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Sample records for genetically distinct environment

  1. Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies.

    Science.gov (United States)

    Sandberg, Troy E; Lloyd, Colton J; Palsson, Bernhard O; Feist, Adam M

    2017-07-01

    Adaptive laboratory evolution (ALE) experiments are often designed to maintain a static culturing environment to minimize confounding variables that could influence the adaptive process, but dynamic nutrient conditions occur frequently in natural and bioprocessing settings. To study the nature of carbon substrate fitness tradeoffs, we evolved batch cultures of Escherichia coli via serial propagation into tubes alternating between glucose and either xylose, glycerol, or acetate. Genome sequencing of evolved cultures revealed several genetic changes preferentially selected for under dynamic conditions and different adaptation strategies depending on the substrates being switched between; in some environments, a persistent "generalist" strain developed, while in another, two "specialist" subpopulations arose that alternated dominance. Diauxic lag phenotype varied across the generalists and specialists, in one case being completely abolished, while gene expression data distinguished the transcriptional strategies implemented by strains in pursuit of growth optimality. Genome-scale metabolic modeling techniques were then used to help explain the inherent substrate differences giving rise to the observed distinct adaptive strategies. This study gives insight into the population dynamics of adaptation in an alternating environment and into the underlying metabolic and genetic mechanisms. Furthermore, ALE-generated optimized strains have phenotypes with potential industrial bioprocessing applications. IMPORTANCE Evolution and natural selection inexorably lead to an organism's improved fitness in a given environment, whether in a laboratory or natural setting. However, despite the frequent natural occurrence of complex and dynamic growth environments, laboratory evolution experiments typically maintain simple, static culturing environments so as to reduce selection pressure complexity. In this study, we investigated the adaptive strategies underlying evolution to

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

    Science.gov (United States)

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

    2008-07-29

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

  3. Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies

    DEFF Research Database (Denmark)

    Sandberg, Troy E.; Lloyd, Colton J.; Palsson, Bernhard O.

    2017-01-01

    and specialists, in one case being completely abolished, while gene expression data distinguished the transcriptional strategies implemented by strains in pursuit of growth optimality. Genome-scale metabolic modeling techniques were then used to help explain the inherent substrate differences giving rise...... applications.IMPORTANCE Evolution and natural selection inexorably lead to an organism's improved fitness in a given environment, whether in a laboratory or natural setting. However, despite the frequent natural occurrence of complex and dynamic growth environments, laboratory evolution experiments typically...... of evolved strains via a number of different data types revealed the various genetic and phenotypic changes implemented in pursuit of growth optimality and how these differed across the different growth substrates and switching protocols. This work not only helps to establish general principles of adaptation...

  4. Different genotypes of Trypanosoma cruzi produce distinctive placental environment genetic response in chronic experimental infection

    Science.gov (United States)

    Juiz, Natalia Anahí; Solana, María Elisa; Acevedo, Gonzalo Raúl; Benatar, Alejandro Francisco; Ramirez, Juan Carlos; da Costa, Priscilla Almeida; Macedo, Andrea Mara; Longhi, Silvia Andrea

    2017-01-01

    Congenital infection of Trypanosoma cruzi allows transmission of this parasite through generations. Despite the problematic that this entails, little is known about the placenta environment genetic response produced against infection. We performed functional genomics by microarray analysis in C57Bl/6J mice comparing placentas from uninfected animals and from animals infected with two different T. cruzi strains: K98, a clone of the non-lethal myotropic CA-I strain (TcI), and VD (TcVI), isolated from a human case of congenital infection. Analysis of networks by GeneMANIA of differentially expressed genes showed that “Secretory Granule” was a pathway down-regulated in both infected groups, whereas “Innate Immune Response” and “Response to Interferon-gamma” were pathways up-regulated in VD infection but not in K98. Applying another approach, the GSEA algorithm that detects small changes in predetermined gene sets, we found that metabolic processes, transcription and macromolecular transport were down-regulated in infected placentas environment and some pathways related to cascade signaling had opposite regulation: over-represented in VD and down-regulated in K98 group. We also have found a stronger tropism to the placental organ by VD strain, by detection of parasite DNA and RNA, suggesting living parasites. Our study is the first one to describe in a murine model the genetic response of placental environment to T. cruzi infection and suggests the development of a strong immune response, parasite genotype-dependent, to the detriment of cellular metabolism, which may contribute to control infection preventing the risk of congenital transmission. PMID:28273076

  5. Quinolone-resistant Escherichia coli isolated from birds of prey in Portugal are genetically distinct from those isolated from water environments and gulls in Portugal, Spain and Sweden.

    Science.gov (United States)

    Vredenburg, Jana; Varela, Ana Rita; Hasan, Badrul; Bertilsson, Stefan; Olsen, Björn; Narciso-da-Rocha, Carlos; Bonnedahl, Jonas; Stedt, Johan; Da Costa, Paulo Martins; Manaia, Célia M

    2014-04-01

    The influence of geographic distribution and type of habitat on the molecular epidemiology of ciprofloxacin resistant Escherichia coli was investigated. Ciprofloxacin resistant E. coli from wastewater, urban water with faecal contamination and faeces of gulls, pigeons and birds of prey, from Portugal, Spain and Sweden were compared based on multi-locus sequence typing (MLST) and quinolone resistance genetic determinants. Multi-locus sequence typing allowed the differentiation of E. coli lineages associated with birds of prey from those inhabiting gulls and waters. E. coli lineages of clinical relevance, such as the complex ST131, were detected in wastewater, streams and gulls in Portugal, Spain and Sweden. Quinolone resistance was due to gyrA and parC mutations, although distinct mutations were detected in birds of prey and in wastewater, streams and gulls isolates. These differences were correlated with specific MLST lineages, suggesting resistance inheritance. Among the plasmid-mediated quinolone resistance genes, only aac(6')-ib-cr and qnrS were detected in wastewater, streams and gulls isolates, but not in birds of prey. The horizontal transfer of the gene aac(6')-ib-cr could be inferred from its occurrence in different MLST lineages. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

  6. Biology, Genetics, and Environment

    Science.gov (United States)

    Wall, Tamara L.; Luczak, Susan E.; Hiller-Sturmhöfel, Susanne

    2016-01-01

    Gene variants encoding several of the alcohol-metabolizing enzymes, alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH), are among the largest genetic associations with risk for alcohol dependence. Certain genetic variants (i.e., alleles)—particularly the ADH1B*2, ADH1B*3, ADH1C*1, and ALDH2*2 alleles—have been associated with lower rates of alcohol dependence. These alleles may lead to an accumulation of acetaldehyde during alcohol metabolism, which can result in heightened subjective and objective effects. The prevalence of these alleles differs among ethnic groups; ADH1B*2 is found frequently in northeast Asians and occasionally Caucasians, ADH1B*3 is found predominantly in people of African ancestry, ADH1C*1 varies substantially across populations, and ALDH2*2 is found almost exclusively in northeast Asians. Differences in the prevalence of these alleles may account at least in part for ethnic differences in alcohol consumption and alcohol use disorder (AUD). However, these alleles do not act in isolation to influence the risk of AUD. For example, the gene effects of ALDH2*2 and ADH1B*2 seem to interact. Moreover, other factors have been found to influence the extent to which these alleles affect a person’s alcohol involvement, including developmental stage, individual characteristics (e.g., ethnicity, antisocial behavior, and behavioral undercontrol), and environmental factors (e.g., culture, religion, family environment, and childhood adversity). PMID:27163368

  7. Genetically distinct Dutch-domesticated Clarias gariepinus used in ...

    African Journals Online (AJOL)

    Because of its potential as an aquaculture species it has been widely used in aquaculture ventures in South Africa, specifically a stock known as Dutch catfish, a domesticated strain developed in the Netherlands. Mitochondrial DNA markers indicate that this stock is genetically distinct from the natural populations of C.

  8. Genetically Distinct Subsets within ANCA-Associated Vasculitis

    Science.gov (United States)

    Lyons, Paul A.; Rayner, Tim F.; Trivedi, Sapna; Holle, Julia U.; Watts, Richard A.; Jayne, David R.W.; Baslund, Bo; Brenchley, Paul; Bruchfeld, Annette; Chaudhry, Afzal N.; Tervaert, Jan Willem Cohen; Deloukas, Panos; Feighery, Conleth; Gross, Wolfgang L.; Guillevin, Loic; Gunnarsson, Iva; P, Lorraine Harper M.R.C; Hrušková, Zdenka; Little, Mark A.; Martorana, Davide; Neumann, Thomas; Ohlsson, Sophie; Padmanabhan, Sandosh; Pusey, Charles D.; Salama, Alan D.; Sanders, Jan-Stephan F.; Savage, Caroline O.; Segelmark, Mårten; Stegeman, Coen A.; Tesař, Vladimir; Vaglio, Augusto; Wieczorek, Stefan; Wilde, Benjamin; Zwerina, Jochen; Rees, Andrew J.; Clayton, David G.; Smith, Kenneth G.C.

    2013-01-01

    BACKGROUND Antineutrophil cytoplasmic antibody (ANCA)–associated vasculitis is a severe condition encompassing two major syndromes: granulomatosis with polyangiitis (formerly known as Wegener’s granulomatosis) and microscopic polyangiitis. Its cause is unknown, and there is debate about whether it is a single disease entity and what role ANCA plays in its pathogenesis. We investigated its genetic basis. METHODS A genomewide association study was performed in a discovery cohort of 1233 U.K. patients with ANCA-associated vasculitis and 5884 controls and was replicated in 1454 Northern European case patients and 1666 controls. Quality control, population stratification, and statistical analyses were performed according to standard criteria. RESULTS We found both major-histocompatibility-complex (MHC) and non-MHC associations with ANCA-associated vasculitis and also that granulomatosis with polyangiitis and microscopic polyangiitis were genetically distinct. The strongest genetic associations were with the antigenic specificity of ANCA, not with the clinical syndrome. Anti–proteinase 3 ANCA was associated with HLA-DP and the genes encoding α1-antitrypsin (SERPINA1) and proteinase 3 (PRTN3) (P = 6.2×10−89, P = 5.6×10−12, and P = 2.6×10−7, respectively). Anti–myeloperoxidase ANCA was associated with HLA-DQ (P = 2.1×10−8). CONCLUSIONS This study confirms that the pathogenesis of ANCA-associated vasculitis has a genetic component, shows genetic distinctions between granulomatosis with polyangiitis and microscopic polyangiitis that are associated with ANCA specificity, and suggests that the response against the autoantigen proteinase 3 is a central pathogenic feature of proteinase 3 ANCA–associated vasculitis. These data provide preliminary support for the concept that proteinase 3 ANCA–associated vasculitis and myeloperoxidase ANCA–associated vasculitis are distinct autoimmune syndromes. (Funded by the British Heart Foundation and others.) PMID

  9. Puerto Rico and Florida manatees represent genetically distinct groups

    Science.gov (United States)

    Hunter, Margaret E.; Mignucci-Giannoni, Antonio A.; Tucker, Kimberly Pause; King, Timothy L.; Bonde, Robert K.; Gray, Brian A.; McGuire, Peter M.

    2012-01-01

    The West Indian manatee (Trichechus manatus) populations in Florida (T. m. latirostris) and Puerto Rico (T. m. manatus) are considered distinct subspecies and are listed together as endangered under the United States Endangered Species Act. Sustained management and conservation efforts for the Florida subspecies have led to the suggested reclassification of the species to a threatened or delisted status. However, the two populations are geographically distant, morphologically distinct, and habitat degradation and boat strikes continue to threaten the Puerto Rico population. Here, 15 microsatellite markers and mitochondrial control region sequences were used to determine the relatedness of the two populations and investigate the genetic diversity and phylogeographic organization of the Puerto Rico population. Highly divergent allele frequencies were identified between Florida and Puerto Rico using microsatellite (F ST = 0.16; R ST = 0.12 (P ST = 0.66; Φ ST = 0.50 (P E = 0.45; NA = 3.9), were similar, but lower than those previously identified in Florida (HE = 0.48, NA = 4.8). Within Puerto Rico, the mitochondrial genetic diversity values (π = 0.001; h = 0.49) were slightly lower than those previously reported (π = 0.002; h = 0.54) and strong phylogeographic structure was identified (F ST global = 0.82; Φ ST global = 0.78 (P population size (N = 250), and distinct threats and habitat emphasize the need for separate protections in Puerto Rico. Conservation efforts including threat mitigation, migration corridors, and protection of subpopulations could lead to improved genetic variation in the endangered Puerto Rico manatee population.

  10. Budgerigar flight in a varying environment: flight at distinct speeds?

    Science.gov (United States)

    Srinivasan, Mandyam V.

    2016-01-01

    How do flying birds respond to changing environments? The behaviour of budgerigars, Melopsittacus undulatus, was filmed as they flew through a tapered tunnel. Unlike flying insects—which vary their speed progressively and continuously by holding constant the optic flow induced by the walls—the birds showed a tendency to fly at only two distinct, fixed speeds. They switched between a high speed in the wider section of the tunnel, and a low speed in the narrower section. The transition between the two speeds was abrupt, and anticipatory. The high speed was close to the energy-efficient, outdoor cruising speed for these birds, while the low speed was approximately half this value. This is the first observation of the existence of two distinct, preferred flight speeds in birds. A dual-speed flight strategy may be beneficial for birds that fly in varying environments, with the high speed set at an energy-efficient value for flight through open spaces, and the low speed suited to safe manoeuvring in a cluttered environment. The constancy of flight speed within each regime enables the distances of obstacles and landmarks to be directly calibrated in terms of optic flow, thus facilitating simple and efficient guidance of flight through changing environments. PMID:27330173

  11. Budgerigar flight in a varying environment: flight at distinct speeds?

    OpenAIRE

    Schiffner, Ingo; Srinivasan, Mandyam V.

    2016-01-01

    How do flying birds respond to changing environments? The behaviour of budgerigars, Melopsittacus undulatus, was filmed as they flew through a tapered tunnel. Unlike flying insects���which vary their speed progressively and continuously by holding constant the optic flow induced by the walls���the birds showed a tendency to fly at only two distinct, fixed speeds. They switched between a high speed in the wider section of the tunnel, and a low speed in the narrower section. The transition betw...

  12. Psoriasis and cardiometabolic traits: modest association but distinct genetic architectures

    Science.gov (United States)

    Koch, Manja; Baurecht, Hansjörg; Ried, Janina S.; Rodriguez, Elke; Schlesinger, Sabrina; Volks, Natalie; Gieger, Christian; Rückert, Ina-Maria; Heinrich, Luise; Willenborg, Christina; Smith, Catherine; Peters, Annette; Thorand, Barbara; Koenig, Wolfgang; Lamina, Claudia; Jansen, Henning; Kronenberg, Florian; Seissler, Jochen; Thiery, Joachim; Rathmann, Wolfgang; Schunkert, Heribert; Erdmann, Jeanette; Barker, Jonathan; Nair, Rajan P; Tsoi, Lam C; Elder, James T; Mrowietz, Ulrich; Weichenthal, Michael; Mucha, Sören; Schreiber, Stefan; Franke, Andre; Schmitt, Jochen; Lieb, Wolfgang; Weidinger, Stephan

    2015-01-01

    Psoriasis has been linked to cardiometabolic diseases, but epidemiological findings are inconsistent. We investigated the association between psoriasis and cardiometabolic outcomes in a German cross-sectional study (n=4.185) and a prospective cohort of German Health Insurance beneficiaries (n=1.811.098). A potential genetic overlap was explored using genome-wide data from >22.000 coronary artery disease (CAD) and >4.000 psoriasis cases, and with a dense genotyping study of cardiometabolic risk loci on 927 psoriasis cases and 3.717 controls. Controlling for major confounders, in the cross-sectional analysis psoriasis was significantly associated with type 2 diabetes (T2D, adjusted odd’s ratio OR=2.36; 95% confidence interval CI=1.26–4.41) and myocardial infarction (MI, OR=2.26, 95% CI=1.03–4.96). In the longitudinal study, psoriasis slightly increased the risk for incident T2D (adjusted relative risk RR=1.11; 95%CI=1.08–1.14) and MI (RR=1.14; 95%CI=1.06–1.22), with highest risk increments in systemically treated psoriasis, which accounted for 11 and 17 excess cases of T2D and MI per 10,000 person-years. Except for weak signals from within the MHC, there was no evidence for genetic risk loci shared between psoriasis and cardiometabolic traits. Our findings suggest that psoriasis, in particular severe psoriasis, increases risk for T2D and MI, and that the genetic architecture of psoriasis and cardiometabolic traits is largely distinct. PMID:25599394

  13. Genetic Algorithms in Noisy Environments

    OpenAIRE

    THEN, T. W.; CHONG, EDWIN K. P.

    1993-01-01

    Genetic Algorithms (GA) have been widely used in the areas of searching, function optimization, and machine learning. In many of these applications, the effect of noise is a critical factor in the performance of the genetic algorithms. While it hals been shown in previous siiudies that genetic algorithms are still able to perform effectively in the presence of noise, the problem of locating the global optimal solution at the end of the search has never been effectively addressed. Furthermore,...

  14. Genetic distinctions between autoimmune hepatitis in Italy and North America.

    Science.gov (United States)

    Muratori, Paolo; Czaja, Albert-J; Muratori, Luigi; Pappas, Georgios; Maccariello, Silvana; Cassani, Fabio; Granito, Alessandro; Ferrari, Rodolfo; Mantovani, Vilma; Lenzi, Marco; Bianchi, Francesco-B

    2005-03-28

    Our goals were to analyze the known genetic predispositions for autoimmune hepatitis (AIH) in AIH Italian population and to compare them with North American counterparts. Human leukocyte antigens (HLA) B8, C7, DR3, DR4, DR7, DR11, DR13, DQ2 and the B8-DR3-DQ2 phenotype were determined by microlymphocytotoxicity and polymerase chain reaction in 74 Italian patients (57 with type 1 and 17 with type 2 AIH) and 149 North American patients with type 1 AIH, and in adequate controls. B8-DR3-DQ2 occurred more frequently in Italian patients with type 1 AIH than in Italian controls (30% vs 7%, P<0.0001), but less frequently than in North American counterparts (30% vs 48%, P = 0.02). DR4 occurred less frequently in Italian patients with type 1 AIH (23% vs 43%, P = 0.01) and in controls (16% vs 34%, P = 0.0003) than in North American counterparts. No differences were found in alleles' frequency between type 1 and type 2 Italian AIH patients. DR11 had a frequency lower in type 1 Italian AIH patients than controls (17% vs 35%, P = 0.01). HLA DR4 is not associated with AIH in Italy. The known HLA risk factors for AIH occur similarly in Italian patients with type 1 and type 2 AIH, and they are less frequent than in North American patients. B8-DR3-DQ2 is the predominant phenotype of type 1 AIH also in Italy, and HLA DR11 may be a regionally distinctive protective factor against type 1 AIH.

  15. Intraocular pressure in genetically distinct mice: an update and strain survey

    Directory of Open Access Journals (Sweden)

    Tomarev Stanislav I

    2001-08-01

    Full Text Available Abstract Background Little is known about genetic factors affecting intraocular pressure (IOP in mice and other mammals. The purpose of this study was to determine the IOPs of genetically distinct mouse strains, assess the effects of factors such as age, sex and time of day on IOP in specific strain backgrounds, and to assess the effects of specific candidate gene mutations on IOP. Results Based on over 30 studied mouse strains, average IOP ranges from approximately 10 to 20 mmHg. Gender does not typically affect IOP and aging results in an IOP decrease in some strains. Most tested strains exhibit a diurnal rhythm with IOP being the highest during the dark period of the day. Homozygosity for a null allele of the carbonic anhydrase II gene (Car2n does not alter IOP while homozygosity for a mutation in the leptin receptor gene (Leprdb that causes obesity and diabetes results in increased IOP. Albino C57BL/6J mice homozygous for a tyrosinase mutation (Tyrc-2J have higher IOPs than their pigmented counterparts. Conclusions Genetically distinct mouse strains housed in the same environment have a broad range of IOPs. These IOP differences are likely due to interstrain genetic differences that create a powerful resource for studying the regulation of IOP. Age, time of day, obesity and diabetes have effects on mouse IOP similar to those in humans and other species. Mutations in two of the assessed candidate genes (Lepr and Tyr result in increased IOP. These studies demonstrate that mice are a practical and powerful experimental system to study the genetics of IOP regulation and disease processes that raise IOP to harmful levels.

  16. Regional differences in seasonal timing of rainfall discriminate between genetically distinct East African giraffe taxa.

    Directory of Open Access Journals (Sweden)

    Henri A Thomassen

    Full Text Available Masai (Giraffa tippelskirchi, Reticulated (G. reticulata and Rothschild's (G. camelopardalis giraffe lineages in East Africa are morphologically and genetically distinct, yet in Kenya their ranges abut. This raises the question of how divergence is maintained among populations of a large mammal capable of long-distance travel, and which readily hybridize in zoos. Here we test four hypotheses concerning the maintenance of the phylogeographic boundaries among the three taxa: 1 isolation-by-distance; 2 physical barriers to dispersal; 3 general habitat differences resulting in habitat segregation; or 4 regional differences in the seasonal timing of rainfall, and resultant timing of browse availability. We used satellite remotely sensed and climate data to characterize the environment at the locations of genotyped giraffes. Canonical variate analysis, random forest algorithms, and generalized dissimilarity modelling were employed in a landscape genetics framework to identify the predictor variables that best explained giraffes' genetic divergence. We found that regional differences in the timing of precipitation, and resulting green-up associated with the abundance of browse, effectively discriminate between taxa. Local habitat conditions, topographic and human-induced barriers, and geographic distance did not aid in discriminating among lineages. Our results suggest that selection associated with regional timing of events in the annual climatic cycle may help maintain genetic and phenotypic divergence in giraffes. We discuss potential mechanisms of maintaining divergence, and suggest that synchronization of reproduction with seasonal rainfall cycles that are geographically distinct may contribute to reproductive isolation. Coordination of weaning with green-up cycles could minimize the costs of lactation and predation on the young. Our findings are consistent with theory and empirical results demonstrating the efficacy of seasonal or phenologically

  17. Regional differences in seasonal timing of rainfall discriminate between genetically distinct East African giraffe taxa.

    Science.gov (United States)

    Thomassen, Henri A; Freedman, Adam H; Brown, David M; Buermann, Wolfgang; Jacobs, David K

    2013-01-01

    Masai (Giraffa tippelskirchi), Reticulated (G. reticulata) and Rothschild's (G. camelopardalis) giraffe lineages in East Africa are morphologically and genetically distinct, yet in Kenya their ranges abut. This raises the question of how divergence is maintained among populations of a large mammal capable of long-distance travel, and which readily hybridize in zoos. Here we test four hypotheses concerning the maintenance of the phylogeographic boundaries among the three taxa: 1) isolation-by-distance; 2) physical barriers to dispersal; 3) general habitat differences resulting in habitat segregation; or 4) regional differences in the seasonal timing of rainfall, and resultant timing of browse availability. We used satellite remotely sensed and climate data to characterize the environment at the locations of genotyped giraffes. Canonical variate analysis, random forest algorithms, and generalized dissimilarity modelling were employed in a landscape genetics framework to identify the predictor variables that best explained giraffes' genetic divergence. We found that regional differences in the timing of precipitation, and resulting green-up associated with the abundance of browse, effectively discriminate between taxa. Local habitat conditions, topographic and human-induced barriers, and geographic distance did not aid in discriminating among lineages. Our results suggest that selection associated with regional timing of events in the annual climatic cycle may help maintain genetic and phenotypic divergence in giraffes. We discuss potential mechanisms of maintaining divergence, and suggest that synchronization of reproduction with seasonal rainfall cycles that are geographically distinct may contribute to reproductive isolation. Coordination of weaning with green-up cycles could minimize the costs of lactation and predation on the young. Our findings are consistent with theory and empirical results demonstrating the efficacy of seasonal or phenologically dictated

  18. Population genetic diversity and fitness in multiple environments

    Directory of Open Access Journals (Sweden)

    McGreevy Thomas J

    2010-07-01

    Full Text Available Abstract Background When a large number of alleles are lost from a population, increases in individual homozygosity may reduce individual fitness through inbreeding depression. Modest losses of allelic diversity may also negatively impact long-term population viability by reducing the capacity of populations to adapt to altered environments. However, it is not clear how much genetic diversity within populations may be lost before populations are put at significant risk. Development of tools to evaluate this relationship would be a valuable contribution to conservation biology. To address these issues, we have created an experimental system that uses laboratory populations of an estuarine crustacean, Americamysis bahia with experimentally manipulated levels of genetic diversity. We created replicate cultures with five distinct levels of genetic diversity and monitored them for 16 weeks in both permissive (ambient seawater and stressful conditions (diluted seawater. The relationship between molecular genetic diversity at presumptive neutral loci and population vulnerability was assessed by AFLP analysis. Results Populations with very low genetic diversity demonstrated reduced fitness relative to high diversity populations even under permissive conditions. Population performance decreased in the stressful environment for all levels of genetic diversity relative to performance in the permissive environment. Twenty percent of the lowest diversity populations went extinct before the end of the study in permissive conditions, whereas 73% of the low diversity lines went extinct in the stressful environment. All high genetic diversity populations persisted for the duration of the study, although population sizes and reproduction were reduced under stressful environmental conditions. Levels of fitness varied more among replicate low diversity populations than among replicate populations with high genetic diversity. There was a significant correlation

  19. Genetically distinct subsets within ANCA-associated vasculitis.

    LENUS (Irish Health Repository)

    Lyons, Paul A

    2012-07-19

    Antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis is a severe condition encompassing two major syndromes: granulomatosis with polyangiitis (formerly known as Wegener\\'s granulomatosis) and microscopic polyangiitis. Its cause is unknown, and there is debate about whether it is a single disease entity and what role ANCA plays in its pathogenesis. We investigated its genetic basis.

  20. Genetic and genotype environment interaction effects for the content ...

    Indian Academy of Sciences (India)

    Administrator

    Oryza sativa L.); nutrient quality; essential amino acid; genetic effect; genotype environment interaction. RESEARCH ARTICLE. Genetic and genotype environment interaction effects for the content of seven essential amino acids in indica rice.

  1. Possible people, complaints, and the distinction between genetic planning and genetic engineering.

    Science.gov (United States)

    Delaney, James J

    2011-07-01

    Advances in the understanding of genetics have led to the belief that it may become possible to use genetic engineering to manipulate the DNA of humans at the embryonic stage to produce certain desirable traits. Although this currently cannot be done on a large scale, many people nevertheless object in principle to such practices. Most often, they argue that genetic enhancements would harm the children who were engineered, cause societal harms, or that the risks of perfecting the procedures are too high to proceed. However, many of these same people do not have serious objections to what is called 'genetic planning' procedures (such as the selection of sperm donors with desirable traits) that essentially have the same ends. The author calls the view that genetic engineering enhancements are impermissible while genetic planning enhancements are permissible the 'popular view', and argues that the typical reasons people give for the popular view fail to distinguish the two practices. This paper provides a principle that can salvage the popular view, which stresses that offspring from genetic engineering practices have grounds for complaint because they are identical to the pre-enhanced embryo, whereas offspring who are the result of genetic planning have no such grounds.

  2. Genetically distinct isolates of Spirocerca sp. from a naturally infected red fox (Vulpes vulpes) from Denmark

    DEFF Research Database (Denmark)

    Al-Sabi, Mohammad Nafi Solaiman; Hansen, Mette Sif; Chriél, Mariann

    2014-01-01

    Spirocerca lupi causes formation of nodules that may transform into sarcoma in the walls ofaorta, esophagus and stomach of infected canids. In February 2013, post mortem examina-tion of a red fox (Vulpes vulpes) hunted in Denmark revealed the presence of several nodulescontaining adult worms...... of the cox1 gene, from individual worms, revealed distinct genetic variation(7–9%) between the Danish worms and isolates of S. lupi from Europe, Asia and Africa.This was confirmed by phylogenetic analysis that clearly separated the Danish worms fromother isolates of S. lupi. The distinct genetic differences...... of the current worms compared toother isolates of S. lupi may suggest the presence of a cryptic species within Spirocerca....

  3. Biology and ecology of Neosho Smallmouth Bass and the genetically distinct Ouachita lineage

    Science.gov (United States)

    Brewer, Shannon K.; Long, James M.; Tringali, Michael D.; Long, James M.; Birdsong, Timothy W.; Allen, Michael S.

    2015-01-01

    We reviewed the published and gray literature associated with Neosho Smallmouth Bass and the genetically-distinct Ouachita lineage. Substantial inter-stream variation appears to occur among these populations, particularly related to age. The Neosho subspecies is more abundant, grows faster, and lives longer than the genetically-distinct Ouachita lineage. Recruitment is highly variable among streams for both populations and appears to be related to some undescribed aspects of hydrology but also likely reflect bias due to sampling gear. Information on annual and seasonal trends is lacking for the Neosho subspecies and the Ouachita lineages, particularly as related to the spawning period. Conservation efforts for these lineages might benefit from agencies partnering to achieve goals that extend beyond a particular agencies responsibilities and state boundaries. Recognition of spatial and temporal considerations, combined with a better understanding of the population dynamics as related to abundance, growth, mortality and reproduction would benefit the creation of more effective conservation and management strategies for genetically-distinct populations of Smallmouth Bass.

  4. Genetic and metabolic regulation of fatty acid deposition in autochthonous bovine breeds with distinct genetic background

    OpenAIRE

    Costa, Ana Sofia Henriques da

    2013-01-01

    Tese de Doutoramento em Ciências Veterinárias. Especialidade de Produção Animal During the finishing phase, bovines deposit large amounts of subcutaneous and visceral fats resulting in production inefficiencies affecting, in particular, meat quality. Intramuscular fat composition of ruminant meats influences the quality of the final product, which explains the importance of assessing meat fatty acid profile using different breeds and feeding strategies. On the other hand, both genetic back...

  5. Congenital hypogonadotropic hypogonadism and constitutional delay of growth and puberty have distinct genetic architectures.

    Science.gov (United States)

    Cassatella, Daniele; Howard, Sasha R; Acierno, James S; Xu, Cheng; Papadakis, Georgios E; Santoni, Federico A; Dwyer, Andrew A; Santini, Sara; Sykiotis, Gerasimos P; Chambion, Caroline; Meylan, Jenny; Marino, Laura; Favre, Lucie; Li, Jiankang; Liu, Xuanzhu; Zhang, Jianguo; Bouloux, Pierre-Marc; Geyter, Christian De; Paepe, Anne De; Dhillo, Waljit S; Ferrara, Jean-Marc; Hauschild, Michael; Lang-Muritano, Mariarosaria; Lemke, Johannes R; Flück, Christa; Nemeth, Attila; Phan-Hug, Franziska; Pignatelli, Duarte; Popovic, Vera; Pekic, Sandra; Quinton, Richard; Szinnai, Gabor; l'Allemand, Dagmar; Konrad, Daniel; Sharif, Saba; Iyidir, Özlem Turhan; Stevenson, Brian J; Yang, Huanming; Dunkel, Leo; Pitteloud, Nelly

    2018-04-01

    Congenital hypogonadotropic hypogonadism (CHH) and constitutional delay of growth and puberty (CDGP) represent rare and common forms of GnRH deficiency, respectively. Both CDGP and CHH present with delayed puberty, and the distinction between these two entities during early adolescence is challenging. More than 30 genes have been implicated in CHH, while the genetic basis of CDGP is poorly understood. We characterized and compared the genetic architectures of CHH and CDGP, to test the hypothesis of a shared genetic basis between these disorders. Exome sequencing data were used to identify rare variants in known genes in CHH ( n  = 116), CDGP ( n  = 72) and control cohorts ( n  = 36 874 ExAC and n  = 405 CoLaus). Mutations in at least one CHH gene were found in 51% of CHH probands, which is significantly higher than in CDGP (7%, P  = 7.6 × 10 -11 ) or controls (18%, P  = 5.5 × 10 -12 ). Similarly, oligogenicity (defined as mutations in more than one gene) was common in CHH patients (15%) relative to CDGP (1.4%, P  = 0.002) and controls (2%, P  = 6.4 × 10 -7 ). Our data suggest that CDGP and CHH have distinct genetic profiles, and this finding may facilitate the differential diagnosis in patients presenting with delayed puberty. © 2018 The authors.

  6. Canine Cutaneous Leishmaniasis: Dissemination and Tissue Tropism of Genetically Distinct Leishmania (Viannia braziliensis Populations

    Directory of Open Access Journals (Sweden)

    Guilherme Marx de Oliveira

    2013-01-01

    Full Text Available Little is known regarding the internal dissemination of initial cutaneous lesions and tissue tropism of Leishmania (Viannia braziliensis populations in naturally infected dogs. The aim of this study was to investigate genetic polymorphisms of L. (V. braziliensis populations in different anatomic sites of naturally infected dogs by using polymerase chain reaction (PCR and low-stringency single specific primer-PCR (LSSP-PCR techniques. The amplified products were analyzed by LSSP-PCR to investigate the genetic variability of the parasite populations present in different anatomical sites. Twenty-three out of the 52 samples gave PCR-positive results. The existence of L. (V. braziliensis strains that remained restricted to cutaneous lesions and others showing characteristics of dissemination to internal organs and healthy skin was observed. LSSP-PCR and numerical analyses revealed that parasite populations that do not disseminate were genetically similar and belonged to a separate phenetic cluster. In contrast, populations that showed spreading to internal organs displayed a more polymorphic genetic profile. Despite the heterogeneity, L. (V. braziliensis populations with identical genetic profiles were observed in popliteal and cervical lymph nodes of the same animal. Our results indicate that infection in dogs can be manifested by dissemination and tissue tropism of genetically distinct populations of L. (V. braziliensis.

  7. Simultaneous infection of human host with genetically distinct isolates of Paracoccidioides brasiliensis

    Directory of Open Access Journals (Sweden)

    João Batista Júnior

    2010-02-01

    Full Text Available This study is the first report on genetic differences between isolates of Paracoccidioides brasiliensis from a single patient. We describe a simultaneous infection with genetically distinct isolates of P. brasiliensis in a patient with chronic paracoccidioidomycosis. The clinical isolates were obtained from lesions in different anatomical sites and were characterised by random amplified polymorphic DNA (RAPD analysis. The RAPD technique can be helpful for distinguishing between clinical isolates. Different random primers were used to characterise these clinical isolates. The RAPD patterns allowed for differentiation between isolates and the construction of a phenetic tree, which showed more than 28% genetic variability in this fungal species, opening new possibilities for clinical studies of P. brasiliensis. Based on these results and preliminary clinical findings, we suggest that different genotypes of P. brasiliensis might infect the same patient, inducing the active form of the disease.

  8. Neuroinformatic analyses of common and distinct genetic components associated with major neuropsychiatric disorders

    Science.gov (United States)

    Lotan, Amit; Fenckova, Michaela; Bralten, Janita; Alttoa, Aet; Dixson, Luanna; Williams, Robert W.; van der Voet, Monique

    2014-01-01

    Major neuropsychiatric disorders are highly heritable, with mounting evidence suggesting that these disorders share overlapping sets of molecular and cellular underpinnings. In the current article we systematically test the degree of genetic commonality across six major neuropsychiatric disorders—attention deficit hyperactivity disorder (ADHD), anxiety disorders (Anx), autistic spectrum disorders (ASD), bipolar disorder (BD), major depressive disorder (MDD), and schizophrenia (SCZ). We curated a well-vetted list of genes based on large-scale human genetic studies based on the NHGRI catalog of published genome-wide association studies (GWAS). A total of 180 genes were accepted into the analysis on the basis of low but liberal GWAS p-values (<10−5). 22% of genes overlapped two or more disorders. The most widely shared subset of genes—common to five of six disorders–included ANK3, AS3MT, CACNA1C, CACNB2, CNNM2, CSMD1, DPCR1, ITIH3, NT5C2, PPP1R11, SYNE1, TCF4, TENM4, TRIM26, and ZNRD1. Using a suite of neuroinformatic resources, we showed that many of the shared genes are implicated in the postsynaptic density (PSD), expressed in immune tissues and co-expressed in developing human brain. Using a translational cross-species approach, we detected two distinct genetic components that were both shared by each of the six disorders; the 1st component is involved in CNS development, neural projections and synaptic transmission, while the 2nd is implicated in various cytoplasmic organelles and cellular processes. Combined, these genetic components account for 20–30% of the genetic load. The remaining risk is conferred by distinct, disorder-specific variants. Our systematic comparative analysis of shared and unique genetic factors highlights key gene sets and molecular processes that may ultimately translate into improved diagnosis and treatment of these debilitating disorders. PMID:25414627

  9. Neuroinformatic Analyses of Common and Distinct Genetic Components Associated with Major Neuropsychiatric Disorders

    Directory of Open Access Journals (Sweden)

    Amit eLotan

    2014-11-01

    Full Text Available Major neuropsychiatric disorders are highly heritable, with mounting evidence suggesting that these disorders share overlapping sets of molecular and cellular underpinnings. In the current article we systematically test the degree of genetic commonality across six major neuropsychiatric disorders—attention deficit hyperactivity disorder, anxiety disorders, autistic spectrum disorders, bipolar disorder, major depressive disorder and schizophrenia. We curated a well-vetted list of genes based on large-scale human genetic studies and verified their appearance on the NHGRI catalog of published genome-wide association studies. A total of 180 genes were accepted into the analysis on the basis of low but liberal GWAS p-values (<10-5. 22% of genes overlapped two or more disorders. The most widely shared subset of genes—common to five of six disorders–included ANK3, AS3MT, CACNA1C, CACNB2, CNNM2, CSMD1, DPCR1, ITIH3, NT5C2, PPP1R11, SYNE1, TCF4, TENM4, TRIM26, and ZNRD1. Using a suite of neuroinformatic resources, we showed that many of the shared genes are implicated in the postsynaptic density, expressed in immune tissues and co-expressed in developing human brain.. Using a translational cross-species approach, we detected two distinct genetic components that were both shared by each of the six disorders; the 1st component is involved in CNS development, neural projections and synaptic transmission, while the 2nd is implicated in various cytoplasmic organelles and cellular processes. Combined, these genetic components account for 20–30% of the genetic load. The remaining risk is conferred by distinct, disorder-specific variants. Nevertheless, the convergence of different analytical approaches on similar targets may bear important implications. Thus, although adding mostly confirmatory findings, higher resolution of shared and unique genetic factors provided in this manuscript could ultimately translate into improved diagnosis and treatment of

  10. Genetic Diversity and Geographic Distribution of Genetically Distinct Rabies Viruses in the Philippines

    Science.gov (United States)

    Saito, Mariko; Oshitani, Hitoshi; Orbina, Jun Ryan C.; Tohma, Kentaro; de Guzman, Alice S.; Kamigaki, Taro; Demetria, Catalino S.; Manalo, Daria L.; Noguchi, Akira; Inoue, Satoshi; Quiambao, Beatriz P.

    2013-01-01

    Background Rabies continues to be a major public health problem in the Philippines, where 200–300 human cases were reported annually between 2001 and 2011. Understanding the phylogeography of rabies viruses is important for establishing a more effective and feasible control strategy. Methods We performed a molecular analysis of rabies viruses in the Philippines using rabied animal brain samples. The samples were collected from 11 of 17 regions, which covered three island groups (Luzon, Visayas, and Mindanao). Partial nucleoprotein (N) gene sequencing was performed on 57 samples and complete glycoprotein (G) gene sequencing was performed on 235 samples collected between 2004 and 2010. Results The Philippine strains of rabies viruses were included in a distinct phylogenetic cluster, previously named Asian 2b, which appeared to have diverged from the Chinese strain named Asian 2a. The Philippine strains were further divided into three major clades, which were found exclusively in different island groups: clades L, V, and M in Luzon, Visayas, and Mindanao, respectively. Clade L was subdivided into nine subclades (L1–L9) and clade V was subdivided into two subclades (V1 and V2). With a few exceptions, most strains in each subclade were distributed in specific geographic areas. There were also four strains that were divided into two genogroups but were not classified into any of the three major clades, and all four strains were found in the island group of Luzon. Conclusion We detected three major clades and two distinct genogroups of rabies viruses in the Philippines. Our data suggest that viruses of each clade and subclade evolved independently in each area without frequent introduction into other areas. An important implication of these data is that geographically targeted dog vaccination using the island group approach may effectively control rabies in the Philippines. PMID:23593515

  11. Multigene Phylogeography of Bactrocera caudata (Insecta: Tephritidae): Distinct Genetic Lineages in Northern and Southern Hemispheres.

    Science.gov (United States)

    Yong, Hoi-Sen; Lim, Phaik-Eem; Tan, Ji; Song, Sze-Looi; Suana, I Wayan; Eamsobhana, Praphathip

    2015-01-01

    Bactrocera caudata is a pest of pumpkin flower. Specimens of B. caudata from the northern hemisphere (mainland Asia) and southern hemisphere (Indonesia) were analysed using the partial DNA sequences of the nuclear 28S rRNA and internal transcribed spacer region 2 (ITS-2) genes, and the mitochondrial cytochrome c oxidase subunit I (COI), cytochrome c oxidase subunit II (COII) and 16S rRNA genes. The COI, COII, 16S rDNA and concatenated COI+COII+16S and COI+COII+16S+28S+ITS-2 nucleotide sequences revealed that B. caudata from the northern hemisphere (Peninsular Malaysia, East Malaysia, Thailand) was distinctly different from the southern hemisphere (Indonesia: Java, Bali and Lombok), without common haplotype between them. Phylogenetic analysis revealed two distinct clades (northern and southern hemispheres), indicating distinct genetic lineage. The uncorrected 'p' distance for the concatenated COI+COII+16S nucleotide sequences between the taxa from the northern and southern hemispheres ('p' = 4.46-4.94%) was several folds higher than the 'p' distance for the taxa in the northern hemisphere ('p' = 0.00-0.77%) and the southern hemisphere ('p' = 0.00%). This distinct difference was also reflected by concatenated COI+COII+16S+28S+ITS-2 nucleotide sequences with an uncorrected 'p' distance of 2.34-2.69% between the taxa of northern and southern hemispheres. In accordance with the type locality the Indonesian taxa belong to the nominal species. Thus the taxa from the northern hemisphere, if they were to constitute a cryptic species of the B. caudata species complex based on molecular data, need to be formally described as a new species. The Thailand and Malaysian B. caudata populations in the northern hemisphere showed distinct genetic structure and phylogeographic pattern.

  12. Environment Changes Genetic Effects on Respiratory Conditions and Allergic Phenotypes

    DEFF Research Database (Denmark)

    Song, Yong; Schwager, Michelle J; Backer, Vibeke

    2017-01-01

    The prevalence of asthma and allergic diseases is disproportionately distributed among different populations, with an increasing trend observed in Western countries. Here we investigated how the environment affected genotype-phenotype association in a genetically homogeneous, but geographically s......-phenotype associations relating to bronchitis and allergy susceptibility are dependent on the environment and that environmental factors/lifestyles modify genetic predisposition and change the genetic effects on diseases.......The prevalence of asthma and allergic diseases is disproportionately distributed among different populations, with an increasing trend observed in Western countries. Here we investigated how the environment affected genotype-phenotype association in a genetically homogeneous, but geographically...... residing either in the westernized environment of Denmark or in the rural area of Greenland. Our results showed that lung function was associated with genetic variants in ORMDL3, with polymorphisms having a significant interaction with place of residence. LT-α SNP rs909253 and rs1041981 were significantly...

  13. Sarcoptes scabiei mites in humans are distributed into three genetically distinct clades.

    Science.gov (United States)

    Andriantsoanirina, V; Ariey, F; Izri, A; Bernigaud, C; Fang, F; Charrel, R; Foulet, F; Botterel, F; Guillot, J; Chosidow, O; Durand, R

    2015-12-01

    Scabies is an ectoparasitic infestation caused by the mite Sarcoptes scabiei. Currently, S. scabiei is taxonomically divided into different varieties on the basis of host origin. Genetics-based research on scabies has been conducted, but the data on genetic diversity of populations of this mite in humans in Europe are lacking. We evaluated the genetic diversity of populations of S. scabiei. A large series of mites obtained from humans in France and the data of mites from various hosts and geographical areas retrieved from GenBank were included to investigate whether mites are divided into distinct populations. The study of cytochrome c oxidase subunit 1 gene polymorphisms were found to be best suited for phylogenetic analysis. S. scabiei mites were distributed into three genetically distinct clades, with most mites clustering in clades B and C. The Fst value and the Nm value calculated for mites included in clades B and C indicated a strong population structure and a very low gene flow between mites of those clades. The results of the present study not only support the rejection of the hypothesis of panmixia for S. scabiei in humans but also suggest that mites belonging to different clades are genetically isolated. Moreover, the results suggest that the subdivision of S. scabies in varieties according to animal or human hosts is not warranted. In conclusion, S. scabiei mites in humans do not constitute a homogeneous population. Further investigations are now required to assess whether different clinical forms of scabies are associated with particular haplotypes or clades. Copyright © 2015 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

  14. High Genetic Diversity and Distinctiveness of Rear-Edge Climate Relicts Maintained by Ancient Tetraploidisation for Alnus glutinosa

    Science.gov (United States)

    Lepais, Olivier; Muller, Serge D.; Ben Saad-Limam, Samia; Benslama, Mohamed; Rhazi, Laila; Belouahem-Abed, Djamila; Daoud-Bouattour, Amina; Gammar, Amor Mokhtar; Ghrabi-Gammar, Zeineb; Bacles, Cécile Fanny Emilie

    2013-01-01

    Populations located at the rear-edge of a species’ distribution may have disproportionate ecological and evolutionary importance for biodiversity conservation in a changing global environment. Yet genetic studies of such populations remain rare. This study investigates the evolutionary history of North-African low latitude marginal populations of Alnus glutinosa Gaertn., a European tree species that plays a significant ecological role as a keystone of riparian ecosystems. We genotyped 551 adults from 19 populations located across North Africa at 12 microsatellite loci and applied a coalescent-based simulation approach to reconstruct the demographic and evolutionary history of these populations. Surprisingly, Moroccan trees were tetraploids demonstrating a strong distinctiveness of these populations within a species otherwise known as diploid. Best-fitting models of demographic reconstruction revealed the relict nature of Moroccan populations that were found to have withstood past climate change events and to be much older than Algerian and Tunisian populations. This study highlights the complex demographic history that can be encountered in rear-edge distribution margins that here consist of both old stable climate relict and more recent populations, distinctively diverse genetically both quantitatively and qualitatively. We emphasize the high evolutionary and conservation value of marginal rear-edge populations of a keystone riparian species in the context of on-going climate change in the Mediterranean region. PMID:24098677

  15. Phylogeographic Evidence for 2 Genetically Distinct Zoonotic Plasmodium knowlesi Parasites, Malaysia.

    Science.gov (United States)

    Yusof, Ruhani; Ahmed, Md Atique; Jelip, Jenarun; Ngian, Hie Ung; Mustakim, Sahlawati; Hussin, Hani Mat; Fong, Mun Yik; Mahmud, Rohela; Sitam, Frankie Anak Thomas; Japning, J Rovie-Ryan; Snounou, Georges; Escalante, Ananias A; Lau, Yee Ling

    2016-08-01

    Infections of humans with the zoonotic simian malaria parasite Plasmodium knowlesi occur throughout Southeast Asia, although most cases have occurred in Malaysia, where P. knowlesi is now the dominant malaria species. This apparently skewed distribution prompted an investigation of the phylogeography of this parasite in 2 geographically separated regions of Malaysia, Peninsular Malaysia and Malaysian Borneo. We investigated samples collected from humans and macaques in these regions. Haplotype network analyses of sequences from 2 P. knowlesi genes, type A small subunit ribosomal 18S RNA and cytochrome c oxidase subunit I, showed 2 genetically distinct divergent clusters, 1 from each of the 2 regions of Malaysia. We propose that these parasites represent 2 distinct P. knowlesi types that independently became zoonotic. These types would have evolved after the sea-level rise at the end of the last ice age, which separated Malaysian Borneo from Peninsular Malaysia.

  16. Salmonella Typhimurium undergoes distinct genetic adaption during chronic infections of mice

    DEFF Research Database (Denmark)

    Søndberg, Emilie; Jelsbak, Lotte

    2016-01-01

    . In the current study genetic adaptation during experimental chronic S. Typhimurium infections of mice, an established model of chronic typhoid fever, was probed as an approach for studying the molecular mechanisms of host-adaptation during long-term host-association. Results Individually sequence-tagged wild....... Typhi and serve as the reservoir for the disease. The specific mechanisms and adaptive strategies enabling S. Typhi to survive inside the host for extended periods are incompletely understood. Yet, elucidation of these processes is of major importance for improvement of therapeutic strategies...... clones were subjected to whole genome sequencing. Dominant clones isolated from either systemic organs or fecal samples exhibited distinct single nucleotide polymorphisms (SNPs). One mouse appeared to have distinct adapted clones in the spleen and liver, respectively. Three mice were colonized...

  17. Induced neural stem cells from distinct genetic backgrounds exhibit different reprogramming status.

    Science.gov (United States)

    Kim, Sung Min; Lim, Kyung Tae; Kwak, Tae Hwan; Lee, Seung Chan; Im, Jung Hyun; Hali, Sai; In Hwang, Seon; Kim, Dajeong; Hwang, Jeongho; Kim, Kee-Pyo; Chung, Hak-Jae; Kim, Jeong Beom; Ko, Kinarm; Chung, Hyung-Min; Lee, Hoon Taek; Schöler, Hans R; Han, Dong Wook

    2016-03-01

    Somatic cells could be directly converted into induced neural stem cells (iNSCs) by ectopic expression of defined transcription factors. However, the underlying mechanism of direct lineage transition into iNSCs is largely unknown. In this study, we examined the effect of genetic background on the direct conversion process into an iNSC state. The iNSCs from two different mouse strains exhibited the distinct efficiency of lineage conversion as well as clonal expansion. Furthermore, the expression levels of endogenous NSC markers, silencing of transgenes, and in vitro differentiation potential were also different between iNSC lines from different strains. Therefore, our data suggest that the genetic background of starting cells influences the conversion efficiency as well as reprogramming status of directly converted iNSCs. Copyright © 2016 University of Texas at Austin Dell Medical School. Published by Elsevier B.V. All rights reserved.

  18. Generator scheduling under competitive environment using genetic ...

    African Journals Online (AJOL)

    In this paper, genetic algorithm (GA) is used to solve the GENCOs profit based unit commitment problem (PBUCP) in a dayahead competitive electricity markets considering power and reserve generations simultaneously, whereas enhanced lambda iteration (ELI) method is used to solve the economic dispatch (ED) ...

  19. Distinct Genetic Lineages of Bactrocera caudata (Insecta: Tephritidae) Revealed by COI and 16S DNA Sequences

    Science.gov (United States)

    Lim, Phaik-Eem; Tan, Ji; Suana, I. Wayan; Eamsobhana, Praphathip; Yong, Hoi Sen

    2012-01-01

    The fruit fly Bactrocera caudata is a pest species of economic importance in Asia. Its larvae feed on the flowers of Cucurbitaceae such as Cucurbita moschata. To-date it is distinguished from related species based on morphological characters. Specimens of B. caudata from Peninsular Malaysia and Indonesia (Bali and Lombok) were analysed using the partial DNA sequences of cytochrome c oxidase subunit I (COI) and 16S rRNA genes. Both gene sequences revealed that B. caudata from Peninsular Malaysia was distinctly different from B. caudata of Bali and Lombok, without common haplotype between them. Phylogenetic analysis revealed two distinct clades, indicating distinct genetic lineage. The uncorrected ‘p’ distance for COI sequences between B. caudata of Malaysia-Thailand-China and B. caudata of Bali-Lombok was 5.65%, for 16S sequences from 2.76 to 2.99%, and for combined COI and 16S sequences 4.45 to 4.46%. The ‘p’ values are distinctly different from intraspecific ‘p’ distance (0–0.23%). Both the B. caudata lineages are distinctly separated from related species in the subgenus Zeugodacus – B. ascita, B. scutellata, B. ishigakiensis, B. diaphora, B. tau, B. cucurbitae, and B. depressa. Molecular phylogenetic analysis indicates that the B. caudata lineages are closely related to B. ascita sp. B, and form a clade with B. scutellata, B. ishigakiensis, B. diaphora and B. ascita sp. A. This study provides additional baseline for the phylogenetic relationships of Bactrocera fruit flies of the subgenus Zeugodacus. Both the COI and 16S genes could be useful markers for the molecular differentiation and phylogenetic analysis of tephritid fruit flies. PMID:22615962

  20. Distinct genetic lineages of Bactrocera caudata (Insecta: Tephritidae revealed by COI and 16S DNA sequences.

    Directory of Open Access Journals (Sweden)

    Phaik-Eem Lim

    Full Text Available The fruit fly Bactrocera caudata is a pest species of economic importance in Asia. Its larvae feed on the flowers of Cucurbitaceae such as Cucurbita moschata. To-date it is distinguished from related species based on morphological characters. Specimens of B. caudata from Peninsular Malaysia and Indonesia (Bali and Lombok were analysed using the partial DNA sequences of cytochrome c oxidase subunit I (COI and 16S rRNA genes. Both gene sequences revealed that B. caudata from Peninsular Malaysia was distinctly different from B. caudata of Bali and Lombok, without common haplotype between them. Phylogenetic analysis revealed two distinct clades, indicating distinct genetic lineage. The uncorrected 'p' distance for COI sequences between B. caudata of Malaysia-Thailand-China and B. caudata of Bali-Lombok was 5.65%, for 16S sequences from 2.76 to 2.99%, and for combined COI and 16S sequences 4.45 to 4.46%. The 'p' values are distinctly different from intraspecific 'p' distance (0-0.23%. Both the B. caudata lineages are distinctly separated from related species in the subgenus Zeugodacus - B. ascita, B. scutellata, B. ishigakiensis, B. diaphora, B. tau, B. cucurbitae, and B. depressa. Molecular phylogenetic analysis indicates that the B. caudata lineages are closely related to B. ascita sp. B, and form a clade with B. scutellata, B. ishigakiensis, B. diaphora and B. ascita sp. A. This study provides additional baseline for the phylogenetic relationships of Bactrocera fruit flies of the subgenus Zeugodacus. Both the COI and 16S genes could be useful markers for the molecular differentiation and phylogenetic analysis of tephritid fruit flies.

  1. Environment Changes Genetic Effects on Respiratory Conditions and Allergic Phenotypes

    DEFF Research Database (Denmark)

    Song, Yong; Schwager, Michelle J; Backer, Vibeke

    2017-01-01

    The prevalence of asthma and allergic diseases is disproportionately distributed among different populations, with an increasing trend observed in Western countries. Here we investigated how the environment affected genotype-phenotype association in a genetically homogeneous, but geographically s...

  2. Genetic and genotype environment interaction effects for the content ...

    Indian Academy of Sciences (India)

    In view of the paucity of genetic information available on essential amino acids in indica rice, we estimated the genetic main effects and genotype × environment (G × E) interaction effects on the content of essential amino acids. Nine cytoplasmic male sterile lines as females and five restorer lines as males were introduced ...

  3. Genetic and genotype × environment interaction effects for the ...

    Indian Academy of Sciences (India)

    In view of the paucity of genetic information available on essential amino acids in indica rice, we estimated the genetic main effects and genotype × environment (G × E) interaction effects on the content of essential amino acids. Nine cytoplasmic male sterile lines as females and five restorer lines as males were introduced ...

  4. Genetically distinct isolates of Spirocerca sp. from a naturally infected red fox (Vulpes vulpes) from Denmark.

    Science.gov (United States)

    Al-Sabi, Mohammad Nafi Solaiman; Hansen, Mette Sif; Chriél, Mariann; Holm, Elisabeth; Larsen, Gitte; Enemark, Heidi Larsen

    2014-09-15

    Spirocerca lupi causes formation of nodules that may transform into sarcoma in the walls of aorta, esophagus and stomach of infected canids. In February 2013, post mortem examination of a red fox (Vulpes vulpes) hunted in Denmark revealed the presence of several nodules containing adult worms of Spirocerca sp. in the stomach and the omentum. The nodules largely consisted of fibrous tissue with infiltration of mononuclear cells, neutrophilic granulocytes and macrophages with hemosiderin deposition. Parasitological examination by three copromicroscopic methods, sedimentation, flotation with saturated sugar-salt solution, and sieving failed to detect eggs of Spirocerca sp. in feces collected from the colon. This is the first report of spirocercosis in Denmark, and may have been caused by a recent introduction by migrating paratenic or definitive host. Analysis of two overlapping partial sequences of the cox1 gene, from individual worms, revealed distinct genetic variation (7-9%) between the Danish worms and isolates of S. lupi from Europe, Asia and Africa. This was confirmed by phylogenetic analysis that clearly separated the Danish worms from other isolates of S. lupi. The distinct genetic differences of the current worms compared to other isolates of S. lupi may suggest the presence of a cryptic species within Spirocerca. Copyright © 2014 Elsevier B.V. All rights reserved.

  5. Clinical characteristics in genetically distinct forms of the congenital long QT syndrome

    International Nuclear Information System (INIS)

    Kawahara, Yosuke; Sawayama, Toshitami; Samukawa, Masanobu; Nezuo, Shoso; Tanaka, Junji; Suetsuna, Ryoji; Kamiyama, Norio

    1998-01-01

    The clinical characteristics in genetically distinct forms of the congenital long QT syndrome (LQTs) were examined on the balance of bilateral sympathetic nerves, and ECG findings. The subjects (mean: 19.4 years old) were three genetically distinct forms of LQTs, including 3 patients in A-family (the high risk family with sudden death), 2 patients in B-family and 3 patients in C-family. All patients met the standard diagnostic criteria according to Schwartz. As the index of the balance of bilateral sympathetic nerves, the dissociation of Tl and MIBG uptake (D) was examined and the radioactivity ratio (the A/L ratio) of anteroseptal wall to posterolateral wall was calculated. The T-wave patterns of ECG and the situation at syncope were examined. In A-family, all 3 patients showed the lowered A/L ratio, D(+), and similar T-wave patterns in ECG. The syndrome developed at exercise, and their QTc extended at exercise. In B-family, all 2 patients showed normal A/L ratio and long T-wave at QT onset, and their QTc shortened at exercise. All patients had developed syncope at rest. In C-family, all 3 patients showed a little decrease of A/L ratio and similar T-wave patterns. Their QTc extended at exercise. These results suggest that the characteristics of the sympathetic nerve balance, ECG wave patterns and the syndrome may depend on each family. (K.H.)

  6. Streptococcus equi subsp. zooepidemicus isolates from equine infectious endometritis belong to a distinct genetic group.

    Science.gov (United States)

    Rasmussen, Camilla Dooleweerdt; Haugaard, Maria Mathilde; Petersen, Morten Roenn; Nielsen, Jesper Møller; Pedersen, Hanne Gervi; Bojesen, Anders Miki

    2013-04-18

    Streptococcus equi subsp. zooepidemicus is the pathogen most commonly isolated from the uterus of mares. S. zooepidemicus is an opportunistic pathogen and part of the resident flora in the caudal reproductive tract. The aim of this study was to investigate whether a genotypically distinct subpopulation of S. zooepidemicus is associated with endometritis in the mare, by genotyping and comparing uterine S. zooepidemicus strains with isolates from the vagina and clitoral fossa. Mares with (n=18) or without (n=11) clinical symptoms of endometritis were included. Uterine samples were obtained using a guarded endometrial biopsy punch, whereas a swab was used to recover samples from the cranial vagina and the clitoral fossa. If S. zooepidemicus was present, up to three colonies were selected from each anatomical location (max. 9 isolates per mare). Bacterial isolates were characterized by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). S. zooepidemicus was isolated from the endometrium of 12 mares. A total of 88 isolates were analyzed by PFGE: 31 from the endometrium, 26 from the cranial vagina and 31 isolates from the clitoral fossa. For MLST 21 isolates were chosen. Results demonstrated a higher genetic similarity of the isolates obtained from infectious endometritis compared to isolates obtained from the caudal reproductive tract. In conclusion, we demonstrate for the first time that a genetically distinct group of S. zooepidemicus is associated with infectious endometritis in the mare.

  7. Hierarchical spatial genetic structure in a distinct population segment of greater sage-grouse

    Science.gov (United States)

    Oyler-McCance, Sara J.; Casazza, Michael L.; Fike, Jennifer A.; Coates, Peter S.

    2014-01-01

    Greater sage-grouse (Centrocercus urophasianus) within the Bi-State Management Zone (area along the border between Nevada and California) are geographically isolated on the southwestern edge of the species’ range. Previous research demonstrated that this population is genetically unique, with a high proportion of unique mitochondrial DNA (mtDNA) haplotypes and with significant differences in microsatellite allele frequencies compared to populations across the species’ range. As a result, this population was considered a distinct population segment (DPS) and was recently proposed for listing as threatened under the U.S. Endangered Species Act. A more comprehensive understanding of the boundaries of this genetically unique population (where the Bi-State population begins) and an examination of genetic structure within the Bi-State is needed to help guide effective management decisions. We collected DNA from eight sampling locales within the Bi-State (N = 181) and compared those samples to previously collected DNA from the two most proximal populations outside of the Bi-State DPS, generating mtDNA sequence data and amplifying 15 nuclear microsatellites. Both mtDNA and microsatellite analyses support the idea that the Bi-State DPS represents a genetically unique population, which has likely been separated for thousands of years. Seven mtDNA haplotypes were found exclusively in the Bi-State population and represented 73 % of individuals, while three haplotypes were shared with neighboring populations. In the microsatellite analyses both STRUCTURE and FCA separate the Bi-State from the neighboring populations. We also found genetic structure within the Bi-State as both types of data revealed differences between the northern and southern part of the Bi-State and there was evidence of isolation-by-distance. STRUCTURE revealed three subpopulations within the Bi-State consisting of the northern Pine Nut Mountains (PNa), mid Bi-State, and White Mountains (WM) following a

  8. Distinct Immunoregulatory Mechanisms in Mesenchymal Stem Cells: Role of the Cytokine Environment

    Czech Academy of Sciences Publication Activity Database

    Holáň, Vladimír; Heřmánková, Barbora; Boháčová, Pavla; Kössl, Jan; Chudíčková, Milada; Hájková, Michaela; Krulová, Magdaléna; Zajícová, Alena; Javorková, Eliška

    2016-01-01

    Roč. 12, č. 6 (2016), s. 654-663 ISSN 1550-8943 R&D Projects: GA ČR(CZ) GA14-12580S; GA MŠk(CZ) ED1.1.00/02.0109; GA MŠk(CZ) LO1508; GA MŠk(CZ) LO1309 Institutional support: RVO:68378041 Keywords : mesenchymal stem cells * regulatory B cells * cytokine environment Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.967, year: 2016

  9. Koalas (Phascolarctos cinereus) From Queensland Are Genetically Distinct From 2 Populations in Victoria.

    Science.gov (United States)

    Ruiz-Rodriguez, Christina T; Ishida, Yasuko; Murray, Neil D; O'Brien, Stephen J; Graves, Jennifer A M; Greenwood, Alex D; Roca, Alfred L

    2016-01-01

    The koala (Phascolarctos cinereus) suffered population declines and local extirpation due to hunting in the early 20th century, especially in southern Australia. Koalas were subsequently reintroduced to the Brisbane Ranges (BR) and Stony Rises (SR) by translocating individuals from a population on French Island descended from a small number of founders. To examine genetic diversity and north-south differentiation, we genotyped 13 microsatellite markers in 46 wild koalas from the BR and SR, and 27 Queensland koalas kept at the US zoos. The Queensland koalas displayed much higher heterozygosity (H O = 0.73) than the 2 southern Australian koala populations examined: H O = 0.49 in the BR, whereas H O = 0.41 in the SR. This is consistent with the historical accounts of bottlenecks and founder events affecting the southern populations and contrasts with reports of high genetic diversity in some southern populations. The 2 southern Australian koala populations were genetically similar (F ST = 0.018, P = 0.052). By contrast, northern and southern Australian koalas were highly differentiated (F ST = 0.27, P < 0.001), thereby suggesting that geographic structuring should be considered in the conservation management of koalas. Sequencing of 648bp of the mtDNA control region in Queensland koalas found 8 distinct haplotypes, one of which had not been previously detected among koalas. Queensland koalas displayed high mitochondrial haplotype diversity (H = 0.753) and nucleotide diversity (π = 0.0072), indicating along with the microsatellite data that North American zoos have maintained high levels of genetic diversity among their Queensland koalas. © The American Genetic Association 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  10. Genetic approach identifies distinct asthma pathways in overweight vs normal weight children.

    Science.gov (United States)

    Butsch Kovacic, M; Martin, L J; Biagini Myers, J M; He, H; Lindsey, M; Mersha, T B; Khurana Hershey, G K

    2015-08-01

    The pathogenesis of asthma in the context of excess body weight may be distinct from asthma that develops in normal weight children. The study's objective was to explore the biology of asthma in the context of obesity and normal weight status using genetic methodologies. Associations between asthma and SNPs in 49 genes were assessed, as well as, interactions between SNPs and overweight status in child participants of the Greater Cincinnati Pediatric Clinic Repository. Asthma was significantly associated with weight (OR = 1.38; P = 0.037). The number of genes and the magnitude of their associations with asthma were notably greater when considering overweight children alone vs normal weight and overweight children together. When considering weight, distinct sets of asthma-associated genes were observed, many times with opposing effects. We demonstrated that the underlying heterogeneity of asthma is likely due in part to distinct pathogenetic pathways that depend on preceding/comorbid overweight and/or allergy. It is therefore important to consider both obesity and asthma when conducting studies of asthma. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  11. Common and distinct genetic properties of ESCRT-II components in Drosophila.

    Directory of Open Access Journals (Sweden)

    Hans-Martin Herz

    Full Text Available BACKGROUND: Genetic studies in yeast have identified class E vps genes that form the ESCRT complexes required for protein sorting at the early endosome. In Drosophila, mutations of the ESCRT-II component vps25 cause endosomal defects leading to accumulation of Notch protein and increased Notch pathway activity. These endosomal and signaling defects are thought to account for several phenotypes. Depending on the developmental context, two different types of overgrowth can be detected. Tissue predominantly mutant for vps25 displays neoplastic tumor characteristics. In contrast, vps25 mutant clones in a wild-type background trigger hyperplastic overgrowth in a non-autonomous manner. In addition, vps25 mutant clones also promote apoptotic resistance in a non-autonomous manner. PRINCIPAL FINDINGS: Here, we genetically characterize the remaining ESCRT-II components vps22 and vps36. Like vps25, mutants of vps22 and vps36 display endosomal defects, accumulate Notch protein and--when the tissue is predominantly mutant--show neoplastic tumor characteristics. However, despite these common phenotypes, they have distinct non-autonomous phenotypes. While vps22 mutations cause strong non-autonomous overgrowth, they do not affect apoptotic resistance. In contrast, vps36 mutations increase apoptotic resistance, but have little effect on non-autonomous proliferation. Further characterization reveals that although all ESCRT-II mutants accumulate Notch protein, only vps22 and vps25 mutations trigger Notch activity. CONCLUSIONS/SIGNIFICANCE: The ESCRT-II components vps22, vps25 and vps36 display common and distinct genetic properties. Our data redefine the role of Notch for hyperplastic and neoplastic overgrowth in these mutants. While Notch is required for hyperplastic growth, it appears to be dispensable for neoplastic transformation.

  12. Shared versus distinct genetic contributions of mental wellbeing with depression and anxiety symptoms in healthy twins.

    Science.gov (United States)

    Routledge, Kylie M; Burton, Karen L O; Williams, Leanne M; Harris, Anthony; Schofield, Peter R; Clark, C Richard; Gatt, Justine M

    2016-10-30

    Mental wellbeing and mental illness symptoms are typically conceptualized as opposite ends of a continuum, despite only sharing about a quarter in common variance. We investigated the normative variation in measures of wellbeing and of depression and anxiety in 1486 twins who did not meet clinical criteria for an overt diagnosis. We quantified the shared versus distinct genetic and environmental variance between wellbeing and depression and anxiety symptoms. The majority of participants (93%) reported levels of depression and anxiety symptoms within the healthy range, yet only 23% reported a wellbeing score within the "flourishing" range: the remainder were within the ranges of "moderate" (67%) or "languishing" (10%). In twin models, measures of wellbeing and of depression and anxiety shared 50.09% of variance due to genetic factors and 18.27% due to environmental factors; the rest of the variance was due to unique variation impacting wellbeing or depression and anxiety symptoms. These findings suggest that an absence of clinically-significant symptoms of depression and anxiety does not necessarily indicate that an individual is flourishing. Both unique and shared genetic and environmental factors may determine why some individuals flourish in the absence of symptoms while others do not. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  13. Complex Genotype by Environment interactions and changing genetic architectures across thermal environments in the Australian field cricket, Teleogryllus oceanicus

    Science.gov (United States)

    2011-01-01

    Background Biologists studying adaptation under sexual selection have spent considerable effort assessing the relative importance of two groups of models, which hinge on the idea that females gain indirect benefits via mate discrimination. These are the good genes and genetic compatibility models. Quantitative genetic studies have advanced our understanding of these models by enabling assessment of whether the genetic architectures underlying focal phenotypes are congruent with either model. In this context, good genes models require underlying additive genetic variance, while compatibility models require non-additive variance. Currently, we know very little about how the expression of genotypes comprised of distinct parental haplotypes, or how levels and types of genetic variance underlying key phenotypes, change across environments. Such knowledge is important, however, because genotype-environment interactions can have major implications on the potential for evolutionary responses to selection. Results We used a full diallel breeding design to screen for complex genotype-environment interactions, and genetic architectures underlying key morphological traits, across two thermal environments (the lab standard 27°C, and the cooler 23°C) in the Australian field cricket, Teleogryllus oceanicus. In males, complex three-way interactions between sire and dam parental haplotypes and the rearing environment accounted for up to 23 per cent of the scaled phenotypic variance in the traits we measured (body mass, pronotum width and testes mass), and each trait harboured significant additive genetic variance in the standard temperature (27°C) only. In females, these three-way interactions were less important, with interactions between the paternal haplotype and rearing environment accounting for about ten per cent of the phenotypic variance (in body mass, pronotum width and ovary mass). Of the female traits measured, only ovary mass for crickets reared at the cooler

  14. Complex Genotype by Environment interactions and changing genetic architectures across thermal environments in the Australian field cricket, Teleogryllus oceanicus

    Directory of Open Access Journals (Sweden)

    Dowling Damian K

    2011-07-01

    Full Text Available Abstract Background Biologists studying adaptation under sexual selection have spent considerable effort assessing the relative importance of two groups of models, which hinge on the idea that females gain indirect benefits via mate discrimination. These are the good genes and genetic compatibility models. Quantitative genetic studies have advanced our understanding of these models by enabling assessment of whether the genetic architectures underlying focal phenotypes are congruent with either model. In this context, good genes models require underlying additive genetic variance, while compatibility models require non-additive variance. Currently, we know very little about how the expression of genotypes comprised of distinct parental haplotypes, or how levels and types of genetic variance underlying key phenotypes, change across environments. Such knowledge is important, however, because genotype-environment interactions can have major implications on the potential for evolutionary responses to selection. Results We used a full diallel breeding design to screen for complex genotype-environment interactions, and genetic architectures underlying key morphological traits, across two thermal environments (the lab standard 27°C, and the cooler 23°C in the Australian field cricket, Teleogryllus oceanicus. In males, complex three-way interactions between sire and dam parental haplotypes and the rearing environment accounted for up to 23 per cent of the scaled phenotypic variance in the traits we measured (body mass, pronotum width and testes mass, and each trait harboured significant additive genetic variance in the standard temperature (27°C only. In females, these three-way interactions were less important, with interactions between the paternal haplotype and rearing environment accounting for about ten per cent of the phenotypic variance (in body mass, pronotum width and ovary mass. Of the female traits measured, only ovary mass for crickets

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

    DEFF Research Database (Denmark)

    McAuliffe, Laura; Kokotovic, Branko; Ayling, Roger D.

    2004-01-01

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

  16. Distinct cellular and molecular environments support aging-related DNA methylation changes in the substantia nigra.

    Science.gov (United States)

    Fasolino, Maria; Liu, Shuo; Wang, Yinsheng; Zhou, Zhaolan

    2017-01-01

    We aimed to couple brain region-specific changes in global DNA methylation over aging to underlying cellular and molecular environments. We measured two major forms of DNA methylation and analyzed Dnmt, Tet and metabolite levels in the striatum and substantia nigra (SN) over aging in healthy male mice. The ratio of 5-hydroxymethylcytosine to 5-methylcytosine increases over aging in the SN, and 5-hydroxymethylcytosine increases preferentially in dopaminergic neurons. Additionally, this age-dependent alteration in methylation correlates with a reduction in the ratio of α-ketoglutarate to succinate in the SN. Distinct cellular and molecular environments correlate with aging-associated methylation changes in the SN, implicating this epigenetic mechanism in the susceptibility of this brain region to age-related cell loss.

  17. Functional Genetic Screen to Identify Interneurons Governing Behaviorally Distinct Aspects of Drosophila Larval Motor Programs

    Directory of Open Access Journals (Sweden)

    Matt Q. Clark

    2016-07-01

    Full Text Available Drosophila larval crawling is an attractive system to study rhythmic motor output at the level of animal behavior. Larval crawling consists of waves of muscle contractions generating forward or reverse locomotion. In addition, larvae undergo additional behaviors, including head casts, turning, and feeding. It is likely that some neurons (e.g., motor neurons are used in all these behaviors, but the identity (or even existence of neurons dedicated to specific aspects of behavior is unclear. To identify neurons that regulate specific aspects of larval locomotion, we performed a genetic screen to identify neurons that, when activated, could elicit distinct motor programs. We used 165 Janelia CRM-Gal4 lines—chosen for sparse neuronal expression—to ectopically express the warmth-inducible neuronal activator TrpA1, and screened for locomotor defects. The primary screen measured forward locomotion velocity, and we identified 63 lines that had locomotion velocities significantly slower than controls following TrpA1 activation (28°. A secondary screen was performed on these lines, revealing multiple discrete behavioral phenotypes, including slow forward locomotion, excessive reverse locomotion, excessive turning, excessive feeding, immobile, rigid paralysis, and delayed paralysis. While many of the Gal4 lines had motor, sensory, or muscle expression that may account for some or all of the phenotype, some lines showed specific expression in a sparse pattern of interneurons. Our results show that distinct motor programs utilize distinct subsets of interneurons, and provide an entry point for characterizing interneurons governing different elements of the larval motor program.

  18. Distinct Mechanisms of Nuclease-Directed DNA-Structure-Induced Genetic Instability in Cancer Genomes.

    Science.gov (United States)

    Zhao, Junhua; Wang, Guliang; Del Mundo, Imee M; McKinney, Jennifer A; Lu, Xiuli; Bacolla, Albino; Boulware, Stephen B; Zhang, Changsheng; Zhang, Haihua; Ren, Pengyu; Freudenreich, Catherine H; Vasquez, Karen M

    2018-01-30

    Sequences with the capacity to adopt alternative DNA structures have been implicated in cancer etiology; however, the mechanisms are unclear. For example, H-DNA-forming sequences within oncogenes have been shown to stimulate genetic instability in mammals. Here, we report that H-DNA-forming sequences are enriched at translocation breakpoints in human cancer genomes, further implicating them in cancer etiology. H-DNA-induced mutations were suppressed in human cells deficient in the nucleotide excision repair nucleases, ERCC1-XPF and XPG, but were stimulated in cells deficient in FEN1, a replication-related endonuclease. Further, we found that these nucleases cleaved H-DNA conformations, and the interactions of modeled H-DNA with ERCC1-XPF, XPG, and FEN1 proteins were explored at the sub-molecular level. The results suggest mechanisms of genetic instability triggered by H-DNA through distinct structure-specific, cleavage-based replication-independent and replication-dependent pathways, providing critical evidence for a role of the DNA structure itself in the etiology of cancer and other human diseases. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

  19. Coffee, Genetic Variants, and Parkinson's Disease: Gene–Environment Interactions

    OpenAIRE

    Yamada-Fowler, Naomi; Söderkvist, Peter

    2015-01-01

    Studies of gene–environment interactions may help us to understand the disease mechanisms of common and complex diseases such as Parkinson's disease (PD). Sporadic PD, the common form of PD, is thought to be a multifactorial disorder caused by combinations of multiple genetic factors and environmental or life-style exposures. Since one of the most extensively studied life-style factors in PD is coffee/caffeine intake, here, the studies of genetic polymorphisms with life-style interactions of ...

  20. Genetic engineering of microorganisms: free release into the environment

    OpenAIRE

    Morgan, J.A.W.

    1990-01-01

    Genetic engineering now makes possible the insertion of DNA from many organisms into other prokaryotic, eukaryotic and viral hosts. This technology has been used to construct a variety of such genetically engineered microorganisms (GEMs). The possibility of accidental or deliberate release of GEMs into the natural environment has recently raised much public concern. The prospect of deliberate release of these microorganisms has prompted an increased need to understand the processes of surviva...

  1. Distinct genetic architecture underlies the emergence of sleep loss and prey-seeking behavior in the Mexican cavefish.

    Science.gov (United States)

    Yoshizawa, Masato; Robinson, Beatriz G; Duboué, Erik R; Masek, Pavel; Jaggard, James B; O'Quin, Kelly E; Borowsky, Richard L; Jeffery, William R; Keene, Alex C

    2015-02-20

    Sleep is characterized by extended periods of quiescence and reduced responsiveness to sensory stimuli. Animals ranging from insects to mammals adapt to environments with limited food by suppressing sleep and enhancing their response to food cues, yet little is known about the genetic and evolutionary relationship between these processes. The blind Mexican cavefish, Astyanax mexicanus is a powerful model for elucidating the genetic mechanisms underlying behavioral evolution. A. mexicanus comprises an extant ancestral-type surface dwelling morph and at least five independently evolved cave populations. Evolutionary convergence on sleep loss and vibration attraction behavior, which is involved in prey seeking, have been documented in cavefish raising the possibility that enhanced sensory responsiveness underlies changes in sleep. We established a system to study sleep and vibration attraction behavior in adult A. mexicanus and used high coverage quantitative trait loci (QTL) mapping to investigate the functional and evolutionary relationship between these traits. Analysis of surface-cave F2 hybrid fish and an outbred cave population indicates that independent genetic factors underlie changes in sleep/locomotor activity and vibration attraction behavior. High-coverage QTL mapping with genotyping-by-sequencing technology identify two novel QTL intervals that associate with locomotor activity and include the narcolepsy-associated tp53 regulating kinase. These QTLs represent the first genomic localization of locomotor activity in cavefish and are distinct from two QTLs previously identified as associating with vibration attraction behavior. Taken together, these results localize genomic regions underlying sleep/locomotor and sensory changes in cavefish populations and provide evidence that sleep loss evolved independently from enhanced sensory responsiveness.

  2. Population genetic analysis and bioclimatic modeling in Agave striata in the Chihuahuan Desert indicate higher genetic variation and lower differentiation in drier and more variable environments.

    Science.gov (United States)

    Trejo, Laura; Alvarado-Cárdenas, Leonardo O; Scheinvar, Enrique; Eguiarte, Luis E

    2016-06-01

    Is there an association between bioclimatic variables and genetic variation within species? This question can be approached by a detailed analysis of population genetics parameters along environmental gradients in recently originated species (so genetic drift does not further obscure the patterns). The genus Agave, with more than 200 recent species encompassing a diversity of morphologies and distributional patterns, is an adequate system for such analyses. We studied Agave striata, a widely distributed species from the Chihuahuan Desert, with a distinctive iteroparous reproductive ecology and two recognized subspecies with clear morphological differences. We used population genetic analyses along with bioclimatic studies to understand the effect of environment on the genetic variation and differentiation of this species. We analyzed six populations of the subspecies A. striata subsp. striata, with a southern distribution, and six populations of A. striata subsp. falcata, with a northern distribution, using 48 ISSR loci and a total of 541 individuals (averaging 45 individuals per population). We assessed correlations between population genetics parameters (the levels of genetic variation and differentiation) and the bioclimatic variables of each population. We modeled each subspecies distribution and used linear correlations and multifactorial analysis of variance. Genetic variation (measured as expected heterozygosity) increased at higher latitudes. Higher levels of genetic variation in populations were associated with a higher variation in environmental temperature and lower precipitation. Stronger population differentiation was associated with wetter and more variable precipitation in the southern distribution of the species. The two subspecies have genetic differences, which coincide with their climatic differences and potential distributions. Differences in genetic variation among populations and the genetic differentiation between A. striata subsp. striata

  3. Distinct Genetic Diversity of Carbapenem-Resistant Acinetobacter baumannii from Colombian Hospitals.

    Science.gov (United States)

    Correa, Adriana; Del Campo, Rosa; Escandón-Vargas, Kevin; Perenguez, Marcela; Rodríguez-Baños, Mercedes; Hernández-Gómez, Cristhian; Pallares, Christian; Perez, Federico; Arias, Cesar A; Cantón, Rafael; Villegas, María V

    The global success of multidrug-resistant Acinetobacter baumannii has been associated with the dissemination of a high-risk clone designated clonal complex (CC) 92 B (Bartual scheme)/CC2 P (Pasteur scheme), which is the most frequent genetic lineage in European, Asian, and North American carbapenem-resistant Acinetobacter isolates. In these isolates, carbapenem resistance is mainly mediated by β-lactamases encoded by bla OXA-23-like , bla OXA-24-like , bla OXA-51-like , and/or bla OXA-58-like genes. In this study, we characterized the population genetics of 121 carbapenem-resistant A. baumannii complex isolates recovered from 14 hospitals in seven cities in Colombia (2008-2010). Multiplex PCR was used to detect bla OXA-23-like , bla OXA-24-like , bla OXA-51-like , and bla OXA-58-like genes. Molecular typing was performed using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). PCR showed that 118 (97.5%) of the isolates were positive for both bla OXA-23-like and bla OXA-51-like genes, and three other isolates were only positive for bla OXA-51-like . PFGE identified 18 different pulsotypes, while MLST identified 11 different sequence types (STs), seven of which had not been previously described in Acinetobacter. None of the STs found in this study was associated with CC92 B /CC2 P . The most widespread STs in our isolates belonged to ST636 and their single-locus variants ST121/ST124/ST634 (CC636 B ) followed by STs belonging to CC110 B . Our observations suggest a wide distribution of diverse A. baumannii complex clones containing bla OXA-23-like in Colombian hospitals (especially CC636 B and CC110 B ) that differ from the high-risk clones commonly found in other regions of the world, indicating a distinct molecular epidemiology of carbapenem-resistant Acinetobacter spp. in Colombia.

  4. Cross-packaging of genetically distinct mouse and primate retroviral RNAs

    Directory of Open Access Journals (Sweden)

    Jaballah Soumeya

    2009-07-01

    Full Text Available Abstract Background The mouse mammary tumor virus (MMTV is unique from other retroviruses in having multiple viral promoters, which can be regulated by hormones in a tissue specific manner. This unique property has lead to increased interest in studying MMTV replication with the hope of developing MMTV based vectors for human gene therapy. However, it has recently been reported that related as well as unrelated retroviruses can cross-package each other's genome raising safety concerns towards the use of candidate retroviral vectors for human gene therapy. Therefore, using a trans complementation assay, we looked at the ability of MMTV RNA to be cross-packaged and propagated by an unrelated primate Mason-Pfizer monkey virus (MPMV that has intracellular assembly process similar to that of MMTV. Results Our results revealed that MMTV and MPMV RNAs could be cross-packaged by the heterologous virus particles reciprocally suggesting that pseudotyping between two genetically distinct retroviruses can take place at the RNA level. However, the cross-packaged RNAs could not be propagated further indicating a block at post-packaging events in the retroviral life cycle. To further confirm that the specificity of cross-packaging was conferred by the packaging sequences (ψ, we cloned the packaging sequences of these viruses on expression plasmids that generated non-viral RNAs. Test of these non-viral RNAs confirmed that the reciprocal cross-packaging was primarily due to the recognition of ψ by the heterologous virus proteins. Conclusion The results presented in this study strongly argue that MPMV and MMTV are promiscuous in their ability to cross-package each other's genome suggesting potential RNA-protein interactions among divergent retroviral RNAs proposing that these interactions are more complicated than originally thought. Furthermore, these observations raise the possibility that MMTV and MPMV genomes could also co-package providing substrates for

  5. The Hydrodynamic Distinctiveness of Living Organisms: Communication in Complex Hydraulic Environments

    Science.gov (United States)

    Johnson, M.

    2015-12-01

    Animals make decisions about the suitability of habitat and their reaction to other organisms based on the sensory information that they first obtain. This information is transmitted, masked and filtered by fluvial processes, such as turbulent flow. Despite governing how animals interact with the environment, limited attention has been paid to the controls on the propagation of sensory signals through rivers. Some animals interpret hydraulic events and use the characteristics of wakes to sense the presence of other organisms. This implies that at least some animals can differentiate turbulent flow generated by the presence of living organisms from ambient environmental turbulence. We investigate whether there are specific flow characteristics, distinct from the ambient environment, that potentially flag the presence of organisms to other animals. ADV and PIV measurements in a series of laboratory flume experiments quantified the flow around living Signal Crayfish (Pacifastacus leniusculus) and two inanimate objects of equivalent shape and size. Experiments were repeated across a gradient of turbulence intensities generated over nine combinations of flow velocity and relative submergence. Flows downstream of living crayfish were distinct from inanimate objects, with greater turbulent intensities, higher energy in low- to intermediate frequencies, and flow structures that were less coherent in comparison to those measured downstream of inanimate objects. However, the hydrodynamic signature of crayfish became masked as the intensity of ambient turbulence exceeded that generated by living crayfish. These results demonstrate the importance of the fluvial processes in the transmission of sensory information and suggest that the ability of animals to perceive hydraulic signatures is likely to be limited in many situations in rivers. Thus, animals may need to rely on other senses, such as sight or hearing, especially where depth is shallow relative to grain size.

  6. Understanding the Science-Learning Environment: A Genetically Sensitive Approach

    Science.gov (United States)

    Haworth, Claire M. A.; Davis, Oliver S. P.; Hanscombe, Ken B.; Kovas, Yulia; Dale, Philip S.; Plomin, Robert

    2013-01-01

    Previous studies have shown that environmental influences on school science performance increase in importance from primary to secondary school. Here we assess for the first time the relationship between the science-learning environment and science performance using a genetically sensitive approach to investigate the aetiology of this link. 3000…

  7. Age of Jupiter inferred from the distinct genetics and formation times of meteorites.

    Science.gov (United States)

    Kruijer, Thomas S; Burkhardt, Christoph; Budde, Gerrit; Kleine, Thorsten

    2017-06-27

    The age of Jupiter, the largest planet in our Solar System, is still unknown. Gas-giant planet formation likely involved the growth of large solid cores, followed by the accumulation of gas onto these cores. Thus, the gas-giant cores must have formed before dissipation of the solar nebula, which likely occurred within less than 10 My after Solar System formation. Although such rapid accretion of the gas-giant cores has successfully been modeled, until now it has not been possible to date their formation. Here, using molybdenum and tungsten isotope measurements on iron meteorites, we demonstrate that meteorites derive from two genetically distinct nebular reservoirs that coexisted and remained spatially separated between ∼1 My and ∼3-4 My after Solar System formation. The most plausible mechanism for this efficient separation is the formation of Jupiter, opening a gap in the disk and preventing the exchange of material between the two reservoirs. As such, our results indicate that Jupiter's core grew to ∼20 Earth masses within Jupiter is the oldest planet of the Solar System, and its solid core formed well before the solar nebula gas dissipated, consistent with the core accretion model for giant planet formation.

  8. Genetic distinctiveness of the Herdwick sheep breed and two other locally adapted hill breeds of the UK.

    Science.gov (United States)

    Bowles, Dianna; Carson, Amanda; Isaac, Peter

    2014-01-01

    There is considerable interest in locally adapted breeds of livestock as reservoirs of genetic diversity that may provide important fitness traits for future use in agriculture. In marginal areas, these animals contribute to food security and extract value from land unsuitable for other systems of farming. In England, close to 50% of the national sheep flock is farmed on grassland designated as disadvantaged areas for agricultural production. Many of these areas are in the uplands, where some native breeds of sheep continue to be commercially farmed only in highly localised geographical regions to which they are adapted. This study focuses on three of these breeds, selected for their adaptation to near identical environments and their geographical concentration in regions close to one another. Our objective has been to use retrotyping, microsatellites and single nucleotide polymorphisms to explore the origins of the breeds and whether, despite their similar adaptations and proximity, they are genetically distinctive. We find the three breeds each have a surprisingly different pattern of retrovirus insertions into their genomes compared with one another and with other UK breeds. Uniquely, there is a high incidence of the R0 retrotype in the Herdwick population, characteristic of a primitive genome found previously in very few breeds worldwide and none in the UK mainland. The Herdwick and Rough Fells carry two rare retroviral insertion events, common only in Texels, suggesting sheep populations in the northern uplands have a historical association with the original pin-tail sheep of Texel Island. Microsatellite data and analyses of SNPs associated with RXFP2 (horn traits) and PRLR (reproductive performance traits) also distinguished the three breeds. Significantly, an SNP linked to TMEM154, a locus controlling susceptibility to infection by Maedi-Visna, indicated that all three native hill breeds have a lower than average risk of infection to the lentivirus.

  9. Genetic distinctiveness of the Herdwick sheep breed and two other locally adapted hill breeds of the UK.

    Directory of Open Access Journals (Sweden)

    Dianna Bowles

    Full Text Available There is considerable interest in locally adapted breeds of livestock as reservoirs of genetic diversity that may provide important fitness traits for future use in agriculture. In marginal areas, these animals contribute to food security and extract value from land unsuitable for other systems of farming. In England, close to 50% of the national sheep flock is farmed on grassland designated as disadvantaged areas for agricultural production. Many of these areas are in the uplands, where some native breeds of sheep continue to be commercially farmed only in highly localised geographical regions to which they are adapted. This study focuses on three of these breeds, selected for their adaptation to near identical environments and their geographical concentration in regions close to one another. Our objective has been to use retrotyping, microsatellites and single nucleotide polymorphisms to explore the origins of the breeds and whether, despite their similar adaptations and proximity, they are genetically distinctive. We find the three breeds each have a surprisingly different pattern of retrovirus insertions into their genomes compared with one another and with other UK breeds. Uniquely, there is a high incidence of the R0 retrotype in the Herdwick population, characteristic of a primitive genome found previously in very few breeds worldwide and none in the UK mainland. The Herdwick and Rough Fells carry two rare retroviral insertion events, common only in Texels, suggesting sheep populations in the northern uplands have a historical association with the original pin-tail sheep of Texel Island. Microsatellite data and analyses of SNPs associated with RXFP2 (horn traits and PRLR (reproductive performance traits also distinguished the three breeds. Significantly, an SNP linked to TMEM154, a locus controlling susceptibility to infection by Maedi-Visna, indicated that all three native hill breeds have a lower than average risk of infection to the

  10. ACPA-Negative RA Consists of Two Genetically Distinct Subsets Based on RF Positivity in Japanese

    Science.gov (United States)

    Terao, Chikashi; Ohmura, Koichiro; Ikari, Katsunori; Kochi, Yuta; Maruya, Etsuko; Katayama, Masaki; Yurugi, Kimiko; Shimada, Kota; Murasawa, Akira; Honjo, Shigeru; Takasugi, Kiyoshi; Matsuo, Keitaro; Tajima, Kazuo; Suzuki, Akari; Yamamoto, Kazuhiko; Momohara, Shigeki; Yamanaka, Hisashi; Yamada, Ryo; Saji, Hiroo; Matsuda, Fumihiko; Mimori, Tsuneyo

    2012-01-01

    HLA-DRB1, especially the shared epitope (SE), is strongly associated with rheumatoid arthritis (RA). However, recent studies have shown that SE is at most weakly associated with RA without anti-citrullinated peptide/protein antibody (ACPA). We have recently reported that ACPA-negative RA is associated with specific HLA-DRB1 alleles and diplotypes. Here, we attempted to detect genetically different subsets of ACPA-negative RA by classifying ACPA-negative RA patients into two groups based on their positivity for rheumatoid factor (RF). HLA-DRB1 genotyping data for totally 954 ACPA-negative RA patients and 2,008 healthy individuals in two independent sets were used. HLA-DRB1 allele and diplotype frequencies were compared among the ACPA-negative RF-positive RA patients, ACPA-negative RF-negative RA patients, and controls in each set. Combined results were also analyzed. A similar analysis was performed in 685 ACPA-positive RA patients classified according to their RF positivity. As a result, HLA-DRB1*04:05 and *09:01 showed strong associations with ACPA-negative RF-positive RA in the combined analysis (p = 8.8×10−6 and 0.0011, OR: 1.57 (1.28–1.91) and 1.37 (1.13–1.65), respectively). We also found that HLA-DR14 and the HLA-DR8 homozygote were associated with ACPA-negative RF-negative RA (p = 0.00022 and 0.00013, OR: 1.52 (1.21–1.89) and 3.08 (1.68–5.64), respectively). These association tendencies were found in each set. On the contrary, we could not detect any significant differences between ACPA-positive RA subsets. As a conclusion, ACPA-negative RA includes two genetically distinct subsets according to RF positivity in Japan, which display different associations with HLA-DRB1. ACPA-negative RF-positive RA is strongly associated with HLA-DRB1*04:05 and *09:01. ACPA-negative RF-negative RA is associated with DR14 and the HLA-DR8 homozygote. PMID:22792215

  11. Distinct Aeromonas Populations in Water Column and Associated with Copepods from Estuarine Environment (Seine, France

    Directory of Open Access Journals (Sweden)

    Gautier Chaix

    2017-07-01

    Full Text Available Aeromonas spp. are ubiquitous bacteria primarily recovered from aquatic ecosystems. They are found in fresh water as well as estuarine and marine waters, and in association with numerous autochthonous aquatic organisms in these environments. However, aeromonads are also etiologic agents of fish diseases and are now recognized as emerging pathogens in humans. The estuary is therefore a key environment, harboring autochthonous aeromonads, and aeromonads originating from humans and animals, mainly released by treated WWTP effluent or watershed run-off via tributaries. The present study compares the abundance and the diversity of Aeromonas populations. Over 2 years of monitoring (eight campaigns from February 2013 to November 2015, the occurrence of Aeromonas was investigated within the water column (water and fluid mud and in association with copepods. Moreover, the diversity of Aeromonas populations was ascertained by analyzing gyrB and radA sequences, and the antibiotic-resistance phenotypes were determined using the disk diffusion method. This study shows, for the first time, the presence of Aeromonas spp. in water (1.1 × 102 to 1.2 ± 0.3 × 103 CFU.100 mL-1, fluid mud (2.6 ± 2.6 × 102 to 9.8 ± 0.9 × 103 CFU.g-1 and in association with living copepods (1.9 ± 0.7 × 102 to >1.1 × 104 CFU.g-1 in the Seine estuary. Moreover, the diversity study, conducted on 36 strains isolated from the water column and 47 strains isolated from copepods, indicates distinct populations within these two compartments. Strains distributed in five clusters corresponding to A. bestiarum (n = 6; 5.45%, A. encheleia (n = 1; 0.91%, A. media (n = 22; 20.0%, A. rivipollensis (n = 34; 30.91% and A. salmonicida (n = 47; 42.73%. A. salmonicida is the most abundant species associated with Eurytemora affinis (n = 35; 74.47%. In contrast, A. salmonicida accounts for only 30.56% (n = 11 of isolates in the water column. This study shows the coexistence of distinct populations

  12. Ovarian carcinomas with genetic and epigenetic BRCA1 loss have distinct molecular abnormalities

    Directory of Open Access Journals (Sweden)

    Miller Dianne M

    2008-01-01

    Full Text Available Background Subclassification of ovarian carcinomas can be used to guide treatment and determine prognosis. Germline and somatic mutations, loss of heterozygosity (LOH, and epigenetic events such as promoter hypermethylation can lead to decreased expression of BRCA1/2 in ovarian cancers. The mechanism of BRCA1/2 loss is a potential method of subclassifying high grade serous carcinomas. Methods A consecutive series of 49 ovarian cancers was assessed for mutations status of BRCA1 and BRCA2, LOH at the BRCA1 and BRCA2 loci, methylation of the BRCA1 promoter, BRCA1, BRCA2, PTEN, and PIK3CA transcript levels, PIK3CA gene copy number, and BRCA1, p21, p53, and WT-1 immunohistochemistry. Results Eighteen (37% of the ovarian carcinomas had germline or somatic BRCA1 mutations, or epigenetic loss of BRCA1. All of these tumours were high-grade serous or undifferentiated type. None of the endometrioid (n = 5, clear cell (n = 4, or low grade serous (n = 2 carcinomas showed loss of BRCA1, whereas 47% of the 38 high-grade serous or undifferentiated carcinomas had loss of BRCA1. It was possible to distinguish high grade serous carcinomas with BRCA1 mutations from those with epigenetic BRCA1 loss: tumours with BRCA1 mutations typically had decreased PTEN mRNA levels while those with epigenetic loss of BRCA1 had copy number gain of PIK3CA. Overexpression of p53 with loss of p21 expression occurred significantly more frequently in high grade serous carcinomas with epigenetic loss of BRCA1, compared to high grade serous tumors without loss of BRCA1. Conclusion High grade serous carcinomas can be subclassified into three groups: BRCA1 loss (genetic, BRCA1 loss (epigenetic, and no BRCA1 loss. Tumors in these groups show distinct molecular alterations involving the PI3K/AKT and p53 pathways.

  13. Ovarian carcinomas with genetic and epigenetic BRCA1 loss have distinct molecular abnormalities

    International Nuclear Information System (INIS)

    Press, Joshua Z; Smith, Margaret; Spellman, Paul T; Wang, Yuker; Miller, Dianne M; Horsman, Doug; Faham, Malek; Gilks, C Blake; Gray, Joe; Huntsman, David G; De Luca, Alessandro; Boyd, Niki; Young, Sean; Troussard, Armelle; Ridge, Yolanda; Kaurah, Pardeep; Kalloger, Steve E; Blood, Katherine A

    2008-01-01

    Subclassification of ovarian carcinomas can be used to guide treatment and determine prognosis. Germline and somatic mutations, loss of heterozygosity (LOH), and epigenetic events such as promoter hypermethylation can lead to decreased expression of BRCA1/2 in ovarian cancers. The mechanism of BRCA1/2 loss is a potential method of subclassifying high grade serous carcinomas. A consecutive series of 49 ovarian cancers was assessed for mutations status of BRCA1 and BRCA2, LOH at the BRCA1 and BRCA2 loci, methylation of the BRCA1 promoter, BRCA1, BRCA2, PTEN, and PIK3CA transcript levels, PIK3CA gene copy number, and BRCA1, p21, p53, and WT-1 immunohistochemistry. Eighteen (37%) of the ovarian carcinomas had germline or somatic BRCA1 mutations, or epigenetic loss of BRCA1. All of these tumours were high-grade serous or undifferentiated type. None of the endometrioid (n = 5), clear cell (n = 4), or low grade serous (n = 2) carcinomas showed loss of BRCA1, whereas 47% of the 38 high-grade serous or undifferentiated carcinomas had loss of BRCA1. It was possible to distinguish high grade serous carcinomas with BRCA1 mutations from those with epigenetic BRCA1 loss: tumours with BRCA1 mutations typically had decreased PTEN mRNA levels while those with epigenetic loss of BRCA1 had copy number gain of PIK3CA. Overexpression of p53 with loss of p21 expression occurred significantly more frequently in high grade serous carcinomas with epigenetic loss of BRCA1, compared to high grade serous tumors without loss of BRCA1. High grade serous carcinomas can be subclassified into three groups: BRCA1 loss (genetic), BRCA1 loss (epigenetic), and no BRCA1 loss. Tumors in these groups show distinct molecular alterations involving the PI3K/AKT and p53 pathways

  14. Ovarian carcinomas with genetic and epigenetic BRCA1 loss have distinct molecular abnormalities

    Energy Technology Data Exchange (ETDEWEB)

    Gilks, C. Blake; Press, Joshua Z.; De Luca, Alessandro; Boyd, Niki; Young, Sean; Troussard, Armelle; Ridge, Yolanda; Kaurah, Pardeep; Kalloger, Steve E.; Blood, Katherine A.; Smith, Margaret; Spellman, Paul T.; Wang, Yuker; Miller, Dianne M.; Horsman, Doug; Faham, Malek; Gilks, C. Blake; Gray, Joe; Huntsman, David G.

    2008-05-02

    Subclassification of ovarian carcinomas can be used to guide treatment and determine prognosis. Germline and somatic mutations, loss of heterozygosity (LOH), and epigenetic events such as promoter hypermethylation can lead to decreased expression of BRCA1/2 in ovarian cancers. The mechanism of BRCA1/2 loss is a potential method of subclassifying high grade serous carcinomas. A consecutive series of 49 ovarian cancers was assessed for mutations status of BRCA1 and BRCA2, LOH at the BRCA1 and BRCA2 loci, methylation of the BRCA1 promoter, BRCA1, BRCA2, PTEN, and PIK3CA transcript levels, PIK3CA gene copy number, and BRCA1, p21, p53, and WT-1 immunohistochemistry. Eighteen (37%) of the ovarian carcinomas had germline or somatic BRCA1 mutations, or epigenetic loss of BRCA1. All of these tumors were high-grade serous or undifferentiated type. None of the endometrioid (n=5), clear cell (n=4), or low grade serous (n=2) carcinomas showed loss of BRCA1, whereas 47% of the 38 high-grade serous or undifferentiated carcinomas had loss of BRCA1. It was possible to distinguish high grade serous carcinomas with BRCA1 mutations from those with epigenetic BRCA1 loss: tumors with BRCA1 mutations typically had decreased PTEN mRNA levels while those with epigenetic loss of BRCA1 had copy number gain of PIK3CA. Overexpression of p53 with loss of p21 expression occurred significantly more frequently in high grade serous carcinomas with epigenetic loss of BRCA1, compared to high grade serous tumors without loss of BRCA1. High grade serous carcinomas can be subclassified into three groups: BRCA1 loss (genetic), BRCA1 loss (epigenetic), and no BRCA1 loss. Tumors in these groups show distinct molecular alterations involving the PI3K/AKT and p53 pathways.

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

    Directory of Open Access Journals (Sweden)

    David W G Stanton

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

  16. The contribution of genetics and environment to obesity.

    Science.gov (United States)

    Albuquerque, David; Nóbrega, Clévio; Manco, Licínio; Padez, Cristina

    2017-09-01

    Obesity is a global health problem mainly attributed to lifestyle changes such as diet, low physical activity or socioeconomics factors. However, several evidences consistently showed that genetics contributes significantly to the weight-gain susceptibility. A systematic literature search of most relevant original, review and meta-analysis, restricted to English was conducted in PubMed, Web of Science and Google scholar up to May 2017 concerning the contribution of genetics and environmental factors to obesity. Several evidences suggest that obesogenic environments contribute to the development of an obese phenotype. However, not every individual from the same population, despite sharing the same obesogenic environment, develop obesity. After more than 10 years of investigation on the genetics of obesity, the variants found associated with obesity represent only 3% of the estimated BMI-heritability, which is around 47-80%. Moreover, genetic factors per se were unable to explain the rapid spread of obesity prevalence. The integration of multi-omics data enables scientists having a better picture and to elucidate unknown pathways contributing to obesity. New studies based on case-control or gene candidate approach will be important to identify new variants associated with obesity susceptibility and consequently unveiling its genetic architecture. This will lead to an improvement of our understanding about underlying mechanisms involved in development and origin of the actual obesity epidemic. The integration of several omics will also provide insights about the interplay between genes and environments contributing to the obese phenotype. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

  17. Comparative linkage meta-analysis reveals regionally-distinct, disparate genetic architectures: application to bipolar disorder and schizophrenia.

    Directory of Open Access Journals (Sweden)

    Brady Tang

    2011-04-01

    Full Text Available New high-throughput, population-based methods and next-generation sequencing capabilities hold great promise in the quest for common and rare variant discovery and in the search for "missing heritability." However, the optimal analytic strategies for approaching such data are still actively debated, representing the latest rate-limiting step in genetic progress. Since it is likely a majority of common variants of modest effect have been identified through the application of tagSNP-based microarray platforms (i.e., GWAS, alternative approaches robust to detection of low-frequency (1-5% MAF and rare (<1% variants are of great importance. Of direct relevance, we have available an accumulated wealth of linkage data collected through traditional genetic methods over several decades, the full value of which has not been exhausted. To that end, we compare results from two different linkage meta-analysis methods--GSMA and MSP--applied to the same set of 13 bipolar disorder and 16 schizophrenia GWLS datasets. Interestingly, we find that the two methods implicate distinct, largely non-overlapping, genomic regions. Furthermore, based on the statistical methods themselves and our contextualization of these results within the larger genetic literatures, our findings suggest, for each disorder, distinct genetic architectures may reside within disparate genomic regions. Thus, comparative linkage meta-analysis (CLMA may be used to optimize low-frequency and rare variant discovery in the modern genomic era.

  18. ASD and schizophrenia show distinct developmental profiles in common genetic overlap with population-based social communication difficulties.

    Science.gov (United States)

    St Pourcain, B; Robinson, E B; Anttila, V; Sullivan, B B; Maller, J; Golding, J; Skuse, D; Ring, S; Evans, D M; Zammit, S; Fisher, S E; Neale, B M; Anney, R J L; Ripke, S; Hollegaard, M V; Werge, T; Ronald, A; Grove, J; Hougaard, D M; Børglum, A D; Mortensen, P B; Daly, M J; Davey Smith, G

    2018-02-01

    Difficulties in social communication are part of the phenotypic overlap between autism spectrum disorders (ASD) and schizophrenia. Both conditions follow, however, distinct developmental patterns. Symptoms of ASD typically occur during early childhood, whereas most symptoms characteristic of schizophrenia do not appear before early adulthood. We investigated whether overlap in common genetic influences between these clinical conditions and impairments in social communication depends on the developmental stage of the assessed trait. Social communication difficulties were measured in typically-developing youth (Avon Longitudinal Study of Parents and Children, N⩽5553, longitudinal assessments at 8, 11, 14 and 17 years) using the Social Communication Disorder Checklist. Data on clinical ASD (PGC-ASD: 5305 cases, 5305 pseudo-controls; iPSYCH-ASD: 7783 cases, 11 359 controls) and schizophrenia (PGC-SCZ2: 34 241 cases, 45 604 controls, 1235 trios) were either obtained through the Psychiatric Genomics Consortium (PGC) or the Danish iPSYCH project. Overlap in genetic influences between ASD and social communication difficulties during development decreased with age, both in the PGC-ASD and the iPSYCH-ASD sample. Genetic overlap between schizophrenia and social communication difficulties, by contrast, persisted across age, as observed within two independent PGC-SCZ2 subsamples, and showed an increase in magnitude for traits assessed during later adolescence. ASD- and schizophrenia-related polygenic effects were unrelated to each other and changes in trait-disorder links reflect the heterogeneity of genetic factors influencing social communication difficulties during childhood versus later adolescence. Thus, both clinical ASD and schizophrenia share some genetic influences with impairments in social communication, but reveal distinct developmental profiles in their genetic links, consistent with the onset of clinical symptoms.

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

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    Jorge Assis

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

  20. Genetic distinction between contiguous urban and rural multimammate mice in Tanzania despite gene flow

    Czech Academy of Sciences Publication Activity Database

    Gryseels, S.; Goüy de Bellocq, Joëlle; Makundi, R.; Vanmechelen, K.; Broeckhove, J.; Mazoch, V.; Šumbera, R.; Zima Jr., Jan; Leirs, H.; Baird, Stuart J. E.

    2016-01-01

    Roč. 29, č. 10 (2016), s. 1952-1967 ISSN 1010-061X R&D Projects: GA ČR GCP502/11/J070; GA ČR GAP506/10/0983; GA MŠk EE2.3.20.0303 Institutional support: RVO:68081766 Keywords : Mastomys natalensis * urbanisation * synanthropy * population genetics * IMa2 * spatial genetics * Tanzania Subject RIV: EG - Zoology Impact factor: 2.792, year: 2016

  1. Assessing Genetic Structure in Common but Ecologically Distinct Carnivores: The Stone Marten and Red Fox.

    Science.gov (United States)

    Basto, Mafalda P; Santos-Reis, Margarida; Simões, Luciana; Grilo, Clara; Cardoso, Luís; Cortes, Helder; Bruford, Michael W; Fernandes, Carlos

    2016-01-01

    The identification of populations and spatial genetic patterns is important for ecological and conservation research, and spatially explicit individual-based methods have been recognised as powerful tools in this context. Mammalian carnivores are intrinsically vulnerable to habitat fragmentation but not much is known about the genetic consequences of fragmentation in common species. Stone martens (Martes foina) and red foxes (Vulpes vulpes) share a widespread Palearctic distribution and are considered habitat generalists, but in the Iberian Peninsula stone martens tend to occur in higher quality habitats. We compared their genetic structure in Portugal to see if they are consistent with their differences in ecological plasticity, and also to illustrate an approach to explicitly delineate the spatial boundaries of consistently identified genetic units. We analysed microsatellite data using spatial Bayesian clustering methods (implemented in the software BAPS, GENELAND and TESS), a progressive partitioning approach and a multivariate technique (Spatial Principal Components Analysis-sPCA). Three consensus Bayesian clusters were identified for the stone marten. No consensus was achieved for the red fox, but one cluster was the most probable clustering solution. Progressive partitioning and sPCA suggested additional clusters in the stone marten but they were not consistent among methods and were geographically incoherent. The contrasting results between the two species are consistent with the literature reporting stricter ecological requirements of the stone marten in the Iberian Peninsula. The observed genetic structure in the stone marten may have been influenced by landscape features, particularly rivers, and fragmentation. We suggest that an approach based on a consensus clustering solution of multiple different algorithms may provide an objective and effective means to delineate potential boundaries of inferred subpopulations. sPCA and progressive partitioning

  2. Assessing Genetic Structure in Common but Ecologically Distinct Carnivores: The Stone Marten and Red Fox.

    Directory of Open Access Journals (Sweden)

    Mafalda P Basto

    Full Text Available The identification of populations and spatial genetic patterns is important for ecological and conservation research, and spatially explicit individual-based methods have been recognised as powerful tools in this context. Mammalian carnivores are intrinsically vulnerable to habitat fragmentation but not much is known about the genetic consequences of fragmentation in common species. Stone martens (Martes foina and red foxes (Vulpes vulpes share a widespread Palearctic distribution and are considered habitat generalists, but in the Iberian Peninsula stone martens tend to occur in higher quality habitats. We compared their genetic structure in Portugal to see if they are consistent with their differences in ecological plasticity, and also to illustrate an approach to explicitly delineate the spatial boundaries of consistently identified genetic units. We analysed microsatellite data using spatial Bayesian clustering methods (implemented in the software BAPS, GENELAND and TESS, a progressive partitioning approach and a multivariate technique (Spatial Principal Components Analysis-sPCA. Three consensus Bayesian clusters were identified for the stone marten. No consensus was achieved for the red fox, but one cluster was the most probable clustering solution. Progressive partitioning and sPCA suggested additional clusters in the stone marten but they were not consistent among methods and were geographically incoherent. The contrasting results between the two species are consistent with the literature reporting stricter ecological requirements of the stone marten in the Iberian Peninsula. The observed genetic structure in the stone marten may have been influenced by landscape features, particularly rivers, and fragmentation. We suggest that an approach based on a consensus clustering solution of multiple different algorithms may provide an objective and effective means to delineate potential boundaries of inferred subpopulations. sPCA and progressive

  3. Short-range phenotypic divergence among genetically distinct parapatric populations of an Australian funnel-web spider.

    Science.gov (United States)

    Wong, Mark K L; Woodman, James D; Rowell, David M

    2017-07-01

    Speciation involves divergence at genetic and phenotypic levels. Where substantial genetic differentiation exists among populations, examining variation in multiple phenotypic characters may elucidate the mechanisms by which divergence and speciation unfold. Previous work on the Australian funnel-web spider Atrax sutherlandi Gray (2010; Records of the Australian Museum 62 , 285-392; Mygalomorphae: Hexathelidae: Atracinae) has revealed a marked genetic structure along a 110-kilometer transect, with six genetically distinct, parapatric populations attributable to past glacial cycles. In the present study, we explore variation in three classes of phenotypic characters (metabolic rate, water loss, and morphological traits) within the context of this phylogeographic structuring. Variation in metabolic and water loss rates shows no detectable association with genetic structure; the little variation observed in these rates may be due to the spiders' behavioral adaptations (i.e., burrowing), which buffer the effects of climatic gradients across the landscape. However, of 17 morphological traits measured, 10 show significant variation among genetic populations, in a disjunct manner that is clearly not latitudinal. Moreover, patterns of variation observed for morphological traits serving different organismic functions (e.g., prey capture, burrowing, and locomotion) are dissimilar. In contrast, a previous study of an ecologically similar sympatric spider with little genetic structure indicated a strong latitudinal response in 10 traits over the same range. The congruence of morphological variation with deep phylogeographic structure in Tallaganda's A. sutherlandi populations, as well as the inconsistent patterns of variation across separate functional traits, suggest that the spiders are likely in early stages of speciation, with parapatric populations independently responding to local selective forces.

  4. Genetic and environmental influences on the ages of drinking and gambling initiation: evidence for distinct aetiologies and sex differences.

    Science.gov (United States)

    Richmond-Rakerd, Leah S; Slutske, Wendy S; Heath, Andrew C; Martin, Nicholas G

    2014-02-01

    To investigate the genetic and environmental contributions to age at first drink (AFD) and age first gambled (AFG), assess their overlap and examine sex differences. Univariate twin models were fitted to decompose the variation in AFD and AFG into additive genetic, shared environmental and unique environmental factors. Bivariate genetic models were fitted to assess the genetic and environmental contributions to the sources of covariation in AFD and AFG. National Australian Twin Registry. A total of 4542 same-sex and opposite-sex twins aged 32-43 years, 42% male and 58% female. AFD and AFG were assessed via structured psychiatric telephone interviews. Age of onset was treated as both continuous and categorical (early/late onset). AFD and AFG were modestly correlated (r = 0.18). Unique environmental influences explained a substantial proportion of the variation in both AFD (0.55, 95% confidence interval [CI] = 0.50-0.61) and AFG (0.66, 95% CI = 0.59-0.72), but these influences were uncorrelated (rE  = 0.01). Additive genetic factors explained a notable proportion of variation in AFG (0.21, 95% CI = 0.003-0.39), while shared environmental factors were important for AFD (0.31, 95% CI = 0.15-0.46). Among men, genetic factors influenced variation in AFG but not in AFD and shared environmental factors influenced variation in AFD but not in AFG. Among women, shared environmental factors influenced variation in both AFD and AFG, but these environmental factors were not significantly correlated (rC  = 0.09). Among Australian twins, age at first drink and age first gambled are influenced by distinct unique environmental factors, and the genetic and environmental underpinnings of both phenotypes differ in men and women. © 2013 Society for the Study of Addiction.

  5. Spatially and genetically distinct control of seed germination by phytochromes A and B

    Czech Academy of Sciences Publication Activity Database

    Lee, K. P.; Piskurewicz, U.; Turečková, Veronika; Carat, S.; Chappuis, R.; Strnad, Miroslav; Fankhauser, Ch.; Lopez-Molina, L.

    2012-01-01

    Roč. 26, č. 17 (2012), s. 1984 -1996 ISSN 0890-9369 Institutional research plan: CEZ:AV0Z50380511 Keywords : ABI5 * DELLA factors * abscisic acid Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 12.444, year: 2012

  6. Adolescent, Parent, and Observer Perceptions of Parenting: Genetic and Environmental Influences on Shared and Distinct Perceptions.

    Science.gov (United States)

    Feinberg, Mark; Neiderhiser, Jenae; Howe, George; Hetherington, E. Mavis

    2001-01-01

    Examined low interrater agreement by decomposing common and unique variance among parent, adolescent, and observer reports of parental warmth and negativity into genetic and environmental factors. Model-fitting analyses findings generally supported predictions for warmth and negativity at Family and Individual levels. At the Social level, genetic…

  7. Using Genetic Algorithms for Navigation Planning in Dynamic Environments

    Directory of Open Access Journals (Sweden)

    Ferhat Uçan

    2012-01-01

    Full Text Available Navigation planning can be considered as a combination of searching and executing the most convenient flight path from an initial waypoint to a destination waypoint. Generally the aim is to follow the flight path, which provides minimum fuel consumption for the air vehicle. For dynamic environments, constraints change dynamically during flight. This is a special case of dynamic path planning. As the main concern of this paper is flight planning, the conditions and objectives that are most probable to be used in navigation problem are considered. In this paper, the genetic algorithm solution of the dynamic flight planning problem is explained. The evolutionary dynamic navigation planning algorithm is developed for compensating the existing deficiencies of the other approaches. The existing fully dynamic algorithms process unit changes to topology one modification at a time, but when there are several such operations occurring in the environment simultaneously, the algorithms are quite inefficient. The proposed algorithm may respond to the concurrent constraint updates in a shorter time for dynamic environment. The most secure navigation of the air vehicle is planned and executed so that the fuel consumption is minimum.

  8. Genotyping of relapsing polychondritis identified novel susceptibility HLA alleles and distinct genetic characteristics from other rheumatic diseases.

    Science.gov (United States)

    Terao, Chikashi; Yoshifuji, Hajime; Yamano, Yoshihisa; Kojima, Hiroto; Yurugi, Kimiko; Miura, Yasuo; Maekawa, Taira; Handa, Hiroshi; Ohmura, Koichiro; Saji, Hiroh; Mimori, Tsuneyo; Matsuda, Fumihiko

    2016-09-01

    To uncover the genetic background of relapsing polychondritis (RPC), a rare autoimmune disease with unknown mechanisms characterized by systemic inflammation of the cartilage, to deepen our understanding of the pathophysiology of RPC and show its distinct genetic characteristics from other rheumatic diseases. A total of 102 patients with RPC and 1000 healthy subjects were recruited for a two-staged genetic association study and genotyped for six HLA classical loci. Haplotype association tests were also performed. The associations of amino acid (AA) residues and positions with susceptibility to RPC were analysed. Frequencies of representative susceptibility HLA alleles to other rheumatic diseases in RPC were also analysed. HLA-DRB1*16:02, HLA-DQB1*05:02 and HLA-B*67:01, which are in linkage disequilibrium with each other, were associated with RPC (P = 1.9 × 10(-6), 1.4 × 10(-5) and 0.00024, respectively). AA residue at position 57 in HLA-DQB1, the most significant position in type I diabetes mellitus, showed the strongest association among AA residues. HLA-DR4, a known susceptibility allele in Germans, showed a trend of susceptibility association without significance (P = 0.067). No associations were observed between the three alleles and clinical phenotypes. Representative susceptibility HLA alleles to RA, SLE, Behçet disease and Takayasu arteritis did not show enrichment in RPC in spite of sufficient statistical power. HLA-DRB1*16:02, HLA-DQB1*05:02 and HLA-B*67:01, in linkage disequilibrium with each other, are associated with susceptibility to RPC Importance of HLA-class II loci in RPC susceptibility is suggested. RPC is considered a genetically distinct disease from other rheumatic diseases. © The Author 2016. Published by Oxford University Press on behalf of the British Society for Rheumatology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  9. Abraham's children in the genome era: major Jewish diaspora populations comprise distinct genetic clusters with shared Middle Eastern Ancestry.

    Science.gov (United States)

    Atzmon, Gil; Hao, Li; Pe'er, Itsik; Velez, Christopher; Pearlman, Alexander; Palamara, Pier Francesco; Morrow, Bernice; Friedman, Eitan; Oddoux, Carole; Burns, Edward; Ostrer, Harry

    2010-06-11

    For more than a century, Jews and non-Jews alike have tried to define the relatedness of contemporary Jewish people. Previous genetic studies of blood group and serum markers suggested that Jewish groups had Middle Eastern origin with greater genetic similarity between paired Jewish populations. However, these and successor studies of monoallelic Y chromosomal and mitochondrial genetic markers did not resolve the issues of within and between-group Jewish genetic identity. Here, genome-wide analysis of seven Jewish groups (Iranian, Iraqi, Syrian, Italian, Turkish, Greek, and Ashkenazi) and comparison with non-Jewish groups demonstrated distinctive Jewish population clusters, each with shared Middle Eastern ancestry, proximity to contemporary Middle Eastern populations, and variable degrees of European and North African admixture. Two major groups were identified by principal component, phylogenetic, and identity by descent (IBD) analysis: Middle Eastern Jews and European/Syrian Jews. The IBD segment sharing and the proximity of European Jews to each other and to southern European populations suggested similar origins for European Jewry and refuted large-scale genetic contributions of Central and Eastern European and Slavic populations to the formation of Ashkenazi Jewry. Rapid decay of IBD in Ashkenazi Jewish genomes was consistent with a severe bottleneck followed by large expansion, such as occurred with the so-called demographic miracle of population expansion from 50,000 people at the beginning of the 15th century to 5,000,000 people at the beginning of the 19th century. Thus, this study demonstrates that European/Syrian and Middle Eastern Jews represent a series of geographical isolates or clusters woven together by shared IBD genetic threads.

  10. Distinct genetic diversity of Oncomelania hupensis, intermediate host of Schistosoma japonicum in mainland China as revealed by ITS sequences.

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    Qin Ping Zhao

    Full Text Available BACKGROUND: Oncomelania hupensis is the unique intermediate host of Schistosoma japonicum, which causes schistosomiasis endemic in the Far East, and especially in mainland China. O. hupensis largely determines the parasite's geographical range. How O. hupensis's genetic diversity is distributed geographically in mainland China has never been well examined with DNA sequence data. METHODOLOGY/PRINCIPAL FINDINGS: In this study we investigate the genetic variation among O. hupensis from different geographical origins using the combined complete internal transcribed spacer 1 (ITS1 and ITS2 regions of nuclear ribosomal DNA. 165 O. hupensis isolates were obtained in 29 localities from 7 provinces across mainland China: lake/marshland and hill regions in Anhui, Hubei, Hunan, Jiangxi and Jiangsu provinces, located along the middle and lower reaches of Yangtze River, and mountainous regions in Sichuan and Yunnan provinces. Phylogenetic and haplotype network analyses showed distinct genetic diversity and no shared haplotypes between populations from lake/marshland regions of the middle and lower reaches of the Yangtze River and populations from mountainous regions of Sichuan and Yunnan provinces. The genetic distance between these two groups is up to 0.81 based on Fst, and branch time was estimated as 2-6 Ma. As revealed in the phylogenetic tree, snails from Sichuan and Yunnan provinces were also clustered separately. Geographical separation appears to be an important factor accounting for the diversification of the two groups of O. hupensis in mainland China, and probably for the separate clades between snails from Sichuan and Yunnan provinces. In lake/marshland and hill regions along the middle and lower reaches of the Yangtze River, three clades were identified in the phylogenetic tree, but without any obvious clustering of snails from different provinces. CONCLUSIONS: O. hupensis in mainland China may have considerable genetic diversity, and a more

  11. Genetic diversity and distinctiveness of the proboscis monkeys (Nasalis larvatus) of the Klias Peninsula, Sabah, Malaysia.

    Science.gov (United States)

    Munshi-South, Jason; Bernard, Henry

    2011-01-01

    In this study, we sequenced a partial segment of the mitochondrial control region from 21 proboscis monkeys of the Klias peninsula, the last large population remaining on the west coast of Sabah, Malaysia. Our results showed that this population retains substantial genetic variation, and subpopulations from different river systems in the central and southern portions of the Klias share multiple haplotypes. We also compared our data with previously generated sequences from 2 eastern populations of proboscis monkeys in Sabah and found little evidence of regional genetic structure. Based on these results, we argue that conservation efforts should focus on restoring connectivity between central and southern Klias peninsula proboscis monkeys and discuss future analyses needed to better understand the mitochondrial structure of proboscis monkeys in Sabah.

  12. Biology, Genetics, and Environment: Underlying Factors Influencing Alcohol Metabolism.

    Science.gov (United States)

    Wall, Tamara L; Luczak, Susan E; Hiller-Sturmhöfel, Susanne

    2016-01-01

    Gene variants encoding several of the alcohol-metabolizing enzymes, alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH), are among the largest genetic associations with risk for alcohol dependence. Certain genetic variants (i.e., alleles)--particularly the ADH1B*2, ADH1B*3, ADH1C*1, and ALDH2*2 alleles--have been associated with lower rates of alcohol dependence. These alleles may lead to an accumulation of acetaldehyde during alcohol metabolism, which can result in heightened subjective and objective effects. The prevalence of these alleles differs among ethnic groups; ADH1B*2 is found frequently in northeast Asians and occasionally Caucasians, ADH1B*3 is found predominantly in people of African ancestry, ADH1C*1 varies substantially across populations, and ALDH2*2 is found almost exclusively in northeast Asians. Differences in the prevalence of these alleles may account at least in part for ethnic differences in alcohol consumption and alcohol use disorder (AUD). However, these alleles do not act in isolation to influence the risk of AUD. For example, the gene effects of ALDH2*2 and ADH1B*2 seem to interact. Moreover, other factors have been found to influence the extent to which these alleles affect a person's alcohol involvement, including developmental stage, individual characteristics (e.g., ethnicity, antisocial behavior, and behavioral undercontrol), and environmental factors (e.g., culture, religion, family environment, and childhood adversity).

  13. Distinct genetic control of parasite elimination, dissemination, and disease after Leishmania major infection

    Czech Academy of Sciences Publication Activity Database

    Kurey, Irina; Kobets, Tetyana; Havelková, Helena; Slapničková, Martina; Quan, L.; Trtková, Kateřina; Grekov, Igor; Svobodová, M.; Stassen, A. P. M.; Hutson, A.; Demant, P.; Lipoldová, Marie

    2009-01-01

    Roč. 61, č. 9 (2009), s. 619-633 ISSN 0093-7711 R&D Projects: GA ČR GA310/06/1745; GA MŠk(CZ) LC06009 Grant - others:EC(XE) 05-1000004-7761 Institutional research plan: CEZ:AV0Z50520514 Keywords : Leishmania major * Parasite elimination * QTL mapping Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.988, year: 2009

  14. Genetic Analysis of Israel Acute Paralysis Virus: Distinct Clusters Are Circulating in the United States▿

    Science.gov (United States)

    Palacios, G.; Hui, J.; Quan, P. L.; Kalkstein, A.; Honkavuori, K. S.; Bussetti, A. V.; Conlan, S.; Evans, J.; Chen, Y. P.; vanEngelsdorp, D.; Efrat, H.; Pettis, J.; Cox-Foster, D.; Holmes, E. C.; Briese, T.; Lipkin, W. I.

    2008-01-01

    Israel acute paralysis virus (IAPV) is associated with colony collapse disorder of honey bees. Nonetheless, its role in the pathogenesis of the disorder and its geographic distribution are unclear. Here, we report phylogenetic analysis of IAPV obtained from bees in the United States, Canada, Australia, and Israel and the establishment of diagnostic real-time PCR assays for IAPV detection. Our data indicate the existence of at least three distinct IAPV lineages, two of them circulating in the United States. Analysis of representatives from each proposed lineage suggested the possibility of recombination events and revealed differences in coding sequences that may have implications for virulence. PMID:18434396

  15. Mycobacteria exploit three genetically distinct DNA double-strand break repair pathways.

    Science.gov (United States)

    Gupta, Richa; Barkan, Daniel; Redelman-Sidi, Gil; Shuman, Stewart; Glickman, Michael S

    2011-01-01

    Bacterial pathogens rely on their DNA repair pathways to resist genomic damage inflicted by the host. DNA double-strand breaks (DSBs) are especially threatening to bacterial viability. DSB repair by homologous recombination (HR) requires nucleases that resect DSB ends and a strand exchange protein that facilitates homology search. RecBCD and RecA perform these functions in Escherichia coli and constitute the major pathway of error-free DSB repair. Mycobacteria, including the human pathogen M. tuberculosis, elaborate an additional error-prone pathway of DSB repair via non-homologous end-joining (NHEJ) catalysed by Ku and DNA ligase D (LigD). Little is known about the relative contributions of HR and NHEJ to mycobacterial chromosome repair, the factors that dictate pathway choice, or the existence of additional DSB repair pathways. Here we demonstrate that Mycobacterium smegmatis has three DSB repair pathway options: HR, NHEJ and a novel mechanism of single-strand annealing (SSA). Inactivation of NHEJ or SSA is compensated by elevated HR. We find that mycobacterial RecBCD does not participate in HR or confer resistance to ionizing radiation (IR), but is required for the RecA-independent SSA pathway. In contrast, the mycobacterial helicase-nuclease AdnAB participates in the RecA-dependent HR pathway, and is a major determinant of resistance to IR and oxidative DNA damage. These findings reveal distinctive features of mycobacterial DSB repair, most notably the dedication of the RecBCD and AdnAB helicase-nuclease machines to distinct repair pathways. © 2010 Blackwell Publishing Ltd.

  16. Presence Relates to Distinct Outcomes in Two Virtual Environments Employing Different Learning Modalities

    Science.gov (United States)

    Persky, Susan; Kaphingst, Kimberly A.; McCall, Cade; Lachance, Christina; Beall, Andrew C.; Blascovich, Jim

    2009-01-01

    Presence in virtual learning environments (VLEs) has been associated with a number of outcome factors related to a user’s ability and motivation to learn. The extant but relatively small body of research suggests that a high level of presence is related to better performance on learning outcomes in VLEs. Different configurations of form and content variables such as those associated with active (self-driven, interactive activities) versus didactic (reading or lecture) learning may, however, influence how presence operates and on what content it operates. We compared the influence of presence between two types of immersive VLEs (i.e., active versus didactic techniques) on comprehension and engagement-related outcomes. The findings revealed that the active VLE promoted greater presence. Although we found no relationship between presence and learning comprehension outcomes for either virtual environment, presence was related to information engagement variables in the didactic immersive VLE but not the active environment. Results demonstrate that presence is not uniformly elicited or effective across immersive VLEs. Educational delivery mode and environment complexity may influence the impact of presence on engagement. PMID:19366319

  17. Inter-specific coral chimerism: genetically distinct multicellular structures associated with tissue loss in Montipora capitata.

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    Thierry M Work

    Full Text Available Montipora white syndrome (MWS results in tissue-loss that is often lethal to Montipora capitata, a major reef building coral that is abundant and dominant in the Hawai'ian Archipelago. Within some MWS-affected colonies in Kane'ohe Bay, Oahu, Hawai'i, we saw unusual motile multicellular structures within gastrovascular canals (hereafter referred to as invasive gastrovascular multicellular structure-IGMS that were associated with thinning and fragmentation of the basal body wall. IGMS were in significantly greater densities in coral fragments manifesting tissue-loss compared to paired normal fragments. Mesenterial filaments from these colonies yielded typical M. capitata mitochondrial haplotypes (CO1, CR, while IGMS from the same colony consistently yielded distinct haplotypes previously only found in a different Montipora species (Montipora flabellata. Protein profiles showed consistent differences between paired mesenterial filaments and IGMS from the same colonies as did seven microsatellite loci that also exhibited an excess of alleles per locus inconsistent with a single diploid organism. We hypothesize that IGMS are a parasitic cellular lineage resulting from the chimeric fusion between M. capitata and M. flabellata larvae followed by morphological reabsorption of M. flabellata and subsequent formation of cell-lineage parasites. We term this disease Montiporaiasis. Although intra-specific chimerism is common in colonial animals, this is the first suspected inter-specific example and the first associated with tissue loss.

  18. Transgene x environment interactions in genetically modified wheat.

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    Simon L Zeller

    Full Text Available BACKGROUND: The introduction of transgenes into plants may cause unintended phenotypic effects which could have an impact on the plant itself and the environment. Little is published in the scientific literature about the interrelation of environmental factors and possible unintended effects in genetically modified (GM plants. METHODS AND FINDINGS: We studied transgenic bread wheat Triticum aestivum lines expressing the wheat Pm3b gene against the fungus powdery mildew Blumeria graminis f.sp. tritici. Four independent offspring pairs, each consisting of a GM line and its corresponding non-GM control line, were grown under different soil nutrient conditions and with and without fungicide treatment in the glasshouse. Furthermore, we performed a field experiment with a similar design to validate our glasshouse results. The transgene increased the resistance to powdery mildew in all environments. However, GM plants reacted sensitive to fungicide spraying in the glasshouse. Without fungicide treatment, in the glasshouse GM lines had increased vegetative biomass and seed number and a twofold yield compared with control lines. In the field these results were reversed. Fertilization generally increased GM/control differences in the glasshouse but not in the field. Two of four GM lines showed up to 56% yield reduction and a 40-fold increase of infection with ergot disease Claviceps purpurea compared with their control lines in the field experiment; one GM line was very similar to its control. CONCLUSIONS: Our results demonstrate that, depending on the insertion event, a particular transgene can have large effects on the entire phenotype of a plant and that these effects can sometimes be reversed when plants are moved from the glasshouse to the field. However, it remains unclear which mechanisms underlie these effects and how they may affect concepts in molecular plant breeding and plant evolutionary ecology.

  19. Phenotypic convergence in genetically distinct lineages of a Rhinolophus species complex (Mammalia, Chiroptera.

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    David S Jacobs

    Full Text Available Phenotypes of distantly related species may converge through adaptation to similar habitats and/or because they share biological constraints that limit the phenotypic variants produced. A common theme in bats is the sympatric occurrence of cryptic species that are convergent in morphology but divergent in echolocation frequency, suggesting that echolocation may facilitate niche partitioning, reducing competition. If so, allopatric populations freed from competition, could converge in both morphology and echolocation provided they occupy similar niches or share biological constraints. We investigated the evolutionary history of a widely distributed African horseshoe bat, Rhinolophus darlingi, in the context of phenotypic convergence. We used phylogenetic inference to identify and date lineage divergence together with phenotypic comparisons and ecological niche modelling to identify morphological and geographical correlates of those lineages. Our results indicate that R. darlingi is paraphyletic, the eastern and western parts of its distribution forming two distinct non-sister lineages that diverged ~9.7 Mya. We retain R. darlingi for the eastern lineage and argue that the western lineage, currently the sub-species R. d. damarensis, should be elevated to full species status. R. damarensis comprises two lineages that diverged ~5 Mya. Our findings concur with patterns of divergence of other co-distributed taxa which are associated with increased regional aridification between 7-5 Mya suggesting possible vicariant evolution. The morphology and echolocation calls of R. darlingi and R. damarensis are convergent despite occupying different biomes. This suggests that adaptation to similar habitats is not responsible for the convergence. Furthermore, R. darlingi forms part of a clade comprising species that are bigger and echolocate at lower frequencies than R. darlingi, suggesting that biological constraints are unlikely to have influenced the

  20. A shared transcriptional program in early breast neoplasias despite genetic and clinical distinctions.

    Science.gov (United States)

    Brunner, Alayne L; Li, Jun; Guo, Xiangqian; Sweeney, Robert T; Varma, Sushama; Zhu, Shirley X; Li, Rui; Tibshirani, Robert; West, Robert B

    2014-05-23

    The earliest recognizable stages of breast neoplasia are lesions that represent a heterogeneous collection of epithelial proliferations currently classified based on morphology. Their role in the development of breast cancer is not well understood but insight into the critical events at this early stage will improve efforts in breast cancer detection and prevention. These microscopic lesions are technically difficult to study so very little is known about their molecular alterations. To characterize the transcriptional changes of early breast neoplasia, we sequenced 3'- end enriched RNAseq libraries from formalin-fixed paraffin-embedded tissue of early neoplasia samples and matched normal breast and carcinoma samples from 25 patients. We find that gene expression patterns within early neoplasias are distinct from both normal and breast cancer patterns and identify a pattern of pro-oncogenic changes, including elevated transcription of ERBB2, FOXA1, and GATA3 at this early stage. We validate these findings on a second independent gene expression profile data set generated by whole transcriptome sequencing. Measurements of protein expression by immunohistochemistry on an independent set of early neoplasias confirms that ER pathway regulators FOXA1 and GATA3, as well as ER itself, are consistently upregulated at this early stage. The early neoplasia samples also demonstrate coordinated changes in long non-coding RNA expression and microenvironment stromal gene expression patterns. This study is the first examination of global gene expression in early breast neoplasia, and the genes identified here represent candidate participants in the earliest molecular events in the development of breast cancer.

  1. Phenotypic convergence in genetically distinct lineages of a Rhinolophus species complex (Mammalia, Chiroptera).

    Science.gov (United States)

    Jacobs, David S; Babiker, Hassan; Bastian, Anna; Kearney, Teresa; van Eeden, Rowen; Bishop, Jacqueline M

    2013-01-01

    Phenotypes of distantly related species may converge through adaptation to similar habitats and/or because they share biological constraints that limit the phenotypic variants produced. A common theme in bats is the sympatric occurrence of cryptic species that are convergent in morphology but divergent in echolocation frequency, suggesting that echolocation may facilitate niche partitioning, reducing competition. If so, allopatric populations freed from competition, could converge in both morphology and echolocation provided they occupy similar niches or share biological constraints. We investigated the evolutionary history of a widely distributed African horseshoe bat, Rhinolophus darlingi, in the context of phenotypic convergence. We used phylogenetic inference to identify and date lineage divergence together with phenotypic comparisons and ecological niche modelling to identify morphological and geographical correlates of those lineages. Our results indicate that R. darlingi is paraphyletic, the eastern and western parts of its distribution forming two distinct non-sister lineages that diverged ~9.7 Mya. We retain R. darlingi for the eastern lineage and argue that the western lineage, currently the sub-species R. d. damarensis, should be elevated to full species status. R. damarensis comprises two lineages that diverged ~5 Mya. Our findings concur with patterns of divergence of other co-distributed taxa which are associated with increased regional aridification between 7-5 Mya suggesting possible vicariant evolution. The morphology and echolocation calls of R. darlingi and R. damarensis are convergent despite occupying different biomes. This suggests that adaptation to similar habitats is not responsible for the convergence. Furthermore, R. darlingi forms part of a clade comprising species that are bigger and echolocate at lower frequencies than R. darlingi, suggesting that biological constraints are unlikely to have influenced the convergence. Instead, the

  2. Phenotype-Environment Interactions in Genetic Syndromes Associated with Severe or Profound Intellectual Disability

    Science.gov (United States)

    Tunnicliffe, Penny; Oliver, Chris

    2011-01-01

    The research literature notes both biological and operant theories of behavior disorder in individuals with intellectual disabilities. These two theories of genetic predisposition and operant reinforcement remain quite distinct; neither theory on its own is sufficient to explain challenging behavior in genetic syndromes and an integrated approach…

  3. ASD and schizophrenia show distinct developmental profiles in common genetic overlap with population-based social communication difficulties

    DEFF Research Database (Denmark)

    St Pourcain, B; Robinson, E B; Anttila, V

    2017-01-01

    -developing youth (Avon Longitudinal Study of Parents and Children, N⩽5553, longitudinal assessments at 8, 11, 14 and 17 years) using the Social Communication Disorder Checklist. Data on clinical ASD (PGC-ASD: 5305 cases, 5305 pseudo-controls; iPSYCH-ASD: 7783 cases, 11 359 controls) and schizophrenia (PGC-SCZ2: 34......Difficulties in social communication are part of the phenotypic overlap between autism spectrum disorders (ASD) and schizophrenia. Both conditions follow, however, distinct developmental patterns. Symptoms of ASD typically occur during early childhood, whereas most symptoms characteristic...... of schizophrenia do not appear before early adulthood. We investigated whether overlap in common genetic influences between these clinical conditions and impairments in social communication depends on the developmental stage of the assessed trait. Social communication difficulties were measured in typically...

  4. Genetic, Ecological and Morphological Distinctness of the Blue Mussels Mytilus trossulus Gould and M. edulis L. in the White Sea

    Science.gov (United States)

    Katolikova, Marina; Khaitov, Vadim; Väinölä, Risto; Gantsevich, Michael; Strelkov, Petr

    2016-01-01

    Two blue mussel lineages of Pliocene origin, Mytilus edulis (ME) and M. trossulus (MT), co-occur and hybridize in several regions on the shores of the North Atlantic. The two species were distinguished from each other by molecular methods in the 1980s, and a large amount of comparative data on them has been accumulated since that time. However, while ME and MT are now routinely distinguished by various genetic markers, they tend to be overlooked in ecological studies since morphological characters for taxonomic identification have been lacking, and no consistent habitat differences between lineages have been reported. Surveying a recently discovered area of ME and MT co-occurrence in the White Sea and employing a set of allozyme markers for identification, we address the issue whether ME and MT are true biological species with distinct ecological characteristics or just virtual genetic entities with no matching morphological and ecological identities. We find that: (1) in the White Sea, the occurrence of MT is largely concentrated in harbors, in line with observations from other subarctic regions of Europe; (2) mixed populations of ME and MT are always dominated by purebred individuals, animals classified as hybrids constituting only ca. 18%; (3) in terms of shell morphology, 80% of MT bear a distinct uninterrupted dark prismatic strip under the ligament while 97% of ME lack this character; (4) at sites of sympatry MT is more common on algal substrates while ME mostly lives directly on the bottom. This segregation by the substrate may contribute to maintaining reproductive isolation and decreasing competition between taxa. We conclude that while ME and MT are not fully reproductively isolated, they do represent clearly distinguishable biological, ecological and morphological entities in the White Sea. It remains to be documented whether the observed morphological and ecological differences are of a local character, or whether they have simply been overlooked in

  5. Genomic tools for evolution and conservation in the chimpanzee: Pan troglodytes ellioti is a genetically distinct population.

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    Rory Bowden

    Full Text Available In spite of its evolutionary significance and conservation importance, the population structure of the common chimpanzee, Pan troglodytes, is still poorly understood. An issue of particular controversy is whether the proposed fourth subspecies of chimpanzee, Pan troglodytes ellioti, from parts of Nigeria and Cameroon, is genetically distinct. Although modern high-throughput SNP genotyping has had a major impact on our understanding of human population structure and demographic history, its application to ecological, demographic, or conservation questions in non-human species has been extremely limited. Here we apply these tools to chimpanzee population structure, using ∼700 autosomal SNPs derived from chimpanzee genomic data and a further ∼100 SNPs from targeted re-sequencing. We demonstrate conclusively the existence of P. t. ellioti as a genetically distinct subgroup. We show that there is clear differentiation between the verus, troglodytes, and ellioti populations at the SNP and haplotype level, on a scale that is greater than that separating continental human populations. Further, we show that only a small set of SNPs (10-20 is needed to successfully assign individuals to these populations. Tellingly, use of only mitochondrial DNA variation to classify individuals is erroneous in 4 of 54 cases, reinforcing the dangers of basing demographic inference on a single locus and implying that the demographic history of the species is more complicated than that suggested analyses based solely on mtDNA. In this study we demonstrate the feasibility of developing economical and robust tests of individual chimpanzee origin as well as in-depth studies of population structure. These findings have important implications for conservation strategies and our understanding of the evolution of chimpanzees. They also act as a proof-of-principle for the use of cheap high-throughput genomic methods for ecological questions.

  6. Genetic, Ecological and Morphological Distinctness of the Blue Mussels Mytilus trossulus Gould and M. edulis L. in the White Sea.

    Directory of Open Access Journals (Sweden)

    Marina Katolikova

    Full Text Available Two blue mussel lineages of Pliocene origin, Mytilus edulis (ME and M. trossulus (MT, co-occur and hybridize in several regions on the shores of the North Atlantic. The two species were distinguished from each other by molecular methods in the 1980s, and a large amount of comparative data on them has been accumulated since that time. However, while ME and MT are now routinely distinguished by various genetic markers, they tend to be overlooked in ecological studies since morphological characters for taxonomic identification have been lacking, and no consistent habitat differences between lineages have been reported. Surveying a recently discovered area of ME and MT co-occurrence in the White Sea and employing a set of allozyme markers for identification, we address the issue whether ME and MT are true biological species with distinct ecological characteristics or just virtual genetic entities with no matching morphological and ecological identities. We find that: (1 in the White Sea, the occurrence of MT is largely concentrated in harbors, in line with observations from other subarctic regions of Europe; (2 mixed populations of ME and MT are always dominated by purebred individuals, animals classified as hybrids constituting only ca. 18%; (3 in terms of shell morphology, 80% of MT bear a distinct uninterrupted dark prismatic strip under the ligament while 97% of ME lack this character; (4 at sites of sympatry MT is more common on algal substrates while ME mostly lives directly on the bottom. This segregation by the substrate may contribute to maintaining reproductive isolation and decreasing competition between taxa. We conclude that while ME and MT are not fully reproductively isolated, they do represent clearly distinguishable biological, ecological and morphological entities in the White Sea. It remains to be documented whether the observed morphological and ecological differences are of a local character, or whether they have simply been

  7. Dubowitz syndrome is a complex comprised of multiple, genetically distinct and phenotypically overlapping disorders.

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    Douglas R Stewart

    Full Text Available Dubowitz syndrome is a rare disorder characterized by multiple congenital anomalies, cognitive delay, growth failure, an immune defect, and an increased risk of blood dyscrasia and malignancy. There is considerable phenotypic variability, suggesting genetic heterogeneity. We clinically characterized and performed exome sequencing and high-density array SNP genotyping on three individuals with Dubowitz syndrome, including a pair of previously-described siblings (Patients 1 and 2, brother and sister and an unpublished patient (Patient 3. Given the siblings' history of bone marrow abnormalities, we also evaluated telomere length and performed radiosensitivity assays. In the siblings, exome sequencing identified compound heterozygosity for a known rare nonsense substitution in the nuclear ligase gene LIG4 (rs104894419, NM_002312.3:c.2440C>T that predicts p.Arg814X (MAF:0.0002 and an NM_002312.3:c.613delT variant that predicts a p.Ser205Leufs*29 frameshift. The frameshift mutation has not been reported in 1000 Genomes, ESP, or ClinSeq. These LIG4 mutations were previously reported in the sibling sister; her brother had not been previously tested. Western blotting showed an absence of a ligase IV band in both siblings. In the third patient, array SNP genotyping revealed a de novo ∼ 3.89 Mb interstitial deletion at chromosome 17q24.2 (chr 17:62,068,463-65,963,102, hg18, which spanned the known Carney complex gene PRKAR1A. In all three patients, a median lymphocyte telomere length of ≤ 1st centile was observed and radiosensitivity assays showed increased sensitivity to ionizing radiation. Our work suggests that, in addition to dyskeratosis congenita, LIG4 and 17q24.2 syndromes also feature shortened telomeres; to confirm this, telomere length testing should be considered in both disorders. Taken together, our work and other reports on Dubowitz syndrome, as currently recognized, suggest that it is not a unitary entity but instead a collection of

  8. Phylogeography of lions (Panthera leo ssp.) reveals three distinct taxa and a late Pleistocene reduction in genetic diversity.

    Science.gov (United States)

    Barnett, Ross; Shapiro, Beth; Barnes, Ian; Ho, Simon Y W; Burger, Joachim; Yamaguchi, Nobuyuki; Higham, Thomas F G; Wheeler, H Todd; Rosendahl, Wilfried; Sher, Andrei V; Sotnikova, Marina; Kuznetsova, Tatiana; Baryshnikov, Gennady F; Martin, Larry D; Harington, C Richard; Burns, James A; Cooper, Alan

    2009-04-01

    Lions were the most widespread carnivores in the late Pleistocene, ranging from southern Africa to the southern USA, but little is known about the evolutionary relationships among these Pleistocene populations or the dynamics that led to their extinction. Using ancient DNA techniques, we obtained mitochondrial sequences from 52 individuals sampled across the present and former range of lions. Phylogenetic analysis revealed three distinct clusters: (i) modern lions, Panthera leo; (ii) extinct Pleistocene cave lions, which formed a homogeneous population extending from Europe across Beringia (Siberia, Alaska and western Canada); and (iii) extinct American lions, which formed a separate population south of the Pleistocene ice sheets. The American lion appears to have become genetically isolated around 340 000 years ago, despite the apparent lack of significant barriers to gene flow with Beringian populations through much of the late Pleistocene. We found potential evidence of a severe population bottleneck in the cave lion during the previous interstadial, sometime after 48 000 years, adding to evidence from bison, mammoths, horses and brown bears that megafaunal populations underwent major genetic alterations throughout the last interstadial, potentially presaging the processes involved in the subsequent end-Pleistocene mass extinctions.

  9. A chemical-genetic strategy reveals distinct temporal requirements for SAD-1 kinase in neuronal polarization and synapse formation

    Directory of Open Access Journals (Sweden)

    Shokat Kevan M

    2008-09-01

    Full Text Available Abstract Background Neurons assemble into a functional network through a sequence of developmental processes including neuronal polarization and synapse formation. In Caenorhabditis elegans, the serine/threonine SAD-1 kinase is essential for proper neuronal polarity and synaptic organization. To determine if SAD-1 activity regulates the establishment or maintenance of these neuronal structures, we examined its temporal requirements using a chemical-genetic method that allows for selective and reversible inactivation of its kinase activity in vivo. Results We generated a PP1 analog-sensitive variant of SAD-1. Through temporal inhibition of SAD-1 kinase activity we show that its activity is required for the establishment of both neuronal polarity and synaptic organization. However, while SAD-1 activity is needed strictly when neurons are polarizing, the temporal requirement for SAD-1 is less stringent in synaptic organization, which can also be re-established during maintenance. Conclusion This study reports the first temporal analysis of a neural kinase activity using the chemical-genetic system. It reveals that neuronal polarity and synaptic organization have distinct temporal requirements for SAD-1.

  10. Genetically Distinct Glossina fuscipes fuscipes Populations in the Lake Kyoga Region of Uganda and Its Relevance for Human African Trypanosomiasis

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    Richard Echodu

    2013-01-01

    Full Text Available Tsetse flies (Glossina spp. are the sole vectors of Trypanosoma brucei—the agent of human (HAT and animal (AAT trypanosomiasis. Glossina fuscipes fuscipes (Gff is the main vector species in Uganda—the only country where the two forms of HAT disease (rhodesiense and gambiense occur, with gambiense limited to the northwest. Gff populations cluster in three genetically distinct groups in northern, southern, and western Uganda, respectively, with a contact zone present in central Uganda. Understanding the dynamics of this contact zone is epidemiologically important as the merger of the two diseases is a major health concern. We used mitochondrial and microsatellite DNA data from Gff samples in the contact zone to understand its spatial extent and temporal stability. We show that this zone is relatively narrow, extending through central Uganda along major rivers with south to north introgression but displaying no sex-biased dispersal. Lack of obvious vicariant barriers suggests that either environmental conditions or reciprocal competitive exclusion could explain the patterns of genetic differentiation observed. Lack of admixture between northern and southern populations may prevent the sympatry of the two forms of HAT disease, although continued control efforts are needed to prevent the recolonization of tsetse-free regions by neighboring populations.

  11. Diabetes mellitus in two genetically distinct populations in Jordan. A comparison between Arabs and Circassians/Chechens living with diabetes

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    Laith N. Al-Eitan

    2017-02-01

    Full Text Available Objectives: To compare clinical, anthropometric, and laboratory characteristics in diabetes type 2 patients of 2 genetically-distinct ethnicities living in Jordan, Arabs and Circassians/Chechens. Methods: This cross sectional ethnic comparison study was conducted in King Abdullah University Hospital, Irbid and The National Center for Diabetes, Endocrinology, and Genetics, Amman, Jordan between June 2013 and February 2014. A sample of 347 (237 Arab and 110 Circassian/Chechen people living with diabetes were included in the study. Data were collected through direct interviews with the participants. Clinical data were collected using a questionnaire and anthropometric measurements. Laboratory data were extracted from the patients’ medical records. Results: More Arabs with diabetes had hypertension as a comorbidity than Circassians/Chechens with diabetes. Arabs living with diabetes were generally more obese, whereas Circassians/Chechens living with diabetes had worse lipid control. Arabs with diabetes had higher means of glycated haemoglobin (HbA1c and fasting blood sugar, and more Arabs with diabetes had unsatisfactory glycemic control (60.6% than Circassians/Chechens with diabetes (38.2% (HbA1c ≥7.0%. Most participants (88.8% had at least one lipid abnormality (dyslipidemia. Conclusion: Multiple discrepancies among the 2 ethnic diabetic populations were found. New diabetes management recommendations and policies should be used when treating people living with diabetes of those ethnicities, particularly in areas of glycemic control, lipid control, and obesity.

  12. Single Particle Tracking reveals two distinct environments for CD4 receptors at the surface of living T lymphocytes

    International Nuclear Information System (INIS)

    Mascalchi, Patrice; Lamort, Anne Sophie; Salomé, Laurence; Dumas, Fabrice

    2012-01-01

    Highlights: ► We studied the diffusion of single CD4 receptors on living lymphocytes. ► This study reveals that CD4 receptors have either a random or confined diffusion. ► The dynamics of unconfined CD4 receptors was accelerated by a temperature raise. ► The dynamics of confined CD4 receptors was unchanged by a temperature raise. ► Our results suggest the existence of two different environments for CD4 receptors. -- Abstract: We investigated the lateral diffusion of the HIV receptor CD4 at the surface of T lymphocytes at 20 °C and 37 °C by Single Particle Tracking using Quantum Dots. We found that the receptors presented two major distinct behaviors that were not equally affected by temperature changes. About half of the receptors showed a random diffusion with a diffusion coefficient increasing upon raising the temperature. The other half of the receptors was permanently or transiently confined with unchanged dynamics on raising the temperature. These observations suggest that two distinct subpopulations of CD4 receptors with different environments are present at the surface of living T lymphocytes.

  13. Some distinctive features of tax control in the contemporary business environment

    Directory of Open Access Journals (Sweden)

    Anđelković Mileva

    2016-01-01

    Full Text Available Traditional tax control has proven to be an insufficiently effective means of verifying the overall real economic power of large taxpayers (multinational corporations and wealthy individuals. As compared to the increasing mobility of taxpayers, tax administration activities are limited by the territorial jurisdiction of the fiscal sovereignty. The crisis of public finances has forced many countries to focus on the prevention of tax evasion and aggressive tax planning, particularly in international tax matters. In this sense, the traditional forms of tax control are supplemented by some additional strategies which are to provide tax authorities with more data on tax payers' business operations, profit, income, expenses and property. In practice, some developed tax administrations already apply a number of specific measures: the disclosure of information about aggressive tax planning schemes, advance pricing agreement, advance tax rulings, the use of financial intermediaries in data exchange processes, improved taxation relations, automatic exchange of tax information, etc. These specific measures are intended to help tax administrations to overcome the discrepancy between the information at their disposal and the information held by the taxpayers, which facilitates a more realistic assessment of tax liabilities. This will ensure a better management of tax risk and better tax compliance, which will ultimately contribute to a more efficient development of tax systems in the contemporary global business environment.

  14. Genetic and genotype environment interaction effects for the content ...

    Indian Academy of Sciences (India)

    Administrator

    It is necessary for rice breeders to understand the genetic basis of nutrient quality traits of rice. Essential amino acids are most important in determining the nutrient quality of rice grain and can affect the health of people who depend on rice as a staple food. In view of the paucity of genetic information available on essential ...

  15. Genetic susceptibility to asthma in a changing environment

    NARCIS (Netherlands)

    Bleecker, ER; Postma, DS; Meyers, DA; Chadwick, DJ; Cardew, G

    1997-01-01

    There is a major interest in investigating the genetic components of allergy and asthma. Four different areas are involved in the study of complex genetic diseases: family studies, assessment of phenotype, segregation analysis and gene mapping. initial assessment of phenotype must be practical,

  16. Deliberate release of genetically modified plants into the environment in Slovenia

    OpenAIRE

    Zlata LUTHAR

    2015-01-01

    Deliberate release of genetically modified higher plants (GMHPs) into the environment in Slovenia is regulated by the Law on the Management of Genetically Modified Organisms (ZRGSO) Ur. l. RS 23/2005 and 21/2010, III chapter. For each deliberate release of GMPs into the environment a license issued by the Ministry of Environment and Spatial Planning (MESP) must be acquired. The application or notification should contain a very accurate and complex description of the GMP, of the field where it...

  17. Appendiceal goblet cell carcinoids and adenocarcinomas ex-goblet cell carcinoid are genetically distinct from primary colorectal-type adenocarcinoma of the appendix

    DEFF Research Database (Denmark)

    Jesinghaus, Moritz; Konukiewitz, Björn; Foersch, Sebastian

    2018-01-01

    The appendix gives rise to goblet cell carcinoids, which represent special carcinomas with distinct biological and histological features. Their genetic background and molecular relationship to colorectal adenocarcinoma is largely unknown. We therefore performed a next-generation sequencing analysis...... a morphomolecular entity, histologically and genetically distinct from appendiceal colorectal-type adenocarcinomas and its colorectal counterparts. Altered Wnt-signaling associated genes, apart from APC, may act as potential drivers of these neoplasms. The absence of KRAS/NRAS mutations might render some...... of these tumors eligible for anti-EGFR directed therapy regimens.Modern Pathology advance online publication, 12 January 2018; doi:10.1038/modpathol.2017.184....

  18. The genetics of music accomplishment: evidence for gene-environment correlation and interaction.

    Science.gov (United States)

    Hambrick, David Z; Tucker-Drob, Elliot M

    2015-02-01

    Theories of skilled performance that emphasize training history, such as K. Anders Ericsson and colleagues' deliberate-practice theory, have received a great deal of recent attention in both the scientific literature and the popular press. Twin studies, however, have demonstrated evidence for moderate-to-strong genetic influences on skilled performance. Focusing on musical accomplishment in a sample of over 800 pairs of twins, we found evidence for gene-environment correlation, in the form of a genetic effect on music practice. However, only about one quarter of the genetic effect on music accomplishment was explained by this genetic effect on music practice, suggesting that genetically influenced factors other than practice contribute to individual differences in music accomplishment. We also found evidence for gene-environment interaction, such that genetic effects on music accomplishment were most pronounced among those engaging in music practice, suggesting that genetic potentials for skilled performance are most fully expressed and fostered by practice.

  19. Bacterial gene transfer by natural genetic transformation in the environment.

    OpenAIRE

    Lorenz, M G; Wackernagel, W

    1994-01-01

    Natural genetic transformation is the active uptake of free DNA by bacterial cells and the heritable incorporation of its genetic information. Since the famous discovery of transformation in Streptococcus pneumoniae by Griffith in 1928 and the demonstration of DNA as the transforming principle by Avery and coworkers in 1944, cellular processes involved in transformation have been studied extensively by in vitro experimentation with a few transformable species. Only more recently has it been c...

  20. NUTM2A-CIC fusion small round cell sarcoma: a genetically distinct variant of CIC-rearranged sarcoma.

    Science.gov (United States)

    Sugita, Shintaro; Arai, Yasuhito; Aoyama, Tomoyuki; Asanuma, Hiroko; Mukai, Wakako; Hama, Natsuko; Emori, Makoto; Shibata, Tatsuhiro; Hasegawa, Tadashi

    2017-07-01

    CIC-rearranged sarcoma is a new entity of undifferentiated small round cell sarcoma characterized by chimeric fusions with CIC rearrangement. We report a NUTM2A-CIC fusion sarcoma in a 43-year-old woman who died of rapidly progressive disease. Histologic analysis revealed multinodular proliferation of small round tumor cells with mild nuclear pleomorphism. The sclerotic fibrous septa separated the tumor into multiple nodules. Immunohistochemistry showed that the tumor cells were diffusely positive for vimentin, focally positive for cytokeratin, and negative for CD99 and NKX2.2. Tumor cells were also negative for ETV4, which was recently identified as a specific marker for CIC-rearranged sarcoma. High-throughput RNA sequencing of a formalin-fixed, paraffin-embedded clinical sample unveiled a novel NUTM2A-CIC fusion between NUTM2A exon 7 and CIC exon 12, and fluorescence in situ hybridization identified CIC and NUTM2A split signals. This case shared several clinicopathological findings with previously reported CIC-rearranged cases. We recognized the tumor as a genetically distinct variant of CIC-rearranged sarcomas with a novel NUTM2A-CIC fusion. Copyright © 2017. Published by Elsevier Inc.

  1. Turtle carapace anomalies: the roles of genetic diversity and environment.

    Directory of Open Access Journals (Sweden)

    Guillermo Velo-Antón

    2011-04-01

    Full Text Available Phenotypic anomalies are common in wild populations and multiple genetic, biotic and abiotic factors might contribute to their formation. Turtles are excellent models for the study of developmental instability because anomalies are easily detected in the form of malformations, additions, or reductions in the number of scutes or scales.In this study, we integrated field observations, manipulative experiments, and climatic and genetic approaches to investigate the origin of carapace scute anomalies across Iberian populations of the European pond turtle, Emys orbicularis. The proportion of anomalous individuals varied from 3% to 69% in local populations, with increasing frequency of anomalies in northern regions. We found no significant effect of climatic and soil moisture, or climatic temperature on the occurrence of anomalies. However, lower genetic diversity and inbreeding were good predictors of the prevalence of scute anomalies among populations. Both decreasing genetic diversity and increasing proportion of anomalous individuals in northern parts of the Iberian distribution may be linked to recolonization events from the Southern Pleistocene refugium.Overall, our results suggest that developmental instability in turtle carapace formation might be caused, at least in part, by genetic factors, although the influence of environmental factors affecting the developmental stability of turtle carapace cannot be ruled out. Further studies of the effects of environmental factors, pollutants and heritability of anomalies would be useful to better understand the complex origin of anomalies in natural populations.

  2. An enriched rearing environment calms adult male rat sexual activity: implication for distinct serotonergic and hormonal responses to females.

    Directory of Open Access Journals (Sweden)

    Susumu Urakawa

    Full Text Available Early life events induce alterations in neural function in adulthood. Although rearing in an enriched environment (EE has a great impact on behavioral development, the effects of enriched rearing on sociosexual behavior remain unclear. In this study, we investigated the effects of rearing in an EE on male copulatory behavior and its underlying neurobiological mechanisms in Wistar-Imamichi rats. Three-week-old, recently weaned rats were continuously subjected to a standard environment (SE or an EE comprised of a large cage with several objects, such as toys, tunnels, ladders, and a running wheel. After 6 weeks, rats reared in an EE (EE rats showed decreased sexual activity compared with rats reared in a SE (SE rats. This included a lower number of ejaculations and longer latencies in three consecutive copulatory tests. In addition, EE rats showed decreased emotional responsiveness and less locomotor behavior in an open field. In a runway test, on the other hand, sexual motivation toward receptive females in EE males was comparable to that of SE males. Furthermore, following exposure to a female, increases in serotonin levels in the nucleus accumbens and the striatum were significantly suppressed in EE males, whereas dopaminergic responses were similar between the groups. Female-exposure-induced increases in the levels of plasma corticosterone and testosterone were also suppressed in EE rats compared to SE rats. These data suggest that rearing in an EE decreases male copulatory behavior, and serotonin and hormonal regulating systems may regulate the differences in sociosexual interactions that result from distinct rearing environments.

  3. Genetics

    DEFF Research Database (Denmark)

    Christensen, Kaare; McGue, Matt

    2016-01-01

    The sequenced genomes of individuals aged ≥80 years, who were highly educated, self-referred volunteers and with no self-reported chronic diseases were compared to young controls. In these data, healthy ageing is a distinct phenotype from exceptional longevity and genetic factors that protect...

  4. Simulation based Virtual Learning Environment in Medical Genetics Counseling

    DEFF Research Database (Denmark)

    Makransky, Guido; Bonde, Mads Tvillinggaard; Wulff, Julie S. G.

    2016-01-01

    Background: Simulation based learning environments are designed to improve the quality of medical education by allowing students to interact with patients, diagnostic laboratory procedures, and patient data in a virtual environment. However, few studies have evaluated whether simulation based...... in medicine, received a 2-hour training session in a simulation based learning environment. The main outcomes were pre- to post- changes in knowledge, intrinsic motivation, and self-efficacy, together with post-intervention evaluation of the effect of the simulation on student understanding of everyday...... feel more confident counseling a patient after the simulation. Conclusions: The simulation based learning environment increased students’ learning, intrinsic motivation, and self-efficacy (although the strength of these effects differed depending on their pre-test knowledge), and increased...

  5. Genetic Characterization of Spondweni and Zika Viruses and Susceptibility of Geographically Distinct Strains of Aedes aegypti, Aedes albopictus and Culex quinquefasciatus (Diptera: Culicidae to Spondweni Virus.

    Directory of Open Access Journals (Sweden)

    Andrew D Haddow

    2016-10-01

    Full Text Available Zika virus (ZIKV has extended its known geographic distribution to the New World and is now responsible for severe clinical complications in a subset of patients. While substantial genetic and vector susceptibility data exist for ZIKV, less is known for the closest related flavivirus, Spondweni virus (SPONV. Both ZIKV and SPONV have been known to circulate in Africa since the mid-1900s, but neither has been genetically characterized by gene and compared in parallel. Furthermore, the susceptibility of peridomestic mosquito species incriminated or suspected in the transmission of ZIKV to SPONV was unknown.In this study, two geographically distinct strains of SPONV were genetically characterized and compared to nine genetically and geographically distinct ZIKV strains. Additionally, the susceptibility of both SPONV strains was determined in three mosquito species. The open reading frame (ORF of the SPONV 1952 Nigerian Chuku strain, exhibited a nucleotide and amino acid identity of 97.8% and 99.2%, respectively, when compared to the SPONV 1954 prototype South African SA Ar 94 strain. The ORF of the SPONV Chuku strain exhibited a nucleotide and amino acid identity that ranged from 68.3% to 69.0% and 74.6% to 75.0%, respectively, when compared to nine geographically and genetically distinct strains of ZIKV. The ORF of the nine African and Asian lineage ZIKV strains exhibited limited nucleotide divergence. Aedes aegypti, Ae. albopictus and Culex quinquefasciatus susceptibility and dissemination was low or non-existent following artificial infectious blood feeding of moderate doses of both SPONV strains.SPONV and ZIKV nucleotide and amino acid divergence coupled with differences in geographic distribution, ecology and vector species support previous reports that these viruses are separate species. Furthermore, the low degree of SPONV infection or dissemination in Ae. albopictus, Ae. aegypti and Cx. quinquefasciatus following exposure to two

  6. Measuring the genetic influence on human life span: gene-environment interaction and sex-specific genetic effects

    DEFF Research Database (Denmark)

    Tan, Qihua; De Benedictis, G; Yashin, Annatoli

    2001-01-01

    New approaches are needed to explore the different ways in which genes affect the human life span. One needs to assess the genetic effects themselves, as well as gene–environment interactions and sex dependency. In this paper, we present a new model that combines both genotypic and demographicinf...

  7. PD-L1 marks a subset of melanomas with a shorter overall survival and distinct genetic and morphological characteristics.

    Science.gov (United States)

    Massi, D; Brusa, D; Merelli, B; Ciano, M; Audrito, V; Serra, S; Buonincontri, R; Baroni, G; Nassini, R; Minocci, D; Cattaneo, L; Tamborini, E; Carobbio, A; Rulli, E; Deaglio, S; Mandalà, M

    2014-12-01

    Programmed cell death ligand 1 (PD-L1) is a cell surface molecule that plays a critical role in suppressing immune responses, mainly through binding of the PD-1 receptor on T lymphocytes. PD-L1 may be expressed by metastatic melanoma (MM). However, its clinical and biological significance remains unclear. Here, we investigated whether expression of PD-L1 in MM identifies a biologically more aggressive form of the disease, carrying prognostic relevance. PD-L1 expression was analyzed by immunohistochemistry using two different antibodies in primary tumors and paired metastases from 81 melanoma patients treated at a single institution. Protein expression levels were correlated with PD-L1 mRNA, BRAF mutational status and clinical outcome. PD-L1(+) and PD-L1(-) subsets of the A375 cell line were stabilized in vitro and compared using gene expression profiling and functional assays. Results were confirmed using xenograft models. PD-L1 membrane positivity was detected in 30/81 (37%) of patients. By multivariate analysis, Breslow thickness and PD-L1 membrane positivity were independent risk factors for melanoma-specific death {PD-L1 5% cutoff [hazard ratio (HR) 3.92, confidence interval (CI) 95% 1.61-9.55 P melanoma. If confirmed, our clinical and experimental data suggest that PD-L1(+) melanomas should be considered a disease subset with distinct genetic and morpho-phenotypic features, leading to enhanced aggressiveness and invasiveness. © The Author 2014. Published by Oxford University Press on behalf of the European Society for Medical Oncology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  8. Maternal environment affects the genetic basis of seed dormancy in Arabidopsis thaliana.

    Science.gov (United States)

    Postma, Froukje M; Ågren, Jon

    2015-02-01

    The genetic basis of seed dormancy, a key life history trait important for adaptive evolution in plant populations, has yet been studied only using seeds produced under controlled conditions in greenhouse environments. However, dormancy is strongly affected by maternal environmental conditions, and interactions between seed genotype and maternal environment have been reported. Consequently, the genetic basis of dormancy of seeds produced under natural field conditions remains unclear. We examined the effect of maternal environment on the genetic architecture of seed dormancy using a recombinant inbred line (RIL) population derived from a cross between two locally adapted populations of Arabidopsis thaliana from Italy and Sweden. We mapped quantitative trait loci (QTL) for dormancy of seeds produced in the greenhouse and at the native field sites of the parental genotypes. The Italian genotype produced seeds with stronger dormancy at fruit maturation than did the Swedish genotype in all three environments, and the maternal field environments induced higher dormancy levels compared to the greenhouse environment in both genotypes. Across the three maternal environments, a total of nine dormancy QTL were detected, three of which were only detected among seeds matured in the field, and six of which showed significant QTL × maternal environment interactions. One QTL had a large effect on dormancy across all three environments and colocalized with the candidate gene DOG1. Our results demonstrate the importance of studying the genetic basis of putatively adaptive traits under relevant conditions. © 2015 John Wiley & Sons Ltd.

  9. Genetic Variability of the Grey Wolf Canis lupus in the Caucasus in Comparison with Europe and the Middle East: Distinct or Intermediary Population?

    Science.gov (United States)

    Pilot, Małgorzata; Dąbrowski, Michał J.; Hayrapetyan, Vahram; Yavruyan, Eduard G.; Kopaliani, Natia; Tsingarska, Elena; Bujalska, Barbara; Kamiński, Stanisław; Bogdanowicz, Wiesław

    2014-01-01

    Despite continuous historical distribution of the grey wolf (Canis lupus) throughout Eurasia, the species displays considerable morphological differentiation that resulted in delimitation of a number of subspecies. However, these morphological discontinuities are not always consistent with patterns of genetic differentiation. Here we assess genetic distinctiveness of grey wolves from the Caucasus (a region at the border between Europe and West Asia) that have been classified as a distinct subspecies C. l. cubanensis. We analysed their genetic variability based on mtDNA control region, microsatellite loci and genome-wide SNP genotypes (obtained for a subset of the samples), and found similar or higher levels of genetic diversity at all these types of loci as compared with other Eurasian populations. Although we found no evidence for a recent genetic bottleneck, genome-wide linkage disequilibrium patterns suggest a long-term demographic decline in the Caucasian population – a trend consistent with other Eurasian populations. Caucasian wolves share mtDNA haplotypes with both Eastern European and West Asian wolves, suggesting past or ongoing gene flow. Microsatellite data also suggest gene flow between the Caucasus and Eastern Europe. We found evidence for moderate admixture between the Caucasian wolves and domestic dogs, at a level comparable with other Eurasian populations. Taken together, our results show that Caucasian wolves are not genetically isolated from other Eurasian populations, share with them the same demographic trends, and are affected by similar conservation problems. PMID:24714198

  10. Human impact on genetic diversity of Toxoplasma gondii: example of the anthropized environment from French Guiana.

    Science.gov (United States)

    Mercier, A; Ajzenberg, D; Devillard, S; Demar, M P; de Thoisy, B; Bonnabau, H; Collinet, F; Boukhari, R; Blanchet, D; Simon, S; Carme, B; Dardé, M-L

    2011-08-01

    In French Guiana, severe cases of toxoplasmosis in immunocompetent patients are associated with atypical strains of Toxoplasma gondii linked to a wild neotropical rainforest cycle and a higher genetic diversity than usually observed for T. gondii isolates from anthropized environment. This raises the question of the impact of anthropization of the natural environment, on genetic diversity and on the population structure of T. gondii. However, few data are available on strains circulating in the anthropized areas from French Guiana. Seropositive animals originating mainly from anthropized sub-urban areas and punctually from wild environment in French Guiana were analyzed for T. gondii isolation and genotyping. Thirty-three strains were obtained by bioassay in mice and compared with 18 previously reported isolates chiefly originating from the Amazon rainforest. The genotyping analysis performed with 15 microsatellite markers located on 12 different chromosomes revealed a lower genetic diversity in the anthropized environment. Results were analyzed in terms of population structure by clustering methods, Neighbor-joining trees reconstruction based on genetic distances, F(ST,) Mantel's tests and linkage disequilibrium. They clearly showed a genetic differentiation between strains associated to the anthropized environment and those associated to the wild, but with some inbreeding between them. The majority of strains from the anthropized environment were clustered into additional lineages of T. gondii that are common in the Caribbean. In conclusion the two environmental populations "wild" and "anthropized" were genetically well differentiated. The anthropization of the environment seems to be accompanied with a decreased diversity of T. gondii associated with a greater structure of the populations. We detected potential interpenetration and genetic exchanges between these two environmental populations. As a higher pathogenicity in human of "wild" genotypes has been

  11. Genetic Interactions with Prenatal Social Environment: Effects on Academic and Behavioral Outcomes

    Science.gov (United States)

    Conley, Dalton; Rauscher, Emily

    2013-01-01

    Numerous studies report gene-environment interactions, suggesting that specific alleles have different effects on social outcomes depending on environment. In all these studies, however, environmental conditions are potentially endogenous to unmeasured genetic characteristics. That is, it could be that the observed interaction effects actually…

  12. Simulation based virtual learning environment in medical genetics counseling

    DEFF Research Database (Denmark)

    Makransky, Guido; Bonde, Mads T.; Wulff, Julie S. G.

    2016-01-01

    learning environments increase students' knowledge, intrinsic motivation, and self-efficacy, and help them generalize from laboratory analyses to clinical practice and health decision-making. METHODS: An entire class of 300 University of Copenhagen first-year undergraduate students, most with a major...

  13. Genetic by environment interaction on fresh root yield, dry matter ...

    African Journals Online (AJOL)

    Eighteen yellow-fleshed cassava genotypes and two released white-fleshed clones (check) were evaluated in five locations representing the major cassava growing agroecological zones of Nigeria to access their performance for fresh root yield, dry matter content, total carotene content and genotypes by environment ...

  14. Evolving Plastic Responses to External and Genetic Environments.

    Science.gov (United States)

    Reuter, Max; Camus, M Florencia; Hill, Mark S; Ruzicka, Filip; Fowler, Kevin

    2017-03-01

    Phenotypic plasticity can mitigate adaptive trade-offs in fluctuating environments but how plasticity arises is little known. New research documents this process in a bacterial system. We highlight remarkable parallels to the evolution of sexual dimorphism and argue that their approach can aid our understanding of adaptive conflicts between the sexes. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. ROAD DETECTION BY NEURAL AND GENETIC ALGORITHM IN URBAN ENVIRONMENT

    Directory of Open Access Journals (Sweden)

    A. Barsi

    2012-07-01

    Full Text Available In the urban object detection challenge organized by the ISPRS WG III/4 high geometric and radiometric resolution aerial images about Vaihingen/Stuttgart, Germany are distributed. The acquired data set contains optical false color, near infrared images and airborne laserscanning data. The presented research focused exclusively on the optical image, so the elevation information was ignored. The road detection procedure has been built up of two main phases: a segmentation done by neural networks and a compilation made by genetic algorithms. The applied neural networks were support vector machines with radial basis kernel function and self-organizing maps with hexagonal network topology and Euclidean distance function for neighborhood management. The neural techniques have been compared by hyperbox classifier, known from the statistical image classification practice. The compilation of the segmentation is realized by a novel application of the common genetic algorithm and by differential evolution technique. The genes were implemented to detect the road elements by evaluating a special binary fitness function. The results have proven that the evolutional technique can automatically find major road segments.

  16. Genetic Characterization of Enterococcus in California Coastal Environments

    OpenAIRE

    Ferguson, Donna Marie

    2014-01-01

    Enterococcus are used as fecal indicator bacteria used to assess the possible presence of fecal contamination of recreational waters. Current enterococci laboratory methods do not distinguish between enterococci from fecal and non-fecal sources, confounding assessments of water quality assessment and efforts to identify and remediate fecal sources. Moreover, the ability of enterococci to grow marine environments indicate that contributions from natural sources may further limit their use as...

  17. Pollen genetic markers for detection of mutagens in the environment

    Energy Technology Data Exchange (ETDEWEB)

    Nilan, R.A.; Rosichan, J.L.; Arenaz, P.; Hodgdon, A.L.; Kleinhofs, A.

    1980-01-01

    To utilize and exploit pollen for in situ mutagen monitoring, screening and toxicology, the range of genetic traits in pollen must be identified and analyzed. To be useful for the development of mutagen detection systems proteins should be: (1) activity stainable or immunologically identifiable in the pollen, (2) the products of one to three loci; and (3) gametophytic and nuclear in origin. Several proteins, including alcohol dehydrogenase in maize, which meet these criteria are discussed. The waxy locus in barley and maize which controls starch deposition for pollen screening and mutant detection. Thirty waxy mutant lines, induced by sodium azide and gamma-rays are characterized for spontaneous and induced reversion frequencies, allelism, karyotype, amylose content, and UDPglucose glucosyltransferase (waxy gene product) activity. Twelve mutant alleles are being mapped by recombinant frequencies.

  18. ASD and schizophrenia show distinct developmental profiles in common genetic overlap with population-based social communication difficulties

    DEFF Research Database (Denmark)

    St Pourcain, B; Robinson, E B; Anttila, V

    2017-01-01

    Difficulties in social communication are part of the phenotypic overlap between autism spectrum disorders (ASD) and schizophrenia. Both conditions follow, however, distinct developmental patterns. Symptoms of ASD typically occur during early childhood, whereas most symptoms characteristic...

  19. A comparison between legume technologies and fallow, and their effects on maize and soil traits, in two distinct environments of the West African savannah

    NARCIS (Netherlands)

    Franke, A.C.; Laberge, G.; Oyewole, B.D.; Schulz, S.; Tobe, O.

    2008-01-01

    Legume¿maize rotation and maize nitrogen (N)-response trials were carried out simultaneously from 1998 to 2004 in two distinct agro-ecological environments of West Africa: the humid derived savannah (Ibadan) and the drier northern Guinea savannah (Zaria). In the N-response trial, maize was grown

  20. Genetic and Epigenetic Tumor Suppressor Gene Silencing are Distinct Molecular Phenotypes Driven by Growth Promoting Mutations in Non small Cell Lung Cancer

    International Nuclear Information System (INIS)

    Marsit, C. J.; Kelsey, K. T.; Houseman, E. A.; Kelsey, K. T.; Houseman, E. A.; Nelson, H. H.

    2008-01-01

    Both genetic and epigenetic alterations characterize human non small cell lung cancer (NSCLC), but the biological processes that create or select these alterations remain incompletely investigated. Our hypothesis posits that a roughly reciprocal relationship between the propensity for promoter hyper methylation and a propensity for genetic deletion leads to distinct molecular phenotypes of lung cancer. To test this hypothesis, we examined promoter hyper methylation of 17 tumor suppressor genes, as a marker of epigenetic alteration propensity, and deletion events at the 3p21 region, as a marker of genetic alteration. To model the complex biology between these somatic alterations, we utilized an item response theory model. We demonstrated that tumors exhibiting LOH at greater than 30% of informative alleles in the 3p21 region have a significantly reduced propensity for hyper methylation. At the same time, tumors with activating KRAS mutations showed a significantly increased propensity for hyper methylation of the loci examined, a result similar to what has been observed in colon cancer. These data suggest that NSCLCs have distinct epigenetic or genetic alteration phenotypes acting upon tumor suppressor genes and that mutation of oncogenic growth promoting genes, such as KRAS, is associated with the epigenetic phenotype.

  1. Menstrual blood closely resembles the uterine immune micro-environment and is clearly distinct from peripheral blood

    NARCIS (Netherlands)

    Molen, R.G. van der; Schutten, J.H.; Cranenbroek, B. van; Meer, M. ter; Donckers, J.; Scholten, R.R.; Heijden, O.W.H. van der; Spaanderman, M.E.A.; Joosten, I.

    2014-01-01

    STUDY QUESTION: Is menstrual blood a suitable source of endometrial derived lymphocytes? SUMMARY ANSWER: Mononuclear cells isolated from menstrual samples (menstrual blood mononuclear cells (MMC)) are clearly distinct from peripheral blood mononuclear cells (PBMC) and show a strong resemblance with

  2. Genetic and social environment interactions and their impact on health policy.

    Science.gov (United States)

    Payne, Perry W; Royal, Charmaine; Kardia, Sharon L R

    2007-01-01

    Genetic and social factors are not as separate as once thought. Researchers within the social sciences are beginning to realize that genetics and the social environment interact synergistically to affect health behaviors and outcomes. This way of thinking is leading to new research models and is influencing the development of research initiatives. The importance of this gene-social environment paradigm is evident in current and proposed health policies, and future research likely will spur further questions related to various areas of public policy.

  3. Genetic diversity of archaea in deep-sea hydrothermal vent environments.

    OpenAIRE

    Takai, K; Horikoshi, K

    1999-01-01

    Molecular phylogenetic analysis of naturally occurring archaeal communities in deep-sea hydrothermal vent environments was carried out by PCR-mediated small subunit rRNA gene (SSU rDNA) sequencing. As determined through partial sequencing of rDNA clones amplified with archaea-specific primers, the archaeal populations in deep-sea hydrothermal vent environments showed a great genetic diversity, and most members of these populations appeared to be uncultivated and unidentified organisms. In the...

  4. Genetic architecture of carbon isotope composition and growth in Eucalyptus across multiple environments.

    Science.gov (United States)

    Bartholomé, Jérôme; Mabiala, André; Savelli, Bruno; Bert, Didier; Brendel, Oliver; Plomion, Christophe; Gion, Jean-Marc

    2015-06-01

    In the context of climate change, the water-use efficiency (WUE) of highly productive tree varieties, such as eucalypts, has become a major issue for breeding programmes. This study set out to dissect the genetic architecture of carbon isotope composition (δ(13) C), a proxy of WUE, across several environments. A family of Eucalyptus urophylla × E. grandis was planted in three trials and phenotyped for δ(13) C and growth traits. High-resolution genetic maps enabled us to target genomic regions underlying δ(13) C quantitative trait loci (QTLs) on the E. grandis genome. Of the 15 QTLs identified for δ(13) C, nine were stable across the environments and three displayed significant QTL-by-environment interaction, suggesting medium to high genetic determinism for this trait. Only one colocalization was found between growth and δ(13) C. Gene ontology (GO) term enrichment analysis suggested candidate genes related to foliar δ(13) C, including two involved in the regulation of stomatal movements. This study provides the first report of the genetic architecture of δ(13) C and its relation to growth in Eucalyptus. The low correlations found between the two traits at phenotypic and genetic levels suggest the possibility of improving the WUE of Eucalyptus varieties without having an impact on breeding for growth. © 2015 CIRAD. New Phytologist © 2015 New Phytologist Trust.

  5. Genetic Analyses and Simulations of Larval Dispersal Reveal Distinct Populations and Directional Connectivity across the Range of the Hawaiian Grouper (Epinephelus quernus

    Directory of Open Access Journals (Sweden)

    Malia Ana J. Rivera

    2011-01-01

    Full Text Available Integration of ecological and genetic data to study patterns of biological connectivity can aid in ecosystem-based management. Here we investigated connectivity of the Hawaiian grouper Epinephelus quernus, a species of management concern within the Main Hawaiian Islands (MHI, by comparing genetic analyses with simulated larval dispersal patterns across the species range in the Hawaiian Archipelago and Johnston Atoll. Larval simulations revealed higher dispersal from the MHI to the Northwestern Hawaiian Islands (NWHI than in the opposite direction and evidence for a dispersal corridor between Johnston and the middle of the Hawaiian Archipelago. Genetic analyses using mitochondrial DNA (mtDNA control region sequences and microsatellites revealed relatively high connectivity across the Hawaiian Archipelago, with the exception of genetically distinct populations and higher mtDNA diversity in the mid-Archipelago. These analyses support the preservation of the mid-archipelago as a source of genetic diversity and a region of connectivity with locations outside the Hawaiian Archipelago. Additionally, our evidence for directional dispersal away from the MHI lends caution to any management decisions that would rely on the NWHI replenishing depleted MHI stocks.

  6. Social science genetics and fertility : Essays on the Interplay Between Genes, Social Environment and Human Fertility

    NARCIS (Netherlands)

    Tropf, Felix

    2016-01-01

    To what extent do genes influence the age at which you have your first child and the number of children that you have? Does the social environment influence genetic effects on fertility? Do genes lead to spurious associations between life outcomes such as education and age at first birth? The social

  7. Genotype-by-environment interaction in genetic mapping of multiple quantitative trait loci

    NARCIS (Netherlands)

    Jansen, R.C.; Ooijen, J.W. van; Stam, P.; Lister, C.; Dean, C.

    1995-01-01

    The interval mapping method is widely used for the genetic mapping of quantitative trait loci (QTLs), though true resolution of quantitative variation into QTLs is hampered with this method. Separation of QTLs is troublesome, because single-QTL is models are fitted. Further, genotype-by-environment

  8. Revealing genetic diversity of eukaryotic microorganisms in aquatic environments by denaturing gradient gel electrophoresis

    NARCIS (Netherlands)

    Van Hannen, E.J.; Van Agterveld, M.P.; Gons, H.J.; Laanbroek, H.J.

    1998-01-01

    A new Eucarya-specific 18S rDNA primer set was constructed and tested using denaturing gradient gel electrophoresis to analyze the genetic diversity of eukaryotic microorganisms in aquatic environments. All eukaryal lines of descent exhibited four or fewer nucleotide mismatches in the forward primer

  9. Gene × Environment Interactions in Schizophrenia: Evidence from Genetic Mouse Models

    Directory of Open Access Journals (Sweden)

    Paula Moran

    2016-01-01

    Full Text Available The study of gene × environment, as well as epistatic interactions in schizophrenia, has provided important insight into the complex etiopathologic basis of schizophrenia. It has also increased our understanding of the role of susceptibility genes in the disorder and is an important consideration as we seek to translate genetic advances into novel antipsychotic treatment targets. This review summarises data arising from research involving the modelling of gene × environment interactions in schizophrenia using preclinical genetic models. Evidence for synergistic effects on the expression of schizophrenia-relevant endophenotypes will be discussed. It is proposed that valid and multifactorial preclinical models are important tools for identifying critical areas, as well as underlying mechanisms, of convergence of genetic and environmental risk factors, and their interaction in schizophrenia.

  10. Gene × Environment Interactions in Schizophrenia: Evidence from Genetic Mouse Models.

    Science.gov (United States)

    Moran, Paula; Stokes, Jennifer; Marr, Julia; Bock, Gavin; Desbonnet, Lieve; Waddington, John; O'Tuathaigh, Colm

    2016-01-01

    The study of gene × environment, as well as epistatic interactions in schizophrenia, has provided important insight into the complex etiopathologic basis of schizophrenia. It has also increased our understanding of the role of susceptibility genes in the disorder and is an important consideration as we seek to translate genetic advances into novel antipsychotic treatment targets. This review summarises data arising from research involving the modelling of gene × environment interactions in schizophrenia using preclinical genetic models. Evidence for synergistic effects on the expression of schizophrenia-relevant endophenotypes will be discussed. It is proposed that valid and multifactorial preclinical models are important tools for identifying critical areas, as well as underlying mechanisms, of convergence of genetic and environmental risk factors, and their interaction in schizophrenia.

  11. Genetic and environmental-genetic interaction rules for the myopia based on a family exposed to risk from a myopic environment.

    Science.gov (United States)

    Wenbo, Li; Congxia, Bai; Hui, Liu

    2017-08-30

    To quantitatively assess the role of heredity and environmental factors in myopia based on the family with enough exposed to risk from myopic environment for establishment of environmental and genetic index (EGI). A pedigree analysis unit was defined as one child (university student), father, and mother. Information pertaining to visual acuity, experience in participating in the college entrance examination in mainland of China (regarded as a strong environmental risk for myopia), and occupation for pedigree analysis units were obtained. The difference between effect of both genetic and environmental factors (myopia prevalence in children with two myopic parents) and environmental factors (myopia prevalence in children of whom neither parent was myopic) was defined as the EGI. Multiple regression analysis was performed for 114 pedigree using diopters of father, mother, average diopters in parents, maximum and minimum diopters in father and mother as variables. A total of 353 farmers and 162 farmer families were used as a control group. A distinct difference in myopia rate (96.2% versus 57.7%) was observed for children from parents with myopia and parents without myopia (EGI=0.385). The maximum diopter was included to regression equation which was statistically significant. The prevalence of myopia was 9.9% in the farmer. The prevalence in children is similar between the farmer and other families. A new genetic rule that myopia in children was directly related with maximum diopters in father and mother may be suggested. Environmental factors may play a leading role in the formation of myopia. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Chemical Variation in a Dominant Tree Species: Population Divergence, Selection and Genetic Stability across Environments

    Science.gov (United States)

    O’Reilly-Wapstra, Julianne M.; Miller, Alison M.; Hamilton, Matthew G.; Williams, Dean; Glancy-Dean, Naomi; Potts, Brad M.

    2013-01-01

    Understanding among and within population genetic variation of ecologically important plant traits provides insight into the potential evolutionary processes affecting those traits. The strength and consistency of selection driving variability in traits would be affected by plasticity in differences among genotypes across environments (G×E). We investigated population divergence, selection and environmental plasticity of foliar plant secondary metabolites (PSMs) in a dominant tree species, Eucalyptus globulus. Using two common garden trials we examined variation in PSMs at multiple genetic scales; among 12 populations covering the full geographic range of the species and among up to 60 families within populations. Significant genetic variation in the expression of many PSMs resides both among and within populations of E. globulus with moderate (e.g., sideroxylonal A h2op = 0.24) to high (e.g., macrocarpal G h2op = 0.48) narrow sense heritabilities and high coefficients of additive genetic variation estimated for some compounds. A comparison of Qst and Fst estimates suggest that variability in some of these traits may be due to selection. Importantly, there was no genetic by environment interaction in the expression of any of the quantitative chemical traits despite often significant site effects. These results provide evidence that natural selection has contributed to population divergence in PSMs in E. globulus, and identifies the formylated phloroglucinol compounds (particularly sideroxylonal) and a dominant oil, 1,8-cineole, as candidates for traits whose genetic architecture has been shaped by divergent selection. Additionally, as the genetic differences in these PSMs that influence community phenotypes is stable across environments, the role of plant genotype in structuring communities is strengthened and these genotypic differences may be relatively stable under global environmental changes. PMID:23526981

  13. Chemical variation in a dominant tree species: population divergence, selection and genetic stability across environments.

    Directory of Open Access Journals (Sweden)

    Julianne M O'Reilly-Wapstra

    Full Text Available Understanding among and within population genetic variation of ecologically important plant traits provides insight into the potential evolutionary processes affecting those traits. The strength and consistency of selection driving variability in traits would be affected by plasticity in differences among genotypes across environments (G×E. We investigated population divergence, selection and environmental plasticity of foliar plant secondary metabolites (PSMs in a dominant tree species, Eucalyptus globulus. Using two common garden trials we examined variation in PSMs at multiple genetic scales; among 12 populations covering the full geographic range of the species and among up to 60 families within populations. Significant genetic variation in the expression of many PSMs resides both among and within populations of E. globulus with moderate (e.g., sideroxylonal A h(2op = 0.24 to high (e.g., macrocarpal G h(2op = 0.48 narrow sense heritabilities and high coefficients of additive genetic variation estimated for some compounds. A comparison of Qst and Fst estimates suggest that variability in some of these traits may be due to selection. Importantly, there was no genetic by environment interaction in the expression of any of the quantitative chemical traits despite often significant site effects. These results provide evidence that natural selection has contributed to population divergence in PSMs in E. globulus, and identifies the formylated phloroglucinol compounds (particularly sideroxylonal and a dominant oil, 1,8-cineole, as candidates for traits whose genetic architecture has been shaped by divergent selection. Additionally, as the genetic differences in these PSMs that influence community phenotypes is stable across environments, the role of plant genotype in structuring communities is strengthened and these genotypic differences may be relatively stable under global environmental changes.

  14. Shift happens: trailing edge contraction associated with recent warming trends threatens a distinct genetic lineage in the marine macroalga Fucus vesiculosus.

    Science.gov (United States)

    Nicastro, Katy R; Zardi, Gerardo I; Teixeira, Sara; Neiva, João; Serrão, Ester A; Pearson, Gareth A

    2013-01-23

    Significant effects of recent global climate change have already been observed in a variety of ecosystems, with evidence for shifts in species ranges, but rarely have such consequences been related to the changes in the species genetic pool. The stretch of Atlantic coast between North Africa and North Iberia is ideal for studying the relationship between species distribution and climate change as it includes the distributional limits of a considerable number of both cold- and warm-water species.We compared temporal changes in distribution of the canopy-forming alga Fucus vesiculosus with historical sea surface temperature (SST) patterns to draw links between range shifts and contemporary climate change. Moreover, we genetically characterized with microsatellite markers previously sampled extinct and extant populations in order to estimate resulting cryptic genetic erosion. Over the past 30 years, a geographic contraction of the southern range edge of this species has occurred, with a northward latitudinal shift of approximately 1,250 km. Additionally, a more restricted distributional decline was recorded in the Bay of Biscay. Coastal SST warming data over the last three decades revealed a significant increase in temperature along most of the studied coastline, averaging 0.214°C/decade. Importantly, the analysis of existing and extinct population samples clearly distinguished two genetically different groups, a northern and a southern clade. Because of the range contraction, the southern group is currently represented by very few extant populations. This southern edge range shift is thus causing the loss of a distinct component of the species genetic background. We reveal a climate-correlated diversity loss below the species level, a process that could render the species more vulnerable to future environmental changes and affect its evolutionary potential. This is a remarkable case of genetic uniqueness of a vanishing cryptic genetic clade (southern clade).

  15. Isotopic and geochemical investigation of two distinct Mars analog environments using evolved gas techniques in Svalbard, Norway

    NARCIS (Netherlands)

    Stern, J.C.; McAdam, A.C.; Kate, I.L. ten; Bish, D.L.; Blake, D.F.; Morris, R.V.; Bowden, R.; Fogel, M.L.; Glamoclija, M.; Mahaffy, P.R.; Steele, A.; Amundsen, H.E.F.

    2013-01-01

    The 2010 Arctic Mars Analog Svalbard Expedition (AMASE) investigated two distinct geologic settings on Svalbard, using methodologies and techniques to be deployed on Mars Science Laboratory (MSL). AMASE-related research comprises both analyses conducted during the expedition and further analyses of

  16. Population differentiation in Pacific salmon: local adaptation, genetic drift, or the environment?

    Science.gov (United States)

    Adkison, Milo D.

    1995-01-01

    Morphological, behavioral, and life-history differences between Pacific salmon (Oncorhynchus spp.) populations are commonly thought to reflect local adaptation, and it is likewise common to assume that salmon populations separated by small distances are locally adapted. Two alternatives to local adaptation exist: random genetic differentiation owing to genetic drift and founder events, and genetic homogeneity among populations, in which differences reflect differential trait expression in differing environments. Population genetics theory and simulations suggest that both alternatives are possible. With selectively neutral alleles, genetic drift can result in random differentiation despite many strays per generation. Even weak selection can prevent genetic drift in stable populations; however, founder effects can result in random differentiation despite selective pressures. Overlapping generations reduce the potential for random differentiation. Genetic homogeneity can occur despite differences in selective regimes when straying rates are high. In sum, localized differences in selection should not always result in local adaptation. Local adaptation is favored when population sizes are large and stable, selection is consistent over large areas, selective diffeentials are large, and straying rates are neither too high nor too low. Consideration of alternatives to local adaptation would improve both biological research and salmon conservation efforts.

  17. Temporally isolated lineages of Pink salmon reveal unique signatures of selection on distinct pools of standing genetic variation

    DEFF Research Database (Denmark)

    Limborg, Morten; Waples, R.K.; Seeb, J.E.

    2014-01-01

    A species’ genetic diversity bears the marks of evolutionary processes that have occurred throughout its history. However, robust detection of selection in wild populations is difficult and often impeded by lack of replicate tests. Here, we investigate selection in pink salmon (Oncorhynchus gorbu...

  18. The melanomas: a synthesis of epidemiological, clinical, histopathological, genetic, and biological aspects, supporting distinct subtypes, causal pathways, and cells of origin

    Science.gov (United States)

    Whiteman, David C.; Pavan, William J; Bastian, Boris C.

    2012-01-01

    Summary Converging lines of evidence from varied scientific disciplines suggest that cutaneous melanomas comprise biologically distinct subtypes that arise through multiple causal pathways. Understanding the respective relationships of each subtype with etiologic factors such as UV radiation and constitutional factors is the first necessary step toward developing refined prevention strategies for the specific forms of melanoma. Furthermore, classifying this disease precisely into biologically distinct subtypes is the key to developing mechanism- based treatments, as highlighted by recent discoveries. In this review, we outline the historical developments that underpin our understanding of melanoma heterogeneity, and we do this from the perspectives of clinical presentation, histopathology, epidemiology, molecular genetics, and developmental biology. We integrate the evidence from these separate trajectories to catalog the emerging major categories of melanomas and conclude with important unanswered questions relating to the development of melanoma and its cells of origin. PMID:21707960

  19. Glacial vicariance in the Pacific Northwest: evidence from a lodgepole pine mitochondrial DNA minisatellite for multiple genetically distinct and widely separated refugia.

    Science.gov (United States)

    Godbout, Julie; Fazekas, Aron; Newton, Craig H; Yeh, Francis C; Bousquet, Jean

    2008-05-01

    The Canadian side of the Pacific Northwest was almost entirely covered by ice during the last glacial maximum, which has induced vicariance and genetic population structure for several plant and animal taxa. Lodgepole pine (Pinus contorta Dougl. ex. Loud.) has a wide latitudinal and longitudinal distribution in the Pacific Northwest. Our main objective was to identify relictual signatures of glacial vicariance in the population structure of the species and search for evidence of distinct glacial refugia in the Pacific Northwest. A maternally inherited mitochondrial DNA minisatellite-like marker was used to decipher haplotype diversity in 91 populations of lodgepole pine located across the natural range. Overall population differentiation was sizeable (G(ST) = 0.365 and R(ST) = 0.568). Four relatively homogeneous groups of populations, possibly representative of as many genetically distinct glacial populations, were identified for the two main subspecies, ssp. latifolia and ssp. contorta. For ssp. contorta, one glacial lineage is suggested to have been located at high latitudes and possibly off the coast of mainland British Columbia (BC), while the other is considered to have been located south of the ice sheet along the Pacific coast. For ssp. latifolia, two genetically distinct glacial populations probably occurred south of the ice sheet: in the area bounded by the Cascades and Rocky Mountains ranges, and on the eastern side of the Rockies. A possible fifth refugium located in the Yukon may have also been present for ssp. latifolia. Zones of contact between these ancestral lineages were also apparent in interior and northern BC. These results indicate the role of the Queen Charlotte Islands and the Alexander Archipelago as a refugial zone for some Pacific Northwest species and the vicariant role played by the Cascades and the American Rocky Mountains during glaciation.

  20. Phenotypic and genetic effects of contrasting ethanol environments on physiological and developmental traits in Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Luis E Castañeda

    Full Text Available A central problem in evolutionary physiology is to understand the relationship between energy metabolism and fitness-related traits. Most attempts to do so have been based on phenotypic correlations that are not informative for the evolutionary potential of natural populations. Here, we explored the effect of contrasting ethanol environments on physiological and developmental traits, their genetic (covariances and genetic architecture in Drosophila melanogaster. Phenotypic and genetic parameters were estimated in two populations (San Fernando and Valdivia, Chile, using a half-sib family design where broods were split into ethanol-free and ethanol-supplemented conditions. Our findings show that metabolic rate, body mass and development times were sensitive (i.e., phenotypic plasticity to ethanol conditions and dependent on population origin. Significant heritabilities were found for all traits, while significant genetic correlations were only found between larval and total development time and between development time and metabolic rate for flies of the San Fernando population developed in ethanol-free conditions. Posterior analyses indicated that the G matrices differed between ethanol conditions for the San Fernando population (mainly explained by differences in genetic (covariances of developmental traits, whereas the Valdivia population exhibited similar G matrices between ethanol conditions. Our findings suggest that ethanol-free environment increases the energy available to reduce development time. Therefore, our results indicate that environmental ethanol could modify the process of energy allocation, which could have consequences on the evolutionary response of natural populations of D. melanogaster.

  1. Phenotypic and Genetic Effects of Contrasting Ethanol Environments on Physiological and Developmental Traits in Drosophila melanogaster

    Science.gov (United States)

    Castañeda, Luis E.; Nespolo, Roberto F.

    2013-01-01

    A central problem in evolutionary physiology is to understand the relationship between energy metabolism and fitness-related traits. Most attempts to do so have been based on phenotypic correlations that are not informative for the evolutionary potential of natural populations. Here, we explored the effect of contrasting ethanol environments on physiological and developmental traits, their genetic (co)variances and genetic architecture in Drosophila melanogaster. Phenotypic and genetic parameters were estimated in two populations (San Fernando and Valdivia, Chile), using a half-sib family design where broods were split into ethanol-free and ethanol-supplemented conditions. Our findings show that metabolic rate, body mass and development times were sensitive (i.e., phenotypic plasticity) to ethanol conditions and dependent on population origin. Significant heritabilities were found for all traits, while significant genetic correlations were only found between larval and total development time and between development time and metabolic rate for flies of the San Fernando population developed in ethanol-free conditions. Posterior analyses indicated that the G matrices differed between ethanol conditions for the San Fernando population (mainly explained by differences in genetic (co)variances of developmental traits), whereas the Valdivia population exhibited similar G matrices between ethanol conditions. Our findings suggest that ethanol-free environment increases the energy available to reduce development time. Therefore, our results indicate that environmental ethanol could modify the process of energy allocation, which could have consequences on the evolutionary response of natural populations of D. melanogaster. PMID:23505567

  2. The yeast Starmerella bacillaris (synonym Candida zemplinina) shows high genetic diversity in winemaking environments.

    Science.gov (United States)

    Masneuf-Pomarede, Isabelle; Juquin, Elodie; Miot-Sertier, Cécile; Renault, Philippe; Laizet, Yec'han; Salin, Franck; Alexandre, Hervé; Capozzi, Vittorio; Cocolin, Luca; Colonna-Ceccaldi, Benoit; Englezos, Vasileios; Girard, Patrick; Gonzalez, Beatriz; Lucas, Patrick; Mas, Albert; Nisiotou, Aspasia; Sipiczki, Matthias; Spano, Giuseppe; Tassou, Chrysoula; Bely, Marina; Albertin, Warren

    2015-08-01

    The yeast Candida zemplinina (Starmerella bacillaris) is frequently isolated from grape and wine environments. Its enological use in mixed fermentation with Saccharomyces cerevisiae has been extensively investigated these last few years, and several interesting features including low ethanol production, fructophily, glycerol and other metabolites production, have been described. In addition, molecular tools allowing the characterization of yeast populations have been developed, both at the inter- and intraspecific levels. However, most of these fingerprinting methods are not compatible with population genetics or ecological studies. In this work, we developed 10 microsatellite markers for the C. zemplinina species that were used for the genotyping of 163 strains from nature or various enological regions (28 vineyards/wineries from seven countries). We show that the genetic diversity of C. zemplinina is shaped by geographical localization. Populations isolated from winemaking environments are quite diverse at the genetic level: neither clonal-like behaviour nor specific genetic signature were associated with the different vineyards/wineries. Altogether, these results suggest that C. zemplinina is not under selective pressure in winemaking environments. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  3. The Drosophila TRPP cation channel, PKD2 and Dmel/Ced-12 act in genetically distinct pathways during apoptotic cell clearance.

    Directory of Open Access Journals (Sweden)

    Emeline Van Goethem

    Full Text Available Apoptosis, a genetically programmed cell death, allows for homeostasis and tissue remodelling during development of all multi-cellular organisms. Phagocytes swiftly recognize, engulf and digest apoptotic cells. Yet, to date the molecular mechanisms underlying this phagocytic process are still poorly understood. To delineate the molecular mechanisms of apoptotic cell clearance in Drosophila, we have carried out a deficiency screen and have identified three overlapping phagocytosis-defective mutants, which all delete the fly homologue of the ced-12 gene, known as Dmel\\ced12. As anticipated, we have found that Dmel\\ced-12 is required for apoptotic cell clearance, as for its C. elegans and mammalian homologues, ced-12 and elmo, respectively. However, the loss of Dmel\\ced-12 did not solely account for the phenotypes of all three deficiencies, as zygotic mutations and germ line clones of Dmel\\ced-12 exhibited weaker phenotypes. Using a nearby genetically interacting deficiency, we have found that the polycystic kidney disease 2 gene, pkd2, which encodes a member of the TRPP channel family, is also required for phagocytosis of apoptotic cells, thereby demonstrating a novel role for PKD2 in this process. We have also observed genetic interactions between pkd2, simu, drpr, rya-r44F, and retinophilin (rtp, also known as undertaker (uta, a gene encoding a MORN-repeat containing molecule, which we have recently found to be implicated in calcium homeostasis during phagocytosis. However, we have not found any genetic interaction between Dmel\\ced-12 and simu. Based on these genetic interactions and recent reports demonstrating a role for the mammalian pkd-2 gene product in ER calcium release during store-operated calcium entry, we propose that PKD2 functions in the DRPR/RTP pathway to regulate calcium homeostasis during this process. Similarly to its C. elegans homologue, Dmel\\Ced-12 appears to function in a genetically distinct pathway.

  4. Distinctive roles of age, sex, and genetics in shaping transcriptional variation of human immune responses to microbial challenges.

    Science.gov (United States)

    Piasecka, Barbara; Duffy, Darragh; Urrutia, Alejandra; Quach, Hélène; Patin, Etienne; Posseme, Céline; Bergstedt, Jacob; Charbit, Bruno; Rouilly, Vincent; MacPherson, Cameron R; Hasan, Milena; Albaud, Benoit; Gentien, David; Fellay, Jacques; Albert, Matthew L; Quintana-Murci, Lluis

    2018-01-16

    The contribution of host genetic and nongenetic factors to immunological differences in humans remains largely undefined. Here, we generated bacterial-, fungal-, and viral-induced immune transcriptional profiles in an age- and sex-balanced cohort of 1,000 healthy individuals and searched for the determinants of immune response variation. We found that age and sex affected the transcriptional response of most immune-related genes, with age effects being more stimulus-specific relative to sex effects, which were largely shared across conditions. Although specific cell populations mediated the effects of age and sex on gene expression, including CD8 + T cells for age and CD4 + T cells and monocytes for sex, we detected a direct effect of these intrinsic factors for the majority of immune genes. The mapping of expression quantitative trait loci (eQTLs) revealed that genetic factors had a stronger effect on immune gene regulation than age and sex, yet they affected a smaller number of genes. Importantly, we identified numerous genetic variants that manifested their regulatory effects exclusively on immune stimulation, including a Candida albicans -specific master regulator at the CR1 locus. These response eQTLs were enriched in disease-associated variants, particularly for autoimmune and inflammatory disorders, indicating that differences in disease risk may result from regulatory variants exerting their effects only in the presence of immune stress. Together, this study quantifies the respective effects of age, sex, genetics, and cellular heterogeneity on the interindividual variability of immune responses and constitutes a valuable resource for further exploration in the context of different infection risks or disease outcomes. Copyright © 2018 the Author(s). Published by PNAS.

  5. Evolutionary Genetic Analysis Uncovers Multiple Species with Distinct Habitat Preferences and Antibiotic Resistance Phenotypes in the Stenotrophomonas maltophilia Complex

    Directory of Open Access Journals (Sweden)

    Luz E. Ochoa-Sánchez

    2017-08-01

    Full Text Available The genus Stenotrophomonas (Gammaproteobacteria has a broad environmental distribution. Stenotrophomonas maltophilia is its best known species because it is a globally emerging, multidrug-resistant (MDR, opportunistic pathogen. Members of this species are known to display high genetic, ecological and phenotypic diversity, forming the so-called S. maltophilia complex (Smc. Heterogeneous resistance and virulence phenotypes have been reported for environmental Smc isolates of diverse ecological origin. We hypothesized that this heterogeneity could be in part due to the potential lumping of several cryptic species in the Smc. Here we used state-of-the-art phylogenetic and population genetics methods to test this hypothesis based on the multilocus dataset available for the genus at pubmlst.org. It was extended with sequences from complete and draft genome sequences to assemble a comprehensive set of reference sequences. This framework was used to analyze 108 environmental isolates obtained in this study from the sediment and water column of four rivers and streams in Central Mexico, affected by contrasting levels of anthropogenic pollution. The aim of the study was to identify species in this collection, defined as genetically cohesive sequence clusters, and to determine the extent of their genetic, ecological and phenotypic differentiation. The multispecies coalescent, coupled with Bayes factor analysis was used to delimit species borders, together with population genetic structure analyses, recombination and gene flow estimates between sequence clusters. These analyses consistently revealed that the Smc contains at least 5 significantly differentiated lineages: S. maltophilia and Smc1 to Smc4. Only S. maltophilia was found to be intrinsically MDR, all its members expressing metallo-β-lactamases (MBLs. The other Smc lineages were not MDR and did not express MBLs. We also obtained isolates related to S. acidaminiphila, S. humi and S. terrae. They

  6. Molecular genetic gene-environment studies using candidate genes in schizophrenia: a systematic review.

    Science.gov (United States)

    Modinos, Gemma; Iyegbe, Conrad; Prata, Diana; Rivera, Margarita; Kempton, Matthew J; Valmaggia, Lucia R; Sham, Pak C; van Os, Jim; McGuire, Philip

    2013-11-01

    The relatively high heritability of schizophrenia suggests that genetic factors play an important role in the etiology of the disorder. On the other hand, a number of environmental factors significantly influence its incidence. As few direct genetic effects have been demonstrated, and there is considerable inter-individual heterogeneity in the response to the known environmental factors, interactions between genetic and environmental factors may be important in determining whether an individual develops the disorder. To date, a considerable number of studies of gene-environment interactions (G×E) in schizophrenia have employed a hypothesis-based molecular genetic approach using candidate genes, which have led to a range of different findings. This systematic review aims to summarize the results from molecular genetic candidate studies and to review challenges and opportunities of this approach in psychosis research. Finally, we discuss the potential of future prospects, such as new studies that combine hypothesis-based molecular genetic candidate approaches with agnostic genome-wide association studies in determining schizophrenia risk. © 2013 Elsevier B.V. All rights reserved.

  7. Beta-hemolytic Streptococcus dysgalactiae strains isolated from horses are a genetically distinct population within the Streptococcus dysgalactiae taxon

    Science.gov (United States)

    Pinho, Marcos D.; Erol, Erdal; Ribeiro-Gonçalves, Bruno; Mendes, Catarina I.; Carriço, João A.; Matos, Sandra C.; Preziuso, Silvia; Luebke-Becker, Antina; Wieler, Lothar H.; Melo-Cristino, Jose; Ramirez, Mario

    2016-01-01

    The pathogenic role of beta-hemolytic Streptococcus dysgalactiae in the equine host is increasingly recognized. A collection of 108 Lancefield group C (n = 96) or L (n = 12) horse isolates recovered in the United States and in three European countries presented multilocus sequence typing (MLST) alleles, sequence types and emm types (only 56% of the isolates could be emm typed) that were, with few exceptions, distinct from those previously found in human Streptococcus dysgalactiae subsp. equisimilis. Characterization of a subset of horse isolates by multilocus sequence analysis (MLSA) and 16S rRNA gene sequence showed that most equine isolates could also be differentiated from S. dysgalactiae strains from other animal species, supporting the existence of a horse specific genomovar. Draft genome information confirms the distinctiveness of the horse genomovar and indicates the presence of potentially horse-specific virulence factors. While this genomovar represents most of the isolates recovered from horses, a smaller MLST and MLSA defined sub-population seems to be able to cause infections in horses, other animals and humans, indicating that transmission between hosts of strains belonging to this group may occur. PMID:27530432

  8. Genetic micro-epidemiology of malaria in Papua Indonesia: Extensive P. vivax diversity and a distinct subpopulation of asymptomatic P. falciparum infections.

    Science.gov (United States)

    Pava, Zuleima; Noviyanti, Rintis; Handayuni, Irene; Trimarsanto, Hidayat; Trianty, Leily; Burdam, Faustina H; Kenangalem, Enny; Utami, Retno A S; Tirta, Yusrifar K; Coutrier, Farah; Poespoprodjo, Jeanne R; Price, Ric N; Marfurt, Jutta; Auburn, Sarah

    2017-01-01

    Genetic analyses of Plasmodium have potential to inform on transmission dynamics, but few studies have evaluated this on a local spatial scale. We used microsatellite genotyping to characterise the micro-epidemiology of P. vivax and P. falciparum diversity to inform malaria control strategies in Timika, Papua Indonesia. Genotyping was undertaken on 713 sympatric P. falciparum and P. vivax isolates from a cross-sectional household survey and clinical studies conducted in Timika. Standard population genetic measures were applied, and the data was compared to published data from Kalimantan, Bangka, Sumba and West Timor. Higher diversity (HE = 0.847 vs 0.625; p = 0.017) and polyclonality (46.2% vs 16.5%, p<0.001) were observed in P. vivax versus P. falciparum. Distinct P. falciparum substructure was observed, with two subpopulations, K1 and K2. K1 was comprised solely of asymptomatic infections and displayed greater relatedness to isolates from Sumba than to K2, possibly reflecting imported infections. The results demonstrate the greater refractoriness of P. vivax versus P. falciparum to control measures, and risk of distinct parasite subpopulations persisting in the community undetected by passive surveillance. These findings highlight the need for complimentary new surveillance strategies to identify transmission patterns that cannot be detected with traditional malariometric methods.

  9. Morphometric differences of Microgramma squamulosa (Kaulf. de la Sota (Polypodiaceae leaves in environments with distinct atmospheric air quality

    Directory of Open Access Journals (Sweden)

    LEDYANE D. ROCHA

    2014-09-01

    Full Text Available Plants growing in environments with different atmospheric conditions may present changes in the morphometric parameters of their leaves. Microgramma squamulosa (Kaulf. de la Sota is a neotropical epiphytic fern found in impacted environments. The aims of this study were to quantitatively compare structural characteristics of leaves in areas with different air quality conditions, and to identify morphometric parameters that are potential indicators of the effects of pollution on these plants. Fertile and sterile leaves growing on isolated trees were collected from an urban (Estância Velha and a rural (Novo Hamburgo environment, in Rio Grande do Sul, Brazil. For each leaf type, macroscopic and microscopic analyses were performed on 192 samples collected in each environment. The sterile and fertile leaves showed significantly greater thickness of the midrib and greater vascular bundle and leaf blade areas in the rural environment, which is characterized by less air pollution. The thickness of the hypodermis and the stomatal density of the fertile leaves were greater in the urban area, which is characterized by more air pollution. Based on the fact that significant changes were found in the parameters of both types of leaves, which could possibly be related to air pollutants, M. squamulosa may be a potential bioindicator.

  10. Comparative safety testing of genetically modified foods in a 90-day rat feeding study design allowing the distinction between primary and secondary effects of the new genetic event

    DEFF Research Database (Denmark)

    Knudsen, Ib; Poulsen, Morten

    2007-01-01

    -349]. The overall objective of the project has been to develop and validate the scientific methodology necessary for assessing the safety of foods from genetically modified plants in accordance with the present EU regulation. The safety assessment in the project is combining the results of the 90-day rat feeding......., Frenzel, T., Danier, J., Rychlik, M., Shu, Q., Emami, K., Taylor, M., Gatehouse, A., Engel, K.-H., Knudsen, I., 2007a. Safety testing of GM-rice expressing PHA-E lectin using a new animal test design. Food Chem. Toxicol. 45, 364-377; Poulsen, M., Kroghsbo, S., Schroder, M., Wilcks, A., Jacobsen, H......., Miller, A., Frenzel, T., Danier, J., Rychlik, M., Shu, Q., Emami, K., Sudhakar, D., Gatehouse, A., Engel, K.-H., Knudsen, I., 2007b. A 90-day safety in Wistar rats fed genetically modified rice expressing snowdrop lectin Galanthus nivalis (GNA). Food Chem. Toxicol. 45, 350-363; Schroder, M., Poulsen, M...

  11. Assembled genomic and tissue-specific transcriptomic data resources for two genetically distinct lines of Cowpea ( Vigna unguiculata (L.) Walp).

    Science.gov (United States)

    Spriggs, Andrew; Henderson, Steven T; Hand, Melanie L; Johnson, Susan D; Taylor, Jennifer M; Koltunow, Anna

    2018-02-09

    Cowpea ( Vigna unguiculata (L.) Walp) is an important legume crop for food security in areas of low-input and smallholder farming throughout Africa and Asia. Genetic improvements are required to increase yield and resilience to biotic and abiotic stress and to enhance cowpea crop performance. An integrated cowpea genomic and gene expression data resource has the potential to greatly accelerate breeding and the delivery of novel genetic traits for cowpea. Extensive genomic resources for cowpea have been absent from the public domain; however, a recent early release reference genome for IT97K-499-35 ( Vigna unguiculata  v1.0, NSF, UCR, USAID, DOE-JGI, http://phytozome.jgi.doe.gov/) has now been established in a collaboration between the Joint Genome Institute (JGI) and University California (UC) Riverside. Here we release supporting genomic and transcriptomic data for IT97K-499-35 and a second transformable cowpea variety, IT86D-1010. The transcriptome resource includes six tissue-specific datasets for each variety, with particular emphasis on reproductive tissues that extend and support the V. unguiculata v1.0 reference. Annotations have been included in our resource to allow direct mapping to the v1.0 cowpea reference. Access to this resource provided here is supported by raw and assembled data downloads.

  12. On the origin of Tibetans and their genetic basis in adapting high-altitude environments.

    Directory of Open Access Journals (Sweden)

    Binbin Wang

    2011-02-01

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

  13. D-VASim: An Interactive Virtual Laboratory Environment for the Simulation and Analysis of Genetic Circuits

    DEFF Research Database (Denmark)

    Baig, Hasan; Madsen, Jan

    2016-01-01

    Simulation and behavioral analysis of genetic circuits is a standard approach of functional verification prior to their physical implementation. Many software tools have been developed to perform in silico analysis for this purpose, but none of them allow users to interact with the model during...... the behavior of genetic logic circuit models represented in an SBML (Systems Biology Markup Language). Hence, SBML models developed in other software environments can be analyzed and simulated in D-VASim. D-VASim offers deterministic as well as stochastic simulation; and differs from other software tools...... runtime. The runtime interaction gives the user a feeling of being in the lab performing a real world experiment. In this work, we present a user-friendly software tool named D-VASim (Dynamic Virtual Analyzer and Simulator), which provides a virtual laboratory environment to simulate and analyze...

  14. Full genome sequencing and genetic characterization of Eubenangee viruses identify Pata virus as a distinct species within the genus Orbivirus.

    Directory of Open Access Journals (Sweden)

    Manjunatha N Belaganahalli

    Full Text Available Eubenangee virus has previously been identified as the cause of Tammar sudden death syndrome (TSDS. Eubenangee virus (EUBV, Tilligery virus (TILV, Pata virus (PATAV and Ngoupe virus (NGOV are currently all classified within the Eubenangee virus species of the genus Orbivirus, family Reoviridae. Full genome sequencing confirmed that EUBV and TILV (both of which are from Australia show high levels of aa sequence identity (>92% in the conserved polymerase VP1(Pol, sub-core VP3(T2 and outer core VP7(T13 proteins, and are therefore appropriately classified within the same virus species. However, they show much lower amino acid (aa identity levels in their larger outer-capsid protein VP2 (<53%, consistent with membership of two different serotypes - EUBV-1 and EUBV-2 (respectively. In contrast PATAV showed significantly lower levels of aa sequence identity with either EUBV or TILV (with <71% in VP1(Pol and VP3(T2, and <57% aa identity in VP7(T13 consistent with membership of a distinct virus species. A proposal has therefore been sent to the Reoviridae Study Group of ICTV to recognise 'Pata virus' as a new Orbivirus species, with the PATAV isolate as serotype 1 (PATAV-1. Amongst the other orbiviruses, PATAV shows closest relationships to Epizootic Haemorrhagic Disease virus (EHDV, with 80.7%, 72.4% and 66.9% aa identity in VP3(T2, VP1(Pol, and VP7(T13 respectively. Although Ngoupe virus was not available for these studies, like PATAV it was isolated in Central Africa, and therefore seems likely to also belong to the new species, possibly as a distinct 'type'. The data presented will facilitate diagnostic assay design and the identification of additional isolates of these viruses.

  15. Full genome sequencing and genetic characterization of Eubenangee viruses identify Pata virus as a distinct species within the genus Orbivirus.

    Science.gov (United States)

    Belaganahalli, Manjunatha N; Maan, Sushila; Maan, Narender S; Nomikou, Kyriaki; Pritchard, Ian; Lunt, Ross; Kirkland, Peter D; Attoui, Houssam; Brownlie, Joe; Mertens, Peter P C

    2012-01-01

    Eubenangee virus has previously been identified as the cause of Tammar sudden death syndrome (TSDS). Eubenangee virus (EUBV), Tilligery virus (TILV), Pata virus (PATAV) and Ngoupe virus (NGOV) are currently all classified within the Eubenangee virus species of the genus Orbivirus, family Reoviridae. Full genome sequencing confirmed that EUBV and TILV (both of which are from Australia) show high levels of aa sequence identity (>92%) in the conserved polymerase VP1(Pol), sub-core VP3(T2) and outer core VP7(T13) proteins, and are therefore appropriately classified within the same virus species. However, they show much lower amino acid (aa) identity levels in their larger outer-capsid protein VP2 (TILV (with <71% in VP1(Pol) and VP3(T2), and <57% aa identity in VP7(T13)) consistent with membership of a distinct virus species. A proposal has therefore been sent to the Reoviridae Study Group of ICTV to recognise 'Pata virus' as a new Orbivirus species, with the PATAV isolate as serotype 1 (PATAV-1). Amongst the other orbiviruses, PATAV shows closest relationships to Epizootic Haemorrhagic Disease virus (EHDV), with 80.7%, 72.4% and 66.9% aa identity in VP3(T2), VP1(Pol), and VP7(T13) respectively. Although Ngoupe virus was not available for these studies, like PATAV it was isolated in Central Africa, and therefore seems likely to also belong to the new species, possibly as a distinct 'type'. The data presented will facilitate diagnostic assay design and the identification of additional isolates of these viruses.

  16. Genetic diversity of Mycobacterium tuberculosis isolates obtained from three distinct population groups in the Central Province, Sri Lanka

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    Dulanthi Weerasekera

    2015-05-01

    Full Text Available Objective: To characterize the Mycobacterium tuberculosis (M. tuberculosis isolates by spoligotyping and mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR typing to understand how M. tuberculosis strains transmit among the study population. Methods: Spoligotyping and MIRU-VNTR were used to genotype M. tuberculosis isolates obtained from three distinct population groups in Sri Lanka. General population suspected of having tuberculosis attending the Chest Clinic, Kandy (n = 78, patients having tuberculosis in Bogambara prison, Kandy (n = 22 and estate workers having tuberculosis in the Central Province, Sri Lanka (n = 50, from January 2012 to April 2014 were included in the study. Results: Among 150 isolates, a total of 19 distinct families were observed including 6 major spoligotyping-based families; East-African-Indian (39.33%, Haarlem (20%, Beijing (8.6%, Central European family T (6.5%, European family X (5.2% and Central and Middle Eastern Asian (0.6%. Beijing strains were only identified among the general population. MANU strains were significant (36.36% among the prisoners who had clustered with the MANU strains of the general population indicating contact cases and a possible transmission index within a particular geographical area. Haarlem 3 (34% was the predominant strain among the estate workers. There was a close epidemiological relationship between the prisoners and the estate workers in the population. Conclusions: The first insight of 15 loci MIRU-VNTR typing in conjunction with spoligotyping in a population in Sri Lanka demonstrated the feasibility and the applicability of these techniques to differentiate strains, their heterogeneity and the predominance of several worldwide distributed spoligotypes.

  17. The Genetic Structure of Natural Populations of DROSOPHILA MELANOGASTER. Xix. Genotype-Environment Interaction in Viability

    OpenAIRE

    Tachida, Hidenori; Mukai, Terumi

    1985-01-01

    To investigate whether or not an excess of additive genetic variance for viability detected in southern natural populations of Drosophila melanogaster was created by diversifying selection, genotype-environment interaction was tested as follows. (1) Two karyotype chromosomes were used: 61 second chromosomes with the standard karyotype and 63 second chromosomes carrying In(2L)t. Their homozygote viabilities were larger than 50% of the average viability of random heterozygotes. (2) The effect...

  18. Comparative analysis of Edwardsiella isolates from fish in the eastern United States identifies two distinct genetic taxa amongst organisms phenotypically classified as E. tarda

    Science.gov (United States)

    Griffin, Matt J.; Quiniou, Sylvie M.; Cody, Theresa; Tabuchi, Maki; Ware, Cynthia; Cipriano, Rocco C.; Mauel, Michael J.; Soto, Esteban

    2013-01-01

    Edwardsiella tarda, a Gram-negative member of the family Enterobacteriaceae, has been implicated in significant losses in aquaculture facilities worldwide. Here, we assessed the intra-specific variability of E. tarda isolates from 4 different fish species in the eastern United States. Repetitive sequence mediated PCR (rep-PCR) using 4 different primer sets (ERIC I & II, ERIC II, BOX, and GTG5) and multi-locus sequence analysis of 16S SSU rDNA, groEl, gyrA, gyrB, pho, pgi, pgm, and rpoA gene fragments identified two distinct genotypes of E. tarda (DNA group I; DNA group II). Isolates that fell into DNA group II demonstrated more similarity to E. ictaluri than DNA group I, which contained the reference E. tarda strain (ATCC #15947). Conventional PCR analysis using published E. tarda-specific primer sets yielded variable results, with several primer sets producing no observable amplification of target DNA from some isolates. Fluorometric determination of G + C content demonstrated 56.4% G + C content for DNA group I, 60.2% for DNA group II, and 58.4% for E. ictaluri. Surprisingly, these isolates were indistinguishable using conventional biochemical techniques, with all isolates demonstrating phenotypic characteristics consistent with E. tarda. Analysis using two commercial test kits identified multiple phenotypes, although no single metabolic characteristic could reliably discriminate between genetic groups. Additionally, anti-microbial susceptibility and fatty acid profiles did not demonstrate remarkable differences between groups. The significant genetic variation (genetically distinct taxa of Edwardsiella that is phenotypically indistinguishable from E. tarda.

  19. The Molecular Epidemiology and Genetic Environment of Carbapenemases Detected in Africa.

    Science.gov (United States)

    Sekyere, John Osei; Govinden, Usha; Essack, Sabiha

    2016-01-01

    Research articles describing carbapenemases and their genetic environments in Gram-negative bacteria were reviewed to determine the molecular epidemiology of carbapenemases in Africa. The emergence of resistance to the carbapenems, the last resort antibiotic for difficult to treat bacterial infections, affords clinicians few therapeutic options, with a resulting increase in morbidities, mortalities, and healthcare costs. However, the molecular epidemiology of carbapenemases throughout Africa is less described. Research articles and conference proceedings describing the genetic environment and molecular epidemiology of carbapenemases in Africa were retrieved from Google Scholar, Scifinder, Pubmed, Web of Science, and Science Direct databases. Predominant carbapenemase genes so far described in Africa include the blaOXA-48 type, blaIMP, blaVIM, and blaNDM in Acinetobacter baumannii, Klebsiella pneumoniae, Enterobacter cloacae, Citrobacter spp., and Escherichia coli carried on various plasmid types and sizes, transposons, and integrons. Class D and class B carbapenemases, mainly prevalent in A. baumannii, K. pneumoniae, E. cloacae, Citrobacter spp., and E. coli were the commonest carbapenemases. Carbapenemases are mainly reported in North and South Africa as under-resourced laboratories, lack of awareness and funding preclude the detection and reporting of carbapenemase-mediated resistance. Consequently, the true molecular epidemiology of carbapenemases and their genetic environment in Africa is still unknown.

  20. Distinct genetic difference between the Duffy binding protein (PkDBPαII) of Plasmodium knowlesi clinical isolates from North Borneo and Peninsular Malaysia.

    Science.gov (United States)

    Fong, Mun-Yik; Rashdi, Sarah A A; Yusof, Ruhani; Lau, Yee-Ling

    2015-02-21

    Plasmodium knowlesi is one of the monkey malaria parasites that can cause human malaria. The Duffy binding protein of P. knowlesi (PkDBPαII) is essential for the parasite's invasion into human and monkey erythrocytes. A previous study on P. knowlesi clinical isolates from Peninsular Malaysia reported high level of genetic diversity in the PkDBPαII. Furthermore, 36 amino acid haplotypes were identified and these haplotypes could be separated into allele group I and allele group II. In the present study, the PkDBPαII of clinical isolates from the Malaysian states of Sarawak and Sabah in North Borneo was investigated, and compared with the PkDBPαII of Peninsular Malaysia isolates. Blood samples from 28 knowlesi malaria patients were used. These samples were collected between 2011 and 2013 from hospitals in North Borneo. The PkDBPαII region of the isolates was amplified by PCR, cloned into Escherichia coli, and sequenced. The genetic diversity, natural selection and phylogenetics of PkDBPαII haplotypes were analysed using MEGA5 and DnaSP ver. 5.10.00 programmes. Forty-nine PkDBPαII sequences were obtained. Comparison at the nucleotide level against P. knowlesi strain H as reference sequence revealed 58 synonymous and 102 non-synonymous mutations. Analysis on these mutations showed that PkDBPαII was under purifying (negative) selection. At the amino acid level, 38 different PkDBPαII haplotypes were identified. Twelve of the 28 blood samples had mixed haplotype infections. Phylogenetic analysis revealed that all the haplotypes were in allele group I, but they formed a sub-group that was distinct from those of Peninsular Malaysia. Wright's FST fixation index indicated high genetic differentiation between the North Borneo and Peninsular Malaysia haplotypes. This study is the first to report the genetic diversity and natural selection of PkDBPαII of P. knowlesi from Borneo Island. The PkDBPαII haplotypes found in this study were distinct from those from

  1. Deliberate release of genetically modified plants into the environment in Slovenia

    Directory of Open Access Journals (Sweden)

    Zlata LUTHAR

    2015-11-01

    Full Text Available Deliberate release of genetically modified higher plants (GMHPs into the environment in Slovenia is regulated by the Law on the Management of Genetically Modified Organisms (ZRGSO Ur. l. RS 23/2005 and 21/2010, III chapter. For each deliberate release of GMPs into the environment a license issued by the Ministry of Environment and Spatial Planning (MESP must be acquired. The application or notification should contain a very accurate and complex description of the GMP, of the field where it will be released and of wider surroundings or environment. The application consists of Annex 2 with accessories: 1. Part A (technical data for the authorization of deliberate GMP release into the environment; 2. Part B (environmental risk assessment; 3. Application summary in Slovenian and English language for the release of GMP into environment, which is transmitted to Brussels by MESP; 4. Extract from the Land Cadastre of the field to which the GMP will be released. The release procedure runs (till here under the above mentioned Law, which has been in place for several years and which clearly defines that it is possible to release GMP in Slovenia. In the case of GM rice in 2011, the law applied till the site selection of the experiment. Here, the law was not sufficiently taken into account. It was prevailed by the regulation of Farmland and Forest Fund of the Republic of Slovenia and municipal decision, which was stronger than the national law and prevented the cultivation of GM rice in an area that is legally suitable for release of GMO into the environment. Rice is not grown in Slovenia and does not have wild ancestors or close relatives with whom it might mate. Nearest area of cultivation is in neighboring Italy, which is from potentially selected location in Slovenia more than 70 km away.

  2. Genetic diversity of archaea in deep-sea hydrothermal vent environments.

    Science.gov (United States)

    Takai, K; Horikoshi, K

    1999-08-01

    Molecular phylogenetic analysis of naturally occurring archaeal communities in deep-sea hydrothermal vent environments was carried out by PCR-mediated small subunit rRNA gene (SSU rDNA) sequencing. As determined through partial sequencing of rDNA clones amplified with archaea-specific primers, the archaeal populations in deep-sea hydrothermal vent environments showed a great genetic diversity, and most members of these populations appeared to be uncultivated and unidentified organisms. In the phylogenetic analysis, a number of rDNA sequences obtained from deep-sea hydrothermal vents were placed in deep lineages of the crenarchaeotic phylum prior to the divergence of cultivated thermophilic members of the crenarchaeota or between thermophilic members of the euryarchaeota and members of the methanogen-halophile clade. Whole cell in situ hybridization analysis suggested that some microorganisms of novel phylotypes predicted by molecular phylogenetic analysis were likely present in deep-sea hydrothermal vent environments. These findings expand our view of the genetic diversity of archaea in deep-sea hydrothermal vent environments and of the phylogenetic organization of archaea.

  3. Cryptic Genetic Variation for Arabidopsis thaliana Seed Germination Speed in a Novel Salt Stress Environment.

    Science.gov (United States)

    Yuan, Wei; Flowers, Jonathan M; Sahraie, Dustin J; Purugganan, Michael D

    2016-10-13

    The expansion of species ranges frequently necessitates responses to novel environments. In plants, the ability of seeds to disperse to marginal areas relies in part to its ability to germinate under stressful conditions. Here we examine the genetic architecture of Arabidopsis thaliana germination speed under a novel, saline environment, using an Extreme QTL (X-QTL) mapping platform we previously developed. We find that early germination in normal and salt conditions both rely on a QTL on the distal arm of chromosome 4, but we also find unique QTL on chromosomes 1, 2, 4, and 5 that are specific to salt stress environments. Moreover, different QTLs are responsible for early vs. late germination, suggesting a temporal component to the expression of life history under these stress conditions. Our results indicate that cryptic genetic variation exists for responses to a novel abiotic stress, which may suggest a role of such variation in adaptation to new climactic conditions or growth environments. Copyright © 2016 Yuan et al.

  4. Genetic Parameters And Selection Response For Yield Traits In Bread Wheat Under Irrigated And Rainfed Environments

    Science.gov (United States)

    Khalil, Iftikhar Hussain; at-ur-Rahman, Hiday; Khan, Imran

    2008-01-01

    A set of 22 F5:7 experimental wheat lines along with four check cultivars (Dera-98, Fakhr-e-Sarhad, Ghaznavi-98 and Tatara) were evaluated as independent experiments under irrigated and rainfed environments using a randomized complete block design at NWFP Agricultural University, Peshawar during 2004-05. The two environments were statistically different for days to heading and spike length only. Highly significant genetic variability existed among the wheat lines (P<0.01) in the combined analysis across environments for all traits. Genotype×environment interactions were non-significant for all traits except 1000-grain weight indicating consistent performance of wheat genotypes across the two environments. Wheat lines and check cultivars were 2 to 5 days early in heading under rainfed environment compared to the irrigated. Plant height, spike length, 1000-grain weight, biological and grain yields were generally reduced under rainfed environment. Genetic variances were of greater magnitude than environmental variances for most of the traits in both environments. The heritability estimates were of higher magnitude (0.74 to 0.96) for days to heading, plant height, spike length, biological and grain yield, while medium (0.31 to 0.51) for 1000-grain weight. Selection differentials were negative for heading (-7.3 days in irrigated vs -9.4 days in rainfed) and plant height (-9.0 cm in irrigated vs -8.7 cm in rainfed) indicating possibility of selecting wheat genotypes with early heading and short plant stature. Positive selection differentials of 1.3 vs 1.6 cm for spike length, 3.8 vs 3.4 g for 1000-grain weight, 2488.2 vs 3139.7 kg ha-1 for biological yield and 691.6 vs 565.4 kg ha-1 for grain yield at 20% selection intensity were observed under irrigated and rainfed environments, respectively. Expected selection responses were 7.98 vs 8.91 days for heading, 8.20 vs 9.52 cm for plant height, 1.01 vs 1.61 cm for spike length, 2.12 vs 1.15 g for 1000-grain weight, 1655

  5. Genetic Polymorphism of the Glutathione S-Transferase M1 and T1 Genes in Three Distinct Arab Populations

    Directory of Open Access Journals (Sweden)

    Abdel Halim Salem

    2011-01-01

    Full Text Available Deletion polymorphisms for the glutathione S-transferase (GST gene are associated with increased risk of cancer, and are implicated in detoxifying mutagenic electrophilic compounds. GST Polymorphic variants were reported for different populations. The aim of this study was to investigate the frequencies of GSTM1 and GSTT1 null genotypes among Bahraini, Lebanese and Tunisian Arabs. GST genotyping was done by multiplex PCR-based methods. Study subjects comprised 167 Bahrainis, 141 Lebanese and 186 Tunisians unrelated healthy individuals. GSTM1 deletion homozygosity of 49.7%, 52.5% and 63.4% were recorded for Bahraini, Lebanese and Tunisians, respectively. Among Bahrainis, the prevalence of GSTT1 null homozygotes was 28.7%, while in higher rates were seen in Lebanese (37.6% and Tunisians (37.1%. Our results indicate that there are no major differences in allelic distribution of GSTM1 and GSTT1 genes between the three Arab populations investigated except between Bahrainis and Tunisians regarding the allelic distribution of GSTM1 gene (P = 0.013. Combined analysis of both genes revealed that 14.4% of Bahrainis, 16.3% of Lebanese and 21.0% of Tunisians harbor the deleted genotype of both genes. This is the first study that addresses GST gene polymorphism in Bahraini and Lebanese Arabs, and will help genetic studies on the association of GSTM1 and GSTT1 polymorphisms with disease risks and drug effects in Arab populations.

  6. Isotopic and Geochemical Investigation of Two Distinct Mars Analog Environments Using Evolved Gas Techniques in Svalbard, Norway

    Science.gov (United States)

    Stern, Jennifer Claire; Mcadam, Amy Catherine; Ten Kate, Inge L.; Bish, David L.; Blake, David F.; Morris, Richard V.; Bowden, Roxane; Fogel, Marilyn L.; Glamoclija, Mihaela; Mahaffy, Paul R.; hide

    2013-01-01

    The 2010 Arctic Mars Analog Svalbard Expedition (AMASE) investigated two distinct geologic settings on Svalbard, using methodologies and techniques to be deployed on Mars Science Laboratory (MSL). AMASErelated research comprises both analyses conducted during the expedition and further analyses of collected samples using laboratory facilities at a variety of institutions. The Sample Analysis at Mars (SAM) instrument suite on MSL includes pyrolysis ovens, a gas-processing manifold, a quadrupole mass spectrometer (QMS), several gas chromatography columns, and a Tunable Laser Spectrometer (TLS). An integral part of SAM development is the deployment of SAM-like instrumentation in the field. During AMASE 2010, two parts of SAM participated as stand-alone instruments. A Hiden Evolved Gas Analysis- Mass Spectrometer (EGA-QMS) system represented the EGA-QMS component of SAM, and a Picarro Cavity Ring Down Spectrometer (EGA-CRDS), represented the EGA-TLS component of SAM. A field analog of CheMin, the XRD/XRF on MSL, was also deployed as part of this field campaign. Carbon isotopic measurements of CO2 evolved during thermal decomposition of carbonates were used together with EGA-QMS geochemical data, mineral composition information and contextual observations made during sample collection to distinguish carbonates formation associated with chemosynthetic activity at a fossil methane seep from abiotic processes forming carbonates associated with subglacial basaltic eruptions. Carbon and oxygen isotopes of the basalt-hosted carbonates suggest cryogenic carbonate formation, though more research is necessary to clarify the history of these rocks.

  7. Poles apart: the "bipolar" pteropod species Limacina helicina is genetically distinct between the Arctic and Antarctic oceans.

    Science.gov (United States)

    Hunt, Brian; Strugnell, Jan; Bednarsek, Nina; Linse, Katrin; Nelson, R John; Pakhomov, Evgeny; Seibel, Brad; Steinke, Dirk; Würzberg, Laura

    2010-03-23

    The shelled pteropod (sea butterfly) Limacina helicina is currently recognised as a species complex comprising two sub-species and at least five "forma". However, at the species level it is considered to be bipolar, occurring in both the Arctic and Antarctic oceans. Due to its aragonite shell and polar distribution L. helicina is particularly vulnerable to ocean acidification. As a key indicator of the acidification process, and a major component of polar ecosystems, L. helicina has become a focus for acidification research. New observations that taxonomic groups may respond quite differently to acidification prompted us to reassess the taxonomic status of this important species. We found a 33.56% (+/-0.09) difference in cytochrome c oxidase subunit I (COI) gene sequences between L. helicina collected from the Arctic and Antarctic oceans. This degree of separation is sufficient for ordinal level taxonomic separation in other organisms and provides strong evidence for the Arctic and Antarctic populations of L. helicina differing at least at the species level. Recent research has highlighted substantial physiological differences between the poles for another supposedly bipolar pteropod species, Clione limacina. Given the large genetic divergence between Arctic and Antarctic L. helicina populations shown here, similarly large physiological differences may exist between the poles for the L. helicina species group. Therefore, in addition to indicating that L. helicina is in fact not bipolar, our study demonstrates the need for acidification research to take into account the possibility that the L. helicina species group may not respond in the same way to ocean acidification in Arctic and Antarctic ecosystems.

  8. Menstrual blood closely resembles the uterine immune micro-environment and is clearly distinct from peripheral blood.

    Science.gov (United States)

    van der Molen, R G; Schutten, J H F; van Cranenbroek, B; ter Meer, M; Donckers, J; Scholten, R R; van der Heijden, O W H; Spaanderman, M E A; Joosten, I

    2014-02-01

    Is menstrual blood a suitable source of endometrial derived lymphocytes? Mononuclear cells isolated from menstrual samples (menstrual blood mononuclear cells (MMC)) are clearly distinct from peripheral blood mononuclear cells (PBMC) and show a strong resemblance with biopsy-derived endometrial mononuclear cells. A critical event in the onset of pregnancy is the implantation of the embryo in the uterine wall. The immune cell composition in the endometrium at the time of implantation is considered pivotal for success. Despite advancing knowledge on the composition of the immune cell population in the uterus, the role of endometrial immune cells in reproductive disorders is still not fully resolved, mainly due to the fact that this type of research requires invasive techniques. Here, we collected menstrual fluid and validated this unique non-invasive technique to obtain and study the endometrium-derived immune cells which would be present around the time of implantation. Five healthy non-pregnant females with regular menstruation cycles and not using oral contraceptives collected their menstrual blood using a menstrual cup in five consecutive cycles. Sampling took place over the first 3 days of menses, with 12 h intervals. Peripheral blood samples, taken before and after each menstruation, were obtained for comparative analysis. MMC and PBMC samples were characterized for the different lymphocyte subsets by flow cytometry, with emphasis on NK cells and T cells. Next, the functional capacity of the MMC-derived NK cells was determined by measuring intracellular production of IFN-γ, granzyme B and perforin after culture in the presence of IL-2 and IL-15. In support of their endometrial origin, MMC samples contained the typical composition of mononuclear cells expected of endometrial tissue, were phenotypically similar to the reported phenotype for biopsy-derived endometrial cells, and were distinct from PBMC. Increased percentages of NK cells and decreased percentages

  9. Monitoring the Short-Term Response to Salt Exposure of Two Genetically Distinct Phragmites australis Clones with Different Salinity Tolerance Levels

    DEFF Research Database (Denmark)

    Achenbach, Luciana; Brix, Hans

    2014-01-01

    Aims: Two genetically distinct clones of Phragmites australis were used to investigate the immediate response induced by osmotic stress. The study aimed at elucidating if the response time, the inhibition rate and the recovery from salinity stress vary between these two genotypes. The experimental...... salt concentrations (20 and 40 parts per thousand salinity). Important findings: The osmotic stress induced stomata closure and reduction of Pmax and E for both clones. The clone-specific responses as measured through physiological parameters were negatively correlated with exposure time and salt...... in the 15-minute experiment. The Greeny-type also recovered after the 70-minute exposure, but not the Land-type. We conclude that the response to osmotic stress is genotype-dependent and that the salt-tolerant clone possesses very efficient signaling pathways to detect changes in the soil water potential...

  10. Correlated Paleoseismic Interpretation of Turbidites from 3 Distinct Sedimentary Environments in the Cascadia Subduction Zone Off Vancouver Island Canada

    Science.gov (United States)

    Enkin, R. J.; Hamilton, T. S.; Rogers, G. C.

    2014-12-01

    Sedimentary sequences containing turbidites can provide important paleoseismic records. We present sedimentary records from 3 distinct sedimentary systems which provide a reliable well-dated paleseismic record. All 3 sites are subject to strong ground shaking in the event of a megathrust earthquake along the Cascadia Subduction Zone near Vancouver Island, Canada. Effingham Inlet is an anoxic fjord on the west coast of Vancouver Island with an age model based on radiocarbon dates from terrestrial plant material (no marine correction), the Mazama Ash, and sedimentation rates constrained by annual laminations [Dallimore et al. 2008, Enkin et al., 2013]. Barkley Canyon [Goldfinger et al., 2012], 150 km SW, has been sampled at the abyssal plain fan in front of a submarine canyon. Slipstream Slump [ms submitted], 40 km north of Barkley Canyon, is a well-preserved 3 km wide sedimentary failure from the frontal ridge of the Cascadia accretionary wedge. At Slipstream, given the 2300 m water depth and the thin weak crust at the outer edge of the accretionary wedge, megathrust earthquake shaking is the most likely trigger for the turbidity currents, with sediments sourced exclusively from the exposed slide scar. Correlations based on sedimentology and physical property logging are made between turbidites observed at Barkley Canyon and Slipstream Slump, and a mutually consistent age model is defined using only planktonic foraminiferal dates and Bayesian analysis with a Poisson-process sedimentation model. A young marine reservoir age of ΔR=0 yr brings the top to the present and produces age correlations consistent with the thickest (>10 cm) Effingham Inlet turbidites. Correlations of physical property logs tie the Effingham Inlet record to the offshore, despite the extreme differences in the sedimentology. Having good marine geophysical data and well positioned core transects allows the facies analysis needed to interpret the turbidite record. This study provides a much

  11. Comparative Genomic Analyses of Multiple Pseudomonas Strains Infecting Corylus avellana Trees Reveal the Occurrence of Two Genetic Clusters with Both Common and Distinctive Virulence and Fitness Traits.

    Directory of Open Access Journals (Sweden)

    Simone Marcelletti

    Full Text Available The European hazelnut (Corylus avellana is threatened in Europe by several pseudomonads which cause symptoms ranging from twig dieback to tree death. A comparison of the draft genomes of nine Pseudomonas strains isolated from symptomatic C. avellana trees was performed to identify common and distinctive genomic traits. The thorough assessment of genetic relationships among the strains revealed two clearly distinct clusters: P. avellanae and P. syringae. The latter including the pathovars avellanae, coryli and syringae. Between these two clusters, no recombination event was found. A genomic island of approximately 20 kb, containing the hrp/hrc type III secretion system gene cluster, was found to be present without any genomic difference in all nine pseudomonads. The type III secretion system effector repertoires were remarkably different in the two groups, with P. avellanae showing a higher number of effectors. Homologue genes of the antimetabolite mangotoxin and ice nucleation activity clusters were found solely in all P. syringae pathovar strains, whereas the siderophore yersiniabactin was only present in P. avellanae. All nine strains have genes coding for pectic enzymes and sucrose metabolism. By contrast, they do not have genes coding for indolacetic acid and anti-insect toxin. Collectively, this study reveals that genomically different Pseudomonas can converge on the same host plant by suppressing the host defence mechanisms with the use of different virulence weapons. The integration into their genomes of a horizontally acquired genomic island could play a fundamental role in their evolution, perhaps giving them the ability to exploit new ecological niches.

  12. Comparative Genomic Analyses of Multiple Pseudomonas Strains Infecting Corylus avellana Trees Reveal the Occurrence of Two Genetic Clusters with Both Common and Distinctive Virulence and Fitness Traits

    Science.gov (United States)

    Marcelletti, Simone; Scortichini, Marco

    2015-01-01

    The European hazelnut (Corylus avellana) is threatened in Europe by several pseudomonads which cause symptoms ranging from twig dieback to tree death. A comparison of the draft genomes of nine Pseudomonas strains isolated from symptomatic C. avellana trees was performed to identify common and distinctive genomic traits. The thorough assessment of genetic relationships among the strains revealed two clearly distinct clusters: P. avellanae and P. syringae. The latter including the pathovars avellanae, coryli and syringae. Between these two clusters, no recombination event was found. A genomic island of approximately 20 kb, containing the hrp/hrc type III secretion system gene cluster, was found to be present without any genomic difference in all nine pseudomonads. The type III secretion system effector repertoires were remarkably different in the two groups, with P. avellanae showing a higher number of effectors. Homologue genes of the antimetabolite mangotoxin and ice nucleation activity clusters were found solely in all P. syringae pathovar strains, whereas the siderophore yersiniabactin was only present in P. avellanae. All nine strains have genes coding for pectic enzymes and sucrose metabolism. By contrast, they do not have genes coding for indolacetic acid and anti-insect toxin. Collectively, this study reveals that genomically different Pseudomonas can converge on the same host plant by suppressing the host defence mechanisms with the use of different virulence weapons. The integration into their genomes of a horizontally acquired genomic island could play a fundamental role in their evolution, perhaps giving them the ability to exploit new ecological niches. PMID:26147218

  13. Production of extracellular nucleic acids by genetically altered bacteria in aquatic-environment microcosms

    International Nuclear Information System (INIS)

    Paul, J.H.; David, A.W.

    1989-01-01

    The factors which affect the production of extracellular DNA by genetically altered strains of Escherichia coli, Pseudomonas aeruginosa, Pseudomonas cepacia, and Bradyrhizobium japonicum in aquatic environments were investigated. Cellular nucleic acids were labeled in vivo by incubation with [ 3 H]thymidine or [ 3 H]adenine, and production of extracellular DNA in marine waters, artificial seawater, or minimal salts media was determined by detecting radiolabeled macromolecules in incubation filtrates. The presence or absence of the ambient microbial community had little effect on the production of extracellular DNA. Three of four organisms produced the greatest amounts of extracellular nucleic acids when incubated in low-salinity media (2% artificial seawater) rather than high-salinity media (10 to 50% artificial seawater). The greatest production of extracellular nucleic acids by P. cepacia occurred at pH 7 and 37 degree C, suggesting that extracellular-DNA production may be a normal physiologic function of the cell. Incubation of labeled P. cepacia cells in water from Bimini Harbor, Bahamas, resulted in labeling of macromolecules of the ambient microbial population. Collectively these results indicate that (i) extracellular-DNA production by genetically altered bacteria released into aquatic environments is more strongly influenced by physicochemical factors than biotic factors, (ii) extracellular-DNA production rates are usually greater for organisms released in freshwater than marine environments, and (iii) ambient microbial populations can readily utilize materials released by these organisms

  14. Quantitative genetic analysis of responses to larval food limitation in a polyphenic butterfly indicates environment- and trait-specific effects

    NARCIS (Netherlands)

    Saastamoinen, M.; Brommer, J.E.; Brakefield, P.M.; Zwaan, B.J.

    2013-01-01

    Different components of heritability, including genetic variance (VG), are influenced by environmental conditions. Here, we assessed phenotypic responses of life-history traits to two different developmental conditions, temperature and food limitation. The former represents an environment that

  15. Distinct effects of Cr bulk doping and surface deposition on the chemical environment and electronic structure of the topological insulator Bi2Se3

    Science.gov (United States)

    Yilmaz, Turgut; Hines, William; Sun, Fu-Chang; Pletikosić, Ivo; Budnick, Joseph; Valla, Tonica; Sinkovic, Boris

    2017-06-01

    In this report, it is shown that Cr doped into the bulk and Cr deposited on the surface of Bi2Se3 films produced by molecular beam epitaxy (MBE) have strikingly different effects on both the electronic structure and chemical environment. Angle resolved photoemission spectroscopy (ARPES) shows that Cr doped into the bulk opens a surface state energy gap which can be seen at room temperature; much higher than the measured ferromagnetic transition temperature of ≈10 K. On the other hand, similar ARPES measurements show that the surface states remain gapless down to 15 K for films with Cr surface deposition. In addition, core-level photoemission spectroscopy of the Bi 5d, Se 3d, and Cr 3p core levels show distinct differences in the chemical environment for the two methods of Cr introduction. Surface deposition of Cr results in the formation of shoulders on the lower binding energy side for the Bi 5d peaks and two distinct Cr 3p peaks indicative of two Cr sites. These striking differences suggests an interesting possibility that better control of doping at only near surface region may offer a path to quantum anomalous Hall states at higher temperatures than reported in the literature.

  16. Redox environment is an intracellular factor to operate distinct pathways for aggregation of Cu,Zn-superoxide dismutase in amyotrophic lateral sclerosis

    Directory of Open Access Journals (Sweden)

    Yoshiaki eFurukawa

    2013-11-01

    Full Text Available Dominant mutations in Cu,Zn-superoxide dismutase (SOD1 cause a familial form of amyotrophic lateral sclerosis (fALS. Misfolding and aggregation of mutant SOD1 proteins are a pathological hallmark of SOD1-related fALS cases; however, the molecular mechanism of SOD1 aggregation remains controversial. Here, I have used E. coli as a model organism and shown multiple distinct pathways of SOD1 aggregation that are dependent upon its thiol-disulfide status. Overexpression of fALS-mutant SOD1s in the cytoplasm of E. coli BL21 and SHuffleTM, where redox environment is reducing and oxidizing, respectively, resulted in the formation of insoluble aggregates with notable differences; a disulfide bond of SOD1 was completely reduced in BL21 or abnormally formed between SOD1 molecules in SHuffleTM. Depending upon intracellular redox environment, therefore, mutant SOD1 is considered to misfold/aggregate through distinct pathways, which would be relevant in description of the pathological heterogeneity of SOD1-related fALS cases.

  17. Development of an RT-qPCR assay for the specific detection of a distinct genetic lineage of the infectious bursal disease virus.

    Science.gov (United States)

    Tomás, Gonzalo; Hernández, Martín; Marandino, Ana; Techera, Claudia; Grecco, Sofia; Hernández, Diego; Banda, Alejandro; Panzera, Yanina; Pérez, Ruben

    2017-04-01

    The infectious bursal disease virus (IBDV) is a major health threat to the world's poultry industry despite intensive controls including proper biosafety practices and vaccination. IBDV (Avibirnavirus, Birnaviridae) is a non-enveloped virus with a bisegmented double-stranded RNA genome. The virus is traditionally classified into classic, variant and very virulent strains, each with different epidemiological relevance and clinical implications. Recently, a novel worldwide spread genetic lineage was described and denoted as distinct (d) IBDV. Here, we report the development and validation of a reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assay for the specific detection of dIBDVs in the global poultry industry. The assay employs a TaqMan-MGB probe that hybridizes with a unique molecular signature of dIBDV. The assay successfully detected all the assessed strains belonging to the dIBDV genetic lineage, showing high specificity and absence of cross-reactivity with non-dIBDVs, IBDV-negative samples and other common avian viruses. Using serial dilutions of in vitro-transcribed RNA we obtained acceptable PCR efficiencies and determination coefficients, and relatively small intra- and inter-assay variability. The assay demonstrated a wide dynamic range between 10 3 and 10 8 RNA copies/reaction. This rapid, specific and quantitative assay is expected to improve IBDV surveillance and control worldwide and to increase our understanding of the molecular epidemiology of this economically detrimental poultry pathogen.

  18. The dominant Australian community-acquired methicillin-resistant Staphylococcus aureus clone ST93-IV [2B] is highly virulent and genetically distinct.

    Directory of Open Access Journals (Sweden)

    Kyra Y L Chua

    Full Text Available Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA USA300 has spread rapidly across North America, and CA-MRSA is also increasing in Australia. However, the dominant Australian CA-MRSA strain, ST93-IV [2B] appears distantly related to USA300 despite strikingly similar clinical and epidemiological profiles. Here, we compared the virulence of a recent Australian ST93 isolate (JKD6159 to other MRSA, including USA300, and found that JKD6159 was the most virulent in a mouse skin infection model. We fully sequenced the genome of JKD6159 and confirmed that JKD6159 is a distinct clone with 7616 single nucleotide polymorphisms (SNPs distinguishing this strain from all other S. aureus genomes. Despite its high virulence there were surprisingly few virulence determinants. However, genes encoding α-hemolysin, Panton-Valentine leukocidin (PVL and α-type phenol soluble modulins were present. Genome comparisons revealed 32 additional CDS in JKD6159 but none appeared to encode new virulence factors, suggesting that this clone's enhanced pathogenicity could lie within subtler genome changes, such as SNPs within regulatory genes. To investigate the role of accessory genome elements in CA-MRSA epidemiology, we next sequenced three additional Australian non-ST93 CA-MRSA strains and compared them with JKD6159, 19 completed S. aureus genomes and 59 additional S. aureus genomes for which unassembled genome sequence data was publicly available (82 genomes in total. These comparisons showed that despite its distinctive genotype, JKD6159 and other CA-MRSA clones (including USA300 share a conserved repertoire of three notable accessory elements (SSCmecIV, PVL prophage, and pMW2. This study demonstrates that the genetically distinct ST93 CA-MRSA from Australia is highly virulent. Our comparisons of geographically and genetically diverse CA-MRSA genomes suggest that apparent convergent evolution in CA-MRSA may be better explained by the rapid

  19. Constant, cycling, hot and cold thermal environments: strong effects on mean viability but not on genetic estimates

    DEFF Research Database (Denmark)

    Ketola, Tarmo; Kellermann, Vanessa; Kristensen, Torsten Nygård

    2012-01-01

    and their fluctuations. How species will respond to these changes is uncertain, particularly as there is a lack of studies which compare genetic performances in constant vs. fluctuating environments. In this study, we used a nested full-sib/half-sib breeding design to examine how the genetic variances and heritabilities...

  20. Genetics of phenotypic plasticity and biomass traits in hybrid willows across contrasting environments and years.

    Science.gov (United States)

    Berlin, Sofia; Hallingbäck, Henrik R; Beyer, Friderike; Nordh, Nils-Erik; Weih, Martin; Rönnberg-Wästljung, Ann-Christin

    2017-07-01

    Phenotypic plasticity can affect the geographical distribution of taxa and greatly impact the productivity of crops across contrasting and variable environments. The main objectives of this study were to identify genotype-phenotype associations in key biomass and phenology traits and the strength of phenotypic plasticity of these traits in a short-rotation coppice willow population across multiple years and contrasting environments to facilitate marker-assisted selection for these traits. A hybrid Salix viminalis  × ( S. viminalis × Salix schwerinii ) population with 463 individuals was clonally propagated and planted in three common garden experiments comprising one climatic contrast between Sweden and Italy and one water availability contrast in Italy. Several key phenotypic traits were measured and phenotypic plasticity was estimated as the trait value difference between experiments. Quantitative trait locus (QTL) mapping analyses were conducted using a dense linkage map and phenotypic effects of S. schwerinii haplotypes derived from detected QTL were assessed. Across the climatic contrast, clone predictor correlations for biomass traits were low and few common biomass QTL were detected. This indicates that the genetic regulation of biomass traits was sensitive to environmental variation. Biomass QTL were, however, frequently shared across years and across the water availability contrast. Phenology QTL were generally shared between all experiments. Substantial phenotypic plasticity was found among the hybrid offspring, that to a large extent had a genetic origin. Individuals carrying influential S. schwerinii haplotypes generally performed well in Sweden but less well in Italy in terms of biomass production. The results indicate that specific genetic elements of S. schwerinii are more suited to Swedish conditions than to those of Italy. Therefore, selection should preferably be conducted separately for such environments in order to maximize biomass

  1. Bayesian inference of selection in a heterogeneous environment from genetic time-series data.

    Science.gov (United States)

    Gompert, Zachariah

    2016-01-01

    Evolutionary geneticists have sought to characterize the causes and molecular targets of selection in natural populations for many years. Although this research programme has been somewhat successful, most statistical methods employed were designed to detect consistent, weak to moderate selection. In contrast, phenotypic studies in nature show that selection varies in time and that individual bouts of selection can be strong. Measurements of the genomic consequences of such fluctuating selection could help test and refine hypotheses concerning the causes of ecological specialization and the maintenance of genetic variation in populations. Herein, I proposed a Bayesian nonhomogeneous hidden Markov model to estimate effective population sizes and quantify variable selection in heterogeneous environments from genetic time-series data. The model is described and then evaluated using a series of simulated data, including cases where selection occurs on a trait with a simple or polygenic molecular basis. The proposed method accurately distinguished neutral loci from non-neutral loci under strong selection, but not from those under weak selection. Selection coefficients were accurately estimated when selection was constant or when the fitness values of genotypes varied linearly with the environment, but these estimates were less accurate when fitness was polygenic or the relationship between the environment and the fitness of genotypes was nonlinear. Past studies of temporal evolutionary dynamics in laboratory populations have been remarkably successful. The proposed method makes similar analyses of genetic time-series data from natural populations more feasible and thereby could help answer fundamental questions about the causes and consequences of evolution in the wild. © 2015 John Wiley & Sons Ltd.

  2. CoaSim: A Flexible Environment for Simulating Genetic Data under Coalescent Models

    DEFF Research Database (Denmark)

    Mailund; Schierup, Mikkel Heide; Pedersen, Christian Nørgaard Storm

    2005-01-01

    Background Coalescent simulations are playing a large role in interpreting large scale intra- polymorphism surveys and for planning and evaluating association studies. Coalescent of data sets under different models can be compared to the actual data to test different evolutionary factors and thus...... get insight into these. Results We have created the CoaSim application as a flexible environment for Monte various types of genetic data under equilibrium and non-equilibrium coalescent variety of applications. Interaction with the tool is through the Guile version scripting language. Scheme scripts...

  3. Comparison of weighting approaches for genetic risk scores in gene-environment interaction studies.

    Science.gov (United States)

    Hüls, Anke; Krämer, Ursula; Carlsten, Christopher; Schikowski, Tamara; Ickstadt, Katja; Schwender, Holger

    2017-12-16

    Weighted genetic risk scores (GRS), defined as weighted sums of risk alleles of single nucleotide polymorphisms (SNPs), are statistically powerful for detection gene-environment (GxE) interactions. To assign weights, the gold standard is to use external weights from an independent study. However, appropriate external weights are not always available. In such situations and in the presence of predominant marginal genetic effects, we have shown in a previous study that GRS with internal weights from marginal genetic effects ("GRS-marginal-internal") are a powerful and reliable alternative to single SNP approaches or the use of unweighted GRS. However, this approach might not be appropriate for detecting predominant interactions, i.e. interactions showing an effect stronger than the marginal genetic effect. In this paper, we present a weighting approach for such predominant interactions ("GRS-interaction-training") in which parts of the data are used to estimate the weights from the interaction terms and the remaining data are used to determine the GRS. We conducted a simulation study for the detection of GxE interactions in which we evaluated power, type I error and sign-misspecification. We compared this new weighting approach to the GRS-marginal-internal approach and to GRS with external weights. Our simulation study showed that in the absence of external weights and with predominant interaction effects, the highest power was reached with the GRS-interaction-training approach. If marginal genetic effects were predominant, the GRS-marginal-internal approach was more appropriate. Furthermore, the power to detect interactions reached by the GRS-interaction-training approach was only slightly lower than the power achieved by GRS with external weights. The power of the GRS-interaction-training approach was confirmed in a real data application to the Traffic, Asthma and Genetics (TAG) Study (N = 4465 observations). When appropriate external weights are unavailable, we

  4. Genetic variability of garlic accessions as revealed by agro-morphological traits evaluated under different environments.

    Science.gov (United States)

    Hoogerheide, E S S; Azevedo Filho, J A; Vencovsky, R; Zucchi, M I; Zago, B W; Pinheiro, J B

    2017-05-31

    The cultivated garlic (Allium sativum L.) displays a wide phenotypic diversity, which is derived from natural mutations and phenotypic plasticity, due to dependence on soil type, moisture, latitude, altitude and cultural practices, leading to a large number of cultivars. This study aimed to evaluate the genetic variability shown by 63 garlic accessions belonging to Instituto Agronômico de Campinas and the Escola Superior de Agricultura "Luiz de Queiroz" germplasm collections. We evaluated ten quantitative characters in experimental trials conducted under two localities of the State of São Paulo: Monte Alegre do Sul and Piracicaba, during the agricultural year of 2007, in a randomized blocks design with five replications. The Mahalanobis distance was used to measure genetic dissimilarities. The UPGMA method and Tocher's method were used as clustering procedures. Results indicated significant variation among accessions (P < 0.01) for all evaluated characters, except for the percentage of secondary bulb growth in MAS, indicating the existence of genetic variation for bulb production, and germplasm evaluation considering different environments is more reliable for the characterization of the genotypic variability among garlic accessions, since it diminishes the environmental effects in the clustering of genotypes.

  5. Genetic data from algae sedimentary DNA reflect the influence of environment over geography.

    Science.gov (United States)

    Stoof-Leichsenring, Kathleen R; Herzschuh, Ulrike; Pestryakova, Luidmila A; Klemm, Juliane; Epp, Laura S; Tiedemann, Ralph

    2015-08-11

    Genetic investigations on eukaryotic plankton confirmed the existence of modern biogeographic patterns, but analyses of palaeoecological data exploring the temporal variability of these patterns have rarely been presented. Ancient sedimentary DNA proved suitable for investigations of past assemblage turnover in the course of environmental change, but genetic relatedness of the identified lineages has not yet been undertaken. Here, we investigate the relatedness of diatom lineages in Siberian lakes along environmental gradients (i.e. across treeline transects), over geographic distance and through time (i.e. the last 7000 years) using modern and ancient sedimentary DNA. Our results indicate that closely-related Staurosira lineages occur in similar environments and less-related lineages in dissimilar environments, in our case different vegetation and co-varying climatic and limnic variables across treeline transects. Thus our study reveals that environmental conditions rather than geographic distance is reflected by diatom-relatedness patterns in space and time. We tentatively speculate that the detected relatedness pattern in Staurosira across the treeline could be a result of adaptation to diverse environmental conditions across the arctic boreal treeline, however, a geographically-driven divergence and subsequent repopulation of ecologically different habitats might also be a potential explanation for the observed pattern.

  6. Genetic architecture of life history traits and environment-specific trade-offs.

    Science.gov (United States)

    Haselhorst, Monia S H; Edwards, Christine E; Rubin, Matthew J; Weinig, Cynthia

    2011-10-01

    Life history theory predicts the evolution of trait combinations that enhance fitness, and the occurrence of trade-offs depends in part on the magnitude of variation in growth rate or acquisition. Using recombinant inbred lines, we examined the genetic architecture of age and size at reproduction across abiotic conditions encountered by cultivars and naturalized populations of Brassica rapa. We found that genotypes are plastic to seasonal setting, such that reproduction was accelerated under conditions encountered by summer annual populations and genetic variances for age at reproduction varied across simulated seasonal settings. Using an acquisition-allocation model, we predicted the likelihood of trade-offs. Consistent with predicted relationships, we observed a trade-off where early maturity is associated with small size at maturity under simulated summer and fall annual conditions but not under winter annual conditions. The trade-off in the summer annual setting was observed despite significant genotypic variation in growth rate, which is often expected to decouple age and size at reproduction because rapidly growing genotypes could mature early and attain a larger size relative to slowly growing genotypes that mature later. The absence of a trade-off in the winter setting is presumably attributable to the absence of genotypic differences in age at reproduction. We observed QTL for age at reproduction that jointly regulated size at reproduction in both the summer and fall annual settings, but these QTL were environment-specific (i.e. different QTL contributed to the trade-off in the fall vs. summer annual settings). Thus, at least some of the genetic mechanisms underlying observed trade-offs differed across environments. © 2011 Blackwell Publishing Ltd.

  7. Hanseniaspora uvarum from Winemaking Environments Show Spatial and Temporal Genetic Clustering

    Science.gov (United States)

    Albertin, Warren; Setati, Mathabatha E.; Miot-Sertier, Cécile; Mostert, Talitha T.; Colonna-Ceccaldi, Benoit; Coulon, Joana; Girard, Patrick; Moine, Virginie; Pillet, Myriam; Salin, Franck; Bely, Marina; Divol, Benoit; Masneuf-Pomarede, Isabelle

    2016-01-01

    Hanseniaspora uvarum is one of the most abundant yeast species found on grapes and in grape must, at least before the onset of alcoholic fermentation (AF) which is usually performed by Saccharomyces species. The aim of this study was to characterize the genetic and phenotypic variability within the H. uvarum species. One hundred and fifteen strains isolated from winemaking environments in different geographical origins were analyzed using 11 microsatellite markers and a subset of 47 strains were analyzed by AFLP. H. uvarum isolates clustered mainly on the basis of their geographical localization as revealed by microsatellites. In addition, a strong clustering based on year of isolation was evidenced, indicating that the genetic diversity of H. uvarum isolates was related to both spatial and temporal variations. Conversely, clustering analysis based on AFLP data provided a different picture with groups showing no particular characteristics, but provided higher strain discrimination. This result indicated that AFLP approaches are inadequate to establish the genetic relationship between individuals, but allowed good strain discrimination. At the phenotypic level, several extracellular enzymatic activities of enological relevance (pectinase, chitinase, protease, β-glucosidase) were measured but showed low diversity. The impact of environmental factors of enological interest (temperature, anaerobia, and copper addition) on growth was also assessed and showed poor variation. Altogether, this work provided both new analytical tool (microsatellites) and new insights into the genetic and phenotypic diversity of H. uvarum, a yeast species that has previously been identified as a potential candidate for co-inoculation in grape must, but whose intraspecific variability had never been fully assessed. PMID:26834719

  8. Review: Role of genetics and the environment in the pathogenesis of canine atopic dermatitis.

    Science.gov (United States)

    Bizikova, Petra; Pucheu-Haston, Cherie M; Eisenschenk, Melissa N C; Marsella, Rosanna; Nuttall, Tim; Santoro, Domenico

    2015-04-01

    Multiple levels of evidence support the role of genetics and the environment in the pathogenesis of canine atopic dermatitis (AD). This review summarizes the current evidence in genetics and the effect of environmental factors on the development and perpetuation of canine AD. Citation databases, abstracts and proceedings from international meetings published between 2001 and 2013 were reviewed in this update. Where necessary, older articles were included for background information. Canine AD is a heritable disease, in which interaction with environmental factors influences disease risk and phenotype. A study of British guide dogs indicated that nearly 50% of the risk of developing AD was determined by an individual's genotype. Genomic studies performed so far in canine AD have uncovered numerous gene candidates likely to be involved in pathogenesis through their role in immunity, skin barrier formation, apoptosis and inflammation. In addition to genetics, there is evidence to suggest that exposure to certain environmental factors influences the prevalence and course of canine AD. For example, living in rural areas or feeding noncommercial diets was negatively associated with the development of AD in dogs, while exposure to high levels of smoke was associated with increased prevalence of allergic skin disease. It is becoming clear that canine AD is genotypically complex and influenced by a variety of environmental factors. Well-designed studies with sufficient statistical power will be critical to identify the complex genetic and environmental factors involved in disease development and progression. Recognition of such factors may help to identify new targets for therapy and enable better disease prevention and management. © 2015 ESVD and ACVD.

  9. Hanseniaspora uvarum from winemaking environments show spatial and temporal genetic clustering

    Directory of Open Access Journals (Sweden)

    Warren eAlbertin

    2016-01-01

    Full Text Available Hanseniaspora uvarum is one of the most abundant yeast species found on grapes and in grape must, at least before the onset of alcoholic fermentation which is usually performed by Saccharomyces species. The aim of this study was to characterise the genetic and phenotypic variability within the H. uvarum species. One hundred and fifteen strains isolated from winemaking environments in different geographical origins were analysed using 11 microsatellite markers and a subset of 47 strains were analysed by AFLP. H. uvarum isolates clustered mainly on the basis of their geographical localisation as revealed by microsatellites. In addition, a strong clustering based on year of isolation was evidenced, indicating that the genetic diversity of Hanseniaspora uvarum isolates was related to both spatial and temporal variations. Conversely, clustering analysis based on AFLP data provided a different picture with groups showing no particular characteristics, but provided higher strain discrimination. This result indicated that AFLP approaches are inadequate to establish the genetic relationship between individuals, but allowed good strain discrimination. At the phenotypic level, several extracellular enzymatic activities of enological relevance (pectinase, chitinase, protease, β-glucosidase were measured but showed low diversity. The impact of environmental factors of enological interest (temperature, anaerobia and copper addition on growth was also assessed and showed poor variation. Altogether, this work provided both new analytical tool (microsatellites and new insights into the genetic and phenotypic diversity of H. uvarum, a yeast species that has previously been identified as a potential candidate for co-inoculation in grape must, but whose intraspecific variability had never been fully assessed.

  10. Birt-Hogg-Dubé renal tumors are genetically distinct from other renal neoplasias and are associated with up-regulation of mitochondrial gene expression

    Directory of Open Access Journals (Sweden)

    Yonneau Laurent

    2010-12-01

    Full Text Available Abstract Background Germline mutations in the folliculin (FLCN gene are associated with the development of Birt-Hogg-Dubé syndrome (BHDS, a disease characterized by papular skin lesions, a high occurrence of spontaneous pneumothorax, and the development of renal neoplasias. The majority of renal tumors that arise in BHDS-affected individuals are histologically similar to sporadic chromophobe renal cell carcinoma (RCC and sporadic renal oncocytoma. However, most sporadic tumors lack FLCN mutations and the extent to which the BHDS-derived renal tumors share genetic defects associated with the sporadic tumors has not been well studied. Methods BHDS individuals were identified symptomatically and FLCN mutations were confirmed by DNA sequencing. Comparative gene expression profiling analyses were carried out on renal tumors isolated from individuals afflicted with BHDS and a panel of sporadic renal tumors of different subtypes using discriminate and clustering approaches. qRT-PCR was used to confirm selected results of the gene expression analyses. We further analyzed differentially expressed genes using gene set enrichment analysis and pathway analysis approaches. Pathway analysis results were confirmed by generation of independent pathway signatures and application to additional datasets. Results Renal tumors isolated from individuals with BHDS showed distinct gene expression and cytogenetic characteristics from sporadic renal oncocytoma and chromophobe RCC. The most prominent molecular feature of BHDS-derived kidney tumors was high expression of mitochondria-and oxidative phosphorylation (OXPHOS-associated genes. This mitochondria expression phenotype was associated with deregulation of the PGC-1α-TFAM signaling axis. Loss of FLCN expression across various tumor types is also associated with increased nuclear mitochondrial gene expression. Conclusions Our results support a genetic distinction between BHDS-associated tumors and other renal

  11. Monitoring and identifying genetically-engineered microorganisms in the environment by time-resolved laser fluorometry

    Energy Technology Data Exchange (ETDEWEB)

    Basile, F.

    1992-01-01

    A large percentage of the applications of Genetically Engineered Microorganisms (GEMs) involve their release into the environment. At the present time there is no rapid analytical method that can accurately identify and quantify the number of microorganisms and their foreign genes. In the past several years the author's laboratory has used successfully laser-based enzymatic assays to identify and differentiate pathogens, microorganisms, and genetically modified microorganisms. This work focused on the use of the above technology to track and identify agricultural beneficially GEMs that have been released into the environment. The first stage of this work dealt with the detection of the marker gene, the lactose operon. It was successfully demonstrated that the laser-based enzymatic assay can detect enzymatic activity in E. coli after 5 minutes of induction. Moreover, the author has achieved quantitation of GEMs in the laboratory down to 10[sup 4] cells with only a 30 minute incubation time. The second stage of this work dealt with the characterization of the analytical blank present in environmental samples. Strategies were devised to circumvent this interference and new substrates were synthesized that improved the S/B of the analysis. The last stage of this research dealt with devising new instrumental methods to detect small number (single cell) of microorganisms. These included incorporation of time-resolved detection in flow cytometry, Capillary Electrophoresis of microorganisms, and two-photon spectroscopy of centrosymmetric probes. The results found here will complement the large array of techniques available for monitoring and identifying GEMs in the environment. Ultimately, the technique chosen will depend heavily on the type of gene being monitored, the sensitivity required, and the environmental conditions.

  12. Genetic variants of FOXP2 and KIAA0319/TTRAP/THEM2 locus are associated with altered brain activation in distinct language-related regions.

    Science.gov (United States)

    Pinel, Philippe; Fauchereau, Fabien; Moreno, Antonio; Barbot, Alexis; Lathrop, Mark; Zelenika, Diana; Le Bihan, Denis; Poline, Jean-Baptiste; Bourgeron, Thomas; Dehaene, Stanislas

    2012-01-18

    Recent advances have been made in the genetics of two human communication skills: speaking and reading. Mutations of the FOXP2 gene cause a severe form of language impairment and orofacial dyspraxia, while single-nucleotide polymorphisms (SNPs) located within a KIAA0319/TTRAP/THEM2 gene cluster and affecting the KIAA0319 gene expression are associated with reading disability. Neuroimaging studies of clinical populations point to partially distinct cerebral bases for language and reading impairments. However, alteration of FOXP2 and KIAA0319/TTRAP/THEM2 polymorphisms on typically developed language networks has never been explored. Here, we genotyped and scanned 94 healthy subjects using fMRI during a reading task. We studied the correlation of genetic polymorphisms with interindividual variability in brain activation and functional asymmetry in frontal and temporal cortices. In FOXP2, SNPs rs6980093 and rs7799109 were associated with variations of activation in the left frontal cortex. In the KIAA0319/TTRAP/THEM2 locus, rs17243157 was associated with asymmetry in functional activation of the superior temporal sulcus (STS). Interestingly, healthy subjects bearing the KIAA0319/TTRAP/THEM2 variants previously identified as enhancing the risk of dyslexia showed a reduced left-hemispheric asymmetry of the STS. Our results confirm that both FOXP2 and KIAA0319/TTRAP/THEM2 genes play an important role in human language development, but probably through different cerebral pathways. The observed cortical effects mirror previous fMRI results in developmental language and reading disorders, and suggest that a continuum may exist between these pathologies and normal interindividual variability.

  13. Genetic Structuration, Demography and Evolutionary History of Mycobacterium tuberculosis LAM9 Sublineage in the Americas as Two Distinct Subpopulations Revealed by Bayesian Analyses

    Science.gov (United States)

    Reynaud, Yann; Millet, Julie; Rastogi, Nalin

    2015-01-01

    Tuberculosis (TB) remains broadly present in the Americas despite intense global efforts for its control and elimination. Starting from a large dataset comprising spoligotyping (n = 21183 isolates) and 12-loci MIRU-VNTRs data (n = 4022 isolates) from a total of 31 countries of the Americas (data extracted from the SITVIT2 database), this study aimed to get an overview of lineages circulating in the Americas. A total of 17119 (80.8%) strains belonged to the Euro-American lineage 4, among which the most predominant genotypic family belonged to the Latin American and Mediterranean (LAM) lineage (n = 6386, 30.1% of strains). By combining classical phylogenetic analyses and Bayesian approaches, this study revealed for the first time a clear genetic structuration of LAM9 sublineage into two subpopulations named LAM9C1 and LAM9C2, with distinct genetic characteristics. LAM9C1 was predominant in Chile, Colombia and USA, while LAM9C2 was predominant in Brazil, Dominican Republic, Guadeloupe and French Guiana. Globally, LAM9C2 was characterized by higher allelic richness as compared to LAM9C1 isolates. Moreover, LAM9C2 sublineage appeared to expand close to twenty times more than LAM9C1 and showed older traces of expansion. Interestingly, a significant proportion of LAM9C2 isolates presented typical signature of ancestral LAM-RDRio MIRU-VNTR type (224226153321). Further studies based on Whole Genome Sequencing of LAM strains will provide the needed resolution to decipher the biogeographical structure and evolutionary history of this successful family. PMID:26517715

  14. Human murine mammary tumour virus-like agents are genetically distinct from endogenous retroviruses and are not detectable in breast cancer cell lines or biopsies

    International Nuclear Information System (INIS)

    Mant, Christine; Gillett, Cheryl; D'Arrigo, Corrado; Cason, John

    2004-01-01

    It has been reported that a human murine mammary tumour virus (MMTV)-like virus (HMLV), which may be an endogenous human retrovirus (HERV), occurs in the human breast cancer cell lines T47D and MCF-7 and, in 38% of human breast cancer biopsies. As the aetiology of most breast cancers remains unknown, it is important to verify these observations in differing breast cancer populations worldwide. Thus, we sought to determine the genetic relationships between HMLVs, MMTVs, and HERVs, and to investigate the association between HMLVs and breast cancer biopsies from South London, UK. Phylogenetic analyses of the env/pol region indicated that HMLVs are indistinct from MMTVs, and that MMTVS/HMLVs exhibit only low sequence homologies with HERVs. A search of the human genome confirmed that HMLVs are not endogenous. Using MMTV polymerase chain reaction (PCR) primers described previously, we amplified DNA from all cell lines except MCF-7 and from 7 of 44 (16%) breast cancer biopsies. A restriction fragment length polymorphism assay was designed to distinguish between HMLVs and MMTVs, and upon analyses, PCR amplicons appeared to be HMLVs. To confirm these findings, amplicons from the T47D cell line and from four randomly selected breast cancer patients were sequenced. Of 106 DNA sequences obtained, 103 were homologous with a short arm of human chromosome (Chr) 3 (3p13), two with Chr 4, and one with Chr 8. None of the sequences exhibited significant nucleotide homology with MMTVs, HMLVs, or with HERVs (all <50%). Thus, we conclude that (i) HMLVs are integral members of the MMTV family; (ii) MMTVs/HMLVs are genetically distinct from HERVs; (iii) MMTV/HMLV DNA is not present in human breast cancer cell lines or clinical biopsies in our locality

  15. Horizontal Transfer of the Plant Virulence Gene, nec1, and Flanking Sequences among Genetically Distinct Streptomyces Strains in the Diastatochromogenes Cluster

    Science.gov (United States)

    Bukhalid, R. A.; Takeuchi, T.; Labeda, D.; Loria, R.

    2002-01-01

    Evidence for the horizontal transfer of a pathogenicity island (PAI) carrying the virulence gene nec1 and flanking sequences among Streptomyces strains in the Diastatochromogenes cluster is presented. Plant-pathogenic, thaxtomin-producing Streptomyces strains, previously classified as S. scabiei based on the conventionally used phenotypic characteristics, were found to be genetically distinct from the type strain of S. scabiei based on DNA relatedness and 16S rDNA sequence analysis. Pairwise DNA-DNA hybridizations between some of these strains and the S. scabiei type strain were as low as 36%, a value much below what is conventionally accepted for species identity (70%). The sequence of the nec1 gene, however, was identical in all the S. scabiei and S. scabiei-like strains tested, irrespective of their DNA relatedness to the type strain of S. scabiei, their geographic origin, or the isolation host. Furthermore, a 26-kb DNA fragment including and flanking nec1 was also conserved among these strains based on restriction and Southern analyses. These data indicate that the etiology of potato scab is more complex than previously recognized; this result has important implications for potato scab management strategies. Previous research has suggested that horizontal transfer of a PAI was the mechanism for evolution of pathogenicity in S. acidiscabies and S. turgidiscabies, species that lie outside of the Diastatochromogenes cluster. Data presented here support this model and indicate that PAI transfer also has occurred frequently in species closely related to S. scabiei. PMID:11823214

  16. Genetic diversity of Acinetobacter spp. adapted to heavy metal polluted environments

    Directory of Open Access Journals (Sweden)

    Šipošová Nikola Š

    2017-06-01

    Full Text Available Multiple metallotolerant bacterial strains were isolated from soil and drainage water samples collected from three industrially heavy metals polluted areas in Slovakia. Obtained bacterial isolates were identified using MALDI-TOF mass spectrometry and bacterial isolates that belonged to the Acinetobacter genus were subjected for the further study. A. calcoaceticus was found to be prevalent species among analyzed Acinetobacter spp. strains, followed by A. lwoffii and A. johnsonii. A. calcoaceticus strains exhibited higher minimum inhibitory concentration to Mn, Zn, and Cu cations compared to A. lwoffii and A. johnsonii. On the other hand minimum inhibitory concentration to Co and Ni were identical in all Acinetobacter spp. isolates. Genetic analyses demonstrated multiple plasmids presence in A. lwoffii and A. johnsonii but not in A. calcoaceticus. Using ERIC-PCR the presence of two different genotypes of A. calcoaceticus was detected in heavy metal polluted environments in Slovakia.

  17. Mobile genetic elements, a key to microbial adaptation in extreme environments

    Science.gov (United States)

    van Houdt, Rob; Mijnendonckx, Kristel; Provoost, Ann; Monsieurs, Pieter; Mergeay, Max; Leys, Natalie

    To ensure well-being of the crew during manned spaceflight, continuous monitoring of different microbial contaminants in air, in water and on surfaces in the spacecraft is vital. Next to microorganisms originating mainly from human activity, strains from the closely related gen-era Cupriavidus and Ralstonia have been identified and isolated during numerous monitoring campaigns from different space-related environments. These strains have been found in the air of the Mars Exploration Rover assembly room, on the surface of the Mars Odyssey Orbiter and in different water sources from the International Space Station, Shuttle and Mir space station. In previous studies, we investigated the response of the model bacterium Cupriavidus metallidurans CH34 when cultured in the international space station (ISS) and space gravity and radiation simulation facilities, to understand it's ways to adapt to space flight conditions. It was also demonstrated that genetic rearrangements due to the movement of IS (insertion sequence) elements, enabled CH34 to adapt to toxic zinc concentrations, in space flight and on ground. In this study, we screened the full genome sequence of C. metallidurans CH34 for the presence of mobile genetic elements (MGEs), with the purpose to identified their putative role in adaptation to the new environments. Eleven genomic islands (GI) were identified in chro-mosome 1, three on the native plasmid pMOL28 and two on the native plasmid pMOL30. On the plasmids pMOL28 and pMOL30, all genes involved in the response to metals were located within GIs. Three of the GIs on chromosome 1 contained genes involved in the response to metals. Three GIs (CMGI-2, -3 and -4) on chromosome 1 belonged to the Tn4371 family, with CMGI-2 containing at least 25 genes involved in the degradation of toluene corresponding to CH34's ability to grow at expense of toluene, benzene or xylene as sole carbon source. CMGI-3 sheltered accessory genes involved in CO2 fixation and

  18. Peer deviance, parental divorce, and genetic risk in the prediction of drug abuse in a nationwide Swedish sample: evidence of environment-environment and gene-environment interaction.

    Science.gov (United States)

    Kendler, Kenneth S; Ohlsson, Henrik; Sundquist, Kristina; Sundquist, Jan

    2014-04-01

    Peer deviance (PD) strongly predicts externalizing psychopathologic conditions but has not been previously assessable in population cohorts. We sought to develop such an index of PD and to clarify its effects on risk of drug abuse (DA). To examine how strongly PD increases the risk of DA and whether this community-level liability indicator interacts with key DA risk factors at the individual and family levels. Studies of future DA registration in 1,401,698 Swedish probands born from January 1, 1970, through December 31, 1985, and their adolescent peers in approximately 9200 small community areas. Peer deviance was defined as the proportion of individuals born within 5 years of the proband living in the same small community when the proband was 15 years old who eventually were registered for DA. Drug abuse recorded in medical, legal, or pharmacy registry records. Peer deviance was associated with future DA in the proband, with rates of DA in older and male peers more strongly predictive than in younger or female peers. The predictive power of PD was only slightly attenuated by adding measures of community deprivation, collective efficacy, or family socioeconomic status. Probands whose parents were divorced were more sensitive to the pathogenic effects of high PD environments. A robust positive interaction was also seen between genetic risk of DA (indexed by rates of DA in first-, second-, and third-degree relatives) and PD exposure. With sufficient data, PD can be measured in populations and strongly predicts DA. In a nationwide sample, risk factors at the level of the individual (genetic vulnerability), family (parental loss), and community (PD) contribute substantially to risk of DA. Individuals at elevated DA risk because of parental divorce or high genetic liability are more sensitive to the pathogenic effects of PD. Although the effect of our PD measure on DA liability cannot be explained by standard measures of community or family risk, we cannot, with

  19. Genetic basis of nitrogen use efficiency and yield stability across environments in winter rapeseed.

    Science.gov (United States)

    Bouchet, Anne-Sophie; Laperche, Anne; Bissuel-Belaygue, Christine; Baron, Cécile; Morice, Jérôme; Rousseau-Gueutin, Mathieu; Dheu, Jean-Eric; George, Pierre; Pinochet, Xavier; Foubert, Thomas; Maes, Olivier; Dugué, Damien; Guinot, Florent; Nesi, Nathalie

    2016-09-15

    Nitrogen use efficiency is an important breeding trait that can be modified to improve the sustainability of many crop species used in agriculture. Rapeseed is a major oil crop with low nitrogen use efficiency, making its production highly dependent on nitrogen input. This complex trait is suspected to be sensitive to genotype × environment interactions, especially genotype × nitrogen interactions. Therefore, phenotyping diverse rapeseed populations under a dense network of trials is a powerful approach to study nitrogen use efficiency in this crop. The present study aimed to determine the quantitative trait loci (QTL) associated with yield in winter oilseed rape and to assess the stability of these regions under contrasting nitrogen conditions for the purpose of increasing nitrogen use efficiency. Genome-wide association studies and linkage analyses were performed on two diversity sets and two doubled-haploid populations. These populations were densely genotyped, and yield-related traits were scored in a multi-environment design including seven French locations, six growing seasons (2009 to 2014) and two nitrogen nutrition levels (optimal versus limited). Very few genotype × nitrogen interactions were detected, and a large proportion of the QTL were stable across nitrogen nutrition conditions. In contrast, strong genotype × trial interactions in which most of the QTL were specific to a single trial were found. To obtain further insight into the QTL × environment interactions, genetic analyses of ecovalence were performed to identify the genomic regions contributing to the genotype × nitrogen and genotype × trial interactions. Fifty-one critical genomic regions contributing to the additive genetic control of yield-associated traits were identified, and the structural organization of these regions in the genome was investigated. Our results demonstrated that the effect of the trial was greater than the effect of nitrogen nutrition

  20. Detection and Tracking of a Novel Genetically Tagged Biological Simulant in the Environment

    Science.gov (United States)

    Emanuel, Peter A.; Buckley, Patricia E.; Sutton, Tiffany A.; Edmonds, Jason M.; Bailey, Andrew M.; Rivers, Bryan A.; Kim, Michael H.; Ginley, William J.; Keiser, Christopher C.; Doherty, Robert W.; Kragl, F. Joseph; Narayanan, Fiona E.; Katoski, Sarah E.; Paikoff, Sari; Leppert, Samuel P.; Strawbridge, John B.; VanReenen, Daniel R.; Biberos, Sally S.; Moore, Douglas; Phillips, Douglas W.; Mingioni, Lisa R.; Melles, Ogba; Ondercin, Daniel G.; Hirsh, Beth; Bieschke, Kendall M.; Harris, Crystal L.; Omberg, Kristin M.; Rastogi, Vipin K.; Van Cuyk, Sheila

    2012-01-01

    A variant of Bacillus thuringiensis subsp. kurstaki containing a single, stable copy of a uniquely amplifiable DNA oligomer integrated into the genome for tracking the fate of biological agents in the environment was developed. The use of genetically tagged spores overcomes the ambiguity of discerning the test material from pre-existing environmental microflora or from previously released background material. In this study, we demonstrate the utility of the genetically “barcoded” simulant in a controlled indoor setting and in an outdoor release. In an ambient breeze tunnel test, spores deposited on tiles were reaerosolized and detected by real-time PCR at distances of 30 m from the point of deposition. Real-time PCR signals were inversely correlated with distance from the seeded tiles. An outdoor release of powdered spore simulant at Aberdeen Proving Ground, Edgewood, MD, was monitored from a distance by a light detection and ranging (LIDAR) laser. Over a 2-week period, an array of air sampling units collected samples were analyzed for the presence of viable spores and using barcode-specific real-time PCR assays. Barcoded B. thuringiensis subsp. kurstaki spores were unambiguously identified on the day of the release, and viable material was recovered in a pattern consistent with the cloud track predicted by prevailing winds and by data tracks provided by the LIDAR system. Finally, the real-time PCR assays successfully differentiated barcoded B. thuringiensis subsp. kurstaki spores from wild-type spores under field conditions. PMID:23001670

  1. Two distinct origins of a common BRCA1 mutation in breast-ovarian cancer families: A genetic study of 15 185delAG-mutation kindreds

    Energy Technology Data Exchange (ETDEWEB)

    Berman, D.B.; Schultz, D.C.; Godwin, A.K. [Creighton Univ., Omaha, NE (United States)] [and others

    1996-06-01

    We screened 163 women from breast-ovarian cancer-prone families, as well as 178 individuals affected with breast and/or ovarian cancer but unselected for family history, for germ-line mutations in exon 2 of BRCA1, by SSCP analysis and direct sequencing. A total of 25 mutations were detected. Thirteen of 64 Jewish Ashkenazi women and 2 non-Jewish individuals were found to possess the 185delAG mutation. Haplotype data for all 15 individuals, with markers intragenic to BRCA1, suggest that the Jewish Ashkenazi individuals share a common ancestry that is distinct from the lineage shared by the other two women. These data provide the first evidence of two distinct lines of transmission for the 185delAG mutation, only one of which has its origins in the Jewish Ashkenazi population. Our screening also uncovered 10 affected individuals with an 11-bp deletion at nucleotide 188 of BRCA1 (188del11), 4 of whom are Ashkenazi Jews. This is only the third reported mutation detected within the Jewish Ashkenazi population and may represent the second most common alteration in BRCA1 found in Ashkenazi Jews in the United States. The observed overrepresentation of specific mutations within a subgroup of the general population may eventually contribute to the development of inexpensive and routine tests for BRCA1 mutations, as well as to the elucidation of other contributory factors (e.g., diet, environment, and chemical exposures) that may play a key role in cancer initiation and development. The implications of the mutational data, as well as the role that founder effect, demographic history, and penetrance play in the resulting observed phenomena, are discussed. 32 refs., 3 figs., 2 tabs.

  2. Genetic risk for schizophrenia, obstetric complications, and adolescent school outcome: evidence for gene-environment interaction.

    Science.gov (United States)

    Forsyth, Jennifer K; Ellman, Lauren M; Tanskanen, Antti; Mustonen, Ulla; Huttunen, Matti O; Suvisaari, Jaana; Cannon, Tyrone D

    2013-09-01

    Low birth weight (LBW) and hypoxia are among the environmental factors most reliably associated with schizophrenia; however, the nature of this relationship is unclear and both gene-environment interaction and gene-environment covariation models have been proposed as explanations. High-risk (HR) designs that explore whether obstetric complications differentially predict outcomes in offspring at low risk (LR) vs HR for schizophrenia, while accounting for differences in rates of maternal risk factors, may shed light on this question. This study used prospectively obtained data to examine relationships between LBW and hypoxia on school outcome at age 15-16 years in a Finnish sample of 1070 offspring at LR for schizophrenia and 373 offspring at HR for schizophrenia, based on parental psychiatric history. Controlling for offspring sex, maternal smoking, social support, parity, age, and number of prenatal care visits, HR offspring performed worse than LR offspring across academic, nonacademic, and physical education domains. LBW predicted poorer academic and physical education performance in HR offspring, but not in LR offspring, and this association was similar for offspring of fathers vs mothers with schizophrenia. Hypoxia predicted poorer physical education score across risk groups. Rates of LBW and hypoxia were similar for LR and HR offspring and for offspring of fathers vs mothers with schizophrenia. Results support the hypothesis that genetic susceptibility to schizophrenia confers augmented vulnerability of the developing brain to the effects of obstetric complications, possibly via epigenetic mechanisms.

  3. cAMP response element binding protein (CREB activates transcription via two distinct genetic elements of the human glucose-6-phosphatase gene

    Directory of Open Access Journals (Sweden)

    Stefano Luisa

    2005-01-01

    /CREB fusion protein and a mutant of the PKA catalytic subunit that is targeted to the nucleus, we have shown that the glucose-6-phosphatase gene has two distinct genetic elements that function as bona fide CRE. This study further shows that the expression vectors encoding C2/CREB and catalytic subunit of PKA are valuable tools for the study of CREB-mediated gene transcription and the biological functions of CREB.

  4. High Prevalence and Genetic Polymorphisms of Legionella in Natural and Man-Made Aquatic Environments in Wenzhou, China

    Directory of Open Access Journals (Sweden)

    Leyi Zhang

    2017-02-01

    Full Text Available Natural and engineered water systems are the main sources of Legionnaires’ disease. It is essential from a public health perspective to survey water environments for the existence of Legionella. To analyze the main serogroups, genotypes and pathogenicity of the pathogen, a stratified sampling method was adopted to collect water samples randomly from shower water, cooling tower water, and local public hot springs in Wenzhou, China. Suspected strains were isolated from concentrated water samples. Serum agglutination assay and real-time PCR (Polymerase chain reaction were used to identify L. pneumophila. Sequence-based typing (SBT and pulsed-field gel electrophoresis (PFGE were used to elucidate the genetic polymorphisms in the collected isolates. The intracellular growth ability of the isolates was determined through their interaction with J774 cells and plating them onto BCYE (Buffered Charcoal Yeast Extract agar plates. Overall, 25.56% (46/180 of water samples were Legionella-positive; fifty-two strains were isolated and two kinds of serogroups were co-detected from six water samples from 2015 to 2016. Bacterial concentrations ranged from 20 CFU/100 mL to 10,720 CFU/100 mL. In detail, the Legionella-positive rates of shower water, cooling tower water and hot springs water were 15.45%, 13.33%, and 62.5%, respectively. The main serogroups were LP1 (30.69% and LP3 (28.85% and all strains carried the dot gene. Among them, 52 isolates and another 10 former isolates were analyzed by PFGE. Nineteen distinct patterns were observed in 52 strains isolated from 2015 to 2016 with three patterns being observed in 10 strains isolated from 2009 to 2014. Seventy-three strains containing 52 from this study and 21 former isolates were selected for SBT analysis and divided into 25 different sequence types in 4 main clonal groups belonging to 4 homomorphic types. Ten strains were chosen to show their abilities to grow and multiply in J744 cells. Taken together

  5. SOX10 mutation causes Waardenburg syndrome associated with distinctive phenotypic features in an Iranian family: A clue for phenotype-directed genetic analysis.

    Science.gov (United States)

    Jalilian, Nazanin; Tabatabaiefar, Mohammad Amin; Alimadadi, Hossein; Noori-Daloii, Mohammad Reza

    2017-05-01

    Waardenburg syndrome (WS) is a neurocristopathy characterized by hearing impairment and pigmentary disturbances in hair, eyes, and skin. WS is clinically heterogeneous and can be subdivided into four major types (WS1-WS4) where WS4 or Shah-Waardenburg is diagnosed when WS2 is accompanied by Hirschsprung disease (HD). Mutations of SOX10, EDN3/EDNRB have been identified in association with WS4. This study was aimed to determine the pathogenic variant in an Iranian pedigree affected with WS4. A two-generation pedigree with three affected members and considerable phenotypic heterogeneity was recruited. The proband was a 15-year-old boy, with severe to profound sensorineural hearing impairment, heterochromia iridis, hypoplastic blue eyes and Hirschprung disease. The other two also presented characteristics of WS2 and complained of chronic constipation with normal anorectal reflex. Sequencing of all exons and exon-intron boundaries of SOX10, EDN3/EDNRB revealed a heterozygous variant c.422T > C in exon 3 of SOX10 confirmed by a series of evidence to be pathogenic. It resulted in p.L141P at the protein level. Leucin 141 is located in Nuclear Export signal, HMG box of the protein. This study is the first report of a WS4 family in the Iranian population. The mutation is associated with distinctive phenotypic profile (association of anosmia and chronic constipation with SOX10 mutations) and could further improve diagnosis and counseling of WS in the Iranian population and can contribute to phenotype-directed genetic analysis. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize

    Energy Technology Data Exchange (ETDEWEB)

    Suzuki, Hitoshi; MacDonald, Jacqueline; Syed, Khajamohiddin; Salamov, Asaf; Hori, Chiaki; Aerts, Andrea; Henrissat, Bernard; Wiebenga, Ad; vanKuyk, Patricia A.; Barry, Kerrie; Lindquist, Erika; LaButti, Kurt; Lapidus, Alla; Lucas, Susan; Coutinho, Pedro; Gong, Yunchen; Samejima, Masahiro; Mahadevan, Radhakrishnan; Abou-Zaid, Mamdouh; de Vries, Ronald P.; Igarashi, Kiyohiko; Yadav, Jagit S.; Grigoriev, Igor V.; Master, Emma R.

    2012-02-17

    Background Softwood is the predominant form of land plant biomass in the Northern hemisphere, and is among the most recalcitrant biomass resources to bioprocess technologies. The white rot fungus, Phanerochaete carnosa, has been isolated almost exclusively from softwoods, while most other known white-rot species, including Phanerochaete chrysosporium, were mainly isolated from hardwoods. Accordingly, it is anticipated that P. carnosa encodes a distinct set of enzymes and proteins that promote softwood decomposition. To elucidate the genetic basis of softwood bioconversion by a white-rot fungus, the present study reports the P. carnosa genome sequence and its comparative analysis with the previously reported P. chrysosporium genome. Results P. carnosa encodes a complete set of lignocellulose-active enzymes. Comparative genomic analysis revealed that P. carnosa is enriched with genes encoding manganese peroxidase, and that the most divergent glycoside hydrolase families were predicted to encode hemicellulases and glycoprotein degrading enzymes. Most remarkably, P. carnosa possesses one of the largest P450 contingents (266 P450s) among the sequenced and annotated wood-rotting basidiomycetes, nearly double that of P. chrysosporium. Along with metabolic pathway modeling, comparative growth studies on model compounds and chemical analyses of decomposed wood components showed greater tolerance of P. carnosa to various substrates including coniferous heartwood. Conclusions The P. carnosa genome is enriched with genes that encode P450 monooxygenases that can participate in extractives degradation, and manganese peroxidases involved in lignin degradation. The significant expansion of P450s in P. carnosa, along with differences in carbohydrate- and lignin-degrading enzymes, could be correlated to the utilization of heartwood and sapwood preparations from both coniferous and hardwood species.

  7. Distinct Contributions of Ice Nucleation, Large-Scale Environment, and Shallow Cumulus Detrainment to Cloud Phase Partitioning With NCAR CAM5

    Science.gov (United States)

    Wang, Yong; Zhang, Damao; Liu, Xiaohong; Wang, Zhien

    2018-01-01

    Mixed-phase clouds containing both liquid droplets and ice particles occur frequently at high latitudes and in the midlatitude storm track regions. Simulations of the cloud phase partitioning between liquid and ice hydrometeors in state-of-the-art global climate models are still associated with large biases. In this study, the phase partitioning in terms of liquid mass phase ratio (MPRliq, defined as the ratio of liquid mass to total condensed water mass) simulated from the NCAR Community Atmosphere Model version 5 (CAM5) is evaluated against the observational data from A-Train satellite remote sensors. Modeled MPRliq is significantly lower than observations on the global scale, especially in the Southern Hemisphere (e.g., Southern Ocean and the Antarctic). Sensitivity tests with CAM5 are conducted to investigate the distinct contributions of heterogeneous ice nucleation, shallow cumulus detrainment, and large-scale environment (e.g., winds, temperature, and water vapor) to the low MPRliq biases. Our results show that an aerosol-aware ice nucleation parameterization increases the MPRliq especially at temperatures colder than -20°C and significantly improves the model agreements with observations in the Polar regions in summer. The decrease of threshold temperature over which all detrained cloud water is liquid from 268 to 253 K enhances the MPRliq and improves the MPRliq mostly over the Southern Ocean. By constraining water vapor in CAM5 toward reanalysis, modeled low biases in many geographical regions are largely reduced through a significant decrease of cloud ice mass mixing ratio.

  8. Alpine bistort (Bistorta vivipara) in edge habitat associates with fewer but distinct ectomycorrhizal fungal species: a comparative study of three contrasting soil environments in Svalbard.

    Science.gov (United States)

    Mundra, Sunil; Bahram, Mohammad; Eidesen, Pernille Bronken

    2016-11-01

    Bistorta vivipara is a widespread arctic-alpine ectomycorrhizal (ECM) plant species. Recent findings suggest that fungal communities associated with B. vivipara roots appear random over short distances, but at larger scales, environmental filtering structure fungal communities. Habitats in highly stressful environments where specialist species with narrower niches may have an advantage represent unique opportunity to test the effect of environmental filtering. We utilised high-throughput amplicon sequencing to identify ECM communities associated with B. vivipara in Svalbard. We compared ECM communities in a core habitat where B. vivipara is frequent (Dryas-heath) with edge habitats representing extremes in terms of nutrient availability where B. vivipara is less frequent (bird-manured meadow and a nutrient-depleted mine tilling). Our analysis revealed that soil conditions in edge habitats favour less diverse but more distinct ECM fungal communities with functional traits adapted to local conditions. ECM richness was overall lower in both edge habitats, and the taxonomic compositions of ECM fungi were in line with our functional expectations. Stress-tolerant genera such as Laccaria and Hebeloma were abundant in nutrient-poor mine site whereas functional competitors genera such as Lactarius and Russula were dominant in the nutrient-rich bird-cliff site. Our results suggest that ECM communities in rare edge habitats are most likely not subsets of the larger pool of ECM fungi found in natural tundra, and they may represent a significant contribution to the overall diversity of ECM fungi in the Arctic.

  9. Identification of New Genetic Susceptibility Loci for Breast Cancer Through Consideration of Gene-Environment Interactions

    Science.gov (United States)

    Schoeps, Anja; Rudolph, Anja; Seibold, Petra; Dunning, Alison M.; Milne, Roger L.; Bojesen, Stig E.; Swerdlow, Anthony; Andrulis, Irene; Brenner, Hermann; Behrens, Sabine; Orr, Nicholas; Jones, Michael; Ashworth, Alan; Li, Jingmei; Cramp, Helen; Connley, Dan; Czene, Kamila; Darabi, Hatef; Chanock, Stephen J.; Lissowska, Jolanta; Figueroa, Jonine D.; Knight, Julia; Glendon, Gord; Mulligan, Anna M.; Dumont, Martine; Severi, Gianluca; Baglietto, Laura; Olson, Janet; Vachon, Celine; Purrington, Kristen; Moisse, Matthieu; Neven, Patrick; Wildiers, Hans; Spurdle, Amanda; Kosma, Veli-Matti; Kataja, Vesa; Hartikainen, Jaana M.; Hamann, Ute; Ko, Yon-Dschun; Dieffenbach, Aida K.; Arndt, Volker; Stegmaier, Christa; Malats, Núria; Arias Perez, JoséI.; Benítez, Javier; Flyger, Henrik; Nordestgaard, Børge G.; Truong, Théresè; Cordina-Duverger, Emilie; Menegaux, Florence; Silva, Isabel dos Santos; Fletcher, Olivia; Johnson, Nichola; Häberle, Lothar; Beckmann, Matthias W.; Ekici, Arif B.; Braaf, Linde; Atsma, Femke; van den Broek, Alexandra J.; Makalic, Enes; Schmidt, Daniel F.; Southey, Melissa C.; Cox, Angela; Simard, Jacques; Giles, Graham G.; Lambrechts, Diether; Mannermaa, Arto; Brauch, Hiltrud; Guénel, Pascal; Peto, Julian; Fasching, Peter A.; Hopper, John; Flesch-Janys, Dieter; Couch, Fergus; Chenevix-Trench, Georgia; Pharoah, Paul D. P.; Garcia-Closas, Montserrat; Schmidt, Marjanka K.; Hall, Per; Easton, Douglas F.; Chang-Claude, Jenny

    2014-01-01

    Genes that alter disease risk only in combination with certain environmental exposures may not be detected in genetic association analysis. By using methods accounting for gene-environment (G × E) interaction, we aimed to identify novel genetic loci associated with breast cancer risk. Up to 34,475 cases and 34,786 controls of European ancestry from up to 23 studies in the Breast Cancer Association Consortium were included. Overall, 71,527 single nucleotide polymorphisms (SNPs), enriched for association with breast cancer, were tested for interaction with 10 environmental risk factors using three recently proposed hybrid methods and a joint test of association and interaction. Analyses were adjusted for age, study, population stratification, and confounding factors as applicable. Three SNPs in two independent loci showed statistically significant association: SNPs rs10483028 and rs2242714 in perfect linkage disequilibrium on chromosome 21 and rs12197388 in ARID1B on chromosome 6. While rs12197388 was identified using the joint test with parity and with age at menarche (P-values = 3 × 10−07), the variants on chromosome 21 q22.12, which showed interaction with adult body mass index (BMI) in 8,891 postmenopausal women, were identified by all methods applied. SNP rs10483028 was associated with breast cancer in women with a BMI below 25 kg/m2 (OR = 1.26, 95% CI 1.15–1.38) but not in women with a BMI of 30 kg/m2 or higher (OR = 0.89, 95% CI 0.72–1.11, P for interaction = 3.2 × 10−05). Our findings confirm comparable power of the recent methods for detecting G × E interaction and the utility of using G × E interaction analyses to identify new susceptibility loci. PMID:24248812

  10. Eco-genetic structure of Bacillus cereus sensu lato populations from different environments in northeastern Poland.

    Science.gov (United States)

    Drewnowska, Justyna M; Swiecicka, Izabela

    2013-01-01

    The Bacillus cereus group, which includes entomopathogens and etiologic agents of foodborne illness or anthrax, persists in various environments. The basis of their ecological diversification remains largely undescribed. Here we present the genetic structure and phylogeny of 273 soil B. cereus s.l. isolates from diverse habitats in northeastern Poland, with samplings acquired from the last European natural forest (Białowieża National Park), the largest marshes in Europe (Biebrza National Park), and a farm. In multi-locus sequence typing (MLST), despite negative selection in seven housekeeping loci, the isolates exhibited high genetic diversity (325 alleles), mostly resulting from mutation events, and represented 148 sequencing types (131 STs new and 17 STs already described) grouped into 19 complexes corresponding with bacterial clones, and 80 singletons. Phylogenetic analyses showed that 74% of the isolates clustered with B. cereus s.l. environmental references (clade III), while only 11 and 15%, respectively, grouped with isolates of clinical origin (clade I), and B. cereus ATCC 14579 and reference B. thuringiensis (clade II). Predominantly within clade III, we found lineages adapted to low temperature (thermal ecotypes), while putative toxigenic isolates (cytK-positive) were scattered in all clades of the marsh and farm samplings. The occurrence of 92% of STs in bacilli originating from one habitat, and the description of new STs for 78% of the isolates, strongly indicate the existence of specific genotypes within the natural B. cereus s.l. populations. In contrast to the human-associated B. cereus s.l. that exhibit a significant level of similarity, the environmental isolates appear more complex. Thus we propose dividing B. cereus s.l. into two groups, the first including environmental isolates, and the second covering those that are of clinical relevance.

  11. Eco-genetic structure of Bacillus cereus sensu lato populations from different environments in northeastern Poland.

    Directory of Open Access Journals (Sweden)

    Justyna M Drewnowska

    Full Text Available The Bacillus cereus group, which includes entomopathogens and etiologic agents of foodborne illness or anthrax, persists in various environments. The basis of their ecological diversification remains largely undescribed. Here we present the genetic structure and phylogeny of 273 soil B. cereus s.l. isolates from diverse habitats in northeastern Poland, with samplings acquired from the last European natural forest (Białowieża National Park, the largest marshes in Europe (Biebrza National Park, and a farm. In multi-locus sequence typing (MLST, despite negative selection in seven housekeeping loci, the isolates exhibited high genetic diversity (325 alleles, mostly resulting from mutation events, and represented 148 sequencing types (131 STs new and 17 STs already described grouped into 19 complexes corresponding with bacterial clones, and 80 singletons. Phylogenetic analyses showed that 74% of the isolates clustered with B. cereus s.l. environmental references (clade III, while only 11 and 15%, respectively, grouped with isolates of clinical origin (clade I, and B. cereus ATCC 14579 and reference B. thuringiensis (clade II. Predominantly within clade III, we found lineages adapted to low temperature (thermal ecotypes, while putative toxigenic isolates (cytK-positive were scattered in all clades of the marsh and farm samplings. The occurrence of 92% of STs in bacilli originating from one habitat, and the description of new STs for 78% of the isolates, strongly indicate the existence of specific genotypes within the natural B. cereus s.l. populations. In contrast to the human-associated B. cereus s.l. that exhibit a significant level of similarity, the environmental isolates appear more complex. Thus we propose dividing B. cereus s.l. into two groups, the first including environmental isolates, and the second covering those that are of clinical relevance.

  12. Digestive efficiency in rabbit does according to environment and genetic type

    Directory of Open Access Journals (Sweden)

    Davi Savietto

    2012-10-01

    Full Text Available Ninety lactating rabbit does of three different genetic types [2 from a line differentiating 20 generations by selection for litter size at weaning (lines V16 and V36 and 1 from a line founded under reproductive longevity criteria and then selected by litter size at weaning (line LP] were subjected to three environmental conditions: NC, females housed under normal conditions (14 to 20oC and fed with a control diet (333 g NDF/kg DM; HC, females housed under heat conditions (25 to 35oC and fed with the control diet; or NF, females housed under normal conditions and fed with a fibrous diet (443 g NDF/kg DM.  The apparent digestible coefficients of dry matter (DMd, organic matter, crude protein (CPd, gross energy, NDF (NDFd and acid detergent fibre, as well as the daily intake of dry matter (DM, digestible protein (DP and digestible energy (DE, were determined (14 to 18 d post-partum.  The environment affected all variables analysed.  In general, heat conditions reduced the daily feed intake (around -30%; P<0.05 and increased main apparent digestible coefficients (+4.5 percentage points for DMd.  In contrast, the use of a fibrous diet led to lower DE intake (-217 kJ/d; P<0.05 and main apparent digestibility coefficients (-13.5 percentage points for DMd.  Females from line V, regardless of generation, showed lower daily DM intake (-19.2 g/d; P<0.05 and NDFd (-1.5 percentage points; P<0.05 than line LP.  Interactions between genetic type and environment were found for daily DM intake, NDFd and CPd.  When receiving fibrous diet, LP females showed a higher increment in daily DM intake (65.6 g/d; P<0.05 than V36 females, compared to control. Under heat conditions, NDFd obtained for LP females were higher to those in normal conditions (+3.14 percentage points, while V females showed similar NDFd.  In addition, the increase in CPd observed under heat conditions was higher for LP (+9.87 percentage points and V36 (+8.74 percentage points than V16

  13. Genetic Background and Environment Influence the Effects of Mutations in pykF and Help Reveal Mechanisms Underlying Their Benefit

    Science.gov (United States)

    2015-08-01

    environment interactions characterize the evolution of drug resistance in yeast. Genetics 192:241–252. Gompel, N., and B. Prud’homme. 2009. The causes...3314–3323. 84 Walk, S. T., E. W. Alm, D. M. Gordon, J. L. Ram, G. A. Toranzos, J. M. Tiedje, and T. S. Whittam. 2009. Cryptic lineages of the genus

  14. Genetic Liability, Environment, and the Development of Fussiness in Toddlers: The Roles of Maternal Depression and Parental Responsiveness

    Science.gov (United States)

    Natsuaki, Misaki N.; Ge, Xiaojia; Leve, Leslie D.; Neiderhiser, Jenae M.; Shaw, Daniel S.; Conger, Rand D.; Scaramella, Laura V.; Reid, John B.; Reiss, David

    2010-01-01

    Using a longitudinal, prospective adoption design, the authors of this study examined the effects of the environment (adoptive parents' depressive symptoms and responsiveness) and genetic liability of maternal depression (inferred by birth mothers' major depressive disorder [MDD]) on the development of fussiness in adopted children between 9 and…

  15. Runaway sexual selection without genetic correlations: social environments and flexible mate choice initiate and enhance the Fisher process.

    Science.gov (United States)

    Bailey, Nathan W; Moore, Allen J

    2012-09-01

    Female mating preferences are often flexible, reflecting the social environment in which they are expressed. Associated indirect genetic effects (IGEs) can affect the rate and direction of evolutionary change, but sexual selection models do not capture these dynamics. We incorporate IGEs into quantitative genetic models to explore how variation in social environments and mate choice flexibility influence Fisherian sexual selection. The importance of IGEs is that runaway sexual selection can occur in the absence of a genetic correlation between male traits and female preferences. Social influences can facilitate the initiation of the runaway process and increase the rate of trait elaboration. Incorporating costs to choice do not alter the main findings. Our model provides testable predictions: (1) genetic covariances between male traits and female preferences may not exist, (2) social flexibility in female choice will be common in populations experiencing strong sexual selection, (3) variation in social environments should be associated with rapid sexual trait divergence, and (4) secondary sexual traits will be more elaborate than previously predicted. Allowing feedback from the social environment resolves discrepancies between theoretical predictions and empirical data, such as why indirect selection on female preferences, theoretically weak, might be sufficient for preferences to become elaborated. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

  16. Air pollution and asthma control in the Epidemiological study on the Genetics and Environment of Asthma.

    Science.gov (United States)

    Jacquemin, Bénédicte; Kauffmann, Francine; Pin, Isabelle; Le Moual, Nicole; Bousquet, Jean; Gormand, Frédéric; Just, Jocelyne; Nadif, Rachel; Pison, Christophe; Vervloet, Daniel; Künzli, Nino; Siroux, Valérie

    2012-09-01

    The associations between exposure to air pollution and asthma control are not well known. The objective of this study was to assess the association between long-term exposure to NO(2), O(3) and PM(10) and asthma control in the follow-up of the Epidemiological study on the Genetics and Environment of Asthma (EGEA2) (2003-2007). Modelled outdoor NO(2), O(3) and PM(10) estimates were linked to each residential address using the 4 km grid air pollutant surface developed by the French Institute of Environment in 2004. Asthma control was assessed in 481 subjects with current asthma using a multidimensional approach following the 2006-2009 Global Initiative for Asthma guidelines. Multinomial and ordinal logistic regressions were conducted adjusted for sex, age, body mass index, education, smoking and use of inhaled corticosteroids. The association between air pollution and the three domains of asthma control (symptoms, exacerbations and lung function) was assessed. ORs are reported per IQR. Median concentrations (in micrograms per cubic metre) were 32 (IQR 25-38) for NO(2) (n=465), 46 (41-52) for O(3) and 21 (18-21) for PM(10) (n=481). In total, 44%, 29% and 27% had controlled, partly controlled and uncontrolled asthma, respectively. The ordinal ORs for O(3) and PM(10) with asthma control were 1.69 (95% CI 1.22 to 2.34) and 1.35 (95% CI 1.13 to 1.64), respectively. When including both pollutants in the same model, both associations persisted. Associations were not modified by sex, smoking status, use of inhaled corticosteroids, atopy, season of examination or body mass index. Both pollutants were associated with each of the three main domains of control. The results suggest that long-term exposure to PM(10) and O(3) is associated with uncontrolled asthma in adults, defined by symptoms, exacerbations and lung function.

  17. Genetic differentiation and selection against migrants in evolutionarily replicated extreme environments.

    Science.gov (United States)

    Plath, Martin; Pfenninger, Markus; Lerp, Hannes; Riesch, Rüdiger; Eschenbrenner, Christoph; Slattery, Patrick A; Bierbach, David; Herrmann, Nina; Schulte, Matthias; Arias-Rodriguez, Lenin; Rimber Indy, Jeane; Passow, Courtney; Tobler, Michael

    2013-09-01

    We investigated mechanisms of reproductive isolation in livebearing fishes (genus Poecilia) inhabiting sulfidic and nonsulfidic habitats in three replicate river drainages. Although sulfide spring fish convergently evolved divergent phenotypes, it was unclear if mechanisms of reproductive isolation also evolved convergently. Using microsatellites, we found strongly reduced gene flow between adjacent populations from different habitat types, suggesting that local adaptation to sulfidic habitats repeatedly caused the emergence of reproductive isolation. Reciprocal translocation experiments indicate strong selection against immigrants into sulfidic waters, but also variation among drainages in the strength of selection against immigrants into nonsulfidic waters. Mate choice experiments revealed the evolution of assortative mating preferences in females from nonsulfidic but not from sulfidic habitats. The inferred strength of sexual selection against immigrants (RI(s)) was negatively correlated with the strength of natural selection (RI(m)), a pattern that could be attributed to reinforcement, whereby natural selection strengthens behavioral isolation due to reduced hybrid fitness. Overall, reproductive isolation and genetic differentiation appear to be replicated and direct consequences of local adaptation to sulfide spring environments, but the relative contributions of different mechanisms of reproductive isolation vary across these evolutionarily independent replicates, highlighting both convergent and nonconvergent evolutionary trajectories of populations in each drainage. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  18. Implications of host genetic variation on the risk and prevalence of infectious diseases transmitted through the environment.

    Science.gov (United States)

    Doeschl-Wilson, Andrea B; Davidson, R; Conington, J; Roughsedge, T; Hutchings, M R; Villanueva, B

    2011-07-01

    Previous studies have shown that host genetic heterogeneity in the response to infectious challenge can affect the emergence risk and the severity of diseases transmitted through direct contact between individuals. However, there is substantial uncertainty about the degree and direction of influence owing to different definitions of genetic variation, most of which are not in line with the current understanding of the genetic architecture of disease traits. Also, the relevance of previous results for diseases transmitted through environmental sources is unclear. In this article a compartmental genetic-epidemiological model was developed to quantify the impact of host genetic diversity on epidemiological characteristics of diseases transmitted through a contaminated environment. The model was parameterized for footrot in sheep. Genetic variation was defined through continuous distributions with varying shape and degree of dispersion for different disease traits. The model predicts a strong impact of genetic heterogeneity on the disease risk and its progression and severity, as well as on observable host phenotypes, when dispersion in key epidemiological parameters is high. The impact of host variation depends on the disease trait for which variation occurs and on environmental conditions affecting pathogen survival. In particular, compared to homogeneous populations with the same average susceptibility, disease risk and severity are substantially higher in populations containing a large proportion of highly susceptible individuals, and the differences are strongest when environmental contamination is low. The implications of our results for the recording and analysis of disease data and for predicting response to selection are discussed.

  19. Environmental influences on the longitudinal covariance of expressive vocabulary: measuring the home literacy environment in a genetically sensitive design.

    Science.gov (United States)

    Hart, Sara A; Petrill, Stephen A; DeThorne, Laura S; Deater-Deckard, Kirby; Thompson, Lee A; Schatschneider, Chris; Cutting, Laurie E

    2009-08-01

    Despite the well-replicated relationship between the home literacy environment and expressive vocabulary, few studies have examined the extent to which the home literacy environment is associated with the development of early vocabulary ability in the context of genetic influences. This study examined the influence of the home literacy environment on the longitudinal covariance of expressive vocabulary within a genetically sensitive design. Participants were drawn from the Western Reserve Reading Project, a longitudinal twin project of 314 twin pairs based in Ohio. Twins were assessed via three annual home visits during early elementary school; expressive vocabulary was measured via the Boston Naming Test (BNT), and the Home Literacy Environment (HLE) was assessed using mothers' report. The heritability of the BNT was moderate and significant at each measurement occasion, h(2) = .29-.49, as were the estimates of the shared environment, c(2) = .27-.39. HLE accounted for between 6-10% of the total variance in each year of vocabulary assessment. Furthermore, 7-9% of the total variance of the stability over time in BNT was accounted for by covariance in the home literacy environment. These results indicate that aspects of the home literacy environment, as reported by mothers, account for some of the shared environmental variance associated with expressive vocabulary in school aged children.

  20. Sensation seeking, peer deviance, and genetic influences on adolescent delinquency: Evidence for person-environment correlation and interaction.

    Science.gov (United States)

    Mann, Frank D; Patterson, Megan W; Grotzinger, Andrew D; Kretsch, Natalie; Tackett, Jennifer L; Tucker-Drob, Elliot M; Harden, K Paige

    2016-07-01

    Both sensation seeking and affiliation with deviant peer groups are risk factors for delinquency in adolescence. In this study, we use a sample of adolescent twins (n = 549), 13 to 20 years old (M age = 15.8 years), in order to test the interactive effects of peer deviance and sensation seeking on delinquency in a genetically informative design. Consistent with a socialization effect, affiliation with deviant peers was associated with higher delinquency even after controlling for selection effects using a co-twin-control comparison. At the same time, there was evidence for person-environment correlation; adolescents with genetic dispositions toward higher sensation seeking were more likely to report having deviant peer groups. Genetic influences on sensation seeking substantially overlapped with genetic influences on adolescent delinquency. Finally, the environmentally mediated effect of peer deviance on adolescent delinquency was moderated by individual differences in sensation seeking. Adolescents reporting high levels of sensation seeking were more susceptible to deviant peers, a Person × Environment interaction. These results are consistent with both selection and socialization processes in adolescent peer relationships, and they highlight the role of sensation seeking as an intermediary phenotype for genetic risk for delinquency. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

  1. From a genetic predisposition to an interactive predisposition: rethinking the ethical implications of screening for gene-environment interactions.

    Science.gov (United States)

    Tabery, James

    2009-02-01

    In a widely acclaimed study from 2002, researchers found a case of gene-environment interaction for a gene controlling neuroenzymatic activity (low vs. high), exposure to childhood maltreatment, and antisocial personality disorder (ASPD). Cases of gene-environment interaction are generally characterized as evincing a genetic predisposition; for example, individuals with low neuroenzymatic activity are generally characterized as having a genetic predisposition to ASPD. I first argue that the concept of a genetic predisposition fundamentally misconstrues these cases of gene-environment interaction. This misconstrual will be diagnosed, and then a new concept--interactive predisposition--will be introduced. I then show how this conceptual shift reconfigures old questions and raises new questions for genetic screening. Attempts to screen embryos or fetuses for the gene associated with low neuroenzymatic activity with an eye toward selecting against the low-activity variant fall prey to the myth of pre-environmental prediction; attempts to screen newborns for the gene associated with low neuroenzymatic activity with an eye toward early intervention will have to face the interventionist's dilemma.

  2. Range-wide genetic differentiation among North American great gray owls (Strix nebulosa) reveals a distinct lineage limited to the Sierra Nevada, California

    Science.gov (United States)

    J.M. Hull; J.J. Keane; W.K. Savage; S.A. Godwin; J. Shafer; E.P. Jepsen; R. Gerhardt; C. Stermer; H.B. Ernest

    2010-01-01

    Investigations of regional genetic differentiation are essential for describing phylogeographic patterns and informing management efforts for species of conservation concern. In this context, we investigated genetic diversity and evolutionary relationships among great gray owl (Strix nebulosa) populations in western North America, which...

  3. Genetic variation in walnuts (Juglans regia, j. sigillata and Juglandaceae) species distinctions, human impacts, and the conservation of agrobiodiversity in yunnan, china

    Science.gov (United States)

    Walnuts are a major crop of many countries and mostly cultivated in large-scale plantations with few cultivars. Landraces provide important genetic reservoirs; thus, understanding factors influencing the geographic distribution of genetic variation in crop resources is a fundamental goal of agrobiod...

  4. Analysis of genetic and genotype X environment interaction effects for agronomic traits of rice (oryza sativa l.) in salt tolerance

    International Nuclear Information System (INIS)

    Zhou, H.K.; Hayat, Y.; Fang, L.J.; Guo, R.F.; He, J.M.; Xu, H.M.

    2010-01-01

    A diallel cross experiment of 4 rice (Oryza sativa L.) female and 6 male varieties was conducted to study the genetic effects and their interaction with salt-stress condition of 7 agronomic traits in normal and salt-stressed planting conditions. The panicle length (PL), effective number of panicles per plant (ENP), plumped number of grains per panicles (PNG), total number of grains per panicles (TNG), 1000-grain weight (W), seed setting ratio (SSR) and grain weight per plant (PGW), were investigated. A genetic model including additive effect, dominance effect and their interaction effects with environment (ADE) was employed for analysis of data. It was observed that significant (p<0.05) additive effects, dominance effects, additive X environment interaction effects and dominance X environment interaction effects exist for most of the agronomic traits of rice. In addition, significant (p<0.05) narrow sense heritabilities of ENP, PNG, TNG, W and PGW were found, indicating that the genetic performance of these traits are greatly affected by salt stress condition. A significant (p<0.05) negative correlations in the additive effects and additive X environment interaction effects detected between ENP and PNG suggesting that selection on increasing of ENP can reduce PNG. In addition, there exist a highly significant (p<0.01) positive dominance correlation among the dominance effects of the ENP, PNG and TNG, which shows that it is possible to breed salt-tolerant rice variety by coordinating large panicle and multi-panicle in utilization of heterosis. (author)

  5. Are Genetics and Environment Substitutes or Complements in Affecting Entrepreneurial Choice?

    DEFF Research Database (Denmark)

    Zunino, Diego

    whether the genetic effect is different across genders, based on the stylized fact that barriers to entrepreneurship entry are stronger for females than for males. Using regression analysis, the study confirms earlier findings showing substantial genetic effects. More interestingly, the study finds...

  6. Modelling the loss of genetic diversity in vole populations in a spatially and temporally varying environment

    DEFF Research Database (Denmark)

    Topping, Christopher John; Østergaard, Siri; Pertoldi, Cino

    2003-01-01

    incorporating explicit genetics provide a promising new approach to the evaluation of the effect of animal behaviour, and random and man-induced events on the genetic composition of populations. They also provide a new platform from which to investigate the implication of real world deviations from assumptions...

  7. Conservation genetics in a globally changing environment : present problems, paradoxes and future challenges

    NARCIS (Netherlands)

    Pertoldi, Cino; Bijlsma, R.; Loeschcke, Volker

    2007-01-01

    Despite recent advances in conservation genetics and related disciplines and the growing impact that conservation genetics is having in conservation biology, our knowledge on several key issues in the field is still insufficient. Here we identify some of these issues together with addressing several

  8. Environment

    DEFF Research Database (Denmark)

    Valentini, Chiara

    2017-01-01

    The term environment refers to the internal and external context in which organizations operate. For some scholars, environment is defined as an arrangement of political, economic, social and cultural factors existing in a given context that have an impact on organizational processes and structures....... For others, environment is a generic term describing a large variety of stakeholders and how these interact and act upon organizations. Organizations and their environment are mutually interdependent and organizational communications are highly affected by the environment. This entry examines the origin...... and development of organization-environment interdependence, the nature of the concept of environment and its relevance for communication scholarships and activities....

  9. Genetics

    Science.gov (United States)

    ... Likelihood of getting certain diseases Mental abilities Natural talents An abnormal trait (anomaly) that is passed down ... one of them has a genetic disorder. Information Human beings have cells with 46 chromosomes . These consist ...

  10. Utilization of farm animal genetic resources in a changing agro-ecological environment in the Nordic countries.

    Science.gov (United States)

    Kantanen, Juha; Løvendahl, Peter; Strandberg, Erling; Eythorsdottir, Emma; Li, Meng-Hua; Kettunen-Præbel, Anne; Berg, Peer; Meuwissen, Theo

    2015-01-01

    Livestock production is the most important component of northern European agriculture and contributes to and will be affected by climate change. Nevertheless, the role of farm animal genetic resources in the adaptation to new agro-ecological conditions and mitigation of animal production's effects on climate change has been inadequately discussed despite there being several important associations between animal genetic resources and climate change issues. The sustainability of animal production systems and future food security require access to a wide diversity of animal genetic resources. There are several genetic questions that should be considered in strategies promoting adaptation to climate change and mitigation of environmental effects of livestock production. For example, it may become important to choose among breeds and even among farm animal species according to their suitability to a future with altered production systems. Some animals with useful phenotypes and genotypes may be more useful than others in the changing environment. Robust animal breeds with the potential to adapt to new agro-ecological conditions and tolerate new diseases will be needed. The key issue in mitigation of harmful greenhouse gas effects induced by livestock production is the reduction of methane (CH4) emissions from ruminants. There are differences in CH4 emissions among breeds and among individual animals within breeds that suggest a potential for improvement in the trait through genetic selection. Characterization of breeds and individuals with modern genomic tools should be applied to identify breeds that have genetically adapted to marginal conditions and to get critical information for breeding and conservation programs for farm animal genetic resources. We conclude that phenotyping and genomic technologies and adoption of new breeding approaches, such as genomic selection introgression, will promote breeding for useful characters in livestock species.

  11. Utilization of farm animal genetic resources in a changing agro-ecological environment in the Nordic countries

    Directory of Open Access Journals (Sweden)

    Juha eKantanen

    2015-02-01

    Full Text Available Livestock production is the most important component of northern European agriculture and contributes to and will be affected by climate change. Nevertheless, the role of farm animal genetic resources in the adaptation to new agro-ecological conditions and mitigation of animal production’s effects on climate change has been inadequately discussed despite there being several important associations between animal genetic resources and climate change issues. The sustainability of animal production systems and future food security require access to a wide diversity of animal genetic resources.There are several genetic questions that should be considered in strategies promoting adaptation to climate change and mitigation of environmental effects of livestock production. For example, it may become important to choose among breeds and even among farm animal species according to their suitability to a future with altered production systems. Some animals with useful phenotypes and genotypes may be more useful than others in the changing environment.Robust animal breeds with the potential to adapt to new agro-ecological conditions and tolerate new diseases will be needed. The key issue in mitigation of harmful greenhouse gas effects induced by livestock production is the reduction of methane (CH4 emissions from ruminants. There are differences in CH4 emissions among breeds and among individual animals within breeds that suggest a potential for improvement in the trait through genetic selection.Characterization of breeds and individuals with modern genomic tools should be applied to identify breeds that have genetically adapted to marginal conditions and to get critical information for breeding and conservation programmes for farm animal genetic resources. We conclude that phenotyping and genomic technologies and adoption of new breeding approaches, such as genomic selection introgression, will promote breeding for useful characters in livestock species.

  12. Establishing a risk-assessment process for release of genetically modified wine yeast into the environment.

    Science.gov (United States)

    Schoeman, Heidi; Wolfaardt, Gideon M; Botha, Alfred; van Rensburg, Pierre; Pretorius, Isak S

    2009-08-01

    The use and release of genetically modified organisms (GMOs) is an issue of intense public concern and, in the case of food and beverages, products containing GMOs or products thereof carry the risk of consumer rejection. The recent commercialization of 2 GM wine yeasts in the United States and Canada has made research and development of risk assessments for GM microorganisms a priority. The purpose of this study was to take a first step in establishing a risk-assessment process for future use and potential release of GM wine yeasts into the environment. The behaviour and spread of a GM wine yeast was monitored in saturated sand columns, saturated sand flow cells, and conventional flow cells. A widely used commercial Saccharomyces cerevisiae wine yeast, VIN13, a VIN13 transgenic strain (LKA1, which carries the LKA1 alpha-amylase gene of Lipomyces kononenkoae), a soil bacterium (Dyadobacter fermentens), and a nonwine soil-borne yeast (Cryptococcus laurentii) were compared in laboratory-scale microcosm systems designed to monitor microbial mobility behaviour, survival, and attachment to surfaces. It was found that LKA1 cells survived in saturated sand columns, but showed little mobility in the porous matrix, suggesting that the cells attached with high efficiency to sand. There was no significant difference between the mobility patterns of LKA1 and VIN13. All 3 yeasts (VIN13, LKA1, and C. laurentii) were shown to form stable biofilms; the 2 S. cerevisiae strains either had no difference in biofilm density or the LKA1 biofilm was less dense than that of VIN13. When co-inoculated with C. laurentii, LKA1 had no negative influence on the breakthrough of the Cryptococcus yeast in a sand column or on its ability to form biofilms. In addition, LKA1 did not successfully integrate into a stable mixed-biofilm community, nor did it disrupt the biofilm community. Overall, it was concluded that the LKA1 transgenic yeast had the same reproductive success as VIN13 in these 3

  13. Metabolite Profiling of Maize Grain: Differentiation due to Genetics, Environment and Input System

    OpenAIRE

    Röhlig, Richard M.

    2011-01-01

    A metabolite profiling approach for maize (Zea mays) based on gas chromatography/mass spectrometry was applied to the simultaneous detection, identification and quantification of a broad spectrum of non-polar (fatty acid methyl esters, free fatty acids, fatty alcohols, sterols, hydrocarbons) and polar (sugars, sugar alcohols, organic and inorganic acids, amino acids, amines) constituents. The non-targeted method allowed the investigation of the influence of genetics (cultivar, genetic modific...

  14. Genetic profiling of two phenotypically distinct outbred rats derived from a colony of the Zucker fatty rats maintained at Tokyo Medical University.

    Science.gov (United States)

    Nakanishi, Satoshi; Kuramoto, Takashi; Kashiwazaki, Naomi; Yokoi, Norihide

    2017-05-03

    The Zucker fatty (ZF) rat is an outbred rat and a well-known model of obesity without diabetes, harboring a missense mutation (fatty, abbreviated as fa) in the leptin receptor gene (Lepr). Slc:Zucker (Slc:ZF) outbred rats exhibit obesity while Hos:ZFDM-Lepr fa (Hos:ZFDM) outbred rats exhibit obesity and type 2 diabetes. Both outbred rats have been derived from an outbred ZF rat colony maintained at Tokyo Medical University. So far, genetic profiles of these outbred rats remain unknown. Here, we applied a simple genotyping method using Ampdirect reagents and FTA cards (Amp-FTA) in combination with simple sequence length polymorphisms (SSLP) markers to determine genetic profiles of Slc:ZF and Hos:ZFDM rats. Among 27 SSLP marker loci, 24 loci (89%) were fixed for specific allele at each locus in Slc:ZF rats and 26 loci (96%) were fixed in Hos:ZFDM rats, respectively. This indicates the low genetic heterogeneity in both colonies of outbred rats. Nine loci (33%) showed different alleles between the two outbred rats, suggesting considerably different genetic profiles between the two outbred rats in spite of the same origin. Additional analysis using 72 SSLP markers further supported these results and clarified the profiles in detail. This study revealed that genetic profiles of the Slc:ZF and Hos:ZFDM outbred rats are different for about 30% of the SSLP marker loci, which is the underlying basis for the phenotypic difference between the two outbred rats.

  15. Establishment of Stably Transfected Cells Constitutively Expressing the Full-Length and Truncated Antigenic Proteins of Two Genetically Distinct Mink Astroviruses

    DEFF Research Database (Denmark)

    Bidokhti, Mehdi R. M.; Ullman, Karin; Jensen, Trine Hammer

    2013-01-01

    to circumvent this drawback, we have developed stably transfected mink fetal cells and BHK21 cells constitutively expressing the full-length and truncated capsid proteins of two distinct genotypes of mink astrovirus. Protein expression in these stably transfected cells was demonstrated by strong signals...

  16. Morphological and genetic evidence for multiple evolutionary distinct lineages in the endangered and commercially exploited red lined torpedo barbs endemic to the Western Ghats of India.

    Science.gov (United States)

    John, Lijo; Philip, Siby; Dahanukar, Neelesh; Anvar Ali, Palakkaparambil Hamsa; Tharian, Josin; Raghavan, Rajeev; Antunes, Agostinho

    2013-01-01

    Red lined torpedo barbs (RLTBS) (Cyprinidae: Puntius) endemic to the Western Ghats Hotspot of India, are popular and highly priced freshwater aquarium fishes. Two decades of indiscriminate exploitation for the pet trade, restricted range, fragmented populations and continuing decline in quality of habitats has resulted in their 'Endangered' listing. Here, we tested whether the isolated RLTB populations demonstrated considerable variation qualifying to be considered as distinct conservation targets. Multivariate morphometric analysis using 24 size-adjusted characters delineated all allopatric populations. Similarly, the species-tree highlighted a phylogeny with 12 distinct RLTB lineages corresponding to each of the different riverine populations. However, coalescence-based methods using mitochondrial DNA markers identified only eight evolutionarily distinct lineages. Divergence time analysis points to recent separation of the populations, owing to the geographical isolation, more than 5 million years ago, after the lineages were split into two ancestral stocks in the Paleocene, on north and south of a major geographical gap in the Western Ghats. Our results revealing the existence of eight evolutionarily distinct RLTB lineages calls for the re-determination of conservation targets for these cryptic and endangered taxa.

  17. Morphological and genetic evidence for multiple evolutionary distinct lineages in the endangered and commercially exploited red lined torpedo barbs endemic to the Western Ghats of India.

    Directory of Open Access Journals (Sweden)

    Lijo John

    Full Text Available Red lined torpedo barbs (RLTBS (Cyprinidae: Puntius endemic to the Western Ghats Hotspot of India, are popular and highly priced freshwater aquarium fishes. Two decades of indiscriminate exploitation for the pet trade, restricted range, fragmented populations and continuing decline in quality of habitats has resulted in their 'Endangered' listing. Here, we tested whether the isolated RLTB populations demonstrated considerable variation qualifying to be considered as distinct conservation targets. Multivariate morphometric analysis using 24 size-adjusted characters delineated all allopatric populations. Similarly, the species-tree highlighted a phylogeny with 12 distinct RLTB lineages corresponding to each of the different riverine populations. However, coalescence-based methods using mitochondrial DNA markers identified only eight evolutionarily distinct lineages. Divergence time analysis points to recent separation of the populations, owing to the geographical isolation, more than 5 million years ago, after the lineages were split into two ancestral stocks in the Paleocene, on north and south of a major geographical gap in the Western Ghats. Our results revealing the existence of eight evolutionarily distinct RLTB lineages calls for the re-determination of conservation targets for these cryptic and endangered taxa.

  18. Genetics

    International Nuclear Information System (INIS)

    Hubitschek, H.E.

    1975-01-01

    Progress is reported on the following research projects: genetic effects of high LET radiations; genetic regulation, alteration, and repair; chromosome replication and the division cycle of Escherichia coli; effects of radioisotope decay in the DNA of microorganisms; initiation and termination of DNA replication in Bacillus subtilis; mutagenesis in mouse myeloma cells; lethal and mutagenic effects of near-uv radiation; effect of 8-methoxypsoralen on photodynamic lethality and mutagenicity in Escherichia coli; DNA repair of the lethal effects of far-uv; and near uv irradiation of bacterial cells

  19. QTL mapping based on different genetic systems for essential amino acid contents in cottonseeds in different environments.

    Science.gov (United States)

    Liu, Haiying; Quampah, Alfred; Chen, Jinhong; Li, Jinrong; Huang, Zhuangrong; He, Qiuling; Zhu, Shuijin; Shi, Chunhai

    2013-01-01

    Cottonseeds are rich in various essential amino acids. However, the inheritance of them at molecular level are still not defined across various genetic systems. In the present study, using a newly developed mapping model that can analyze the embryo and maternal main effects as well as QTL × environment interaction effects on quantitative quality trait loci (QTLs) in cottonseeds, a study on QTL located in the tetraploid embryo and tetraploid maternal plant genomes for essential amino acid contents in cottonseeds under different environments was carried out, using the immortal F2 (IF2) populations from a set of 188 recombinant inbred lines derived from an intraspecific hybrid cross of two upland cotton germplasms HS46 and MARKCBUCAG8US-1-88 as experimental materials. The results showed a total of 35 QTLs associated with these quality traits in cottonseeds. Nineteen QTLs were subsequently mapped on chromosome 5, 6 and 8 in sub-A genome and chromosome 15, 18, 22 and 23 in sub-D genome. Eighteen QTLs were also found having QTL × environment (QE) interaction effects. The genetic main effects from QTLs located on chromosomes in the embryo and maternal plant genomes and their QE effects in different environments were all important for these essential amino acids in cottonseeds. The results suggested that the influence of environmental factors on the expression of some QTLs located in different genetic systems should be considered when improving for these amino acids. This study can serve as the foundation for the improvement of these essential amino acids in cottonseeds.

  20. AFLPs reveal different population genetic structure under contrasting environments in the marine snail Nucella lapillus L.

    Directory of Open Access Journals (Sweden)

    Belén Carro

    Full Text Available Dispersal has received growing attention in marine ecology, particularly since evidence obtained with up-to-date techniques challenged the traditional view. The dogwhelk Nucella lapillus L., a sedentary gastropod with direct development, is a good example: dispersal was traditionally assumed to be limited until studies with microsatellites disputed this idea. To shed some light on this controversy, the genetic structure of dogwhelk populations in northwest Spain was investigated with highly polymorphic AFLP markers giving special attention to the influence of hydrodynamic stress. In agreement with the expectations for a poor disperser, our results show a significant genetic structure at regional (<200 km and areal scales (<15 km. However, the spatial genetic structure varied with wave-exposure in the present case study: IBD was evident under sheltered conditions but absent from the exposed area where genetic differentiation was stronger. Our results provide evidence that differences in wave-exposure can exert a detectable influence on the genetic structure of coastal organisms, even in species without a planktonic larva.

  1. Distinct composition of bovine milk from Jersey and Holstein-Friesian cows with good, poor or non-coagulation properties as reflected in protein genetic variants and isoforms

    DEFF Research Database (Denmark)

    Jensen, Hanne Bak; Poulsen, Nina Aagaard; Andersen, Kell Kleiner

    2012-01-01

    , relative to total αS1-CN, along with a lower fraction of glycosylated κ-CN relative to total κ-CN. Thus, apparent variation was observed in the milk and protein composition, in the genetic makeup of the major milk proteins, and in the posttranslational modification level of CN between milk samples...

  2. Analysis of genetic distance between Peruvian Alpaca (Vicugna Pacos showing two distinct fleece phenotypes, Suri and Huacaya, by means of microsatellite markers

    Directory of Open Access Journals (Sweden)

    Carlo Renieri

    2011-10-01

    Full Text Available Two coat phenotypes exist in Alpaca, Huacaya and Suri. The two coats show different fleece structure, textile characteristics and prices on the market. Although present scientific knowledge suggests a simple genetic model of inheritance, there is a tendency to manage and consider the two phenotypes as two different breeds. A 13 microsatellite panel was used in this study to assess genetic distance between Suri and Huacaya alpacas in a sample of non-related animals from two phenotypically pure flocks at the Illpa-Puno experimental station in Quimsachata, Peru. The animals are part of a germplasm established approximately 20 years ago and have been bred separately according to their coat type since then. Genetic variability parameters were also calculated. The data were statistically analyzed using the software Genalex 6.3, Phylip 3.69 and Fstat 2.9.3.2. The sample was tested for Hardy-Weinberg equilibrium (HWE and after strict Bonferroni correction only one locus (LCA37 showed deviation from equilibrium (Ploci associations showed significant disequilibrium. Observed heterozygosis (Ho= 0.766; SE=0.044, expected heterozygosis (He=0.769; SE=0.033, number of alleles (Na=9.667, SE=0.772 and Fixation index (F=0.004; SE=0.036 are comparable to data from previous studies. Measures of genetic distance were 0.06 for Nei’s and 0.03 for Cavalli-Sforza’s. The analysis of molecular variance reported no existing variance between populations. Considering the origin of the animals, their post domestication evolution and the reproductive practices in place, the results do not show genetic differentiation between the two populations for the studied loci.

  3. Methods for detecting interactions between genetic polymorphisms and prenatal environment exposure with a mother-child design.

    Science.gov (United States)

    Wang, Shuang; Zheng, Tian; Chanock, Stephen; Jedrychowski, Wieslaw; Perera, Frederica P

    2010-02-01

    Prenatal exposures such as polycyclic aromatic hydrocarbons and early postnatal environmental exposures are of particular concern because of the heightened susceptibility of the fetus and infant to diverse environmental pollutants. Marked inter-individual variation in response to the same level of exposure was observed in both mothers and their newborns, indicating that susceptibility might be due to genetic factors. With the mother-child pair design, existing methods developed for parent-child trio data or random sample data are either not applicable or not designed to optimally use the information. To take full advantage of this unique design, which provides partial information on genetic transmission and has both maternal and newborn outcome status collected, we developed a likelihood-based method that uses both the maternal and the newborn information together and jointly models gene-environment interactions on maternal and newborn outcomes. Through intensive simulation studies, the proposed method has demonstrated much improved power in detecting gene-environment interactions. The application on a real mother-child pair data from a study conducted in Krakow, Poland, suggested four significant gene-environment interactions after multiple comparisons adjustment. 2009 Wiley-Liss, Inc.

  4. Needle parameter variation of mature black spruce families displaying a genetic x environment interaction in growth

    Science.gov (United States)

    John E. Major; Kurt H. Johnsen; Debby C. Barsi; Moira Campbell

    2013-01-01

    To examine soil moisture stress, light, and genetic effects on individual needle parameters and investigate total needle contribution to productivity, individual and total needle parameter variation were quantified in 32-year-old black spruce from five crown positions from four full-sib families studied previously for drought tolerance and differential productivity on...

  5. Developmental and genetic modulation of arsenic biotransformation: A gene by environment interaction?

    International Nuclear Information System (INIS)

    Meza, Mercedes; Gandolfi, A. Jay; Klimecki, Walter T.

    2007-01-01

    The complexity of arsenic toxicology has confounded the identification of specific pathways of disease causation. One focal point of arsenic research is aimed at fully characterizing arsenic biotransformation in humans, a process that appears to be quite variable, producing a mixture of several arsenic species with greatly differing toxic potencies. In an effort to characterize genetic determinants of variability in arsenic biotransformation, a genetic association study of 135 subjects in western Sonora, Mexico was performed by testing 23 polymorphic sites in three arsenic biotransformation candidate genes. One gene, arsenic 3 methyltransferase (AS3MT), was strongly associated with the ratio of urinary dimethylarsinic acid to monomethylarsonic acid (D/M) in children (7-11 years) but not in adults (18-79 years). Subsequent analyses revealed that the high D/M values associated with variant AS3MT alleles were primarily due to lower levels of monomethylarsonic acid as percent of total urinary arsenic (%MMA5). In light of several reports of arsenic-induced disease being associated with relatively high %MMA5 levels, these findings raise the possibility that variant AS3MT individuals may suffer less risk from arsenic exposure than non-variant individuals. These analyses also provide evidence that, in this population, regardless of AS3MT variant status, children tend to have lower %MMA5 values than adults, suggesting that the global developmental regulation of arsenic biotransformation may interact with genetic variants in metabolic genes to result in novel genetic effects such as those in this report

  6. Fine-mapping the MHC locus in juvenile idiopathic arthritis (JIA) reveals genetic heterogeneity corresponding to distinct adult inflammatory arthritic diseases.

    Science.gov (United States)

    Hinks, A; Bowes, J; Cobb, J; Ainsworth, H C; Marion, M C; Comeau, M E; Sudman, M; Han, B; Becker, M L; Bohnsack, J F; de Bakker, P I W; Haas, J P; Hazen, M; Lovell, D J; Nigrovic, P A; Nordal, E; Punnaro, M; Rosenberg, A M; Rygg, M; Smith, S L; Wise, C A; Videm, V; Wedderburn, L R; Yarwood, A; Yeung, R S M; Prahalad, S; Langefeld, C D; Raychaudhuri, S; Thompson, S D; Thomson, W

    2017-04-01

    Juvenile idiopathic arthritis (JIA) is a heterogeneous group of diseases, comprising seven categories. Genetic data could potentially be used to help redefine JIA categories and improve the current classification system. The human leucocyte antigen (HLA) region is strongly associated with JIA. Fine-mapping of the region was performed to look for similarities and differences in HLA associations between the JIA categories and define correspondences with adult inflammatory arthritides. Dense genotype data from the HLA region, from the Immunochip array for 5043 JIA cases and 14 390 controls, were used to impute single-nucleotide polymorphisms, HLA classical alleles and amino acids. Bivariate analysis was performed to investigate genetic correlation between the JIA categories. Conditional analysis was used to identify additional effects within the region. Comparison of the findings with those in adult inflammatory arthritic diseases was performed. We identified category-specific associations and have demonstrated for the first time that rheumatoid factor (RF)-negative polyarticular JIA and oligoarticular JIA are genetically similar in their HLA associations. We also observe that each JIA category potentially has an adult counterpart. The RF-positive polyarthritis association at HLA-DRB1 amino acid at position 13 mirrors the association in adult seropositive rheumatoid arthritis (RA). Interestingly, the combined oligoarthritis and RF-negative polyarthritis dataset shares the same association with adult seronegative RA. The findings suggest the value of using genetic data in helping to classify the categories of this heterogeneous disease. Mapping JIA categories to adult counterparts could enable shared knowledge of disease pathogenesis and aetiology and facilitate transition from paediatric to adult services. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

  7. Responses to the change in the environment in pairs of male rats genetically selected for activity level.

    Science.gov (United States)

    Franková, S; Tikal, K

    1989-12-01

    Laboratory Wistar strain rats were genetically selected for high (+A) and low (-A) activity level. In thirteen pairs of adult males of the 23rd filial generation reactions to changes in the external environment were studied. The animals were housed in breeding cages four each. Two parallel studies were conducted: in pairs simultaneously placed into a novel environment (NOV), empty cages of the same dimensions as the home cage (HC), in the second, behaviour of the second pair that remained in the HC, after removal of two cage-mates, was tested. Once a minute, for a period of one hour, the type of activity was recorded and noted whether it was an element effected in contact with the partner or without any contact. The animals +A and -A differed in the frequency of various types of activity and immobility, in the ratio between behavioural manifestations shown in or without contact as well as in the response to the type of modified environment. To changes in the situation, whether removed cage-mates from the HC or placed into NOV +A animals reacted with a high wave of environment exploration which gradually habituated. -A rats equally responded with exploration but on a lower level. In +rats we recorded more frequently exploration without contact with the partner in HC and NOV in comparison with -A, more frequent grooming, less immobility in contact and with no contact. Between +A partners there was a greater number of contacts in NOV than in HC whereas in the -A group the incidence of contact did not differ between HC and NOV. ANOVA revealed the influence of factors of genetics and environment and interaction in several behavioural categories. The simple and in time economical method demonstrated the possibility of use for the detection of differences between +A and -A lines even at relatively small changes in the external stimulatory situation.

  8. Environment

    Science.gov (United States)

    2005-01-01

    biodiversity. Consequently, the major environmental challenges facing us in the 21st century include: global climate change , energy, population and food...technological prowess, and security interests. Challenges Global Climate Change – Evidence shows that our environment and the global climate ... urbanization will continue to pressure the regional environment . Although most countries have environmental protection ministries or agencies, a lack of

  9. Genetic liability, prenatal health, stress and family environment: risk factors in the Harvard Adolescent Family High Risk for schizophrenia study.

    Science.gov (United States)

    Walder, Deborah J; Faraone, Stephen V; Glatt, Stephen J; Tsuang, Ming T; Seidman, Larry J

    2014-08-01

    The familial ("genetic") high-risk (FHR) paradigm enables assessment of individuals at risk for schizophrenia based on a positive family history of schizophrenia in first-degree, biological relatives. This strategy presumes genetic transmission of abnormal traits given high heritability of the illness. It is plausible, however, that adverse environmental factors are also transmitted in these families. Few studies have evaluated both biological and environmental factors within a FHR study of adolescents. We conceptualize four precursors to psychosis pathogenesis: two biological (genetic predisposition, prenatal health issues (PHIs)) and two environmental (family environment, stressful life events (SLEs)). Participants assessed between 1998 and 2007 (ages 13-25) included 40 (20F/20M) adolescents at FHR for schizophrenia (FHRs) and 55 (31F/24M) community controls. 'Genetic load' indexed number of affected family members relative to pedigree size. PHI was significantly greater among FHRs, and family cohesion and expressiveness were less (and family conflict was higher) among FHRs; however, groups did not significantly differ in SLE indices. Among FHRs, genetic liability was significantly associated with PHI and family expressiveness. Prenatal and family environmental disruptions are elevated in families with a first-degree relative with schizophrenia. Findings support our proposed 'polygenic neurodevelopmental diathesis-stress model' whereby psychosis susceptibility (and resilience) involves the independent and synergistic confluence of (temporally-sensitive) biological and environmental factors across development. Recognition of biological and social environmental influences across critical developmental periods points to key issues relevant for enhanced identification of psychosis susceptibility, facilitation of more precise models of illness risk, and development of novel prevention strategies. Copyright © 2014 Elsevier B.V. All rights reserved.

  10. Genetic consequences of radioactive pollution of the environment caused by the chernobyl accident for plants populations

    International Nuclear Information System (INIS)

    Shevchenko, V.A.; Abramov, V.I.; Kal'chenko, V.A.; Fedotov, I.S.

    1996-01-01

    Populations of Arabidopsis thaliana Heynh, and Sylvestris L., growing within 30 km of Chernobyl and Bransk region have been analyzed for the frequency of embryonic lethal mutations on arabidopsis and frequency of chlorophill mutations and chromosome aberrations by pine. On pine also have been analyzed rate of mutations at enzyme loci in endosperms of seeds. Dose dependence of the value genetic damage on level of radioactive pollution was observed. Refs. 30, figs. 4, tabs. 6

  11. Genetic diversity and molecular characterization of Saccharomyces cerevisiae strains from winemaking environments

    OpenAIRE

    Schuller, Dorit Elisabeth

    2004-01-01

    Tese de doutoramento em Ciências The principal aim of the present work is to assess the genetic diversity of fermenting Saccharomyces cerevisiae strains found in vineyards belonging to the Vinho Verde Region in order to create a strain collection representing the region’s biodiversity wealth as a basis for future strain selection and improvement programs. Validation of molecular techniques for accurate genotyping is an indispensable prerequisite for biogeographical surveys. Molecular ty...

  12. Epigenetic understanding of gene-environment interactions in psychiatric disorders: a new concept of clinical genetics

    OpenAIRE

    Kubota, Takeo; Miyake, Kunio; Hirasawa, Takae

    2012-01-01

    Abstract Epigenetics is a mechanism that regulates gene expression independently of the underlying DNA sequence, relying instead on the chemical modification of DNA and histone proteins. Although environmental and genetic factors were thought to be independently associated with disorders, several recent lines of evidence suggest that epigenetics bridges these two factors. Epigenetic gene regulation is essential for normal development, thus defects in epigenetics cause various rare congenital ...

  13. Genetic monogamy despite variable ecological conditions and social environment in the cooperatively breeding apostlebird.

    Science.gov (United States)

    Warrington, Miyako H; Rollins, Lee Ann; Raihani, Nichola J; Russell, Andrew F; Griffith, Simon C

    2013-11-01

    Mating strategies may be context-dependent and may vary across ecological and social contexts, demonstrating the role of these factors in driving the variation in genetic polyandry within and among species. Here, we took a longitudinal approach across 5 years (2006-2010), to study the apostlebird (Struthidea cinerea), an Australian cooperatively breeding bird, whose reproduction is affected by ecological "boom and bust" cycles. Climatic variation drives variation in the social (i.e., group sizes, proportion of males and females) and ecological (i.e., plant and insect abundance) context in which mating occurs. By quantifying variation in both social and ecological factors and characterizing the genetic mating system across multiple years using a molecular parentage analysis, we found that the genetic mating strategy did not vary among years despite significant variation in rainfall, driving primary production, and insect abundance, and corresponding variation in social parameters such as breeding group size. Group sizes in 2010, an ecologically good year, were significantly smaller (mean = 5.8 ± 0.9, n = 16) than in the drought affected years, between 2006 and 2008, (mean = 9.1 ± 0.5, n = 63). Overall, apostlebirds were consistently monogamous with few cases of multiple maternity or paternity (8 of 78 nests) across all years.

  14. Radioprotection of the environment: on the context of biodiversity and evolutionary theory. A reference organism has no genetic properties

    International Nuclear Information System (INIS)

    Cedervall, Bjoern

    2008-01-01

    The recent efforts to define a basis for radioprotection of the environment include some concepts and ideas related to various endpoints which need a clarification. This paper focuses on the biodiversity concept and the context of individuals of a species as well as that of the species as a gene pool. A major problem with the ambition to radioprotect biodiversity is the concept 'reference organism' which has no genetic properties and therefore is in contradiction with a real biological species. Biodiversity and the species (gene pool) concept are, just as any other areas of biology, integral parts of evolutionary theory. With the reference organism as a basis no meaningful reasoning can take place which relates data on radioactivity levels or mutations to potential effects on populations or biodiversity. It is therefore suggested that the national and international bodies involved in radioprotection of the environment take advantage of evolutionary theory as a reference frame. (author)

  15. Effect of Genetics, Environment, and Phenotype on the Metabolome of Maize Hybrids Using GC/MS and LC/MS.

    Science.gov (United States)

    Tang, Weijuan; Hazebroek, Jan; Zhong, Cathy; Harp, Teresa; Vlahakis, Chris; Baumhover, Brian; Asiago, Vincent

    2017-06-28

    We evaluated the variability of metabolites in various maize hybrids due to the effect of environment, genotype, phenotype as well as the interaction of the first two factors. We analyzed 480 forage and the same number of grain samples from 21 genetically diverse non-GM Pioneer brand maize hybrids, including some with drought tolerance and viral resistance phenotypes, grown at eight North American locations. As complementary platforms, both GC/MS and LC/MS were utilized to detect a wide diversity of metabolites. GC/MS revealed 166 and 137 metabolites in forage and grain samples, respectively, while LC/MS captured 1341 and 635 metabolites in forage and grain samples, respectively. Univariate and multivariate analyses were utilized to investigate the response of the maize metabolome to the environment, genotype, phenotype, and their interaction. Based on combined percentages from GC/MS and LC/MS datasets, the environment affected 36% to 84% of forage metabolites, while less than 7% were affected by genotype. The environment affected 12% to 90% of grain metabolites, whereas less than 27% were affected by genotype. Less than 10% and 11% of the metabolites were affected by phenotype in forage and grain, respectively. Unsupervised PCA and HCA analyses revealed similar trends, i.e., environmental effect was much stronger than genotype or phenotype effects. On the basis of comparisons of disease tolerant and disease susceptible hybrids, neither forage nor grain samples originating from different locations showed obvious phenotype effects. Our findings demonstrate that the combination of GC/MS and LC/MS based metabolite profiling followed by broad statistical analysis is an effective approach to identify the relative impact of environmental, genetic and phenotypic effects on the forage and grain composition of maize hybrids.

  16. Nature, nurture, and capital punishment: How evidence of a genetic-environment interaction, future dangerousness, and deliberation affect sentencing decisions.

    Science.gov (United States)

    Gordon, Natalie; Greene, Edie

    2018-01-01

    Research has shown that the low-activity MAOA genotype in conjunction with a history of childhood maltreatment increases the likelihood of violent behaviors. This genetic-environment (G × E) interaction has been introduced as mitigation during the sentencing phase of capital trials, yet there is scant data on its effectiveness. This study addressed that issue. In a factorial design that varied mitigating evidence offered by the defense [environmental (i.e., childhood maltreatment), genetic, G × E, or none] and the likelihood of the defendant's future dangerousness (low or high), 600 mock jurors read sentencing phase evidence in a capital murder trial, rendered individual verdicts, and half deliberated as members of a jury to decide a sentence of death or life imprisonment. The G × E evidence had little mitigating effect on sentencing preferences: participants who received the G × E evidence were no less likely to sentence the defendant to death than those who received evidence of childhood maltreatment or a control group that received neither genetic nor maltreatment evidence. Participants with evidence of a G × E interaction were more likely to sentence the defendant to death when there was a high risk of future dangerousness than when there was a low risk. Sentencing preferences were more lenient after deliberation than before. We discuss limitations and future directions. Copyright © 2017 John Wiley & Sons, Ltd.

  17. Genetic similarity of the Hainan medaka populations collected from hyper- and hypo-osmotic environments in northern Vietnam

    Science.gov (United States)

    Hayakawa, Hideki; Le, Quang Dung; Kinoshita, Masato; Takehana, Yusuke; Sakuma, Kei; Takeshima, Hirohiko; Kojima, Shigeaki; Naruse, Kiyoshi; Inoue, Koji

    2015-06-01

    Ricefishes of the genus Oryzias, including Japanese medaka ( O. latipes), are known as excellent model organisms for studies in various fields of science. Some species of the genus inhabit brackish water, and such species are recognized to be useful to investigate physiological phenomena in seawater. However, only a limited number of species have been recorded from brackish waters. In addition, there is no information about the genetic relationship among populations inhabiting sites with different salinities. Here we report the discovery of Oryzias fish in two locations near Haiphong, northern Vietnam, a brackish mangrove planting area and a freshwater pond. A phylogenetic analysis using mitochondrial 12S and 16S ribosomal RNA (rRNA) gene sequences indicated that the fish from the two localities are the same species, Hainan medaka, O. curvinotus. Population genetic analysis using the mitochondrial 12S and 16S rRNA gene sequences revealed a close genetic relationship between the two populations. These results suggest that O. curvinotus is adaptable to both hyperosmotic and hypoosmotic environments. Due to its osmotic adaptability and ease of rearing in the laboratory, this species is expected to become a model for marine environmental and toxicological studies, as well as for studies of osmotic adaptation mechanisms.

  18. A forward genetic screen with a thalamocortical axon reporter mouse yields novel neurodevelopment mutants and a distinct emx2 mutant phenotype

    Directory of Open Access Journals (Sweden)

    Vock Vita M

    2011-01-01

    Full Text Available Abstract Background The dorsal thalamus acts as a gateway and modulator for information going to and from the cerebral cortex. This activity requires the formation of reciprocal topographic axon connections between thalamus and cortex. The axons grow along a complex multistep pathway, making sharp turns, crossing expression boundaries, and encountering intermediate targets. However, the cellular and molecular components mediating these steps remain poorly understood. Results To further elucidate the development of the thalamocortical system, we first created a thalamocortical axon reporter line to use as a genetic tool for sensitive analysis of mutant mouse phenotypes. The TCA-tau-lacZ reporter mouse shows specific, robust, and reproducible labeling of thalamocortical axons (TCAs, but not the overlapping corticothalamic axons, during development. Moreover, it readily reveals TCA pathfinding abnormalities in known cortical mutants such as reeler. Next, we performed an unbiased screen for genes involved in thalamocortical development using random mutagenesis with the TCA reporter. Six independent mutant lines show aberrant TCA phenotypes at different steps of the pathway. These include ventral misrouting, overfasciculation, stalling at the corticostriatal boundary, and invasion of ectopic cortical cell clusters. An outcross breeding strategy coupled with a genomic panel of single nucleotide polymorphisms facilitated genetic mapping with small numbers of mutant mice. We mapped a ventral misrouting mutant to the Emx2 gene, and discovered that some TCAs extend to the olfactory bulbs in this mutant. Mapping data suggest that other lines carry mutations in genes not previously known for roles in thalamocortical development. Conclusions These data demonstrate the feasibility of a forward genetic approach to understanding mammalian brain morphogenesis and wiring. A robust axonal reporter enabled sensitive analysis of a specific axon tract inside the

  19. Male Reproductive Disorders and Fertility Trends: Influences of Environment and Genetic Susceptibility

    Science.gov (United States)

    Skakkebaek, Niels E.; Rajpert-De Meyts, Ewa; Buck Louis, Germaine M.; Toppari, Jorma; Andersson, Anna-Maria; Eisenberg, Michael L.; Jensen, Tina Kold; Jørgensen, Niels; Swan, Shanna H.; Sapra, Katherine J.; Ziebe, Søren; Priskorn, Lærke; Juul, Anders

    2015-01-01

    It is predicted that Japan and European Union will soon experience appreciable decreases in their populations due to persistently low total fertility rates (TFR) below replacement level (2.1 child per woman). In the United States, where TFR has also declined, there are ethnic differences. Caucasians have rates below replacement, while TFRs among African-Americans and Hispanics are higher. We review possible links between TFR and trends in a range of male reproductive problems, including testicular cancer, disorders of sex development, cryptorchidism, hypospadias, low testosterone levels, poor semen quality, childlessness, changed sex ratio, and increasing demand for assisted reproductive techniques. We present evidence that several adult male reproductive problems arise in utero and are signs of testicular dysgenesis syndrome (TDS). Although TDS might result from genetic mutations, recent evidence suggests that it most often is related to environmental exposures of the fetal testis. However, environmental factors can also affect the adult endocrine system. Based on our review of genetic and environmental factors, we conclude that environmental exposures arising from modern lifestyle, rather than genetics, are the most important factors in the observed trends. These environmental factors might act either directly or via epigenetic mechanisms. In the latter case, the effects of exposures might have an impact for several generations post-exposure. In conclusion, there is an urgent need to prioritize research in reproductive physiology and pathophysiology, particularly in highly industrialized countries facing decreasing populations. We highlight a number of topics that need attention by researchers in human physiology, pathophysiology, environmental health sciences, and demography. PMID:26582516

  20. Genetics, environment, and asthma associated with celiac disease in the extended family of an affected child.

    Science.gov (United States)

    Sigala-Robles, R; Aguayo-Patrón, S V; Calderón de la Barca, A M

    2017-11-18

    Celiac disease (CD) is an autoimmune enteropathy associated with gluten ingestion. In extended families of celiac patients that live in close proximity of one another, shared genetic and environmental factors can predispose them to CD. The aim of this study was to provide evidence about the genetic and environmental factors involved in the development of CD in the extended family of a pediatric patient. The medical history, environmental conditions, and participant weight, height, and peripheral blood samples were evaluated. The HLA-DQ2/DQ8 haplotypes were genotyped through qPCR testing and the IgA anti-gliadin and anti-transglutaminase antibodies were quantified using the ELISA test. Twelve close-living maternal relatives of the index case participated in the study. Eight of them presented with the HLA-DQ2 haplotype, inherited from the grandfather, and 7/12 and 9/12 were positive for IgA anti-gliadin and IgA anti-transglutaminase antibodies, respectively. The main intestinal symptoms stated by the participants were abdominal bloating, excess flatulence, constipation, and gastroesophageal reflux. The most frequent extra-intestinal symptoms were fatigue, stress, and anxiety. In addition, 6/13 participants had bronchial asthma. The extended family living in close proximity of one another shared a genetic predisposition, environmental conditions, and asthma, which could have predisposed them to celiac disease. Copyright © 2017 Asociación Mexicana de Gastroenterología. Publicado por Masson Doyma México S.A. All rights reserved.

  1. A genetic algorithm solution for the operation of green LTE networks with energy and environment considerations

    KAUST Repository

    Ghazzai, Hakim

    2012-01-01

    The Base Station (BS) sleeping strategy has become a well-known technique to achieve energy savings in cellular networks by switching off redundant BSs mainly for lightly loaded networks. Besides, the exploitation of renewable energies, as additional power sources in smart grids, becomes a real challenge to network operators to reduce power costs. In this paper, we propose a method based on genetic algorithms that decreases the energy consumption of a Long-Term Evolution (LTE) cellular network by not only shutting down underutilized BSs but also by optimizing the amounts of energy procured from the smart grid without affecting the desired Quality of Service. © 2012 Springer-Verlag.

  2. Genetic variation in TAS1R2 (Ile191Val) is associated with consumption of sugars in overweight and obese individuals in 2 distinct populations.

    Science.gov (United States)

    Eny, Karen M; Wolever, Thomas Ms; Corey, Paul N; El-Sohemy, Ahmed

    2010-12-01

    Taste is an important determinant of food consumption, and genetic variations in the sweet taste receptor subunit TAS1R2 may contribute to interindividual variations in sugar consumption. We determined whether Ser9Cys and Ile191Val variations in TAS1R2 were associated with differences in the consumption of sugars in 2 populations. Population 1 included 1037 diabetes-free young adults in whom we assessed dietary intake by using a 1-mo, 196-item food-frequency questionnaire. Population 2 consisted of 100 individuals with type 2 diabetes with dietary intakes assessed by using 2 sets of 3-d food records administered 2 wk apart. Dietary counseling was provided between food records 1 and 2. Dietary intakes between genotypes were compared by using analysis of covariance adjusted for potential confounders. In population 1, a significant Ile191Val × body mass index (BMI; in kg/m²) interaction was detected for the consumption of sugars, and the effect of genotype was significant only in individuals with a BMI ≥ 25 (n = 205). In comparison with individuals homozygous for the Ile allele, Val carriers consumed fewer sugars (122 ± 6 compared with 103 ± 6 g sugar/d, respectively; P = 0.01). Regression estimates that associated BMI with total sugar consumption by Ile/Ile and Val-carrier genotype intersected at a BMI of 23.5. In population 2, Val carriers also consumed less sugar than did individuals with the Ile/Ile genotype (99 ± 6 compared with 83 ± 6 g sugar/d, respectively; P = 0.04) on food record 2, and sugar was the only macronutrient that decreased significantly (-9 ± 4 g sugar/d, P = 0.02) in Val carriers who received dietary counseling. Our findings show that a genetic variation in TAS1R2 affects habitual consumption of sugars and may contribute to interindividual differences in changing behaviors in response to dietary counseling.

  3. Expected genetic gain and genotype- environment interaction in Acacia mangium in the northern region of Costa Rica

    Directory of Open Access Journals (Sweden)

    Benjamín Pavlotzky

    2014-12-01

    Full Text Available Two Acacia mangium Willd. progeny tests were evaluated, pursuing an increment in the profitability of commercial plantations. The 25 open-pollinated families were established in Los Chiles and San Carlos, northern region of Costa Rica, in year 2006, and evaluated in 2007 and in 2010. Genetic material came from plus tree selections obtained by GENFORES, a costarican tree-improvement and gene-conservation cooperative. In each trial, families were represented by 48 progenies, planted in 4 pairs randomly distributed within each of the 6 blocks. In 2010, DBH, survival rate, commercial number of logs per tree, forking, forking height and log quality in the first 4 logs, were evaluated. Based on these measurements, wood commercial volume per tree and per hectare were estimated. Data was analyzed with SELEGEN software from EMBRAPA, Brasil, in order to determine all genetic parameters of the breeding population. All traits evaluated showed family mean heritability values over 0.46. Genetic gain in commercial volume per hectare was estimated as 55.8%, when selecting as parents the 2 best individuals from the top 12 families, which would correspond to an expected commercial volume.ha -1 , at 4 years age, of 78.93 m 3 .ha -1 (around 20 m 3 .ha -1 .year -1 . The 2 Colombian provenances were significantly superior in growth to the rest of the evaluated materials. No significant gene-environment interaction was observed between both sites. Genetic correlations among evaluated traits showed that diameter growth rate is expressed early in this tree species, thus could be used in shortening future selections.

  4. Macro-environment of breast carcinoma: frequent genetic alterations in the normal appearing skins of patients with breast cancer.

    Science.gov (United States)

    Moinfar, Farid; Beham, Alfred; Friedrich, Gerhard; Deutsch, Alexander; Hrzenjak, Andelko; Luschin, Gero; Tavassoli, Fattaneh A

    2008-05-01

    Genetic abnormalities in microenvironmental tissues with subsequent alterations of reciprocal interactions between epithelial and mesenchymal cells play a key role in the breast carcinogenesis. Although a few reports have demonstrated abnormal fibroblastic functions in normal-appearing fibroblasts taken from the skins of breast cancer patients, the genetic basis of this phenomenon and its implication for carcinogenesis are unexplored. We analyzed 12 mastectomy specimens showing invasive ductal carcinomas. In each case, morphologically normal epidermis and dermis, carcinoma, normal stroma close to carcinoma, and stroma at a distant from carcinoma were microdissected. Metastatic-free lymphatic tissues from lymph nodes served as a control. Using PCR, DNA extracts were examined with 11 microsatellite markers known for a high frequency of allelic imbalances in breast cancer. Losses of heterozygosity and/or microsatellite instability were detected in 83% of the skin samples occurring either concurrently with or independently from the cancerous tissues. In 80% of these cases at least one microsatellite marker displayed loss of heterozygosity or microsatellite instability in the skin, which was absent in carcinoma. A total of 41% of samples showed alterations of certain loci observed exclusively in the carcinoma but not in the skin compartments. Our study suggests that breast cancer is not just a localized genetic disorder, but rather part of a larger field of genetic alterations/instabilities affecting multiple cell populations in the organ with various cellular elements, ultimately contributing to the manifestation of the more 'localized' carcinoma. These data indicate that more global assessment of tumor micro- and macro-environment is crucial for our understanding of breast carcinogenesis.

  5. Genetic Dissection of QTL Associated with Grain Yield in Diverse Environments

    Directory of Open Access Journals (Sweden)

    Junli Zhang

    2014-12-01

    Full Text Available Wheat (Triticum aestivum L. breeding programs strive to increase grain yield; however, the progress is hampered due to its quantitative inheritance, low heritability, and confounding environmental effects. In the present study, a winter wheat population of 159 recombinant inbred lines (RILs was evaluated in six trials under rainfed, terminal drought, and fully-irrigated conditions, over four years. Quantitative trait locus/loci (QTL mapping was conducted for grain yield main effect (GY and the genotype × environment interaction (GEI effect. A total of 17 QTL were associated with GY and 13 QTL associated with GEI, and nine QTL were mapped in the flanking chromosomal regions for both GY and GEI. One major QTL Q.Gy.ui-1B.2, explaining up to 22% of grain yield, was identified in all six trials. Besides the additive effect of QTL associated with GY, interactions among QTL (QTL × QTL interaction, QTL × environment, and QTL × QTL × environment were also observed. When combining the interaction effects, QTL Q.Gy.ui-1B.2 along with other QTL explained up to 52% of the variation in grain yield over the six trials. This study suggests that QTL mapping of complex traits such as grain yield should include interaction effects of QTL and environments in marker-assisted selection.

  6. Genetic analysis of nile tilapia (oreochromis niloticus) selection line reared in two input environments.

    NARCIS (Netherlands)

    Khaw, H.L.; Bovenhuis, H.; Ponzoni, R.W.; Rezk, M.A.; Charo, H.; Komen, J.

    2009-01-01

    Ascertaining the appropriate selection environment for Nile tilapia (Oreochromis niloticus) in Africa is a critical issue. Two data sets derived from two selection lines originating from a common base population were analysed in this study. The lines were selected in two different input

  7. Commentary: Gene-Environment Interplay in the Context of Genetics, Epigenetics, and Gene Expression.

    Science.gov (United States)

    Kramer, Douglas A.

    2005-01-01

    Objective: To comment on the article in this issue of the Journal by Professor Michael Rutter, "Environmentally Mediated Risks for Psychopathology: Research Strategies and Findings," in the context of current research findings on gene-environment interaction, epigenetics, and gene expression. Method: Animal and human studies are reviewed that…

  8. The release of genetically modified crops into the environment - Part II. Overview of ecological risk assessment

    NARCIS (Netherlands)

    Conner, A.J.; Glare, T.R.; Nap, J.P.H.

    2003-01-01

    Despite numerous future promises, there is a multitude of concerns about the impact of GM crops on the environment. Key issues in the environmental assessment of GM crops are putative invasiveness, vertical or horizontal gene flow, other ecological impacts, effects on biodiversity and the impact of

  9. Population subdivision in marine environments: the contributions of biogeography, geographical distance and discontinuous habitat to genetic differentiation in a blennioid fish, Axoclinus nigricaudus.

    Science.gov (United States)

    Riginos, C; Nachman, M W

    2001-06-01

    The relative importance of factors that may promote genetic differentiation in marine organisms is largely unknown. Here, contributions to population structure from a biogeographic boundary, geographical distance and the distribution of suitable habitat were investigated in Axoclinus nigricaudus, a small subtidal rock-reef fish, throughout its range in the Gulf of California. A 408-bp fragment of the mitochondrial control region was sequenced from 105 individuals. Variation was significantly partitioned between 28 of 36 possible combinations of population pairs. Phylogenetic analyses, hierarchical analyses of variance and a modified Mantel test substantiated a major break between two putative biogeographic regions. This genetic discontinuity coincides with an abrupt change in ecological characteristics, including temperature and salinity, but does not coincide with known oceanographic circulation patterns or any known historic barriers. There was an overall relationship of increasing genetic distance with increasing geographical distance between population pairs, in a manner consistent with isolation-by-distance. A significant habitat-by-geographical-distance interaction term indicated that, for a given geographical distance, populations separated by discontinuous habitat (sand) are more distinct genetically than are populations separated by continuous habitat (rock). In addition, populations separated by deep open waters were more genetically distinct than populations separated by continuous habitat (rock). These results indicate that levels of genetic differentiation among populations of A. nigricaudus cannot be explained by a single factor, but are due to the combined influences of biogeography, geographical distance and availability of suitable habitat.

  10. Genetic parameters for egg and related characteristics of white Leghorn hens in a subtropical environment

    Directory of Open Access Journals (Sweden)

    Hani M. Sabri

    1999-06-01

    Full Text Available Estimates of heritability and phenotypic and genetic correlations between egg number, weight, specific gravity, mass, and estimated shell weight were obtained, along with phenotypic and genetic correlations of specific gravity and weight with body weight, weight change, metabolizable energy intake, residual feed consumption, and weight and age at sexual maturity. Data were from 350 White Leghorn hens by 50 sires and 175 dams. Heritabilities of the egg traits ranged from 0.20 to 0.55, increasing with age of bird from 26 to 54 weeks of age. Their standard errors ranged from 0.07 (all data to 0.17 (26 to 29 weeks. Phenotypic correlations ranged from 0.80 to -0.13, and genetic correlations from 0.91 to -0.27, depending on egg trait. The highest phenotypic and genetic correlations were between egg number and mass. Genetic correlations for specific gravity and estimated shell weight were, with body weight, -0.02 and 0.56; weight change, 0.29 and 0.44; daily metabolizable energy intake, -0.10 and 0.33; residual consumption, -0.16 and 0.11; age at sexual maturity, -0.61 and -0.46, and weight at sexual maturity, 0.02 and 0.63. Results should contribute to the design of efficient selection programs for economically important traits in hens.Estimativas de herdabilidade e correlações fenotípicas e genéticas entre o número de ovos, peso, gravidade específica, massa e peso estimado da casca foram obtidas, assim como correlações fenotípicas e genéticas de gravidade específica e peso com peso corporal, alterações ponderais, ingestão de energia metabolizável, consumo alimentar residual e peso e idade ao atingir a maturidade sexual. Os dados foram obtidos de 350 galinhas da raça Leghorn Branca obtidas de 50 pais e 175 mães. A herdabilidade dos caracteres dos ovos variou de 0,20 a 0,55, aumentando com a idade da ave de 26 a 54 semanas. O desvio padrão variou de 0,07 (todos os dados a 0,17 (26 a 29 semanas. As correlações fenotípicas variaram

  11. Longitudinal study of distributions of similar antimicrobial-resistant Salmonella serovars in pigs and their environment in two distinct swine production systems.

    Science.gov (United States)

    Keelara, Shivaramu; Scott, H Morgan; Morrow, William M; Gebreyes, Wondwossen A; Correa, Maria; Nayak, Rajesh; Stefanova, Rossina; Thakur, Siddhartha

    2013-09-01

    The aim of this longitudinal study was to determine and compare the prevalences and genotypic profiles of antimicrobial-resistant (AR) Salmonella isolates from pigs reared in antimicrobial-free (ABF) and conventional production systems at farm, at slaughter, and in their environment. We collected 2,889 pig fecal and 2,122 environmental (feed, water, soil, lagoon, truck, and floor swabs) samples from 10 conventional and eight ABF longitudinal cohorts at different stages of production (farrowing, nursery, finishing) and slaughter (postevisceration, postchill, and mesenteric lymph nodes [MLN]). In addition, we collected 1,363 carcass swabs and 205 lairage and truck samples at slaughter. A total of 1,090 Salmonella isolates were recovered from the samples; these were isolated with a significantly higher prevalence in conventionally reared pigs (4.0%; n = 66) and their environment (11.7%; n = 156) than in ABF pigs (0.2%; n = 2) and their environment (0.6%; n = 5) (P antimicrobial resistance (AR) were exhibited to tetracycline (71%), sulfisoxazole (42%), and streptomycin (17%). Multidrug resistance (resistance to ≥ 3 antimicrobials; MDR) was detected in 27% (n = 254) of the Salmonella isolates from the conventional system. Our study reports a low prevalence of Salmonella in both production systems in pigs on farms, while a higher prevalence was detected among the carcasses at slaughter. The dynamics of Salmonella prevalence in pigs and carcasses were reciprocated in the farm and slaughter environment, clearly indicating an exchange of this pathogen between the pigs and their surroundings. Furthermore, the phenotypic and genotypic fingerprint profile results underscore the potential role played by environmental factors in dissemination of AR Salmonella to pigs.

  12. The ARG1-LIKE2 gene of Arabidopsis functions in a gravity signal transduction pathway that is genetically distinct from the PGM pathway

    Science.gov (United States)

    Guan, Changhui; Rosen, Elizabeth S.; Boonsirichai, Kanokporn; Poff, Kenneth L.; Masson, Patrick H.

    2003-01-01

    The arl2 mutants of Arabidopsis display altered root and hypocotyl gravitropism, whereas their inflorescence stems are fully gravitropic. Interestingly, mutant roots respond like the wild type to phytohormones and an inhibitor of polar auxin transport. Also, their cap columella cells accumulate starch similarly to wild-type cells, and mutant hypocotyls display strong phototropic responses to lateral light stimulation. The ARL2 gene encodes a DnaJ-like protein similar to ARG1, another protein previously implicated in gravity signal transduction in Arabidopsis seedlings. ARL2 is expressed at low levels in all organs of seedlings and plants. arl2-1 arg1-2 double mutant roots display kinetics of gravitropism similar to those of single mutants. However, double mutants carrying both arl2-1 and pgm-1 (a mutation in the starch-biosynthetic gene PHOSPHOGLUCOMUTASE) at the homozygous state display a more pronounced root gravitropic defect than the single mutants. On the other hand, seedlings with a null mutation in ARL1, a paralog of ARG1 and ARL2, behave similarly to the wild type in gravitropism and other related assays. Taken together, the results suggest that ARG1 and ARL2 function in the same gravity signal transduction pathway in the hypocotyl and root of Arabidopsis seedlings, distinct from the pathway involving PGM.

  13. Transgenerational latent early-life associated regulation unites environment and genetics across generations.

    Science.gov (United States)

    Lahiri, Debomoy K; Maloney, Bryan; Bayon, Baindu L; Chopra, Nipun; White, Fletcher A; Greig, Nigel H; Nurnberger, John I

    2016-03-01

    The origin of idiopathic diseases is still poorly understood. The latent early-life associated regulation (LEARn) model unites environmental exposures and gene expression while providing a mechanistic underpinning for later-occurring disorders. We propose that this process can occur across generations via transgenerational LEARn (tLEARn). In tLEARn, each person is a 'unit' accumulating preclinical or subclinical 'hits' as in the original LEARn model. These changes can then be epigenomically passed along to offspring. Transgenerational accumulation of 'hits' determines a sporadic disease state. Few significant transgenerational hits would accompany conception or gestation of most people, but these may suffice to 'prime' someone to respond to later-life hits. Hits need not produce symptoms or microphenotypes to have a transgenerational effect. Testing tLEARn requires longitudinal approaches. A recently proposed longitudinal epigenome/envirome-wide association study would unite genetic sequence, epigenomic markers, environmental exposures, patient personal history taken at multiple time points and family history.

  14. Influence of ROBO1 and RORA on risk of age-related macular degeneration reveals genetically distinct phenotypes in disease pathophysiology.

    Directory of Open Access Journals (Sweden)

    Gyungah Jun

    Full Text Available ROBO1 is a strong candidate gene for age-related macular degeneration (AMD based upon its location under a linkage peak on chromosome 3p12, its expression pattern, and its purported function in a pathway that includes RORA, a gene previously associated with risk for neovascular AMD. Previously, we observed that expression of ROBO1 and RORA is down-regulated among wet AMD cases, as compared to their unaffected siblings. Thus, we hypothesized that contribution of association signals in ROBO1, and interaction between these two genes may be important for both wet and dry AMD. We evaluated association of 19 single nucleotide polymorphisms (SNPs in ROBO1 with wet and dry stages of AMD in a sibling cohort and a Greek case-control cohort containing 491 wet AMD cases, 174 dry AMD cases and 411 controls. Association signals and interaction results were replicated in an independent prospective cohort (1070 controls, 164 wet AMD cases, 293 dry AMD cases. The most significantly associated ROBO1 SNPs were rs1387665 under an additive model (meta P = 0.028 for wet AMD and rs9309833 under a recessive model (meta P = 6 × 10(-4 for dry AMD. Further analyses revealed interaction between ROBO1 rs9309833 and RORA rs8034864 for both wet and dry AMD (interaction P<0.05. These studies were further supported by whole transcriptome expression profile studies from 66 human donor eyes and chromatin immunoprecipitation assays from mouse retinas. These findings suggest that distinct ROBO1 variants may influence the risk of wet and dry AMD, and the effects of ROBO1 on AMD risk may be modulated by RORA variants.

  15. Adolescent Age Moderates Genetic and Environmental Influences on Parent-Adolescent Positivity and Negativity: Implications for Genotype-Environment Correlation

    Science.gov (United States)

    Marceau, Kristine; Knopik, Valerie S.; Neiderhiser, Jenae M.; Lichtenstein, Paul; Spotts, Erica L.; Ganiban, Jody M.; Reiss, David

    2015-01-01

    In the present study we examined how genotype-environment correlation processes differ as a function of adolescent age. We tested whether adolescent age moderates genetic and environmental influences on positivity and negativity in mother-adolescent and father-adolescent relationships using parallel samples of twin parents from the Twin and Offspring Study in Sweden and twin/sibling adolescents from the Nonshared Environment in Adolescent Development Study. We inferred differences in the role of passive and non-passive genotype-environment correlation based on biometric moderation findings. Findings indicated that non-passive rGE played a stronger role for positivity in mother- and father- adolescent relationships in families with older adolescents than families with younger adolescents, and that passive rGE played a stronger role for positivity in the mother-adolescent relationship in families with younger adolescents than in families with older adolescents. Implications of these findings for the timing and targeting of interventions on family relationships are discussed. PMID:25924807

  16. Application of multi-objective optimization based on genetic algorithm for sustainable strategic supplier selection under fuzzy environment

    Directory of Open Access Journals (Sweden)

    Muhammad Hashim

    2017-05-01

    Full Text Available Purpose:  The incorporation of environmental objective into the conventional supplier selection practices is crucial for corporations seeking to promote green supply chain management (GSCM. Challenges and risks associated with green supplier selection have been broadly recognized by procurement and supplier management professionals. This paper aims to solve a Tetra “S” (SSSS problem based on a fuzzy multi-objective optimization with genetic algorithm in a holistic supply chain environment. In this empirical study, a mathematical model with fuzzy coefficients is considered for sustainable strategic supplier selection (SSSS problem and a corresponding model is developed to tackle this problem. Design/methodology/approach: Sustainable strategic supplier selection (SSSS decisions are typically multi-objectives in nature and it is an important part of green production and supply chain management for many firms. The proposed uncertain model is transferred into deterministic model by applying the expected value mesurement (EVM and genetic algorithm with weighted sum approach for solving the multi-objective problem. This research focus on a multi-objective optimization model for minimizing lean cost, maximizing sustainable service and greener product quality level. Finally, a mathematical case of textile sector is presented to exemplify the effectiveness of the proposed model with a sensitivity analysis. Findings: This study makes a certain contribution by introducing the Tetra ‘S’ concept in both the theoretical and practical research related to multi-objective optimization as well as in the study of sustainable strategic supplier selection (SSSS under uncertain environment. Our results suggest that decision makers tend to select strategic supplier first then enhance the sustainability. Research limitations/implications: Although the fuzzy expected value model (EVM with fuzzy coefficients constructed in present research should be helpful for

  17. Application of multi-objective optimization based on genetic algorithm for sustainable strategic supplier selection under fuzzy environment

    Energy Technology Data Exchange (ETDEWEB)

    Hashim, M.; Nazam, M.; Yao, L.; Baig, S.A.; Abrar, M.; Zia-ur-Rehman, M.

    2017-07-01

    The incorporation of environmental objective into the conventional supplier selection practices is crucial for corporations seeking to promote green supply chain management (GSCM). Challenges and risks associated with green supplier selection have been broadly recognized by procurement and supplier management professionals. This paper aims to solve a Tetra “S” (SSSS) problem based on a fuzzy multi-objective optimization with genetic algorithm in a holistic supply chain environment. In this empirical study, a mathematical model with fuzzy coefficients is considered for sustainable strategic supplier selection (SSSS) problem and a corresponding model is developed to tackle this problem. Design/methodology/approach: Sustainable strategic supplier selection (SSSS) decisions are typically multi-objectives in nature and it is an important part of green production and supply chain management for many firms. The proposed uncertain model is transferred into deterministic model by applying the expected value mesurement (EVM) and genetic algorithm with weighted sum approach for solving the multi-objective problem. This research focus on a multi-objective optimization model for minimizing lean cost, maximizing sustainable service and greener product quality level. Finally, a mathematical case of textile sector is presented to exemplify the effectiveness of the proposed model with a sensitivity analysis. Findings: This study makes a certain contribution by introducing the Tetra ‘S’ concept in both the theoretical and practical research related to multi-objective optimization as well as in the study of sustainable strategic supplier selection (SSSS) under uncertain environment. Our results suggest that decision makers tend to select strategic supplier first then enhance the sustainability. Research limitations/implications: Although the fuzzy expected value model (EVM) with fuzzy coefficients constructed in present research should be helpful for solving real world

  18. Application of multi-objective optimization based on genetic algorithm for sustainable strategic supplier selection under fuzzy environment

    International Nuclear Information System (INIS)

    Hashim, M.; Nazam, M.; Yao, L.; Baig, S.A.; Abrar, M.; Zia-ur-Rehman, M.

    2017-01-01

    The incorporation of environmental objective into the conventional supplier selection practices is crucial for corporations seeking to promote green supply chain management (GSCM). Challenges and risks associated with green supplier selection have been broadly recognized by procurement and supplier management professionals. This paper aims to solve a Tetra “S” (SSSS) problem based on a fuzzy multi-objective optimization with genetic algorithm in a holistic supply chain environment. In this empirical study, a mathematical model with fuzzy coefficients is considered for sustainable strategic supplier selection (SSSS) problem and a corresponding model is developed to tackle this problem. Design/methodology/approach: Sustainable strategic supplier selection (SSSS) decisions are typically multi-objectives in nature and it is an important part of green production and supply chain management for many firms. The proposed uncertain model is transferred into deterministic model by applying the expected value mesurement (EVM) and genetic algorithm with weighted sum approach for solving the multi-objective problem. This research focus on a multi-objective optimization model for minimizing lean cost, maximizing sustainable service and greener product quality level. Finally, a mathematical case of textile sector is presented to exemplify the effectiveness of the proposed model with a sensitivity analysis. Findings: This study makes a certain contribution by introducing the Tetra ‘S’ concept in both the theoretical and practical research related to multi-objective optimization as well as in the study of sustainable strategic supplier selection (SSSS) under uncertain environment. Our results suggest that decision makers tend to select strategic supplier first then enhance the sustainability. Research limitations/implications: Although the fuzzy expected value model (EVM) with fuzzy coefficients constructed in present research should be helpful for solving real world

  19. Anticitrullinated protein/peptide antibody multiplexing defines an extended group of ACPA-positive rheumatoid arthritis patients with distinct genetic and environmental determinants.

    Science.gov (United States)

    Rönnelid, Johan; Hansson, Monika; Mathsson-Alm, Linda; Cornillet, Martin; Reed, Evan; Jakobsson, Per-Johan; Alfredsson, Lars; Holmdahl, Rikard; Skriner, Karl; Serre, Guy; Lundberg, Karin; Klareskog, Lars

    2018-02-01

    The second generation anticycliccitrullinated peptide (anti-CCP2) assay detects the majority but not all anticitrullinated protein/peptide antibodies (ACPA). Anti-CCP2-positive rheumatoid arthritis (RA) is associated with HLA-DRB1* shared epitope (SE) alleles and smoking. Using a multiplex assay to detect multiple specific ACPA, we have investigated the fine specificity of individual ACPA responses and the biological impact of additional ACPA reactivity among anti-CCP2-negative patients. We investigated 2825 patients with RA and 551 healthy controls with full data on anti-CCP2, HLA-DRB1* alleles and smoking history concerning reactivity against 16 citrullinated peptides and arginine control peptides with a multiplex array. The prevalence of the 16 ACPA specificities ranged from 9% to 58%. When reactivity to arginine peptides was subtracted, the mean diagnostic sensitivity increased by 3.2% with maintained 98% specificity. Of the anti-CCP2-negative patients, 16% were found to be ACPA positive. All ACPA specificities associated with SE, and all but one with smoking. Correction for arginine reactivity also conveyed a stronger association with SE for 13/16 peptides. Importantly, when all ACPA specificities were analysed together, SE and smoking associated with RA in synergy among ACPA positive, but not among ACPA-negative subjects also in the anti-CCP2-negative subset. Multiplexing detects an enlarged group of ACPA-positive but anti-CCP2-negative patients with genetic and environmental attributes previously assigned to anti-CCP2-positive patients. The individual correction for arginine peptide reactivity confers both higher diagnostic sensitivity and stronger association to SE than gross ACPA measurement. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  20. Digestive efficiency in rabbit does according to environment and genetic type

    DEFF Research Database (Denmark)

    Savietto, D; Blas, E; Cervera, C

    2012-01-01

    subjected to three environmental conditions: NC, females housed under normal conditions (14 to 20oC) and fed with a control diet (333 g NDF/kg DM); HC, females housed under heat conditions (25 to 35oC) and fed with the control diet; or NF, females housed under normal conditions and fed with a fibrous diet......-partum). The environment affected all variables analysed. In general, heat conditions reduced the daily feed intake (around -30%; Pdiet led to lower DE intake (-217 kJ/d; P.... When receiving fibrous diet, LP females showed a higher increment in daily DM intake (65.6 g/d; P

  1. GENETIC DIVERSITY IN ARABICA COFFEE GROWN IN POTASSIUM-CONSTRAINED ENVIRONMENT

    Directory of Open Access Journals (Sweden)

    Waldênia de Melo Moura

    2015-02-01

    Full Text Available Potassium is a source of non-renewable natural resource, and is used in large quantities in coffee fertilization through basically imported formulations in the form of potassium chloride. An alternative to make production systems more sustainable would be obtaining cultivars more efficient in the use of this nutrient. This study aimed to evaluate the genetic diversity among 20 cultivars of coffee, in conditions of low availability of potassium to identify the best combinations for composing future populations to be used in breeding programs. The experiment was arranged in a randomized block design with three replications of nutrient solution. Agronomic characteristics and efficiencies of rooting, absorption, translocation, biomass production and potassium utilization were evaluated. The clustering analysis was based on the unweighted pair group method with arithmetic mean clustering algorithm (UPGMA and canonical variables. Variability was observed for most treatments. The multivariate procedures produced similar discrimination of genotypes, with the formation of five groups. Hybridizations between the cultivar Icatu Precoce IAC 3283 with cultivars Catuaí Amarelo IAC 62, Araponga MG1, Caturra Vermelho IAC 477, Catuaí Vermelho IAC 15, Rubi MG 1192 and Catucaí 785/15, and between the cultivar Tupi IAC 1669-33 with cultivars Icatu Vermelho IAC 4045, Acaiá Cerrado MG 1474 and Oeiras MG 6851 are the most promising for obtaining segregating populations or heterotic hybrids in breeding programs aiming more efficiency in potassium utilization.

  2. Physiological Aspects of Female Fertility: Role of the Environment, Modern Lifestyle, and Genetics.

    Science.gov (United States)

    Hart, Roger J

    2016-07-01

    Across the Western World there is an increasing trend to postpone childbearing. Consequently, the negative influence of age on oocyte quality may lead to a difficulty in conceiving for many couples. Furthermore, lifestyle factors may exacerbate a couple's difficulty in conceiving due mainly to the metabolic influence of obesity; however, the negative impacts of low peripheral body fat, excessive exercise, the increasing prevalence of sexually transmitted diseases, and smoking all have significant negative effects on fertility. Other factors that impede conception are the perceived increasing prevalence of the polycystic ovary syndrome, which is further exacerbated by obesity, and the presence of uterine fibroids and endometriosis (a progressive pelvic inflammatory disorder) which are more prevalent in older women. A tendency for an earlier sexual debut and to have more sexual partners has led to an increase in sexually transmitted diseases. In addition, there are several genetic influences that may limit the number of oocytes within the ovary; consequently, by postponing attempts at childbearing, a limitation of oocyte number may become evident, whereas in previous generations with earlier conception this potentially reduced reproductive life span did not manifest in infertility. Environmental influences on reproduction are under increasing scrutiny. Although firm evidence is lacking however, dioxin exposure may be linked to endometriosis, phthalate exposure may influence ovarian reserve, and bisphenol A may interfere with oocyte development and maturation. However, chemotherapy or radiotherapy is recognized to lead to ovarian damage and predispose the woman to ovarian failure. Copyright © 2016 the American Physiological Society.

  3. Genetic Diversity in Salmonella Isolates from Ducks and their Environments in Penang, Malaysia using Enterobacterial Repetitive Intergenic Consensus

    Directory of Open Access Journals (Sweden)

    Frederick Adzitey 1, Gulam Rusul Rahmat Ali2*, Nurul Huda2 and Rosma Ahmad3

    2013-07-01

    Full Text Available A total of 107 Salmonella isolates (37 S. typhimurium, 26 S. hadar, 15 S. enteritidis, 15 S. braenderup, and 14 S. albany isolated from ducks and their environments in Penang, Malaysia were typed using enterobacterial repetitive intergenic consensus (ERIC to determine their genetic diversity. Analysis of the Salmonella strains by ERIC produced DNA fingerprints of different sizes for differentiation purposes. The DNA fingerprints or band sizes ranged from 14-8300bp for S. Typhimurium, 146-6593bp for S. hadar, 15-4929bp for S. enteritidis, 14-5142bp for S. braenderup and 7-5712bp for S. albany. Cluster analysis at a coefficient of 0.85 grouped the Salmonella strains into various clusters and singletons. S. typhimurium were grouped into 10 clusters and 6 singletons, S. Hadar were grouped into 3 clusters and 18 singletons, S. enteritidis were grouped into 3 clusters and 7 singletons, S. braenderup were grouped into 4 clusters and 7 singletons, and S. albany were grouped into 3 clusters and 7 singletons with discriminatory index (D ranging from 0.92-0.98. ERIC proved to be a useful typing tool for determining the genetic diversity of the duck Salmonella strains.

  4. Genetic basis and importance of metal resistant genes in bacteria for bioremediation of contaminated environments with toxic metal pollutants.

    Science.gov (United States)

    Das, Surajit; Dash, Hirak R; Chakraborty, Jaya

    2016-04-01

    Metal pollution is one of the most persistent and complex environmental issues, causing threat to the ecosystem and human health. On exposure to several toxic metals such as arsenic, cadmium, chromium, copper, lead, and mercury, several bacteria has evolved with many metal-resistant genes as a means of their adaptation. These genes can be further exploited for bioremediation of the metal-contaminated environments. Many operon-clustered metal-resistant genes such as cadB, chrA, copAB, pbrA, merA, and NiCoT have been reported in bacterial systems for cadmium, chromium, copper, lead, mercury, and nickel resistance and detoxification, respectively. The field of environmental bioremediation has been ameliorated by exploiting diverse bacterial detoxification genes. Genetic engineering integrated with bioremediation assists in manipulation of bacterial genome which can enhance toxic metal detoxification that is not usually performed by normal bacteria. These techniques include genetic engineering with single genes or operons, pathway construction, and alternations of the sequences of existing genes. However, numerous facets of bacterial novel metal-resistant genes are yet to be explored for application in microbial bioremediation practices. This review describes the role of bacteria and their adaptive mechanisms for toxic metal detoxification and restoration of contaminated sites.

  5. Application of the distributed genetic algorithm for in-core fuel optimization problems under parallel computational environment

    International Nuclear Information System (INIS)

    Yamamoto, Akio; Hashimoto, Hiroshi

    2002-01-01

    The distributed genetic algorithm (DGA) is applied for loading pattern optimization problems of the pressurized water reactors. A basic concept of DGA follows that of the conventional genetic algorithm (GA). However, DGA equally distributes candidates of solutions (i.e. loading patterns) to several independent ''islands'' and evolves them in each island. Communications between islands, i.e. migrations of some candidates between islands are performed with a certain period. Since candidates of solutions independently evolve in each island while accepting different genes of migrants, premature convergence in the conventional GA can be prevented. Because many candidate loading patterns should be evaluated in GA or DGA, the parallelization is efficient to reduce turn around time. Parallel efficiency of DGA was measured using our optimization code and good efficiency was attained even in a heterogeneous cluster environment due to dynamic distribution of the calculation load. The optimization code is based on the client/server architecture with the TCP/IP native socket and a client (optimization) module and calculation server modules communicate the objects of loading patterns each other. Throughout the sensitivity study on optimization parameters of DGA, a suitable set of the parameters for a test problem was identified. Finally, optimization capability of DGA and the conventional GA was compared in the test problem and DGA provided better optimization results than the conventional GA. (author)

  6. SOCIAL CULTURE OF EDUCATIONAL ENVIRONMENT OF AN INSTITUTION OF HIGHER EDUCATION AS A FACTOR OF INFLUENCE ON PSYCHO-EMOTIONAL DISTINCTIVE FEATURES OF STUDENTS

    Directory of Open Access Journals (Sweden)

    Ruslan Vyacheslavovich Kostrigin

    2017-04-01

    Full Text Available Purpose. The article examines the influence of socio-cultural space of educational institution on the formation and manifestation of mental and emotional characteristics of students. The authors present the social culture of the University educational space as a socio-cultural environment, significant living space, which is in the process of formation of a student personality. Methodology. The basis of the research is the fundamental principles of modern psychology on the social conditioning of personality development in activity, communication and vocational training, the modern ideas of humanistic psychology and pedagogy, the system-structural approach to the analysis of the personality, the role of education and vocational training in its development were the methodological and theoretical basis of the work. Results. The results of this research consist of the fact that the authors represent the range of types of project activities with its potential enable to shape moral consciousness, value orientation, and sustainable world view, related to the solution of life issues. The conclusion has been made about a direct relationship of quality of educational space and the manifestation of psycho-emotional characteristics of students and development and self-development of emotional sphere of personality. Practical implications. The results of the study can be applied in the sphere of education, work with the students, and for the work of psychological pedagogical services.

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

    Science.gov (United States)

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

    2014-08-01

    The high-altitude hypoxic environment represents one of the most extreme challenges for mammals. Previous studies of humans on the Tibetan plateau and in the Andes Mountains have identified statistical signatures of selection in different sets of loci. Here, we first measured the hemoglobin levels in village dogs from Tibet and those from Chinese lowlands. We found that the hemoglobin levels are very similar between the two groups, suggesting that Tibetan dogs might share similar adaptive strategies as the Tibetan people. Through a whole-genome sequencing approach, we have identified EPAS1 and HBB as candidate genes for the hypoxic adaptation on the Tibetan plateau. The population genetic analysis shows a significant convergence between humans and dogs in Tibet. The similarities in the sets of loci that exhibit putative signatures of selection and the hemoglobin levels between humans and dogs of the same environment, but not between human populations in different regions, suggests an extraordinary landscape of convergent evolution between human beings and their best friend on the Tibetan plateau. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  8. Optimising ketocarotenoid production in potato tubers: effect of genetic background, transgene combinations and environment.

    Science.gov (United States)

    Campbell, Raymond; Morris, Wayne L; Mortimer, Cara L; Misawa, Norihiko; Ducreux, Laurence J M; Morris, Jenny A; Hedley, Pete E; Fraser, Paul D; Taylor, Mark A

    2015-05-01

    Astaxanthin is a high value carotenoid produced by some bacteria, a few green algae, several fungi but only a limited number of plants from the genus Adonis. Astaxanthin has been industrially exploited as a feed supplement in poultry farming and aquaculture. Consumption of ketocarotenoids, most notably astaxanthin, is also increasingly associated with a wide range of health benefits, as demonstrated in numerous clinical studies. Currently astaxanthin is produced commercially by chemical synthesis or from algal production systems. Several studies have used a metabolic engineering approach to produce astaxanthin in transgenic plants. Previous attempts to produce transgenic potato tubers biofortified with astaxanthin have met with limited success. In this study we have investigated approaches to optimising tuber astaxanthin content. It is demonstrated that the selection of appropriate parental genotype for transgenic approaches and stacking carotenoid biosynthetic pathway genes with the cauliflower Or gene result in enhanced astaxanthin content, to give six-fold higher tuber astaxanthin content than has been achieved previously. Additionally we demonstrate the effects of growth environment on tuber carotenoid content in both wild type and astaxanthin-producing transgenic lines and describe the associated transcriptome and metabolome restructuring. Crown Copyright © 2015. Published by Elsevier Ireland Ltd. All rights reserved.

  9. Role of genetic & environment risk factors in the aetiology of colorectal cancer in Malaysia

    Directory of Open Access Journals (Sweden)

    Nurul Hanis Ramzi

    2014-01-01

    Full Text Available Background & objectives: Colorectal cancer (CRC is second only to breast cancer as the leading cause of cancer-related deaths in Malaysia. In the Asia-Pacific area, it is the highest emerging gastrointestinal cancer. The aim of this study was to identify single nucleotide polymorphisms (SNPs and environmental factors associated with CRC risk in Malaysia from a panel of cancer associated SNPs. Methods: In this case-control study, 160 Malaysian subjects were recruited, including both with CRC and controls. A total of 768 SNPs were genotyped and analyzed to distinguish risk and protective alleles. Genotyping was carried out using Illumina′s BeadArray platform. Information on blood group, occupation, medical history, family history of cancer, intake of red meat and vegetables, exposure to radiation, smoking and drinking habits, etc was collected. Odds ratio (OR, 95% confidence interval (CI were calculated. Results: A panel of 23 SNPs significantly associated with colorectal cancer risk was identified ( p0 <0.01. Of these, 12 SNPs increased the risk of CRC and 11 reduced the risk. Among the environmental risk factors investigated, high intake of red meat (more than 50% daily proportion was found to be significantly associated with increased risk of CRC (OR=6.52, 95% CI :1.93 - 2.04, P=0.003. Two SNPs including rs2069521 and rs10046 in genes of cytochrome P450 (CYP superfamily were found significantly associated with CRC risk. For gene-environment analysis, the A allele of rs2069521 showed a significant association with CRC risk when stratified by red meat intake. Interpretation & conclusions: In this preliminary study, a panel of SNPs found to be significantly associated with CRC in Malaysian population, was identified. Also, red meat consumption and lack of physical exercise were risk factors for CRC, while consumption of fruits and vegetables served as protective factor.

  10. Role of genetic & environment risk factors in the aetiology of colorectal cancer in Malaysia.

    Science.gov (United States)

    Ramzi, Nurul Hanis; Chahil, Jagdish Kaur; Lye, Say Hean; Munretnam, Khamsigan; Sahadevappa, Kavitha Itagi; Velapasamy, Sharmila; Hashim, Nikman Adli Nor; Cheah, Soon Keat; Lim, Gerard Chin Chye; Hussein, Heselynn; Haron, Mohd Roslan; Alex, Livy; Ler, Lian Wee

    2014-06-01

    Colorectal cancer (CRC) is second only to breast cancer as the leading cause of cancer-related deaths in Malaysia. In the Asia-Pacific area, it is the highest emerging gastrointestinal cancer. The aim of this study was to identify single nucleotide polymorphisms (SNPs) and environmental factors associated with CRC risk in Malaysia from a panel of cancer associated SNPs. In this case-control study, 160 Malaysian subjects were recruited, including both with CRC and controls. A total of 768 SNPs were genotyped and analyzed to distinguish risk and protective alleles. Genotyping was carried out using Illumina's BeadArray platform. Information on blood group, occupation, medical history, family history of cancer, intake of red meat and vegetables, exposure to radiation, smoking and drinking habits, etc was collected. Odds ratio (OR), 95% confidence interval (CI) were calculated. A panel of 23 SNPs significantly associated with colorectal cancer risk was identified (P<0.01). Of these, 12 SNPs increased the risk of CRC and 11 reduced the risk. Among the environmental risk factors investigated, high intake of red meat (more than 50% daily proportion) was found to be significantly associated with increased risk of CRC (OR=6.52, 95% CI :1.93-2.04, P=0.003). Two SNPs including rs2069521 and rs10046 in genes of cytochrome P450 (CYP) superfamily were found significantly associated with CRC risk. For gene-environment analysis, the A allele of rs2069521 showed a significant association with CRC risk when stratified by red meat intake. In this preliminary study, a panel of SNPs found to be significantly associated with CRC in Malaysian population, was identified. Also, red meat consumption and lack of physical exercise were risk factors for CRC, while consumption of fruits and vegetables served as protective factor.

  11. Environment

    International Nuclear Information System (INIS)

    McIntyre, A.D.; Turnbull, R.G.H.

    1992-01-01

    The development of the hydrocarbon resources of the North Sea has resulted in both offshore and onshore environmental repercussions, involving the existing physical attributes of the sea and seabed, the coastline and adjoining land. The social and economic repercussions of the industry were equally widespread. The dramatic and speedy impact of the exploration and exploitation of the northern North Sea resources in the early 1970s, on the physical resources of Scotland was quickly realised together with the concern that any environmental and social damage to the physical and social fabric should be kept to a minimum. To this end, a wide range of research and other activities by central and local government, and other interested agencies was undertaken to extend existing knowledge on the marine and terrestrial environments that might be affected by the oil and gas industry. The outcome of these activities is summarized in this paper. The topics covered include a survey of the marine ecosystems of the North Sea, the fishing industry, the impact of oil pollution on seabirds and fish stocks, the ecology of the Scottish coastline and the impact of the petroleum industry on a selection of particular sites. (author)

  12. An Underlying Common Factor, Influenced by Genetics and Unique Environment, Explains the Covariation Between Major Depressive Disorder, Generalized Anxiety Disorder, and Burnout: A Swedish Twin Study.

    Science.gov (United States)

    Mather, Lisa; Blom, Victoria; Bergström, Gunnar; Svedberg, Pia

    2016-12-01

    Depression and anxiety are highly comorbid due to shared genetic risk factors, but less is known about whether burnout shares these risk factors. We aimed to examine whether the covariation between major depressive disorder (MDD), generalized anxiety disorder (GAD), and burnout is explained by common genetic and/or environmental factors. This cross-sectional study included 25,378 Swedish twins responding to a survey in 2005-2006. Structural equation models were used to analyze whether the trait variances and covariances were due to additive genetics, non-additive genetics, shared environment, and unique environment. Univariate analyses tested sex limitation models and multivariate analysis tested Cholesky, independent pathway, and common pathway models. The phenotypic correlations were 0.71 (0.69-0.74) between MDD and GAD, 0.58 (0.56-0.60) between MDD and burnout, and 0.53 (0.50-0.56) between GAD and burnout. Heritabilities were 45% for MDD, 49% for GAD, and 38% for burnout; no statistically significant sex differences were found. A common pathway model was chosen as the final model. The common factor was influenced by genetics (58%) and unique environment (42%), and explained 77% of the variation in MDD, 69% in GAD, and 44% in burnout. GAD and burnout had additive genetic factors unique to the phenotypes (11% each), while MDD did not. Unique environment explained 23% of the variability in MDD, 20% in GAD, and 45% in burnout. In conclusion, the covariation was explained by an underlying common factor, largely influenced by genetics. Burnout was to a large degree influenced by unique environmental factors not shared with MDD and GAD.

  13. Accounting for Genotype-by-Environment Interactions and Residual Genetic Variation in Genomic Selection for Water-Soluble Carbohydrate Concentration in Wheat.

    Science.gov (United States)

    Ovenden, Ben; Milgate, Andrew; Wade, Len J; Rebetzke, Greg J; Holland, James B

    2018-04-16

    Abiotic stress tolerance traits are often complex and recalcitrant targets for conventional breeding improvement in many crop species. This study evaluated the potential of genomic selection to predict water-soluble carbohydrate concentration (WSCC), an important drought tolerance trait, in wheat under field conditions. A panel of 358 varieties and breeding lines constrained for maturity was evaluated under rainfed and irrigated treatments across two locations and two years. Whole-genome marker profiles and factor analytic mixed models were used to generate genomic estimated breeding values (GEBVs) for specific environments and environment groups. Additive genetic variance was smaller than residual genetic variance for WSCC, such that genotypic values were dominated by residual genetic effects rather than additive breeding values. As a result, GEBVs were not accurate predictors of genotypic values of the extant lines, but GEBVs should be reliable selection criteria to choose parents for intermating to produce new populations. The accuracy of GEBVs for untested lines was sufficient to increase predicted genetic gain from genomic selection per unit time compared to phenotypic selection if the breeding cycle is reduced by half by the use of GEBVs in off-season generations. Further, genomic prediction accuracy depended on having phenotypic data from environments with strong correlations with target production environments to build prediction models. By combining high-density marker genotypes, stress-managed field evaluations, and mixed models that model simultaneously covariances among genotypes and covariances of complex trait performance between pairs of environments, we were able to train models with good accuracy to facilitate genetic gain from genomic selection. Copyright © 2018, G3: Genes, Genomes, Genetics.

  14. Sensitivity to cocaine in adult mice is due to interplay between genetic makeup, early environment and later experience.

    Science.gov (United States)

    Di Segni, Matteo; Andolina, Diego; Coassin, Alessandra; Accoto, Alessandra; Luchetti, Alessandra; Pascucci, Tiziana; Luzi, Carla; Lizzi, Anna Rita; D'Amato, Francesca R; Ventura, Rossella

    2017-10-01

    Although early aversive postnatal events are known to increase the risk to develop psychiatric disorders later in life, rarely they determine alone the nature and outcome of the psychopathology, indicating that interaction with genetic factors is crucial for expression of psychopathologies in adulthood. Moreover, it has been suggested that early life experiences could have negative consequences or confer adaptive value in different individuals. Here we suggest that resilience or vulnerability to adult cocaine sensitivity depends on a "triple interaction" between genetic makeup x early environment x later experience. We have recently showed that Repeated Cross Fostering (RCF; RCF pups were fostered by four adoptive mothers from postnatal day 1 to postnatal day 4. Pups were left with the last adoptive mother until weaning) experienced by pups affected the response to a negative experience in adulthood in opposite direction in two genotypes leading DBA2/J, but not C57BL/6J mice, toward an "anhedonia-like" phenotype. Here we investigate whether exposure to a rewarding stimulus, instead of a negative one, in adulthood induces an opposite behavioral outcome. To test this hypothesis, we investigated the long-lasting effects of RCF on cocaine sensitivity in C57 and DBA female mice by evaluating conditioned place preference induced by different cocaine doses and catecholamine prefrontal-accumbal response to cocaine using a "dual probe" in vivo microdialysis procedure. Moreover, cocaine-induced c-Fos activity was assessed in different brain regions involved in processing of rewarding stimuli. Finally, cocaine-induced spine changes were evaluated in the prefrontal-accumbal system. RCF experience strongly affected the behavioral, neurochemical and morphological responses to cocaine in adulthood in opposite direction in the two genotypes increasing and reducing, respectively, the sensitivity to cocaine in C57 and DBA mice. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments.

    Science.gov (United States)

    Librado, Pablo; Der Sarkissian, Clio; Ermini, Luca; Schubert, Mikkel; Jónsson, Hákon; Albrechtsen, Anders; Fumagalli, Matteo; Yang, Melinda A; Gamba, Cristina; Seguin-Orlando, Andaine; Mortensen, Cecilie D; Petersen, Bent; Hoover, Cindi A; Lorente-Galdos, Belen; Nedoluzhko, Artem; Boulygina, Eugenia; Tsygankova, Svetlana; Neuditschko, Markus; Jagannathan, Vidhya; Thèves, Catherine; Alfarhan, Ahmed H; Alquraishi, Saleh A; Al-Rasheid, Khaled A S; Sicheritz-Ponten, Thomas; Popov, Ruslan; Grigoriev, Semyon; Alekseev, Anatoly N; Rubin, Edward M; McCue, Molly; Rieder, Stefan; Leeb, Tosso; Tikhonov, Alexei; Crubézy, Eric; Slatkin, Montgomery; Marques-Bonet, Tomas; Nielsen, Rasmus; Willerslev, Eske; Kantanen, Juha; Prokhortchouk, Egor; Orlando, Ludovic

    2015-12-15

    Yakutia, Sakha Republic, in the Siberian Far East, represents one of the coldest places on Earth, with winter record temperatures dropping below -70 °C. Nevertheless, Yakutian horses survive all year round in the open air due to striking phenotypic adaptations, including compact body conformations, extremely hairy winter coats, and acute seasonal differences in metabolic activities. The evolutionary origins of Yakutian horses and the genetic basis of their adaptations remain, however, contentious. Here, we present the complete genomes of nine present-day Yakutian horses and two ancient specimens dating from the early 19th century and ∼5,200 y ago. By comparing these genomes with the genomes of two Late Pleistocene, 27 domesticated, and three wild Przewalski's horses, we find that contemporary Yakutian horses do not descend from the native horses that populated the region until the mid-Holocene, but were most likely introduced following the migration of the Yakut people a few centuries ago. Thus, they represent one of the fastest cases of adaptation to the extreme temperatures of the Arctic. We find cis-regulatory mutations to have contributed more than nonsynonymous changes to their adaptation, likely due to the comparatively limited standing variation within gene bodies at the time the population was founded. Genes involved in hair development, body size, and metabolic and hormone signaling pathways represent an essential part of the Yakutian horse adaptive genetic toolkit. Finally, we find evidence for convergent evolution with native human populations and woolly mammoths, suggesting that only a few evolutionary strategies are compatible with survival in extremely cold environments.

  16. Low genetic differentiation among morphologically distinct ...

    African Journals Online (AJOL)

    Labeobarbus altianalis and L. bynni bynni are hexaploid cyprinid fishes in the genus Labeobarbus. In the Great Lakes region of Africa, these two large-bodied barbs exhibit considerable morphological variations. Their intraspecific classification, currently based on geographical distribution and morphological variation, is of ...

  17. Non-genetic polymorphisms in rotifers: environmental and endogenous controls, development, and features for predictable or unpredictable environments.

    Science.gov (United States)

    Gilbert, John J

    2017-05-01

    Pronounced non-genetic polymorphisms, or polyphenisms, occur in some monogonont rotifers reproducing by diploid, female parthenogenesis. In many brachionids, there is great variation in spine length. In trimorphic species of Asplanchna, females can vary in size and shape, from a small saccate morph to giant cruciform and campanulate morphs. In species that also reproduce sexually, diploid eggs can develop into two types of females. Amictic females produce diploid eggs that develop parthenogenetically into females; mictic females produce haploid eggs that develop parthenogenetically into males or, if fertilized, into resting eggs. In a species of Synchaeta, amictic females produce diploid eggs that can be either thin-shelled and subitaneous or thicker-shelled and diapausing. In all cases, morph determination occurs during the oogenesis or embryological development of diploid eggs in the maternal body cavity. For the first time, these polymorphisms are reviewed together and compared regarding a number of features associated with transitions from default to induced morphs: (i) type of variation (morphological, physiological, or both; continuous or discrete); (ii) inducing signal (environmental, endogenous, or both); (iii) universality of response to that signal (all or only some individuals); (iv) fitness cost; (v) reversibility; and (vi) ecological significance. Most of the polymorphisms fall into two major categories regarding these features. Transitions suitable for predictable environments involve: universal responses to environmental signals; continuous morphological variation; low reproductive cost; rapid reversibility; and adaptations for defence, hydrodynamics or prey ingestion. Transitions suitable for unpredictable environments are bet-hedging strategies and usually involve: partial (stochastic) responses to environmental or endogenous signals; discontinuous physiological variation; initiation of diapause, and thus high reproductive cost and slow

  18. The Dynamics of Genetic Interactions between Vibrio metoecus and Vibrio cholerae, Two Close Relatives Co-Occurring in the Environment.

    Science.gov (United States)

    Orata, Fabini D; Kirchberger, Paul C; Méheust, Raphaël; Barlow, E Jed; Tarr, Cheryl L; Boucher, Yan

    2015-10-09

    Vibrio metoecus is the closest relative of Vibrio cholerae, the causative agent of the potent diarrheal disease cholera. Although the pathogenic potential of this new species is yet to be studied in depth, it has been co-isolated with V. cholerae in coastal waters and found in clinical specimens in the United States. We used these two organisms to investigate the genetic interaction between closely related species in their natural environment. The genomes of 20 V. cholerae and 4 V. metoecus strains isolated from a brackish coastal pond on the US east coast, as well as 4 clinical V. metoecus strains were sequenced and compared with reference strains. Whole genome comparison shows 86-87% average nucleotide identity (ANI) in their core genes between the two species. On the other hand, the chromosomal integron, which occupies approximately 3% of their genomes, shows higher conservation in ANI between species than any other region of their genomes. The ANI of 93-94% observed in this region is not significantly greater within than between species, meaning that it does not follow species boundaries. Vibrio metoecus does not encode toxigenic V. cholerae major virulence factors, the cholera toxin and toxin-coregulated pilus. However, some of the pathogenicity islands found in pandemic V. cholerae were either present in the common ancestor it shares with V. metoecus, or acquired by clinical and environmental V. metoecus in partial fragments. The virulence factors of V. cholerae are therefore both more ancient and more widespread than previously believed. There is high interspecies recombination in the core genome, which has been detected in 24% of the single-copy core genes, including genes involved in pathogenicity. Vibrio metoecus was six times more often the recipient of DNA from V. cholerae as it was the donor, indicating a strong bias in the direction of gene transfer in the environment. © The Author(s) 2015. Published by Oxford University Press on behalf of the

  19. Babesia divergens-like organisms from free-ranging chamois (Rupicapra r. rupicapra) and roe deer (Capreolus c. capreolus) are distinct from B. divergens of cattle origin - an epidemiological and molecular genetic investigation.

    Science.gov (United States)

    Schmid, Nicole; Deplazes, Peter; Hoby, Stefan; Ryser-Degiorgis, Marie-Pierre; Edelhofer, Renate; Mathis, Alexander

    2008-06-14

    In 2005 and 2006, three adult female chamois (Rupicapra r. rupicapra) were found dead with signs of acute babesial infection in the eastern Swiss Alps. PCR on DNA extracted from blood or spleen of the carcasses revealed sequence identity of the amplified part of the 18S rRNA gene with GenBank entries attributed to Babesia divergens of cattle origin or B. capreoli of wild ruminant origin which have never been described before in this region. Examination of 424 blood samples from 314 head of cattle from this area by IFAT, microscopy and PCR provided no evidence for babesial infection. Six of 887 ticks collected from cattle were PCR-positive, and sequencing revealed Babesia sp. genotype EU1 in five and B. divergens/B. capreoli in one of them. A Babesia isolate of chamois, two isolates of roe deer from the same region and one isolate of a roe deer from the north-western Swiss Alps were genetically compared with two Swiss B. divergens isolates of cattle origin by analysing the genomic rDNA locus. Whereas the near full length sequences of the 18S rRNA gene were virtually identical among all six isolates (>99.4% identity), distinct differences between the two isolates from cattle on the one hand and the four isolates from free-ranging ruminants on the other hand were observed in the sequences of the internal transcribed spacers 1 and 2 (ITS1, ITS2) and part of the 28S rRNA gene. These results indicate that, albeit genetically very closely related, these babesial organisms from cattle and from free-ranging ruminants indeed are distinguishable organisms with different host specificities, and they support the use of the discrete species name B. capreoli for the B. divergens-like organisms from chamois and roe deer.

  20. Comparative epigenetic and genetic spatial structure of the perennial herbHelleborus foetidus: Isolation by environment, isolation by distance, and functional trait divergence.

    Science.gov (United States)

    Herrera, Carlos M; Medrano, Mónica; Bazaga, Pilar

    2017-08-16

    Epigenetic variation can play a role in local adaptation; thus, there should be associations among epigenetic variation, environmental variation, and functional trait variation across populations. This study examines these relationships in the perennial herb Helleborus foetidus (Ranunculaceae). Plants from 10 subpopulations were characterized genetically (AFLP, SSR markers), epigenetically (MSAP markers), and phenotypically (20 functional traits). Habitats were characterized using six environmental variables. Isolation-by-distance (IBD) and isolation-by-environment (IBE) patterns of genetic and epigenetic divergence were assessed, as was the comparative explanatory value of geographical and environmental distance as predictors of epigenetic, genetic, and functional differentiation. Subpopulations were differentiated genetically, epigenetically, and phenotypically. Genetic differentiation was best explained by geographical distance, while epigenetic differentiation was best explained by environmental distance. Divergence in functional traits was correlated with environmental and epigenetic distances, but not with geographical and genetic distances. Results are compatible with the hypothesis that epigenetic IBE and functional divergence reflected responses to environmental variation. Spatial analyses simultaneously considering epigenetic, genetic, phenotypic and environmental information provide a useful tool to evaluate the role of environmental features as drivers of natural epigenetic variation between populations. © 2017 Botanical Society of America.

  1. Genetic characterization of EV71 isolates from 2004 to 2010 reveals predominance and persistent circulation of the newly proposed genotype D and recent emergence of a distinct lineage of subgenotype C2 in Hong Kong.

    Science.gov (United States)

    Yip, Cyril C Y; Lau, Susanna K P; Lo, Janice Y C; Chan, Kwok-Hung; Woo, Patrick C Y; Yuen, Kwok-Yung

    2013-07-04

    Enterovirus 71 (EV71) is a common etiological agent of hand, foot and mouth disease (HFMD) in children. EV71 epidemics have been reported in Hong Kong in recent years, and yet the genetic information of EV71 strains circulating in our locality is limited. The objective of this study was to investigate the genetic evolution of these EV71 isolates in Hong Kong over a 7-year period. Twenty-two EV71 isolates from Hong Kong during 2004-2010 were included for phylogenetic analysis using partial VP2-VP3, 2C and 3D regions. Eight EV71 strains were selected for complete genome sequencing and recombination analysis. Among the 22 EV71 isolates, 20 belonged to subgenotype C4 and 2 belonged to subgenotype C2 based on the phylogenetic analysis of partial VP2-VP3, 2C and 3D gene regions. Phylogenetic, similarity plot and bootscan analyses using complete genome sequences of seven EV71 isolates of subgenotype C4 supported that the "double-recombinant" strains of subgenotype C4 persistently circulating in Hong Kong should belong to a newly proposed genotype D. Further analysis revealed two clusters, subgenotypes C4b and C4a (proposed genotypes D1a and D1b respectively), with "genotype D1b" strains being predominant in recent years in Hong Kong. A distinct lineage of EV71 subgenotype C2 has emerged in Hong Kong in 2008. The evolutionary rate of EV71 was 3.1 × 10-3 nucleotide substitutions per site per year similar to that of other enterovirus, such as EV68, but was relatively lower than those of echovirus 30 and poliovirus. Molecular clock analysis using VP1 gene dated the time to the most recent common ancestor of all EV71 genotypes to 1900s, while the EV71 "double-recombinant" strains of "genotype D" were detected as early as 1998. This study provides the molecular basis for proposing a new "genotype D" of EV71 and assigning a discrete lineage of subgenotype C2. EV71 strains of "genotype D" have been circulating in Hong Kong for over 7 years, with "genotype D1b" being predominant.

  2. Modelling individual space?time exposure opportunities: A novel approach to unravelling the genetic or environment disease causation debate

    DEFF Research Database (Denmark)

    Sabel, Clive E; Boyle, Paul; Raab, Gillian

    2009-01-01

    clustering of ALS at the time of birth in south-east Finland and this could support either a genetic or an environmental hypothesis. We know that south-east Finland is an environmentally degraded area, but the population in this region may also be genetically susceptible to this condition. We therefore...

  3. Enriching an intraspecific genetic map and identifying QTL for fiber quality and yield component traits across multiple environments in Upland cotton (Gossypium hirsutum L.).

    Science.gov (United States)

    Liu, Xueying; Teng, Zhonghua; Wang, Jinxia; Wu, Tiantian; Zhang, Zhiqin; Deng, Xianping; Fang, Xiaomei; Tan, Zhaoyun; Ali, Iftikhar; Liu, Dexin; Zhang, Jian; Liu, Dajun; Liu, Fang; Zhang, Zhengsheng

    2017-12-01

    Cotton is a significant commercial crop that plays an indispensable role in many domains. Constructing high-density genetic maps and identifying stable quantitative trait locus (QTL) controlling agronomic traits are necessary prerequisites for marker-assisted selection (MAS). A total of 14,899 SSR primer pairs designed from the genome sequence of G. raimondii were screened for polymorphic markers between mapping parents CCRI 35 and Yumian 1, and 712 SSR markers showing polymorphism were used to genotype 180 lines from a (CCRI 35 × Yumian 1) recombinant inbred line (RIL) population. Genetic linkage analysis was conducted on 726 loci obtained from the 712 polymorphic SSR markers, along with 1379 SSR loci obtained in our previous study, and a high-density genetic map with 2051 loci was constructed, which spanned 3508.29 cM with an average distance of 1.71 cM between adjacent markers. Marker orders on the linkage map are highly consistent with the corresponding physical orders on a G. hirsutum genome sequence. Based on fiber quality and yield component trait data collected from six environments, 113 QTLs were identified through two analytical methods. Among these 113 QTLs, 50 were considered stable (detected in multiple environments or for which phenotypic variance explained by additive effect was greater than environment effect), and 18 of these 50 were identified with stability by both methods. These 18 QTLs, including eleven for fiber quality and seven for yield component traits, could be priorities for MAS.

  4. Spatial genetic diversity in the Cape mole-rat, Georychus capensis: Extreme isolation of populations in a subterranean environment.

    Science.gov (United States)

    Visser, Jacobus H; Bennett, Nigel C; Jansen van Vuuren, Bettine

    2018-01-01

    The subterranean niche harbours animals with extreme adaptations. These adaptations decrease the vagility of taxa and, along with other behavioural adaptations, often result in isolated populations characterized by small effective population sizes, high inbreeding, population bottlenecks, genetic drift and consequently, high spatial genetic structure. Although information is available for some species, estimates of genetic diversity and whether this variation is spatially structured, is lacking for the Cape mole-rat (Georychus capensis). By adopting a range-wide sampling regime and employing two variable mitochondrial markers (cytochrome b and control region), we report on the effects that life-history, population demography and geographic barriers had in shaping genetic variation and population genetic patterns in G. capensis. We also compare our results to information available for the sister taxon of the study species, Bathyergus suillus. Our results show that Georychus capensis exhibits low genetic diversity relative to the concomitantly distributed B. suillus, most likely due to differences in habitat specificity, habitat fragmentation and historical population declines. In addition, the isolated nature of G. capensis populations and low levels of population connectivity has led to small effective population sizes and genetic differentiation, possibly aided by genetic drift. Not surprisingly therefore, G. capensis exhibits pronounced spatial structure across its range in South Africa. Along with geographic distance and demography, other factors shaping the genetic structure of G. capensis include the historical and contemporary impacts of mountains, rivers, sea-level fluctuations and elevation. Given the isolation and differentiation among G. capensis populations, the monotypic genus Georychus may represent a species complex.

  5. The Glass is Half Full and Half Empty: A population-representative twin study testing if Optimism and Pessimism are distinct systems

    Science.gov (United States)

    Bates, Timothy C.

    2015-01-01

    Optimism and pessimism are associated with important outcomes including health and depression. Yet it is unclear if these apparent polar opposites form a single dimension or reflect two distinct systems. The extent to which personality accounts for differences in optimism/pessimism is also controversial. Here, we addressed these questions in a genetically informative sample of 852 pairs of twins. Distinct genetic influences on optimism and pessimism were found. Significant family-level environment effects also emerged, accounting for much of the negative relationship between optimism and pessimism, as well as a link to neuroticism. A general positive genetics factor exerted significant links among both personality and life-orientation traits. Both optimism bias and pessimism also showed genetic variance distinct from all effects of personality, and from each other. PMID:26561494

  6. Utilization of farm animal genetic resources in a changing agro-ecological environment in the Nordic countries

    DEFF Research Database (Denmark)

    Kantanen, Juha; Løvendahl, Peter; Strandberg, Erling

    2015-01-01

    Livestock production is the most important component of northern European agriculture and contributes to and will be affected by climate change. Nevertheless, the role of farm animal genetic resources in the adaptation to new agro-ecological conditions and mitigation of animal production’s effects....... There are several genetic questions that should be considered in strategies promoting adaptation to climate change and mitigation of environmental effects of livestock production. For example, it may become important to choose among breeds and even among farm animal species according to their suitability...... on climate change has been inadequately discussed despite there being several important associations between animal genetic resources and climate change issues. The sustainability of animal production systems and future food security require access to a wide diversity of animal genetic resources...

  7. Genetic versus rearing-environment effects on phenotype: hatchery and natural rearing effects on hatchery- and wild-born coho salmon.

    Directory of Open Access Journals (Sweden)

    Cedar M Chittenden

    Full Text Available With the current trends in climate and fisheries, well-designed mitigative strategies for conserving fish stocks may become increasingly necessary. The poor post-release survival of hatchery-reared Pacific salmon indicates that salmon enhancement programs require assessment. The objective of this study was to determine the relative roles that genotype and rearing environment play in the phenotypic expression of young salmon, including their survival, growth, physiology, swimming endurance, predator avoidance and migratory behaviour. Wild- and hatchery-born coho salmon adults (Oncorhynchus kisutch returning to the Chehalis River in British Columbia, Canada, were crossed to create pure hatchery, pure wild, and hybrid offspring. A proportion of the progeny from each cross was reared in a traditional hatchery environment, whereas the remaining fry were reared naturally in a contained side channel. The resulting phenotypic differences between replicates, between rearing environments, and between cross types were compared. While there were few phenotypic differences noted between genetic groups reared in the same habitat, rearing environment played a significant role in smolt size, survival, swimming endurance, predator avoidance and migratory behaviour. The lack of any observed genetic differences between wild- and hatchery-born salmon may be due to the long-term mixing of these genotypes from hatchery introgression into wild populations, or conversely, due to strong selection in nature--capable of maintaining highly fit genotypes whether or not fish have experienced part of their life history under cultured conditions.

  8. Computational visual distinctness metric

    NARCIS (Netherlands)

    Martínez-Baena, J.; Toet, A.; Fdez-Vidal, X.R.; Garrido, A.; Rodríguez-Sánchez, R.

    1998-01-01

    A new computational visual distinctness metric based on principles of the early human visual system is presented. The metric is applied to quantify (1) the visual distinctness of targets in complex natural scenes and (2) the perceptual differences between compressed and uncompressed images. The new

  9. Discovering candidate genes that regulate resin canal number in Pinus taeda stems by integrating genetic analysis across environments, ages, and populations

    Energy Technology Data Exchange (ETDEWEB)

    Westbrook, JW; Walker, AR; Neves, LG; Munoz, P; Resende, MFR; Neale, DB; Wegrzyn, JL; Huber, DA; Kirst, M; Davis, JM; Peter, GF

    2014-09-30

    Genetically improving constitutive resin canal development in Pinus stems may enhance the capacity to synthesize terpenes for bark beetle resistance, chemical feedstocks, and biofuels. To discover genes that potentially regulate axial resin canal number (RCN), single nucleotide polymorphisms (SNPs) in 4027 genes were tested for association with RCN in two growth rings and three environments in a complex pedigree of 520 Pinus taeda individuals (CCLONES). The map locations of associated genes were compared with RCN quantitative trait loci (QTLs) in a (P.taedaxPinuselliottii)xP.elliottii pseudo-backcross of 345 full-sibs (BC1). Resin canal number was heritable (h(2)0.12-0.21) and positively genetically correlated with xylem growth (r(g)0.32-0.72) and oleoresin flow (r(g)0.15-0.51). Sixteen well-supported candidate regulators of RCN were discovered in CCLONES, including genes associated across sites and ages, unidirectionally associated with oleoresin flow and xylem growth, and mapped to RCN QTLs in BC1. Breeding is predicted to increase RCN 11% in one generation and could be accelerated with genomic selection at accuracies of 0.45-0.52 across environments. There is significant genetic variation for RCN in loblolly pine, which can be exploited in breeding for elevated terpene content.

  10. Discovering candidate genes that regulate resin canal number in Pinus taeda stems by integrating genetic analysis across environments, ages, and populations.

    Science.gov (United States)

    Westbrook, Jared W; Walker, Alejandro R; Neves, Leandro G; Munoz, Patricio; Resende, Marcio F R; Neale, David B; Wegrzyn, Jill L; Huber, Dudley A; Kirst, Matias; Davis, John M; Peter, Gary F

    2015-01-01

    Genetically improving constitutive resin canal development in Pinus stems may enhance the capacity to synthesize terpenes for bark beetle resistance, chemical feedstocks, and biofuels. To discover genes that potentially regulate axial resin canal number (RCN), single nucleotide polymorphisms (SNPs) in 4027 genes were tested for association with RCN in two growth rings and three environments in a complex pedigree of 520 Pinus taeda individuals (CCLONES). The map locations of associated genes were compared with RCN quantitative trait loci (QTLs) in a (P. taeda × Pinus elliottii) × P. elliottii pseudo-backcross of 345 full-sibs (BC1). Resin canal number was heritable (h(2) ˜ 0.12-0.21) and positively genetically correlated with xylem growth (rg ˜ 0.32-0.72) and oleoresin flow (rg ˜ 0.15-0.51). Sixteen well-supported candidate regulators of RCN were discovered in CCLONES, including genes associated across sites and ages, unidirectionally associated with oleoresin flow and xylem growth, and mapped to RCN QTLs in BC1. Breeding is predicted to increase RCN 11% in one generation and could be accelerated with genomic selection at accuracies of 0.45-0.52 across environments. There is significant genetic variation for RCN in loblolly pine, which can be exploited in breeding for elevated terpene content. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

  11. Influence of Host Genetics and Environment on Nasal Carriage of Staphylococcus aureus in Danish Middle-Aged and Elderly Twins

    DEFF Research Database (Denmark)

    Andersen, Paal Skytt; Pedersen, Jacob Krabbe; Fode, Peder

    2012-01-01

    Background. Nasal carriage is a major risk factor for Staphylococcus aureus infection. Approximately, one-quarter of adults carry S. aureus. However, the role of host genetics on S. aureus nasal carriage is unknown. Methods. Nasal swabs were obtained from a national cohort of middle-aged and elde......Background. Nasal carriage is a major risk factor for Staphylococcus aureus infection. Approximately, one-quarter of adults carry S. aureus. However, the role of host genetics on S. aureus nasal carriage is unknown. Methods. Nasal swabs were obtained from a national cohort of middle.......4%-34.5%), and opposite sex (21.4%; 95% CI, 12.0%-33.4%) dizygotic twins. Despite shared childhoods, only 1 of 617 pairs was concordant with respect to lineage. Although heritability increased for S. aureus and lineage persistency, no significant heritability was detected. Conclusion. In this study, host genetic factors...

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

    Science.gov (United States)

    Kandi, Kamala M.

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

  13. Genotype-environment interaction and the number of test sites for the genetic improvement of rubber trees (Hevea in São Paulo State, Brazil

    Directory of Open Access Journals (Sweden)

    Costa Reginaldo Brito da

    2000-01-01

    Full Text Available The present study quantifies the possible genotype-environment interactions and determines the ideal number of test sites for rubber trees [Hevea brasiliensis (Willd ex Adr. de Juss. Muell Arg] in the plateau region of São Paulo State. The study was based on the genetic correlation among progenies at three different sites and on estimates of genetic gains with indirect selection of rubber trees. Twenty-two half-sib progenies were planted at the Jaú, Pindorama and Votuporanga experimental stations using random blocks with five replications and 10 plants per plot. At three years of age, the plants were evaluated for their total number of latex ring vessels (NR, rubber production (RP, bark thickness (BT and girth (SG. There was significant genetic variability in the characters RP, SG and BT, mainly among progenies from Pindorama and Votuporanga. The effects of genotype-site interactions were significant for RP and SG. The finding of significant interactions was not a complicating factor because of the large genetic correlation detected. These results indicate that the use of two sites is more profitable when the gains in efficiency of selection are greater than 10%. Thus, Pindorama and Votuporanga will satisfactorily attend the studied region.

  14. Interaction between Social/Psychosocial Factors and Genetic Variants on Body Mass Index: A Gene-Environment Interaction Analysis in a Longitudinal Setting

    Directory of Open Access Journals (Sweden)

    Wei Zhao

    2017-09-01

    Full Text Available Obesity, which develops over time, is one of the leading causes of chronic diseases such as cardiovascular disease. However, hundreds of BMI (body mass index-associated genetic loci identified through large-scale genome-wide association studies (GWAS only explain about 2.7% of BMI variation. Most common human traits are believed to be influenced by both genetic and environmental factors. Past studies suggest a variety of environmental features that are associated with obesity, including socioeconomic status and psychosocial factors. This study combines both gene/regions and environmental factors to explore whether social/psychosocial factors (childhood and adult socioeconomic status, social support, anger, chronic burden, stressful life events, and depressive symptoms modify the effect of sets of genetic variants on BMI in European American and African American participants in the Health and Retirement Study (HRS. In order to incorporate longitudinal phenotype data collected in the HRS and investigate entire sets of single nucleotide polymorphisms (SNPs within gene/region simultaneously, we applied a novel set-based test for gene-environment interaction in longitudinal studies (LGEWIS. Childhood socioeconomic status (parental education was found to modify the genetic effect in the gene/region around SNP rs9540493 on BMI in European Americans in the HRS. The most significant SNP (rs9540488 by childhood socioeconomic status interaction within the rs9540493 gene/region was suggestively replicated in the Multi-Ethnic Study of Atherosclerosis (MESA (p = 0.07.

  15. Access and benefits sharing of genetic resources and associated traditional knowledge in northern Canada: understanding the legal environment and creating effective research agreements.

    Science.gov (United States)

    Geary, Janis; Jardine, Cynthia G; Guebert, Jenilee; Bubela, Tania

    2013-01-01

    Research in northern Canada focused on Aboriginal peoples has historically benefited academia with little consideration for the people being researched or their traditional knowledge (TK). Although this attitude is changing, the complexity of TK makes it difficult to develop mechanisms to preserve and protect it. Protecting TK becomes even more important when outside groups become interested in using TK or materials with associated TK. In the latter category are genetic resources, which may have commercial value and are the focus of this article. This article addresses access to and use of genetic resources and associated TK in the context of the historical power-imbalances in research relationships in Canadian north. Review. Research involving genetic resources and TK is becoming increasingly relevant in northern Canada. The legal framework related to genetic resources and the cultural shift of universities towards commercial goals in research influence the environment for negotiating research agreements. Current guidelines for research agreements do not offer appropriate guidelines to achieve mutual benefit, reflect unequal bargaining power or take the relationship between parties into account. Relational contract theory may be a useful framework to address the social, cultural and legal hurdles inherent in creating research agreements.

  16. Access and benefits sharing of genetic resources and associated traditional knowledge in northern Canada: understanding the legal environment and creating effective research agreements

    Directory of Open Access Journals (Sweden)

    Janis Geary

    2013-08-01

    Full Text Available Background. Research in northern Canada focused on Aboriginal peoples has historically benefited academia with little consideration for the people being researched or their traditional knowledge (TK. Although this attitude is changing, the complexity of TK makes it difficult to develop mechanisms to preserve and protect it. Protecting TK becomes even more important when outside groups become interested in using TK or materials with associated TK. In the latter category are genetic resources, which may have commercial value and are the focus of this article. Objective. This article addresses access to and use of genetic resources and associated TK in the context of the historical power-imbalances in research relationships in Canadian north. Design. Review. Results. Research involving genetic resources and TK is becoming increasingly relevant in northern Canada. The legal framework related to genetic resources and the cultural shift of universities towards commercial goals in research influence the environment for negotiating research agreements. Current guidelines for research agreements do not offer appropriate guidelines to achieve mutual benefit, reflect unequal bargaining power or take the relationship between parties into account. Conclusions. Relational contract theory may be a useful framework to address the social, cultural and legal hurdles inherent in creating research agreements.

  17. Optimizing T-Learning Course Scheduling Based on Genetic Algorithm in Benefit-Oriented Data Broadcast Environments

    Science.gov (United States)

    Huang, Yong-Ming; Chen, Chao-Chun; Wang, Ding-Chau

    2012-01-01

    Ubiquitous learning receives much attention in these few years due to its wide spectrum of applications, such as the T-learning application. The learner can use mobile devices to watch the digital TV based course content, and thus, the T-learning provides the ubiquitous learning environment. However, in real-world data broadcast environments, the…

  18. Combining ability × environment interaction and genetic analysis for agronomic traits in safflower (Carthamus tinctorius L.: biplot as a tool for diallel data

    Directory of Open Access Journals (Sweden)

    Pooran Golkar

    2017-09-01

    Full Text Available Combining ability × environment interaction is considerable to identify the effect of environment on the combining ability and gene action of the traits to select appropriate parents for safflower hybrid production. The 36 genotype (28 F2 progenies of eight-parent half-diallel crosses across 8 parental genotypes of safflower were studied to investigate the mentioned parameters across different geographical regions of Iran. The results indicated significant differences among parents for general and specific combining ability, except for seeds per capitulum across three environments. The overall results indicated that K21 and Mex.22-191 were excellent parents with greater general combining ability for the improvement of seed yield in safflower. The K21 × Mex.22-191 hybrid could be, therefore, employed for the production of high seed yield in safflower breeding. The estimates of genetic variance components recommended the importance of additive- dominance genetic effects that contributed to variation in yield per plant. Such gene action expression for seed yield needs auxiliary methods based on hybridization and selection for seed yield advancement in safflower.

  19. Genetic evaluation of weight gain and feed-to-gain ratio of White New Zealand rabbits raised in different environments

    NARCIS (Netherlands)

    Santos, A.L.; Scapinello, C.; Nunes Martins, E.; Granzotto, F.; Carneiro Paula, M.; Marubayashi Hidalgo, A.

    2010-01-01

    This research evaluates whether the selection for feed-to-gain ratio (FGR) and weight gain (WG), based on individual and/or collective performance of rabbits, can lead to genetic gain in collectively-raised rabbit progenies. Animals were submitted to an evaluation period at the age of 50 to 70 days,

  20. Selection for water-soluble carbohydrate accumulation and investigation of genetic × environment interactions in an elite wheat breeding population

    Science.gov (United States)

    The potential to increase the genetic capacity for water-soluble carbohydrate (WSC) accumulation is an opportunity to improve the drought tolerance capability of rainfed wheat varieties, particularly in Australia where terminal drought is a significant constraint to wheat production. A population of...

  1. The importance of shared environment in mother-infant attachment security: A behavioral genetic study [IF: 3.272

    NARCIS (Netherlands)

    Bokhorst, C.L.; Bakermans-Kranenburg, M.J.; Fearon, R.M.; van IJzendoorn, M.H.; Fonagy, P.; Schuengel, C.

    2003-01-01

    In a sample of 157 monozygotic and dizygotic twins, genetic and environmental influences on infant attachment and temperament were quantified. Only unique environmental or error components could explain the variance in disorganized versus organized attachment as assessed in the Ainsworth Strange

  2. Genotype x environment interactions in pig breeding programmes. V. Genetic parameters and sire x herd interaction in commercial fattening.

    NARCIS (Netherlands)

    Merks, J.W.M.; Kemenade, van P.G.M.

    1989-01-01

    An experimental progeny test of 107 Dutch Yorkshire AI boars was designed under commercial fattening conditions to estimate genetic parameters and to examine sire x herd interactions under these conditions. Individual records of 8148 crossbred fattening pigs, born on 27 sow herds and fattened on 35

  3. Genetics or environment in drug transport: the case of organic anion transporting polypeptides and adverse drug reactions.

    Science.gov (United States)

    Clarke, John D; Cherrington, Nathan J

    2012-03-01

    Organic anion transporting polypeptide (OATP) uptake transporters are important for the disposition of many drugs and perturbed OATP activity can contribute to adverse drug reactions (ADRs). It is well documented that both genetic and environmental factors can alter OATP expression and activity. Genetic factors include single nucleotide polymorphisms (SNPs) that change OATP activity and epigenetic regulation that modify OATP expression levels. SNPs in OATPs contribute to ADRs. Environmental factors include the pharmacological context of drug-drug interactions and the physiological context of liver diseases. Liver diseases such as non-alcoholic fatty liver disease, cholestasis and hepatocellular carcinoma change the expression of multiple OATP isoforms. The role of liver diseases in the occurrence of ADRs is unknown. This article covers the roles OATPs play in ADRs when considered in the context of genetic or environmental factors. The reader will gain a greater appreciation for the current evidence regarding the salience and importance of each factor in OATP-mediated ADRs. A SNP in a single OATP transporter can cause changes in drug pharmacokinetics and contribute to ADRs but, because of overlap in substrate specificities, there is potential for compensatory transport by other OATP isoforms. By contrast, the expression of multiple OATP isoforms is decreased in liver diseases, reducing compensatory transport and thereby increasing the probability of ADRs. To date, most research has focused on the genetic factors in OATP-mediated ADRs while the impact of environmental factors has largely been ignored.

  4. Developmental windows and environment as important factors in the expression of genetic information: a cardiovascular physiologist's view

    Czech Academy of Sciences Publication Activity Database

    Kuneš, Jaroslav; Zicha, Josef

    2006-01-01

    Roč. 111, č. 5 (2006), s. 295-305 ISSN 0143-5221 R&D Projects: GA MZd(CZ) NR7786 Institutional research plan: CEZ:AV0Z50110509 Keywords : developmental window * genetic determinants * environmental stimuli Subject RIV: ED - Physiology Impact factor: 3.263, year: 2006

  5. A novel genetic score approach using instruments to investigate interactions between pathways and environment: application to air pollution.

    Directory of Open Access Journals (Sweden)

    Marie-Abele Bind

    Full Text Available Air pollution has been associated with increased systemic inflammation markers. We developed a new pathway analysis approach to investigate whether gene variants within relevant pathways (oxidative stress, endothelial function, and metal processing modified the association between particulate air pollution and fibrinogen, C-reactive protein (CRP, intercellular adhesion molecule-1 (ICAM-1, and vascular cell adhesion molecule-1 (VCAM-1. Our study population consisted of 822 elderly participants of the Normative Aging Study (1999-2011. To investigate the role of biological mechanisms and to reduce the number of comparisons in the analysis, we created pathway-specific scores using gene variants related to each pathway. To select the most appropriate gene variants, we used the least absolute shrinkage and selection operator (Lasso to relate independent outcomes representative of each pathway (8-hydroxydeoxyguanosine for oxidative stress, augmentation index for endothelial function, and patella lead for metal processing to gene variants. A high genetic score corresponds to a higher allelic risk profile. We fit mixed-effects models to examine modification by the genetic score of the weekly air pollution association with the outcome. Among participants with higher genetic scores within the oxidative stress pathway, we observed significant associations between particle number and fibrinogen, while we did not find any association among participants with lower scores (p(interaction = 0.04. Compared to individuals with low genetic scores of metal processing gene variants, participants with higher scores had greater effects of particle number on fibrinogen (p(interaction = 0.12, CRP (p(interaction = 0.02, and ICAM-1 (pinteraction = 0.08. This two-stage penalization method is easy to implement and can be used for large-scale genetic applications.

  6. A novel genetic score approach using instruments to investigate interactions between pathways and environment: application to air pollution.

    Science.gov (United States)

    Bind, Marie-Abele; Coull, Brent; Suh, Helen; Wright, Robert; Baccarelli, Andrea; Vokonas, Pantel; Schwartz, Joel

    2014-01-01

    Air pollution has been associated with increased systemic inflammation markers. We developed a new pathway analysis approach to investigate whether gene variants within relevant pathways (oxidative stress, endothelial function, and metal processing) modified the association between particulate air pollution and fibrinogen, C-reactive protein (CRP), intercellular adhesion molecule-1 (ICAM-1), and vascular cell adhesion molecule-1 (VCAM-1). Our study population consisted of 822 elderly participants of the Normative Aging Study (1999-2011). To investigate the role of biological mechanisms and to reduce the number of comparisons in the analysis, we created pathway-specific scores using gene variants related to each pathway. To select the most appropriate gene variants, we used the least absolute shrinkage and selection operator (Lasso) to relate independent outcomes representative of each pathway (8-hydroxydeoxyguanosine for oxidative stress, augmentation index for endothelial function, and patella lead for metal processing) to gene variants. A high genetic score corresponds to a higher allelic risk profile. We fit mixed-effects models to examine modification by the genetic score of the weekly air pollution association with the outcome. Among participants with higher genetic scores within the oxidative stress pathway, we observed significant associations between particle number and fibrinogen, while we did not find any association among participants with lower scores (p(interaction) = 0.04). Compared to individuals with low genetic scores of metal processing gene variants, participants with higher scores had greater effects of particle number on fibrinogen (p(interaction) = 0.12), CRP (p(interaction) = 0.02), and ICAM-1 (pinteraction = 0.08). This two-stage penalization method is easy to implement and can be used for large-scale genetic applications.

  7. Handling of Astyanax sp. for biomonitoring in Cangüiri Farm within a fountainhead (Iraí River Environment Preservation Area) through the use of genetic biomarkers.

    Science.gov (United States)

    Ramsdorf, Wanessa Algarte; Vicari, Taynah; de Almeida, Marina I M; Artoni, Roberto Ferreira; Cestari, Marta Margarete

    2012-10-01

    Aquatic environmental pollution may cause biodiversity loss. Thus, monitoring studies are very important because fish health reflects both quality and sustainability of the environment, as well as of the individuals that live there. In the present report, genetic biomarkers (piscine micronucleus test; comet assay with blood, liver, and kidney cells) were used in specimens of Astyanax sp. to analyze the contamination level of the Cangüiri Farm through biomonitoring. The Cangüiri Farm, the old school farm of the Federal University of Paraná, is inside the Iraí River Environment Preservation Area, created in 1996 to preserve the sources of public water supply in Curitiba and metropolitan area. We verified that the fishes collected within the Cangüiri Farm area presented high damage levels, showing more environment contamination when compared to the specimens collected in the Costa Ecologic Park, used as reference in the present report. The results indicate that the Cangüiri Farm, which is inside an environment protection area, created especially for the protection of the fountainhead for water supply, may be contaminated. These toxic residues, which were remarkably persistent in the environment, are possibly derived from agricultural activities in the wider area. Thus, we suggest the analysis of the area with other biomarkers and for a longer time period.

  8. [PHENOTYPICAL CHARACTERISTICS AND GENETICAL DETERMINANTS OF PATHOGENICITY OF STAPHYLOCOCCUS AUREUS, ISOLATED FROM BACTERIAL CARRIERS, RESIDING ON THE TERRITORIES WITH VARIOUS LEVELS OF ANTHROPOGENIC POLLUTION OF AIR ENVIRONMENT].

    Science.gov (United States)

    Utkina, T M; Popova, L P; Kartashova, O L; Khazeeva, G D; Khaliullina, A A

    2015-01-01

    Comparative phenotypical and genetical evaluation of pathogenic potential of Staphylococcus aureus strains, isolated from resident bacterial carriers, residing on the territories with anthropogenic pollution of air environment of varying intensity. S. aureus, isolated 3 times from mucous membrane of the anterior of nose from 210 children, were the object of the study. Anti-carnosine activity and biofilm formation was determined by a photometric method, antibiotics resistance--by a disc diffusion method. lukS, lukF, sec 3, clfA, clfB, agr and mecA gene detection, that are associated with S. aureus, was carried out by PCR. S. aureus strains, isolated from children, residing on the territories with a high level of anthropogenic pollution of air environment, were characterized by antibiotics resistance, higher values of anti-carnosine activity, 2 times more frequently formed biofilms with higher values of the parameter. clfA and clfB genes, that determine colonization of mucous membranes, and agr gene were detected in all the studied S. aureus strains, lukF and sec 3 genes were detected in 20-40% of the strains, isolated from children, residing on both territories. mecA and lukS genetical determinants were not detected. S. aureus, isolated from children, residing on the territories with high levels of anthropogenic pollution of air environment; were characterized by higher values of the studied factors of persistence and stability against antibiotics. Genetical determinants of pathogenicity were not detected in S. aureus, isolated from individuals, residing on both territories.

  9. A Non-Invasive Genetic Survey of Otters (Lutra lutra) in an Urban Environment: A Pilot Study with Citizen Scientists

    OpenAIRE

    Shane White; David O’Neill; Denise B. O’Meara; Carolyn Shores; Catherine O’Reilly; Andrew P. Harrington; Gill Weyman; D. P. Sleeman

    2013-01-01

    Acquiring reliable estimates for an elusive species' distribution and population size can be problematic. For cryptic species such as the Eurasian otter (Lutra lutra), traditional monitoring approaches rely heavily on identifying field signs that may under or overestimate population sizes. Increasingly, non-invasive genetic sampling is effectively applied to assess the abundance and population structure of otters by genotyping faeces (spraints). Here we present the results of a non-invasive s...

  10. Behavioral, ecological and genetic differentiation in an open environment--a study of a mysid population in the Baltic Sea.

    Science.gov (United States)

    Ogonowski, Martin; Duberg, Jon; Hansson, Sture; Gorokhova, Elena

    2013-01-01

    Diel vertical migration (DVM) is often assumed to encompass an entire population. However, bimodal nighttime vertical distributions have been observed in various taxa. Mysid shrimp populations also display this pattern with one group concentrated in the pelagia and the other near the bottom. This may indicate alternative migratory strategies, resembling the seasonal partial migrations seen in birds, fishes and amphibians, where only a subset of the population migrates. To assess the persistence of these alternative strategies, we analyzed the nitrogen and carbon stable isotope signatures (as proxies for diet), biochemical indices (as proxies for growth condition), and genetic population divergence in the Baltic mysid Mysis salemaai collected at night in the pelagia and close to the bottom. Stable isotope signatures were significantly different between migrants (pelagic samples) and residents (benthic samples), indicating persistent diet differences, with pelagic mysids having a more uniform and carnivorous diet. Sequencing of the mitochondrial cytochrome subunit I (COI) gene showed genetic differentiation attributable to geographic location but not between benthic and pelagic groups. Divergent migration strategies were however supported by significantly lower gene flow between benthic populations indicating that these groups have a lower predisposition for horizontal migrations compared to pelagic ones. Different migration strategies did not convey measurable growth benefits as pelagic and benthic mysids had similar growth condition indices. Thus, the combination of ecological, biochemical and genetic markers indicate that this partial migration may be a plastic behavioral trait that yields equal growth benefits.

  11. Home environmental influences on children's language and reading skills in a genetically sensitive design: Are socioeconomic status and home literacy environment environmental mediators and moderators?

    Science.gov (United States)

    Chow, Bonnie Wing-Yin; Ho, Connie Suk-Han; Wong, Simpson W L; Waye, Mary M Y; Zheng, Mo

    2017-12-01

    This twin study examined how family socioeconomic status (SES) and home literacy environment (HLE) contributes to Chinese language and reading skills. It included 312 Chinese twin pairs aged 3 to 11. Children were individually administered tasks of Chinese word reading, receptive vocabulary and reading-related cognitive skills, and nonverbal reasoning ability. Information on home environment was collected through parent-reported questionnaires. Results showed that SES and HLE mediated shared environmental influences but did not moderate genetic influences on general language and reading abilities. Also, SES and HLE mediated shared environmental contributions to receptive vocabulary and syllable and rhyme awareness, but not orthographic skills. The findings of this study add to past twin studies that focused on alphabetic languages, suggesting that these links could be universal across languages. They also extend existing findings on SES and HLE's contributions to reading-related cognitive skills. © 2017 Scandinavian Psychological Associations and John Wiley & Sons Ltd.

  12. Gene, environment and cognitive function

    DEFF Research Database (Denmark)

    Xu, Chunsheng; Sun, Jianping; Duan, Haiping

    2015-01-01

    population living under distinct environmental condition as the Western populations. OBJECTIVE: this study aims to explore the genetic and environmental impact on normal cognitive ageing in the Chinese twins. DESIGN/SETTING: cognitive function was measured on 384 complete twin pairs with median age of 50...... factors accounting for 23-33% of the total variances. In contrast, all cognitive performances showed moderate to high influences by the unique environmental factors. CONCLUSIONS: genetic factor and common family environment have a limited contribution to cognitive function in the Chinese adults......BACKGROUND: the genetic and environmental contributions to cognitive function in the old people have been well addressed for the Western populations using twin modelling showing moderate to high heritability. No similar study has been conducted in the world largest and rapidly ageing Chinese...

  13. Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments

    DEFF Research Database (Denmark)

    Librado, Pablo; Der Sarkissian, Clio; Ermini, Luca

    2015-01-01

    Yakutia, Sakha Republic, in the Siberian Far East, represents one of the coldest places on Earth, with winter record temperatures dropping below −70 °C. Nevertheless, Yakutian horses survive all year round in the open air due to striking phenotypic adaptations, including compact body conformations...... dating from the early 19th century and ∼5,200 y ago. By comparing these genomes with the genomes of two Late Pleistocene, 27 domesticated, and three wild Przewalski’s horses, we find that contemporary Yakutian horses do not descend from the native horses that populated the region until the mid......, likely due to the comparatively limited standing variation within gene bodies at the time the population was founded. Genes involved in hair development, body size, and metabolic and hormone signaling pathways represent an essential part of the Yakutian horse adaptive genetic toolkit. Finally, we find...

  14. Simulation based virtual learning environment in medical genetics counseling: an example of bridging the gap between theory and practice in medical education.

    Science.gov (United States)

    Makransky, Guido; Bonde, Mads T; Wulff, Julie S G; Wandall, Jakob; Hood, Michelle; Creed, Peter A; Bache, Iben; Silahtaroglu, Asli; Nørremølle, Anne

    2016-03-25

    Simulation based learning environments are designed to improve the quality of medical education by allowing students to interact with patients, diagnostic laboratory procedures, and patient data in a virtual environment. However, few studies have evaluated whether simulation based learning environments increase students' knowledge, intrinsic motivation, and self-efficacy, and help them generalize from laboratory analyses to clinical practice and health decision-making. An entire class of 300 University of Copenhagen first-year undergraduate students, most with a major in medicine, received a 2-h training session in a simulation based learning environment. The main outcomes were pre- to post- changes in knowledge, intrinsic motivation, and self-efficacy, together with post-intervention evaluation of the effect of the simulation on student understanding of everyday clinical practice were demonstrated. Knowledge (Cohen's d = 0.73), intrinsic motivation (d = 0.24), and self-efficacy (d = 0.46) significantly increased from the pre- to post-test. Low knowledge students showed the greatest increases in knowledge (d = 3.35) and self-efficacy (d = 0.61), but a non-significant increase in intrinsic motivation (d = 0.22). The medium and high knowledge students showed significant increases in knowledge (d = 1.45 and 0.36, respectively), motivation (d = 0.22 and 0.31), and self-efficacy (d = 0.36 and 0.52, respectively). Additionally, 90 % of students reported a greater understanding of medical genetics, 82 % thought that medical genetics was more interesting, 93 % indicated that they were more interested and motivated, and had gained confidence by having experienced working on a case story that resembled the real working situation of a doctor, and 78 % indicated that they would feel more confident counseling a patient after the simulation. The simulation based learning environment increased students' learning, intrinsic motivation, and

  15. Estimation of genetic parameters and genotype-by-environment interactions related to acute ammonia stress in Pacific white shrimp (Litopenaeus vannamei) juveniles at two different salinity levels.

    Science.gov (United States)

    Lu, Xia; Luan, Sheng; Cao, Baoxiang; Meng, Xianhong; Sui, Juan; Dai, Ping; Luo, Kun; Shi, Xiaoli; Hao, Dengchun; Han, Guomin; Kong, Jie

    2017-01-01

    Regarding the practical farming of Litopenaeus vannamei, the deterioration of water quality from intensive culture systems and environmental pollution is a common but troublesome problem in the cultivation of this species. The toxicities that result from deteriorating water quality, such as that from ammonia stress, have lethal effects on juvenile shrimp and can increase their susceptibility to pathogens. The toxicity of ammonia plays an important role in the frequently high mortality during the early stage on shrimp farms. However, little information is available regarding the genetic parameters of the ammonia tolerance of juveniles in the early stage, but this information is necessary to understand the potential for the genetic improvement of this trait. Considering the euryhalinity of L. vannamei and the fact that low salinity can increase the toxicity of ammonia stress, we estimated the heritability of ammonia tolerance in juveniles in 30‰ (normal) and 5‰ (low) salinity in this study using the survival time (ST) at individual level and the survival status at the half-lethal time (SS50) at the family level. In the normal and low salinity conditions and for the merged data, the heritability estimates of the ST (0.784±0.070, 0.575±0.068, and 0.517±0.058, respectively) and SS50 (0.402±0.061, 0.216±0.050, and 0.264±0.050, respectively) were all significantly greater than zero, which indicates that the ammonia-tolerance of shrimp can be greatly improved. So it might provide an alternative method to reduce mortality, help to enhance resistance to pathogens and reduce the occurrence of infectious diseases. The significant positive genetic correlation between ST and body length suggested that ammonia is more toxic to shrimp in the early stage. The medium-strength genetic correlations of the ST and SS50 between the two environments (0.394±0.097 and 0.377±0.098, respectively) indicate a strong genotype-by-environment (G×E) interaction for ammonia tolerance

  16. Detection of gene-environment interactions in the presence of linkage disequilibrium and noise by using genetic risk scores with internal weights from elastic net regression.

    Science.gov (United States)

    Hüls, Anke; Ickstadt, Katja; Schikowski, Tamara; Krämer, Ursula

    2017-06-12

    For the analysis of gene-environment (GxE) interactions commonly single nucleotide polymorphisms (SNPs) are used to characterize genetic susceptibility, an approach that mostly lacks power and has poor reproducibility. One promising approach to overcome this problem might be the use of weighted genetic risk scores (GRS), which are defined as weighted sums of risk alleles of gene variants. The gold-standard is to use external weights from published meta-analyses. In this study, we used internal weights from the marginal genetic effects of the SNPs estimated by a multivariate elastic net regression and thereby provided a method that can be used if there are no external weights available. We conducted a simulation study for the detection of GxE interactions and compared power and type I error of single SNPs analyses with Bonferroni correction and corresponding analysis with unweighted and our weighted GRS approach in scenarios with six risk SNPs and an increasing number of highly correlated (up to 210) and noise SNPs (up to 840). Applying weighted GRS increased the power enormously in comparison to the common single SNPs approach (e.g. 94.2% vs. 35.4%, respectively, to detect a weak interaction with an OR ≈ 1.04 for six uncorrelated risk SNPs and n = 700 with a well-controlled type I error). Furthermore, weighted GRS outperformed the unweighted GRS, in particular in the presence of SNPs without any effect on the phenotype (e.g. 90.1% vs. 43.9%, respectively, when 20 noise SNPs were added to the six risk SNPs). This outperforming of the weighted GRS was confirmed in a real data application on lung inflammation in the SALIA cohort (n = 402). However, in scenarios with a high number of noise SNPs (>200 vs. 6 risk SNPs), larger sample sizes are needed to avoid an increased type I error, whereas a high number of correlated SNPs can be handled even in small samples (e.g. n = 400). In conclusion, weighted GRS with weights from the marginal genetic effects of the

  17. qnr, aac(6')-Ib-cr and qepA genes in Escherichia coli and Klebsiella spp.: genetic environments and plasmid and chromosomal location.

    Science.gov (United States)

    Ruiz, Elena; Sáenz, Yolanda; Zarazaga, Myriam; Rocha-Gracia, Rosa; Martínez-Martínez, Luis; Arlet, Guillaume; Torres, Carmen

    2012-04-01

    To characterize the location and genetic environments of qnr, aac(6')-Ib-cr and qepA genes related to quinolone resistance in 19 Escherichia coli, Klebsiella pneumoniae and Klebsiella oxytoca strains. Genetic environments of the indicated genes were studied by cloning, PCR mapping and sequencing. The location of these genes was analysed by S1-PFGE and PFGE-I-CeuI and hybridization with specific probes. Associated antibiotic resistance mechanisms and molecular typing of strains were also investigated. The studied strains carried the aac(6')-Ib-cr, qepA, qnrS1, qnrB6, qnrB4 and oqxAB genes, with aac(6')-Ib-cr being the most prevalent. E. coli strains belonged to sequence types (STs) ST648, ST131, ST224 and ST205, and K. pneumoniae strains to ST433, ST341, ST152, ST15 and ST431. Different genetic environments of quinolone resistance genes were observed, and some of them had not been previously detected and registered in GenBank. The aac(6')-Ib-cr gene was mainly located in class 1 integrons or associated with the Tn1721 transposon in E. coli and associated with the aac(3)-II gene in Klebsiella. All these structures contained mechanisms of gene acquisition and/or dissemination, such as IS26. The studied quinolone resistance genes were mostly detected in IncF and IncN plasmids in E. coli and in IncR plasmids in Klebsiella, but in some strains the chromosomal location of the aac(6')-Ib-cr gene was detected for the first time. The bla(CTX-M-15), bla(OXA-1), tet(A), aac(3)-II and aph(3')-Ia genes and class 1 integrons were found in most strains. The aac(6')-Ib-cr gene was detected for the first time in the chromosome, although a plasmidic location was the most frequently found, with differentiation of plasmids types in E. coli versus Klebsiella.

  18. Protocol for Assessing the Relative Effects of Environment and Genetics on Antler and Body Growth for a Long-lived Cervid.

    Science.gov (United States)

    Michel, Eric S; Flinn, Emily B; Demarais, Stephen; Strickland, Bronson K; Wang, Guiming; Dacus, Chad M

    2017-08-08

    Cervid phenotype can be placed into one of two categories: efficiency, which promotes survival over extravagant morphometric growth, and luxury, which promotes growth of large weaponry and body size. Populations of the same species display each phenotype depending on environmental conditions. Although antler and body size of male white-tailed deer (Odocoileus virginianus) varies by physiographic region in Mississippi, USA and is strongly correlated with regional variation in nutritional quality, the effects of population-level genetics from native stocks and previous re-stocking efforts cannot be disregarded. This protocol describes how we designed a controlled study, where other factors that influence phenotype, such as age and nutrition, are controlled. We brought wild-caught pregnant females and six-month-old fawns from three distinct physiographic regions in Mississippi, USA to the Mississippi State University Rusty Dawkins Memorial Deer Unit. Deer from the same region were bred to produce a second generation of offspring, allowing us to assess generational responses and maternal effects. All deer ate the same high-quality (20% crude protein deer pellet) diet ad libitum. We uniquely marked each neonate and recorded body mass, hind foot, and total body length. Each subsequent fall, we sedated individuals via remote injection and sampled the same morphometrics plus antlers of adults. We found that all morphometrics increased in size from first to second generation, with full compensation of antler size (regional variation no longer present) and partial compensation of body mass (some evidence of regional variation) evident in the second generation. Second generation males that originated from our poorest quality soil region displayed about a 40% increase in antler size and about a 25% increase in body mass when compared to their wild harvested counterparts. Our results suggest phenotypic variation of wild male white-tailed deer in Mississippi are more related to

  19. Genetic and Environmental Risk Factors, Sleeping Environment, for Allergic Diseases in Infant: Analysis of a Data Subset from the South Kyushu and Okinawa Study Area of Japan Environment and Children's Study.

    Science.gov (United States)

    Miyazaki, Wataru; Lu, Xi; Oda, Masako; Kuroda, Yoshiki; Aoki, Kazuo; Mitsubuchi, Hiroshi; Ohba, Takashi; Katoh, Takahiko

    2016-01-01

    The incidence of infant allergic diseases have increased recently, and it may be caused by multiple influences of both genetic and environmental factors from the fetal stage through infancy. In this study, we analyzed a data subset from the South Kyushu and Okinawa (SKO) Study Area of Japan Environment and Children's Study (JECS) to determine the relationship of allergic diseases in infants with mothers' characteristics and/or infants' life habits, especially sleeping. A total of 3873 mother-infant pairs from the SKO Regional Center of JECS were included. The mothers responded to questionnaires in the first trimester of their pregnancy and the self-reported questionnaire when their infants were 1 year old. Student's t-test, chi-square test, trend test, and logistic regression analysis were carried out to analyze the associations between the infants' allergic diseases and the mothers' genetic characteristics and/or sleeping habits of infants. Maternal allergic diseases were significantly associated with increased infant allergy risk (OR: 1.93, 95% CI: 1.63-2.27). The number of allergic diseases of mothers was also significantly associated with infant allergy, and the trend test showed an increasing risk of infant allergy (phabits, the infants who sleep in the prone position had a higher allergic disease risk than those who sleep in other positions (OR: 1.46, 95% CI: 1.17-1.83). These significant associations were observed regardless of the presence of allergy in mothers. This study suggests that the development of allergic diseases in infants may be caused by the multiple participation of both genetic and environmental factors.

  20. Genetic and Toxigenic Variability within Aspergillus flavus Population Isolated from Maize in Two Diverse Environments in Kenya

    Directory of Open Access Journals (Sweden)

    Sheila Okoth

    2018-01-01

    Full Text Available Aspergillus flavus is the main producer of carcinogenic aflatoxins in agricultural commodities such as maize. This fungus occurs naturally on crops, and produces aflatoxins when environmental conditions are favorable. The aim of this study is to analyse the genetic variability among 109 A. flavus isolates previously recovered from maize sampled from a known aflatoxin-hotspot (Eastern region, Kenya and the major maize-growing area in the Rift Valley (Kenya, and to determine their toxigenic potential. DNA analyses of internal transcribed spacer (ITS regions of ribosomal DNA, partial β-tubulin gene (benA and calmodulin gene (CaM sequences were used. The strains were further analyzed for the presence of four aflatoxin-biosynthesis genes in relation to their capability to produce aflatoxins and other metabolites, targeting the regulatory gene aflR and the structural genes aflP, aflD, and aflQ. In addition, the metabolic profile of the fungal strains was unraveled using state-of-the-art LC-MS/MS instrumentation. The three gene-sequence data grouped the isolates into two major clades, A. minisclerotigenes and A. flavus. A. minisclerotigenes was most prevalent in Eastern Kenya, while A. flavus was common in both regions. A. parasiticus was represented by a single isolate collected from Rift Valley. Diversity existed within the A. flavus population, which formed several subclades. An inconsistency in identification of some isolates using the three markers was observed. The calmodulin gene sequences showed wider variation of polymorphisms. The aflatoxin production pattern was not consistent with the presence of aflatoxigenic genes, suggesting an inability of the primers to always detect the genes or presence of genetic mutations. Significant variation was observed in toxin profiles of the isolates. This is the first time that a profound metabolic profiling of A. flavus isolates was done in Kenya. Positive associations were evident for some metabolites

  1. Genetic and Toxigenic Variability within Aspergillus flavus Population Isolated from Maize in Two Diverse Environments in Kenya.

    Science.gov (United States)

    Okoth, Sheila; De Boevre, Marthe; Vidal, Arnau; Diana Di Mavungu, José; Landschoot, Sofie; Kyallo, Martina; Njuguna, Joyce; Harvey, Jagger; De Saeger, Sarah

    2018-01-01

    Aspergillus flavus is the main producer of carcinogenic aflatoxins in agricultural commodities such as maize. This fungus occurs naturally on crops, and produces aflatoxins when environmental conditions are favorable. The aim of this study is to analyse the genetic variability among 109 A. flavus isolates previously recovered from maize sampled from a known aflatoxin-hotspot (Eastern region, Kenya) and the major maize-growing area in the Rift Valley (Kenya), and to determine their toxigenic potential. DNA analyses of internal transcribed spacer (ITS) regions of ribosomal DNA, partial β-tubulin gene (benA) and calmodulin gene (CaM) sequences were used. The strains were further analyzed for the presence of four aflatoxin-biosynthesis genes in relation to their capability to produce aflatoxins and other metabolites, targeting the regulatory gene aflR and the structural genes aflP, aflD, and aflQ. In addition, the metabolic profile of the fungal strains was unraveled using state-of-the-art LC-MS/MS instrumentation. The three gene-sequence data grouped the isolates into two major clades, A. minisclerotigenes and A. flavus . A. minisclerotigenes was most prevalent in Eastern Kenya, while A. flavus was common in both regions. A. parasiticus was represented by a single isolate collected from Rift Valley. Diversity existed within the A. flavus population, which formed several subclades. An inconsistency in identification of some isolates using the three markers was observed. The calmodulin gene sequences showed wider variation of polymorphisms. The aflatoxin production pattern was not consistent with the presence of aflatoxigenic genes, suggesting an inability of the primers to always detect the genes or presence of genetic mutations. Significant variation was observed in toxin profiles of the isolates. This is the first time that a profound metabolic profiling of A. flavus isolates was done in Kenya. Positive associations were evident for some metabolites, while for

  2. Genetic susceptibility loci, environmental exposures, and Parkinson's disease: a case-control study of gene-environment interactions.

    Science.gov (United States)

    Chung, Sun Ju; Armasu, Sebastian M; Anderson, Kari J; Biernacka, Joanna M; Lesnick, Timothy G; Rider, David N; Cunningham, Julie M; Ahlskog, J Eric; Frigerio, Roberta; Maraganore, Demetrius M

    2013-06-01

    Prior studies causally linked mutations in SNCA, MAPT, and LRRK2 genes with familial Parkinsonism. Genome-wide association studies have demonstrated association of single nucleotide polymorphisms (SNPs) in those three genes with sporadic Parkinson's disease (PD) susceptibility worldwide. Here we investigated the interactions between SNPs in those three susceptibility genes and environmental exposures (pesticides application, tobacco smoking, coffee drinking, and alcohol drinking) also associated with PD susceptibility. Pairwise interactions between environmental exposures and 18 variants (16 SNPs and two variable number tandem repeats, or "VNTRs") in SNCA, MAPT and LRRK2, were investigated using data from 1098 PD cases from the upper Midwest, USA and 1098 matched controls. Environmental exposures were assessed using a validated telephone interview script. Five pairwise interactions had uncorrected P-values coffee drinking × MAPT H1/H2 haplotype or MAPT rs16940806, and alcohol drinking × MAPT rs2435211. None of these interactions remained significant after Bonferroni correction. Secondary analyses in strata defined by type of control (sibling or unrelated), sex, or age at onset of the case also did not identify significant interactions after Bonferroni correction. This study documented limited pairwise interactions between established genetic and environmental risk factors for PD; however, the associations were not significant after correction for multiple testing. Copyright © 2013 Elsevier Ltd. All rights reserved.

  3. Neuregulin 1: a prime candidate for research into gene-environment interactions in schizophrenia? Insights from genetic rodent models

    Directory of Open Access Journals (Sweden)

    Tim eKarl

    2013-08-01

    Full Text Available Schizophrenia is a multi-factorial disease characterized by a high heritability and environmental risk factors. In recent years, an increasing number of researchers worldwide have started investigating the ‘two-hit hypothesis’ of schizophrenia predicting that genetic and environmental risk factors (GxE interactively cause the development of the disorder. This work is starting to produce valuable new animal models and reveal novel insights into the pathophysiology of schizophrenia. This mini review will focus on recent advancements in the field made by challenging mutant and transgenic rodent models for the schizophrenia candidate gene neuregulin 1 (NRG1 with particular environmental factors. It will outline results obtained from mouse and rat models for various Nrg1 isoforms/isoform types (e.g. transmembrane domain Nrg1, Type II Nrg1, which have been exposed to different forms of stress (acute versus chronic, restraint versus social and housing conditions (standard laboratory versus minimally enriched housing. These studies suggest Nrg1 as a prime candidate for GxE interactions in schizophrenia rodent models and that the use of rodent models will enable a better understanding of GxE interactions and the underlying mechanisms.

  4. Detection and Genetic Environment of Pleuromutilin-Lincosamide-Streptogramin A Resistance Genes in Staphylococci Isolated from Pets.

    Science.gov (United States)

    Deng, Fengru; Wang, Huiwen; Liao, Yifei; Li, Jun; Feßler, Andrea T; Michael, Geovana B; Schwarz, Stefan; Wang, Yang

    2017-01-01

    Increasing emergence of staphylococci resistant to pleuromutilins, lincosamides, and streptogramin A (PLS A ) and isolated from humans and pets is a growing public health concern worldwide. Currently, there was only one published study regarding one of the PLS A genes, vga (A) detected in staphylococci isolated from cat. In this study, eleven pleuromutilin-resistant staphylococci from pets and two from their owners were isolated and further characterized for their antimicrobial susceptibilities, plasmid profiles, genotypes, and genetic context of the PLS A resistance genes. The gene sal (A) identified in 11 staphylococcal isolates was found for the first time in Staphylococcus haemolyticus, Staphylococcus epidermidis , and Staphylococcus xylosus . Moreover, these 11 isolates shared the identical regions flanking the sal (A) gene located in the chromosomal DNA. Two S. haemolyticus isolates from a cat and its owner carried similar vga (A) LC plasmids and displayed indistinguishable PFGE patterns. A novel chromosomal multidrug resistance genomic island (MDRGI) containing 13 resistance genes, including lsa (E), was firstly identified in S. epidermidis . In addition, vga (A) LC , sal (A), and lsa (E) were for the first time identified in staphylococcal isolates originating from pet animals. The plasmids, chromosomal DNA region, and MDRGI associated with the PLS A resistance genes vga (A), vga (A) LC , sal (A), and lsa (E) are present in staphylococci isolated from pets and humans and present significant challenges for the clinical management of infections by limiting therapeutic options.

  5. A hybrid genetic-simulated annealing algorithm for the location-inventory-routing problem considering returns under e-supply chain environment.

    Science.gov (United States)

    Li, Yanhui; Guo, Hao; Wang, Lin; Fu, Jing

    2013-01-01

    Facility location, inventory control, and vehicle routes scheduling are critical and highly related problems in the design of logistics system for e-business. Meanwhile, the return ratio in Internet sales was significantly higher than in the traditional business. Many of returned merchandise have no quality defects, which can reenter sales channels just after a simple repackaging process. Focusing on the existing problem in e-commerce logistics system, we formulate a location-inventory-routing problem model with no quality defects returns. To solve this NP-hard problem, an effective hybrid genetic simulated annealing algorithm (HGSAA) is proposed. Results of numerical examples show that HGSAA outperforms GA on computing time, optimal solution, and computing stability. The proposed model is very useful to help managers make the right decisions under e-supply chain environment.

  6. A Hybrid Genetic-Simulated Annealing Algorithm for the Location-Inventory-Routing Problem Considering Returns under E-Supply Chain Environment

    Directory of Open Access Journals (Sweden)

    Yanhui Li

    2013-01-01

    Full Text Available Facility location, inventory control, and vehicle routes scheduling are critical and highly related problems in the design of logistics system for e-business. Meanwhile, the return ratio in Internet sales was significantly higher than in the traditional business. Many of returned merchandise have no quality defects, which can reenter sales channels just after a simple repackaging process. Focusing on the existing problem in e-commerce logistics system, we formulate a location-inventory-routing problem model with no quality defects returns. To solve this NP-hard problem, an effective hybrid genetic simulated annealing algorithm (HGSAA is proposed. Results of numerical examples show that HGSAA outperforms GA on computing time, optimal solution, and computing stability. The proposed model is very useful to help managers make the right decisions under e-supply chain environment.

  7. A Hybrid Genetic-Simulated Annealing Algorithm for the Location-Inventory-Routing Problem Considering Returns under E-Supply Chain Environment

    Science.gov (United States)

    Guo, Hao; Fu, Jing

    2013-01-01

    Facility location, inventory control, and vehicle routes scheduling are critical and highly related problems in the design of logistics system for e-business. Meanwhile, the return ratio in Internet sales was significantly higher than in the traditional business. Many of returned merchandise have no quality defects, which can reenter sales channels just after a simple repackaging process. Focusing on the existing problem in e-commerce logistics system, we formulate a location-inventory-routing problem model with no quality defects returns. To solve this NP-hard problem, an effective hybrid genetic simulated annealing algorithm (HGSAA) is proposed. Results of numerical examples show that HGSAA outperforms GA on computing time, optimal solution, and computing stability. The proposed model is very useful to help managers make the right decisions under e-supply chain environment. PMID:24489489

  8. Automatic Laser Pointer Detection Algorithm for Environment Control Device Systems Based on Template Matching and Genetic Tuning of Fuzzy Rule-Based Systems

    Directory of Open Access Journals (Sweden)

    F.

    2012-04-01

    Full Text Available In this paper we propose a new approach for laser-based environment device control systems based on the automatic design of a Fuzzy Rule-Based System for laser pointer detection. The idea is to improve the success rate of the previous approaches decreasing as much as possible the false offs and increasing the success rate in images with laser spot, i.e., the detection of a false laser spot (since this could lead to dangerous situations. To this end, we propose to analyze both, the morphology and color of a laser spot image together, thus developing a new robust algorithm. Genetic Fuzzy Systems have also been employed to improve the laser spot system detection by means of a fine tuning of the involved membership functions thus reducing the system false offs, which is the main objective in this problem. The system presented in this paper, makes use of a Fuzzy Rule-Based System adjusted by a Genetic Algorithm, which, based on laser morphology and color analysis, shows a better success rate than previous approaches.

  9. Temporal genetic variability and host sources of Escherichia coli associated with fecal pollution from domesticated animals in the shellfish culture environment of Xiangshan Bay, East China Sea

    Energy Technology Data Exchange (ETDEWEB)

    Fu Linglin, E-mail: full1103@yahoo.com.cn [Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310035 (China); Shuai Jiangbing [Zhejiang Entry and Exit Inspection and Quarantine Bureau, Hangzhou 310012 (China); Wang Yanbo; Ma Hongjia [Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310035 (China); Li Jianrong, E-mail: lijianrong@mail.zjgsu.edu.cn [Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310035 (China)

    2011-10-15

    This study was conducted to analyze the genetic variability of Escherichia coli from domesticated animal wastes for microbial source tracking (MST) application in fecal contaminated shellfish growing waters of Xiangshan Bay, East China Sea. (GTG){sub 5} primer was used to generate 1363 fingerprints from E. coli isolated from feces of known 9 domesticated animal sources around this shellfish culture area. Jackknife analysis of the complete (GTG){sub 5}-PCR DNA fingerprint library indicated that isolates were assigned to the correct source groups with an 84.28% average rate of correct classification. Based on one-year source tracking data, the dominant sources of E. coli were swine, chickens, ducks and cows in this water area. Moreover, annual and spatial changes of E. coli concentrations and host sources may affect the level and distribution of zoonotic pathogen species in waters. Our findings will further contribute to preventing fecal pollution in aquatic environments and quality control of shellfish. - Highlights: > The host-origin library developed by (GTG){sub 5}-PCR could be used to shellfish water MST. > Fecal pollution of Xiangshan Bay arose from multiple sources of agricultural wastes. > High level of E. coli concentration in shellfish water increases the health risk. > Annual changes of E. coli host sources affect distribution of zoonotic pathogens. - The temporal genetic variability and dominant host sources of E. coli in fecal contaminated shellfish growing waters of Xiangshan Bay was characterized.

  10. Temporal genetic variability and host sources of Escherichia coli associated with fecal pollution from domesticated animals in the shellfish culture environment of Xiangshan Bay, East China Sea

    International Nuclear Information System (INIS)

    Fu Linglin; Shuai Jiangbing; Wang Yanbo; Ma Hongjia; Li Jianrong

    2011-01-01

    This study was conducted to analyze the genetic variability of Escherichia coli from domesticated animal wastes for microbial source tracking (MST) application in fecal contaminated shellfish growing waters of Xiangshan Bay, East China Sea. (GTG) 5 primer was used to generate 1363 fingerprints from E. coli isolated from feces of known 9 domesticated animal sources around this shellfish culture area. Jackknife analysis of the complete (GTG) 5 -PCR DNA fingerprint library indicated that isolates were assigned to the correct source groups with an 84.28% average rate of correct classification. Based on one-year source tracking data, the dominant sources of E. coli were swine, chickens, ducks and cows in this water area. Moreover, annual and spatial changes of E. coli concentrations and host sources may affect the level and distribution of zoonotic pathogen species in waters. Our findings will further contribute to preventing fecal pollution in aquatic environments and quality control of shellfish. - Highlights: → The host-origin library developed by (GTG) 5 -PCR could be used to shellfish water MST. → Fecal pollution of Xiangshan Bay arose from multiple sources of agricultural wastes. → High level of E. coli concentration in shellfish water increases the health risk. → Annual changes of E. coli host sources affect distribution of zoonotic pathogens. - The temporal genetic variability and dominant host sources of E. coli in fecal contaminated shellfish growing waters of Xiangshan Bay was characterized.

  11. Genetic susceptibility to breast cancer in French-Canadians: role of carcinogen-metabolizing enzymes and gene-environment interactions.

    Science.gov (United States)

    Krajinovic, M; Ghadirian, P; Richer, C; Sinnett, H; Gandini, S; Perret, C; Lacroix, A; Labuda, D; Sinnett, D

    2001-04-15

    Breast cancer is the most frequent malignancy among women. Since genetic factors such as BRCA1 and BRCA2 as well as reproductive history constitute only 30% of the cause, environmental exposure may play a significant role in the development of breast cancer. Likewise, the relevant enzymes involved in the biotransformation of xenobiotics (from tobacco smoke, diet or other environmental sources) might play a role in breast carcinogenesis. Since individuals with modified ability to metabolize these carcinogens could have a different risk for breast cancer, we investigated the role of cytochromes P-450 (CYP1A1, CYP2D6), glutathione-S-transferases (GSTM1, GSTT1, GSTP1) and N-acetyltransferases (NAT1, NAT2) gene variants in breast carcinogenesis. A case-control study was conducted on 149 women with breast carcinoma and 207 healthy controls, both of French-Canadian origin. The CYP1A1*4 allele was found to be a significant risk determinant of breast carcinoma (OR = 3.3, 95% CI 1.1-9.7), particularly among post-menopausal women (OR = 4.0, 95% CI 1.2-13.8). The frequency of NAT2 rapid acetylators was increased among smokers (OR = 2.6, 95% CI 0.8-8.2), while the NAT1*10 allele conferred a 4-fold increase in risk among women who consumed well-done meat (OR = 4.4, 95% CI 1.0-18.9). These data suggest that CYP1A1*4, NAT1 and NAT2 variants are involved in the susceptibility to breast carcinoma by modifying the impact of exogenous and/or endogenous exposures. Copyright 2001 Wiley-Liss, Inc.

  12. Distinctiveness of Saudi Arabian EFL Learners

    Directory of Open Access Journals (Sweden)

    Manssour Habbash

    2016-04-01

    Full Text Available In view of the increasing concern among English language teachers dealing with students from Saudi Arabia, as it manifests in TESOL community discussions, about the uniqueness of Saudi Arabian EFL learners, this paper attempts to document the outcome of a study of their distinctiveness from the perspective of expatriate teachers working for PYPs (Preparatory Year Programs in Saudi Arabia. This study examines the distinctiveness with regard to the learning attitudes of Saudi students that are often cultivated by the culture and academic environment in their homeland. Employing an emic approach for collecting the required data an analysis was carried out in light of the other studies on ‘education’ in Saudi Arabia that have particular reference to the factors that can positively influence student motivation, student success and the academic environment. The findings were used in constructing the rationale behind such distinctiveness. Assuming that the outcome of the discussion on the findings of this exploration can be helpful for teachers in adapting their teaching methodology and improving their teacher efficacy in dealing with students both from the kingdom and in the kingdom, some recommendations are made. Keywords: China Distinctiveness, Saudi Arabian University context, Expatriate teachers’ perspective, Distinctiveness Theory

  13. A circulating reservoir of pathogenic-like CD4+ T cells shares a genetic and phenotypic signature with the inflamed synovial micro-environment.

    Science.gov (United States)

    Spreafico, Roberto; Rossetti, Maura; van Loosdregt, Jorg; Wallace, Carol A; Massa, Margherita; Magni-Manzoni, Silvia; Gattorno, Marco; Martini, Alberto; Lovell, Daniel J; Albani, Salvatore

    2016-02-01

    Systemic immunological processes are profoundly shaped by the micro-environments where antigen recognition occurs. Identifying molecular signatures distinctive of such processes is pivotal to understand pathogenic immune responses and manipulate them for therapeutic purposes. Unfortunately, direct investigation of peripheral tissues, enriched in pathogenic T cells, is often impossible or imposingly invasive in humans. Conversely, blood is easily accessible, but pathogenic signatures are diluted systemically as a result of the strict compartmentalisation of immune responses. In this work, we aimed at defining immune mediators shared between the bloodstream and the synovial micro-environment, and relevant for disease activity in autoimmune arthritis. CD4(+) T cells from blood and synovium of patients with juvenile idiopathic arthritis (JIA) were immunophenotyped by flow cytometry. The TCR repertoire of a circulating subset showing similarity with the synovium was analysed through next-generation sequencing of TCR β-chain CDR3 to confirm enrichment in synovial clonotypes. Finally, clinical relevance was established by monitoring the size of this subset in the blood of patients with JIA and rheumatoid arthritis (RA). We identified a small subset of circulating CD4(+) T cells replicating the phenotypical signature of lymphocytes infiltrating the inflamed synovium. These circulating pathogenic-like lymphocytes (CPLs) were enriched in synovial clonotypes and they exhibited strong production of pro-inflammatory cytokines. Importantly, CPLs were expanded in patients with JIA, who did not respond to therapy, and also correlated with disease activity in patients with RA. CPLs provide an accessible reservoir of pathogenic cells recirculating into the bloodstream and correlating with disease activity, to be exploited for diagnostic and research purposes. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go

  14. Genetic variation and control of chloroplast pigment concentrations in Picea rubens, Picea mariana and their hybrids. I. Ambient and elevated [CO2] environments

    International Nuclear Information System (INIS)

    Major, J.E.; Barsi, D.C.; Mosseler, A.; Campbell, M.

    2007-01-01

    A significant decline has been noted in the red spruce component of the Acadian forest region in eastern Canada and the northeastern United States as a result of excessive harvesting, acid rain, and global warming. Two experiments were performed to acquire benchmark adaptive traits for information from a red spruce (RS) (Picea rubens Sargand) and black spruce (BS) (P. mariana (Mill.) B.S.P.) genetic complex grown in ambient carbon dioxide concentration ([CO 2 ]). The first experiment involved RS-BS seed sources from across the RS geographical range, while the second experiment involved an intra- and interspecific controlled-cross experiment to determine if RS and BS have unique chloroplast pigment concentrations and traits that reflect adaptations to different ecological niches. The objective was to determine species origin and hybrid variations in chloroplast pigment concentrations; examine the effect of elevated [CO 2 ] on chloroplast pigments; determine the inheritance of chloroplast pigments and examine the relationship of chloroplast pigment concentrations of trees grown at ambient [CO 2 ] with productivity traits and nitrogen concentrations. The traits related to light-energy processing have pronounced ecological implications for plant health. Results from the species origin experiment showed that total chlorophyll concentration was about 15 per cent higher in ambient [CO 2 ] than in elevated [CO 2 ]. In ambient [CO 2 ], BS populations had 11 per cent higher total chlorophyll and carotenoid concentrations than RS populations. Results from the controlled-cross experiment showed that families with a hybrid index of 25 per cent RS had the highest total chlorophyll concentrations, and families with hybrid indices of 75 and 100 had the lowest amounts. A predominant male effect for chlorophyll concentration was noted. In ambient and elevated [CO 2 ] environments, crosses with BS males had 10.6 and 17.6 per cent higher total chlorophyll concentrations than crosses

  15. Convergent Metabolic Specialization through Distinct Evolutionary Paths in Pseudomonas aeruginosa

    DEFF Research Database (Denmark)

    La Rosa, Ruggero; Johansen, Helle Krogh; Molin, Søren

    2018-01-01

    Evolution by natural selection under complex and dynamic environmental conditions occurs through intricate and often counterintuitive trajectories affecting many genes and metabolic solutions. To study short- and long-term evolution of bacteria in vivo, we used the natural model system of cystic...... of adaptive evolution. We show that central metabolic pathways of three distinct Pseudomonas aeruginosa lineages coevolving within the same environment become restructured at the cost of versatility during long-term colonization. Cell physiology changes from naive to adapted phenotypes resulted in (i...... requirements. Interestingly, although convergence was evidenced at the phenotypic level of metabolic specialization, comparative genomics disclosed diverse mutational patterns underlying the different evolutionary trajectories. Therefore, distinct combinations of genetic and regulatory changes converge...

  16. Genetic characterization of Shiga toxin-producing Escherichia coli (STEC) and atypical enteropathogenic Escherichia coli (EPEC) isolates from goat's milk and goat farm environment.

    Science.gov (United States)

    Álvarez-Suárez, María-Elena; Otero, Andrés; García-López, María-Luisa; Dahbi, Ghizlane; Blanco, Miguel; Mora, Azucena; Blanco, Jorge; Santos, Jesús A

    2016-11-07

    The aim of this study was to characterize a collection of 44 Shiga toxin-producing (STEC) and enteropathogenic Escherichia coli (EPEC) isolated from goat milk and goat farm environment. Of the 19 STEC isolates, five (26.3%) carried the stx1 gene, four (21.1%) the stx2 gene and 10 (52.6%) presented both stx genes. Six (31.6%) STEC strains were eae-positive and belonged to serotypes related to severe human disease (O157:H7 and O5:HNM). Another seven STEC strains were of serotype O146:H21 and three of serotype O166:H28, also linked to human disease. The STEC strains isolated from goat milk were of serotypes potentially pathogenic for humans. All the 25 EPEC isolates were considered atypical (aEPEC) and one aEPEC strain was of serotype O26:H11, a serotype frequently isolated in children with diarrhea. Multilocus sequence typing (MLST) was carried out with seven housekeeping genes and 23 sequence types (ST) were detected, 14 of them newly described. Twelve STs grouped STEC isolates and 11 STs grouped EPEC isolates. Genetic typing by pulsed field gel electrophoresis (PFGE) resulted in 38 patterns which grouped in 10 clusters. Well-defined groups were also observed for strains of pathogenic serotypes. In conclusion, strains of STEC and aEPEC belonging to serotypes related to severe human disease have been detected in goat milk and the goat farm environment. Ruminants are an important reservoir of STEC strains and the role of these animals as carriers of other pathogenic types of E. coli seems to be an emerging concern. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. Distinctive Dynamic Capabilities for New Business Creation

    DEFF Research Database (Denmark)

    Rosenø, Axel; Enkel, Ellen; Mezger, Florian

    2013-01-01

    This study examines the distinctive dynamic capabilities for new business creation in established companies. We argue that these are very different from those for managing incremental innovation within a company's core business. We also propose that such capabilities are needed in both slow...... and fast-paced industries, and that similarities exist across industries. Hence, the study contributes to dynamic capabilities literature by: 1) identifying the distinctive dynamic capabilities for new business creation; 2) shifting focus away from dynamic capabilities in environments characterised by high...... clock-speed and uncertainty towards considering dynamic capabilities for the purpose of developing new businesses, which also implies a high degree of uncertainty. Based on interviews with 33 companies, we identify distinctive dynamic capabilities for new business creation, find that dynamic...

  18. Temporal genetic variability and host sources of Escherichia coli associated with fecal pollution from domesticated animals in the shellfish culture environment of Xiangshan Bay, East China Sea.

    Science.gov (United States)

    Fu, Ling-Lin; Shuai, Jiang-Bing; Wang, Yanbo; Ma, Hong-Jia; Li, Jian-Rong

    2011-10-01

    This study was conducted to analyze the genetic variability of Escherichia coli from domesticated animal wastes for microbial source tracking (MST) application in fecal contaminated shellfish growing waters of Xiangshan Bay, East China Sea. (GTG)(5) primer was used to generate 1363 fingerprints from E. coli isolated from feces of known 9 domesticated animal sources around this shellfish culture area. Jackknife analysis of the complete (GTG)(5)-PCR DNA fingerprint library indicated that isolates were assigned to the correct source groups with an 84.28% average rate of correct classification. Based on one-year source tracking data, the dominant sources of E. coli were swine, chickens, ducks and cows in this water area. Moreover, annual and spatial changes of E. coli concentrations and host sources may affect the level and distribution of zoonotic pathogen species in waters. Our findings will further contribute to preventing fecal pollution in aquatic environments and quality control of shellfish. Copyright © 2011 Elsevier Ltd. All rights reserved.

  19. Phosphate Fertilizer and Growing Environment Change the Phytochemicals, Oil Quality, and Nutritional Composition of Roundup Ready Genetically Modified and Conventional Soybean.

    Science.gov (United States)

    Scilewski da Costa Zanatta, Tatiane; Manica-Berto, Roberta; Ferreira, Cristiano Dietrich; Cardozo, Michele Maciel Crizel; Rombaldi, Cesar Valmor; Zambiazi, Rui Carlos; Dias, Álvaro Renato Guerra

    2017-04-05

    Phosphorus (P) intake, genotype, and growth environment in soybean cultivation can affect the composition of the soybean. This experiment was conducted in two locations (microregions I and II) using a randomized complete block design, including conventional soybean (BRS Sambaíba) and genetically modified (GM) [Msoy 9144 Roundup Ready (RR)] cultivars and varying doses of phosphorus fertilizer (0, 60, 120, and 240 kg/ha P 2 O 5 ). Soybeans were evaluated for chemical composition, total phenols, phytic acid content, individual isoflavone content, antioxidant activity, oil quality, fatty acid profile, total carotenoid content, and individual tocopherol contents. Multivariate analysis facilitated reduction in the number of variables with respect to soybean genotype (conventional BRS Sambaíba and GM Msoy 9144 RR), dose of P 2 O 5 fertilizer, and place of cultivation (microregion I and II). BRS Sambaíba had higher concentrations of β-glucosides, malonylglucosides, glycitein, and genistein than Msoy 9144 RR, which showed a higher concentration of daidzein. The highest concentrations of isoflavones and fatty acids were observed in soybeans treated with 120 and 240 kg/ha P 2 O 5 , regardless of the location and cultivar.

  20. Prenatal screening and genetics

    DEFF Research Database (Denmark)

    Alderson, P; Aro, A R; Dragonas, T

    2001-01-01

    Although the term 'genetic screening' has been used for decades, this paper discusses how, in its most precise meaning, genetic screening has not yet been widely introduced. 'Prenatal screening' is often confused with 'genetic screening'. As we show, these terms have different meanings, and we...... examine definitions of the relevant concepts in order to illustrate this point. The concepts are i) prenatal, ii) genetic screening, iii) screening, scanning and testing, iv) maternal and foetal tests, v) test techniques and vi) genetic conditions. So far, prenatal screening has little connection...... with precisely defined genetics. There are benefits but also disadvantages in overstating current links between them in the term genetic screening. Policy making and professional and public understandings about screening could be clarified if the distinct meanings of prenatal screening and genetic screening were...

  1. Genetics of complex disorders.

    Science.gov (United States)

    Kere, Juha

    2010-05-21

    The success stories of identifying genes in Mendelian disorders have stimulated research that aims at identifying the genetic determinants in complex disorders, in which both genetics, environment and chance affect the pathogenetic processes. This review summarizes the brief history and lessons learned from genetic analysis of complex disorders and outlines some landscapes ahead for medical research. 2010. Published by Elsevier Inc.

  2. Education and Training: Is There Any Longer a Useful Distinction?

    Science.gov (United States)

    Hager, Paul; Laurent, John

    1990-01-01

    Although education and training were distinct concepts when Taylorism dominated the workplace, it is no longer appropriate to separate them. Today's highly competitive environment requires the education of a flexible, multiskilled workforce, not training for narrowly defined employment tasks. (SK)

  3. Prevalence and characterization of plasmid-mediated blaESBL with their genetic environment in Escherichia coli and Klebsiella pneumoniae in patients with pneumonia.

    Science.gov (United States)

    Wang, Xiao-rong; Chen, Ji-chao; Kang, Yu; Jiang, Ning; An, Shu-chang; Gao, Zhan-cheng

    2012-03-01

    The extended spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli) and Klebsiella pneumoniae (K. pneumoniae) are the major pathogens causing pneumonia and have a significant impact on the clinical course. Limited data exist on molecular characterization of ESBL-producing E. coli and K. pneumoniae that cause pneumonia. The aim of this study was to investigate the comprehensive multilevel characteristics of E. coli and K. pneumoniae causing pneumonia in China for the first time. E. coli (17) and K. pneumoniae (21) isolates responsible for pneumonia were isolated from 1270 specimens collected in a prospective multi-center study in eight teaching hospitals in China from June to December in 2007. The susceptibilities, ESBL confirmation, sequence typing, blaCTX-M and blaSHV genes, their genetic environment and plasmid Inc/rep types were determined. Sixteen E. coli (94.1%) and eleven K. pneumoniae (52.4%) isolates were ESBL producers. About 77.8% and 66.7% of them were resistance to ciprofloxacin and levofloxacin, and 100% were susceptible to imipenem. The most prevalent ESBL gene was CTX-M-14, followed by SHV-2, CTX-M-15, CTX-M-3, CTX-M-65, SHV-12, SHV-26 and SHV-28. SHV-1 and SHV-11 were also detected and coexisted with blaCTX-Ms in five strains, and three strains contained only SHV-1. All CTX-M-14 were detected ISEcp1 upstream and nine were found IS903 downstream and the majority of them (64.3%) were carried by IncF plasmids. All blaSHV were flanked by recF and deoR, located on IncF, IncN, IncX and IncH plasmids. Two SHV-2, one SHV-1 and the only SHV-28 were further preceded by IS26. Genes lacY and lacZ were detected at further upstream of two blaSHV-1. The K. pneumoniae carrying SHV-28 was susceptible to β-lactams, and no mutations or deletions in gene or promoter sequences were identified to account for susceptibility. Multilocus sequence typing experiments showed the ESBL-producing strains were genetically diverse. The rate of occurrence of blaESBL in E

  4. Distinct signatures of diversifying selection revealed by genome analysis of respiratory tract and invasive bacterial populations.

    Science.gov (United States)

    Shea, Patrick R; Beres, Stephen B; Flores, Anthony R; Ewbank, Amy L; Gonzalez-Lugo, Javier H; Martagon-Rosado, Alexandro J; Martinez-Gutierrez, Juan C; Rehman, Hina A; Serrano-Gonzalez, Monica; Fittipaldi, Nahuel; Ayers, Stephen D; Webb, Paul; Willey, Barbara M; Low, Donald E; Musser, James M

    2011-03-22

    Many pathogens colonize different anatomical sites, but the selective pressures contributing to survival in the diverse niches are poorly understood. Group A Streptococcus (GAS) is a human-adapted bacterium that causes a range of infections. Much effort has been expended to dissect the molecular basis of invasive (sterile-site) infections, but little is known about the genomes of strains causing pharyngitis (streptococcal "sore throat"). Additionally, there is essentially nothing known about the genetic relationships between populations of invasive and pharyngitis strains. In particular, it is unclear if invasive strains represent a distinct genetic subpopulation of strains that cause pharyngitis. We compared the genomes of 86 serotype M3 GAS pharyngitis strains with those of 215 invasive M3 strains from the same geographical location. The pharyngitis and invasive groups were highly related to each other and had virtually identical phylogenetic structures, indicating they belong to the same genetic pool. Despite the overall high degree of genetic similarity, we discovered that strains from different host environments (i.e., throat, normally sterile sites) have distinct patterns of diversifying selection at the nucleotide level. In particular, the pattern of polymorphisms in the hyaluronic acid capsule synthesis operon was especially different between the two strain populations. This finding was mirrored by data obtained from full-genome analysis of strains sequentially cultured from nonhuman primates. Our results answer the long-standing question of the genetic relationship between GAS pharyngitis and invasive strains. The data provide previously undescribed information about the evolutionary history of pathogenic microbes that cause disease in different anatomical sites.

  5. Moral Fantasy in Genetic Engineering.

    Science.gov (United States)

    Boone, C. Keith

    1984-01-01

    Discusses the main ethical issues generated by the new genetics and suggests ways to think about them. Concerns include "playing God," violation of the natural order of the universe, and abuse of genetic technology. Critical distinctions for making difficult decisions about genetic engineering issues are noted. (DH)

  6. Genetic conservation and management of the California endemic, Torrey pine (Pinus torreyanaParry): Implications of genetic rescue in a genetically depauperate species.

    Science.gov (United States)

    Hamilton, Jill A; Royauté, Raphaël; Wright, Jessica W; Hodgskiss, Paul; Ledig, F Thomas

    2017-09-01

    Rare species present a challenge under changing environmental conditions as the genetic consequences of rarity may limit species ability to adapt to environmental change. To evaluate the evolutionary potential of a rare species, we assessed variation in traits important to plant fitness using multigenerational common garden experiments. Torrey pine, Pinus torreyana Parry, is one of the rarest pines in the world, restricted to one mainland and one island population. Morphological differentiation between island and mainland populations suggests adaptation to local environments may have contributed to trait variation. The distribution of phenotypic variances within the common garden suggests distinct population-specific growth trajectories underlay genetic differences, with the island population exhibiting substantially reduced genetic variance for growth relative to the mainland population. Furthermore, F1 hybrids, representing a cross between mainland and island trees, exhibit increased height accumulation and fecundity relative to mainland and island parents. This may indicate genetic rescue via intraspecific hybridization could provide the necessary genetic variation to persist in environments modified as a result of climate change. Long-term common garden experiments, such as these, provide invaluable resources to assess the distribution of genetic variance that may inform conservation strategies to preserve evolutionary potential of rare species, including genetic rescue.

  7. Serum club cell protein 16 is associated with asymptomatic airway responsiveness in adults: Findings from the French epidemiological study on the genetics and environment of asthma.

    Science.gov (United States)

    Rava, Marta; Le Moual, Nicole; Dumont, Xavier; Guerra, Stefano; Siroux, Valerie; Jacquemin, Benedicte; Kauffmann, Francine; Bernard, Alfred; Nadif, Rachel

    2015-11-01

    Club cell secretory protein (CC-16) is a sensitive biomarker of airways epithelium integrity. It has gained interest as a biological marker in chronic lung diseases because of its presumed relationship to inflammation. Little is known about the association between CC-16 serum level and asthma, lung function and airway responsiveness (AR). Serum CC-16 level was determined by latex immunoassay in 1298 participants from the French Epidemiological case-control and family-based study on Genetics and Environment of Asthma (EGEA) (mean age 43 years; 49% men, 38% with asthma). Pre-bronchodilator lung function (forced expiratory volume in 1 s (FEV1 ), forced vital capacity (FVC) and FEV1 /FVC) and degree of AR, expressed as a function of the dose-response slope to methacholine test were measured. Standardized residuals CC-16 z-scores were obtained by regressing CC-16 level on the glomerular filtration rate. CC-16 z-scores were correlated with asthma, lung function and AR in participants with and without asthma. CC-16 geometric mean level was 12.4 μg/L (range: 2.2-70.6 μg/L). In participants without asthma, lower CC-16 z-scores was associated with impaired FEV1 /FVC% (β = 0.50 (95% CI: 0.06, 0.95) and with higher degree of AR (β = 0.24 (95% CI: 0.09, 0.39)). CC-16 was not associated with impaired lung function or AR in participants with asthma. Lower CC-16 serum level was associated with impaired lung function and AR, suggesting that serum CC-16 level may reflect early damages to the lung epithelium in adults without asthma. © 2015 Asian Pacific Society of Respirology.

  8. Limited Pollen Dispersal Contributes to Population Genetic Structure but Not Local Adaptation in Quercus oleoides Forests of Costa Rica.

    Directory of Open Access Journals (Sweden)

    Nicholas John Deacon

    Full Text Available Quercus oleoides Cham. and Schlect., tropical live oak, is a species of conservation importance in its southern range limit of northwestern Costa Rica. It occurs in high-density stands across a fragmented landscape spanning a contrasting elevation and precipitation gradient. We examined genetic diversity and spatial genetic structure in this geographically isolated and genetically distinct population. We characterized population genetic diversity at 11 nuclear microsatellite loci in 260 individuals from 13 sites. We monitored flowering time at 10 sites, and characterized the local environment in order to compare observed spatial genetic structure to hypotheses of isolation-by-distance and isolation-by-environment. Finally, we quantified pollen dispersal distances and tested for local adaptation through a reciprocal transplant experiment in order to experimentally address these hypotheses.High genetic diversity is maintained in the population and the genetic variation is significantly structured among sampled sites. We identified 5 distinct genetic clusters and average pollen dispersal predominately occurred over short distances. Differences among sites in flowering phenology and environmental factors, however, were not strictly associated with genetic differentiation. Growth and survival of upland and lowland progeny in their native and foreign environments was expected to exhibit evidence of local adaptation due to the more extreme dry season in the lowlands. Seedlings planted in the lowland garden experienced much higher mortality than seedlings in the upland garden, but we did not identify evidence for local adaptation.Overall, this study indicates that the Costa Rican Q. oleoides population has a rich population genetic history. Despite environmental heterogeneity and habitat fragmentation, isolation-by-distance and isolation-by-environment alone do not explain spatial genetic structure. These results add to studies of genetic structure by

  9. Counselor Identity: Conformity or Distinction?

    Science.gov (United States)

    McLaughlin, Jerry E.; Boettcher, Kathryn

    2009-01-01

    The authors explore 3 debates in other disciplines similar to counseling's identity debate in order to learn about common themes and outcomes. Conformity, distinction, and cohesion emerged as common themes. They conclude that counselors should retain their distinctive, humanistic approach rather than conforming to the dominant, medical approach.

  10. Distinct patterns of epigenetic marks and transcription factor binding ...

    Indian Academy of Sciences (India)

    Distinct patterns of epigenetic marks and transcription factor binding sites across promoters of sense-intronic long noncoding RNAs. Sourav Ghosh, Satish Sati, Shantanu Sengupta and Vinod Scaria. J. Genet. 94, 17–25. Gencode V9 lncRNA gene : 11004. Known lncRNA : 1175. Novel lncRNA : 5898. Putative lncRNA :.

  11. Distinction

    OpenAIRE

    2010-01-01

    Pr Serge Haroche La Médaille d’or 2009 du CNRS est décernée au Pr Serge Haroche, titulaire de la chaire de Physique quantique depuis 2001. Serge Haroche est spécialiste de physique atomique et d’optique quantique. Il est l’un des fondateurs de l’électrodynamique quantique en cavité, domaine qui permet, par des expériences conceptuellement simples, d’éclairer les fondements de la théorie quantique et de réaliser des prototypes de systèmes de traitement quantique de l’information. Serge Haroche...

  12. Circular Lows, a Genetically Distinct Subset of Coronae?

    Science.gov (United States)

    McDaniel, K.; Hansen, V. L.

    2005-03-01

    We mapped several circular lows, coronae marked by amphitheater-like depressions to evaluate models of formation. These features are not easily accommodated by a diapiric model and suggest that coronae may form by more than one mechanism.

  13. Genetically distinct subsets within ANCA-associated vasculitis

    DEFF Research Database (Denmark)

    Lyons, Paul A; Rayner, Tim F; Trivedi, Sapna

    2012-01-01

    Antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis is a severe condition encompassing two major syndromes: granulomatosis with polyangiitis (formerly known as Wegener's granulomatosis) and microscopic polyangiitis. Its cause is unknown, and there is debate about whether it is a single...

  14. The Genetic Architecture of Type 1 Diabetes

    Directory of Open Access Journals (Sweden)

    Samuel T Jerram

    2017-08-01

    Full Text Available Type 1 diabetes (T1D is classically characterised by the clinical need for insulin, the presence of disease-associated serum autoantibodies, and an onset in childhood. The disease, as with other autoimmune diseases, is due to the interaction of genetic and non-genetic effects, which induce a destructive process damaging insulin-secreting cells. In this review, we focus on the nature of this interaction, and how our understanding of that gene–environment interaction has changed our understanding of the nature of the disease. We discuss the early onset of the disease, the development of distinct immunogenotypes, and the declining heritability with increasing age at diagnosis. Whilst Human Leukocyte Antigens (HLA have a major role in causing T1D, we note that some of these HLA genes have a protective role, especially in children, whilst other non-HLA genes are also important. In adult-onset T1D, the disease is often not insulin-dependent at diagnosis, and has a dissimilar immunogenotype with reduced genetic predisposition. Finally, we discuss the putative nature of the non-genetic factors and how they might interact with genetic susceptibility, including preliminary studies of the epigenome associated with T1D.

  15. Genetic Engineering and Human Mental Ecology: Interlocking Effects and Educational Considerations.

    Science.gov (United States)

    Affifi, Ramsey

    2017-01-01

    This paper describes some likely semiotic consequences of genetic engineering on what Gregory Bateson has called "the mental ecology" (1979) of future humans, consequences that are less often raised in discussions surrounding the safety of GMOs (genetically modified organisms). The effects are as follows: an increased 1) habituation to the presence of GMOs in the environment, 2) normalization of empirically false assumptions grounding genetic reductionism, 3) acceptance that humans are capable and entitled to decide what constitutes an evolutionary improvement for a species, 4) perception that the main source of creativity and problem solving in the biosphere is anthropogenic. Though there are some tensions between them, these effects tend to produce self-validating webs of ideas, actions, and environments, which may reinforce destructive habits of thought. Humans are unlikely to safely develop genetic technologies without confronting these escalating processes directly. Intervening in this mental ecology presents distinct challenges for educators, as will be discussed.

  16. Genetic Variability, Genotype × Environment Interaction, Correlation, and GGE Biplot Analysis for Grain Iron and Zinc Concentration and Other Agronomic Traits in RIL Population of Sorghum (Sorghum bicolor L. Moench)

    Science.gov (United States)

    Phuke, Rahul M.; Anuradha, Kotla; Radhika, Kommineni; Jabeen, Farzana; Anuradha, Ghanta; Ramesh, Thatikunta; Hariprasanna, K.; Mehtre, Shivaji P.; Deshpande, Santosh P.; Anil, Gaddameedi; Das, Roma R.; Rathore, Abhishek; Hash, Tom; Reddy, Belum V. S.; Kumar, Are Ashok

    2017-01-01

    The low grain iron and zinc densities are well documented problems in food crops, affecting crop nutritional quality especially in cereals. Sorghum is a major source of energy and micronutrients for majority of population in Africa and central India. Understanding genetic variation, genotype × environment interaction and association between these traits is critical for development of improved cultivars with high iron and zinc. A total of 336 sorghum RILs (Recombinant Inbred Lines) were evaluated for grain iron and zinc concentration along with other agronomic traits for 2 years at three locations. The results showed that large variability exists in RIL population for both micronutrients (Iron = 10.8 to 76.4 mg kg−1 and Zinc = 10.2 to 58.7 mg kg−1, across environments) and agronomic traits. Genotype × environment interaction for both micronutrients (iron and zinc) was highly significant. GGE biplots comparison for grain iron and zinc showed greater variation across environments. The results also showed that G × E was substantial for grain iron and zinc, hence wider testing needed for taking care of G × E interaction to breed micronutrient rich sorghum lines. Iron and zinc concentration showed high significant positive correlation (across environment = 0.79; p 0.60, in individual environments) for Fe and Zn and other traits studied indicating its suitability to map QTL for iron and zinc. PMID:28529518

  17. Genetic engineering compared to natural genetic variations.

    Science.gov (United States)

    Arber, Werner

    2010-11-30

    By comparing strategies of genetic alterations introduced in genetic engineering with spontaneously occurring genetic variation, we have come to conclude that both processes depend on several distinct and specific molecular mechanisms. These mechanisms can be attributed, with regard to their evolutionary impact, to three different strategies of genetic variation. These are local nucleotide sequence changes, intragenomic rearrangement of DNA segments and the acquisition of a foreign DNA segment by horizontal gene transfer. Both the strategies followed in genetic engineering and the amounts of DNA sequences thereby involved are identical to, or at least very comparable with, those involved in natural genetic variation. Therefore, conjectural risks of genetic engineering must be of the same order as those for natural biological evolution and for conventional breeding methods. These risks are known to be quite low. There is no scientific reason to assume special long-term risks for GM crops. For future agricultural developments, a road map is designed that can be expected to lead, by a combination of genetic engineering and conventional plant breeding, to crops that can insure food security and eliminate malnutrition and hunger for the entire human population on our planet. Public-private partnerships should be formed with the mission to reach the set goals in the coming decades. Copyright © 2010 Elsevier B.V. All rights reserved.

  18. Genetic differentiation across multiple spatial scales of the Red Sea of the corals Stylophora pistillata and Pocillopora verrucosa

    KAUST Repository

    Monroe, Alison

    2015-12-01

    Observing populations at different spatial scales gives greater insight into the specific processes driving genetic differentiation and population structure. Here we determined population connectivity across multiple spatial scales in the Red Sea to determine the population structures of two reef building corals Stylophora pistillata and Pocillopora verrucosa. The Red sea is a 2,250 km long body of water with extremely variable latitudinal environmental gradients. Mitochondrial and microsatellite markers were used to determine distinct lineages and to look for genetic differentiation among sampling sites. No distinctive population structure across the latitudinal gradient was discovered within this study suggesting a phenotypic plasticity of both these species to various environments. Stylophora pistillata displayed a heterogeneous distribution of three distinct genetic populations on both a fine and large scale. Fst, Gst, and Dest were all significant (p-value<0.05) and showed moderate genetic differentiation between all sampling sites. However this seems to be byproduct of the heterogeneous distribution, as no distinct genetic population breaks were found. Stylophora pistillata showed greater population structure on a fine scale suggesting genetic selection based on fine scale environmental variations. However, further environmental and oceanographic data is needed to make more inferences on this structure at small spatial scales. This study highlights the deficits of knowledge of both the Red Sea and coral plasticity in regards to local environmental conditions.

  19. Etiological Distinction of Working Memory Components in Relation to Mathematics.

    Science.gov (United States)

    Lukowski, Sarah L; Soden, Brooke; Hart, Sara A; Thompson, Lee A; Kovas, Yulia; Petrill, Stephen A

    2014-11-01

    Working memory has been consistently associated with mathematics achievement, although the etiology of these relations remains poorly understood. The present study examined the genetic and environmental underpinnings of math story problem solving, timed calculation, and untimed calculation alongside working memory components in 12-year-old monozygotic ( n = 105) and same-sex dizygotic ( n = 143) twin pairs. Results indicated significant phenotypic correlation between each working memory component and all mathematics outcomes ( r = 0.18 - 0.33). Additive genetic influences shared between the visuo-spatial sketchpad and mathematics achievement was significant, accounting for roughly 89% of the observed correlation. In addition, genetic covariance was found between the phonological loop and math story problem solving. In contrast, despite there being a significant observed relationship between phonological loop and timed and untimed calculation, there was no significant genetic or environmental covariance between the phonological loop and timed or untimed calculation skills. Further analyses indicated that genetic overlap between the visuo-spatial sketchpad and math story problem solving and math fluency was distinct from general genetic factors, whereas g , phonological loop, and mathematics shared generalist genes. Thus, although each working memory component was related to mathematics, the etiology of their relationships may be distinct.

  20. Mitochondrial Genetics and Cancer

    Directory of Open Access Journals (Sweden)

    Safarina G. Malik

    2017-02-01

    Full Text Available The first modern human, the Mitochondrial Eve, was traced back to Africa about 200,000 years ago, based on the variation in the mitochondrial DNA (mtDNA. An eruption of a super volcano, Mount Toba, in Sumatra 70,000 years ago may have led to a 'nuclear winter', followed by a 1,000-year ice age. This cold snap would have made life difficult; genetic evidence indicated a sharp reduction in population size around this time, reaching approximately 10,000 individuals. Once the climate started to improve, our ancestors recovered from this near-extinction event. The population expanded, and some courageous explorers ventured beyond Africa. Around 50,000 years ago some of these brave ancestors had successfully crossed the globe to South East Asia and Australia. Some of them settled in the Indonesian archipelago, forming the first settlement of prehistoric Indonesia. The second migration happened around 10,000 years ago, where a group of hunter-gatherers followed the now-submerged river systems that once ran from mainland Asia between the modern islands of Sumatera, Java, and Borneo. Then, around 4,000 years ago the third group of ancestors arrived. This agricultural community brought along their culture of pottery, plant cultivation, and animal domestication, co-inciding with the vast spread of Austronesian languages. Therefore, it is likely that the Indonesian archipelago hosts a wide range of linguistic, ethnic and genetic diversity.1 Nowadays, the modern Indonesia is home to around 700 ethnic populations, each with distinct cultural and linguistic characteristics, representing vast genome diversity. Our ancestors’ decision to embark on a sea travel and take on its related lifestyle has influenced the development of susceptibility and resistance to various diseases observed today. During the prolonged travel, our ancestors were subjected to changes in global climate and geographic dynamic, which strongly influenced and shaped the genetic background

  1. Caging and Uncaging Genetics.

    Directory of Open Access Journals (Sweden)

    Tom J Little

    2016-07-01

    Full Text Available It is important for biology to understand if observations made in highly reductionist laboratory settings generalise to harsh and noisy natural environments in which genetic variation is sorted to produce adaptation. But what do we learn by studying, in the laboratory, a genetically diverse population that mirrors the wild? What is the best design for studying genetic variation? When should we consider it at all? The right experimental approach depends on what you want to know.

  2. Host Genetic and Environmental Effects on Mouse Cecum Microbiota

    Energy Technology Data Exchange (ETDEWEB)

    Campbell, James H [ORNL; Foster, Carmen M [ORNL; Vishnivetskaya, Tatiana A [ORNL; Campbell, Alisha G [ORNL; Yang, Zamin Koo [ORNL; Wymore, Ann [ORNL; Palumbo, Anthony Vito [ORNL; Podar, Mircea [ORNL

    2012-01-01

    The mammalian gut harbors complex and variable microbial communities, across both host phylogenetic space and conspecific individuals. A synergy of host genetic and environmental factors shape these communities and account for their variability, but their individual contributions and the selective pressures involved are still not well understood. We employed barcoded pyrosequencing of V1-2 and V4 regions of bacterial small subunit ribosomal RNA genes to characterize the effects of host genetics and environment on cecum assemblages in 10 genetically distinct, inbred mouse strains. Eight of these strains are the foundation of the Collaborative Cross (CC), a panel of mice derived from a genetically diverse set of inbred founder strains, designed specifically for complex trait analysis. Diversity of gut microbiota was characterized by complementing phylogenetic and distance-based, sequence-clustering approaches. Significant correlations were found between the mouse strains and their gut microbiota, reflected by distinct bacterial communities. Cohabitation and litter had a reduced, although detectable effect, and the microbiota response to these factors varied by strain. We identified bacterial phylotypes that appear to be discriminative and strain-specific to each mouse line used. Cohabitation of different strains of mice revealed an interaction of host genetic and environmental factors in shaping gut bacterial consortia, in which bacterial communities became more similar but retained strain specificity. This study provides a baseline analysis of intestinal bacterial communities in the eight CC progenitor strains and will be linked to integrated host genotype, phenotype and microbiota research on the resulting CC panel.

  3. Defining poverty as distinctively human

    Directory of Open Access Journals (Sweden)

    H.P.P. Lötter

    2007-05-01

    Full Text Available While it is relatively easy for most people to identify human beings suffering from poverty, it is rather more difficult to come to a proper understanding of poverty. In this article the author wants to deepen our understanding of poverty by interpreting the conventional definitions of poverty in a new light. The article starts with a defence of a claim that poverty is a concept uniquely applicable to humans. It then present a critical discussion of the distinction between absolute and relative poverty and it is then argued that a revision of this distinction can provide general standards applicable to humans everywhere.

  4. Genetic divergence across habitats in the widespread coral Seriatopora hystrix and its associated Symbiodinium.

    Directory of Open Access Journals (Sweden)

    Pim Bongaerts

    2010-05-01

    Full Text Available Coral reefs are hotspots of biodiversity, yet processes of diversification in these ecosystems are poorly understood. The environmental heterogeneity of coral reef environments could be an important contributor to diversification, however, evidence supporting ecological speciation in corals is sparse. Here, we present data from a widespread coral species that reveals a strong association of host and symbiont lineages with specific habitats, consistent with distinct, sympatric gene pools that are maintained through ecologically-based selection.Populations of a common brooding coral, Seriatopora hystrix, were sampled from three adjacent reef habitats (spanning a approximately 30 m depth range at three locations on the Great Barrier Reef (n = 336. The populations were assessed for genetic structure using a combination of mitochondrial (putative control region and nuclear (three microsatellites markers for the coral host, and the ITS2 region of the ribosomal DNA for the algal symbionts (Symbiodinium. Our results show concordant genetic partitioning of both the coral host and its symbionts across the different habitats, independent of sampling location.This study demonstrates that coral populations and their associated symbionts can be highly structured across habitats on a single reef. Coral populations from adjacent habitats were found to be genetically isolated from each other, whereas genetic similarity was maintained across similar habitat types at different locations. The most parsimonious explanation for the observed genetic partitioning across habitats is that adaptation to the local environment has caused ecological divergence of distinct genetic groups within S. hystrix.

  5. Outbreak caused by a multi-resistant Klebsiella pneumoniae strain of new sequence type ST341 carrying new genetic environments of aac(6')-Ib-cr and qnrS1 genes in a neonatal intensive care unit in Spain.

    Science.gov (United States)

    Ruiz, Elena; Rojo-Bezares, Beatriz; Sáenz, Yolanda; Olarte, Inés; Esteban, Inés; Rocha-Gracia, Rosa; Zarazaga, Myriam; Torres, Carmen

    2010-11-01

    An outbreak due to a Klebsiella pneumoniae clone occurred in a neonatal intensive care unit of a Spanish Hospital in which three newborns were infected (all with gestational age ≤29 weeks; two of them died) and seven were colonized (gestational age >32 weeks; none died). One K. pneumoniae strain per patient was further characterized. The 10 strains showed an indistinguishable pulsed-field-gel-electrophoresis pattern, were typed in the phylogenetic group KpI and were ascribed into a new sequence type registered as ST341. All 10 strains presented the same multiple-antibiotic-resistant phenotype, showed extended-spectrum-beta-lactamase production, and harbored the bla(CTX-M-15), bla(SHV-11), bla(OXA-1,)aac(6')-Ib-cr, qnrS1, aac(3)-II, aph(3')-Ia and aadA5 resistance genes. No class 1 or class 2 integrons were detected. The bla(CTX-M-15) gene presented the following genetic environment: ISEcp1-bla(CTX-M-15)-orf477. These strains contained two copies of the aac(6')-Ib-cr gene included in the following new genetic environments: aac(3)-II-IS26-aac(6')-Ib-cr-bla(OXA-1) and aac(3)-II-IS26-ΔcatB3-bla(OXA-1)-aac(6')-Ib-cr (registered at GenBank with accession numbers GQ438247 and GQ438248, respectively). The genetic environment of the qnrS1 gene (IS26-ΔISEcl2-qnrS1) (GenBank accession number GQ438249) was also not described previously. The aac(6')-Ib-cr, qnrS1, bla(CTX-M-15), aac(3)-II, and bla(OXA-1) genes, located in a plasmid of 33.5 kb, could be transferred to Escherichia coli by transformation. Copyright © 2010 Elsevier GmbH. All rights reserved.

  6. Educational Psychology: The Distinctive Contribution

    Science.gov (United States)

    Cameron, R. J.

    2006-01-01

    This paper, written in the twenty-first anniversary year of the journal "Educational Psychology in Practice", attempts to uncover those distinctive aspects of the discipline and the practice of applied psychology in general and educational psychology in particular. After considering some of the reasons for attempting this task at this point in…

  7. Qualitative genetics - examples from soybean and other crops

    Science.gov (United States)

    Qualitative genetics, also known as Mendelian genetics or transmission genetics, refers to those genetic traits that have a distinct appearance (phenotype) and are controlled by one or few genes. Examples of qualitative genetics include response to abiotic and biotic stresses, and anatomical, morpho...

  8. KEYNOTE ADDRESS: CONSERVATION GENETICS OF FRESHWATER ORGANISMS

    OpenAIRE

    WEISS S.

    2005-01-01

    This manuscript serves as a summary of both the importance of genetics in conservation, and the range of methodological approaches available. Two somewhat distinct realms of conservation genetics are outlined. The first theoretically rests upon the field of population genetics, and primarily concerns itself with the conservation of genetic diversity within and among populations, both in the wild and captivity. Basic concepts such as heterozygosity, genetic drift, and effective population size...

  9. A shifting mutational landscape in 6 nutritional states: Stress-induced mutagenesis as a series of distinct stress input-mutation output relationships.

    Directory of Open Access Journals (Sweden)

    Ram P Maharjan

    2017-06-01

    Full Text Available Environmental stresses increase genetic variation in bacteria, plants, and human cancer cells. The linkage between various environments and mutational outcomes has not been systematically investigated, however. Here, we established the influence of nutritional stresses commonly found in the biosphere (carbon, phosphate, nitrogen, oxygen, or iron limitation on both the rate and spectrum of mutations in Escherichia coli. We found that each limitation was associated with a remarkably distinct mutational profile. Overall mutation rates were not always elevated, and nitrogen, iron, and oxygen limitation resulted in major spectral changes but no net increase in rate. Our results thus suggest that stress-induced mutagenesis is a diverse series of stress input-mutation output linkages that is distinct in every condition. Environment-specific spectra resulted in the differential emergence of traits needing particular mutations in these settings. Mutations requiring transpositions were highest under iron and oxygen limitation, whereas base-pair substitutions and indels were highest under phosphate limitation. The unexpected diversity of input-output effects explains some important phenomena in the mutational biases of evolving genomes. The prevalence of bacterial insertion sequence transpositions in the mammalian gut or in anaerobically stored cultures is due to environmentally determined mutation availability. Likewise, the much-discussed genomic bias towards transition base substitutions in evolving genomes can now be explained as an environment-specific output. Altogether, our conclusion is that environments influence genetic variation as well as selection.

  10. A shifting mutational landscape in 6 nutritional states: Stress-induced mutagenesis as a series of distinct stress input-mutation output relationships.

    Science.gov (United States)

    Maharjan, Ram P; Ferenci, Thomas

    2017-06-01

    Environmental stresses increase genetic variation in bacteria, plants, and human cancer cells. The linkage between various environments and mutational outcomes has not been systematically investigated, however. Here, we established the influence of nutritional stresses commonly found in the biosphere (carbon, phosphate, nitrogen, oxygen, or iron limitation) on both the rate and spectrum of mutations in Escherichia coli. We found that each limitation was associated with a remarkably distinct mutational profile. Overall mutation rates were not always elevated, and nitrogen, iron, and oxygen limitation resulted in major spectral changes but no net increase in rate. Our results thus suggest that stress-induced mutagenesis is a diverse series of stress input-mutation output linkages that is distinct in every condition. Environment-specific spectra resulted in the differential emergence of traits needing particular mutations in these settings. Mutations requiring transpositions were highest under iron and oxygen limitation, whereas base-pair substitutions and indels were highest under phosphate limitation. The unexpected diversity of input-output effects explains some important phenomena in the mutational biases of evolving genomes. The prevalence of bacterial insertion sequence transpositions in the mammalian gut or in anaerobically stored cultures is due to environmentally determined mutation availability. Likewise, the much-discussed genomic bias towards transition base substitutions in evolving genomes can now be explained as an environment-specific output. Altogether, our conclusion is that environments influence genetic variation as well as selection.

  11. Genetic Gains in Yield and Yield Related Traits under Drought Stress and Favorable Environments in a Maize Population Improved Using Marker Assisted Recurrent Selection

    Directory of Open Access Journals (Sweden)

    Folusho Bankole

    2017-05-01

    Full Text Available The objective of marker assisted recurrent selection (MARS is to increase the frequency of favorable marker alleles in a population before inbred line extraction. This approach was used to improve drought tolerance and grain yield (GY in a biparental cross of two elite drought tolerant lines. The testcrosses of randomly selected 50 S1 lines from each of the three selection cycles (C0, C1, C2 of the MARS population, parental testcrosses and the cross between the two parents (F1 were evaluated under drought stress (DS and well watered (WW well as under rainfed conditions to determine genetic gains in GY and other agronomic traits. Also, the S1 lines derived from each selection types were genotyped with single nucleotide polymorphism (SNP markers. Testcrosses derived from C2 produced significantly higher grain field under DS than those derived from C0 with a relative genetic gain of 7% per cycle. Also, the testcrosses of S1 lines from C2 showed an average genetic gain of 1% per cycle under WW condition and 3% per cycle under rainfed condition. Molecular analysis revealed that the frequency of favorable marker alleles increased from 0.510 at C0 to 0.515 at C2, while the effective number of alleles (Ne per locus decreased from C0 (1.93 to C2 (1.87. Our results underscore the effectiveness of MARS for improvement of GY under DS condition.

  12. Genetic analysis of the rates of conception using a longitudinal threshold model with random regression in dairy crossbreeding within a tropical environment.

    Science.gov (United States)

    Buaban, Sayan; Kuchida, Keigo; Suzuki, Mitsuyoshi; Masuda, Yutaka; Boonkum, Wuttigrai; Duangjinda, Monchai

    2016-08-01

    This study was designed to: (i) estimate genetic parameters and breeding values for conception rates (CR) using the repeatability threshold model (RP-THM) and random regression threshold models (RR-THM); and (ii) compare covariance functions for modeling the additive genetic (AG) and permanent environmental (PE) effects in the RR-THM. The CR was defined as the outcome of an insemination. A data set of 130 592 first-lactation insemination records of 55 789 Thai dairy cows, calving between 1996 and 2011, was used in the analyses. All models included fixed effects of year × month of insemination, breed × day in milk to insemination class and age at calving. The random effects consisted of herd × year interaction, service sire, PE, AG and residual. Variance components were estimated using a Bayesian method via Gibbs sampling. Heritability estimates of CR ranged from 0.032 to 0.067, 0.037 to 0.165 and 0.045 to 0.218 for RR-THM with the second, third and fourth-order of Legendre polynomials, respectively. The heritability estimated from RP-THM was 0.056. Model comparisons based on goodness of fit, predictive abilities, predicted service results of animal, and pattern of genetic parameter estimates, indicated that the model which fit the desired outcome of insemination was the RR-THM with two regression coefficients. © 2015 Japanese Society of Animal Science.

  13. Genetic connectivity across marginal habitats: the elephants of the Namib Desert.

    Science.gov (United States)

    Ishida, Yasuko; Van Coeverden de Groot, Peter J; Leggett, Keith E A; Putnam, Andrea S; Fox, Virginia E; Lai, Jesse; Boag, Peter T; Georgiadis, Nicholas J; Roca, Alfred L

    2016-09-01

    Locally isolated populations in marginal habitats may be genetically distinctive and of heightened conservation concern. Elephants inhabiting the Namib Desert have been reported to show distinctive behavioral and phenotypic adaptations in that severely arid environment. The genetic distinctiveness of Namibian desert elephants relative to other African savanna elephant (Loxodonta africana) populations has not been established. To investigate the genetic structure of elephants in Namibia, we determined the mitochondrial (mt) DNA control region sequences and genotyped 17 microsatellite loci in desert elephants (n = 8) from the Hoanib River catchment and the Hoarusib River catchment. We compared these to the genotypes of elephants (n = 77) from other localities in Namibia. The mtDNA haplotype sequences and frequencies among desert elephants were similar to those of elephants in Etosha National Park, the Huab River catchment, the Ugab River catchment, and central Kunene, although the geographically distant Caprivi Strip had different mtDNA haplotypes. Likewise, analysis of the microsatellite genotypes of desert-dwelling elephants revealed that they were not genetically distinctive from Etosha elephants, and there was no evidence for isolation by distance across the Etosha region. These results, and a review of the historical record, suggest that a high learning capacity and long-distance migrations allowed Namibian elephants to regularly shift their ranges to survive in the face of high variability in climate and in hunting pressure.

  14. Grima: A Distinct Emotion Concept?

    Science.gov (United States)

    Schweiger Gallo, Inge; Fernández-Dols, José-Miguel; Gollwitzer, Peter M; Keil, Andreas

    2017-01-01

    People experience an unpleasant sensation when hearing a scratch on a board or plate. The present research focuses on this aversive experience known in Spanish as 'grima' with no equivalent term in English and German. We hypothesized that this aversive experience constitutes a distinctive, separate emotional concept. In Study 1, we found that the affective meaning of 'grima' was closer to disgust than to other emotion concepts. Thus, in Study 2 we explored the features of grima and compared them with disgust . As grima was reported to be predominantly elicited by certain auditory stimuli and associated with a distinctive physiological pattern, Study 3 used direct measures of physiological arousal to test the assumption of a distinctive pattern of physiological responses elicited by auditory stimuli of grima and disgust, and found different effects on heart rate but not on skin conductance. In Study 4, we hypothesized that only participants with an implementation intention geared toward down-regulating grima would be able to successfully weaken the grima- but not disgust- experience. Importantly, this effect was specific as it held true for the grima-eliciting sounds only, but did not affect disgust-related sounds. Finally, Study 5 found that English and German speakers lack a single accessible linguistic label for the pattern of aversive reactions termed by Spanish speaking individuals as 'grima', whereas the elicitors of other emotions were accessible and accurately identified by German, English, as well as Spanish speakers.

  15. Occlusal and facial features in Amazon indigenous: An insight into the role of genetics and environment in the etiology dental malocclusion.

    Science.gov (United States)

    de Souza, Bento Sousa; Bichara, Livia Monteiro; Guerreiro, João Farias; Quintão, Cátia Cardoso Abdo; Normando, David

    2015-09-01

    Indigenous people of the Xingu river present a similar tooth wear pattern, practise exclusive breast-feeding, no pacifier use, and have a large intertribal genetic distance. To revisit the etiology of dental malocclusion features considering these population characteristics. Occlusion and facial features of five semi-isolated Amazon indigenous populations (n=351) were evaluated and compared to previously published data from urban Amazon people. Malocclusion prevalence ranged from 33.8% to 66.7%. Overall this prevalence is lower when compared to urban people mainly regarding posterior crossbite. A high intertribal diversity was found. The Arara-Laranjal village had a population with a normal face profile (98%) and a high rate of normal occlusion (66.2%), while another group from the same ethnicity presented a high prevalence of malocclusion, the highest occurrence of Class III malocclusion (32.6%) and long face (34.8%). In Pat-Krô village the population had the highest prevalence of Class II malocclusion (43.9%), convex profile (38.6%), increased overjet (36.8%) and deep bite (15.8%). Another village's population, from the same ethnicity, had a high frequency of anterior open bite (22.6%) and anterior crossbite (12.9%). The highest occurrence of bi-protrusion was found in the group with the lowest prevalence of dental crowding, and vice versa. Supported by previous genetic studies and given their similar environmental conditions, the high intertribal diversity of occlusal and facial features suggests that genetic factors contribute substantially to the morphology of occlusal and facial features in the indigenous groups studied. The low prevalence of posterior crossbite in the remote indigenous populations compared with urban populations may relate to prolonged breastfeeding and an absence of pacifiers in the indigenous groups. Copyright © 2015 Elsevier Ltd. All rights reserved.

  16. Genetic variation and population structure in Oryza ...

    Indian Academy of Sciences (India)

    We assessed the nature and distribution of genetic variation among 11 populations of O. malampuzhaensis using random amplified polymorphic DNA markers. The analysis revealed low genetic variation in O. malampuzhaensis. Cluster analysis of pairwise genetic distances of populations revealed three distinct clusters ...

  17. Genetic and Nongenetic Determinants of Cell Growth Variation Assessed by High-Throughput Microscopy

    Science.gov (United States)

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

    2013-01-01

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

  18. The genetic epidemiology of irrational fears and phobias in men.

    Science.gov (United States)

    Kendler, K S; Myers, J; Prescott, C A; Neale, M C

    2001-03-01

    Much of our knowledge of the role of genetic factors in the etiology of phobias comes from one population-based sample of female twins. We examined the sources of individual differences in the risks for phobias and their associated irrational fears in male twins. In personal interviews with both members of 1198 male-male twin pairs (707 monozygotic [MZ] and 491 dizygotic [DZ]) ascertained from a population-based registry, we assessed the lifetime history of agoraphobia and social, animal, situational, and blood/injury phobias as well as their associated irrational fears. Twin resemblance was assessed by means of probandwise concordance, odds ratios, tetrachoric correlations, and univariate and multivariate biometrical model fitting. The suggestive results obtained by analysis of phobias only were supported by analyzing both fears and phobias. All 5 phobia subtypes aggregate within twin-pairs. This aggregation is due largely or solely to genetic factors with heritability of liabilities ranging from 25% to 37%. Multivariate analysis revealed a common genetic factor, genetic factors specific to each subtype, and a common familial-environmental factor. In male subjects, genetic risk factors, which are partially common across all subtypes and partially subtype specific, play a moderate role in the etiology of phobias and their associated irrational fears. Family environment probably has an impact on risk for agoraphobia and social phobia. The genetic liability to blood/injury phobias is not distinct from those of the more typical phobias.

  19. An Investigation into the Use of Hypermutation as an Adaptive Operator in Genetic Algorithms Having Continuous, Time-Dependent Nonstationary Environments

    Science.gov (United States)

    1990-12-11

    1989. Astrom , Karl Johan and Wittenmark, Bjom, Adaptive Control, Addison-Wesley Publishing Company, Reading, Massachusetts (1989). Deb, 1989. Deb...quality. In water turbines, the blade angle giving the max- imum output power varies with the water speed ( Astrom , 1989). , " Distribution/__ Manuscript...dominance and codomi- nance operators, to transform a population structure into a form that can be evaluated by the environment. 8. References Astrom

  20. Is the atopic march related to confounding by genetics and early-life environment? A systematic review of sibship and twin data.

    Science.gov (United States)

    Khan, S J; Dharmage, S C; Matheson, M C; Gurrin, L C

    2018-01-01

    A popular hypothesis known as the atopic march proposes a set of sequential allergy and respiratory disorders in early childhood contributes enormously to the burden of disease in developed countries. Although the concept of the atopic march has been refined and strengthened by many cross-sectional and longitudinal studies linking eczema as the initial manifestation with progression to hay fever and then asthma, there is yet no definitive proof that the atopic march is the primary causal factor in childhood allergic disease. This debate is mainly related to the controversy around potential confounding of these associations by genetic and environmental factors. Family studies are ideally suited to unravelling the role of these factors. While multiple reviews have synthesized evidence from studies investigating this question, no review to date has explored specific evidence generated by twin and sibling studies to understand the aetiology of atopic march diseases. Our aim was to conduct a systematic review of twin and sibling studies that examine the allergic phenotypes that form the atopic march, to determine whether such analyses of data from these studies attempt to control for the effect confounding by shared factors, and to report estimates of the magnitude of associations between multiple phenotypes. Our review suggests that (1) genetics play a bigger role predisposing eczema to hay fever and eczema to asthma than environmental factors, and (2) the link between eczema and asthma and hay fever is independent of shared early-life environmental factors. © 2017 EAACI and John Wiley and Sons A/S. Published by John Wiley and Sons Ltd.

  1. Objectives, criteria and methods for using molecular genetic data in priority setting for conservation of animal genetic resources.

    Science.gov (United States)

    Boettcher, P J; Tixier-Boichard, M; Toro, M A; Simianer, H; Eding, H; Gandini, G; Joost, S; Garcia, D; Colli, L; Ajmone-Marsan, P

    2010-05-01

    The genetic diversity of the world's livestock populations is decreasing, both within and across breeds. A wide variety of factors has contributed to the loss, replacement or genetic dilution of many local breeds. Genetic variability within the more common commercial breeds has been greatly decreased by selectively intense breeding programmes. Conservation of livestock genetic variability is thus important, especially when considering possible future changes in production environments. The world has more than 7500 livestock breeds and conservation of all of them is not feasible. Therefore, prioritization is needed. The objective of this article is to review the state of the art in approaches for prioritization of breeds for conservation, particularly those approaches that consider molecular genetic information, and to identify any shortcomings that may restrict their application. The Weitzman method was among the first and most well-known approaches for utilization of molecular genetic information in conservation prioritization. This approach balances diversity and extinction probability to yield an objective measure of conservation potential. However, this approach was designed for decision making across species and measures diversity as distinctiveness. For livestock, prioritization will most commonly be performed among breeds within species, so alternatives that measure diversity as co-ancestry (i.e. also within-breed variability) have been proposed. Although these methods are technically sound, their application has generally been limited to research studies; most existing conservation programmes have effectively primarily based decisions on extinction risk. The development of user-friendly software incorporating these approaches may increase their rate of utilization.

  2. Cryptic relatedness in epidemiologic collections accessed for genetic association studies: experiences from the Epidemiologic Architecture for Genes Linked to Environment (EAGLE) study and the National Health and Nutrition Examination Surveys (NHANES).

    Science.gov (United States)

    Malinowski, Jennifer; Goodloe, Robert; Brown-Gentry, Kristin; Crawford, Dana C

    2015-01-01

    Epidemiologic collections have been a major resource for genotype-phenotype studies of complex disease given their large sample size, racial/ethnic diversity, and breadth and depth of phenotypes, traits, and exposures. A major disadvantage of these collections is they often survey households and communities without collecting extensive pedigree data. Failure to account for substantial relatedness can lead to inflated estimates and spurious associations. To examine the extent of cryptic relatedness in an epidemiologic collection, we as the Epidemiologic Architecture for Genes Linked to Environment (EAGLE) study accessed the National Health and Nutrition Examination Surveys (NHANES) linked to DNA samples ("Genetic NHANES") from NHANES III and NHANES 1999-2002. NHANES are population-based cross-sectional surveys conducted by the National Center for Health Statistics at the Centers for Disease Control and Prevention. Genome-wide genetic data is not yet available in NHANES, and current data use agreements prohibit the generation of GWAS-level data in NHANES samples due issues in maintaining confidentiality among other ethical concerns. To date, only hundreds of single nucleotide polymorphisms (SNPs) genotyped in a variety of candidate genes are available for analysis in NHANES. We performed identity-by-descent (IBD) estimates in three self-identified subpopulations of Genetic NHANES (non-Hispanic white, non- Hispanic black, and Mexican American) using PLINK software to identify potential familial relationships from presumed unrelated subjects. We then compared the PLINKidentified relationships to those identified by an alternative method implemented in Kinship-based INference for Genome-wide association studies (KING). Overall, both methods identified familial relationships in NHANES III and NHANES 1999-2002 for all three subpopulations, but little concordance was observed between the two methods due in major part to the limited SNP data available in Genetic NHANES

  3. THE ATTITUDE TOWARDS GENETICALLY MODIFIED ORGANISMS (GMO’S) AND THEIR EFFECT ON HEALTH AND ENVIRONMENT IN SOUTHWESTERN NIGERIA : SCIENTISTS’ PERCEPTION

    OpenAIRE

    O OLADELE; O Akinsorotan

    2007-01-01

    The study was carried out in South Western Nigeria to evaluate the perception of scientists at Universities and Research Institutes on the effect of GMO’s on health and environment. It is proposed that scientists’ perception would influence the on-going debate as preclude to Nigeria being a signatory to the use of GMO’s. Using a simple random sampling technique, a total of one hundred and eighty respondents were selected from a population of 760 and then interviewed. Data were collected th...

  4. Review of genetic concepts

    International Nuclear Information System (INIS)

    Robinson, A.

    1984-01-01

    In recent years, practitioners of medicine have become increasingly aware of the importance of genetics in the understanding of physical and mental health and in the management of disease. The last decades have witnessed unprecedented developments in genetics that have increased our understanding of the basic processes of heredity enormously. New techniques and understanding have provided insights directly applicable to medicine. The fundamental fact of heredity may be considered the ability of living organisms to produce offspring that resemble their parents more than others. One of the basic characteristics of the human condition is the uniqueness and diversity of all individuals. This results from their genetic individuality (with the exception of identical twins) and the interaction of the genetic constitution (the genome) with the environment, which is generally unique to the individual as well. In short, the interaction of genes with the environment is what confers biologic uniqueness to all humans

  5. Genetics, lifestyle and environment. UK Biobank is an open access resource following the lives of 500,000 participants to improve the health of future generations.

    Science.gov (United States)

    Trehearne, Andrew

    2016-03-01

    UK Biobank is a long-term prospective epidemiology study having recruited and now following the lives of 500,000 people in England, Scotland and Wales, aged 40-69 years when they joined the study (Sudlow et al., PLoS Med 12(3):e1001779, 2015). Participants were recruited by letter and asked to attend one of 22 assessment centres in towns and cities across Britain, where they provided consent, answered detailed questions about their health and lifestyle, had body measures taken and donated blood, urine and saliva. Participants provided consent for the long-term follow-up of their health via medical records, such as general practice and hospital records, cancer and death records. Samples are being stored long term for a wide range of analyses, including genetic. The resource is open to all bona fide scientists from the UK and overseas, academic and industry who register via its access management system. Summary of UK Biobank data can be viewed via its Data Showcase and the resource will be strengthened over time as the results of new analyses and studies are returned, health links and participants provide additional information about themselves. Some will attend full repeat assessment visits. UK Biobank is open for business, and it hopes researchers will find it a valuable tool to improve the health of future generations.

  6. Gene-environment interaction affects substance P and neurokinin A in the entorhinal cortex and periaqueductal grey in a genetic animal model of depression: implications for the pathophysiology of depression

    DEFF Research Database (Denmark)

    Husum, Henriette; Wörtwein, Gitta; Andersson, Weronika

    2008-01-01

    Evidence implies a role for corticotropin-releasing hormone (CRH) and tachykinins, e.g. substance P (SP) and neurokinin A (NKA) in the pathophysiology of depression. We have previously shown that SP- and NKA-like immunoreactivity (-LI) concentrations were altered in the frontal cortex and striatum...... of the congenitally 'depressed' Flinders Sensitive Line (FSL) compared to the Flinders Resistant Line (FRL) control rats. It is also known that environmental stress may affect brain levels of tachykinins. In view of these results we decided to superimpose maternal deprivation, an early life environmental stressor......, onto the genetically predisposed 'depressed' FSL rats and the FRL control rats and use this paradigm as a model of gene-environment interaction. The adult animals were sacrificed, adrenal glands and brains dissected out and SP-, NKA- and CRH-LI levels were determined in ten discrete brain regions...

  7. A genetic model based on evapoconcentration for sediment-hosted exotic-Cu mineralization in arid environments: the case of the El Tesoro Central copper deposit, Atacama Desert, Chile

    Science.gov (United States)

    Fernández-Mort, A.; Riquelme, R.; Alonso-Zarza, A. M.; Campos, E.; Bissig, T.; Mpodozis, C.; Carretier, S.; Herrera, C.; Tapia, M.; Pizarro, H.; Muñoz, S.

    2017-12-01

    Although the formation of exotic-Cu deposits is controlled by multiple factors, the role of the sedimentary environment has not been well defined. We present a case study of the El Tesoro Central exotic-Cu deposit located in the Atacama Desert of northern Chile. This deposit consists of two mineralized bodies hosted within Late Cenozoic gravels deposited in an arid continental environment dominated by alluvial fans with sub-surficial ponded water bodies formed at the foot of these fans or within the interfan areas. Both exotic-Cu orebodies mostly consist of chrysocolla, copper wad, atacamite, paratacamite, quartz, opal, and calcite. The most commonly observed paragenesis comprises chrysocolla, silica minerals, and calcite and records a progressive increase in pH, which is notably influenced by evaporation. The results of stable isotope analyses (δ13C and δ18O) and hydrogeochemical simulations confirm that evapoconcentration is the main controlling factor in the exotic-Cu mineralization at El Tesoro Central. This conclusion complements the traditional genetic model based on the gradual neutralization of highly oversaturated Cu-bearing solutions that progressively cement the gravels and underlying bedrock regardless of the depositional environment. This study concludes that in exotic-Cu deposits formed relatively far from the source, a favorable sedimentary environment and particular hydrologic and climatic conditions are essential to trap, accumulate, evapoconcentrate, neutralize and saturate Cu-bearing solutions to trigger mineralization. Thus, detailed sedimentological studies should be incorporated when devising exploration strategies in order to discover new exotic-Cu resources, particularly if they are expected to have formed relatively far from the metal sources.

  8. Prevalence, mechanisms and genetic relatedness of the human pathogenic fungus Aspergillus fumigatus exhibiting resistance to medical azoles in the environment of Taiwan.

    Science.gov (United States)

    Wang, Hsuan-Chen; Huang, Jui-Chang; Lin, Yong-Hong; Chen, Yu-Hsin; Hsieh, Ming-I; Choi, Pui-Ching; Lo, Hsiu-Jung; Liu, Wei-Lun; Hsu, Ching-Shan; Shih, Hsin-I; Wu, Chi-Jung; Chen, Yee-Chun

    2018-01-01

    Emerging azole resistance in Aspergillus fumigatus poses a serious threat to human health. This nationwide surveillance study investigated the prevalence and molecular characteristics of azole-resistant A. fumigatus environmental isolates in Taiwan, an island country with increasing use of azole fungicides. Of the 2760 air and soil samples screened from 2014 to 2016, 451 A. fumigatus isolates were recovered from 266 samples and 34 isolates from 29 samples displayed resistance to medical azoles (itraconazole, voriconazole or posaconazole). The resistance prevalence was 10.9% and 7.5% in A. fumigatus-positive samples and isolates respectively. Most (29, 85.3%) azole-resistant isolates harboured TR 34 /L98H mutations, which were widely distributed, clustered genetically with clinical isolates, and had growth rates that were similar to those of the wild-type isolates. Microsatellite genotyping revealed both the global spread of the TR 34 /L98H isolates and the occurrence of TR 34 /L98H/S297T/F495I isolates belonging to local microsatellite genotypes. AfuMDR3 and atrF, two efflux transporter genes, were constitutively upregulated in two individual resistant isolates without cyp51A mutations, highlighting their potential roles in azole resistance. These results emphasize the need for periodic environmental surveillance at the molecular level in regions in which azole fungicides are applied, and agricultural fungicide management strategies that generate less selective pressure should be investigated. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

  9. Complex relationships between occupation, environment, DNA adducts, genetic polymorphisms and bladder cancer in a case-control study using a structural equation modeling.

    Directory of Open Access Journals (Sweden)

    Stefano Porru

    Full Text Available DNA adducts are considered an integrate measure of carcinogen exposure and the initial step of carcinogenesis. Their levels in more accessible peripheral blood lymphocytes (PBLs mirror that in the bladder tissue. In this study we explore whether the formation of PBL DNA adducts may be associated with bladder cancer (BC risk, and how this relationship is modulated by genetic polymorphisms, environmental and occupational risk factors for BC. These complex interrelationships, including direct and indirect effects of each variable, were appraised using the structural equation modeling (SEM analysis. Within the framework of a hospital-based case/control study, study population included 199 BC cases and 213 non-cancer controls, all Caucasian males. Data were collected on lifetime smoking, coffee drinking, dietary habits and lifetime occupation, with particular reference to exposure to aromatic amines (AAs and polycyclic aromatic hydrocarbons (PAHs. No indirect paths were found, disproving hypothesis on association between PBL DNA adducts and BC risk. DNA adducts were instead positively associated with occupational cumulative exposure to AAs (p = 0.028, whereas XRCC1 Arg 399 (p<0.006 was related with a decreased adduct levels, but with no impact on BC risk. Previous findings on increased BC risk by packyears (p<0.001, coffee (p<0.001, cumulative AAs exposure (p = 0.041 and MnSOD (p = 0.009 and a decreased risk by MPO (p<0.008 were also confirmed by SEM analysis. Our results for the first time make evident an association between occupational cumulative exposure to AAs with DNA adducts and BC risk, strengthening the central role of AAs in bladder carcinogenesis. However the lack of an association between PBL DNA adducts and BC risk advises that these snapshot measurements are not representative of relevant exposures. This would envisage new scenarios for biomarker discovery and new challenges such as repeated measurements at different

  10. Nonclinical and Clinical Enterococcus faecium Strains, but Not Enterococcus faecalis Strains, Have Distinct Structural and Functional Genomic Features

    Science.gov (United States)

    Kim, Eun Bae

    2014-01-01

    Certain strains of Enterococcus faecium and Enterococcus faecalis contribute beneficially to animal health and food production, while others are associated with nosocomial infections. To determine whether there are structural and functional genomic features that are distinct between nonclinical (NC) and clinical (CL) strains of those species, we analyzed the genomes of 31 E. faecium and 38 E. faecalis strains. Hierarchical clustering of 7,017 orthologs found in the E. faecium pangenome revealed that NC strains clustered into two clades and are distinct from CL strains. NC E. faecium genomes are significantly smaller than CL genomes, and this difference was partly explained by significantly fewer mobile genetic elements (ME), virulence factors (VF), and antibiotic resistance (AR) genes. E. faecium ortholog comparisons identified 68 and 153 genes that are enriched for NC and CL strains, respectively. Proximity analysis showed that CL-enriched loci, and not NC-enriched loci, are more frequently colocalized on the genome with ME. In CL genomes, AR genes are also colocalized with ME, and VF are more frequently associated with CL-enriched loci. Genes in 23 functional groups are also differentially enriched between NC and CL E. faecium genomes. In contrast, differences were not observed between NC and CL E. faecalis genomes despite their having larger genomes than E. faecium. Our findings show that unlike E. faecalis, NC and CL E. faecium strains are equipped with distinct structural and functional genomic features indicative of adaptation to different environments. PMID:24141120

  11. Journal of Genetics | Indian Academy of Sciences

    Indian Academy of Sciences (India)

    Keywords. antagonistic pleiotropy; balancer chromosomes; environmental heterogeneity; maintenance of genetic variation; trade-offs. Abstract. A fundamental assumption of models for the maintenance of genetic variation by environmental heterogeneity is that selection favours different genotypes in different environments.

  12. Genetic diversity of the crustacean parasite Hematodinium (Alveolata, Syndinea).

    Science.gov (United States)

    Hamilton, Kristina M; Morritt, D; Shaw, Paul W

    2010-01-01

    In the absence of distinct morphological characteristics, knowledge of genetic relationships within and between protist parasite species is important for determining reservoir hosts and understanding the biology of the causative agents of emerging diseases. The genus Hematodinium is a member of Syndinea, an ubiquitous alveolate group found in all oceanic environments. Hematodinium parasites cause epizootics in crustaceans, yet their life cycle, genotypic variety and their phylogeny is poorly understood. By combining phylogenetic methods with analyses of secondary structures of variable ribosomal RNA genes we show that Hematodinium from the east and west North-Atlantic is comprised of distinct ribotypes or clades. These did not correspond to a specific area, but varied in host specificity. For example, a Hematodinium 'Langoustine' clade was only found in Nephrops norvegicus langoustines, whereas other clades were specific to crabs or seem to be generalist parasites. Copyright (c) 2009 Elsevier GmbH. All rights reserved.

  13. THE ATTITUDE TOWARDS GENETICALLY MODIFIED ORGANISMS (GMO’S AND THEIR EFFECT ON HEALTH AND ENVIRONMENT IN SOUTHWESTERN NIGERIA : SCIENTISTS’ PERCEPTION

    Directory of Open Access Journals (Sweden)

    O OLADELE

    2007-11-01

    Full Text Available The study was carried out in South Western Nigeria to evaluate the perception of scientists at Universities and Research Institutes on the effect of GMO’s on health and environment. It is proposed that scientists’ perception would influence the on-going debate as preclude to Nigeria being a signatory to the use of GMO’s. Using a simple random sampling technique, a total of one hundred and eighty respondents were selected from a population of 760 and then interviewed. Data were collected through the use of a structured questionnaire with a reliability coefficient of 0.92 and analysis was done using frequency counts, percentages and probit regression model. Scientists were between 31 and 40 years (59.40%, were MSC holders (44.44%, got their information on GMO’s from journals (89.60% and were male (56.70%. Majority of the scientists had low awareness of the GMO’s products (52.8%, low perception (54.5 percent. There is significant relationship between awareness, age, religion, sources of information (radio, newspaper, scientific periodicals and their perception toward GMOs. There is no significant difference in perception and awareness between scientists at Universities and research institutes.

  14. Genetic basis of autism: is there a way forward?

    Science.gov (United States)

    Eapen, Valsamma

    2011-05-01

    This paper outlines some of the key findings from genetic research carried out in the last 12-18 months, which indicate that autism spectrum disorder (ASD) is a complex disorder involving interactions between genetic, epigenetic and environmental factors. The current literature highlights the presence of genetic and phenotypic heterogeneity in ASD with a number of underlying pathogenetic mechanisms. In this regard, there are at least three phenotypic presentations with distinct genetic underpinnings: autism plus phenotype characterized by syndromic ASD caused by rare, single-gene disorders; broad autism phenotype caused by genetic variations in single or multiple genes, each of these variations being common and distributed continually in the general population, but resulting in varying clinical phenotypes when it reaches a certain threshold through complex gene-gene and gene-environment interactions; and severe and specific phenotype caused by 'de-novo' mutations in the patient or transmitted through asymptomatic carriers of such mutation. Understanding the neurobiological processes by which genotypes become phenotypes, along with the advances in developmental neuroscience and neuronal networks at the cellular and molecular level, is paving the way for translational research involving targeted interventions of affected molecular pathways and early intervention programs that promote normal brain responses to stimuli and alter the developmental trajectory.

  15. Family environment and child development

    Directory of Open Access Journals (Sweden)

    Tina Kavčič

    2005-04-01

    Full Text Available The paper presents an overview of research findings on influence of family environment, especially parental behaviour, on child's development. Contemporary authors question early socialization researchers' claims that family characteristics and parental behaviour have important influence on behaviour of their children. Later researchers examined the size and durability of possible effects of family environment on child development. In addition, they focused on establishing whether it is actually the parental behaviour that influences child's development or, on the contrary, parental behaviour represents mainly a reaction to child's characteristics. Behaviour genetic studies have provided evidence that many traditional measures of family environment, including measures of parental behaviour, show genetic influence, thus reflecting genetically influenced child characteristics. Behaviour geneticists also suggest that environmental influences on child (personality development include predominantly non-shared environment, i.e. individual child's specific experiences, his/her own perceptions and interpretations of objectively same events. Based on empirically determined significant genetic effects on most behavioural traits and inconclusive results of studies on effects of family environment on child development some authors believe that it is not the parents, but rather genetic factor and/or peers who have the key role in child development. With respect to findings of behaviour genetics numerous recent studies of relations between family environment and child development involve child specific measures of (extrafamilial environment and examine the interactions between characteristics of an individual and those of his/her environment.

  16. Identification and mapping in spring wheat of genetic factors controlling stem rust resistance and the study of their epistatic interactions across multiple environments.

    Science.gov (United States)

    Singh, A; Knox, R E; DePauw, R M; Singh, A K; Cuthbert, R D; Campbell, H L; Singh, D; Bhavani, S; Fetch, T; Clarke, F

    2013-08-01

    Stem rust (Puccinia graminis f. sp. tritici) is responsible for major production losses in hexaploid wheat (Triticum aestivum L.) around the world. The spread of stem rust race Ug99 and variants is a threat to worldwide wheat production and efforts are ongoing to identify and incorporate resistance. The objectives of this research were to identify quantitative trait loci (QTL) and to study their epistatic interactions for stem rust resistance in a population derived from the Canadian wheat cultivars AC Cadillac and Carberry. A doubled haploid (DH) population was developed and genotyped with DArT(®) and SSR markers. The parents and DH lines were phenotyped for stem rust severity and infection response to Ug99 and variant races in 2009, 2010 and 2011 in field rust nurseries near Njoro, Kenya, and to North American races in 2011 and 2012 near Swift Current, SK, Canada. Seedling infection type to race TTKSK was assessed in a bio-containment facility in 2009 and 2012 near Morden, MB. Eight QTL for stem rust resistance and three QTL for pseudo-black chaff on nine wheat chromosomes were identified. The phenotypic variance (PV) explained by the stem rust resistance QTL ranged from 2.4 to 48.8 %. AC Cadillac contributed stem rust resistance QTL on chromosomes 2B, 3B, 5B, 6D, 7B and 7D. Carberry contributed resistance QTL on 4B and 5A. Epistatic interactions were observed between loci on 4B and 5B, 4B and 7B, 6D and 3B, 6D and 5B, and 6D and 7B. The stem rust resistance locus on 6D interacted synergistically with 5B to improve the disease resistance through both crossover and non-crossover interactions depending on the environment. Results from this study will assist in planning breeding for stem rust resistance by maximizing QTL main effects and epistatic interactions.

  17. Distinctiveness of Ugandapithecus from Proconsul

    Directory of Open Access Journals (Sweden)

    Gommery, D.

    2009-12-01

    Full Text Available The decision to create the genus Ugandapithecus by Senut et al., 2000 has been criticised, either directly and in detail by MacLatchy & Rossie (2005b who argued that it is a junior synonym of Proconsul, or indirectly without providing reasons, firstly by Harrison (2001 who wrote that he did not retain it as a genus distinct from Proconsul, and then by Suwa et al., (2007 who employed the name “Ugandapithecus” with inverted commas, implying some degree of doubt about its validity as a genus, but without providing details. More recently Harrison & Andrews (2009 have recognised the Meswa sample as a separate species but they argue that it should be maintained within Proconsul, despite the morphological differences that it has from other species of the genus. We here re-examine the question by comparing, on the one hand, the holotype maxilla of Proconsul africanus, the type species of the genus, with the upper dentition of Ugandapithecus major, and, on the other hand, the holotype mandible of Ugandapithecus major with the lower dentition and mandibles previously attributed to Proconsul africanus. We conclude that the differences between the known upper and lower dentitions of P. africanus and U. major are of such a degree that the two taxa warrant generic separation, and that the differences are not related to sexual dimorphism. Where Proconsul africanus differs from Ugandapithecus major, it approaches Proconsul nyanzae and Proconsul heseloni from Rusinga.Furthermore, the range of morphometric variation within the fossil samples previously attributed to Ugandapithecus major is so great that it far surpasses variation in any other hominoid, fossil or extant. Previously this great amount of variation was interpreted to mean that U. major was extremely dimorphic, with huge males and small females, but if this is true, then U. major would be unique among hominoids in having females in which the cheek teeth fall completely outside the range of

  18. Municipal solid waste landfills harbor distinct microbiomes

    Science.gov (United States)

    Stamps, Blake W.; Lyles, Christopher N.; Suflita, Joseph M.; Masoner, Jason R.; Cozzarelli, Isabelle M.; Kolpin, Dana W.; Stevenson, Bradley S.

    2016-01-01

    Landfills are the final repository for most of the discarded material from human society and its “built environments.” Microorganisms subsequently degrade this discarded material in the landfill, releasing gases (largely CH4 and CO2) and a complex mixture of soluble chemical compounds in leachate. Characterization of “landfill microbiomes” and their comparison across several landfills should allow the identification of environmental or operational properties that influence the composition of these microbiomes and potentially their biodegradation capabilities. To this end, the composition of landfill microbiomes was characterized as part of an ongoing USGS national survey studying the chemical composition of leachates from 19 non-hazardous landfills across 16 states in the continental U.S. The landfills varied in parameters such as size, waste composition, management strategy, geography, and climate zone. The diversity and composition of bacterial and archaeal populations in leachate samples were characterized by 16S rRNA gene sequence analysis, and compared against a variety of physical and chemical parameters in an attempt to identify their impact on selection. Members of the Epsilonproteobacteria, Gammaproteobacteria, Clostridia, and candidate division OP3 were the most abundant. The distribution of the observed phylogenetic diversity could best be explained by a combination of variables and was correlated most strongly with the concentrations of chloride and barium, rate of evapotranspiration, age of waste, and the number of detected household chemicals. This study illustrates how leachate microbiomes are distinct from those of other natural or built environments, and sheds light on the major selective forces responsible for this microbial diversity.

  19. Municipal Solid Waste Landfills Harbor Distinct Microbiomes

    Directory of Open Access Journals (Sweden)

    Blake Warren Stamps

    2016-04-01

    Full Text Available Landfills are the final repository for most of the discarded material from human society and its built environments. Microorganisms subsequently degrade this discarded material in the landfill, releasing gases (largely CH4 and CO2 and a complex mixture of soluble chemical compounds in leachate. Characterization of landfill microbiomes and their comparison across several landfills should allow the identification of environmental or operational properties that influence the composition of these microbiomes and potentially their biodegradation capabilities. To this end, the composition of landfill microbiomes was characterized as part of an ongoing USGS national survey studying the chemical composition of leachates from 19 non-hazardous landfills across 16 states in the continental U.S. The landfills varied in parameters such as size, waste composition, management strategy, geography, and climate zone. The diversity and composition of bacterial and archaeal populations in leachate samples were characterized by 16S rRNA gene sequence analysis, and compared against a variety of physical and chemical parameters in an attempt to identify their impact on selection. Members of the Epsilonproteobacteria, Gammaproteobacteria, Clostridia, and candidate division OP3 were the most abundant. The distribution of the observed phylogenetic diversity could best be explained by a combination of variables and was correlated most strongly with the concentrations of chloride and barium, rate of evapotranspiration, age of waste, and the number of detected household chemicals. This study illustrates how leachate microbiomes are distinct from those of other natural or built environments, and sheds light on the major selective forces responsible for this microbial diversity.

  20. Immunological commonalities and distinctions between airway and digestive immunity.

    Science.gov (United States)

    Kunisawa, Jun; Nochi, Tomonori; Kiyono, Hiroshi

    2008-11-01

    Airway and digestive tissues are the frontlines of the body's defense, being continuously exposed to the outside environment and encountering large numbers of antigens and microorganisms. To achieve immunosurveillance and immunological homeostasis in the harsh environments of the mucosal surfaces, the mucosal immune system tightly regulates a state of opposing but harmonized immune activation and quiescence. Recently, accumulating evidence has revealed that although the respiratory and intestinal immune systems share common mucosa-associated immunological features that are different from those of the systemic immune system, they also show distinctive immunological phenotypes, functions, and developmental pathways. We describe here the common and distinct immunological features of respiratory and intestinal immune systems and its application to the development of mucosal vaccines.

  1. Genetic profiles distinguish different types of hereditary ovarian cancer

    DEFF Research Database (Denmark)

    Domanska, Katarina; Malander, Susanne; Staaf, Johan

    2010-01-01

    Heredity represents the strongest risk factor for ovarian cancer with disease predisposing mutations identified in 15% of the tumors. With the aim to identify genetic classifiers for hereditary ovarian cancer, we profiled hereditary ovarian cancers linked to the hereditary breast and ovarian cancer...... as a control group. Unsupervised cluster analysis identified two distinct subgroups related to genetic complexity. Sporadic and HBOC associated tumors had complex genetic profiles with an average 41% of the genome altered, whereas the mismatch repair defective tumors had stable genetic profiles...... that HBOC and HNPCC associated ovarian cancer develop along distinct genetic pathways and genetic profiles can thus be applied to distinguish between different types of hereditary ovarian cancer....

  2. Two distinct classes of QTL determine rust resistance in sorghum.

    Science.gov (United States)

    Wang, Xuemin; Mace, Emma; Hunt, Colleen; Cruickshank, Alan; Henzell, Robert; Parkes, Heidi; Jordan, David

    2014-12-31

    Agriculture is facing enormous challenges to feed a growing population in the face of rapidly evolving pests and pathogens. The rusts, in particular, are a major pathogen of cereal crops with the potential to cause large reductions in yield. Improving stable disease resistance is an on-going major and challenging focus for many plant breeding programs, due to the rapidly evolving nature of the pathogen. Sorghum is a major summer cereal crop that is also a host for a rust pathogen Puccinia purpurea, which occurs in almost all sorghum growing areas of the world, causing direct and indirect yield losses in sorghum worldwide, however knowledge about its genetic control is still limited. In order to further investigate this issue, QTL and association mapping methods were implemented to study rust resistance in three bi-parental populations and an association mapping set of elite breeding lines in different environments. In total, 64 significant or highly significant QTL and 21 suggestive rust resistance QTL were identified representing 55 unique genomic regions. Comparisons across populations within the current study and with rust QTL identified previously in both sorghum and maize revealed a high degree of correspondence in QTL location. Negative phenotypic correlations were observed between rust, maturity and height, indicating a trend for both early maturing and shorter genotypes to be more susceptible to rust. The significant amount of QTL co-location across traits, in addition to the consistency in the direction of QTL allele effects, has provided evidence to support pleiotropic QTL action across rust, height, maturity and stay-green, supporting the role of carbon stress in susceptibility to rust. Classical rust resistance QTL regions that did not co-locate with height, maturity or stay-green QTL were found to be significantly enriched for the defence-related NBS-encoding gene family, in contrast to the lack of defence-related gene enrichment in multi-trait effect

  3. Graphical models for genetic analyses

    DEFF Research Database (Denmark)

    Lauritzen, Steffen Lilholt; Sheehan, Nuala A.

    2003-01-01

    This paper introduces graphical models as a natural environment in which to formulate and solve problems in genetics and related areas. Particular emphasis is given to the relationships among various local computation algorithms which have been developed within the hitherto mostly separate areas...... of graphical models and genetics. The potential of graphical models is explored and illustrated through a number of example applications where the genetic element is substantial or dominating....

  4. The genetic basis of divergent pigment patterns in juvenile threespine sticklebacks.

    Science.gov (United States)

    Greenwood, A K; Jones, F C; Chan, Y F; Brady, S D; Absher, D M; Grimwood, J; Schmutz, J; Myers, R M; Kingsley, D M; Peichel, C L

    2011-08-01

    Animal pigment patterns are important for a range of functions, including camouflage and communication. Repeating pigment patterns, such as stripes, bars and spots have been of particular interest to developmental and theoretical biologists, but the genetic basis of natural variation in such patterns is largely unexplored. In this study, we identify a difference in a periodic pigment pattern among juvenile threespine sticklebacks (Gasterosteus aculeatus) from different environments. Freshwater sticklebacks exhibit prominent vertical bars that visually break up the body shape, but sticklebacks from marine populations do not. We hypothesize that these distinct pigment patterns are tuned to provide crypsis in different habitats. This phenotypic difference is widespread and appears in most of the freshwater populations that we sampled. We used quantitative trait locus (QTL) mapping in freshwater-marine F2 hybrids to elucidate the genetic architecture underlying divergence in this pigmentation pattern. We identified two QTL that were significantly associated with variation in barring. Interestingly, these QTL were associated with two distinct aspects of the pigment pattern: melanophore number and overall pigment level. We compared the QTL locations with positions of known pigment candidate genes in the stickleback genome. We also identified two major QTL for juvenile body size, providing new insights into the genetic basis of juvenile growth rates in natural populations. In summary, although there is a growing literature describing simple genetic bases for adaptive coloration differences, this study emphasizes that pigment patterns can also possess a more complex genetic architecture.

  5. Genetic Mapping

    Science.gov (United States)

    ... Links for Patient Care Education All About the Human Genome Project Fact Sheets Genetic Education Resources for Teachers Genomic ... genetic mapping? Among the main goals of the Human Genome Project (HGP) was to develop new, better and cheaper ...

  6. Genetic Disorders

    Science.gov (United States)

    ... This can cause a medical condition called a genetic disorder. You can inherit a gene mutation from ... during your lifetime. There are three types of genetic disorders: Single-gene disorders, where a mutation affects ...

  7. Genetic Testing

    Science.gov (United States)

    ... risk factor for the development of celiac disease, genetic predisposition. Without this factor, it is impossible that the ... with antibody testing in the future. When the genetic predisposition for celiac disease was detected (on Chromosome 6) ...

  8. Genetic counseling

    Science.gov (United States)

    ... have a high risk of having babies with Tay-Sachs or Canavan's disease. African-Americans, who may risk ... yours to make. Images Genetic counseling and prenatal diagnosis References Simpson JL, Holzgreve W, Driscoll DA. Genetic ...

  9. Environmental factors influence both abundance and genetic diversity in a widespread bird species

    Science.gov (United States)

    Liu, Yang; Webber, Simone; Bowgen, Katharine; Schmaltz, Lucie; Bradley, Katharine; Halvarsson, Peter; Abdelgadir, Mohanad; Griesser, Michael

    2013-01-01

    Genetic diversity is one of the key evolutionary variables that correlate with population size, being of critical importance for population viability and the persistence of species. Genetic diversity can also have important ecological consequences within populations, and in turn, ecological factors may drive patterns of genetic diversity. However, the relationship between the genetic diversity of a population and how this interacts with ecological processes has so far only been investigated in a few studies. Here, we investigate the link between ecological factors, local population size, and allelic diversity, using a field study of a common bird species, the house sparrow (Passer domesticus). We studied sparrows outside the breeding season in a confined small valley dominated by dispersed farms and small-scale agriculture in southern France. Population surveys at 36 locations revealed that sparrows were more abundant in locations with high food availability. We then captured and genotyped 891 house sparrows at 10 microsatellite loci from a subset of these locations (N = 12). Population genetic analyses revealed weak genetic structure, where each locality represented a distinct substructure within the study area. We found that food availability was the main factor among others tested to influence the genetic structure between locations. These results suggest that ecological factors can have strong impacts on both population size per se and intrapopulation genetic variation even at a small scale. On a more general level, our data indicate that a patchy environment and low dispersal rate can result in fine-scale patterns of genetic diversity. Given the importance of genetic diversity for population viability, combining ecological and genetic data can help to identify factors limiting population size and determine the conservation potential of populations. PMID:24363897

  10. Genetic risk

    OpenAIRE

    ten Kate, Leo P.

    2012-01-01

    In this paper I will review different aspects of genetic risk in the context of preconception care. I restrict myself to the knowledge of risk which is relevant for care and/or enables reproductive choice. The paper deals with chromosomes, genes and the genetic classification of diseases, and it explains why Mendelian disorders frequently do not show the expected pattern of occurrence in families. Factors that amplify genetic risk are also discussed. Of the two methods of genetic risk assessm...

  11. [The genetics of addictions].

    Science.gov (United States)

    Ibañez Cuadrado, Angela

    2008-01-01

    The addictions are common chronic psychiatric diseases which represent a serious worldwide public-health problem. They have a high prevalence and negative effects at individual, family and societal level, with a high sanitary cost. Epidemiological genetic research has revealed that addictions are moderately to highly heritable. Also the investigation has evidenced that environmental and genetic factors contribute to individual differences in vulnerability to addictions. Advances in the neurobiology of addiction joined to the development of new molecular genetic technologies, have led to the identification of a variety of underlying genes and pathways in addiction process, leading to the description of common molecular mechanisms in substance and behaviour dependencies. Identifying gene-environment interactions is a crucial issue in future research. Other major goal in genetic research is the identification of new therapeutic targets for treatment and prevention.

  12. Imaging Genetics

    Science.gov (United States)

    Munoz, Karen E.; Hyde, Luke W.; Hariri, Ahmad R.

    2009-01-01

    Imaging genetics is an experimental strategy that integrates molecular genetics and neuroimaging technology to examine biological mechanisms that mediate differences in behavior and the risks for psychiatric disorder. The basic principles in imaging genetics and the development of the field are discussed.

  13. Genetic variation between ecotypic populations of Chloris ...

    African Journals Online (AJOL)

    Genetic variation between ecotypic populations of Chloris roxburghiana grass detected through RAPD analysis. ... frequency indicated that the four populations of C. roxburghiana were genetically distinct, probably as a result of variation in soil fertility, geographical isolation and socio-ecological history of the study sites.

  14. Journal of Genetics | Indian Academy of Sciences

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics. DIOVANI PISCOR. Articles written in Journal of Genetics. Volume 96 Issue 4 September 2017 pp 665-671 RESEARCH ARTICLE. Distinct classical and molecular cytogenetics of Astyanax marionae and A. fasciatus (Characiformes: Characidae): a comparative study of the organization ...

  15. Journal of Genetics | Indian Academy of Sciences

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics. ZHONGJIE CHANG. Articles written in Journal of Genetics. Volume 89 Issue 2 August 2010 pp 183-192 Research Article. cDNA cloning and expression analysis of two distinct Sox8 genes in Paramisgurnus dabryanus (Cypriniformes) · Xiaohua Xia Jie Zhao Qiyan Du Zhongjie Chang.

  16. Intraspecific chromosomal and genetic polymorphism in Brassica ...

    Indian Academy of Sciences (India)

    2014-04-16

    Apr 16, 2014 ... A. V., Lemesh V. A. and Muravenko O. V. 2014 Intraspecific chromosomal and genetic polymorphism in Brassica napus L. detected by cytogenetic and molecular markers. J. Genet. ...... Howell E. C., Kearsey M. J., Jones G. H., King G. J. and Armstrong. S. J. 2008 A and C genome distinction and ...

  17. Genetic diversity in European Pisum germplasm collections

    NARCIS (Netherlands)

    Jing, R.; Ambrose, M.A.; Knox, M.R.; Smykal, P.; Hybl, M.; Ramos, A.; Caminero, C.; Burstin, J.; Duc, G.; Soest, van L.J.; Swiecicki, W.K.; Pereira, M.G.; Vishnyakova, M.; Davenport, G.F.; Flavell, A.J.; Ellis, T.

    2012-01-01

    The distinctness of, and overlap between, pea genotypes held in several Pisum germplasm collections has been used to determine their relatedness and to test previous ideas about the genetic diversity of Pisum. Our characterisation of genetic diversity among 4,538 Pisum accessions held in 7 European

  18. Genetic Aspects of Nephrotic Syndrome

    DEFF Research Database (Denmark)

    Joshi, Shivani

    steroid dependence or become frequent relapsers. Repeated courses of corticosteroid treatment often cause significant associated morbidity. Familial occurrence of SSNS is rare and suggests a potential genetic origin. However, very little data on molecular genetics of familial SSNS is available...... with SSNS are rare, but do indicate a genetic predisposition. In study III we investigated a potential genetic linkage in 9 European SSNS families with at least two affected siblings. Using SNP6 whole genome linkage analysis we could establish linkage of the disease phenotype to chromosome 15 with a maximum...... immunosuppressive treatment in future patients with the same genotype. Our findings also demonstrate that inheritance of different alleles at independent genetic loci in NS may contribute to the disease phenotype. SSNS is clinically distinct from SRNS and its pathogenesis is still unclear. Our study showed linkage...

  19. Genetically engineered tissue to screen for glycan function in tissue formation

    DEFF Research Database (Denmark)

    M., Adamopoulou; E.M., Pallesen; A., Levann

    2017-01-01

    . We use genetic engineering with CRISPR/Cas9 combined with 3D organotypic skin models to examine how distinct glycans influence epithelial formation. We have performed knockout and knockin of more than 100 select genes in the genome of human immortalized human keratinocytes, enabling a systematic...... analysis of the impact of specific glycans in the formation and transformation of the human skin. The genetic engineered human skin models (GlycoSkin) was designed with and without all major biosynthetic pathways in mammalian glycan biosynthesis, including GalNAc-O-glycans, O-fucosylation, O......-mannosylation, with and without complex N-linked gly-cans, and with and without elongated glycosphingolipids. We believe that this is the first time tissue is developed presenting a repertoire of all human glycan structures in a com-binatorial design presenting all possible glycoforms in their native environment. Such genetic...

  20. About Genetic Counselors

    Science.gov (United States)

    ... clinical care in many areas of medicine. Assisted Reproductive Technology/Infertility Genetics Cancer Genetics Cardiovascular Genetics Cystic Fibrosis Genetics Fetal Intervention and Therapy Genetics Hematology Genetics Metabolic Genetics ...

  1. Feature selection environment for genomic applications

    Directory of Open Access Journals (Sweden)

    Martins David

    2008-10-01

    Full Text Available Abstract Background Feature selection is a pattern recognition approach to choose important variables according to some criteria in order to distinguish or explain certain phenomena (i.e., for dimensionality reduction. There are many genomic and proteomic applications that rely on feature selection to answer questions such as selecting signature genes which are informative about some biological state, e.g., normal tissues and several types of cancer; or inferring a prediction network among elements such as genes, proteins and external stimuli. In these applications, a recurrent problem is the lack of samples to perform an adequate estimate of the joint probabilities between element states. A myriad of feature selection algorithms and criterion functions have been proposed, although it is difficult to point the best solution for each application. Results The intent of this work is to provide an open-source multiplataform graphical environment for bioinformatics problems, which supports many feature selection algorithms, criterion functions and graphic visualization tools such as scatterplots, parallel coordinates and graphs. A feature selection approach for growing genetic networks from seed genes (targets or predictors is also implemented in the system. Conclusion The proposed feature selection environment allows data analysis using several algorithms, criterion functions and graphic visualization tools. Our experiments have shown the software effectiveness in two distinct types of biological problems. Besides, the environment can be used in different pattern recognition applications, although the main concern regards bioinformatics tasks.

  2. Epigenetics and the environment in bioethics.

    Science.gov (United States)

    Dupras, Charles; Ravitsky, Vardit; Williams-Jones, Bryn

    2014-09-01

    A rich literature in public health has demonstrated that health is strongly influenced by a host of environmental factors that can vary according to social, economic, geographic, cultural or physical contexts. Bioethicists should, we argue, recognize this and--where appropriate--work to integrate environmental concerns into their field of study and their ethical deliberations. In this article, we present an argument grounded in scientific research at the molecular level that will be familiar to--and so hopefully more persuasive for--the biomedically-inclined in the bioethics community. Specifically, we argue that the relatively new field of molecular epigenetics provides novel information that should serve as additional justification for expanding the scope of bioethics to include environmental and public health concerns. We begin by presenting two distinct visions of bioethics: the individualistic and rights-oriented and the communitarian and responsibility-oriented. We follow with a description of biochemical characteristics distinguishing epigenetics from genetics, in order to emphasize the very close relationship that exists between the environment and gene expression. This then leads to a discussion of the importance of the environment in determining individual and population health, which, we argue, should shift bioethics towards a Potterian view that promotes a communitarian-based sense of responsibility for the environment, in order to fully account for justice considerations and improve public health. © 2012 John Wiley & Sons Ltd.

  3. Photostability and photodegradation pathways of distinctive pesticides.

    Science.gov (United States)

    Kiss, Attila; Virág, Diána

    2009-01-01

    Transformation of pesticides in the environment is a highly complex process affected by different factors. Biological and physical-chemical factors may play a role in the degradation to variable extent. Photodecomposition might be regarded as one of the most crucial factors affecting the fate of pesticides. Therefore, our study focused on revealing specific details of the photolytic degradation of pesticides. The toxicity of the examined pesticides is well known; however, little information is available regarding their natural degradation processes. More detailed examinations are required to reveal the exact mechanism of the pesticide decomposition and the biological impacts of the degradates. Significance of this study is enhanced by the fact that decomposition of pesticides may result in the formation of toxic degradation products. The photolytic degradation of frequently applied pesticides (e.g., acetochlor, simazine, chlorpyrifos, and carbendazim) with different chemical structures was investigated. An immersible ultraviolet light source was applied to induce photodegradation. The degradation processes were followed by thin-layer chromatography and gas chromatography/mass spectrometry techniques. Electron ionization mass spectrometry was used to identify the degradation species. Detailed mechanisms of photolytic transformation were established by identification of each degradate. The photolytic degradation of pesticides of distinctive chemical character exhibited markedly different photodecomposition mechanisms. At least four degradation species were detected and identified in each case. Loss of alkyl, chloro, and hydroxyl groups as well as cleavage of alkyloxy, amide, amino-alkyl, and ester bonds might be regarded as typical decomposition patterns. Deamination and ring opening might be observed at the last stages of decomposition.

  4. Genetic loci for serum magnesium among African-Americans and gene-environment interaction at MUC1 and TRPM6 in European-Americans: the Atherosclerosis Risk in Communities (ARIC) study.

    Science.gov (United States)

    Tin, Adrienne; Köttgen, Anna; Folsom, Aaron R; Maruthur, Nisa M; Tajuddin, Salman M; Nalls, Mike A; Evans, Michele K; Zonderman, Alan B; Friedrich, Christopher A; Boerwinkle, Eric; Coresh, Josef; Kao, Wen Hong Linda

    2015-05-29

    Low serum magnesium levels have been associated with multiple chronic diseases. The regulation of serum magnesium homeostasis is not well understood. A previous genome-wide association study (GWAS) of European ancestry (EA) populations identified nine loci for serum magnesium. No such study has been conducted in African-Americans, nor has there been an evaluation of the interaction of magnesium-associated SNPs with environmental factors. The goals of this study were to identify genetic loci associated with serum magnesium in an African-American (AA) population using both genome-wide and candidate region interrogation approaches and to evaluate gene-environment interaction for the magnesium-associated variants in both EA and AA populations. We conducted a GWAS of serum magnesium in 2737 AA participants of the Atherosclerosis Risk in Communities (ARIC) Study and interrogated the regions of the nine published candidate loci in these results. Literature search identified the influence of progesterone on MUC1 expression and insulin on TRPM6 expression. The GWAS approach in African-American participants identified a locus near MUC1 as genome-wide significant (rs2974937, beta=-0.013, p=6.1x10(-9)). The candidate region interrogation approach identified two of the nine loci previously discovered in EA populations as containing SNPs that were significantly associated in African-American participants (SHROOM3 and TRPM6). The index variants at these three loci together explained 2.8 % of the variance in serum magnesium concentration in ARIC African-American participants. On the test of gene-environment interaction in ARIC EA participants, the index variant at MUC1 had 2.5 times stronger association in postmenopausal women with progestin use (beta=-0.028, p=7.3x10(-5)) than in those without any hormone use (beta=-0.011, p=7.0x10(-8), p for interaction 0.03). At TRPM6, the index variant had 1.6 times stronger association in those with lower fasting insulin levels (African

  5. Acute myeloid leukemia ontogeny is defined by distinct somatic mutations.

    Science.gov (United States)

    Lindsley, R Coleman; Mar, Brenton G; Mazzola, Emanuele; Grauman, Peter V; Shareef, Sarah; Allen, Steven L; Pigneux, Arnaud; Wetzler, Meir; Stuart, Robert K; Erba, Harry P; Damon, Lloyd E; Powell, Bayard L; Lindeman, Neal; Steensma, David P; Wadleigh, Martha; DeAngelo, Daniel J; Neuberg, Donna; Stone, Richard M; Ebert, Benjamin L

    2015-02-26

    Acute myeloid leukemia (AML) can develop after an antecedent myeloid malignancy (secondary AML [s-AML]), after leukemogenic therapy (therapy-related AML [t-AML]), or without an identifiable prodrome or known exposure (de novo AML). The genetic basis of these distinct pathways of AML development has not been determined. We performed targeted mutational analysis of 194 patients with rigorously defined s-AML or t-AML and 105 unselected AML patients. The presence of a mutation in SRSF2, SF3B1, U2AF1, ZRSR2, ASXL1, EZH2, BCOR, or STAG2 was >95% specific for the diagnosis of s-AML. Analysis of serial samples from individual patients revealed that these mutations occur early in leukemogenesis and often persist in clonal remissions. In t-AML and elderly de novo AML populations, these alterations define a distinct genetic subtype that shares clinicopathologic properties with clinically confirmed s-AML and highlights a subset of patients with worse clinical outcomes, including a lower complete remission rate, more frequent reinduction, and decreased event-free survival. This trial was registered at www.clinicaltrials.gov as #NCT00715637. © 2015 by The American Society of Hematology.

  6. Genetic Diversity and Population Structure of Ethiopian Sheep Populations Revealed by High-Density SNP Markers

    Directory of Open Access Journals (Sweden)

    Zewdu Edea

    2017-12-01

    Full Text Available Sheep in Ethiopia are adapted to a wide range of environments, including extreme habitats. Elucidating their genetic diversity is critical for improving breeding strategies and mapping quantitative trait loci associated with productivity. To this end, the present study investigated the genetic diversity and population structure of five Ethiopian sheep populations exhibiting distinct phenotypes and sampled from distinct production environments, including arid lowlands and highlands. To investigate the genetic relationships in greater detail and infer population structure of Ethiopian sheep breeds at the continental and global levels, we analyzed genotypic data of selected sheep breeds from the Ovine SNP50K HapMap dataset. All Ethiopian sheep samples were genotyped with Ovine Infinium HD SNP BeadChip (600K. Mean genetic diversity ra