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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

Ægisdóttir, Hafdís Hanna; Kuss, Patrick; Stöcklin, Jürg

2009-01-01

2

Analysis of Genetic Interaction Networks Shows That Alternatively Spliced Genes Are Highly Versatile  

PubMed Central

Alternative splicing has the potential to increase the diversity of the transcriptome and proteome. Where more than one transcript arises from a gene they are often so different that they are quite unlikely to have the same function. However, it remains unclear if alternative splicing generally leads to a gene being involved in multiple biological processes or whether it alters the function within a single process. Knowing that genetic interactions occur between functionally related genes, we have used them as a proxy for functional versatility, and have analysed the sets of genes of two well-characterised model organisms: Caenorhabditis elegans and Drosophila melanogaster. Using network analyses we find that few genes are functionally homogenous (only involved in a few functionally-related biological processes). Moreover, there are differences between alternatively spliced genes and genes with a single transcript; specifically, genes with alternatively splicing are, on average, involved in more biological processes. Finally, we suggest that factors other than specific functional classes determine whether a gene is alternatively spliced. PMID:23409018

Talavera, David; Sheoran, Ritika; Lovell, Simon C.

2013-01-01

3

Batrachochytrium dendrobatidis Shows High Genetic Diversity and Ecological Niche Specificity among Haplotypes in the Maya Mountains of Belize  

PubMed Central

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

Kaiser, Kristine; Pollinger, John

2012-01-01

4

A new genome scan for primary nonsyndromic vesicoureteric reflux emphasizes high genetic heterogeneity and shows linkage and association with various genes already implicated in urinary tract development.  

PubMed

Primary vesicoureteric reflux (VUR), the retrograde flow of urine from the bladder toward the kidneys, results from a developmental anomaly of the vesicoureteric valve mechanism, and is often associated with other urinary tract anomalies. It is the most common urological problem in children, with an estimated prevalence of 1-2%, and is a major cause of hypertension in childhood and of renal failure in childhood or adult life. We present the results of a genetic linkage and association scan using 900,000 markers. Our linkage results show a large number of suggestive linkage peaks, with different results in two groups of families, suggesting that VUR is even more genetically heterogeneous than previously imagined. The only marker achieving P?

Darlow, J M; Dobson, M G; Darlay, R; Molony, C M; Hunziker, M; Green, A J; Cordell, H J; Puri, P; Barton, D E

2014-01-01

5

A new genome scan for primary nonsyndromic vesicoureteric reflux emphasizes high genetic heterogeneity and shows linkage and association with various genes already implicated in urinary tract development  

PubMed Central

Primary vesicoureteric reflux (VUR), the retrograde flow of urine from the bladder toward the kidneys, results from a developmental anomaly of the vesicoureteric valve mechanism, and is often associated with other urinary tract anomalies. It is the most common urological problem in children, with an estimated prevalence of 1–2%, and is a major cause of hypertension in childhood and of renal failure in childhood or adult life. We present the results of a genetic linkage and association scan using 900,000 markers. Our linkage results show a large number of suggestive linkage peaks, with different results in two groups of families, suggesting that VUR is even more genetically heterogeneous than previously imagined. The only marker achieving P?

Darlow, J M; Dobson, M G; Darlay, R; Molony, C M; Hunziker, M; Green, A J; Cordell, H J; Puri, P; Barton, D E

2014-01-01

6

Three genetic grapevine leafroll-associated virus 3 variants identified from South African vineyards show high variability in their 5?UTR  

Microsoft Academic Search

Three genetic variants of grapevine leafroll-associated virus 3 (GLRaV-3) were identified in vineyards of the Western Cape,\\u000a South Africa. The GLRaV-3 variants were identified by single-strand conformation polymorphism (SSCP) profiles generated from\\u000a a region amplified in ORF5. ORF5 sequence data confirmed the three genetic variant groups, and a specific SSCP profile was\\u000a assigned to each variant group. The results of

A. E. C. Jooste; H. J. Maree; D. U. Bellstedt; D. E. Goszczynski; G. Pietersen; J. T. Burger

2010-01-01

7

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

8

ORIGINAL PAPER Genetic variation of xylem hydraulic properties shows  

E-print Network

ORIGINAL PAPER Genetic variation of xylem hydraulic properties shows that wood density is involved understanding of the role of wood density in the hydraulic properties of xylem and may clarify the role of wood to cell wall proportion of the xylem is closely related to wood density (Bucci et al. 2004; Hacke et al

Boyer, Edmond

9

High Points of Human Genetics  

ERIC Educational Resources Information Center

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

Stern, Curt

1975-01-01

10

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.

11

New Genetic and Linguistic Analyses Show Ancient Human Influence on Baobab Evolution and Distribution in Australia  

PubMed Central

This study investigates the role of human agency in the gene flow and geographical distribution of the Australian baobab, Adansonia gregorii. The genus Adansonia is a charismatic tree endemic to Africa, Madagascar, and northwest Australia that has long been valued by humans for its multiple uses. The distribution of genetic variation in baobabs in Africa has been partially attributed to human-mediated dispersal over millennia, but this relationship has never been investigated for the Australian species. We combined genetic and linguistic data to analyse geographic patterns of gene flow and movement of word-forms for A. gregorii in the Aboriginal languages of northwest Australia. Comprehensive assessment of genetic diversity showed weak geographic structure and high gene flow. Of potential dispersal vectors, humans were identified as most likely to have enabled gene flow across biogeographic barriers in northwest Australia. Genetic-linguistic analysis demonstrated congruence of gene flow patterns and directional movement of Aboriginal loanwords for A. gregorii. These findings, along with previous archaeobotanical evidence from the Late Pleistocene and Holocene, suggest that ancient humans significantly influenced the geographic distribution of Adansonia in northwest Australia. PMID:25830225

Rangan, Haripriya; Bell, Karen L.; Baum, David A.; Fowler, Rachael; McConvell, Patrick; Saunders, Thomas; Spronck, Stef; Kull, Christian A.; Murphy, Daniel J.

2015-01-01

12

New genetic and linguistic analyses show ancient human influence on baobab evolution and distribution in australia.  

PubMed

This study investigates the role of human agency in the gene flow and geographical distribution of the Australian baobab, Adansonia gregorii. The genus Adansonia is a charismatic tree endemic to Africa, Madagascar, and northwest Australia that has long been valued by humans for its multiple uses. The distribution of genetic variation in baobabs in Africa has been partially attributed to human-mediated dispersal over millennia, but this relationship has never been investigated for the Australian species. We combined genetic and linguistic data to analyse geographic patterns of gene flow and movement of word-forms for A. gregorii in the Aboriginal languages of northwest Australia. Comprehensive assessment of genetic diversity showed weak geographic structure and high gene flow. Of potential dispersal vectors, humans were identified as most likely to have enabled gene flow across biogeographic barriers in northwest Australia. Genetic-linguistic analysis demonstrated congruence of gene flow patterns and directional movement of Aboriginal loanwords for A. gregorii. These findings, along with previous archaeobotanical evidence from the Late Pleistocene and Holocene, suggest that ancient humans significantly influenced the geographic distribution of Adansonia in northwest Australia. PMID:25830225

Rangan, Haripriya; Bell, Karen L; Baum, David A; Fowler, Rachael; McConvell, Patrick; Saunders, Thomas; Spronck, Stef; Kull, Christian A; Murphy, Daniel J

2015-01-01

13

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

14

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

15

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

16

Genetics Show Current Decline and Pleistocene Expansion in Northern Spotted Owls  

USGS Publications Warehouse

The northern spotted owl (Strix occidentalis caurina) is one of the most controversial threatened subspecies ever listed under the U.S. Endangered Species Act. Because of concern for persistence of the subspecies, logging on Federal lands in the U.S. Pacific Northwest was dramatically reduced under the Northwest Forest Plan in 1994. Despite protection of its remaining forest habitat, recent field studies show continued demographic declines of northern spotted owls. One potential threat to northern spotted owls that has not yet been shown is loss of genetic variation from population bottlenecks that can increase inbreeding depression and decrease adaptive potential. Here, we show recent genetic bottlenecks in northern spotted owls using a large genetic dataset (352 individuals from across the subspecies' range and 11 microsatellite loci). The signature of bottlenecks was strongest in Washington State, in agreement with field data. Interestingly, we also found a genetic signature of Pleistocene expansion in the same study areas where recent bottlenecks were shown. Our results provide independent evidence that northern spotted owls have recently declined, and suggest that loss of genetic variation is an emerging threat to the subspecies' persistence. Reduced effective population size (Ne), shown here in addition to field evidence for demographic decline, highlights the increasing vulnerability of this bird to extinction.

Funk, W. Chris; Forsman, Eric D.; Mullins, Thomas D.; Haig, Susan M.

2008-01-01

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

Graphene oxide immobilized enzymes show high thermal and solvent stability  

NASA Astrophysics Data System (ADS)

The thermal and solvent tolerance of enzymes is highly important for their industrial use. We show here that the enzyme lipase from Rhizopus oryzae exhibits exceptionally high thermal stability and high solvent tolerance and even increased activity in acetone when immobilized onto a graphene oxide (GO) nanosupport prepared by Staudenmaier and Brodie methods. We studied various forms of immobilization of the enzyme: by physical adsorption, covalent attachment, and additional crosslinking. The activity recovery was shown to be dependent on the support type, enzyme loading and immobilization procedure. Covalently immobilized lipase showed significantly better resistance to heat inactivation (the activity recovery was 65% at 70 °C) in comparison with the soluble counterpart (the activity recovery was 65% at 40 °C). Physically adsorbed lipase achieved over 100% of the initial activity in a series of organic solvents. These findings, showing enhanced thermal stability and solvent tolerance of graphene oxide immobilized enzyme, will have a profound impact on practical industrial scale uses of enzymes for the conversion of lipids into fuels.The thermal and solvent tolerance of enzymes is highly important for their industrial use. We show here that the enzyme lipase from Rhizopus oryzae exhibits exceptionally high thermal stability and high solvent tolerance and even increased activity in acetone when immobilized onto a graphene oxide (GO) nanosupport prepared by Staudenmaier and Brodie methods. We studied various forms of immobilization of the enzyme: by physical adsorption, covalent attachment, and additional crosslinking. The activity recovery was shown to be dependent on the support type, enzyme loading and immobilization procedure. Covalently immobilized lipase showed significantly better resistance to heat inactivation (the activity recovery was 65% at 70 °C) in comparison with the soluble counterpart (the activity recovery was 65% at 40 °C). Physically adsorbed lipase achieved over 100% of the initial activity in a series of organic solvents. These findings, showing enhanced thermal stability and solvent tolerance of graphene oxide immobilized enzyme, will have a profound impact on practical industrial scale uses of enzymes for the conversion of lipids into fuels. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr00438a

Hermanová, So?a; Zarevúcká, Marie; Bouša, Daniel; Pumera, Martin; Sofer, Zden?k

2015-03-01

19

Graphene oxide immobilized enzymes show high thermal and solvent stability.  

PubMed

The thermal and solvent tolerance of enzymes is highly important for their industrial use. We show here that the enzyme lipase from Rhizopus oryzae exhibits exceptionally high thermal stability and high solvent tolerance and even increased activity in acetone when immobilized onto a graphene oxide (GO) nanosupport prepared by Staudenmaier and Brodie methods. We studied various forms of immobilization of the enzyme: by physical adsorption, covalent attachment, and additional crosslinking. The activity recovery was shown to be dependent on the support type, enzyme loading and immobilization procedure. Covalently immobilized lipase showed significantly better resistance to heat inactivation (the activity recovery was 65% at 70 °C) in comparison with the soluble counterpart (the activity recovery was 65% at 40 °C). Physically adsorbed lipase achieved over 100% of the initial activity in a series of organic solvents. These findings, showing enhanced thermal stability and solvent tolerance of graphene oxide immobilized enzyme, will have a profound impact on practical industrial scale uses of enzymes for the conversion of lipids into fuels. PMID:25757536

Hermanová, So?a; Zarevúcká, Marie; Bouša, Daniel; Pumera, Martin; Sofer, Zden?k

2015-03-19

20

Genetic relations of First Stallion Inspection traits with dressage and show-jumping performance in competition of Dutch Warmblood horses  

Microsoft Academic Search

Genetic parameters for traits evaluated at the First Stallion Inspection (FSI) and genetic correlations with dressage and show-jumping performance in competition were estimated. Data comprised 2361 stallions with FSI-observations from 1994 through 1999. Genetic analyses were performed using univariate and bivariate animal models. Heritability estimates of the FSI-traits ranged from 0.25 to 0.61. FSI-traits related to gaits showed strong genetic

B. J. Ducro; E. P. C. Koenen; J. M. F. M. van Tartwijk; J. A. M. van Arendonk

2007-01-01

21

A UV-induced genetic network links the RSC complex to nucleotide excision repair and shows dose-dependent rewiring.  

PubMed

Efficient repair of UV-induced DNA damage requires the precise coordination of nucleotide excision repair (NER) with numerous other biological processes. To map this crosstalk, we generated a differential genetic interaction map centered on quantitative growth measurements of >45,000 double mutants before and after different doses of UV radiation. Integration of genetic data with physical interaction networks identified a global map of 89 UV-induced functional interactions among 62 protein complexes, including a number of links between the RSC complex and several NER factors. We show that RSC is recruited to both silenced and transcribed loci following UV damage where it facilitates efficient repair by promoting nucleosome remodeling. Finally, a comparison of the response to high versus low levels of UV shows that the degree of genetic rewiring correlates with dose of UV and reveals a network of dose-specific interactions. This study makes available a large resource of UV-induced interactions, and it illustrates a methodology for identifying dose-dependent interactions based on quantitative shifts in genetic networks. PMID:24360959

Srivas, Rohith; Costelloe, Thomas; Carvunis, Anne-Ruxandra; Sarkar, Sovan; Malta, Erik; Sun, Su Ming; Pool, Marijke; Licon, Katherine; van Welsem, Tibor; van Leeuwen, Fred; McHugh, Peter J; van Attikum, Haico; Ideker, Trey

2013-12-26

22

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

23

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

24

Resistance to oxidative stress shows low heritability and high common environmental variance in a wild bird.  

PubMed

Oxidative stress was recently demonstrated to affect several fitness-related traits and is now well recognized to shape animal life-history evolution. However, very little is known about how much resistance to oxidative stress is determined by genetic and environmental effects and hence about its potential for evolution, especially in wild populations. In addition, our knowledge of phenotypic sexual dimorphism and cross-sex genetic correlations in resistance to oxidative stress remains extremely limited despite important evolutionary implications. In free-living great tits (Parus major), we quantified heritability, common environmental effect, sexual dimorphism and cross-sex genetic correlation in offspring resistance to oxidative stress by performing a split-nest cross-fostering experiment where 155 broods were split, and all siblings (n = 791) translocated and raised in two other nests. Resistance to oxidative stress was measured as both oxidative damage to lipids and erythrocyte resistance to a controlled free-radical attack. Both measurements of oxidative stress showed low additive genetic variances, high common environmental effects and phenotypic sexual dimorphism with males showing a higher resistance to oxidative stress. Cross-sex genetic correlations were not different from unity, and we found no substantial heritability in resistance to oxidative stress at adult age measured on 39 individuals that recruited the subsequent year. Our study shows that individual ability to resist to oxidative stress is primarily influenced by the common environment and has a low heritability with a consequent low potential for evolution, at least at an early stage of life. PMID:25040169

Losdat, S; Helfenstein, F; Blount, J D; Richner, H

2014-09-01

25

Molecular Epidemiological Analysis of Mycoplasma bovis Isolates from the United Kingdom Shows Two Genetically Distinct Clusters  

PubMed Central

Mycoplasma bovis is an important veterinary pathogen causing pneumonia, arthritis, and mastitis in infected cattle. We investigated the genetic diversity of 53 isolates collected in the United Kingdom between 1996 and 2002 with pulsed-field gel electrophoresis (PFGE), amplified fragment length polymorphism (AFLP), and random amplified polymorphic DNA (RAPD) analysis. In addition, the influence of variable surface protein (Vsp) profiles on the profiles generated with molecular typing techniques was studied. Both AFLP and RAPD separated the isolates into two distinct groups, but PFGE showed less congruence with the other techniques. There was no clear relationship between the geographic origin or year of isolation of the isolates and the profiles produced. No correlation between Vsp profiles and any of the molecular typing techniques was observed. We propose that RAPD and AFLP provide valuable tools for molecular typing of M. bovis. PMID:15472309

McAuliffe, Laura; Kokotovic, Branko; Ayling, Roger D.; Nicholas, Robin A. J.

2004-01-01

26

Molecular epidemiological analysis of Mycoplasma bovis isolates from the United Kingdom shows two genetically distinct clusters.  

PubMed

Mycoplasma bovis is an important veterinary pathogen causing pneumonia, arthritis, and mastitis in infected cattle. We investigated the genetic diversity of 53 isolates collected in the United Kingdom between 1996 and 2002 with pulsed-field gel electrophoresis (PFGE), amplified fragment length polymorphism (AFLP), and random amplified polymorphic DNA (RAPD) analysis. In addition, the influence of variable surface protein (Vsp) profiles on the profiles generated with molecular typing techniques was studied. Both AFLP and RAPD separated the isolates into two distinct groups, but PFGE showed less congruence with the other techniques. There was no clear relationship between the geographic origin or year of isolation of the isolates and the profiles produced. No correlation between Vsp profiles and any of the molecular typing techniques was observed. We propose that RAPD and AFLP provide valuable tools for molecular typing of M. bovis. PMID:15472309

McAuliffe, Laura; Kokotovic, Branko; Ayling, Roger D; Nicholas, Robin A J

2004-10-01

27

Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment  

PubMed Central

The subseafloor marine biosphere may be one of the largest reservoirs of microbial biomass on Earth and has recently been the subject of debate in terms of the composition of its microbial inhabitants, particularly on sediments from the Peru Margin. A metagenomic analysis was made by using whole-genome amplification and pyrosequencing of sediments from Ocean Drilling Program Site 1229 on the Peru Margin to further explore the microbial diversity and overall community composition within this environment. A total of 61.9 Mb of genetic material was sequenced from sediments at horizons 1, 16, 32, and 50 m below the seafloor. These depths include sediments from both primarily sulfate-reducing methane-generating regions of the sediment column. Many genes of the annotated genes, including those encoding ribosomal proteins, corresponded to those from the Chloroflexi and Euryarchaeota. However, analysis of the 16S small-subunit ribosomal genes suggests that Crenarchaeota are the abundant microbial member. Quantitative PCR confirms that uncultivated Crenarchaeota are indeed a major microbial group in these subsurface samples. These findings show that the marine subsurface is a distinct microbial habitat and is different from environments studied by metagenomics, especially because of the predominance of uncultivated archaeal groups. PMID:18650394

Biddle, Jennifer F.; Fitz-Gibbon, Sorel; Schuster, Stephan C.; Brenchley, Jean E.; House, Christopher H.

2008-01-01

28

UNC study shows genetic, non-invasive test could improve colon cancer screening  

Cancer.gov

A non-invasive test that includes detection of the genetic abnormalities related to cancer could significantly improve the effectiveness of colon cancer screening, according to research from the UNC School of Medicine and UNC Lineberger Comprehensive Cancer Center.

29

Thinking positively: The genetics of high intelligence  

PubMed Central

High intelligence (general cognitive ability) is fundamental to the human capital that drives societies in the information age. Understanding the origins of this intellectual capital is important for government policy, for neuroscience, and for genetics. For genetics, a key question is whether the genetic causes of high intelligence are qualitatively or quantitatively different from the normal distribution of intelligence. We report results from a sibling and twin study of high intelligence and its links with the normal distribution. We identified 360,000 sibling pairs and 9000 twin pairs from 3 million 18-year-old males with cognitive assessments administered as part of conscription to military service in Sweden between 1968 and 2010. We found that high intelligence is familial, heritable, and caused by the same genetic and environmental factors responsible for the normal distribution of intelligence. High intelligence is a good candidate for “positive genetics” — going beyond the negative effects of DNA sequence variation on disease and disorders to consider the positive end of the distribution of genetic effects. PMID:25593376

Shakeshaft, Nicholas G.; Trzaskowski, Maciej; McMillan, Andrew; Krapohl, Eva; Simpson, Michael A.; Reichenberg, Avi; Cederlöf, Martin; Larsson, Henrik; Lichtenstein, Paul; Plomin, Robert

2015-01-01

30

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

ERIC Educational Resources Information Center

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

Malone, Molly

2012-01-01

31

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

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

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

34

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

PubMed

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

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

2012-01-01

35

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

Microsoft Academic Search

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

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

2011-01-01

36

Systems Level Analysis of Systemic Sclerosis Shows a Network of Immune and Profibrotic Pathways Connected with Genetic Polymorphisms  

PubMed Central

Systemic sclerosis (SSc) is a rare systemic autoimmune disease characterized by skin and organ fibrosis. The pathogenesis of SSc and its progression are poorly understood. The SSc intrinsic gene expression subsets (inflammatory, fibroproliferative, normal-like, and limited) are observed in multiple clinical cohorts of patients with SSc. Analysis of longitudinal skin biopsies suggests that a patient's subset assignment is stable over 6–12 months. Genetically, SSc is multi-factorial with many genetic risk loci for SSc generally and for specific clinical manifestations. Here we identify the genes consistently associated with the intrinsic subsets across three independent cohorts, show the relationship between these genes using a gene-gene interaction network, and place the genetic risk loci in the context of the intrinsic subsets. To identify gene expression modules common to three independent datasets from three different clinical centers, we developed a consensus clustering procedure based on mutual information of partitions, an information theory concept, and performed a meta-analysis of these genome-wide gene expression datasets. We created a gene-gene interaction network of the conserved molecular features across the intrinsic subsets and analyzed their connections with SSc-associated genetic polymorphisms. The network is composed of distinct, but interconnected, components related to interferon activation, M2 macrophages, adaptive immunity, extracellular matrix remodeling, and cell proliferation. The network shows extensive connections between the inflammatory- and fibroproliferative-specific genes. The network also shows connections between these subset-specific genes and 30 SSc-associated polymorphic genes including STAT4, BLK, IRF7, NOTCH4, PLAUR, CSK, IRAK1, and several human leukocyte antigen (HLA) genes. Our analyses suggest that the gene expression changes underlying the SSc subsets may be long-lived, but mechanistically interconnected and related to a patients underlying genetic risk. PMID:25569146

Mahoney, J. Matthew; Taroni, Jaclyn; Martyanov, Viktor; Wood, Tammara A.; Greene, Casey S.; Pioli, Patricia A.; Hinchcliff, Monique E.; Whitfield, Michael L.

2015-01-01

37

Systems level analysis of systemic sclerosis shows a network of immune and profibrotic pathways connected with genetic polymorphisms.  

PubMed

Systemic sclerosis (SSc) is a rare systemic autoimmune disease characterized by skin and organ fibrosis. The pathogenesis of SSc and its progression are poorly understood. The SSc intrinsic gene expression subsets (inflammatory, fibroproliferative, normal-like, and limited) are observed in multiple clinical cohorts of patients with SSc. Analysis of longitudinal skin biopsies suggests that a patient's subset assignment is stable over 6-12 months. Genetically, SSc is multi-factorial with many genetic risk loci for SSc generally and for specific clinical manifestations. Here we identify the genes consistently associated with the intrinsic subsets across three independent cohorts, show the relationship between these genes using a gene-gene interaction network, and place the genetic risk loci in the context of the intrinsic subsets. To identify gene expression modules common to three independent datasets from three different clinical centers, we developed a consensus clustering procedure based on mutual information of partitions, an information theory concept, and performed a meta-analysis of these genome-wide gene expression datasets. We created a gene-gene interaction network of the conserved molecular features across the intrinsic subsets and analyzed their connections with SSc-associated genetic polymorphisms. The network is composed of distinct, but interconnected, components related to interferon activation, M2 macrophages, adaptive immunity, extracellular matrix remodeling, and cell proliferation. The network shows extensive connections between the inflammatory- and fibroproliferative-specific genes. The network also shows connections between these subset-specific genes and 30 SSc-associated polymorphic genes including STAT4, BLK, IRF7, NOTCH4, PLAUR, CSK, IRAK1, and several human leukocyte antigen (HLA) genes. Our analyses suggest that the gene expression changes underlying the SSc subsets may be long-lived, but mechanistically interconnected and related to a patients underlying genetic risk. PMID:25569146

Mahoney, J Matthew; Taroni, Jaclyn; Martyanov, Viktor; Wood, Tammara A; Greene, Casey S; Pioli, Patricia A; Hinchcliff, Monique E; Whitfield, Michael L

2015-01-01

38

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

39

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

40

Synthetic incoherent feedforward circuits show adaptation to the amount of their genetic template  

PubMed Central

Natural and synthetic biological networks must function reliably in the face of fluctuating stoichiometry of their molecular components. These fluctuations are caused in part by changes in relative expression efficiency and the DNA template amount of the network-coding genes. Gene product levels could potentially be decoupled from these changes via built-in adaptation mechanisms, thereby boosting network reliability. Here, we show that a mechanism based on an incoherent feedforward motif enables adaptive gene expression in mammalian cells. We modeled, synthesized, and tested transcriptional and post-transcriptional incoherent loops and found that in all cases the gene product adapts to changes in DNA template abundance. We also observed that the post-transcriptional form results in superior adaptation behavior, higher absolute expression levels, and lower intrinsic fluctuations. Our results support a previously hypothesized endogenous role in gene dosage compensation for such motifs and suggest that their incorporation in synthetic networks will improve their robustness and reliability. PMID:21811230

Bleris, Leonidas; Xie, Zhen; Glass, David; Adadey, Asa; Sontag, Eduardo; Benenson, Yaakov

2011-01-01

41

Pediatric Brainstem Gangliogliomas Show BRAFV600E Mutation in a High Percentage of Cases  

PubMed Central

Brainstem gangliogliomas (GGs) often cannot be resected, have a much poorer prognosis than those located in more common supratentorial sites, and may benefit from novel therapeutic approaches. Therapeutically-targetable BRAF c.1799T>A (p.V600E) (BRAFV600E) mutations are harbored in roughly 50% of collective GGs taken from all anatomical sites. Large numbers of pediatric brainstem GGs, however, have not been specifically assessed and anatomic- and age-restricted assessment of genetic and biological factors are becoming increasingly important. Pediatric brainstem GGs (n=13), non-brainstem GGs (n=11), and brainstem pilocytic astrocytomas (PAs) (n=8) were screened by standard Sanger DNA sequencing of BRAF exon 15. Five of 13 (38%) pediatric GG harbored a definitive BRAFV600E mutation, with 2 others exhibiting an equivocal result by this method. BRAFV600E was also seen in 5/11 (45%) non-brainstem GGs and 1/8 (13%) brainstem PAs. VE1 immunostaining for BRAFV600E showed concordance with sequencing in 9/9 brainstem GGs including the two cases equivocal by Sanger. The equivocal brainstem GGs were subsequently shown to harbor BRAFV600E using a novel, more sensitive, RNA-sequencing approach, yielding a final BRAFV600E mutation frequency of 54% (7/13) in brainstem GGs. BRAFV600E-targeted therapeutics should be a consideration for the high percentage of pediatric brainstem GGs refractory to conventional therapies. PMID:24238153

Donson, Andrew M.; Kleinschmidt-DeMasters, B. K.; Aisner, Dara L.; Bemis, Lynne T.; Birks, Diane K.; Mulcahy Levy, Jean M.; Smith, Amy A.; Handler, Michael H.; Foreman, Nicholas K.; Rush, Sarah Z.

2014-01-01

42

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

43

Landscape genetics of high mountain frog metapopulations  

USGS Publications Warehouse

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.

Murphy, M.A.; Dezzani, R.; Pilliod, D.S.; Storfer, A.

2010-01-01

44

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

PubMed Central

The obesity epidemic is responsible for a substantial economic burden in developed countries and is a major risk factor for type 2 diabetes and cardiovascular disease. The disease is the result not only of several environmental risk factors, but also of genetic predisposition. To take advantage of recent advances in gene-mapping technology, we executed a genome-wide association scan to identify genetic variants associated with obesity-related quantitative traits in the genetically isolated population of Sardinia. Initial analysis suggested that several SNPs in the FTO and PFKP genes were associated with increased BMI, hip circumference, and weight. Within the FTO gene, rs9930506 showed the strongest association with BMI (p = 8.6 ×10?7), hip circumference (p = 3.4 × 10?8), and weight (p = 9.1 × 10?7). In Sardinia, homozygotes for the rare “G” allele of this SNP (minor allele frequency = 0.46) were 1.3 BMI units heavier than homozygotes for the common “A” allele. Within the PFKP gene, rs6602024 showed very strong association with BMI (p = 4.9 × 10?6). Homozygotes for the rare “A” allele of this SNP (minor allele frequency = 0.12) were 1.8 BMI units heavier than homozygotes for the common “G” allele. To replicate our findings, we genotyped these two SNPs in the GenNet study. In European Americans (N = 1,496) and in Hispanic Americans (N = 839), we replicated significant association between rs9930506 in the FTO gene and BMI (p-value for meta-analysis of European American and Hispanic American follow-up samples, p = 0.001), weight (p = 0.001), and hip circumference (p = 0.0005). We did not replicate association between rs6602024 and obesity-related traits in the GenNet sample, although we found that in European Americans, Hispanic Americans, and African Americans, homozygotes for the rare “A” allele were, on average, 1.0–3.0 BMI units heavier than homozygotes for the more common “G” allele. In summary, we have completed a whole genome–association scan for three obesity-related quantitative traits and report that common genetic variants in the FTO gene are associated with substantial changes in BMI, hip circumference, and body weight. These changes could have a significant impact on the risk of obesity-related morbidity in the general population. PMID:17658951

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

2007-01-01

45

Genetic Analysis of High Angular Resolution Diffusion Images (HARDI)  

E-print Network

Diffusion Imaging, tensor distribution function, structural equation model, twins, quantitative geneticsGenetic Analysis of High Angular Resolution Diffusion Images (HARDI) Liang Zhan1 , Alex D. Leow2 of Medical Research, Brisbane, Australia Abstract. Imaging genetics is a new field that extends methods from

Thompson, Paul

46

MULTIPARENTAL POPULATIONS High-Resolution Genetic Mapping of Complex Traits  

E-print Network

to fearful or stressful events (Mahan and Ressler 2012). Twin and family studies support a genetic basisMULTIPARENTAL POPULATIONS High-Resolution Genetic Mapping of Complex Traits from a Combined in Neuroscience, Middlebury College, Middlebury, Vermont 05753, and Department of Human Genetics and Department

Abney, Mark

47

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

ERIC Educational Resources Information Center

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

Haddow, Paula K.

1982-01-01

48

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

ERIC Educational Resources Information Center

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

Biological Sciences Curriculum Study Journal, 1980

1980-01-01

49

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

PubMed

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. PMID:25567926

Arnaud, Jean-François; Fénart, Stéphane; Cordellier, Mathilde; Cuguen, Joël

2010-05-01

50

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. PMID:25567926

Arnaud, Jean-François; Fénart, Stéphane; Cordellier, Mathilde; Cuguen, Joël

2010-01-01

51

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

PubMed Central

Most of our knowledge on learning and memory formation results from extensive studies on a small number of animal species. Although features and cellular pathways of learning and memory are highly similar in this diverse group of species, there are also subtle differences. Closely related species of parasitic wasps display substantial variation in memory dynamics and can be instrumental to understanding both the adaptive benefit of and mechanisms underlying this variation. Parasitic wasps of the genus Nasonia offer excellent opportunities for multidisciplinary research on this topic. Genetic and genomic resources available for Nasonia are unrivaled among parasitic wasps, providing tools for genetic dissection of mechanisms that cause differences in learning. This study presents a robust, high-throughput method for olfactory conditioning of Nasonia using a host encounter as reward. A T-maze olfactometer facilitates high-throughput memory retention testing and employs standardized odors of equal detectability, as quantified by electroantennogram recordings. Using this setup, differences in memory retention between Nasonia species were shown. In both Nasonia vitripennis and Nasonia longicornis, memory was observed up to at least 5 days after a single conditioning trial, whereas Nasonia giraulti lost its memory after 2 days. This difference in learning may be an adaptation to species-specific differences in ecological factors, for example, host preference. The high-throughput methods for conditioning and memory retention testing are essential tools to study both ultimate and proximate factors that cause variation in learning and memory formation in Nasonia and other parasitic wasp species. PMID:22804968

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

2012-01-01

52

The age related markers lipofuscin and apoptosis show different genetic architecture by QTL mapping in short-lived Nothobranchius fish  

PubMed Central

Annual fish of the genus Nothobranchius show large variations in lifespan and expression of age-related phenotypes between closely related populations. We studied N. kadleci and its sister species N. furzeri GRZ strain, and found that N.kadleci is longer-lived than the N. furzeri. Lipofuscin and apoptosis measured in the liver increased with age in N. kadleci with different profiles: lipofuscin increased linearly, while apoptosis declined in the oldest animals. More lipofuscin (P < 0.001) and apoptosis (P < 0.001) was observed in N. furzeri than in N. kadleci at 16w age. Lipofuscin and apoptotic cells were then quantified in hybrids from the mating of N. furzeri to N. kadleci. F1 individuals showed heterosis for lipofuscin but additive effects for apoptosis. These two age-related phenotypes were not correlated in F2 hybrids. Quantitative trait loci analysis of 287 F2 fish using 237 markers identified two QTL accounting for 10% of lipofuscin variance (P < 0.001) with overdominance effect. Apoptotic cells revealed three significant- and two suggestive QTL explaining 19% of variance (P < 0.001), showing additive and dominance effects, and two interacting loci. Our results show that lipofuscin and apoptosis are markers of different age-dependent biological processes controlled by different genetic mechanisms. PMID:25093339

Ng'oma, Enoch; Reichwald, Kathrin; Dorn, Alexander; Wittig, Michael; Balschun, Tobias; Franke, Andre; Platzer, Matthias; Cellerino, Allesandro

2014-01-01

53

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

54

Student Problem Solving in High School Genetics.  

ERIC Educational Resources Information Center

Describes set of specific steps (procedural knowledge) used when solving monohybrid/dihybrid cross problems and extent to which students could justify execution of each step in terms of their conceptual knowledge of genetics and meiosis. Implications for genetics instruction are discussed. (JN)

Stewart, James

1983-01-01

55

68. Joe Moore, Photographer. September, 1996. B51 SHOWING HIGH BAY ...  

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

68. Joe Moore, Photographer. September, 1996. B51 SHOWING HIGH BAY DOOR (C) and B51L IN FOREGROUND - University of California Radiation Laboratory, Bevatron, 1 Cyclotron Road, Berkeley, Alameda County, CA

56

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 Beach and Belle Glade had waited to hear for so long. On Tuesday, with new record-breaking academic of struggles, the improved grades at Boynton Beach, Lake Worth and Glades Central High were cause

Belogay, Eugene A.

57

Phylogenetic character mapping of proteomic diversity shows high correlation with subspecific phylogenetic diversity in Trypanosoma cruzi.  

PubMed

We performed a phylogenetic character mapping on 26 stocks of Trypanosoma cruzi, the parasite responsible for Chagas disease, and 2 stocks of the sister taxon T. cruzi marinkellei to test for possible associations between T. cruzi-subspecific phylogenetic diversity and levels of protein expression, as examined by proteomic analysis and mass spectrometry. We observed a high level of correlation (P < 10(-4)) between genetic distance, as established by multilocus enzyme electrophoresis, and proteomic dissimilarities estimated by proteomic Euclidian distances. Several proteins were found to be specifically associated to T. cruzi phylogenetic subdivisions (discrete typing units). This study explores the previously uncharacterized links between infraspecific phylogenetic diversity and gene expression in a human pathogen. It opens the way to searching for new vaccine and drug targets and for identification of specific biomarkers at the subspecific level of pathogens. PMID:21059959

Telleria, Jenny; Biron, David G; Brizard, Jean-Paul; Demettre, Edith; Séveno, Martial; Barnabé, Christian; Ayala, Francisco J; Tibayrenc, Michel

2010-11-23

58

Phylogenetic character mapping of proteomic diversity shows high correlation with subspecific phylogenetic diversity in Trypanosoma cruzi  

PubMed Central

We performed a phylogenetic character mapping on 26 stocks of Trypanosoma cruzi, the parasite responsible for Chagas disease, and 2 stocks of the sister taxon T. cruzi marinkellei to test for possible associations between T. cruzi–subspecific phylogenetic diversity and levels of protein expression, as examined by proteomic analysis and mass spectrometry. We observed a high level of correlation (P < 10?4) between genetic distance, as established by multilocus enzyme electrophoresis, and proteomic dissimilarities estimated by proteomic Euclidian distances. Several proteins were found to be specifically associated to T. cruzi phylogenetic subdivisions (discrete typing units). This study explores the previously uncharacterized links between infraspecific phylogenetic diversity and gene expression in a human pathogen. It opens the way to searching for new vaccine and drug targets and for identification of specific biomarkers at the subspecific level of pathogens. PMID:21059959

Telleria, Jenny; Biron, David G.; Brizard, Jean-Paul; Demettre, Edith; Séveno, Martial; Barnabé, Christian; Ayala, Francisco J.; Tibayrenc, Michel

2010-01-01

59

Mice fed on a diet enriched with genetically engineered multivitamin corn show no sub-acute toxic effects and no sub-chronic toxicity.  

PubMed

Multivitamin corn is a novel genetically engineered variety that simultaneously produces high levels of ?-carotene, ascorbate and folate, and therefore has the potential to address simultaneously multiple micronutrient deficiencies caused by the lack of vitamins A, B9 and C in developing country populations. As part of the development process for genetically engineered crops and following European Food Safety Authority (EFSA) recommendations, multivitamin corn must be tested in whole food/feed sub-chronic animal feeding studies to ensure there are no adverse effects, and potential allergens must be identified. We carried out a 28-day toxicity assessment in mice, which showed no short-term sub-acute evidence of diet-related adverse health effects and no difference in clinical markers (food consumption, body weight, organ/tissue weight, haematological and biochemical blood parameters and histopathology) compared to mice fed on a control diet. A subsequent 90-day sub-chronic feeding study again showed no indications of toxicity compared to mice fed on control diets. Our data confirm that diets enriched with multivitamin corn have no adverse effects on mice, do not induce any clinical signs of toxicity and do not contain known allergens. PMID:22928600

Arjó, Gemma; Capell, Teresa; Matias-Guiu, Xavier; Zhu, Changfu; Christou, Paul; Piñol, Carme

2012-12-01

60

Synthesis of high-impedance FSSs using genetic algorithms  

Microsoft Academic Search

In this paper, a genetic algorithm-based technique for synthesizing high impedance surfaces is presented. These surfaces behave like a perfect magnetic conductor (PMC) in a certain frequency range; to achieve this result, a multilayered dielectric structure in conjunction with an FSS screen and a perfectly electric conductor (PEC) ground plane have been used. The genetic algorithm (GA) uses an electromagnetic

Luigi Lanuzza; Agostino Monorchio; Giuliano Manara

2002-01-01

61

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

62

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

Microsoft Academic Search

Dynamic changes in protein conformation in response to external stimuli are important in biological processes, but it has proved difficult to directly visualize such structural changes under physiological conditions. Here, we show that high-speed atomic force microscopy can be used to visualize dynamic changes in stimulated proteins. High-resolution movies of a light-driven proton pump, bacteriorhodopsin, reveal that, upon illumination, a

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

2010-01-01

63

Multilocus Phylogenetics Show High Levels of Endemic Fusaria Inhabiting Sardinian Soils (Tyrrhenian Islands)  

Technology Transfer Automated Retrieval System (TEKTRAN)

The Mediterranean island of Sardinia is well known for high levels of vascular plant diversity and endemism, but little is known about its microbial diversity. Under the hypothesis that Fusarium species would show similar patterns, we estimated variability in Fusarium species composition among ten ...

64

Executive deficits in Individuals at High Genetic Risk of Schizophrenia   

E-print Network

Background. Studies of individuals at high genetic risk (HR) of schizophrenia have shown subtle deficits in the domains of executive functions. However, executive abilities also depend on working memory, which is one of the most prominent...

Dimitrova, R

2012-11-28

65

Computational methods for high-throughput pooled genetic experiments  

E-print Network

Advances in high-throughput DNA sequencing have created new avenues of attack for classical genetics problems. This thesis develops and applies principled methods for analyzing DNA sequencing data from multiple pools of ...

Edwards, Matthew Douglas

2011-01-01

66

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

Microsoft Academic Search

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

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

67

Chipping away at the common epilepsies with complex genetics: the 15q13.3 microdeletion shows the way  

PubMed Central

The idiopathic epilepsies are genetically heterogeneous with more than 50 clinical classifications. They are characterized by episodic seizures arising from erratic neuronal discharge in susceptible individuals. The most common predisposing genetic cause is the recently discovered chromosome 15q13.3 microdeletion. Other disorders previously attributed to the same lesion include autism, intellectual disability and schizophrenia. This phenotypic spectrum is most easily imagined as a contiguous gene syndrome with idiopathic generalized epilepsy as the most common clinical manifestation. Expressivity of the microdeletion in carriers is too variable for antenatal prediction of phenotype to be possible; however, when it is detected in living affected cases, it can be taken as the major predisposing cause for the observed phenotype. The discovery of this small 15q13.3 lesion barely scratches the surface that conceals what we ultimately need to know about the molecular genetic mechanisms behind the common epilepsies with complex genetics, but it provides valuable insight into how to proceed toward that goal. PMID:19341504

2009-01-01

68

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

Microsoft Academic Search

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

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

2007-01-01

69

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

Technology Transfer Automated Retrieval System (TEKTRAN)

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

70

A Multifunctional Drug Combination Shows Highly Potent Therapeutic Efficacy against Human Cancer Xenografts in Athymic Mice  

PubMed Central

The tumor microenvironment plays a crucial role during tumor development. Integrated combination of drugs that target tumor microenvironment is a promising approach to anticancer therapy. Here, we report a multifunctional combination of low-cytotoxic drugs composed of dipyridamole, bestatin and dexamethasone (DBDx) which mainly acts on the tumor microenvironment shows highly potent antitumor efficacy in vivo. In mouse hepatoma H22 model, the triple drug combination showed synergistic and highly potent antitumor efficacy. The combination indices of various combinations of the triple drugs were between 0.2 and 0.5. DBDx inhibited the growth of a panel of human tumor xenografts and showed no obvious systemic toxicity. At tolerated doses, DBDx suppressed the growth of human hepatocellular carcinoma BEL-7402, HepG2, and lung adenocarcinoma A549 xenografts by 94.5%, 93.7% and 96.9%, respectively. Clonogenic assay demonstrated that DBDx showed weak cytotoxicity. Western blot showed that Flk1 and Nos3 were down-regulated in the DBDx-treated group. Proteomic analysis showed that DBDx mainly affected the metabolic process and immune system process; in addition, the angiogenesis and VEGF signaling pathway were also affected. Conclusively, DBDx, a multifunctional drug combination of three low-cytotoxic drugs, shows synergistic and highly potent antitumor efficacy evidently mediated by the modulation of tumor microenvironment. Based on its low-cytotoxic attributes and its broad-spectrum antitumor therapeutic efficacy, this multifunctional combination might be useful in the treatment of cancers, especially those refractory to conventional chemotherapeutics. PMID:25531414

Li, Yi; Wu, Shu-Ying; Zhen, Yong-Su

2014-01-01

71

The fission yeast chromo domain encoding gene chp1(+) is required for chromosome segregation and shows a genetic interaction with alpha-tubulin.  

PubMed Central

In eukaryotes, the segregation of chromosomes is co-ordinated by the centromere and must proceed accurately if aneuploidy and cell death are to be avoided. The fission yeast centromere is complex, containing highly repetitive regions of DNA showing the characteristics of heterochromatin. Two proteins, Swi6p and Clr4p, that are associated with the fission yeast centromere also contain a chromo (chromatin organisation modifier) domain and are required for centromere function. We have analysed a novel fission yeast gene encoding a putative chromo domain called chp 1(+) (chromo domain protein in Schizosaccharomyces p ombe ). In the absence of Chp1p protein, cells are viable but show chromosome segregation defects such as lagging chromosomes on the spindle during anaphase and high rates of minichromosome loss, phenotypes which are also displayed by swi 6 and clr 4. A fusion protein between green fluorescent protein (GFP) and Chp1p, like Swi6p, is localized to discrete sites within the nucleus. In contrast to Swi6p and Clr4p, Chp1p is not required to repress silent mating-type genes. We demonstrate a genetic interaction between chp 1(+) and alpha-tubulin ( nda 2(+)) and between swi 6(+) and beta-tubulin ( nda 3(+)). Chp1p and Swi6p proteins may be components of the kinetochore which captures and stabilizes the microtubules of the spindle. PMID:9722643

Doe, C L; Wang, G; Chow, C; Fricker, M D; Singh, P B; Mellor, E J

1998-01-01

72

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

73

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

74

Ecotypic differentiation in Medicago polymorpha L. along an environmental gradient in central Chile. RAPDs studies show little genetic divergence  

Microsoft Academic Search

Burr medic (Medicago polymorpha) is distributed in a wide range of bioclimatic and edaphic conditions throughout the mediterranean-climate region of Chile.\\u000a Previous studies on populations of M. polymorpha collected along this gradient revealed a remarkable ecotypic differentiation in many adaptive traits. Random amplified polymorphic\\u000a DNA (RAPD) was used to evaluate genetic divergence in 36 accessions collected along the entire gradient.

M. Paredes; V. Becerra; C. Rojo; A. Del Pozo; C. Ovalle; J. Aronson

2002-01-01

75

Villous, hypermucinous mucosa in long standing ulcerative colitis shows high frequency of K-ras mutations  

PubMed Central

BACKGROUND—K-ras mutation is one of the first genetic alterations in classical colorectal carcinogenesis.?AIMS—To investigate the role of K-ras mutations in carcinogenesis, in long standing ulcerative colitis.?METHODS—A total of 161 microdissected and 100 DNA samples from 13 patients were analysed for K-ras codons 12 and 13 mutations by means of a combination of enriched polymerase chain reaction amplification and temporal temperature gradient electrophoresis.?RESULTS—K-ras mutations were found in 21/161 (13%) microdissected samples in 7/13 large bowels (16 and five in codons 12 and 13, respectively), and in 10/100 (10%) mucosal DNA samples (six and four, respectively). One of four patients with six adenocarcinomas had a K-ras mutation in a carcinoma, as well as one of two patients with large dysplasia associated lesion or mass (DALM). Eight of 13 (61%) areas with villous architecture and large, distended goblet cells, had a K-ras mutation, which was significantly more frequent than in low grade dysplasia (one of 23, 4%) but did not reach significance versus high grade dysplasia (four of 14, 28.5%). K-ras mutations were found in one of 20 (5%) flat lesions indefinite for dysplasia, two of 14 (14%) in non-villous, hypermucinous mucosa, and in one of 57 flat areas negative for dysplasia.?CONCLUSION—The highest K-ras mutation frequency was found in villous, hypermucinous mucosa. We suggest that this entity should be investigated further as a potential risk lesion for cancer development. It may represent a pathway directly from non-classical dysplasia to cancer, not previously described.???Keywords: K-ras mutations; ulcerative colitis; dysplasia; dysplasia associated lesion or mass PMID:10517904

Andersen, S; Lovig, T; Clausen, O; Bakka, A; Fausa, O; Rognum, T

1999-01-01

76

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

ERIC Educational Resources Information Center

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

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

2011-01-01

77

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

78

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

79

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

PubMed

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

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

2011-01-01

80

Genetic engineering for high methionine grain legumes.  

PubMed

Methionine (Met) is the primary limiting essential amino acid in grain legumes. The imbalance in amino acid composition restricts their biological value (BV) to 55 to 75% of that of animal protein. So far improvement of the BV could not be achieved by conventional breeding. Therefore, genetic engineering was employed by several laboratories to resolve the problem. Three strategies have been followed. A) Engineering for increased free Met levels; B) engineering of endogenous storage proteins with increased numbers of Met residues; C) transfer of foreign genes encoding Met-rich proteins, e.g. the Brazil nut 2S albumin (BNA) and its homologue from sunflower, into grain legumes. The latter strategy turned out to be most promising. In all cases the gene was put under the control of a developmentally regulated seed specific promoter and transferred into grain legumes using the bacterial Agrobacterium tumefaciens-system. Integration into and copy numbers in the plant genome as well as Mendelian inheritance and gene dosage effects were verified. After correct precursor processing the mature 2S albumin was intracellularly deposited in protein bodies which are part of the vacuolar compartment. The foreign protein amounted to 5 to 10% of the total seed protein in the best transgenic lines of narbon bean (Vicia narbonensis L., used in the authors' laboratories), lupins (Lupinus angustifolius L., used in CSIRO, Australia), and soybean (Glycine max (L.) Merr., used by Pioneer Hi-Bred, Inc., USA). In the narbon bean the increase of Met was directly related to the amount of 2S albumin in the transgenic seeds, but in soybean it remained below the theoretically expected value. Nevertheless, trangenic soybean reached 100%, whereas narbon bean and lupins reached approximately 80% of the FAO-standard for nutritionally balanced food proteins. These results document that the Met problem of grain legumes can be resolved by genetic engineering. PMID:9739551

Müntz, K; Christov, V; Saalbach, G; Saalbach, I; Waddell, D; Pickardt, T; Schieder, O; Wüstenhagen, T

1998-08-01

81

Genetic analysis shows low levels of hybridization between African wildcats (Felis silvestris lybica) and domestic cats (F. s. catus) in South Africa.  

PubMed

Hybridization between domestic and wild animals is a major concern for biodiversity conservation, and as habitats become increasingly fragmented, conserving biodiversity at all levels, including genetic, becomes increasingly important. Except for tropical forests and true deserts, African wildcats occur across the African continent; however, almost no work has been carried out to assess its genetic status and extent of hybridization with domestic cats. For example, in South Africa it has been argued that the long-term viability of maintaining pure wildcat populations lies in large protected areas only, isolated from human populations. Two of the largest protected areas in Africa, the Kgalagadi Transfrontier and Kruger National Parks, as well as the size of South Africa and range of landscape uses, provide a model situation to assess how habitat fragmentation and heterogeneity influences the genetic purity of African wildcats. Using population genetic and home range data, we examined the genetic purity of African wildcats and their suspected hybrids across South Africa, including areas within and outside of protected areas. Overall, we found African wildcat populations to be genetically relatively pure, but instances of hybridization and a significant relationship between the genetic distinctiveness (purity) of wildcats and human population pressure were evident. The genetically purest African wildcats were found in the Kgalagadi Transfrontier Park, while samples from around Kruger National Park showed cause for concern, especially combined with the substantial human population density along the park's boundary. While African wildcat populations in South Africa generally appear to be genetically pure, with low levels of hybridization, our genetic data do suggest that protected areas may play an important role in maintaining genetic purity by reducing the likelihood of contact with domestic cats. We suggest that approaches such as corridors between protected areas are unlikely to remain effective for wildcat conservation, as the proximity to human settlements around these areas is projected to increase the wild/domestic animal interface. Thus, large, isolated protected areas will become increasingly important for wildcat conservation and efforts need to be made to prevent introduction of domestic cats into these areas. PMID:25691958

Le Roux, Johannes J; Foxcroft, Llewellyn C; Herbst, Marna; MacFadyen, Sandra

2015-01-01

82

Genetic analysis shows low levels of hybridization between African wildcats (Felis silvestris lybica) and domestic cats (F. s. catus) in South Africa  

PubMed Central

Hybridization between domestic and wild animals is a major concern for biodiversity conservation, and as habitats become increasingly fragmented, conserving biodiversity at all levels, including genetic, becomes increasingly important. Except for tropical forests and true deserts, African wildcats occur across the African continent; however, almost no work has been carried out to assess its genetic status and extent of hybridization with domestic cats. For example, in South Africa it has been argued that the long-term viability of maintaining pure wildcat populations lies in large protected areas only, isolated from human populations. Two of the largest protected areas in Africa, the Kgalagadi Transfrontier and Kruger National Parks, as well as the size of South Africa and range of landscape uses, provide a model situation to assess how habitat fragmentation and heterogeneity influences the genetic purity of African wildcats. Using population genetic and home range data, we examined the genetic purity of African wildcats and their suspected hybrids across South Africa, including areas within and outside of protected areas. Overall, we found African wildcat populations to be genetically relatively pure, but instances of hybridization and a significant relationship between the genetic distinctiveness (purity) of wildcats and human population pressure were evident. The genetically purest African wildcats were found in the Kgalagadi Transfrontier Park, while samples from around Kruger National Park showed cause for concern, especially combined with the substantial human population density along the park's boundary. While African wildcat populations in South Africa generally appear to be genetically pure, with low levels of hybridization, our genetic data do suggest that protected areas may play an important role in maintaining genetic purity by reducing the likelihood of contact with domestic cats. We suggest that approaches such as corridors between protected areas are unlikely to remain effective for wildcat conservation, as the proximity to human settlements around these areas is projected to increase the wild/domestic animal interface. Thus, large, isolated protected areas will become increasingly important for wildcat conservation and efforts need to be made to prevent introduction of domestic cats into these areas. PMID:25691958

Le Roux, Johannes J; Foxcroft, Llewellyn C; Herbst, Marna; MacFadyen, Sandra

2015-01-01

83

Genome-wide meta-analysis of observational studies shows common genetic variants associated with macronutrient intake1234  

PubMed Central

Background: Macronutrient intake varies substantially between individuals, and there is evidence that this variation is partly accounted for by genetic variants. Objective: The objective of the study was to identify common genetic variants that are associated with macronutrient intake. Design: We performed 2-stage genome-wide association (GWA) meta-analysis of macronutrient intake in populations of European descent. Macronutrients were assessed by using food-frequency questionnaires and analyzed as percentages of total energy consumption from total fat, protein, and carbohydrate. From the discovery GWA (n = 38,360), 35 independent loci associated with macronutrient intake at P < 5 × 10?6 were identified and taken forward to replication in 3 additional cohorts (n = 33,533) from the DietGen Consortium. For one locus, fat mass obesity-associated protein (FTO), cohorts with Illumina MetaboChip genotype data (n = 7724) provided additional replication data. Results: A variant in the chromosome 19 locus (rs838145) was associated with higher carbohydrate (? ± SE: 0.25 ± 0.04%; P = 1.68 × 10?8) and lower fat (? ± SE: ?0.21 ± 0.04%; P = 1.57 × 10?9) consumption. A candidate gene in this region, fibroblast growth factor 21 (FGF21), encodes a fibroblast growth factor involved in glucose and lipid metabolism. The variants in this locus were associated with circulating FGF21 protein concentrations (P < 0.05) but not mRNA concentrations in blood or brain. The body mass index (BMI)–increasing allele of the FTO variant (rs1421085) was associated with higher protein intake (? ± SE: 0.10 ± 0.02%; P = 9.96 × 10?10), independent of BMI (after adjustment for BMI, ? ± SE: 0.08 ± 0.02%; P = 3.15 × 10?7). Conclusion: Our results indicate that variants in genes involved in nutrient metabolism and obesity are associated with macronutrient consumption in humans. Trials related to this study were registered at clinicaltrials.gov as NCT00005131 (Atherosclerosis Risk in Communities), NCT00005133 (Cardiovascular Health Study), NCT00005136 (Family Heart Study), NCT00005121 (Framingham Heart Study), NCT00083369 (Genetic and Environmental Determinants of Triglycerides), NCT01331512 (InCHIANTI Study), and NCT00005487 (Multi-Ethnic Study of Atherosclerosis). PMID:23636237

Tanaka, Toshiko; Ngwa, Julius S; van Rooij, Frank JA; Zillikens, M Carola; Wojczynski, Mary K; Frazier-Wood, Alexis C; Houston, Denise K; Kanoni, Stavroula; Lemaitre, Rozenn N; Luan, Jian'an; Mikkilä, Vera; Renstrom, Frida; Sonestedt, Emily; Zhao, Jing Hua; Chu, Audrey Y; Qi, Lu; Chasman, Daniel I; de Oliveira Otto, Marcia C; Dhurandhar, Emily J; Feitosa, Mary F; Johansson, Ingegerd; Khaw, Kay-Tee; Lohman, Kurt K; Manichaikul, Ani; McKeown, Nicola M; Mozaffarian, Dariush; Singleton, Andrew; Stirrups, Kathleen; Viikari, Jorma; Ye, Zheng; Bandinelli, Stefania; Barroso, Inês; Deloukas, Panos; Forouhi, Nita G; Hofman, Albert; Liu, Yongmei; Lyytikäinen, Leo-Pekka; North, Kari E; Dimitriou, Maria; Hallmans, Goran; Kähönen, Mika; Langenberg, Claudia; Ordovas, Jose M; Uitterlinden, André G; Hu, Frank B; Kalafati, Ioanna-Panagiota; Raitakari, Olli; Franco, Oscar H; Johnson, Andrew; Emilsson, Valur; Schrack, Jennifer A; Semba, Richard D; Siscovick, David S; Arnett, Donna K; Borecki, Ingrid B; Franks, Paul W; Kritchevsky, Stephen B; Lehtimäki, Terho; Loos, Ruth JF; Orho-Melander, Marju; Rotter, Jerome I; Wareham, Nicholas J; Witteman, Jacqueline CM; Ferrucci, Luigi; Dedoussis, George; Cupples, L Adrienne; Nettleton, Jennifer A

2013-01-01

84

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; Gonçalves, Priscila; Miyaki, Cristina Yumi; Baker, Allan J.

2011-01-01

85

Low genetic variability in the highly endangered mediterranean monk seal.  

PubMed

Genetic variability is an important component in the ability of populations to adapt in the face of environmental change. Here we report the first description of nuclear genetic variability in the only remaining sizable colony of the Mediterranean monk seal (Monachus monachus), located at Cap Blanc (Western Sahara, Mauritania), whose estimated size during the study period (1994-May 1997) was about 320 individuals. We tested 42 microsatellite loci isolated from five pinniped species in a sample of 52 pups. Three loci failed to give any product, and of the remaining 39, only 15 were polymorphic, with a maximum of 3 alleles detected. Three loci appeared to be X-linked. No departures from Hardy-Weinberg equilibrium were detected and no genetic structure was found between the two nursing caves currently occupied by the seals. Several analytical methods show that, as a consequence of a severe bottleneck, the population has suffered a decrease in genetic variability over the last few centuries. PMID:15247308

Pastor, T; Garza, J C; Allen, P; Amos, W; Aguilar, A

2004-01-01

86

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, Valérie; Guilloton, Fabien; Espagnolle, Nicolas; Cordonier, Thomas; Heymann, Dominique; Layrolle, Pierre; Sensébé, Luc; Deschaseaux, Frédéric

2012-01-01

87

Linkage and LOH studies in 19 cylindromatosis families show no evidence of genetic heterogeneity and refine the CYLD locus on chromosome 16q12-q13.  

PubMed

Familial cylindromatosis is an autosomal dominant predisposition to multiple neoplasms of the skin appendages. The susceptibility gene has previously been mapped to chromosome 16q12-q13 and has features of a recessive oncogene/tumour suppressor gene. We have now evaluated 19 families with this disease by a combination of genetic linkage analysis and loss of heterozygosity in cylindromas from affected individuals. All 15 informative families show linkage to this locus, providing no evidence for genetic heterogeneity. Recombinant mapping has placed the gene in an interval of approximately 1 Mb. There is no evidence, between families, of haplotype sharing that might be indicative of common founder mutations. PMID:10982183

Takahashi, M; Rapley, E; Biggs, P J; Lakhani, S R; Cooke, D; Hansen, J; Blair, E; Hofmann, B; Siebert, R; Turner, G; Evans, D G; Schrander-Stumpel, C; Beemer, F A; van Vloten, W A; Breuning, M H; van den Ouweland, A; Halley, D; Delpech, B; Cleveland, M; Leigh, I; Chapman, P; Burn, J; Hohl, D; Görög, J P; Seal, S; Mangion, J

2000-01-01

88

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

Microsoft Academic Search

Holoprosencephaly (HPE), the most common structural malformation of the forebrain in humans, can be detected early during\\u000a pregnancy using prenatal ultrasonography . Among foetuses with a normal karyotype, 14% have mutations in the four main HPE\\u000a genes (SHH, ZIC2, SIX3 and TGIF). Genomic rearrangements have now been implicated in many genetic diseases, so we hypothesized that microdeletions in the\\u000a major

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

2006-01-01

89

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

90

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

PubMed Central

Peptide Nucleic Acids (PNAs), nucleic acid analogues showing high stability to enzyme degradation and strong affinity and specificity of binding toward DNA and RNA are widely investigated as tools to interfere in gene expression. Several studies have been focused on PNA analogues with modifications on the backbone and bases in the attempt to overcome solubility, uptake and aggregation issues. ? PNAs, PNA derivatives having a substituent in the ? position of the backbone show interesting properties in terms of secondary structure and affinity of binding toward complementary nucleic acids. In this paper we illustrate our results obtained on new analogues, bearing a sulphate in the ? position of the backbone, developed to be more DNA-like in terms of polarity and charge. The synthesis of monomers and oligomers is described. NMR studies on the conformational properties of monomers and studies on the secondary structure of single strands and triplexes are reported. Furthermore the hybrid stability and the effect of mismatches on the stability have also been investigated. Finally, the ability of the new analogue to work as antigene, interfering with the transcription of the ErbB2 gene on a human cell line overexpressing ErbB2 (SKBR3), assessed by FACS and qPCR, is described. PMID:22586450

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

2012-01-01

91

? Sulphate PNA (PNA S): highly selective DNA binding molecule showing promising antigene activity.  

PubMed

Peptide Nucleic Acids (PNAs), nucleic acid analogues showing high stability to enzyme degradation and strong affinity and specificity of binding toward DNA and RNA are widely investigated as tools to interfere in gene expression. Several studies have been focused on PNA analogues with modifications on the backbone and bases in the attempt to overcome solubility, uptake and aggregation issues. ? PNAs, PNA derivatives having a substituent in the ? position of the backbone show interesting properties in terms of secondary structure and affinity of binding toward complementary nucleic acids. In this paper we illustrate our results obtained on new analogues, bearing a sulphate in the ? position of the backbone, developed to be more DNA-like in terms of polarity and charge. The synthesis of monomers and oligomers is described. NMR studies on the conformational properties of monomers and studies on the secondary structure of single strands and triplexes are reported. Furthermore the hybrid stability and the effect of mismatches on the stability have also been investigated. Finally, the ability of the new analogue to work as antigene, interfering with the transcription of the ErbB2 gene on a human cell line overexpressing ErbB2 (SKBR3), assessed by FACS and qPCR, is described. PMID:22586450

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

2012-01-01

92

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

PubMed Central

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

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

2012-01-01

93

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

94

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

PubMed Central

A novel lectin was isolated from the mushroom Agrocybe aegerita (designated AAL-2) by affinity chromatography with GlcNAc (N-acetylglucosamine)-coupled Sepharose 6B after ammonium sulfate precipitation. The AAL-2 coding sequence (1224 bp) was identified by performing a homologous search of the five tryptic peptides identified by MS against the translated transcriptome of A. aegerita. The molecular mass of AAL-2 was calculated to be 43.175 kDa from MS, which was consistent with the data calculated from the amino acid sequence. To analyse the carbohydrate-binding properties of AAL-2, a glycan array composed of 465 glycan candidates was employed, and the result showed that AAL-2 bound with high selectivity to terminal non-reducing GlcNAc residues, and further analysis revealed that AAL-2 bound to terminal non-reducing GlcNAc residues with higher affinity than previously well-known GlcNAc-binding lectins such as WGA (wheatgerm agglutinin) and GSL-II (Griffonia simplicifolia lectin-II). ITC (isothermal titration calorimetry) showed further that GlcNAc bound to AAL-2 in a sequential manner with moderate affinity. In the present study, we also evaluated the anti-tumour activity of AAL-2. The results showed that AAL-2 could bind to the surface of hepatoma cells, leading to induced cell apoptosis in vitro. Furthermore, AAL-2 exerted an anti-hepatoma effect via inhibition of tumour growth and prolongation of survival time of tumour-bearing mice in vivo. PMID:22268569

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

2012-01-01

95

Culturable associated-bacteria of the sponge Theonella swinhoei show tolerance to high arsenic concentrations  

PubMed Central

Sponges are potent filter feeders and as such are exposed to high fluxes of toxic trace elements, which can accumulate in their body over time. Such is the case of the Red Sea sponge Theonella swinhoei, which has been shown to accumulate up to 8500 mg/Kg of the highly toxicelement arsenic. T. swinhoei is known to harbor a multitude of sponge-associated bacteria, so it is hypothesized that the associated-bacteria will be tolerant to high arsenic concentration. This study also investigates the fate of the arsenic accumulated in the sponge to test if the associated-bacteria have an important role in the arsenic accumulation process of their host, since bacteria are key players in the natural arsenic cycle. Separation of the sponge to sponge cells and bacteria enriched fractions showed that arsenic is accumulated by the bacteria. Sponge-associated, arsenic-tolerant bacteria were cultured in the presence of 5 mM of either arsenate or arsenite (equivalent to 6150 mg/Kg arsenic, dry weight). The 54 isolated bacteria were grouped to 15 operational taxonomic units (OTUs) and isolates belonging to 12 OTUs were assessed for tolerance to arsenate at increased concentrations up to 100 mM. Eight of the 12 OTUs tolerated an order of magnitude increase in the concentration of arsenate, and some exhibited external biomineralization of arsenic–magnesium salts. The biomineralization of this unique mineral was directly observed in bacteria for the first time. These results may provide an explanation for the ability of the sponge to accumulate considerable amounts of arsenic. Furthermore arsenic-mineralizing bacteria can potentially be used for the study of bioremediation, as arsenic toxicity affects millions of people worldwide.

Keren, Ray; Lavy, Adi; Mayzel, Boaz; Ilan, Micha

2015-01-01

96

Biological Invasions: Paradox Lost and Paradise Gained A new study shows how an invasive snail species accrues elevated genetic  

E-print Network

Dispatches Biological Invasions: Paradox Lost and Paradise Gained A new study shows how an invasive human interference in animal and plant dispersal, biological invasions are wreaking havoc that can become economically and ecologically threatening. Recent studies of biological invasions, however

Hufbauer, Ruth A.

97

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

NASA Astrophysics Data System (ADS)

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

Stengler, E.; Sirera, J. M.

2011-09-01

98

[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

99

High-performance of geometric primitives detection usinig genetic algorithm  

Microsoft Academic Search

In this paper, we present some new methods for high performance of geometric primitives detection using a genetic algorithm (GA). At first, we describe the detection algorithm based on minimal subset and improvement of fitness function of geometric primitives. Secondly, we analyze the structure of minimal subsets and its probability properties in a digital image, and we improved the probability

Yao Dong Wang; Noboru FUNAKUBO

1999-01-01

100

Genetics  

Technology Transfer Automated Retrieval System (TEKTRAN)

Maintaining genetic variation in wild populations of Arctic organisms is fundamental to the long-term persistence of high latitude biodiversity. Variability is important because it provides options for species to respond to changing environmental conditions and novel challenges such as emerging path...

101

European Invasion of North American Pinus strobus at Large and Fine Scales: High Genetic Diversity and Fine-Scale Genetic Clustering over Time in the Adventive Range  

PubMed Central

Background North American Pinus strobus is a highly invasive tree species in Central Europe. Using ten polymorphic microsatellite loci we compared various aspects of the large-scale genetic diversity of individuals from 30 sites in the native distribution range with those from 30 sites in the European adventive distribution range. To investigate the ascertained pattern of genetic diversity of this intercontinental comparison further, we surveyed fine-scale genetic diversity patterns and changes over time within four highly invasive populations in the adventive range. Results Our data show that at the large scale the genetic diversity found within the relatively small adventive range in Central Europe, surprisingly, equals the diversity found within the sampled area in the native range, which is about thirty times larger. Bayesian assignment grouped individuals into two genetic clusters separating North American native populations from the European, non-native populations, without any strong genetic structure shown over either range. In the case of the fine scale, our comparison of genetic diversity parameters among the localities and age classes yielded no evidence of genetic diversity increase over time. We found that SGS differed across age classes within the populations under study. Old trees in general completely lacked any SGS, which increased over time and reached its maximum in the sapling stage. Conclusions Based on (1) the absence of difference in genetic diversity between the native and adventive ranges, together with the lack of structure in the native range, and (2) the lack of any evidence of any temporal increase in genetic diversity at four highly invasive populations in the adventive range, we conclude that population amalgamation probably first happened in the native range, prior to introduction. In such case, there would have been no need for multiple introductions from previously isolated populations, but only several introductions from genetically diverse populations. PMID:23874648

Mandák, Bohumil; Hadincová, V?roslava; Mahelka, Václav; Wildová, Radka

2013-01-01

102

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

103

Facial emotion perception differs in young persons at genetic and clinical high-risk for psychosis.  

PubMed

A large body of literature has documented facial emotion perception impairments in schizophrenia. More recently, emotion perception has been investigated in persons at genetic and clinical high-risk for psychosis. This study compared emotion perception abilities in groups of young persons with schizophrenia, clinical high-risk, genetic risk and healthy controls. Groups, ages 13-25, included 24 persons at clinical high-risk, 52 first-degree relatives at genetic risk, 91 persons with schizophrenia and 90 low risk persons who completed computerized testing of emotion recognition and differentiation. Groups differed by overall emotion recognition abilities and recognition of happy, sad, anger and fear expressions. Pairwise comparisons revealed comparable impairments in recognition of happy, angry, and fearful expressions for persons at clinical high-risk and schizophrenia, while genetic risk participants were less impaired, showing reduced recognition of fearful expressions. Groups also differed for differentiation of happy and sad expressions, but differences were mainly between schizophrenia and control groups. Emotion perception impairments are observable in young persons at-risk for psychosis. Preliminary results with clinical high-risk participants, when considered along findings in genetic risk relatives, suggest social cognition abilities to reflect pathophysiological processes involved in risk of schizophrenia. PMID:24582775

Kohler, Christian G; Richard, Jan A; Brensinger, Colleen M; Borgmann-Winter, Karin E; Conroy, Catherine G; Moberg, Paul J; Gur, Ruben C; Gur, Raquel E; Calkins, Monica E

2014-05-15

104

In Vivo High-Resolution 7 Tesla MRI Shows Early and Diffuse Cortical Alterations in CADASIL  

PubMed Central

Background and Purpose Recent data suggest that early symptoms may be related to cortex alterations in CADASIL (Cerebral Autosomal-Dominant Arteriopathy with Subcortical Infarcts and Leukoencephalopathy), a monogenic model of cerebral small vessel disease (SVD). The aim of this study was to investigate cortical alterations using both high-resolution T2* acquisitions obtained with 7 Tesla MRI and structural T1 images with 3 Tesla MRI in CADASIL patients with no or only mild symptomatology (modified Rankin’s scale ?1 and Mini Mental State Examination (MMSE) ?24). Methods Complete reconstructions of the cortex using 7 Tesla T2* acquisitions with 0.7 mm isotropic resolution were obtained in 11 patients (52.1±13.2 years, 36% male) and 24 controls (54.8±11.0 years, 42% male). Seven Tesla T2* within the cortex and cortical thickness and morphology obtained from 3 Tesla images were compared between CADASIL and control subjects using general linear models. Results MMSE, brain volume, cortical thickness and global sulcal morphology did not differ between groups. By contrast, T2* measured by 7 Tesla MRI was significantly increased in frontal, parietal, occipital and cingulate cortices in patients after correction for multiple testing. These changes were not related to white matter lesions, lacunes or microhemorrhages in patients having no brain atrophy compared to controls. Conclusions Seven Tesla MRI, by contrast to state of the art post-processing of 3 Tesla acquisitions, shows diffuse T2* alterations within the cortical mantle in CADASIL whose origin remains to be determined. PMID:25165824

De Guio, François; Reyes, Sonia; Vignaud, Alexandre; Duering, Marco; Ropele, Stefan; Duchesnay, Edouard; Chabriat, Hugues; Jouvent, Eric

2014-01-01

105

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

106

Mammary and vaginal myofibroblastomas are genetically related lesions: fluorescence in situ hybridization analysis shows deletion of 13q14 region.  

PubMed

Partial monosomy 13q, a chromosomal alteration originally reported in spindle cell lipoma, has also been documented in a few cases of mammary myofibroblastoma. Subsequently, a monoallelic loss of RB1 and FOXO1, located on 13q14, was identified in some cases of cellular angiofibroma, a benign stromal tumor of the lower female genital tract. This cytogenetic finding and the overlapping morphologic and immunohistochemical features shared by spindle cell lipoma, mammary myofibroblastoma, and cellular angiofibroma strongly suggest a histogenetic link among these tumors. Recently, we have emphasized morphologic and immunohistochemical similarities between mammary and vulvovaginal myofibroblastoma. The aim of the present study was to asses if these 2 tumors share the same chromosomal alteration. We studied the chromosome 13q14 region by fluorescence in situ hybridization analysis in a series of mammary and vaginal myofibroblastomas, with a readable signal in 7 of 13 mammary myofibroblastomas and 5 of 7 cases of vaginal myofibroblastomas. Despite histologic variation, most of the mammary (5/7) and vaginal (3/5) myofibroblastomas showed monoallelic deletion of FOXO1 in more than 22% of the cell populations. Our findings confirm that mammary myofibroblastoma is a tumor that exhibits chromosome abnormalities associated with the loss of the 13q14 region. In addition, we show for the first time that myofibroblastoma of the lower female genital tract also exhibits the same chromosomal abnormality, supporting the hypothesis that both tumors are in the spectrum of a single entity, likely arising from a common precursor cell. PMID:22575260

Magro, Gaetano; Righi, Alberto; Casorzo, Laura; Antonietta, Torrisi; Salvatorelli, Lucia; Kacerovská, Denisa; Kazakov, Dmitry; Michal, Michal

2012-11-01

107

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

PubMed Central

Background Ants typically distinguish nestmates from non-nestmates based on the perception of colony-specific chemicals, particularly cuticular hydrocarbons present on the surface of the ants' exoskeleton. These recognition cues are believed to play an important role in the formation of vast so-called supercolonies that have been described for some invasive ant species, but general conclusions about the role of these cues are hampered by only few species being studied. Here we use data on cuticular hydrocarbons, aggression and microsatellite genetic markers to investigate the interdependence of chemical recognition cues, genetic distance and nestmate discrimination in the pharaoh ant (Monomorium pharaonis), a widespread pest species, and ask whether introduced populations of this species are genetically differentiated and exhibit intraspecific aggression. Results Microsatellite analyses of a total of 35 colonies from four continents revealed extremely high levels of genetic differentiation between almost all colonies (FST = 0.751 ± 0.006 SE) and very low within-colony diversity. This implies that at least 34 and likely hundreds more independent lineages of this ant have spread worldwide. Aggression tests involving workers from 14 different colonies showed only low levels of aggression, even between colonies that were geographically and/or genetically very distant. Chemical analyses of groups of worker ants showed that all colonies had the same cuticular compounds, which varied only quantitatively among colonies. There was a positive correlation between geographical and genetic distance, but no other significant relationships were detected between aggression, chemical profile, genetic distance and geographical distance. Conclusions The pharaoh ant has a global invasion history of numerous independent introductions resulting in genetically highly differentiated colonies typically displaying surprisingly low levels of intraspecific aggression, a behaviour that may have evolved in the native range or by lineage selection in the introduced range. PMID:20591186

2010-01-01

108

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

109

Spatial Heterogeneity as a Genetic Mixing Mechanism in Highly Philopatric Colonial Seabirds  

PubMed Central

How genetic diversity is maintained in philopatric colonial systems remains unclear, and understanding the dynamic balance of philopatry and dispersal at all spatial scales is essential to the study of the evolution of coloniality. In the King penguin, Aptenodytes patagonicus, return rates of post-fledging chicks to their natal sub-colony are remarkably high. Empirical studies have shown that adults return year after year to their previous breeding territories within a radius of a few meters. Yet, little reliable data are available on intra- and inter-colonial dispersal in this species. Here, we present the first fine-scale study of the genetic structure in a king penguin colony in the Crozet Archipelago. Samples were collected from individual chicks and analysed at 8 microsatellite loci. Precise geolocation data of hatching sites and selective pressures associated with habitat features were recorded for all sampling locations. We found that despite strong natal and breeding site fidelity, king penguins retain a high degree of panmixia and genetic diversity. Yet, genetic structure appears markedly heterogeneous across the colony, with higher-than-expected inbreeding levels, and local inbreeding and relatedness hotspots that overlap predicted higher-quality nesting locations. This points towards heterogeneous population structure at the sub-colony level, in which fine-scale environmental features drive local philopatric behaviour, while lower-quality patches may act as genetic mixing mechanisms at the colony level. These findings show how a lack of global genetic structuring can emerge from small-scale heterogeneity in ecological parameters, as opposed to the classical model of homogeneous dispersal. Our results also emphasize the importance of sampling design for estimation of population parameters in colonial seabirds, as at high spatial resolution, basic genetic features are shown to be location-dependent. Finally, this study stresses the importance of understanding intra-colonial dispersal and genetic mixing mechanisms in order to better estimate species-wide gene flows and population dynamics. PMID:25680103

Cristofari, Robin; Trucchi, Emiliano; Whittington, Jason D.; Vigetta, Stéphanie; Gachot-Neveu, Hélène; Stenseth, Nils Christian; Le Maho, Yvon; Le Bohec, Céline

2015-01-01

110

DNA markers indicate low genetic diversity and high genetic divergence in the landlocked freshwater goby, Rhinogobius sp. YB, in the Ryukyu Archipelago, Japan.  

PubMed

Genetic diversity and genetic divergence were investigated in the landlocked goby Rhinogobius sp. YB by analysis of seven microsatellite DNA loci and the mtDNA control region sequence, and were compared with those of the closely related amphidromous species Rhinogobius sp. DA. Samples of Rhinogobius sp. YB and Rhinogobius sp. DA were collected from seven and four rivers, respectively. All pairwise Fst tests based on microsatellite DNA showed significant genetic differences, except for one pair of populations of Rhinogobius sp. DA (P<0.00064, alpha=78). The average Nei's genetic distance was 0.616 in Rhinogobius sp. YB and 0.394 in Rhinogobius sp. DA. Forty-two haplotypes were detected in both species, and almost all Rhinogobius sp. YB populations included different haplotypes. The means of allelic richness, Ho, and He in Rhinogobius sp. YB (2.057, 0.149, and 0.156, respectively) were significantly lower than in Rhinogobius sp. DA (4.868, 0.366, and 0.403, respectively; P<0.05). The high genetic divergence and low genetic diversity in Rhinogobius sp. YB may have resulted from repeated colonizations of rivers by different founders. Efforts to conserve genetic resources should take these evolutionarily significant units (ESU) of Rhinogobius sp. YB into account. The genetic markers used in this study provide simple and highly informative indicators for Rhinogobius sp. YB population management. PMID:18459821

Ohara, Kenichi; Takagi, Motohiro; Hashimoto, Miho; Miyazaki, Kazunori; Hirashima, Kentaro

2008-04-01

111

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

112

Comparison of Microbial Diversity of Korean Commercial Makgeolli Showing High ?-Glucan Content and High Antihypertensive Activity, Respectively.  

PubMed

We measured physiological functionalities, including antihypertensive angiotensin I-converting enzyme inhibitory activity and immun-stimulating ?-glucan content for sixty kinds of Makgeolli that is commercially available from the market. As a result, we selected R-12 commercial raw Makgeolli, with a high content of immuno-stimulating ?-glucan, and R-14 commercial raw Makgeolli, exhibiting high antihypertensive activity. Due to the similarities in their overall physicochemical properties and raw materials used for fermentation, we compared the microbial flora in order to investigate the reason for the differences in their functionalities. Nested PCR and denaturing gradient gel electrophoresis for yeasts and bacteria were performed for analysis of microbial diversity of two different kinds of Makgeolli (i.e., R-12, R-14), which showed immuno-stimulating ?-glucan content and exhibited a very high level of antihypertensive activity, respectively. Analysis of the 18S rDNA amplicon revealed a major presence of the yeast strain Pichia burtonii in every Makgeolli sample. Analysis of the 16S rDNA amplicon revealed a predominance of lactic acid bacteria, and the most frequent lactic acid bacteria were Lactobacillus ingluviei, L. fermentum, and L. harbinensis, and Lactobacillus sp. Among these, L. harbinensis was detected only in R-12 and L. ingluviei was found only in R-14. Different functionalities from the individual commercially available Makgeolli may be attributed to actions of different microbial flora during fermentation. PMID:22870058

Min, Jin-Hong; Kim, Young-Hun; Kim, Jae-Ho; Choi, Shin-Yang; Lee, Jong-Soo; Kim, Ha-Kun

2012-06-01

113

Genetic causes of high and low serum HDL-cholesterol  

PubMed Central

Plasma levels of HDL cholesterol (HDL-C) have a strong inherited basis with heritability estimates of 40-60%. The well-established inverse relationship between plasma HDL-C levels and the risk of coronary artery disease (CAD) has led to an extensive search for genetic factors influencing HDL-C concentrations. Over the past 30 years, candidate gene, genome-wide linkage, and most recently genome-wide association (GWA) studies have identified several genetic variations for plasma HDL-C levels. However, the functional role of several of these variants remains unknown, and they do not always correlate with CAD. In this review, we will first summarize what is known about HDL metabolism, monogenic disorders associated with both low and high HDL-C levels, and candidate gene studies. Then we will focus this review on recent genetic findings from the GWA studies and future strategies to elucidate the remaining substantial proportion of HDL-C heritability. Comprehensive investigation of the genetic factors conferring to low and high HDL-C levels using integrative approaches is important to unravel novel pathways and their relations to CAD, so that more effective means of diagnosis, treatment, and prevention will be identified. PMID:20421590

Weissglas-Volkov, Daphna; Pajukanta, Päivi

2010-01-01

114

WT1 mutations are secondary events in AML, show varying frequencies and impact on prognosis between genetic subgroups.  

PubMed

To investigate frequency and prognostic impact of Wilms tumor 1 (WT1) mutations (mut), we analyzed 3157 unselected acute myeloid leukemia patients for WT1mut in exons 7 and 9. In total, 188 WT1 mutations were detected (exon 7: n=150, exon 9: n=38); 141 were frameshift, 24 missense, 14 non-sense, 7 splice site and 2 indel mutations. In 175/3157 (5.5%) patients, a WT1mut was found. Higher frequencies were detected in patients with biallelic CEBPAmut (13.6%; P=0.001), followed by t(15;17)/PML-RARA (11.0%, P=0.004), and FLT3-ITD (8.5%, P<0.001). WT1mut were rare in DNMT3Amut (4.4%, P=0.014), ASXL1mut (1.7%, P<0.001), IDH2R140 (1.7%, P=0.001) and IDH1R132 (0.9%, P<0.001), and not detected in complex karyotypes (P=0.047). They were more frequent in females than in males (6.6 vs 4.7%; P=0.014) and in patients <60 years (P<0.001). Analysis of paired samples of 35 patients revealed a relatively unstable character of WT1mut (65.7% retained, 34.3% lost WT1mut at relapse). In the total cohort and subgroups with high WT1mut incidences (biallelic CEBPAmut, PML-RARA), WT1mut had no impact on prognosis. In normal karyotype AML, WT1mut patients had shorter event-free survival (EFS) (10.8 vs 17.9 m, P=0.008). In multivariate analysis, WT1mut had an independent adverse impact on EFS (P=0.002, hazard ratio (HR): 1.64) besides FLT3-ITD status (P<0.001, HR: 1.71) and age (P<0.001, HR: 1.28). PMID:25110071

Krauth, M-T; Alpermann, T; Bacher, U; Eder, C; Dicker, F; Ulke, M; Kuznia, S; Nadarajah, N; Kern, W; Haferlach, C; Haferlach, T; Schnittger, S

2015-03-01

115

Study Shows Aspirin Reduces Colorectal Cancer in Those at High Risk  

Cancer.gov

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

116

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

117

High genetic polymorphism among Giardia duodenalis isolates from Sahrawi children.  

PubMed

Human giardiasis, the gastrointestinal infection caused by two genetically different groups (or assemblages) of Giardia duodenalis, is very common worldwide, and its prevalence is higher in developing countries. However, few surveys in these regions have been performed to include a genetic characterization of the parasite, which is necessary to unravel the complex epidemiology of the infection. In this work, we screened 120 faecal samples collected from Sahrawi children in 2003-2005, and found 41 (34.2%) of them to be positive, using immunofluorescent microscopy, for the presence of G. duodenalis cysts. Molecular characterization of the isolates was performed by RFLP and/or sequence analysis of the triose phosphate isomerase (tpi) and the glutamate dehydrogenase (gdh) genes. The results disclosed an unexpectedly high genetic polymorphism among isolates of both assemblages A and B, and a large percentage of the sequences (50% for the tpi gene, and 90% for the gdh gene) from assemblage B isolates characterized by the presence of overlapping nucleotide peaks at specific positions in the chromatograms, which can be attributed to mixed infections or to allelic sequence heterozygosity of single cysts. Notably, this phenomenon was not observed in sequences from assemblage A isolates. These results suggest that the genetic structure is different in isolates of assemblages A and B. PMID:19477474

Lalle, Marco; Bruschi, Fabrizio; Castagna, Barbara; Campa, Mario; Pozio, Edoardo; Cacciò, Simone M

2009-08-01

118

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

2012-01-01

119

Breeding for improved potato nutrition: High amylose starch potatoes show promise as fiber source  

Technology Transfer Automated Retrieval System (TEKTRAN)

Potato starch is composed of approximately 75% amylopectin and 25% amylose. We are interested in breeding for higher amylose content, which would increase the fiber content of potato and decrease glycemic index. In order to make progress in a breeding program, we have developed a high throughput ass...

120

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.

121

Source-Sink Estimates of Genetic Introgression Show Influence of Hatchery Strays on Wild Chum Salmon Populations in Prince William Sound, Alaska  

PubMed Central

The extent to which stray, hatchery-reared salmon affect wild populations is much debated. Although experiments show that artificial breeding and culture influence the genetics of hatchery salmon, little is known about the interaction between hatchery and wild salmon in a natural setting. Here, we estimated historical and contemporary genetic population structures of chum salmon (Oncorhynchus keta) in Prince William Sound (PWS), Alaska, with 135 single nucleotide polymorphism (SNP) markers. Historical population structure was inferred from the analysis of DNA from fish scales, which had been archived since the late 1960’s for several populations in PWS. Parallel analyses with microsatellites and a test based on Hardy-Weinberg proportions showed that about 50% of the fish-scale DNA was cross-contaminated with DNA from other fish. These samples were removed from the analysis. We used a novel application of the classical source-sink model to compare SNP allele frequencies in these archived fish-scales (1964–1982) with frequencies in contemporary samples (2008–2010) and found a temporal shift toward hatchery allele frequencies in some wild populations. Other populations showed markedly less introgression, despite moderate amounts of hatchery straying. The extent of introgression may reflect similarities in spawning time and life-history traits between hatchery and wild fish, or the degree that hybrids return to a natal spawning area. The source-sink model is a powerful means of detecting low levels of introgression over several generations. PMID:24349150

Jasper, James R.; Habicht, Christopher; Moffitt, Steve; Brenner, Rich; Marsh, Jennifer; Lewis, Bert; Creelman Fox, Elisabeth; Grauvogel, Zac; Rogers Olive, Serena D.; Grant, W. Stewart

2013-01-01

122

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

123

RXTE shows a transition to the high-soft state in MAXI J1659-152  

NASA Astrophysics Data System (ADS)

The last two RXTE observations of the new galactic black hole candidate MAXI J1659-152 (Atels #2873,#2877,#2881) performed on October 17, 2010, 04:16 UT and 18:52 UT have clearly shown changes in the source spectral and variability properties consistent with a transition to the high soft state. Specifically, the power density spectrum have shown the rms variability level of about 5% presented by the low frequency red noise only.

Shaposhnikov, Nikolai; Yamaoka, Kazutaka

2010-10-01

124

[Developing and applying of a parentage identification approach based on high density genetic markers].  

PubMed

Pedigree is an important information source in the studies on human genetics and animal/plant breeding. Pedigree error is a common data error in breeding practice. It can affect the reliability of results from researches such as gene mapping, genetic or phenotypic value prediction. By using genetic markers, several approaches can identify the suspected pedigrees, but most of them are complex and the allowed number of genetic markers is limited, such as Cervus. Since the wide use of high density single nucleotide polymorphisms (SNPs) in human genetic and animal/plant breeding, a new parentage identification approach (named EasyPC, Easy Pedigree Checking) based on whole genome genetic data was proposed in this study. EasyPC was compared with Cervus on efficiency, and validated with a Chinese Holstein cattle (n=2180) and a Duroc swine (n=191) population. Results showed that EasyPC was much less time demanding than Cervus, and pedigree error rates were 20% for cattle and 6% for swine. Result from the cattle population is in accordance with previous study. By analyzing the empirical distribution of Mendelian error rate calculated in a population using all available SNPs, EasyPC not only can identify the correctness of a pedigree in a simple, fast, and accurate manner, but also can correct the wrong pedigree. EasyPC provides a promising alternative solution to traditional pedigree correction approaches and eases the data analysis of whole genome related studies. PMID:25143282

Zhang, Zhe; Luo, Yuanyu; Li, Qingqing; He, Jinlong; Gao, Ning; Zhang, Hao; Ding, Xiangdong; Zhang, Qin; Li, Jiaqi

2014-08-01

125

Genetic Signatures Reveal High-Altitude Adaptation in a Set of Ethiopian Populations  

E-print Network

Article Genetic Signatures Reveal High-Altitude Adaptation in a Set of Ethiopian Populations Emilia, the genetic targets of selection may, in part, have differed be- tween these populations: for example and Center of Human Genetic Diversity, Addis Ababa, Ethiopia 6 The Centre for Genetic Anthropology

Nielsen, Rasmus

126

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

127

Assembly of three coordination polymers based on a sulfonic-carboxylic ligand showing high proton conductivity.  

PubMed

Three new coordination polymers (CPs)/metal-organic frameworks (MOFs) with different structures have been synthesized using 4,8-disulfonyl-2,6-naphthalenedicarboxylic acid (H4L) and metal ions, Cu(2+), Ca(2+) and Cd(2+). The Cu compound features a one-dimensional chain structure, further extending into a 2D layer network through H-bond interactions. Both the Ca and Cd compounds show 3D frameworks with (4,4)-connected PtS-type topology and (3,6)-connected bct-type topology, respectively. These CPs/MOFs all exhibit proton conduction behavior, especially for the Cu compound with a proton conductivity of 3.46 × 10(-3) S cm(-1) at 368 K and 95% relative humidity (RH). Additionally, the activation energy (Ea) has also been investigated to deeply understand the proton-conduction mechanism. PMID:25406590

Zhao, Shu-Na; Song, Xue-Zhi; Zhu, Min; Meng, Xing; Wu, Lan-Lan; Song, Shu-Yan; Wang, Cheng; Zhang, Hong-Jie

2015-01-21

128

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.

129

Decarbonizing urban transport in European cities: four cases show possibly high co-benefits  

NASA Astrophysics Data System (ADS)

Cities worldwide are increasingly becoming agents of climate change mitigation, while simultaneously aiming for other goals, such as improved accessibility and clean air. Based on stakeholder interviews and data analysis, we assess the current state of urban mobility in the four European cities of Barcelona, Malmö, Sofia and Freiburg. We then provide scenarios of increasingly ambitious policy packages, reducing greenhouse gas emissions from urban transport by up to 80% from 2010 to 2040. We find significant concurrent co-benefits in cleaner air, reduced noise ambience, fewer traffic-related injuries and deaths, more physical activity, less congestion and monetary fuel savings. Our scenarios suggest that non-motorized transport, especially bicycles, can occupy high modal shares, particularly in cities with less than 0.5 million inhabitants. We think that this kind of multi-criteria assessment of social costs and benefits is a useful complement to cost-benefit analysis of climate change mitigation measures.

Creutzig, Felix; Mühlhoff, Rainer; Römer, Julia

2012-12-01

130

Map showing high-purity silica sand of Middle Ordovician age in the Midwestern states  

USGS Publications Warehouse

Certain quartz sands of Middle Ordovician age in the Midwestern States are well known for their purity and are exploited for a wide variety of industrial uses. The principal Middle Ordovician formations containing high-purity sands are the St. Peter Sandstone which crops out extensively from Minnesota to Arkansas; the Everton Formation principally of Arkansas; and the Oil Creek, McLish, and Tulip Creek Formations (all of the Simpson Group) of Oklahoma. The St. Peter and sandy beds in the other formations are commonly called "sandstones," but a more appropriate term is "sands" for in most fresh exposures they are completely uncemented or very weakly cemented. On exposure to air, uncemented sands usually become "case hardened" where evaporating ground water precipitates mineral matter at the surface; but this is a surficial effect. This report summarizes the available information on the extent of exposures, range of grain size, and chemical composition of the Middle Ordovician sands.

Ketner, Keith B.

1979-01-01

131

High Genetic Variability of Schistosoma haematobium in Mali and Nigeria  

PubMed Central

Schistosoma haematobium is one of the most prevalent parasitic flatworms, infecting over 112 million people in Africa. However, little is known about the genetic diversity of natural S. haematobium populations from the human host because of the inaccessible location of adult worms in the host. We used 4 microsatellite loci to genotype individually pooled S. haematobium eggs directly from each patient sampled at 4 endemic locations in Africa. We found that the average allele number of individuals from Mali was significantly higher than that from Nigeria. In addition, no significant difference in allelic composition was detected among the populations within Nigeria; however, the allelic composition was significantly different between Mali and Nigeria populations. This study demonstrated a high level of genetic variability of S. haematobium in the populations from Mali and Nigeria, the 2 major African endemic countries, suggesting that geographical population differentiation may occur in the regions. PMID:25748721

Ezeh, Charles; Yin, Mingbo; Li, Hongyan; Zhang, Ting; Xu, Bin; Sacko, Moussa; Feng, Zheng; Hu, Wei

2015-01-01

132

High risks of losing genetic diversity in an endemic Mauritian gecko: implications for conservation.  

PubMed

Genetic structure can be a consequence of recent population fragmentation and isolation, or a remnant of historical localised adaptation. This poses a challenge for conservationists since misinterpreting patterns of genetic structure may lead to inappropriate management. Of 17 species of reptile originally found in Mauritius, only five survive on the main island. One of these, Phelsuma guimbeaui (lowland forest day gecko), is now restricted to 30 small isolated subpopulations following severe forest fragmentation and isolation due to human colonisation. We used 20 microsatellites in ten subpopulations and two mitochondrial DNA (mtDNA) markers in 13 subpopulations to: (i) assess genetic diversity, population structure and genetic differentiation of subpopulations; (ii) estimate effective population sizes and migration rates of subpopulations; and (iii) examine the phylogenetic relationships of haplotypes found in different subpopulations. Microsatellite data revealed significant population structure with high levels of genetic diversity and isolation by distance, substantial genetic differentiation and no migration between most subpopulations. MtDNA, however, showed no evidence of population structure, indicating that there was once a genetically panmictic population. Effective population sizes of ten subpopulations, based on microsatellite markers, were small, ranging from 44 to 167. Simulations suggested that the chance of survival and allelic diversity of some subpopulations will decrease dramatically over the next 50 years if no migration occurs. Our DNA-based evidence reveals an urgent need for a management plan for the conservation of P. guimbeaui. We identified 18 threatened and 12 viable subpopulations and discuss a range of management options that include translocation of threatened subpopulations to retain maximum allelic diversity, and habitat restoration and assisted migration to decrease genetic erosion and inbreeding for the viable subpopulations. PMID:24963708

Buckland, Steeves; Cole, Nik C; Groombridge, Jim J; Küpper, Clemens; Burke, Terry; Dawson, Deborah A; Gallagher, Laura E; Harris, Stephen

2014-01-01

133

High and Distinct Range-Edge Genetic Diversity despite Local Bottlenecks  

PubMed Central

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

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

2013-01-01

134

High Risks of Losing Genetic Diversity in an Endemic Mauritian Gecko: Implications for Conservation  

PubMed Central

Genetic structure can be a consequence of recent population fragmentation and isolation, or a remnant of historical localised adaptation. This poses a challenge for conservationists since misinterpreting patterns of genetic structure may lead to inappropriate management. Of 17 species of reptile originally found in Mauritius, only five survive on the main island. One of these, Phelsuma guimbeaui (lowland forest day gecko), is now restricted to 30 small isolated subpopulations following severe forest fragmentation and isolation due to human colonisation. We used 20 microsatellites in ten subpopulations and two mitochondrial DNA (mtDNA) markers in 13 subpopulations to: (i) assess genetic diversity, population structure and genetic differentiation of subpopulations; (ii) estimate effective population sizes and migration rates of subpopulations; and (iii) examine the phylogenetic relationships of haplotypes found in different subpopulations. Microsatellite data revealed significant population structure with high levels of genetic diversity and isolation by distance, substantial genetic differentiation and no migration between most subpopulations. MtDNA, however, showed no evidence of population structure, indicating that there was once a genetically panmictic population. Effective population sizes of ten subpopulations, based on microsatellite markers, were small, ranging from 44 to 167. Simulations suggested that the chance of survival and allelic diversity of some subpopulations will decrease dramatically over the next 50 years if no migration occurs. Our DNA-based evidence reveals an urgent need for a management plan for the conservation of P. guimbeaui. We identified 18 threatened and 12 viable subpopulations and discuss a range of management options that include translocation of threatened subpopulations to retain maximum allelic diversity, and habitat restoration and assisted migration to decrease genetic erosion and inbreeding for the viable subpopulations. PMID:24963708

Buckland, Steeves; Cole, Nik C.; Groombridge, Jim J.; Küpper, Clemens; Burke, Terry; Dawson, Deborah A.; Gallagher, Laura E.; Harris, Stephen

2014-01-01

135

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

PubMed

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

Ley, A C; Hardy, O J

2013-04-01

136

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

PubMed Central

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

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

2011-01-01

137

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

PubMed

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

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

2011-02-01

138

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

139

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

140

A High Fuel Consumption Efficiency Management Scheme for PHEVs Using an Adaptive Genetic Algorithm  

PubMed Central

A high fuel efficiency management scheme for plug-in hybrid electric vehicles (PHEVs) has been developed. In order to achieve fuel consumption reduction, an adaptive genetic algorithm scheme has been designed to adaptively manage the energy resource usage. The objective function of the genetic algorithm is implemented by designing a fuzzy logic controller which closely monitors and resembles the driving conditions and environment of PHEVs, thus trading off between petrol versus electricity for optimal driving efficiency. Comparison between calculated results and publicized data shows that the achieved efficiency of the fuzzified genetic algorithm is better by 10% than existing schemes. The developed scheme, if fully adopted, would help reduce over 600 tons of CO2 emissions worldwide every day. PMID:25587974

Lee, Wah Ching; Tsang, Kim Fung; Chi, Hao Ran; Hung, Faan Hei; Wu, Chung Kit; Chui, Kwok Tai; Lau, Wing Hong; Leung, Yat Wah

2015-01-01

141

A high fuel consumption efficiency management scheme for PHEVs using an adaptive genetic algorithm.  

PubMed

A high fuel efficiency management scheme for plug-in hybrid electric vehicles (PHEVs) has been developed. In order to achieve fuel consumption reduction, an adaptive genetic algorithm scheme has been designed to adaptively manage the energy resource usage. The objective function of the genetic algorithm is implemented by designing a fuzzy logic controller which closely monitors and resembles the driving conditions and environment of PHEVs, thus trading off between petrol versus electricity for optimal driving efficiency. Comparison between calculated results and publicized data shows that the achieved efficiency of the fuzzified genetic algorithm is better by 10% than existing schemes. The developed scheme, if fully adopted, would help reduce over 600 tons of CO2 emissions worldwide every day. PMID:25587974

Lee, Wah Ching; Tsang, Kim Fung; Chi, Hao Ran; Hung, Faan Hei; Wu, Chung Kit; Chui, Kwok Tai; Lau, Wing Hong; Leung, Yat Wah

2015-01-01

142

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

143

Genetics  

MedlinePLUS

... Inheritance; Heterozygous; Inheritance patterns; Heredity and disease; Heritable; Genetic markers ... The chromosomes are made up of strands of genetic information called DNA. Each chromosome contains sections of ...

144

Targeted exome sequencing for mitochondrial disorders reveals high genetic heterogeneity  

PubMed Central

Background Mitochondrial disorders are difficult to diagnose due to extreme genetic and phenotypic heterogeneities. Methods We explored the utility of targeted next-generation sequencing for the diagnosis of mitochondrial disorders in 148 patients submitted for clinical testing. A panel of 447 nuclear genes encoding mitochondrial respiratory chain complexes, and other genes inducing secondary mitochondrial dysfunction or that cause diseases which mimic mitochondrial disorders were tested. Results We identified variants considered to be possibly disease-causing based on family segregation data and/or variants already known to cause disease in twelve genes in thirteen patients. Rare or novel variants of unknown significance were identified in 45 additional genes for various metabolic, genetic or neurogenetic disorders. Conclusions Primary mitochondrial defects were confirmed only in four patients indicating that majority of patients with suspected mitochondrial disorders are presumably not the result of direct impairment of energy production. Our results support that clinical and routine laboratory ascertainment for mitochondrial disorders are challenging due to significant overlapping non-specific clinical symptoms and lack of specific biomarkers. While next-generation sequencing shows promise for diagnosing suspected mitochondrial disorders, the challenges remain as the underlying genetic heterogeneity may be greater than suspected and it is further confounded by the similarity of symptoms with other conditions as we report here. PMID:24215330

2013-01-01

145

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.Emília; Salzburger, Walter

2011-01-01

146

Comparative transcriptomics of Eastern African cichlid fishes shows signs of positive selection and a large contribution of untranslated regions to genetic diversity.  

PubMed

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 Emília; Salzburger, Walter

2011-01-01

147

Application of suppressive subtractive hybridization to the identification of genetic differences between two Lactococcus garvieae strains showing distinct differences in virulence for rainbow trout and mouse.  

PubMed

Lactococcus garvieae is the causative microbial agent of lactococcosis, an important and damaging fish disease in aquaculture. This bacterium has also been isolated from vegetables, milk, cheese, meat and sausages, from cow and buffalo as a mastitis agent, and even from humans, as an opportunistic infectious agent. In this work pathogenicity experiments were performed in rainbow trout and mouse models with strains isolated from human (L. garvieae HF) and rainbow trout (L. garvieae UNIUDO74; henceforth referred to as 074). The mean LD(50) value in rainbow trout obtained for strain 074 was 2.1 × 10(2) ± 84 per fish. High doses of the bacteria caused specific signs of disease as well as histological alterations in mice. In contrast, strain HF did not prove to be pathogenic either for rainbow trout or for mice. Based on these virulence differences, two suppressive subtractive hybridizations were carried out to identify unique genetic sequences present in L. garvieae HF (SSHI) and L. garvieae 074 (SSHII). Differential dot-blot screening of the subtracted libraries allowed the identification of 26 and 13 putative ORFs specific for L. garvieae HF and L. garvieae 074, respectively. Additionally, a PCR-based screening of 12 of the 26 HF-specific putative ORFs and the 13 074-specific ones was conducted to identify their presence/absence in 25 L. garvieae strains isolated from different origins and geographical areas. This study demonstrates the existence of genetic heterogeneity within L. garvieae isolates and provides a more complete picture of the genetic background of this bacterium. PMID:21546587

Reimundo, Pilar; Rivas, Amable J; Osorio, Carlos R; Méndez, Jéssica; Pérez-Pascual, David; Navais, Roberto; Gómez, Esther; Sotelo, Miguel; Lemos, Manuel L; Guijarro, José A

2011-07-01

148

Highly-multiplexed SNP genotyping for genetic mapping and germplasm diversity studies in pea  

PubMed Central

Background Single Nucleotide Polymorphisms (SNPs) can be used as genetic markers for applications such as genetic diversity studies or genetic mapping. New technologies now allow genotyping hundreds to thousands of SNPs in a single reaction. In order to evaluate the potential of these technologies in pea, we selected a custom 384-SNP set using SNPs discovered in Pisum through the resequencing of gene fragments in different genotypes and by compiling genomic sequence data present in databases. We then designed an Illumina GoldenGate assay to genotype both a Pisum germplasm collection and a genetic mapping population with the SNP set. Results We obtained clear allelic data for more than 92% of the SNPs (356 out of 384). Interestingly, the technique was successful for all the genotypes present in the germplasm collection, including those from species or subspecies different from the P. sativum ssp sativum used to generate sequences. By genotyping the mapping population with the SNP set, we obtained a genetic map and map positions for 37 new gene markers. Conclusion Our results show that the Illumina GoldenGate assay can be used successfully for high-throughput SNP genotyping of diverse germplasm in pea. This genotyping approach will simplify genotyping procedures for association mapping or diversity studies purposes and open new perspectives in legume genomics. PMID:20701750

2010-01-01

149

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

150

A Phalaenopsis variety with floral organs showing C class homeotic transformation and its revertant may enable Phalaenopsis as a potential molecular genetic material.  

PubMed

The Orchidaceae is one of the most famous garden plants, and improvement of the orchid is very important in horticulture field. However, molecular information is largely unknown. We found a Phalaenopsis variety harboring floral organs showing C class homeotic change. Column is composed of the anthers with the receptive stigmatic surface just underneath them in wild type. However the C class variety produced column with sepal or petal like structure at the abaxial side. This is the typical abnormality as C class mutants in plants. Further, wild type looking revertant was found from the meristem tissue cultured population. This result strongly indicates the existence of active transposable element in Phalaenopsis genome. This transposon may enable Phalaenopsis as a good material for molecular genetic analysis in Orchidaceae. PMID:21670548

Ejima, Chika; Kobayashi, Yuuki; Honda, Hiroaki; Shimizu, Noriko; Kiyohara, Shunsuke; Hamasaki, Ryota; Sawa, Shinichiro

2011-01-01

151

High-throughput neuroimaging-genetics computational infrastructure.  

PubMed

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 infrastructure. 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

152

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

153

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

154

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

155

Genetic connectivity of the moth pollinated tree Glionnetia sericea in a highly fragmented habitat.  

PubMed

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; Kaiser-Bunbury, Christopher N; Kettle, Chris J; Valentin, Terence; Ghazoul, Jaboury

2014-01-01

156

ISSR and DAMD markers revealed high genetic variability within Flavoparmelia caperata in Western Himalaya (India).  

PubMed

Flavoparmelia caperata (L.) Hale is medicinally very important and possesses antifungal and antibacterial activities. F. caperata is the only species found in India. Inter simple sequence repeat (ISSR) and Directed amplification of minisatellite DNA (DAMD) methods were used to analyze the genetic variability within F. caperata from the Western Himalayan region of India. Eleven ISSR and 10 DAMD primers produced 139 and 117 polymorphic bands, and detected 91.44 and 82.34 % polymorphisms, respectively. Cumulative band data generated for ISSR and DAMD markers resulted in 86.86 % polymorphism across all the accessions of F. caperata. The average Polymorphic information content (PIC) value obtained with ISSR, DAMD, and cumulative band data were 0.28, 0.27, and 0.27, respectively. The clustering of the F. caperata accessions in the UPGMA dendrogram showed that these accessions are intermingled with each other in different subclusters irrespective of their geographical affiliations. The pattern of genetic variations within F. caperata accessions could be due to free exchange of spores that might have taken place among these accessions in the wild. ISSR and DAMD markers efficiently and reliably resulted in discrete banding patterns and polymorphic profiles. These markers despite targeting different regions of genome, revealed almost similar levels of polymorphism across all the accessions. The wide range of genetic distance and high level of polymorphism detected by ISSR and DAMD reflected a high genetic variability among the different accessions of F. caperata. PMID:25320473

Singh, Niraj; Bajpai, Rajesh; Mahar, K S; Tiwari, Vandana; Upreti, D K; Rana, T S

2014-10-01

157

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

Microsoft Academic Search

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

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

2008-01-01

158

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

159

Fine genetic characterization of elite maize germplasm using high-throughput SNP genotyping.  

PubMed

To investigate the genetic structure of Chinese maize germplasm, the MaizeSNP50 BeadChip with 56,110 single nucleotide polymorphisms (SNPs) was used to genotype a collection of 367 inbred lines widely used in maize breeding of China. A total of 41,819 informative SNPs with minor allele number of more than 0.05 were used to estimate the genetic diversity, relatedness, and linkage disequilibrium (LD) decay. Totally 1,015 SNPs evenly distributed in the genome were selected randomly to evaluate the population structure of these accessions. Results showed that two main groups could be determined i.e., the introduced germplasm and the local germplasm. Further, five subgroups corresponding to different heterotic groups, that is, Reid Yellow Dent (Reid), Lancaster Sure Crop (Lancaster), P group (P), Tang Sipingtou (TSPT), and Tem-tropic I group (Tem-tropic I), were determined. The genetic diversity of within subgroups was highest in the Tem-Tropic I and lowest in the P. Most lines in this panel showed limited relatedness with each other. Comparisons of gene diversity showed that there existed some conservative genetic regions in specific subgroups across the ten chromosomes, i.e., seven in the Lancaster, seven in the Reid, six in the TSPT, five in the P, and two in the Tem-Tropical I. In addition, the results also revealed that there existed fifteen conservative regions transmitted from Huangzaosi, an important foundation parent, to its descendants. These are important for further studies since the outcomes may provide clues to understand why Huangzaosi could become a foundation parent in Chinese maize breeding. For the panel of 367 elite lines, average LD distance was 391 kb and varied among different chromosomes as well as in different genomic regions of one chromosome. This analysis uncovered a high natural genetic diversity in the elite maize inbred set, suggesting that the panel can be used in association study, esp. for temperate regions. PMID:24343198

Wu, Xun; Li, Yongxiang; Shi, Yunsu; Song, Yanchun; Wang, Tianyu; Huang, Yubi; Li, Yu

2014-03-01

160

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

161

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

162

High genetic homogeneity of an intertidal marine invertebrate along 8000 km of the Atlantic coast  

E-print Network

High genetic homogeneity of an intertidal marine invertebrate along 8000 km of the Atlantic coast diagnostic characters in benthic invertebrate species. Almost invariably, genetic studies have demonstrated.28) so that P. nigra has genetic variation levels more related with other invertebrates than to their

Solé-Cava, Antonio M.

163

Genetic mapping of high caries experience on human chromosome 13  

PubMed Central

Background Our previous genome-wide linkage scan mapped five loci for caries experience. The purpose of this study was to fine map one of these loci, the locus 13q31.1, in order to identify genetic contributors to caries. Methods Seventy-two pedigrees from the Philippines were studied. Caries experience was recorded and DNA was extracted from blood samples obtained from all subjects. Sixty-one single nucleotide polymorphisms (SNPs) in 13q31.1 were genotyped. Association between caries experience and alleles was tested. We also studied 1,481 DNA samples obtained from saliva of subjects from the USA, 918 children from Brazil, and 275 children from Turkey, in order to follow up the results found in the Filipino families. We used the AliBaba2.1 software to determine if the nucleotide changes of the associated SNPs changed the prediction of the presence of transcription-binding site sequences and we also analyzed the gene expression of the genes selected based on binding predictions. Mutation analysis was also performed in 33 Filipino individuals of a segment of 13q31.1 that is highly conserved in mammals. Results Statistically significant association with high caries experience was found for 11 markers in 13q31.1 in the Filipino families. Haplotype analysis also confirmed these results. In the populations used for follow-up purposes, associations were found between high caries experience and a subset of these markers. Regarding the prediction of the transcription-binding site, the base change of the SNP rs17074565 was found to change the predicted-binding of genes that could be involved in the pathogenesis of caries. When the sequence has the allele C of rs17074565, the potential transcription factors binding the sequence are GR and GATA1. When the subject carries the G allele of rs17074565, the potential transcription factor predicted to bind to the sequence is GATA3. The expression of GR in whole saliva was higher in individuals with low caries experience when compared to individuals with high caries experience (p =?0.046). No mutations were found in the highly conserved sequence. Conclusions Genetic factors contributing to caries experience may exist in 13q31.1. The rs17074565 is located in an intergenic region and is predicted to disrupt the binding sites of two different transcription factors that might be involved with caries experience. GR expression in saliva may be a biomarker for caries risk and should be further explored. PMID:24192446

2013-01-01

164

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...

165

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...

166

Abstract Recent studies show that SouthEast Indian Ocean (SEIO) SSTs are a highly significant precursor  

E-print Network

Abstract Recent studies show that SouthEast Indian Ocean (SEIO) SSTs are a highly significant Ocean Dipole Mode (IODM) events are significantly influ- enced by the SEIO temperature perturbations. A reversed evo- lution is simulated for a cold SEIO perturbation. It is shown that the life cycle

Ribes, Aurélien

167

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

PubMed

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

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

2010-11-15

168

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

169

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, Luís; Robertson, Kelly M.; Sequeira, Marina; Stockin, Karen A.; Coelho, M. Manuela; Möller, Luciana M.

2012-01-01

170

High genetic diversity with moderate differentiation in Juniperus excelsa from Lebanon and the eastern Mediterranean region  

PubMed Central

Background and aims Juniperus excelsa is an important woody species in the high mountain ecosystems of the eastern Mediterranean Basin where it constitutes the only coniferous species found at the tree line. The genetic diversity within and among J. excelsa populations of the eastern Mediterranean Basin is studied in the light of their historical fragmentation. Methodology Nuclear microsatellites originally developed for Juniperus communis and J. przewalskii were tested on 320 individuals from 12 different populations originating from Lebanon, Turkey, Cyprus, Greece and the Ukraine. Principal results Among the 31 nuclear microsatellite primers tested, only three produced specific amplification products, with orthology confirmed by sequence analysis. They were then used for genetic diversity studies. The mean number of alleles and the expected heterozygosity means were Na=8.78 and He=0.76, respectively. The fixation index showed a significant deviation from Hardy–Weinberg equilibrium and an excess of homozygotes (FIS=0.27–0.56). A moderate level of genetic differentiation was observed among the populations (FST=0.075, P<0.001). The most differentiated populations corresponded to old vestigial stands found at the tree line (>2000 m) in Lebanon. These populations were differentiated from the other populations that are grouped into three sub-clusters. Conclusions High levels of genetic diversity were observed at species and population levels. The high level of differentiation in the high-mountain Lebanese populations reflects a long period of isolation or possibly a different origin. The admixture observed in other populations from Lebanon suggests a more recent separation from the Turkish–southeastern European populations. PMID:22476474

Douaihy, Bouchra; Vendramin, Giovanni G.; Boraty?ski, Adam; Machon, Nathalie; Bou Dagher-Kharrat, Magda

2011-01-01

171

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

NASA Astrophysics Data System (ADS)

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

Zhang, Changjiang; Wang, Xiaodong

2008-11-01

172

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

SciTech Connect

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

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

2008-11-06

173

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

174

Low Genetic Variability in the Highly Endangered Mediterranean Monk Seal  

Microsoft Academic Search

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

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

2004-01-01

175

High School Students' Use of Meiosis When Solving Genetics Problems.  

ERIC Educational Resources Information Center

Paints a different picture of students' reasoning with meiosis as they solved complex, computer-generated genetics problems, some of which required them to revise their understanding of meiosis in response to anomalous data. Students were able to develop a rich understanding of meiosis and can utilize that knowledge to solve genetics problems.…

Wynne, Cynthia F.; Stewart, Jim; Passmore, Cindy

2001-01-01

176

Transcriptome analysis of the Bombyx mori fat body after constant high temperature treatment shows differences between the sexes.  

PubMed

Ambient temperature plays a large role in insect growth, development and even their distribution. The elucidation of the associated molecular mechanism that underlies the effect of constant high temperature will enables us to further understand the stress responses. We constructed four digital gene expression libraries from the fat body of female and male Bombyx mori. Differential gene expression was analyzed after constant high temperature treatment. The results showed that there were significant changes to the gene expression in the fat body after heat treatment, especially in binding, catalytic, cellular and metabolic processes. Constant high temperature may induce more traditional cryoprotectants, such as glycerol, glycogen, sorbitol and lipids, to protect cells from damage, and induce heat oxidative stress in conjunction with the heat shock proteins. The data also indicated a difference between males and females. The heat shock protein-related genes were up-regulated in both sexes but the expression of Hsp25.4 and DnaJ5 were down-regulated in the male fat body of B. mori. This is the first report of such a result. Constant high temperature also affected the expression of other functional genes and differences were observed between male and female fat bodies in the expression of RPS2, RPL37A and MREL. These findings provide abundant data on the effect of high temperature on insects at the molecular level. The data will also be beneficial to the study of differences between the sexes, manifested in variations in gene expression under high temperature. PMID:24972568

Wang, Hua; Fang, Yan; Wang, Lipeng; Zhu, Wenjuan; Ji, Haipeng; Wang, Haiying; Xu, Shiqing; Sima, Yanghu

2014-09-01

177

A case of fatal drug intoxication showing a high-density duodenal content by postmortem computed tomography.  

PubMed

A 22-year-old woman was found dead in her bed, and subsequent postmortem examination was performed using ordinary methods such as external examination, Triage®, and computed tomography (CT) scan which demonstrated a high-density content of the duodenum. Autopsy and quantitative analysis of drugs present in the GI tract showed that high amounts of radiopaque psychotic agents such as fluvoxamine maleate, carbamazepine, and zolpidem tartrate had been responsible for the high-density profile of the duodenum. Postmortem quantitative analysis of drugs in the blood suggested that death had been caused by fatal intoxication with fluvoxamine maleate. Thus, postmortem CT could offer an opportunity to suspect drug intoxication due to radiopaque psychotic agents such as chloral hydrate, phenothiazine, bromovaleryl urea, fluvoxamine maleate, and probably zolpidem tartrate, although it is neither a specific nor a quantitative test for drugs. Therefore, postmortem CT happened to provide clues to investigation of drug intoxication in the present case. PMID:21134778

Sano, Rie; Takahashi, Keiko; Kominato, Yoshihiko; Araki, Takuya; Yamamoto, Koujiro; Takei, Hiroyuki; Otake, Hidenori; Awata, Sachiko; Akuzawa, Hisashi; Tago, Yoko; Aoki, Hideo

2011-01-01

178

Genetics  

Microsoft Academic Search

The author draws on modern research to introduce genetics in a molecular and cellular context. This work covers the structure of DNA and the gene and gene expression, replication, mutation, and recombination, looks at the gene in the context of the cell and organism, describes the elements of genetic analysis and the basic principles of inheritance, and examines classic experiments

1990-01-01

179

A Web-Based Genetic Polymorphism Learning Approach for High School Students and Science Teachers  

ERIC Educational Resources Information Center

Variation and polymorphism are concepts that are central to genetics and genomics, primary biological disciplines in which high school students and undergraduates require a solid foundation. From 1998 through 2002, a web-based genetics education program was developed for high school teachers and students. The program included an exercise on using…

Amenkhienan, Ehichoya; Smith, Edward J.

2006-01-01

180

High efficiency genetic modification of hair follicles and growing hair shafts  

Microsoft Academic Search

A technique for genetic modification of hair follicles was developed which results in efficient alteration of the hair shaft phenotype. High-level in vivo transgene expression was maintained in hair follicles such that growing hair shafts were phenotypically altered. Mouse anagen skin fragments, maintained in histoculture, were genetically modified at high efficiency with adenoviral-GFP. The histocultured skin fragments were treated with

Norimitsu Saito; Ming Zhao; Lingna Li; Eugene Baranov; Meng Yang; Yukinori Ohta; Kensei Katsuoka; Sheldon Penman; Robert M. Hoffman

2002-01-01

181

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

PubMed Central

We describe the generation of a family of high-signal-to-noise single-wavelength genetically encoded indicators for maltose. This was achieved by insertion of circularly permuted fluorescent proteins into a bacterial periplasmic binding protein (PBP), Escherichia coli maltodextrin-binding protein, resulting in a four-color family of maltose indicators. The sensors were iteratively optimized to have sufficient brightness and maltose-dependent fluorescence increases for imaging, under both one- and two-photon illumination. We demonstrate that maltose affinity of the sensors can be tuned in a fashion largely independent of the fluorescent readout mechanism. Using literature mutations, the binding specificity could be altered to moderate sucrose preference, but with a significant loss of affinity. We use the soluble sensors in individual E. coli bacteria to observe rapid maltose transport across the plasma membrane, and membrane fusion versions of the sensors on mammalian cells to visualize the addition of maltose to extracellular media. The PBP superfamily includes scaffolds specific for a number of analytes whose visualization would be critical to the reverse engineering of complex systems such as neural networks, biosynthetic pathways, and signal transduction cascades. We expect the methodology outlined here to be useful in the development of indicators for many such analytes. PMID:21989929

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

2011-01-01

182

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

183

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

PubMed

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. PMID:21989929

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

2011-11-01

184

Magic Show  

Microsoft Academic Search

With a concentration in theatre, I created a magic show from scratch. Over the course of the semester, I researched both the effects (more commonly known as magic tricks) in a variety of styles, especially mentalism, along with the patter, or script, that is integral in making a good effect into something utterly amazing. I chose a certain set of

Zachary Brass

2012-01-01

185

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

PubMed Central

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

Kung, Johnny T.; Gelbart, Marnie E.

2012-01-01

186

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

187

Population Genetic Studies Revealed Local Adaptation in a High Gene-Flow Marine Fish, the Small Yellow Croaker (Larimichthys polyactis)  

PubMed Central

The genetic differentiation of many marine fish species is low. Yet local adaptation may be common in marine fish species as the vast and changing marine environment provides more chances for natural selection. Here, we used anonymous as well as known protein gene linked microsatellites and mitochondrial DNA to detect the population structure of the small yellow croaker (Larimichthys polyactis) in the Northwest Pacific marginal seas. Among these loci, we detected at least two microsatellites, anonymous H16 and HSP27 to be clearly under diversifying selection in outlier tests. Sequence cloning and analysis revealed that H16 was located in the intron of BAHCC1 gene. Landscape genetic analysis showed that H16 mutations were significantly associated with temperature, which further supported the diversifying selection at this locus. These marker types presented different patterns of population structure: (i) mitochondrial DNA phylogeny showed no evidence of genetic divergence and demonstrated only one glacial linage; (ii) population differentiation using putatively neutral microsatellites presented a pattern of high gene flow in the L. polyactis. In addition, several genetic barriers were identified; (iii) the population differentiation pattern revealed by loci under diversifying selection was rather different from that revealed by putatively neutral loci. The results above suggest local adaptation in the small yellow croaker. In summary, population genetic studies based on different marker types disentangle the effects of demographic history, migration, genetic drift and local adaptation on population structure and also provide valuable new insights for the design of management strategies in L. polyactis. PMID:24349521

Wang, Le; Liu, Shufang; Zhuang, Zhimeng; Guo, Liang; Meng, Zining; Lin, Haoran

2013-01-01

188

Distinct and Diverse: Range-Wide Phylogeography Reveals Ancient Lineages and High Genetic Variation in the Endangered Okapi (Okapia johnstoni)  

PubMed Central

The okapi is an endangered, evolutionarily distinctive even-toed ungulate classified within the giraffidae family that is endemic to the Democratic Republic of Congo. The okapi is currently under major anthropogenic threat, yet to date nothing is known about its genetic structure and evolutionary history, information important for conservation management given the species' current plight. The distribution of the okapi, being confined to the Congo Basin and yet spanning the Congo River, also makes it an important species for testing general biogeographic hypotheses for Congo Basin fauna, a currently understudied area of research. Here we describe the evolutionary history and genetic structure of okapi, in the context of other African ungulates including the giraffe, and use this information to shed light on the biogeographic history of Congo Basin fauna in general. Using nuclear and mitochondrial DNA sequence analysis of mainly non-invasively collected samples, we show that the okapi is both highly genetically distinct and highly genetically diverse, an unusual combination of genetic traits for an endangered species, and feature a complex evolutionary history. Genetic data are consistent with repeated climatic cycles leading to multiple Plio-Pleistocene refugia in isolated forests in the Congo catchment but also imply historic gene flow across the Congo River. PMID:25007188

Stanton, David W. G.; Hart, John; Galbusera, Peter; Helsen, Philippe; Shephard, Jill; Kümpel, Noëlle F.; Wang, Jinliang; Ewen, John G.; Bruford, Michael W.

2014-01-01

189

Distinct and diverse: range-wide phylogeography reveals ancient lineages and high genetic variation in the endangered okapi (Okapia johnstoni).  

PubMed

The okapi is an endangered, evolutionarily distinctive even-toed ungulate classified within the giraffidae family that is endemic to the Democratic Republic of Congo. The okapi is currently under major anthropogenic threat, yet to date nothing is known about its genetic structure and evolutionary history, information important for conservation management given the species' current plight. The distribution of the okapi, being confined to the Congo Basin and yet spanning the Congo River, also makes it an important species for testing general biogeographic hypotheses for Congo Basin fauna, a currently understudied area of research. Here we describe the evolutionary history and genetic structure of okapi, in the context of other African ungulates including the giraffe, and use this information to shed light on the biogeographic history of Congo Basin fauna in general. Using nuclear and mitochondrial DNA sequence analysis of mainly non-invasively collected samples, we show that the okapi is both highly genetically distinct and highly genetically diverse, an unusual combination of genetic traits for an endangered species, and feature a complex evolutionary history. Genetic data are consistent with repeated climatic cycles leading to multiple Plio-Pleistocene refugia in isolated forests in the Congo catchment but also imply historic gene flow across the Congo River. PMID:25007188

Stanton, David W G; Hart, John; Galbusera, Peter; Helsen, Philippe; Shephard, Jill; Kümpel, Noëlle F; Wang, Jinliang; Ewen, John G; Bruford, Michael W

2014-01-01

190

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.; Kilpeläinen, Tuomas O.; Esko, Tõnu; Mägi, 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, Amélie; 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.; Grönberg, 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, Åsa; 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, André G.; Hofman, Albert; Zillikens, M. Carola; den Heijer, Martin; Kiemeney, Lambertus A.; Maschio, Andrea; Hall, Per; Tyrer, Jonathan; Teumer, Alexander; Völzke, Henry; Kovacs, Peter; Tönjes, 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.; Lehtimäki, Terho; Raitakari, Olli; Absher, Devin; Iribarren, Carlos; Basart, Hanneke; Hovingh, Kees G.; Hyppönen, 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; Lindström, 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; KrjutÅ¡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, Göran; Shungin, Dmitry; Morris, Andrew David; Palmer, Colin N. A.; Erbel, Raimund; Moebus, Susanne; Nöthen, 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; Müller-Nurasyid, Martina; Peters, Annette; Boehm, Bernhard O.; Kleber, Marcus E.; März, 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.; Njølstad, Inger; Wilsgaard, Tom; Ganna, Andrea; Rehnberg, Emil; Hingorani, Aroon; Kivimaki, Mika; Kumari, Meena; Assimes, Themistocles L.; Barroso, Inês; Boehnke, Michael; Borecki, Ingrid B.; Deloukas, Panos; Fox, Caroline S.; Frayling, Timothy; Groop, Leif C.; Haritunians, Talin; Hunter, David

2013-01-01

191

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.

Jennifer Doherty

192

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

193

Evaluation of Four Genetic Variants in Han Chinese Subjects with High Myopia  

PubMed Central

High myopia is one of the leading causes of blindness worldwide. However, the exact etiology of high myopia remains unraveled despite numerous attempts of elucidation. Previous genome-wide association study (GWAS) has revealed that four single nucleotide polymorphisms (SNPs), including rs2969180, rs1652333, rs9307551, and rs7837791, were associated with high myopia in Caucasians. The present study was conducted to investigate whether these genetic variants were associated with high myopia in Han Chinese. These four SNPs were genotyped by SNaPshot method in a Han Chinese cohort composed of 827 patients with high myopia and 988 healthy controls. Among the SNPs genotyped, only rs9307551 was found to be significantly associated with high myopia in this study. Carriers of rs9307551A allele, AA, and AC genotypes had an increased risk of high myopia (OR = 1.33, 95% CI 1.14–1.54; OR = 1.75, 95% CI 1.28–2.38; OR = 1.59, 95% CI 1.24–2.01, resp.). Interestingly, when split by gender, the association between rs9307551 and high myopia proved to be gender-specific with significance observed only in females but not males. These findings suggested that the SNP of rs9307551 showed a gender-specific association with high myopia in the Han Chinese population. In addition, LOC100506035, a lincRNA gene, might play a crucial role in the susceptibility to high myopia. PMID:25628894

Ye, Zimeng; Luo, Huaichao; Gong, Bo; Lin, Ying; Shuai, Ping; Wang, Pu; Ye, Changning; Yang, Zhenglin; Wang, Wanjun; Shi, Yi

2015-01-01

194

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

195

DRD4 Long Allele Carriers Show Heightened Attention to High-Priority Items Relative to Low-Priority Items  

PubMed Central

Humans with 7 or more repeats in exon III of the DRD4 gene (long DRD4 carriers) sometimes demonstrate impaired attention, as seen in ADHD, and at other times demonstrate heightened attention, as seen in addictive behavior. Though the clinical effects of DRD4 are the focus of much work, this gene may not necessarily serve as a ‘risk’ gene for attentional deficits, but as a plasticity gene where attention is heightened for priority items in the environment and impaired for minor items. Here we examine the role of DRD4 in two tasks that benefit from selective attention to high-priority information. We examine a category learning task where performance is supported by focusing on features and updating verbal rules. Here selective attention to the most salient features is associated with good performance. In addition, we examine the Operation Span Task (OSPAN), a working memory capacity task that relies on selective attention to update and maintain items in memory while also performing a secondary task. Long DRD4 carriers show superior performance relative to short DRD4 homozygotes (six or less tandem repeats) in both the category learning and OSPAN tasks. These results suggest that DRD4 may serve as a ‘plasticity’ gene where individuals with the long allele show heightened selective attention to high-priority items in the environment, which can be beneficial in the appropriate context. PMID:25244120

Gorlick, Marissa A.; Worthy, Darrell A.; Knopik, Valerie S.; McGeary, John E.; Beevers, Christopher G.; Maddox, W. Todd

2014-01-01

196

Awareness of Societal Issues Among High School Biology Teachers Teaching Genetics  

Microsoft Academic Search

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

Reuven Lazarowitz; Ilit Bloch

2005-01-01

197

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

198

A comprehensive platform for highly multiplexed mammalian functional genetic screens  

PubMed Central

Background Genome-wide screening in human and mouse cells using RNA interference and open reading frame over-expression libraries is rapidly becoming a viable experimental approach for many research labs. There are a variety of gene expression modulation libraries commercially available, however, detailed and validated protocols as well as the reagents necessary for deconvolving genome-scale gene screens using these libraries are lacking. As a solution, we designed a comprehensive platform for highly multiplexed functional genetic screens in human, mouse and yeast cells using popular, commercially available gene modulation libraries. The Gene Modulation Array Platform (GMAP) is a single microarray-based detection solution for deconvolution of loss and gain-of-function pooled screens. Results Experiments with specially constructed lentiviral-based plasmid pools containing ~78,000 shRNAs demonstrated that the GMAP is capable of deconvolving genome-wide shRNA "dropout" screens. Further experiments with a larger, ~90,000 shRNA pool demonstrate that equivalent results are obtained from plasmid pools and from genomic DNA derived from lentivirus infected cells. Parallel testing of large shRNA pools using GMAP and next-generation sequencing methods revealed that the two methods provide valid and complementary approaches to deconvolution of genome-wide shRNA screens. Additional experiments demonstrated that GMAP is equivalent to similar microarray-based products when used for deconvolution of open reading frame over-expression screens. Conclusion Herein, we demonstrate four major applications for the GMAP resource, including deconvolution of pooled RNAi screens in cells with at least 90,000 distinct shRNAs. We also provide detailed methodologies for pooled shRNA screen readout using GMAP and compare next-generation sequencing to GMAP (i.e. microarray) based deconvolution methods. PMID:21548937

2011-01-01

199

Optimized design on condensing tubes high-speed TIG welding technology magnetic control based on genetic algorithm  

NASA Astrophysics Data System (ADS)

An orthogonal experiment was conducted by the means of multivariate nonlinear regression equation to adjust the influence of external transverse magnetic field and Ar flow rate on welding quality in the process of welding condenser pipe by high-speed argon tungsten-arc welding (TIG for short). The magnetic induction and flow rate of Ar gas were used as optimum variables, and tensile strength of weld was set to objective function on the base of genetic algorithm theory, and then an optimal design was conducted. According to the request of physical production, the optimum variables were restrained. The genetic algorithm in the MATLAB was used for computing. A comparison between optimum results and experiment parameters was made. The results showed that the optimum technologic parameters could be chosen by the means of genetic algorithm with the conditions of excessive optimum variables in the process of high-speed welding. And optimum technologic parameters of welding coincided with experiment results.

Lu, Lin; Chang, Yunlong; Li, Yingmin; Lu, Ming

2013-05-01

200

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

PubMed

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

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

2012-07-01

201

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.

202

[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

203

Linkage and LOH studies in 19 cylindromatosis families show no evidence of genetic heterogeneity and refine the CYLD locus on chromosome 16q12-q13  

Microsoft Academic Search

Familial cylindromatosis is an autosomal dominant predisposition to multiple neoplasms of the skin appendages. The susceptibility gene has previously been mapped to chromosome 16q12-q13 and has features of a recessive oncogene\\/tumour suppressor gene. We have now evaluated 19 families with this disease by a combination of genetic linkage analysis and loss of heterozygosity in cylindromas from affected individuals. All 15

Meiko Takahashi; Elizabeth Rapley; Patrick J. Biggs; Sunil R. Lakhani; David Cooke; Juliana Hansen; Edward Blair; B. Hofmann; Reiner Siebert; Gwen Turner; D. Gareth Evans; Connie Schrander-Stumpel; Frits A. Beemer; Willem A. van Vloten; Martijn H. Breuning; Ans van den Ouweland; Dicky Halley; Bertrand Delpech; Mark Cleveland; Irene Leigh; Pam Chapman; John Burn; Daniel Hohl; Jean-Philippe Görög; Sheila Seal; Jon Mangion; William Warren; Graham Bignell; Michael R. Stratton

2000-01-01

204

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

Cibrián-Jaramillo, Angélica; 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

205

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

206

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

207

Genetic dissection of an alien chromosomal segment may enable the production of a rice (Oryza sativa L.) genotype showing shoot developmental instability.  

PubMed

During the course of evolutionary history, organisms have acquired genes which cooperate harmoniously and subsequently express a stable pattern of development. In an earlier study we introduced a large chromosomal segment of chromosome 6 from a rice (Oryza sativa L.) ecotype, carrying the two flowering-time genes, which showed complex epistatic interactions in relation to environmental change, into a different ecotype by successive backcrossings. Four-near-isogenic lines (NILs) with respect to these two loci were obtained by subsequent hybridization with the recurrent parent. In the study reported here, these four NILs were the major plant material used to evaluate changes in days to leaf appearance (DLA) during shoot development using a quadratic-polynomial regression. The regressions were regarded as developmental norms because of the high values of R (2). Absolute Y-residuals (AYRs) (or size of deviation) of DLA from the norms were significantly affected by genotype. Dissections of the alien chromosomal segment resulted in one NIL that showed an increased level of AYR. Since this NIL also expressed a low survival rate in a stress environment, we suggest that the increased level of AYR during development might indicate an increased level of instability in shoot development. PMID:25677854

Itoh, Youki; Sato, Yoshikazu

2015-04-01

208

High Genetic Diversity Despite the Potential for Stepping-Stone Colonizations in an Invasive Species of Gecko on Moorea, French Polynesia  

PubMed Central

Invasive species often have reduced genetic diversity, but the opposite can be true if there have been multiple introductions and genetic admixture. Reduced diversity is most likely soon after establishment, in remote locations, when there is lower propagule pressure and with stepping-stone colonizations. The common house gecko (Hemidactylus frenatus) was introduced to Moorea, French Polynesia in the remote eastern Pacific within the last two decades and accordingly is expected to exhibit low diversity. In contrast, we show that H. frenatus on Moorea has exceptionally high genetic diversity, similar to that near the native range in Asia and much higher than reported for other Pacific island reptiles. The high diversity in this recently founded population likely reflects extensive genetic admixture in source population(s) and a life history that promotes retention of diversity. These observations point to the importance of understanding range-wide dynamics of genetic admixture in highly invasive species. PMID:22073211

Tonione, Maria A.; Reeder, Natalie; Moritz, Craig C.

2011-01-01

209

High fidelity of RecA-catalyzed recombination: a watchdog of genetic diversity  

E-print Network

High fidelity of RecA-catalyzed recombination: a watchdog of genetic diversity Dror Sagi, Tsvi recombination plays a key role in generating genetic diversity, while maintaining protein functionality of heterology was studied in vitro, using fluores- cence resonant energy transfer. RecA can detect single

Tlusty, Tsvi

210

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.

211

Frequency of Truancy at High School: Evidence for Genetic and Twin Specific Shared Environmental Influences  

Microsoft Academic Search

PurposeThe purpose of this study was to examine the relative influence of genetic and environmental factors on variation in truancy during high school. We examined the significance of genetic and shared and nonshared environmental influences. In addition, we tested for the presence of environmental factors specifically shared by twins, but not by their siblings.

Niels van der Aa; Irene Rebollo-Mesa; Gonneke Willemsen; Dorret I. Boomsma; Meike Bartels

2009-01-01

212

Spatio-temporal Genetic Structure of a Tropical Bee Species Suggests High Dispersal Over a Fragmented Landscape  

PubMed Central

Habitat destruction threatens biodiversity by reducing the amount of available resources and connectivity among geographic areas. For organisms living in fragmented habitats, population persistence may depend on dispersal, which maintains gene flow among fragments and can prevent inbreeding within them. It is centrally important to understand patterns of dispersal for bees living in fragmented areas given the importance of pollination systems and recently documented declines in bee populations. We used population and landscape genetic techniques to characterize patterns of dispersal over a large fragmented area in southern Costa Rica for the orchid bee species Euglossa championi. First, we estimated levels of genetic differentiation among forest fragments as ?pt, an analog to the traditional summary statistic Fst, as well as two statistics that may more adequately represent levels of differentiation, G’st and Dest. Second, we used a Bayesian approach to determine the number and composition of genetic groups in our sample. Third we investigated how genetic differentiation changes with distance. Fourth, we determined the extent to which deforested areas restrict dispersal. Finally, we estimated the extent to which there were temporal differences in allele frequencies within the same forest fragments. Within years we found low levels of differentiation even over 80 km, and no effect of land use type on level of genetic differentiation. However, we found significant genetic differentiation between years. Taken together our results suggest that there are high levels of gene flow over this geographic area, and that individuals show low site fidelity over time. PMID:24659825

Suni, Sevan S.; Bronstein, Judith L.; Brosi, Berry J.

2014-01-01

213

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

214

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

215

A High-Resolution Single Nucleotide Polymorphism Genetic Map  

E-print Network

.pbio.0040395 Introduction The current genetic map of the mouse is based on data from crosses between inbred be combined to form a map using this approach [8], recombination rates are not constant across the genome [9 to estimate fine-scale recombination rates from linkage-disequilibrium (LD) data, using a coalescent

Nachman, Michael

216

New high density genetic marker technology for use in breeding  

Technology Transfer Automated Retrieval System (TEKTRAN)

Recent advances in genetic marker technology have enhanced our ability to evaluate rice breeding materials more quickly and with greater coverage. In 2005, as a result of an international collaboration, the japonica rice variety, Nipponbare, was the first crop plant to be completely sequenced. Subse...

217

Genetics  

Technology Transfer Automated Retrieval System (TEKTRAN)

The genus Capsicum represents one of several well characterized Solanaceous genera. A wealth of classical and molecular genetics research is available for the genus. Information gleaned from its cultivated relatives, tomato and potato, provide further insight for basic and applied studies. Early ...

218

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

219

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

220

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

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

221

An EGFR/HER2-Bispecific and Enediyne-Energized Fusion Protein Shows High Efficacy against Esophageal Cancer  

PubMed Central

Esophageal cancer is one of the most common cancers, and the 5-year survival rate is less than 10% due to lack of effective therapeutic agents. This study was to evaluate antitumor activity of Ec-LDP-Hr-AE, a recently developed bispecific enediyne-energized fusion protein targeting both epidermal growth factor receptor (EGFR) and epidermal growth factor receptor 2 (HER2), on esophageal cancer. The fusion protein Ec-LDP-Hr-AE consists of two oligopeptide ligands and an enediyne antibiotic lidamycin (LDM) for receptor binding and cell killing, respectively. The current study demonstrated that Ec-LDP-Hr had high affinity to bind to esophageal squamous cell carcinoma (ESCC) cells, and enediyne-energized fusion protein Ec-LDP-Hr-AE showed potent cytotoxicity to ESCC cells with differential expression of EGFR and HER2. Ec-LDP-Hr-AE could cause significant G2-M arrest in EC9706 and KYSE150 cells, and it also induced apoptosis in ESCC cells in a dosage-dependent manner. Western blot assays showed that Ec-LDP-Hr-AE promoted caspase-3 and caspase-7 activities as well as PARP cleavage. Moreover, Ec-LDP-Hr-AE inhibited cell proliferation via decreasing phosphorylation of EGFR and HER2, and further exerted inhibition of the activation of their downstream signaling molecules. In vivo, at a tolerated dose, Ec-LDP-Hr-AE inhibited tumor growth by 88% when it was administered to nude mice bearing human ESCC cell KYSE150 xenografts. These results indicated that Ec-LDP-Hr-AE exhibited potent anti-caner efficacy on ESCC, suggesting it could be a promising candidate for targeted therapy of esophageal cancer. PMID:24664246

Yang, Wan-Cai; Zhang, Sheng-Hua; Zhen, Yong-Su

2014-01-01

222

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

PubMed Central

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

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

2013-01-01

223

Genetic algorithm for the design of high frequency diffraction gratings for high power laser applications  

NASA Astrophysics Data System (ADS)

We present a genetic algorithm with small population sizes for the design of diffraction gratings in the rigorous domain. A general crossover and mutation scheme is defined, forming fifteen offspring from 3 parents, which enables the algorithm to be used for designing gratings with diverse optical properties by careful definition of the merit function. The initial parents are randomly selected and the parents of the subsequent generations are selected by survival of the fittest. The performance of the algorithm is demonstrated by designing diffraction gratings with specific application to high power laser beam lines. Gratings are designed that act as beam deflectors, polarisers, polarising beam splitters, harmonic separation gratings and pulse compression gratings. By imposing fabrication constraints within the design process, we determine which of these elements have true potential for application within high power laser beam lines.

Thomson, Martin J.; Waddie, Andrew J.; Taghizadeh, Mohammad R.

2006-04-01

224

High Genetic Diversity and Clonal Growth in Relict Populations of Olea europaea subsp. laperrinei (Oleaceae) from Hoggar, Algeria  

PubMed Central

• Background and Aims The Laperrine's olive (Olea europaea subsp. laperrinei) is an endemic tree from Saharan massifs. Its populations have substantially regressed since the Pleistocene and are presently distributed in a fragmented habitat. Long-term persistence of this taxon is uncertain and programmes of preservation have to be urgently implemented. To define a conservation strategy, the genetic diversity and breeding system of this tree have to be investigated. • Methods One hundred and eleven ramets were prospected in the laperrinei populations from the Tamanrasset region, southern Algeria. Genetic polymorphism was revealed at nuclear and chloroplast DNA (cpDNA) microsatellite loci allowing a comparative assessment of the genetic diversity of laperrinei and Mediterranean populations based on bi-parental and maternal markers. Additionally, nuclear microsatellite markers enabled the genotypes to be identified unambiguously. • Key Results Based on nuclear microsatellite data, the total diversity was high (Ht = 0·61) in laperrinei populations and similar to that observed in western Mediterranean populations. A substantial cpDNA diversity (Ht = 0·19) was also observed. Genetically identical ramets originated from the same stump (which can cover >80?m2) were identified in each population. Sixteen per cent of genets exhibited more than one ramet. In addition, several cases of somatic mutations were unambiguously revealed in distinct ramets stemming from the same stump. • Conclusions These data show that highly isolated and small laperrinei populations are able to maintain a high genetic diversity. This supports the existence of relict trees persisting for a very long time (probably since the last humid transition, 3000 years ago). It is proposed that the very long persistence associated with an asexual multiplication of highly adapted trees could be a strategy of survival in extreme conditions avoiding a mutational meltdown due to reproduction in reduced populations. PMID:16043438

BAALI-CHERIF, DJAMEL; BESNARD, GUILLAUME

2005-01-01

225

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

E-print Network

The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis of human, CA, and approved May 29, 2009 (received for review December 30, 2008) Down syndrome (DS), or trisomy

Gerstein, Mark

226

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

PubMed

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

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

2012-02-01

227

High-resolution structural analysis shows how Tah1 tethers Hsp90 to the R2TP complex.  

PubMed

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

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

2013-10-01

228

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

Pietiläinen, Maria; Korpelainen, Helena

2013-01-01

229

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

PubMed

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 (H O) and expected (H E) heterozygosities averaged 0.522 and 0.445, respectively. Typically negative but non-significant F IS values (mean -0.173) were found in S. oppositifolia populations. F ST 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

Pietiläinen, Maria; Korpelainen, Helena

2013-01-01

230

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

231

Capturing the Molecular and Biological Diversity of High-Grade Astrocytoma in Genetically Engineered Mouse Models  

PubMed Central

High-grade astrocytoma remains a significant challenge to the clinician and researcher alike. Intense study of the molecular pathogenesis of these tumors has allowed identification of frequent genetic alterations and critical core pathways in this disease. The use of novel mouse genetic tools to study the consequence of specific mutations in brain has led to the development of multiple representative genetically engineered mouse models that provided novel insights into gliomagenesis. As we learn more about the biology of high-grade astrocytoma from the study of these models, we anticipate that our improved understanding will eventually lead to greater success in clinical trials and improved outcome for patients. PMID:22287481

Chow, Lionel M.L.; Baker, Suzanne J.

2012-01-01

232

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

233

Adaptive color polymorphism and unusually high local genetic diversity in the side-blotched lizard, Uta stansburiana.  

PubMed

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

234

The dipeptide H-Trp-Glu-OH shows highly antagonistic activity against PPARgamma: bioassay with molecular modeling simulation.  

PubMed

The peroxisome proliferator-activated receptor gamma (PPARgamma) is an important therapeutic drug target for several conditions, including diabetes, inflammation, dyslipidemia, hypertension, and cancer. It is shown that an antagonist or partial agonist of PPARgamma has attractive potential applications in the discovery of novel antidiabetic agents that may retain efficacious insulin-sensitizing properties and minimize potential side effects. In this work, the dipeptide H-Trp-Glu-OH (G3335) was discovered to be a novel PPARgamma antagonist. Biacore 3000 results based on the surface plasmon resonance (SPR) technique showed that G3335 exhibits a highly specific binding affinity against PPARgamma (K(D) = 8.34 microM) and is able to block rosiglitazone, a potent PPARgamma agonist, in the stimulation of the interaction between the PPARgamma ligand-binding domain (LBD) and RXRalpha-LBD. Yeast two-hybrid assays demonstrated that G3335 exhibits strong antagonistic activity (IC50 = 8.67 microM) in perturbing rosiglitazone in the promotion of the PPARgamma-LBD-CBP interaction. Moreover, in transactivation assays, G3335 was further confirmed as an antagonist of PPARgamma in that G3335 could competitively bind to PPARgamma against 0.1 microM rosiglitazone to repress reporter-gene expression with an IC50 value of 31.9 muM. In addition, homology modeling and molecular-docking analyses were performed to investigate the binding mode of PPARgamma-LBD with G3335 at the atomic level. The results suggested that residues Cys285, Arg288, Ser289, and His449 in PPARgamma play vital roles in PPARgamma-LBD-G3335 binding. The significance of Cys285 for PPARgamma-LBD-G3335 interaction was further demonstrated by PPARgamma point mutation (PPARgamma-LBD-Cys285Ala). It is hoped our current work will provide a powerful approach for the discovery of PPARgamma antagonists, and that G3335 might be developed as a possible lead compound in diabetes research. PMID:16317783

Ye, Fei; Zhang, Zhen-Shan; Luo, Hai-Bin; Shen, Jian-Hua; Chen, Kai-Xian; Shen, Xu; Jiang, Hua-Liang

2006-01-01

235

High Resolution Synchronisation Of Climate Archives Shows Evidence For A Time-Transgressive Abrupt Climate Change During The Younger Dryas  

NASA Astrophysics Data System (ADS)

Understanding regional variations in climatic changes is critical the understanding of the dynamics of the atmospheric climate system. One key tool is the past record of climatic oscillations, which provide evidence of large abrupt shifts. The last major reorganisation of the North Atlantic realm took place during the Younger Dryas (YD), a ~1100 year long cold period at the end of the last glaciation, thought to be induced through increased meltwater and a reduction in North Atlantic overturning. Within this region, the YD had at least two phases an earlier cold phase followed by a second phase of climatic amelioration related to a resumption of North Atlantic overturning and reorganisation of the atmospheric system. Previously studies suggest this shift between climate states occurred at the same time across the North Atlantic, however often the available chronological resolution is insufficient to determine synchroneity of this transition between records. We now show that this transition was locally abrupt, but time-transgressive across the region through the direct synchronisation of high resolution continental records. This observation has become possible through the correlation of independent annually resolved records using isochronous volcanic ash layers, we thus avoid any circularity involved in aligning records through palaeoclimate signals. This independent synchronisation also allows us to resolve differences between archives at an annual to decadal scale. As a result of this we can now infer that atmospheric response to the gradual resumption of North Atlantic overturning was very rapid at individual sites but was a-synchronous at a regional scale. This has significant implications for both palaeoclimate modelling and also our understanding of the dynamic nature of atmospheric response to climate change.

Lane, C. S.; Brauer, A.; Blockley, S.; Dulski, P.

2012-12-01

236

Genetic consequences of forest fragmentation for a highly specialized arboreal mammal--the edible dormouse.  

PubMed

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, Jürgen; Loeschcke, Volker; Weis-Dootz, Tanja; Segelbacher, Gernot

2014-01-01

237

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, Jürgen; Loeschcke, Volker; Weis-Dootz, Tanja; Segelbacher, Gernot

2014-01-01

238

Essay Contest Reveals Misconceptions of High School Students in Genetics Content  

PubMed Central

National educational organizations have called upon scientists to become involved in K–12 education reform. From sporadic interaction with students to more sustained partnerships with teachers, the engagement of scientists takes many forms. In this case, scientists from the American Society of Human Genetics (ASHG), the Genetics Society of America (GSA), and the National Society of Genetic Counselors (NSGC) have partnered to organize an essay contest for high school students as part of the activities surrounding National DNA Day. We describe a systematic analysis of 500 of 2443 total essays submitted in response to this contest over 2 years. Our analysis reveals the nature of student misconceptions in genetics, the possible sources of these misconceptions, and potential ways to galvanize genetics education. PMID:18245328

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

2008-01-01

239

Genetic Interactions Show the Importance of rRNA Modification Machinery for the Role of Rps15p during Ribosome Biogenesis in S. cerevisiæ  

PubMed Central

Rps15p, an essential ribosomal protein, was previously shown to be critical for nuclear export of small subunit pre-particles. We have designed a synthetic lethal screen in Saccharomyces cerevisiæ to identify its genetic partners and further elucidate its role during ribosomal biogenesis. Our screen revealed interactions with mutants affected at various stages during ribosome biogenesis, from early nucleolar steps to nuclear export. Mutations were identified in genes encoding proteins involved in early ribosome biogenesis steps, like the small subunit processome component Utp15p, the 90S pre-ribosome factor Slx9p and the H/ACA snoRNP core protein Nhp2p. In addition, we found a synthetic lethality with BUD23, a gene encoding a methyltransferase involved both in rRNA modification and small subunit nuclear export. Interestingly, deletion of snR36 or snR85, two H/ACA snoRNAs that direct modifications close to Rps15p's binding site on the rRNA, produces mild and opposite effects on growth in an rps15 hypomorphic background. These data uncover an unreported link between a ribosomal protein and rRNA modification machinery. PMID:20454621

Bellemer, Clément; Chabosseau, Pauline; Gallardo, Franck; Gleizes, Pierre-Emmanuel; Stahl, Guillaume

2010-01-01

240

Awareness of Societal Issues Among High School Biology Teachers Teaching Genetics  

NASA Astrophysics Data System (ADS)

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

Lazarowitz, Reuven; Bloch, Ilit

2005-12-01

241

A high throughput genotyping approach reveals distinctive autosomal genetic signatures for European and Near Eastern wild boar.  

PubMed

The lack of a Near Eastern genetic signature in modern European porcine breeds indicates that, although domestic pigs from the Fertile Crescent entered Europe during the Neolithic, they were completely replaced by their European counterparts in a short window of time. Whilst the absence of such genetic signature has been convincingly demonstrated at the mitochondrial level, variation at the autosomal genomes of European and Near Eastern Sus scrofa has not been compared yet. Herewith, we have explored the genetic relationships among 43 wild boar from Europe (N?=?21), Near East (N?=?19) and Korea (N?=?3), and 40 Iberian (N?=?16), Canarian (N?=?4) and Mangalitza (N?=?20) pigs by using a high throughput SNP genotyping platform. After data filtering, 37,167 autosomal SNPs were used to perform population genetics analyses. A multidimensional scaling plot based on genome-wide identity-by-state pairwise distances inferred with PLINK showed that Near Eastern and European wild boar populations are genetically differentiated. Maximum likelihood trees built with TreeMix supported this conclusion i.e. an early population split between Near Eastern and European Sus scrofa was observed. Moreover, analysis of the data with Structure evidenced that the sampled Iberian, Canarian and Mangalitza pigs did not carry any autosomal signature compatible with a Near Eastern ancestry, a finding that agrees well with previous mitochondrial studies. PMID:23460788

Manunza, Arianna; Zidi, Ali; Yeghoyan, Seryozha; Balteanu, Valentin Adrian; Carsai, Teodora Crina; Scherbakov, Oleg; Ramírez, Oscar; Eghbalsaied, Shahin; Castelló, Anna; Mercadé, Anna; Amills, Marcel

2013-01-01

242

Genetic structure is correlated with phenotypic divergence rather than geographic isolation in the highly polymorphic strawberry poison-dart frog.  

PubMed

Phenotypic and genetic divergence can be influenced by a variety of factors, including sexual and natural selection, genetic drift and geographic isolation. Investigating the roles of these factors in natural systems can provide insight into the relative influences of allopatric and ecological modes of biological diversification in nature. The strawberry poison frog, Dendrobates pumilio, presents an excellent opportunity for this kind of research, displaying a diverse array of colour morphs and inhabiting a heterogeneous landscape that includes oceanic islands, fragmented rainforest patches and wide expanses of suitable habitat. In this study, we use 15 highly polymorphic microsatellite loci to estimate population structure and gene flow among populations from across the range of D. pumilio and a causal modelling framework to statistically test 12 hypotheses regarding the geographic and phenotypic variables that explain genetic differentiation within this system. Our results demonstrate that the genetic distance between populations is most strongly associated with differences in dorsal coloration. Previous experimental studies have shown that phenotypic differences can result in sexual and natural selection against non-native phenotypes, and our results now show that these forces lead to genetic isolation between different colour morphs in the wild, presenting a potential case of incipient speciation through selection. PMID:20025652

Wang, Ian J; Summers, Kyle

2010-02-01

243

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

PubMed

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

Raymond, Lucie; Plantegenest, Manuel; Vialatte, Aude

2013-11-01

244

Genetics  

NSDL National Science Digital Library

Genetics is the branch of biology that studies the ways in which hereditary information is passed on from the parents to their offspring. As we study this unit, I will be asking you to visit the following websites to emphasize concepts brought up during class. DNA Structure and Replication Build a DNA molecule Use this website to practice matching up complementary nucleotides in the DNA molecule. How DNA Replicates Take a look at this short video clip that demonstrates how the DNA molecule replicates. A Science Odyssey :You Try It: DNA Workshop When you get to this website, click on \\"Go directly to the DNA Workshop\\". Click on DNA replication on the left ...

Miss Goodfellow

2007-10-23

245

Genetics  

NSDL National Science Digital Library

This online tutorial from the TheTech Museum of Innovation focuses on genetics. The interactive topics will initially introduce the user to the DNA, chromosomes, and the make up of human genes. Further topics will examine forensic science, the history of forensics, fingerprinting, and cloning background research and community response to cloning. Finally, the resource provides connections to gallery exhibits, science labs, and a design challenge that engages the learner to write a persuasive letter to a group or organization responsible for cloning or DNA decision making. Copyright 2005 International Technology Education Association

The Tech Museum of Innovation

2004-01-01

246

Inference of selection based on temporal genetic differentiation in the study of highly polymorphic multigene families.  

PubMed

The co-evolutionary arms race between host immune genes and parasite virulence genes is known as Red Queen dynamics. Temporal fluctuations in allele frequencies, or the 'turnover' of alleles at immune genes, are concordant with predictions of the Red Queen hypothesis. Such observations are often taken as evidence of host-parasite co-evolution. Here, we use computer simulations of the Major Histocompatibility Complex (MHC) of guppies (Poecilia reticulata) to study the turnover rate of alleles (temporal genetic differentiation, G'(ST)). Temporal fluctuations in MHC allele frequencies can be ??order of magnitude larger than changes observed at neutral loci. Although such large fluctuations in the MHC are consistent with Red Queen dynamics, simulations show that other demographic and population genetic processes can account for this observation, these include: (1) overdominant selection, (2) fluctuating population size within a metapopulation, and (3) the number of novel MHC alleles introduced by immigrants when there are multiple duplicated genes. Synergy between these forces combined with migration rate and the effective population size can drive the rapid turnover in MHC alleles. We posit that rapid allelic turnover is an inherent property of highly polymorphic multigene families and that it cannot be taken as evidence of Red Queen dynamics. Furthermore, combining temporal samples in spatial F(ST) outlier analysis may obscure the signal of selection. PMID:22900006

McMullan, Mark; van Oosterhout, Cock

2012-01-01

247

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

248

High Urban Breeding Densities Do Not Disrupt Genetic Monogamy in a Bird Species  

PubMed Central

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

249

Phylogenetic analysis of Portuguese Feline Immunodeficiency Virus sequences reveals high genetic diversity.  

PubMed

Feline Immunodeficiency Virus (FIV) is a Lentivirus responsible for an immunodeficiency like disease in domestic cats. Based on the genetic diversity of the V3-V5 region of env gene FIV is divided in five phylogenetic subtypes (A, B, C, D and E) with a world-wide distribution. To understand the subtype diversity of FIV in Portugal a serological survey was conducted during 1 year in the Veterinary Faculty Hospital, Lisbon, Portugal to identify seropositive animals. Two viral genomic regions were amplified by a nested PCR, sequenced and the phylogenetic relationships between 24 new Portuguese FIV sequences and other previously published FIV isolates were assessed. The introduction of these sequences induced a subclustering in subtype B including most of the new Portuguese sequences. Moreover, a new cluster emerged, with two highly divergent new sequences that might represent a new subtype. The study of these new FIV isolates showed the presence in Portugal of a unique viral population subclustering within subtype B and of sequences clearly divergent from the five known subtypes, providing a contribution for the understanding of FIV's genetic diversity. PMID:16384661

Duarte, Ana; Tavares, Luis

2006-04-16

250

Genetic analysis of axial length genes in high grade myopia from Indian population?  

PubMed Central

Purpose To study the putative association of Membrane frizzled related protein (MFRP) and Visual system homeobox protein (VSX2) gene variants with axial length (AL) in myopia. Method A total of 189 samples with (N = 98) and without (N = 91) myopia were genotyped for the MRFP and VSX2 variations in ABI Prism 3100 AVANT genetic analyzer. Genotype/haplotype analysis was performed using PLINK, Haploview and THESIAS softwares. Results Fifteen variations were observed in the MFRP gene of which, rs36015759 (c.492C > T, T164T) in exon 5 was distributed at a high frequency in the controls and significantly associated with a low risk for myopia (P = 4.10 ? e? 07 OR < 1.0). An increased frequency for the coding haplotype block [CGTCGG] harboring rs36015759 was observed in controls (31%) than cases (8%) that also correlated with a decreased mean AL (? 1.35085; P = 0.000444) by THESIAS analysis. The ‘T’ allele of rs36015759 was predicted to abolish the binding site for splicing enhancer (SRp40) by FASTSNP analysis. Conclusion Myopia is a complex disorder influenced by genetic and environmental factors. Our work shows evidence of association of a specific MFRP haplotype which was more prevalent in controls with decreased AL. However, replication and functional studies are warranted to confirm these findings. PMID:25606400

Sharmila, Ferdinamarie; Abinayapriya; Ramprabhu, Karthikeyan; Kumaramanickavel, Govindasamy; R.R.Sudhir; Sripriya, Sarangapani

2014-01-01

251

[Human genetics studies in areas of high natural radiation. VII. Genetic load].  

PubMed

Two methods to estimate the inbreeding load (Morton, Crow and Muller17 1956; Freire-Maia and Freire-Maia6 1965) are reviewed. Both are employed in the analysis of our data. Besides the total population, a sample constituted of individuals with no alien ancestral is also analysed. No clean effect of natural radioactivity, as measured by genetic load models, has been found (this is especially valid for abortions, pre-natal mortality, anomalies, and abnormalities in general). The results on stillbirths and post-natal and total mortalities are discussed, and it is concluded that most probably the differences found are due to uncontrolled concomitant variables (if not to chance alone). Further analysis are under way. PMID:1215578

Freire-Maia, A

1975-01-01

252

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

253

Genetic structure is associated with phenotypic divergence in floral traits and reproductive investment in a high-altitude orchid from the iron quadrangle, southeastern Brazil.  

PubMed

Knowledge of the role of Neotropical montane landscapes in shaping genetic connectivity and local adaptation is essential for understanding the evolutionary processes that have shaped the extraordinary species diversity in these regions. In the present study, we examined the landscape genetics, estimated genetic diversity, and explored genetic relationships with morphological variability and reproductive strategies in seven natural populations of Cattleya liliputana (Orchidaceae). Nuclear microsatellite markers were used for genetic analyses. Spatial Bayesian clustering and population-based analyses revealed significant genetic structuring and high genetic diversity (He = 0.733 ± 0.03). Strong differentiation was found between populations over short spatial scales (FST = 0.138, p < 0.001), reflecting the landscape discontinuity and isolation. Monmonier´s maximum difference algorithm, Bayesian analysis on STRUCTURE and principal component analysis identified one major genetic discontinuity between populations. Divergent genetic groups showed phenotypic divergence in flower traits and reproductive strategies. Increased sexual reproductive effort was associated with rock outcrop type and may be a response to adverse conditions for growth and vegetative reproduction. Here we discuss the effect of restricted gene flow, local adaptation and phenotypic plasticity as drivers of population differentiation in Neotropical montane rock outcrops. PMID:25756994

Leles, Bruno; Chaves, Anderson V; Russo, Philip; Batista, João A N; Lovato, Maria Bernadete

2015-01-01

254

Genetic Structure Is Associated with Phenotypic Divergence in Floral Traits and Reproductive Investment in a High-Altitude Orchid from the Iron Quadrangle, Southeastern Brazil  

PubMed Central

Knowledge of the role of Neotropical montane landscapes in shaping genetic connectivity and local adaptation is essential for understanding the evolutionary processes that have shaped the extraordinary species diversity in these regions. In the present study, we examined the landscape genetics, estimated genetic diversity, and explored genetic relationships with morphological variability and reproductive strategies in seven natural populations of Cattleya liliputana (Orchidaceae). Nuclear microsatellite markers were used for genetic analyses. Spatial Bayesian clustering and population-based analyses revealed significant genetic structuring and high genetic diversity (He = 0.733 ± 0.03). Strong differentiation was found between populations over short spatial scales (FST = 0.138, p < 0.001), reflecting the landscape discontinuity and isolation. Monmonier´s maximum difference algorithm, Bayesian analysis on STRUCTURE and principal component analysis identified one major genetic discontinuity between populations. Divergent genetic groups showed phenotypic divergence in flower traits and reproductive strategies. Increased sexual reproductive effort was associated with rock outcrop type and may be a response to adverse conditions for growth and vegetative reproduction. Here we discuss the effect of restricted gene flow, local adaptation and phenotypic plasticity as drivers of population differentiation in Neotropical montane rock outcrops. PMID:25756994

Leles, Bruno; Chaves, Anderson V.; Russo, Philip; Batista, João A. N.; Lovato, Maria Bernadete

2015-01-01

255

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

256

Informed consent form challenges for genetic research in a developing arab country with high risk for genetic disease.  

PubMed

The prevalence of genetic disease is high in the Middle East, particularly in the United Arab Emirates. Our study assesses the information provided in, and the readability ease of, informed consent forms (ICF) for genetic research studies. A multicenter retrospective cross-sectional review of 54 ICFs was conducted to assess compliance by comparing them with standard good clinical practice guidelines for developing consent forms. Readability of the forms was determined using the Flesch-Kincaid scale. Overall Good Clinical Practice compliance for the ICFs averaged at 63 %. Information regarding privacy, confidentiality, specimen collection and storage were absent from the majority of the ICFs. Readability ease score was low (36.7?±?4.6) and required college-level (11.8?±?1.4) reading skills to understand the information. Our study highlights the need to improve the readability and information contained in the ICFs for genetic research studies in our setting. Our findings may be generalized to similar cultures in the Middle East and Asia. PMID:25228356

Nair, Satish Chandrasekhar; Ibrahim, Halah

2015-04-01

257

Patients with type 1 diabetes show signs of vascular dysfunction in response to multiple high-fat meals  

PubMed Central

Background A high-fat diet promotes postprandial systemic inflammation and metabolic endotoxemia. We investigated the effects of three consecutive high-fat meals on endotoxemia, inflammation, vascular function, and postprandial lipid metabolism in patients with type 1 diabetes. Methods Non-diabetic controls (n?=?34) and patients with type 1 diabetes (n?=?37) were given three high-caloric, fat-containing meals during one day. Blood samples were drawn at fasting (8:00) and every two hours thereafter until 18:00. Applanation tonometry was used to assess changes in the augmentation index during the investigation day. Results Three consecutive high-fat meals had only a modest effect on serum LPS-activity levels and inflammatory markers throughout the day in both groups. Of note, patients with type 1 diabetes were unable to decrease the augmentation index in response to the high-fat meals. The most profound effects of the consecutive fat loads were seen in chylomicron and HDL-metabolism. The triglyceride-rich lipoprotein remnant marker, apoB-48, was elevated in patients compared to controls both at fasting (p?=?0.014) and postprandially (p?=?0.035). The activities of the HDL-associated enzymes PLTP (p?high-fat meals, early signs of vascular dysfunction alongside accumulation of chylomicron remnants, higher augmentation index, and decreased PON-1 activity were observed in patients with type 1 diabetes. The high-fat meals had no significant impact on postprandial LPS-activity in non-diabetic subjects or patients with type 1 diabetes suggesting that metabolic endotoxemia may be more central in patients with chronic metabolic disturbances such as obesity, type 2 diabetes, or diabetic kidney disease. PMID:24959195

2014-01-01

258

Many Infants Prenatally Exposed to High Levels of Alcohol Show One Particular Anomaly of the Corpus Callosum  

Microsoft Academic Search

Introduction: Effects of prenatal alcohol exposure on the brain are seen at every age. The earlier they can be quantified, the better the prognosis for the affected child. Here we show measurable alcohol effects at birth on a structure currently used for nosology only much later in life. Methods: Midline shape of the corpus callosum was imaged in infants via

Fred L. Bookstein; Paul D. Connor; Janet E. Huggins; Helen M. Barr; Kristi D. Pimentel; Ann P. Streissguth

2007-01-01

259

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

260

A new supramolecular system of racemic-bis-beta-naphthol, benzoquinone and aromatic hydrocarbon, which shows high molecular recognition ability.  

PubMed

Racemic-bis-beta-naphthol, benzoquinone and aromatic hydrocarbons formed a new three component supramolecular system as black crystals. X-ray analysis of the crystals shows that (+)- and (-)-bis-beta-naphthol and benzoquinone form a quinhydrone-type crystalline lattice with aromatic stacking and hydrogen bonding in which the third aromatic hydrocarbon component is accommodated. As the cavity created has a definite shape and size, only hydrocarbons which fit the cavity are selectively included. PMID:12197000

Toda, Fumio; Senzaki, Mami; Kuroda, Reiko

2002-08-21

261

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

262

Smoking habit and genetic factors associated with lung cancer in a population highly exposed to arsenic.  

PubMed

In order to find some relationship between genetic differences in metabolic activation and detoxification of environmental carcinogens and host susceptibility to chemically induced cancers, we have investigated the distribution of the GSTM1 null genotype and CYP450 *1A1 MspI polymorphism in lung cancer patients and healthy volunteers of the second region in the north of Chile highly exposed to arsenic. The main sources of environmental arsenic exposure in Chile are copper smelting and drinking water, specially in the second region, the most important copper mining region in the world that shows the highest lung cancer mortality rate in the country (35/100.00). The population of Antofagasta, the main city of the region was exposed between 1958 and 1970 to arsenic concentrations in drinking water of 860 microg/m3, presently declining to 40 microg/m3. For men the MspI CYP1A1 *2A genotype was associated with a highly significant estimated relative lung cancer risk (O.R. = 2.60), but not GSTM1 by itself. The relative lung cancer risk for the combined 2A/null GSTM1 genotypes was 2.51, which increased with the smoking habits (O.R. = 2.98). In the second region the cancer mortality rate for As associated cancers, might be related at least part to differences in As biotransformation. In this work we demonstrate that genetic biomarkers such as CYP1A1 2A and GSTM1 polymorphisms in addition to DR70 as screening biomarkers might provide relevant information to identify individuals with higher risk for lung cancer, due to arsenic exposure. PMID:16099114

Adonis, M; Martínez, V; Marín, P; Berrios, D; Gil, L

2005-10-15

263

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

264

Highly resolved early Eocene food webs show development of modern trophic structure after the end-Cretaceous extinction.  

PubMed

Generalities of food web structure have been identified for extant ecosystems. However, the trophic organization of ancient ecosystems is unresolved, as prior studies of fossil webs have been limited by low-resolution, high-uncertainty data. We compiled highly resolved, well-documented feeding interaction data for 700 taxa from the 48 million-year-old latest early Eocene Messel Shale, which contains a species assemblage that developed after an interval of protracted environmental and biotal change during and following the end-Cretaceous extinction. We compared the network structure of Messel lake and forest food webs to extant webs using analyses that account for scale dependence of structure with diversity and complexity. The Messel lake web, with 94 taxa, displays unambiguous similarities in structure to extant webs. While the Messel forest web, with 630 taxa, displays differences compared to extant webs, they appear to result from high diversity and resolution of insect-plant interactions, rather than substantive differences in structure. The evidence presented here suggests that modern trophic organization developed along with the modern Messel biota during an 18 Myr interval of dramatic post-extinction change. Our study also has methodological implications, as the Messel forest web analysis highlights limitations of current food web data and models. PMID:24648225

Dunne, Jennifer A; Labandeira, Conrad C; Williams, Richard J

2014-05-01

265

Highly resolved early Eocene food webs show development of modern trophic structure after the end-Cretaceous extinction  

PubMed Central

Generalities of food web structure have been identified for extant ecosystems. However, the trophic organization of ancient ecosystems is unresolved, as prior studies of fossil webs have been limited by low-resolution, high-uncertainty data. We compiled highly resolved, well-documented feeding interaction data for 700 taxa from the 48 million-year-old latest early Eocene Messel Shale, which contains a species assemblage that developed after an interval of protracted environmental and biotal change during and following the end-Cretaceous extinction. We compared the network structure of Messel lake and forest food webs to extant webs using analyses that account for scale dependence of structure with diversity and complexity. The Messel lake web, with 94 taxa, displays unambiguous similarities in structure to extant webs. While the Messel forest web, with 630 taxa, displays differences compared to extant webs, they appear to result from high diversity and resolution of insect–plant interactions, rather than substantive differences in structure. The evidence presented here suggests that modern trophic organization developed along with the modern Messel biota during an 18 Myr interval of dramatic post-extinction change. Our study also has methodological implications, as the Messel forest web analysis highlights limitations of current food web data and models. PMID:24648225

Dunne, Jennifer A.; Labandeira, Conrad C.; Williams, Richard J.

2014-01-01

266

High Genetic Diversity in the Chemoreceptor Superfamily of Caenorhabditis elegans  

PubMed Central

We investigated genetic polymorphism in the Caenorhabditis elegans srh and str chemoreceptor gene families, each of which consists of ?300 genes encoding seven-pass G-protein-coupled receptors. Almost one-third of the genes in each family are annotated as pseudogenes because of apparent functional defects in N2, the sequenced wild-type strain of C. elegans. More than half of these “pseudogenes” have only one apparent defect, usually a stop codon or deletion. We sequenced the defective region for 31 such genes in 22 wild isolates of C. elegans. For 10 of the 31 genes, we found an apparently functional allele in one or more wild isolates, suggesting that these are not pseudogenes but instead functional genes with a defective allele in N2. We suggest the term “flatliner” to describe genes whose functional vs. pseudogene status is unclear. Investigations of flatliner gene positions, dN/dS ratios, and phylogenetic trees indicate that they are not readily distinguished from functional genes in N2. We also report striking heterogeneity in the frequency of other polymorphisms among these genes. Finally, the large majority of polymorphism was found in just two strains from geographically isolated islands, Hawaii and Madeira. This suggests that our sampling of wild diversity in C. elegans is narrow and that identification of additional strains from similarly isolated regions will greatly expand the diversity available for study. PMID:15520260

Stewart, Mary K.; Clark, Nathaniel L.; Merrihew, Gennifer; Galloway, Evan M.; Thomas, James H.

2005-01-01

267

Dissecting High-Dimensional Phenotypes with Bayesian Sparse Factor Analysis of Genetic Covariance Matrices  

PubMed Central

Quantitative genetic studies that model complex, multivariate phenotypes are important for both evolutionary prediction and artificial selection. For example, changes in gene expression can provide insight into developmental and physiological mechanisms that link genotype and phenotype. However, classical analytical techniques are poorly suited to quantitative genetic studies of gene expression where the number of traits assayed per individual can reach many thousand. Here, we derive a Bayesian genetic sparse factor model for estimating the genetic covariance matrix (G-matrix) of high-dimensional traits, such as gene expression, in a mixed-effects model. The key idea of our model is that we need consider only G-matrices that are biologically plausible. An organism’s entire phenotype is the result of processes that are modular and have limited complexity. This implies that the G-matrix will be highly structured. In particular, we assume that a limited number of intermediate traits (or factors, e.g., variations in development or physiology) control the variation in the high-dimensional phenotype, and that each of these intermediate traits is sparse – affecting only a few observed traits. The advantages of this approach are twofold. First, sparse factors are interpretable and provide biological insight into mechanisms underlying the genetic architecture. Second, enforcing sparsity helps prevent sampling errors from swamping out the true signal in high-dimensional data. We demonstrate the advantages of our model on simulated data and in an analysis of a published Drosophila melanogaster gene expression data set. PMID:23636737

Runcie, Daniel E.; Mukherjee, Sayan

2013-01-01

268

ARCING HIGH IMPEDANCE FAULT DETECTION USING REAL CODED GENETIC ALGORITHM  

Microsoft Academic Search

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

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

269

Constitutive expression of high-affinity sulfate transporter (HAST) gene in Indian mustard showed enhanced sulfur uptake and assimilation  

Microsoft Academic Search

Lycopersicon esculantum sulfate transporter gene (LeST 1.1) encodes a high-affinity sulfate transporter (HAST) located in root epidermis. In this\\u000a study, the LeST 1.1 gene was constitutively expressed in Indian mustard (Brassica juncea cv. Pusa Jai Kisan). Transgenic as well as untransformed plants were grown in sulfur-insufficient (25 and 50 ?M) and sulfur-sufficient\\u000a (1,000 ?M) conditions for 30 days. Two-fold increase was noticed in

M. Z. Abdin; M. Akmal; M. Ram; T. Nafis; P. Alam; M. Nadeem; M. A. Khan; A. Ahmad

270

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.

271

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.; Bagnéris, Claire; Dumas, Christian; Henderson, Brian; Ward, John; Keep, Nicholas H.; Cohen-Gonsaud, Martin

2014-01-01

272

Next generation sequencing shows high variation of the intestinal microbial species composition in Atlantic cod caught at a single location  

PubMed Central

Background The observation that specific members of the microbial intestinal community can be shared among vertebrate hosts has promoted the concept of a core microbiota whose composition is determined by host-specific selection. Most studies investigating this concept in individual hosts have focused on mammals, yet the diversity of fish lineages provides unique comparative opportunities from an evolutionary, immunological and environmental perspective. Here we describe microbial intestinal communities of eleven individual Atlantic cod (Gadus morhua) caught at a single location based on an extensively 454 sequenced 16S rRNA library of the V3 region. Results We obtained a total of 280447 sequences and identify 573 Operational Taxonomic Units (OTUs) at 97% sequence similarity level, ranging from 40 to 228 OTUs per individual. We find that ten OTUs are shared, though the number of reads of these OTUs is highly variable. This variation is further illustrated by community diversity estimates that fluctuate several orders of magnitude among specimens. The shared OTUs belong to the orders of Vibrionales, which quantitatively dominate the Atlantic cod intestinal microbiota, followed by variable numbers of Bacteroidales, Erysipelotrichales, Clostridiales, Alteromonadales and Deferribacterales. Conclusions The microbial intestinal community composition varies significantly in individual Atlantic cod specimens caught at a single location. This high variation among specimens suggests that a complex combination of factors influence the species distribution of these intestinal communities. PMID:24206635

2013-01-01

273

A highly efficient ligand-regulated Cre recombinase mouse line shows that LoxP recombination is position dependent  

PubMed Central

Conditional gene inactivation using the Cre/loxP system is widely used, but the difficulty in properly regulating Cre expression remains one of the bottlenecks. One approach to regulate Cre activity utilizes a mutant estrogen hormone-binding domain (ERT) to keep Cre inactive unless the non-steroidal estrogen analog 4-hydroxytamoxifen (OHT) is present. Here we describe a mouse strain expressing Cre-ERT from the ubiquitously expressed ROSA26 (R26) locus. We demonstrate efficient temporal and spatial regulation of Cre recombination in vivo and in primary cells derived from these mice. We show the existence of marked differences in recombination frequencies between different substrates within the same cell. This has important consequences when concurrent switching of multiple alleles within the same cell is needed, and highlights one of the difficulties that may be encountered when using reporter mice as indicator strains. PMID:11306549

Vooijs, Marc; Jonkers, Jos; Berns, Anton

2001-01-01

274

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

275

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

276

High genetic diversity and low population structure in Porter's sunflower (Helianthus porteri).  

PubMed

Granite outcrops in the southeastern United States are rare and isolated habitats that support edaphically controlled communities dominated by herbaceous plants. They harbor rare and endemic species that are expected to have low genetic variability and high population structure due to small population sizes and their disjunct habitat. We test this expectation for an annual outcrop endemic, Helianthus porteri (Porter's sunflower). Contrary to expectation, H. porteri has relatively high genetic diversity (H e = 0.681) and relatively low genetic structure among the native populations (F ST = 0.077) when compared to 5 other Helianthus species (N = 288; 18 expressed sequence tag-SSR markers). These findings suggest greater gene flow than expected. The potential for gene flow is supported by the analysis of transplant populations established with propagules from a common source in 1959. One population established close to a native population (1.5 km) at the edge of the natural range is genetically similar to and shares rare alleles with the adjacent native population and is distinct from the central source population. In contrast, a transplant population established north of the native range has remained similar to the source population. The relatively high genetic diversity and low population structure of this species, combined with the long-term success of transplanted populations, bode well for its persistence as long as the habitat persists. PMID:23487323

Gevaert, Scott D; Mandel, Jennifer R; Burke, John M; Donovan, Lisa A

2013-01-01

277

High-resolution MRI assessment of dactylitis in psoriatic arthritis shows flexor tendon pulley and sheath-related enthesitis  

PubMed Central

Objective Dactylitis is a hallmark of psoriatic arthritis (PsA) where flexor tenosynovitis is common. This study explored the microanatomical basis of dactylitis using high-resolution MRI (hrMRI) to visualise the small entheses around the digits. Methods Twelve patients with psoriatic dactylitis (4 fingers, 8 toes), and 10 healthy volunteers (6 fingers, 4 toes) had hrMRI of the digits using a ‘microscopy’ coil and contrast enhancement. All structures were evaluated including the tendons and ligaments, related enthesis organs, pulleys, volar/plantar plates and tendon sheaths. Results In dactylitis, collateral ligament enthesitis was seen in nine digits (75%), extensor tendon enthesitis in six digits (50%), functional enthesitis (5 digits, 42%), abnormal enhancement at the volar plates (2/5 joints, 40%) and the plantar plate (1/5 joints, 20%). Nine cases (75%) demonstrated flexor tenosynovitis, with flexor tendon pulley/flexor sheath microenthesopathy observed in 50% of all cases. Less abnormalities which were milder was observed in the normal controls, none of whom had any signal changes in the tendon pulleys or fibrous sheaths. Conclusions This study provides proof of concept for a link between dactylitis and ‘digital polyenthesitis’ including disease of the miniature enthesis pulleys of the flexor tendons, further affirming the concept of enthesitis in PsA. PMID:25261575

Tan, Ai Lyn; Fukuba, Eiji; Halliday, Nicola Ann; Tanner, Steven F; Emery, Paul; McGonagle, Dennis

2015-01-01

278

Non-random expression of ribosomal DNA units in a grasshopper showing high intragenomic variation for the ITS2 region.  

PubMed

We analyse intragenomic variation of the ITS2 internal transcribed spacer of ribosomal DNA (rDNA) in the grasshopper Eyprepocnemis plorans, by means of tagged PCR 454 amplicon sequencing performed on both genomic DNA (gDNA) and RNA-derived complementary DNA (cDNA), using part of the ITS2 flanking coding regions (5.8S and 28S rDNA) as an internal control for sequencing errors. Six different ITS2 haplotypes (i.e. variants for at least one nucleotide in the complete ITS2 sequence) were found in a single population, one of them (Hap4) being specific to a supernumerary (B) chromosome. The analysis of both gDNA and cDNA from the same individuals provided an estimate of the expression efficiency of the different haplotypes. We found random expression (i.e. about similar recovery in gDNA and cDNA) for three haplotypes (Hap1, Hap2 and Hap5), but significant underexpression for three others (Hap3, Hap4 and Hap6). Hap4 was the most extremely underexpressed and, remarkably, it showed the lowest sequence conservation for the flanking 5.8-28S coding regions in the gDNA reads but the highest conservation (100%) in the cDNA ones, suggesting the preferential expression of mutation-free rDNA units carrying this ITS2 haplotype. These results indicate that the ITS2 region of rDNA is far from complete homogenization in this species, and that the different rDNA units are not expressed at random, with some of them being severely downregulated. PMID:25565136

Ruiz-Estévez, M; Ruiz-Ruano, F J; Cabrero, J; Bakkali, M; Perfectti, F; López-León, M D; Camacho, J P M

2015-06-01

279

T cells from chronic bone infection show reduced proliferation and a high proportion of CD28- CD4 T cells  

PubMed Central

Chronic bone infection is associated with bone resorption. From animal studies, CD3/CD28-activated T cells are known to enhance osteoclastogenesis and bone resorption. Because CD28 is expressed constitutively on T cells and its expression is down-regulated by chronic exposure to the inflammatory environment, we characterized co-stimulatory molecule expression on T cells from chronically infected patients. We used cytofluorometric techniques to phenotypically characterize T cells, its co-stimulatory molecules and perforin secretion from infected and non-infected human bones. Chronic bone infection was defined as infection lasting for more than a month. We show a higher T cell activation [human leucocyte antigen D-related (HLA-DR+)] in infected compared to non-infected bones: median being 16 versus 7%, P?=?0·009 for CD4 T cells, and 33 versus 15%, P?=?0·038 for CD8 T cells, respectively. However, T cell proliferation (Ki67+) was lower for CD8 T cells in infected bones: 26 versus 34%, P?=?0·045. In contrast, we detected no difference in apoptosis and regulatory T cells. In infected bone, we found higher CD28-negative CD4+ T cells compared to non-infected bone: 20 versus 8%, respectively (P?=?0·005); this T cell subset had higher CD11b expression and perforin secretion. Chronically infected human bones are characterized by an increase of CD28-negative CD4+ T cells, indicating long-term activated cells with cytotoxic ability. Therefore, this alteration of co-stimulatory molecules may modify interactions with osteoclasts and impact bone resorption. PMID:24298980

Kumar, G; Roger, P-M; Ticchioni, M; Trojani, C; Bernard de Dompsur, R; Bronsard, N; Carles, M; Bernard, E

2014-01-01

280

Opportunistic computed tomography screening shows a high incidence of osteoporosis in ankylosing spondylitis patients with acute vertebral fractures.  

PubMed

Advanced ankylosing spondylitis is associated with reductions in bone mineral density (BMD), contributing to pain and predisposing to fractures. Quantifying this reduction is complicated because overgrowth of bone and loss of trabecular bone occur concurrently. Traditional methods such as dual-energy X-ray absorptiometry struggle to generate accurate estimates of BMD in these patients. The aim of this study was to evaluate the utility of computed tomography (CT) attenuation in generating estimates of BMD in patients with severe AS who had sustained vertebral fractures. Patients with severe AS and bridging syndesmophytes who presented, with acute fractures of the spine, were reviewed to assess whether they had a CT scan in the 6 mo before or after injury that included an image of the L1 vertebra; if it did, the scans were selected for analysis. A total of 17 patients were evaluated. Using a CT attenuation threshold of 135 HU balanced for sensitivity and specificity, 14 of 17 (82%) patients were osteoporotic. Using a CT attenuation threshold for higher sensitivity (160 HU), 15 of 17 (88%) patients were osteoporotic. Even using the L1 CT attenuation threshold of 110 HU for higher specificity, 14 of 17 (82%) patients were osteoporotic. CT attenuation demonstrates that a high proportion of AS patients who sustain fractures have osteoporosis. This overcomes some of the difficulties that have been encountered with the use of dual-energy X-ray absorptiometry in this group of patients. This simple and accessible method saves on time, cost, and exposure to radiation and can help in the planning of a patient's management. PMID:25172008

Emohare, Osa; Cagan, Amanda; Polly, David W; Gertner, Elie

2015-01-01

281

High-Impact Event Prediction by Temporal Data Mining through Genetic Algorithms  

Microsoft Academic Search

This paper describes a genetic algorithm based approach to detect and predict high-impact events. While, these events occur infrequently, they are quite costly, meaning that they have a high-impact on the system key performance indicators. This approach is based on mining for these events and subsequences that are predictive of these high-impact events from historical data and then classifying these

Narayan Srinivasa; Qin Jiang; Leandro G. Barajas

2008-01-01

282

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

283

MUTANT SCREEN REPORT A Genetic Screen for High Copy Number  

E-print Network

platform for DNA repair enzymes, undergoes modification by the ubiquitin-like mole- cule SUMO. PCNA for functions related to DNA- and chromatin-binding, chromatin packaging and modification, and mRNA export from. This modification takes place during S-phase or after high doses of DNA damage. An additional residue, lysine 127

Shamir, Ron

284

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

285

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

PubMed

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

Fortunato, Angelo

2009-04-01

286

Doing the lesson or doing science: Argument in high school genetics  

NASA Astrophysics Data System (ADS)

This article focuses on the capacity of students to develop and assess arguments during a high school genetics instructional sequence. The research focused on the locating distinction in argumentation discourse between doing science vs. doing school or doing the lesson (Bloome, Puro, & Theodorou, 1989). Participants in this classroom case study were high school (9th grade) students in Galicia (Spain). Students were observed, videotaped, and audiotaped while working in groups over six class sessions. Toulmin's argument pattern was used as a tool for the analysis of students' conversation and other frames were used for analyzing other dimensions of students' dialogue; (e.g., epistemic operations, use of analogies, appeal to consistency, and causal relations). Instances of doing science and instances of doing the lesson are identified and discussed as moments when the classroom discourse is dominated either by talking science or displaying the roles of students. The different arguments constructed and co-constructed by students, the elements of the arguments, and the sequence are also discussed, showing a dominance of claims and a lesser frequence of justifications or warrants. Implications for developing effective contexts to promote argumentation and science dialogue in the classroom are discussed.

Jiménez-Aleixandre, M. Pilar; Bugallo Rodríguez, Anxela; Duschl, Richard A.

2000-11-01

287

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

288

Lumbar spinal stenosis is a highly genetic condition partly mediated by disc degeneration.  

PubMed

Objective. Lumbar spinal stenosis is one of the most commonly diagnosed spinal disorders in older adults. Although the pathophysiology of the clinical syndrome is not well understood, a narrow central canal or intervertebral foramen is an essential or defining feature. The aim of the present study was to estimate the magnitude of genetic versus environmental influences on central lumbar spinal stenosis and to investigate disc degeneration and stature or bone development as possible genetic pathways.Methods. A classic twin study with multivariate analyses considering lumbar level and other covariates was conducted. The study sample comprised 598 male twins (147 monozygotic and 152 dizygotic pairs), 35-70 years of age, from the population-based Finnish Twin Cohort. The primary phenotypes were central lumbar stenosis as assessed qualitatively on magnetic resonance imaging (MRI) and quantitatively measured dural sac cross-sectional area. Additional phenotypes (to examine possible genetic pathways) included disc bulging and standing height, as an indicator of overall skeletal size or development.Results. The heritability estimate (h²) for qualitatively assessed central lumbar spinal stenosis on MRI was 66.9% (95% confidence interval [95% CI] 56.8,74.5). The broad-sense heritability estimate for dural sac cross-sectional area was 81.2% (95% CI 74.5, 86.1),with a similar magnitude of genetic influences across lumbar levels (h²=72.4–75.6). The additive genetic correlation of quantitatively assessed stenosis and disc bulging was extremely high. There was no indication of shared genetic influences between stenosis and stature.Conclusion. Central lumbar spinal stenosis and associated dural sac dimensions are highly genetic, and disc degeneration (bulging) appears to be one pathway through which genes influence spinal stenosis. PMID:25155712

Battié, Michele C; Ortega-Alonso, Alfredo; Niemelainen, Riikka; Gill, Kevin; Levalahti, Esko; Videman, Tapio; Kaprio, Jaakko

2014-12-01

289

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

290

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

291

High local genetic diversity and low outcrossing rate in Caenorhabditis elegans natural populations  

E-print Network

of natural populations through sexual reproduction. Previous studies showed that males do not reproduce. elegans are genetically uniform and whether males and sexual reproduction occur. Understanding the biology about its biology outside the laboratory. Especially, its unusual mode of reproduction with self

Paris-Sud XI, Université de

292

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...

293

Short Communication Non-monophyly of Retortamonadida and high genetic diversity of the genus  

E-print Network

Short Communication Non-monophyly of Retortamonadida and high genetic diversity of the genus in Prague, Vinicna 7, 128 44 Prague, Czech Republic b Department of Anatomy and Physiology of Farm Animals have attracted attention because of their evolutionary history. Their cells lack some typically

Flegr, Jaroslav

294

High Functional Diversity in Mycobacterium tuberculosis Driven by Genetic Drift and  

E-print Network

High Functional Diversity in Mycobacterium tuberculosis Driven by Genetic Drift and Human Research, London, United Kingdom Mycobacterium tuberculosis infects one third of the human world population.pbio.0060311 Introduction Mycobacterium tuberculosis is a gram-positive bacterium and the causative agent

Petrov, Dmitri

295

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

296

Oxidative and thermal stabilities of genetically modified high oleic sunflower oil  

Microsoft Academic Search

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

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

2007-01-01

297

The HapMap project has raised high hopes for mapping genetic determinants of complex human  

E-print Network

The HapMap project has raised high hopes for mapping genetic determinants of complex human disease for mapping studies in human populations around the world. The HapMap project has characterized haplotype structures across the genome for four human populations with the goal of enabling genome-wide sets of SNPs

Rosenberg, Noah

298

A high resolution genetic map anchoring scaffolds of the sequenced watermelon genome  

Technology Transfer Automated Retrieval System (TEKTRAN)

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 ...

299

Characterization of new bacterial catabolic genes and mobile genetic elements by high throughput genetic screening of a soil metagenomic library.  

PubMed

A mix of oligonucleotide probes was used to hybridize soil metagenomic DNA from a fosmid clone library spotted on high density membranes. The pooled radio-labeled probes were designed to target genes encoding glycoside hydrolases GH18, dehalogenases, bacterial laccases and mobile genetic elements (integrases from integrons and insertion sequences). Positive hybridizing spots were affiliated to the corresponding clones in the library and the metagenomic inserts were sequenced. After assembly and annotation, new coding DNA sequences related to genes of interest were identified with low protein similarity against the closest hits in databases. This work highlights the sensitivity of DNA/DNA hybridization techniques as an effective and complementary way to recover novel genes from large metagenomic clone libraries. This study also supports that some of the identified catabolic genes might be associated with horizontal transfer events. PMID:24721211

Jacquiod, Samuel; Demanèche, Sandrine; Franqueville, Laure; Ausec, Luka; Xu, Zhuofei; Delmont, Tom O; Dunon, Vincent; Cagnon, Christine; Mandic-Mulec, Ines; Vogel, Timothy M; Simonet, Pascal

2014-11-20

300

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

301

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

302

High genetic diversity detected in the endemic Primula apennina Widmer (Primulaceae) using ISSR fingerprinting  

Microsoft Academic Search

Primula apennina Widmer is endemic to the North Apennines (Italy). ISSR were used to detect the genetic diversity within and among six populations\\u000a representative of the species distribution range. High levels of genetic diversity were revealed both at population percentage\\u000a of polymorphic band (PPB = 75.92%, H\\u000a S = 0.204, H\\u000a pop = 0.319) and at species level (PPB = 96.95%, H\\u000a T = 0.242, H\\u000a sp = 0.381). Nei gene diversity

Silvia Crema; Giovanni Cristofolini; Martina Rossi; Lucia Conte

2009-01-01

303

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

304

High Genetic Diversity and Insignificant Interspecific Differentiation in Opisthopappus Shih, an Endangered Cliff Genus Endemic to the Taihang Mountains of China  

PubMed Central

Opisthopappus Shih is endemic to the Taihang Mountains, China. It grows in the crevice of cliffs and is in fragmented distribution. This genus consists of two species, namely, O. taihangensis (Ling) Shih and O. longilobus Shih, which are both endangered plants in China. This study adopted intersimple sequence repeat markers (ISSR) to analyze the genetic diversity and genetic structure from different levels (genus, species, and population) in this genus. A total of 253 loci were obtained from 27 primers, 230 of which were polymorphic loci with a proportion of polymorphic bands (PPB) of up to 90.91% at genus level. At species level, both O. taihangensis (PPB = 90.12%, H = 0.1842, and I = 0.289) and O. longilobus (PPB = 95.21%, H = 0.2226, and I = 0.3542) have high genetic diversity. Their respective genetic variation mostly existed within the population. And genetic variation in O. longilobus (84.95%) was higher than that in O. taihangensis (80.45%). A certain genetic differentiation among populations in O. taihangensis was found (Gst = 0.2740, ?st = 0.196) and genetic differentiation in O. longilobus was very small (Gst = 0.1034, ?st = 0.151). Gene flow in different degrees (Nm = 1.325 and 4.336, resp.) and mating system can form the existing genetic structures of these two species. Furthermore, genetic differentiation coefficient (Gst = 0.0453) between species and the clustering result based on the genetic distance showed that interspecific differentiation between O. taihangensis and O. longilobus was not significant and could occur lately. PMID:24453824

Guo, Rongmin; Zhou, Lihua; Zhao, Hongbo

2013-01-01

305

Multilocus spacer analysis revealed highly homogeneous genetic background of Asian type of Borrelia miyamotoi.  

PubMed

Borrelia miyamotoi, a member of the relapsing fever group borreliae, was first isolated in Japan and subsequently found in Ixodes ticks in North America, Europe and Russia. Currently, there are three types of B. miyamotoi: Asian or Siberian (transmitted mainly by Ixodes persulcatus), European (Ixodesricinus) and American (Ixodesscapularis and Ixodespacificus). Despite the great genetic distances between B. miyamotoi types, isolates within a type are characterised by an extremely low genetic variability. In particular, strains of B. miyamotoi of Asian type, isolated in Russia from the Baltic sea to the Far East, have been shown to be identical based on the analysis of several conventional genetic markers, such as 16S rRNA, flagellin, outer membrane protein p66 and glpQ genes. Thus, protein or rRNA - coding genes were shown not to be informative enough in studying genetic diversity of B. miyamotoi within a type. In the present paper, we have attempted to design a new multilocus technique based on eight non-coding intergenic spacers (3686bp in total) and have applied it to the analysis of intra-type genetic variability of ?. miyamotoi detected in different regions of Russia and from two tick species, I. persulcatus and Ixodespavlovskyi. However, even though potentially the most variable loci were selected, no genetic variability between studied DNA samples was found, except for one nucleotide substitution in two of them. The sequences obtained were identical to those of the reference strain FR64b. Analysis of the data obtained with the GenBank sequences indicates a highly homogeneous genetic background of B. miyamotoi from the Baltic Sea to the Japanese Islands. In this paper, a hypothesis of clonal expansion of B. miyamotoi is discussed, as well as possible mechanisms for the rapid dissemination of one B. miyamotoi clone over large distances. PMID:25697887

Mukhacheva, Tatyana A; Salikhova, Irina I; Kovalev, Sergey Y

2015-04-01

306

The genetic landscape of high-risk neuroblastoma  

PubMed Central

Neuroblastoma is a malignancy of the developing sympathetic nervous system that often presents with widespread metastatic disease, resulting in survival rates of less than 50%1. To determine the spectrum of somatic mutation in high-risk neuroblastoma, we studied 240 cases using a combination of whole exome, genome and transcriptome sequencing as part of the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) initiative. Here we report a low median exonic mutation frequency of 0.60 per megabase (0.48 non-silent), and remarkably few recurrently mutated genes in these tumors. Genes with significant somatic mutation frequencies included ALK (9.2% of cases), PTPN11 (2.9%), ATRX (2.5%, an additional 7.1% had focal deletions), MYCN (1.7%, a recurrent p.Pro44Leu alteration), and NRAS (0.83%). Rare, potentially pathogenic germline variants were significantly enriched in ALK, CHEK2, PINK1, and BARD1. The relative paucity of recurrent somatic mutations in neuroblastoma challenges current therapeutic strategies reliant upon frequently altered oncogenic drivers. PMID:23334666

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

2013-01-01

307

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

PubMed

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 mitochondrial 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 portion of its range. However, some populations are found on isolated habitat patches, which were recently separated from one another by large expanses of uninhabitable terrain, in the form of row crop agriculture. The goal of this study was to compare levels of genetic differentiation and diversity among populations found in relatively continuous habitat to populations in both recently and historically isolated habitat. Four microsatellite loci were used to genotype over 300 individuals from five populations in continuous habitat, five populations in recently fragmented habitat, and one historically isolated population. Results from the historically isolated population were concordant with previous analyses and suggest significant differentiation. Also, microsatellite data were consistent with the genetic effects of habitat fragmentation for the recently isolated populations, in the form of increased differentiation and decreased genetic diversity when compared to nonfragmented populations. These results suggest that given the appropriate control populations, microsatellite markers can be used to detect the effects of recent habitat fragmentation in natural populations, even at a large geographical scale in high gene flow species. PMID:12492874

Williams, Barry L; Brawn, Jeffrey D; Paige, Ken N

2003-01-01

308

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

PubMed Central

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

2013-01-01

309

Effects of voluntary exercise and genetic selection for high activity levels on HSP72 expression in house mice  

E-print Network

in calcium homeostasis, and glucose deprivation (4, 17, 34). In various tissues of rats, exercise has beenEffects of voluntary exercise and genetic selection for high activity levels on HSP72 expression. Effects of voluntary exercise and genetic selection for high activity levels on HSP72 expression in house

Garland Jr., Theodore

310

Genetic Characterization of Highly Pathogenic Avian Influenza (H5N8) Virus from Domestic Ducks, England, November 2014.  

PubMed

Genetic sequences of a highly pathogenic avian influenza (H5N8) virus in England have high homology to those detected in mainland Europe and Asia during 2014. Genetic characterization suggests this virus is an avian-adapted virus without specific affinity for zoonoses. Spatio-temporal detections of H5N8 imply a role for wild birds in virus spread. PMID:25898126

Hanna, Amanda; Banks, Jill; Marston, Denise A; Ellis, Richard J; Brookes, Sharon M; Brown, Ian H

2015-05-01

311

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

Faculty of Natural Sciences 2007 Department of Physics Review The Blackett Laboratory #12;Cover: The cover shows two photographs illustrating the participation of the Imperial High Energy Physics group, which are segmented into narrow strips typically 80 m wide by 10-20cm long. The lower photograph shows

312

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

313

High-grade endometrial stromal sarcomas: a clinicopathologic study of a group of tumors with heterogenous morphologic and genetic features.  

PubMed

The existence of a "high-grade endometrial stromal sarcoma" category of tumors has been a controversial subject owing to, among other things, the difficulty in establishing consistent diagnostic criteria. Currently, the recommended classification for such tumors is undifferentiated uterine/endometrial sarcoma. Interest in this subject has recently increased markedly with the identification of recurrent molecular genetic abnormalities. At Mayo Clinic, a group of neoplasms has been observed that morphologically resemble, either cytologically or architecturally, classic "low-grade" endometrial stromal sarcoma but feature obvious deviations, specifically, 17 tumors with unequivocally high-grade morphology. These high-grade tumors displayed 3 morphologic themes: (1) tumors with a component that is identical to low-grade ESS that transitions abruptly into an obviously higher-grade component; (2) tumors composed exclusively of high-grade cells with uniform nuclear features but with a permeative pattern of infiltration; (3) tumors similar to the second group but with a different, yet characteristic, cytomorphology featuring enlarged round to ovoid cells (larger than those found in low-grade ESS) with smooth nuclear membranes and distinct chromatin clearing but lacking prominent nucleoli. We collected clinicopathologic data, applied immunohistochemical studies, and also tested tumors by fluorescence in situ hybridization for abnormalities in JAZF1, PHF1, YWHAE, and CCND1. Tumors from these 3 groups were found to be immunohistochemically and genetically distinct from one another. Most notable was the fact that category 3 contained all the cases that tested positive for YWHAE rearrangement, did not show any classic translocations for JAZF1, PHF1, or CCND1, often presented at a high stage, and behaved aggressively. This study demonstrates the morphologic, immunophenotypic, and molecular genetic heterogeneity that exists within "undifferentiated endometrial sarcomas" as currently defined and lends credence to the effort of subclassifying some tumors as truly "high-grade endometrial stromal sarcomas." Our study also shows that, in the context of undifferentiated endometrial sarcomas, recognition of cytomorphologic features on routine hematoxylin and eosin-stained sections may be used to select tumors with specific molecular genetic changes-that is, translocations involving YWHAE. Our conclusions will help further efforts towards proper sub-classification of these tumors which will aid in diagnosis and potentially affect clinical management. PMID:25133706

Sciallis, Andrew P; Bedroske, Patrick P; Schoolmeester, John K; Sukov, William R; Keeney, Gary L; Hodge, Jennelle C; Bell, Debra A

2014-09-01

314

High Prevalence, Genetic Diversity and Intracellular Growth Ability of Legionella in Hot Spring Environments  

PubMed Central

Background Legionella is the causative agent of Legionnaires' disease, and hot springs are a major source of outbreaks of this disease. It is important from a public health perspective to survey hot spring environments for the presence of Legionella. Methods Prospective surveillance of the extent of Legionella pollution was conducted at three hot spring recreational areas in Beijing, China in 2011. Pulsed-field gel electrophoresis (PFGE) and sequence-based typing (SBT) were used to describe the genetic polymorphism of isolates. The intracellular growth ability of the isolates was determined by interacting with J774 cells and plating the dilutions onto BCYE agar plates. Results Overall, 51.9% of spring water samples showed Legionella-positive, and their concentrations ranged from 1 CFU/liter to 2,218 CFU/liter. The positive rates of Legionella were significantly associated with a free chlorine concentration of ?0.2 mg/L, urea concentration of ?0.05 mg/L, total microbial counts of ?400 CFU/ml and total coliform of ?3 MPN/L (p<0.01). The Legionella concentrations were significantly associated with sample temperature, pH, total microbial counts and total coliform (p<0.01). Legionella pneumophila was the most frequently isolated species (98.9%), and the isolated serogroups included serogroups 3 (25.3%), 6 (23.4%), 5 (19.2%), 1 (18.5%), 2 (10.2%), 8 (0.4%), 10 (0.8%), 9 (1.9%) and 12 (0.4%). Two hundred and twenty-eight isolates were analyzed by PFGE and 62 different patterns were obtained. Fifty-seven L. pneumophila isolates were selected for SBT analysis and divided into 35 different sequence types with 5 main clonal groups. All the 57 isolates had high intracellular growth ability. Conclusions Our results demonstrated high prevalence and genetic polymorphism of Legionella in springs in Beijing, China, and the SBT and intracellular growth assay results suggested that the Legionella isolates of hot spring environments were pathogenic. Improved control and prevention strategies are urgently needed. PMID:23527075

Zhou, Haijian; Wang, Huanxin; Xu, Ying; Zhao, Mingqiang; Guan, Hong; Li, Machao; Shao, Zhujun

2013-01-01

315

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

316

Genetic diversity of high-elevation populations of an endangered medicinal plant  

PubMed Central

Intraspecific genetic variation in natural populations governs their potential to overcome challenging ecological and environmental conditions. In addition, knowledge of this variation is critical for the conservation and management of endangered plant taxa. Found in the Himalayas, Podophyllum hexandrum is an endangered high-elevation plant species that has great medicinal importance. Here we report on the genetic diversity analysis of 24 P. hexandrum populations (209 individuals), representing the whole of the Indian Himalayas. In the present study, seven amplified fragment length polymorphism (AFLP) primer pairs generated 1677 fragments, of which 866 were found to be polymorphic. Neighbour joining clustering, principal coordinate analysis and STRUCTURE analysis clustered 209 individuals from 24 populations of the Indian Himalayan mountains into two major groups with a significant amount of gene flow (Nm = 2.13) and moderate genetic differentiation Fst(0.196), G?st(0.20). This suggests that, regardless of geographical location, all of the populations from the Indian Himalayas are intermixed and are composed broadly of two types of genetic populations. High variance partitioned within populations (80 %) suggests that most of the diversity is restricted to the within-population level. These results suggest two possibilities about the ancient population structure of P. hexandrum: either all of the populations in the geographical region of the Indian Himalayas are remnants of a once-widespread ancient population, or they originated from two types of genetic populations, which coexisted a long time ago, but subsequently separated as a result of long-distance dispersal and natural selection. High variance partitioned within the populations indicates that these populations have evolved in response to their respective environments over time, but low levels of heterozygosity suggest the presence of historical population bottlenecks. PMID:25416728

Nag, Akshay; Ahuja, Paramvir Singh; Sharma, Ram Kumar

2015-01-01

317

Genetic diversity of high-elevation populations of an endangered medicinal plant.  

PubMed

Intraspecific genetic variation in natural populations governs their potential to overcome challenging ecological and environmental conditions. In addition, knowledge of this variation is critical for the conservation and management of endangered plant taxa. Found in the Himalayas, Podophyllum hexandrum is an endangered high-elevation plant species that has great medicinal importance. Here we report on the genetic diversity analysis of 24 P. hexandrum populations (209 individuals), representing the whole of the Indian Himalayas. In the present study, seven amplified fragment length polymorphism (AFLP) primer pairs generated 1677 fragments, of which 866 were found to be polymorphic. Neighbour joining clustering, principal coordinate analysis and STRUCTURE analysis clustered 209 individuals from 24 populations of the Indian Himalayan mountains into two major groups with a significant amount of gene flow (Nm = 2.13) and moderate genetic differentiation Fst(0.196), G'st(0.20). This suggests that, regardless of geographical location, all of the populations from the Indian Himalayas are intermixed and are composed broadly of two types of genetic populations. High variance partitioned within populations (80 %) suggests that most of the diversity is restricted to the within-population level. These results suggest two possibilities about the ancient population structure of P. hexandrum: either all of the populations in the geographical region of the Indian Himalayas are remnants of a once-widespread ancient population, or they originated from two types of genetic populations, which coexisted a long time ago, but subsequently separated as a result of long-distance dispersal and natural selection. High variance partitioned within the populations indicates that these populations have evolved in response to their respective environments over time, but low levels of heterozygosity suggest the presence of historical population bottlenecks. PMID:25416728

Nag, Akshay; Ahuja, Paramvir Singh; Sharma, Ram Kumar

2014-01-01

318

Developmental, genetic, and environmental components of aerobic capacity at high altitude.  

PubMed

The aerobic capacity of 268 subjects (158 males and 110 females) was evaluated in La Paz, Bolivia situated at 3,750 m. The sample included 1) 39 high altitude rural natives (all male); 2) 67 high altitude urban natives (32 male, 35 female); 3) 69 Bolivians of foreign ancestry acclimatized to high altitude since birth (37 male, 32 female); 4) 50 Bolivians of foreign ancestry acclimatized to high altitude during growth (25 male, 25 female); and 5) 42 non-Bolivians of either European or North American ancestry acclimatized to high altitude during adulthood (25 male, 18 female). Data analyses indicate that 1) high altitude urban natives, acclimatized to high altitude since birth or during growth, attained higher aerobic capacity than subjects acclimatized to high altitude during adulthood; 2) age at arrival to high altitude is inversely related to maximum oxygen consumption (VO2 max) expressed in terms L/min or ml/min/kg of lean body mass, but not in terms of ml/min/kg of body weight; 3) among subjects acclimatized to high altitude during growth, approximately 25% of the variability in aerobic capacity can be explained by developmental factors; 4) as inferred from evaluations of skin color reflectance and sibling similarities, approximately 20 to 25% of the variability in aerobic capacity at high altitude can be explained by genetic factors; 5) except among the non-Bolivians acclimatized to high altitude during adulthood, the aerobic capacity of individuals with high occupational activity level is equal to the aerobic capacity of high altitude rural natives; and 6) the relationship between occupational activity level and aerobic capacity is much greater among subjects acclimatized to high altitude before the age of 10 years than afterwards. Together these data suggest that the attainment of normal aerobic capacity at high altitude is related to both developmental acclimatization and genetic factors but its expression is highly mediated by environmental factors, such as occupational activity level and body composition. PMID:7604895

Frisancho, A R; Frisancho, H G; Milotich, M; Brutsaert, T; Albalak, R; Spielvogel, H; Villena, M; Vargas, E; Soria, R

1995-04-01

319

[Genetic analysis and mapping of high-tillering and dwarf mutant htd1-2 in rice].  

PubMed

Tillering is one of the most important agronomic traits of rice. In order to explore the molecular mechanism of rice tillering, a high-tillering dwarf 1-2 (htd1-2) mutant was isolated from the offspring of the indica rice (Oryza sativa L. ssp. indica) variety 9311 treated with 350Gy 60Co gamma-radiation. Genetic analysis showed that both high tillering and dwarf phenotypes of htd1-2 were controlled by a single recessive nuclear gene. By means of molecular marker technique, the HIGH-TILLERING DWARF1-2(HTD1-2) gene was mapped between two CAPS markers A6 and E2 on chromosome 4 within 116 kilobases. Within this region, there is a cloned gene HIGH-TILLERING DWARF1(HTD1), which controls rice tillering. By comparing sequences of HTD1 between htd1-2 and 9311, in combination with the results from dCAPS analysis, we believed that HTD1 is an orthologue of the gene HTD1-2. Because of different genetic backgrounds, htd1 and htd1-2 have different phenotypes although they are the allelic mutants. Furthermore, removal of axillary buds proved that dwarfism of htd1-2 mutant is partly attributed to its excessive tillers. PMID:19586849

Jiang, Hai-Pai; Zhang, Shu-Ying; Bao, Jin-Song; Wang, Bo-Lun; Wang, Shu

2009-05-01

320

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

2014-01-01

321

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

322

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

323

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

PubMed Central

OBJECTIVE: To conduct clinical and molecular genetic analyses of the members of an extended family in Central Indiana with a high prevalence of restless legs syndrome (RLS). PARTICIPANTS AND METHODS: From February 1, 2006, through August 31, 2008, we collected data from members of this family, which is of English descent. Genealogical methods were used to expand the family tree, and family members were screened with an RLS questionnaire. Telephone interviews and personal examinations were performed at Mayo Clinic and during a field trip to Central Indiana. Blood samples were collected for molecular genetic analysis. A follow-up telephone interview was conducted 1 year later. RESULTS: The family tree spans 7 generations with 88 living members, 30 of whom meet the criteria for diagnosis of RLS established by the International Restless Legs Syndrome Study Group. Three affected family members also have Parkinson disease or essential tremor. The mode of RLS inheritance is compatible with an autosomal dominant pattern. The affected family members do not exhibit linkage to the 5 known RLS loci or mutations in the RLS susceptibility genes MEIS1 and BTBD9. CONCLUSION: Of 88 members of this single extended family in Central Indiana, 30 were diagnosed as having RLS. Because our analysis shows that the disease is not linked to any of the known RLS loci or risk-associated genes, we postulate that members of this family may carry a gene mutation in a novel genetic locus. PMID:19181647

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

2009-01-01

324

A High-Density Genetic Map for Soybean Based on Specific Length Amplified Fragment Sequencing  

PubMed Central

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

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

2014-01-01

325

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

326

Functional genetic divergence in high CO2 adapted Emiliania huxleyi populations.  

PubMed

Predicting the impacts of environmental change on marine organisms, food webs, and biogeochemical cycles presently relies almost exclusively on short-term physiological studies, while the possibility of adaptive evolution is often ignored. Here, we assess adaptive evolution in the coccolithophore Emiliania huxleyi, a well-established model species in biological oceanography, in response to ocean acidification. We previously demonstrated that this globally important marine phytoplankton species adapts within 500 generations to elevated CO2 . After 750 and 1000 generations, no further fitness increase occurred, and we observed phenotypic convergence between replicate populations. We then exposed adapted populations to two novel environments to investigate whether or not the underlying basis for high CO2 -adaptation involves functional genetic divergence, assuming that different novel mutations become apparent via divergent pleiotropic effects. The novel environment "high light" did not reveal such genetic divergence whereas growth in a low-salinity environment revealed strong pleiotropic effects in high CO2 adapted populations, indicating divergent genetic bases for adaptation to high CO2 . This suggests that pleiotropy plays an important role in adaptation of natural E. huxleyi populations to ocean acidification. Our study highlights the potential mutual benefits for oceanography and evolutionary biology of using ecologically important marine phytoplankton for microbial evolution experiments. PMID:23815647

Lohbeck, Kai T; Riebesell, Ulf; Collins, Sinéad; Reusch, Thorsten B H

2013-07-01

327

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

PubMed

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

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

2012-11-01

328

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

329

Can crayfish take the heat? Procambarus clarkii show nociceptive behaviour to high temperature stimuli, but not low temperature or chemical stimuli  

PubMed Central

Nociceptors are sensory neurons that are tuned to tissue damage. In many species, nociceptors are often stimulated by noxious extreme temperatures and by chemical agonists that do not damage tissue (e.g., capsaicin and isothiocyanate). We test whether crustaceans have nociceptors by examining nociceptive behaviours and neurophysiological responses to extreme temperatures and potentially nocigenic chemicals. Crayfish (Procambarus clarkii) respond quickly and strongly to high temperatures, and neurons in the antenna show increased responses to transient high temperature stimuli. Crayfish showed no difference in behavioural response to low temperature stimuli. Crayfish also showed no significant changes in behaviour when stimulated with capsaicin or isothiocyanate compared to controls, and neurons in the antenna did not change their firing rate following application of capsaicin or isothiocyanate. Noxious high temperatures appear to be a potentially ecologically relevant noxious stimulus for crayfish that can be detected by sensory neurons, which may be specialized nociceptors. PMID:25819841

Puri, Sakshi; Faulkes, Zen

2015-01-01

330

High Altitude Pulmonary Edema in an Experienced Mountaineer. Possible Genetic Predisposition  

PubMed Central

High altitude pulmonary edema (HAPE) is a form of high altitude illness characterized by cough, dyspnea upon exertion progressing to dyspnea at rest and eventual death, seen in patients who ascend over 2,500 meters, particularly if that ascent is rapid. This case describes a patient with no prior history of HAPE and extensive experience hiking above 2,500 meters who developed progressive dyspnea and cough while ascending to 3,200 meters. His risk factors included rapid ascent, high altitude, male sex, and a possible genetic predisposition for HAPE. PMID:25493133

Whitlow, Kenneth S.; Davis, Babette W.

2014-01-01

331

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

332

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

333

Human high-altitude adaptation: forward genetics meets the HIF pathway  

PubMed Central

Humans have adapted to the chronic hypoxia of high altitude in several locations, and recent genome-wide studies have indicated a genetic basis. In some populations, genetic signatures have been identified in the hypoxia-inducible factor (HIF) pathway, which orchestrates the transcriptional response to hypoxia. In Tibetans, they have been found in the HIF2A (EPAS1) gene, which encodes for HIF-2?, and the prolyl hydroxylase domain protein 2 (PHD2, also known as EGLN1) gene, which encodes for one of its key regulators, PHD2. High-altitude adaptation may be due to multiple genes that act in concert with one another. Unraveling their mechanism of action can offer new therapeutic approaches toward treating common human diseases characterized by chronic hypoxia. PMID:25319824

Bigham, Abigail W.

2014-01-01

334

Phenotypic plasticity and genetic adaptation to high-altitude hypoxia in vertebrates  

PubMed Central

High-altitude environments provide ideal testing grounds for investigations of mechanism and process in physiological adaptation. In vertebrates, much of our understanding of the acclimatization response to high-altitude hypoxia derives from studies of animal species that are native to lowland environments. Such studies can indicate whether phenotypic plasticity will generally facilitate or impede adaptation to high altitude. Here, we review general mechanisms of physiological acclimatization and genetic adaptation to high-altitude hypoxia in birds and mammals. We evaluate whether the acclimatization response to environmental hypoxia can be regarded generally as a mechanism of adaptive phenotypic plasticity, or whether it might sometimes represent a misdirected response that acts as a hindrance to genetic adaptation. In cases in which the acclimatization response to hypoxia is maladaptive, selection will favor an attenuation of the induced phenotypic change. This can result in a form of cryptic adaptive evolution in which phenotypic similarity between high- and low-altitude populations is attributable to directional selection on genetically based trait variation that offsets environmentally induced changes. The blunted erythropoietic and pulmonary vasoconstriction responses to hypoxia in Tibetan humans and numerous high-altitude birds and mammals provide possible examples of this phenomenon. When lowland animals colonize high-altitude environments, adaptive phenotypic plasticity can mitigate the costs of selection, thereby enhancing prospects for population establishment and persistence. By contrast, maladaptive plasticity has the opposite effect. Thus, insights into the acclimatization response of lowland animals to high-altitude hypoxia can provide a basis for predicting how altitudinal range limits might shift in response to climate change. PMID:21112992

Storz, Jay F.; Scott, Graham R.; Cheviron, Zachary A.

2010-01-01

335

Particle size analysis of high density lipoproteins in patients with genetic cholesteryl ester transfer protein deficiency  

Microsoft Academic Search

We investigated the detailed distribution of high-density lipoproteins (HDL) particle size in patients with cholesteryl ester transfer protein (CETP) deficiency. Serum samples pre-stained with Sudan black B were electrophoresed using 4–30% polyacrylamide gradient gels, and the Stokes diameter of HDL particles was determined in 23 patients with genetic CETP deficiency, nine patients with hyperalphalipoproteinemia and seven subjects with normal HDL

Tomoko Arai; Toshihiko Tsukada; Toshio Murase; Kojiro Matsumoto

2000-01-01

336

A scalable pipeline for highly effective genetic modification of a malaria parasite  

Microsoft Academic Search

In malaria parasites, the systematic experimental validation of drug and vaccine targets by reverse genetics is constrained by the inefficiency of homologous recombination and by the difficulty of manipulating adenine and thymine (A+T)-rich DNA of most Plasmodium species in Escherichia coli. We overcame these roadblocks by creating a high-integrity library of Plasmodium berghei genomic DNA (>77% A+T content) in a

Claudia Pfander; Burcu Anar; Frank Schwach; Thomas D Otto; Mathieu Brochet; Katrin Volkmann; Michael A Quail; Arnab Pain; Barry Rosen; William Skarnes; Julian C Rayner; Oliver Billker

2011-01-01

337

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

338

Relocation, high-latitude warming and host genetic identity shape the foliar fungal microbiome of poplars.  

PubMed

Micro-organisms associated with plants and animals affect host fitness, shape community structure and influence ecosystem properties. Climate change is expected to influence microbial communities, but their reactions are not well understood. Host-associated micro-organisms are influenced by the climate reactions of their hosts, which may undergo range shifts due to climatic niche tracking, or may be actively relocated to mitigate the effects of climate change. We used a common-garden experiment and rDNA metabarcoding to examine the effect of host relocation and high-latitude warming on the complex fungal endophytic microbiome associated with leaves of an ecologically dominant boreal forest tree (Populus balsamifera L.). We also considered the potential effects of poplar genetic identity in defining the reactions of the microbiome to the treatments. The relocation of hosts to the north increased the diversity of the microbiome and influenced its structure, with results indicating enemy release from plausible pathogens. High-latitude warming decreased microbiome diversity in comparison with natural northern conditions. The warming also caused structural changes, which made the fungal communities distinct in comparison with both low-latitude and high-latitude natural communities, and increased the abundance of plausible pathogens. The reactions of the microbiome to relocation and warming were strongly dependent on host genetic identity. This suggests that climate change effects on host-microbiome systems may be mediated by the interaction of environmental factors and the population genetic processes of the hosts. PMID:25443313

Bálint, Miklós; Bartha, László; O'Hara, Robert B; Olson, Matthew S; Otte, Jürgen; Pfenninger, Markus; Robertson, Amanda L; Tiffin, Peter; Schmitt, Imke

2015-01-01

339

A High Through-Put Reverse Genetic Screen Identifies Two Genes Involved in Remote Memory in Mice  

E-print Network

A High Through-Put Reverse Genetic Screen Identifies Two Genes Involved in Remote Memory in Mice Through-Put Reverse Genetic Screen Identifies Two Genes Involved in Remote Memory in Mice. PLoS ONE 3 required for remote memory, we screened randomly selected mouse strains harboring known mutations. In our

Anagnostaras, Stephan

340

Chromosome rearrangements during domestication of cucumber as revealed from high-density genetic mapping and draft genome assembly  

Technology Transfer Automated Retrieval System (TEKTRAN)

Cucumber is an economically important vegetable crop, but available genetic and genomics resources for cucumber are limited that hinders progress in cucumber breeding. In this study, we made significant contributions to the cucumber research community by developing a high-density genetic map for cul...

341

Copyright 1999 by the Genetics Society of America High-Resolution Mapping of Quantitative Trait Loci for Sternopleural Bristle  

E-print Network

Loci for Sternopleural Bristle Number in Drosophila melanogaster Marjorie C. Gurganus,1 Sergey VCopyright © 1999 by the Genetics Society of America High-Resolution Mapping of Quantitative Trait. Nuzhdin,2 Jeff W. Leips and Trudy F. C. Mackay Department of Genetics, North Carolina State University

Mackay, Trudy F.C.

342

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

PubMed

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

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

2012-07-01

343

In many cases, tsunami waveheights and effects show a high variability along the coast. The possible causes are insecurities about the tectonic  

E-print Network

In many cases, tsunami waveheights and effects show a high variability along the coast area in propagation direction of a tsunami wave can produce largely amplified waves by near coast tsunami waveguiding, see [1]. The waveguiding is caused by the fact that different propagation speeds

Al Hanbali, Ahmad

344

An intensely luminescent metal-organic framework based on a highly light-harvesting dyclo-metalated iridium(III) unit showing effective detection of explosives.  

PubMed

An intense visible yellow-orange emission with long lifetime and enhanced quantum yield has been achieved for a metal-organic framework based on a highly light-harvesting dyclo-metalated iridium(III) unit, which shows effective detection of nitroaromatic explosives on the ppm scale. PMID:24144427

Li, Lina; Zhang, Shuquan; Xu, Liangjin; Han, Liang; Chen, Zhong-Ning; Luo, Junhua

2013-11-01

345

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

346

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

347

Colored polydimethylsiloxane micropillar arrays for high throughput measurements of forces applied by genetic model organisms.  

PubMed

Measuring forces applied by multi-cellular organisms is valuable in investigating biomechanics of their locomotion. Several technologies have been developed to measure such forces, for example, strain gauges, micro-machined sensors, and calibrated cantilevers. We introduce an innovative combination of techniques as a high throughput screening tool to assess forces applied by multiple genetic model organisms. First, we fabricated colored Polydimethylsiloxane (PDMS) micropillars where the color enhances contrast making it easier to detect and track pillar displacement driven by the organism. Second, we developed a semi-automated graphical user interface to analyze the images for pillar displacement, thus reducing the analysis time for each animal to minutes. The addition of color reduced the Young's modulus of PDMS. Therefore, the dye-PDMS composite was characterized using Yeoh's hyperelastic model and the pillars were calibrated using a silicon based force sensor. We used our device to measure forces exerted by wild type and mutant Caenorhabditis elegans moving on an agarose surface. Wild type C. elegans exert an average force of ?1??N on an individual pillar and a total average force of ?7.68??N. We show that the middle of C. elegans exerts more force than its extremities. We find that C. elegans mutants with defective body wall muscles apply significantly lower force on individual pillars, while mutants defective in sensing externally applied mechanical forces still apply the same average force per pillar compared to wild type animals. Average forces applied per pillar are independent of the length, diameter, or cuticle stiffness of the animal. We also used the device to measure, for the first time, forces applied by Drosophila melanogaster larvae. Peristaltic waves occurred at 0.4?Hz applying an average force of ?1.58??N on a single pillar. Our colored microfluidic device along with its displacement tracking software allows us to measure forces applied by multiple model organisms that crawl or slither to travel through their environment. PMID:25713693

Khare, Siddharth M; Awasthi, Anjali; Venkataraman, V; Koushika, Sandhya P

2015-01-01

348

Determination of genetic transferrin variants in human serum by high-resolution capillary zone electrophoresis(†).  

PubMed

High-resolution capillary zone electrophoresis in the routine arena with stringent quality assurance is employed for the determination of carbohydrate-deficient transferrin in human serum. The assay comprises mixing of human serum with a Fe(III) -containing solution prior to analysis of the iron-saturated mixture in a dynamically double-coated capillary using a commercial buffer at alkaline pH. In contrast to other assays, it provides sufficient resolution for proper recognition of genetic transferrin variants. Analysis of 7290 patient sera revealed 166 isoform patterns that could be assigned to genetic variants, namely, 109 BC, 53 CD, one BD and three CC variants. Several subtypes of transferrin D can be distinguished as they have large enough differences in pI values. Subtypes of transferrin C and B cannot be resolved. However, analysis of the detection time ratios of tetrasialo isoforms of transferrin BC and transferrin CD variants revealed multimodal frequency histograms, indicating the presence of subtypes of transferrin C, B and D. The data gathered over 11 years demonstrate the robustness of the high-resolution capillary zone electrophoresis assay. This is the first account of a capillary zone electrophoresis based carbohydrate-deficient transferrin assay with a broad overview on transferrin isoform patterns associated with genetic transferrin variants. PMID:24737700

Caslavska, Jitka; Joneli, Jeannine; Wanzenried, Ursula; Schiess, Jeannette; Lanz, Christian; Thormann, Wolfgang

2014-07-01

349

High-resolution mapping reveals hundreds of genetic incompatibilities in hybridizing fish species.  

PubMed

Hybridization is increasingly being recognized as a common process in both animal and plant species. Negative epistatic interactions between genes from different parental genomes decrease the fitness of hybrids and can limit gene flow between species. However, little is known about the number and genome-wide distribution of genetic incompatibilities separating species. To detect interacting genes, we perform a high-resolution genome scan for linkage disequilibrium between unlinked genomic regions in naturally occurring hybrid populations of swordtail fish. We estimate that hundreds of pairs of genomic regions contribute to reproductive isolation between these species, despite them being recently diverged. Many of these incompatibilities are likely the result of natural or sexual selection on hybrids, since intrinsic isolation is known to be weak. Patterns of genomic divergence at these regions imply that genetic incompatibilities play a significant role in limiting gene flow even in young species. PMID:24898754

Schumer, Molly; Cui, Rongfeng; Powell, Daniel L; Dresner, Rebecca; Rosenthal, Gil G; Andolfatto, Peter

2014-01-01

350

High-Level Genetic Diversity and Complex Population Structure of Siberian Apricot (Prunus sibirica L.) in China as Revealed by Nuclear SSR Markers  

PubMed Central

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

351

Genetic dissection of Al tolerance QTLs in the maize genome by high density SNP scan  

PubMed Central

Background Aluminum (Al) toxicity is an important limitation to food security in tropical and subtropical regions. High Al saturation on acid soils limits root development, reducing water and nutrient uptake. In addition to naturally occurring acid soils, agricultural practices may decrease soil pH, leading to yield losses due to Al toxicity. Elucidating the genetic and molecular mechanisms underlying maize Al tolerance is expected to accelerate the development of Al-tolerant cultivars. Results Five genomic regions were significantly associated with Al tolerance, using 54,455 SNP markers in a recombinant inbred line population derived from Cateto Al237. Candidate genes co-localized with Al tolerance QTLs were further investigated. Near-isogenic lines (NILs) developed for ZmMATE2 were as Al-sensitive as the recurrent line, indicating that this candidate gene was not responsible for the Al tolerance QTL on chromosome 5, qALT5. However, ZmNrat1, a maize homolog to OsNrat1, which encodes an Al3+ specific transporter previously implicated in rice Al tolerance, was mapped at ~40 Mbp from qALT5. We demonstrate for the first time that ZmNrat1 is preferentially expressed in maize root tips and is up-regulated by Al, similarly to OsNrat1 in rice, suggesting a role of this gene in maize Al tolerance. The strongest-effect QTL was mapped on chromosome 6 (qALT6), within a 0.5 Mbp region where three copies of the Al tolerance gene, ZmMATE1, were found in tandem configuration. qALT6 was shown to increase Al tolerance in maize; the qALT6-NILs carrying three copies of ZmMATE1 exhibited a two-fold increase in Al tolerance, and higher expression of ZmMATE1 compared to the Al sensitive recurrent parent. Interestingly, a new source of Al tolerance via ZmMATE1 was identified in a Brazilian elite line that showed high expression of ZmMATE1 but carries a single copy of ZmMATE1. Conclusions High ZmMATE1 expression, controlled either by three copies of the target gene or by an unknown molecular mechanism, is responsible for Al tolerance mediated by qALT6. As Al tolerant alleles at qALT6 are rare in maize, marker-assisted introgression of this QTL is an important strategy to improve maize adaptation to acid soils worldwide. PMID:24564817

2014-01-01

352

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

PubMed

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

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

2013-04-01

353

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

354

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

355

Wavelets meet genetic imaging  

NASA Astrophysics Data System (ADS)

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

Wang, Yu-Ping

2005-08-01

356

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

357

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

358

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

NASA Astrophysics Data System (ADS)

The resilience of Symbiodinium harboured by corals is dependent on the genetic diversity and extent of connectivity among reef populations. This study presents genetic analyses of Great Barrier Reef (GBR) populations of clade C Symbiodinium hosted by the alcyonacean coral, Sinularia flexibilis. Allelic variation at four newly developed microsatellite loci demonstrated that Symbiodinium populations are genetically differentiated at all spatial scales from 16 to 1,360 km (pairwise ?ST = 0.01-0.47, mean = 0.22); the only exception being two neighbouring populations in the Cairns region separated by 17 km. This indicates that gene flow is restricted for Symbiodinium C hosted by S. flexibilis on the GBR. Patterns of population structure reflect longshore circulation patterns and limited cross-shelf mixing, suggesting that passive transport by currents is the primary mechanism of dispersal in Symbiodinium types that are acquired horizontally. There was no correlation between the genetic structure of Symbiodinium populations and their host S. flexibilis, most likely because different factors affect the dispersal and recruitment of each partner in the symbiosis. The genetic diversity of these Symbiodinium reef populations is on average 1.5 times lower on inshore reefs than on offshore reefs. Lower inshore diversity may reflect the impact of recent bleaching events on Sinularia assemblages, which have been more widespread and severe on inshore reefs, but may also have been shaped by historical sea level fluctuations or recent migration patterns.

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

2009-03-01

359

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

Microsoft Academic Search

[3H]Adenine has previously been used to label the newly discovered G protein-coupled murine adenine receptors. Recent reports\\u000a 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\\u000a of mammalian protein. In this study, we showed that specific [3H]adenine binding to various mammalian membrane preparations increased linearly with

Anke C. Schiedel; Heiko Meyer; Bernt B. A. Alsdorf; Simone Gorzalka; Hannelore Brüssel; Christa E. Müller

2007-01-01

360

Population structure and genetic diversity of the orchid bee Eufriesea violacea (Hymenoptera,  

E-print Network

Population structure and genetic diversity of the orchid bee Eufriesea violacea (Hymenoptera Abstract ­ In this study, both the genetic diversity and population genetic structure of Eufriesea violacea microsatellite markers. The results showed that genetic diversity was high in all populations and the genetic

361

Construction of a genetic map based on high-throughput SNP genotyping and genetic mapping of a TuMV resistance locus in Brassica rapa.  

PubMed

Brassica rapa is a member of the Brassicaceae family and includes vegetables and oil crops that are cultivated worldwide. The introduction of durable resistance against turnip mosaic virus (TuMV) into agronomically important cultivars has been a significant challenge for genetic and horticultural breeding studies of B. rapa. Based on our previous genome-wide analysis of DNA polymorphisms between the TuMV-resistant doubled haploid (DH) line VC40 and the TuMV-susceptible DH line SR5, we constructed a core genetic map of the VCS-13M DH population, which is composed of 83 individuals derived from microspore cultures of a F1 cross between VC40 and SR5, by analyzing the segregation of 314 sequence-characterized genetic markers. The genetic markers correspond to 221 SNPs and 31 InDels of genes as well as 62 SSRs, covering 1,115.9 cM with an average distance of 3.6 cM between the adjacent marker loci. The alignment and orientation of the constructed map showed good agreement with the draft genome sequence of Chiifu, thus providing an efficient strategy to map genic sequences. Using the genetic map, a novel dominant TuMV resistance locus (TuMV-R) in the VCS-13M DH population was identified as a 0.34 Mb region in the short arm of chromosome A6 in which four CC-NBS-LRR resistance genes and two pathogenesis-related-1 genes reside. The genetic map developed in this study can play an important role in the genetic study of TuMV resistance and the molecular breeding of B. rapa. PMID:24326528

Chung, Hee; Jeong, Young-Min; Mun, Jeong-Hwan; Lee, Soo-Seong; Chung, Won-Hyong; Yu, Hee-Ju

2014-04-01

362

Analysis of genetic variation and diversity of Rice stripe virus populations through high-throughput sequencing  

PubMed Central

Plant RNA viruses often generate diverse populations in their host plants through error-prone replication and recombination. Recent studies on the genetic diversity of plant RNA viruses in various host plants have provided valuable information about RNA virus evolution and emergence of new diseases caused by RNA viruses. We analyzed and compared the genetic diversity of Rice stripe virus (RSV) populations in Oryza sativa (a natural host of RSV) and compared it with that of the RSV populations generated in an infection of Nicotiana benthamiana, an experimental host of RSV, using the high-throughput sequencing technology. From infected O. sativa and N. benthamiana plants, a total of 341 and 1675 site substitutions were identified in the RSV genome, respectively, and the average substitution ratio in these sites was 1.47 and 7.05 %, respectively, indicating that the RSV populations from infected N. benthamiana plant are more diverse than those from infected O. sativa plant. Our result gives a direct evidence that virus might allow higher genetic diversity for host adaptation.

Huang, Lingzhe; Li, Zefeng; Wu, Jianxiang; Xu, Yi; Yang, Xiuling; Fan, Longjiang; Fang, Rongxiang; Zhou, Xueping

2015-01-01

363

Rapid recombination mapping for high-throughput genetic screens in Drosophila.  

PubMed

Mutagenesis screens are a staple of classical genetics. Chemical-induced mutations, however, are often difficult and time-consuming to identify. Here, we report that recombination analysis with pairs of dominant visible markers provides a rapid and reliable strategy to map mutations in Drosophila melanogaster. This method requires only two generations and a total of six crosses in vials to estimate the genetic map position of the responsible lesion with high accuracy. This genetic map position can then be reliably used to identify the mutated gene through complementation testing with an average of nine deficiencies and Sanger sequencing. We have used this approach to successfully map a collection of mutations from an ethyl methanesulfonate-based mutagenesis screen on the third chromosome. We propose that this method also may be used in conjunction with whole-genome sequencing, particularly when multiple independent alleles of the mutated locus are not available. By facilitating the rapid identification of mutated genes, our mapping strategy removes a primary obstacle to the widespread use of powerful chemical mutagenesis screens to understand fundamental biological phenomena. PMID:24170736

Sapiro, Anne L; Ihry, Robert J; Buhr, Derek L; Konieczko, Kevin M; Ives, Sarah M; Engstrom, Anna K; Wleklinski, Nicholas P; Kopish, Kristin J; Bashirullah, Arash

2013-12-01

364

Population analysis of Vibrio parahaemolyticus originating from different geographical regions demonstrates a high genetic diversity  

PubMed Central

Background Vibrio parahaemolyticus is frequently isolated from environmental and seafood samples and associated with gastroenteritis outbreakes in American, European, Asian and African countries. To distinguish between different lineages of V. parahaemolyticus various genotyping techniques have been used, incl. multilocus sequence typing (MLST). Even though some studies have already applied MLST analysis to characterize V. parahaemolyticus strain sets, these studies have been restricted to specific geographical areas (e.g. U.S. coast, Thailand and Peru), have focused exclusively on pandemic or non-pandemic pathogenic isolates or have been based on a limited strain number. Results To generate a global picture of V. parahaemolyticus genotype distribution, a collection of 130 environmental and seafood related V. parahaemolyticus isolates of different geographical origins (Sri Lanka, Ecuador, North Sea and Baltic Sea as well as German retail) was subjected to MLST analysis after modification of gyrB and recA PCRs. The V. parahaemolyticus population was composed of 82 unique Sequence Types (STs), of which 68 (82.9%) were new to the pubMLST database. After translating the in-frame nucleotide sequences into amino acid sequences, less diversity was detectable: a total of 31 different peptide Sequence Types (pSTs) with 19 (61.3%) new pSTs were generated from the analyzed isolates. Most STs did not show a global dissemination, but some were supra-regionally distributed and clusters of STs were dependent on geographical origin. On peptide level no general clustering of strains from specific geographical regions was observed, thereby the most common pSTs were found on all continents (Asia, South America and Europe) and rare pSTs were restricted to distinct countries or even geographical regions. One lineage of pSTs associated only with strains from North and Baltic Sea strains was identified. Conclusions Our study reveals a high genetic diversity in the analyzed V. parahaemolyticus strain set as well as for geographical strain subsets, with a high proportion of newly discovered alleles and STs. Differences between the subsets were identified. Our data support the postulated population structure of V. parahaemolyticus which follows the ‘epidemic’ model of clonal expansion. Application of peptide based AA-MLST allowed the identification of reliable relationships between strains. PMID:24606756

2014-01-01

365

A high-density genetic map of cucumber derived from Specific Length Amplified Fragment sequencing (SLAF-seq)  

PubMed Central

High-density genetic map provides an essential framework for accurate and efficient genome assembly and QTL fine mapping. Construction of high-density genetic maps appears more feasible since the advent of next-generation sequencing (NGS), which eases SNP discovery and high-throughput genotyping of large population. In this research, a high-density genetic map of cucumber (Cucumis sativus L.) was successfully constructed across an F2 population by a recently developed Specific Length Amplified Fragment sequencing (SLAF-seq) method. In total, 18.69 GB of data containing 93,460,000 paired-end reads were obtained after preprocessing. The average sequencing depth was 44.92 in the D8 (female parent), 42.16 in the Jin5-508 (male parent), and 5.01 in each progeny. 79,092 high-quality SLAFs were detected, of which 6784 SLAFs were polymorphic, and 1892 of the polymorphic markers met the requirements for constructing genetic map. The genetic map spanned 845.87 cm with an average genetic distance of 0.45 cm. It is a reliable linkage map for fine mapping and molecular breeding of cucumber for its high marker density and well-ordered markers. PMID:25610449

Xu, Xuewen; Xu, Ruixue; Zhu, Biyun; Yu, Ting; Qu, Wenqin; Lu, Lu; Xu, Qiang; Qi, Xiaohua; Chen, Xuehao

2015-01-01

366

RPL39L is an example of a recently evolved ribosomal protein paralog that shows highly specific tissue expression patterns and is upregulated in ESCs and HCC tumors.  

PubMed

Ribosomal proteins (RPs) have been shown to be able to impart selectivity on the translating ribosome implicating them in gene expression control. Many ribosomal proteins are highly conserved and recently a number of ribosomal protein paralogs have been described in mammals. We examined the expression pattern of RPs in differentiating mouse Embryonic Stem Cells (ESCs), paying particular attention to the RP paralogs. We find the RP paralog Rpl39l is highly expressed in ESC and its expression strongly correlates with hepatocellular carcinoma tumor (HCC) samples with high tumor grading and alpha-fetoprotein level giving it diagnostic potential. We further screen the expression pattern of all RPs and their paralogs across 22 different tissues. We find that the more recently evolved RP paralogs show a much greater level of tissue-specific expression. We propose that these RP paralogs evolved more recently to provide a greater level of gene expression control to higher eukaryotes. PMID:24452241

Wong, Queenie Wing-Lei; Li, Jia; Ng, Sheng Rong; Lim, Seng Gee; Yang, Henry; Vardy, Leah A

2014-01-01

367

RPL39L is an example of a recently evolved ribosomal protein paralog that shows highly specific tissue expression patterns and is upregulated in ESCs and HCC tumors  

PubMed Central

Ribosomal proteins (RPs) have been shown to be able to impart selectivity on the translating ribosome implicating them in gene expression control. Many ribosomal proteins are highly conserved and recently a number of ribosomal protein paralogs have been described in mammals. We examined the expression pattern of RPs in differentiating mouse Embryonic Stem Cells (ESCs), paying particular attention to the RP paralogs. We find the RP paralog Rpl39l is highly expressed in ESC and its expression strongly correlates with hepatocellular carcinoma tumor (HCC) samples with high tumor grading and alpha-fetoprotein level giving it diagnostic potential. We further screen the expression pattern of all RPs and their paralogs across 22 different tissues. We find that the more recently evolved RP paralogs show a much greater level of tissue-specific expression. We propose that these RP paralogs evolved more recently to provide a greater level of gene expression control to higher eukaryotes. PMID:24452241

Wong, Queenie Wing-Lei; Li, Jia; Ng, Sheng Rong; Lim, Seng Gee; Yang, Henry; Vardy, Leah A

2014-01-01

368

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

PubMed

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

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

2012-04-01

369

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

/08August/Pages/sporadic-genetic-mutation-schizophrenia.aspx[8/9/2011 10:05:12 AM] Categories All Headlines Monday August 8 2011 Schizophrenia can affect those without a family history of it "Scientists say they have `fundamentally transformed' the understanding of the genetics of schizophrenia," BBC News has

370

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

371

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

PubMed

Forward genetic screens have been highly successful in revealing roles of genes and pathways in complex biological events. Traditionally these screens have focused on isolating mutants with the greatest phenotypic deviance, with the hopes of discovering genes that are central to the biological event being investigated. Behavioral screens in mice typically use simple activity-based assays as endophenotypes for more complex emotional states of the animal. They generally set the selection threshold for a putative mutant at 3 SDs (z score of 3) from the average behavior of normal animals to minimize false-positive results. Behavioral screens using a high threshold for detection have generally had limited success, with high false-positive rates and subtle phenotypic differences that have made mapping and cloning difficult. In addition, targeted reverse genetic approaches have shown that when genes central to behaviors such as open field behavior, psychostimulant response, and learning and memory tasks are mutated, they produce subtle phenotypes that differ from wild-type animals by 1 to 2 SDs (z scores of 1 to 2). We have conducted a second-generation (G2) dominant N-ethyl-N-nitrosourea (ENU) screen especially designed to detect subtle behavioral mutants for open field activity and psychostimulant response behaviors. We successfully detect mutant lines with only 1 to 2 SD shifts in mean response compared with wild-type control animals and present a robust statistical and methodological framework for conducting such forward genetic screens. Using this methodology we have screened 229 ENU mutant lines and have identified 15 heritable mutant lines. We conclude that for screens in mice that use activity-based endophenotypic measurements for complex behavioral states, this G2 screening approach yields better results. PMID:21896739

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

2011-09-13

372

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

PubMed Central

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

2014-01-01

373

Application of Homozygosity Haplotype Analysis to Genetic Mapping with High-Density SNP Genotype Data  

PubMed Central

Background In families segregating a monogenic genetic disorder with a single disease gene introduction, patients share a mutation-carrying chromosomal interval with identity-by-descent (IBD). Such a shared chromosomal interval or haplotype, surrounding the actual pathogenic mutation, is typically detected and defined by multipoint linkage and phased haplotype analysis using microsatellite or SNP genotype data. High-density SNP genotype data presents a computational challenge for conventional genetic analyses. A novel non-parametric method termed Homozygosity Haplotype (HH) was recently proposed for the genome-wide search of the autosomal segments shared among patients using high density SNP genotype data. Methodology/Principal Findings The applicability and the effectiveness of HH in identifying the potential linkage of disease causative gene with high-density SNP genotype data were studied with a series of monogenic disorders ascertained in eastern Canadian populations. The HH approach was validated using the genotypes of patients from a family affected with a rare autosomal dominant disease Schnyder crystalline corneal dystrophy. HH accurately detected the ?1 Mb genomic interval encompassing the causative gene UBIAD1 using the genotypes of only four affected subjects. The successful application of HH to identify the potential linkage for a family with pericentral retinal disorder indicates that HH can be applied to perform family-based association analysis by treating affected and unaffected family members as cases and controls respectively. A new strategy for the genome-wide screening of known causative genes or loci with HH was proposed, as shown the applications to a myoclonus dystonia and a renal failure cohort. Conclusions/Significance Our study of the HH approach demonstrates that HH is very efficient and effective in identifying potential disease linked region. HH has the potential to be used as an efficient alternative approach to sequencing or microsatellite-based fine mapping for screening the known causative genes in genetic disease study. PMID:19399176

Jiang, Haiyan; Orr, Andrew; Guernsey, Duane L.; Robitaille, Johane; Asselin, Géraldine; Samuels, Mark E.; Dubé, Marie-Pierre

2009-01-01

374

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

375

Gaussian models for genetic linkage analysis using complete high-resolution maps of identity by descent.  

PubMed Central

Gaussian-process models are developed to detect genetic linkage using complete high-resolution maps of identity by descent between affected relative pairs. Approximations are given for the significance level and power of the likelihood-ratio test of no linkage and for likelihood-ratio confidence regions for trait loci. The sample sizes required to detect linkage by using different classes of affected relative pairs are compared, and the problem of combining data from different classes of relatives is discussed. PMID:8317489

Feingold, E; Brown, P O; Siegmund, D

1993-01-01

376

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

377

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 José; 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

378

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

PubMed Central

High throughput sequencing technologies are being applied to an increasing number of model species with a high-quality reference genome. The application and analyses of whole-genome sequence data in non-model species with no prior genomic information are currently under way. Recent sequencing technologies provide new opportunities for gathering genomic data in natural populations, laying the empirical foundation for future research in the field of conservation and population genomics. Here we present the case study of the Bornean elephant, which is the most endangered subspecies of Asian elephant and exhibits very low genetic diversity. We used two different sequencing platforms, the Roche 454 FLX (shotgun) and Illumina, GAIIx (Restriction site associated DNA, RAD) to evaluate the feasibility of the two methodologies for the discovery of de novo markers (single nucleotide polymorphism, SNPs and microsatellites) using low coverage data. Approximately, 6,683 (shotgun) and 14,724 (RAD) SNPs were detected within our elephant sequence dataset. Genotyping of a representative sample of 194 SNPs resulted in a SNP validation rate of ? 83 to 94% and 17% of the loci were polymorphic with a low diversity (Ho?=?0.057). Different numbers of microsatellites were identified through shotgun (27,226) and RAD (868) techniques. Out of all di-, tri-, and tetra-microsatellite loci, 1,706 loci had sufficient flanking regions (shotgun) while only 7 were found with RAD. All microsatellites were monomorphic in the Bornean but polymorphic in another elephant subspecies. Despite using different sample sizes, and the well known differences in the two platforms used regarding sequence length and throughput, the two approaches showed high validation rate. The approaches used here for marker development in a threatened species demonstrate the utility of high throughput sequencing technologies as a starting point for the development of genomic tools in a non-model species and in particular for a species with low genetic diversity. PMID:23185354

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

2012-01-01

379

On a high-dimensional objective genetic algorithm and its nonlinear dynamic properties  

NASA Astrophysics Data System (ADS)

The revival of multi-objective optimization is mainly resulted from the recent development of multi-objective evolutionary optimization that allows the generation of the overall Pareto front. This paper presents an algorithm called HOGA (High-dimensional Objective Genetic Algorithm) for high-dimensional objective optimization on the basis of evolutionary computing. It adopts the principle of Shannon entropy to calculate the weight for each object since the well-known multi-objective evolutionary algorithms work poorly on the high-dimensional optimization problem. To further discuss the nonlinear dynamic property of HOGA, a martingale analysis approach is then employed; some mathematical derivations of the convergent theorems are obtained. The obtained results indicate that this new algorithm is indeed capable of achieving convergence and the suggested martingale analysis approach provides a new methodology for nonlinear dynamic analysis of evolutionary algorithms.

Huang, Jun; Huang, Xiaohong; Ma, Yan; Liu, Yanbing

2011-09-01

380

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

381

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

382

Artificially created stimuli produced by a genetic algorithm using a saliency model as its fitness function show that Inattentional Blindness modulates performance in a pop-out visual search paradigm.  

PubMed

Salient stimuli are more readily detected than less salient stimuli, and individual differences in such detection may be relevant to why some people fail to notice an unexpected stimulus that appears in their visual field whereas others do notice it. This failure to notice unexpected stimuli is termed 'Inattentional Blindness' and is more likely to occur when we are engaged in a resource-consuming task. A genetic algorithm is described in which artificial stimuli are created using a saliency model as its fitness function. These generated stimuli, which vary in their saliency level, are used in two studies that implement a pop-out visual search task to evaluate the power of the model to discriminate the performance of people who were and were not Inattentionally Blind (IB). In one study the number of orientational filters in the model was increased to check if discriminatory power and the saliency estimation for low-level images could be improved. Results show that the performance of the model does improve when additional filters are included, leading to the conclusion that low-level images may require a higher number of orientational filters for the model to better predict participants' performance. In both studies we found that given the same target patch image (i.e. same saliency value) IB individuals take longer to identify a target compared to non-IB individuals. This suggests that IB individuals require a higher level of saliency for low-level visual features in order to identify target patches. PMID:24508072

Papera, Massimiliano; Cooper, Richard P; Richards, Anne

2014-04-01

383

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

384

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

PubMed

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

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

2013-02-01

385

High Levels of Genetic Connectivity among Populations of Yellowtail Snapper, Ocyurus chrysurus (Lutjanidae - Perciformes), in the Western South Atlantic Revealed through Multilocus Analysis.  

PubMed

In the present study, five loci (mitochondrial and nuclear) were sequenced to determine the genetic diversity, population structure, and demographic history of populations of the yellowtail snapper, Ocyurus chrysurus, found along the coast of the western South Atlantic. O. chrysurus is a lutjanid species that is commonly associated with coral reefs and exhibits an ample geographic distribution, and it can therefore be considered a good model for the investigation of phylogeographic patterns and genetic connectivity in marine environments. The results reflected a marked congruence between the mitochondrial and nuclear markers as well as intense gene flow among the analyzed populations, which represent a single genetic stock along the entire coast of Brazil between the states of Pará and Espírito Santo. Our data also showed high levels of genetic diversity in the species (mainly mtDNA), as well a major historic population expansion, which most likely coincided with the sea level oscillations at the end of the Pleistocene. In addition, this species is intensively exploited by commercial fisheries, and data on the genetic structure of its populations will be essential for the development of effective conservation and management plans. PMID:25769032

da Silva, Raimundo; Veneza, Ivana; Sampaio, Iracilda; Araripe, Juliana; Schneider, Horacio; Gomes, Grazielle

2015-01-01

386

High Levels of Genetic Connectivity among Populations of Yellowtail Snapper, Ocyurus chrysurus (Lutjanidae – Perciformes), in the Western South Atlantic Revealed through Multilocus Analysis  

PubMed Central

In the present study, five loci (mitochondrial and nuclear) were sequenced to determine the genetic diversity, population structure, and demographic history of populations of the yellowtail snapper, Ocyurus chrysurus, found along the coast of the western South Atlantic. O. chrysurus is a lutjanid species that is commonly associated with coral reefs and exhibits an ample geographic distribution, and it can therefore be considered a good model for the investigation of phylogeographic patterns and genetic connectivity in marine environments. The results reflected a marked congruence between the mitochondrial and nuclear markers as well as intense gene flow among the analyzed populations, which represent a single genetic stock along the entire coast of Brazil between the states of Pará and Espírito Santo. Our data also showed high levels of genetic diversity in the species (mainly mtDNA), as well a major historic population expansion, which most likely coincided with the sea level oscillations at the end of the Pleistocene. In addition, this species is intensively exploited by commercial fisheries, and data on the genetic structure of its populations will be essential for the development of effective conservation and management plans. PMID:25769032

da Silva, Raimundo; Veneza, Ivana; Sampaio, Iracilda; Araripe, Juliana; Schneider, Horacio; Gomes, Grazielle

2015-01-01

387

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

PubMed Central

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