum S; McClain, Donald A; Jorde, Lynn B; Prchal, Josef T

2012-04-01

104

PCR-based detection of genetically modified soybean and maize in raw and highly processed foodstuffs.  

PubMed

The PCR method has proved to be an invaluable tool for the specific and sensitive detection of genetically modified material (e.g., Roundup Ready Soybean and Bt-176 "Maximizer" Maize) in foodstuffs. The first step in the procedure, namely the purification of nucleic acids from the sample, is often the deciding factor in the production of meaningful results. In this study, we present two procedures that enable an efficient isolation of trace amounts of genetic material from both raw and highly processed foodstuffs. We show that for optimal, PCR-ready DNA purification from highly processed foodstuffs and PCR inhibitor-rich substances--such as cocoa-containing products--adapted protocols for the QIAGEN QIAamp DNA Stool Mini Kit can be utilized. For complete DNA isolation from raw foodstuffs, a protocol using the DNeasy Plant Mini Kit is presented. PMID:11515380

Tengel, C; Schüssler, P; Setzke, E; Balles, J; Sprenger-Haussels, M

2001-08-01

105

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

106

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. PMID:21885828

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

2011-01-01

107

A comprehensive analysis of high school genetics standards: are states keeping pace with modern genetics?  

PubMed

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. PMID:21885828

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

2011-01-01

108

Mapping migration in a songbird using high-resolution genetic markers.  

PubMed

Neotropic migratory birds are declining across the Western Hemisphere, but conservation efforts have been hampered by the inability to assess where migrants are most limited-the breeding grounds, migratory stopover sites or wintering areas. A major challenge has been the lack of an efficient, reliable and broadly applicable method for measuring the strength of migratory connections between populations across the annual cycle. Here, we show how high-resolution genetic markers can be used to identify genetically distinct groups of a migratory bird, the Wilson's warbler (Cardellina pusilla), at fine enough spatial scales to facilitate assessing regional drivers of demographic trends. By screening 1626 samples using 96 highly divergent single nucleotide polymorphisms selected from a large pool of candidates (~450 000), we identify novel region-specific migratory routes and timetables of migration along the Pacific Flyway. Our results illustrate that high-resolution genetic markers are more reliable, precise and amenable to high throughput screening than previously described intrinsic marking techniques, making them broadly applicable to large-scale monitoring and conservation of migratory organisms. PMID:25346105

Ruegg, Kristen C; Anderson, Eric C; Paxton, Kristina L; Apkenas, Vanessa; Lao, Sirena; Siegel, Rodney B; DeSante, David F; Moore, Frank; Smith, Thomas B

2014-12-01

109

Isolation of thermophilic L-lactic acid producing bacteria showing homo-fermentative manner under high aeration condition.  

PubMed

By applying non-sterile open fermentation of food waste, various thermotolerant l-lactic acid-producing bacteria were isolated and identified. The predominant bacterial isolates showing higher accumulation of l-lactic acid belong to 3 groups of Bacillus coagulans, according to their 16S rRNA gene sequence similarities. B. coagulans strains M21 and M36 produced high amounts of l-lactic acid of high optical purity and lactic acid selectivity in model kitchen refuse medium and glucose-yeast extract-peptone medium. Other thermotolerant isolates resembling to Bacillus humi, B. ruris, B. subtilis, B. niacini and B. soli were also identified. These bacteria produced low amounts of l-lactic acid of more than 99% optical purity. All isolated strains showed the highest growth rate at temperatures around 55-60°C. They showed unique responses to various oxygen supply conditions. The majority of isolates produced l-lactic acid at a low overall oxygen transfer coefficient (KLa); however, acetic acid was produced instead of l-lactic acid at a high KLa. B. coagulans M21 was the only strain that produced high, consistent, and reproducible amounts of optically pure l-lactic acid (>99% optical purity) under high and low KLa conditions in a homo-fermentative manner. PMID:24119530

Tongpim, Saowanit; Meidong, Ratchanu; Poudel, Pramod; Yoshino, Satoshi; Okugawa, Yuki; Tashiro, Yukihiro; Taniguchi, Masayuki; Sakai, Kenji

2014-03-01

110

High-density genome scan in Crohn disease shows confirmed linkage to chromosome 14q11-12.  

PubMed Central

Epidemiological studies have shown that genetic factors contribute to the pathogenesis of the idiopathic inflammatory bowel diseases (IBD), Crohn disease (CD) and ulcerative colitis (UC). Recent genome scans and replication studies have identified replicated linkage between CD and a locus on chromosome 16 (the IBD1 locus), replicated linkage between IBD (especially UC) and a locus on chromosome 12q (the IBD2 locus), and replicated linkage between IBD (especially CD) and a locus on chromosome 6p (the IBD3 locus). Since the estimated locus-specific lambdas values for the regions of replicated linkage do not account for the overall lambdas in CD, and since the published genome scans in IBD show at least nominal evidence for linkage to regions on all but two chromosomes, we performed an independent genome scan using 751 microsatellite loci in 127 CD-affected relative pairs from 62 families. Single-point nonparametric linkage analysis using the GENEHUNTER-PLUS program shows evidence for linkage to the adjacent D14S261 and D14S283 loci on chromosome 14q11-12 (LOD = 3.00 and 1.70, respectively), and the maximal multipoint LOD score is observed at D14S261 (LOD = 3.60). In the multipoint analysis, nominal evidence for linkage (P<.05) is observed near D2S117 (LOD = 1.25), near D3S3045 (LOD = 1.31), between D7S40 and D7S648 (LOD = 0.91), and near D18S61 (LOD = 1.15). Our finding of significant linkage to D14S261 and the finding of suggestive linkage to the same locus in an independent study (multipoint LOD = 2.8) satisfies criteria for confirmed linkage, so we propose that the region of interest on chromosome 14q11-12 should be designated the IBD4 locus. PMID:10747815

Duerr, R H; Barmada, M M; Zhang, L; Pfutzer, R; Weeks, D E

2000-01-01

111

Genetic and nongenetic determinants of cell growth variation assessed by high-throughput microscopy.  

PubMed

In microbial populations, growth initiation and proliferation rates are major components of fitness and therefore likely targets of selection. We used a high-throughput microscopy assay, which enables simultaneous analysis of tens of thousands of microcolonies, to determine the sources and extent of growth rate variation in the budding yeast (Saccharomyces cerevisiae) in different glucose environments. We find that cell growth rates are regulated by the extracellular concentration of glucose as proposed by Monod (1949), but that significant heterogeneity in growth rates is observed among genetically identical individuals within an environment. Yeast strains isolated from different geographic locations and habitats differ in their growth rate responses to different glucose concentrations. Inheritance patterns suggest that the genetic determinants of growth rates in different glucose concentrations are distinct. In addition, we identified genotypes that differ in the extent of variation in growth rate within an environment despite nearly identical mean growth rates, providing evidence that alleles controlling phenotypic variability segregate in yeast populations. We find that the time to reinitiation of growth (lag) is negatively correlated with growth rate, yet this relationship is strain-dependent. Between environments, the respirative activity of individual cells negatively correlates with glucose abundance and growth rate, but within an environment respirative activity and growth rate show a positive correlation, which we propose reflects differences in protein expression capacity. Our study quantifies the sources of genetic and nongenetic variation in cell growth rates in different glucose environments with unprecedented precision, facilitating their molecular genetic dissection. PMID:23938868

Ziv, Naomi; Siegal, Mark L; Gresham, David

2013-12-01

112

31-year-old female shows marked improvement in depression, agitation, and panic attacks after genetic testing was used to inform treatment.  

PubMed

This case describes a 31-year-old female Caucasian patient with complaints of ongoing depression, agitation, and severe panic attacks. The patient was untreated until a recent unsuccessful trial of citalopram followed by venlafaxine which produced a partial response. Genetic testing was performed to assist in treatment decisions and revealed the patient to be heterozygous for polymorphisms in 5HT2C, ANK3, and MTHFR and homozygous for a polymorphism in SLC6A4 and the low activity (Met/Met) COMT allele. In response to genetic results and clinical presentation, venlafaxine was maintained and lamotrigine was added leading to remission of agitation and depression. PMID:24744941

Lawrence, Scott

2014-01-01

113

31-Year-Old Female Shows Marked Improvement in Depression, Agitation, and Panic Attacks after Genetic Testing Was Used to Inform Treatment  

PubMed Central

This case describes a 31-year-old female Caucasian patient with complaints of ongoing depression, agitation, and severe panic attacks. The patient was untreated until a recent unsuccessful trial of citalopram followed by venlafaxine which produced a partial response. Genetic testing was performed to assist in treatment decisions and revealed the patient to be heterozygous for polymorphisms in 5HT2C, ANK3, and MTHFR and homozygous for a polymorphism in SLC6A4 and the low activity (Met/Met) COMT allele. In response to genetic results and clinical presentation, venlafaxine was maintained and lamotrigine was added leading to remission of agitation and depression. PMID:24744941

Lawrence, Scott

2014-01-01

114

Seascape Genetics of a Globally Distributed, Highly Mobile Marine Mammal: The Short-Beaked Common Dolphin (Genus Delphinus)  

PubMed Central

Identifying which factors shape the distribution of intraspecific genetic diversity is central in evolutionary and conservation biology. In the marine realm, the absence of obvious barriers to dispersal can make this task more difficult. Nevertheless, recent studies have provided valuable insights into which factors may be shaping genetic structure in the world's oceans. These studies were, however, generally conducted on marine organisms with larval dispersal. Here, using a seascape genetics approach, we show that marine productivity and sea surface temperature are correlated with genetic structure in a highly mobile, widely distributed marine mammal species, the short-beaked common dolphin. Isolation by distance also appears to influence population divergence over larger geographical scales (i.e. across different ocean basins). We suggest that the relationship between environmental variables and population structure may be caused by prey behaviour, which is believed to determine common dolphins' movement patterns and preferred associations with certain oceanographic conditions. Our study highlights the role of oceanography in shaping genetic structure of a highly mobile and widely distributed top marine predator. Thus, seascape genetic studies can potentially track the biological effects of ongoing climate-change at oceanographic interfaces and also inform marine reserve design in relation to the distribution and genetic connectivity of charismatic and ecologically important megafauna. PMID:22319634

Amaral, Ana R.; Beheregaray, Luciano B.; Bilgmann, Kerstin; Boutov, Dmitri; Freitas, Luis; Robertson, Kelly M.; Sequeira, Marina; Stockin, Karen A.; Coelho, M. Manuela; Moller, Luciana M.

2012-01-01

115

Sex-stratified Genome-wide Association Studies Including 270,000 Individuals Show Sexual Dimorphism in Genetic Loci for Anthropometric Traits  

PubMed Central

Given the anthropometric differences between men and women and previous evidence of sex-difference in genetic effects, we conducted a genome-wide search for sexually dimorphic associations with height, weight, body mass index, waist circumference, hip circumference, and waist-to-hip-ratio (133,723 individuals) and took forward 348 SNPs into follow-up (additional 137,052 individuals) in a total of 94 studies. Seven loci displayed significant sex-difference (FDR<5%), including four previously established (near GRB14/COBLL1, LYPLAL1/SLC30A10, VEGFA, ADAMTS9) and three novel anthropometric trait loci (near MAP3K1, HSD17B4, PPARG), all of which were genome-wide significant in women (P<5×10?8), but not in men. Sex-differences were apparent only for waist phenotypes, not for height, weight, BMI, or hip circumference. Moreover, we found no evidence for genetic effects with opposite directions in men versus women. The PPARG locus is of specific interest due to its role in diabetes genetics and therapy. Our results demonstrate the value of sex-specific GWAS to unravel the sexually dimorphic genetic underpinning of complex traits. PMID:23754948

Jackson, Anne U.; Monda, Keri L.; Kilpelainen, Tuomas O.; Esko, Tonu; Magi, Reedik; Li, Shengxu; Workalemahu, Tsegaselassie; Feitosa, Mary F.; Croteau-Chonka, Damien C.; Day, Felix R.; Fall, Tove; Ferreira, Teresa; Gustafsson, Stefan; Locke, Adam E.; Mathieson, Iain; Scherag, Andre; Vedantam, Sailaja; Wood, Andrew R.; Liang, Liming; Steinthorsdottir, Valgerdur; Thorleifsson, Gudmar; Dermitzakis, Emmanouil T.; Dimas, Antigone S.; Karpe, Fredrik; Min, Josine L.; Nicholson, George; Clegg, Deborah J.; Person, Thomas; Krohn, Jon P.; Bauer, Sabrina; Buechler, Christa; Eisinger, Kristina; Bonnefond, Amelie; Froguel, Philippe; Hottenga, Jouke-Jan; Prokopenko, Inga; Waite, Lindsay L.; Harris, Tamara B.; Smith, Albert Vernon; Shuldiner, Alan R.; McArdle, Wendy L.; Caulfield, Mark J.; Munroe, Patricia B.; Gronberg, Henrik; Chen, Yii-Der Ida; Li, Guo; Beckmann, Jacques S.; Johnson, Toby; Thorsteinsdottir, Unnur; Teder-Laving, Maris; Khaw, Kay-Tee; Wareham, Nicholas J.; Zhao, Jing Hua; Amin, Najaf; Oostra, Ben A.; Kraja, Aldi T.; Province, Michael A.; Cupples, L. Adrienne; Heard-Costa, Nancy L.; Kaprio, Jaakko; Ripatti, Samuli; Surakka, Ida; Collins, Francis S.; Saramies, Jouko; Tuomilehto, Jaakko; Jula, Antti; Salomaa, Veikko; Erdmann, Jeanette; Hengstenberg, Christian; Loley, Christina; Schunkert, Heribert; Lamina, Claudia; Wichmann, H. Erich; Albrecht, Eva; Gieger, Christian; Hicks, Andrew A.; Johansson, Asa; Pramstaller, Peter P.; Kathiresan, Sekar; Speliotes, Elizabeth K.; Penninx, Brenda; Hartikainen, Anna-Liisa; Jarvelin, Marjo-Riitta; Gyllensten, Ulf; Boomsma, Dorret I.; Campbell, Harry; Wilson, James F.; Chanock, Stephen J.; Farrall, Martin; Goel, Anuj; Medina-Gomez, Carolina; Rivadeneira, Fernando; Estrada, Karol; Uitterlinden, Andre G.; Hofman, Albert; Zillikens, M. Carola; den Heijer, Martin; Kiemeney, Lambertus A.; Maschio, Andrea; Hall, Per; Tyrer, Jonathan; Teumer, Alexander; Volzke, Henry; Kovacs, Peter; Tonjes, Anke; Mangino, Massimo; Spector, Tim D.; Hayward, Caroline; Rudan, Igor; Hall, Alistair S.; Samani, Nilesh J.; Attwood, Antony Paul; Sambrook, Jennifer G.; Hung, Joseph; Palmer, Lyle J.; Lokki, Marja-Liisa; Sinisalo, Juha; Boucher, Gabrielle; Huikuri, Heikki; Lorentzon, Mattias; Ohlsson, Claes; Eklund, Niina; Eriksson, Johan G.; Barlassina, Cristina; Rivolta, Carlo; Nolte, Ilja M.; Snieder, Harold; Van der Klauw, Melanie M.; Van Vliet-Ostaptchouk, Jana V.; Gejman, Pablo V.; Shi, Jianxin; Jacobs, Kevin B.; Wang, Zhaoming; Bakker, Stephan J. L.; Mateo Leach, Irene; Navis, Gerjan; van der Harst, Pim; Martin, Nicholas G.; Medland, Sarah E.; Montgomery, Grant W.; Yang, Jian; Chasman, Daniel I.; Ridker, Paul M.; Rose, Lynda M.; Lehtimaki, Terho; Raitakari, Olli; Absher, Devin; Iribarren, Carlos; Basart, Hanneke; Hovingh, Kees G.; Hypponen, Elina; Power, Chris; Anderson, Denise; Beilby, John P.; Hui, Jennie; Jolley, Jennifer; Sager, Hendrik; Bornstein, Stefan R.; Schwarz, Peter E. H.; Kristiansson, Kati; Perola, Markus; Lindstrom, Jaana; Swift, Amy J.; Uusitupa, Matti; Atalay, Mustafa; Lakka, Timo A.; Rauramaa, Rainer; Bolton, Jennifer L.; Fowkes, Gerry; Fraser, Ross M.; Price, Jackie F.; Fischer, Krista; KrjutA?kov, Kaarel; Metspalu, Andres; Mihailov, Evelin; Langenberg, Claudia; Luan, Jian'an; Ong, Ken K.; Chines, Peter S.; Keinanen-Kiukaanniemi, Sirkka M.; Saaristo, Timo E.; Edkins, Sarah; Franks, Paul W.; Hallmans, Goran; Shungin, Dmitry; Morris, Andrew David; Palmer, Colin N. A.; Erbel, Raimund; Moebus, Susanne; Nothen, Markus M.; Pechlivanis, Sonali; Hveem, Kristian; Narisu, Narisu; Hamsten, Anders; Humphries, Steve E.; Strawbridge, Rona J.; Tremoli, Elena; Grallert, Harald; Thorand, Barbara; Illig, Thomas; Koenig, Wolfgang; Muller-Nurasyid, Martina; Peters, Annette; Boehm, Bernhard O.; Kleber, Marcus E.; Marz, Winfried; Winkelmann, Bernhard R.; Kuusisto, Johanna; Laakso, Markku; Arveiler, Dominique; Cesana, Giancarlo; Kuulasmaa, Kari; Virtamo, Jarmo; Yarnell, John W. G.; Kuh, Diana; Wong, Andrew; Lind, Lars; de Faire, Ulf; Gigante, Bruna; Magnusson, Patrik K. E.; Pedersen, Nancy L.; Dedoussis, George; Dimitriou, Maria; Kolovou, Genovefa; Kanoni, Stavroula; Stirrups, Kathleen; Bonnycastle, Lori L.; Nj?lstad, Inger; Wilsgaard, Tom; Ganna, Andrea; Rehnberg, Emil; Hingorani, Aroon; Kivimaki, Mika; Kumari, Meena; Assimes, Themistocles L.; Barroso, Ines; Boehnke, Michael; Borecki, Ingrid B.; Deloukas, Panos; Fox, Caroline S.; Frayling, Timothy; Groop, Leif C.; Haritunians, Talin; Hunter, David; Ingelsson, Erik; Kaplan, Robert; Mohlke, Karen L.; O'Connell, Jeffrey R.; Schlessinger, David

2013-01-01

116

"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

117

Genetics  

NSDL National Science Digital Library

This activity helps students to understand basic principles of genetics, including relationships of genotype to phenotype, concepts of recessive and dominant alleles, and how understanding meiosis and fertilization provides the basis for understanding inheritance, as summarized in Punnett squares. The Student Handout includes an analysis of the inheritance of albinism that teaches all of these concepts, a Coin Toss Genetics activity that helps students understand the probabilistic nature of Punnett square predictions, and an analysis of the inheritance of sickle cell anemia that reinforces the basic concepts and introduces some of the complexities of genetics. The Genetics Supplement includes two additional activities, an analysis of student data on the sex makeup of sibships and pedigree analyses of recessive and dominant alleles with challenge questions that introduce the role of mutations and an evaluation of Punnett squares and pedigrees as models of inheritance.

Doherty, Jennifer; Waldron, Ingrid; Poethig, Scott

118

AFLP analysis reveals high genetic diversity but low population structure in Coccidioides posadasii isolates from Mexico and Argentina  

PubMed Central

Background Coccidioides immitis and C. posadasii cause coccidioidomycosis, a disease that is endemic to North and South America, but for Central America, the incidence of coccidioidomycosis has not been clearly established. Several studies suggest genetic variability in these fungi; however, little definitive information has been discovered about the variability of Coccidioides fungi in Mexico (MX) and Argentina (AR). Thus, the goals for this work were to study 32 Coccidioides spp. isolates from MX and AR, identify the species of these Coccidioides spp. isolates, analyse their phenotypic variability, examine their genetic variability and investigate the Coccidioides reproductive system and its level of genetic differentiation. Methods Coccidioides spp. isolates from MX and AR were taxonomically identified by phylogenetic inference analysis using partial sequences of the Ag2/PRA gene and their phenotypic characteristics analysed. The genetic variability, reproductive system and level of differentiation were estimated using AFLP markers. The level of genetic variability was assessed measuring the percentage of polymorphic loci, number of effective allele, expected heterocygosity and Index of Association (IA). The degree of genetic differentiation was determined by AMOVA. Genetic similarities among isolates were estimated using Jaccard index. The UPGMA was used to contsruct the corresponding dendrogram. Finally, a network of haplotypes was built to evaluate the genealogical relationships among AFLP haplotypes. Results All isolates of Coccidioides spp. from MX and AR were identified as C. posadasii. No phenotypic variability was observed among the C. posadasii isolates from MX and AR. Analyses of genetic diversity and population structure were conducted using AFLP markers. Different estimators of genetic variability indicated that the C. posadasii isolates from MX and AR had high genetic variability. Furthermore, AMOVA, dendrogram and haplotype network showed a small genetic differentiation among the C. posadasii populations analysed from MX and AR. Additionally, the IA calculated for the isolates suggested that the species has a recombinant reproductive system. Conclusions No phenotypic variability was observed among the C. posadasii isolates from MX and AR. The high genetic variability observed in the isolates from MX and AR and the small genetic differentiation observed among the C. posadasii isolates analysed, suggest that this species could be distributed as a single genetic population in Latin America. PMID:24004977

2013-01-01

119

Sci Show  

NSDL National Science Digital Library

The Sci Show, an entertaining series of quirky YouTube videos, tackles topics ranging from âÂÂHow Do Polarized Sunglasses Workâ to âÂÂStrong Interaction: The Four Fundamental Forces of Physics.â Most episodes are less than five minutes long, but they pack a wallop of handy science info. Anyone short on time but long on big questions will benefit from the series. Episodes will be helpful to teachers and parents looking to spark enthusiasm in young minds. Viewers may want to start with recent episodes like âÂÂTodayâÂÂs Mass Extinction,â and the âÂÂWorldâÂÂs First See-Through Animalâ and âÂÂHow Do Animals Change Color?â before digging into the archives for gems like âÂÂThe Truth About Gingersâ and âÂÂThe Science of Lying.âÂÂ

120

IgG4-related lung disease showing high standardized uptake values on FDG-PET: report of two cases  

PubMed Central

Immunoglobulin G4 (IgG4)-related lung disease is a disease in which IgG4-positive plasma cells and lymphocytes infiltrate lung tissues along with immunohistochemically evident fibrous interstitial proliferation in the background, in addition to hyper-IgG4 disease. The diagnosis of this disease can be difficult. Here, we report 2 cases with IgG4-related lung disease that was difficult to differentiate from malignant tumors because both cases had pulmonary lesions showing high standardized uptake values (SUV) on positron emission tomography (PET). Case 1: A 75-year-old man under treatment for autoimmune pancreatitis and diabetes mellitus was noted to have multiple nodular opacities in both lungs and a mass density in the right paravertebral region on computed tomography (CT). As high SUVmax was noted for both lesions on exploration by fluorodeoxyglucose (FDG)-PET/CT, an advanced malignant tumor was diagnosed and a video-assisted thoracoscopic (VATS) biopsy was performed and diagnosed IgG4-related lung disease. Case 2: A 48-year-old woman consulted our clinic with a chief complaint of bloody sputum. Chest CT revealed a mass density with 12-, 13-, and 16-mm spiculations in the S2 segment of the right upper lobe and irregular thickening of the pleura including the paravertebral region. The lesion was a mass showing high SUV in the S2 segment on FDG-PET. Malignancy was suspected from the imaging findings, and a VATS biopsy was performed and diagnosed IgG4-related lung disease. Actively undertaking VATS biopsy in cases with this disease is valuable for making the differential diagnosis between malignant tumors and IgG4-related lung disease, since the diagnosis can be difficult in some patients showing high SUV. PMID:23800259

2013-01-01

121

IgG4-related lung disease showing high standardized uptake values on FDG-PET: report of two cases.  

PubMed

Immunoglobulin G4 (IgG4)-related lung disease is a disease in which IgG4-positive plasma cells and lymphocytes infiltrate lung tissues along with immunohistochemically evident fibrous interstitial proliferation in the background, in addition to hyper-IgG4 disease. The diagnosis of this disease can be difficult. Here, we report 2 cases with IgG4-related lung disease that was difficult to differentiate from malignant tumors because both cases had pulmonary lesions showing high standardized uptake values (SUV) on positron emission tomography (PET). Case 1: A 75-year-old man under treatment for autoimmune pancreatitis and diabetes mellitus was noted to have multiple nodular opacities in both lungs and a mass density in the right paravertebral region on computed tomography (CT). As high SUVmax was noted for both lesions on exploration by fluorodeoxyglucose (FDG)-PET/CT, an advanced malignant tumor was diagnosed and a video-assisted thoracoscopic (VATS) biopsy was performed and diagnosed IgG4-related lung disease. Case 2: A 48-year-old woman consulted our clinic with a chief complaint of bloody sputum. Chest CT revealed a mass density with 12-, 13-, and 16-mm spiculations in the S2 segment of the right upper lobe and irregular thickening of the pleura including the paravertebral region. The lesion was a mass showing high SUV in the S2 segment on FDG-PET. Malignancy was suspected from the imaging findings, and a VATS biopsy was performed and diagnosed IgG4-related lung disease. Actively undertaking VATS biopsy in cases with this disease is valuable for making the differential diagnosis between malignant tumors and IgG4-related lung disease, since the diagnosis can be difficult in some patients showing high SUV. PMID:23800259

Kitada, Masahiro; Matuda, Yoshinari; Hayashi, Satoshi; Ishibashi, Kei; Oikawa, Kensuke; Miyokawa, Naoyuki; Ohsaki, Yoshinobu

2013-01-01

122

Extending glacial refugia for a European tree: genetic markers show that Iberian populations of white elm are native relicts and not introductions.  

PubMed

Conservation policies usually focus on in situ protection of native populations, a priority that requires accurate assessment of population status. Distinction between native and introduced status can be particularly difficult (and at the same time, is most important) for species whose natural habitat has become both rare and highly fragmented. Here, we address the status of the white elm (Ulmus laevis Pallas), a European riparian tree species whose populations have been fragmented by human activity and is protected wherever it is considered native. Small populations of this species are located in Iberia, where they are unprotected because they are considered introductions due to their rarity. However, Iberia and neighbouring regions in southwestern France have been shown to support discrete glacial refuge populations of many European trees, and the possibility remains that Iberian white elms are native relicts. We used chloroplast RFLPs and nuclear microsatellites to establish the relationship between populations in Iberia and the Central European core distribution. Bayesian approaches revealed significant spatial structure across populations. Those in Iberia and southwestern France shared alleles absent from Central Europe, and showed spatial population structure within Iberia common in recognized native taxa. Iberian populations show a demographic signature of ancient population bottlenecks, while those in Central European show a signature of recent population bottlenecks. These patterns are not consistent with historical introduction of white elm to Iberia, and instead strongly support native status, arguing for immediate implementation of conservation measures for white elm populations in Spain and contiguous areas of southern France. PMID:24022495

Fuentes-Utrilla, P; Venturas, M; Hollingsworth, P M; Squirrell, J; Collada, C; Stone, G N; Gil, L

2014-02-01

123

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

124

In vivo methods for testing allergenicity show that high hydrostatic pressure hydrolysates of ?-lactoglobulin are immunologically inert.  

PubMed

The major milk allergen ?-lactoglobulin (?-LG) exhibits an enhanced susceptibility to proteolysis under high hydrostatic pressure and this may be an efficient method to produce hypoallergenic hydrolysates. The aim of this work was to evaluate the in vivo allergenicity of 3 ?-LG hydrolysates produced under atmospheric pressure or high-pressure conditions. Hydrolysates were chosen based on previous experiments that showed that they provide a complete removal of intact ?-LG but differed in vitro IgE-binding properties that could be traced to the peptide pattern. The ability to trigger systemic anaphylaxis was assessed using C3H/HeJ mice orally sensitized to ?-LG. Outcome measures included symptom score, body temperature, serum mouse mast cell protease 1 (mMCP-1), and quantification of circulating basophils. Mast cell degranulation in vivo was assessed by passive cutaneous anaphylaxis. The 3 tested hydrolysates showed an abrogated allergenicity as revealed by the absence of anaphylactic symptoms and a decrease in body temperature. We demonstrated that the peptides present in the hydrolysates had lost their ability to cross-link 2 human IgE antibodies to induce mast cell degranulation, thus indicating that most of the peptides formed retain just one relevant IgE-binding epitope. The orally sensitized mouse model is a useful tool to address the in vivo allergenicity of novel milk formulas and demonstrates the safety of hydrolysates produced under high-pressure conditions. PMID:22281318

López-Expósito, I; Chicón, R; Belloque, J; López-Fandiño, R; Berin, M C

2012-02-01

125

High school students' problem-solving performance on realistic genetics problems  

Microsoft Academic Search

Problem solving is recognized as a valuable educational experience in science. Thus genetics, essentially a problem-solving science included in almost all high school biology courses, offers a fruitful area for studying student problem-solving performance. The research reported in this article describes the performance of 30 high school students solving 119 problems generated by the computer program GENETICS CONSTRUCTION KIT (Jungck

Susie Johnston Slack; Jim Stewart

1990-01-01

126

Accessing Genetic Information with High-Density DNA Arrays  

Microsoft Academic Search

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

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

1996-01-01

127

Mapping IS6110 in high-copy number Mycobacterium tuberculosis strains shows specific insertion points in the Beijing genotype  

PubMed Central

Background Mycobacterium tuberculosis Beijing strains are characterized by a large number of IS6110 copies, suggesting the potential implication of this element in the virulence and capacity for rapid dissemination characteristic of this family. This work studies the insetion points of IS6110 in high-copy clinical isolates specifically focusing on the Beijing genotype. Results In the present work we mapped the insertion points of IS6110 in all the Beijing strains available in the literature and in the DNA sequence databases. We generated a representative primer collection of the IS6110 locations, which was used to analyse 61 high-copy clinical isolates. A total of 440 points of insertion were identified and analysis of their flanking regions determined the exact location, the direct repeats (DRs), the orientation and the distance to neighboring genes of each copy of IS6110. We identified specific points of insertion in Beijing strains that enabled us to obtain a dendrogram that groups the Beijing genotype. Conclusions This work presents a detailed analysis of locations of IS6110 in high-copy clinical isolates, showing points of insertion present with high frequency in the Beijing family and absent in other strains. PMID:23800083

2013-01-01

128

Transnuclear TRP1-specific CD8 T cells with high or low affinity TCRs show equivalent anti-tumor activity  

PubMed Central

We have generated, via somatic cell nuclear transfer, two independent lines of transnuclear (TN) mice, using as nuclear donors CD8 T cells, sorted by tetramer staining, that recognize the endogenous melanoma antigen TRP1. These two lines of nominally identical specificity differ greatly in their affinity for antigen (TRP1high or TRP1low) as inferred from tetramer dissociation and peptide responsiveness. Ex vivo-activated CD8 T cells from either TRP1high or TRP1low mice show cytolytic activity in 3D tissue culture and in vivo, and slow the progression of subcutaneous B16 melanoma. Although naïve TRP1low CD8 T cells do not affect tumor growth, upon activation these cells function indistinguishably from TRP1high cells in vivo, limiting tumor cell growth and increasing mouse survival. The anti-tumor effect of both TRP1high and TRP1low CD8 T cells is enhanced in RAG-deficient hosts. However, tumor outgrowth eventually occurs, likely due to T cell exhaustion. The TRP1 TN mice are an excellent model for examining the functional attributes of T cells conferred by TCR affinity, and they may serve as a platform for screening immunomodulatory cancer therapies. PMID:24459675

Dougan, Stephanie K.; Dougan, Michael; Kim, Jun; Turner, Jacob A.; Ogata, Souichi; Cho, Hyun-Il; Jaenisch, Rudolf; Celis, Esteban; Ploegh, Hidde L.

2013-01-01

129

Genetics  

NSDL National Science Digital Library

What affects how physical characteristics are transmitted from parent to offspring? This is a question that can be answered at many levels. Molecular biologists examine the pattern of nucleotides in deoxyribonucleic acid (DNA) and the effect of mutations on the proteins produced. Classical geneticists explore the patterns by which traits are transmitted through families. Medical geneticists attempt to describe and develop treatments for diseases that have a genetic component. Genetic engineers analyze how traits can be altered in organisms through modern technology. These are only a few of the strategies that scientists employ to explain the nature of heredity. Explore historical perspectives on the study of genetics and investigate how cutting-edge technology is being used to expand our understanding of heredity.

National Science Teachers Association (NSTA)

2005-04-01

130

Population genetics of the understory fishtail palm Chamaedorea ernesti-augusti in Belize: high genetic connectivity with local differentiation  

Microsoft Academic Search

BACKGROUND: Developing a greater understanding of population genetic structure in lowland tropical plant species is highly relevant to our knowledge of increasingly fragmented forests and to the conservation of threatened species. Specific studies are particularly needed for taxa whose population dynamics are further impacted by human harvesting practices. One such case is the fishtail or xaté palm (Chamaedorea ernesti-augusti) of

Angélica Cibrián-Jaramillo; Christine D Bacon; Nancy C Garwood; Richard M Bateman; Meredith M Thomas; Steve Russell; C Donovan Bailey; William J Hahn; Samuel GM Bridgewater; Rob DeSalle

2009-01-01

131

Transcriptome sequencing for high throughput SNP development and genetic mapping in Pea  

PubMed Central

Background Pea has a complex genome of 4.3 Gb for which only limited genomic resources are available to date. Although SNP markers are now highly valuable for research and modern breeding, only a few are described and used in pea for genetic diversity and linkage analysis. Results We developed a large resource by cDNA sequencing of 8 genotypes representative of modern breeding material using the Roche 454 technology, combining both long reads (400 bp) and high coverage (3.8 million reads, reaching a total of 1,369 megabases). Sequencing data were assembled and generated a 68 K unigene set, from which 41 K were annotated from their best blast hit against the model species Medicago truncatula. Annotated contigs showed an even distribution along M. truncatula pseudochromosomes, suggesting a good representation of the pea genome. 10 K pea contigs were found to be polymorphic among the genetic material surveyed, corresponding to 35 K SNPs. We validated a subset of 1538 SNPs through the GoldenGate assay, proving their ability to structure a diversity panel of breeding germplasm. Among them, 1340 were genetically mapped and used to build a new consensus map comprising a total of 2070 markers. Based on blast analysis, we could establish 1252 bridges between our pea consensus map and the pseudochromosomes of M. truncatula, which provides new insight on synteny between the two species. Conclusions Our approach created significant new resources in pea, i.e. the most comprehensive genetic map to date tightly linked to the model species M. truncatula and a large SNP resource for both academic research and breeding. PMID:24521263

2014-01-01

132

High Genetic Diversity and Structured Populations of the Oriental Fruit Moth in Its Range of Origin  

PubMed Central

The oriental fruit moth Grapholita (?=?Cydia) molesta is a key fruit pest globally. Despite its economic importance, little is known about its population genetics in its putative native range that includes China. We used five polymorphic microsatellite loci and two mitochondrial gene sequences to characterize the population genetic diversity and genetic structure of G. molesta from nine sublocations in three regions of a major fruit growing area of China. Larval samples were collected throughout the season from peach, and in late season, after host switch by the moth to pome fruit, also from apple and pear. We found high numbers of microsatellite alleles and mitochondrial DNA haplotypes in all regions, together with a high number of private alleles and of haplotypes at all sublocations, providing strong evidence that the sampled area belongs to the origin of this species. Samples collected from peach at all sublocations were geographically structured, and a significant albeit weak pattern of isolation-by-distance was found among populations, likely reflecting the low flight capacity of this moth. Interestingly, populations sampled from apple and pear in the late season showed a structure differing from that of populations sampled from peach throughout the season, indicating a selective host switch of a certain part of the population only. The recently detected various olfactory genotypes in G. molesta may underly this selective host switch. These genetic data yield, for the first time, an understanding of population dynamics of G. molesta in its native range, and of a selective host switch from peach to pome fruit, which may have a broad applicability to other global fruit production areas for designing suitable pest management strategies. PMID:24265692

Zheng, Yan; Peng, Xiong; Liu, Gaoming; Pan, Hongyan; Dorn, Silvia; Chen, Maohua

2013-01-01

133

High genetic diversity and structured populations of the oriental fruit moth in its range of origin.  

PubMed

The oriental fruit moth Grapholita (?=?Cydia) molesta is a key fruit pest globally. Despite its economic importance, little is known about its population genetics in its putative native range that includes China. We used five polymorphic microsatellite loci and two mitochondrial gene sequences to characterize the population genetic diversity and genetic structure of G. molesta from nine sublocations in three regions of a major fruit growing area of China. Larval samples were collected throughout the season from peach, and in late season, after host switch by the moth to pome fruit, also from apple and pear. We found high numbers of microsatellite alleles and mitochondrial DNA haplotypes in all regions, together with a high number of private alleles and of haplotypes at all sublocations, providing strong evidence that the sampled area belongs to the origin of this species. Samples collected from peach at all sublocations were geographically structured, and a significant albeit weak pattern of isolation-by-distance was found among populations, likely reflecting the low flight capacity of this moth. Interestingly, populations sampled from apple and pear in the late season showed a structure differing from that of populations sampled from peach throughout the season, indicating a selective host switch of a certain part of the population only. The recently detected various olfactory genotypes in G. molesta may underly this selective host switch. These genetic data yield, for the first time, an understanding of population dynamics of G. molesta in its native range, and of a selective host switch from peach to pome fruit, which may have a broad applicability to other global fruit production areas for designing suitable pest management strategies. PMID:24265692

Zheng, Yan; Peng, Xiong; Liu, Gaoming; Pan, Hongyan; Dorn, Silvia; Chen, Maohua

2013-01-01

134

High school students' understanding and problem solving in population genetics  

NASA Astrophysics Data System (ADS)

This study is an investigation of student understanding of population genetics and how students developed, used and revised conceptual models to solve problems. The students in this study participated in three rounds of problem solving. The first round involved the use of a population genetics model to predict the number of carriers in a population. The second round required them to revise their model of simple dominance population genetics to make inferences about populations containing three phenotype variations. The third round of problem solving required the students to revise their model of population genetics to explain anomalous data where the proportions of males and females with a trait varied significantly. As the students solved problems, they were involved in basic scientific processes as they observed population phenomena, constructed explanatory models to explain the data they observed, and attempted to persuade their peers as to the adequacy of their models. In this study, the students produced new knowledge about the genetics of a trait in a population through the revision and use of explanatory population genetics models using reasoning that was similar to what scientists do. The students learned, used and revised a model of Hardy-Weinberg equilibrium to generate and test hypotheses about the genetics of phenotypes given only population data. Students were also interviewed prior to and following instruction. This study suggests that a commonly held intuitive belief about the predominance of a dominant variation in populations is resistant to change, despite instruction and interferes with a student's ability to understand Hardy-Weinberg equilibrium and microevolution.

Soderberg, Patti D.

135

genetics  

NSDL National Science Digital Library

learning about our genetic make up We've been learning about DNA. Go to each web site, read and follow the instructions of the activities provided. On a piece of paper write your answers to the following questions and submit your work. Put the site for each of the questions you are answering. The first site is, ...

Curran, Carolyn

2011-12-05

136

Complete genome sequences from three genetically distinct strains reveal high intraspecies genetic diversity in the microsporidian Encephalitozoon cuniculi.  

PubMed

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. PMID:23291622

Pombert, Jean-François; Xu, Jinshan; Smith, David R; Heiman, David; Young, Sarah; Cuomo, Christina A; Weiss, Louis M; Keeling, Patrick J

2013-04-01

137

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. PMID:23291622

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

2013-01-01

138

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

139

Arterial Reactivity Is Enhanced in Genetic Males Taking High Dose Estrogens  

Microsoft Academic Search

Objectives. We sought to assess whether high dose estrogen treatment is associated with enhanced arterial reactivity in genetic males.Background. Although estrogens have been shown to enhance arterial reactivity in women, and are thereby thought to confer cardiovascular benefit, the vascular effects of long-term estrogen therapy in genetic males is unknown.Methods. We studied the arterial physiology of 30 genetic males—15 male

Jane A McCrohon; William A. W Walters; Jacqui T. C Robinson; Robyn J McCredie; Leo Turner; Mark R Adams; David J Handelsman; David S Celermajer

1997-01-01

140

Human, food and animal Campylobacter spp. isolated in Portugal: High genetic diversity and antibiotic resistance rates.  

PubMed

Infections by Campylobacter jejuni and Campylobacter coli are considered the major cause of bacterial gastroenteritis in humans, with food being the main source of infection. In this study, a total of 196 Campylobacter strains (125 isolates from humans, 39 from retail food and 32 from food animal sources) isolated in Portugal between 2009 and 2012 were characterised by multilocus sequence typing (MLST) and flaA short variable region (SVR) typing. Susceptibility to six antibiotics as well as the mechanisms underlying antibiotic resistance phenotypes was also studied. Based on MLST typing, C. coli strains were genetically more conserved, with a predominant clonal complex (CC828), than C. jejuni strains. In contrast, C. coli isolates were genetically more variable than C. jejuni with regard to flaA-SVR typing. A high rate of resistance was observed for quinolones (100% to nalidixic acid, >90% to ciprofloxacin) and, in general, resistance was more common among C. coli, especially for erythromycin (40.2% vs. 6.7%). In addition, most isolates (86%) were resistant to multiple antimicrobial families. Besides the expected point mutations associated with antibiotic resistance, detected polymorphisms in the cmeABC locus likely play a role in the multiresistant phenotype. This study provides for the first time an overview of the genetic diversity of Campylobacter strains from Portugal. It also shows a worrying antibiotic multiresistance rate and the emergence of Campylobacter strains resistant to antibiotics of human use. PMID:25130097

Duarte, Andreia; Santos, Andrea; Manageiro, Vera; Martins, Ana; Fraqueza, Maria J; Caniça, Manuela; Domingues, Fernanda C; Oleastro, Mónica

2014-10-01

141

Population genetics of the understory fishtail palm Chamaedorea ernesti-augusti in Belize: high genetic connectivity with local differentiation  

PubMed Central

Background Developing a greater understanding of population genetic structure in lowland tropical plant species is highly relevant to our knowledge of increasingly fragmented forests and to the conservation of threatened species. Specific studies are particularly needed for taxa whose population dynamics are further impacted by human harvesting practices. One such case is the fishtail or xaté palm (Chamaedorea ernesti-augusti) of Central America, whose wild-collected leaves are becoming progressively more important to the global ornamental industry. We use microsatellite markers to describe the population genetics of this species in Belize and test the effects of climate change and deforestation on its recent and historical effective population size. Results We found high levels of inbreeding coupled with moderate or high allelic diversity within populations. Overall high gene flow was observed, with a north and south gradient and ongoing differentiation at smaller spatial scales. Immigration rates among populations were more difficult to discern, with minimal evidence for isolation by distance. We infer a tenfold reduction in effective population size ca. 10,000 years ago, but fail to detect changes attributable to Mayan or contemporary deforestation. Conclusion Populations of C. ernesti-augusti are genetically heterogeneous demes at a local spatial scale, but are widely connected at a regional level in Belize. We suggest that the inferred patterns in population genetic structure are the result of the colonization of this species into Belize following expansion of humid forests in combination with demographic and mating patterns. Within populations, we hypothesize that low aggregated population density over large areas, short distance pollen dispersal via thrips, low adult survival, and low fruiting combined with early flowering may contribute towards local inbreeding via genetic drift. Relatively high levels of regional connectivity are likely the result of animal-mediated long-distance seed dispersal. The greatest present threat to the species is the potential onset of inbreeding depression as the result of increased human harvesting activities. Future genetic studies in understory palms should focus on both fine-scale and landscape-level genetic structure. PMID:19818141

Cibrian-Jaramillo, Angelica; Bacon, Christine D; Garwood, Nancy C; Bateman, Richard M; Thomas, Meredith M; Russell, Steve; Bailey, C Donovan; Hahn, William J; Bridgewater, Samuel GM; DeSalle, Rob

2009-01-01

142

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

2012-01-01

143

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

144

UNCORRECTEDPROOF High levels of genetic structuring as a result  

E-print Network

levels of deforestation have led to the fragmentation of many natural popu- lations of plant and animal extinctions, are only now starting to become apparent. Whilst not as obviously apparent, the genetic effects the population less able to adapt to changes in its environment, increasing the risk of extinction (Keller

Provan, Jim

145

High Functional Diversity in Mycobacterium tuberculosis Driven by Genetic Drift and  

E-print Network

tuberculosis driven by genetic drift and human demography. PLoS Biol 6(12): e311. doi:10.1371/journalHigh Functional Diversity in Mycobacterium tuberculosis Driven by Genetic Drift and Human Demography Ruth Hershberg1[ , Mikhail Lipatov1[ , Peter M. Small2,3 , Hadar Sheffer2 , Stefan Niemann4

Petrov, Dmitri

146

A Genetic Algorithm For The High-Level Synthesis Of DSP Systems For Low Power  

Microsoft Academic Search

This paper presents a Genetic Algorithm for the synthesis of Very Large Scale Integration low power Digital Signal Processing systems. The genetic algorithm operates on a high level signal flow graph of the system, which contains functional blocks such as adders, multipliers, etc. Evaluation of each design involves consideration of issues at different levels throughout the design hierarchy, such as

M. S. Bright; T. Arslan

1997-01-01

147

Optimization of High Pressure Common Rail Electro-injector using Genetic Algorithms  

Microsoft Academic Search

The aim of the present investigation is the implementation of an innovative procedure to optimise the design of a high pressure common rail electro- injector. The optimization method is based on the use of genetic programming, a search procedure developed by John Holland at the University of Michigan. A genetic algorithm (GA) creates a random population which evolves combining the

Teresa Donateo; Arturo de Risi; Domenico Laforgia

148

High-Density SNP Genotyping of Tomato (Solanum lycopersicum L.) Reveals Patterns of Genetic Variation  

E-print Network

High-Density SNP Genotyping of Tomato (Solanum lycopersicum L.) Reveals Patterns of Genetic. M. Rick Tomato Genetic Resource Center, University of California Davis, Davis, California, United of America Abstract The effects of selection on genome variation were investigated and visualized in tomato

Douches, David S.

149

Effect of Bead and Illustrations Models on High School Students' Achievement in Molecular Genetics  

ERIC Educational Resources Information Center

Our main goal in this study was to explore whether the use of models in molecular genetics instruction in high school can contribute to students' understanding of concepts and processes in genetics. Three comparable groups of 11th and 12th graders participated: The control group (116 students) was taught in the traditional lecture format, while…

Rotbain, Yosi; Marbach-Ad, Gili; Stavy, Ruth

2006-01-01

150

[Establishment of high efficiency genetic transformation system of maize mediated by Agrobacterium tumefaciens].  

PubMed

In order to establish high-frequency regeneration and high-efficiency genetic transformation system in maize, the significance of the 11 factors influencing maize embryonic callus induction and 9 factors affecting embryonic callus differentiation was researched by orthogonal experiment. The results showed that genotype had highly significant impact on induction of embryonic callus. The concentration of 6-BA, AgNO3, 2,4-D, ABA, and medium are the significant factors. The Multi-comparison showed that ABA 2 mg/L has a significant influence. Among the callus differentiation factors, the genotype and 6-BA concentration showed a strong main effect, the concentrations of NAA, medium, KT and 2,4-D had significant impacts on callus differentiation. Southern blotting analysis demonstrated that the resistant callus rate under the selection pressure of 25 mg/L hygromycin was a reliable indicator for system optimization in resistance screening. The concentration of acetosyringone (AS) showed sensitive differences among genotypes. The highest transformation rate was found with the optimized combination of 24-25 degrees C for co-culture temperature, 0.7 ODx15 min for Agrobacterium tumefa-ciens concentration and incubation-time, and pH 5.5-6.2. By this optimized combination, the survival rate of resistant calli as an index for the stable transformation rates of inbred lines Huangzao 4 and Zong 31 by introducing GUS gene into maize inbred lines was as high as 48.6% and 46.2%, respectively. PMID:19933098

WEI, Kai-Fa

2009-11-01

151

Detecting Genetic Association of Common Human Facial Morphological Variation Using High Density 3D Image Registration  

PubMed Central

Human facial morphology is a combination of many complex traits. Little is known about the genetic basis of common facial morphological variation. Existing association studies have largely used simple landmark-distances as surrogates for the complex morphological phenotypes of the face. However, this can result in decreased statistical power and unclear inference of shape changes. In this study, we applied a new image registration approach that automatically identified the salient landmarks and aligned the sample faces using high density pixel points. Based on this high density registration, three different phenotype data schemes were used to test the association between the common facial morphological variation and 10 candidate SNPs, and their performances were compared. The first scheme used traditional landmark-distances; the second relied on the geometric analysis of 15 landmarks and the third used geometric analysis of a dense registration of ?30,000 3D points. We found that the two geometric approaches were highly consistent in their detection of morphological changes. The geometric method using dense registration further demonstrated superiority in the fine inference of shape changes and 3D face modeling. Several candidate SNPs showed potential associations with different facial features. In particular, one SNP, a known risk factor of non-syndromic cleft lips/palates, rs642961 in the IRF6 gene, was validated to strongly predict normal lip shape variation in female Han Chinese. This study further demonstrated that dense face registration may substantially improve the detection and characterization of genetic association in common facial variation. PMID:24339768

Hu, Sile; Zhou, Hang; Guo, Jing; Jin, Li; Tang, Kun

2013-01-01

152

Detecting genetic association of common human facial morphological variation using high density 3D image registration.  

PubMed

Human facial morphology is a combination of many complex traits. Little is known about the genetic basis of common facial morphological variation. Existing association studies have largely used simple landmark-distances as surrogates for the complex morphological phenotypes of the face. However, this can result in decreased statistical power and unclear inference of shape changes. In this study, we applied a new image registration approach that automatically identified the salient landmarks and aligned the sample faces using high density pixel points. Based on this high density registration, three different phenotype data schemes were used to test the association between the common facial morphological variation and 10 candidate SNPs, and their performances were compared. The first scheme used traditional landmark-distances; the second relied on the geometric analysis of 15 landmarks and the third used geometric analysis of a dense registration of ?30,000 3D points. We found that the two geometric approaches were highly consistent in their detection of morphological changes. The geometric method using dense registration further demonstrated superiority in the fine inference of shape changes and 3D face modeling. Several candidate SNPs showed potential associations with different facial features. In particular, one SNP, a known risk factor of non-syndromic cleft lips/palates, rs642961 in the IRF6 gene, was validated to strongly predict normal lip shape variation in female Han Chinese. This study further demonstrated that dense face registration may substantially improve the detection and characterization of genetic association in common facial variation. PMID:24339768

Peng, Shouneng; Tan, Jingze; Hu, Sile; Zhou, Hang; Guo, Jing; Jin, Li; Tang, Kun

2013-01-01

153

Enriching the Genetic Counseling Recruitment Pipeline: A National Cross-Sectional Study of Public High School Counselors  

Microsoft Academic Search

Early awareness of careers is helpful in recruiting students into a career pipeline. School counselors are among the top resources\\u000a that students turn to when seeking advice about choosing their career. Studies show that high school is the ideal time to\\u000a generate interest in the genetic counseling career, especially for minorities. This novel study of 291 high school counselors\\u000a working

Sharanya N. Kumaravel; Meredith E. Tabangin; Kerry E. Sebera; Nancy Steinberg Warren

154

Mitochondrial DNA markers reveal high genetic diversity but low genetic differentiation in the black fly Simulium tani Takaoka & Davies along an elevational gradient in Malaysia.  

PubMed

The population genetic structure of Simulium tani was inferred from mitochondria-encoded sequences of cytochrome c oxidase subunits I (COI) and II (COII) along an elevational gradient in Cameron Highlands, Malaysia. A statistical parsimony network of 71 individuals revealed 71 haplotypes in the COI gene and 43 haplotypes in the COII gene; the concatenated sequences of the COI and COII genes revealed 71 haplotypes. High levels of genetic diversity but low levels of genetic differentiation were observed among populations of S. tani at five elevations. The degree of genetic diversity, however, was not in accordance with an altitudinal gradient, and a Mantel test indicated that elevation did not have a limiting effect on gene flow. No ancestral haplotype of S. tani was found among the populations. Pupae with unique structural characters at the highest elevation showed a tendency to form their own haplotype cluster, as revealed by the COII gene. Tajima's D, Fu's Fs, and mismatch distribution tests revealed population expansion of S. tani in Cameron Highlands. A strong correlation was found between nucleotide diversity and the levels of dissolved oxygen in the streams where S. tani was collected. PMID:24941043

Low, Van Lun; Adler, Peter H; Takaoka, Hiroyuki; Ya'cob, Zubaidah; Lim, Phaik Eem; Tan, Tiong Kai; Lim, Yvonne A L; Chen, Chee Dhang; Norma-Rashid, Yusoff; Sofian-Azirun, Mohd

2014-01-01

155

Mitochondrial DNA Markers Reveal High Genetic Diversity but Low Genetic Differentiation in the Black Fly Simulium tani Takaoka & Davies along an Elevational Gradient in Malaysia  

PubMed Central

The population genetic structure of Simulium tani was inferred from mitochondria-encoded sequences of cytochrome c oxidase subunits I (COI) and II (COII) along an elevational gradient in Cameron Highlands, Malaysia. A statistical parsimony network of 71 individuals revealed 71 haplotypes in the COI gene and 43 haplotypes in the COII gene; the concatenated sequences of the COI and COII genes revealed 71 haplotypes. High levels of genetic diversity but low levels of genetic differentiation were observed among populations of S. tani at five elevations. The degree of genetic diversity, however, was not in accordance with an altitudinal gradient, and a Mantel test indicated that elevation did not have a limiting effect on gene flow. No ancestral haplotype of S. tani was found among the populations. Pupae with unique structural characters at the highest elevation showed a tendency to form their own haplotype cluster, as revealed by the COII gene. Tajima’s D, Fu’s Fs, and mismatch distribution tests revealed population expansion of S. tani in Cameron Highlands. A strong correlation was found between nucleotide diversity and the levels of dissolved oxygen in the streams where S. tani was collected. PMID:24941043

Low, Van Lun; Adler, Peter H.; Takaoka, Hiroyuki; Ya'cob, Zubaidah; Lim, Phaik Eem; Tan, Tiong Kai; Lim, Yvonne A. L.; Chen, Chee Dhang; Norma-Rashid, Yusoff; Sofian-Azirun, Mohd

2014-01-01

156

Colorectal cancers show distinct mutation spectra in members of the canonical WNT signaling pathway according to their anatomical location and type of genetic instability.  

PubMed

It is unclear whether the mutation spectra in WNT genes vary among distinct types of colorectal tumors. We have analyzed mutations in specific WNT genes in a cohort of 52 colorectal tumors and performed a meta-analysis of previous studies. Notably, significant differences were found among the mutation spectra. We have previously shown that in familial adenomatous polyposis, APC somatic mutations are selected to provide the "just-right" level of WNT signaling for tumor formation. Here, we found that APC mutations encompassing at least two beta-catenin down-regulating motifs (20 a.a. repeats) are significantly more frequent in microsatellite unstable (MSI-H) than in microsatellite stable (MSS) tumors where truncations retaining less than two repeats are more frequent (P = 0.0009). Moreover, in cases where both APC hits are detected, selection for mutations retaining a cumulative number of two 20 a.a. repeats became apparent in MSI-H tumors (P = 0.001). This type of mutations were also more frequent in proximal versus distal colonic tumors, regardless of MSI status (P = 0.0008). Among MSI-H tumors, CTNNB1 mutations were significantly more frequent in HNPCC than in sporadic lesions (28% versus 6%, P < 10-6) and were preferentially detected in the proximal colon, independently of MSI status (P = 0.017). In conclusion, the observed spectra of WNT gene mutations in colorectal tumors are likely the result from selection of specific levels of beta-catenin signaling, optimal for tumor formation in the context of specific anatomical locations and forms of genetic instability. We suggest that this may underlie the preferential location of MMR deficient tumors in the proximal colon. PMID:20544848

Albuquerque, Cristina; Baltazar, Célia; Filipe, Bruno; Penha, Filipa; Pereira, Teresa; Smits, Ron; Cravo, Marília; Lage, Pedro; Fidalgo, Paulo; Claro, Isabel; Rodrigues, Paula; Veiga, Isabel; Ramos, José Silva; Fonseca, Isabel; Leitão, Carlos Nobre; Fodde, Riccardo

2010-08-01

157

Breeding high-yielding drought-tolerant rice: genetic variations and conventional and molecular approaches.  

PubMed

The increased occurrence and severity of drought stress have led to a high yield decline in rice in recent years in drought-affected areas. Drought research at the International Rice Research Institute (IRRI) over the past decade has concentrated on direct selection for grain yield under drought. This approach has led to the successful development and release of 17 high-yielding drought-tolerant rice varieties in South Asia, Southeast Asia, and Africa. In addition to this, 14 quantitative trait loci (QTLs) showing a large effect against high-yielding drought-susceptible popular varieties were identified using grain yield as a selection criterion. Six of these (qDTY 1.1 , qDTY 2.2 , qDTY 3.1 , qDTY 3.2 , qDTY 6.1 , and qDTY 12.1 ) showed an effect against two or more high-yielding genetic backgrounds in both the lowland and upland ecosystem, indicating their usefulness in increasing the grain yield of rice under drought. The yield of popular rice varieties IR64 and Vandana has been successfully improved through a well-planned marker-assisted backcross breeding approach, and QTL introgression in several other popular varieties is in progress. The identification of large-effect QTLs for grain yield under drought and the higher yield increase under drought obtained through the use of these QTLs (which has not been reported in other cereals) indicate that rice, because of its continuous cultivation in two diverse ecosystems (upland, drought tolerant, and lowland, drought susceptible), has benefited from the existence of larger genetic variability than in other cereals. This can be successfully exploited using marker-assisted breeding. PMID:25205576

Kumar, Arvind; Dixit, Shalabh; Ram, T; Yadaw, R B; Mishra, K K; Mandal, N P

2014-11-01

158

Breeding high-yielding drought-tolerant rice: genetic variations and conventional and molecular approaches  

PubMed Central

The increased occurrence and severity of drought stress have led to a high yield decline in rice in recent years in drought-affected areas. Drought research at the International Rice Research Institute (IRRI) over the past decade has concentrated on direct selection for grain yield under drought. This approach has led to the successful development and release of 17 high-yielding drought-tolerant rice varieties in South Asia, Southeast Asia, and Africa. In addition to this, 14 quantitative trait loci (QTLs) showing a large effect against high-yielding drought-susceptible popular varieties were identified using grain yield as a selection criterion. Six of these (qDTY 1.1, qDTY 2.2, qDTY 3.1, qDTY 3.2, qDTY 6.1, and qDTY 12.1) showed an effect against two or more high-yielding genetic backgrounds in both the lowland and upland ecosystem, indicating their usefulness in increasing the grain yield of rice under drought. The yield of popular rice varieties IR64 and Vandana has been successfully improved through a well-planned marker-assisted backcross breeding approach, and QTL introgression in several other popular varieties is in progress. The identification of large-effect QTLs for grain yield under drought and the higher yield increase under drought obtained through the use of these QTLs (which has not been reported in other cereals) indicate that rice, because of its continuous cultivation in two diverse ecosystems (upland, drought tolerant, and lowland, drought susceptible), has benefited from the existence of larger genetic variability than in other cereals. This can be successfully exploited using marker-assisted breeding. PMID:25205576

Kumar, Arvind; Dixit, Shalabh; Ram, T.; Yadaw, R. B.; Mishra, K. K.; Mandal, N. P.

2014-01-01

159

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

160

High Genetic Diversity among Community-Associated Staphylococcus aureus in Europe: Results from a Multicenter Study  

PubMed Central

Background Several studies have addressed the epidemiology of community-associated Staphylococcus aureus (CA-SA) in Europe; nonetheless, a comprehensive perspective remains unclear. In this study, we aimed to describe the population structure of CA-SA and to shed light on the origin of methicillin-resistant S. aureus (MRSA) in this continent. Methods and Findings A total of 568 colonization and infection isolates, comprising both MRSA and methicillin-susceptible S. aureus (MSSA), were recovered in 16 European countries, from community and community-onset infections. The genetic background of isolates was characterized by molecular typing techniques (spa typing, pulsed-field gel electrophoresis and multilocus sequence typing) and the presence of PVL and ACME was tested by PCR. MRSA were further characterized by SCCmec typing. We found that 59% of all isolates were associated with community-associated clones. Most MRSA were related with USA300 (ST8-IVa and variants) (40%), followed by the European clone (ST80-IVc and derivatives) (28%) and the Taiwan clone (ST59-IVa and related clonal types) (15%). A total of 83% of MRSA carried Panton-Valentine leukocidin (PVL) and 14% carried the arginine catabolic mobile element (ACME). Surprisingly, we found a high genetic diversity among MRSA clonal types (ST-SCCmec), Simpson’s index of diversity?=?0.852 (0.788–0.916). Specifically, about half of the isolates carried novel associations between genetic background and SCCmec. Analysis by BURP showed that some CA-MSSA and CA-MRSA isolates were highly related, suggesting a probable local acquisition/loss of SCCmec. Conclusions Our results imply that CA-MRSA origin, epidemiology and population structure in Europe is very dissimilar from that of USA. PMID:22558099

Rolo, Joana; Miragaia, Maria; Turlej-Rogacka, Agata; Empel, Joanna; Bouchami, Ons; Faria, Nuno A.; Tavares, Ana; Hryniewicz, Waleria; Fluit, Ad C.; de Lencastre, Herminia

2012-01-01

161

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. PMID:23700503

Pietilainen, Maria; Korpelainen, Helena

2013-01-01

162

Comparison of Fluorescence In Situ Hybridization and Chromogenic In Situ Hybridization for Low and High Throughput HER2 Genetic Testing  

PubMed Central

The purpose was to evaluate and compare 5 different HER2 genetic assays with different characteristics that could affect the performance to analyze the human epidermal growth factor 2 (HER2) gene copy number under low and high throughput conditions. The study included 108 tissue samples from breast cancer patients with HER2 immunohistochemistry (IHC) results scored as 0/1+, 2+, and 3+. HER2 genetic status was analysed using chromogenic in situ hybridization (CISH) and fluorescence in situ hybridization (FISH). Scoring results were documented through digital image analysis. The cancer region of interest was identified from a serial H&E stained slide following tissue cores were transferred to a tissue microarrays (TMA). When using TMA in a routine flow, all patients will be tested for HER2 status with IHC followed by CISH or FISH, thereby providing individual HER2 results. In conclusion, our results show that the differences between the HER2 genetic assays do not have an effect on the analytic performance and the CISH technology is superior to high throughput HER2 genetic testing due to scanning speed, while the IQ-FISH may still be a choice for fast low throughput HER2 genetic testing. PMID:24383005

Poulsen, Tim S.; Espersen, Maiken L. M.; Kofoed, Vibeke; Dabetic, Tanja; H?gdall, Estrid; Balslev, Eva

2013-01-01

163

Genetic Consequences of Forest Fragmentation for a Highly Specialized Arboreal Mammal - the Edible Dormouse  

PubMed Central

Habitat loss and fragmentation represent the most serious extinction threats for many species and have been demonstrated to be especially detrimental for mammals. Particularly, highly specialized species with low dispersal abilities will encounter a high risk of extinction in fragmented landscapes. Here we studied the edible dormouse (Glis glis), a small arboreal mammal that is distributed throughout Central Europe, where forests are mostly fragmented at different spatial scales. The aim of this study was to investigate the effect of habitat fragmentation on genetic population structures using the example of edible dormouse populations inhabiting forest fragments in south western Germany. We genotyped 380 adult individuals captured between 2001 and 2009 in four different forest fragments and one large continuous forest using 14 species-specific microsatellites. We hypothesised, that populations in small forest patches have a lower genetic diversity and are more isolated compared to populations living in continuous forests. In accordance with our expectations we found that dormice inhabiting forest fragments were isolated from each other. Furthermore, their genetic population structure was more unstable over the study period than in the large continuous forest. Even though we could not detect lower genetic variability within individuals inhabiting forest fragments, strong genetic isolation and an overall high risk to mate with close relatives might be precursors to a reduced genetic variability and the onset of inbreeding depression. Results of this study highlight that connectivity among habitat fragments can already be strongly hampered before genetic erosion within small and isolated populations becomes evident. PMID:24505390

Fietz, Joanna; Tomiuk, Jurgen; Loeschcke, Volker; Weis-Dootz, Tanja; Segelbacher, Gernot

2014-01-01

164

Ocean circulation model predicts high genetic structure observed in a long-lived pelagic developer.  

PubMed

Understanding the movement of genes and individuals across marine seascapes is a long-standing challenge in marine ecology and can inform our understanding of local adaptation, the persistence and movement of populations, and the spatial scale of effective management. Patterns of gene flow in the ocean are often inferred based on population genetic analyses coupled with knowledge of species' dispersive life histories. However, genetic structure is the result of time-integrated processes and may not capture present-day connectivity between populations. Here, we use a high-resolution oceanographic circulation model to predict larval dispersal along the complex coastline of western Canada that includes the transition between two well-studied zoogeographic provinces. We simulate dispersal in a benthic sea star with a 6-10 week pelagic larval phase and test predictions of this model against previously observed genetic structure including a strong phylogeographic break within the zoogeographical transition zone. We also test predictions with new genetic sampling in a site within the phylogeographic break. We find that the coupled genetic and circulation model predicts the high degree of genetic structure observed in this species, despite its long pelagic duration. High genetic structure on this complex coastline can thus be explained through ocean circulation patterns, which tend to retain passive larvae within 20-50 km of their parents, suggesting a necessity for close-knit design of Marine Protected Area networks. PMID:25231198

Sunday, J M; Popovic, I; Palen, W J; Foreman, M G G; Hart, M W

2014-10-01

165

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. PMID:20056691

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

2010-01-01

166

Adaptive Color Polymorphism and Unusually High Local Genetic Diversity in the Side-Blotched Lizard, Uta stansburiana  

PubMed Central

Recently, studies of adaptive color variation have become popular as models for examining the genetics of natural selection. We examined color pattern polymorphism and genetic variation in a population of side-blotched lizards (Uta stansburiana) that is found in habitats with both dark (lava) and light colored (granite) substrates. We conducted a limited experiment for adult phenotypic plasticity in laboratory conditions. We recorded both substrate and lizard color patterns in the field to determine whether lizards tended to match their substrate. Finally we examined genetic variation in a gene (melanocortin 1 receptor) that has been shown to affect lizard color in other species and in a presumably neutral gene (mitochondrial cytochrome b). Populations were sampled in the immediate area of the lava flows as well as from a more distant site to examine the role of population structure. Our captive Uta did not change color to match their background. We show that side-blotched lizards tend to match the substrate on which it was caught in the field and that variation in the melanocortin 1 receptor gene does not correlate well with color pattern in this population. Perhaps the most remarkable result is that this population of side-blotched lizards shows extremely high levels of variation at both genetic markers, in the sense of allele numbers, with relatively low levels of between-allele sequence variation. Genetic variation across this small region was as great or greater than that seen in samples of pelagic fish species collected worldwide. Statistical analysis of genetic variation suggests rapid population expansion may be responsible for the high levels of variation. PMID:23133520

Micheletti, Steven; Parra, Eliseo; Routman, Eric J.

2012-01-01

167

High urban breeding densities do not disrupt genetic monogamy in a bird species.  

PubMed

Urbanization causes widespread endangerment of biodiversity worldwide. However, some species successfully colonize cities reaching higher densities than in their rural habitats. In these cases, although urban city dwellers may apparently be taking advantage of these new environments, they also face new ecological conditions that may induce behavioural changes. For example, the frequency of alternative reproductive behaviours such as extra-pair paternity and intraspecific brood parasitism might increase with breeding densities. Here, using a panel of 17 microsatellites, we tested whether increments in breeding densities such as those associated with urban invasion processes alter genetic monogamy in the burrowing owl Athene cunicularia. Our results show low rates of extra-pair paternity (1.47%), but relatively high levels of intraspecific brood parasitism (8.82%). However, we were not able to detect differences in the frequency at which either alternative reproductive behaviour occurs along a strong breeding density gradient. Further research is needed to properly ascertain the role of other social and ecological factors in the frequency at which this species presents alternative reproductive strategies. Meanwhile, our results suggest that genetic monogamy is maintained despite the increment in conspecific density associated with a recent urban invasion process. PMID:24614308

Rodriguez-Martínez, Sol; Carrete, Martina; Roques, Séverine; Rebolo-Ifrán, Natalia; Tella, José L

2014-01-01

168

High School Biology\\/Life Science Teachers’ Presentation of Genetic Counseling and Health Care Career Options in Their Classrooms  

Microsoft Academic Search

Studies show teachers play an influential role in the career decision-making process of students and early knowledge of genetic\\u000a counseling (GC) increases the likelihood students will consider this career option. This quantitative study is the first to\\u000a explore the presentation of GC and other health care career options by high school (HS) biology\\/life science (B\\/LS) teachers\\u000a in their classrooms. Our

Thea A. Owens; Meredith E. Tabangin; Carl A. Huether; Bethany Vice Bowling; Nancy Steinberg Warren

2009-01-01

169

Photosynthetic metabolism of C3 plants shows highly cooperative regulation under changing environments: A systems biological analysis  

PubMed Central

We studied the robustness of photosynthetic metabolism in the chloroplasts of C3 plants under drought stress and at high CO2 concentration conditions by using a method called Minimization of Metabolic Adjustment Dynamic Flux Balance Analysis (M_DFBA). Photosynthetic metabolism in the chloroplasts of C3 plants applies highly cooperative regulation to minimize the fluctuation of metabolite concentration profiles in the face of transient perturbations. Our work suggests that highly cooperative regulation assures the robustness of the biological system and that there is closer cooperation under perturbation conditions than under normal conditions. This results in minimizing fluctuations in the profiles of metabolite concentrations, which is the key to maintaining a system's function. Our methods help in understanding such phenomena and the mechanisms of robustness for complex metabolic networks in dynamic processes. PMID:19129487

Luo, Ruoyu; Wei, Haibin; Ye, Lin; Wang, Kankan; Chen, Fan; Luo, Lijun; Liu, Lei; Li, Yuanyuan; Crabbe, M. James C.; Jin, Li; Li, Yixue; Zhong, Yang

2009-01-01

170

Biodegradable polymeric nanoparticles show high efficacy and specificity at DNA delivery to human glioblastoma in vitro and in vivo.  

PubMed

Current glioblastoma therapies are insufficient to prevent tumor recurrence and eventual death. Here, we describe a method to treat malignant glioma by nonviral DNA delivery using biodegradable poly(?-amino ester)s (PBAEs), with a focus on the brain tumor initiating cells (BTICs), the tumor cell population believed to be responsible for the formation of new tumors and resistance to many conventional therapies. We show transfection efficacy of >60% and low biomaterial-mediated cytotoxicity in primary human BTICs in vitro even when the BTICs are grown as 3-D oncospheres. Intriguingly, we find that these polymeric nanoparticles show intrinsic specificity for nonviral transfection of primary human BTICs over primary healthy human neural progenitor cells and that this specificity is not due to differences in cellular growth rate or total cellular uptake of nanoparticles. Moreover, we demonstrate that biodegradable PBAE/DNA nanoparticles can be fabricated, lyophilized, and then stored for at least 2 years without losing efficacy, increasing the translational relevance of this technology. Using lyophilized nanoparticles, we show transgene expression by tumor cells after intratumoral injection into an orthotopic murine model of human glioblastoma. PBAE/DNA nanoparticles were more effective than naked DNA at exogenous gene expression in vivo, and tumor cells were transfected more effectively than noninvaded brain parenchyma in vivo. This work shows the potential of nonviral gene delivery tools to target human brain tumors. PMID:24766032

Guerrero-Cázares, Hugo; Tzeng, Stephany Y; Young, Noah P; Abutaleb, Ameer O; Quiñones-Hinojosa, Alfredo; Green, Jordan J

2014-05-27

171

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

USGS Publications Warehouse

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

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

2008-01-01

172

Leveraging High-Dimensional Neuroimaging Data in Genetic Studies of Neuropsychiatric Disease  

Microsoft Academic Search

The current state of biomedical science is such that both the number and sophistication of methods available to investigate\\u000a the genetic determinants of disease is unprecedented. For example, the introduction of high-throughput technologies such as\\u000a DNA microarrays, allow researchers to comprehensively assess the human genome for single nucleotide polymorphisms that confer\\u000a genetic susceptibility. Indeed, while these, and other similarly sophisticated

Cinnamon S. Bloss; Trygve E. Bakken; Alexander H. Joyner; Nicholas J. Schork

173

High-Efficiency Genetic Transformation of Maize by a Mixture of Pollen and Exogenous DNA  

Microsoft Academic Search

High-efficiency genetic transformation was induced in a genetic stock of maize, Zea mays Linnaeus, by self-pollination of the recipient plants along with DNA of the donor. The highest frequency of transformed endosperm per ear was 9.29%. DNA was applied onto silks in a pollen\\/DNA pasty mixture. The exogenous DNA transferred into endosperm expressed itself in endosperm formation. It is not

Yasuo Ohta

1986-01-01

174

Genetic algorithms  

NASA Technical Reports Server (NTRS)

Genetic algorithms are mathematical, highly parallel, adaptive search procedures (i.e., problem solving methods) based loosely on the processes of natural genetics and Darwinian survival of the fittest. Basic genetic algorithms concepts are introduced, genetic algorithm applications are introduced, and results are presented from a project to develop a software tool that will enable the widespread use of genetic algorithm technology.

Wang, Lui; Bayer, Steven E.

1991-01-01

175

High Genetic Diversity and Novelty in Eukaryotic Plankton Assemblages Inhabiting Saline Lakes in the Qaidam Basin  

PubMed Central

Saline lakes are intriguing ecosystems harboring extremely productive microbial communities in spite of their extreme environmental conditions. We performed a comprehensive analysis of the genetic diversity (18S rRNA gene) of the planktonic microbial eukaryotes (nano- and picoeukaryotes) in six different inland saline lakes located in the Qaidam Basin. The novelty level are high, with about 11.23% of the whole dataset showing <90% identity to any previously reported sequence in GenBank. At least 4 operational taxonomic units (OTUs) in mesosaline lakes, while up to eighteen OTUs in hypersaline lakes show very low CCM and CEM scores, indicating that these sequences are highly distantly related to any existing sequence. Most of the 18S rRNA gene sequence reads obtained in investigated mesosaline lakes is closely related to Holozoa group (48.13%), whereas Stramenopiles (26.65%) and Alveolates (10.84%) are the next most common groups. Hypersaline lakes in the Qaidam Basin are also dominated by Holozoa group, accounting for 26.65% of the total number of sequence reads. Notably, Chlorophyta group are only found in high abundance in Lake Gasikule (28.00%), whereas less represented in other hypersaline lakes such as Gahai (0.50%) and Xiaochaidan (1.15%). Further analysis show that the compositions of planktonic eukaryotic assemblages are also most variable between different sampling sites in the same lake. Out of the parameters, four show significant correlation to this CCA: altitude, calcium, sodium and potassium concentrations. Overall, this study shows important gaps in the current knowledge about planktonic microbial eukaryotes inhabiting Qaidam Basin (hyper) saline water bodies. The identified diversity and novelty patterns among eukaryotic plankton assemblages in saline lake are of great importance for understanding and interpreting their ecology and evolution. PMID:25401703

Wang, Jiali; Wang, Fang; Chu, Limin; Wang, Hao; Zhong, Zhiping; Liu, Zhipei; Gao, Jianyong; Duan, Hairong

2014-01-01

176

The human and murine protocadherin-? one-exon gene families show high evolutionary conservation, despite the difference in gene number  

Microsoft Academic Search

Extensive cDNA analysis demonstrated that all human and mouse protocadherin-? genes are one-exon genes. The protein sequences of these genes are highly conserved, especially the three most membrane-proximal extracellular domains. Phylogenetic analysis suggested that this unique gene family evolved by duplication of one single protocadherin-? gene to 15 copies. The final difference in the number of protocadherin-? genes in man

Koen Vanhalst; Patrick Kools; Eveline Vanden Eynde; Frans van Roy

2001-01-01

177

Spherical aggregates of -amyloid (amylospheroid) show high neurotoxicity and activate tau protein kinase I\\/glycogen synthase kinase-3  

Microsoft Academic Search

-Amyloid (A) acquires toxicity by self-aggregation. To identify and characterize the toxic form(s) of A aggregates, we examined in vitro aggregation conditions by using large quantities of homogenous, chemically synthesized A1-40 peptide. We found that slow rotation of A1-40 solution reproducibly gave self-aggregated A1-40 containing a stable and highly toxic moiety. Examination of the aggregates purified by glycerol-gradient centrifugation by

Minako Hoshi; Michio Sato; Shinichiro Matsumoto; Akihiko Noguchi; Kaori Yasutake; Natsuko Yoshida; Kazuki Sato

2003-01-01

178

The RpfC (Rv1884) atomic structure shows high structural conservation within the resuscitation-promoting factor catalytic domain  

PubMed Central

The first structure of the catalytic domain of RpfC (Rv1884), one of the resuscitation-promoting factors (RPFs) from Mycobacterium tuberculosis, is reported. The structure was solved using molecular replacement once the space group had been correctly identified as twinned P21 rather than the apparent C2221 by searching for anomalous scattering sites in P1. The structure displays a very high degree of structural conservation with the previously published structures of the catalytic domains of RpfB (Rv1009) and RpfE (Rv2450). This structural conservation highlights the importance of the versatile domain composition of the RPF family. PMID:25084374

Chauviac, Francois-Xavier; Robertson, Giles; Quay, Doris H. X.; Bagneris, Claire; Dumas, Christian; Henderson, Brian; Ward, John; Keep, Nicholas H.; Cohen-Gonsaud, Martin

2014-01-01

179

Sheep CENPB and CENPC genes show a high level of sequence similarity and conserved synteny with their human homologs.  

PubMed

Sheep CENPB and CENPC clones were isolated from a lung cDNA library. The DNA and predicted amino acid sequences of these clones were compared with their human and mouse homologs and shown to contain a high degree of sequence similarity. Sheep chromosomal assignments were made using a sheep x hamster somatic cell hybrid mini-panel. CENPB was assigned to sheep chromosome 13 and CENPC to chromosome 6. The previously reported assignments of CENPB and CENPC to human chromosomes 20 and 4, respectively, suggest conserved synteny between sheep chromosome 13 and human chromosome 20 and support conserved synteny between sheep chromosome 6 and human chromosome 4. PMID:8893808

Burkin, D J; Jones, C; Burkin, H R; McGrew, J A; Broad, T E

1996-01-01

180

Dana-Farber study shows promise of hormone-depleting drug against localized high-risk prostate tumors  

Cancer.gov

A hormone-depleting drug approved last year for the treatment of metastatic prostate cancer can help eliminate or nearly eliminate tumors in many patients with aggressive cancers that have yet to spread beyond the prostate, according to a clinical study to be presented at the annual meeting of the American Society of Clinical Oncology (ASCO), June 1-5 in Chicago. The phase II clinical trial, led by investigators at Dana-Farber Cancer Institute and other research centers, examined the use of the drug abiraterone acetate (Zytiga) in combination with prednisone and surgery in 58 men with high-risk prostate cancer isolated to the prostate gland.

181

Fine-scale genetic structure and clinal variation in silene acaulis despite high gene flow  

PubMed

We investigated whether the distribution of genes reflects the patchy distribution of individuals of Silene acaulis on Pennsylvania Mountain in central Colorado. Five polymorphic protein loci were analysed using both F-statistics and spatial autocorrelation. Low thetaPOP (FST) indicated little genetic differentiation between populations approximately 1 km apart. This indicates high gene flow within our study site, perhaps as a result of long-distance pollen dispersal. Despite little differentiation between populations, there was clinal variation at the 6-Pgd-1 locus and significant within-population genetic structure (indicated by both thetaPATCH and spatial autocorrelation). We infer that this fine-scale genetic structure is the result of limited seed dispersal combined with genetic drift. The level of genetic structure varied markedly among populations, with the greatest genetic structure (highest Moran's I and thetaPATCH values) in two low-altitude, small, low-density populations. Intensive sampling such as used in this study may reveal similar patterns of fine-scale genetic differentiation in other patchily distributed plant species, particularly those with limited seed dispersal. PMID:10383684

Gehring; Delph

1999-06-01

182

APPLIED ISSUES Population genetic structure of the endangered crayfish  

E-print Network

APPLIED ISSUES Population genetic structure of the endangered crayfish Austropotamobius pallipes different within population levels of genetic diversity (0.000 to northern and southern French populations, showed a high degree of genetic differentiation in both allele

Paris-Sud XI, Université de

183

EST Analysis of Ostreococcus lucimarinus, the Most Compact Eukaryotic Genome, Shows an Excess of Introns in Highly Expressed Genes  

PubMed Central

Background The genome of the pico-eukaryotic (bacterial-sized) prasinophyte green alga Ostreococcus lucimarinus has one of the highest gene densities known in eukaryotes, yet it contains many introns. Phylogenetic studies suggest this unusually compact genome (13.2 Mb) is an evolutionarily derived state among prasinophytes. The presence of introns in the highly reduced O. lucimarinus genome appears to be in opposition to simple explanations of genome evolution based on unidirectional tendencies, either neutral or selective. Therefore, patterns of intron retention in this species can potentially provide insights into the forces governing intron evolution. Methodology/Principal Findings Here we studied intron features and levels of expression in O. lucimarinus using expressed sequence tags (ESTs) to annotate the current genome assembly. ESTs were assembled into unigene clusters that were mapped back to the O. lucimarinus Build 2.0 assembly using BLAST and the level of gene expression was inferred from the number of ESTs in each cluster. We find a positive correlation between expression levels and both intron number (R?=?+0.0893, p?=?<0.0005) and intron density (number of introns/kb of CDS; R?=?+0.0753, p?=?<0.005). Conclusions/Significance In a species with a genome that has been recently subjected to a great reduction of non-coding DNA, these results imply the existence of selective/functional roles for introns that are principally detectable in highly expressed genes. In these cases, introns are likely maintained by balancing the selective forces favoring their maintenance with other mutational and/or selective forces acting on genome size. PMID:18478122

Lanier, William; Moustafa, Ahmed; Bhattacharya, Debashish; Comeron, Josep M.

2008-01-01

184

Subpicomolar diphenyleneiodonium inhibits microglial NADPH oxidase with high specificity and shows great potential as a therapeutic agent for neurodegenerative diseases.  

PubMed

Activation of microglial NADPH oxidase (NOX2) plays a critical role in mediating neuroinflammation, which is closely linked with the pathogenesis of a variety of neurodegenerative diseases, including Parkinson's disease (PD). The inhibition of NOX2-generated superoxide has become an effective strategy for developing disease-modifying therapies for PD. However, the lack of specific and potent NOX2 inhibitors has hampered the progress of this approach. Diphenyleneiodonium (DPI) is a widely used, long-acting NOX2 inhibitor. However, due to its non-specificity for NOX2 and high cytotoxicity at standard doses (µM), DPI has been precluded from human studies. In this study, using ultra-low doses of DPI, we aimed to: (1) investigate whether these problems could be circumvented and (2) determine whether ultra-low doses of DPI were able to preserve its utility as a potent NOX2 inhibitor. We found that DPI at subpicomolar concentrations (10(-14) and 10(-13) M) displays no toxicity in primary midbrain neuron-glia cultures. More importantly, we observed that subpicomolar DPI inhibited phorbol myristate acetate (PMA)-induced activation of NOX2. The same concentrations of DPI did not inhibit the activities of a series of flavoprotein-containing enzymes. Furthermore, potent neuroprotective efficacy was demonstrated in a post-treatment study. When subpicomolar DPI was added to neuron-glia cultures pretreated with lipopolysaccharide, 1-methyl-4-phenylpyridinium or rotenone, it potently protected the dopaminergic neurons. In summary, DPI's unique combination of high specificity toward NOX2, low cytotoxicity and potent neuroprotective efficacy in post-treatment regimens suggests that subpicomolar DPI may be an ideal candidate for further animal studies and potential clinical trials. GLIA 2014;62:2034-2043. PMID:25043383

Wang, Qingshan; Chu, Chun-Hsien; Oyarzabal, Esteban; Jiang, Lulu; Chen, Shih-Heng; Wilson, Belinda; Qian, Li; Hong, Jau-Shyong

2014-12-01

185

A genetic code alteration generates a proteome of high diversity in the human pathogen Candida albicans  

PubMed Central

Background Genetic code alterations have been reported in mitochondrial, prokaryotic, and eukaryotic cytoplasmic translation systems, but their evolution and how organisms cope and survive such dramatic genetic events are not understood. Results Here we used an unusual decoding of leucine CUG codons as serine in the main human fungal pathogen Candida albicans to elucidate the global impact of genetic code alterations on the proteome. We show that C. albicans decodes CUG codons ambiguously and tolerates partial reversion of their identity from serine back to leucine on a genome-wide scale. Conclusion Such codon ambiguity expands the proteome of this human pathogen exponentially and is used to generate important phenotypic diversity. This study highlights novel features of C. albicans biology and unanticipated roles for codon ambiguity in the evolution of the genetic code. PMID:17916231

Gomes, Ana C; Miranda, Isabel; Silva, Raquel M; Moura, Gabriela R; Thomas, Benjamin; Akoulitchev, Alexandre; Santos, Manuel AS

2007-01-01

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

High genetic variability in a population of Tridacna maxima from the Great Barrier Reef  

Microsoft Academic Search

A population of the bivalve mollusk Tridacna maxima (Röding) from Hron Island, Great Barrier Reef, Australia, was studied by gel electrophoresis, and proved to be highly variable genetically, with an average heterozygosity of about 22%. This compares closely with a population of T. maxima from Enewetak (Eniwetok) Atoll, with an average heterozygosity of about 20%, very high for marine organisms.

C. A. Campbell; J. W. Valentine; F. J. Ayala

1975-01-01

188

Landscape scale genetic effects of habitat fragmentation on a high gene flow species: Speyeria idalia (Nymphalidae)  

Microsoft Academic Search

Detection of the genetic effects of recent habitat fragmentation in natural populations can be a difficult task, especially for high gene flow species. Previous analyses of mitochon- drial DNA data from across the current range of Speyeria idalia indicated that the species exhibited high levels of gene flow among populations, with the exception of an isolated population in the eastern

BARRY L. W ILLIAMS; JEFFREY D. BRAWN; KEN N. P AIGE

2003-01-01

189

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

PubMed Central

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

2012-01-01

190

High genetic diversity and population differentiation in Boechera fecunda, a rare relative of Arabidopsis.  

PubMed

Conservation of endangered species becomes a critical issue with the increasing rates of extinction. In this study, we use 13 microsatellite loci and 27 single-copy nuclear loci to investigate the population genetics of Boechera fecunda, a rare relative of Arabidopsis thaliana, known from only 21 populations in Montana. We investigated levels of genetic diversity and population structure in comparison to its widespread congener, Boechera stricta, which shares similar life history and mating system. Despite its rarity, B. fecunda had levels of genetic diversity similar to B. stricta for both microsatellites and nucleotide polymorphism. Populations of B. fecunda are highly differentiated, with a majority of genetic diversity existing among populations (F(ST) = 0.57). Differences in molecular diversity and allele frequencies between western and eastern population groups suggest they experienced very different evolutionary histories. PMID:17784916

Song, Bao-Hua; Mitchell-Olds, Thomas

2007-10-01

191

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

192

High-throughput Genetic Screen for Synaptogenic Factors: Identification of LRP6 as Critical for Excitatory Synapse Development  

PubMed Central

SUMMARY Genetic screens in invertebrates have discovered many synaptogenic genes and pathways. However, similar genetic studies have not been possible in mammals. We have optimized an automated high-throughput platform that employs automated liquid handling and imaging of primary mammalian neurons. Using this platform we have screened 3200 shRNAs targeting 800 proteins. One of the hits identified was LRP6, a co-receptor for canonical Wnt ligands. LRP6 regulates excitatory synaptogenesis, and is selectively localized to excitatory synapses. In vivo knockdown of LRP6 leads to a reduction in the number of functional synapses. Moreover, we show that the canonical Wnt ligand, Wnt8A, promotes synaptogenesis via LRP6. These results provide a proof of principle for using a high content approach to screen for synaptogenic factors in the mammalian nervous system, and identify and characterize a Wnt ligand receptor complex that is critical for development of functional synapses in vivo. PMID:24316074

Sharma, Kamal; Choi, Se-Young; Zhang, Yong; Nieland, Thomas J.F.; Long, Shunyou; Li, Min; Huganir, Richard

2014-01-01

193

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

194

Combined analyses of kinship and FST suggest potential drivers of chaotic genetic patchiness in high gene-flow populations  

PubMed Central

We combine kinship estimates with traditional F-statistics to explain contemporary drivers of population genetic differentiation despite high gene flow. We investigate range-wide population genetic structure of the California spiny (or red rock) lobster (Panulirus interruptus) and find slight, but significant global population differentiation in mtDNA (?ST = 0.006, P = 0.001; Dest_Chao = 0.025) and seven nuclear microsatellites (FST = 0.004, P < 0.001; Dest_Chao = 0.03), despite the species’ 240- to 330-day pelagic larval duration. Significant population structure does not correlate with distance between sampling locations, and pairwise FST between adjacent sites often exceeds that among geographically distant locations. This result would typically be interpreted as unexplainable, chaotic genetic patchiness. However, kinship levels differ significantly among sites (pseudo-F16,988 = 1.39, P = 0.001), and ten of 17 sample sites have significantly greater numbers of kin than expected by chance (P < 0.05). Moreover, a higher proportion of kin within sites strongly correlates with greater genetic differentiation among sites (Dest_Chao, R2 = 0.66, P < 0.005). Sites with elevated mean kinship were geographically proximate to regions of high upwelling intensity (R2 = 0.41, P = 0.0009). These results indicate that P. interruptus does not maintain a single homogenous population, despite extreme dispersal potential. Instead, these lobsters appear to either have substantial localized recruitment or maintain planktonic larval cohesiveness whereby siblings more likely settle together than disperse across sites. More broadly, our results contribute to a growing number of studies showing that low FST and high family structure across populations can coexist, illuminating the foundations of cryptic genetic patterns and the nature of marine dispersal. PMID:23802550

Iacchei, Matthew; Ben-Horin, Tal; Selkoe, Kimberly A; Bird, Christopher E; García-Rodríguez, Francisco J; Toonen, Robert J

2013-01-01

195

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

2013-01-01

196

Nuclear Genetic Diversity in Human Lice (Pediculus humanus) Reveals Continental Differences and High Inbreeding among Worldwide Populations  

PubMed Central

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.

2013-01-01

197

Population genetics of the understory fishtail palm Chamaedorea ernesti-augusti in Belize: high genetic connectivity with local differentiation  

E-print Network

deforestation. Conclusion Populations of C. ernesti-augusti are genetically heterogeneous demes at a local spatial scale, but are widely connected at a regional level in Belize. We suggest that the inferred patterns in population genetic structure are the result...

Cibrian-Jaramillo, Angelica; Bacon, Christine D; Garwood, Nancy C; Bateman, Richard M; Thomas, Meredith M; Russell, Steven R; Bailey, Donovan C; Hahn, William J; Bridgewater, Samuel G M; DeSalle, Rob

2009-10-09

198

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

199

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. PMID:19473382

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

2009-01-01

200

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

201

High genetic diversity at the regional scale and possible speciation in Sebacina epigaea and S. incrustans  

PubMed Central

Background Phylogenetic studies, particularly those based on rDNA sequences from plant roots and basidiomata, have revealed a strikingly high genetic diversity in the Sebacinales. However, the factors determining this genetic diversity at higher and lower taxonomic levels within this order are still unknown. In this study, we analysed patterns of genetic variation within two morphological species, Sebacina epigaea and S. incrustans, based on 340 DNA haplotype sequences of independent genetic markers from the nuclear (ITS?+?5.8S?+?D1/D2, RPB2) and mitochondrial (ATP6) genomes for 98 population samples. By characterising the genetic population structure within these species, we provide insights into species boundaries and the possible factors responsible for genetic diversity at a regional geographic scale. Results We found that recombination events are relatively common between natural populations within Sebacina epigaea and S. incrustans, and play a significant role in generating intraspecific genetic diversity. Furthermore, we also found that RPB2 and ATP6 genes display higher levels of intraspecific synonymous polymorphism. Phylogenetic and demographic analyses based on nuclear and mitochondrial loci revealed three distinct phylogenetic lineages within of each of the morphospecies S. epigaea and S. incrustans: one major and widely distributed lineage, and two geographically restricted lineages, respectively. We found almost no differential morphological or ecological characteristics that could be used to discriminate between these lineages. Conclusions Our results suggest that recombination and negative selection have played significant roles in generating genetic diversity within these morphological species at small geographical scales. Concordance between gene genealogies identified lineages/cryptic species that have evolved independently for a relatively long period of time. These putative species were not associated with geographic provenance, geographic barrier, host preference or distinct phenotypic innovations. PMID:23697379

2013-01-01

202

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

203

High Nuclear Genetic Diversity, High Levels of Outcrossing and Low Differentiation Among Remnant Populations of Quercus petraea at the Margin of its Range in Ireland  

PubMed Central

• Background and Aims Quercus petraea colonized Ireland after the last glaciation from refugia on mainland Europe. Deforestation, however, beginning in Neolithic times, has resulted in small, scattered forest fragments, now covering less than 12 000 ha. • Methods Plastid (three fragments) and microsatellite variation (13 loci) were characterized in seven Irish populations sampled along a north–south gradient. Using Bayesian approaches and Wright’s F?statistics, the effects of colonization and fragmentation on the genetic structure and mating patterns of extant oak populations were investigated. • Key Results All populations possessed cytotypes common to the Iberian Peninsula. Despite the distance from the refugial core and the extensive deforestation in Ireland, nuclear genetic variation was high and comparable to mainland Europe. Low population differentiation was observed within Ireland and populations showed no evidence for isolation by distance. As expected of a marker with an effective population size of one?quarter relative to the nuclear genome, plastid variation indicated higher differentiation. Individual inbreeding coefficients indicated high levels of outcrossing. • Conclusions Consistent with a large effective population size in the historical migrant gene pool and/or with high gene flow among populations, high within?population diversity and low population differentiation was observed within Ireland. It is proposed that native Q. petraea populations in Ireland share a common phylogeographic history and that the present genetic structure does not reflect founder effects. PMID:15087303

MUIR, GRAHAM; LOWE, ANDREW J.; FLEMING, COLIN C.; VOGL, CLAUS

2004-01-01

204

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. PMID:19956580

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

2009-01-01

205

High Levels of Genetic Diversity Throughout the Range of the Portuguese Wheat Landrace ‘Barbela’  

PubMed Central

• Background and Aims Landrace populations represent an important intra-crop reservoir of biodiversity and source of novel gene alleles for use in breeding programmes. Here the aim was to measure the diversity of a wheat landrace, ‘Barbela’, from the north of Portugal. • Methods DNA was extracted from 59 accessions of Barbela collected across its geographical range. Diversity was measured by microsatellite length polymorphisms using 27 primer pairs amplifying 34 polymorphic microsatellite loci. • Key Results High levels of polymorphism were found, with an average polymorphism information content of 0·52; an average of 4·77 alleles (range 2–11) were present at each locus, and half of these loci showed an additional allele in the reference variety ‘Chinese Spring’. • Conclusions ‘Barbela’ is maintained from seeds collected by farmers, but it maintains high allelic variation, and no groupings of accessions were detected when analysed by geographical region, farm or climate, indicating that the wheat landrace is a homogeneous entity. The diversity within the farmer-maintained landrace demonstrates the importance of characterization and maintenance of landrace collections before valuable genetic combinations are lost as uniform commercial crops are introduced. PMID:15355867

RIBEIRO-CARVALHO, C.; GUEDES-PINTO, H.; IGREJAS, G.; STEPHENSON, P.; SCHWARZACHER, T.; HESLOP-HARRISON, J. S.

2004-01-01

206

Genetic algorithm-based feature selection in high-resolution NMR spectra  

PubMed Central

High-resolution nuclear magnetic resonance (NMR) spectroscopy has provided a new means for detection and recognition of metabolic changes in biological systems in response to pathophysiological stimuli and to the intake of toxins or nutrition. To identify meaningful patterns from NMR spectra, various statistical pattern recognition methods have been applied to reduce their complexity and uncover implicit metabolic patterns. In this paper, we present a genetic algorithm (GA)-based feature selection method to determine major metabolite features to play a significant role in discrimination of samples among different conditions in high-resolution NMR spectra. In addition, an orthogonal signal filter was employed as a preprocessor of NMR spectra in order to remove any unwanted variation of the data that is unrelated to the discrimination of different conditions. The results of k-nearest neighbors and the partial least squares discriminant analysis of the experimental NMR spectra from human plasma showed the potential advantage of the features obtained from GA-based feature selection combined with an orthogonal signal filter. PMID:21472035

Cho, Hyun-Woo; Jeong, Myong K.; Park, Youngja; Ziegler, Thomas R.; Jones, Dean P.

2011-01-01

207

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. PMID:21807117

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

2011-01-01

208

Fine-scale genetic structure and clinal variation in Silene acaulis despite high gene flow  

Microsoft Academic Search

We investigated whether the distribution of genes reflects the patchy distribution of individuals of Silene acaulis on Pennsylvania Mountain in central Colorado. Five polymorphic protein loci were analysed using both F-statistics and spatial autocorrelation. Low ?POP (FST) indicated little genetic differentiation between populations ?1 km apart. This indicates high gene flow within our study site, perhaps as a result of

JANET L. GEHRING; Lynda F Delph

1999-01-01

209

Unusually high genetic diversity in COI sequences of Chimarra obscura (Trichoptera: Philopotamidae)  

EPA Science Inventory

Chimarra obscura (Walker 1852) is a philopotamid caddisfly found throughout much of North America. Using the COI DNA barcode locus, we have found unexpectedly high amounts of genetic diversity and distances within C. obscura. Of the approximately 150 specimens sampled, we have fo...

210

Search for genetic determinants of individual variability of the erythropoietin response to high altitude  

Microsoft Academic Search

There is marked variability in the erythropoietin (Epo) and erythrocytic response to extreme high altitude among mountain dwellers, as well as to hypoxic training among athletes, at least in part because of the variation in the erythropoietic response to hypoxia. We hypothesized that this may be genetically determined. Forty-eight athletes were exposed to 24 h of simulated altitude to 2800

Katerina Jedlickova; David W. Stockton; Hua Chen; James Stray-Gundersen; Sarah Witkowski; Ge Ri-Li; Jaroslav Jelinek; Benjamin D. Levine; Josef T. Prchala

2003-01-01

211

Range-wide analysis of genetic structure in a widespread, highly mobile species (Odocoileus hemionus) reveals the importance of historical biogeography.  

PubMed

Highly mobile species that thrive in a wide range of habitats are expected to show little genetic differentiation across their range. A limited but growing number of studies have revealed that patterns of broad-scale genetic differentiation can and do emerge in vagile, continuously distributed species. However, these patterns are complex and often shaped by both historical and ecological factors. Comprehensive surveys of genetic variation at a broad scale and at high resolution are useful for detecting cryptic spatial genetic structure and for investigating the relative roles of historical and ecological processes in structuring widespread, highly mobile species. In this study, we analysed 10 microsatellite loci from over 1900 samples collected across the full range of mule deer (Odocoileus hemionus), one of the most widely distributed and abundant of all large mammal species in North America. Through both individual- and population-based analyses, we found evidence for three main genetic lineages, one corresponding to the 'mule deer' morphological type and two to the 'black-tailed deer' type. Historical biogeographic events likely are the primary drivers of genetic divergence in this species; boundaries of the three lineages correspond well with predictions based on Pleistocene glacial cycles, and substructure within each lineage demonstrates island vicariance. However, across large geographic areas, including the entire mule deer lineage, we found that genetic variation fit an isolation-by-distance pattern rather than discrete clusters. A lack of genetic structure across wide geographic areas of the continental west indicates that ecological processes have not resulted in restrictions to gene flow sufficient for spatial genetic structure to emerge. Our results have important implications for our understanding of evolutionary mechanisms of divergence, as well as for taxonomy, conservation and management. PMID:24863151

Latch, Emily K; Reding, Dawn M; Heffelfinger, James R; Alcalá-Galván, Carlos H; Rhodes, Olin E

2014-07-01

212

Construction of a high-coverage bacterial artificial chromosome library and comprehensive genetic linkage map of yellowtail Seriola quinqueradiata  

PubMed Central

Background Japanese amberjack/yellowtail (Seriola quinqueradiata) is a commonly cultured marine fish in Japan. For cost effective fish production, a breeding program that increases commercially important traits is one of the major solutions. In selective breeding, information of genetic markers is useful and sufficient to identify individuals carrying advantageous traits but if the aim is to determine the genetic basis of the trait, large insert genomic DNA libraries are essential. In this study, toward prospective understanding of genetic basis of several economically important traits, we constructed a high-coverage bacterial artificial chromosome (BAC) library, obtained sequences from the BAC-end, and constructed comprehensive female and male linkage maps of yellowtail using Simple Sequence Repeat (SSR) markers developed from the BAC-end sequences and a yellowtail genomic library. Results The total insert length of the BAC library we constructed here was estimated to be approximately 11 Gb and hence 16-times larger than the yellowtail genome. Sequencing of the BAC-ends showed a low fraction of repetitive sequences comparable to that in Tetraodon and fugu. A total of 837 SSR markers developed here were distributed among 24 linkage groups spanning 1,026.70 and 1,057.83 cM with an average interval of 4.96 and 4.32 cM in female and male map respectively without any segregation distortion. Oxford grids suggested conserved synteny between yellowtail and stickleback. Conclusions In addition to characteristics of yellowtail genome such as low repetitive sequences and conserved synteny with stickleback, our genomic and genetic resources constructed and revealed here will be powerful tools for the yellowtail breeding program and also for studies regarding the genetic basis of traits. PMID:24684753

2014-01-01

213

A high-density simple sequence repeat and single nucleotide polymorphism genetic map of the tetraploid cotton genome.  

PubMed

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. PMID:22384381

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

214

Genetic Diversity Analysis of Highly Incomplete SNP Genotype Data with Imputations: An Empirical Assessment  

PubMed Central

Genotyping by sequencing (GBS) recently has emerged as a promising genomic approach for assessing genetic diversity on a genome-wide scale. However, concerns are not lacking about the uniquely large unbalance in GBS genotype data. Although some genotype imputation has been proposed to infer missing observations, little is known about the reliability of a genetic diversity analysis of GBS data, with up to 90% of observations missing. Here we performed an empirical assessment of accuracy in genetic diversity analysis of highly incomplete single nucleotide polymorphism genotypes with imputations. Three large single-nucleotide polymorphism genotype data sets for corn, wheat, and rice were acquired, and missing data with up to 90% of missing observations were randomly generated and then imputed for missing genotypes with three map-independent imputation methods. Estimating heterozygosity and inbreeding coefficient from original, missing, and imputed data revealed variable patterns of bias from assessed levels of missingness and genotype imputation, but the estimation biases were smaller for missing data without genotype imputation. The estimates of genetic differentiation were rather robust up to 90% of missing observations but became substantially biased when missing genotypes were imputed. The estimates of topology accuracy for four representative samples of interested groups generally were reduced with increased levels of missing genotypes. Probabilistic principal component analysis based imputation performed better in terms of topology accuracy than those analyses of missing data without genotype imputation. These findings are not only significant for understanding the reliability of the genetic diversity analysis with respect to large missing data and genotype imputation but also are instructive for performing a proper genetic diversity analysis of highly incomplete GBS or other genotype data. PMID:24626289

Fu, Yong-Bi

2014-01-01

215

High genetic diversity on a sample of pre-Columbian bone remains from Guane territories in northwestern Colombia.  

PubMed

Ancient DNA was recovered from 17 individuals found in a rock shelter in the district of "La Purnia" (Santander, Colombia). This region is the homeland of pre-Columbian Guane, whom spread over the "Río Suarez" to the "Río de Oro", and were surrounded to the west by the Central Andes, south and east by foothills of Eastern Andes, and north by the "Chicamocha" river canyon. Guanes established in a region that straddles the Andes and the northern Amazon basin, possibly making it an unavoidable conduit for people moving to and from South America. We amplified mtDNA hypervariable region I (HVI) segments from ancient bone remains, and the resulting sequences were compared with both ancient and modern mitochondrial haplogroups from American and non-American populations. Samples showed a distribution of 35% for haplogroup A, 41% for haplogroup B and 24% for haplogroup D. Nine haplotypes were found in 17 samples, indicating an unusually high genetic diversity on a single site ancient population. Among them, three haplotypes have not been previously found in America, two are shared in Asia, and one is a private haplotype. Despite geographical barriers that eventually isolated them, an important influence of gene flow from neighboring pre-Columbian communities, mainly Muiscas, could explain the high genetic polymorphism of this community before the Spanish conquest, and argues against Guanes as being a genetic isolate. PMID:21990065

Casas-Vargas, Andrea; Gómez, Alberto; Briceño, Ignacio; Díaz-Matallana, Marcela; Bernal, Jaime E; Rodríguez, José Vicente

2011-12-01

216

Unexpected genetic differentiation between recently recolonized populations of a long-lived and highly vagile marine mammal  

PubMed Central

Many species have been heavily exploited by man leading to local extirpations, yet few studies have attempted to unravel subsequent recolonization histories. This has led to a significant gap in our knowledge of the long-term effects of exploitation on the amount and structure of contemporary genetic variation, with important implications for conservation. The Antarctic fur seal provides an interesting case in point, having been virtually exterminated in the nineteenth century but subsequently staged a dramatic recovery to recolonize much of its original range. Consequently, we evaluated the hypothesis that South Georgia (SG), where a few million seals currently breed, was the main source of immigrants to other locations including Livingston Island (LI), by genotyping 366 individuals from these two populations at 17 microsatellite loci and sequencing a 263 bp fragment of the mitochondrial hypervariable region 1. Contrary to expectations, we found highly significant genetic differences at both types of marker, with 51% of LI individuals carrying haplotypes that were not observed in 246 animals from SG. Moreover, the youngest of three sequentially founded colonies at LI showed greater similarity to SG at mitochondrial DNA than microsatellites, implying temporal and sex-specific variation in recolonization. Our findings emphasize the importance of relict populations and provide insights into the mechanisms by which severely depleted populations can recover while maintaining surprisingly high levels of genetic diversity. PMID:24198934

Bonin, Carolina A; Goebel, Michael E; Forcada, Jaume; Burton, Ronald S; Hoffman, Joseph I

2013-01-01

217

http://www.tcd.ie/Genetics/staff/Miguel_DeArce_Bioinf_01/bioinformatics_01/htm/air.htm Name; The links show a rotable 3D model of each molecule.  

E-print Network

#12;#12;#12;#12;#12;http://www.tcd.ie/Genetics/staff/Miguel_DeArce_Bioinf_01/bioinformatics_01/htm with the side chain projecting downwards. Codons; This is the Standard Genetic Code. The codon usage reported

Morante, Silvia

218

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

2012-01-01

219

AFLP Polymorphisms Allow High Resolution Genetic Analysis of American Tegumentary Leishmaniasis Agents Circulating in Panama and Other Members of the Leishmania Genus  

PubMed Central

American Tegumentary Leishmaniasis is caused by parasites of the genus Leishmania, and causes significant health problems throughout the Americas. In Panama, Leishmania parasites are endemic, causing thousands of new cases every year, mostly of the cutaneous form. In the last years, the burden of the disease has increased, coincident with increasing disturbances in its natural sylvatic environments. The study of genetic variation in parasites is important for a better understanding of the biology, population genetics, and ultimately the evolution and epidemiology of these organisms. Very few attempts have been made to characterize genetic polymorphisms of parasites isolated from Panamanian patients of cutaneous leishmaniasis. Here we present data on the genetic variability of local isolates of Leishmania, as well as specimens from several other species, by means of Amplified Fragment Length Polymorphisms (AFLP), a technique seldom used to study genetic makeup of parasites. We demonstrate that this technique allows detection of very high levels of genetic variability in local isolates of Leishmania panamensis in a highly reproducible manner. The analysis of AFLP fingerprints generated by unique selective primer combinations in L. panamensis suggests a predominant clonal mode of reproduction. Using fluorescently labeled primers, many taxon-specific fragments were identified which may show potential as species diagnostic fragments. The AFLP permitted a high resolution genetic analysis of the Leishmania genus, clearly separating certain groups among L. panamensis specimens and highly related species such as L. panamensis and L. guyanensis. The phylogenetic networks reconstructed from our AFLP data are congruent with established taxonomy for the genus Leishmania, even when using single selective primer combinations. Results of this study demonstrate that AFLP polymorphisms can be informative for genetic characterization in Leishmania parasites, at both intra and inter-specific levels. PMID:24039881

Restrepo, Carlos M.; De La Guardia, Carolina; Sousa, Octavio E.; Calzada, Jose E.; Fernandez, Patricia L.; Lleonart, Ricardo

2013-01-01

220

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. 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

2013-01-01

221

Genetic risk factors in two Utah pedigrees at high risk for suicide  

PubMed Central

We have used unique population-based data resources to identify 22 high-risk extended pedigrees that show clustering of suicide over twice that expected from demographically adjusted incidence rates. In this initial study of genetic risk factors, we focused on two high-risk pedigrees. In the first of these (pedigree 12), 10/19 (53%) of the related suicides were female, and the average age at death was 30.95. In the second (pedigree 5), 7/51 (14%) of the suicides were female and the average age at death was 36.90. Six decedents in pedigree 12 and nine in pedigree 5 were genotyped with the Illumina HumanExome BeadChip. Genotypes were analyzed using the Variant Annotation, Analysis, and Search program package that computes likelihoods of risk variants using the functional impact of the DNA variation, aggregative scoring of multiple variants across each gene and pedigree structure. We prioritized variants that were: (1) shared across pedigree members, (2) rare in other Utah suicides not related to these pedigrees, (3) ? 5% in genotyping data from 398 other Utah population controls and (4) ?5% frequency in publicly available sequence data from 1358 controls and/or in dbSNP. Results included several membrane protein genes (ANO5, and TMEM141 for pedigree 12 and FAM38A and HRCT1 for pedigree 5). Other genes with known neuronal involvement and/or previous associations with psychiatric conditions were also identified, including NFKB1, CASP9, PLXNB1 and PDE11A in pedigree 12, and THOC1, and AUTS2 in pedigree 5. Although the study is limited to variants included on the HumanExome BeadChip, these findings warrant further exploration, and demonstrate the utility of this high-risk pedigree resource to identify potential genes or gene pathways for future development of targeted interventions. PMID:24252905

Coon, H; Darlington, T; Pimentel, R; Smith, K R; Huff, C D; Hu, H; Jerominski, L; Hansen, J; Klein, M; Callor, W B; Byrd, J; Bakian, A; Crowell, S E; McMahon, W M; Rajamanickam, V; Camp, N J; McGlade, E; Yurgelun-Todd, D; Grey, T; Gray, D

2013-01-01

222

Showing What They Know  

ERIC Educational Resources Information Center

Having students show their skills in three dimensions, known as performance-based assessment, dates back at least to Socrates. Individual schools such as Barrington High School--located just outside of Providence--have been requiring students to actively demonstrate their knowledge for years. The Rhode Island's high school graduating class became…

Cech, Scott J.

2008-01-01

223

High density SNP and SSR-based genetic maps of two independent oil palm hybrids  

PubMed Central

Background Oil palm is an important perennial oil crop with an extremely long selection cycle of 10 to 12 years. As such, any tool that speeds up its genetic improvement process, such as marker-assisted breeding is invaluable. Previously, genetic linkage maps based on AFLP, RFLP and SSR markers were developed and QTLs for fatty acid composition and yield components identified. High density genetic maps of crosses of different genetic backgrounds are indispensable tools for investigating oil palm genetics. They are also useful for comparative mapping analyses to identify markers closely linked to traits of interest. Results A 4.5 K customized oil palm SNP array was developed using the Illumina Infinium platform. The SNPs and 252 SSRs were genotyped on two mapping populations, an intraspecific cross with 87 palms and an interspecific cross with 108 palms. Parental maps with 16 linkage groups (LGs), were constructed for the three fruit forms of E. guineensis (dura, pisifera and tenera). Map resolution was further increased by integrating the dura and pisifera maps into an intraspecific integrated map with 1,331 markers spanning 1,867 cM. We also report the first map of a Colombian E. oleifera, comprising 10 LGs with 65 markers spanning 471 cM. Although not very dense due to the high level of homozygosity in E. oleifera, the LGs were successfully integrated with the LGs of the tenera map. Direct comparison between the parental maps identified 603 transferable markers polymorphic in at least two of the parents. Further analysis revealed a high degree of marker transferability covering 1,075 cM, between the intra- and interspecific integrated maps. The interspecific cross displayed higher segregation distortion than the intraspecific cross. However, inclusion of distorted markers in the genetic maps did not disrupt the marker order and no map expansion was observed. Conclusions The high density SNP and SSR-based genetic maps reported in this paper have greatly improved marker density and genome coverage in comparison with the first reference map based on AFLP and SSR markers. Therefore, it is foreseen that they will be more useful for fine mapping of QTLs and whole genome association mapping studies in oil palm. PMID:24767304

2014-01-01

224

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. PMID:22247776

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

2012-01-01

225

A CD44high/EGFRlow Subpopulation within Head and Neck Cancer Cell Lines Shows an Epithelial-Mesenchymal Transition Phenotype and Resistance to Treatment  

PubMed Central

Mortality in head and neck squamous cell carcinoma (HNSCC) is high due to emergence of therapy resistance which results in local and regional recurrences that may have their origin in resistant cancer stem cells (CSCs) or cells with an epithelial-mesenchymal transition (EMT) phenotype. In the present study, we investigate the possibility of using the cell surface expression of CD44 and epidermal growth factor receptor (EGFR), both of which have been used as stem cell markers, to identify subpopulations within HNSCC cell lines that differ with respect to phenotype and treatment sensitivity. Three subpopulations, consisting of CD44high/EGFRlow, CD44high/EGFRhigh and CD44low cells, respectively, were collected by fluorescence-activated cell sorting. The CD44high/EGFRlow population showed a spindle-shaped EMT-like morphology, while the CD44low population was dominated by cobblestone-shaped cells. The CD44high/EGFRlow population was enriched with cells in G0/G1 and showed a relatively low proliferation rate and a high plating efficiency. Using a real time PCR array, 27 genes, of which 14 were related to an EMT phenotype and two with stemness, were found to be differentially expressed in CD44high/EGFRlow cells in comparison to CD44low cells. Moreover, CD44high/EGFRlow cells showed a low sensitivity to radiation, cisplatin, cetuximab and gefitinib, and a high sensitivity to dasatinib relative to its CD44high/EGFRhigh and CD44low counterparts. In conclusion, our results show that the combination of CD44 (high) and EGFR (low) cell surface expression can be used to identify a treatment resistant subpopulation with an EMT phenotype in HNSCC cell lines. PMID:23049743

La Fleur, Linnea; Johansson, Ann-Charlotte; Roberg, Karin

2012-01-01

226

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

227

Combined genetic and high-throughput strategies for molecular diagnosis of inherited retinal dystrophies.  

PubMed

Most diagnostic laboratories are confronted with the increasing demand for molecular diagnosis from patients and families and the ever-increasing genetic heterogeneity of visual disorders. Concerning Retinal Dystrophies (RD), almost 200 causative genes have been reported to date, and most families carry private mutations. We aimed to approach RD genetic diagnosis using all the available genetic information to prioritize candidates for mutational screening, and then restrict the number of cases to be analyzed by massive sequencing. We constructed and optimized a comprehensive cosegregation RD-chip based on SNP genotyping and haplotype analysis. The RD-chip allows to genotype 768 selected SNPs (closely linked to 100 RD causative genes) in a single cost-, time-effective step. Full diagnosis was attained in 17/36 Spanish pedigrees, yielding 12 new and 12 previously reported mutations in 9 RD genes. The most frequently mutated genes were USH2A and CRB1. Notably, RD3-up to now only associated to Leber Congenital Amaurosis- was identified as causative of Retinitis Pigmentosa. The main assets of the RD-chip are: i) the robustness of the genetic information that underscores the most probable candidates, ii) the invaluable clues in cases of shared haplotypes, which are indicative of a common founder effect, and iii) the detection of extended haplotypes over closely mapping genes, which substantiates cosegregation, although the assumptions in which the genetic analysis is based could exceptionally lead astray. The combination of the genetic approach with whole exome sequencing (WES) greatly increases the diagnosis efficiency, and revealed novel mutations in USH2A and GUCY2D. Overall, the RD-chip diagnosis efficiency ranges from 16% in dominant, to 80% in consanguineous recessive pedigrees, with an average of 47%, well within the upper range of massive sequencing approaches, highlighting the validity of this time- and cost-effective approach whilst high-throughput methodologies become amenable for routine diagnosis in medium sized labs. PMID:24516651

de Castro-Miró, Marta; Pomares, Esther; Lorés-Motta, Laura; Tonda, Raul; Dopazo, Joaquín; Marfany, Gemma; Gonzàlez-Duarte, Roser

2014-01-01

228

Combined Genetic and High-Throughput Strategies for Molecular Diagnosis of Inherited Retinal Dystrophies  

PubMed Central

Most diagnostic laboratories are confronted with the increasing demand for molecular diagnosis from patients and families and the ever-increasing genetic heterogeneity of visual disorders. Concerning Retinal Dystrophies (RD), almost 200 causative genes have been reported to date, and most families carry private mutations. We aimed to approach RD genetic diagnosis using all the available genetic information to prioritize candidates for mutational screening, and then restrict the number of cases to be analyzed by massive sequencing. We constructed and optimized a comprehensive cosegregation RD-chip based on SNP genotyping and haplotype analysis. The RD-chip allows to genotype 768 selected SNPs (closely linked to 100 RD causative genes) in a single cost-, time-effective step. Full diagnosis was attained in 17/36 Spanish pedigrees, yielding 12 new and 12 previously reported mutations in 9 RD genes. The most frequently mutated genes were USH2A and CRB1. Notably, RD3–up to now only associated to Leber Congenital Amaurosis– was identified as causative of Retinitis Pigmentosa. The main assets of the RD-chip are: i) the robustness of the genetic information that underscores the most probable candidates, ii) the invaluable clues in cases of shared haplotypes, which are indicative of a common founder effect, and iii) the detection of extended haplotypes over closely mapping genes, which substantiates cosegregation, although the assumptions in which the genetic analysis is based could exceptionally lead astray. The combination of the genetic approach with whole exome sequencing (WES) greatly increases the diagnosis efficiency, and revealed novel mutations in USH2A and GUCY2D. Overall, the RD-chip diagnosis efficiency ranges from 16% in dominant, to 80% in consanguineous recessive pedigrees, with an average of 47%, well within the upper range of massive sequencing approaches, highlighting the validity of this time- and cost-effective approach whilst high-throughput methodologies become amenable for routine diagnosis in medium sized labs. PMID:24516651

de Castro-Miro, Marta; Pomares, Esther; Lores-Motta, Laura; Tonda, Raul; Dopazo, Joaquin; Marfany, Gemma; Gonzalez-Duarte, Roser

2014-01-01

229

Investigating Population Genetic Structure in a Highly Mobile Marine Organism: The Minke Whale Balaenoptera acutorostrata acutorostrata in the North East Atlantic  

PubMed Central

Inferring the number of genetically distinct populations and their levels of connectivity is of key importance for the sustainable management and conservation of wildlife. This represents an extra challenge in the marine environment where there are few physical barriers to gene-flow, and populations may overlap in time and space. Several studies have investigated the population genetic structure within the North Atlantic minke whale with contrasting results. In order to address this issue, we analyzed ten microsatellite loci and 331 bp of the mitochondrial D-loop on 2990 whales sampled in the North East Atlantic in the period 2004 and 2007–2011. The primary findings were: (1) No spatial or temporal genetic differentiations were observed for either class of genetic marker. (2) mtDNA identified three distinct mitochondrial lineages without any underlying geographical pattern. (3) Nuclear markers showed evidence of a single panmictic population in the NE Atlantic according STRUCTURE's highest average likelihood found at K?=?1. (4) When K?=?2 was accepted, based on the Evanno's test, whales were divided into two more or less equally sized groups that showed significant genetic differentiation between them but without any sign of underlying geographic pattern. However, mtDNA for these individuals did not corroborate the differentiation. (5) In order to further evaluate the potential for cryptic structuring, a set of 100 in silico generated panmictic populations was examined using the same procedures as above showing genetic differentiation between two artificially divided groups, similar to the aforementioned observations. This demonstrates that clustering methods may spuriously reveal cryptic genetic structure. Based upon these data, we find no evidence to support the existence of spatial or cryptic population genetic structure of minke whales within the NE Atlantic. However, in order to conclusively evaluate population structure within this highly mobile species, more markers will be required. PMID:25268591

Quintela, Maria; Skaug, Hans J.; ?ien, Nils; Haug, Tore; Seliussen, Bj?rghild B.; Solvang, Hiroko K.; Pampoulie, Christophe; Kanda, Naohisa; Pastene, Luis A.; Glover, Kevin A.

2014-01-01

230

A high-density genetic map for soybean based on specific length amplified fragment sequencing.  

PubMed

Soybean is an important oil seed crop, but very few high-density genetic maps have been published for this species. Specific length amplified fragment sequencing (SLAF-seq) is a recently developed high-resolution strategy for large scale de novo discovery and genotyping of single nucleotide polymorphisms. SLAF-seq was employed in this study to obtain sufficient markers to construct a high-density genetic map for soybean. In total, 33.10 Gb of data containing 171,001,333 paired-end reads were obtained after preprocessing. The average sequencing depth was 42.29 in the Dongnong594, 56.63 in the Charleston, and 3.92 in each progeny. In total, 164,197 high-quality SLAFs were detected, of which 12,577 SLAFs were polymorphic, and 5,308 of the polymorphic markers met the requirements for use in constructing a genetic map. The final map included 5,308 markers on 20 linkage groups and was 2,655.68 cM in length, with an average distance of 0.5 cM between adjacent markers. To our knowledge, this map has the shortest average distance of adjacent markers for soybean. We report here a high-density genetic map for soybean. The map was constructed using a recombinant inbred line population and the SLAF-seq approach, which allowed the efficient development of a large number of polymorphic markers in a short time. Results of this study will not only provide a platform for gene/quantitative trait loci fine mapping, but will also serve as a reference for molecular breeding of soybean. PMID:25118194

Qi, Zhaoming; Huang, Long; Zhu, Rongsheng; Xin, Dawei; Liu, Chunyan; Han, Xue; Jiang, Hongwei; Hong, Weiguo; Hu, Guohua; Zheng, Hongkun; Chen, Qingshan

2014-01-01

231

Automatic Compilation from High-Level Biologically-Oriented Programming Language to Genetic Regulatory Networks  

PubMed Central

Background The field of synthetic biology promises to revolutionize our ability to engineer biological systems, providing important benefits for a variety of applications. Recent advances in DNA synthesis and automated DNA assembly technologies suggest that it is now possible to construct synthetic systems of significant complexity. However, while a variety of novel genetic devices and small engineered gene networks have been successfully demonstrated, the regulatory complexity of synthetic systems that have been reported recently has somewhat plateaued due to a variety of factors, including the complexity of biology itself and the lag in our ability to design and optimize sophisticated biological circuitry. Methodology/Principal Findings To address the gap between DNA synthesis and circuit design capabilities, we present a platform that enables synthetic biologists to express desired behavior using a convenient high-level biologically-oriented programming language, Proto. The high level specification is compiled, using a regulatory motif based mechanism, to a gene network, optimized, and then converted to a computational simulation for numerical verification. Through several example programs we illustrate the automated process of biological system design with our platform, and show that our compiler optimizations can yield significant reductions in the number of genes () and latency of the optimized engineered gene networks. Conclusions/Significance Our platform provides a convenient and accessible tool for the automated design of sophisticated synthetic biological systems, bridging an important gap between DNA synthesis and circuit design capabilities. Our platform is user-friendly and features biologically relevant compiler optimizations, providing an important foundation for the development of sophisticated biological systems. PMID:21850228

Beal, Jacob; Lu, Ting; Weiss, Ron

2011-01-01

232

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

2014-01-01

233

Exploration of genetically determined resistance against hepatitis C infection in high-risk injecting drug users.  

PubMed

Genetic resistance to specific infections is well recognized. In hepatitis C virus (HCV) infection, genetic polymorphisms in IL-28B and the killer cell immunoglobulin-like receptors (KIR) and their HLA class I ligands have been shown to affect clearance of the virus following infection. There are limited data regarding resistance to established HCV infection. Reliable quantification of repeated exposure in high-risk populations, such as injecting drug users (IDU), is a key limitation of previous studies of resistance. Behavioural data and DNA from IDU (n = 210) in the Hepatitis C Incidence and Transmission Study in prisons (HITS-p) cohort were genotyped for polymorphisms in: IL-28B, peptidyl-prolyl isomerase A (PPIA), HLA-C and KIR2. To quantify risk, a composite risk index based on factors predictive of incident HCV infection was derived. Logistic regression analysis revealed the risk index was strongly associated with incident HCV infection (P < 0.0001). The upper tertile of the uninfected individuals had risk indices comparable to the incident cases, but remained uninfected. There were no significant differences in the frequencies of IL-28B or PPIA polymorphisms between these exposed-uninfected cases, or in the frequencies of KIR2-DL3, HLA-C1, or their combination. A framework for the investigation of genetic determinants of resistance to HCV infection has been developed. Several candidate gene associations were investigated and excluded. Further investigation of genetic determinants of resistance to HCV infection is warranted. PMID:24612442

Sugden, P B; Cameron, B; Luciani, F; Lloyd, A R

2014-08-01

234

High levels of genetic variability and inbreeding in two Neotropical dioecious palms with contrasting life histories.  

PubMed

We characterized the population genetics of two Neotropical dioecious palm species of Chamaedorea with contrasting life strategies from the region that is both the northernmost extent and most species rich of the genus. Chamaedorea tepejilote is a common, wind-pollinated arboreal understory palm. Although most adult plants reproduce each year, only a few individuals produce the majority of flowers and seeds. Chamaedorea elatior, conversely, is an uncommon climbing subcanopy palm with entomophilous flowers (insect-pollinated characteristics). Most of the mature palms do not reproduce in consecutive years and fruiting is episodic. Isozymes with a total of 107 alleles for 27 loci of 17 enzymes from six populations were assessed. For both species, co-occurrence of high levels of genetic variation and homozygosity was observed (C. tepejilote: He: 0.385-0.442, f: 0.431-0.486; C. elatior: He: 0.278-0.342, f: 0.466-0.535). Genetic differentiation of C. elatior was much lower (theta=0.0315) than that for C. tepejilote (theta=0.152). The contrast in differentiation may be influenced by differences in the spatial scale of the genetic neighborhoods of the two species. The simultaneous maintenance of inbreeding and of a large number of alleles within the populations is attributable to the low and variable number of mating pairs. Demographic studies indicate that this pattern could be explained by low reproductive frequency among individuals and over years in C. elatior and by reproductive dominance in C. tepejilote. PMID:17637694

Luna, R; Epperson, B K; Oyama, K

2007-10-01

235

Ecological opportunities and specializations shaped genetic divergence in a highly mobile marine top predator.  

PubMed

Environmental conditions can shape genetic and morphological divergence. Release of new habitats during historical environmental changes was a major driver of evolutionary diversification. Here, forces shaping population structure and ecotype differentiation ('pelagic' and 'coastal') of bottlenose dolphins in the North-east Atlantic were investigated using complementary evolutionary and ecological approaches. Inference of population demographic history using approximate Bayesian computation indicated that coastal populations were likely founded by the Atlantic pelagic population after the Last Glacial Maxima probably as a result of newly available coastal ecological niches. Pelagic dolphins from the Atlantic and the Mediterranean Sea likely diverged during a period of high productivity in the Mediterranean Sea. Genetic differentiation between coastal and pelagic ecotypes may be maintained by niche specializations, as indicated by stable isotope and stomach content analyses, and social behaviour. The two ecotypes were only weakly morphologically segregated in contrast to other parts of the World Ocean. This may be linked to weak contrasts between coastal and pelagic habitats and/or a relatively recent divergence. We suggest that ecological opportunity to specialize is a major driver of genetic and morphological divergence. Combining genetic, ecological and morphological approaches is essential to understanding the population structure of mobile and cryptic species. PMID:25297864

Louis, Marie; Fontaine, Michael C; Spitz, Jérôme; Schlund, Erika; Dabin, Willy; Deaville, Rob; Caurant, Florence; Cherel, Yves; Guinet, Christophe; Simon-Bouhet, Benoit

2014-11-22

236

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. PMID:22605985

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

2012-01-01

237

“ Nafion”-functionalized mesoporous MCM-41 silica shows high activity and selectivity for carboxylic acid esterification and Friedel–Crafts acylation reactions  

Microsoft Academic Search

Hybrid organic–inorganic MCM-41 silicas functionalized with perfluoroalkylsulfonic acid groups analogous to that of Nafion were prepared in a simple single step by a condensation reaction between surface silanol groups of the mesoporous silicas and 1,2,2-trifluoro-2-hydroxy-1-trifluoromethyl-ethane sulfonic acid Beta-sultone. The catalysts showed very high activity for the esterification of long-chain fatty acids with ethanol and high-molecular-weight alcohols with essentially complete selectivity

Mercedes Alvaro; Avelino Corma; Debasish Das; Vicente Fornés; Hermenegildo García

2005-01-01

238

Determining Signalling Nodes for Apoptosis by a Genetic High-Throughput Screen  

Microsoft Academic Search

BackgroundWith the ever-increasing information emerging from the various sequencing and gene annotation projects, there is an urgent need to elucidate the cellular functions of the newly discovered genes. The genetically regulated cell suicide of apoptosis is especially suitable for such endeavours as it is governed by a vast number of factors.Methodology\\/Principal FindingsWe have set up a high-throughput screen in 96-well

Bevan Lin; Derek Huntley; Ghada Abuali; Sarah R. Langley; George Sindelar; Enrico Petretto; Sarah Butcher; Stefan Grimm; Matthew Bogyo

2011-01-01

239

Risk-Reduction Surgery Decisions in High-Risk Women Seen for Genetic Counseling  

Microsoft Academic Search

Women at greatest risk for hereditary breast and ovarian cancer may consider prophylactic removal of breasts or ovaries as\\u000a a risk-reduction measure. This report describes uptake of risk-reduction mastectomy (RRM), risk-reduction oophorectomy (RRO),\\u000a and related factors in 62 high-risk women who received genetic counseling. Seven (11%) participants underwent RRM and 13 (21%)\\u000a underwent RRO. Of these women, 37% did not

Jessica A. Ray; Lois J. Loescher; Molly Brewer

2005-01-01

240

Comparative landscape genetics of two pond-breeding amphibian species in a highly modified agricultural landscape.  

PubMed

Evaluating fine-scale population structure of multiple species in the same landscape increases our ability to identify common patterns as well as discern ecological differences among species' landscape genetic relationships. In the Palouse bioregion of northern Idaho, USA, 99% of the native prairie has been converted to nonirrigated agriculture and exotic grasslands. Columbia spotted frogs (Rana luteiventris) and long-toed salamanders (Ambystoma macrodactylum) in this area breed almost entirely in artificial ponds on private land. We used genetic distances (F(ST) and D(c)) derived from eight microsatellite loci in 783 samples to evaluate the relationships among sympatric breeding populations (N = 20 and 26) of these species in a 213-km(2) landscape. Both species showed a pattern of isolation by distance that was not improved when distance was measured along drainages instead of topographically corrected straight lines (P < 0.01). After testing for autocorrelation among genetic distances, we used an information theoretic approach to model landscape resistance based on slope, soil type, solar insolation, and land cover, and multi-model inference to rank the resistance of landscape surfaces to dispersal (represented by genetic distance). For both species, urban and rural developed land cover provided the highest landscape resistances. Resistance values for long-toed salamanders followed a moisture gradient where forest provided the least resistance, while agriculture and shrub/clearcut provided the least resistance for Columbia spotted frogs. Comparative landscape genetics can be a powerful tool for detecting similarities and differences between codistributed species, and resulting models can be used to predict species-specific responses to landscape change. PMID:20723062

Goldberg, Caren S; Waits, L P

2010-09-01

241

High genetic diversity in a small population: the case of Chilean blue whales  

PubMed Central

It is generally assumed that species with low population sizes have lower genetic diversities than larger populations and vice versa. However, this would not be the case for long-lived species with long generation times, and which populations have declined due to anthropogenic effects, such as the blue whale (Balaenoptera musculus). This species was intensively decimated globally to near extinction during the 20th century. Along the Chilean coast, it is estimated that at least 4288 blue whales were hunted from an apparently pre-exploitation population size (k) of a maximum of 6200 individuals (Southeastern Pacific). Thus, here, we describe the mtDNA (control region) and nDNA (microsatellites) diversities of the Chilean blue whale aggregation site in order to verify the expectation of low genetic diversity in small populations. We then compare our findings with other blue whale aggregations in the Southern Hemisphere. Interestingly, although the estimated population size is small compared with the pre-whaling era, there is still considerable genetic diversity, even after the population crash, both in mitochondrial (N = 46) and nuclear (N = 52) markers (Hd = 0.890 and Ho = 0.692, respectively). Our results suggest that this diversity could be a consequence of the long generation times and the relatively short period of time elapsed since the end of whaling, which has been observed in other heavily-exploited whale populations. The genetic variability of blue whales on their southern Chile feeding grounds was similar to that found in other Southern Hemisphere blue whale feeding grounds. Our phylogenetic analysis of mtDNA haplotypes does not show extensive differentiation of populations among Southern Hemisphere blue whale feeding grounds. The present study suggests that although levels of genetic diversity are frequently used as estimators of population health, these parameters depend on the biology of the species and should be taken into account in a monitoring framework study to obtain a more complete picture of the conservation status of a population. PMID:24834336

Torres-Florez, Juan P; Hucke-Gaete, Rodrigo; Rosenbaum, Howard; Figueroa, Christian C

2014-01-01

242

High genetic diversity in a small population: the case of Chilean blue whales.  

PubMed

It is generally assumed that species with low population sizes have lower genetic diversities than larger populations and vice versa. However, this would not be the case for long-lived species with long generation times, and which populations have declined due to anthropogenic effects, such as the blue whale (Balaenoptera musculus). This species was intensively decimated globally to near extinction during the 20th century. Along the Chilean coast, it is estimated that at least 4288 blue whales were hunted from an apparently pre-exploitation population size (k) of a maximum of 6200 individuals (Southeastern Pacific). Thus, here, we describe the mtDNA (control region) and nDNA (microsatellites) diversities of the Chilean blue whale aggregation site in order to verify the expectation of low genetic diversity in small populations. We then compare our findings with other blue whale aggregations in the Southern Hemisphere. Interestingly, although the estimated population size is small compared with the pre-whaling era, there is still considerable genetic diversity, even after the population crash, both in mitochondrial (N = 46) and nuclear (N = 52) markers (Hd = 0.890 and Ho = 0.692, respectively). Our results suggest that this diversity could be a consequence of the long generation times and the relatively short period of time elapsed since the end of whaling, which has been observed in other heavily-exploited whale populations. The genetic variability of blue whales on their southern Chile feeding grounds was similar to that found in other Southern Hemisphere blue whale feeding grounds. Our phylogenetic analysis of mtDNA haplotypes does not show extensive differentiation of populations among Southern Hemisphere blue whale feeding grounds. The present study suggests that although levels of genetic diversity are frequently used as estimators of population health, these parameters depend on the biology of the species and should be taken into account in a monitoring framework study to obtain a more complete picture of the conservation status of a population. PMID:24834336

Torres-Florez, Juan P; Hucke-Gaete, Rodrigo; Rosenbaum, Howard; Figueroa, Christian C

2014-04-01

243

Genotype-Phenotype Correlations in a Mountain Population Community with High Prevalence of Wilson's Disease: Genetic and Clinical Homogeneity  

PubMed Central

Wilson’s disease is an autosomal recessive disorder caused by more than 500 mutations in ATP7B gene presenting considerably clinical manifestations heterogeneity even in patients with a particular mutation. Previous findings suggested a potential role of additional genetic modifiers and environment factors on phenotypic expression among the affected patients. We conducted clinical and genetic investigations to perform genotype-phenotype correlation in two large families living in a socio-culturally isolated community with the highest prevalence of Wilson’s disease ever reported of 1?1130. Sequencing of ATP7B gene in seven affected individuals and 43 family members identified a common compound heterozygous genotype, H1069Q/M769H-fs, in five symptomatic and two asymptomatic patients and detected the presence of two out of seven identified single nucleotide polymorphisms in all affected patients. Symptomatic patients had similar clinical phenotype and age at onset (18±1 years) showing dysarthria and dysphagia as common clinical features at the time of diagnosis. Moreover, all symptomatic patients presented Kayser-Fleischer rings and lack of dystonia accompanied by unfavourable clinical outcomes. Our findings add value for understanding of genotype-phenotype correlations in Wilson’s disease based on a multifamily study in an isolated population with high extent of genetic and environmental homogeneity as opposed to majority of reports. We observed an equal influence of presumed other genetic modifiers and environmental factors on clinical presentation and age at onset of Wilson’s disease in patients with a particular genotype. These data provide valuable inferences that could be applied for predicting clinical management in asymptomatic patients in such communities. PMID:24897373

Cocos, Relu; Sendroiu, Alina; Schipor, Sorina; Bohiltea, Laurentiu Camil; Sendroiu, Ionut; Raicu, Florina

2014-01-01

244

Natural Sciences 2007 Cover: The cover shows two photographs illustrating the participation of the Imperial High Energy Physics group in the Compact  

E-print Network

measures energy deposited by hadronic particles, such as pions and protons. A large, apparently, missing in energy efficient lighting and displays and for water sterilisation and the scientific and technological: The cover shows two photographs illustrating the participation of the Imperial High Energy Physics group

245

Cover image: Soft x-ray microtomography images showing high-resolution reconstructed biofilm cells grown at Pacific Northwest National Laboratory. Characterizing the chemical and physical interactions of  

E-print Network

#12;Cover image: Soft x-ray microtomography images showing high-resolution reconstructed biofilm sources. With these and other new capabilities in chemical imaging, we are accelerating scientific Lung Imaging Research Gets Second Wind Scientists use computational fluid dynamics (CFD

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

Implications of genetic risk information in families with a high density of bipolar disorder: an exploratory study  

Microsoft Academic Search

While major susceptibility genes for bipolar disorder are yet to be identified, the opportunity exists to systematically ascertain the important issues and societal implications of genetic risk determination for bipolar disorder prior to these technological advances becoming widely available. This study explores, in a sample of families with a high density of bipolar disorder: (i) attitudes to predictive genetic and

Bettina Meiser; Philip B. Mitchell; H. McGirr; M. Van Herten; Peter R. Schofield

2005-01-01

248

Copyright 1998 by the Genetics Society of America High-Efficiency Transformation of Chlamydomonas reinhardtii by Electroporation  

E-print Network

Copyright © 1998 by the Genetics Society of America High-Efficiency Transformation of Chlamydomonas, (3) it is amenable to classical genetic analysis, to 1000 transformants per g DNA. However, this fre for various uni- mutation to be immediately expressed, (5) character- cellular organisms (e.g., yeast, E. coli

249

High Genetic Diversity and Adaptive Potential of Two Simian Hemorrhagic Fever Viruses in a Wild Primate Population  

PubMed Central

Key biological properties such as high genetic diversity and high evolutionary rate enhance the potential of certain RNA viruses to adapt and emerge. Identifying viruses with these properties in their natural hosts could dramatically improve disease forecasting and surveillance. Recently, we discovered two novel members of the viral family Arteriviridae: simian hemorrhagic fever virus (SHFV)-krc1 and SHFV-krc2, infecting a single wild red colobus (Procolobus rufomitratus tephrosceles) in Kibale National Park, Uganda. Nearly nothing is known about the biological properties of SHFVs in nature, although the SHFV type strain, SHFV-LVR, has caused devastating outbreaks of viral hemorrhagic fever in captive macaques. Here we detected SHFV-krc1 and SHFV-krc2 in 40% and 47% of 60 wild red colobus tested, respectively. We found viral loads in excess of 106–107 RNA copies per milliliter of blood plasma for each of these viruses. SHFV-krc1 and SHFV-krc2 also showed high genetic diversity at both the inter- and intra-host levels. Analyses of synonymous and non-synonymous nucleotide diversity across viral genomes revealed patterns suggestive of positive selection in SHFV open reading frames (ORF) 5 (SHFV-krc2 only) and 7 (SHFV-krc1 and SHFV-krc2). Thus, these viruses share several important properties with some of the most rapidly evolving, emergent RNA viruses. PMID:24651479

Weiler, Andrea; Sibley, Samuel D.; Dinis, Jorge M.; Bergman, Zachary; Nelson, Chase W.; Correll, Michael; Gleicher, Michael; Hyeroba, David; Tumukunde, Alex; Weny, Geoffrey; Chapman, Colin; Kuhn, Jens H.; Hughes, Austin L.; Friedrich, Thomas C.; Goldberg, Tony L.; O'Connor, David H.

2014-01-01

250

Schizophrenics 'show new mutations' -Health News -NHS Choices http://www.nhs.uk/news/2011/08August/Pages/sporadic-genetic-mutation-schizophrenia.aspx[8/9/2011 10:05:12 AM  

E-print Network

Food/diet (400) Lifestyle/exercise (393) Pregnancy/child (385) Cancer (342) Medication (312) Heart on Schizophrenia and Depression. The study was published in the peer-reviewed scientific journal Nature Genetics mouse sperm from stem cells (August 5 2011) Music therapy for depression (August 1 2011) Genetic clue

251

High genetic diversity in RdRp gene of Brazilian porcine sapovirus strains.  

PubMed

Sapovirus is one genus within Caliciviridae family that causes diarrhea in humans and animals. Sapovirus (SaV) has been classified into seven genogroups (GI to GVII). The GIII, GVI, and GVII, which prototype is Cowden, JJ681, and K7/JP strains, respectively, infect pigs. The objective of this study was to characterize wild-type Brazilian SaV strains from piglet stool samples and determine SaV infection frequency, age distribution and association with diarrheic disease. Stool samples from 113 piglets up to 28-days-old were collected from 34 pig farms located in the States of Minas Gerais (MG), Mato Grosso do Sul (MS), Paraná (PR), Santa Catarina (SC), and Rio Grande do Sul (RS), during 2004 and 2005. The specimens were evaluated for enteric calicivirus by RT-PCR assay with primers p289/290, designed to detect the polymerase gene of SaV and norovirus. Thirty four (30.1%) samples were positive for SaV and five amplicons were sequenced. Phylogenetic analyses placed BRA29-MS/04 and BRA52-PR/05 sequences into the GIII of SaV genus. BRA04-SC/04, BRA21-RS/04, and BRA37-MG/05 demonstrated low identity with the Cowden strain but were closely related (up to 86.3%) to the Japanese and Dutch SaV strains, grouping together in a new cluster (GVIII?) in the phylogenetic tree. SaV infection was detected more frequently (p=0.0001) in animals between 22 and 28 days of age, in equal frequencies in piglets with and without diarrhea (p=0.59), and in the five Brazilian States. In this study, such as other unclassified worldwide SaVs, the Brazilian strains showed high genetic variability. Furthermore, the distribution and frequency of SaV infection provides evidence that the virus is circulating in Brazilian pig herds. PMID:18403136

Barry, Aline F; Alfieri, Alice F; Alfieri, Amauri A

2008-09-18

252

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

2011-07-01

253

Intact genetic structure and high levels of genetic diversity in bottlenecked sockeye salmon ( Oncorhynchus nerka ) populations of the Fraser River, British Columbia, Canada  

Microsoft Academic Search

Analysis of six microsatellite loci in 5800 sockeye salmon (Oncorhynchus nerka) from 29 Fraser River pop- ulations provided little evidence of genetic bottlenecks or mass straying in upper Fraser sockeye salmon resulting from reduced abundances following 1913-1914 rockslides in the Fraser canyon and successive decades of high exploitation. Upper Fraser populations were not characterized by a paucity of rare alleles,

Ruth E. Withler; Khai D. Le; R. John Nelson; Kristina M. Miller; Terry D. Beacham

2000-01-01

254

Development of a large SNP genotyping array and generation of high-density genetic maps in tomato.  

PubMed

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 F(2) 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. PMID:22802968

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

2012-01-01

255

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. PMID:22802968

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

256

High-level genetic diversity and complex population structure of Siberian apricot (Prunus sibirica L.) in China as revealed by nuclear SSR markers.  

PubMed

Siberian apricot (Prunus sibirica L.), an ecologically and economically important tree species with a high degree of tolerance to a variety of extreme environmental conditions, is widely distributed across the mountains of northeastern and northern China, eastern and southeastern regions of Mongolia, Eastern Siberia, and the Maritime Territory of Russia. However, few studies have examined the genetic diversity and population structure of this species. Using 31 nuclear microsatellites, we investigated the level of genetic diversity and population structure of Siberian apricot sampled from 22 populations across China. The number of alleles per locus ranged from 5 to 33, with an average of 19.323 alleles. The observed heterozygosity and expected heterozygosity ranged from 0.037 to 0.874 and 0.040 to 0.924 with average values of 0.639 and 0.774, respectively. A STRUCTURE-based analysis clustered all of the populations into four genetic clusters. Significant genetic differentiation was observed between all population pairs. A hierarchical analysis of molecular variance attributed about 94% of the variation to within populations. No significant difference was detected between the wild and semi-wild groups, indicating that recent cultivation practices have had little impact on the genetic diversity of Siberian apricot. The Mantel test showed that the genetic distance among the populations was not significantly correlated with geographic distance (r?=?0.4651, p?=?0.9940). Our study represents the most comprehensive investigation of the genetic diversity and population structure of Siberian apricot in China to date, and it provides valuable information for the collection of genetic resources for the breeding of Siberian apricot and related species. PMID:24516551

Wang, Zhe; Kang, Ming; Liu, Huabo; Gao, Jiao; Zhang, Zhengdong; Li, Yingyue; Wu, Rongling; Pang, Xiaoming

2014-01-01

257

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. PMID:11254456

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

2001-01-01

258

High efficiency and reliability of inter-simple sequence repeats (ISSR) markers for evaluation of genetic diversity in Brazilian cultivated Jatropha curcas L. accessions.  

PubMed

Jatropha curcas L. is found in all tropical regions and has garnered lot of attention for its potential as a source of biodiesel. As J. curcas is a plant that is still in the process of being domesticated, interest in improving its agronomic traits has increased in an attempt to select more productive varieties, aiming at sustainable utilization of this plant for biodiesel production. Therefore, the study of genetic diversity in different accessions of J. curcas in Brazil constitutes a necessary first step in genetic programs designed to improve this species. In this study we have used ISSR markers to assess the genetic variability of 332 accessions from eight states in Brazil that produce J. curcas seeds for commercialization. Seven ISSR primers amplified a total of 21,253 bands, of which 19,472 bands (91%) showed polymorphism. Among the polymorphic bands 275 rare bands were identified (present in fewer than 15% of the accessions). Polymorphic information content (PIC), marker index (MI) and resolving power (RP) averaged 0.26, 17.86 and 19.87 per primer, respectively, showing the high efficiency and reliability of the markers used. ISSR markers analyses as number of polymorphic loci, genetic diversity and accession relationships through UPGMA-phenogram and MDS showed that Brazilian accessions are closely related but have a higher level of genetic diversity than accessions from other countries, and the accessions from Natal (RN) are the most diverse, having high value as a source of genetic diversity for breeding programs of J. curcas in the world. PMID:21113672

Grativol, Clícia; da Fonseca Lira-Medeiros, Catarina; Hemerly, Adriana Silva; Ferreira, Paulo Cavalcanti Gomes

2011-10-01

259

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

NASA Astrophysics Data System (ADS)

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 cells permits genetic transformation. Our method involves exposure of a Campylobacter cell suspension to a high-voltage exponential decay discharge (5-13 kV/cm) for a brief period of time (resistance-capacitance time constant = 2.4-26 msec) in the presence of plasmid DNA. Electrical transformation of C. jejuni results in frequencies as high as 1.2 × 106 transformants per ? g of DNA. We have investigated the effects of pulse amplitude and duration, cell growth conditions, divalent cations, and DNA concentration on the efficiency of transformation. Transformants of C. jejuni obtained by electroporation contained structurally intact plasmid molecules. In addition, evidence is presented that indicates that C. jejuni possesses DNA restriction and modification systems. The use of electroporation as a method for transforming other bacterial species and guidelines for its implementation are also discussed.

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

1988-02-01

260

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. PMID:23432809

2013-01-01

261

Genetic Pool Information Reflects Highly Suitable Areas: The Case of Two Parapatric Endangered Species of Tuco-tucos (Rodentia: Ctenomiydae)  

PubMed Central

Conservation of small mammals requires knowledge of the genetically and ecologically meaningful spatial scales at which species respond to habitat modifications. Conservation strategies can be improved through the use of ecological niche models and genetic data to classify areas of high environmental suitability. In this study, we applied a Maxent model integrated with genetic information (nucleotide diversity, haplotype diversity and Fu's Fs neutrality tests) to evaluate potential genetic pool populations with highly suitable areas for two parapatric endangered species of tuco-tucos (Ctenomys minutus and C. lami). Our results demonstrated that both species were largely influenced by vegetation and soil variables at a landscape scale and inhabit a highly specific niche. Ctenomys minutus was also influenced by the variable altitude; the species was associated with low altitudes (sea level). Our model of genetic data associated with environmental suitability indicate that the genetic pool data were associated with highly suitable areas for C. minutus. This pattern was not evident for C. lami, but this outcome could be a consequence of the restricted range of the species. The preservation of species requires not only detailed knowledge of their natural history and genetic structure but also information on the availability of suitable areas where species can survive, and such knowledge can aid significantly in conservation planning. This finding reinforces the use of these two techniques for planning conservation actions. PMID:24819251

Galiano, Daniel; Bernardo-Silva, Jorge; de Freitas, Thales R. O.

2014-01-01

262

Genetic pool information reflects highly suitable areas: the case of two parapatric endangered species of Tuco-tucos (Rodentia: Ctenomiydae).  

PubMed

Conservation of small mammals requires knowledge of the genetically and ecologically meaningful spatial scales at which species respond to habitat modifications. Conservation strategies can be improved through the use of ecological niche models and genetic data to classify areas of high environmental suitability. In this study, we applied a Maxent model integrated with genetic information (nucleotide diversity, haplotype diversity and Fu's Fs neutrality tests) to evaluate potential genetic pool populations with highly suitable areas for two parapatric endangered species of tuco-tucos (Ctenomys minutus and C. lami). Our results demonstrated that both species were largely influenced by vegetation and soil variables at a landscape scale and inhabit a highly specific niche. Ctenomys minutus was also influenced by the variable altitude; the species was associated with low altitudes (sea level). Our model of genetic data associated with environmental suitability indicate that the genetic pool data were associated with highly suitable areas for C. minutus. This pattern was not evident for C. lami, but this outcome could be a consequence of the restricted range of the species. The preservation of species requires not only detailed knowledge of their natural history and genetic structure but also information on the availability of suitable areas where species can survive, and such knowledge can aid significantly in conservation planning. This finding reinforces the use of these two techniques for planning conservation actions. PMID:24819251

Galiano, Daniel; Bernardo-Silva, Jorge; Freitas, Thales R O de

2014-01-01

263

Mapping of Genetic Abnormalities of Primary Tumours from Metastatic CRC by High-Resolution SNP Arrays  

PubMed Central

Background For years, the genetics of metastatic colorectal cancer (CRC) have been studied using a variety of techniques. However, most of the approaches employed so far have a relatively limited resolution which hampers detailed characterization of the common recurrent chromosomal breakpoints as well as the identification of small regions carrying genetic changes and the genes involved in them. Methodology/Principal Findings Here we applied 500K SNP arrays to map the most common chromosomal lesions present at diagnosis in a series of 23 primary tumours from sporadic CRC patients who had developed liver metastasis. Overall our results confirm that the genetic profile of metastatic CRC is defined by imbalanced gains of chromosomes 7, 8q, 11q, 13q, 20q and X together with losses of the 1p, 8p, 17p and 18q chromosome regions. In addition, SNP-array studies allowed the identification of small (<1.3 Mb) and extensive/large (>1.5 Mb) altered DNA sequences, many of which contain cancer genes known to be involved in CRC and the metastatic process. Detailed characterization of the breakpoint regions for the altered chromosomes showed four recurrent breakpoints at chromosomes 1p12, 8p12, 17p11.2 and 20p12.1; interestingly, the most frequently observed recurrent chromosomal breakpoint was localized at 17p11.2 and systematically targeted the FAM27L gene, whose role in CRC deserves further investigations. Conclusions/Significance In summary, in the present study we provide a detailed map of the genetic abnormalities of primary tumours from metastatic CRC patients, which confirm and extend on previous observations as regards the identification of genes potentially involved in development of CRC and the metastatic process. PMID:21060790

Sayagues, Jose Maria; Fontanillo, Celia; Abad, Maria del Mar; Gonzalez-Gonzalez, Maria; Sarasquete, Maria Eugenia; del Carmen Chillon, Maria; Garcia, Eva; Bengoechea, Oscar; Fonseca, Emilio; Gonzalez-Diaz, Marcos; De Las Rivas, Javier

2010-01-01

264

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

265

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 PMID:23433259

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

266

Surprising roles for phospholipid binding proteins revealed by high throughput genetics.  

PubMed

Saccharomyces cerevisiae remains an ideal organism for studying the cell biological roles of lipids in vivo, as yeast has phospholipid metabolic pathways similar to mammalian cells, is easy and economical to manipulate, and is genetically tractable. The availability of isogenic strains containing specific genetic inactivation of each non-essential gene allowed for the development of a high-throughput method, called synthetic genetic analysis (SGA), to identify and describe precise pathways or functions associated with specific genes. This review describes the use of SGA to aid in elucidating the function of two lipid-binding proteins that regulate vesicular transport, Sec14 and Kes1. Sec14 was first identified as a phosphatidylcholine (PC) - phosphatidylinositol (PI) transfer protein required for viability, with reduced Sec14 function resulting in diminished vesicular transport out of the trans-Golgi. Although Sec14 is required for cell viability, inactivating the KES1 gene that encodes for a member of the oxysterol binding protein family in cells lacking Sec14 function results in restoration of vesicular transport and cell growth. SGA analysis identified a role for Kes1 and Sec14 in regulating the level and function of Golgi PI-4-phosphate (PI-4-P). SGA also determined that Sec14 not only regulates vesicular transport out of the trans-Golgi, but also transport from endosomes to the trans-Golgi. Comparing SGA screens in databases, coupled with genetic and cell biological analyses, further determined that the PI-4-P pool affected by Kes1 is generated by the PI 4-kinase Pik1. An important biological role for Sec14 and Kes1 revealed by SGA is coordinate regulation of the Pik1-generated Golgi PI-4-P pool that in turn is essential for vesicular transport into and out of the trans-Golgi. PMID:20651827

LeBlanc, Marissa A; McMaster, Christopher R

2010-08-01

267

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. PMID:19890482

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

2009-01-01

268

Multivariate genetic analysis of plant responses to water deficit and high temperature revealed contrasting adaptive strategies.  

PubMed

How genetic factors control plant performance under stressful environmental conditions is a central question in ecology and for crop breeding. A multivariate framework was developed to examine the genetic architecture of performance-related traits in response to interacting environmental stresses. Ecophysiological and life history traits were quantified in the Arabidopsis thaliana Ler×Cvi mapping population exposed to constant soil water deficit and high air temperature. The plasticity of the genetic variance-covariance matrix ( G: -matrix) was examined using mixed-effects models after regression into principal components. Quantitative trait locus (QTL) analysis was performed on the predictors of genotype effects and genotype by environment interactions (G×E). Three QTLs previously identified for flowering time had antagonistic G×E effects on carbon acquisition and the other traits (phenology, growth, leaf morphology, and transpiration). This resulted in a size-dependent response of water use efficiency (WUE) to high temperature but not soil water deficit, indicating that most of the plasticity of carbon acquisition and WUE to temperature is controlled by the loci that control variation of development, size, growth, and transpiration. A fourth QTL, MSAT2.22, controlled the response of carbon acquisition to specific combinations of watering and temperature irrespective of plant size and development, growth, and transpiration rate, which resulted in size-independent plasticity of WUE. These findings highlight how the strategies to optimize plant performance may differ in response to water deficit and high temperature (or their combination), and how different G×E effects could be targeted to improve plant tolerance to these stresses. PMID:25246443

Vasseur, François; Bontpart, Thibaut; Dauzat, Myriam; Granier, Christine; Vile, Denis

2014-12-01

269

[3H]Adenine is a suitable radioligand for the labeling of G protein-coupled adenine receptors but shows high affinity to bacterial contaminations in buffer solutions  

PubMed Central

[3H]Adenine has previously been used to label the newly discovered G protein-coupled murine adenine receptors. Recent reports have questioned the suitability of [3H]adenine for adenine receptor binding studies because of curious results, e.g. high specific binding even in the absence of mammalian protein. In this study, we showed that specific [3H]adenine binding to various mammalian membrane preparations increased linearly with protein concentration. Furthermore, we found that Tris-buffer solutions typically used for radioligand binding studies (50 mM, pH 7.4) that have not been freshly prepared but stored at 4°C for some time may contain bacterial contaminations that exhibit high affinity binding for [3H]adenine. Specific binding is abolished by heating the contaminated buffer or filtering it through 0.2-?m filters. Three different, aerobic, gram-negative bacteria were isolated from a contaminated buffer solution and identified as Achromobacter xylosoxidans, A. denitrificans, and Acinetobacter lwoffii. A. xylosoxidans, a common bacterium that can cause nosocomial infections, showed a particularly high affinity for [3H]adenine in the low nanomolar range. Structure–activity relationships revealed that hypoxanthine also bound with high affinity to A. xylosoxidans, whereas other nucleobases (uracil, xanthine) and nucleosides (adenosine, uridine) did not. The nature of the labeled site in bacteria is not known, but preliminary results indicate that it may be a high-affinity purine transporter. We conclude that [3H]adenine is a well-suitable radioligand for adenine receptor binding studies but that bacterial contamination of the employed buffer solutions must be avoided. PMID:18404448

Schiedel, Anke C.; Meyer, Heiko; Alsdorf, Bernt B.A.; Gorzalka, Simone; Brussel, Hannelore

2007-01-01

270

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. PMID:23550116

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

271

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

PubMed

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 3,696 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 (RILs) 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 ultra-dense map allowed syntenic studies between lettuce and Vitis vinifera as well as other plant species. PMID:23550116

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

2013-03-22

272

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

273

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 PMID:16593713

Haufler, Christopher H.; Soltis, Douglas E.

1986-01-01

274

The Combined Anti-HIV-1 Activities of Emtricitabine and Tenofovir plus the Integrase Inhibitor Elvitegravir or Raltegravir Show High Levels of Synergy In Vitro.  

PubMed

Highly active antiretroviral therapy (HAART) involves combination treatment with three or more antiretroviral agents. The antiviral effects of combinations of emtricitabine (FTC) plus tenofovir (TFV) plus antiretroviral agents of all the major drug classes were investigated. Combinations of FTC and TFV with a nonnucleoside reverse transcriptase inhibitor (NNRTI) (efavirenz or rilpivirine) or with a protease inhibitor (PI) (atazanavir, lopinavir, or darunavir) showed additive to synergistic anti-HIV-1 activity. FTC-TFV with an HIV-1 integrase strand transfer inhibitor (INSTI) (elvitegravir or raltegravir) showed the strongest synergy. Anti-HIV-1 synergy suggests enhancement of individual anti-HIV-1 activities within cells that may contribute to potent treatment efficacy and open new areas of research into interactions between reverse transcriptase (RT) and integrase inhibitors. PMID:25092710

Kulkarni, Rima; Hluhanich, Rebecca; McColl, Damian M; Miller, Michael D; White, Kirsten L

2014-10-01

275

Post Genome-Wide Association Studies of Novel Genes Associated with Type 2 Diabetes Show Gene-Gene Interaction and High Predictive Value  

PubMed Central

Background Recently, several Genome Wide Association (GWA) studies in populations of European descent have identified and validated novel single nucleotide polymorphisms (SNPs), highly associated with type 2 diabetes (T2D). Our aims were to validate these markers in other European and non-European populations, then to assess their combined effect in a large French study comparing T2D and normal glucose tolerant (NGT) individuals. Methodology/Principal Findings In the same French population analyzed in our previous GWA study (3,295 T2D and 3,595 NGT), strong associations with T2D were found for CDKAL1 (ORrs7756992?=?1.30[1.19–1.42], P?=?2.3×10?9), CDKN2A/2B (ORrs10811661?=?0.74[0.66–0.82], P?=?3.5×10?8) and more modestly for IGFBP2 (ORrs1470579?=?1.17[1.07–1.27], P?=?0.0003) SNPs. These results were replicated in both Israeli Ashkenazi (577 T2D and 552 NGT) and Austrian (504 T2D and 753 NGT) populations (except for CDKAL1) but not in the Moroccan population (521 T2D and 423 NGT). In the overall group of French subjects (4,232 T2D and 4,595 NGT), IGFBP2 and CXCR4 synergistically interacted with (LOC38776, SLC30A8, HHEX) and (NGN3, CDKN2A/2B), respectively, encoding for proteins presumably regulating pancreatic endocrine cell development and function. The T2D risk increased strongly when risk alleles, including the previously discovered T2D-associated TCF7L2 rs7903146 SNP, were combined (8.68-fold for the 14% of French individuals carrying 18 to 30 risk alleles with an allelic OR of 1.24). With an area under the ROC curve of 0.86, only 15 novel loci were necessary to discriminate French individuals susceptible to develop T2D. Conclusions/Significance In addition to TCF7L2, SLC30A8 and HHEX, initially identified by the French GWA scan, CDKAL1, IGFBP2 and CDKN2A/2B strongly associate with T2D in French individuals, and mostly in populations of Central European descent but not in Moroccan subjects. Genes expressed in the pancreas interact together and their combined effect dramatically increases the risk for T2D, opening avenues for the development of genetic prediction tests. PMID:18461161

Cauchi, Stephane; Meyre, David; Durand, Emmanuelle; Proenca, Christine; Marre, Michel; Hadjadj, Samy; Choquet, Helene; De Graeve, Franck; Gaget, Stefan; Allegaert, Frederic; Delplanque, Jerome; Permutt, Marshall Alan; Wasson, Jon; Blech, Ilana; Charpentier, Guillaume; Balkau, Beverley; Vergnaud, Anne-Claire; Czernichow, Sebastien; Patsch, Wolfgang; Chikri, Mohamed; Glaser, Benjamin; Sladek, Robert; Froguel, Philippe

2008-01-01

276

The high heritability of educational achievement reflects many genetically influenced traits, not just intelligence  

PubMed Central

Because educational achievement at the end of compulsory schooling represents a major tipping point in life, understanding its causes and correlates is important for individual children, their families, and society. Here we identify the general ingredients of educational achievement using a multivariate design that goes beyond intelligence to consider a wide range of predictors, such as self-efficacy, personality, and behavior problems, to assess their independent and joint contributions to educational achievement. We use a genetically sensitive design to address the question of why educational achievement is so highly heritable. We focus on the results of a United Kingdom-wide examination, the General Certificate of Secondary Education (GCSE), which is administered at the end of compulsory education at age 16. GCSE scores were obtained for 13,306 twins at age 16, whom we also assessed contemporaneously on 83 scales that were condensed to nine broad psychological domains, including intelligence, self-efficacy, personality, well-being, and behavior problems. The mean of GCSE core subjects (English, mathematics, science) is more heritable (62%) than the nine predictor domains (35–58%). Each of the domains correlates significantly with GCSE results, and these correlations are largely mediated genetically. The main finding is that, although intelligence accounts for more of the heritability of GCSE than any other single domain, the other domains collectively account for about as much GCSE heritability as intelligence. Together with intelligence, these domains account for 75% of the heritability of GCSE. We conclude that the high heritability of educational achievement reflects many genetically influenced traits, not just intelligence. PMID:25288728

Krapohl, Eva; Rimfeld, Kaili; Shakeshaft, Nicholas G.; Trzaskowski, Maciej; McMillan, Andrew; Pingault, Jean-Baptiste; Asbury, Kathryn; Harlaar, Nicole; Kovas, Yulia; Dale, Philip S.; Plomin, Robert

2014-01-01

277

The high heritability of educational achievement reflects many genetically influenced traits, not just intelligence.  

PubMed

Because educational achievement at the end of compulsory schooling represents a major tipping point in life, understanding its causes and correlates is important for individual children, their families, and society. Here we identify the general ingredients of educational achievement using a multivariate design that goes beyond intelligence to consider a wide range of predictors, such as self-efficacy, personality, and behavior problems, to assess their independent and joint contributions to educational achievement. We use a genetically sensitive design to address the question of why educational achievement is so highly heritable. We focus on the results of a United Kingdom-wide examination, the General Certificate of Secondary Education (GCSE), which is administered at the end of compulsory education at age 16. GCSE scores were obtained for 13,306 twins at age 16, whom we also assessed contemporaneously on 83 scales that were condensed to nine broad psychological domains, including intelligence, self-efficacy, personality, well-being, and behavior problems. The mean of GCSE core subjects (English, mathematics, science) is more heritable (62%) than the nine predictor domains (35-58%). Each of the domains correlates significantly with GCSE results, and these correlations are largely mediated genetically. The main finding is that, although intelligence accounts for more of the heritability of GCSE than any other single domain, the other domains collectively account for about as much GCSE heritability as intelligence. Together with intelligence, these domains account for 75% of the heritability of GCSE. We conclude that the high heritability of educational achievement reflects many genetically influenced traits, not just intelligence. PMID:25288728

Krapohl, Eva; Rimfeld, Kaili; Shakeshaft, Nicholas G; Trzaskowski, Maciej; McMillan, Andrew; Pingault, Jean-Baptiste; Asbury, Kathryn; Harlaar, Nicole; Kovas, Yulia; Dale, Philip S; Plomin, Robert

2014-10-21

278

BORDERLINE PERSONALITY TRAITS AND SUBSTANCE USE: GENETIC FACTORS UNDERLIE THE ASSOCIATION WITH SMOKING AND EVER USE OF CANNABIS, BUT NOT WITH HIGH ALCOHOL CONSUMPTION  

PubMed Central

Borderline personality disorder (BPD) and substance use disorders often co-occur. Both disorders are heritable and family studies showed that there are familial factors that increase the risk for BPD as well as substance use/abuse. This is the first study that investigates whether the association of borderline personality traits (BPT) with substance use reflects an underlying genetic vulnerability or nongenetic familial influences. To this end we analyzed data of 5,638 Dutch and Belgian twins aged between 21–50 years from 3,567 families. Significant associations between BPT and high alcohol consumption (r = .192), regular smoking (r = .299), and ever use of cannabis (r = .254) were found. Bivariate genetic analyses showed that the associations of BPT and substance use had different etiologies. For regular smoking and for ever use of cannabis, the correlation with BPT was explained by common genetic factors. Interestingly, for high alcohol consumption and BPT the association was explained by unique environmental factors that influence both traits rather than common genetic factors. PMID:23281672

Distel, Marijn A.; Trull, Tim J.; de Moor, Marleen M. H.; Vink, Jacqueline M.; Geels, Lot M.; van Beek, Jenny H. D. A.; Bartels, Meike; Willemsen, Gonneke; Thiery, Evert; Derom, Catherine A.; Neale, Michael C.; Boomsma, Dorret I.

2013-01-01

279

Expression of genes controlling fat deposition in two genetically diverse beef cattle breeds fed high or low silage diets  

PubMed Central

Background Both genetic background and finishing system can alter fat deposition, thus indicating their influence on adipogenic and lipogenic factors. However, the molecular mechanisms underlying fat deposition and fatty acid composition in beef cattle are not fully understood. This study aimed to assess the effect of breed and dietary silage level on the expression patterns of key genes controlling lipid metabolism in subcutaneous adipose tissue (SAT) and longissimus lumborum (LL) muscle of cattle. To that purpose, forty bulls from two genetically diverse Portuguese bovine breeds with distinct maturity rates, Alentejana and Barrosã, were selected and fed either low (30% maize silage/70% concentrate) or high silage (70% maize silage/30% concentrate) diets. Results The results suggested that enhanced deposition of fatty acids in the SAT from Barrosã bulls, when compared to Alentejana, could be due to higher expression levels of lipogenesis (SCD and LPL) and ?-oxidation (CRAT) related genes. Our results also indicated that SREBF1 expression in the SAT is increased by feeding the low silage diet. Together, these results point out to a higher lipid turnover in the SAT of Barrosã bulls when compared to Alentejana. In turn, lipid deposition in the LL muscle is related to the expression of adipogenic (PPARG and FABP4) and lipogenic (ACACA and SCD) genes. The positive correlation between ACACA expression levels and total lipids, as well trans fatty acids, points to ACACA as a major player in intramuscular deposition in ruminants. Moreover, results reinforce the role of FABP4 in intramuscular fat development and the SAT as the major site for lipid metabolism in ruminants. Conclusions Overall, the results showed that SAT and LL muscle fatty acid composition are mostly dependent on the genetic background. In addition, dietary silage level impacted on muscle lipid metabolism to a greater extent than on that of SAT, as evaluated by gene expression levels of adipogenic and lipogenic factors. Moreover, the response to diet composition evaluated through mRNA levels and fatty acid composition showed interesting differences between Alentejana and Barrosã bulls. These findings provide evidence that the genetic background should be taken into account while devising diet-based strategies to manipulate fatty acid composition of beef cattle tissues. PMID:23767408

2013-01-01

280

Obesity in show cats.  

PubMed

Obesity is an important disease with a high prevalence in cats. Because obesity is related to several other diseases, it is important to identify the population at risk. Several risk factors for obesity have been described in the literature. A higher incidence of obesity in certain cat breeds has been suggested. The aim of this study was to determine whether obesity occurs more often in certain breeds. The second aim was to relate the increased prevalence of obesity in certain breeds to the official standards of that breed. To this end, 268 cats of 22 different breeds investigated by determining their body condition score (BCS) on a nine-point scale by inspection and palpation, at two different cat shows. Overall, 45.5% of the show cats had a BCS > 5, and 4.5% of the show cats had a BCS > 7. There were significant differences between breeds, which could be related to the breed standards. Most overweight and obese cats were in the neutered group. It warrants firm discussions with breeders and cat show judges to come to different interpretations of the standards in order to prevent overweight conditions in certain breeds from being the standard of beauty. Neutering predisposes for obesity and requires early nutritional intervention to prevent obese conditions. PMID:24612018

Corbee, R J

2014-12-01

281

Blacktip reef sharks, Carcharhinus melanopterus, have high genetic structure and varying demographic histories in their Indo-Pacific range.  

PubMed

For free-swimming marine species like sharks, only population genetics and demographic history analyses can be used to assess population health/status as baseline population numbers are usually unknown. We investigated the population genetics of blacktip reef sharks, Carcharhinus melanopterus; one of the most abundant reef-associated sharks and the apex predator of many shallow water reefs of the Indian and Pacific Oceans. Our sampling includes 4 widely separated locations in the Indo-Pacific and 11 islands in French Polynesia with different levels of coastal development. Four-teen microsatellite loci were analysed for samples from all locations and two mitochondrial DNA fragments, the control region and cytochrome b, were examined for 10 locations. For microsatellites, genetic diversity is higher for the locations in the large open systems of the Red Sea and Australia than for the fragmented habitat of the smaller islands of French Polynesia. Strong significant structure was found for distant locations with FST values as high as ~0.3, and a smaller but still significant structure is found within French Polynesia. Both mitochondrial genes show only a few mutations across the sequences with a dominant shared haplotype in French Polynesia and New Caledonia suggesting a common lineage different to that of East Australia. Demographic history analyses indicate population expansions in the Red Sea and Australia that may coincide with sea level changes after climatic events. Expansions and flat signals are indicated for French Polynesia as well as a significant recent bottleneck for Moorea, the most human-impacted lagoon of the locations in French Polynesia. PMID:25251515

Vignaud, Thomas M; Mourier, Johann; Maynard, Jeffrey A; Leblois, Raphael; Spaet, Julia; Clua, Eric; Neglia, Valentina; Planes, Serge

2014-11-01

282

Mutation Scanning in a Single and a Stacked Genetically Modified (GM) Event by Real-Time PCR and High Resolution Melting (HRM) Analysis.  

PubMed

Genetic mutations must be avoided during the production and use of seeds. In the European Union (EU), Directive 2001/18/EC requires any DNA construct introduced via transformation to be stable. Establishing genetic stability is critical for the approval of genetically modified organisms (GMOs). In this study, genetic stability of two GMOs was examined using high resolution melting (HRM) analysis and real-time polymerase chain reaction (PCR) employing Scorpion primers for amplification. The genetic variability of the transgenic insert and that of the flanking regions in a single oilseed rape variety (GT73) and a stacked maize (MON88017 × MON810) was studied. The GT73 and the 5' region of MON810 showed no instabilities in the examined regions. However; two out of 100 analyzed samples carried a heterozygous point mutation in the 3' region of MON810 in the stacked variety. These results were verified by direct sequencing of the amplified PCR products as well as by sequencing of cloned PCR fragments. The occurrence of the mutation suggests that the 5' region is more suitable than the 3' region for the quantification of MON810. The identification of the single nucleotide polymorphism (SNP) in a stacked event is in contrast to the results of earlier studies of the same MON810 region in a single event where no DNA polymorphism was found. PMID:25365178

Ali, Sina-Elisabeth Ben; Madi, Zita Erika; Hochegger, Rupert; Quist, David; Prewein, Bernhard; Haslberger, Alexander G; Brandes, Christian

2014-01-01

283

Direct 2-Arm Comparison Shows Benefit of High-Dose-Rate Brachytherapy Boost vs External Beam Radiation Therapy Alone for Prostate Cancer  

SciTech Connect

Purpose: To evaluate the outcomes of patients treated for intermediate- and high-risk prostate cancer with a single schedule of either external beam radiation therapy (EBRT) and high-dose-rate brachytherapy (HDRB) boost or EBRT alone. Methods and Materials: From 2001-2006, 344 patients received EBRT with HDRB boost for definitive treatment of intermediate- or high-risk prostate cancer. The prescribed EBRT dose was 46 Gy in 23 fractions, with a HDR boost of 19.5 Gy in 3 fractions. This cohort was compared to a contemporaneously treated cohort who received EBRT to 74 Gy in 37 fractions, using a matched pair analysis. Three-dimensional conformal EBRT was used. Matching was performed using a propensity score matching technique. High-risk patients constituted 41% of the matched cohorts. Five-year clinical and biochemical outcomes were analyzed. Results: Initial significant differences in prognostic indicators between the unmatched treatment cohorts were rendered negligible after matching, providing a total of 688 patients. Median biochemical follow-up was 60.5 months. The 5-year freedom from biochemical failure was 79.8% (95% confidence interval [CI], 74.3%-85.0%) and 70.9% (95% CI, 65.4%-76.0%) for the HDRB and EBRT groups, respectively, equating to a hazard ratio of 0.59 (95% CI, 0.43-0.81, P=.0011). Interaction analyses showed no alteration in HDR efficacy when planned androgen deprivation therapy was administered (P=.95), but a strong trend toward reduced efficacy was shown compared to EBRT in high-risk cases (P=.06). Rates of grade 3 urethral stricture were 0.3% (95% CI, 0%-0.9%) and 11.8% (95% CI, 8.1%-16.5%) for EBRT and HDRB, respectively (P<.0001). No differences in clinical outcomes were observed. Conclusions: This comparison of 2 individual contemporaneously treated HDRB and EBRT approaches showed improved freedom from biochemical progression with the HDR approach. The benefit was more pronounced in intermediate- risk patients but needs to be weighed against an increased risk of urethral toxicity.

Khor, Richard [Division of Radiation Oncology and Cancer Imaging, Peter MacCallum Cancer Centre, and University of Melbourne, Melbourne (Australia)] [Division of Radiation Oncology and Cancer Imaging, Peter MacCallum Cancer Centre, and University of Melbourne, Melbourne (Australia); Duchesne, Gillian [Division of Radiation Oncology and Cancer Imaging, Peter MacCallum Cancer Centre, and University of Melbourne, Melbourne (Australia) [Division of Radiation Oncology and Cancer Imaging, Peter MacCallum Cancer Centre, and University of Melbourne, Melbourne (Australia); Monash University, Melbourne (Australia); Tai, Keen-Hun; Foroudi, Farshad; Chander, Sarat; Van Dyk, Sylvia; Garth, Margaret [Division of Radiation Oncology and Cancer Imaging, Peter MacCallum Cancer Centre, and University of Melbourne, Melbourne (Australia)] [Division of Radiation Oncology and Cancer Imaging, Peter MacCallum Cancer Centre, and University of Melbourne, Melbourne (Australia); Williams, Scott, E-mail: Scott.Williams@petermac.org [Division of Radiation Oncology and Cancer Imaging, Peter MacCallum Cancer Centre, and University of Melbourne, Melbourne (Australia)] [Division of Radiation Oncology and Cancer Imaging, Peter MacCallum Cancer Centre, and University of Melbourne, Melbourne (Australia)

2013-03-01

284

A high-density simple sequence repeat-based genetic linkage map of switchgrass.  

PubMed

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. PMID:22413090

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

2012-03-01

285

Genetic Variants in EPAS1 Contribute to Adaptation to High-Altitude Hypoxia in Sherpas  

PubMed Central

Sherpas comprise a population of Tibetan ancestry in the Himalayan region that is renowned for its mountaineering prowess. The very small amount of available genetic information for Sherpas is insufficient to explain their physiological ability to adapt to high-altitude hypoxia. Recent genetic evidence has indicated that natural selection on the endothelial PAS domain protein 1 (EPAS1) gene was occurred in the Tibetan population during their occupation in the Tibetan Plateau for millennia. Tibetan-specific variations in EPAS1 may regulate the physiological responses to high-altitude hypoxia via a hypoxia-inducible transcription factor pathway. We examined three significant tag single-nucleotide polymorphisms (SNPs, rs13419896, rs4953354, and rs4953388) in the EPAS1 gene in Sherpas, and compared these variants with Tibetan highlanders on the Tibetan Plateau as well as with non-Sherpa lowlanders. We found that Sherpas and Tibetans on the Tibetan Plateau exhibit similar patterns in three EPAS1 significant tag SNPs, but these patterns are the reverse of those in non-Sherpa lowlanders. The three SNPs were in strong linkage in Sherpas, but in weak linkage in non-Sherpas. Importantly, the haplotype structured by the Sherpa-dominant alleles was present in Sherpas but rarely present in non-Sherpas. Surprisingly, the average level of serum erythropoietin in Sherpas at 3440 m was equal to that in non-Sherpas at 1300 m, indicating a resistant response of erythropoietin to high-altitude hypoxia in Sherpas. These observations strongly suggest that EPAS1 is under selection for adaptation to the high-altitude life of Tibetan populations, including Sherpas. Understanding of the mechanism of hypoxia tolerance in Tibetans is expected to provide lights to the therapeutic solutions of some hypoxia-related human diseases, such as cardiovascular disease and cancer. PMID:23227185

Basnyat, Buddha; Ito, Michiko; Kobayashi, Nobumitsu; Katsuyama, Yoshihiko; Kubo, Keishi; Ota, Masao

2012-01-01

286

Foraging segregation and genetic divergence between geographically proximate colonies of a highly mobile seabird  

USGS Publications Warehouse

Foraging segregation may play an important role in the maintenance of animal diversity, and is a proposed mechanism for promoting genetic divergence within seabird species. However, little information exists regarding its presence among seabird populations. 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 mitochondrial Cytochrome b gene and carbon, nitrogen and hydrogen isotope values (?? 13C, ?? 15N and ??D, respectively) of feathers. Genetic analyses revealed strong differentiation between colonies on Hawaii and Kauai, with ?? ST = 0. 50 (p < 0. 0001). Coalescent-based analyses gave estimates of <1 migration event per 1,000 generations. Hatch-year birds from Kauai had significantly lower ?? 13C and ?? 15N values than those from Hawaii. This is consistent with Kauai birds provisioning chicks with prey derived from near or north of the Hawaiian Islands, and Hawaii birds provisioning young with prey from regions of the equatorial Pacific characterized by elevated ?? 15N values at the food web base. ?? 15N values of Kauai and Hawaii adults differed significantly, indicating additional foraging segregation during molt. Feather ??D varied from -69 to 53???. This variation cannot be related solely to an isotopically homogeneous ocean water source or evaporative water loss. Instead, we propose the involvement of salt gland excretion. Our data demonstrate the presence of foraging segregation between proximately nesting seabird populations, despite high species mobility. This ecological diversity may facilitate population coexistence, and its preservation should be a focus of conservation strategies. ?? 2011 Springer-Verlag (outside the USA).

Wiley, A.E.; Welch, A.J.; Ostrom, P.H.; James, H.F.; Stricker, C.A.; Fleischer, R.C.; Gandhi, H.; Adams, J.; Ainley, D.G.; Duvall, F.; Holmes, N.; Hu, D.; Judge, S.; Penniman, J.; Swindle, K.A.

2012-01-01

287

Foraging segregation and genetic divergence between geographically proximate colonies of a highly mobile seabird.  

PubMed

Foraging segregation may play an important role in the maintenance of animal diversity, and is a proposed mechanism for promoting genetic divergence within seabird species. However, little information exists regarding its presence among seabird populations. 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 mitochondrial Cytochrome b gene and carbon, nitrogen and hydrogen isotope values (?(13)C, ?(15)N and ?D, respectively) of feathers. Genetic analyses revealed strong differentiation between colonies on Hawaii and Kauai, with ?(ST) = 0.50 (p < 0.0001). Coalescent-based analyses gave estimates of <1 migration event per 1,000 generations. Hatch-year birds from Kauai had significantly lower ?(13)C and ?(15)N values than those from Hawaii. This is consistent with Kauai birds provisioning chicks with prey derived from near or north of the Hawaiian Islands, and Hawaii birds provisioning young with prey from regions of the equatorial Pacific characterized by elevated ?(15)N values at the food web base. ?(15)N values of Kauai and Hawaii adults differed significantly, indicating additional foraging segregation during molt. Feather ?D varied from -69 to 53‰. This variation cannot be related solely to an isotopically homogeneous ocean water source or evaporative water loss. Instead, we propose the involvement of salt gland excretion. Our data demonstrate the presence of foraging segregation between proximately nesting seabird populations, despite high species mobility. This ecological diversity may facilitate population coexistence, and its preservation should be a focus of conservation strategies. PMID:21837410

Wiley, Anne E; Welch, Andreanna J; Ostrom, Peggy H; James, Helen F; Stricker, Craig A; Fleischer, Robert C; Gandhi, Hasand; Adams, Josh; Ainley, David G; Duvall, Fern; Holmes, Nick; Hu, Darcy; Judge, Seth; Penniman, Jay; Swindle, Keith A

2012-01-01

288

Application of somatic embryogenesis in high-value clonal forestry: Deployment, genetic control, and stability of cryopreserved clones  

Microsoft Academic Search

Summary  The most important advantage of cloning conifers by somatic embryogenesis (SE) is that the embryogenic tissue can be cryopreserved\\u000a without changing its genetic make-up and without loss of juvenility. This offers an opportunity to develop high-value clonal\\u000a varieties by defrosting and repropagating cryopreserved clones after genetic testing has shown which clones are the best performers.\\u000a In the current absence of

Y. S. Park; J. D. Barrett; J. M. Bonga

1998-01-01

289

Chemometric Analysis of Chromatographic Fingerprints Shows Potential of Cyclopia maculata (Andrews) Kies for Production of Standardized Extracts with High Xanthone Content.  

PubMed

Cyclopia species are used for the production of honeybush tea and food ingredient extracts associated with many health benefits. A species-specific high-performance liquid chromatography (HPLC) method for Cyclopia maculata, developed and validated, allowed quantification of the major compounds in extracts from "unfermented" and fermented C. maculata. Two xanthones were tentatively identified for the first time in a Cyclopia species, whereas an additional four compounds were tentatively identified for the first time in C. maculata. "Fermentation" (oxidation) decreased the content of all compounds, with the exception of vicenin-2. Similarity analysis of the chromatographic fingerprints of unfermented C. maculata aqueous extracts showed extremely low variation (r ? 0.97) between samples. Some differences between wild-harvested and cultivated seedling plants were, however, demonstrated using principal component analysis. Quantitative data of selected compounds confirmed the low level of variation, making this Cyclopia species ideal for the production of standardized food ingredient extracts. PMID:25329526

Schulze, Alexandra E; de Beer, Dalene; de Villiers, André; Manley, Marena; Joubert, Elizabeth

2014-10-29

290

Males with high genetic similarity to females sire more offspring in sperm competition in Peron's tree frog Litoria peronii  

PubMed Central

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

2008-01-01

291

High levels of genetic diversity in Nosema ceranae within Apis mellifera colonies.  

PubMed

Nosema ceranae is a widespread honeybee parasite, considered to be one of the pathogens involved in the colony losses phenomenon. To date, little is known about its intraspecific genetic variability. The few studies on N. ceranae variation have focused on the subunits of ribosomal DNA, which are not ideal for this purpose and have limited resolution. Here we characterized three single copy loci (Actin, Hsp70 and RPB1) in three N. ceranae isolates from Hungary and Hawaii. Our results provide evidence of unexpectedly high levels of intraspecific polymorphism, the coexistence of a wide variety of haplotypes within each bee colony, and the occurrence of genetic recombination in RPB1. Most haplotypes are not shared across isolates and derive from a few frequent haplotypes by a reduced number of singletons (mutations that appear usually just once in the sample), which suggest that they have a fairly recent origin. Overall, our data indicate that this pathogen has experienced a recent population expansion. The presence of multiple haplotypes within individual isolates could be explained by the existence of different strains of N. ceranae infecting honeybee colonies in the field which complicates, and must not be overlooked, further analysis of host-parasite interactions. PMID:24238365

Gómez-Moracho, Tamara; Maside, Xulio; Martín-Hernández, Raquel; Higes, Mariano; Bartolomé, Carolina

2014-04-01

292

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

293

Single-molecule imaging and fluorescence lifetime imaging microscopy show different structures for high- and low-affinity epidermal growth factor receptors in A431 cells.  

PubMed

Epidermal growth factor (EGF) receptor (EGFR) modulates mitosis and apoptosis through signaling by its high-affinity (HA) and low-affinity (LA) EGF-binding states. The prevailing model of EGFR activation-derived from x-ray crystallography-involves the transition from tethered ectodomain monomers to extended back-to-back dimers and cannot explain these EGFR affinities or their different functions. Here, we use single-molecule Förster resonant energy transfer analysis in combination with ensemble fluorescence lifetime imaging microscopy to investigate the three-dimensional architecture of HA and LA EGFR-EGF complexes in cells by measuring the inter-EGF distances within discrete EGF pairs and the vertical distance from EGF to the plasma membrane. Our results show that EGFR ectodomains form interfaces resulting in two inter-EGF distances ( approximately 8 nm and < 5.5 nm), different from the back-to-back EGFR ectodomain interface ( approximately 11 nm). Distance measurements from EGF to the plasma membrane show that HA EGFR ectodomains are oriented flat on the membrane, whereas LA ectodomains stand proud from it. Their flat orientation confers on HA EGFR ectodomains the exclusive ability to interact via asymmetric interfaces, head-to-head with respect to the EGF-binding site, whereas LA EGFRs must interact only side-by-side. Our results support a structural model in which asymmetric EGFR head-to-head interfaces may be relevant for HA EGFR oligomerization. PMID:17890389

Webb, Stephen E D; Roberts, Selene K; Needham, Sarah R; Tynan, Christopher J; Rolfe, Daniel J; Winn, Martyn D; Clarke, David T; Barraclough, Roger; Martin-Fernandez, Marisa L

2008-02-01

294

Two promising alkaline ?-glucosidases isolated by functional metagenomics from agricultural soil, including one showing high tolerance towards harsh detergents, oxidants and glucose.  

PubMed

New ?-glucosidase activities were identified by screening metagenomic libraries constructed with DNA isolated from the topsoil of a winter wheat field. Two of the corresponding proteins, displaying an unusual preference for alkaline conditions, were selected for purification by Ni-NTA chromatography. AS-Esc6, a 762-amino-acid enzyme belonging to glycoside hydrolase family 3, proved to be a mesophilic aryl-?-glucosidase with maximal activity around pH 8 and 40 °C. A similar pH optimum was found for AS-Esc10, a 475-amino-acid GH1-family enzyme, but this enzyme remained significantly active across a wider pH range and was also markedly more stable than AS-Esc6 at pH greater than 10. AS-Esc10 was found to degrade cellobiose and diverse aryl glycosides, with an optimal temperature of 60 °C and good stability up to 50 °C. Unlike AS-Esc6, which showed a classically low inhibitory constant for glucose (14 mM), AS-Esc10 showed enhanced activity in the presence of molar concentrations of glucose. AS-Esc10 was highly tolerant to hydrogen peroxide and also to sodium dodecyl sulfate, this being indicative of kinetic stability. This unique combination of properties makes AS-Esc10 a particularly promising candidate whose potential in biotechnological applications is worth exploring further. PMID:24414432

Biver, Sophie; Stroobants, Aurore; Portetelle, Daniel; Vandenbol, Micheline

2014-03-01

295

Solar Light Show  

NSDL National Science Digital Library

Over the last few days, the Earth has been buffeted by a geomagnetic storm caused by a major solar flare. In addition to disruptions in radio, telecommunications, and electric service, the flare may also produce a dramatic light show as it peaks tonight. Weather permitting, the aurora borealis, or northern lights, may be visible as far south as Washington, D.C. The best viewing time will be local midnight. The sun is currently at the peak of its eleven-year solar cycle, spawning flares and "coronal mass ejections" (CME), violent outbursts of gas from the sun's corona that can carry up to 10 billion tons of electrified gas traveling at speeds as high as 2000 km/s. Geomagnetic storms result when solar winds compress the magnetosphere, sometimes interfering with electric power transmission and satellites, but also creating beautiful aurorae, as many stargazers hope will occur tonight.

De Nie, Michael W.

296

Why do satellite imageries show exceptionally high chlorophyll in the Gulf of Mannar and the Palk Bay during the Norteast Monsoon?  

PubMed

The Gulf of Mannar (GoM) and the Palk Bay (PB) are two least studied marine environments located between India and Sri Lanka. Exceptionally high chlorophyll a concentration in the GoM and the PB during the Northeast Monsoon (November-February) is a consistent feature in satellite imageries, which has been attributed to the intrusion of the Bay of Bengal (BoB) waters. The analyses of the Moderate Resolution Imaging Spectroradiometer (MODIS) and field chlorophyll data collected from 30 locations in the Indian sector of the GoM and the PB in January 2011 showed significant overestimations in the satellite data. This error was much higher in the PB (60-80 %) as compared to the GoM (18-28 %). The multivariate analyses evidenced that the exceptionally high satellite chlorophyll in the PB is contributed largely by turbidity, colored dissolved organic matter (CDOM), and bottom reflectance. The paper cautions that though MODIS is superior in estimating chlorophyll a in optically complex waters, there are still chances of overestimations in regions like the PB. PMID:25142503

Jyothibabu, R; Madhu, N V; Jagadeesan, L; Anjusha, A; Mohan, Arya P; Ullas, N; Sudheesh, K; Karnan, C

2014-11-01

297

First-degree relatives of early-onset gastric cancer patients show a high risk for gastric cancer: phenotype and genotype profile.  

PubMed

First-degree relatives (FDR) of early-onset gastric cancer (EOGC) is presumed to be a population with a distinct molecular and phenotypic profile, regarding the prevalence of gastric premalignant conditions and the association with Helicobacter pylori infection and host proinflammatory gene polymorphisms. A case-control study was conducted with FDR of EOGC patients (n?=?103) and age and gender matched controls (n?=?101; ranging from spouses to neighbors and dyspeptics). Upper endoscopy was performed, Operative Link on Gastritis Assessment (OLGA) system used for staging and H. pylori (cagA and vacA) and host IL1B-511, IL1RN intron2 VNTR and IFNGR1-56 genotyping. Seventy percent of cases showed atrophy, while 19 % presented with high-stage gastritis (OLGA stage III or IV) (p?high-risk OLGA stages and dysplasia that seem to be associated with high virulence H. pylori strains and pro-inflammatory host genotypes, including a possible population-specific risk marker. FDR of EOGC patients may merit specific management through endoscopic and histopathological adequate assessment of gastric mucosa and surveillance. PMID:23887584

Marcos-Pinto, Ricardo; Dinis-Ribeiro, Mário; Carneiro, Fátima; Wen, Xiaogang; Lopes, Carlos; Figueiredo, Céu; Machado, José Carlos; Ferreira, Rui M; Reis, Celso A; Canedo, Paulo; Durães, Cecília; Ferreira, José; Pedroto, Isabel; Areias, Jorge

2013-09-01

298

Impact of virtual learning environment (VLE): A technological approach to genetics teaching on high school students' content knowledge, self-efficacy and career goal aspirations  

NASA Astrophysics Data System (ADS)

This study examines the effect of a technology-based instructional tool 'Geniverse' on the content knowledge gains, Science Self-Efficacy, Technology Self-Efficacy, and Career Goal Aspirations among 283 high school learners. The study was conducted in four urban high schools, two of which have achieved Adequate Yearly Progress (AYP) and two have not. Students in both types of schools were taught genetics either through Geniverse, a virtual learning environment or Dragon genetics, a paper-pencil activity embedded in traditional instructional method. Results indicated that students in all schools increased their knowledge of genetics using either type of instructional approach. Students who were taught using Geniverse demonstrated an advantage for genetics knowledge although the effect was small. These increases were more pronounced in the schools that had been meeting the AYP goal. The other significant effect for Geniverse was that students in the technology-enhanced classrooms increased in science Self-Efficacy while students in the non-technology enhanced classrooms decreased. In addition, students from Non-AYP schools showed an improvement in Science and Technology Self-Efficacy; however the effects were small. The implications of these results for the future use of technology-enriched classrooms were discussed. Keywords: Technology-based instruction, Self-Efficacy, career goals and Adequate Yearly Progress (AYP).

Kandi, Kamala M.

299

Genetic structuring in three closely related circumpolar plant species: AFLP versus microsatellite markers and high-arctic versus arctic-alpine distributions.  

PubMed

Genetic structuring in response to the glacial cycles has been investigated for many plant species, but exclusively high-arctic ones have not been studied. Such extremely cold-adapted species have probably experienced range reductions under the present climate. Here we compare three predominantly selfing species of Draba with different distributions and hardiness (D. subcapitata, high-arctic; D. nivalis, arctic to arctic-alpine; D. fladnizensis, arctic-alpine) for genetic structuring on the basis of two different types of molecular markers (10 microsatellite loci and 160 amplified fragment length polymorphisms (AFLPs)). The degree of genetic structuring within these species is of particular interest because it has been shown that they contain many cryptic biological species. The high-arctic D. subcapitata had less phylogeographic structure, less diversity and fewer private alleles than the other two species, suggesting that long-distance dispersal may occur more frequently in the high arctic, that hardy plants may have higher probability for establishment after dispersal under high-arctic conditions and that high-arctic species may have experienced a bottleneck during the present interglacial. In contrast, D. fladnizensis and D. nivalis showed distinct phylogeographic structure and more diversity, suggesting separate long-term refugia in Eurasia and North America/Beringia. The AFLP markers revealed more phylogeographic structuring than the microsatellites, possibly because of the higher number of loci surveyed and/or because structure at very large geographic scales is blurred by high mutation rate leading to homoplasy at microsatellite loci. The number of genetic groups detected was in any case insignificant compared with the numerous cryptic biological species known within these species, supporting rapid development of sterility barriers. PMID:19066622

Skrede, I; Borgen, L; Brochmann, C

2009-03-01

300

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

E-print Network

Development of a Large SNP Genotyping Array and Generation of High-Density Genetic Maps in Tomato developed an array for tomato with 8,784 Single Nucleotide Polymorphisms (SNPs) mainly discovered based and could be scored in tomato germplasm. The array was used to generate high-density linkage maps for three

Douches, David S.

301

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

302

St. Jude-led study finds new genetic defects in high-risk childhood leukemia subtypes  

Cancer.gov

Research led by St. Jude Children’s Research Hospital scientists has identified a possible lead in treatment of two childhood leukemia subtypes known for their dramatic loss of chromosomes and poor treatment outcomes. The findings also provide the first evidence of the genetic basis for this high-risk leukemia, which is known as hypodiploid acute lymphoblastic leukemia (ALL). St. Jude researchers led the study in collaboration with investigators from the Children’s Oncology Group, the world’s largest organization devoted exclusively to childhood and adolescent cancer research. The study's whole genome sequencing was done in conjunction with the St. Jude Children’s Research Hospital – Washington University Pediatric Cancer Genome Project.

303

A high-performance genetic algorithm: using traveling salesman problem as a case.  

PubMed

This paper presents a simple but efficient algorithm for reducing the computation time of genetic algorithm (GA) and its variants. The proposed algorithm is motivated by the observation that genes common to all the individuals of a GA have a high probability of surviving the evolution and ending up being part of the final solution; as such, they can be saved away to eliminate the redundant computations at the later generations of a GA. To evaluate the performance of the proposed algorithm, we use it not only to solve the traveling salesman problem but also to provide an extensive analysis on the impact it may have on the quality of the end result. Our experimental results indicate that the proposed algorithm can significantly reduce the computation time of GA and GA-based algorithms while limiting the degradation of the quality of the end result to a very small percentage compared to traditional GA. PMID:24892038

Tsai, Chun-Wei; Tseng, Shih-Pang; Chiang, Ming-Chao; Yang, Chu-Sing; Hong, Tzung-Pei

2014-01-01

304

Plasmid Metagenome Reveals High Levels of Antibiotic Resistance Genes and Mobile Genetic Elements in Activated Sludge  

PubMed Central

The overuse or misuse of antibiotics has accelerated antibiotic resistance, creating a major challenge for the public health in the world. Sewage treatment plants (STPs) are considered as important reservoirs for antibiotic resistance genes (ARGs) and activated sludge characterized with high microbial density and diversity facilitates ARG horizontal gene transfer (HGT) via mobile genetic elements (MGEs). However, little is known regarding the pool of ARGs and MGEs in sludge microbiome. In this study, the transposon aided capture (TRACA) system was employed to isolate novel plasmids from activated sludge of one STP in Hong Kong, China. We also used Illumina Hiseq 2000 high-throughput sequencing and metagenomics analysis to investigate the plasmid metagenome. Two novel plasmids were acquired from the sludge microbiome by using TRACA system and one novel plasmid was identified through metagenomics analysis. Our results revealed high levels of various ARGs as well as MGEs for HGT, including integrons, transposons and plasmids. The application of the TRACA system to isolate novel plasmids from the environmental metagenome, coupled with subsequent high-throughput sequencing and metagenomic analysis, highlighted the prevalence of ARGs and MGEs in microbial community of STPs. PMID:22016806

Zhang, Tong; Zhang, Xu-Xiang; Ye, Lin

2011-01-01

305

Disclosing the Genetic Structure of Brazil through Analysis of Male Lineages with Highly Discriminating Haplotypes  

PubMed Central

In a large variety of genetic studies, probabilistic inferences are made based on information available in population databases. The accuracy of the estimates based on population samples are highly dependent on the number of chromosomes being analyzed as well as the correct representation of the reference population. For frequency calculations the size of a database is especially critical for haploid markers, and for countries with complex admixture histories it is important to assess possible substructure effects that can influence the coverage of the database. Aiming to establish a representative Brazilian population database for haplotypes based on 23 Y chromosome STRs, more than 2,500 Y chromosomes belonging to Brazilian, European and African populations were analyzed. No matter the differences in the colonization history of the five geopolitical regions that currently exist in Brazil, for the Y chromosome haplotypes of the 23 studied Y-STRs, a lack of genetic heterogeneity was found, together with a predominance of European male lineages in all regions of the country. Therefore, if we do not consider the diverse Native American or Afro-descendent isolates, which are spread through the country, a single Y chromosome haplotype frequency database will adequately represent the urban populations in Brazil. In comparison to the most commonly studied group of 17 Y-STRs, the 23 markers included in this work allowed a high discrimination capacity between haplotypes from non-related individuals within a population and also increased the capacity to discriminate between paternal relatives. Nevertheless, the expected haplotype mutation rate is still not enough to distinguish the Y chromosome profiles of paternally related individuals. Indeed, even for rapidly mutating Y-STRs, a very large number of markers will be necessary to differentiate male lineages from paternal relatives. PMID:22808085

Palha, Teresinha; Gusmão, Leonor; Ribeiro-Rodrigues, Elzemar; Guerreiro, João Farias; Ribeiro-dos-Santos, Ândrea; Santos, Sidney

2012-01-01

306

Pathogenic Serum Amyloid A 1.1 Shows a Long Oligomer-rich Fibrillation Lag Phase Contrary to the Highly Amyloidogenic Non-pathogenic SAA2.2*  

PubMed Central

Serum amyloid A (SAA) is best known for being the main component of amyloid in the inflammation-related disease amyloid A (AA) amyloidosis. Despite the high sequence identity among different SAA isoforms, not all SAA proteins are pathogenic. In most mouse strains, the AA deposits mostly consist of SAA1.1. Conversely, the CE/J type mouse expresses a single non-pathogenic SAA2.2 protein that is 94% identical to SAA1.1. Here we show that SAA1.1 and SAA2.2 differ in their quaternary structure, fibrillation kinetics, prefibrillar oligomers, and fibril morphology. At 37 °C and inflammation-related SAA concentrations, SAA1.1 exhibits an oligomer-rich fibrillation lag phase of a few days, whereas SAA2.2 shows virtually no lag phase and forms small fibrils within a few hours. Deep UV resonance Raman, far UV-circular dichroism, atomic force microscopy, and fibrillation cross-seeding experiments suggest that SAA1.1 and SAA2.2 fibrils possess different morphology. Both the long-lived oligomers of pathogenic SAA1.1 and the fleeting prefibrillar oligomers of non-pathogenic SAA2.2, but not their respective amyloid fibrils, permeabilized synthetic bilayer membranes in vitro. This study represents the first comprehensive comparison between the biophysical properties of SAA isoforms with distinct pathogenicities, and the results suggest that structural and kinetic differences in the oligomerization-fibrillation of SAA1.1 and SAA2.2, more than their intrinsic amyloidogenicity, may contribute to their diverse pathogenicity. PMID:23223242

Srinivasan, Saipraveen; Patke, Sanket; Wang, Yun; Ye, Zhuqiu; Litt, Jeffrey; Srivastava, Sunit K.; Lopez, Maria M.; Kurouski, Dmitry; Lednev, Igor K.; Kane, Ravi S.; Colón, Wilfredo

2013-01-01

307

High-throughput DNA analysis shows the importance of methylation in the control of immune inflammatory gene transcription in chronic periodontitis  

PubMed Central

Background Chronic periodontitis represents a complex disease that is hard to control and is not completely understood. Evidence from past studies suggests that there is a key role for DNA methylation in the pathogenesis of periodontitis. However, all reports have applied technologies that investigate genes in a low throughput. In order to advance in the knowledge of the disease, we analyzed DNA methylation variations associated with gene transcription using a high-throughput assay. Infinium® HumanMethylation450 (Illumina) was performed on gingival samples from 12 periodontitis cases and 11 age-matched healthy individuals. Methylation data of 1,284 immune-related genes and 1,038 cell cycle-related genes from Gene Ontology (GO) and 575 genes from a dataset of stably expressed genes (genes with consistent expression in different physiological states and tissues) were extracted from a microarray dataset and analyzed using bioinformatics tools. DNA methylation variations ranging from ?2,000 to +2,000 bp from the transcription start site (TSS) were analyzed, and the results were tested against a differential expression microarray dataset between healthy and periodontitis gingival tissues. Differences were evaluated using tests from the R Statistical Project. Results The comparison of probes between periodontitis and normal gingival tissues showed that the mean methylation scores and the frequency of methylated probes were significantly lower in genes related to the immune process. In the immune group, these parameters were negatively correlated with gene expression (Mann-Whitney test, p?show that variations in DNA methylation between healthy and periodontitis cases are higher in genes related to the immune-inflammatory process. Thus, DNA methylation must be modulating chromatin regions and, consequently, modulating the mRNA transcription of immune-inflammatory genes related with periodontitis, impacting the prognosis of disease. PMID:25147584

2014-01-01

308

Putative osmosensor - OsHK3b - a histidine kinase protein from rice shows high structural conservation with its ortholog AtHK1 from Arabidopsis  

PubMed Central

Prokaryotes and eukaryotes respond to various environmental stimuli using the two-component system (TCS). Essentially, it consists of membrane-bound histidine kinase (HK) which senses the stimuli and further transfers the signal to the response regulator, which in turn, regulates expression of various target genes. Recently, sequence-based genome wide analysis has been carried out in Arabidopsis and rice to identify all the putative members of TCS family. One of the members of this family i.e. AtHK1, (a putative osmosensor, hybrid-type sensory histidine kinase) is known to interact with AtHPt1 (phosphotransfer proteins) in Arabidopsis. Based on predicted rice interactome network (PRIN), the ortholog of AtHK1 in rice, OsHK3b, was found to be interacting with OsHPt2. The analysis of amino acid sequence of AtHK1 showed the presence of transmitter domain (TD) and receiver domain (RD), while OsHK3b showed presence of three conserved domains namely CHASE (signaling domain), TD, and RD. In order to elaborate on structural details of functional domains of hybrid-type HK and phosphotransfer proteins in both these genera, we have modeled them using homology modeling approach. The structural motifs present in various functional domains of the orthologous proteins were found to be highly conserved. Binding analysis of the RD domain of these sensory proteins in Arabidopsis and rice revealed the role of various residues such as histidine in HPt protein which are essential for their interaction. PMID:23869567

Kushwaha, Hemant Ritturaj; Singla-Pareek, Sneh Lata; Pareek, Ashwani

2013-01-01

309

Post-Doctoral Fellow in Cardiovascular Genetics A research position is available for a highly motivated post-doctoral fellow to join the  

E-print Network

Post-Doctoral Fellow in Cardiovascular Genetics A research position is available for a highly laboratory is interested in molecular and genetic mechanisms of inherited cardiomyopathies and arrhythmias a combination of biochemical, genetic and cell biological approaches. The project is focused on the role of cell

de Leon, Alex R.

310

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. PMID:21811587

Gutierrez, Maria Laura; Munoz-Bellvis, Luis; Abad, Maria del Mar; Bengoechea, Oscar; Gonzalez-Gonzalez, Maria

2011-01-01

311

Genetic structure and systematic relationships within the Ophrys fuciflora aggregate (Orchidaceae: Orchidinae): high diversity in Kent and a wind-induced discontinuity bisecting the Adriatic  

PubMed Central

Background and Aims A recent phylogenetic study based on multiple datasets is used as the framework for a more detailed examination of one of the ten molecularly circumscribed groups identified, the Ophrys fuciflora aggregate. The group is highly morphologically variable, prone to phenotypic convergence, shows low levels of sequence divergence and contains an unusually large proportion of threatened taxa, including the rarest Ophrys species in the UK. The aims of this study were to (a) circumscribe minimum resolvable genetically distinct entities within the O. fuciflora aggregate, and (b) assess the likelihood of gene flow between genetically and geographically distinct entities at the species and population levels. Methods Fifty-five accessions sampled in Europe and Asia Minor from the O. fuciflora aggregate were studied using the AFLP genetic fingerprinting technique to evaluate levels of infraspecific and interspecific genetic variation and to assess genetic relationships between UK populations of O. fuciflora s.s. in Kent and in their continental European and Mediterranean counterparts. Key Results The two genetically and geographically distinct groups recovered, one located in England and central Europe and one in south-eastern Europe, are incongruent with current species delimitation within the aggregate as a whole and also within O. fuciflora s.s. Genetic diversity is higher in Kent than in the rest of western and central Europe. Conclusions Gene flow is more likely to occur between populations in closer geographical proximity than those that are morphologically more similar. Little if any gene flow occurs between populations located in the south-eastern Mediterranean and those dispersed throughout the remainder of the distribution, revealing a genetic discontinuity that runs north–south through the Adriatic. This discontinuity is also evident in other clades of Ophrys and is tentatively attributed to the long-term influence of prevailing winds on the long-distance distribution of pollinia and especially seeds. A cline of gene flow connects populations from Kent and central and southern Europe; these individuals should therefore be considered part of an extensive meta-population. Gene flow is also evident among populations from Kent, which appear to constitute a single metapopulation. They show some evidence of hybridization, and possibly also introgression, with O. apifera. PMID:19251716

Devey, Dion S.; Bateman, Richard M.; Fay, Michael F.; Hawkins, Julie A.

2009-01-01

312

Monascus-fermented yellow pigments monascin and ankaflavin showed antiobesity effect via the suppression of differentiation and lipogenesis in obese rats fed a high-fat diet.  

PubMed

Monascus-fermented monascin and ankaflavin are found to strongly inhibit differentiation and lipogenesis and stimulate lipolysis effects in a 3T3-L1 preadipocyte model, but the in vivo regulation mechanism is unclear. This study uses obese rats caused by a high-fat diet to examine the effects of daily monascin and ankaflavin feeding (8 weeks) on antiobesity effects and modulation of differentiation, lipogenesis, and lipid absorption. The results show that monascin and ankaflavin had a significant antiobesity effect, which should result from the modulation of monascin and ankaflavin on the inhibition of differentiation by inhibiting CCAT/enhancer-binding protein ? (C/EBP?) expression (36.4% and 48.3%) and its downstream peroxisome proliferator-activated receptor ? (PPAR?) (55.6% and 64.5%) and CCAT/enhancer-binding protein ? (C/EBP?) expressions (25.2% and 33.2%) and the inhibition of lipogenesis by increasing lipase activity (14.0% and 10.7%) and decreasing heparin releasable lipoprotein lipase (HR-LPL) activity (34.8% and 30.5%). Furthermore, monascin and ankaflavin are the first agents found to suppress Niemann-Pick C1 Like 1 (NPC1L1) protein expression (73.6% and 26.1%) associated with small intestine tissue lipid absorption. Importantly, monascin and ankaflavin are not like monacolin K, which increases creatine phosphokinase (CPK) activity, known as a rhabdomyolysis indicator. PMID:23360447

Lee, Chun-Lin; Wen, Ja-Yan; Hsu, Ya-Wen; Pan, Tzu-Ming

2013-02-20

313

A genetic algorithm optimization technique for compact high intensity cooler design  

SciTech Connect

This paper initially reviews the operation and design criteria for a compact high intensity cooler (CHIC) unit as used in avionic equipment. Here high heat loads are dissipated via multiple impinging jets fed sequentially through a series of fins connected with a bus bar to the heat source. The analytical basis for the heat transfer design, most of which has been published previously, is shown to predict the performance of CHIC units to a high degree of accuracy. This then permits an approach at optimizing the design. Most optimization techniques depend on continuous variables, while in the design of a CHIC unit many of the critical geometrical variables must assume discrete values. A genetic algorithm, generally not well known in engineering circles, that looks for an optimum by simulating an evolutionary process was found to be satisfactory for this problem with its mixture of discrete and continuous variables. It is also shown that in an actual optimization problem, where the fluid pressure drop across the unit has to be balanced against a low overall thermal resistance, an optimum geometrical design can be determined. This design is an improvement over the empirical best design previously reported the literature.

Schmit, T.S.; Dhingra, A.K.; Landis, F.; Kojasoy, G. [Univ. of Wisconsin, Milwaukee, WI (United States). Dept. of Mechanical Engineering

1995-12-31

314

Noncanonical self-assembly of highly asymmetric genetically encoded polypeptide amphiphiles into cylindrical micelles.  

PubMed

Elastin-like polypeptides (ELPs) are a class of biopolymers consisting of the pentameric repeat (VPG?G)n based on the sequence of mammalian tropoelastin that display a thermally induced soluble-to-insoluble phase transition in aqueous solution. We have discovered a remarkably simple approach to driving the spontaneous self-assembly of high molecular weight ELPs into nanostructures by genetically fusing a short 1.5 kDa (XGy)z assembly domain to one end of the ELP. Classical theories of self-assembly based on the geometric mass balance of hydrophilic and hydrophobic block copolymers suggest that these highly asymmetric polypeptides should form spherical micelles. Surprisingly, when sufficiently hydrophobic amino acids (X) are presented in a periodic sequence such as (FGG)8 or (YG)8, these highly asymmetric polypeptides self-assemble into cylindrical micelles whose length can be tuned by the sequence of the morphogenic tag. These nanostructures were characterized by light scattering, tunable resistive pulse sensing, fluorescence spectrophotometry, and thermal turbidimetry, as well as by cryogenic transmission electron microscopy (cryo-TEM) and small-angle neutron scattering (SANS). These short assembly domains provide a facile strategy to control the size, shape, and stability of stimuli responsive polypeptide nanostructures. PMID:25268037

McDaniel, Jonathan R; Weitzhandler, Isaac; Prevost, Sylvain; Vargo, Kevin B; Appavou, Marie-Sousai; Hammer, Daniel A; Gradzielski, Michael; Chilkoti, Ashutosh

2014-11-12

315

High altitude genetic adaptation in Tibetans: no role of increased hemoglobin-oxygen affinity.  

PubMed

High altitude exerts selective evolutionary pressure primarily due to its hypoxic environment, resulting in multiple adaptive responses. High hemoglobin-oxygen affinity is postulated to be one such adaptive change, which has been reported in Sherpas of the Himalayas. Tibetans have lived on the Qinghai-Tibetan plateau for thousands of years and have developed unique phenotypes, such as protection from polycythemia which has been linked to PDH2 mutation, resulting in the downregulation of the HIF pathway. In order to see if Tibetans also developed high hemoglobin-oxygen affinity as a part of their genetic adaptation, we conducted this study assessing hemoglobin-oxygen affinity and their fetal hemoglobin levels in Tibetan subjects from 3 different altitudes. We found normal hemoglobin-oxygen affinity in all subjects, fetal hemoglobin levels were normal in all except one and no hemoglobin variants in any of the subjects. We conclude that increased hemoglobin-oxygen affinity or increased fetal hemoglobin are not adaptive phenotypes of the Tibetan highlanders. PMID:24618341

Tashi, Tsewang; Feng, Tang; Koul, Parvaiz; Amaru, Ricardo; Hussey, Dottie; Lorenzo, Felipe R; RiLi, Ge; Prchal, Josef T

2014-01-01

316

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. PMID:9482872

Simpson, Peter C.; Roach, David; Woolley, Adam T.; Thorsen, Todd; Johnston, Rick; Sensabaugh, George F.; Mathies, Richard A.

1998-01-01

317

Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing  

PubMed Central

Background Genetic mapping and QTL detection are powerful methodologies in plant improvement and breeding. Construction of a high-density and high-quality genetic map would be of great benefit in the production of superior grapes to meet human demand. High throughput and low cost of the recently developed next generation sequencing (NGS) technology have resulted in its wide application in genome research. Sequencing restriction-site associated DNA (RAD) might be an efficient strategy to simplify genotyping. Combining NGS with RAD has proven to be powerful for single nucleotide polymorphism (SNP) marker development. Results An F1 population of 100 individual plants was developed. In-silico digestion-site prediction was used to select an appropriate restriction enzyme for construction of a RAD sequencing library. Next generation RAD sequencing was applied to genotype the F1 population and its parents. Applying a cluster strategy for SNP modulation, a total of 1,814 high-quality SNP markers were developed: 1,121 of these were mapped to the female genetic map, 759 to the male map, and 1,646 to the integrated map. A comparison of the genetic maps to the published Vitis vinifera genome revealed both conservation and variations. Conclusions The applicability of next generation RAD sequencing for genotyping a grape F1 population was demonstrated, leading to the successful development of a genetic map with high density and quality using our designed SNP markers. Detailed analysis revealed that this newly developed genetic map can be used for a variety of genome investigations, such as QTL detection, sequence assembly and genome comparison. PMID:22908993

2012-01-01

318

Enhanced characteristics of genetically modified switchgrass (Panicum virgatum L.) for high biofuel production  

PubMed Central

Background Lignocellulosic biomass is one of the most promising renewable and clean energy resources to reduce greenhouse gas emissions and dependence on fossil fuels. However, the resistance to accessibility of sugars embedded in plant cell walls (so-called recalcitrance) is a major barrier to economically viable cellulosic ethanol production. A recent report from the US National Academy of Sciences indicated that, “absent technological breakthroughs”, it was unlikely that the US would meet the congressionally mandated renewable fuel standard of 35 billion gallons of ethanol-equivalent biofuels plus 1 billion gallons of biodiesel by 2022. We here describe the properties of switchgrass (Panicum virgatum) biomass that has been genetically engineered to increase the cellulosic ethanol yield by more than 2-fold. Results We have increased the cellulosic ethanol yield from switchgrass by 2.6-fold through overexpression of the transcription factor PvMYB4. This strategy reduces carbon deposition into lignin and phenolic fermentation inhibitors while maintaining the availability of potentially fermentable soluble sugars and pectic polysaccharides. Detailed biomass characterization analyses revealed that the levels and nature of phenolic acids embedded in the cell-wall, the lignin content and polymer size, lignin internal linkage levels, linkages between lignin and xylans/pectins, and levels of wall-bound fucose are all altered in PvMYB4-OX lines. Genetically engineered PvMYB4-OX switchgrass therefore provides a novel system for further understanding cell wall recalcitrance. Conclusions Our results have demonstrated that overexpression of PvMYB4, a general transcriptional repressor of the phenylpropanoid/lignin biosynthesis pathway, can lead to very high yield ethanol production through dramatic reduction of recalcitrance. MYB4-OX switchgrass is an excellent model system for understanding recalcitrance, and provides new germplasm for developing switchgrass cultivars as biomass feedstocks for biofuel production. PMID:23651942

2013-01-01

319

High genetic divergence characterizes populations of the endemic plant Lithophragma maximum (Saxifragaceae) on San Clemente Island  

Microsoft Academic Search

Narrowly-ranging species frequently harbor less genetic variability relative to widespread relatives and face graver extinction\\u000a threats due to the heightened impacts of stochastic events on ecological and genetic diversity. In this study, we examined\\u000a the impact of historical and current threats to the maintenance of genetic variation in Lithophragma maximum (Saxifragaceae), a perennial herb endemic to San Clemente Island, California.

M. Steven Furches; L. E. Wallace; K. Helenurm

2009-01-01

320

High-throughput deep sequencing shows that microRNAs play important roles in switchgrass responses to drought and salinity stress.  

PubMed

MicroRNAs (miRNAs) are an important class of small regulatory RNAs. The goal of this study was to analyse stress-responsive miRNAs in switchgrass (Panicum virgatum), the emerging biofuel crop, to facilitate choosing gene targets for improving biomass and biofuel yield. After sequencing three small RNA libraries constructed from control, salt- and drought-treated switchgrass using Illumina sequencing technology, we identified 670 known miRNA families from a total of more than 50 million short reads. A total of 273 miRNAs were identified with precursors: 126 conserved miRNAs and 147 novel miRNAs. Of them, 265 miRNAs were found to have their opposite sequences (miRNA*) with 2-nt overhang on the 3' end. Of them, 194 were detected in switchgrass transcriptome sequences generated from 31 high-throughput RNA sequencing (RNA-Seq) data sets in NCBI. Many miRNAs were differentially or uniquely expressed during salinity or drought stress treatment. We also discovered 11 miRNA clusters containing 29 miRNAs. These identified miRNAs potentially targeted 28549 genes with a various function, including transcription factors, stress-response proteins and cellulose biosynthesis-related proteins. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the identified miRNAs and their targets were classified to 3779 GO terms including 1534 molecular functions, 1851 biological processes and 394 cellular components and were enriched to 147 KEGG pathways. Interestingly, 195 miRNA families and 450 targets were involved in the biosynthesis pathways of carbon, glucose, starch, fatty acid and lignin and in xylem formation, which could aid in designing next-generation switchgrass for biomass and biofuel. PMID:24283289

Xie, Fuliang; Stewart, Charles Neal; Taki, Faten A; He, Qiuling; Liu, Huawei; Zhang, Baohong

2014-04-01

321

High-molecular weight hyaluronan reduced renal PKC activation in genetically diabetic mice.  

PubMed

The cluster determinant (CD44) seems to play a key role in tissues injured by diabetes type 2. CD44 stimulation activates the protein kinase C (PKC) family which in turn activates the transcriptional nuclear factor kappa B (NF-?B) responsible for the expression of the inflammation mediators such as tumor necrosis factor alpha (TNF-?), interleukin-6 (IL-6), interleukin-18 (IL-18), inducible nitric oxide synthase (iNOS), and matrix metalloproteinases (MMPs). Regulation of CD44 interaction with its ligands depends greatly upon PKC. We investigated the effect of the treatment with high-molecular weight hyaluronan (HA) on diabetic nephropathy in genetically diabetic mice. BKS.Cg-m+/+Lepr(db) mice had elevated plasma insulin from 15 days of age and high blood sugar levels at 4 weeks. The severe nephropathy that developed was characterized by a marked increased in CD44 receptors, protein kinase C betaI, betaII, and epsilon (PKC(?I), PKC(?II), and PKC?) mRNA expression and the related protein products in kidney tissue. High levels of mRNA and related protein levels were also detected in the damaged kidney for NF-?B, TNF-?, IL-6, IL-18, MMP-7, and iNOS. Chronic daily administration of high-molecular mass HA for 2 weeks significantly reduced CD44, PKC(?I), PKC(?II), and PKC? gene expression and the related protein production in kidney tissue and TNF-?, IL-6, IL-18, MMP-7, and iNOS expression and levels also decreased. Histological analysis confirmed the biochemical data. However, blood parameters of diabetes were unchanged. These results suggest that the CD44 and PKC play an important role in diabetes and interaction of high-molecular weight HA with these proteins may reduce inflammation and secondary pathologies due to this disease. PMID:20713153

Campo, Giuseppe M; Avenoso, Angela; Micali, Antonio; Nastasi, Giancarlo; Squadrito, Francesco; Altavilla, Domenica; Bitto, Alessandra; Polito, Francesca; Rinaldi, Maria Grazia; Calatroni, Alberto; D'Ascola, Angela; Campo, Salvatore

2010-11-01

322

SMARTPOP: inferring the impact of social dynamics on genetic diversity through high speed simulations  

PubMed Central

Background Social behavior has long been known to influence patterns of genetic diversity, but the effect of social processes on population genetics remains poorly quantified – partly due to limited community-level genetic sampling (which is increasingly being remedied), and partly to a lack of fast simulation software to jointly model genetic evolution and complex social behavior, such as marriage rules. Results To fill this gap, we have developed SMARTPOP – a fast, forward-in-time genetic simulator – to facilitate large-scale statistical inference on interactions between social factors, such as mating systems, and population genetic diversity. By simultaneously modeling genetic inheritance and dynamic social processes at the level of the individual, SMARTPOP can simulate a wide range of genetic systems (autosomal, X-linked, Y chromosomal and mitochondrial DNA) under a range of mating systems and demographic models. Specifically designed to enable resource-intensive statistical inference tasks, such as Approximate Bayesian Computation, SMARTPOP has been coded in C++ and is heavily optimized for speed and reduced memory usage. Conclusion SMARTPOP rapidly simulates population genetic data under a wide range of demographic scenarios and social behaviors, thus allowing quantitative analyses to address complex socio-ecological questions. PMID:24913447

2014-01-01

323

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. PMID:19304815

Gentekaki, E.; Lynn, D. H.

2009-01-01

324

High-density SNP genotyping of tomato (Solanum lycopersicum L.) reveals patterns of genetic variation due to breeding.  

PubMed

The effects of selection on genome variation were investigated and visualized in tomato using a high-density single nucleotide polymorphism (SNP) array. 7,720 SNPs were genotyped on a collection of 426 tomato accessions (410 inbreds and 16 hybrids) and over 97% of the markers were polymorphic in the entire collection. Principal component analysis (PCA) and pairwise estimates of F(st) supported that the inbred accessions represented seven sub-populations including processing, large-fruited fresh market, large-fruited vintage, cultivated cherry, landrace, wild cherry, and S. pimpinellifolium. Further divisions were found within both the contemporary processing and fresh market sub-populations. These sub-populations showed higher levels of genetic diversity relative to the vintage sub-population. The array provided a large number of polymorphic SNP markers across each sub-population, ranging from 3,159 in the vintage accessions to 6,234 in the cultivated cherry accessions. Visualization of minor allele frequency revealed regions of the genome that distinguished three representative sub-populations of cultivated tomato (processing, fresh market, and vintage), particularly on chromosomes 2, 4, 5, 6, and 11. The PCA loadings and F(st) outlier analysis between these three sub-populations identified a large number of candidate loci under positive selection on chromosomes 4, 5, and 11. The extent of linkage disequilibrium (LD) was examined within each chromosome for these sub-populations. LD decay varied between chromosomes and sub-populations, with large differences reflective of breeding history. For example, on chromosome 11, decay occurred over 0.8 cM for processing accessions and over 19.7 cM for fresh market accessions. The observed SNP variation and LD decay suggest that different patterns of genetic variation in cultivated tomato are due to introgression from wild species and selection for market specialization. PMID:23029069

Sim, Sung-Chur; Van Deynze, Allen; Stoffel, Kevin; Douches, David S; Zarka, Daniel; Ganal, Martin W; Chetelat, Roger T; Hutton, Samuel F; Scott, John W; Gardner, Randolph G; Panthee, Dilip R; Mutschler, Martha; Myers, James R; Francis, David M

2012-01-01

325

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

326

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

327

"Cosmic Collisions" Planetarium Show  

E-print Network

of a broader learning experience. What you will see in the Cosmic Collisions program: · Meteors ("shooting to Align Program Material with National SoLs #12;High School see High School Alignment Table "Strong

Mathis, Wayne N.

328

Utilization of the genetic resources of wild species to create a nontransgenic high flavonoid tomato.  

PubMed

Flavonoids represent a large and important group of plant natural products that are ubiquitous in the plant kingdom. Epidemiological studies have shown the health benefits of a diet high in flavonoids. However, the dietary intake of flavonoids in most western populations is limited, creating a need to find alternative food sources for these polyphenolic secondary metabolites. The domestication of many of our cultivated food crops has resulted in alterations in the biosynthetic pathways of many essential micronutrients and vitamins through inadvertent counterselection against nutritional traits in favor of agronomic ones. Flavonoids are nearly absent from fruits of cultivated tomato (Lycopersicon esculentum Mill.), a major vegetable in human diets. Previous attempts to restore the flavonoid pathway in tomato fruits have been limited to transgenic strategies, suggesting that the problem was intractable through traditional methods. Here, we describe for the first time a nontransgenic metabolic engineering approach to developing a high flavonoid tomato using a wild tomato species (Lycopersicon pennelliiv. puberulum) and demonstrate the opportunities for restoring functional pathways using the genetic resources of wild species, resulting in production of healthier foods. PMID:15713046

Willits, Michael G; Kramer, Catherine M; Prata, Rogerio T N; De Luca, Vincenzo; Potter, Brian G; Steffens, John C; Graser, Gerson

2005-02-23

329

Antiviral resistance among highly pathogenic influenza A (H5N1) viruses isolated worldwide in 2002-2012 shows need for continued monitoring  

PubMed Central

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.

2013-01-01

330

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

Microsoft Academic Search

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

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

2011-01-01

331

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

332

High genetic diversity and population differentiation in Boechera fecunda , a rare relative of Arabidopsis  

Microsoft Academic Search

Conservation of endangered species becomes a critical issue with the increasing rates of extinction. In this study, we use 13 microsatellite loci and 27 single-copy nuclear loci to investigate the population genetics of Boechera fecunda, a rare relative of Arabidopsis thaliana, known from only 21 populations in Montana. We investigated levels of genetic diversity and population structure in comparison to

BAO-HUA SONG; THOMAS MITCHELL-OLDS

2007-01-01

333

Am. J. Hum. Genet. 77:685693, 2005 High-Resolution Whole-Genome Association Study of Parkinson Disease  

E-print Network

of Parkinson disease (PD [MIM 168600]). Our findings contribute to the cre- ation of a genomic predispositionAm. J. Hum. Genet. 77:685­693, 2005 685 High-Resolution Whole-Genome Association Study of Parkinson Disease Demetrius M. Maraganore,1 Mariza de Andrade,2 Timothy G. Lesnick,2 Kari J. Strain,2 Matthew J

Jin, Jiashun

334

Genetic Polymorphisms in the Renin-Angiotensin System in High-Altitude and Low-Altitude Native  

E-print Network

to angiotensin I (AT-I), a decapeptide with mild vasoconstrictive properties, by the proteolytic enzyme reninGenetic Polymorphisms in the Renin-Angiotensin System in High-Altitude and Low-Altitude Native loci in genes encoding components of the renin-angiotensin system (RAS) that have alleles associated

Kidd, Kenneth

335

The Art Show  

ERIC Educational Resources Information Center

This article describes what once was thought to be impossible--a formal art show extravaganza at an elementary school with 1,000 students, a Department of Defense Dependent School (DODDS) located overseas, on RAF Lakenheath, England. The dream of this this event involved the transformation of the school cafeteria into an elegant art show

Scolarici, Alicia

2004-01-01

336

Shallow gene pools in the high intertidal: extreme loss of genetic diversity in viviparous sea stars (Parvulastra).  

PubMed

We document an extreme example of reproductive trait evolution that affects population genetic structure in sister species of Parvulastra cushion stars from Australia. Self-fertilization by hermaphroditic adults and brood protection of benthic larvae causes strong inbreeding and range-wide genetic poverty. Most samples were fixed for a single allele at nearly all nuclear loci; heterozygotes were extremely rare (0.18%); mitochondrial DNA sequences were more variable, but few populations shared haplotypes in common. Isolation-with-migration models suggest that these patterns are caused by population bottlenecks (relative to ancestral population size) and low gene flow. Loss of genetic diversity and low potential for dispersal between high-intertidal habitats may have dire consequences for extinction risk and potential for future adaptive evolution in response to climate and other selective agents. PMID:23925835

Keever, Carson C; Puritz, Jonathan B; Addison, Jason A; Byrne, Maria; Grosberg, Richard K; Toonen, Robert J; Hart, Michael W

2013-10-23

337

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.

338

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. PMID:18414665

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

339

11q21 rearrangement is a frequent and highly specific genetic alteration in mucoepidermoid carcinoma.  

PubMed

Mucoepidermoid carcinoma (MEC) is the most common malignant salivary gland tumor. Translocation t(11;19)(q21;p13) involving the MECT1 and MAML2 genes has been suggested as a diagnostic marker in these tumors. To determine the specificity of 11q21 locus rearrangements for MEC, fluorescence in situ hybridization analysis with specific MEC-I Dual Color Break Apart Probe was performed on a tissue microarray containing samples from almost 1200 salivary gland adenomas and carcinomas. Rearrangements of 11q21 were observed in 40% of 217 MECs. The frequency of rearrangements decreased with tumor grade and was found in 53% of G1, 43% of G2, and 31% of G3 tumors (P=0.015). There were no 11q21 rearrangements found in other salivary gland carcinomas including 142 adenoid cystic carcinomas, 104 acinic cell adenocarcinomas, 76 adenocarcinoma not otherwise specified, 38 epithelial-myoepithelial carcinomas, 15 polymorphous low-grade adenocarcinomas, 18 basal cell adenocarcinomas, 19 myoepithelial carcinomas, 12 papillary cystadenocarcinomas, 6 salivary duct carcinomas, and 10 oncocytic carcinomas. Furthermore, all analyzed salivary gland adenomas, including 39 cases of Warthin tumor and control samples, either from the salivary gland or from other organs were negative for 11q21 rearrangements. It is concluded that MECT1-MAML2 gene fusion is a highly specific genetic alteration in MEC with predominance in low-grade and intermediate-grade tumors. PMID:22847156

Clauditz, Till Sebastian; Gontarewicz, Artur; Wang, Chia-Jung; Münscher, Adrian; Laban, Simon; Tsourlakis, Maria Christina; Knecht, Rainald; Sauter, Guido; Wilczak, Waldemar

2012-09-01

340

Genetic Risk Assessments in Individuals at High Risk for Inherited Breast Cancer in the Breast Oncology Care Setting  

PubMed Central

Background It has become increasingly common to consider BRCA mutation status when determining optimal cancer risk management and treatment options in order to improve patient outcomes. Knowledge about the risk for hereditary cancer at or as close as possible to the time of diagnosis allows patients access to the most risk reduction options available. Methods This paper illustrates the role of genetic risk assessment for hereditary breast cancer, using hereditary breast and ovarian cancer (HBOC) syndrome as a model due to germline mutations in the BRCA1 and BRCA2. Specifically, the value of genetic counseling and testing for HBOC across the cancer prevention and control continuum is outlined as it pertains to breast cancer. Results In recognition of the importance of risk assessment for hereditary breast cancer, leading health professional organizations have developed specific guidelines and recommendations to providers for identification of women at increased risk for carrying a BRCA mutation. Conclusions Institutional efforts specific to genetic counseling and testing have resulted in the implementation of a model driven by physician recommendation as a referral system for high-risk breast cancer patients. Establishing an infrastructure to support research, education, and outreach initiatives focused on BRCA genetic counseling and testing will provide information that can improve the delivery of cancer genetics services. PMID:23037493

Pal, Tuya; Vadaparampil, Susan T.

2014-01-01

341

Storytelling Slide Shows to Improve Diabetes and High Blood Pressure Knowledge and Self-Efficacy: Three-Year Results among Community Dwelling Older African Americans  

ERIC Educational Resources Information Center

This study combined the African American tradition of oral storytelling with the Hispanic medium of "Fotonovelas." A staggered pretest posttest control group design was used to evaluate four Storytelling Slide Shows on health that featured community members. A total of 212 participants were recruited for the intervention and 217 for the…

Bertera, Elizabeth M.

2014-01-01

342

Sro9, a Multicopy Suppressor of the Bud Growth Defect in the Saccharomyces Cerevisiae Rho3-Deficient Cells, Shows Strong Genetic Interactions with Tropomyosin Genes, Suggesting Its Role in Organization of the Actin Cytoskeleton  

PubMed Central

RHO3 encodes a Rho-type small GTPase in the yeast Saccharomyces cerevisiae and is involved in the proper organization of the actin cytoskeleton required for bud growth. SRO9 (YCL37c) was isolated as a multicopy suppressor of a rho3? mutation. An Sro9p domain required for function is similar to a domain in the La protein (an RNA-binding protein). Disruption of SRO9 did not affect vegetative growth, even with the simultaneous disruption of an SRO9 homologue, SRO99. However, sro9? was synthetically lethal with a disruption of TPM1, which encodes tropomyosin; sro9? tpm1? cells did not distribute cortical actin patches properly and lysed. We isolated TPM2, the other gene for tropomyosin, as a multicopy suppressor of a tpm1? sro9? double mutant. Genetic analysis suggests that TPM2 is functionally related to TPM1 and that tropomyosin is important but not essential for cell growth. Overexpression of SRO9 suppressed the growth defect in tpm1? tpm2? cells, disappearance of cables of actin filaments in both rho3? cells and tpm1? cells, and temperature sensitivity of actin mutant cells (act1-1 cells), suggesting that Sro9p has a function that overlaps or is related to tropomyosin function. Unlike tropomyosin, Sro9p does not colocalize with actin cables but is diffusely cytoplasmic. These results suggest that Sro9p is a new cytoplasmic factor involved in the organization of actin filaments. PMID:9383048

Kagami, M.; Toh-e, A.; Matsui, Y.

1997-01-01

343

Women with elevated food addiction symptoms show accelerated reactions, but no impaired inhibitory control, in response to pictures of high-calorie food-cues.  

PubMed

Addictive behaviors are accompanied by a lack of inhibitory control, specifically when individuals are confronted with substance-related cues. Thus, we expected women with symptoms of food addiction to be impaired in inhibitory control, when confronted with palatable, high-calorie food-cues. Female college students (N=50) were divided in low and high food addiction groups based on the symptom count of the Yale Food Addiction Scale. Participants performed a Go/No-go-task with high-calorie food-cues or neutral pictures presented behind the targets. Self-reported impulsivity was also assessed. The high food addiction group had faster reaction times in response to food-cues as compared to neutral cues and reported higher attentional impulsivity than the low food addiction group. Commission and omission errors did not differ between groups or picture types. Hence, women with food addiction symptoms reported higher attentional impulsivity and reacted faster in response to food-cues, although neither increased self-reported motor impulsivity nor impaired behavioral inhibition was found. Food addiction symptoms seem to be related to attentional aspects of impulsivity but not other facets of impulsivity. PMID:23121803

Meule, Adrian; Lutz, Annika; Vögele, Claus; Kübler, Andrea

2012-12-01

344

Mobile robot localization from large-scale appearance mosaics has been showing increasing promise as a low-cost, high-perfor-  

E-print Network

a mobile robot requires a solution to the dual problems of recovering the motion history of the robot localization and motion estima- tion capabilities to autonomous vehicles, both on land and in the sea. Mosaic-based localization [10] is a technique employing real- time imagery to track motion over a previously stored high

Kelly, Alonzo

345

The zebrafish Pax3 and Pax7 homologues are highly conserved, encode multiple isoforms and show dynamic segment-like expression in the developing brain  

Microsoft Academic Search

This study describes the isolation and characterization of zebrafish homologues of the mammalian Pax3 and Pax7 genes. The proteins encoded by both zebrafish genes are highly conserved (>83%) relative to the known mammalian sequences. Also the neural expression patterns during embryogenesis are very similar to the murine homologues. However, observed differences in neural crest and mesodermal expression relative to mammals

Hee-Chan Seo; Bjørn O Sætre; Bjarte Håvik; Ståle Ellingsen; Anders Fjose

1998-01-01

346

An ultra-high throughput mutational spectrometer for human genetic diagnostics  

E-print Network

Discovering the genetic causes of common diseases may require scanning for mutations in all of the genes in a million people, a significant undertaking. Such discoveries would revolutionize biotechnology, potentially ...

Forest, Craig Richard, 1978-

2007-01-01

347

The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis  

E-print Network

, Monika Y. Cohenn , Eric Dorano , Tzipora Falik-Zaccaip , Susan O. Lewinq , Ira T. Lotto , Barbara C. McDepartment of Medical Genetics, Women's Health Centre, University of British Columbia, Vancouver, BC, Canada V6H 3V5; s

Gerstein, Mark

348

High-performance genetically targetable optical neural silencing by proton pumps  

E-print Network

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 ...

Chow, Brian Yichiun

349

Genetic convergence in the adaptation of dogs and humans to the high-altitude environment of the tibetan plateau.  

PubMed

The high-altitude hypoxic environment represents one of the most extreme challenges for mammals. Previous studies of humans on the Tibetan plateau and in the Andes Mountains have identified statistical signatures of selection in different sets of loci. Here, we first measured the hemoglobin levels in village dogs from Tibet and those from Chinese lowlands. We found that the hemoglobin levels are very similar between the two groups, suggesting that Tibetan dogs might share similar adaptive strategies as the Tibetan people. Through a whole-genome sequencing approach, we have identified EPAS1 and HBB as candidate genes for the hypoxic adaptation on the Tibetan plateau. The population genetic analysis shows a significant convergence between humans and dogs in Tibet. The similarities in the sets of loci that exhibit putative signatures of selection and the hemoglobin levels between humans and dogs of the same environment, but not between human populations in different regions, suggests an extraordinary landscape of convergent evolution between human beings and their best friend on the Tibetan plateau. PMID:25091388

Wang, Guo-Dong; Fan, Ruo-Xi; Zhai, Weiwei; Liu, Fei; Wang, Lu; Zhong, Li; Wu, Hong; Yang, He-Chuan; Wu, Shi-Fang; Zhu, Chun-Ling; Li, Yan; Gao, Yun; Ge, Ri-Li; Wu, Chung-I; Zhang, Ya-Ping

2014-08-01

350

Deep sequencing identifies two genotypes and high viral genetic diversity of human pegivirus (GB virus C) in rural Ugandan patients.  

PubMed

Human pegivirus (HPgV), formerly 'GB virus C' or 'hepatitis G virus', is a member of the genus Flavivirus (Flaviviridae) that has garnered significant attention due to its inhibition of HIV, including slowing disease progression and prolonging survival in HIV-infected patients. Currently, there are six proposed HPgV genotypes that have roughly distinct geographical distributions. Genotypes 2 and 3 are the most comprehensively characterized, whereas those genotypes occurring on the African continent, where HPgV prevalence is highest, are less well studied. Using deep sequencing methods, we identified complete coding HPgV sequences in four of 28 patients (14.3%) in rural Uganda, east Africa. One of these sequences corresponds to genotype 1 and is the first complete genome of this genotype from east Africa. The remaining three sequences correspond to genotype 5, a genotype that was previously considered exclusively South African. All four positive samples were collected within a geographical area of less than 25 km(2), showing that multiple HPgV genotypes co-circulate in this area. Analysis of intra-host viral genetic diversity revealed that total single-nucleotide polymorphism frequency was approximately tenfold lower in HPgV than in hepatitis C virus. Finally, one patient was co-infected with HPgV and HIV, which, in combination with the high prevalence of HIV, suggests that this region would be a useful locale to study the interactions and co-evolution of these viruses. PMID:24077364

Ghai, Ria R; Sibley, Samuel D; Lauck, Michael; Dinis, Jorge M; Bailey, Adam L; Chapman, Colin A; Omeja, Patrick; Friedrich, Thomas C; O'Connor, David H; Goldberg, Tony L

2013-12-01

351

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. PMID:18160430

Pierro, Dennis J.; Powers, Erik L.; Olson, Ken E.

2008-01-01

352

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

353

The Ozone Show.  

ERIC Educational Resources Information Center

Uses a talk show activity for a final assessment tool for students to debate about the ozone hole. Students are assessed on five areas: (1) cooperative learning; (2) the written component; (3) content; (4) self-evaluation; and (5) peer evaluation. (SAH)

Mathieu, Aaron

2000-01-01

354

Chemistry Game Shows  

Microsoft Academic Search

We present a technological improvement to the use of game shows to help students review for tests. Our approach uses HTML files interpreted with a browser on a computer attached to an LCD projector. The HTML files can be easily modified for use of the game in a variety of courses.

Susan Campbell; Jennifer Muzyka

2002-01-01

355

Histological Analysis of SLC38A6 (SNAT6) Expression in Mouse Brain Shows Selective Expression in Excitatory Neurons with High Expression in the Synapses  

PubMed Central

SLC38A6 is one of the newly found members of the solute carrier 38 family consisting of total 11 members, of which only 6 have been characterized so far. Being the only glutamine transporter family expressed in the brain, this family of proteins are most probably involved in the regulation of the glutamate-glutamine cycle, responsible for preventing excitotoxicity. We used immunohistochemistry to show that SLC38A6 is primarily expressed in excitatory neurons and is not expressed in the astrocytes. Using proximity ligation assay, we have quantified the interactions of this SLC38 family protein with other proteins with known localization in the cells, showing that this transporter is expressed at the synapses. Moreover, this study has enabled us to come up with a model suggesting sub-cellular localization of SLC38A6 at the synaptic membrane of the excitatory neurons. PMID:24752331

Bagchi, Sonchita; Baomar, Hajar Ali; Al-Walai, Somar; Al-Sadi, Saifaddin; Fredriksson, Robert

2014-01-01

356

The GAA triplet-repeat sequence in Friedreich ataxia shows a high level of somatic instability in vivo, with a significant predilection for large contractions  

Microsoft Academic Search

Friedreich ataxia is commonly caused by large expansions of a GAA triplet-repeat (GAA-TR) sequence in the first intron of the FRDA gene. We used small-pool PCR to analyze somatic variability among 7190 individual FRDA molecules from peripheral blood DNA of subjects carrying 12 different expanded alleles, ranging in size from 241 to 1105 triplets. Expanded alleles showed a length-dependent increase

Rajesh Sharma; Saeeda Bhatti; Mariluz Gomez; Rhonda M. Clark; Cynthia Murray; Tetsuo Ashizawa; Sanjay I. Bidichandani

2002-01-01

357

High genetic diversity in cryptic populations of the migratory sutchi catfish Pangasianodon hypophthalmus in the Mekong River.  

PubMed

The detection and conservation of spawning units is of crucial importance in highly migratory species. The sutchi catfish Pangasianodon hypophthalmus (Pangasiidae; Teleostei) is a common large-sized tropical fish, which migrates annually to several upstream spawning sites on the Lower Mekong River and feeds on the huge floodplain of the Lower Mekong and Tonle Sap for the other half of the year. We hypothesised that because of the relative size of the feeding and spawning habitat, genetic variability would be high and homogeneous in foraging populations, but that spawning stocks would be distinct in space and time. To test these predictions, 567 individuals from 10 geographic locations separated by up to 1230 km along the Lower Mekong River were genotyped at seven microsatellite loci. The level of genetic diversity was much higher than other freshwater fish and reached values comparable to marine species (mean H(e)=0.757). All samples collected at the potential spawning sites deviated from Hardy-Weinberg expectations, suggesting admixture. Individual-based clustering methods revealed genetic heterogeneity and enabled the detection of three genetically distinct sympatric populations. There was no evidence of recent reduction in effective population size in any population. Contrasting with the vast extent of the feeding grounds, the shortage of spawning grounds seems to have moved sutchi catfish towards diachronous spawning. Hence the sustainable exploitation of this natural resource hinges on the conservation of the limited spawning grounds and open migration routes between the spawning and feeding grounds. PMID:16369576

So, N; Maes, G E; Volckaert, F A M

2006-02-01

358

Show-Me Center  

NSDL National Science Digital Library

The Show-Me Center is a partnership of four NSF-sponsored middle grades mathematics curriculum development Satellite Centers (University of Wisconsin, Michigan State University, University of Montana, and the Educational Development Center). The group's website provides "information and resources needed to support selection and implementation of standards-based middle grades mathematics curricula." The Video Showcase includes segments on Number, Algebra, Geometry, Measure, and Data Analysis, with information on ways to obtain the complete video set. The Curricula Showcase provides general information, unit goals, sample lessons and teacher pages spanning four projects: the Connected Mathematics Project (CMP), Mathematics in Context (MiC), MathScape: Seeing and Thinking Mathematically, and Middle Grades Math Thematics. The website also posts Show-Me Center newsletters, information on upcoming conferences and workshops, and links to resources including published articles and unpublished commentary on mathematics school reform.

359

Show-Me Magazine  

NSDL National Science Digital Library

Come along as the folks at the University of Missouri show you the history of their college days through the Show Me magazine. It's a wonderful collection of college humor published from 1946 to 1963. First-time visitors would do well to read about the magazine's colorful past, courtesy of Jerry Smith. A good place to start is the November 1920 issue (easily found when you browse by date), which contains a number of parody advertisements along with some doggerels poking good natured fun at the football team and an assortment of deans. Also, it's worth noting that visitors can scroll through issues and save them to an online "bookbag" for later use.

2008-01-01

360

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

361

The Graphing Game Show  

NSDL National Science Digital Library

This lesson plan assesses student interpretation of graphs utilizing cooperative learning to further students understanding. Types of graphs used are horizontal and vertical bar graphs, picture graphs, and pictographs. In the lesson students play a game called the Graphing Game Show, in which they must work as a team to answer questions about specific graphs. The lesson includes four student resource worksheets and suggestions for extension and differentiation.

2011-01-01

362

A genetic response to high altitude hypoxia: high hemoglobin-oxygen affinity in chicken (Gallus gallus) from the Peruvian Andes.  

PubMed

A population of chicken (Gallus gallus) from the Peruvian Andes (4,000 m) carrying a high hemoglobin-oxygen affinity has been identified. This property remained stable after over 1 year residence at sea level and was transmitted to the descendants born at sea level. Chicken were introduced in South America during the Spanish conquest and therefore their adaptation time to high altitude is less than 500 years. This finding shows that a genotypic change in hemoglobin function can occur in an extremely short evolutionary time and leads to some reflections on the high altitude adaptation of the mammals that migrated to South America during the great Plio-Pleistocene interchange. PMID:1756413

Velarde, F L; Espinoza, D; Monge, C; de Muizon, C

1991-01-01

363

Novel H7N9 Influenza Virus Shows Low Infectious Dose, High Growth Rate, and Efficient Contact Transmission in the Guinea Pig Model  

PubMed Central

The zoonotic outbreak of H7N9 subtype avian influenza virus that occurred in eastern China in the spring of 2013 resulted in 135 confirmed human cases, 44 of which were lethal. Sequencing of the viral genome revealed a number of molecular signatures associated with virulence or transmission in mammals. We report here that, in the guinea pig model, a human isolate of novel H7N9 influenza virus, A/Anhui/1/2013 (An/13), is highly dissimilar to an H7N1 avian isolate and instead behaves similarly to a human seasonal strain in several respects. An/13 was found to have a low 50% infectious dose, grow to high titers in the upper respiratory tract, and transmit efficiently among cocaged guinea pigs. The pH of fusion of the hemagglutinin (HA) and the binding of virus to fixed guinea pig tissues were also examined. The An/13 HA displayed a relatively elevated pH of fusion characteristic of many avian strains, and An/13 resembled avian viruses in terms of attachment to tissues. One important difference was seen between An/13 and both the H3N2 human and the H7N1 avian viruses: when inoculated intranasally at a high dose, only the An/13 virus led to productive infection of the lower respiratory tract of guinea pigs. In sum, An/13 was found to retain fusion and attachment properties of an avian influenza virus but displayed robust growth and contact transmission in the guinea pig model atypical of avian strains and indicative of mammalian adaptation. PMID:24227867

Gabbard, Jon D.; Dlugolenski, Daniel; Van Riel, Debby; Marshall, Nicolle; Galloway, Summer E.; Howerth, Elizabeth W.; Campbell, Patricia J.; Jones, Cheryl; Johnson, Scott; Byrd-Leotis, Lauren; Steinhauer, David A.; Kuiken, Thijs; Tompkins, S. Mark; Tripp, Ralph; Lowen, Anice C.

2014-01-01

364

NanA, a Neuraminidase from Streptococcus pneumoniae, Shows High Levels of Sequence Diversity, at Least in Part through Recombination with Streptococcus oralis  

PubMed Central

Streptococcus pneumoniae, an important human pathogen, contains at least two genes, nanA and nanB, that express sialidase activity. NanA is a virulence determinant of pneumococci which is important in animal models of colonization and middle ear infections. The gene encoding NanA was detected in all 106 pneumococcal strains screened that represented 59 restriction profiles. Sequencing confirmed a high level of diversity, up to 17.2% at the nucleotide level and 14.8% at the amino acid level. NanA diversity is due to a number of mechanisms including insertions, point mutations, and recombination generating mosaic genes. The level of nucleotide divergence for each recombinant block is greater than 30% and much higher than the 20% identified within mosaic pbp genes, suggesting that a high selective pressure exists for these alterations. These data indicate that at least one of the four recombinant blocks identified originated from a Streptococcus oralis isolate, demonstrating for the first time that protein virulence determinants of pneumococci have, as identified previously for genes encoding penicillin binding proteins, evolved by recombination with oral streptococci. No amino acid alterations were identified within the aspartic boxes or predicted active site, suggesting that sequence variation may be important in evading the adaptive immune response. Furthermore, this suggests that nanA is an important target of the immune system in the interaction between the pneumococcus and host. PMID:16030232

King, Samantha J.; Whatmore, Adrian M.; Dowson, Christopher G.

2005-01-01

365

Metapopulations in temporary streams - The role of drought-flood cycles in promoting high genetic diversity in a critically endangered freshwater fish and its consequences for the future.  

PubMed

Genetic factors have direct and indirect impacts in the viability of endangered species. Assessing their genetic diversity levels and population structure is thus fundamental for conservation and management. In this paper we use mitochondrial and nuclear markers to address phylogeographic and demographic data on the critically endangered Anaecypris hispanica, using a broad sampling set which covered its known distribution area in the Iberian Peninsula. Our results showed that the populations of A. hispanica are strongly differentiated (high and significant ?ST and FST values, corroborated by the results from AMOVA and SAMOVA) and genetically diversified. We suggest that the restricted gene flow between populations may have been potentiated by ecological, hydrological and anthropogenic causes. Bayesian skyline plots revealed a signal for expansion for all populations (tMRCA between 68kya and 1.33Mya) and a genetic diversity latitudinal gradient was detected between the populations from the Upper (more diversified) and the Lower (less diversified) Guadiana river basin. We postulate a Pleistocenic westwards colonization route for A. hispanica in the Guadiana river basin, which is in agreement with the tempo and mode of paleoevolution of this drainage. The colonization of River Guadalquivir around 60kya with migrants from the Upper Guadiana, most likely by stream capture, is also suggested. This study highlights the view that critically endangered species facing range retreats (about 47% of its known populations have disappeared in the last 15years) are not necessarily small and genetically depleted. However, the extinction risk is not negligible since A. hispanica faces the combined effect of several deterministic and stochastic negative factors and, moreover, recolonization events after localized extinctions are very unlikely to occur due to the strong isolation of populations and to the patchily ecologically-conditioned distribution of fish. The inferred species distribution models highlight the significant contribution of temperature seasonality and isothermality to A. hispanica occurrence in Guadiana environments and emphasize the importance of stable climatic conditions for the preservation of this species. Given the strong population structure, high percentage of private haplotypes and virtual absence of inter-basin gene flow we suggest that each A. hispanica population should be considered as an independent Operational Conservation Unit and that ex-situ and in-situ actions should be conducted in parallel to allow for the long-term survival of the species and the preservation of the genetic integrity of its populations. PMID:25132127

Sousa-Santos, Carla; Robalo, Joana I; Francisco, Sara M; Carrapato, Carlos; Cardoso, Ana Cristina; Doadrio, Ignacio

2014-11-01

366

A Genetic Algorithm for the Multidimensional Knapsack Problem  

Microsoft Academic Search

In this paper we present a heuristic based upon genetic algorithms for the multidimensional knapsack problem. A heuristic operator which utilises problem-specific knowledge is incorporated into the standard genetic algorithm approach. Computational results show that the genetic algorithm heuristic is capable of obtaining high-quality solutions for problems of various characteristics, whilst requiring only a modest amount of computational effort. Computational

P. C. Chu; J. E. Beasley

1998-01-01

367

Molecular cloning and characterization of a novel orphan receptor (P2P) expressed in human pancreas that shows high structural homology to the P2U purinoceptor.  

PubMed

Here we report the cloning of a gene encoding a new member of the superfamily of G protein-coupled receptors. The gene encodes a protein of 365 amino acids closely resembling two recently cloned nucleotide binding receptors, called P2U and P2Y purinoceptors (71% and 49% sequence identity within the transmembrane domains, respectively). Our studies show that this new putative purinoceptor (designated P2P) is encoded by an intronless single copy gene that is exclusively expressed in pancreas, in contrast to the P2U and the P2Y purinoceptors which are widely distributed throughout the periphery. The identification of a pancreas-specific human putative P2 purinoceptor makes it attractive to speculate that the reported actions of ADP/ATP analogues in pancreas on insulin secretion are mediated through this receptor. PMID:8617367

Stam, N J; Klomp, J; Van de Heuvel, N; Olijve, W

1996-04-22

368

Obesity in show dogs.  

PubMed

Obesity is an important disease with a growing incidence. Because obesity is related to several other diseases, and decreases life span, it is important to identify the population at risk. Several risk factors for obesity have been described in the literature. A higher incidence of obesity in certain breeds is often suggested. The aim of this study was to determine whether obesity occurs more often in certain breeds. The second aim was to relate the increased prevalence of obesity in certain breeds to the official standards of that breed. To this end, we investigated 1379 dogs of 128 different breeds by determining their body condition score (BCS). Overall, 18.6% of the show dogs had a BCS >5, and 1.1% of the show dogs had a BCS>7. There were significant differences between breeds, which could be correlated to the breed standards. It warrants firm discussions with breeders and judges in order to come to different interpretations of the standards to prevent overweight conditions from being the standard of beauty. PMID:22882163

Corbee, R J

2012-08-11

369

The high frequency of genetic diseases in hypotonic infants referred by neuropediatrics.  

PubMed

Neonatal hypotonia is a relatively common cause of consultation in daily pediatric practice. It is part of the clinical presentation of a large group of heterogeneous diseases, many of which have an important and classifiable genetic background. Identification of the specific disorder can help optimize the management and treatment of the patient and inform genetic counseling for the family, and therefore input from clinical geneticists is critical at the earliest stages of medical management. Here we present 30 patients with hypotonia of unknown etiology referred by a neuropediatrician to clinical genetics. Clinical, genetic, and molecular evaluation of each patient was performed. Sixty-nine percent of the patients included in the study had a genetic disease, including eight with Prader-Willi syndrome, three with spinal muscular atrophy, one with Rett syndrome, and one with Sotos syndrome harboring a previously undescribed mutation. Our data demonstrate that a multidisciplinary approach used from the outset that includes molecular analysis can help improve diagnosis and management of hypotonic infants. PMID:24715477

Vilchis, Zacil; Najera, Nayelli; Pérez-Duran, Javier; Najera, Zenyesen; Gonzalez, Lourdes; del Refugio Rivera, Maria; Queipo, Gloria

2014-07-01

370

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.

371

Not a "reality" show.  

PubMed

The authors of the preceding articles raise legitimate questions about patient and staff rights and the unintended consequences of allowing ABC News to film inside teaching hospitals. We explain why we regard their fears as baseless and not supported by what we heard from individuals portrayed in the filming, our decade-long experience making medical documentaries, and the full un-aired context of the scenes shown in the broadcast. The authors don't and can't know what conversations we had, what documents we reviewed, and what protections we put in place in each televised scene. Finally, we hope to correct several misleading examples cited by the authors as well as their offhand mischaracterization of our program as a "reality" show. PMID:23631336

Wrong, Terence; Baumgart, Erica

2013-01-01

372

A High Resolution Case Study of a Patient with Recurrent Plasmodium vivax Infections Shows That Relapses Were Caused by Meiotic Siblings  

PubMed Central

Plasmodium vivax infects a hundred million people annually and endangers 40% of the world's population. Unlike Plasmodium falciparum, P. vivax parasites can persist as a dormant stage in the liver, known as the hypnozoite, and these dormant forms can cause malaria relapses months or years after the initial mosquito bite. Here we analyze whole genome sequencing data from parasites in the blood of a patient who experienced consecutive P. vivax relapses over 33 months in a non-endemic country. By analyzing patterns of identity, read coverage, and the presence or absence of minor alleles in the initial polyclonal and subsequent monoclonal infections, we show that the parasites in the three infections are likely meiotic siblings. We infer that these siblings are descended from a single tetrad-like form that developed in the infecting mosquito midgut shortly after fertilization. In this natural cross we find the recombination rate for P. vivax to be 10 kb per centimorgan and we further observe areas of disequilibrium surrounding major drug resistance genes. Our data provide new strategies for studying multiclonal infections, which are common in all types of infectious diseases, and for distinguishing P. vivax relapses from reinfections in malaria endemic regions. This work provides a theoretical foundation for studies that aim to determine if new or existing drugs can provide a radical cure of P. vivax malaria. PMID:24901334

Bright, Andrew Taylor; Manary, Micah J.; Tewhey, Ryan; Arango, Eliana M.; Wang, Tina; Schork, Nicholas J.; Yanow, Stephanie K.; Winzeler, Elizabeth A.

2014-01-01

373

High genetic differentiation among French populations of the Orsini's viper (Vipera ursinii ursinii) based on mitochondrial and microsatellite data: implications for conservation management.  

PubMed

The Orsini's viper (Vipera ursinii) is one of the most threatened snakes in Europe due to its highly fragmented distribution and specific open environment (steppic habitat) requirement. French populations are isolated on top of mountain massifs of the southern Prealps/Alps. Mitochondrial sequences (cytochrome b) and 6 microsatellite loci have been used to estimate the levels of genetic diversity and isolation within and among 11 French fragmented populations (a total of 157 individuals). Eleven cytochrome b haplotypes with a limited divergence were observed (mean divergence between haplotypes: 0.31%). However, we detected considerable genetic differentiation among populations (global F(ST) = 0.76 and 0.26 for mitochondrial and nuclear DNA, respectively). Results indicate that 3 populations possibly went through a bottleneck and 1 population showed low genetic diversity compared with the others. Although a significant isolation by distance was detected for both markers, strong differentiation was also observed between geographically close populations, probably due to the ragged landscape that constitutes a serious barrier to gene flow owing to the limited dispersal capability of the viper. Despite some discrepancies between the 2 markers, 8 Management Units have been identified and should be considered for future management projects. PMID:20841316

Ferchaud, Anne-Laure; Lyet, Arnaud; Cheylan, Marc; Arnal, Véronique; Baron, Jean-Pierre; Montgelard, Claudine; Ursenbacher, Sylvain

2011-01-01

374

Genetic interaction analysis of point mutations enables interrogation of gene function at a residue-level resolution: exploring the applications of high-resolution genetic interaction mapping of point mutations.  

PubMed

We have achieved a residue-level resolution of genetic interaction mapping - a technique that measures how the function of one gene is affected by the alteration of a second gene - by analyzing point mutations. Here, we describe how to interpret point mutant genetic interactions, and outline key applications for the approach, including interrogation of protein interaction interfaces and active sites, and examination of post-translational modifications. Genetic interaction analysis has proven effective for characterizing cellular processes; however, to date, systematic high-throughput genetic interaction screens have relied on gene deletions or knockdowns, which limits the resolution of gene function analysis and poses problems for multifunctional genes. Our point mutant approach addresses these issues, and further provides a tool for in vivo structure-function analysis that complements traditional biophysical methods. We also discuss the potential for genetic interaction mapping of point mutations in human cells and its application to personalized medicine. PMID:24842270

Braberg, Hannes; Moehle, Erica A; Shales, Michael; Guthrie, Christine; Krogan, Nevan J

2014-07-01

375

Light-harvesting mutants show differential gene expression upon shift to high light as a consequence of photosynthetic redox and reactive oxygen species metabolism.  

PubMed

The amount of light energy that is harvested and directed to the photosynthetic machinery is regulated in order to control the production of reactive oxygen species (ROS) in leaf tissues. ROS have important roles as signalling factors that instigate and mediate a range of cellular responses, suggesting that the mechanisms regulating light-harvesting and photosynthetic energy transduction also affect cell signalling. In this study, we exposed wild-type (WT) Arabidopsis and mutants impaired in the regulation of photosynthetic light-harvesting (stn7, tap38 and npq4) to transient high light (HL) stress in order to study the role of these mechanisms for up- and downregulation of gene expression under HL stress. The mutants, all of which have disturbed regulation of excitation energy transfer and distribution, responded to transient HL treatment with surprising similarity to the WT in terms of general 'abiotic stress-regulated' genes associated with hydrogen peroxide and 12-oxo-phytodienoic acid signalling. However, we identified distinct expression profiles in each genotype with respect to induction of singlet oxygen and jasmonic acid-dependent responses. The results of this study suggest that the control of excitation energy transfer interacts with hormonal regulation. Furthermore, the photosynthetic pigment-protein complexes appear to operate as receptors that sense the energetic balance between the photosynthetic light reactions and downstream metabolism. PMID:24591716

Tikkanen, Mikko; Gollan, Peter J; Mekala, Nageswara Rao; Isojärvi, Janne; Aro, Eva-Mari

2014-04-19

376

Student world view as a framework for learning genetics and evolution in high school biology  

NASA Astrophysics Data System (ADS)

Statement of the problem. Few studies in biology education have examined the underlying presuppositions which guide thinking and concept learning in adolescents. The purpose of this study was to describe and understand the biological world views of a variety of high school students before they take biology courses. Specifically, the study examined student world views in the domains of Classification, Relationship and Causation related to the concepts of heredity, evolution and biotechnology. The following served as guiding questions: (1) What are the personal world views of high school students entering biology classes, related to the domain of Classification, Relationship and Causality? (2) How do these student world views confound or enhance the learning of basic concepts in genetics and evolution? Methods. An interpretive method was chosen for this study. The six student participants were ninth graders and represented a wide range of world view backgrounds. A series of three interviews was conducted with each participant, with a focus group used for triangulation of data. The constant comparative method was used to categorize the data and facilitate the search for meaningful patterns. The analysis included a thick description of each student's personal views of classification, evolution and the appropriate use of biotechnology. Results. The study demonstrates that world view is the basis upon which students build knowledge in biology. The logic of their everyday thinking may not match that of scientists. The words they use are sometimes inconsistent with scientific terminology. This study provides evidence that students voice different opinions depending on the social situation, since they are strongly influenced by peers. Students classify animals based on behaviors. They largely believe that the natural world is unpredictable, and that humans are not really part of that world. Half are unlikely to accept the evolution of humans, but may accept it in other species. Their views on causation of evolution vary widely, focusing on intentional changes made by animals. Students who hold world views which differ from scientific world views may become marginalized unless differences in world view are addressed. Researchers and teachers must be mindful of social pressures which cause students to reject certain ideas which may appear to be in opposition to their existing world view.

McCoy, Roger Wesley

377

Genetic alterations of chromosomes, p53 and p16 genes in low- and high-grade bladder cancer  

PubMed Central

A majority of patients with bladder cancer present with superficial disease and subsequently, some patients show progression to muscle invasive or metastatic disease. Bladder cancer has a complex genetic process and identification of the genetic alterations which occur during progression may lead to