1601
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Abstract
For two decades the scientific community has sought to understand why some people clear hepatitis C virus (HCV) and others do not. Recently, several large genome-wide association studies have identified single nucleotide polymorphisms (SNPs) linked to interferon lambda 3 (IFNλ3) that are associated with the spontaneous resolution and successful treatment of HCV infection. These observations are generating intense research activity; the hope is that IFNλ3 genetic variants may serve as important predictive biomarkers of treatment outcome and offer new insights into the biological pathways involved in viral control. A pharmacogenomic treatment approach for HCV can now be envisaged, with the incorporation of host genetic variants into a predictive treatment algorithm with other factors. The SNPs associated with the clinical outcome of HCV infection are located some distance from the IFNλ3 gene itself, and causal genetic variants have yet to be clearly defined. Locating these causal variants, mapping in detail the IFNλ3 signalling pathways and determining the downstream genetic signature so induced will clarify the role of IFNλ3 in the pathogenesis of HCV. Clinical studies assessing safety and efficacy in the treatment of HCV with exogenous IFNλ3 are currently underway. Early results suggest that IFNλ3 treatment inhibits HCV replication and is associated with a limited side effect profile. However, hepatotoxicity in both healthy volunteers and HCV-infected patients has been described. This review discusses the genetic studies that link IFNλ3 to both the spontaneous resolution and treatment-induced clearance of HCV and the potential impact of this in clinical practice, the biology of IFNλ3 as currently understood and how this may impact on HCV infection, and describes the early studies that assess the role of this cytokine in the treatment of patients with HCV.
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Affiliation(s)
- Christabel Kelly
- Peter Medawar Building for Pathogen Research, Oxford NIHR Biomedical Research Centre, Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
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1602
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Qi Q, Bray GA, Smith SR, Hu FB, Sacks FM, Qi L. Insulin receptor substrate 1 gene variation modifies insulin resistance response to weight-loss diets in a 2-year randomized trial: the Preventing Overweight Using Novel Dietary Strategies (POUNDS LOST) trial. Circulation 2011; 124:563-71. [PMID: 21747052 PMCID: PMC3171189 DOI: 10.1161/circulationaha.111.025767] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Common genetic variants in the insulin receptor substrate 1 (IRS1) gene have been recently associated with insulin resistance and hyperinsulinemia. We examined whether the best-associated variant modifies the long-term changes in insulin resistance and body weight in response to weight-loss diets in Preventing Overweight Using Novel Dietary Strategies (POUNDS LOST) trial. METHODS AND RESULTS We genotyped IRS1 rs2943641 in 738 overweight adults (61% were women) who were randomly assigned to 1 of 4 diets varying in macronutrient contents for 2 years. We assessed the progress in fasting insulin, homeostasis model assessment of insulin resistance (HOMA-IR) and weight loss by genotypes. At 6 months, participants with the risk-conferring CC genotype had greater decreases in insulin (P=0.009), HOMA-IR (P=0.015), and weight loss (P=0.018) than those without this genotype in the highest-carbohydrate diet group whereas an opposite genotype effect on changes in insulin and HOMA-IR (P≤0.05) was observed in participants assigned to the lowest-carbohydrate diet group. No significant differences were observed across genotypes in the other 2 diet groups. The tests for genotype by intervention interactions were all significant (P<0.05). At 2 years, the genotype effect on changes in insulin and HOMA-IR remained significant in the highest-carbohydrate diet group (P<0.05). The highest carbohydrate diet led to a greater improvement of insulin and HOMA-IR (P for genotype-time interaction ≤0.009) in participants with the CC genotype than those without this genotype across 2-year intervention. CONCLUSIONS Individuals with the IRS1 rs2943641 CC genotype might obtain more benefits in weight loss and improvement of insulin resistance than those without this genotype by choosing a high-carbohydrate and low-fat diet. CLINICAL TRIAL REGISTRATION http:www.clinicaltrials.gov. Unique identifier: NCT00072995.
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Affiliation(s)
- Qibin Qi
- Department of Nutrition, Harvard School of Public Health, Boston, MA 02115, USA
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1603
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Del Castillo RF, Trujillo-Argueta S, Sánchez-Vargas N, Newton AC. Genetic factors associated with population size may increase extinction risks and decrease colonization potential in a keystone tropical pine. Evol Appl 2011; 4:574-88. [PMID: 25568006 PMCID: PMC3352421 DOI: 10.1111/j.1752-4571.2010.00177.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 11/14/2010] [Indexed: 12/03/2022] Open
Abstract
Pioneer species are essential for forest regeneration and ecosystem resilience. Pinus chiapensis is an endangered pioneer key species for tropical montane cloud forest regeneration in Mesoamerica. Human activities have severely reduced some P. chiapensis populations, which exhibited a small or null colonization potential suggesting the involvement of genetic factors associated with small populations. We explored the relationships between (i) population genetic diversity (allozymes) and population size, including sampling size effects, (ii) fitness estimates associated with colonization potential (seed viability and seedling performance) in a common environment and population size, and (iii) fitness estimates and observed heterozygosity in populations with sizes spanning five orders of magnitude. All the estimates of genetic diversity and fitness increased significantly with population size. Low fitness was detected in progenies of small populations of disturbed and undisturbed habitats. Progenies with the lowest observed heterozygosity displayed the lowest fitness estimates, which, in turn, increased with heterozygosity, but seed viability peaked at intermediate heterozygosity values suggesting inbreeding and outbreeding depression. Inbreeding depression appears to be the most immediate genetic factor in population decline. Conservation efforts should try to maintain large and genetically diverse populations, enhance gene flow by restoring connectivity between adjacent populations, and avoid genetically distant individuals.
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Affiliation(s)
- Rafael F Del Castillo
- Instituto Politécnico Nacional CIIDIR Oaxaca, Hornos, Santa Cruz Xoxocotlán; Oaxaca, Mexico
| | - Sonia Trujillo-Argueta
- Instituto Politécnico Nacional CIIDIR Oaxaca, Hornos, Santa Cruz Xoxocotlán; Oaxaca, Mexico
| | - Nahúm Sánchez-Vargas
- Instituto de Investigaciones Agropecuarias y Forestales, Universidad Michoacana de San Nicolás de Hidalgo, (IIAF-UMSNH) Morelia-Zinapécuaro, Tarímbaro, Michoacán, México
| | - Adrian C Newton
- School of Conservation Sciences, Bournemouth University Talbot Campus, Fern Barrow, Poole, Dorset, UK
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1604
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Ranjan SK, Mallick CB, Saha D, Vidyarthi AS, Ramani R. Genetic variation among species, races, forms and inbred lines of lac insects belonging to the genus Kerria (Homoptera, Tachardiidae). Genet Mol Biol 2011; 34:511-9. [PMID: 21931527 PMCID: PMC3168195 DOI: 10.1590/s1415-47572011000300023] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Accepted: 05/04/2011] [Indexed: 11/22/2022] Open
Abstract
The lac insects (Homoptera: Tachardiidae), belonging to the genus Kerria, are commercially exploited for the production of lac. Kerria lacca is the most commonly used species in India. RAPD markers were used for assessing genetic variation in forty-eight lines of Kerria, especially among geographic races, infrasubspecific forms, cultivated lines, inbred lines, etc., of K. lacca. In the 48 lines studied, the 26 RAPD primers generated 173 loci, showing 97.7% polymorphism. By using neighbor-joining, the dendrogram generated from the similarity matrix resolved the lines into basically two clusters and outgroups. The major cluster, comprising 32 lines, included mainly cultivated lines of the rangeeni form, geographic races and inbred lines of K. lacca. The second cluster consisted of eight lines of K. lacca, seven of the kusmi form and one of the rangeeni from the southern state of Karnataka. The remaining eight lines formed a series of outgroups, this including a group of three yellow mutant lines of K. lacca and other species of the Kerria studied, among others. Color mutants always showed distinctive banding patterns compared to their wild-type counterparts from the same population. This study also adds support to the current status of kusmi and rangeeni, as infraspecific forms of K. lacca.
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Affiliation(s)
- Sanjeev Kumar Ranjan
- Lac Production Division, Indian Institute of Natural Resins and Gums, Indian Council of Agricultural Research, Ranchi, India
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1605
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McFarlane SE, Lane JE, Taylor RW, Gorrell JC, Coltman DW, Humphries MM, Boutin S, McAdam AG. The heritability of multiple male mating in a promiscuous mammal. Biol Lett 2011; 7:368-71. [PMID: 21159688 PMCID: PMC3097859 DOI: 10.1098/rsbl.2010.1003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Accepted: 11/23/2010] [Indexed: 11/12/2022] Open
Abstract
The tendency of females to mate with multiple males is often explained by direct and indirect benefits that could outweigh the many potential costs of multiple mating. However, behaviour can only evolve in response to costs and benefits if there is sufficient genetic variation on which selection can act. We followed 108 mating chases of 85 North American red squirrels (Tamiasciurus hudsonicus) during 4 years, to measure each female's degree of multiple male mating (MMM), and used an animal model analysis of our multi-generational pedigree to provide what we believe is the first estimate of the heritability of MMM in the wild. Female red squirrels were highly polyandrous, mating with an average of 7.0 ± 0.2 males on their day of oestrus. Although we found evidence for moderate levels of additive genetic variation (CV(A) = 5.1), environmental variation was very high (CV(E) = 32.3), which resulted in a very low heritability estimate (h(2) < 0.01). So, while there is genetic variation in this trait, the large environmental variation suggests that any costs or benefits associated with differences among females in MMM are primarily owing to environmental and not genetic differences, which could constrain the evolutionary response to natural selection on this trait.
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Affiliation(s)
- S. Eryn McFarlane
- Department of Integrative Biology, University of Guelph, Guelph, ON, CanadaN1G 2W1
| | - Jeffrey E. Lane
- Institute of Evolutionary Biology, University of Edinburgh, Kings Buildings, Edinburgh EH9 3JT, UK
| | - Ryan W. Taylor
- Department of Zoology, Michigan State University, 203 Natural Sciences, East Lansing, MI 48824, USA
| | - Jamieson C. Gorrell
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, CanadaT6G 2E9
| | - David W. Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, CanadaT6G 2E9
| | - Murray M. Humphries
- Department of Natural Resource Sciences, McGill University, Macdonald Campus, Ste-Anne-de-Bellevue, Québec, CanadaH9X 3V9
| | - Stan Boutin
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, CanadaT6G 2E9
| | - Andrew G. McAdam
- Department of Integrative Biology, University of Guelph, Guelph, ON, CanadaN1G 2W1
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1606
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Sznajder B, Sabelis MW, Egas M. Innate responses of the predatory mite Phytoseiulus persimilis to a herbivore-induced plant volatile. Exp Appl Acarol 2011; 54:125-138. [PMID: 21321807 PMCID: PMC3084430 DOI: 10.1007/s10493-011-9430-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Accepted: 02/01/2011] [Indexed: 05/27/2023]
Abstract
The responses of the predatory mite P. persimilis to herbivore-induced plant volatiles are at least partly genetically determined. Thus, there is potential for the evolution of this behaviour by natural selection. We tested whether distinct predator genotypes with contrasting responses to a specific herbivore-induced plant volatile, i.e. methyl salicylate (MeSa), could be found in a base population collected in the field (Sicily). To this end, we imposed purifying selection on individuals within iso-female lines of P. persimilis such that the lines were propagated only via the individual that showed either a preference or avoidance of MeSa. The responses of the lines were characterized as the mean proportion of individuals choosing MeSa when given a choice between MeSa and clean air. Significant variation in predator responses was detected among iso-female lines, thus confirming the presence of a genetic component for this behaviour. Nevertheless, we did not find a significant difference in the response to MeSa between the lines that were selected to avoid MeSa and the lines selected to prefer MeSa. Instead, in the course of selection the lines selected to avoid MeSa shifted their mean response towards a preference for MeSa. An inverse, albeit weaker, shift was detected for the lines selected to prefer MeSa. We discuss the factors that may have caused the apparent lack of a response to selection within iso-female line in this study and propose experimental approaches that address them.
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Affiliation(s)
- B. Sznajder
- Department of Population Biology, Institute for Biodiversity and Ecosystems Dynamics, University of Amsterdam, Science Park 904, P.O.Box 94240, 1090 GE, Amsterdam, The Netherlands
| | - M. W. Sabelis
- Department of Population Biology, Institute for Biodiversity and Ecosystems Dynamics, University of Amsterdam, Science Park 904, P.O.Box 94240, 1090 GE, Amsterdam, The Netherlands
| | - M. Egas
- Department of Population Biology, Institute for Biodiversity and Ecosystems Dynamics, University of Amsterdam, Science Park 904, P.O.Box 94240, 1090 GE, Amsterdam, The Netherlands
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1607
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Abstract
Dampening of insulin/insulin-like growth factor-1 (IGF1) signaling results in the extension of lifespan in invertebrate as well as murine models. The impact of this evolutionarily conserved pathway on the modulation of human lifespan remains unclear. We previously identified two IGF1R mutations (Ala-37-Thr and Arg-407-His) that are enriched in Ashkenazi Jewish centenarians as compared to younger controls and are associated with the reduced activity of the IGF1 receptor as measured in immortalized lymphocytes. To determine whether these human longevity-associated IGF1R mutations affect IGF1 signaling, we engineered mouse embryonic fibroblasts (MEFs) expressing the different human IGF1R variants in a mouse Igf1r null background. The results indicate that MEFs expressing the human longevity-associated IGF1R mutations attenuated IGF1 signaling, as demonstrated by significant reduction in phosphorylation of both IGF1R and AKT after IGF1 treatment, in comparison with MEFs expressing the wild-type IGF1R. The impaired IGF1 signaling caused by the IGF1R mutations resulted in the reduced induction of the major IGF1-activated genes in MEFs, including EGR1, mCSF, IL3Rα, and TDAG51. Furthermore, the IGF1R mutations caused a delay in cell cycle progression after IGF1 treatment, indicating a dysfunctional physiological response to a cell proliferation signal. These results demonstrate that the human longevity-associated IGF1R variants are reduced-function mutations, implying that dampening of IGF1 signaling may be a longevity mechanism in humans.
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Affiliation(s)
- Cagdas Tazearslan
- Departments of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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1608
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McKinney LV, Nielsen LR, Hansen JK, Kjær ED. Presence of natural genetic resistance in Fraxinus excelsior (Oleraceae) to Chalara fraxinea (Ascomycota): an emerging infectious disease. Heredity (Edinb) 2011; 106:788-97. [PMID: 20823903 PMCID: PMC3186218 DOI: 10.1038/hdy.2010.119] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Revised: 06/29/2010] [Accepted: 07/15/2010] [Indexed: 11/09/2022] Open
Abstract
Fraxinus excelsior, common ash native to Europe, is threatened by a recently identified pathogenic fungus Chalara fraxinea, which causes extensive damage on ash trees across Europe. In Denmark, most stands are severely affected leaving many trees with dead crowns. However, single trees show notably fewer symptoms. In this study, the impact of the emerging infectious disease on native Danish ash trees is assessed by estimating presence of inherent resistance in natural populations. Disease symptoms were assessed from 2007 to 2009 at two different sites with grafted ramets of 39 selected clones representing native F. excelsior trees. A strong genetic variation in susceptibility to C. fraxinea infections was observed. No genetic or geographic structure can explain the differences, but strong genetic correlations to leaf senescence were observed. The results suggest that a small fraction of trees in the Danish population of ash possess substantial resistance against the damage. Though this fraction is probably too low to avoid population collapse in most natural or managed ash forests, the observed presence of putative resistance against the emerging infectious disease in natural stands is likely to be of evolutionary importance. This provides prospects of future maintenance of the species through natural or artificial selection in favour of remaining healthy individuals.
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Affiliation(s)
- L V McKinney
- Department of Forest Genetic Resources, Forest and Landscape Denmark, Faculty of Life Sciences, University of Copenhagen, Rolighedsvej 23, Frederiksberg, Denmark.
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1609
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Abstract
OBJECTIVE To examine whether a polymorphism (5-HTTLPR: serotonin transporter linked polymorphic region) in the promoter of the serotonin transporter gene (SLC6A4) moderates cardiovascular reactivity to social threat. METHODS Psychologically healthy young adults delivered a speech and performed mental arithmetic in one of three conditions: a) an evaluative audience condition that gave disapproving and negative nonverbal social signals (n = 59); b) an evaluative audience condition that provided supportive social signals (n = 60); or c) a no audience condition (n = 65). Heart rate (HR) and systolic and diastolic blood pressures (DBP) were measured before, during, and after the stress tasks to assess cardiovascular reactivity and recovery. RESULTS In the negative audience condition, there was a significant association between the 5-HTTLPR and systolic blood pressure, DBP, and HR reactivity. Individuals with the short/short genotype showed the greatest reactivity. The DBP and HR reactivity of short/short individuals in the negative audience condition was also greater than that of individuals with the short/short genotype in the no audience condition. These associations of the 5-HTLPR with HR reactivity were moderated by gender, being limited to females. With respect to cardiovascular recovery, short/short individuals in the negative audience condition exhibited impaired DBP recovery relative to other genotypes in the same condition, as well as short/short individuals in the no audience condition. CONCLUSIONS The 5-HTTLPR moderates cardiovascular reactivity to stress in a threatening evaluative social context, which suggests that the serotonin system may be involved in the processes by which stressful, conflict-ridden social environments affect risk for cardiovascular-related health outcomes.
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1610
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SAFER STEFAN, TREMETSBERGER KARIN, GUO YANPING, KOHL GUDRUN, SAMUEL MARYR, STUESSY TODF, STUPPNER HERMANN. Phylogenetic relationships in the genus Leontopodium (Asteraceae: Gnaphalieae) based on AFLP data. Bot J Linn Soc 2011; 165:364-377. [PMID: 23258943 PMCID: PMC3524420 DOI: 10.1111/j.1095-8339.2011.01117.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The genus Leontopodium comprises 30-41 species. The centre of diversity is the Sino-Himalayan region in south-western China, where about 15 species occur. The two species native to Europe, L. alpinum (known as the common 'Edelweiss') and L. nivale, are part of the cultural heritage of the people living there. Despite its importance, very little is known about the systematics of the genus. Because recent molecular studies have shown that species within this genus are closely related and difficult to distinguish with rDNA and cpDNA data, we used AFLPs to obtain a more detailed understanding of the phylogeny of the genus. Our main aims were as follows: (1) to clarify species relationships within the genus; and (2) to reveal information about the biogeography of the genus. We used AFLPs with six primer combinations to investigate 216 individuals in 38 populations of 16 different species. With AFLPs, we were able to recognize 10 different groups, all of which had strong bootstrap support. These results were also congruent with the morphology-based taxonomy of the genus. Most private and rare fragments were found in the Yunnan region (south-western China) relative to Europe and Mongolia/central China, suggesting a long-lasting in situ history of populations in the centre of diversity of the genus. Our results illustrate the utility of AFLPs to resolve phylogenetic relationships between these closely related species.
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Affiliation(s)
- STEFAN SAFER
- Institute of Pharmacy/Pharmacognosy, Faculty of Chemistry and Pharmacy, University of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria
| | - KARIN TREMETSBERGER
- Institute of Botany, Department of Integrative Biology and Biodiversity Research, University of Natural Resources and Life Sciences, Gregor-Mendel-Straße 33, 1180 Vienna, Austria
| | - YAN-PING GUO
- College of Life Sciences, Beijing Normal University, no. 19 Xinjiekouwai Street, Beijing 100875, China
| | - GUDRUN KOHL
- Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, 1030 Vienna, Austria
| | - MARY R. SAMUEL
- Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, 1030 Vienna, Austria
| | - TOD F. STUESSY
- Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, 1030 Vienna, Austria
| | - HERMANN STUPPNER
- Institute of Pharmacy/Pharmacognosy, Faculty of Chemistry and Pharmacy, University of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria
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1611
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Abstract
Biological databases are an important resource for the life sciences community. Accessing the hundreds of databases supporting molecular biology and related fields is a daunting and time-consuming task. Integrating this information into one access point is a necessity for the life sciences community, which includes researchers focusing on human disease. Here we discuss the Ensembl genome browser, which acts as a single entry point with Graphical User Interface to data from multiple projects, including OMIM, dbSNP, and the NHGRI GWAS catalog. Ensembl provides a comprehensive source of annotation for the human genome, along with other species of biomedical interest. In this unit, we explore how to use the Ensembl genome browser in example queries related to human genetic diseases. Support protocols demonstrate quick sequence export using the BioMart tool.
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1612
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Bömcke E, Gengler N, Cothran EG. Genetic variability in the Skyros pony and its relationship with other Greek and foreign horse breeds. Genet Mol Biol 2011; 34:68-76. [PMID: 21637546 PMCID: PMC3085377 DOI: 10.1590/s1415-47572010005000113] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Accepted: 11/26/2010] [Indexed: 11/22/2022] Open
Abstract
In Greece, seven native horse breeds have been identified so far. Among these, the Skyros pony is outstanding through having a distinct phenotype. In the present study, the aim was to assess genetic diversity in this breed, by using different types of genetic loci and available genealogical information. Its relationships with the other Greek, as well as foreign, domestic breeds were also investigated. Through microsatellite and pedigree analysis it appeared that the Skyros presented a similar level of genetic diversity to the other European breeds. Nevertheless, comparisons between DNA-based and pedigree-based results revealed that a loss of genetic diversity had probably already occurred before the beginning of breed registration. Tests indicated the possible existence of a recent bottleneck in two of the three main herds of Skyros pony. Nonetheless, relatively high levels of heterozygosity and Polymorphism Information Content indicated sufficient residual genetic variability, probably useful in planning future strategies for breed conservation. Three other Greek breeds were also analyzed. A comparison of these with domestic breeds elsewhere, revealed the closest relationships to be with the Middle Eastern types, whereas the Skyros itself remained isolated, without any close relationship, whatsoever.
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Affiliation(s)
- Elisabeth Bömcke
- Animal Science Unit, Gembloux Agricultural University, Gembloux, Belgium
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1613
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Tranchida-Lombardo V, Cafasso D, Cristaudo A, Cozzolino S. Phylogeographic patterns, genetic affinities and morphological differentiation between Epipactis helleborine and related lineages in a Mediterranean glacial refugium. Ann Bot 2011; 107:427-36. [PMID: 21193482 PMCID: PMC3043932 DOI: 10.1093/aob/mcq256] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
BACKGROUND AND AIMS In the Mediterranean basin, the Italian peninsula has been suggested to be one of the most important glacial refugia for temperate tree species. The orchid genus Epipactis is widely represented in the Italian peninsula by widespread species and several endemic, localized taxa, including selfing and outcrossing taxa. Here the phylogenetic and phylogeographic relationships in a group of closely related taxa in Epipactis are investigated with the aim of understanding the role of this refugial area for cladogenesis and speciation in herbaceous species, such as terrestrial orchids. METHODS Ribosomal DNA (rDNA) was employed to assess phylogenetic relationships, and plastid sequence variation in the rbcL-accD spacer was used to reveal phylogeographic patterns among plastid haplotypes using a parsimony network. KEY RESULTS Low genetic variation and shared ribotypes were detected in rDNA, whereas high levels of sequence variation and a strong phylogeographic structure were found in the examined plastid region. The parsimony plastid haplotype network identified two main haplotype groups, one including E. atrorubens/microphylla/muelleri/leptochila and the other including all accessions of E. helleborine and several localized and endemic taxa, with a combination of widespread and rare haplotypes detected across the Italian peninsula. A greater genetic divergence separated the Italian and other European accessions of E. helleborine. CONCLUSIONS Phylogenetic and phylogeographic patterns support a working hypothesis in which the Italian peninsula has only recently been colonized by Epipactis, probably during the most recent phase of the Quaternary age and, nevertheless, it acted as a remarkable centre of diversification for this orchid lineage. Changes in pollination strategy and recurrent shifts in mating system (from allogamy to autogamy) could have represented the mechanism promoting this rapid diversification and the observed high taxonomic complexity detected in the E. helleborine species complex.
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Affiliation(s)
- Valentina Tranchida-Lombardo
- Sezione di Biologia ed Ecologia Vegetale DACPA, Università di Catania, via Vadisavoia 5, 95123, Catania, Italy
- Dipartimento di Biologia strutturale e funzionale, Università ‘Federico II’, complesso MSA, 80126 Napoli, Italy
| | - Donata Cafasso
- Dipartimento di Biologia strutturale e funzionale, Università ‘Federico II’, complesso MSA, 80126 Napoli, Italy
| | - Antonia Cristaudo
- Sezione di Biologia ed Ecologia Vegetale DACPA, Università di Catania, via Vadisavoia 5, 95123, Catania, Italy
| | - Salvatore Cozzolino
- Dipartimento di Biologia strutturale e funzionale, Università ‘Federico II’, complesso MSA, 80126 Napoli, Italy
- For correspondence. E-mail
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1614
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Abstract
Environmental change challenges local and global survival of populations and species. In a species-poor environment like the Baltic Sea this is particularly critical as major ecosystem functions may be upheld by single species. A complex interplay between demographic and genetic characteristics of species and populations determines risks of local extinction, chances of re-establishment of lost populations, and tolerance to environmental changes by evolution of new adaptations. Recent studies show that Baltic populations of dominant marine species are locally adapted, have lost genetic variation and are relatively isolated. In addition, some have evolved unusually high degrees of clonality and others are representatives of endemic (unique) evolutionary lineages. We here suggest that a consequence of local adaptation, isolation and genetic endemism is an increased risk of failure in restoring extinct Baltic populations. Additionally, restricted availability of genetic variation owing to lost variation and isolation may negatively impact the potential for evolutionary rescue following environmental change.
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Affiliation(s)
- Kerstin Johannesson
- Department of Marine Ecology-Tjärnö, University of Gothenburg, 452 96 Strömstad, Sweden
| | - Katarzyna Smolarz
- Centre for Baltic and East European Studies, Södertörn University, 141 89 Huddinge, Sweden
| | - Mats Grahn
- School of Life Sciences, Södertörn University, 141 89 Huddinge, Sweden
| | - Carl André
- Department of Marine Ecology-Tjärnö, University of Gothenburg, 452 96 Strömstad, Sweden
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1615
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Abstract
Abstract Given molecular genetic data from diploid individuals that, at present, reproduce mostly or exclusively asexually without recombination, an important problem in evolutionary biology is detecting evidence of past sexual reproduction (i.e., meiosis and mating) and recombination (both meiotic and mitotic). However, currently there is a lack of computational tools for carrying out such a study. In this article, we formulate a new problem of reconstructing diploid genealogies under the assumption of no sexual reproduction or recombination, with the ultimate goal being to devise genealogy-based tools for testing deviation from these assumptions. We first consider the infinite-sites model of mutation and develop linear-time algorithms to test the existence of an asexual diploid genealogy compatible with the infinite-sites model of mutation, and to construct one if it exists. In this ideal case, our chance of detecting signatures of past sexual reproduction is maximized. Then, we relax the infinite-sites assumption and develop an integer linear programming formulation to reconstruct asexual diploid genealogies with the minimum number of homoplasy (back or recurrent mutation) events. If this number is substantially larger than that expected for typical asexual organisms, then it may suggest that sexual reproduction or recombination may have played an important role in the evolutionary history. We apply our algorithms on simulated data sets with sizes of biological interest.
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Affiliation(s)
- Fumei Lam
- Department of Computer Science, University of California, Davis, California, USA.
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1616
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Abstract
Genetic variability in reaction norms reflects differences in the ability of individuals, populations and ultimately species to respond to environmental change. By increasing our understanding of how genotype × environment interactions influence evolution, studies of genetic variation in phenotypic plasticity serve to refine our capacity to predict how populations will respond to natural and anthropogenic environmental variability, including climate change. Given the extraordinary variability in morphology, behaviour and life history in salmonids, one might anticipate the research milieu on reaction norms in these fishes to be empirically rich and intellectually engaging. Here, I undertake a review of genetic variability in continuous and discontinuous (threshold) norms of reaction in salmonid fishes, as determined primarily (but not exclusively) by common-garden experiments. Although in its infancy from a numerical publication perspective, there is taxonomically broad evidence of genetic differentiation in continuous, threshold and bivariate reaction norms among individuals, families and populations (including inter-population hybrids and backcrosses) for traits as divergent as embryonic development, age and size at maturity, and gene expression. There is compelling inferential evidence that plasticity is heritable and that population differences in reaction norms can reflect adaptive responses, by natural selection, to local environments. As a stimulus for future work, a series of 20 research questions are identified that focus on reaction-norm variability, selection, costs and constraints, demographic and conservation consequences, and genetic markers and correlates of phenotypic plasticity.
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Affiliation(s)
- J A Hutchings
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada.
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1617
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Abstract
INTRODUCTION PXR polymorphisms have been implicated in modulating CYP3A4 and PXR expression, potentially accounting for interindividual differences in drug metabolism. The prevalence of PXR polymorphisms varies among ethnic groups and data on the allelic distribution in the highly mixed Brazilian population is lacking. The aim of this study was to analyze genetic variations in the PXR gene in Brazilians and to compare the results to other ethnic groups. METHODS DNA samples from 117 healthy Brazilians underwent PCR amplification and sequencing. RESULTS Eleven polymorphisms were identified, 3 of which are highly associated with differences in CYP3A4 expression. We also identified 1 new synonymous variant in 1.3% of the alleles. Among the functional polymorphisms, -25913 C>T and -6994T>C occurred at a higher frequency comparedtothe Africanalleles (p < 0.05) but at a lower frequency compared to Caucasian alleles. The 8055 C>T allele was found at a similar frequency to those described in Caucasians and Africans (p > 0.05). CONCLUSION We observed that functional variants of the PXR were frequent in our sample of the Brazilian population. Our results suggest that PXR gene variants may be of interest in pharmacogenetic studies involving Brazilians.
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Affiliation(s)
- Ricardo P P Moreira
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM 42, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
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1618
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Prudent M, Lecomte A, Bouchet JP, Bertin N, Causse M, Génard M. Combining ecophysiological modelling and quantitative trait locus analysis to identify key elementary processes underlying tomato fruit sugar concentration. J Exp Bot 2011; 62:907-19. [PMID: 21036926 PMCID: PMC3022390 DOI: 10.1093/jxb/erq318] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Revised: 09/20/2010] [Accepted: 09/21/2010] [Indexed: 05/18/2023]
Abstract
A mechanistic model predicting the accumulation of tomato fruit sugars was developed in order (i) to dissect the relative influence of three underlying processes: assimilate supply (S), metabolic transformation of sugars into other compounds (M), and dilution by water uptake (D); and (ii) to estimate the genetic variability of S, M, and D. The latter was estimated in a population of 20 introgression lines derived from the introgression of a wild tomato species (Solanum chmielewskii) into S. lycopersicum, grown under two contrasted fruit load conditions. Low load systematically decreased D in the whole population, while S and M were targets of genotype × fruit load interactions. The sugar concentration positively correlated to S and D when the variation was due to genetic introgressions, while it positively correlated to S and M when the variation was due to changes in fruit load. Co-localizations between quantitative trait loci (QTLs) for sugar concentration and QTLs for S, M, and D allowed hypotheses to be proposed on the processes putatively involved at the QTLs. Among the five QTLs for sugar concentration, four co-localized with QTLs for S, M, and D with similar allele effects. Moreover, the processes underlying QTLs for sugar accumulation changed according to the fruit load condition. Finally, for some genotypes, the processes underlying sugar concentration compensated in such a way that they did not modify the sugar concentration. By uncoupling genetic from physiological relationships between processes, these results provide new insights into further understanding of tomato fruit sugar accumulation.
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Affiliation(s)
- Marion Prudent
- INRA, UR1115 Plantes et Systèmes de culture Horticoles, F-84000 Avignon, France.
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1619
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Kim ST, Cheng Y, Hsu FC, Jin T, Kader AK, Zheng SL, Isaacs WB, Xu J, Sun J. Prostate cancer risk-associated variants reported from genome-wide association studies: meta-analysis and their contribution to genetic Variation. Prostate 2010; 70:1729-38. [PMID: 20564319 PMCID: PMC3013361 DOI: 10.1002/pros.21208] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
BACKGROUND Genome-wide association studies (GWAS) have led to the discovery of multiple single nucleotide polymorphisms (SNPs) that are associated with prostate cancer (PCa) risk. These SNPs may potentially be used for risk prediction. To date, there is not a stable estimate of their effect on PCa risk and their contribution to the genetic variation both of which are important for future risk prediction. METHODS A literature review was conducted to identify SNPs associated with PCa risk with the following criteria: (1) GWAS in the Caucasian population; (2) SNPs with P-value <1.0×10(-6); and (3) one SNP from each independent LD block. A meta-analysis was performed to estimate combined odds ratio (OR) and its 95% confidence interval (CI) for the identified SNPs. The proportion of total genetic variance that is attributable by each of these SNPs was also estimated. RESULTS Thirty PCa risk-associated SNPs were identified. These SNPs had OR estimates between 1.12 and 1.47 except for marker rs16901979 (OR=1.80). Significant heterogeneity in OR estimates was found among different studies for 13 SNPs. The proportion of total genetic variance attributed by each SNP ranged between 0.2% and 0.9%. These 30 SNPs explained ∼13.5% of the total genetic variance of PCa risk in the Caucasian population. CONCLUSION This study provides more stable OR estimates for PCa risk-associated SNPs, which is an important baseline for the effect of these SNPs in risk prediction. These SNPs explain a considerable proportion of genetic variance, however, the majority of genetic variance has yet to be explained.
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Affiliation(s)
- Seong-Tae Kim
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Yu Cheng
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Fang-Chi Hsu
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
- Department of Biostatistical Sciences, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Tao Jin
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - A. Karim Kader
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
- Department of Urology, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - S. Lilly Zheng
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - William B. Isaacs
- The Brady Institute, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Jianfeng Xu
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
- Department of Urology, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Jielin Sun
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
- Address for correspondence: Dr. Jielin Sun, Center for Cancer Genomics, Medical Center Blvd, Winston-Salem, NC 27157, Phone: (336) 713-7500, Fax: (336) 713-7566,
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1620
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Witte AV, Jansen S, Schirmacher A, Young P, Flöel A. COMT Val158Met Polymorphism Modulates Cognitive Effects of Dietary Intervention. Front Aging Neurosci 2010; 2:146. [PMID: 21119769 PMCID: PMC2990456 DOI: 10.3389/fnagi.2010.00146] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Accepted: 10/04/2010] [Indexed: 01/03/2023] Open
Abstract
A common single nucleotide polymorphism (SNP) in the gene encoding catechol-O-methyltransferase (COMT), Val158Met, is thought to influence cognitive performance due to differences in prefrontal dopaminergic neurotransmission. Previous studies lend support for the hypothesis that the "at risk" genotype comprising two Val-alleles (low dopamine) might benefit more from plasticity-enhancing interventions than carriers of one or two Met-alleles. This study aimed to determine whether the response to dietary interventions, known to modulate cognition, is dependent on COMT genotype. Blood samples of 35 healthy elderly subjects (61.3 years ±8 SD; 19 women, 16 men, BMI: 28.2 kg/m(2) ±4 SD) were genotyped for COMT Val158Met by standard procedures (Val/Val = 6; Val/Met = 20; Met/Met = 9). Subjects had previously completed a randomized controlled trial investigating the effects of caloric restriction (CR) or enhancement of unsaturated fatty acids (UFA) on immediate and delayed verbal recognition memory. Homozygous Val/Val-carriers had significantly lower memory scores than Met-carriers at baseline (p < 0.001). Significant interactions of genotype and dietary intervention with regard to cognition were found: CR- and UFA enhancement-induced memory improvements of Val/Val-carriers were considerably greater than those of Met-carriers (ANOVA p's < 0.02). The current study shows for the first time that cognitive effects of dietary interventions are dependent on COMT Val158Met genotype. Our findings lend further support to the hypothesis that an "at risk" genotype might benefit more from plasticity-enhancing interventions than the "not at risk" genotype. This might help to develop individualized therapies in future research based on genetic background.
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Affiliation(s)
- Anja Veronica Witte
- Department of Neurology, Charité - Universitätsmedizin Berlin Berlin, Germany
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1621
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Haworth CM, Wright MJ, Luciano M, Martin NG, de Geus EJ, van Beijsterveldt CE, Bartels M, Posthuma D, Boomsma DI, Davis OS, Kovas Y, Corley RP, Defries JC, Hewitt JK, Olson RK, Rhea SA, Wadsworth SJ, Iacono WG, McGue M, Thompson LA, Hart SA, Petrill SA, Lubinski D, Plomin R. The heritability of general cognitive ability increases linearly from childhood to young adulthood. Mol Psychiatry 2010; 15:1112-20. [PMID: 19488046 DOI: 10.1038/mp.2009.55] [Citation(s) in RCA: 334] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Although common sense suggests that environmental influences increasingly account for individual differences in behavior as experiences accumulate during the course of life, this hypothesis has not previously been tested, in part because of the large sample sizes needed for an adequately powered analysis. Here we show for general cognitive ability that, to the contrary, genetic influence increases with age. The heritability of general cognitive ability increases significantly and linearly from 41% in childhood (9 years) to 55% in adolescence (12 years) and to 66% in young adulthood (17 years) in a sample of 11 000 pairs of twins from four countries, a larger sample than all previous studies combined. In addition to its far-reaching implications for neuroscience and molecular genetics, this finding suggests new ways of thinking about the interface between nature and nurture during the school years. Why, despite life's 'slings and arrows of outrageous fortune', do genetically driven differences increasingly account for differences in general cognitive ability? We suggest that the answer lies with genotype-environment correlation: as children grow up, they increasingly select, modify and even create their own experiences in part based on their genetic propensities.
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1622
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Reese AC, Hardin J, Cheng I, Casey G, Witte JS. Non-Steroidal Anti-Inflammatory Drugs, Variation in Inflammatory Genes, and Aggressive Prostate Cancer. Pharmaceuticals (Basel) 2010; 3:3127-3142. [PMID: 24023525 PMCID: PMC3766748 DOI: 10.3390/ph3103127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Increasing evidence suggests that prostatic inflammation plays a key role in the development of prostate cancer. It remains controversial whether non-steroidal anti-inflammatory drugs (NSAIDs) reduce the risk of prostate cancer. Here, we investigate how a previously reported inverse association between NSAID use and the risk of aggressive prostate cancer is modulated by variants in several inflammatory genes. We found that NSAIDs may have differential effects on prostate cancer development, depending on one’s genetic makeup. Further study of these inflammatory pathways may clarify the mechanisms through which NSAIDs impact prostate cancer risk.
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Affiliation(s)
- Adam C. Reese
- Department of Urology, University of California at San Francisco, 1450 3 Street, San Francisco, CA 94158, USA; E-Mail: (A.C.R.)
| | - Jill Hardin
- Epidemiology and Biostatistics and Institute for Human Genetics, University of California at San Francisco, 1450 3 Street, San Francisco, CA 94158, USA; E-Mail: (J.H.)
| | - Iona Cheng
- Epidemiology Program, Cancer Research Center of Hawai`i, University of Hawai`i, Honolulu, HI 96813, USA
| | - Graham Casey
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - John S. Witte
- Department of Urology, University of California at San Francisco, 1450 3 Street, San Francisco, CA 94158, USA; E-Mail: (A.C.R.)
- Epidemiology and Biostatistics and Institute for Human Genetics, University of California at San Francisco, 1450 3 Street, San Francisco, CA 94158, USA; E-Mail: (J.H.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-415-502-6882; Fax: +1-415-476-1356
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1623
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Manzaneda AJ, Prasad KVSK, Mitchell-Olds T. Variation and fitness costs for tolerance to different types of herbivore damage in Boechera stricta genotypes with contrasting glucosinolate structures. New Phytol 2010; 188:464-77. [PMID: 20663059 PMCID: PMC2950872 DOI: 10.1111/j.1469-8137.2010.03385.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
• Analyses of plant tolerance in response to different modes of herbivory are essential to an understanding of plant defense evolution, yet are still scarce. Allocation costs and trade-offs between tolerance and plant chemical defenses may influence genetic variation for tolerance. However, variation in defenses also occurs for the presence or absence of discrete chemical structures; yet, the effects of intraspecific polymorphisms on tolerance to multiple herbivores have not been evaluated. • Here, in a glasshouse experiment, we investigated the variation for tolerance to different types of herbivore damage, and direct allocation costs, in 10 genotypes of Boechera stricta (Brassicaceae), a wild relative of Arabidopsis, with contrasting foliar glucosinolate chemical structures (methionine-derived glucosinolates vs glucosinolates derived from branched-chain amino acids). • We found significant genetic variation for tolerance to different types of herbivore. Structural variations in the glucosinolate profile did not influence tolerance to damage, but predicted plant fitness. Levels of constitutive and induced glucosinolates varied between genotypes with different structural profiles, but we did not detect any cost of tolerance explaining the genetic variation in tolerance among genotypes. • Trade-offs between plant tolerance to multiple herbivores may not explain the existence of intermediate levels of tolerance to damage in plants with contrasting chemical defensive profiles.
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Affiliation(s)
- Antonio J Manzaneda
- Institute for Genome Sciences and Policy, Department of Biology, Duke University, Durham, NC 27708, USA.
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1624
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Lee NH. Pharmacogenetics of drug metabolizing enzymes and transporters: effects on pharmacokinetics and pharmacodynamics of anticancer agents. Anticancer Agents Med Chem 2010; 10:583-92. [PMID: 21194402 PMCID: PMC3770187 DOI: 10.2174/187152010794474019] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Accepted: 11/17/2010] [Indexed: 11/22/2022]
Abstract
There is wide interpatient variability in drug response and toxicity to standard doses of most anticancer medications. Genetic polymorphisms in genes encoding metabolic enzymes, receptors and drug transporters targeted by anticancer medications are often found, in part, to be responsible for the observed variability. Approximately 80% of all sequence variations residing in genes is in the form of single nucleotide polymorphisms or SNPs. The location of SNPs can be in the protein coding sequence, regulatory regions or at exon-intron boundaries of genes. Adverse drug reactions resulting from these sequence variations are due to changes in the activity of the encoded protein (in many instances the protein is non-functional) or perturbations in the level of gene expression. The goal of pharmacogenetic testing is to identify genetic polymorphisms that predispose patients to an adverse drug reaction, thereby allowing the health care provider to make informed decisions pertaining to the type of drug, dosage and dosage scheduling to be administered.
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Affiliation(s)
- Norman H Lee
- Department of Pharmacology and Physiology, The George Washington University Medical Center, Washington, DC 20037, USA.
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1625
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Chande A, Kövics GJ, Sandhu SS, Rai MK. Morphological and genetic differentiation among four pigment producing Indian species of Phoma (Saccardo, 1899). Indian J Microbiol 2010; 50:110-6. [PMID: 22815582 PMCID: PMC3396407 DOI: 10.1007/s12088-010-0067-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2008] [Accepted: 05/28/2008] [Indexed: 11/30/2022] Open
Abstract
A PCR-based technique, involving the random amplification of polymorphic DNA (RAPD), was used for assessing genetic relatedness among isolates of the genus Phoma. Randomly Amplified Polymorphic DNA (RAPD) revealed the presence of interspecific genetic variation among the pigment producing isolates of Phoma and has shown distinct phylogenetic cluster. The major objective of the study was to study the genetic variation, if any. Study was aimed to differentiate four pigment producing species of Phoma based on morphological studies and molecular markers in general and RAPD in particular. We found that the test species of Phoma can be very well differentiated using molecular markers. Phoma sorghina was differentiated from P. exigua, P. fimeti and P. herbarum. RAPD profiles of P. herbarum and P. fimeti has shown the maximum similarity, which indicates the genetic relatedness among these two species which were considered earlier as distinct species based on morphological observation.
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Affiliation(s)
- Ajit Chande
- />Department of Biotechnology, SGB Amravati University, Amravati, 444 602 Maharashtra India
| | - G. J. Kövics
- />Faculty of Agriculture, Department of Plant Protection, Debrecen University, H-4015 Debrecen, P.O. Box 36, Hungary
| | - S. S. Sandhu
- />Department of Bioscience, RD University, Jabalpur, M.P. India
| | - M. K. Rai
- />Department of Biotechnology, SGB Amravati University, Amravati, 444 602 Maharashtra India
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1626
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Sampedro L, Moreira X, Llusia J, Peñuelas J, Zas R. Genetics, phosphorus availability, and herbivore-derived induction as sources of phenotypic variation of leaf volatile terpenes in a pine species. J Exp Bot 2010; 61:4437-47. [PMID: 20952630 PMCID: PMC2955752 DOI: 10.1093/jxb/erq246] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Revised: 07/14/2010] [Accepted: 07/19/2010] [Indexed: 05/20/2023]
Abstract
Oleoresin produced and stored in pine tree leaves provides direct resistance to herbivores, while leaf volatile terpenes (LVT) in the resin are also powerful airborne infochemicals. Resin concentration and profile show considerable spatial and temporal phenotypic variation within and among pine populations. LVT biochemistry is known to be under genetic control, and although LVT should be plastic to diverse abiotic and biotic environmental factors such as nutrient availability and herbivore attack, little is known about their relative contributions and interactive effects. The aim of this paper was to clarify whether reduced phosphorus availability could increase the LVT concentration and affect the expression of herbivore-derived induced defences, and how plasticity would contribute to the phenotypic variation of LVT. The constitutive and methyl-jasmonate (MeJa) induced LVT concentration and profile were analysed in 17 half-sib Pinus pinaster families growing under two levels of P-availability (complete and P-limited fertilization). Individual terpene concentrations showed large additive genetic variation, which was more pronounced in the control than in MeJa-induced pines. MeJa application did not affect the LVT concentration, but significantly modified the LVT profile by depleting the α-pinene content and reducing the sesquiterpene fraction. Low P-availability strongly reduced plant growth and foliar nutrient concentrations, but did not affect LVT concentration and profile, and did not interact with MeJa-induction. Results indicate a strong homeostasis of LVT concentration to P-availability, and minor changes in the LVT profile due to MeJa-induction. Genetic variation appears to be the main source of phenotypic variation affecting the LVT concentration in this pine species.
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Affiliation(s)
- Luis Sampedro
- Centro de Investigación Forestal de Lourizán - Unidad Asociada MBG-CSIC, Apdo 127, E-36080 Pontevedra, Galicia, Spain.
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1627
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Allen AR, Minozzi G, Glass EJ, Skuce RA, McDowell SWJ, Woolliams JA, Bishop SC. Bovine tuberculosis: the genetic basis of host susceptibility. Proc Biol Sci 2010; 277:2737-45. [PMID: 20519223 PMCID: PMC2981996 DOI: 10.1098/rspb.2010.0830] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Accepted: 05/13/2010] [Indexed: 01/01/2023] Open
Abstract
The prevalence of bovine tuberculosis (BTB) in the UK remains a significant economic burden and problem for the agri-food industry. Much effort has been directed towards improving diagnostics, finding vaccine candidates and assessing the usefulness of badger culling. The contribution that host genotype makes to disease outcome has, until recently, been overlooked; yet, it is biologically untenable that genetic variation does not play a role. In this review, we highlight the evidence, past and present, for a role of host genetics in determining susceptibility to BTB in livestock. We then address some of the major issues surrounding the design of future studies tasked with finding the exact causative genetic variation underpinning the TB susceptibility phenotype. Finally, we discuss some of the potential future benefits, and problems, that a knowledge of the genetic component to BTB resistance/susceptibility may bring to the agricultural industries and the wider scientific community.
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Affiliation(s)
- A R Allen
- Veterinary Sciences Division, Bacteriology Branch, Agri-Food and Biosciences Institute, Stormont, , Stoney Road, Belfast BT4 3SD, UK.
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1628
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Abstract
An important question for the conservation of species dwelling in fragmented habitats is whether changes to the intervening landscape create a barrier to gene flow. Here, we make use of the spatial distribution of the granite outcrop-dwelling lizard, Ctenophorus ornatus, to compare inferred levels of gene flow between outcrops in a nature reserve with that between outcrops in the adjacent agricultural land. Genetic variation, relatedness and subdivision were compared within groups of individuals from different outcrops similar in size and distance apart at each site. In the agricultural land, we found significantly lower genetic variation within outcrops and greater genetic differentiation between outcrops than in the reserve. Further, the rate at which genetic divergence between outcrops increased over geographical distance was significantly greater in the agricultural land than in the reserve. We also found that individuals were more closely related within outcrops but more distantly related between outcrops in the cleared land. These effects occur over a small spatial scale with an average distance between outcrops of less than five kilometres. Thus, even though land clearing around the outcrops leaves outcrop size unchanged, it restricts gene flow, reducing genetic variation and increasing population structure, with potentially negative consequences for the long-term persistence of the lizards on these outcrops.
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Affiliation(s)
- Esther Levy
- Centre for Evolutionary Biology, School of Animal Biology, The University of Western Australia, M092, 35 Stirling Hwy, Crawley, WA 6009, Australia
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1629
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Polito L, Kehoe PG, Forloni G, Albani D. The molecular genetics of sirtuins: association with human longevity and age-related diseases. Int J Mol Epidemiol Genet 2010; 1:214-225. [PMID: 21537393 PMCID: PMC3076766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Accepted: 06/15/2010] [Indexed: 05/30/2023]
Abstract
The sirtuins are a family of proteins remarkably conserved from yeast to humans. In organisms such as yeast, worms and flies it is quite well established that the activity of sirtuins prolongs lifespan. As a result of promising findings in simple organisms, sirtuins are now investigated in higher organisms in relation to the ageing process. In mammals there are seven different sirtuin proteins each encoded by individual genes (SIRT1-7). Although sirtuins share a highly conserved catalytic domain, they differ in their biological function. Some mammalian sirtuins have been implicated in different ageing pathways and their modulation has been deemed to be beneficial in different models of age-associated diseases. Overall, sirtuins could contribute to mechanisms of human longevity and avoid or delay the onset of age-associated disorders. Here we review and discuss the potential impact of genetic variation in the sirtuin genes in relation to human longevity and age-related diseases.
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Affiliation(s)
- Letizia Polito
- Laboratory of Biology of Neurodegenerative Disorders, Department of Neuroscience, Mario Negri Institute for Pharmacological ResearchMilan, Italy
- Golgi Cenci Research CenterAbbiategrasso, Italy
| | - Patrick G Kehoe
- Dementia Research Group, Institute of Clinical Neurosciences, Department of Clinical Science at North Bristol, University of Bristol, Frenchay HospitalBristol BS16 1LE, UK
| | - Gianluigi Forloni
- Laboratory of Biology of Neurodegenerative Disorders, Department of Neuroscience, Mario Negri Institute for Pharmacological ResearchMilan, Italy
| | - Diego Albani
- Laboratory of Biology of Neurodegenerative Disorders, Department of Neuroscience, Mario Negri Institute for Pharmacological ResearchMilan, Italy
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1630
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Scheinfeldt LB, Soi S, Tishkoff SA. Colloquium paper: working toward a synthesis of archaeological, linguistic, and genetic data for inferring African population history. Proc Natl Acad Sci U S A 2010; 107 Suppl 2:8931-8. [PMID: 20445100 PMCID: PMC3024023 DOI: 10.1073/pnas.1002563107] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although Africa is the origin of modern humans, the pattern and distribution of genetic variation and correlations with cultural and linguistic diversity in Africa have been understudied. Recent advances in genomic technology, however, have led to genomewide studies of African samples. In this article, we discuss genetic variation in African populations contextualized with what is known about archaeological and linguistic variation. What emerges from this review is the importance of using independent lines of evidence in the interpretation of genetic and genomic data in the reconstruction of past population histories.
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Affiliation(s)
| | - Sameer Soi
- Genomics and Computational Biology Graduate Group, and
| | - Sarah A. Tishkoff
- Department of Genetics
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
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1631
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Winston JB, Erlich JM, Green CA, Aluko A, Kaiser KA, Takematsu M, Barlow RS, Sureka AO, LaPage MJ, Janss LL, Jay PY. Heterogeneity of genetic modifiers ensures normal cardiac development. Circulation 2010; 121:1313-21. [PMID: 20212279 PMCID: PMC2953850 DOI: 10.1161/circulationaha.109.887687] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Mutations of the transcription factor Nkx2-5 cause pleiotropic heart defects with incomplete penetrance. This variability suggests that additional factors can affect or prevent the mutant phenotype. We assess here the role of genetic modifiers and their interactions. METHODS AND RESULTS Heterozygous Nkx2-5 knockout mice in the inbred strain background C57Bl/6 frequently have atrial and ventricular septal defects. The incidences are substantially reduced in the Nkx2-5(+/-) progeny of first-generation (F1) outcrosses to the strains FVB/N or A/J. Defects recur in the second generation (F2) of the F1 X F1 intercross or backcrosses to the parental strains. Analysis of >3000 Nkx2-5(+/-) hearts from 5 F2 crosses demonstrates the profound influence of genetic modifiers on disease presentation. On the basis of their incidences and coincidences, anatomically distinct malformations have shared and unique modifiers. All 3 strains carry susceptibility alleles at different loci for atrial and ventricular septal defects. Relative to the other 2 strains, A/J carries polymorphisms that confer greater susceptibility to atrial septal defect and atrioventricular septal defects and C57Bl/6 to muscular ventricular septal defects. Segregation analyses reveal that > or = 2 loci influence membranous ventricular septal defect susceptibility, whereas > or = loci and at least 1 epistatic interaction affect muscular ventricular and atrial septal defects. CONCLUSIONS Alleles of modifier genes can either buffer perturbations on cardiac development or direct the manifestation of a defect. In a genetically heterogeneous population, the predominant effect of modifier genes is health. (Circulation. 2010;121:1313-1321.)
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MESH Headings
- Animals
- Disease Models, Animal
- Female
- Genetic Predisposition to Disease/genetics
- Heart/embryology
- Heart Defects, Congenital/epidemiology
- Heart Defects, Congenital/genetics
- Heart Septal Defects, Atrial/epidemiology
- Heart Septal Defects, Atrial/genetics
- Heart Septal Defects, Ventricular/epidemiology
- Heart Septal Defects, Ventricular/genetics
- Homeobox Protein Nkx-2.5
- Homeodomain Proteins/genetics
- Incidence
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Inbred Strains
- Mice, Knockout
- Mutation/genetics
- Phenotype
- Risk Factors
- Transcription Factors/genetics
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Affiliation(s)
- Julia B Winston
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
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1632
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Peery MZ, Hall LA, Sellas A, Beissinger SR, Moritz C, Bérubé M, Raphael MG, Nelson SK, Golightly RT, McFarlane-Tranquilla L, Newman S, Palsbøll PJ. Genetic analyses of historic and modern marbled murrelets suggest decoupling of migration and gene flow after habitat fragmentation. Proc Biol Sci 2010; 277:697-706. [PMID: 19906669 PMCID: PMC2842750 DOI: 10.1098/rspb.2009.1666] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Accepted: 10/19/2009] [Indexed: 11/12/2022] Open
Abstract
The dispersal of individuals among fragmented populations is generally thought to prevent genetic and demographic isolation, and ultimately reduce extinction risk. In this study, we show that a century of reduction in coastal old-growth forests, as well as a number of other environmental factors, has probably resulted in the genetic divergence of marbled murrelets (Brachyramphus marmoratus) in central California, despite the fact that 7 per cent of modern-sampled murrelets in this population were classified as migrants using genetic assignment tests. Genetic differentiation appears to persist because individuals dispersing from northern populations contributed relatively few young to the central California population, as indicated by the fact that migrants were much less likely to be members of parent-offspring pairs than residents (10.5% versus 45.4%). Moreover, a recent 1.4 per cent annual increase in the proportion of migrants in central California, without appreciable reproduction, may have masked an underlying decline in the resident population without resulting in demographic rescue. Our results emphasize the need to understand the behaviour of migrants and the extent to which they contribute offspring in order to determine whether dispersal results in gene flow and prevents declines in resident populations.
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Affiliation(s)
- M Zachariah Peery
- Department of Forest and Wildlife Ecology, 1630 Linden Drive Madison, University of Wisconsin-Madison, Madison, WI 53706, USA.
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1633
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Abstract
Genome-wide association studies have proven to be a highly successful method for identification of genetic loci for complex phenotypes in both humans and model organisms. These large scale studies rely on the collection of hundreds of thousands of single nucleotide polymorphisms (SNPs) across the genome. Standard high-throughput genotyping technologies capture only a fraction of the total genetic variation. Recent efforts have shown that it is possible to "impute" with high accuracy the genotypes of SNPs that are not collected in the study provided that they are present in a reference data set which contains both SNPs collected in the study as well as other SNPs. We here introduce a novel HMM based technique to solve the imputation problem that addresses several shortcomings of existing methods. First, our method is adaptive which lets it estimate population genetic parameters from the data and be applied to model organisms that have very different evolutionary histories. Compared to previous methods, our method is up to ten times more accurate on model organisms such as mouse. Second, our algorithm scales in memory usage in the number of collected markers as opposed to the number of known SNPs. This issue is very relevant due to the size of the reference data sets currently being generated. We compare our method over mouse and human data sets to existing methods, and show that each has either comparable or better performance and much lower memory usage. The method is available for download at http://genetics.cs.ucla.edu/eminim.
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Affiliation(s)
- Hyun Min Kang
- Biostatistics Department, University of Michigan, Ann Arbor, Ann Arbor, Michigan
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Ann Arbor, Michigan
| | - Noah A. Zaitlen
- Bioinformatics Program, University of California, San Diego, La Jolla, California
| | - Eleazar Eskin
- Departments of Computer Science and Human Genetics, University of California, Los Angeles, Los Angeles, California
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1634
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Raduski AR, Rieseberg LH, Strasburg JL. Effective population size, gene flow, and species status in a narrow endemic sunflower, Helianthus neglectus, compared to its widespread sister species, H. petiolaris. Int J Mol Sci 2010; 11:492-506. [PMID: 20386650 PMCID: PMC2852850 DOI: 10.3390/ijms11020492] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Revised: 01/17/2010] [Accepted: 01/21/2010] [Indexed: 11/16/2022] Open
Abstract
Species delimitation has long been a difficult and controversial process, and different operational criteria often lead to different results. In particular, investigators using phenotypic vs. molecular data to delineate species may recognize different boundaries, especially if morphologically or ecologically differentiated populations have only recently diverged. Here we examine the genetic relationship between the widespread sunflower species Helianthus petiolaris and its narrowly distributed sand dune endemic sister species H. neglectus using sequence data from nine nuclear loci. The two species were initially described as distinct based on a number of minor morphological differences, somewhat different ecological tolerances, and at least one chromosomal rearrangement distinguishing them; but detailed molecular data has not been available until now. We find that, consistent with previous work, H. petiolaris is exceptionally genetically diverse. Surprisingly, H. neglectus harbors very similar levels of genetic diversity (average diversity across loci is actually slightly higher in H. neglectus). It is extremely unlikely that such a geographically restricted species could maintain these levels of genetic variation in isolation. In addition, the two species show very little evidence of any genetic divergence, and estimates of interspecific gene flow are comparable to gene flow estimates among regions within H. petiolaris. These results indicate that H. petiolaris and H. neglectus likely do not represent two distinct, isolated gene pools; H. neglectus is probably more accurately thought of as a geographically restricted, morphologically and ecologically distinct subspecies of H. petiolaris rather than a separate species.
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Affiliation(s)
- Andrew R. Raduski
- Department of Biology, Indiana University, Bloomington, IN 47405, USA; E-Mail:
| | - Loren H. Rieseberg
- Department of Botany, University of British Columbia, Vancouver, B.C. V6T 1Z4, Canada; E-Mail:
| | - Jared L. Strasburg
- Department of Biology, Indiana University, Bloomington, IN 47405, USA; E-Mail:
- Author to whom correspondence should be addressed; E-Mail:
; Tel.: +1-812-855-9018; Fax: +1-812-855-6705
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1635
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Agalliu I, Kwon EM, Salinas CA, Koopmeiners JS, Ostrander EA, Stanford JL. Genetic variation in DNA repair genes and prostate cancer risk: results from a population-based study. Cancer Causes Control 2010; 21:289-300. [PMID: 19902366 PMCID: PMC2811225 DOI: 10.1007/s10552-009-9461-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Accepted: 10/22/2009] [Indexed: 01/07/2023]
Abstract
OBJECTIVE DNA repair pathways are crucial to prevent accumulation of DNA damage and maintain genomic stability. Alterations of this pathway have been reported in many cancers. An increase in oxidative DNA damage or decrease in DNA repair capacity with aging or due to germline genetic variation may affect prostate cancer risk. METHODS Pooled data from two population-based studies (1,457 cases and 1,351 controls) were analyzed to examine associations between 28 single-nucleotide polymorphisms (SNPs) in nine DNA repair genes (APEX1, BRCA2, ERCC2, ERCC4, MGMT, MUTYH, OGG1, XPC, and XRCC1) and prostate cancer risk. We also explored whether associations varied by smoking, by family history or clinical features of prostate cancer. RESULTS There were no associations between these SNPs and overall risk of prostate cancer. Risks by genotype also did not vary by smoking or by family history of prostate cancer. Although two SNPs in BRCA2 (rs144848, rs1801406) and two SNPs in ERCC2 (rs1799793, rs13181) showed stronger associations with high Gleason score or advanced-stage tumors when comparing homozygous men carrying the minor versus major allele, results were not statistically significantly different between clinically aggressive and non-aggressive tumors. CONCLUSION Overall, this study found no associations between prostate cancer and the SNPs in DNA repair genes. Given the complexity of this pathway and its crucial role in maintenance of genomic stability, a pathway-based analysis of all 150 genes in DNA repair pathways, as well as exploration of gene-environment interactions may be warranted.
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Affiliation(s)
- Ilir Agalliu
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA.
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1636
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Kanojia PC, Paingankar MS, Patil AA, Gokhale MD, Deobagkar DN. Morphometric and allozyme variation in Culex tritaeniorhynchus mosquito populations from India. J Insect Sci 2010; 10:138. [PMID: 20883134 PMCID: PMC3388975 DOI: 10.1673/031.010.13801] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2008] [Accepted: 10/21/2009] [Indexed: 05/29/2023]
Abstract
Four populations of Culex tritaeniorhynchus (Giles) (Diptera: Culicidae), collected from Bellary, Cuddalore, Pune, and the Microbial Containment Complex laboratory culture in India were analyzed for morphological and allozyme variation. Multivariate analysis based on eight morphological characteristics and three morphometric indices was used to investigate the morphological variations among the four populations. Principal component analysis of the data suggested that siphon, saddle, and anal gills related variables were most important. Discriminant factor analysis of morphological data revealed that the four populations form significantly different clusters which can be differentiated from each other based on siphon, saddle, and pectin teeth related variables. Allozyme electrophoresis of the four populations revealed that the mean heterozygosity per locus value had high variation, ranging from 0.0879 to 1.794. Fst values between 0 and 0.519 suggested genetic differentiation within these populations. Fis values ranged from 0 to 1 with most of the values closer to 1. The allelic frequencies and Nei's genetic identity values showed that genetic differences between populations were small, but significant. Some of the morphological and allozyme variations in the Cx. tritaeniorhynchus populations could be partly attributed to the environmental conditions. The findings suggested that transition of morphological characters and allozyme variations in Cx. tritaeniorhynchus populations seem to be consequences of influence and selection by the environmental conditions. These results indicated that populations of Cx. tritaeniorhynchus in non-endemic areas of Japanese encephalitis (JE) virus infection have higher adaptability as compared to endemic areas of JE infection.
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Affiliation(s)
- Phul Chand Kanojia
- Department of Medical Entomology and Zoology, National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune 411001, India
| | - Mandar S. Paingankar
- Molecular Biology Research Laboratory, Department of Zoology, University of Pune, Pune 411007, India
| | - Avinash A. Patil
- Department of Medical Entomology and Zoology, National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune 411001, India
| | - Mangesh D. Gokhale
- Department of Medical Entomology and Zoology, National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune 411001, India
| | - Dileep N. Deobagkar
- Molecular Biology Research Laboratory, Department of Zoology, University of Pune, Pune 411007, India
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1637
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Downie DA. Baubles, bangles, and biotypes: a critical review of the use and abuse of the biotype concept. J Insect Sci 2010; 10:176. [PMID: 21062149 PMCID: PMC3016951 DOI: 10.1673/031.010.14136] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Accepted: 05/28/2010] [Indexed: 05/26/2023]
Abstract
Pest species of insects are notoriously prone to escape the weapons deployed in management efforts against them. This is particularly true in herbivorous insects. When a previously successful tactic fails the insect population has apparently adapted to it and is often considered to be a new or distinct entity, and given the non-formal category 'biotype'. The entities falling under the umbrella term 'biotype' are not consistent either within or between biotypes, and their underlying genetic composition and origins, while generally unknown, are likely heterogeneous within and variable between biotypes. In some cases race or species may be more appropriate referents. Some examples of applications of the concept in the context of host plant resistance are discussed. It is argued here that the term 'biotype' and its applications are overly simplistic, confused, have not proved useful in current pest management, and lack predictive power for future management.
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Affiliation(s)
- D A Downie
- Department of Zoology and Entomology, Rhodes University, Grahamstown, 6140 South Africa.
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1638
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Small HJ, Shields JD, Haas LW, Vogelbein WK, Moss J, Reece KS. GENETIC VARIATION AMONG STRAINS OF PSEUDOPFIESTERIA SHUMWAYAE AND PFIESTERIA PISCICIDA (DINOPHYCEAE)(1). J Phycol 2009; 45:1315-1322. [PMID: 27032589 DOI: 10.1111/j.1529-8817.2009.00754.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The putatively toxic dinoflagellates Pseudopfiesteria shumwayae (Glasgow et J. M. Burkh.) Litaker, Steid., P. L. Mason, Shields et P. A. Tester and Pfiesteria piscicida Steid. et J. M. Burkh. have been implicated in massive fish kills and of having negative impacts on human health along the mid-Atlantic seaboard of the USA. Considerable debate still remains as to the mechanisms responsible for fish mortality (toxicity vs. micropredation) caused by these dinoflagellates. Genetic differences among these cultures have not been adequately investigated and may account for or correlate with phenotypic variability among strains within each species. Genetic variation among strains of Ps. shumwayae and P. piscicida was examined by PCR-RFLP analysis using cultures obtained from the Provasoli-Guillard National Center for Culture of Marine Phytoplankton (CCMP), as well as those from our own and other colleagues' collection efforts. Examination of restriction digest banding profiles for 22 strains of Ps. shumwayae revealed the presence of 10 polymorphic restriction endonuclease sites within the first and second internal transcribed spacers (ITS1 and ITS2) and the 5.8S gene of the rDNA complex, and the cytochrome oxidase subunit I (COI) gene. Three compound genotypes were represented within the 22 Ps. shumwayae strains. Conversely, PCR-RFLP examination of 14 strains of P. piscicida at the same ITS1, 5.8S, and ITS2 regions revealed only one variable restriction endonuclease site, located in the ITS1 region. In addition, a dinoflagellate culture listed as P. piscicida (CCMP 1928) and analyzed as part of this study was identified as closely related to Luciella masanensis P. L. Mason, H. J. Jeong, Litaker, Reece et Steid.
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Affiliation(s)
- Hamish J Small
- Department of Environmental & Aquatic Animal Health, Virginia Institute of Marine Science, The College of William and Mary, P.O. Box 1346, Gloucester Point, Virginia, 23062-1346, USA
| | - Jeffrey D Shields
- Department of Environmental & Aquatic Animal Health, Virginia Institute of Marine Science, The College of William and Mary, P.O. Box 1346, Gloucester Point, Virginia, 23062-1346, USA
| | - Leonard W Haas
- Department of Environmental & Aquatic Animal Health, Virginia Institute of Marine Science, The College of William and Mary, P.O. Box 1346, Gloucester Point, Virginia, 23062-1346, USA
| | - Wolfgang K Vogelbein
- Department of Environmental & Aquatic Animal Health, Virginia Institute of Marine Science, The College of William and Mary, P.O. Box 1346, Gloucester Point, Virginia, 23062-1346, USA
| | - Jessica Moss
- Department of Environmental & Aquatic Animal Health, Virginia Institute of Marine Science, The College of William and Mary, P.O. Box 1346, Gloucester Point, Virginia, 23062-1346, USA
| | - Kimberly S Reece
- Department of Environmental & Aquatic Animal Health, Virginia Institute of Marine Science, The College of William and Mary, P.O. Box 1346, Gloucester Point, Virginia, 23062-1346, USA
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1639
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Flatt T, Schmidt PS. Integrating evolutionary and molecular genetics of aging. Biochim Biophys Acta 2009; 1790:951-62. [PMID: 19619612 PMCID: PMC2972575 DOI: 10.1016/j.bbagen.2009.07.010] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2009] [Revised: 07/07/2009] [Accepted: 07/10/2009] [Indexed: 12/25/2022]
Abstract
Aging or senescence is an age-dependent decline in physiological function, demographically manifest as decreased survival and fecundity with increasing age. Since aging is disadvantageous it should not evolve by natural selection. So why do organisms age and die? In the 1940s and 1950s evolutionary geneticists resolved this paradox by positing that aging evolves because selection is inefficient at maintaining function late in life. By the 1980s and 1990s this evolutionary theory of aging had received firm empirical support, but little was known about the mechanisms of aging. Around the same time biologists began to apply the tools of molecular genetics to aging and successfully identified mutations that affect longevity. Today, the molecular genetics of aging is a burgeoning field, but progress in evolutionary genetics of aging has largely stalled. Here we argue that some of the most exciting and unresolved questions about aging require an integration of molecular and evolutionary approaches. Is aging a universal process? Why do species age at different rates? Are the mechanisms of aging conserved or lineage-specific? Are longevity genes identified in the laboratory under selection in natural populations? What is the genetic basis of plasticity in aging in response to environmental cues and is this plasticity adaptive? What are the mechanisms underlying trade-offs between early fitness traits and life span? To answer these questions evolutionary biologists must adopt the tools of molecular biology, while molecular biologists must put their experiments into an evolutionary framework. The time is ripe for a synthesis of molecular biogerontology and the evolutionary biology of aging.
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Affiliation(s)
- Thomas Flatt
- Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Josef Baumann Gasse 1, A-1210 Wien, Austria
| | - Paul S. Schmidt
- University of Pennsylvania, Department of Biology, 433 South University Avenue, Philadelphia, PA 19104-6018, USA.
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1640
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Tung J, Fédrigo O, Haygood R, Mukherjee S, Wray GA. Genomic features that predict allelic imbalance in humans suggest patterns of constraint on gene expression variation. Mol Biol Evol 2009; 26:2047-59. [PMID: 19506001 PMCID: PMC2734157 DOI: 10.1093/molbev/msp113] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2009] [Indexed: 12/29/2022] Open
Abstract
Variation in gene expression is an important contributor to phenotypic diversity within and between species. Although this variation often has a genetic component, identification of the genetic variants driving this relationship remains challenging. In particular, measurements of gene expression usually do not reveal whether the genetic basis for any observed variation lies in cis or in trans to the gene, a distinction that has direct relevance to the physical location of the underlying genetic variant, and which may also impact its evolutionary trajectory. Allelic imbalance measurements identify cis-acting genetic effects by assaying the relative contribution of the two alleles of a cis-regulatory region to gene expression within individuals. Identification of patterns that predict commonly imbalanced genes could therefore serve as a useful tool and also shed light on the evolution of cis-regulatory variation itself. Here, we show that sequence motifs, polymorphism levels, and divergence levels around a gene can be used to predict commonly imbalanced genes in a human data set. Reduction of this feature set to four factors revealed that only one factor significantly differentiated between commonly imbalanced and nonimbalanced genes. We demonstrate that these results are consistent between the original data set and a second published data set in humans obtained using different technical and statistical methods. Finally, we show that variation in the single allelic imbalance-associated factor is partially explained by the density of genes in the region of a target gene (allelic imbalance is less probable for genes in gene-dense regions), and, to a lesser extent, the evenness of expression of the gene across tissues and the magnitude of negative selection on putative regulatory regions of the gene. These results suggest that the genomic distribution of functional cis-regulatory variants in the human genome is nonrandom, perhaps due to local differences in evolutionary constraint.
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Affiliation(s)
- Jenny Tung
- Department of Biology, Duke University, Durham, NC, USA.
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1641
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Agola LE, Steinauer ML, Mburu DN, Mungai BN, Mwangi IN, Magoma GN, Loker ES, Mkoji GM. Genetic diversity and population structure of Schistosoma mansoni within human infrapopulations in Mwea, central Kenya assessed by microsatellite markers. Acta Trop 2009; 111:219-25. [PMID: 19427295 PMCID: PMC2763435 DOI: 10.1016/j.actatropica.2009.04.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Revised: 04/20/2009] [Accepted: 04/29/2009] [Indexed: 10/20/2022]
Abstract
A recently developed high-throughput technique that allows multi-locus microsatellite analysis of individual miracidia of Schistosoma mansoni was used to assess the levels of genetic diversity and population structure in 12 infrapopulations of the parasite, each infrapopulation derived from an infected school child from the Mwea area, central Kenya. The mean number of alleles per locus was in the range 8.22-10.22, expected heterozygosity in Hardy-Weinberg equilibrium was 0.68-0.70, and pairwise F(ST) values ranged from 0.16% to 3.98% for the 12 infrapopulations. Although the genetic diversity within each infrapopulation of S. mansoni in this area was generally high, low levels of genetic structure were observed, suggestive of high levels of gene flow among infrapopulations. Private alleles were found in 8 of the 12 infrapopulation, the highest number of private alleles recorded per infrapopulation was 3. Our data suggest that the level of gene flow among infrapopulations of S. mansoni in Mwea is extremely high, thus providing opportunity for spread of rare alleles, including those that may confer character traits such as drug resistance and virulence.
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Affiliation(s)
- L E Agola
- Centre for Biotechnology Research and Development, Kenya Medical Research Institute, P.O. Box 54840-00200, Nairobi, Kenya.
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1642
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Hogan KJ, Burmester JK, Caldwell MD, Hogan QH, Coursin DB, Green DN, Selzer RMR, Broderick TP, Rusy DA, Poroli M, Lutz AL, Sanders AM, Oldenburg MC, Koelbl JA, de Arruda-Indig M, Halsey JL, Day SP, Domanico MJ. Perioperative genomic profiles using structure-specific oligonucleotide probes. Clin Med Res 2009; 7:69-84. [PMID: 19474452 PMCID: PMC2757430 DOI: 10.3121/cmr.2009.837] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
OBJECTIVES Many complications in the perioperative interval are associated with genetic susceptibilities that may be unknown in advance of surgery and anesthesia, including drug toxicity and inefficacy, thrombosis, prolonged neuromuscular blockade, organ failure and sepsis. The aims of this study were to design and validate the first genetic testing platform and panel designed for use in perioperative care, to establish allele frequencies in a target population, and to determine the number of mutant alleles per patient undergoing surgery. DESIGN/SETTING/PARTICIPANTS AND METHODS: One hundred fifty patients at Marshfield Clinic, Marshfield, Wisconsin, 100 patients at the Medical College of Wisconsin Zablocki Veteran's Administration Medical Center, Milwaukee, Wisconsin, and 200 patients at the University of Wisconsin Hospitals and Clinics, Madison, Wisconsin undergoing surgery and anesthesia were tested for 48 polymorphisms in 22 genes including ABC, BChE, ACE, CYP2C9, CYP2C19, CYP2D6, CYP3A4, CYP3A5, beta2AR, TPMT, F2, F5, F7, MTHFR, TNFalpha, TNFbeta, CCR5, ApoE, HBB, MYH7, ABO and Gender (PRKY, PFKFB1). Using structure-specific cleavage of oligonucleotide probes (Invader, Third Wave Technologies, Inc., Madison, WI), 96-well plates were configured so that each well contained reagents for detection of both the wild type and mutant alleles at each locus. RESULTS There were 21,600 genotypes confirmed in duplicate. After withdrawal of polymorphisms in non-pathogenic genes (i.e., the ABO blood group and gender-specific alleles), 376 of 450 patients were found to be homozygous for mutant alleles at one or more loci. Modes of two mutant homozygous loci and 10 mutant alleles in aggregate (i.e., the sum of homozygous and heterozygous mutant polymorphisms) were observed per patient. CONCLUSIONS Significant genetic heterogeneity that may not be accounted for by taking a family medical history, or by obtaining routine laboratory test results, is present in most patients presenting for surgery and may be detected using a newly developed genotyping platform.
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Affiliation(s)
- Kirk J Hogan
- Department of Anesthesiology, University of Wisconsin School of Medicine and Public Health, B6/319 Clinical Sciences Center, 600 Highland Avenue, Madison, WI 53792, USA.
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1643
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Abstract
Hepatitis C virus (HCV) infections are treated with interferon alpha plus ribavirin, but it is unknown how ribavirin works against HCV. Ribavirin is a guanosine analogue that can be a substrate for the viral RNA polymerase. HCV is genetically variable, and this genetic variation could affect the polymerase's use of ribavirin triphosphate. Thirteen patients infected with HCV who failed interferon alpha monotherapy and were retreated with interferon alpha plus ribavirin were identified; seven were responders and six were nonresponders to combination therapy. The consensus sequences encoding the 13 polymerases plus seven sequences from treatment-naive controls were determined. The responder sequences were more genetically variable than the nonresponders and controls, the amino acid variations unique to responders had lower BLOSUM90 scores than variations in nonresponders and controls, and the amino acid variations correlated with response to therapy clustered around the RNA-binding channel of the polymerase. These data imply that that the responder enzymes were probably more functionally variable than the nonresponder enzymes. Enzymatic activity was measured for 10 recombinant polymerases; RNA synthesis activity varied by over sevenfold and polymerases from two of the responders used GTP much better than UTP, but technical limitations prevented direct measurement of ribavirin triphosphate use. Because response to combination therapy in these patients was primarily due to addition of ribavirin to the treatment regimen, these data imply that genetic variation in the polymerase may have affected the efficiency of ribavirin incorporation into the viral genome and hence may have modulated ribavirin's efficacy against HCV.
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Affiliation(s)
- Nathan A. Cannon
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine
| | - Maureen J. Donlin
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine
| | - Lisa M. Mayes
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine
| | - Andre C. Lyra
- Division of Gastroenterology and Hepatology, Saint Louis University School of Medicine
| | - Adrian M. Di Bisceglie
- Division of Gastroenterology and Hepatology, Saint Louis University School of Medicine,Saint Louis University Liver Center, Saint Louis University School of Medicine
| | - John E. Tavis
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine,Saint Louis University Liver Center, Saint Louis University School of Medicine
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1644
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Abstract
Coronary heart disease (CHD) is a complex disease that is affected by environmental as well as genetic factors. Research is ongoing that probes the relationship of human genetic variation to disease, potentially leading to better diagnosis and therapy. Variation in factors such as low-density lipoprotein cholesterol, apolipoprotein E, high-density lipoprotein cholesterol, apolipoprotein A-I/CIII/A-IV, lipoprotein lipase, cholesteryl ester transfer protein, lipoprotein (a), and homocysteine may affect CHD risk via genetic or environmental mechanisms or their interactions.
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Affiliation(s)
- J L Breslow
- Rockefeller University, Laboratory of Biochemical Genetics and Metabolism, New York, New York 10021, USA.
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1645
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Ren X, Yin J, Ma D, Li G. Characterization and membrane gene-based phylogenetic analysis of avian infectious bronchitis virus Chinese strain HH06. Virus Genes 2009; 38:39-45. [PMID: 18792774 PMCID: PMC7089277 DOI: 10.1007/s11262-008-0280-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Accepted: 08/19/2008] [Indexed: 11/10/2022]
Abstract
A Chinese isolate of avian infectious bronchitis virus (IBV) designated HH06 was isolated from the kidney tissues of a chicken flock experiencing an outbreak of nephritis. In vivo pathogenicity of the IBV isolate HH06 was determined by inoculating specific pathogen-free (SPF) chickens. The clinical signs and related gross lesions of HH06 infected chickens were similar with those of the field-infected chickens. SPF embryonated eggs were inoculated with virus suspension for serial passage and their genomic RNA was extracted. RT-PCR technique was utilized to amplify the M gene sequence encoding membrane protein of IBV. Recombinant plasmid named T-vector-M was constructed via inserting the M gene into the TA cloning vector, pMD 18-T. The sequenced M gene and its deduced amino acid (aa) sequences were compared with the published sequences of reference strains. The M gene is of 687 bp in length encoding the M protein of 228 amino acids with a predicted molecular weight of 25.4 kDa. The sequences of the M gene and M protein share 83.9-97.9% and 83.6-96.5% homologous identities, respectively, compared with 29 IBV reference strains derived from different regions or countries, which revealed that there are still significant variations between strains. Furthermore, a phylogenetic tree based on these M DNA sequences was generated, and the tree topology suggests that some Chinese IBV strains may have a common ancestor; however, HH06 is a new local IBV isolate that is responsible for the field outbreak of nephritis.
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Affiliation(s)
- Xiaofeng Ren
- College of Veterinary Medicine, Northeast Agricultural University, 59 Mucai Street, 150030 Harbin, People’s Republic of China
| | - Jiechao Yin
- College of Life Sciences, Northeast Agricultural University, 59 Mucai Street, 150030 Harbin, People’s Republic of China
| | - Dexing Ma
- College of Veterinary Medicine, Northeast Agricultural University, 59 Mucai Street, 150030 Harbin, People’s Republic of China
| | - Guangxing Li
- College of Veterinary Medicine, Northeast Agricultural University, 59 Mucai Street, 150030 Harbin, People’s Republic of China
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1646
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Rahman SMZ, Khan MR, Islam S, Alam S. Genetic variation of wild and hatchery populations of the catla Indian major carp (Catla catla Hamilton 1822: Cypriniformes, Cyprinidae) revealed by RAPD markers. Genet Mol Biol 2009; 32:197-201. [PMID: 21637668 PMCID: PMC3032962 DOI: 10.1590/s1415-47572009005000013] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Accepted: 07/03/2008] [Indexed: 11/30/2022] Open
Abstract
Genetic variation is a key component for improving a stock through selective breeding programs. Randomly amplified polymorphic DNA (RAPD) markers were used to assess genetic variation in three wild population of the catla carp (Catla catla Hamilton 1822) in the Halda, Jamuna and Padma rivers and one hatchery population in Bangladesh. Five decamer random primers were used to amplify RAPD markers from 30 fish from each population. Thirty of the 55 scorable bands were polymorphic, indicating some degree of genetic variation in all the populations. The proportion of polymorphic loci and gene diversity values reflected a relatively higher level of genetic variation in the Halda population. Sixteen of the 30 polymorphic loci showed a significant (p < 0.05, p < 0.01, p < 0.001) departure from homogeneity and the F(ST) values in the different populations indicated some degree of genetic differentiation in the population pairs. Estimated genetic distances between populations were directly correlated with geographical distances. The unweighted pair group method with averages (UPGMA) dendrogram showed two clusters, the Halda population forming one cluster and the other populations the second cluster. Genetic variation of C. catla is a useful trait for developing a good management strategy for maintaining genetic quality of the species.
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Affiliation(s)
- S M Zakiur Rahman
- Department of Biotechnology, Bangladesh Agricultural University, Mymensingh Bangladesh
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1647
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Mellman TA, Alim T, Brown DD, Gorodetsky E, Buzas B, Lawson WB, Goldman D, Charney DS. Serotonin polymorphisms and posttraumatic stress disorder in a trauma exposed African American population. Depress Anxiety 2009; 26:993-7. [PMID: 19842167 PMCID: PMC2963151 DOI: 10.1002/da.20627] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Genetic polymorphisms that influence serotonin (5-hydroxytryptamine, 5HT) neurotransmission are candidates for contributing to susceptibility to posttraumatic stress disorder (PTSD). The objective of our study was to determine if a variable length polymorphism for the promoter regions of the 5HT transporter (5HTTLPR), and/or a substitution polymorphism in the promoter region for the 5HT2A receptor, would be associated with PTSD in a trauma exposed population of adult African-Americans. METHODS Using a case control design, 118 participants recruited from the primary care clinics and the campus of a historically black university who met inclusion criteria including trauma exposure provided blood samples for genomic DNA. PTSD criteria were determined by the Clinician Assessment of PTSD Scale (CAPS) and criteria for other psychiatric disorders by the Structured Clinical Interview for DSM-IV (SCID). 5HTTLPR and 5HT2A-1438A/G were genotyped using established methods. Associations of genotypes with lifetime PTSD, and models testing associations of allele "dose", were analyzed. RESULTS Fifty-five (47%) participants met lifetime criteria for PTSD and 26 (22%) met criteria for (mostly comorbid) major depression. The 5HT2A (lower expressing) G allele was significantly associated with PTSD. We did not find significant associations with 5HTTLPR. CONCLUSIONS Our findings suggest a relationship between genetic variation in the 5HT2A promoter region and PTSD.
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Affiliation(s)
- Thomas A. Mellman
- Howard University College of Medicine, Department of Psychiatry, Washington, District of Columbia,Correspondence to: Thomas A. Mellman, Department of Psychiatry, Howard University Hospital, 2041 Georgia Ave., Washington, DC 20060.
| | - Tanya Alim
- Howard University College of Medicine, Department of Psychiatry, Washington, District of Columbia
| | - Denver D. Brown
- Howard University College of Medicine, Department of Psychiatry, Washington, District of Columbia
| | - Elena Gorodetsky
- Laboratory of Neurogenetics, National Institute of Alcohol Abuse and Alcoholism, National Institute of Health, Bethesda, Maryland
| | - Beata Buzas
- Laboratory of Neurogenetics, National Institute of Alcohol Abuse and Alcoholism, National Institute of Health, Bethesda, Maryland
| | - William B. Lawson
- Howard University College of Medicine, Department of Psychiatry, Washington, District of Columbia
| | - David Goldman
- Laboratory of Neurogenetics, National Institute of Alcohol Abuse and Alcoholism, National Institute of Health, Bethesda, Maryland
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1648
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Williams RN, Bos DH, Gopurenko D, Dewoody JA. Amphibian malformations and inbreeding. Biol Lett 2008; 4:549-52. [PMID: 18593670 PMCID: PMC2610075 DOI: 10.1098/rsbl.2008.0233] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2008] [Revised: 06/03/2008] [Accepted: 06/10/2008] [Indexed: 11/12/2022] Open
Abstract
Inbreeding may lead to morphological malformations in a wide variety of taxa. We used genetic markers to evaluate whether malformed urodeles were more inbred and/or had less genetic diversity than normal salamanders. We captured 687 adult and 1,259 larval tiger salamanders (Ambystoma tigrinum tigrinum), assessed each individual for gross malformations, and surveyed genetic variation among malformed and normal individuals using both cytoplasmic and nuclear markers. The most common malformations in both adults and larvae were brachydactyly, ectrodactyly and polyphalangy. The overall frequency of adults with malformations was 0.078 compared to 0.081 in larval samples. Genetic diversity was high in both normal and malformed salamanders, and there were no significant difference in measures of inbreeding (f and F), allele frequencies, mean individual heterozygosity or mean internal relatedness. Environmental contaminants or other extrinsic factors may lead to genome alternations that ultimately cause malformations, but our data indicate that inbreeding is not a causal mechanism.
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Affiliation(s)
- Rod N Williams
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907, USA.
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1649
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Abstract
Is genetic evolution predictable? Evolutionary developmental biologists have argued that, at least for morphological traits, the answer is a resounding yes. Most mutations causing morphological variation are expected to reside in the cis-regulatory, rather than the coding, regions of developmental genes. This "cis-regulatory hypothesis" has recently come under attack. In this review, we first describe and critique the arguments that have been proposed in support of the cis-regulatory hypothesis. We then test the empirical support for the cis-regulatory hypothesis with a comprehensive survey of mutations responsible for phenotypic evolution in multicellular organisms. Cis-regulatory mutations currently represent approximately 22% of 331 identified genetic changes although the number of cis-regulatory changes published annually is rapidly increasing. Above the species level, cis-regulatory mutations altering morphology are more common than coding changes. Also, above the species level cis-regulatory mutations predominate for genes not involved in terminal differentiation. These patterns imply that the simple question "Do coding or cis-regulatory mutations cause more phenotypic evolution?" hides more interesting phenomena. Evolution in different kinds of populations and over different durations may result in selection of different kinds of mutations. Predicting the genetic basis of evolution requires a comprehensive synthesis of molecular developmental biology and population genetics.
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Affiliation(s)
- David L Stern
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544, USA.
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1650
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Roscher C, Schumacher J, Weisser WW, Schulze ED. Genetic identity affects performance of species in grasslands of different plant diversity: an experiment with Lolium perenne cultivars. Ann Bot 2008; 102:113-25. [PMID: 18463110 PMCID: PMC2712428 DOI: 10.1093/aob/mcn070] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2008] [Revised: 03/04/2008] [Accepted: 04/08/2008] [Indexed: 05/21/2023]
Abstract
BACKGROUND AND AIMS Recent biodiversity research has focused on ecosystem processes, but less is known about responses of populations of individual plant species to changing community diversity and implications of genetic variation within species. To address these issues, effects of plant community diversity on the performance of different cultivars of Lolium perenne were analysed. METHODS Populations of 15 genetic cultivars of Lolium perenne were established in experimental grasslands varying in richness of species (from 1 to 60) and functional groups (from 1 to 4). Population sizes, mean size of individual plants, biomass of individual shoots and seed production were measured in the first and second growing season after establishment. KEY RESULTS Population sizes of all cultivars decreased with increasing community species richness. Plant individuals formed fewer shoots with a lower shoot mass in more species-rich plant communities. A large proportion of variation in plant size and relative population growth was attributable to effects of community species and functional group richness, but the inclusion of cultivar identity explained additional 4-7 % of variation. Cultivar identity explained most variation (28-51 %) at the shoot level (biomass of individual tillers and reproductive shoots, seed production, heading stage). Coefficients of variation of the measured variables across plant communities were larger in cultivars with a lower average performance, indicating that this variation was predominantly due to passive growth reductions and not a consequence of larger adaptive plastic responses. No single cultivar performed best in all communities. CONCLUSIONS The decreasing performance of Lolium perenne in plant communities of increasing species richness suggests a regulation of competitive interactions by species diversity. Genetic variation within species provides a base for larger phenotypic variation and may affect competitive ability. However, heterogeneous biotic environments (= plant communities of different species composition) are important for the maintenance of intra-specific genetic variation.
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Affiliation(s)
- Christiane Roscher
- Institute of Ecology, Friedrich Schiller University Jena, Dornburger Strasse 159, D-07743 Jena, Germany.
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