Science.gov

Sample records for estimated genetic barrier

  1. Psoriasis genetics: breaking the barrier

    PubMed Central

    Roberson, Elisha D.O.; Bowcock, Anne M.

    2010-01-01

    Psoriasis is a common incurable inflammatory skin disease affecting 2–3% of the European population. Psoriatic skin contains large numbers of immune cells which produce many cytokines, chemokines and inflammatory molecules. The epidermis divides much faster than normal and has a defective outer layer or barrier which under normal circumstances protects from infection and dehydration. Psoriatic skin is characterized by a distinct set of inflammation and epidermal proliferation and differentiation markers, and it has not been clear if the genetic basis of psoriasis is due to defects of the immune system or the skin. One genetic determinant lies within the major histocompatibility complex class 1 region. Genome-wide association studies have revealed genetic susceptibility factors that play a role in the formation of immune cells found in psoriasis lesions. Others affect epidermal proliferation and the formation of the skin’s barrier. Hence, genetic components of both the immune system and the epidermis predispose to disease. PMID:20692714

  2. [Resistance profile and genetic barrier of dolutegravir].

    PubMed

    Llibre, Josep M; Clotet, Bonaventura

    2015-03-01

    The resistance profile of dolutegravir differs significantly from those of earlier integrase inhibitors (INI). Dolutegravir displays in vitro activity against mutant HIV-1 harboring any isolated resistance mutations selected during failures to raltegravir or elvitegravir (Y143C/H/, N155H, Q148H/K/R, E92G/Q, T66A/I/K, T97A, E138A/K, G140A/S). Its activity is only compromised by Q148X mutations combined with other mutations, particularly > 1 mutation. The drug has pharmacokinetic/pharmacodynamic properties (plasmatic t1/2 15.3 h, inhibitory quotient 19, dissociative t1/2 from the IN-DNA complex 71 h) that favor a high genetic barrier to resistance. In vitro the selection of HIV-1 resistance to dolutegravir is extremely difficult to achieve. The mutations eventually selected (R263K, H51Y and E138K) do not confer significant resistance, and induce a fitness cost that prevents HIV-1 from evading drug pressure. Suprisingly, HIV-1 is not able to compensate, leading the virus to a previously unnoticed evolutionary pathway with very low chances of developing resistance to INI or the backbone. No treatment-naïve patients starting dolutegravir therapy (+TDF/FTC o ABC/3TC) have selected resistance in IN or against the backbone. No INI- naïve patients with prior virologic failure selected phenotypic dolutegravir resistance. Only 4 out of 354 patients selected resistance mutations in IN, and rates of selection of mutations in IN or against the backbone were significantly lower than with raltegravir. In multitreated patients with widespread resistance including IN resistance, the high efficacy of dolutegravir was confirmed, irrespective of the previous pattern of IN mutations, provided that Q148X associated with other mutations was absent. PMID:25858608

  3. The estimation of genetic divergence

    NASA Technical Reports Server (NTRS)

    Holmquist, R.; Conroy, T.

    1981-01-01

    Consideration is given to the criticism of Nei and Tateno (1978) of the REH (random evolutionary hits) theory of genetic divergence in nucleic acids and proteins, and to their proposed alternative estimator of total fixed mutations designated X2. It is argued that the assumption of nonuniform amino acid or nucleotide substitution will necessarily increase REH estimates relative to those made for a model where each locus has an equal likelihood of fixing mutations, thus the resulting value will not be an overestimation. The relative values of X2 and measures calculated on the basis of the PAM and REH theories for the number of nucleotide substitutions necessary to explain a given number of observed amino acid differences between two homologous proteins are compared, and the smaller values of X2 are attributed to (1) a mathematical model based on the incorrect assumption that an entire structural gene is free to fix mutations and (2) the assumptions of different numbers of variable codons for the X2 and REH calculations. Results of a repeat of the computer simulations of Nei and Tateno are presented which, in contrast to the original results, confirm the REH theory. It is pointed out that while a negative correlation is observed between estimations of the fixation intensity per varion and the number of varions for a given pair of sequences, the correlation between the two fixation intensities and varion numbers of two different pairs of sequences need not be negative. Finally, REH theory is used to resolve a paradox concerning the high rate of covarion turnover and the nature of general function sites as permanent covarions.

  4. Exploring barriers to payer utilization of genetic counselors.

    PubMed

    Doyle, Nan; Cirino, Allison; Trivedi, Amber; Flynn, Maureen

    2015-02-01

    Access to genetic counselors' services is neither universal nor automatic, due in part to the gatekeeper role of healthcare payers--the companies and agencies that purchase healthcare services on patients' behalf and control the bulk of healthcare spending. This pilot study surveyed and analyzed the relative importance of barriers to expanded payer coverage of genetic counselors' services. Surveys were mailed to 263 medical directors and quality assurance directors at health insurance carriers throughout the United States. Respondents provided demographic information and indicated the importance of nine possible barriers, plus an optional write-in "other." Twenty-two surveys were analyzed. "Evidence that use of genetic counselors improves health outcomes" led the list of factors having a significant/very significant influence on coverage policy. Sixteen respondents (73 %) rated this factor "4" or "5" on a Likert scale; it also received the most #1 rankings and the highest score using a weighted-mean analysis. Provider practice guidelines, CMS/Medicare regulations, and genetic counselor licensure-all of which are outside of payers' direct control-also ranked highly. The research demonstrates that although the potential barriers to expanded reimbursement for genetic counselors are numerous and complex, some are more consistently identified as important and therefore more deserving of legislative and advocacy resources to effect change. Future research should endeavor to increase survey response and include providers as well as payers. PMID:25138080

  5. Ecological and Genetic Barriers Differentiate Natural Populations of Saccharomyces cerevisiae.

    PubMed

    Clowers, Katie J; Heilberger, Justin; Piotrowski, Jeff S; Will, Jessica L; Gasch, Audrey P

    2015-09-01

    How populations that inhabit the same geographical area become genetically differentiated is not clear. To investigate this, we characterized phenotypic and genetic differences between two populations of Saccharomyces cerevisiae that in some cases inhabit the same environment but show relatively little gene flow. We profiled stress sensitivity in a group of vineyard isolates and a group of oak-soil strains and found several niche-related phenotypes that distinguish the populations. We performed bulk-segregant mapping on two of the distinguishing traits: The vineyard-specific ability to grow in grape juice and oak-specific tolerance to the cell wall damaging drug Congo red. To implicate causal genes, we also performed a chemical genomic screen in the lab-strain deletion collection and identified many important genes that fell under quantitative trait loci peaks. One gene important for growth in grape juice and identified by both the mapping and the screen was SSU1, a sulfite-nitrite pump implicated in wine fermentations. The beneficial allele is generated by a known translocation that we reasoned may also serve as a genetic barrier. We found that the translocation is prevalent in vineyard strains, but absent in oak strains, and presents a postzygotic barrier to spore viability. Furthermore, the translocation was associated with a fitness cost to the rapid growth rate seen in oak-soil strains. Our results reveal the translocation as a dual-function locus that enforces ecological differentiation while producing a genetic barrier to gene flow in these sympatric populations. PMID:25953281

  6. Ecological and Genetic Barriers Differentiate Natural Populations of Saccharomyces cerevisiae

    PubMed Central

    Clowers, Katie J.; Heilberger, Justin; Piotrowski, Jeff S.; Will, Jessica L.; Gasch, Audrey P.

    2015-01-01

    How populations that inhabit the same geographical area become genetically differentiated is not clear. To investigate this, we characterized phenotypic and genetic differences between two populations of Saccharomyces cerevisiae that in some cases inhabit the same environment but show relatively little gene flow. We profiled stress sensitivity in a group of vineyard isolates and a group of oak-soil strains and found several niche-related phenotypes that distinguish the populations. We performed bulk-segregant mapping on two of the distinguishing traits: The vineyard-specific ability to grow in grape juice and oak-specific tolerance to the cell wall damaging drug Congo red. To implicate causal genes, we also performed a chemical genomic screen in the lab-strain deletion collection and identified many important genes that fell under quantitative trait loci peaks. One gene important for growth in grape juice and identified by both the mapping and the screen was SSU1, a sulfite-nitrite pump implicated in wine fermentations. The beneficial allele is generated by a known translocation that we reasoned may also serve as a genetic barrier. We found that the translocation is prevalent in vineyard strains, but absent in oak strains, and presents a postzygotic barrier to spore viability. Furthermore, the translocation was associated with a fitness cost to the rapid growth rate seen in oak-soil strains. Our results reveal the translocation as a dual-function locus that enforces ecological differentiation while producing a genetic barrier to gene flow in these sympatric populations. PMID:25953281

  7. Disentangle the Causes of the Road Barrier Effect in Small Mammals through Genetic Patterns.

    PubMed

    Ascensão, Fernando; Mata, Cristina; Malo, Juan E; Ruiz-Capillas, Pablo; Silva, Catarina; Silva, André P; Santos-Reis, Margarida; Fernandes, Carlos

    2016-01-01

    Road barrier effect is among the foremost negative impacts of roads on wildlife. Knowledge of the factors responsible for the road barrier effect is crucial to understand and predict species' responses to roads, and to improve mitigation measures in the context of management and conservation. We built a set of hypothesis aiming to infer the most probable cause of road barrier effect (traffic effect or road surface avoidance), while controlling for the potentially confounding effects road width, traffic volume and road age. The wood mouse Apodemus sylvaticus was used as a model species of small and forest-dwelling mammals, which are more likely to be affected by gaps in cover such as those resulting from road construction. We confront genetic patterns from opposite and same roadsides from samples of three highways and used computer simulations to infer migration rates between opposite roadsides. Genetic patterns from 302 samples (ca. 100 per highway) suggest that the highway barrier effect for wood mouse is due to road surface avoidance. However, from the simulations we estimated a migration rate of about 5% between opposite roadsides, indicating that some limited gene flow across highways does occur. To reduce highway impact on population genetic diversity and structure, possible mitigation measures could include retrofitting of culverts and underpasses to increase their attractiveness and facilitate their use by wood mice and other species, and setting aside roadside strips without vegetation removal to facilitate establishment and dispersal of small mammals. PMID:26978779

  8. Disentangle the Causes of the Road Barrier Effect in Small Mammals through Genetic Patterns

    PubMed Central

    Ascensão, Fernando; Mata, Cristina; Malo, Juan E.; Ruiz-Capillas, Pablo; Silva, Catarina; Silva, André P.; Santos-Reis, Margarida; Fernandes, Carlos

    2016-01-01

    Road barrier effect is among the foremost negative impacts of roads on wildlife. Knowledge of the factors responsible for the road barrier effect is crucial to understand and predict species’ responses to roads, and to improve mitigation measures in the context of management and conservation. We built a set of hypothesis aiming to infer the most probable cause of road barrier effect (traffic effect or road surface avoidance), while controlling for the potentially confounding effects road width, traffic volume and road age. The wood mouse Apodemus sylvaticus was used as a model species of small and forest-dwelling mammals, which are more likely to be affected by gaps in cover such as those resulting from road construction. We confront genetic patterns from opposite and same roadsides from samples of three highways and used computer simulations to infer migration rates between opposite roadsides. Genetic patterns from 302 samples (ca. 100 per highway) suggest that the highway barrier effect for wood mouse is due to road surface avoidance. However, from the simulations we estimated a migration rate of about 5% between opposite roadsides, indicating that some limited gene flow across highways does occur. To reduce highway impact on population genetic diversity and structure, possible mitigation measures could include retrofitting of culverts and underpasses to increase their attractiveness and facilitate their use by wood mice and other species, and setting aside roadside strips without vegetation removal to facilitate establishment and dispersal of small mammals. PMID:26978779

  9. Estimating Genetic Ancestry Proportions from Faces

    PubMed Central

    Klimentidis, Yann C.; Shriver, Mark D.

    2009-01-01

    Ethnicity can be a means by which people identify themselves and others. This type of identification mediates many kinds of social interactions and may reflect adaptations to a long history of group living in humans. Recent admixture in the US between groups from different continents, and the historically strong emphasis on phenotypic differences between members of these groups, presents an opportunity to examine the degree of concordance between estimates of group membership based on genetic markers and on visually-based estimates of facial features. We first measured the degree of Native American, European, African and East Asian genetic admixture in a sample of 14 self-identified Hispanic individuals, chosen to cover a broad range of Native American and European genetic admixture proportions. We showed frontal and side-view photographs of the 14 individuals to 241 subjects living in New Mexico, and asked them to estimate the degree of NA admixture for each individual. We assess the overall concordance for each observer based on an aggregated measure of the difference between the observer and the genetic estimates. We find that observers reach a significantly higher degree of concordance than expected by chance, and that the degree of concordance as well as the direction of the discrepancy in estimates differs based on the ethnicity of the observer, but not on the observers' age or sex. This study highlights the potentially high degree of discordance between physical appearance and genetic measures of ethnicity, as well as how perceptions of ethnic affiliation are context-specific. We compare our findings to those of previous studies and discuss their implications. PMID:19223962

  10. Molecular barriers to processes of genetic reprogramming and cell transformation.

    PubMed

    Chestkov, I V; Khomyakova, E A; Vasilieva, E A; Lagarkova, M A; Kiselev, S L

    2014-12-01

    Genetic reprogramming by ectopic expression of transcription factor genes induces the pluripotent state in somatic cells. This technology provides an opportunity to establish pluripotent stem cells for each person, as well as to get better understanding of epigenetic mechanisms controlling cell state. Interestingly, some of the molecular processes that accompany somatic cell reprogramming in vitro are also characteristic for tumor manifestation. Thus, similar "molecular barriers" that control the stability of epigenetic state exist for both processes of pluripotency induction and malignant transformation. The reprogramming of tumor cells is interesting in two aspects: first, it will determine the contribution of epigenetic changes in carcinogenesis; second, it gives an approach to evaluate tumor stem cells that are supposed to form the entire cell mass of the tumor. This review discusses the key stages of genetic reprogramming, the similarity and difference between the reprogramming process and malignant transformation. PMID:25716723

  11. Estimation of genetic purging under competitive conditions.

    PubMed

    López-Cortegano, Eugenio; Vilas, Ana; Caballero, Armando; García-Dorado, Aurora

    2016-08-01

    Inbreeding depression for fitness traits is a key issue in evolutionary biology and conservation genetics. The magnitude of inbreeding depression, though, may critically depend on the efficiency of genetic purging, the elimination or recessive deleterious mutations by natural selection after they are exposed by inbreeding. However, the detection and quantification of genetic purging for nonlethal mutations is a rather difficult task. Here, we present two comprehensive sets of experiments with Drosophila aimed at detecting genetic purging in competitive conditions and quantifying its magnitude. We obtain, for the first time in competitive conditions, an estimate for the predictive parameter, the purging coefficient (d), that quantifies the magnitude of genetic purging, either against overall inbreeding depression (d ≈ 0.3), or against the component ascribed to nonlethal alleles (dNL ≈ 0.2). We find that competitive fitness declines at a high rate when inbreeding increases in the absence of purging. However, in moderate size populations under competitive conditions, inbreeding depression need not be too dramatic in the medium to short term, as the efficiency of purging is also very high. Furthermore, we find that purging occurred under competitive conditions also reduced the inbreeding depression that is expressed in the absence of competition. PMID:27302839

  12. Debris flow impact estimation on a rigid barrier

    NASA Astrophysics Data System (ADS)

    Vagnon, Federico; Segalini, Andrea

    2016-07-01

    The aim of this paper is to analyse debris flow impact against rigid and undrained barrier in order to propose a new formulation for the estimation of acting force after the flow impact to safe design protection structures. For this reason, this work concentrates on the flow impact, by performing a series of small scale tests in a specifically created flume. Flow characteristics (flow height and velocity) and applied loads (dynamic and static) on barrier were measured using four ultrasonic devices, four load cells and a contact surface pressure gauge. The results obtained were compared with main existing models and a new equation is proposed. Furthermore, a brief review of the small scale theory was provided to analyse the scale effects that can affect the results.

  13. Instrumental noise estimates stabilize and quantify endothelial cell micro-impedance barrier function parameter estimates

    SciTech Connect

    English, Anthony E; Moy, Alan B; Kruse, Kara L; Ward, Richard C; Kirkpatrick, Stacy S; GoldmanM.D., Mitchell H

    2009-04-01

    A novel transcellular micro-impedance biosensor, referred to as the electric cell-substrate impedance sensor or ECIS, has become increasingly applied to the study and quantification of endothelial cell physiology. In principle, frequency dependent impedance measurements obtained from this sensor can be used to estimate the cell cell and cell matrix impedance components of endothelial cell barrier function based on simple geometric models. Few studies, however, have examined the numerical optimization of these barrier function parameters and established their error bounds. This study, therefore, illustrates the implementation of a multi-response Levenberg Marquardt algorithm that includes instrumental noise estimates and applies it to frequency dependent porcine pulmonary artery endothelial cell impedance measurements. The stability of cell cell, cell matrix and membrane impedance parameter estimates based on this approach is carefully examined, and several forms of parameter instability and refinement illustrated. Including frequency dependent noise variance estimates in the numerical optimization reduced the parameter value dependence on the frequency range of measured impedances. The increased stability provided by a multi-response non-linear fit over one-dimensional algorithms indicated that both real and imaginary data should be used in the parameter optimization. Error estimates based on single fits and Monte Carlo simulations showed that the model barrier parameters were often highly correlated with each other. Independently resolving the different parameters can, therefore, present a challenge to the experimentalist and demand the use of non-linear multivariate statistical methods when comparing different sets of parameters.

  14. Crossing the impassable: genetic connections in 20 reef fishes across the eastern Pacific barrier

    PubMed Central

    Lessios, H.A; Robertson, D.R

    2006-01-01

    The ‘impassable’ Eastern Pacific Barrier (EPB), ca 5000 km of deep water separating the eastern from the central Pacific, is the World's widest marine biogeographic barrier. Sequencing of mitochondrial DNA in 20 reef fish morphospecies encountered on both sides of the barrier revealed cryptic speciation in two. Among the other 18 species only two showed significant differentiation (as revealed by haplotype networks and FST statistics) between the eastern and the central Pacific. Coalescence analyses indicated that genetic similarity in the 18 truly transpacific species resulted from different combinations of ages of most recent invasion and of levels of recurrent gene flow, with estimated times of initial separation ranging from approximately 30 000 to 1 Myr (ago). There is no suggestion of simultaneous interruptions of gene flow among the species. Migration across the EPB was previously thought to be exclusively eastward, but our evidence showed two invasions from east to west and eight cases in which subsequent gene flow possibly proceeded in the same direction. Thus, the EPB is sporadically permeable to propagules originating on either side. PMID:16901840

  15. Mechanisms and genetic control of interspecific crossing barriers in Lycopersicon

    SciTech Connect

    Mutschler, M.A. ); McCormick, S. . Plant Gene Expression Center)

    1993-03-27

    This study employs Lycopersicon esculentum and L. pennellii as model systems to study the interspecific reproductive barriers unilateral incongruity (UI), hybrid breakdown and interspecific aberrant ratio syndrome (IARS).

  16. Fragmentation reduces regional-scale spatial genetic structure in a wind-pollinated tree because genetic barriers are removed

    PubMed Central

    Wang, Rong; Compton, Stephen G; Shi, Yi-Su; Chen, Xiao-Yong

    2012-01-01

    Gene flow strongly influences the regional genetic structuring of plant populations. Seed and pollen dispersal patterns can respond differently to the increased isolation resulting from habitat fragmentation, with unpredictable consequences for gene flow and population structuring. In a recently fragmented landscape we compared the pre- and post-fragmentation genetic structure of populations of a tree species where pollen and seed dispersal respond differentially to forest fragmentation generated by flooding. Castanopsis sclerophylla is wind-pollinated, with seeds that are dispersed by gravity and rodents. Using microsatellites, we found no significant difference in genetic diversity between pre- and post-fragmentation cohorts. Significant genetic structure was observed in pre-fragmentation cohorts, due to an unknown genetic barrier that had isolated one small population. Among post-fragmentation cohorts this genetic barrier had disappeared and genetic structure was significantly weakened. The strengths of genetic structuring were at a similar level in both cohorts, suggesting that overall gene flow of C. sclerophylla has been unchanged by fragmentation at the regional scale. Fragmentation has blocked seed dispersal among habitats, but this appears to have been compensated for by enhanced pollen dispersal, as indicated by the disappearance of a genetic barrier, probably as a result of increased wind speeds and easier pollen movement over water. Extensive pollen flow can counteract some negative effects of fragmentation and assist the long-term persistence of small remnant populations. PMID:23139883

  17. Genetic background of skin barrier dysfunction in the pathogenesis of psoriasis vulgaris

    PubMed Central

    Szczerkowska-Dobosz, Aneta; Rębała, Krzysztof; Purzycka-Bohdan, Dorota

    2015-01-01

    Psoriasis is a common inflammatory skin disease. It is known to be a complex condition with multifactorial mode of inheritance, however the associations between particular pathogenic pathways remain unclear. A novel report on the pathogenesis of psoriasis has recently included the genetic determination of the skin barrier dysfunction. In this paper, we focus on specific genetic variants associated with formation of the epidermal barrier and their role in the complex pathogenesis of the disease. PMID:26015782

  18. A systematic review of factors that act as barriers to patient referral to genetic services

    PubMed Central

    Delikurt, Türem; Williamson, Graham R; Anastasiadou, Violetta; Skirton, Heather

    2015-01-01

    Patients who might benefit from genetic services may be denied access through failure to be referred. To investigate the evidence on barriers to referral to genetic services, we conducted a systematic review of empirical evidence on this topic. Nine studies were included in the review. Barriers related to non-genetic healthcare professionals were: lack of awareness of patient risk factors, failure to obtain adequate family history, lack of knowledge of genetics and genetic conditions, lack of awareness of genetic services, inadequate coordination of referral and lack of genetics workforce. Those related to individuals affected by or at risk of a genetic condition were: lack of awareness of personal risk, lack of knowledge and/or awareness of medical history of family members and lack of knowledge of genetic services. Research on access to genetic services is heterogeneous; stronger empirical evidence is needed on factors that are barriers, and further research is needed to develop ‘targeted interventions' for equitable access to genetic services in a range of populations. PMID:25205405

  19. Genetic structure of juvenile cohorts of bicolor damselfish ( Stegastes partitus) along the Mesoamerican barrier reef: chaos through time

    NASA Astrophysics Data System (ADS)

    Hepburn, R. I.; Sale, P. F.; Dixon, B.; Heath, Daniel D.

    2009-03-01

    Dispersal in marine systems is a critical component of the ecology, evolution, and conservation of such systems; however, estimating dispersal is logistically difficult, especially in coral reef fish. Juvenile bicolor damselfish ( Stegastes partitus) were sampled at 13 sites along the Mesoamerican Barrier Reef System (MBRS), the barrier reefs on the east coast of Central America extending from the Yucatan, Mexico to Honduras, to evaluate genetic structure among recently settled cohorts. Using genotype data at eight microsatellite loci genetic structure was estimated at large and small spatial scales using exact tests for allele frequency differences and hierarchical analysis of molecular variance (AMOVA). Isolation-by-distance models of divergence were assessed at both spatial scales. Results showed genetic homogeneity of recently settled S. partitus at large geographic scales with subtle, but significant, genetic structure at smaller geographic scales. Genetic temporal stability was tested for using archived juvenile S. partitus collected earlier in the same year (nine sites), and in the previous year (six sites). The temporal analyses indicated that allele frequency differences among sites were not generally conserved over time, nor were pairwise genetic distances correlated through time, indicative of temporal instability. These results indicate that S. partitus larvae undergo high levels of dispersal along the MBRS, and that the structure detected at smaller spatial scales is likely driven by stochastic effects on dispersal coupled with microgeographic effects. Temporal variation in juvenile cohort genetic signature may be a fundamental characteristic of connectivity patterns in coral reef fishes, with various species and populations differing only in the magnitude of that instability. Such a scenario provides a basis for the reconciliation of conflicting views regarding levels of genetic structuring in S. partitus and possibly other coral reef fish species.

  20. Influence of barriers to movement on within-watershed genetic variation of coastal cutthroat trout

    USGS Publications Warehouse

    Wofford, John E.B.; Gresswell, Robert E.; Banks, M.A.

    2005-01-01

    Because human land use activities often result in increased fragmentation of aquatic and terrestrial habitats, a better understanding of the effects of fragmentation on the genetic heterogeneity of animal populations may be useful for effective management. We used eight microsatellites to examine the genetic structure of coastal cutthroat trout (Oncorhynchus clarki clarki) in Camp Creek, an isolated headwater stream in western Oregon. Our objectives were to determine if coastal cutthroat trout were genetically structured within streams and to assess the effects of natural and anthropogenic barriers on coastal cutthroat trout genetic variation. Fish sampling occurred at 10 locations, and allele frequencies differed significantly among all sampling sections. Dispersal barriers strongly influenced coastal cutthroat trout genetic structure and were associated with reduced genetic diversity and increased genetic differentiation. Results indicate that Camp Creek coastal cutthroat trout exist as many small, partially independent populations that are strongly affected by genetic drift. In headwater streams, barriers to movement can result in genetic and demographic isolation leading to reduced coastal cutthroat trout genetic diversity, and potentially compromising long-term population persistence. When habitat fragmentation eliminates gene flow among small populations, similar results may occur in other species.

  1. Genetic mouse models to study blood–brain barrier development and function

    PubMed Central

    2013-01-01

    The blood–brain barrier (BBB) is a complex physiological structure formed by the blood vessels of the central nervous system (CNS) that tightly regulates the movement of substances between the blood and the neural tissue. Recently, the generation and analysis of different genetic mouse models has allowed for greater understanding of BBB development, how the barrier is regulated during health, and its response to disease. Here we discuss: 1) Genetic mouse models that have been used to study the BBB, 2) Available mouse genetic tools that can aid in the study of the BBB, and 3) Potential tools that if generated could greatly aid in our understanding of the BBB. PMID:23305182

  2. Estimates of genetic parameters for fat yield in Murrah buffaloes

    PubMed Central

    Kumar, Manoj; Vohra, Vikas; Ratwan, Poonam; Valsalan, Jamuna; Patil, C. S.; Chakravarty, A. K.

    2016-01-01

    Aim: The present study was performed to investigate the effect of genetic and non-genetic factors affecting milk fat yield and to estimate genetic parameters of monthly test day fat yields (MTDFY) and lactation 305-day fat yield (L305FY) in Murrah buffaloes. Materials and Methods: The data on total of 10381 MTDFY records comprising the first four lactations of 470 Murrah buffaloes calved from 1993 to 2014 were assessed. These buffaloes were sired by 75 bulls maintained in an organized farm at ICAR-National Dairy Research Institute, Karnal. Least squares maximum likelihood program was used to estimate genetic and non-genetic parameters. Heritability estimates were obtained using paternal half-sib correlation method. Genetic and phenotypic correlations among MTDFY, and 305-day fat yield were calculated from the analysis of variance and covariance matrix among sire groups. Results: The overall least squares mean of L305FY was found to be 175.74±4.12 kg. The least squares mean of overall MTDFY ranged from 3.33±0.14 kg (TD-11) to 7.06±0.17 kg (TD-3). The h2 estimate of L305FY was found to be 0.33±0.16 in this study. The estimates of phenotypic and genetic correlations between 305-day fat yield and different MTDFY ranged from 0.32 to 0.48 and 0.51 to 0.99, respectively. Conclusions: In this study, all the genetic and non-genetic factors except age at the first calving group, significantly affected the traits under study. The estimates of phenotypic and genetic correlations of MTDFY with 305-day fat yield was generally higher in the MTDFY-5 of lactation suggesting that this TD yields could be used as the selection criteria for early evaluation and selection of Murrah buffaloes. PMID:27057114

  3. A Rapid Genetic Assay for the Identification of the Most Common Pocillopora damicornis Genetic Lineages on the Great Barrier Reef

    PubMed Central

    Torda, Gergely; Schmidt-Roach, Sebastian; Peplow, Lesa M.; Lundgren, Petra; van Oppen, Madeleine J. H.

    2013-01-01

    Pocillopora damicornis (Linnaeus, 1758; Scleractinia, Pocilloporidae) has recently been found to comprise at least five distinct genetic lineages in Eastern Australia, some of which likely represent cryptic species. Due to similar and plastic gross morphology of these lineages, field identification is often difficult. Here we present a quick, cost effective genetic assay as well as three novel microsatellite markers that distinguish the two most common lineages found on the Great Barrier Reef. The assay is based on PCR amplification of two regions within the mitochondrial putative control region, which show consistent and easily identifiable fragment size differences for the two genetic lineages after Alu1 restriction enzyme digestion of the amplicons. PMID:23505507

  4. Vicariance and dispersal across an intermittent barrier: population genetic structure of marine animals across the Torres Strait land bridge

    NASA Astrophysics Data System (ADS)

    Mirams, A. G. K.; Treml, E. A.; Shields, J. L.; Liggins, L.; Riginos, C.

    2011-12-01

    Biogeographic barriers, some transitory in duration, are likely to have been important contributing factors to modern marine biodiversity in the Indo-Pacific region. One such barrier was the Torres Strait land bridge between continental Australia and New Guinea that persisted through much of the late Pleistocene and separated Indian and Pacific Ocean taxa. Here, we examine the patterns of mitochondrial DNA diversity for marine animals with present-day distributions spanning the Torres Strait. Specifically, we investigate whether there are concordant signatures across species, consistent with either vicariance or recent colonization from either ocean basin. We survey four species of reef fishes ( Apogon doederleini, Pomacentrus coelestis, Dascyllus trimaculatus, and Acanthurus triostegus) for mtDNA cytochrome oxidase 1 and control region variation and contrast these results to previous mtDNA studies in diverse marine animals with similar distributions. We find substantial genetic partitioning (estimated from F-statistics and coalescent approaches) between Indian and Pacific Ocean populations for many species, consistent with regional persistence through the late Pleistocene in both ocean basins. The species-specific estimates of genetic divergence, however, vary greatly and for reef fishes we estimate substantially different divergence times among species. It is likely that Indian and Pacific Ocean populations have been isolated for multiple glacial cycles for some species, whereas for other species genetic connections have been more recent. Regional estimates of genetic diversity and directionality of gene flow also vary among species. Thus, there is no apparent consistency among historical patterns across the Torres Strait for these co-distributed marine animals.

  5. How to perform meaningful estimates of genetic effects.

    PubMed

    Alvarez-Castro, José M; Le Rouzic, Arnaud; Carlborg, Orjan

    2008-05-01

    Although the genotype-phenotype map plays a central role both in Quantitative and Evolutionary Genetics, the formalization of a completely general and satisfactory model of genetic effects, particularly accounting for epistasis, remains a theoretical challenge. Here, we use a two-locus genetic system in simulated populations with epistasis to show the convenience of using a recently developed model, NOIA, to perform estimates of genetic effects and the decomposition of the genetic variance that are orthogonal even under deviations from the Hardy-Weinberg proportions. We develop the theory for how to use this model in interval mapping of quantitative trait loci using Halley-Knott regressions, and we analyze a real data set to illustrate the advantage of using this approach in practice. In this example, we show that departures from the Hardy-Weinberg proportions that are expected by sampling alone substantially alter the orthogonal estimates of genetic effects when other statistical models, like F2 or G2A, are used instead of NOIA. Finally, for the first time from real data, we provide estimates of functional genetic effects as sets of effects of natural allele substitutions in a particular genotype, which enriches the debate on the interpretation of genetic effects as implemented both in functional and in statistical models. We also discuss further implementations leading to a completely general genotype-phenotype map. PMID:18451979

  6. Concordant genetic structure in two species of woodpecker distributed across the primary West African biogeographic barriers.

    PubMed

    Fuchs, Jérôme; Bowie, Rauri C K

    2015-07-01

    The lowland forests of western and central tropical Africa are separated by several potential biogeographic barriers to dispersal for forest adapted vertebrates. The two primary barriers are (1) the Dahomey Gap, a savanna corridor that reaches the coast of southern Ghana, Togo and Benin, and separates the West African rainforest into the Upper (Ghana west to Guinea) and Lower Guinea (Nigeria to Uganda and Angola) forest blocks, and (2) the Lower Niger River, a large delta that separates Western and Eastern Nigeria. Previous studies on terrestrial vertebrates (lizards, mammals and birds) have highlighted a genetic break in the Dahomey Gap/Lower Niger River area although the relative importance of each barrier has not been assessed due to limitations in geographic sampling. We compared the phylogeographic history of two co-distributed sister-species of woodpeckers (Campethera caroli and C. nivosa) using data from three loci representing all inheritance modes. Our analyses revealed that both the Dahomey Gap and possibly the Lower Niger River acted as strong biogeographic barriers for the two woodpecker species, with the Lower Niger River being the first barrier to have formed, leading to three distinct populations of C. nivosa. Our divergence time analyses revealed that both these biogeographic barriers formed during the Pleistocene, supporting the Pleistocene refuge hypothesis, with the Dahomey Gap likely appearing about 0.5 myr BP. No genetic structure was recovered among sampled populations in either the Upper or the Lower Guinea Forest Block for both species, despite the considerable geographic area covered. PMID:25800284

  7. [Influence of maternal genetic effect on genetic parameter estimates of production traits of cashmere goat].

    PubMed

    Bai, Jun-Yan; Li, Jin-Quan; Jia, Xiao-Ping; Zhang, Qin; Dao, Er-Ji

    2006-09-01

    The derivative-free restricted maximum likelihood (DFREML) method was used to compare the differences of genetic parameter estimates of Inner Mongolian Cashmere Goats under two models, which differ in whether maternal genetic effect is taken into account. The differences between the two models were, tested by likelihood ratio test. The results show that maternal genetic effect highly affects live body weight and cashmere thickness while has no significant effect on raw cashmere weight, staple length, fibre diameter and fibre length. PMID:16963416

  8. Transethnic Genetic-Correlation Estimates from Summary Statistics.

    PubMed

    Brown, Brielin C; Ye, Chun Jimmie; Price, Alkes L; Zaitlen, Noah

    2016-07-01

    The increasing number of genetic association studies conducted in multiple populations provides an unprecedented opportunity to study how the genetic architecture of complex phenotypes varies between populations, a problem important for both medical and population genetics. Here, we have developed a method for estimating the transethnic genetic correlation: the correlation of causal-variant effect sizes at SNPs common in populations. This methods takes advantage of the entire spectrum of SNP associations and uses only summary-level data from genome-wide association studies. This avoids the computational costs and privacy concerns associated with genotype-level information while remaining scalable to hundreds of thousands of individuals and millions of SNPs. We applied our method to data on gene expression, rheumatoid arthritis, and type 2 diabetes and overwhelmingly found that the genetic correlation was significantly less than 1. Our method is implemented in a Python package called Popcorn. PMID:27321947

  9. Genetics in geographically structured populations: defining, estimating and interpreting FST

    PubMed Central

    Holsinger, Kent E.; Weir, Bruce S.

    2015-01-01

    Wright’s F-statistics, and especially FST, provide important insights into the evolutionary processes that influence the structure of genetic variation within and among populations, and they are among the most widely used descriptive statistics in population and evolutionary genetics. Estimates of FST can identify regions of the genome that have been the target of selection, and comparisons of FST from different parts of the genome can provide insights into the demographic history of populations. For these reasons and others, FST has a central role in population and evolutionary genetics and has wide applications in fields that range from disease association mapping to forensic science. This Review clarifies how FST is defined, how it should be estimated, how it is related to similar statistics and how estimates of FST should be interpreted. PMID:19687804

  10. Genetic engineering of yellow betalain pigments beyond the species barrier.

    PubMed

    Nakatsuka, Takashi; Yamada, Eri; Takahashi, Hideyuki; Imamura, Tomohiro; Suzuki, Mariko; Ozeki, Yoshihiro; Tsujimura, Ikuko; Saito, Misa; Sakamoto, Yuichi; Sasaki, Nobuhiro; Nishihara, Masahiro

    2013-01-01

    Betalains are one of the major plant pigment groups found in some higher plants and higher fungi. They are not produced naturally in any plant species outside of the order Caryophyllales, nor are they produced by anthocyanin-accumulating Caryophyllales. Here, we attempted to reconstruct the betalain biosynthetic pathway as a self-contained system in an anthocyanin-producing plant species. The combined expressions of a tyrosinase gene from shiitake mushroom and a DOPA 4,5-dioxygenase gene from the four-o'clock plant resulted in successful betalain production in cultured cells of tobacco BY2 and Arabidopsis T87. Transgenic tobacco BY2 cells were bright yellow because of the accumulation of betaxanthins. LC-TOF-MS analyses showed that proline-betaxanthin (Pro-Bx) accumulated as the major betaxanthin in these transgenic BY2 cells. Transgenic Arabidopsis T87 cells also produced betaxanthins, but produced lower levels than transgenic BY2 cells. These results illustrate the success of a novel genetic engineering strategy for betalain biosynthesis. PMID:23760173

  11. Genetic engineering of yellow betalain pigments beyond the species barrier

    PubMed Central

    Nakatsuka, Takashi; Yamada, Eri; Takahashi, Hideyuki; Imamura, Tomohiro; Suzuki, Mariko; Ozeki, Yoshihiro; Tsujimura, Ikuko; Saito, Misa; Sakamoto, Yuichi; Sasaki, Nobuhiro; Nishihara, Masahiro

    2013-01-01

    Betalains are one of the major plant pigment groups found in some higher plants and higher fungi. They are not produced naturally in any plant species outside of the order Caryophyllales, nor are they produced by anthocyanin-accumulating Caryophyllales. Here, we attempted to reconstruct the betalain biosynthetic pathway as a self-contained system in an anthocyanin-producing plant species. The combined expressions of a tyrosinase gene from shiitake mushroom and a DOPA 4,5-dioxygenase gene from the four-o'clock plant resulted in successful betalain production in cultured cells of tobacco BY2 and Arabidopsis T87. Transgenic tobacco BY2 cells were bright yellow because of the accumulation of betaxanthins. LC-TOF-MS analyses showed that proline-betaxanthin (Pro-Bx) accumulated as the major betaxanthin in these transgenic BY2 cells. Transgenic Arabidopsis T87 cells also produced betaxanthins, but produced lower levels than transgenic BY2 cells. These results illustrate the success of a novel genetic engineering strategy for betalain biosynthesis. PMID:23760173

  12. Practical Barriers and Ethical Challenges in Genetic Data Sharing

    PubMed Central

    Simpson, Claire L.; Goldenberg, Aaron J.; Culverhouse, Rob; Daley, Denise; Igo, Robert P.; Jarvik, Gail P.; Mandal, Diptasri M.; Mascalzoni, Deborah; Montgomery, Courtney Gray; Pierce, Brandon L.; Plaetke, Rosemarie; Shete, Sanjay; Goddard, Katrina A. B.; Stein, Catherine M.

    2014-01-01

    The underlying ethos of dbGaP is that access to these data by secondary data analysts facilitates advancement of science. NIH has required that genome-wide association study data be deposited in the Database of Genotypes and Phenotypes (dbGaP) since 2003. In 2013, a proposed updated policy extended this requirement to next-generation sequencing data. However, recent literature and anecdotal reports suggest lingering logistical and ethical concerns about subject identifiability, informed consent, publication embargo enforcement, and difficulty in accessing dbGaP data. We surveyed the International Genetic Epidemiology Society (IGES) membership about their experiences. One hundred and seventy five (175) individuals completed the survey, a response rate of 27%. Of respondents who received data from dbGaP (43%), only 32% perceived the application process as easy but most (75%) received data within five months. Remaining challenges include difficulty in identifying an institutional signing official and an overlong application process. Only 24% of respondents had contributed data to dbGaP. Of these, 31% reported local IRB restrictions on data release; an additional 15% had to reconsent study participants before depositing data. The majority of respondents (56%) disagreed that the publication embargo period was sufficient. In response, we recommend longer embargo periods and use of varied data-sharing models rather than a one-size-fits-all approach. PMID:25153467

  13. Model-free Estimation of Recent Genetic Relatedness

    PubMed Central

    Conomos, Matthew P.; Reiner, Alexander P.; Weir, Bruce S.; Thornton, Timothy A.

    2016-01-01

    Genealogical inference from genetic data is essential for a variety of applications in human genetics. In genome-wide and sequencing association studies, for example, accurate inference on both recent genetic relatedness, such as family structure, and more distant genetic relatedness, such as population structure, is necessary for protection against spurious associations. Distinguishing familial relatedness from population structure with genotype data, however, is difficult because both manifest as genetic similarity through the sharing of alleles. Existing approaches for inference on recent genetic relatedness have limitations in the presence of population structure, where they either (1) make strong and simplifying assumptions about population structure, which are often untenable, or (2) require correct specification of and appropriate reference population panels for the ancestries in the sample, which might be unknown or not well defined. Here, we propose PC-Relate, a model-free approach for estimating commonly used measures of recent genetic relatedness, such as kinship coefficients and IBD sharing probabilities, in the presence of unspecified structure. PC-Relate uses principal components calculated from genome-screen data to partition genetic correlations among sampled individuals due to the sharing of recent ancestors and more distant common ancestry into two separate components, without requiring specification of the ancestral populations or reference population panels. In simulation studies with population structure, including admixture, we demonstrate that PC-Relate provides accurate estimates of genetic relatedness and improved relationship classification over widely used approaches. We further demonstrate the utility of PC-Relate in applications to three ancestrally diverse samples that vary in both size and genealogical complexity. PMID:26748516

  14. Use of a portable electric barrier to estimate Chinook salmon escapement in a turbid Alaskan river

    USGS Publications Warehouse

    Palmisano, A.; Burger, C.V.

    1988-01-01

    We developed a portable electric barrier to aid in the capture of adult chinook salmon Oncorhynchus tshawytscha undergoing spawning migrations up a turbid stream in south-central Alaska. In 1981, we tagged and released 157 chinook salmon after diverting them from the main-stem Killey River into a conventional trap with the aid of the electric barrier. On the basis of returns of tagged salmon to Benjamin Creek, a clear-water tributary of the upper Killey River, we estimated spawners in the drainage to number 8,000 fish. Two different statistical approaches to the mark–recapture data yielded similar estimates. Through several modifications of the electric barrier, we were able to reduce mortality associated with the barrier's use.

  15. Estimates of genetic correlations among growth traits including competition effects

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective was to estimate genetic parameters of direct and competition effects for traits measured at the end of a growth test utilizing multi-trait analyses. A total of 9,720 boars were tested with 15 boars per pen from about 71 to 161 d of age and weight from 31 to 120 kg. Traits analyzed wi...

  16. Estimation of genetic parameters for reproductive traits in alpacas.

    PubMed

    Cruz, A; Cervantes, I; Burgos, A; Morante, R; Gutiérrez, J P

    2015-12-01

    One of the main deficiencies affecting animal breeding programs in Peruvian alpacas is the low reproductive performance leading to low number of animals available to select from, decreasing strongly the selection intensity. Some reproductive traits could be improved by artificial selection, but very few information about genetic parameters exists for these traits in this specie. The aim of this study was to estimate genetic parameters for six reproductive traits in alpacas both in Suri (SU) and Huacaya (HU) ecotypes, as well as their genetic relationship with fiber and morphological traits. Dataset belonging to Pacomarca experimental farm collected between 2000 and 2014 was used. Number of records for age at first service (AFS), age at first calving (AFC), copulation time (CT), pregnancy diagnosis (PD), gestation length (GL), and calving interval (CI) were, respectively, 1704, 854, 19,770, 5874, 4290 and 934. Pedigree consisted of 7742 animals. Regarding reproductive traits, model of analysis included additive and residual random effects for all traits, and also permanent environmental effect for CT, PD, GL and CI traits, with color and year of recording as fixed effects for all the reproductive traits and also age at mating and sex of calf for GL trait. Estimated heritabilities, respectively for HU and SU were 0.19 and 0.09 for AFS, 0.45 and 0.59 for AFC, 0.04 and 0.05 for CT, 0.07 and 0.05 for PD, 0.12 and 0.20 for GL, and 0.14 and 0.09 for CI. Genetic correlations between them ranged from -0.96 to 0.70. No important genetic correlations were found between reproductive traits and fiber or morphological traits in HU. However, some moderate favorable genetic correlations were found between reproductive and either fiber and morphological traits in SU. According to estimated genetic correlations, some reproductive traits might be included as additional selection criteria in HU. PMID:26490188

  17. Estimated genetic parameters for carcass traits of Brahman cattle.

    PubMed

    Riley, D G; Chase, C C; Hammond, A C; West, R L; Johnson, D D; Olson, T A; Coleman, S W

    2002-04-01

    Heritabilities and genetic and phenotypic correlations were estimated from feedlot and carcass data collected from Brahman calves (n = 504) in central Florida from 1996 to 2000. Data were analyzed using animal models in MTDFREML. Models included contemporary group (n = 44; groups of calves of the same sex, fed in the same pen, slaughtered on the same day) as a fixed effect and calf age in days at slaughter as a continuous variable. Estimated feedlot trait heritabilities were 0.64, 0.67, 0.47, and 0.26 for ADG, hip height at slaughter, slaughter weight, and shrink. The USDA yield grade estimated heritability was 0.71; heritabilities for component traits of yield grade, including hot carcass weight, adjusted 12th rib backfat thickness, loin muscle area, and percentage kidney, pelvic, and heart fat were 0.55, 0.63, 0.44, and 0.46, respectively. Heritability estimates for dressing percentage, marbling score, USDA quality grade, cutability, retail yield, and carcass hump height were 0.77, 0.44, 0.47, 0.71, 0.5, and 0.54, respectively. Estimated genetic correlations of adjusted 12th rib backfat thickness with ADG, slaughter weight, marbling score, percentage kidney, pelvic, and heart fat, and yield grade (0.49, 0.46, 0.56, 0.63, and 0.93, respectively) were generally larger than most literature estimates. Estimated genetic correlations of marbling score with ADG, percentage shrink, loin muscle area, percentage kidney, pelvic, and heart fat, USDA yield grade, cutability, retail yield, and carcass hump height were 0.28, 0.49, 0.44, 0.27, 0.45, -0.43, 0.27, and 0.43, respectively. Results indicate that sufficient genetic variation exists within the Brahman breed for design and implementation of effective selection programs for important carcass quality and yield traits. PMID:12008662

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

    NASA Astrophysics Data System (ADS)

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

    2009-03-01

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

  19. Genetic variability of Wagyu cattle estimated by statistical approaches.

    PubMed

    Oyama, Kenji

    2011-06-01

    The genetic evaluation of economically important traits utilizes estimates of genetic variability, which are represented by heritability. This review summarizes the published heritabilities of traits estimated in Wagyu cattle. Two different mean heritabilities, unweighted and weighted by standard errors, were calculated. In Japanese Black cattle, the average unweighted and weighted direct heritabilities of birth weight were 0.35 and 0.28, respectively, whereas the respective maternal heritabilities were 0.17 and 0.07. The mean unweighted heritability of calf market weight was estimated to be 0.30 in Japanese Black cattle. The mean unweighted heritability of daily gain during performance testing was 0.29 in Japanese Black and 0.40 in Japanese Shorthorn cattle. In Japanese Black cattle, the unweighted mean heritability was 0.48 for carcass weight, 0.46 for rib-eye area, 0.38 for rib thickness, 0.39 for subcutaneous fat thickness, and 0.55 for marbling. The mean weighted heritability of the calving interval was low, and estimated to be 0.05. In general, the heritabilities estimated in Wagyu cattle were similar to those estimated in other beef breeds. PMID:21615828

  20. Genetic roadmap of the Arctic: plant dispersal highways, traffic barriers and capitals of diversity.

    PubMed

    Eidesen, Pernille Bronken; Ehrich, Dorothee; Bakkestuen, Vegar; Alsos, Inger Greve; Gilg, Oliver; Taberlet, Pierre; Brochmann, Christian

    2013-11-01

    We provide the first comparative multispecies analysis of spatial genetic structure and diversity in the circumpolar Arctic using a common strategy for sampling and genetic analyses. We aimed to identify and explain potential general patterns of genetic discontinuity/connectivity and diversity, and to compare our findings with previously published hypotheses. We collected and analyzed 7707 samples of 17 widespread arctic-alpine plant species for amplified fragment length polymorphisms (AFLPs). Genetic structure, diversity and distinctiveness were analyzed for each species, and extrapolated to cover the geographic range of each species. The resulting maps were overlaid to produce metamaps. The Arctic and Atlantic Oceans, the Greenlandic ice cap, the Urals, and lowland areas between southern mountain ranges and the Arctic were the strongest barriers against gene flow. Diversity was highest in Beringia and gradually decreased into formerly glaciated areas. The highest degrees of distinctiveness were observed in Siberia. We conclude that large-scale general patterns exist in the Arctic, shaped by the Pleistocene glaciations combined with long-standing physical barriers against gene flow. Beringia served as both refugium and source for interglacial (re)colonization, whereas areas further west in Siberia served as refugia, but less as sources for (re)colonization. PMID:23869846

  1. [Integral estimation of genetic effects of ionizing radiation].

    PubMed

    Shevchenko, V A

    1997-01-01

    A system of criteria (direct, indirect, extrapolational, integral, populational, evolutional) has been proposed to estimate the consequences of irradiation of flora, fauna and human population. This system makes it possible to obtain the most comprehensive estimate of genetic effects from exposure of live organisms to ionizing radiations. An attempt has been made to use extrapolational approaches for assessing the genetic risk on the basis of the results of cytogenetic examination of the human population in a number of regions exposed to the action of ionizing radiations as a result of the Chernobyl accident, in connection with the activity of the chemical plant Mayak in the Chelyabinsk region, nuclear explosions at the Semipalatinsk nuclear test site, the accident at the Three Mile Island nuclear power plant in the U.S.A. PMID:9599614

  2. Genetic differentiation among populations of the brooding soft coral Clavularia koellikeri on the Great Barrier Reef

    NASA Astrophysics Data System (ADS)

    Bastidas, C.; Benzie, J.; Fabricius, K.

    2002-09-01

    The contribution of sexual and asexual reproduction, the spatial patterns of genetic structure, and the potential gene flow among populations were determined for the soft coral Clavularia koellikeri (Octocorallia: Alcyonacea, Clavulariidae) at ten sites among six reefs from two well-separated regions of the Great Barrier Reef (GBR), Australia. Eight allozyme loci indicated that colonies of C. koellikeri separated ≥3 m were produced sexually. Genetic diversity was lower in the southern (18°S) compared with the northern (10°S) populations, suggesting that reefs closer to the southernmost limit of the distribution of C. koellikeri within the GBR (19°S) may represent a more marginal habitat for this species. High levels of genetic differentiation were significant at all spatial scales (sites within reefs, reefs, and regions) from <4 km up to 1,000 km, indicating that C. koellikeri has restricted dispersal, consistent with having brooded larvae.

  3. HCV-1b intra-subtype variability: Impact on genetic barrier to protease inhibitors.

    PubMed

    Ferraro, Donatella; Urone, Noemi; Di Marco, Vito; Craxì, Antonio

    2014-04-01

    Due to error-prone RNA polymerase and the lack of proofreading mechanisms, to the spread worldwide and probable long-term presence in human population, HCV showed a high degree of inter- and intra-subtype genetic variability. Protease inhibitors (PIs), a new class of drugs, have been designed specifically on the HCV genotype 1 NS3 protease three-dimensional structure. The viral genetic barrier limits the efficacy of PIs, and fourteen loci in the HCV NS3 gene are involved in resistance to PIs. A sensitive method (15UI/ml) for study the HCV genetic profile of 125 strains from patients naïve to PIs, was developed through the use of new degenerate primers for subtype 1b. We observed the presence of naturally resistance-associated variants in 14% of the HCV strains (V36L, F43S, T54S, I153V, R155Q, D168A/G). T54S was the most common mutation (4%) detected. We investigated, through minimal score (m.s.) calculating, how the HCV intra-subtype 1b variability modifies the genetic barrier to PIs. For >60% of strains a single transition (m.s. of 1) was required for selection of low to medium resistance mutations, while more than one transition/transversion (m.s. ⩾2.5) or one transition plus one transversion (m.s. ⩾3.5) was necessary for most of the high level PI-resistant-associated mutations, except for A156V, for which a single transition was sufficient (m.s. of 1). However, the presence at locus 36 of the amino acid polymorphism S36 in one case and the wild type V36 in 6 isolates, encoded by unusual GTA or GTG codons, might determined a higher probability of V36L/M mutations because of the reduction of the genetic barrier. Instead, the presence of the CGA and CGT codons in the 155(th) position increases the genetic barrier for R155M or R155Q/M. The large intra-subtype variability, suggests that a routine baseline resistance test must be used before PIs-treatment. PMID:24508244

  4. Estimating Meiotic Gene Conversion Rates From Population Genetic Data

    PubMed Central

    Gay, J.; Myers, S.; McVean, G.

    2007-01-01

    Gene conversion plays an important part in shaping genetic diversity in populations, yet estimating the rate at which it occurs is difficult because of the short lengths of DNA involved. We have developed a new statistical approach to estimating gene conversion rates from genetic variation, by extending an existing model for haplotype data in the presence of crossover events. We show, by simulation, that when the rate of gene conversion events is at least comparable to the rate of crossover events, the method provides a powerful approach to the detection of gene conversion and estimation of its rate. Application of the method to data from the telomeric X chromosome of Drosophila melanogaster, in which crossover activity is suppressed, indicates that gene conversion occurs ∼400 times more often than crossover events. We also extend the method to estimating variable crossover and gene conversion rates and estimate the rate of gene conversion to be ∼1.5 times higher than the crossover rate in a region of human chromosome 1 with known recombination hotspots. PMID:17660532

  5. Torus mandibularis: an estimation of the degree of genetic determination.

    PubMed

    Eggen, S

    1989-12-01

    Torus mandibularis has frustrated several attempts to make family patterns of variation fit modifications of Mendelian models. It is suggested that the quasi-continuous model of inheritance provides a rational explanation for the diverging opinions. The model implies an underlying continuous and normally distributed variable, 'liability', with a threshold value beyond which individuals will be affected. Both genetic and environmental factors determine liability, making the system multifactorial. The incidence of variable degrees of torus was examined in two groups of patients with different stresses on the jaws: one group with bruxism and one comparison group. The transformation of incidences to group means and variances of liability was demonstrated. Muscular forces during bruxism were shown to influence liability. The relative importance of environmental and genetic components of variance could, however, not be estimated directly from the entire groups, since both were mixed with regard to the genetic predisposition. To achieve materials with uniform genotypes, all individuals without torus were omitted. The estimate of the genotypic variance (VG) was obtained by subtracting the variance of the bruxism sub-group--the environmental component associated with bruxism (VEB)--from the total phenotypic variance of the comparison sub-group (VP). The estimate of the genetic determination of torus (VG/VP) turned out to be about 30%, whereas approximately 70% of the causes seemed to be attributable to environmental influence in terms of occlusal stress. Gene effects on the morphologic level are usually pleiotropic, and it is suggested that the correlation of torus mandibularis with other clinical variables might make an interesting subject for further investigation. PMID:2609949

  6. Using genetic data to estimate diffusion rates in heterogeneous landscapes.

    PubMed

    Roques, L; Walker, E; Franck, P; Soubeyrand, S; Klein, E K

    2016-08-01

    Having a precise knowledge of the dispersal ability of a population in a heterogeneous environment is of critical importance in agroecology and conservation biology as it can provide management tools to limit the effects of pests or to increase the survival of endangered species. In this paper, we propose a mechanistic-statistical method to estimate space-dependent diffusion parameters of spatially-explicit models based on stochastic differential equations, using genetic data. Dividing the total population into subpopulations corresponding to different habitat patches with known allele frequencies, the expected proportions of individuals from each subpopulation at each position is computed by solving a system of reaction-diffusion equations. Modelling the capture and genotyping of the individuals with a statistical approach, we derive a numerically tractable formula for the likelihood function associated with the diffusion parameters. In a simulated environment made of three types of regions, each associated with a different diffusion coefficient, we successfully estimate the diffusion parameters with a maximum-likelihood approach. Although higher genetic differentiation among subpopulations leads to more accurate estimations, once a certain level of differentiation has been reached, the finite size of the genotyped population becomes the limiting factor for accurate estimation. PMID:26707856

  7. GAz: a genetic algorithm for photometric redshift estimation

    NASA Astrophysics Data System (ADS)

    Hogan, Robert; Fairbairn, Malcolm; Seeburn, Navin

    2015-05-01

    We present a new approach to the problem of estimating the redshift of galaxies from photometric data. The approach uses a genetic algorithm combined with non-linear regression to model the 2SLAQ LRG data set with SDSS DR7 photometry. The genetic algorithm explores the very large space of high order polynomials while only requiring optimization of a small number of terms. We find a σrms = 0.0408 ± 0.0006 for redshifts in the range 0.4 < z < 0.7. These results are competitive with the current state-of-the-art but can be presented simply as a polynomial which does not require the user to run any code. We demonstrate that the method generalizes well to other data sets and redshift ranges by testing it on SDSS DR11 and on simulated data. For other data sets or applications the code has been made available at https://github.com/rbrthogan/GAz.

  8. Evaluating noninvasive genetic sampling techniques to estimate large carnivore abundance.

    PubMed

    Mumma, Matthew A; Zieminski, Chris; Fuller, Todd K; Mahoney, Shane P; Waits, Lisette P

    2015-09-01

    Monitoring large carnivores is difficult because of intrinsically low densities and can be dangerous if physical capture is required. Noninvasive genetic sampling (NGS) is a safe and cost-effective alternative to physical capture. We evaluated the utility of two NGS methods (scat detection dogs and hair sampling) to obtain genetic samples for abundance estimation of coyotes, black bears and Canada lynx in three areas of Newfoundland, Canada. We calculated abundance estimates using program capwire, compared sampling costs, and the cost/sample for each method relative to species and study site, and performed simulations to determine the sampling intensity necessary to achieve abundance estimates with coefficients of variation (CV) of <10%. Scat sampling was effective for both coyotes and bears and hair snags effectively sampled bears in two of three study sites. Rub pads were ineffective in sampling coyotes and lynx. The precision of abundance estimates was dependent upon the number of captures/individual. Our simulations suggested that ~3.4 captures/individual will result in a < 10% CV for abundance estimates when populations are small (23-39), but fewer captures/individual may be sufficient for larger populations. We found scat sampling was more cost-effective for sampling multiple species, but suggest that hair sampling may be less expensive at study sites with limited road access for bears. Given the dependence of sampling scheme on species and study site, the optimal sampling scheme is likely to be study-specific warranting pilot studies in most circumstances. PMID:25693632

  9. Using genetic markers to estimate the pollen dispersal curve.

    PubMed

    Austerlitz, Frederic; Dick, Christopher W; Dutech, Cyril; Klein, Etienne K; Oddou-Muratorio, Sylvie; Smouse, Peter E; Sork, Victoria L

    2004-04-01

    Pollen dispersal is a critical process that shapes genetic diversity in natural populations of plants. Estimating the pollen dispersal curve can provide insight into the evolutionary dynamics of populations and is essential background for making predictions about changes induced by perturbations. Specifically, we would like to know whether the dispersal curve is exponential, thin-tailed (decreasing faster than exponential), or fat-tailed (decreasing slower than the exponential). In the latter case, rare events of long-distance dispersal will be much more likely. Here we generalize the previously developed TWOGENER method, assuming that the pollen dispersal curve belongs to particular one- or two-parameter families of dispersal curves and estimating simultaneously the parameters of the dispersal curve and the effective density of reproducing individuals in the population. We tested this method on simulated data, using an exponential power distribution, under thin-tailed, exponential and fat-tailed conditions. We find that even if our estimates show some bias and large mean squared error (MSE), we are able to estimate correctly the general trend of the curve - thin-tailed or fat-tailed - and the effective density. Moreover, the mean distance of dispersal can be correctly estimated with low bias and MSE, even if another family of dispersal curve is used for the estimation. Finally, we consider three case studies based on forest tree species. We find that dispersal is fat-tailed in all cases, and that the effective density estimated by our model is below the measured density in two of the cases. This latter result may reflect the difficulty of estimating two parameters, or it may be a biological consequence of variance in reproductive success of males in the population. Both the simulated and empirical findings demonstrate the strong potential of TWOGENER for evaluating the shape of the dispersal curve and the effective density of the population (d(e)). PMID:15012767

  10. [Transfer of genetic constructions through the transplacental barrier into mice embryos].

    PubMed

    Efremov, A M; Buglaeva, A O; Orlov, S V; Burov, S V; Ignatovich, I A; Dizhe, E B; Shavva, V S; Perevozchikov, A P

    2010-01-01

    Genetic modification of mammalian embryos is an important way to model various changes in human development; also, it is an instrument for studying the functions of certain genes in mammals. Using our own experience in developing modes of delivery of genetic constructions to mammals in a nonviral way, we present here data on the delivery of a eukaryotic expression vector to mice embryos through the transplacental barrier with the use of hydrodynamic intravenous injections of DNA-hybrid peptide complexes to pregnant females. The peptide has a cationic part for interaction with DNA and includes a ligand structure towards receptors of the releasing factor of luteinizing hormone (RFLH, luliberin). Advantages of the suggested method are simplicity, economy, nonimmunogenicity for females, and the ability to multiply repeat the procedure. On the basis of the method, systemic gene delivery into tissues of mammalian embryos may be developed. PMID:20429369

  11. Robust Sparse Matching and Motion Estimation Using Genetic Algorithms

    NASA Astrophysics Data System (ADS)

    Shahbazi, M.; Sohn, G.; Théau, J.; Ménard, P.

    2015-03-01

    In this paper, we propose a robust technique using genetic algorithm for detecting inliers and estimating accurate motion parameters from putative correspondences containing any percentage of outliers. The proposed technique aims to increase computational efficiency and modelling accuracy in comparison with the state-of-the-art via the following contributions: i) guided generation of initial populations for both avoiding degenerate solutions and increasing the rate of useful hypotheses, ii) replacing random search with evolutionary search, iii) possibility of evaluating the individuals of every population by parallel computation, iv) being performable on images with unknown internal orientation parameters, iv) estimating the motion model via detecting a minimum, however more than enough, set of inliers, v) ensuring the robustness of the motion model against outliers, degeneracy and poorperspective camera models, vi) making no assumptions about the probability distribution of inliers and/or outliers residuals from the estimated motion model, vii) detecting all the inliers by setting the threshold on their residuals adaptively with regard to the uncertainty of the estimated motion model and the position of the matches. The proposed method was evaluated both on synthetic data and real images. The results were compared with the most popular techniques from the state-of-the-art, including RANSAC, MSAC, MLESAC, Least Trimmed Squares and Least Median of Squares. Experimental results proved that the proposed approach perform better than others in terms of accuracy of motion estimation, accuracy of inlier detection and the computational efficiency.

  12. Estimating microsatellite based genetic diversity in Rhode Island Red chicken.

    PubMed

    Das, A K; Kumar, S; Rahim, A

    2015-01-01

    This study aimed to estimate microsatellite based genetic diversity in two lines (the selected RIR(S) and control line RIR(C)) of Rhode Island Red (RIR) chicken. Genomic DNA of 24 randomly selected birds maintained at Central Avian Research Institute (India) and 24 microsatellite markers were used. Microsatellite alleles were determined on 6% urea-PAGE, recorded using GelDoc system and the samples were genotyped. Nei's heterozygosity and Botstein's polymorphic information content (PIC) at each microsatellite locus were estimated. Wright's fixation indices and gene flow were estimated using POPGENE software. All the microsatellite loci were polymorphic and the estimated PIC ranged from 0.3648 (MCW0059) to 0.7819 (ADL0267) in RIR(S) and from 0.2392 (MCW0059) to 0.8620 (ADL0136) in RIR(C). Most of the loci were highly informative (PIC>0.50) in the both lines, except for five loci in RIR(S) and six loci in RIR(C) line. Nei's heterozygosity per locus ranged from 0.4800 (MCW0059) to 0.8056 (ADL0267) in RIR(S) and from 0.2778 (MCW0059) to 0.875 (ADL0136) in RIR(C). Out of 24 loci, 15 (62.5%) in RIR(S) and 14 loci (58.33%) in RIR(C) revealed moderate to high negative FIS index indicating heterozygote excess for these loci in corresponding lines, but the rest revealed positive FIS indicating heterozygosity deficiency. A mean FIS across the both lines indicated overall 10.77% heterozygosity deficit and a mean FIT indicated 17.19% inbreeding co-efficient favoring homozygosity over the two lines. The mean FST indicated that 10.18% of the microsatellite variation between the two lines was due to their genetic difference. PMID:27175188

  13. Genetic and anatomical basis of the barrier separating wakefulness and anesthetic-induced unresponsiveness.

    PubMed

    Joiner, William J; Friedman, Eliot B; Hung, Hsiao-Tung; Koh, Kyunghee; Sowcik, Mallory; Sehgal, Amita; Kelz, Max B

    2013-01-01

    A robust, bistable switch regulates the fluctuations between wakefulness and natural sleep as well as those between wakefulness and anesthetic-induced unresponsiveness. We previously provided experimental evidence for the existence of a behavioral barrier to transitions between these states of arousal, which we call neural inertia. Here we show that neural inertia is controlled by processes that contribute to sleep homeostasis and requires four genes involved in electrical excitability: Sh, sss, na and unc79. Although loss of function mutations in these genes can increase or decrease sensitivity to anesthesia induction, surprisingly, they all collapse neural inertia. These effects are genetically selective: neural inertia is not perturbed by loss-of-function mutations in all genes required for the sleep/wake cycle. These effects are also anatomically selective: sss acts in different neurons to influence arousal-promoting and arousal-suppressing processes underlying neural inertia. Supporting the idea that anesthesia and sleep share some, but not all, genetic and anatomical arousal-regulating pathways, we demonstrate that increasing homeostatic sleep drive widens the neural inertial barrier. We propose that processes selectively contributing to sleep homeostasis and neural inertia may be impaired in pathophysiological conditions such as coma and persistent vegetative states. PMID:24039590

  14. Genetic and Anatomical Basis of the Barrier Separating Wakefulness and Anesthetic-Induced Unresponsiveness

    PubMed Central

    Hung, Hsiao-Tung; Koh, Kyunghee; Sowcik, Mallory; Sehgal, Amita; Kelz, Max B.

    2013-01-01

    A robust, bistable switch regulates the fluctuations between wakefulness and natural sleep as well as those between wakefulness and anesthetic-induced unresponsiveness. We previously provided experimental evidence for the existence of a behavioral barrier to transitions between these states of arousal, which we call neural inertia. Here we show that neural inertia is controlled by processes that contribute to sleep homeostasis and requires four genes involved in electrical excitability: Sh, sss, na and unc79. Although loss of function mutations in these genes can increase or decrease sensitivity to anesthesia induction, surprisingly, they all collapse neural inertia. These effects are genetically selective: neural inertia is not perturbed by loss-of-function mutations in all genes required for the sleep/wake cycle. These effects are also anatomically selective: sss acts in different neurons to influence arousal-promoting and arousal-suppressing processes underlying neural inertia. Supporting the idea that anesthesia and sleep share some, but not all, genetic and anatomical arousal-regulating pathways, we demonstrate that increasing homeostatic sleep drive widens the neural inertial barrier. We propose that processes selectively contributing to sleep homeostasis and neural inertia may be impaired in pathophysiological conditions such as coma and persistent vegetative states. PMID:24039590

  15. A Genetic Algorithm Based Support Vector Machine Model for Blood-Brain Barrier Penetration Prediction

    PubMed Central

    Zhang, Daqing; Xiao, Jianfeng; Zhou, Nannan; Zheng, Mingyue; Luo, Xiaomin; Jiang, Hualiang; Chen, Kaixian

    2015-01-01

    Blood-brain barrier (BBB) is a highly complex physical barrier determining what substances are allowed to enter the brain. Support vector machine (SVM) is a kernel-based machine learning method that is widely used in QSAR study. For a successful SVM model, the kernel parameters for SVM and feature subset selection are the most important factors affecting prediction accuracy. In most studies, they are treated as two independent problems, but it has been proven that they could affect each other. We designed and implemented genetic algorithm (GA) to optimize kernel parameters and feature subset selection for SVM regression and applied it to the BBB penetration prediction. The results show that our GA/SVM model is more accurate than other currently available log BB models. Therefore, to optimize both SVM parameters and feature subset simultaneously with genetic algorithm is a better approach than other methods that treat the two problems separately. Analysis of our log BB model suggests that carboxylic acid group, polar surface area (PSA)/hydrogen-bonding ability, lipophilicity, and molecular charge play important role in BBB penetration. Among those properties relevant to BBB penetration, lipophilicity could enhance the BBB penetration while all the others are negatively correlated with BBB penetration. PMID:26504797

  16. Marker-based estimation of genetic parameters in genomics.

    PubMed

    Hu, Zhiqiu; Yang, Rong-Cai

    2014-01-01

    Linear mixed model (LMM) analysis has been recently used extensively for estimating additive genetic variances and narrow-sense heritability in many genomic studies. While the LMM analysis is computationally less intensive than the Bayesian algorithms, it remains infeasible for large-scale genomic data sets. In this paper, we advocate the use of a statistical procedure known as symmetric differences squared (SDS) as it may serve as a viable alternative when the LMM methods have difficulty or fail to work with large datasets. The SDS procedure is a general and computationally simple method based only on the least squares regression analysis. We carry out computer simulations and empirical analyses to compare the SDS procedure with two commonly used LMM-based procedures. Our results show that the SDS method is not as good as the LMM methods for small data sets, but it becomes progressively better and can match well with the precision of estimation by the LMM methods for data sets with large sample sizes. Its major advantage is that with larger and larger samples, it continues to work with the increasing precision of estimation while the commonly used LMM methods are no longer able to work under our current typical computing capacity. Thus, these results suggest that the SDS method can serve as a viable alternative particularly when analyzing 'big' genomic data sets. PMID:25025305

  17. Marker-Based Estimation of Genetic Parameters in Genomics

    PubMed Central

    Hu, Zhiqiu; Yang, Rong-Cai

    2014-01-01

    Linear mixed model (LMM) analysis has been recently used extensively for estimating additive genetic variances and narrow-sense heritability in many genomic studies. While the LMM analysis is computationally less intensive than the Bayesian algorithms, it remains infeasible for large-scale genomic data sets. In this paper, we advocate the use of a statistical procedure known as symmetric differences squared (SDS) as it may serve as a viable alternative when the LMM methods have difficulty or fail to work with large datasets. The SDS procedure is a general and computationally simple method based only on the least squares regression analysis. We carry out computer simulations and empirical analyses to compare the SDS procedure with two commonly used LMM-based procedures. Our results show that the SDS method is not as good as the LMM methods for small data sets, but it becomes progressively better and can match well with the precision of estimation by the LMM methods for data sets with large sample sizes. Its major advantage is that with larger and larger samples, it continues to work with the increasing precision of estimation while the commonly used LMM methods are no longer able to work under our current typical computing capacity. Thus, these results suggest that the SDS method can serve as a viable alternative particularly when analyzing ‘big’ genomic data sets. PMID:25025305

  18. Genetic Barrier to Direct Acting Antivirals in HCV Sequences Deposited in the European Databank

    PubMed Central

    Tovo, Cristiane Valle; Gorini da Veiga, Ana Beatriz; Machado, André Luiz; West, John

    2016-01-01

    Background & Aims Development of resistance results from mutations in the viral genome, and the presence of selective drug pressure leads to the emergence of a resistant virus population. The aim of this study was to analyze the impact of genetic variability on the genetic barrier to drug resistance to DAAs. Methods The genetic barrier was quantified based on the number and type of nucleotide mutations required to impart resistance, considering full-length HCV NS3, NS5A and NS5B regions segregated by genotype into subtypes 1a, 1b, 2a, 2b and 3a. This study analyzeds 789 NS3 sequences, 708 sequences and 536 NS5B sequences deposited in the European Hepatitis C Virus Database, in the following resistance-associated positions: NS3: F43/I/L/S/V, Q80K/R, R155K/G, A156G/S/T and D168A/C/E/G/H/N/T/V/Y; NS5A: L/M28A/T/V, Q30E/H/R, L31F/I/M/V, H58D or P58S and Y93C/F/H/N/S; NS5B: S282P/R/T, C316H/N/Y, S368T, Y448C/H, S556G/R, D559R. Results Variants that require only one transversion in NS3 were found in 4 positions and include F43S, R80K, R155K/G and A156T. The genetic barrier to resistance shows subtypic differences at position 155 of the NS3 gene where a single transition is necessary in subtype 1a. In the NS5A gene, 5 positions where only one nucleotide change can confer resistance were found, such as L31M which requires one transversion in all subtypes, except in 0.28% of 1b sequences; and R30H, generated by a single transition, which was found in 10.25% of the sequences of genotype 1b. Other subtypic differences were observed at position 58, where resistance is less likely in genotype 1a because a transversion is required to create the variant 58S. For the NS5B inhibitors, the genetic barrier at positions conferring resistance was nearly identical in subtypes 1a and 1b, and single transitions or transversions were necessary in 5 positions to generate a drug-resistant variant of HCV. The positions C316Y and S556D required only one transition in all genotypes, Y448H and S

  19. 78 FR 50481 - Request for Public Comments Regarding the National Trade Estimate Report on Foreign Trade Barriers

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-19

    ... Foreign Trade Barriers (NTE). With this notice, the Trade Policy Staff Committee (TPSC) is requesting... TRADE REPRESENTATIVE Request for Public Comments Regarding the National Trade Estimate Report on Foreign Trade Barriers AGENCY: Office of the United States Trade Representative. ACTION: Notice....

  20. Estimating Sampling Selection Bias in Human Genetics: A Phenomenological Approach

    PubMed Central

    Risso, Davide; Taglioli, Luca; De Iasio, Sergio; Gueresi, Paola; Alfani, Guido; Nelli, Sergio; Rossi, Paolo; Paoli, Giorgio; Tofanelli, Sergio

    2015-01-01

    This research is the first empirical attempt to calculate the various components of the hidden bias associated with the sampling strategies routinely-used in human genetics, with special reference to surname-based strategies. We reconstructed surname distributions of 26 Italian communities with different demographic features across the last six centuries (years 1447–2001). The degree of overlapping between "reference founding core" distributions and the distributions obtained from sampling the present day communities by probabilistic and selective methods was quantified under different conditions and models. When taking into account only one individual per surname (low kinship model), the average discrepancy was 59.5%, with a peak of 84% by random sampling. When multiple individuals per surname were considered (high kinship model), the discrepancy decreased by 8–30% at the cost of a larger variance. Criteria aimed at maximizing locally-spread patrilineages and long-term residency appeared to be affected by recent gene flows much more than expected. Selection of the more frequent family names following low kinship criteria proved to be a suitable approach only for historically stable communities. In any other case true random sampling, despite its high variance, did not return more biased estimates than other selective methods. Our results indicate that the sampling of individuals bearing historically documented surnames (founders' method) should be applied, especially when studying the male-specific genome, to prevent an over-stratification of ancient and recent genetic components that heavily biases inferences and statistics. PMID:26452043

  1. Microgeographic Population Genetic Structure of Baylisascaris procyonis (Nematoda: Ascaroidae) in Western Michigan Indicates the Grand River Is a Barrier to Gene Flow.

    PubMed

    Sarkissian, Christina A; Campbell, Sara K; Dharmarajan, Guha; Jacquot, Joseph; Page, L Kristen; Graham, Douglas H

    2015-12-01

    Baylisascaris procyonis , the raccoon roundworm, is increasingly being recognized for its zoonotic and public health importance. Fine-scale analyses of the population genetics of this species have been hampered due to a lack of appropriate genetic markers. To this end, we developed 8 novel polymorphic microsatellites for B. procyonis and used these markers to elucidate microgeographic structuring of this parasite in a 500-km(2) study area in western Michigan. Our analyses revealed significant levels of genetic differentiation amongst the 74 worms collected from 10 different raccoons. Critically, Bayesian clustering indicated 2 genetically distinct groups, one on either side of the Grand River which bisects our study area. Estimates of F(ST), and results from AMOVA and isolation by distance, further corroborated a scenario whereby the river is acting as a barrier to gene flow, a rather unexpected finding given the high vagility of raccoons and microgeographic scale of the analysis. It is possible that the Grand River is a major dispersal barrier for B. procyonis because raccoons are most likely to disperse across the river when it is frozen, and worm burden in raccoons approaches zero during the winter. PMID:26284339

  2. Genetic control and estimation of genetic parameters for seed-coat darkening of carioca beans.

    PubMed

    Silva, F C; Melo, P G S; Pereira, H S; Melo, L C

    2014-01-01

    The maintenance of the light color of the grains of carioca beans is a requirement for the development of new cultivars of common beans because it enables the storage of grains for long periods so that they may be traded at a proper opportunity. Crosses of cultivar BRSMG Madrepérola, which presents slow grain darkening, were made to 10 elite lines presenting normal darkening to obtain information about the genetic control of the trait and estimates of phenotypic and genotypic parameters. Progenies at the tegument generations F3 and F4 and their parents were evaluated at the locations of Santo Antônio de Goiás and Ponta Grossa at 71, 106, and 155 days of storage for seed-coat darkening using a rank of scores ranging from 1 (very light colored grains) to 5 (very dark colored grains). Genotypic and phenotypic variances and broad-sense heritabilities were estimated for each population. The segregation ratios were subjected to the chi-square test to establish the genetic control. Some populations did not present consistent patterns of genetic control, while others presented monogenic or double-recessive digenic segregation, indicating that the trait is controlled by few genes. Six segregant populations were identified with both low means for darkening and high expected gain under selection. Despite the strong environmental influence on the expression of the traits and the occurrence of the genotype by environment interaction, the estimates of genotypic and phenotypic parameters indicate the possibility of successful selection to develop lines with slow seed-coat darkening. PMID:25158267

  3. Efficient dynamical correction of the transition state theory rate estimate for a flat energy barrier.

    PubMed

    Mökkönen, Harri; Ala-Nissila, Tapio; Jónsson, Hannes

    2016-09-01

    The recrossing correction to the transition state theory estimate of a thermal rate can be difficult to calculate when the energy barrier is flat. This problem arises, for example, in polymer escape if the polymer is long enough to stretch between the initial and final state energy wells while the polymer beads undergo diffusive motion back and forth over the barrier. We present an efficient method for evaluating the correction factor by constructing a sequence of hyperplanes starting at the transition state and calculating the probability that the system advances from one hyperplane to another towards the product. This is analogous to what is done in forward flux sampling except that there the hyperplane sequence starts at the initial state. The method is applied to the escape of polymers with up to 64 beads from a potential well. For high temperature, the results are compared with direct Langevin dynamics simulations as well as forward flux sampling and excellent agreement between the three rate estimates is found. The use of a sequence of hyperplanes in the evaluation of the recrossing correction speeds up the calculation by an order of magnitude as compared with the traditional approach. As the temperature is lowered, the direct Langevin dynamics simulations as well as the forward flux simulations become computationally too demanding, while the harmonic transition state theory estimate corrected for recrossings can be calculated without significant increase in the computational effort. PMID:27609008

  4. Models for estimation of service life of concrete barriers in low-level radioactive waste disposal

    SciTech Connect

    Walton, J.C.; Plansky, L.E.; Smith, R.W. )

    1990-09-01

    Concrete barriers will be used as intimate parts of systems for isolation of low level radioactive wastes subsequent to disposal. This work reviews mathematical models for estimating the degradation rate of concrete in typical service environments. The models considered cover sulfate attack, reinforcement corrosion, calcium hydroxide leaching, carbonation, freeze/thaw, and cracking. Additionally, fluid flow, mass transport, and geochemical properties of concrete are briefly reviewed. Example calculations included illustrate the types of predictions expected of the models. 79 refs., 24 figs., 6 tabs.

  5. Using adult learning theory concepts to address barriers to cancer genetic risk assessment in the African American community.

    PubMed

    Kendall, Jeff; Kendall, Colleen; Catts, Zohra Ali-Khan; Radford, Cristi; Dasch, Kimberly

    2007-06-01

    Utilization of cancer genetic risk assessment can be profoundly influenced by an individuals' knowledge of risk assessment, attitudes regarding illness and healthcare, and affective reactions derived from social norms. Race and ethnicity play a powerful role in the development of an individual's attitudes and should be considered when attempting to understand a person's openness to cancer genetic risk assessment (Lannin et al., 1998). Until recently, however, cancer screening and prevention programs have been primarily based on data from studies conducted with the Caucasian population, yielding data that are not fully applicable to the African American community. In the last several years, research findings regarding African American's knowledge, attitudes, and feelings about genetic counseling and testing have grown (Matthews et al., 2000; Singer et al., 2004; Thompson et al., 2003). However, to the authors' knowledge, these data have yet to be presented in a manner that both summarizes the barriers that African Americans have reported regarding cancer genetic risk assessment, while at the same time suggesting methods individual genetic counselors can utilize during community presentations to help address these barriers. This article will first summarize previous empirical findings regarding African Americans' knowledge, attitudes, and feelings about cancer genetic risk assessment. The article will then apply adult learning theory to those findings to provide genetic counselors with practical, theory based techniques to apply toward community based educational programs with African American groups. PMID:17473964

  6. Historical habitat barriers prevent ring-like genetic continuity throughout the distribution of threatened Alameda Striped Racers (Coluber lateralis euryxanthus)

    USGS Publications Warehouse

    Richmond, Jonathan Q.; Wood, Dustin A.; Swaim, Karen; Fisher, Robert N.; Vandergast, Amy

    2016-01-01

    We used microsatellites and mtDNA sequences to examine the mixed effects of geophysical, habitat, and contemporary urban barriers on the genetics of threatened Alameda Striped Racers (Coluber lateralis euryxanthus), a species with close ties to declining coastal scrub and chaparral habitat in the eastern San Francisco Bay area of California. We used cluster assignments to characterize population genetic structuring with respect to land management units and approximate Bayesian analysis to rank the ability of five alternative evolutionary hypotheses to explain the inferred structure. Then, we estimated rates of contemporary and historical migration among the major clusters and measured the fit of different historical migration models to better understand the formation of the current population structure. Our results reveal a ring-like pattern of historical connectivity around the Tri-Valley area of the East Bay (i.e., San Ramon, Amador, and Livermore valleys), with clusters largely corresponding to different management units. We found no evidence of continuous gene flow throughout the ring, however, and that the main gap in continuity is centered across the Livermore Valley. Historical migration models support higher rates of gene flow away from the terminal ends of the ring on the north and south sides of the Valley, compared with rates into those areas from western sites that border the interior San Francisco Bay. We attribute the break in ring-like connectivity to the presence of unsuitable habitat within the Livermore Valley that has been reinforced by 20th century urbanization, and the asymmetry in gene flow rates to spatial constraints on movement and east–west environmental gradients influenced by the proximity of the San Francisco Bay.

  7. Orbit design and estimation for surveillance missions using genetic algorithms

    NASA Astrophysics Data System (ADS)

    Abdelkhalik, Osama Mohamed Omar

    2005-11-01

    The problem of observing a given set of Earth target sites within an assigned time frame is examined. Attention is given mainly to visiting these sites as sub-satellite nadir points. Solutions to this problem in the literature require thrusters to continuously maneuver the satellite from one site to another. A natural solution is proposed. A natural solution is a gravitational orbit that enables the spacecraft to satisfy the mission requirements without maneuvering. Optimization of a penalty function is performed to find natural solutions for satellite orbit configurations. This penalty function depends on the mission objectives. Two mission objectives are considered: maximum observation time and maximum resolution. The penalty function poses multi minima and a genetic algorithm technique is used to solve this problem. In the case that there is no one orbit satisfying the mission requirements, a multi-orbit solution is proposed. In a multi-orbit solution, the set of target sites is split into two groups. Then the developed algorithm is used to search for a natural solution for each group. The satellite has to be maneuvered between the two solution orbits. Genetic algorithms are used to find the optimal orbit transfer between the two orbits using impulsive thrusters. A new formulation for solving the orbit maneuver problem using genetic algorithms is developed. The developed formulation searches for a minimum fuel consumption maneuver and guarantees that the satellite will be transferred exactly to the final orbit even if the solution is non-optimal. The results obtained demonstrate the feasibility of finding natural solutions for many case studies. The problem of the design of suitable satellite constellation for Earth observing applications is addressed. Two cases are considered. The first is the remote sensing missions for a particular region with high frequency and small swath width. The second is the interferometry radar Earth observation missions. In satellite

  8. Effect of Enhanced Information, Values Clarification, and Removal of Financial Barriers on Use of Prenatal Genetic Testing

    PubMed Central

    Kuppermann, Miriam; Pena, Sherri; Bishop, Judith T.; Nakagawa, Sanae; Gregorich, Steven E.; Sit, Anita; Vargas, Juan; Caughey, Aaron B.; Sykes, Susan; Pierce, Lasha; Norton, Mary E.

    2015-01-01

    Importance Prenatal genetic testing guidelines recommend providing patients with detailed information to allow informed, preference-based screening and diagnostic testing decisions. The effect of implementing these guidelines is not well understood. Objective Toanalyze the effect of a decision support guide and elimination of financial barriers to testing on use of prenatal genetic testing and decision-making among women of varying literacy and numeracy levels. Design Randomized trial conducted from 2010-2013. Setting Prenatal clinics at three county hospitals, a community clinic, an academic center, and three medical centers of an integrated health care delivery system in the San Francisco Bay area. Participants English- or Spanish-speaking women who had not yet undergone screening and/or diagnostic testing and remained pregnant at 11 weeks gestation (n=710). Interventions A computerized, interactive decision support guide and access to prenatal testing with no out-of-pocket expense (n=357) or usual care as per current guidelines (n=353). Main Outcome Measures The primary outcome was invasive diagnostic test use, obtained via medical record review. Secondary outcomes included testing strategy undergone, and knowledge, risk comprehension, decisional conflict and decision regret at 24-36 weeks' gestation. Results Women randomized to the intervention group, compared to those randomized to the control group, were less likely to have invasive testing [5.9% vs. 12.3%, odds ratio (OR) 0.45, 95% CI 0.25-0.80] and more likely to forego testing altogether [25.6% vs. 20.4%, OR 3.30 (reference group screening followed by invasive testing), CI 1.43-7.64]. They also had higher knowledge scores (9.4 vs. 8.6 on a 15-point scale, mean group difference 0.82, CI 0.34-1.31), and were more likely to correctly estimate the amniocentesis-related miscarriage risk (73.8% vs. 59.0%, OR 1.95, CI 1.39-2.75) and their age-adjusted chance of carrying a fetus with trisomy 21 (58.7% vs. 46

  9. Joint estimation of crown of thorns (Acanthaster planci) densities on the Great Barrier Reef

    PubMed Central

    Mellin, Camille; Pratchett, Morgan S.; Hoey, Jessica; Anthony, Kenneth R.N.; Cheal, Alistair J.; Miller, Ian; Sweatman, Hugh; Cowan, Zara L.; Taylor, Sascha; Moon, Steven; Fonnesbeck, Chris J.

    2016-01-01

    Crown-of-thorns starfish (CoTS; Acanthaster spp.) are an outbreaking pest among many Indo-Pacific coral reefs that cause substantial ecological and economic damage. Despite ongoing CoTS research, there remain critical gaps in observing CoTS populations and accurately estimating their numbers, greatly limiting understanding of the causes and sources of CoTS outbreaks. Here we address two of these gaps by (1) estimating the detectability of adult CoTS on typical underwater visual count (UVC) surveys using covariates and (2) inter-calibrating multiple data sources to estimate CoTS densities within the Cairns sector of the Great Barrier Reef (GBR). We find that, on average, CoTS detectability is high at 0.82 [0.77, 0.87] (median highest posterior density (HPD) and [95% uncertainty intervals]), with CoTS disc width having the greatest influence on detection. Integrating this information with coincident surveys from alternative sampling programs, we estimate CoTS densities in the Cairns sector of the GBR averaged 44 [41, 48] adults per hectare in 2014.

  10. Landscape-scale evaluation of genetic structure among barrier-isolated populations of coastal cutthroat trout, Oncorhynchus clarkii clarkii

    USGS Publications Warehouse

    Guy, T.J.; Gresswell, R.E.; Banks, M.A.

    2008-01-01

    Relationships among landscape structure, stochastic disturbance, and genetic diversity were assessed by examining interactions between watershed-scale environmental factors and genetic diversity of coastal cutthroat trout (Oncorhynchus clarkii clarkii) in 27 barrier-isolated watersheds from western Oregon, USA. Headwater populations of coastal cutthroat trout were genetically differentiated (mean FST = 0.33) using data from seven microsatellite loci (2232 individuals), but intrapopulation microsatellite genetic diversity (mean number of alleles per locus = 5, mean He = 0.60) was only moderate. Genetic diversity of coastal cutthroat trout was greater (P = 0.02) in the Coast Range ecoregion (mean alleles = 47) than in the Cascades ecoregion (mean alleles = 30), and differences coincided with indices of regional within-watershed complexity and connectivity. Furthermore, regional patterns of diversity evident from isolation-by-distance plots suggested that retention of within-population genetic diversity in the Coast Range ecoregion is higher than that in the Cascades, where genetic drift is the dominant factor influencing genetic patterns. Thus, it appears that physical landscape features have influenced genetic patterns in these populations isolated from short-term immigration. ?? 2008 NRC.

  11. The Individualized Genetic Barrier Predicts Treatment Response in a Large Cohort of HIV-1 Infected Patients

    PubMed Central

    Beerenwinkel, Niko; Montazeri, Hesam; Schuhmacher, Heike; Knupfer, Patrick; von Wyl, Viktor; Furrer, Hansjakob; Battegay, Manuel; Hirschel, Bernard; Cavassini, Matthias; Vernazza, Pietro; Bernasconi, Enos; Yerly, Sabine; Böni, Jürg; Klimkait, Thomas; Cellerai, Cristina; Günthard, Huldrych F.

    2013-01-01

    The success of combination antiretroviral therapy is limited by the evolutionary escape dynamics of HIV-1. We used Isotonic Conjunctive Bayesian Networks (I-CBNs), a class of probabilistic graphical models, to describe this process. We employed partial order constraints among viral resistance mutations, which give rise to a limited set of mutational pathways, and we modeled phenotypic drug resistance as monotonically increasing along any escape pathway. Using this model, the individualized genetic barrier (IGB) to each drug is derived as the probability of the virus not acquiring additional mutations that confer resistance. Drug-specific IGBs were combined to obtain the IGB to an entire regimen, which quantifies the virus' genetic potential for developing drug resistance under combination therapy. The IGB was tested as a predictor of therapeutic outcome using between 2,185 and 2,631 treatment change episodes of subtype B infected patients from the Swiss HIV Cohort Study Database, a large observational cohort. Using logistic regression, significant univariate predictors included most of the 18 drugs and single-drug IGBs, the IGB to the entire regimen, the expert rules-based genotypic susceptibility score (GSS), several individual mutations, and the peak viral load before treatment change. In the multivariate analysis, the only genotype-derived variables that remained significantly associated with virological success were GSS and, with 10-fold stronger association, IGB to regimen. When predicting suppression of viral load below 400 cps/ml, IGB outperformed GSS and also improved GSS-containing predictors significantly, but the difference was not significant for suppression below 50 cps/ml. Thus, the IGB to regimen is a novel data-derived predictor of treatment outcome that has potential to improve the interpretation of genotypic drug resistance tests. PMID:24009493

  12. Could refuge theory and rivers acting as barriers explain the genetic variability distribution in the Atlantic Forest?

    PubMed

    Cazé, Ana Luiza R; Mäder, Geraldo; Nunes, Teonildes S; Queiroz, Luciano P; de Oliveira, Guilherme; Diniz-Filho, José Alexandre F; Bonatto, Sandro L; Freitas, Loreta B

    2016-08-01

    The Atlantic Forest is one of the most species-rich ecoregions in the world. The historical origins of this richness and the evolutionary processes that produced diversification and promoted speciation in this ecosystem remain poorly understood. In this context, focusing on Passiflora contracta, an endemic species from the Atlantic Forest distributed exclusively at sea level along forest edges, this study aimed to characterize the patterns of genetic variability and explore two hypotheses that attempt to explain the possible causes of the genetic diversity in this region: the refuge and riverine barrier theories. We employed Bayesian methods combined with niche modeling to identify genetically homogeneous groups, to determine the diversification age, and identify long-term climate stability areas to species survival. The analyses were performed using molecular markers from nuclear and plastid genomes, with samples collected throughout the entire geographic distribution of the species, and comparisons with congeners species. The results indicated that populations were genetically structured and provided evidence of demographic stability. The molecular markers indicated the existence of a clear structure and the presence of five homogeneous groups. Interestingly, the separation of the groups coincides with the geographical locations of local rivers, corroborating the hypothesis of rivers acting as barriers to gene flow in this species. The highest levels of genetic diversity and the areas identified as having long-term climate stability were found in the same region reported for other species as a possible refuge area during the climatic changes of the Quaternary. PMID:27188539

  13. A comparison of binary and continuous genetic algorithm in parameter estimation of a logistic growth model

    NASA Astrophysics Data System (ADS)

    Windarto, Indratno, S. W.; Nuraini, N.; Soewono, E.

    2014-02-01

    Genetic algorithm is an optimization method based on the principles of genetics and natural selection in life organisms. The algorithm begins by defining the optimization variables, defining the cost function (in a minimization problem) or the fitness function (in a maximization problem) and selecting genetic algorithm parameters. The main procedures in genetic algorithm are generating initial population, selecting some chromosomes (individual) as parent's individual, mating, and mutation. In this paper, binary and continuous genetic algorithms were implemented to estimate growth rate and carrying capacity parameter from poultry data cited from literature. For simplicity, all genetic algorithm parameters (selection rate and mutation rate) are set to be constant along implementation of the algorithm. It was found that by selecting suitable mutation rate, both algorithms can estimate these parameters well. Suitable range for mutation rate in continuous genetic algorithm is wider than the binary one.

  14. An implementation of continuous genetic algorithm in parameter estimation of predator-prey model

    NASA Astrophysics Data System (ADS)

    Windarto

    2016-03-01

    Genetic algorithm is an optimization method based on the principles of genetics and natural selection in life organisms. The main components of this algorithm are chromosomes population (individuals population), parent selection, crossover to produce new offspring, and random mutation. In this paper, continuous genetic algorithm was implemented to estimate parameters in a predator-prey model of Lotka-Volterra type. For simplicity, all genetic algorithm parameters (selection rate and mutation rate) are set to be constant along implementation of the algorithm. It was found that by selecting suitable mutation rate, the algorithms can estimate these parameters well.

  15. Chromosomal Rearrangements as Barriers to Genetic Homogenization between Archaic and Modern Humans.

    PubMed

    Rogers, Rebekah L

    2015-12-01

    Chromosomal rearrangements, which shuffle DNA throughout the genome, are an important source of divergence across taxa. Using a paired-end read approach with Illumina sequence data for archaic humans, I identify changes in genome structure that occurred recently in human evolution. Hundreds of rearrangements indicate genomic trafficking between the sex chromosomes and autosomes, raising the possibility of sex-specific changes. Additionally, genes adjacent to genome structure changes in Neanderthals are associated with testis-specific expression, consistent with evolutionary theory that new genes commonly form with expression in the testes. I identify one case of new-gene creation through transposition from the Y chromosome to chromosome 10 that combines the 5'-end of the testis-specific gene Fank1 with previously untranscribed sequence. This new transcript experienced copy number expansion in archaic genomes, indicating rapid genomic change. Among rearrangements identified in Neanderthals, 13% are transposition of selfish genetic elements, whereas 32% appear to be ectopic exchange between repeats. In Denisovan, the pattern is similar but numbers are significantly higher with 18% of rearrangements reflecting transposition and 40% ectopic exchange between distantly related repeats. There is an excess of divergent rearrangements relative to polymorphism in Denisovan, which might result from nonuniform rates of mutation, possibly reflecting a burst of transposable element activity in the lineage that led to Denisovan. Finally, loci containing genome structure changes show diminished rates of introgression from Neanderthals into modern humans, consistent with the hypothesis that rearrangements serve as barriers to gene flow during hybridization. Together, these results suggest that this previously unidentified source of genomic variation has important biological consequences in human evolution. PMID:26399483

  16. Role of recent and old riverine barriers in fine-scale population genetic structure of Geoffroy's tamarin (Saguinus geoffroyi) in the Panama Canal watershed

    PubMed Central

    Díaz-Muñoz, Samuel L

    2012-01-01

    The role of physical barriers in promoting population divergence and genetic structuring is well known. While it is well established that animals can show genetic structuring at small spatial scales, less well-resolved is how the timing of the appearance of barriers affects population structure. This study uses the Panama Canal watershed as a test of the effects of old and recent riverine barriers in creating population structure in Saguinus geoffroyi, a small cooperatively breeding Neotropical primate. Mitochondrial sequences and microsatellite genotypes from three sampling localities revealed genetic structure across the Chagres River and the Panama Canal, suggesting that both waterways act as barriers to gene flow. F-statistics and exact tests of population differentiation suggest population structure on either side of both riverine barriers. Genetic differentiation across the Canal, however, was less than observed across the Chagres. Accordingly, Bayesian clustering algorithms detected between two and three populations, with localities across the older Chagres River always assigned as distinct populations. While conclusions represent a preliminary assessment of genetic structure of S. geoffroyi, this study adds to the evidence indicating that riverine barriers create genetic structure across a wide variety of taxa in the Panama Canal watershed and highlights the potential of this study area for discerning modern from historical influences on observed patterns of population genetic structure. PMID:22423325

  17. Role of recent and old riverine barriers in fine-scale population genetic structure of Geoffroy's tamarin (Saguinus geoffroyi) in the Panama Canal watershed.

    PubMed

    Díaz-Muñoz, Samuel L

    2012-02-01

    The role of physical barriers in promoting population divergence and genetic structuring is well known. While it is well established that animals can show genetic structuring at small spatial scales, less well-resolved is how the timing of the appearance of barriers affects population structure. This study uses the Panama Canal watershed as a test of the effects of old and recent riverine barriers in creating population structure in Saguinus geoffroyi, a small cooperatively breeding Neotropical primate. Mitochondrial sequences and microsatellite genotypes from three sampling localities revealed genetic structure across the Chagres River and the Panama Canal, suggesting that both waterways act as barriers to gene flow. F-statistics and exact tests of population differentiation suggest population structure on either side of both riverine barriers. Genetic differentiation across the Canal, however, was less than observed across the Chagres. Accordingly, Bayesian clustering algorithms detected between two and three populations, with localities across the older Chagres River always assigned as distinct populations. While conclusions represent a preliminary assessment of genetic structure of S. geoffroyi, this study adds to the evidence indicating that riverine barriers create genetic structure across a wide variety of taxa in the Panama Canal watershed and highlights the potential of this study area for discerning modern from historical influences on observed patterns of population genetic structure. PMID:22423325

  18. Genetic study of skin thickness and its association with postweaning growth in Nellore cattle: estimation of the genetic parameters.

    PubMed

    Maiorano, A M; Oliveira, M C S; Cyrillo, J N S G; Albuquerque, L G; Curi, R A; Silva, J A Iiv

    2016-01-01

    The objective of the present study was to estimate genetic parameters for skin thickness (ST) and postweaning weight gain (PWG550) in Nellore cattle. Records were obtained from 152,392 Nellore animals born between 2001 and 2011. ST was measured in the posterior region of the animal's scapula with a millimeter caliper. The animals were assigned to different contemporary groups, formed on the basis of farm, year, sex, feeding regimen at weaning, date of weaning, feeding regimen at 450 days of age, and date of weighing at 450 days of age. The genetic parameters were estimated by Bayesian analysis using the GIBBS1F90 program. The mean ST and PWG550 observed were 7.71 ± 2.04 mm and 115.95 ± 36.17 kg, respectively. The posterior mean estimates of heritability (h2) were 0.12 ± 0.02 and 0.29 ± 0.02 for ST and PWG550, respectively. The posterior mean estimates of the phenotypic, genetic, and environmental correlations between the traits were 0.16 ± 0.0, 0.17 ± 0.02, and 0.17 ± 0.09, respectively. The traits ST and PWG550 showed sufficient additive genetic variance to be used as selection criteria in breeding programs. The low genetic correlation obtained indicates that genes favoring the expression of one trait may not influence the other. Consequently, a selection favoring ST would be less efficient in increasing PWG550. PMID:26909980

  19. Genetic parameter estimation for pre- and post-weaning traits in Brahman cattle in Brazil.

    PubMed

    Vargas, Giovana; Buzanskas, Marcos Eli; Guidolin, Diego Gomes Freire; Grossi, Daniela do Amaral; Bonifácio, Alexandre da Silva; Lôbo, Raysildo Barbosa; da Fonseca, Ricardo; Oliveira, João Ademir de; Munari, Danísio Prado

    2014-10-01

    Beef cattle producers in Brazil use body weight traits as breeding program selection criteria due to their great economic importance. The objectives of this study were to evaluate different animal models, estimate genetic parameters, and define the most fitting model for Brahman cattle body weight standardized at 120 (BW120), 210 (BW210), 365 (BW365), 450 (BW450), and 550 (BW550) days of age. To estimate genetic parameters, single-, two-, and multi-trait analyses were performed using the animal model. The likelihood ratio test was verified between all models. For BW120 and BW210, additive direct genetic, maternal genetic, maternal permanent environment, and residual effects were considered, while for BW365 and BW450, additive direct genetic, maternal genetic, and residual effects were considered. Finally, for BW550, additive direct genetic and residual effects were considered. Estimates of direct heritability for BW120 were similar in all analyses; however, for the other traits, multi-trait analysis resulted in higher estimates. The maternal heritability and proportion of maternal permanent environmental variance to total variance were minimal in multi-trait analyses. Genetic, environmental, and phenotypic correlations were of high magnitude between all traits. Multi-trait analyses would aid in the parameter estimation for body weight at older ages because they are usually affected by a lower number of animals with phenotypic information due to culling and mortality. PMID:25037588

  20. Mechanisms and genetic control of interspecific crossing barriers in Lycopersicon. Second yearly progress report

    SciTech Connect

    Mutschler, M.A.; McCormick, S.

    1993-03-27

    This study employs Lycopersicon esculentum and L. pennellii as model systems to study the interspecific reproductive barriers unilateral incongruity (UI), hybrid breakdown and interspecific aberrant ratio syndrome (IARS).

  1. Genetic structure and rabies spread potential in raccoons: the role of landscape barriers and sex-biased dispersal.

    PubMed

    Côté, Héloïse; Garant, Dany; Robert, Karine; Mainguy, Julien; Pelletier, Fanie

    2012-06-01

    Identifying natural barriers to movements of hosts associated with infectious diseases is essential for developing effective control strategies. Raccoon rabies variant (RRV) is a zoonosis of concern for humans because its main vector, the raccoon (Procyon lotor), is found near residential areas. In Québec, Canada, all cases of RRV found in raccoons since 2006 were detected on the eastern side of the Richelieu River, suggesting that this river acts as a barrier to gene flow and thus the potential for RRV to spread. The objectives of this study were to characterize the genetic structure of raccoon populations and assess the effect of the Richelieu River on the population structure in southern Québec, Canada. We also evaluated whether RRV spread potential differed between sex and at a larger spatial scale. Our analyses revealed a weak signal of genetic differentiation among individuals located on each side of the Richelieu River. At a larger spatial scale, genetic structuring was weak. Our results suggest that rivers might not always efficiently restrain raccoon movements and spread of RRV. We suggest that the difference in genetic structure found between sexes can be partly explained by male movements during the breeding season in winter, when ice bridges allow passage over most rivers in Québec. PMID:25568059

  2. Genetic structure and rabies spread potential in raccoons: the role of landscape barriers and sex-biased dispersal

    PubMed Central

    Côté, Héloïse; Garant, Dany; Robert, Karine; Mainguy, Julien; Pelletier, Fanie

    2012-01-01

    Identifying natural barriers to movements of hosts associated with infectious diseases is essential for developing effective control strategies. Raccoon rabies variant (RRV) is a zoonosis of concern for humans because its main vector, the raccoon (Procyon lotor), is found near residential areas. In Québec, Canada, all cases of RRV found in raccoons since 2006 were detected on the eastern side of the Richelieu River, suggesting that this river acts as a barrier to gene flow and thus the potential for RRV to spread. The objectives of this study were to characterize the genetic structure of raccoon populations and assess the effect of the Richelieu River on the population structure in southern Québec, Canada. We also evaluated whether RRV spread potential differed between sex and at a larger spatial scale. Our analyses revealed a weak signal of genetic differentiation among individuals located on each side of the Richelieu River. At a larger spatial scale, genetic structuring was weak. Our results suggest that rivers might not always efficiently restrain raccoon movements and spread of RRV. We suggest that the difference in genetic structure found between sexes can be partly explained by male movements during the breeding season in winter, when ice bridges allow passage over most rivers in Québec. PMID:25568059

  3. 77 FR 49055 - Request for Public Comments To Compile the National Trade Estimate Report on Foreign Trade Barriers

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-15

    ... Foreign Trade Barriers (NTE). With this notice, the Trade Policy Staff Committee (TPSC) is requesting... field on the home page. Douglas M. Bell, Chair, Trade Policy Staff Committee. BILLING CODE 3290-F2-P ... TRADE REPRESENTATIVE Request for Public Comments To Compile the National Trade Estimate Report...

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

    SciTech Connect

    Duster, T.

    1998-11-01

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

  5. Estimation of genetic diversity using SSR markers in sunflower

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sunflower is a major oilseed crop in central Asia, but little is known of the molecular diversity among collections of sunflower from Pakistan region. This paper described inherent genetic relationships among sunflower collections using Simple Sequence Repeat molecular markers. Results should help...

  6. Population-genetic influences on genomic estimates of the inbreeding coefficient: a global perspective

    PubMed Central

    Pemberton, Trevor J.; Rosenberg, Noah A.

    2014-01-01

    Background/Aims Culturally-driven marital practices provide a key instance of an interaction between social and genetic processes in shaping patterns of human genetic variation, producing, for example, increased identity by descent through consanguineous marriage. A commonly used measure to quantify identity by descent in an individual is the inbreeding coefficient, a quantity that reflects not only consanguinity, but also other aspects of kinship in the population to which the individual belongs. Here, in populations worldwide, we examine the relationship between genomic estimates of the inbreeding coefficient and population patterns in genetic variation. Methods Using genotypes at 645 microsatellites, we compare inbreeding coefficients from 5,043 individuals representing 237 worldwide populations to demographic consanguinity frequency estimates available for 26 populations, as well as to other quantities that can illuminate population-genetic influences on inbreeding coefficients. Results We observe higher inbreeding coefficient estimates in populations and geographic regions with known high levels of consanguinity or genetic isolation, and in populations with an increased effect of genetic drift and decreased genetic diversity with increasing distance from Africa. For the small number of populations with specific consanguinity estimates, we find a correlation between inbreeding coefficients and consanguinity frequency (r=0.349, P=0.040). Conclusions The results emphasize the importance of both consanguinity and population-genetic factors in influencing variation in inbreeding coefficients, and they provide insight into factors useful for assessing the effect of consanguinity on genomic patterns in different populations. PMID:25060268

  7. Estimating soybean genetic gain for yield in the northern United States – Influence of cropping history

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mean on-farm USA soybean yield increased at a rate of 21.3 kg per ha per year between 1924 and 2010, due to adoption of yield-enhancing genetic and agronomic technologies. To estimate annual rates of genetic yield gain in three northern USA soybean maturity groups (MG) and determine if these estimat...

  8. Genetic divergence among sweet corn lines estimated by microsatellite markers.

    PubMed

    Lopes, A D; Scapim, C A; Mangolin, C A; Machado, M F P S

    2014-01-01

    The purpose of this study was to analyze the genetic diversity of 15 sugary-1 sweet corn lines by microsatellite markers. One hundred pairs of simple sequence repeat primers that were mapped for field corn were tested. Of these primers, 15% were polymorphic, and all were selected for the evaluation. These primers identified a total of 39 alleles among the 15 loci that were evaluated. The number of alleles per locus in the genotypes ranged from 2 to 4, with an average of 2.60 alleles per locus; the highest number of alleles was observed at the loci Bnlg1083, Umc1241, and Umc1590. The occurrence of null alleles at locus Umc1363 was evident only in line DN44. The proportion of polymorphic loci was the highest in lines DN17.1 and DN6 (73.33%), whereas lines DN47, DN23, and DN28 were more monomorphic than other lines. The loci Bnlg1083 and Umc1506 were polymorphic in 8 and 7 lines, respectively, indicating that these loci might be effective and promising for the identification of polymorphism in other sweet corn lines. The genetic diversity calculated by Rogers' genetic distances indicated the lowest genetic similarity between lines DN9 and DN28 (0.7603) and the highest similarity between lines DN19 and DN6 (0.3724). The dendrogram obtained by the unweighted pair-group method based on arithmetic averages indicated the formation of 4 major groups, showing the crossing of the genotypes DN19 and DN6 with DN8 as a possible alternative for the expression of heterozygosis. PMID:25511025

  9. Genetic diversity and population differentiation in the cockle Cerastoderma edule estimated by microsatellite markers

    NASA Astrophysics Data System (ADS)

    Martínez, L.; Méndez, J.; Insua, A.; Arias-Pérez, A.; Freire, R.

    2013-03-01

    The edible cockle Cerastoderma edule is a marine bivalve commercially fished in several European countries that have lately suffered a significant decrease in production. Despite its commercial importance, genetic studies in this species are scarce. In this work, genetic diversity and population differentiation of C. edule has been assessed using 11 microsatellite markers in eight locations from the European Atlantic coast. All localities showed similar observed and expected heterozygosity values, but displayed differences in allelic richness, with lowest values obtained for localities situated farther north. Global Fst value revealed the existence of significant genetic structure; all but one locality from the Iberian Peninsula were genetically homogeneous, while more remote localities from France, The Netherlands, and Scotland were significantly different from all other localities. A combined effect of isolation by distance and the existence of barriers that limit gene flow may explain the differentiation observed.

  10. The influence of acculturation and breast cancer-specific distress on perceived barriers to genetic testing for breast cancer among women of African descent

    PubMed Central

    Sussner, Katarina M.; Thompson, Hayley S.; Jandorf, Lina; Edwards, Tiffany A.; Forman, Andrea; Brown, Karen; Kapil-Pair, Nidhi; Bovbjerg, Dana H.; Schwartz, Marc D.; Valdimarsdottir, Heiddis B.

    2009-01-01

    Objective Rising health disparities are increasingly evident in relation to use of genetic services (including genetic counseling and testing) for breast cancer risk, with women of African descent less likely to use genetic services compared with Whites. Meanwhile, little is known regarding potential within-group acculturation and psychological differences underlying perceived barriers to genetic testing among women of African descent. Methods Hypothesized contributions of acculturation factors and breast cancer-specific distress to perceived barriers to genetic testing were examined with a statistical analysis of baseline data from 146 women of African descent (56% US born and 44% foreign born) meeting genetic breast cancer risk criteria and participating in a larger longitudinal study that included the opportunity for free genetic counseling and testing. Perceived barriers assessed included: (1) anticipation of negative emotional reactions, (2) stigma, (3) confidentiality concerns, (4) family-related worry, and (5) family-related guilt associated with genetic testing. Results In multivariate analyses, being foreign born was a significant predictor of anticipated negative emotional reactions about genetic testing (β= 0.26; SE=0.11; p = 0.01). Breast cancer-specific distress scores (avoidance symptoms) were positively related to anticipated negative emotional reactions (β = 0.02; SE= 0.005; p = <0.0001), confidentiality concerns (β = 0.02; SE = 0.01; p = 0.02), and family-related guilt (β = 0.02; SE=0.01; p = 0.0009) associated with genetic testing. Conclusions Results suggest an influence of acculturation and breast cancer-specific distress on perceived barriers to genetic testing among women of African descent. The potential utility of culturally tailored genetic counseling services taking into account such influences and addressing emotional and psychological concerns of women considering genetic testing for breast cancer should be investigated. PMID

  11. Estimating black bear population density and genetic diversity at Tensas River, Louisiana using microsatellite DNA markers

    USGS Publications Warehouse

    Boersen, Mark R.; Clark, Joseph D.; King, Tim L.

    2003-01-01

    The Recovery Plan for the federally threatened Louisiana black bear (Ursus americanus luteolus) mandates that remnant populations be estimated and monitored. In 1999 we obtained genetic material with barbed-wire hair traps to estimate bear population size and genetic diversity at the 329-km2 Tensas River Tract, Louisiana. We constructed and monitored 122 hair traps, which produced 1,939 hair samples. Of those, we randomly selected 116 subsamples for genetic analysis and used up to 12 microsatellite DNA markers to obtain multilocus genotypes for 58 individuals. We used Program CAPTURE to compute estimates of population size using multiple mark-recapture models. The area of study was almost entirely circumscribed by agricultural land, thus the population was geographically closed. Also, study-area boundaries were biologically discreet, enabling us to accurately estimate population density. Using model Chao Mh to account for possible effects of individual heterogeneity in capture probabilities, we estimated the population size to be 119 (SE=29.4) bears, or 0.36 bears/km2. We were forced to examine a substantial number of loci to differentiate between some individuals because of low genetic variation. Despite the probable introduction of genes from Minnesota bears in the 1960s, the isolated population at Tensas exhibited characteristics consistent with inbreeding and genetic drift. Consequently, the effective population size at Tensas may be as few as 32, which warrants continued monitoring or possibly genetic augmentation.

  12. An alternative covariance estimator to investigate genetic heterogeneity in populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genomic predictions and GWAS have used mixed models for identification of associations and trait predictions. In both cases, the covariance between individuals for performance is estimated using molecular markers. Mixed model properties indicate that the use of the data for prediction is optimal if ...

  13. A Genetic Algorithm Approach to Nonlinear Least Squares Estimation

    ERIC Educational Resources Information Center

    Olinsky, Alan D.; Quinn, John T.; Mangiameli, Paul M.; Chen, Shaw K.

    2004-01-01

    A common type of problem encountered in mathematics is optimizing nonlinear functions. Many popular algorithms that are currently available for finding nonlinear least squares estimators, a special class of nonlinear problems, are sometimes inadequate. They might not converge to an optimal value, or if they do, it could be to a local rather than…

  14. Optimization of multiple edge barriers with genetic algorithms coupled with a Nelder--Mead local search

    NASA Astrophysics Data System (ADS)

    Baulac, Marine; Defrance, Jérôme; Jean, Philippe

    2007-02-01

    This research work aims at developing a new multi-criteria optimization method dedicated to complex road noise barriers. Numerical simulations of the acoustical propagation have been achieved using MICADO, a 2D boundary element method (BEM) code developed at CSTB. The optimization part is carried out with the help of a Nelder-Mead algorithm (direct local search method) coupled with an evolutionary strategy in order to globalize the approach. A first application of this combination between an outdoor sound propagation numerical code and an optimization algorithm concerns the optimization of noise barrier caps with the following varying parameters: the cap size, its shape and its surface impedance. The cost function to be minimized is defined through a mean value of the insertion loss due to the added crowning compared to the straight, rigid barrier solution of same overall height, averaged on several receiver points within the barrier shadow zone. Final results show a significant improvement of the efficiency of a multiple edge noise barrier by optimizing values of both size and impedance.

  15. Genetic parameter estimates of growth curve and reproduction traits in Japanese quail.

    PubMed

    Narinc, Dogan; Karaman, Emre; Aksoy, Tulin; Firat, Mehmet Ziya

    2014-01-01

    The goal of selection studies in broilers is to obtain genetically superior chicks in terms of major economic traits, which are mainly growth rate, meat yield, and feed conversion ratio. Multiple selection schedules for growth and reproduction are used in selection programs within commercial broiler dam lines. Modern genetic improvement methods have not been applied in experimental quail lines. The current research was conducted to estimate heritabilities and genetic correlations for growth and reproduction traits in a Japanese quail flock. The Gompertz equation was used to determine growth curve parameters. The Gibbs sampling under a multi-trait animal model was applied to estimate the heritabilities and genetic correlations for these traits. A total of 948 quail were used with complete pedigree information to estimate the genetic parameters. Heritability estimates of BW, absolute and relative growth rates at 5 wk of age (AGR and RGR), β0 and β2 parameters, and age at point of inflection (IPT) of Gompertz growth curve, total egg number (EN) from the day of first lay to 24 wk of age were moderate to high, with values ranging from 0.25 to 0.40. A low heritability (0.07) for fertility (FR) and a strong genetic correlation (0.83) between FR and EN were estimated in our study. Body weight exhibited negative genetic correlation with EN, FR, RGR, and IPT. This genetic antagonism among the mentioned traits may be overcome using modern poultry breeding methods such as selection using multi-trait best linear unbiased prediction and crossbreeding. PMID:24570419

  16. Spatial and temporal genetic structure of Symbiodinium populations within a common reef-building coral on the Great Barrier Reef.

    PubMed

    Howells, Emily J; Willis, Bette L; Bay, Line K; van Oppen, Madeleine J H

    2013-07-01

    The dinoflagellate photosymbiont Symbiodinium plays a fundamental role in defining the physiological tolerances of coral holobionts, but little is known about the dynamics of these endosymbiotic populations on coral reefs. Sparse data indicate that Symbiodinium populations show limited spatial connectivity; however, no studies have investigated temporal dynamics for in hospite Symbiodinium populations following significant mortality and recruitment events in coral populations. We investigated the combined influences of spatial isolation and disturbance on the population dynamics of the generalist Symbiodinium type C2 (ITS1 rDNA) hosted by the scleractinian coral Acropora millepora in the central Great Barrier Reef. Using eight microsatellite markers, we genotyped Symbiodinium in a total of 401 coral colonies, which were sampled from seven sites across a 12-year period including during flood plume-induced coral bleaching. Genetic differentiation of Symbiodinium was greatest within sites, explaining 70-86% of the total genetic variation. An additional 9-27% of variation was explained by significant differentiation of populations among sites separated by 0.4-13 km, which is consistent with low levels of dispersal via water movement and historical disturbance regimes. Sampling year accounted for 6-7% of total genetic variation and was related to significant coral mortality following severe bleaching in 1998 and a cyclone in 2006. Only 3% of the total genetic variation was related to coral bleaching status, reflecting generally small (8%) reductions in allelic diversity within bleached corals. This reduction probably reflected a loss of genotypes in hospite during bleaching, although no site-wide changes in genetic diversity were observed. Combined, our results indicate the importance of disturbance regimes acting together with limited oceanographic transport to determine the genetic composition of Symbiodinium types within reefs. PMID:23730715

  17. Blood-Brain Barrier Breakdown Determines Differential Therapeutic Outcome in Genetically Diverse Forms of Medulloblastoma.

    PubMed

    Guerit, Sylvaine; Liebner, Stefan

    2016-04-11

    Medulloblastoma driven by Wnt/β-catenin and Sonic hedgehog pathway mutations show favorable and poor patient survival upon treatment, respectively. In this Cancer Cell issue, Phoenix and colleagues (2016) report disruption of the blood-brain barrier by Wif1 specifically in Wnt-driven medulloblastoma, resulting in increased treatment response and survival in mouse models. PMID:27070693

  18. Estimation of genetic parameters and their sampling variances of quantitative traits in the type 2 modified augmented design

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We proposed a method to estimate the error variance among non-replicated genotypes, thus to estimate the genetic parameters by using replicated controls. We derived formulas to estimate sampling variances of the genetic parameters. Computer simulation indicated that the proposed methods of estimatin...

  19. Estimating non-genetic and genetic parameters of pre-weaning growth traits in Raini Cashmere goat.

    PubMed

    Barazandeh, Arsalan; Moghbeli, Sadrollah Molaei; Vatankhah, Mahmood; Mohammadabadi, Mohammadreza

    2012-04-01

    Data and pedigree information used in the present study were 3,022 records of kids obtained from the breeding station of Raini goat. The studied traits were birth weight (BW), weaning weight (WW), average daily gain from birth to weaning (ADG) and Kleiber ratio at weaning (KR). The model included the fixed effects of sex of kid, type of birth, age of dam, year of birth, month of birth, and age of kid (days) as covariate that had significant effects, and random effects direct additive genetic, maternal additive genetic, maternal permanent environmental effects and residual. (Co) variance components were estimated using univariate and multivariate analysis by WOMBAT software applying four animal models including and ignoring maternal effects. Likelihood ratio test used to determine the most appropriate models. Heritability (h(a)(2)) estimates for BW, WW, ADG, and KR according to suitable model were 0.12 ± 0.05, 0.08 ± 0.06, 0.10 ± 0.06, and 0.06 ± 0.05, respectively. Estimates of the proportion of maternal permanent environmental effect to phenotypic variance (c(2)) were 0.17 ± 0.03, 0.07 ± 0.03, and 0.07 ± 0.03 for BW, WW, and ADG, respectively. Genetic correlations among traits were positive and ranged from 0.53 (BW-ADG) to 1.00 (WW-ADG, WW-KR, and ADG-KR). The maternal permanent environmental correlations between BW-WW, BW-ADG, and WW-ADG were 0.54, 0.48, and 0.99, respectively. Results indicated that maternal effects, especially maternal permanent environmental effects are an important source of variation in pre-weaning growth trait and ignoring those in the model redound incorrect genetic evaluation of kids. PMID:21901301

  20. Estimates of genetic parameters for growth traits in Brahman cattle using random regression and multitrait models.

    PubMed

    Bertipaglia, T S; Carreño, L O D; Aspilcueta-Borquis, R R; Boligon, A A; Farah, M M; Gomes, F J; Machado, C H C; Rey, F S B; da Fonseca, R

    2015-08-01

    Random regression models (RRM) and multitrait models (MTM) were used to estimate genetic parameters for growth traits in Brazilian Brahman cattle and to compare the estimated breeding values obtained by these 2 methodologies. For RRM, 78,641 weight records taken between 60 and 550 d of age from 16,204 cattle were analyzed, and for MTM, the analysis consisted of 17,385 weight records taken at the same ages from 12,925 cattle. All models included the fixed effects of contemporary group and the additive genetic, maternal genetic, and animal permanent environmental effects and the quadratic effect of age at calving (AAC) as covariate. For RRM, the AAC was nested in the animal's age class. The best RRM considered cubic polynomials and the residual variance heterogeneity (5 levels). For MTM, the weights were adjusted for standard ages. For RRM, additive heritability estimates ranged from 0.42 to 0.75, and for MTM, the estimates ranged from 0.44 to 0.72 for both models at 60, 120, 205, 365, and 550 d of age. The maximum maternal heritability estimate (0.08) was at 140 d for RRM, but for MTM, it was highest at weaning (0.09). The magnitude of the genetic correlations was generally from moderate to high. The RRM adequately modeled changes in variance or covariance with age, and provided there was sufficient number of samples, increased accuracy in the estimation of the genetic parameters can be expected. Correlation of bull classifications were different in both methods and at all the ages evaluated, especially at high selection intensities, which could affect the response to selection. PMID:26440161

  1. Estimating Genetic Effects and Quantifying Missing Heritability Explained by Identified Rare-Variant Associations

    PubMed Central

    Liu, Dajiang J.; Leal, Suzanne M.

    2012-01-01

    Next-generation sequencing has led to many complex-trait rare-variant (RV) association studies. Although single-variant association analysis can be performed, it is grossly underpowered. Therefore, researchers have developed many RV association tests that aggregate multiple variant sites across a genetic region (e.g., gene), and test for the association between the trait and the aggregated genotype. After these aggregate tests detect an association, it is only possible to estimate the average genetic effect for a group of RVs. As a result of the "winner’s curse," such an estimate can be biased. Although for common variants one can obtain unbiased estimates of genetic parameters by analyzing a replication sample, for RVs it is desirable to obtain unbiased genetic estimates for the study where the association is identified. This is because there can be substantial heterogeneity of RV sites and frequencies even among closely related populations. In order to obtain an unbiased estimate for aggregated RV analysis, we developed bootstrap-sample-split algorithms to reduce the bias of the winner’s curse. The unbiased estimates are greatly important for understanding the population-specific contribution of RVs to the heritability of complex traits. We also demonstrate both theoretically and via simulations that for aggregate RV analysis the genetic variance for a gene or region will always be underestimated, sometimes substantially, because of the presence of noncausal variants or because of the presence of causal variants with effects of different magnitudes or directions. Therefore, even if RVs play a major role in the complex-trait etiologies, a portion of the heritability will remain missing, and the contribution of RVs to the complex-trait etiologies will be underestimated. PMID:23022102

  2. Estimation of Additive, Dominance, and Imprinting Genetic Variance Using Genomic Data

    PubMed Central

    Lopes, Marcos S.; Bastiaansen, John W. M.; Janss, Luc; Knol, Egbert F.; Bovenhuis, Henk

    2015-01-01

    Traditionally, exploration of genetic variance in humans, plants, and livestock species has been limited mostly to the use of additive effects estimated using pedigree data. However, with the development of dense panels of single-nucleotide polymorphisms (SNPs), the exploration of genetic variation of complex traits is moving from quantifying the resemblance between family members to the dissection of genetic variation at individual loci. With SNPs, we were able to quantify the contribution of additive, dominance, and imprinting variance to the total genetic variance by using a SNP regression method. The method was validated in simulated data and applied to three traits (number of teats, backfat, and lifetime daily gain) in three purebred pig populations. In simulated data, the estimates of additive, dominance, and imprinting variance were very close to the simulated values. In real data, dominance effects account for a substantial proportion of the total genetic variance (up to 44%) for these traits in these populations. The contribution of imprinting to the total phenotypic variance of the evaluated traits was relatively small (1–3%). Our results indicate a strong relationship between additive variance explained per chromosome and chromosome length, which has been described previously for other traits in other species. We also show that a similar linear relationship exists for dominance and imprinting variance. These novel results improve our understanding of the genetic architecture of the evaluated traits and shows promise to apply the SNP regression method to other traits and species, including human diseases. PMID:26438289

  3. A Fast and Reliable Computational Method for Estimating Population Genetic Parameters

    PubMed Central

    Vasco, Daniel A.

    2008-01-01

    The estimation of ancestral and current effective population sizes in expanding populations is a fundamental problem in population genetics. Recently it has become possible to scan entire genomes of several individuals within a population. These genomic data sets can be used to estimate basic population parameters such as the effective population size and population growth rate. Full-data-likelihood methods potentially offer a powerful statistical framework for inferring population genetic parameters. However, for large data sets, computationally intensive methods based upon full-likelihood estimates may encounter difficulties. First, the computational method may be prohibitively slow or difficult to implement for large data. Second, estimation bias may markedly affect the accuracy and reliability of parameter estimates, as suggested from past work on coalescent methods. To address these problems, a fast and computationally efficient least-squares method for estimating population parameters from genomic data is presented here. Instead of modeling genomic data using a full likelihood, this new approach uses an analogous function, in which the full data are replaced with a vector of summary statistics. Furthermore, these least-squares estimators may show significantly less estimation bias for growth rate and genetic diversity than a corresponding maximum-likelihood estimator for the same coalescent process. The least-squares statistics also scale up to genome-sized data sets with many nucleotides and loci. These results demonstrate that least-squares statistics will likely prove useful for nonlinear parameter estimation when the underlying population genomic processes have complex evolutionary dynamics involving interactions between mutation, selection, demography, and recombination. PMID:18505868

  4. Estimation of radiative and conductive properties of a semitransparent medium using genetic algorithms

    NASA Astrophysics Data System (ADS)

    Braiek, A.; Adili, A.; Albouchi, F.; Karkri, M.; Ben Nasrallah, S.

    2016-06-01

    The aim of this work is to simultaneously identify the conductive and radiative parameters of a semitransparent sample using a photothermal method associated with an inverse problem. The identification of the conductive and radiative proprieties is performed by the minimization of an objective function that represents the errors between calculated temperature and measured signal. The calculated temperature is obtained from a theoretical model built with the thermal quadrupole formalism. Measurement is obtained in the rear face of the sample whose front face is excited by a crenel of heat flux. For identification procedure, a genetic algorithm is developed and used. The genetic algorithm is a useful tool in the simultaneous estimation of correlated or nearly correlated parameters, which can be a limiting factor for the gradient-based methods. The results of the identification procedure show the efficiency and the stability of the genetic algorithm to simultaneously estimate the conductive and radiative properties of clear glass.

  5. Estimation of the Proportion of Genetic Variation Accounted for by DNA Tests

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An increasingly relevant question in evaluating commercial DNA tests is "What proportion of the additive genetic variation in the target trait is accounted for by the test?" Therefore, several estimators of this quantity were evaluated by simulation of a population of 1000 animals with 100 sires, ea...

  6. Genetic and phenotypic parameter estimates for feed intake and other traits in growing beef cattle

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic parameters for dry matter intake (DMI), residual feed intake (RFI), average daily gain (ADG), mid-period body weight (MBW), gain to feed ratio (G:F) and flight speed (FS) were estimated using 1165 steers from a mixed-breed population using restricted maximum likelihood methodology applied to...

  7. Application of marker selection to enhance estimation of genetic effects and gene interaction in cattle

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Selection on important genetic markers can improve estimates of additive and dominance association effects. A composite population of beef cattle was selected for intermediate frequencies of myostatin (GDF8) F94L and µ-calpain (CAPN1) polymorphisms. Important additive associations of the GDF8 locu...

  8. Estimates of genetic parameters among scale activity scores, growth, and fatness in pigs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic parameters for scale activity score were estimated from generations 5, 6, and 7 of a randomly selected, composite population composed of Duroc, Large White, and two sources of Landrace (n = 2,186). At approximately 156 d of age, pigs were weighed (WT) and ultrasound backfat measurements (BF1...

  9. Estimates of genetic parameters for kyphosis in two crossbred swine populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic parameters for degree of kyphosis were estimated from a Duroc-Landrace F2 population (n = 316) and from a composite population (Line C) composed of Duroc, Large White, and two sources of Landrace (n = 1,552). Live presentation did not indicate kyphosis in pigs or sows. Degree of kyphosis was...

  10. NESTED THRESHOLD SIRE MODELS FOR ESTIMATING GENETIC PARAMETERS FOR STAYABILITY IN BEEF COWS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Stayability is the ability of a beef cow to remain in production to a specified age. In this study, the interest was in determining the genetic relationship between stayability to an early age with the stayability to a later age. A nested threshold sire model for stayability was used to estimate t...

  11. Estimates of genetic variation for feed intake and other characteristics in growing beef cattle

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Calves born between 2003 and 2006 at the U.S. Meat Animal Research Center provided data for estimation of genetic and phenotypic parameters for measures of body weight and gain and feed intake during the finishing phase. At average age 278 d, cattle were started on a high-energy diet of corn, alfalf...

  12. A Genetic Model for the Female Sterility Barrier Between Asian and African Cultivated Rice Species

    PubMed Central

    Garavito, Andrea; Guyot, Romain; Lozano, Jaime; Gavory, Frédérick; Samain, Sylvie; Panaud, Olivier; Tohme, Joe; Ghesquière, Alain; Lorieux, Mathias

    2010-01-01

    S1 is the most important locus acting as a reproductive barrier between Oryza sativa and O. glaberrima. It is a complex locus, with factors that may affect male and female fertility separately. Recently, the component causing the allelic elimination of pollen was fine mapped. However, the position and nature of the component causing female sterility remains unknown. To fine map the factor of the S1 locus affecting female fertility, we developed a mapping approach based on the evaluation of the degree of female transmission ratio distortion (fTRD) of markers. Through implementing this methodology in four O. sativa × O. glaberrima crosses, the female component of the S1 locus was mapped into a 27.8-kb (O. sativa) and 50.3-kb (O. glaberrima) region included within the interval bearing the male component of the locus. Moreover, evidence of additional factors interacting with S1 was also found. In light of the available data, a model where incompatibilities in epistatic interactions between S1 and the additional factors are the cause of the female sterility barrier between O. sativa and O. glaberrima was developed to explain the female sterility and the TRD mediated by S1. According to our model, the recombination ratio and allelic combinations between these factors would determine the final allelic frequencies observed for a given cross. PMID:20457876

  13. The use and abuse of genetic marker-based estimates of relatedness and inbreeding

    PubMed Central

    Taylor, Helen R

    2015-01-01

    Genetic marker-based estimators remain a popular tool for measuring relatedness (rxy) and inbreeding (F) coefficients at both the population and individual level. The performance of these estimators fluctuates with the number and variability of markers available, and the relatedness composition and demographic history of a population. Several methods are available to evaluate the reliability of the estimates of rxy and F, some of which are implemented in the program COANCESTRY. I used the simulation module in COANCESTRY since assess the performance of marker-based estimators of rxy and F in a species with very low genetic diversity, New Zealand’s little spotted kiwi (Apteryx owenii). I also conducted a review of published papers that have used COANCESTRY as its release to assess whether and how the reliability of the estimates of rxy and F produced by genetic markers are being measured and reported in published studies. My simulation results show that even when the correlation between true (simulated) and estimated rxy or F is relatively high (Pearson’s r = 0.66–0.72 and 0.81–0.85, respectively) the imprecision of the estimates renders them highly unreliable on an individual basis. The literature review demonstrates that the majority of studies do not report the reliability of marker-based estimates of rxy and F. There is currently no standard practice for selecting the best estimator for a given data set or reporting an estimator’s performance. This could lead to experimental results being interpreted out of context and render the robustness of conclusions based on measures of rxy and F debatable. PMID:26357542

  14. Perceived barriers to Internet-based health communication on human genetics.

    PubMed

    Bernhardt, Jay M; Lariscy, Ruth Ann Weaver; Parrott, Roxanne L; Silk, Kami J; Felter, Elizabeth M

    2002-01-01

    The Internet has emerged as potential vehicle for distributing health communication to millions of individuals because it is interactive, user controlled, and offers breadth and depth of information. However, its widespread use by the public may be limited due to three overarching concerns: privacy and confidentiality, information accuracy and perceptions of credibility, including limited credibility of some government-sponsored web sites. To explore the potential of using the Internet, especially for delivering information on human genetics communication, 15 focus groups and one interview were conducted with African American and European American adult males and females in a southeastern town. We found that the participants recognized great potential in the Internet for health communication on human genetics, but they also voiced concerns about the credibility and accuracy of online information, lack of trust in many web sites, and fear of safeguarding privacy. Their concerns are summarized here, along with potential remedies health communicators could implement and should research further. The Internet cannot achieve its full potential for human genetics communication until the public's concerns are addressed and resolved. PMID:12356290

  15. Population Growth Rates of Reef Sharks with and without Fishing on the Great Barrier Reef: Robust Estimation with Multiple Models

    PubMed Central

    Hisano, Mizue; Connolly, Sean R.; Robbins, William D.

    2011-01-01

    Overfishing of sharks is a global concern, with increasing numbers of species threatened by overfishing. For many sharks, both catch rates and underwater visual surveys have been criticized as indices of abundance. In this context, estimation of population trends using individual demographic rates provides an important alternative means of assessing population status. However, such estimates involve uncertainties that must be appropriately characterized to credibly and effectively inform conservation efforts and management. Incorporating uncertainties into population assessment is especially important when key demographic rates are obtained via indirect methods, as is often the case for mortality rates of marine organisms subject to fishing. Here, focusing on two reef shark species on the Great Barrier Reef, Australia, we estimated natural and total mortality rates using several indirect methods, and determined the population growth rates resulting from each. We used bootstrapping to quantify the uncertainty associated with each estimate, and to evaluate the extent of agreement between estimates. Multiple models produced highly concordant natural and total mortality rates, and associated population growth rates, once the uncertainties associated with the individual estimates were taken into account. Consensus estimates of natural and total population growth across multiple models support the hypothesis that these species are declining rapidly due to fishing, in contrast to conclusions previously drawn from catch rate trends. Moreover, quantitative projections of abundance differences on fished versus unfished reefs, based on the population growth rate estimates, are comparable to those found in previous studies using underwater visual surveys. These findings appear to justify management actions to substantially reduce the fishing mortality of reef sharks. They also highlight the potential utility of rigorously characterizing uncertainty, and applying multiple

  16. Population growth rates of reef sharks with and without fishing on the great barrier reef: robust estimation with multiple models.

    PubMed

    Hisano, Mizue; Connolly, Sean R; Robbins, William D

    2011-01-01

    Overfishing of sharks is a global concern, with increasing numbers of species threatened by overfishing. For many sharks, both catch rates and underwater visual surveys have been criticized as indices of abundance. In this context, estimation of population trends using individual demographic rates provides an important alternative means of assessing population status. However, such estimates involve uncertainties that must be appropriately characterized to credibly and effectively inform conservation efforts and management. Incorporating uncertainties into population assessment is especially important when key demographic rates are obtained via indirect methods, as is often the case for mortality rates of marine organisms subject to fishing. Here, focusing on two reef shark species on the Great Barrier Reef, Australia, we estimated natural and total mortality rates using several indirect methods, and determined the population growth rates resulting from each. We used bootstrapping to quantify the uncertainty associated with each estimate, and to evaluate the extent of agreement between estimates. Multiple models produced highly concordant natural and total mortality rates, and associated population growth rates, once the uncertainties associated with the individual estimates were taken into account. Consensus estimates of natural and total population growth across multiple models support the hypothesis that these species are declining rapidly due to fishing, in contrast to conclusions previously drawn from catch rate trends. Moreover, quantitative projections of abundance differences on fished versus unfished reefs, based on the population growth rate estimates, are comparable to those found in previous studies using underwater visual surveys. These findings appear to justify management actions to substantially reduce the fishing mortality of reef sharks. They also highlight the potential utility of rigorously characterizing uncertainty, and applying multiple

  17. Problems and solutions in the estimation of genetic risks from radiation and chemicals

    SciTech Connect

    Russell, W. L.

    1980-01-01

    Extensive investigations with mice on the effects of various physical and biological factors, such as dose rate, sex and cell stage, on radiation-induced mutation have provided an evaluation of the genetics hazards of radiation in man. The mutational results obtained in both sexes with progressive lowering of the radiation dose rate have permitted estimation of the mutation frequency expected under the low-level radiation conditions of most human exposure. Supplementing the studies on mutation frequency are investigations on the phenotypic effects of mutations in mice, particularly anatomical disorders of the skeleton, which allow an estimation of the degree of human handicap associated with the occurrence of parallel defects in man. Estimation of the genetic risk from chemical mutagens is much more difficult, and the research is much less advanced. Results on transmitted mutations in mice indicate a poor correlation with mutation induction in non-mammalian organisms.

  18. Six genetically distinct clades of Palola (Eunicidae, Annelida) from Lizard Island, Great Barrier Reef, Australia.

    PubMed

    Schulze, Anja

    2015-01-01

    A total of 36 lots of Palola spp. (Eunicidae, Annelida) were collected during the Lizard Island Polychaete Workshop on Lizard Island, Great Barrier Reef, Queensland, Australia. Of these, 21 specimens were sequenced for a portion of the mitochondrial cytochrome c oxidase I gene. These sequences were analysed in conjunction with existing sequences of Palola spp. from other geographic regions. The samples from Lizard Island form six distinct clades, although none of them can clearly be assigned to any of the nominal species. Four of the six Lizard Island clades fall into species group A and the remaining two into species group B (which also includes the type species, Palola viridis). All sequenced specimens were characterized morphologically as far as possible and a dichotomous key was assembled. Based on this key, the remaining samples were identified as belonging to one of the clades. PMID:26624083

  19. Estimated genetic parameters for palatability traits of steaks from Brahman cattle.

    PubMed

    Riley, D G; Chase, C C; Hammond, A C; West, R L; Johnson, D D; Olson, T A; Coleman, S W

    2003-01-01

    Heritabilities and genetic and phenotypic correlations were estimated from carcass and beef palatability data collected from Brahman calves (n = 504) born in central Florida from 1996 to 2000. Traits evaluated included Warner-Bratzler shear force (after 7, 14, and 21 d of aging), panel tenderness score, connective tissue amount, juiciness, flavor intensity, and off flavor (after 14 d of aging), percentages of raw and cooked lipids, and milligrams per gram of muscle calpastatin activity. Parameters were estimated using an animal model and derivative-free restricted maximum likelihood procedures. Estimated heritabilities for d 7, 14, and 21 shear force were 0.14,0.14, and 0.06, respectively, indicating that improvement in these traits by selection would be slow. Estimated heritabilities of sensory panel attributes were 0.11, 0.12, 0.05, 0.04, and 0.01 for tenderness, connective tissue amount, juiciness, flavor intensity, and off flavor, respectively. The estimated heritabilities for percentages of raw and cooked lipids, and calpastatin activity were 0.34, 0.17, and 0.07, respectively. Most of the estimated genetic correlations among palatability traits and for palatability traits with fat thickness, marbling score, and loin muscle area were consistent with other estimates from the literature. Results indicated that improvement in tenderness based on selection for favorable shear force, sensory panel tenderness, or calpastatin activity would be slow; therefore, postslaughter intervention programs should also be considered. PMID:12597372

  20. Population Genetic Analysis of Streptomyces albidoflavus Reveals Habitat Barriers to Homologous Recombination in the Diversification of Streptomycetes

    PubMed Central

    Cheng, Kun; Rong, Xiaoying; Pinto-Tomás, Adrián A.; Fernández-Villalobos, Marcela; Murillo-Cruz, Catalina

    2014-01-01

    Examining the population structure and the influence of recombination and ecology on microbial populations makes great sense for understanding microbial evolution and speciation. Streptomycetes are a diverse group of bacteria that are widely distributed in nature and a rich source of useful bioactive compounds; however, they are rarely subjected to population genetic investigations. In this study, we applied a five-gene-based multilocus sequence analysis (MLSA) scheme to 41 strains of Streptomyces albidoflavus derived from diverse sources, mainly insects, sea, and soil. Frequent recombination was detected in S. albidoflavus, supported by multiple lines of evidence from the pairwise homoplasy index (Φw) test, phylogenetic discordance, the Shimodaira-Hasegawa (SH) test, and network analysis, underpinning the predominance of homologous recombination within Streptomyces species. A strong habitat signal was also observed in both phylogenetic and Structure 2.3.3 analyses, indicating the importance of ecological difference in shaping the population structure. Moreover, all three habitat-associated groups, particularly the entomic group, demonstrated significantly reduced levels of gene flow with one another, generally revealing habitat barriers to recombination. Therefore, a combined effect of homologous recombination and ecology is inferred for S. albidoflavus, where dynamic evolution is at least partly balanced by the extent that differential distributions of strains among habitats limit genetic exchange. Our study stresses the significance of ecology in microbial speciation and reveals the coexistence of homologous recombination and ecological divergence in the evolution of streptomycetes. PMID:25416769

  1. Population genetic analysis of Streptomyces albidoflavus reveals habitat barriers to homologous recombination in the diversification of streptomycetes.

    PubMed

    Cheng, Kun; Rong, Xiaoying; Pinto-Tomás, Adrián A; Fernández-Villalobos, Marcela; Murillo-Cruz, Catalina; Huang, Ying

    2015-02-01

    Examining the population structure and the influence of recombination and ecology on microbial populations makes great sense for understanding microbial evolution and speciation. Streptomycetes are a diverse group of bacteria that are widely distributed in nature and a rich source of useful bioactive compounds; however, they are rarely subjected to population genetic investigations. In this study, we applied a five-gene-based multilocus sequence analysis (MLSA) scheme to 41 strains of Streptomyces albidoflavus derived from diverse sources, mainly insects, sea, and soil. Frequent recombination was detected in S. albidoflavus, supported by multiple lines of evidence from the pairwise homoplasy index (Φw) test, phylogenetic discordance, the Shimodaira-Hasegawa (SH) test, and network analysis, underpinning the predominance of homologous recombination within Streptomyces species. A strong habitat signal was also observed in both phylogenetic and Structure 2.3.3 analyses, indicating the importance of ecological difference in shaping the population structure. Moreover, all three habitat-associated groups, particularly the entomic group, demonstrated significantly reduced levels of gene flow with one another, generally revealing habitat barriers to recombination. Therefore, a combined effect of homologous recombination and ecology is inferred for S. albidoflavus, where dynamic evolution is at least partly balanced by the extent that differential distributions of strains among habitats limit genetic exchange. Our study stresses the significance of ecology in microbial speciation and reveals the coexistence of homologous recombination and ecological divergence in the evolution of streptomycetes. PMID:25416769

  2. A New Barrier to Dispersal Trapped Old Genetic Clines That Escaped the Easter Microplate Tension Zone of the Pacific Vent Mussels

    PubMed Central

    Plouviez, Sophie; Faure, Baptiste; Le Guen, Dominique; Lallier, François H.; Bierne, Nicolas; Jollivet, Didier

    2013-01-01

    Comparative phylogeography of deep-sea hydrothermal vent species has uncovered several genetic breaks between populations inhabiting northern and southern latitudes of the East Pacific Rise. However, the geographic width and position of genetic clines are variable among species. In this report, we further characterize the position and strength of barriers to gene flow between populations of the deep-sea vent mussel Bathymodiolus thermophilus. Eight allozyme loci and DNA sequences of four nuclear genes were added to previously published sequences of the cytochrome c oxidase subunit I gene. Our data confirm the presence of two barriers to gene flow, one located at the Easter Microplate (between 21°33′S and 31°S) recently described as a hybrid zone, and the second positioned between 7°25′S and 14°S with each affecting different loci. Coalescence analysis indicates a single vicariant event at the origin of divergence between clades for all nuclear loci, although the clines are now spatially discordant. We thus hypothesize that the Easter Microplate barrier has recently been relaxed after a long period of isolation and that some genetic clines have escaped the barrier and moved northward where they have subsequently been trapped by a reinforcing barrier to gene flow between 7°25′S and 14°S. PMID:24312557

  3. ESTIMATES OF GENETIC PARAMETERS AND AN EVALUATION OF GENOTYPE X ENVIRONMENT INTERACTION FOR WEANING WEIGHT IN NELLORE CATTLE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Records of 105,645 Nellore calves born from 1977 to 1994 in eight different regions of Brazil were used to estimate genetic parameters for weaning weight (kg). The objective of this study was to estimate genetic and environmental parameters and evaluate genotype x environment interaction for weaning...

  4. Overcoming the Barrier of Low Efficiency during Genetic Transformation of Streptococcus mitis

    PubMed Central

    Salvadori, Gabriela; Junges, Roger; Morrison, Donald A.; Petersen, Fernanda C.

    2016-01-01

    Objective: Streptococcus mitis is a predominant oral colonizer, but difficulties in genetic manipulation of this species have hampered our understanding of the mechanisms it uses for colonization of oral surfaces. The aim of this study was to reveal optimal conditions for natural genetic transformation in S. mitis and illustrate its application in direct genome editing. Methods: Luciferase reporter assays were used to assess gene expression of the alternative sigma factor (σX) in combination with natural transformation experiments to evaluate the efficiency by which S. mitis activates the competence system and incorporates exogenous DNA. Optimal amounts and sources of donor DNA (chromosomal, amplicon, or replicative plasmid), concentrations of synthetic competence-stimulating peptide, and transformation media were assessed. Results: A semi-defined medium showed much improved results for response to the competence stimulating peptide when compared to rich media. The use of a donor amplicon with large homology flanking regions also provided higher transformation rates. Overall, an increase of transformation efficiencies from 0.001% or less to over 30% was achieved with the developed protocol. We further describe the construction of a markerless mutant based on this high efficiency strategy. Conclusion: We optimized competence development in S. mitis, by use of semi-defined medium and appropriate concentrations of synthetic competence factor. Combined with the use of a large amplicon of donor DNA, this method allowed easy and direct editing of the S. mitis genome, broadening the spectrum of possible downstream applications of natural transformation in this species. PMID:27458432

  5. A genetic resampling particle filter for freeway traffic-state estimation

    NASA Astrophysics Data System (ADS)

    Bi, Jun; Guan, Wei; Qi, Long-Tao

    2012-06-01

    On-line estimation of the state of traffic based on data sampled by electronic detectors is important for intelligent traffic management and control. Because a nonlinear feature exists in the traffic state, and because particle filters have good characteristics when it comes to solving the nonlinear problem, a genetic resampling particle filter is proposed to estimate the state of freeway traffic. In this paper, a freeway section of the northern third ring road in the city of Beijing in China is considered as the experimental object. By analysing the traffic-state characteristics of the freeway, the traffic is modeled based on the second-order validated macroscopic traffic flow model. In order to solve the particle degeneration issue in the performance of the particle filter, a genetic mechanism is introduced into the resampling process. The realization of a genetic particle filter for freeway traffic-state estimation is discussed in detail, and the filter estimation performance is validated and evaluated by the achieved experimental data.

  6. Estimates of genetic parameters for direct and maternal effects on embryonic survival in swine.

    PubMed

    Gama, L T; Boldman, K G; Johnson, R K

    1991-12-01

    Survival of 16,838 potential embryos was determined by counting corpora lutea and fetuses at 50 d of gestation for 1,081 litters by 225 sires. These data, coded as 1 or 0 depending on whether an ovulation was represented by a fetus, were used to estimate direct and maternal additive genetic variances and their covariance for embryonic survival. Data were from first-parity gilts of a Large White-Landrace composite population subdivided into two lines, one selected for an index of ovulation rate and embryonic survival for seven generations and a contemporary control line. Variance components were obtained by ANOVA and expectations of covariances among relatives and by derivative-free restricted maximum likelihood (DFREML) in an animal model. As a trait of the embryo, heritability of direct effects obtained with ANOVA was 3.8%, heritability of maternal effects was 1.5%, and the genetic correlation between them was -.51. After adjustment of embryonic survival for ovulation rate, lower estimates of each parameter were obtained with ANOVA. Heritability of embryonic survival as a trait of the dam was 9 to 10%. Estimates of heritability of both direct and maternal effects obtained with DFREML were less than 1% and the genetic correlation between them was -.64. When survival of embryos from only those dams with 15 or more ovulations was analyzed, heritability of maternal effects was 4.4%. Estimates of common environmental effects on embryonic survival ranged from 5 to 7%. PMID:1808176

  7. EDDY CURRENT INVERSION AND ESTIMATION METRICS FOR EVALUATING THERMAL BARRIER COATINGS

    SciTech Connect

    Sabbagh, Harold A.; Murphy, R. Kim; Sabbagh, Elias H.; Knopp, Jeremy S.; Aldrin, John C.; Nyenhuis, John

    2010-02-22

    In this paper, sophisticated eddy-current techniques incorporating model-based inverse methods were successfully demonstrated to measure the thickness and remaining-life of high-temperature coatings. To further assure the performance of these inverse methods, several estimation metrics including Fisher Information, Cramer-Rao Lower Bound (CRLB), covariance, and singular value decomposition (SVD) are introduced. The connections and utility of these metrics are illustrated in the design of eddy current methods for estimating layer thickness, conductivity and probe liftoff.

  8. Eddy Current Inversion and Estimation Metrics for Evaluating Thermal Barrier Coatings

    NASA Astrophysics Data System (ADS)

    Sabbagh, Harold A.; Knopp, Jeremy S.; Aldrin, John C.; Murphy, R. Kim; Sabbagh, Elias H.; Nyenhuis, John

    2010-02-01

    In this paper, sophisticated eddy-current techniques incorporating model-based inverse methods were successfully demonstrated to measure the thickness and remaining-life of high-temperature coatings. To further assure the performance of these inverse methods, several estimation metrics including Fisher Information, Cramer-Rao Lower Bound (CRLB), covariance, and singular value decomposition (SVD) are introduced. The connections and utility of these metrics are illustrated in the design of eddy current methods for estimating layer thickness, conductivity and probe liftoff.

  9. Estimating sampling error of evolutionary statistics based on genetic covariance matrices using maximum likelihood.

    PubMed

    Houle, D; Meyer, K

    2015-08-01

    We explore the estimation of uncertainty in evolutionary parameters using a recently devised approach for resampling entire additive genetic variance-covariance matrices (G). Large-sample theory shows that maximum-likelihood estimates (including restricted maximum likelihood, REML) asymptotically have a multivariate normal distribution, with covariance matrix derived from the inverse of the information matrix, and mean equal to the estimated G. This suggests that sampling estimates of G from this distribution can be used to assess the variability of estimates of G, and of functions of G. We refer to this as the REML-MVN method. This has been implemented in the mixed-model program WOMBAT. Estimates of sampling variances from REML-MVN were compared to those from the parametric bootstrap and from a Bayesian Markov chain Monte Carlo (MCMC) approach (implemented in the R package MCMCglmm). We apply each approach to evolvability statistics previously estimated for a large, 20-dimensional data set for Drosophila wings. REML-MVN and MCMC sampling variances are close to those estimated with the parametric bootstrap. Both slightly underestimate the error in the best-estimated aspects of the G matrix. REML analysis supports the previous conclusion that the G matrix for this population is full rank. REML-MVN is computationally very efficient, making it an attractive alternative to both data resampling and MCMC approaches to assessing confidence in parameters of evolutionary interest. PMID:26079756

  10. Lack of Genetic Structure and Female-Specific Effect of Dispersal Barriers in a Rabies Vector, the Striped Skunk (Mephitis mephitis)

    PubMed Central

    Talbot, Benoit; Garant, Dany; Rioux Paquette, Sébastien; Mainguy, Julien; Pelletier, Fanie

    2012-01-01

    Evaluating the permeability of potential barriers to movement, dispersal and gene exchanges can help describe spreading patterns of wildlife diseases. Here, we used landscape genetics methods to assess the genetic structure of the striped skunk (Mephitis mephitis), which is a frequent vector of rabies, a lethal zoonosis of great concern for public health. Our main objective was to identify landscape elements shaping the genetic structure of this species in Southern Québec, Canada, in an area where the raccoon rabies variant has been detected. We hypothesised that geographic distance and landscape barriers, such as highways and major rivers, would modulate genetic structure. We genotyped a total of 289 individuals sampled across a large area (22,000 km2) at nice microsatellite loci. Genetic structure analyses identified a single genetic cluster in the study area. Major rivers and highways, however, influenced the genetic relatedness among sampled individuals. Sex-specific analyses revealed that rivers significantly limited dispersal only for females while highways only had marginal effects. Rivers and highways did not significantly affect male dispersal. These results support the contention that female skunks are more philopatric than males. Overall, our results suggest that the effects of major rivers and highways on dispersal are sex-specific and rather weak and are thus unlikely to prevent the spread of rabies within and among striped skunk populations. PMID:23166760

  11. Estimation of genetic parameters for hip dysplasia in Czech Labrador Retrievers.

    PubMed

    Vostrý, L; Capková, Z; Sebková, N; Přibyl, J

    2012-02-01

    The objective of this study was to estimate the genetic parameters, genetic trends and breeding values using linear model (LM) and threshold model (TM) for the development of hip dysplasia (HD) in Labrador Retrievers in the Czech Republic (n = 3151). The right and left hip joints were evaluated separately using the Fédération Cynologique Internationale scoring system. Four linear and four TMs were tested for the correct estimation of genetic parameters. All the tested models utilized fixed effects of sex, assessor, year of birth, regression of age at evaluation, random direct genetic effects and the effect of the animals' permanent environments. The models differed in the inclusion of the following effects: fixed effects of regression of inbreeding coefficient, random maternal effect and random effect of the maternal permanent environment. Compared to the TM, the LM provided lower coefficients of direct (0.25-0.29 versus 0.26-0.35) and maternal heritability (0.01-0.02 versus 0.03-0.05), repeatability (0.76-0.77 versus 0.78-0.83) and of the correlation between direct and maternal effects (-0.55 to -0.21 versus -0.80 to -0.27). In the tested models, no statistical significance was found for fixed regression of inbreeding coefficients or for the random effect of the permanent maternal environment. In spite of the similarity of the LM and TM results, the TM is recommended as the more suitable model for estimating genetic parameters and subsequent breeding values for HD in Labrador Retrievers in the Czech Republic. PMID:22225585

  12. Simultaneous Estimation of Additive and Mutational Genetic Variance in an Outbred Population of Drosophila serrata.

    PubMed

    McGuigan, Katrina; Aguirre, J David; Blows, Mark W

    2015-11-01

    How new mutations contribute to genetic variation is a key question in biology. Although the evolutionary fate of an allele is largely determined by its heterozygous effect, most estimates of mutational variance and mutational effects derive from highly inbred lines, where new mutations are present in homozygous form. In an attempt to overcome this limitation, middle-class neighborhood (MCN) experiments have been used to assess the fitness effect of new mutations in heterozygous form. However, because MCN populations harbor substantial standing genetic variance, estimates of mutational variance have not typically been available from such experiments. Here we employ a modification of the animal model to analyze data from 22 generations of Drosophila serrata bred in an MCN design. Mutational heritability, measured for eight cuticular hydrocarbons, 10 wing-shape traits, and wing size in this outbred genetic background, ranged from 0.0006 to 0.006 (with one exception), a similar range to that reported from studies employing inbred lines. Simultaneously partitioning the additive and mutational variance in the same outbred population allowed us to quantitatively test the ability of mutation-selection balance models to explain the observed levels of additive and mutational genetic variance. The Gaussian allelic approximation and house-of-cards models, which assume real stabilizing selection on single traits, both overestimated the genetic variance maintained at equilibrium, but the house-of-cards model was a closer fit to the data. This analytical approach has the potential to be broadly applied, expanding our understanding of the dynamics of genetic variance in natural populations. PMID:26384357

  13. Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivars.

    PubMed

    Shahin, Arwa; Smulders, Marinus J M; van Tuyl, Jaap M; Arens, Paul; Bakker, Freek T

    2014-01-01

    Next Generation Sequencing (NGS) may enable estimating relationships among genotypes using allelic variation of multiple nuclear genes simultaneously. We explored the potential and caveats of this strategy in four genetically distant Lilium cultivars to estimate their genetic divergence from transcriptome sequences using three approaches: POFAD (Phylogeny of Organisms from Allelic Data, uses allelic information of sequence data), RAxML (Randomized Accelerated Maximum Likelihood, tree building based on concatenated consensus sequences) and Consensus Network (constructing a network summarizing among gene tree conflicts). Twenty six gene contigs were chosen based on the presence of orthologous sequences in all cultivars, seven of which also had an orthologous sequence in Tulipa, used as out-group. The three approaches generated the same topology. Although the resolution offered by these approaches is high, in this case there was no extra benefit in using allelic information. We conclude that these 26 genes can be widely applied to construct a species tree for the genus Lilium. PMID:25368628

  14. Applications in genetic risk estimation of data on the induction of dominant skeletal mutations in mice

    SciTech Connect

    Selby, P.B.

    1982-01-01

    Studies on the induction of dominant skeleton mutations and of dominant cataract mutations provide means of estimating genetic hazard to humans from radiation. The breeding-test method of studying the induction of dominant skeletal mutations is slow and cumbersome. In an attempt to devise a more rapid method, three non-breeding-test methods have been developed which are likely to have wider application in mutagenicity testing. (ACR)

  15. Sub-sampling genetic data to estimate black bear population size: A case study

    USGS Publications Warehouse

    Tredick, C.A.; Vaughan, M.R.; Stauffer, D.F.; Simek, S.L.; Eason, T.

    2007-01-01

    Costs for genetic analysis of hair samples collected for individual identification of bears average approximately US$50 [2004] per sample. This can easily exceed budgetary allowances for large-scale studies or studies of high-density bear populations. We used 2 genetic datasets from 2 areas in the southeastern United States to explore how reducing costs of analysis by sub-sampling affected precision and accuracy of resulting population estimates. We used several sub-sampling scenarios to create subsets of the full datasets and compared summary statistics, population estimates, and precision of estimates generated from these subsets to estimates generated from the complete datasets. Our results suggested that bias and precision of estimates improved as the proportion of total samples used increased, and heterogeneity models (e.g., Mh[CHAO]) were more robust to reduced sample sizes than other models (e.g., behavior models). We recommend that only high-quality samples (>5 hair follicles) be used when budgets are constrained, and efforts should be made to maximize capture and recapture rates in the field.

  16. Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs.

    PubMed

    Lee, S Hong; Ripke, Stephan; Neale, Benjamin M; Faraone, Stephen V; Purcell, Shaun M; Perlis, Roy H; Mowry, Bryan J; Thapar, Anita; Goddard, Michael E; Witte, John S; Absher, Devin; Agartz, Ingrid; Akil, Huda; Amin, Farooq; Andreassen, Ole A; Anjorin, Adebayo; Anney, Richard; Anttila, Verneri; Arking, Dan E; Asherson, Philip; Azevedo, Maria H; Backlund, Lena; Badner, Judith A; Bailey, Anthony J; Banaschewski, Tobias; Barchas, Jack D; Barnes, Michael R; Barrett, Thomas B; Bass, Nicholas; Battaglia, Agatino; Bauer, Michael; Bayés, Mònica; Bellivier, Frank; Bergen, Sarah E; Berrettini, Wade; Betancur, Catalina; Bettecken, Thomas; Biederman, Joseph; Binder, Elisabeth B; Black, Donald W; Blackwood, Douglas H R; Bloss, Cinnamon S; Boehnke, Michael; Boomsma, Dorret I; Breen, Gerome; Breuer, René; Bruggeman, Richard; Cormican, Paul; Buccola, Nancy G; Buitelaar, Jan K; Bunney, William E; Buxbaum, Joseph D; Byerley, William F; Byrne, Enda M; Caesar, Sian; Cahn, Wiepke; Cantor, Rita M; Casas, Miguel; Chakravarti, Aravinda; Chambert, Kimberly; Choudhury, Khalid; Cichon, Sven; Cloninger, C Robert; Collier, David A; Cook, Edwin H; Coon, Hilary; Cormand, Bru; Corvin, Aiden; Coryell, William H; Craig, David W; Craig, Ian W; Crosbie, Jennifer; Cuccaro, Michael L; Curtis, David; Czamara, Darina; Datta, Susmita; Dawson, Geraldine; Day, Richard; De Geus, Eco J; Degenhardt, Franziska; Djurovic, Srdjan; Donohoe, Gary J; Doyle, Alysa E; Duan, Jubao; Dudbridge, Frank; Duketis, Eftichia; Ebstein, Richard P; Edenberg, Howard J; Elia, Josephine; Ennis, Sean; Etain, Bruno; Fanous, Ayman; Farmer, Anne E; Ferrier, I Nicol; Flickinger, Matthew; Fombonne, Eric; Foroud, Tatiana; Frank, Josef; Franke, Barbara; Fraser, Christine; Freedman, Robert; Freimer, Nelson B; Freitag, Christine M; Friedl, Marion; Frisén, Louise; Gallagher, Louise; Gejman, Pablo V; Georgieva, Lyudmila; Gershon, Elliot S; Geschwind, Daniel H; Giegling, Ina; Gill, Michael; Gordon, Scott D; Gordon-Smith, Katherine; Green, Elaine K; Greenwood, Tiffany A; Grice, Dorothy E; Gross, Magdalena; Grozeva, Detelina; Guan, Weihua; Gurling, Hugh; De Haan, Lieuwe; Haines, Jonathan L; Hakonarson, Hakon; Hallmayer, Joachim; Hamilton, Steven P; Hamshere, Marian L; Hansen, Thomas F; Hartmann, Annette M; Hautzinger, Martin; Heath, Andrew C; Henders, Anjali K; Herms, Stefan; Hickie, Ian B; Hipolito, Maria; Hoefels, Susanne; Holmans, Peter A; Holsboer, Florian; Hoogendijk, Witte J; Hottenga, Jouke-Jan; Hultman, Christina M; Hus, Vanessa; Ingason, Andrés; Ising, Marcus; Jamain, Stéphane; Jones, Edward G; Jones, Ian; Jones, Lisa; Tzeng, Jung-Ying; Kähler, Anna K; Kahn, René S; Kandaswamy, Radhika; Keller, Matthew C; Kennedy, James L; Kenny, Elaine; Kent, Lindsey; Kim, Yunjung; Kirov, George K; Klauck, Sabine M; Klei, Lambertus; Knowles, James A; Kohli, Martin A; Koller, Daniel L; Konte, Bettina; Korszun, Ania; Krabbendam, Lydia; Krasucki, Robert; Kuntsi, Jonna; Kwan, Phoenix; Landén, Mikael; Långström, Niklas; Lathrop, Mark; Lawrence, Jacob; Lawson, William B; Leboyer, Marion; Ledbetter, David H; Lee, Phil H; Lencz, Todd; Lesch, Klaus-Peter; Levinson, Douglas F; Lewis, Cathryn M; Li, Jun; Lichtenstein, Paul; Lieberman, Jeffrey A; Lin, Dan-Yu; Linszen, Don H; Liu, Chunyu; Lohoff, Falk W; Loo, Sandra K; Lord, Catherine; Lowe, Jennifer K; Lucae, Susanne; MacIntyre, Donald J; Madden, Pamela A F; Maestrini, Elena; Magnusson, Patrik K E; Mahon, Pamela B; Maier, Wolfgang; Malhotra, Anil K; Mane, Shrikant M; Martin, Christa L; Martin, Nicholas G; Mattheisen, Manuel; Matthews, Keith; Mattingsdal, Morten; McCarroll, Steven A; McGhee, Kevin A; McGough, James J; McGrath, Patrick J; McGuffin, Peter; McInnis, Melvin G; McIntosh, Andrew; McKinney, Rebecca; McLean, Alan W; McMahon, Francis J; McMahon, William M; McQuillin, Andrew; Medeiros, Helena; Medland, Sarah E; Meier, Sandra; Melle, Ingrid; Meng, Fan; Meyer, Jobst; Middeldorp, Christel M; Middleton, Lefkos; Milanova, Vihra; Miranda, Ana; Monaco, Anthony P; Montgomery, Grant W; Moran, Jennifer L; Moreno-De-Luca, Daniel; Morken, Gunnar; Morris, Derek W; Morrow, Eric M; Moskvina, Valentina; Muglia, Pierandrea; Mühleisen, Thomas W; Muir, Walter J; Müller-Myhsok, Bertram; Murtha, Michael; Myers, Richard M; Myin-Germeys, Inez; Neale, Michael C; Nelson, Stan F; Nievergelt, Caroline M; Nikolov, Ivan; Nimgaonkar, Vishwajit; Nolen, Willem A; Nöthen, Markus M; Nurnberger, John I; Nwulia, Evaristus A; Nyholt, Dale R; O'Dushlaine, Colm; Oades, Robert D; Olincy, Ann; Oliveira, Guiomar; Olsen, Line; Ophoff, Roel A; Osby, Urban; Owen, Michael J; Palotie, Aarno; Parr, Jeremy R

    2013-09-01

    Most psychiatric disorders are moderately to highly heritable. The degree to which genetic variation is unique to individual disorders or shared across disorders is unclear. To examine shared genetic etiology, we use genome-wide genotype data from the Psychiatric Genomics Consortium (PGC) for cases and controls in schizophrenia, bipolar disorder, major depressive disorder, autism spectrum disorders (ASD) and attention-deficit/hyperactivity disorder (ADHD). We apply univariate and bivariate methods for the estimation of genetic variation within and covariation between disorders. SNPs explained 17-29% of the variance in liability. The genetic correlation calculated using common SNPs was high between schizophrenia and bipolar disorder (0.68 ± 0.04 s.e.), moderate between schizophrenia and major depressive disorder (0.43 ± 0.06 s.e.), bipolar disorder and major depressive disorder (0.47 ± 0.06 s.e.), and ADHD and major depressive disorder (0.32 ± 0.07 s.e.), low between schizophrenia and ASD (0.16 ± 0.06 s.e.) and non-significant for other pairs of disorders as well as between psychiatric disorders and the negative control of Crohn's disease. This empirical evidence of shared genetic etiology for psychiatric disorders can inform nosology and encourages the investigation of common pathophysiologies for related disorders. PMID:23933821

  17. Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs

    PubMed Central

    2013-01-01

    Most psychiatric disorders are moderately to highly heritable. The degree to which genetic variation is unique to individual disorders or shared across disorders is unclear. To examine shared genetic etiology, we use genome-wide genotype data from the Psychiatric Genomics Consortium (PGC) for cases and controls in schizophrenia, bipolar disorder, major depressive disorder, autism spectrum disorders (ASD) and attention-deficit/hyperactivity disorder (ADHD). We apply univariate and bivariate methods for the estimation of genetic variation within and covariation between disorders. SNPs explained 17–29% of the variance in liability. The genetic correlation calculated using common SNPs was high between schizophrenia and bipolar disorder (0.68 ± 0.04 s.e.), moderate between schizophrenia and major depressive disorder (0.43 ± 0.06 s.e.), bipolar disorder and major depressive disorder (0.47 ± 0.06 s.e.), and ADHD and major depressive disorder (0.32 ± 0.07 s.e.), low between schizophrenia and ASD (0.16 ± 0.06 s.e.) and non-significant for other pairs of disorders as well as between psychiatric disorders and the negative control of Crohn’s disease. This empirical evidence of shared genetic etiology for psychiatric disorders can inform nosology and encourages the investigation of common pathophysiologies for related disorders. PMID:23933821

  18. Estimation of genetic structure of a Mycosphaerella musicola population using inter-simple sequence repeat markers.

    PubMed

    Peixouto, Y S; Dórea Bragança, C A; Andrade, W B; Ferreira, C F; Haddad, F; Oliveira, S A S; Darosci Brito, F S; Miller, R N G; Amorim, E P

    2015-01-01

    Among the diseases affecting banana (Musa sp), yellow Sigatoka, caused by the fungal pathogen Mycosphaerella musicola Leach, is considered one of the most important in Brazil, causing losses throughout the year. Understanding the genetic structure of pathogen populations will provide insight into the life history of pathogens, including the evolutionary processes occurring in agrosystems. Tools for estimating the possible emergence of pathogen variants with altered pathogenicity, virulence, or aggressiveness, as well as resistance to systemic fungicides, can also be developed from such data. The objective of this study was to analyze the genetic diversity and population genetics of M. musicola in the main banana-producing regions in Brazil. A total of 83 isolates collected from different banana cultivars in the Brazilian states of Bahia, Rio Grande do Norte, and Minas Gerais were evaluated using inter-simple sequence repeat markers. High variability was detected between the isolates, and 85.5% of the haplotypes were singletons in the populations. The highest source of genetic diversity (97.22%) was attributed to variations within populations. Bayesian cluster analysis revealed the presence of 2 probable ancestral groups, however, showed no relationship to population structure in terms of collection site, state of origin, or cultivar. Similarly, we detected noevidence of genetic recombination between individuals within different states, indicating that asexual cycles play a major role in M. musicola reproduction and that long-distance dispersal of the pathogen is the main factor contributing to the lack of population structure in the fungus. PMID:26214487

  19. Genetic parameter estimates for carcass and yearling ultrasound measurements in Brangus cattle.

    PubMed

    Moser, D W; Bertrand, J K; Misztal, I; Kriese, L A; Benyshek, L L

    1998-10-01

    Carcass measurements of 12th-rib fat thickness (CARCFAT), longissimus muscle area (CARCLMA), and weight (CARCWT) on 2,028 Brangus and Brangus-sired fed steers and heifers, as well as yearling weights (YWT) and ultrasound measures of 12th-rib fat thickness (USFAT) and longissimus muscle area (USLMA) on 3,583 Brangus bulls and heifers were analyzed to estimate genetic parameters. Data were analyzed using a six-trait animal model and an average information REML algorithm. The model included fixed effects for contemporary group and breed of dam, covariates for age at slaughter or measurement, and random animal and residual effects. Heritabilities for CARCFAT, CARCLMA, CARCWT, USFAT, USLMA, and YWT were .27+/-.05, .39+/-.05, .59+/-.06, .11+/-.03, .29+/-.04, and .40+/-.04, respectively. Genetic correlations between CARCFAT and USFAT, CARCLMA and USLMA, and CARCWT and YWT were .69+/-.18, .66+/-.14, and .61+/-.11, respectively. The favorable and moderately strong genetic correlations between carcass measurements and similar yearling breeding-animal ultrasound measurements indicate that such measurements of 12th-rib fat and longissimus muscle area are useful in predicting genetic values for carcass leanness and longissimus muscle area. Selection using yearling ultrasound measurements of breeding cattle should result in predictable genetic improvement for carcass characteristics. Inclusion of yearling ultrasound measurements for fat thickness and longissimus muscle area should enhance national cattle evaluation programs. PMID:9814892

  20. Estimation of genetic parameters for carcass defects of Japanese Black cattle in Kagoshima.

    PubMed

    Nishi, Kazutaka; Shimogiri, Takeshi; Kusano, Akinori; Sakamoto, Shinichi; Shiromoto, Kiyomi; Kawabe, Kotaro; Okamoto, Shin; Honda, Takeshi; Oyama, Kenji

    2016-05-01

    Cattle exhibit a range of carcass defects, including blood splash (BLS), intramuscular edema (INE), muscle steatosis (MUS), bruising (BR), trim loss (TRL) and others (OTH). These defects lower the carcass value and can result in significant economic loss to producers. We estimated the incidence, relationship with inbreeding coefficients and genetic parameters of carcass defects in Japanese Black cattle using 561 619 carcass records from Kagoshima, Japan during April 1988 through March 2011. The defect incidence ranged from 0.22% for TRL to 5.73% for BR. The incidence of MUS and BR increased from 1.21% to 6.57% and from 1.06% to 9.31%, respectively. The incidence of INE peaked at 7.44% in 1999 and decreased thereafter. We observed a positive linear relationship between the defect incidence and the inbreeding coefficients in MUS, BR and TRL (P < 0.01). The heritabilities estimated by univariate animal model with Gibbs sampling for BLS, INE, MUS, BR and TRL were 0.24, 0.06, 0.18, 0.05 and 0.02, respectively. The contribution of farm variance to phenotypic variance was negligible (0.01 to 0.04). Significant genetic correlations of TRL were estimated with MUS (0.63) and BR (0.63). Our results suggest that genetic factors contribute to the incidence of BLS and MUS. PMID:26419703

  1. Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data

    PubMed Central

    Beerenwinkel, Niko; Günthard, Huldrych F.; Roth, Volker; Metzner, Karin J.

    2012-01-01

    Many viruses, including the clinically relevant RNA viruses HIV (human immunodeficiency virus) and HCV (hepatitis C virus), exist in large populations and display high genetic heterogeneity within and between infected hosts. Assessing intra-patient viral genetic diversity is essential for understanding the evolutionary dynamics of viruses, for designing effective vaccines, and for the success of antiviral therapy. Next-generation sequencing (NGS) technologies allow the rapid and cost-effective acquisition of thousands to millions of short DNA sequences from a single sample. However, this approach entails several challenges in experimental design and computational data analysis. Here, we review the entire process of inferring viral diversity from sample collection to computing measures of genetic diversity. We discuss sample preparation, including reverse transcription and amplification, and the effect of experimental conditions on diversity estimates due to in vitro base substitutions, insertions, deletions, and recombination. The use of different NGS platforms and their sequencing error profiles are compared in the context of various applications of diversity estimation, ranging from the detection of single nucleotide variants (SNVs) to the reconstruction of whole-genome haplotypes. We describe the statistical and computational challenges arising from these technical artifacts, and we review existing approaches, including available software, for their solution. Finally, we discuss open problems, and highlight successful biomedical applications and potential future clinical use of NGS to estimate viral diversity. PMID:22973268

  2. Genetic parameter estimates of yearling live animal ultrasonic measurements in Brangus cattle.

    PubMed

    Stelzleni, A M; Perkins, T L; Brown, A H; Pohlman, F W; Johnson, Z B; Sandelin, B A

    2002-12-01

    The objective of this study was to estimate genetic parameters for real-time ultrasound measurements of longissimus muscle area (LMA), 12th rib backfat thickness (FT), percent intramuscular fat (IMF), and yearling weight (YW) for 1,299 yearling Brangus bulls and heifers. A single ultrasound technician performed all measurements. The number of observations was 1,298, 1,298, 1,215, and 1,170 for LMA, FT, IMF, and YW, respectively. Genetic parameters were estimated for each trait using single- and multiple-trait derivative-free restricted maximal likelihood. Fixed effects were contemporary group (defined as same sex, same age within six months, and same environment), and days of age as a covariate. Correlations were estimated from two-trait models. Heritabilities for LMA, FT, IMF, and YW were 0.31, 0.26, 0.16, and 0.53, respectively. Genetic correlations between LMA and FT, LMA and IMF, LMA and YW, FT and IMF, FT and YW, and IMF and YW were 0.09, 0.25, 0.44, 0.36, 0.42, and 0.31, respectively. Yearling live animal ultrasonic measurements can be used as a selection tool in breeding cattle for the improvement of carcass traits. PMID:12542155

  3. Estimation of the incidence of a rare genetic disease through a two-tier mutation survey

    SciTech Connect

    Chakraborty, R.; Srinivasan, M.R. ); Raskin, S. Universidade Federal do Parana, Curitiba )

    1993-06-01

    Recent attempts to detect mutations involving single base changes or small deletions that are specific to genetic diseases provide an opportunity to develop a two-tier mutation-screening program through which incidence of rare genetic disorders and gene carriers may be precisely estimated. A two-tier survey consists of mutation screening in a sample of patients with specific genetic disorders and in a second sample of newborns from the same population in which mutation frequency is evaluated. The authors provide the statistical basis for evaluating the incidence of affected and gene carriers in such two-tier mutation-screening surveys, from which the precision of the estimates is derived. Sample-size requirements of such two-tier mutation-screening surveys are evaluated. Considering examples of cystic fibrosis (CF) and medium-chain acyl-CoA dehydrogenase deficiency (MCAD), the two most frequent autosomal recessive diseases in Caucasian populations and the two most frequent mutations ([Delta]F508 and G985) that occur on these disease allele-bearing chromosomes, the authors show that, with 50--100 patients and a 20-fold larger sample of newborns screened for these mutations, the incidence of such diseases and their gene carriers in a population may be quite reliably estimated. The theory developed here is also applicable to rare autosomal dominant diseases for which disease-specific mutations are found. 21 refs., 1 fig., 3 tabs.

  4. Investigations into modeling and further estimation of detection limits of the liquid electrode dielectric barrier discharge.

    PubMed

    Krähling, Tobias; Michels, Antje; Geisler, Sebastian; Florek, Stefan; Franzke, Joachim

    2014-06-17

    The liquid electrode dielectric barrier discharge (LE-DBD) is a miniaturized atmospheric pressure plasma as emission excitation source for elemental determination with pulsed behavior. Metals dissolved in liquids are detectable in flow systems with low flow rates of 20 μL min(-1) by means of optical emission spectrometry using a simple portable spectrometer. Time-resolved determination of the hydrogen excitation temperature Tαβ indicates that the LE-DBD does not reach a stable state during a burning phase, whereat the maximum and minimum Tαβ is independent of the flow rate. Adding dissolved metals to the liquid electrode does not influence the minimum Tαβ at the end of a burning phase. With the help of measured doubly charged lanthanum lines and spatially resolved measurements, the mechanism of the liquid transfer into the plasma will be clarified. Emissions from metal oxides indicate a thermal evaporation transfer mechanism, but only an additional electrospray-like transfer mechanism can explain the observed La III emissions and nonhomogeneous spatial distribution of exited species. The reaction pathways for electrosprayed hydrated metal ions are discussed for triply and doubly charged ions. The analytical performance is evaluated for 23 elements from the categories of alkali, alkaline earth, transition, and poor metals. The achieved detection limits are between 0.016 mg L(-1) for Li and 41 mg L(-1) for Bi. PMID:24831065

  5. Estimating observing locations for advancing beyond the winter predictability barrier of Indian Ocean dipole event predictions

    NASA Astrophysics Data System (ADS)

    Feng, Rong; Duan, Wansuo; Mu, Mu

    2016-04-01

    In this paper, we explored potential observing locations (i.e., the sensitive areas) of positive Indian Ocean dipole (IOD) events to advance beyond the winter predictability barrier (WPB) using the geophysical fluid dynamics laboratory climate model version 2p1 (GFDL CM2p1). The sensitivity analysis is conducted through perfect model predictability experiments, in which the model is assumed to be perfect and so any prediction errors are caused by initial errors. The results show that the initial errors with an east-west dipole pattern are more likely to result in a significant WPB than spatially correlated noises; the areas where the large values of the dipole pattern initial errors are located have great effects on prediction uncertainties in winter and provide useful information regarding the sensitive areas. Further, the prediction uncertainties in winter are more sensitive to the initial errors in the subsurface large value areas than to those in the surface large value areas. The results indicate that the subsurface large value areas are sensitive areas for advancing beyond the WPB of IOD predictions and if we carry out intensive observations across these areas, the prediction errors in winter may be largely reduced. This will lead to large improvements in the skill of wintertime IOD event forecasts.

  6. Genetic Parameter Estimates of Carcass Traits under National Scale Breeding Scheme for Beef Cattle.

    PubMed

    Do, ChangHee; Park, ByungHo; Kim, SiDong; Choi, TaeJung; Yang, BohSuk; Park, SuBong; Song, HyungJun

    2016-08-01

    Carcass and price traits of 72,969 Hanwoo cows, bulls and steers aged 16 to 80 months at slaughter collected from 2002 to 2013 at 75 beef packing plants in Korea were analyzed to determine heritability, correlation and breeding value using the Multi-Trait restricted maximum likelihood (REML) animal model procedure. The traits included carcass measurements, scores and grades at 24 h postmortem and bid prices at auction. Relatively high heritability was found for maturity (0.41±0.031), while moderate heritability estimates were obtained for backfat thickness (0.20±0.018), longissimus muscle (LM) area (0.23±0.020), carcass weight (0.28±0.019), yield index (0.20±0.018), yield grade (0.16±0.017), marbling (0.28±0.021), texture (0.14±0.016), quality grade (0.26±0.016) and price/kg (0.24±0.025). Relatively low heritability estimates were observed for meat color (0.06±0.013) and fat color (0.06±0.012). Heritability estimates for most traits were lower than those in the literature. Genetic correlations of carcass measurements with characteristic scores or quality grade of carcass ranged from -0.27 to +0.21. Genetic correlations of yield grade with backfat thickness, LM area and carcass weight were 0.91, -0.43, and -0.09, respectively. Genetic correlations of quality grade with scores of marbling, meat color, fat color and texture were -0.99, 0.48, 0.47, and 0.98, respectively. Genetic correlations of price/kg with LM area, carcass weight, marbling, meat color, texture and maturity were 0.57, 0.64, 0.76, -0.41, -0.79, and -0.42, respectively. Genetic correlations of carcass price with LM area, carcass weight, marbling and texture were 0.61, 0.57, 0.64, and -0.73, respectively, with standard errors ranging from ±0.047 to ±0.058. The mean carcass weight breeding values increased by more than 8 kg, whereas the mean marbling scores decreased by approximately 0.2 from 2000 through 2009. Overall, the results suggest that genetic improvement of productivity and

  7. Genetic Parameter Estimates of Carcass Traits under National Scale Breeding Scheme for Beef Cattle

    PubMed Central

    Do, ChangHee; Park, ByungHo; Kim, SiDong; Choi, TaeJung; Yang, BohSuk; Park, SuBong; Song, HyungJun

    2016-01-01

    Carcass and price traits of 72,969 Hanwoo cows, bulls and steers aged 16 to 80 months at slaughter collected from 2002 to 2013 at 75 beef packing plants in Korea were analyzed to determine heritability, correlation and breeding value using the Multi-Trait restricted maximum likelihood (REML) animal model procedure. The traits included carcass measurements, scores and grades at 24 h postmortem and bid prices at auction. Relatively high heritability was found for maturity (0.41±0.031), while moderate heritability estimates were obtained for backfat thickness (0.20±0.018), longissimus muscle (LM) area (0.23±0.020), carcass weight (0.28±0.019), yield index (0.20±0.018), yield grade (0.16±0.017), marbling (0.28±0.021), texture (0.14±0.016), quality grade (0.26±0.016) and price/kg (0.24±0.025). Relatively low heritability estimates were observed for meat color (0.06±0.013) and fat color (0.06±0.012). Heritability estimates for most traits were lower than those in the literature. Genetic correlations of carcass measurements with characteristic scores or quality grade of carcass ranged from −0.27 to +0.21. Genetic correlations of yield grade with backfat thickness, LM area and carcass weight were 0.91, −0.43, and −0.09, respectively. Genetic correlations of quality grade with scores of marbling, meat color, fat color and texture were −0.99, 0.48, 0.47, and 0.98, respectively. Genetic correlations of price/kg with LM area, carcass weight, marbling, meat color, texture and maturity were 0.57, 0.64, 0.76, −0.41, −0.79, and −0.42, respectively. Genetic correlations of carcass price with LM area, carcass weight, marbling and texture were 0.61, 0.57, 0.64, and −0.73, respectively, with standard errors ranging from ±0.047 to ±0.058. The mean carcass weight breeding values increased by more than 8 kg, whereas the mean marbling scores decreased by approximately 0.2 from 2000 through 2009. Overall, the results suggest that genetic improvement of

  8. Population genetics of autopolyploids under a mixed mating model and the estimation of selfing rate.

    PubMed

    Hardy, Olivier J

    2016-01-01

    Nowadays, the population genetics analysis of autopolyploid species faces many difficulties due to (i) limited development of population genetics tools under polysomic inheritance, (ii) difficulties to assess allelic dosage when genotyping individuals and (iii) a form of inbreeding resulting from the mechanism of 'double reduction'. Consequently, few data analysis computer programs are applicable to autopolyploids. To contribute bridging this gap, this article first derives theoretical expectations for the inbreeding and identity disequilibrium coefficients under polysomic inheritance in a mixed mating model. Moment estimators of these coefficients are proposed when exact genotypes or just markers phenotypes (i.e. allelic dosage unknown) are available. This led to the development of estimators of the selfing rate based on adult genotypes or phenotypes and applicable to any even-ploidy level. Their statistical performances and robustness were assessed by numerical simulations. Contrary to inbreeding-based estimators, the identity disequilibrium-based estimator using phenotypes is robust (absolute bias generally < 0.05), even in the presence of double reduction, null alleles or biparental inbreeding due to isolation by distance. A fairly good precision of the selfing rate estimates (root mean squared error < 0.1) is already achievable using a sample of 30-50 individuals phenotyped at 10 loci bearing 5-10 alleles each, conditions reachable using microsatellite markers. Diallelic markers (e.g. SNP) can also perform satisfactorily in diploids and tetraploids but more polymorphic markers are necessary for higher ploidy levels. The method is implemented in the software SPAGeDi and should contribute to reduce the lack of population genetics tools applicable to autopolyploids. PMID:25981126

  9. Estimating genetic parameters for fertility in dairy cows from in-line milk progesterone profiles.

    PubMed

    Tenghe, A M M; Bouwman, A C; Berglund, B; Strandberg, E; Blom, J Y; Veerkamp, R F

    2015-08-01

    The aim of this study was to define endocrine fertility traits from in-line milk progesterone (P4) records and to estimate genetic parameters for these traits. Correlations of classical fertility (calving interval and calving to first service) and milk production traits with endocrine fertility traits were also estimated. In-line milk P4 records (n=160,952) collected from June 2009 through November 2013 for 2,273 lactations of 1,561 Holstein-Friesian cows in 12 commercial herds in the Netherlands were analyzed for (the log of) the number of days from calving till commencement of luteal activity (lnC-LA), proportion of samples between 25 and 60 d in milk with luteal activity (PLA), presence or absence of luteal activity for a cow between 25 and 60 d in milk, interval from commencement of luteal activity to first service (CLAFS), first luteal phase length, length of first interluteal interval, and length of first interovulatory interval. Milk P4 records were sampled, on average, every 2 d. Genetic parameters were estimated using a mixed linear animal model. Heritability estimates (±SE) of endocrine fertility traits were 0.12±0.05 for lnC-LA, 0.12±0.05 for PLA, and 0.11±0.06 for CLAFS, and their repeatability estimates were 0.29±0.04, 0.21±0.04, and 0.15±0.06, respectively. The genetic correlation of lnC-LA with PLA was -0.91±0.06 and with CLAFS was -0.56±0.25. The genetic correlations of lnC-LA were 0.26±0.33 with calving interval and 0.37±0.21 with calving to first service. Genetic correlations of the milk production traits with lnC-LA ranged from 0.04 to 0.18 and 0.07 to 0.65 with classical fertility traits. The phenotypic correlations of all endocrine fertility traits with milk production traits were close to zero (0.01 to 0.07). This study shows that in-line P4 records can be used to define and explore several heritable endocrine fertility traits in dairy cows and might help in selection for improved fertility. PMID:26004838

  10. Ocean currents influence the genetic structure of an intertidal mollusc in southeastern Australia – implications for predicting the movement of passive dispersers across a marine biogeographic barrier

    PubMed Central

    Miller, Adam D; Versace, Vincent L; Matthews, Ty G; Montgomery, Steven; Bowie, Kate C

    2013-01-01

    Major disjunctions among marine communities in southeastern Australia have been well documented, although explanations for biogeographic structuring remain uncertain. Converging ocean currents, environmental gradients, and habitat discontinuities have been hypothesized as likely drivers of structuring in many species, although the extent to which species are affected appears largely dependent on specific life histories and ecologies. Understanding these relationships is critical to the management of native and invasive species, and the preservation of evolutionary processes that shape biodiversity in this region. In this study we test the direct influence of ocean currents on the genetic structure of a passive disperser across a major biogeographic barrier. Donax deltoides (Veneroida: Donacidae) is an intertidal, soft-sediment mollusc and an ideal surrogate for testing this relationship, given its lack of habitat constraints in this region, and its immense dispersal potential driven by year-long spawning and long-lived planktonic larvae. We assessed allele frequencies at 10 polymorphic microsatellite loci across 11 sample locations spanning the barrier region and identified genetic structure consistent with the major ocean currents of southeastern Australia. Analysis of mitochondrial DNA sequence data indicated no evidence of genetic structuring, but signatures of a species range expansion corresponding with historical inundations of the Bassian Isthmus. Our results indicate that ocean currents are likely to be the most influential factor affecting the genetic structure of D. deltoides and a likely physical barrier for passive dispersing marine fauna generally in southeastern Australia. PMID:23762511

  11. Finite-Size Effects on Liquid-Solid Phase Coexistence and the Estimation of Crystal Nucleation Barriers

    NASA Astrophysics Data System (ADS)

    Statt, Antonia; Virnau, Peter; Binder, Kurt

    2015-01-01

    A fluid in equilibrium in a finite volume V with particle number N at a density ρ =N /V exceeding the onset density ρf of freezing may exhibit phase coexistence between a crystalline nucleus and surrounding fluid. Using a method suitable for the estimation of the chemical potential of dense fluids, we obtain the excess free energy due to the surface of the crystalline nucleus. There is neither a need to precisely locate the interface nor to compute the (anisotropic) interfacial tension. As a test case, a soft version of the Asakura-Oosawa model for colloid-polymer mixtures is treated. While our analysis is appropriate for crystal nuclei of arbitrary shape, we find the nucleation barrier to be compatible with a spherical shape and consistent with classical nucleation theory.

  12. Limitations to estimating bacterial cross-speciestransmission using genetic and genomic markers: inferencesfrom simulation modeling

    USGS Publications Warehouse

    Julio Andre, Benavides; Cross, Paul C.; Luikart, Gordon; Scott, Creel

    2014-01-01

    Cross-species transmission (CST) of bacterial pathogens has major implications for human health, livestock, and wildlife management because it determines whether control actions in one species may have subsequent effects on other potential host species. The study of bacterial transmission has benefitted from methods measuring two types of genetic variation: variable number of tandem repeats (VNTRs) and single nucleotide polymorphisms (SNPs). However, it is unclear whether these data can distinguish between different epidemiological scenarios. We used a simulation model with two host species and known transmission rates (within and between species) to evaluate the utility of these markers for inferring CST. We found that CST estimates are biased for a wide range of parameters when based on VNTRs and a most parsimonious reconstructed phylogeny. However, estimations of CST rates lower than 5% can be achieved with relatively low bias using as low as 250 SNPs. CST estimates are sensitive to several parameters, including the number of mutations accumulated since introduction, stochasticity, the genetic difference of strains introduced, and the sampling effort. Our results suggest that, even with whole-genome sequences, unbiased estimates of CST will be difficult when sampling is limited, mutation rates are low, or for pathogens that were recently introduced.

  13. Estimating effective population size and migration rates from genetic samples over space and time.

    PubMed Central

    Wang, Jinliang; Whitlock, Michael C

    2003-01-01

    In the past, moment and likelihood methods have been developed to estimate the effective population size (N(e)) on the basis of the observed changes of marker allele frequencies over time, and these have been applied to a large variety of species and populations. Such methods invariably make the critical assumption of a single isolated population receiving no immigrants over the study interval. For most populations in the real world, however, migration is not negligible and can substantially bias estimates of N(e) if it is not accounted for. Here we extend previous moment and maximum-likelihood methods to allow the joint estimation of N(e) and migration rate (m) using genetic samples over space and time. It is shown that, compared to genetic drift acting alone, migration results in changes in allele frequency that are greater in the short term and smaller in the long term, leading to under- and overestimation of N(e), respectively, if it is ignored. Extensive simulations are run to evaluate the newly developed moment and likelihood methods, which yield generally satisfactory estimates of both N(e) and m for populations with widely different effective sizes and migration rates and patterns, given a reasonably large sample size and number of markers. PMID:12586728

  14. Estimating aquifer recharge in Mission River watershed, Texas: model development and calibration using genetic algorithms

    NASA Astrophysics Data System (ADS)

    Uddameri, V.; Kuchanur, M.

    2007-01-01

    Soil moisture balance studies provide a convenient approach to estimate aquifer recharge when only limited site-specific data are available. A monthly mass-balance approach has been utilized in this study to estimate recharge in a small watershed in the coastal bend of South Texas. The developed lumped parameter model employs four adjustable parameters to calibrate model predicted stream runoff to observations at a gaging station. A new procedure was developed to correctly capture the intermittent nature of rainfall. The total monthly rainfall was assigned to a single-equivalent storm whose duration was obtained via calibration. A total of four calibrations were carried out using an evolutionary computing technique called genetic algorithms as well as the conventional gradient descent (GD) technique. Ordinary least squares and the heteroscedastic maximum likelihood error (HMLE) based objective functions were evaluated as part of this study as well. While the genetic algorithm based calibrations were relatively better in capturing the peak runoff events, the GD based calibration did slightly better in capturing the low flow events. Treating the Box-Cox exponent in the HMLE function as a calibration parameter did not yield better estimates and the study corroborates the suggestion made in the literature of fixing this exponent at 0.3. The model outputs were compared against available information and results indicate that the developed modeling approach provides a conservative estimate of recharge.

  15. Estimation of genetic parameters on conformation traits of the Iranian Arab horses population.

    PubMed

    Gharahveysi, S; Kashan, N Emam Jome; Gerami, A; Torshizi, R Vaez

    2008-01-15

    Arab horse is a popular pure breed in Iran and is registered by World Arabian Horse Organization (WAHO). There is no scientific study and research about this breed. In this research 13 conformation traits on a random sample of the Iranian Arab horses studied. The estimate of variance components estimated by Animal Model and Derivative Free Restricted Maximum Likelihood (DF-REML) approach and DF-REML software. Heritability of conformation traits is also evaluated. The range of estimated heritability were (0.050 +/- 0.008) neck length and (0.614 +/- 0.087) croup height. Results indicated that, conformation traits were good traits for selection and horse genetic evaluation. PMID:18817204

  16. [Estimation of population genetic parameters for radiographical findings of elbow dsyplasia in the Labrador Retriever].

    PubMed

    Engler, Jennifer; Hamann, Henning; Distl, Ottmar

    2009-01-01

    The aim of this study was the analysis of non-genetic and genetic factors influencing elbow dysplasia (ED) in a Labrador retriever population. We analysed scores of elbow dysplasia from the official screening programme of the Labrador Club Deutschland (LCD) following the protocol of the International Elbow Working Group. The data set included X-rays from 2931 Labrador retrievers. These dogs were born between 2000 and 2004 and originated from 834 litters and 315 kennels. The pedigree file contained 27 305 dogs pertaining to 20 generations. We analysed four different traits including ED-Mit as the averaged result of ED scores from both elbow joints, ED-Max as the higher score of both elbow joints and ED-links and ED-rechts as the ED score of left or right elbow joint. Animal models were employed to estimate heritabilities, additive genetic correlation and residual correlation using residual maximum likelihood (REML). Significant effects for all four ED-traits were gender, month of birth and inbreeding coefficient. The fixed effect of birth year showed only significant effects for ED-Mit and ED-rechts. Age at examination was not significant. Heritability estimates for ED-Mit were 0.12 +/- 0.03, for ED-Max 0.11 +/- 0.03 and 0.13 +/- 0.03 for ED-links as well as 0.07 +/- 0.02 for ED-rechts. Heritability for female dogs was 0.12 +/- 0.03 and 0.10 +/- 0.03 for male dogs. The additive genetic correlation between ED-links and ED-rechts was 1 and the residual correlation 0.64. The heritabilities for ED were low to moderate based on models employed here and taking this into consideration, selection response will be small when employing phenotypic ED scores from breeding animals as the sole selection criterion. Therefore, breeding programmes should be supported by breeding values as tools for selection of breeding dogs. There was no difference in heritabilities between the mean ED score of the joints or the ED score of the joint with the higher ED grade. Furthermore, either

  17. Multivariable Mendelian randomization: the use of pleiotropic genetic variants to estimate causal effects.

    PubMed

    Burgess, Stephen; Thompson, Simon G

    2015-02-15

    A conventional Mendelian randomization analysis assesses the causal effect of a risk factor on an outcome by using genetic variants that are solely associated with the risk factor of interest as instrumental variables. However, in some cases, such as the case of triglyceride level as a risk factor for cardiovascular disease, it may be difficult to find a relevant genetic variant that is not also associated with related risk factors, such as other lipid fractions. Such a variant is known as pleiotropic. In this paper, we propose an extension of Mendelian randomization that uses multiple genetic variants associated with several measured risk factors to simultaneously estimate the causal effect of each of the risk factors on the outcome. This "multivariable Mendelian randomization" approach is similar to the simultaneous assessment of several treatments in a factorial randomized trial. In this paper, methods for estimating the causal effects are presented and compared using real and simulated data, and the assumptions necessary for a valid multivariable Mendelian randomization analysis are discussed. Subject to these assumptions, we demonstrate that triglyceride-related pathways have a causal effect on the risk of coronary heart disease independent of the effects of low-density lipoprotein cholesterol and high-density lipoprotein cholesterol. PMID:25632051

  18. Estimates of genetic parameters for hip and elbow dysplasia in Finnish Rottweilers.

    PubMed

    Mäki, K; Liinamo, A E; Ojala, M

    2000-05-01

    Data from 2,764 Rottweiler dogs born from 1987 to 1996 were analyzed with a Restricted Maximum Likelihood procedure using a mixed linear animal model to obtain variance component estimates for hip and elbow dysplasia. The data included 2,764 hip dysplasia and 2,278 elbow dysplasia records. Hip joints were scored as normal (0), borderline (1), slight (2), moderate (3), and severe (4, 4.5, and 5) hip dysplasia. Elbow joints were graded normal or borderline (0), slight (1), moderate (2), and severe (3) elbow dysplasia. The mean for the hip scores was 1.07 and for the elbow scores .60. Environmental effects influencing hip dysplasia were age, birth year, birth year x season interaction, and experience of the veterinarian responsible for x-raying the dog. For elbow dysplasia, statistically significant effects were age, birth year, sex of the dog, and panelist responsible for each screening. Estimates of heritability for hip and elbow dysplasia were .58 +/- .04 and .31 +/- .04, respectively, with a genetic correlation of .37 +/- .08 between the traits. Genetic improvement of almost one genetic standard deviation was observed in both traits during the 10 yr covered by the data. PMID:10834565

  19. Accounting for missing data in the estimation of contemporary genetic effective population size (N(e) ).

    PubMed

    Peel, D; Waples, R S; Macbeth, G M; Do, C; Ovenden, J R

    2013-03-01

    Theoretical models are often applied to population genetic data sets without fully considering the effect of missing data. Researchers can deal with missing data by removing individuals that have failed to yield genotypes and/or by removing loci that have failed to yield allelic determinations, but despite their best efforts, most data sets still contain some missing data. As a consequence, realized sample size differs among loci, and this poses a problem for unbiased methods that must explicitly account for random sampling error. One commonly used solution for the calculation of contemporary effective population size (N(e) ) is to calculate the effective sample size as an unweighted mean or harmonic mean across loci. This is not ideal because it fails to account for the fact that loci with different numbers of alleles have different information content. Here we consider this problem for genetic estimators of contemporary effective population size (N(e) ). To evaluate bias and precision of several statistical approaches for dealing with missing data, we simulated populations with known N(e) and various degrees of missing data. Across all scenarios, one method of correcting for missing data (fixed-inverse variance-weighted harmonic mean) consistently performed the best for both single-sample and two-sample (temporal) methods of estimating N(e) and outperformed some methods currently in widespread use. The approach adopted here may be a starting point to adjust other population genetics methods that include per-locus sample size components. PMID:23280157

  20. Multivariable Mendelian Randomization: The Use of Pleiotropic Genetic Variants to Estimate Causal Effects

    PubMed Central

    Burgess, Stephen; Thompson, Simon G.

    2015-01-01

    A conventional Mendelian randomization analysis assesses the causal effect of a risk factor on an outcome by using genetic variants that are solely associated with the risk factor of interest as instrumental variables. However, in some cases, such as the case of triglyceride level as a risk factor for cardiovascular disease, it may be difficult to find a relevant genetic variant that is not also associated with related risk factors, such as other lipid fractions. Such a variant is known as pleiotropic. In this paper, we propose an extension of Mendelian randomization that uses multiple genetic variants associated with several measured risk factors to simultaneously estimate the causal effect of each of the risk factors on the outcome. This “multivariable Mendelian randomization” approach is similar to the simultaneous assessment of several treatments in a factorial randomized trial. In this paper, methods for estimating the causal effects are presented and compared using real and simulated data, and the assumptions necessary for a valid multivariable Mendelian randomization analysis are discussed. Subject to these assumptions, we demonstrate that triglyceride-related pathways have a causal effect on the risk of coronary heart disease independent of the effects of low-density lipoprotein cholesterol and high-density lipoprotein cholesterol. PMID:25632051

  1. Multilevel Selection 2: Estimating the Genetic Parameters Determining Inheritance and Response to Selection

    PubMed Central

    Bijma, Piter; Muir, William M.; Ellen, Esther D.; Wolf, Jason B.; Van Arendonk, Johan A. M.

    2007-01-01

    Interactions among individuals are universal, both in animals and in plants and in natural as well as domestic populations. Understanding the consequences of these interactions for the evolution of populations by either natural or artificial selection requires knowledge of the heritable components underlying them. Here we present statistical methodology to estimate the genetic parameters determining response to multilevel selection of traits affected by interactions among individuals in general populations. We apply these methods to obtain estimates of genetic parameters for survival days in a population of layer chickens with high mortality due to pecking behavior. We find that heritable variation is threefold greater than that obtained from classical analyses, meaning that two-thirds of the full heritable variation is hidden to classical analysis due to social interactions. As a consequence, predicted responses to multilevel selection applied to this population are threefold greater than classical predictions. This work, combined with the quantitative genetic theory for response to multilevel selection presented in an accompanying article in this issue, enables the design of selection programs to effectively reduce competitive interactions in livestock and plants and the prediction of the effects of social interactions on evolution in natural populations undergoing multilevel selection. PMID:17110493

  2. Genetic clines in the Bay of Biscay provide estimates of migration for Sardina pilchardus.

    PubMed

    Laurent, V; Voisin, M; Planes, S

    2006-01-01

    Nine allozymic loci in 1,635 individuals of Sardina pilchardus obtained at 33 sites ranging from the North to the South limits of the Bay of Biscay were analyzed to provide a description of the genetic structure of the sardine population. Individual body size and age were also recorded and analyzed. In the study population, weak but significant genetic differences were found, and a cline was observed between multilocus heterozygosity and longitude. The cline was predominantly driven by allelic frequencies of two loci, PGM-1* and PEP-lt*, and using a cline model, we estimated a migration rate of 103.1 km/gen (dispersal distance per generation). In addition, we observed that the cline was linked to biological data such as mean length and mean age of the fish. Two hypotheses may explain this cline: mixing of two different populations in the Bay of Biscay or a selective process. The weak genetic differences, the important dispersal distance per generation, and the link between genetic and biological data suggest that selection is likely to be the primary factor that maintains the cline. PMID:16407528

  3. Estimation of genetic parameters for resistance to gastro-intestinal nematodes in pure blood Arabian horses.

    PubMed

    Kornaś, Sławomir; Sallé, Guillaume; Skalska, Marta; David, Ingrid; Ricard, Anne; Cabaret, Jacques

    2015-03-01

    Equine internal parasites, mostly cyathostomins, affect both horse welfare and performance. The appearance of anthelmintic-resistant parasites creates a pressing need for optimising drenching schemes. This optimization may be achieved by identifying genetic markers associated with host susceptibility to infection and then to drench carriers of these markers. The aim of our study was to characterise the genetics of horse resistance to strongyle infection by estimating heritability of this trait in an Arabian pure blood population. A population of 789 Arabian pure blood horses from the Michałów stud farm, Poland were measured for strongyle egg excretion twice a year, over 8 years. Low repeatability values were found for faecal egg counts. Our analyses showed that less than 10% of the observed variation for strongyle faecal egg counts in this population had a genetic origin. However, additional analyses highlighted an age-dependent increase in heritability which was 0.04 (±0.02) in young horses (up to 3 years of age) but 0.21 (±0.04) in older ones. These results suggest that a significant part of the inter-individual variation has a genetic origin. This paves the way to a genomic dissection of horse-nematode interactions which might provide predictive markers of susceptibility, allowing individualised drenching schemes. PMID:25592965

  4. Multilocus Bayesian Estimates of Intra-Oceanic Genetic Differentiation, Connectivity, and Admixture in Atlantic Swordfish (Xiphias gladius L.)

    PubMed Central

    Smith, Brad L.; Lu, Ching-Ping; García-Cortés, Blanca; Viñas, Jordi; Yeh, Shean-Ya; Alvarado Bremer, Jaime R.

    2015-01-01

    Previous genetic studies of Atlantic swordfish (Xiphias gladius L.) revealed significant differentiation among Mediterranean, North Atlantic and South Atlantic populations using both mitochondrial and nuclear DNA data. However, limitations in geographic sampling coverage, and the use of single loci, precluded an accurate placement of boundaries and of estimates of admixture. In this study, we present multilocus analyses of 26 single nucleotide polymorphisms (SNPs) within 10 nuclear genes to estimate population differentiation and admixture based on the characterization of 774 individuals representing North Atlantic, South Atlantic, and Mediterranean swordfish populations. Pairwise FST values, AMOVA, PCoA, and Bayesian individual assignments support the differentiation of swordfish inhabiting these three basins, but not the current placement of the boundaries that separate them. Specifically, the range of the South Atlantic population extends beyond 5°N management boundary to 20°N-25°N from 45°W. Likewise the Mediterranean population extends beyond the current management boundary at the Strait of Gibraltar to approximately 10°W. Further, admixture zones, characterized by asymmetric contributions of adjacent populations within samples, are confined to the Northeast Atlantic. While South Atlantic and Mediterranean migrants were identified within these Northeast Atlantic admixture zones no North Atlantic migrants were identified respectively in these two neighboring basins. Owing to both, the characterization of larger number of loci and a more ample spatial sampling coverage, it was possible to provide a finer resolution of the boundaries separating Atlantic swordfish populations than previous studies. Finally, the patterns of population structure and admixture are discussed in the light of the reproductive biology, the known patterns of dispersal, and oceanographic features that may act as barriers to gene flow to Atlantic swordfish. PMID:26057382

  5. Assumption-free estimation of the genetic contribution to refractive error across childhood

    PubMed Central

    St Pourcain, Beate; McMahon, George; Timpson, Nicholas J.; Evans, David M.; Williams, Cathy

    2015-01-01

    Purpose Studies in relatives have generally yielded high heritability estimates for refractive error: twins 75–90%, families 15–70%. However, because related individuals often share a common environment, these estimates are inflated (via misallocation of unique/common environment variance). We calculated a lower-bound heritability estimate for refractive error free from such bias. Methods Between the ages 7 and 15 years, participants in the Avon Longitudinal Study of Parents and Children (ALSPAC) underwent non-cycloplegic autorefraction at regular research clinics. At each age, an estimate of the variance in refractive error explained by single nucleotide polymorphism (SNP) genetic variants was calculated using genome-wide complex trait analysis (GCTA) using high-density genome-wide SNP genotype information (minimum N at each age=3,404). Results The variance in refractive error explained by the SNPs (“SNP heritability”) was stable over childhood: Across age 7–15 years, SNP heritability averaged 0.28 (SE=0.08, p<0.001). The genetic correlation for refractive error between visits varied from 0.77 to 1.00 (all p<0.001) demonstrating that a common set of SNPs was responsible for the genetic contribution to refractive error across this period of childhood. Simulations suggested lack of cycloplegia during autorefraction led to a small underestimation of SNP heritability (adjusted SNP heritability=0.35; SE=0.09). To put these results in context, the variance in refractive error explained (or predicted) by the time participants spent outdoors was <0.005 and by the time spent reading was <0.01, based on a parental questionnaire completed when the child was aged 8–9 years old. Conclusions Genetic variation captured by common SNPs explained approximately 35% of the variation in refractive error between unrelated subjects. This value sets an upper limit for predicting refractive error using existing SNP genotyping arrays, although higher-density genotyping in

  6. Genetic Structure of the Tree Peony (Paeonia rockii) and the Qinling Mountains as a Geographic Barrier Driving the Fragmentation of a Large Population

    PubMed Central

    Yuan, Jun–hui; Cheng, Fang–Yun; Zhou, Shi–Liang

    2012-01-01

    Background Tree peonies are great ornamental plants associated with a rich ethnobotanical history in Chinese culture and have recently been used as an evolutionary model. The Qinling Mountains represent a significant geographic barrier in Asia, dividing mainland China into northern (temperate) and southern (semi–tropical) regions; however, their flora has not been well analyzed. In this study, the genetic differentiation and genetic structure of Paeonia rockii and the role of the Qinling Mountains as a barrier that has driven intraspecific fragmentation were evaluated using 14 microsatellite markers. Methodology/Principal Findings Twenty wild populations were sampled from the distributional range of P. rockii. Significant population differentiation was suggested (FST value of 0.302). Moderate genetic diversity at the population level (HS of 0.516) and high population diversity at the species level (HT of 0.749) were detected. Significant excess homozygosity (FIS of 0.076) and recent population bottlenecks were detected in three populations. Bayesian clusters, population genetic trees and principal coordinate analysis all classified the P. rockii populations into three genetic groups and one admixed Wenxian population. An isolation-by-distance model for P. rockii was suggested by Mantel tests (r = 0.6074, P<0.001) and supported by AMOVA (P<0.001), revealing a significant molecular variance among the groups (11.32%) and their populations (21.22%). These data support the five geographic boundaries surrounding the Qinling Mountains and adjacent areas that were detected with Monmonier's maximum-difference algorithm. Conclusions/Significance Our data suggest that the current genetic structure of P. rockii has resulted from the fragmentation of a formerly continuously distributed large population following the restriction of gene flow between populations of this species by the Qinling Mountains. This study provides a fundamental genetic profile for the conservation

  7. Estimating the Population Size and Genetic Diversity of Amur Tigers in Northeast China

    PubMed Central

    Dou, Hailong; Yang, Haitao; Feng, Limin; Mou, Pu; Wang, Tianming; Ge, Jianping

    2016-01-01

    Over the past century, the endangered Amur tiger (Panthera tigris altaica) has experienced a severe contraction in demography and geographic range because of habitat loss, poaching, and prey depletion. In its historical home in Northeast China, there appears to be a single tiger population that includes tigers in Southwest Primorye and Northeast China; however, the current demographic status of this population is uncertain. Information on the abundance, distribution and genetic diversity of this population for assessing the efficacy of conservation interventions are scarce. We used noninvasive genetic detection data from scats, capture-recapture models and an accumulation curve method to estimate the abundance of Amur tigers in Northeast China. We identified 11 individual tigers (6 females and 5 males) using 10 microsatellite loci in three nature reserves between April 2013 and May 2015. These tigers are confined primarily to a Hunchun Nature Reserve along the border with Russia, with an estimated population abundance of 9–11 tigers during the winter of 2014–2015. They showed a low level of genetic diversity. The mean number of alleles per locus was 2.60 and expected and observed heterozygosity were 0.42 and 0.49, respectively. We also documented long-distance dispersal (~270 km) of a male Amur tiger to Huangnihe Nature Reserve from the border, suggesting that the expansion of neighboring Russian populations may eventually help sustain Chinese populations. However, the small and isolated population recorded by this study demonstrate that there is an urgent need for more intensive regional management to create a tiger-permeable landscape and increased genetic connectivity with other populations. PMID:27100387

  8. Estimating the Population Size and Genetic Diversity of Amur Tigers in Northeast China.

    PubMed

    Dou, Hailong; Yang, Haitao; Feng, Limin; Mou, Pu; Wang, Tianming; Ge, Jianping

    2016-01-01

    Over the past century, the endangered Amur tiger (Panthera tigris altaica) has experienced a severe contraction in demography and geographic range because of habitat loss, poaching, and prey depletion. In its historical home in Northeast China, there appears to be a single tiger population that includes tigers in Southwest Primorye and Northeast China; however, the current demographic status of this population is uncertain. Information on the abundance, distribution and genetic diversity of this population for assessing the efficacy of conservation interventions are scarce. We used noninvasive genetic detection data from scats, capture-recapture models and an accumulation curve method to estimate the abundance of Amur tigers in Northeast China. We identified 11 individual tigers (6 females and 5 males) using 10 microsatellite loci in three nature reserves between April 2013 and May 2015. These tigers are confined primarily to a Hunchun Nature Reserve along the border with Russia, with an estimated population abundance of 9-11 tigers during the winter of 2014-2015. They showed a low level of genetic diversity. The mean number of alleles per locus was 2.60 and expected and observed heterozygosity were 0.42 and 0.49, respectively. We also documented long-distance dispersal (~270 km) of a male Amur tiger to Huangnihe Nature Reserve from the border, suggesting that the expansion of neighboring Russian populations may eventually help sustain Chinese populations. However, the small and isolated population recorded by this study demonstrate that there is an urgent need for more intensive regional management to create a tiger-permeable landscape and increased genetic connectivity with other populations. PMID:27100387

  9. Optimizing scheduling problem using an estimation of distribution algorithm and genetic algorithm

    NASA Astrophysics Data System (ADS)

    Qun, Jiang; Yang, Ou; Dong, Shi-Du

    2007-12-01

    This paper presents a methodology for using heuristic search methods to optimize scheduling problem. Specifically, an Estimation of Distribution Algorithm (EDA)- Population Based Incremental Learning (PBIL), and Genetic Algorithm (GA) have been applied to finding effective arrangement of curriculum schedule of Universities. To our knowledge, EDAs have been applied to fewer real world problems compared to GAs, and the goal of the present paper is to expand the application domain of this technique. The experimental results indicate a good applicability of PBIL to optimize scheduling problem.

  10. Estimation of genetic parameters and response to selection for a continuous trait subject to culling before testing.

    PubMed

    Arnason, T; Albertsdóttir, E; Fikse, W F; Eriksson, S; Sigurdsson, A

    2012-02-01

    The consequences of assuming a zero environmental covariance between a binary trait 'test-status' and a continuous trait on the estimates of genetic parameters by restricted maximum likelihood and Gibbs sampling and on response from genetic selection when the true environmental covariance deviates from zero were studied. Data were simulated for two traits (one that culling was based on and a continuous trait) using the following true parameters, on the underlying scale: h² = 0.4; r(A) = 0.5; r(E) = 0.5, 0.0 or -0.5. The selection on the continuous trait was applied to five subsequent generations where 25 sires and 500 dams produced 1500 offspring per generation. Mass selection was applied in the analysis of the effect on estimation of genetic parameters. Estimated breeding values were used in the study of the effect of genetic selection on response and accuracy. The culling frequency was either 0.5 or 0.8 within each generation. Each of 10 replicates included 7500 records on 'test-status' and 9600 animals in the pedigree file. Results from bivariate analysis showed unbiased estimates of variance components and genetic parameters when true r(E) = 0.0. For r(E) = 0.5, variance components (13-19% bias) and especially (50-80%) were underestimated for the continuous trait, while heritability estimates were unbiased. For r(E) = -0.5, heritability estimates of test-status were unbiased, while genetic variance and heritability of the continuous trait together with were overestimated (25-50%). The bias was larger for the higher culling frequency. Culling always reduced genetic progress from selection, but the genetic progress was found to be robust to the use of wrong parameter values of the true environmental correlation between test-status and the continuous trait. Use of a bivariate linear-linear model reduced bias in genetic evaluations, when data were subject to culling. PMID:22225584

  11. Reinforcement genetic approach to coefficient estimation for multivariable nonlinear discrete-time dynamical systems

    NASA Astrophysics Data System (ADS)

    Chang, Wei-Der; Yan, Jun-Juh

    2006-10-01

    In this paper, we propose a novel genetic algorithm (GA) with a multi-crossover fashion to estimate the associated coefficients for a class of nonlinear discrete-time multivariable dynamical systems. Unlike the traditional crossover method of using two chromosomes, the proposed method uses three chromosomes to achieve a crossover. According to the adjusting direction by crossing three chromosomes, more excellent offspring can be produced. To solve the identification problem of multivariable nonlinear discrete-time systems, each of estimated system coefficients represents a gene, and a collection of genes is referred to as a chromosome in the view of GA. The chromosomes in the population are then evolved using the proposed multi-crossover method. An illustrative example of multivariable nonlinear systems is given to demonstrate the effectiveness, as compared with the traditional crossover method, of the proposed method.

  12. A self-adaptive genetic algorithm to estimate JA model parameters considering minor loops

    NASA Astrophysics Data System (ADS)

    Lu, Hai-liang; Wen, Xi-shan; Lan, Lei; An, Yun-zhu; Li, Xiao-ping

    2015-01-01

    A self-adaptive genetic algorithm for estimating Jiles-Atherton (JA) magnetic hysteresis model parameters is presented. The fitness function is established based on the distances between equidistant key points of normalized hysteresis loops. Linearity function and logarithm function are both adopted to code the five parameters of JA model. Roulette wheel selection is used and the selection pressure is adjusted adaptively by deducting a proportional which depends on current generation common value. The Crossover operator is established by combining arithmetic crossover and multipoint crossover. Nonuniform mutation is improved by adjusting the mutation ratio adaptively. The algorithm is used to estimate the parameters of one kind of silicon-steel sheet's hysteresis loops, and the results are in good agreement with published data.

  13. Central role of the gut epithelial barrier in the pathogenesis of chronic intestinal inflammation: lessons learned from animal models and human genetics.

    PubMed

    Pastorelli, Luca; De Salvo, Carlo; Mercado, Joseph R; Vecchi, Maurizio; Pizarro, Theresa T

    2013-01-01

    The gut mucosa is constantly challenged by a bombardment of foreign antigens and environmental microorganisms. As such, the precise regulation of the intestinal barrier allows the maintenance of mucosal immune homeostasis and prevents the onset of uncontrolled inflammation. In support of this concept, emerging evidence points to defects in components of the epithelial barrier as etiologic factors in the pathogenesis of inflammatory bowel diseases (IBDs). In fact, the integrity of the intestinal barrier relies on different elements, including robust innate immune responses, epithelial paracellular permeability, epithelial cell integrity, as well as the production of mucus. The purpose of this review is to systematically evaluate how alterations in the aforementioned epithelial components can lead to the disruption of intestinal immune homeostasis, and subsequent inflammation. In this regard, the wealth of data from mouse models of intestinal inflammation and human genetics are pivotal in understanding pathogenic pathways, for example, that are initiated from the specific loss of function of a single protein leading to the onset of intestinal disease. On the other hand, several recently proposed therapeutic approaches to treat human IBD are targeted at enhancing different elements of gut barrier function, further supporting a primary role of the epithelium in the pathogenesis of chronic intestinal inflammation and emphasizing the importance of maintaining a healthy and effective intestinal barrier. PMID:24062746

  14. Grizzly Bear Noninvasive Genetic Tagging Surveys: Estimating the Magnitude of Missed Detections.

    PubMed

    Fisher, Jason T; Heim, Nicole; Code, Sandra; Paczkowski, John

    2016-01-01

    Sound wildlife conservation decisions require sound information, and scientists increasingly rely on remotely collected data over large spatial scales, such as noninvasive genetic tagging (NGT). Grizzly bears (Ursus arctos), for example, are difficult to study at population scales except with noninvasive data, and NGT via hair trapping informs management over much of grizzly bears' range. Considerable statistical effort has gone into estimating sources of heterogeneity, but detection error-arising when a visiting bear fails to leave a hair sample-has not been independently estimated. We used camera traps to survey grizzly bear occurrence at fixed hair traps and multi-method hierarchical occupancy models to estimate the probability that a visiting bear actually leaves a hair sample with viable DNA. We surveyed grizzly bears via hair trapping and camera trapping for 8 monthly surveys at 50 (2012) and 76 (2013) sites in the Rocky Mountains of Alberta, Canada. We used multi-method occupancy models to estimate site occupancy, probability of detection, and conditional occupancy at a hair trap. We tested the prediction that detection error in NGT studies could be induced by temporal variability within season, leading to underestimation of occupancy. NGT via hair trapping consistently underestimated grizzly bear occupancy at a site when compared to camera trapping. At best occupancy was underestimated by 50%; at worst, by 95%. Probability of false absence was reduced through successive surveys, but this mainly accounts for error imparted by movement among repeated surveys, not necessarily missed detections by extant bears. The implications of missed detections and biased occupancy estimates for density estimation-which form the crux of management plans-require consideration. We suggest hair-trap NGT studies should estimate and correct detection error using independent survey methods such as cameras, to ensure the reliability of the data upon which species management and

  15. Optimal sampling strategy for estimation of spatial genetic structure in tree populations.

    PubMed

    Cavers, S; Degen, B; Caron, H; Lemes, M R; Margis, R; Salgueiro, F; Lowe, A J

    2005-10-01

    Fine-scale spatial genetic structure (SGS) in natural tree populations is largely a result of restricted pollen and seed dispersal. Understanding the link between limitations to dispersal in gene vectors and SGS is of key interest to biologists and the availability of highly variable molecular markers has facilitated fine-scale analysis of populations. However, estimation of SGS may depend strongly on the type of genetic marker and sampling strategy (of both loci and individuals). To explore sampling limits, we created a model population with simulated distributions of dominant and codominant alleles, resulting from natural regeneration with restricted gene flow. SGS estimates from subsamples (simulating collection and analysis with amplified fragment length polymorphism (AFLP) and microsatellite markers) were correlated with the 'real' estimate (from the full model population). For both marker types, sampling ranges were evident, with lower limits below which estimation was poorly correlated and upper limits above which sampling became inefficient. Lower limits (correlation of 0.9) were 100 individuals, 10 loci for microsatellites and 150 individuals, 100 loci for AFLPs. Upper limits were 200 individuals, five loci for microsatellites and 200 individuals, 100 loci for AFLPs. The limits indicated by simulation were compared with data sets from real species. Instances where sampling effort had been either insufficient or inefficient were identified. The model results should form practical boundaries for studies aiming to detect SGS. However, greater sample sizes will be required in cases where SGS is weaker than for our simulated population, for example, in species with effective pollen/seed dispersal mechanisms. PMID:16030529

  16. [Genetic and demographic structure of the State of Aragua, Venezuela, estimated through the surnames].

    PubMed

    Rodríguez Larralde, A; Casique, J

    1993-01-01

    The genetic structure of the State of Aragua, Venezuela, has been studied through the analysis of surnames obtained from the register of electors. The analysis covered 23 counties and included a total of 99,593 individuals and 6,338 different surnames. Estimators of isolation, consanguinity, microdifferentiation and four measures of genetic distance, were studied. When our results were compared with those obtained in other States of Venezuela studied previously (Falcón, Lara, Mérida, Nueva Esparta and Yaracuy), Aragua appears as the State most open to new migrants, probably due to its nearness to Caracas, Venezuela's capital city. Within Aragua, the counties most isolated are Choronií, Ocumare de la Costa and Tovar, while those less isolated are El Limón, Turmero, La Victoria, San Mateo and Cagua. The correlations between the logarithmic transformations of genetic and geographic distances were all significant, revealing surname differentiation by distance. The dendrogram built with the Euclidean distance matrix shows a first group of counties formed by those localized towards the central portion of the State, to which southern counties are added. Choroní and Ocumare de la Costa form a group which enters the dendrogram just before Tovar, the last county to be included in the analysis. Seven surnames with a focal distribution within the State were identified: Ayala and Calanche in Choroní; Kanzler, Misle and Ruh in Tovar; Lira in San Mateo and Santaella in Barbacoas. PMID:7483965

  17. Estimation of genetic parameters for semen quality traits and growth rate in a paternal rabbit line.

    PubMed

    Lavara, R; Vicente, J S; Baselga, M

    2012-08-01

    Variance components of sperm quality traits were estimated in a paternal line of rabbits selected on the basis of daily weight gain (DG, g/day) between 28 and 63 days of age. Features of the marginal posterior distributions for the genetic variance ratios, variance due to non-additive plus environmental permanent male effects, and variance due to litter of birth effects with respect to phenotypic variance are reported. The correlation between sperm quality traits and the selection criteria were also estimated. Nine sets of two-trait analyses were performed involving 12 908 DG records, 2231 ejaculates corresponding to 412 males, and 14 700 animals in the pedigree file. Heritability values (h(2)) of sperm quality traits commonly evaluated in a classic spermiogram were 0.18, 0.19, and 0.12 for normal acrosome status (NAR) (%, percentage of sperm with intact acrosome), sperm abnormalities (ANR) (%, percentage of sperm abnormalities), and sperm motility (MOT) (%, percentage of total motile sperm cells), respectively. The h(2) of some motion computer-assisted sperm analysis (CASA) Parameters 0.09, 0.11, 0.10, 0.11, 0.11 and 0.11 for average path velocity (VAP) (μm/sec; average path velocity), straight-line velocity (VSL) (μm/sec; straight-line velocity), curvilinear velocity (VCL) (μm/sec; curvilinear velocity), linearity index (LIN) (%, linearity index), amplitude of lateral head displacement (ALH) (μm; amplitude of the lateral head displacement) and straightness (STR) (%, straightness) were also estimated. Permanent environmental effects were lower than the corresponding values of h(2) and varied between 0.04 and 0.14. Genetic correlations between DG and sperm traits showed a high interval of highest density of 95% (HPD)(95%) (interval of highest density of 95%). However, there is some consistent evidence of the negativity of the genetic correlations of DG with NAR and MOT (-0.40 and -0.53, respectively). Permanent correlations were low, including the zero in the

  18. Estimates of genetic parameters for reproductive traits in Brahman cattle breed.

    PubMed

    Cavani, L; Garcia, D A; Carreño, L O D; Ono, R K; Pires, M P; Farah, M M; Ventura, H T; Millen, D D; Fonseca, R

    2015-07-01

    This study was designed to estimate genetic parameters for the following traits of Brahman cattle in Brazil: age at first calving (AFC), calving interval (CI), rebreeding (REB), and stayability (STAY). For REB, the value 1 was assigned to heifers that rebred and calved after first calving and the value 0 was assigned to heifers that failed to rebreed after first calving. Likewise, for STAY, the value 1 was assigned to cows that calved at least 3 times by the time they reach 6 yr of age; otherwise, the value 0 was assigned. A bivariate analysis was used to estimate covariances components by using linear animal model for CI and AFC and threshold animal model for REB and STAY. The mean h(2) were 0.10, 0.02, 0.22, and 0.10 for AFC, CI, REB, and STAY, respectively. The genetic correlations were –0.13 between AFC and CI, –0.35 between AFC and REB, –0.57 between AFC and STAY, and 0.32 between REB and STAY, which reveal that cows that remain productive for longer periods in the herd also start breeding younger and present greater chances to REB. The selection of Brahman cattle for reproductive traits, such as AFC, CI, REB, and STAY, will render low magnitude and long-term responses. PMID:26439997

  19. A comparison of genetic risk score with family history for estimating prostate cancer risk

    PubMed Central

    Helfand, Brian T

    2016-01-01

    Prostate cancer (PCa) testing is recommended by most authoritative groups for high-risk men including those with a family history of the disease. However, family history information is often limited by patient knowledge and clinician intake, and thus, many men are incorrectly assigned to different risk groups. Alternate methods to assess PCa risk are required. In this review, we discuss how genetic variants, referred to as PCa-risk single-nucleotide polymorphisms, can be used to calculate a genetic risk score (GRS). GRS assigns a relatively unique value to all men based on the number of PCa-risk SNPs that an individual carries. This GRS value can provide a more precise estimate of a man's PCa risk. This is particularly relevant in situations when an individual is unaware of his family history. In addition, GRS has utility and can provide a more precise estimate of risk even among men with a positive family history. It can even distinguish risk among relatives with the same degree of family relationships. Taken together, this review serves to provide support for the clinical utility of GRS as an independent test to provide supplemental information to family history. As such, GRS can serve as a platform to help guide-shared decision-making processes regarding the timing and frequency of PCa testing and biopsies. PMID:27004541

  20. Estimating Information Processing in a Memory System: The Utility of Meta-analytic Methods for Genetics

    PubMed Central

    Yildizoglu, Tugce; Weislogel, Jan-Marek; Mohammad, Farhan; Chan, Edwin S.-Y.; Assam, Pryseley N.; Claridge-Chang, Adam

    2015-01-01

    Genetic studies in Drosophila reveal that olfactory memory relies on a brain structure called the mushroom body. The mainstream view is that each of the three lobes of the mushroom body play specialized roles in short-term aversive olfactory memory, but a number of studies have made divergent conclusions based on their varying experimental findings. Like many fields, neurogenetics uses null hypothesis significance testing for data analysis. Critics of significance testing claim that this method promotes discrepancies by using arbitrary thresholds (α) to apply reject/accept dichotomies to continuous data, which is not reflective of the biological reality of quantitative phenotypes. We explored using estimation statistics, an alternative data analysis framework, to examine published fly short-term memory data. Systematic review was used to identify behavioral experiments examining the physiological basis of olfactory memory and meta-analytic approaches were applied to assess the role of lobular specialization. Multivariate meta-regression models revealed that short-term memory lobular specialization is not supported by the data; it identified the cellular extent of a transgenic driver as the major predictor of its effect on short-term memory. These findings demonstrate that effect sizes, meta-analysis, meta-regression, hierarchical models and estimation methods in general can be successfully harnessed to identify knowledge gaps, synthesize divergent results, accommodate heterogeneous experimental design and quantify genetic mechanisms. PMID:26647168

  1. Using a genetic algorithm to estimate the details of earthquake slip distributions from point surface displacements

    NASA Astrophysics Data System (ADS)

    Lindsay, A.; McCloskey, J.; Nic Bhloscaidh, M.

    2016-03-01

    Examining fault activity over several earthquake cycles is necessary for long-term modeling of the fault strain budget and stress state. While this requires knowledge of coseismic slip distributions for successive earthquakes along the fault, these exist only for the most recent events. However, overlying the Sunda Trench, sparsely distributed coral microatolls are sensitive to tectonically induced changes in relative sea levels and provide a century-spanning paleogeodetic and paleoseismic record. Here we present a new technique called the Genetic Algorithm Slip Estimator to constrain slip distributions from observed surface deformations of corals. We identify a suite of models consistent with the observations, and from them we compute an ensemble estimate of the causative slip. We systematically test our technique using synthetic data. Applying the technique to observed coral displacements for the 2005 Nias-Simeulue earthquake and 2007 Mentawai sequence, we reproduce key features of slip present in previously published inversions such as the magnitude and location of slip asperities. From the displacement data available for the 1797 and 1833 Mentawai earthquakes, we present slip estimates reproducing observed displacements. The areas of highest modeled slip in the paleoearthquake are nonoverlapping, and our solutions appear to tile the plate interface, complementing one another. This observation is supported by the complex rupture pattern of the 2007 Mentawai sequence, underlining the need to examine earthquake occurrence through long-term strain budget and stress modeling. Although developed to estimate earthquake slip, the technique is readily adaptable for a wider range of applications.

  2. Estimate of genetic gain in popcorn after cycles of phenotypic recurrent selection.

    PubMed

    Ematné, H J; Nunes, J A R; Dias, K O G; Prado, P E R; Souza, J C

    2016-01-01

    Popcorn is widely consumed in Brazil, yet there are few breeding programs for this crop. Recurrent selection (RS) is a viable breeding alternative for popcorn; however, the gains achieved must be frequently checked. The aim of this study was to assess the effect of selection for grain type (round and pointed) after four cycles of phenotypic RS on the main agronomic traits of popcorn, to estimate the genetic gain achieved for the trait of expansion volume (EV), and to obtain estimates of phenotypic correlations for the main traits of the crop in the UFLA E and UFLA R populations. The zero, one, two, and three cycles of the UFLA E and UFLA R populations, the fourth cycle, and the controls IAC-112 and IAC-125 were used. The experiments were conducted at the experimental farm of Universidade Federal de Lavras (UFLA; Environment 1) and at the experimental area of the Genetics and Plant Breeding Sector of the Department of Biology at UFLA (Environment 2) in the 2010/11 crop season. Nine agronomic traits were evaluated, including EV and grain yield (GY). The UFLA R and UFLA E populations showed similar behavior for all evaluated traits. The type of grain did not affect the genetic gain for EV, which was 5 and 3.7% in each cycle carried out in the UFLA E and UFLA R population, respectively. Phenotypic selection carried out during recombination for EV is an effective method for increasing expression of the trait. EV and GY did not show a linear association. PMID:27323058

  3. Elevation as a barrier: genetic structure for an Atlantic rain forest tree (Bathysa australis) in the Serra do Mar mountain range, SE Brazil.

    PubMed

    Reis, Talita Soares; Ciampi-Guillardi, Maísa; Bajay, Miklos Maximiliano; de Souza, Anete Pereira; Dos Santos, Flavio Antonio Maës

    2015-05-01

    Distance and discrete geographic barriers play a role in isolating populations, as seed and pollen dispersal become limited. Nearby populations without any geographic barrier between them may also suffer from ecological isolation driven by habitat heterogeneity, which may promote divergence by local adaptation and drift. Likewise, elevation gradients may influence the genetic structure and diversity of populations, particularly those marginally distributed. Bathysa australis (Rubiaceae) is a widespread tree along the elevation gradient of the Serra do Mar, SE Brazil. This self-compatible species is pollinated by bees and wasps and has autochoric seeds, suggesting restricted gene dispersal. We investigated the distribution of genetic diversity in six B. australis populations at two extreme sites along an elevation gradient: a lowland site (80-216 m) and an upland site (1010-1100 m.a.s.l.). Nine microsatellite loci were used to test for genetic structure and to verify differences in genetic diversity between sites. We found a marked genetic structure on a scale as small as 6 km (F ST = 0.21), and two distinct clusters were identified, each corresponding to a site. Although B. australis is continuously distributed along the elevation gradient, we have not observed a gene flow between the extreme populations. This might be related to B. australis biological features and creates a potential scenario for adaptation to the different conditions imposed by the elevation gradient. We failed to find an isolation-by-distance pattern; although on the fine scale, all populations showed spatial autocorrelation until ∼10-20 m. Elevation difference was a relevant factor though, but we need further sampling effort to check its correlation with genetic distance. The lowland populations had a higher allelic richness and showed higher rare allele counts than the upland ones. The upland site may be more selective, eliminating rare alleles, as we did not find any evidence for

  4. Elevation as a barrier: genetic structure for an Atlantic rain forest tree (Bathysa australis) in the Serra do Mar mountain range, SE Brazil

    PubMed Central

    Reis, Talita Soares; Ciampi-Guillardi, Maísa; Bajay, Miklos Maximiliano; de Souza, Anete Pereira; dos Santos, Flavio Antonio Maës

    2015-01-01

    Distance and discrete geographic barriers play a role in isolating populations, as seed and pollen dispersal become limited. Nearby populations without any geographic barrier between them may also suffer from ecological isolation driven by habitat heterogeneity, which may promote divergence by local adaptation and drift. Likewise, elevation gradients may influence the genetic structure and diversity of populations, particularly those marginally distributed. Bathysa australis (Rubiaceae) is a widespread tree along the elevation gradient of the Serra do Mar, SE Brazil. This self-compatible species is pollinated by bees and wasps and has autochoric seeds, suggesting restricted gene dispersal. We investigated the distribution of genetic diversity in six B. australis populations at two extreme sites along an elevation gradient: a lowland site (80–216 m) and an upland site (1010–1100 m.a.s.l.). Nine microsatellite loci were used to test for genetic structure and to verify differences in genetic diversity between sites. We found a marked genetic structure on a scale as small as 6 km (FST = 0.21), and two distinct clusters were identified, each corresponding to a site. Although B. australis is continuously distributed along the elevation gradient, we have not observed a gene flow between the extreme populations. This might be related to B. australis biological features and creates a potential scenario for adaptation to the different conditions imposed by the elevation gradient. We failed to find an isolation-by-distance pattern; although on the fine scale, all populations showed spatial autocorrelation until ∼10-20 m. Elevation difference was a relevant factor though, but we need further sampling effort to check its correlation with genetic distance. The lowland populations had a higher allelic richness and showed higher rare allele counts than the upland ones. The upland site may be more selective, eliminating rare alleles, as we did not find any evidence

  5. Genetics

    MedlinePlus

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

  6. Genetics

    MedlinePlus

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

  7. THREaD Mapper Studio: a novel, visual web server for the estimation of genetic linkage maps.

    PubMed

    Cheema, Jitender; Ellis, T H Noel; Dicks, Jo

    2010-07-01

    The estimation of genetic linkage maps is a key component in plant and animal research, providing both an indication of the genetic structure of an organism and a mechanism for identifying candidate genes associated with traits of interest. Because of this importance, several computational solutions to genetic map estimation exist, mostly implemented as stand-alone software packages. However, the estimation process is often largely hidden from the user. Consequently, problems such as a program crashing may occur that leave a user baffled. THREaD Mapper Studio (http://cbr.jic.ac.uk/threadmapper) is a new web site that implements a novel, visual and interactive method for the estimation of genetic linkage maps from DNA markers. The rationale behind the web site is to make the estimation process as transparent and robust as possible, while also allowing users to use their expert knowledge during analysis. Indeed, the 3D visual nature of the tool allows users to spot features in a data set, such as outlying markers and potential structural rearrangements that could cause problems with the estimation procedure and to account for them in their analysis. Furthermore, THREaD Mapper Studio facilitates the visual comparison of genetic map solutions from third party software, aiding users in developing robust solutions for their data sets. PMID:20494977

  8. [Estimation of population genetic parameters and breeding values for elbow dysplasia in Rottweilers].

    PubMed

    Heine, Andrea; Hamann, Henning; Tellhelm, Bernd; Distl, Ottmar

    2009-01-01

    We analysed scores of elbow dysplasia following the IEWG protocol from the official screening programme of the Allgemeiner Deutscher Rottweiler Club (ADRK). The data set included X-rays from 5100 Rottweiler dogs born between 1995 and 2004. Out of these 5,100 dogs, 46.9% were free from ED, 9.8% showed borderline signs (ED-UG), 31.8% ED-grade 1 (mild ED), 10% ED-grade 2 (moderate ED) und 1.6% ED-grade 3 (severe ED). Male dogs were more often affected by ED-grade 2 and 3 than female dogs. Traits analysed were ED-grade (dogs free from ED and dogs with ED-grades 1 to 3) and borderline ED (ED-UG). Birth year, birth season and inbreeding coefficient were significant for ED-grade. Higher inbreeding coefficients were associated with higher ED scores. ED-UG was significantly influenced by birth year and the interaction of birth year and birth season. A bivariate linear animal model was employed to estimate heritabilities using Residual Maximum Likelihood (REML) for ED-grade and ED-UG. Heritability estimates and their standard errors were 0.387 +/- 0.028 for ED-grade and 0.017 +/- 0.009 for ED-UG. The additive genetic correlation between ED-grade and ED-UG was -0.5. Heritabilities for ED-grade in female and male dogs were 0.350 +/- 0.033 and 0.497 +/- 0.047. We do not recommend use of ED-UG in breeding work because of the low heritability estimate and the negative additive genetic correlation with ED-grade. PMID:19350808

  9. Web application for genetic modification flux with database to estimate metabolic fluxes of genetic mutants.

    PubMed

    Mohd Ali, Noorlin; Tsuboi, Ryo; Matsumoto, Yuta; Koishi, Daisuke; Inoue, Kentaro; Maeda, Kazuhiro; Kurata, Hiroyuki

    2016-07-01

    Computational analysis of metabolic fluxes is essential in understanding the structure and function of a metabolic network and in rationally designing genetically modified mutants for an engineering purpose. We had presented the genetic modification flux (GMF) that predicts the flux distribution of a broad range of genetically modified mutants. To enhance the feasibility and usability of GMF, we have developed a web application with a metabolic network database to predict a flux distribution of genetically modified mutants. One hundred and twelve data sets of Escherichia coli, Corynebacterium glutamicum, Saccharomyces cerevisiae, and Chinese hamster ovary were registered as standard models. PMID:26777238

  10. Fine-scale genetic breaks driven by historical range dynamics and ongoing density-barrier effects in the estuarine seaweed Fucus ceranoides L.

    PubMed Central

    2012-01-01

    Background Factors promoting the emergence of sharp phylogeographic breaks include restricted dispersal, habitat discontinuity, physical barriers, disruptive selection, mating incompatibility, genetic surfing and secondary contact. Disentangling the role of each in any particular system can be difficult, especially when species are evenly distributed across transition zones and dispersal barriers are not evident. The estuarine seaweed Fucus ceranoides provides a good example of highly differentiated populations along its most persistent distributional range at the present rear edge of the species distribution, in NW Iberia. Intrinsic dispersal restrictions are obvious in this species, but have not prevented F. ceranoides from vastly expanding its range northwards following the last glaciation, implying that additional factors are responsible for the lack of connectivity between neighbouring southern populations. In this study we analyze 22 consecutive populations of F. ceranoides along NW Iberia to investigate the processes generating and maintaining the observed high levels of regional genetic divergence. Results Variation at seven microsatellite loci and at mtDNA spacer sequences was concordant in revealing that Iberian F. ceranoides is composed of three divergent genetic clusters displaying nearly disjunct geographical distributions. Structure and AFC analyses detected two populations with an admixed nuclear background. Haplotypic diversity was high in the W sector and very low in the N sector. Within each genetic cluster, population structure was also pervasive, although shallower. Conclusions The deep divergence between sectors coupled with the lack of support for a role of oceanographic barriers in defining the location of breaks suggested 1) that the parapatric genetic sectors result from the regional reassembly of formerly vicariant sub-populations, and 2) that the genetic discontinuities at secondary contact zones (and elsewhere) are maintained despite

  11. Novel Morphologic and Genetic Analysis of Cancer Cells in a 3D Microenvironment Identifies STAT3 as a Regulator of Tumor Permeability Barrier Function.

    PubMed

    Park, Min Chul; Jeong, Hyobin; Son, Sung Hwa; Kim, YounHa; Han, Daeyoung; Goughnour, Peter C; Kang, Taehee; Kwon, Nam Hoon; Moon, Hyo Eun; Paek, Sun Ha; Hwang, Daehee; Seol, Ho Jun; Nam, Do-Hyun; Kim, Sunghoon

    2016-03-01

    Tumor permeability is a critical determinant of drug delivery and sensitivity, but systematic methods to identify factors that perform permeability barrier functions in the tumor microenvironment are not yet available. Multicellular tumor spheroids have become tractable in vitro models to study the impact of a three-dimensional (3D) environment on cellular behavior. In this study, we characterized the spheroid-forming potential of cancer cells and correlated the resulting spheroid morphologies with genetic information to identify conserved cellular processes associated with spheroid structure. Spheroids generated from 100 different cancer cell lines were classified into four distinct groups based on morphology. In particular, round and compact spheroids exhibited highly hypoxic inner cores and permeability barriers against anticancer drugs. Through systematic and correlative analysis, we reveal JAK-STAT signaling as one of the signature pathways activated in round spheroids. Accordingly, STAT3 inhibition in spheroids generated from the established cancer cells and primary glioblastoma patient-derived cells altered the rounded morphology and increased drug sensitivity. Furthermore, combined administration of the STAT3 inhibitor and 5-fluorouracil to a mouse xenograft model markedly reduced tumor growth compared with monotherapy. Collectively, our findings demonstrate the ability to integrate 3D culture and genetic profiling to determine the factors underlying the integrity of the permeability barrier in the tumor microenvironment, and may help to identify and exploit novel mechanisms of drug resistance. PMID:26676754

  12. Estimating Typhoon Rainfall over Sea from SSM/I Satellite Data Using an Improved Genetic Programming

    NASA Astrophysics Data System (ADS)

    Yeh, K.; Wei, H.; Chen, L.; Liu, G.

    2010-12-01

    Estimating Typhoon Rainfall over Sea from SSM/I Satellite Data Using an Improved Genetic Programming Keh-Chia Yeha, Hsiao-Ping Weia,d, Li Chenb, and Gin-Rong Liuc a Department of Civil Engineering, National Chiao Tung University, Hsinchu, Taiwan, 300, R.O.C. b Department of Civil Engineering and Engineering Informatics, Chung Hua University, Hsinchu, Taiwan, 300, R.O.C. c Center for Space and Remote Sensing Research, National Central University, Tao-Yuan, Taiwan, 320, R.O.C. d National Science and Technology Center for Disaster Reduction, Taipei County, Taiwan, 231, R.O.C. Abstract This paper proposes an improved multi-run genetic programming (GP) and applies it to predict the rainfall using meteorological satellite data. GP is a well-known evolutionary programming and data mining method, used to automatically discover the complex relationships among nonlinear systems. The main advantage of GP is to optimize appropriate types of function and their associated coefficients simultaneously. This study makes an improvement to enhance escape ability from local optimums during the optimization procedure. The GP continuously runs several times by replacing the terminal nodes at the next run with the best solution at the current run. The current novel model improves GP, obtaining a highly nonlinear mathematical equation to estimate the rainfall. In the case study, this improved GP described above combining with SSM/I satellite data is employed to establish a suitable method for estimating rainfall at sea surface during typhoon periods. These estimated rainfalls are then verified with the data from four rainfall stations located at Peng-Jia-Yu, Don-Gji-Dao, Lan-Yu, and Green Island, which are four small islands around Taiwan. From the results, the improved GP can generate sophisticated and accurate nonlinear mathematical equation through two-run learning procedures which outperforms the traditional multiple linear regression, empirical equations and back-propagated network

  13. Multi Population Genetic Algorithm to estimate snow properties from GPR data

    NASA Astrophysics Data System (ADS)

    Godio, A.

    2016-08-01

    Multi-population genetic algorithms (DGA or MGA) are based on the partition of the population into several semi-isolated subpopulations (demes). Each sub-population is associated to an independent GA and explores different promising regions of the search space. We evaluate the sensitivity of some parameters to solve a non-linear problem in georadar data analysis. Particularly, we adapt the DGAs to optimize the model parameters of a data set of variable-offset data, collected in variable offset modality with Ground Penetrating Radar, to estimate porosity, saturation and density of snowpack in a glacial environment. The data set comes from investigation on glaciers to estimate the thickness and density of the seasonal snow. The main strategies to select the best parameters of the optimization process are outlined. We analyze the sensitivity on the solution of the optimization problems of some parameters of DGA; we deal with the effects of population and sub-population, and mutation properties. We consider the reflection traveltimes in a layered medium including a relationship between the traveltimes, porosity and saturation of the snow. We solve the problem for the layer thickness and the porosity, saturation and structural exponent of the snow. Reliable results are obtained in the snow density estimating, while the evaluation of free water content into the snow still remains challenging.

  14. Estimates of phenotypic and genetic parameters for birth weight of Brown Swiss calves in Turkey using an animal model.

    PubMed

    Sahin, A; Ulutas, Z; Yilmaz Adkinson, A; Adkinson, R W

    2012-06-01

    A study was conducted to assess the influence of genetic and environmental factors on Brown Swiss calf birth weight, and to estimate variance components, genetic parameters, and breeding values. Data were collected on 1,761 Brown Swiss calves born from 1990 to 2005 in the Konuklar State Farm in Turkey. Mean birth weight for all calves was 39.3 ± 0.09 kg. Least squares mean birth weights for male and female Brown Swiss calves were 40.3 ± 0.02 and 39.0 ± 0.02 kg, respectively. Variance components, genetic parameters, and breeding values for birth weight in Brown Swiss calves were estimated by restricted error maximum likelihood (REML)-best linear unbiased prediction(BLUP) procedures using an MTDFREML (multiple trait derivative free restricted maximum likelihood) program employing an animal model. Direct heritability (h(d)(2)), maternal heritability (h(m)(2)), total heritability (h(T)(2)), r(am) and c(am) estimates were 0.12, 0.09, 0.23, -0.58, and -0.06, respectively. The estimated maternal permanent environmental variance expressed as a proportion of the phenotypic variance (c(2)) was 0.05. Breeding values were estimated for the trait and used to evaluate genetic trends across the time period investigated. The genetic trend linear regression was not different from zero. No genetic trend for birth weight was expected, since there had been no direct selection pressure on the trait. Absence of a trend confirms that there was no change due to selection pressure on correlated traits. Genetic and environmental parameter estimates were similar to literature values indicating that effective selection methods used in more developed improvement programs would be effective in Turkey as well. PMID:22203217

  15. Estimating genetic covariance functions assuming a parametric correlation structure for environmental effects

    PubMed Central

    Meyer, Karin

    2001-01-01

    A random regression model for the analysis of "repeated" records in animal breeding is described which combines a random regression approach for additive genetic and other random effects with the assumption of a parametric correlation structure for within animal covariances. Both stationary and non-stationary correlation models involving a small number of parameters are considered. Heterogeneity in within animal variances is modelled through polynomial variance functions. Estimation of parameters describing the dispersion structure of such model by restricted maximum likelihood via an "average information" algorithm is outlined. An application to mature weight records of beef cow is given, and results are contrasted to those from analyses fitting sets of random regression coefficients for permanent environmental effects. PMID:11742630

  16. Estimates of population genetic diversity in brown bullhead catfish by DNA fingerprinting

    SciTech Connect

    Roth, A.C.; Wessendarp, T.K.; Gordon, D.A.; Smith, M.K.; Lattier, D.L.; Hertzberg, V.; Leonard, A.

    1994-12-31

    Estimates of population genetic diversity may be a sensitive indicator of environmental impact, since limiting the effective breeding population by any means will result in loss of some variant genotypes, as has been demonstrated by allozyme analysis. DNA fingerprinting techniques are also coming into use for population analyses, and the authors chose to apply fingerprinting analysis three populations of brown bullhead catfish collected in Northern Ohio. DNA was isolated from the red blood cells of individual fish. Purified DNAs were digested with EcoR1 restriction enzyme; the digests were then sized on a 1% agarose gel, transferred to nylon membranes and probed with a radiolabeled M13 probe using the Westneat hybridization protocol (Southern blotting). This method effects fragments containing VNTR (variable number of tandem repeat) sequences complementary to the M13, which are highly variable among individual catfish. Hybridized bands were visualized by a Molecular Dynamics phosphorimager and recorded and analyzed with its proprietary Imagequant image analysis program, Excel and SAS. A total of 10 variable bands were identified and their presence or absence scored in each individual. These data were analyzed to determine between and within-population similarity indices as well as population heterozygosity and genetic diversity measures.

  17. Genetic differentiation among populations of Brachytrupes portentosus (Lichtenstein 1796) (Orthoptera: Gryllidae) in Thailand and the Lao PDR: the Mekong River as a biogeographic barrier.

    PubMed

    Tantrawatpan, C; Saijuntha, W; Pilab, W; Sakdakham, K; Pasorn, P; Thanonkeo, S; Thiha; Satrawaha, R; Petney, T

    2011-12-01

    The Mekong River is known to act as a boundary between a number of terrestrial and freshwater species, including various parasites and their intermediate hosts as well as endangered mammal species. Little information is available, however, on the genetic differentiation between terrestrial invertebrates to the east and the west of this wide river. The genetic diversity among eight natural populations of Brachytrupes portentosus (Lichtenstein, 1796) (Orthoptera: Gryllidae) collected from Thailand and the Lao People's Democratic Republic (PDR) were analyzed by multilocus enzyme electrophoresis. The allelic profiles of 20 enzymes encoding 23 loci were analyzed. An average of 41% fixed differences was detected between the populations from Thailand and Lao PDR, which are separated by the Mekong River. The percent fixed differences ranged between 4% and 26% within the populations from Thailand and between 4% and 22% within the populations from Lao PDR. A phenogram shows that the eight populations fell into two major clusters based on the Thai and Lao sampling sites. The genetic distance between the samples within Thailand and within Lao PDR was related to the distances between sampling areas. The genetic variability between populations of this cricket indicates that genetic relationships are influenced by a natural barrier as well as by the geographical distance between these allopatric populations. PMID:21554800

  18. Estimation of Genetic Associations between Production and Meat Quality Traits in Duroc Pigs

    PubMed Central

    Cabling, M. M.; Kang, H. S.; Lopez, B. M.; Jang, M.; Kim, H. S.; Nam, K. C.; Choi, J. G.; Seo, K. S.

    2015-01-01

    Data collected from 690 purebred Duroc pigs from 2009 to 2012 were used to estimate the heritability, and genetic and phenotypic correlations between production and meat quality traits. Variance components were obtained through the restricted maximum likelihood procedure using Wombat and SAS version 9.0. Animals were raised under the same management in five different breeding farms. The average daily gain, loin muscle area (LMA), backfat thickness (BF), and lean percent (LP) were measured as production traits. Meat quality traits included pH, cooking loss, lightness (L*), redness (a*), yellowness (b*), marbling score (MS), moisture content (MC), water holding capacity (WHC), and shear force. The results showed that the heritability estimates for meat quality traits varied largely from 0.19 to 0.79. Production traits were moderate to highly heritable from 0.41 to 0.73. Genotypically, the BF was positively correlated (p<0.05) with MC (0.786), WHC (0.904), and pH (0.328) but negatively correlated with shear force (−0.533). The results of genetic correlations indicated that selection for less BF could decrease pH, moisture content, and WHC and increase the shear force of meat. Additionally, a significant positive correlation was recorded between average daily gain and WHC, which indicates pork from faster-growing animals has higher WHC. Furthermore, selection for larger LMA and LP could increase MS and lightness color of meat. The meat quality and production traits could be improved simultaneously if desired. Hence, to avoid further deterioration of pork characteristics, appropriate selection of traits should be considered. PMID:26104512

  19. A hybrid neural networks-fuzzy logic-genetic algorithm for grade estimation

    PubMed Central

    Tahmasebi, Pejman; Hezarkhani, Ardeshir

    2012-01-01

    The grade estimation is a quite important and money/time-consuming stage in a mine project, which is considered as a challenge for the geologists and mining engineers due to the structural complexities in mineral ore deposits. To overcome this problem, several artificial intelligence techniques such as Artificial Neural Networks (ANN) and Fuzzy Logic (FL) have recently been employed with various architectures and properties. However, due to the constraints of both methods, they yield the desired results only under the specific circumstances. As an example, one major problem in FL is the difficulty of constructing the membership functions (MFs).Other problems such as architecture and local minima could also be located in ANN designing. Therefore, a new methodology is presented in this paper for grade estimation. This method which is based on ANN and FL is called “Coactive Neuro-Fuzzy Inference System” (CANFIS) which combines two approaches, ANN and FL. The combination of these two artificial intelligence approaches is achieved via the verbal and numerical power of intelligent systems. To improve the performance of this system, a Genetic Algorithm (GA) – as a well-known technique to solve the complex optimization problems – is also employed to optimize the network parameters including learning rate, momentum of the network and the number of MFs for each input. A comparison of these techniques (ANN, Adaptive Neuro-Fuzzy Inference System or ANFIS) with this new method (CANFIS–GA) is also carried out through a case study in Sungun copper deposit, located in East-Azerbaijan, Iran. The results show that CANFIS–GA could be a faster and more accurate alternative to the existing time-consuming methodologies for ore grade estimation and that is, therefore, suggested to be applied for grade estimation in similar problems. PMID:25540468

  20. A hybrid neural networks-fuzzy logic-genetic algorithm for grade estimation

    NASA Astrophysics Data System (ADS)

    Tahmasebi, Pejman; Hezarkhani, Ardeshir

    2012-05-01

    The grade estimation is a quite important and money/time-consuming stage in a mine project, which is considered as a challenge for the geologists and mining engineers due to the structural complexities in mineral ore deposits. To overcome this problem, several artificial intelligence techniques such as Artificial Neural Networks (ANN) and Fuzzy Logic (FL) have recently been employed with various architectures and properties. However, due to the constraints of both methods, they yield the desired results only under the specific circumstances. As an example, one major problem in FL is the difficulty of constructing the membership functions (MFs).Other problems such as architecture and local minima could also be located in ANN designing. Therefore, a new methodology is presented in this paper for grade estimation. This method which is based on ANN and FL is called "Coactive Neuro-Fuzzy Inference System" (CANFIS) which combines two approaches, ANN and FL. The combination of these two artificial intelligence approaches is achieved via the verbal and numerical power of intelligent systems. To improve the performance of this system, a Genetic Algorithm (GA) - as a well-known technique to solve the complex optimization problems - is also employed to optimize the network parameters including learning rate, momentum of the network and the number of MFs for each input. A comparison of these techniques (ANN, Adaptive Neuro-Fuzzy Inference System or ANFIS) with this new method (CANFIS-GA) is also carried out through a case study in Sungun copper deposit, located in East-Azerbaijan, Iran. The results show that CANFIS-GA could be a faster and more accurate alternative to the existing time-consuming methodologies for ore grade estimation and that is, therefore, suggested to be applied for grade estimation in similar problems.

  1. Estimation of genetic parameters for individual udder quarter milk content traits in Brown Swiss cattle.

    PubMed

    Kramer, M; Erbe, M; Bapst, B; Bieber, A; Simianer, H

    2013-09-01

    The aim of this study was to estimate genetic parameters and accuracies of breeding values for milk content traits of individual udder quarters in Brown Swiss cattle. Data of 1,799 phenotyped cows from 40 Swiss dairy herds were analyzed, taking the complete pedigree into account. Fat, protein, lactose, and urea contents, somatic cell score (SCS), and information about hyperkeratosis were available for each udder quarter. The milk of rear udder quarters was found to have significantly higher lactose content and significantly lower fat content than milk of the front udder quarters. The same trend found for fat content was observed for protein content, whereas no differences between the udder quarters were observed for urea content, SCS, or hyperkeratosis. Heritabilities for each udder quarter were in the following ranges: fat content 0.09±0.06 to 0.14±0.06, protein content 0.20±0.09 to 0.33±0.07, lactose content 0.04±0.03 to 0.16±0.07, urea content 0.13±0.07 to 0.22±0.08, SCS 0.18±0.06 to 0.32±0.07, and hyperkeratosis 0.12±0.04 to 0.26±0.05. In our study, hyperkeratosis, protein content, and SCS showed higher heritabilities in the front udder quarters, fat content had higher heritabilities in the rear udder quarters, and no systematic pattern in heritability was observed for lactose content or urea content. Additive genetic correlations between all udder quarters were >0.90 for protein and urea contents, whereas they were remarkably low (<0.60) for SCS. For fat and lactose contents, the genetic correlations between the 2 front or between the 2 rear quarters, respectively, were notably higher than correlations between 1 front and 1 rear quarter, suggesting that the front and the rear udders could be considered as partly genetically different organs. The variability within the udder as such was found to be of low heritability (<0.10) in general, but repeatability was moderate to high for some traits (lactose content: 0.33±0.05, protein content: 0.53±0

  2. Random regression test day models to estimate genetic parameters for milk yield and milk components in Philippine dairy buffaloes.

    PubMed

    Flores, E B; van der Werf, J

    2015-08-01

    Heritabilities and genetic correlations for milk production traits were estimated from first-parity test day records on 1022 Philippine dairy buffalo cows. Traits analysed included milk (MY), fat (FY) and protein (PY) yields, and fat (Fat%) and protein (Prot%) concentrations. Varying orders of Legendre polynomials (Leg(m)) as well as the Wilmink function (Wil) were used in random regression models. These various models were compared based on log likelihood, Akaike's information criterion, Bayesian information criterion and genetic variance estimates. Six residual variance classes were sufficient for MY, FY, PY and Fat%, while seven residual classes for Prot%. Multivariate analysis gave higher estimates of genetic variance and heritability compared with univariate analysis for all traits. Heritability estimates ranged from 0.25 to 0.44, 0.13 to 0.31 and 0.21 to 0.36 for MY, FY and PY, respectively. Wilmink's function was the better fitting function for additive genetic effects for all traits. It was also the preferred function for permanent environment effects for Fat% and Prot%, but for MY, FY and PY, the Legm was the appropriate function. Genetic correlations of MY with FY and PY were high and they were moderately negative with Fat% and Prot%. To prevent deterioration in Fat% and Prot% and improve milk quality, more weight should be applied to milk component traits. PMID:25727642

  3. Breed effects and genetic parameter estimates for calving difficulty and birth weight in a multibreed population.

    PubMed

    Ahlberg, C M; Kuehn, L A; Thallman, R M; Kachman, S D; Snelling, W M; Spangler, M L

    2016-05-01

    Birth weight (BWT) and calving difficulty (CD) were recorded on 4,579 first-parity females from the Germplasm Evaluation Program at the U.S. Meat Animal Research Center (USMARC). Both traits were analyzed using a bivariate animal model with direct and maternal effects. Calving difficulty was transformed from the USMARC scores to corresponding -scores from the standard normal distribution based on the incidence rate of the USMARC scores. Breed fraction covariates were included to estimate breed differences. Heritability estimates (SE) for BWT direct, CD direct, BWT maternal, and CD maternal were 0.34 (0.10), 0.29 (0.10), 0.15 (0.08), and 0.13 (0.08), respectively. Calving difficulty direct breed effects deviated from Angus ranged from -0.13 to 0.77 and maternal breed effects deviated from Angus ranged from -0.27 to 0.36. Hereford-, Angus-, Gelbvieh-, and Brangus-sired calves would be the least likely to require assistance at birth, whereas Chiangus-, Charolais-, and Limousin-sired calves would be the most likely to require assistance at birth. Maternal breed effects for CD were least for Simmental and Charolais and greatest for Red Angus and Chiangus. Results showed that the diverse biological types of cattle have different effects on both BWT and CD. Furthermore, results provide a mechanism whereby beef cattle producers can compare EBV for CD direct and maternal arising from disjoined and breed-specific genetic evaluations. PMID:27285683

  4. Diversity and genetic parameter estimates for yield and its components in Jatropha curcas L.

    PubMed

    Freitas, R G; Dias, L A S; Cardoso, P M R; Evaristo, A B; Silva, M F; Araújo, N M

    2016-01-01

    Jatropha curcas L. is one of the most promising oilseeds for biodiesel and biokerosene production, but few basic studies or breeding programs have been conducted for the species. We estimated genetic parameters and diversity based on 10 yield traits in 77 half-sib progenies of J. curcas after 52 months in the field, and evaluated correlations between them and the oil content of the seeds. The mean grain yield per plant was 377.9 g (ranging from 169.8 to 772.1 g) and the mean oil content was 36.2% (ranging from 30 to 39.6%). Moderate estimates of heritability at the mean progeny level were obtained for the length of the fruit (84.7%), length (69.1%) and width (68.2%) of the seed, and grain yield per plant (62.2%). Oil content was only positively and significantly correlated with 100-seed weight. Our study revealed a range of possible crosses to be investigated in J. curcas. Progeny production should be evaluated over several crop seasons for the accurate selection of the best progenies. PMID:27050981

  5. Short-Term Genetic Changes: Evaluating Effective Population Size Estimates in a Comprehensively Described Brown Trout (Salmo trutta) Population

    PubMed Central

    Serbezov, Dimitar; Jorde, Per Erik; Bernatchez, Louis; Olsen, Esben Moland; Vøllestad, L. Asbjørn

    2012-01-01

    The effective population size (Ne) is notoriously difficult to accurately estimate in wild populations as it is influenced by a number of parameters that are difficult to delineate in natural systems. The different methods that are used to estimate Ne are affected variously by different processes at the population level, such as the life-history characteristics of the organism, gene flow, and population substructure, as well as by the frequency patterns of genetic markers used and the sampling design. Here, we compare Ne estimates obtained by different genetic methods and from demographic data and elucidate how the estimates are affected by various factors in an exhaustively sampled and comprehensively described natural brown trout (Salmo trutta) system. In general, the methods yielded rather congruent estimates, and we ascribe that to the adequate genotyping and exhaustive sampling. Effects of violating the assumptions of the different methods were nevertheless apparent. In accordance with theoretical studies, skewed allele frequencies would underestimate temporal allele frequency changes and thereby upwardly bias Ne if not accounted for. Overlapping generations and iteroparity would also upwardly bias Ne when applied to temporal samples taken over short time spans. Gene flow from a genetically not very dissimilar source population decreases temporal allele frequency changes and thereby acts to increase estimates of Ne. Our study reiterates the importance of adequate sampling, quantification of life-history parameters and gene flow, and incorporating these data into the Ne estimation. PMID:22466040

  6. Estimates of genetic parameters for visual scores and daily weight gain in Brangus animals.

    PubMed

    Queiroz, S A; Oliveira, J A; Costa, G Z; Fries, L A

    2011-05-01

    (Co)variance components were estimated for visual scores of conformation (CY), early finishing (PY) and muscling (MY) at 550 days of age (yearling), average daily gain from weaning to yearling (GWY), conformation (CW), early finishing (PW) and muscling (MW) scores at weaning, and average daily gain from birth to weaning (GBW) in animals forming the Brazilian Brangus breed born between 1986 and 2002 from the livestock files of GenSys Consultants Associados S/C Ltda. The data set contained 53 683; 45 136; 52 937; 56 471; 24 531; 21 166; 24 006 and 25 419 records for CW, PW, MW, GBW, CY, PY, MY and GWY, respectively. Data were analyzed by the restricted maximum likelihood method using single- and two-trait animal models. Direct heritability estimates obtained by single-trait analysis were 0.12, 0.14, 0.13 and 0.14 for CY, PY and MY scores and GWY, respectively. A positive association was observed between the same visual scores at weaning and yearling, with correlations ranging from 0.64 to 0.94. Estimated correlations between GBW and weaning and yearling scores ranged from 0.60 to 0.77. The genetic correlation between GBW and GWY was low (0.10), whereas correlations of 0.55, 0.37 and 0.47 were observed between GWY and CY, PY and MY, respectively. Moreover, GWY showed a weak correlation with CW (0.10), PW (-0.08) and MW (-0.03) scores. These results indicate that selection of the traits that was studied would result in a small response. In addition, selection based on average daily gain may have an indirect effect on visual scores as the correlations between GWY and visual scores were generally strong. PMID:22440022

  7. Considerations when combining data from multiple nutrition experiments to estimate genetic parameters for feed efficiency.

    PubMed

    Hardie, L C; Armentano, L E; Shaver, R D; VandeHaar, M J; Spurlock, D M; Yao, C; Bertics, S J; Contreras-Govea, F E; Weigel, K A

    2015-04-01

    Prior to genomic selection on a trait, a reference population needs to be established to link marker genotypes with phenotypes. For costly and difficult-to-measure traits, international collaboration and sharing of data between disciplines may be necessary. Our aim was to characterize the combining of data from nutrition studies carried out under similar climate and management conditions to estimate genetic parameters for feed efficiency. Furthermore, we postulated that data from the experimental cohorts within these studies can be used to estimate the net energy of lactation (NE(L)) densities of diets, which can provide estimates of energy intakes for use in the calculation of the feed efficiency metric, residual feed intake (RFI), and potentially reduce the effect of variation in energy density of diets. Individual feed intakes and corresponding production and body measurements were obtained from 13 Midwestern nutrition experiments. Two measures of RFI were considered, RFI(Mcal) and RFI(kg), which involved the regression of NE(L )intake (Mcal/d) or dry matter intake (DMI; kg/d) on 3 expenditures: milk energy, energy gained or lost in body weight change, and energy for maintenance. In total, 677 records from 600 lactating cows between 50 and 275 d in milk were used. Cows were divided into 46 cohorts based on dietary or nondietary treatments as dictated by the nutrition experiments. The realized NE(L) densities of the diets (Mcal/kg of DMI) were estimated for each cohort by totaling the average daily energy used in the 3 expenditures for cohort members and dividing by the cohort's total average daily DMI. The NE(L) intake for each cow was then calculated by multiplying her DMI by her cohort's realized energy density. Mean energy density was 1.58 Mcal/kg. Heritability estimates for RFI(kg), and RFI(Mcal) in a single-trait animal model did not differ at 0.04 for both measures. Information about realized energy density could be useful in standardizing intake data from

  8. Genetic diversity estimates point to immediate efforts for conserving the endangered Tibetan sheep of India

    PubMed Central

    Sharma, Rekha; Kumar, Brijesh; Arora, Reena; Ahlawat, Sonika; Mishra, A.K.; Tantia, M.S.

    2016-01-01

    Tibetan is a valuable Himalayan sheep breed classified as endangered. Knowledge of the level and distribution of genetic diversity in Tibetan sheep is important for designing conservation strategies for their sustainable survival and to preserve their evolutionary potential. Thus, for the first time, genetic variability in the Tibetan population was accessed with twenty five inter-simple sequence repeat markers. All the microsatellites were polymorphic and a total of 148 alleles were detected across these loci. The observed number of alleles across all the loci was more than the effective number of alleles and ranged from 3 (BM6506) to 11 (BM6526) with 5.920 ± 0.387 mean number of alleles per locus. The average observed heterozygosity was less than the expected heterozygosity. The observed and expected heterozygosity values ranged from 0.150 (BM1314) to 0.9 (OarCP20) with an overall mean of 0.473 ± 0.044 and from 0.329 (BM8125) to 0.885 (BM6526) with an overall mean 0.672 ± 0.030, respectively. The lower heterozygosity pointed towards diminished genetic diversity in the population. Thirteen microsatellite loci exhibited significant (P < 0.05) departures from the Hardy–Weinberg proportions in the population. The estimate of heterozygote deficiency varied from − 0.443 (OarCP20) to 0.668 (OarFCB128) with a mean positive value of 0.302 ± 0.057. A normal ‘L’ shaped distribution of mode-shift test and non-significant heterozygote excess on the basis of different models suggested absence of recent bottleneck in the existing Tibetan population. In view of the declining population of Tibetan sheep (less than 250) in the breeding tract, need of the hour is immediate scientific management of the population so as to increase the population hand in hand with retaining the founder alleles to the maximum possible extent. PMID:27014586

  9. Genetic diversity estimates point to immediate efforts for conserving the endangered Tibetan sheep of India.

    PubMed

    Sharma, Rekha; Kumar, Brijesh; Arora, Reena; Ahlawat, Sonika; Mishra, A K; Tantia, M S

    2016-06-01

    Tibetan is a valuable Himalayan sheep breed classified as endangered. Knowledge of the level and distribution of genetic diversity in Tibetan sheep is important for designing conservation strategies for their sustainable survival and to preserve their evolutionary potential. Thus, for the first time, genetic variability in the Tibetan population was accessed with twenty five inter-simple sequence repeat markers. All the microsatellites were polymorphic and a total of 148 alleles were detected across these loci. The observed number of alleles across all the loci was more than the effective number of alleles and ranged from 3 (BM6506) to 11 (BM6526) with 5.920 ± 0.387 mean number of alleles per locus. The average observed heterozygosity was less than the expected heterozygosity. The observed and expected heterozygosity values ranged from 0.150 (BM1314) to 0.9 (OarCP20) with an overall mean of 0.473 ± 0.044 and from 0.329 (BM8125) to 0.885 (BM6526) with an overall mean 0.672 ± 0.030, respectively. The lower heterozygosity pointed towards diminished genetic diversity in the population. Thirteen microsatellite loci exhibited significant (P < 0.05) departures from the Hardy-Weinberg proportions in the population. The estimate of heterozygote deficiency varied from - 0.443 (OarCP20) to 0.668 (OarFCB128) with a mean positive value of 0.302 ± 0.057. A normal 'L' shaped distribution of mode-shift test and non-significant heterozygote excess on the basis of different models suggested absence of recent bottleneck in the existing Tibetan population. In view of the declining population of Tibetan sheep (less than 250) in the breeding tract, need of the hour is immediate scientific management of the population so as to increase the population hand in hand with retaining the founder alleles to the maximum possible extent. PMID:27014586

  10. Multiple-trait random regression models for the estimation of genetic parameters for milk, fat, and protein yield in buffaloes.

    PubMed

    Borquis, Rusbel Raul Aspilcueta; Neto, Francisco Ribeiro de Araujo; Baldi, Fernando; Hurtado-Lugo, Naudin; de Camargo, Gregório M F; Muñoz-Berrocal, Milthon; Tonhati, Humberto

    2013-09-01

    In this study, genetic parameters for test-day milk, fat, and protein yield were estimated for the first lactation. The data analyzed consisted of 1,433 first lactations of Murrah buffaloes, daughters of 113 sires from 12 herds in the state of São Paulo, Brazil, with calvings from 1985 to 2007. Ten-month classes of lactation days were considered for the test-day yields. The (co)variance components for the 3 traits were estimated using the regression analyses by Bayesian inference applying an animal model by Gibbs sampling. The contemporary groups were defined as herd-year-month of the test day. In the model, the random effects were additive genetic, permanent environment, and residual. The fixed effects were contemporary group and number of milkings (1 or 2), the linear and quadratic effects of the covariable age of the buffalo at calving, as well as the mean lactation curve of the population, which was modeled by orthogonal Legendre polynomials of fourth order. The random effects for the traits studied were modeled by Legendre polynomials of third and fourth order for additive genetic and permanent environment, respectively, the residual variances were modeled considering 4 residual classes. The heritability estimates for the traits were moderate (from 0.21-0.38), with higher estimates in the intermediate lactation phase. The genetic correlation estimates within and among the traits varied from 0.05 to 0.99. The results indicate that the selection for any trait test day will result in an indirect genetic gain for milk, fat, and protein yield in all periods of the lactation curve. The accuracy associated with estimated breeding values obtained using multi-trait random regression was slightly higher (around 8%) compared with single-trait random regression. This difference may be because to the greater amount of information available per animal. PMID:23831097

  11. Pharmacological Characterization of the Spectrum of Antiviral Activity and Genetic Barrier to Drug Resistance of M2-S31N Channel Blockers.

    PubMed

    Ma, Chunlong; Zhang, Jiantao; Wang, Jun

    2016-09-01

    Adamantanes (amantadine and rimantadine) are one of the two classes of Food and Drug Administration-approved antiviral drugs used for the prevention and treatment of influenza A virus infections. They inhibit viral replication by blocking the wild-type (WT) M2 proton channel, thus preventing viral uncoating. However, their use was discontinued due to widespread drug resistance. Among a handful of drug-resistant mutants, M2-S31N is the predominant mutation and persists in more than 95% of currently circulating influenza A strains. We recently designed two classes of M2-S31N inhibitors, S31N-specific inhibitors and S31N/WT dual inhibitors, which are represented by N-[(5-cyclopropyl-1,2-oxazol-3-yl)methyl]adamantan-1-amine (WJ379) and N-[(5-bromothiophen-2-yl)methyl]adamantan-1-amine (BC035), respectively. However, their antiviral activities against currently circulating influenza A viruses and their genetic barrier to drug resistance are unknown. In this report, we evaluated the therapeutic potential of these two classes of M2-S31N inhibitors (WJ379 and BC035) by profiling their antiviral efficacy against multidrug-resistant influenza A viruses, in vitro drug resistance barrier, and synergistic effect with oseltamivir. We found that M2-S31N inhibitors were active against several influenza A viruses that are resistant to one or both classes of Food and Drug Administration-approved anti-influenza drugs. In addition, M2-S31N inhibitors display a higher in vitro genetic barrier to drug resistance than amantadine. The antiviral effect of WJ379 was also synergistic with oseltamivir carboxylate. Overall, these results reaffirm that M2-S31N inhibitors are promising antiviral drug candidates that warrant further development. PMID:27385729

  12. Estimates of genetic parameters for Holstein cows for test-day yield traits with a random regression cubic spline model

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic parameters were estimated with REML for individual test-day milk, fat, and protein yields and SCS with a random regression cubic spline model. Test-day records of Holstein cows that calved from 1994 through early 1999 were obtained from Dairy Records Management Systems in Raleigh, North Car...

  13. ESTIMATES OF GENETIC PARAMETERS FOR FIRST LACTATION TEST-DAY YIELDS OF HOLSTEIN COWS WITH A CUBIC SPLINE MODEL

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective was to estimate genetic parameters for individual test-day milk, fat, and protein yields with a cubic spline model. A total of 196,687 test-day records in the first 305-d of 38,172 first lactation Holstein cows that calved between 1994 and early 1999 were obtained from Dairy Records Ma...

  14. Genetic and phenotypic parameter estimates for feed intake and other traits in growing beef cattle, and opportunities for selection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Growth, feed intake, and temperament indicator data, collected over 5 yr on a total of 1,141 to 1,183 mixed-breed steers, were used to estimate genetic and phenotypic parameters. All steers had a portion of either Hereford or Angus or both plus varying percentages also of Simmental, Charolais, Limo...

  15. Genome-wide association study of swine farrowing traits. Part I: Genetic and genomic parameter estimates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The primary objective of this study was to determine genetic and genomic parameters among swine farrowing traits. Genetic parameters were obtained by using MTDFREML and genomic parameters were obtained using GenSel. Genetic and residual variances obtained from MTDFREML were used as priors for the ...

  16. Random regression models to estimate genetic parameters for test-day milk yield in Brazilian Murrah buffaloes.

    PubMed

    Sesana, R C; Bignardi, A B; Borquis, R R A; El Faro, L; Baldi, F; Albuquerque, L G; Tonhati, H

    2010-10-01

    The objective of this work was to estimate covariance functions for additive genetic and permanent environmental effects and, subsequently, to obtain genetic parameters for buffalo's test-day milk production using random regression models on Legendre polynomials (LPs). A total of 17 935 test-day milk yield (TDMY) from 1433 first lactations of Murrah buffaloes, calving from 1985 to 2005 and belonging to 12 herds located in São Paulo state, Brazil, were analysed. Contemporary groups (CGs) were defined by herd, year and month of milk test. Residual variances were modelled through variance functions, from second to fourth order and also by a step function with 1, 4, 6, 22 and 42 classes. The model of analyses included the fixed effect of CGs, number of milking, age of cow at calving as a covariable (linear and quadratic) and the mean trend of the population. As random effects were included the additive genetic and permanent environmental effects. The additive genetic and permanent environmental random effects were modelled by LP of days in milk from quadratic to seventh degree polynomial functions. The model with additive genetic and animal permanent environmental effects adjusted by quintic and sixth order LP, respectively, and residual variance modelled through a step function with six classes was the most adequate model to describe the covariance structure of the data. Heritability estimates decreased from 0.44 (first week) to 0.18 (fourth week). Unexpected negative genetic correlation estimates were obtained between TDMY records at first weeks with records from middle to the end of lactation, being the values varied from -0.07 (second with eighth week) to -0.34 (1st with 42nd week). TDMY heritability estimates were moderate in the course of the lactation, suggesting that this trait could be applied as selection criteria in milking buffaloes. PMID:20831561

  17. Estimation of heritabilities, genetic correlations, and breeding values of four traits that collectively define hip dysplasia in dogs.

    PubMed

    Zhang, Zhiwu; Zhu, Lan; Sandler, Jody; Friedenberg, Steven S; Egelhoff, Jill; Williams, Alma J; Dykes, Nathan L; Hornbuckle, William; Krotscheck, Ursula; Moise, N Sydney; Lust, George; Todhunter, Rory J

    2009-04-01

    OBJECTIVE-To estimate heritabilities and genetic correlations among 4 traits of hip joints (distraction index [DI], dorsolateral subluxation [DLS] score, Norberg angle [NA], and extended-hip joint radiograph [EHR] score) and to derive the breeding values for these traits in dogs. ANIMALS-2,716 dogs of 17 breeds (1,551 dogs in which at least 1 hip joint trait was measured). PROCEDURES-The NA was measured, and an EHR score was assigned. Hip joint radiographs were obtained from some dogs to allow calculation of the DI and DLS score. Heritabilities, genetic correlations, and breeding values among the DI, DLS score, NA, and EHR score were calculated by use of a set of multiple-trait, derivative-free, restricted maximum likelihood computer programs. RESULTS-Among 2,716 dogs, 1,411 (52%) had an estimated inbreeding coefficient of 0%; the remaining dogs had a mean inbreeding coefficient of 6.21%. Estimated heritabilities were 0.61, 0.54, 0.73, and 0.76 for the DI, DLS score, NA, and EHR score, respectively. The EHR score was highly genetically correlated with the NA (r = -0.89) and was moderately genetically correlated with the DI (r = 0.69) and DLS score (r = -0.70). The NA was moderately genetically correlated with the DI (r = -0.69) and DLS score (r = 0.58). Genetic correlation between the DI and DLS score was high (r = -0.91). CONCLUSIONS AND CLINICAL RELEVANCE-Establishment of a selection index that makes use of breeding values jointly estimated from the DI, DLS score, NA, and EHR score should enhance breeding programs to reduce the incidence of hip dysplasia in dogs. PMID:19335104

  18. Genetic Characterization and Linkage Disequilibrium Estimation of a Global Maize Collection Using SNP Markers

    PubMed Central

    Yan, Jianbing; Shah, Trushar; Warburton, Marilyn L.; Buckler, Edward S.; McMullen, Michael D.; Crouch, Jonathan

    2009-01-01

    A newly developed maize Illumina GoldenGate Assay with 1536 SNPs from 582 loci was used to genotype a highly diverse global maize collection of 632 inbred lines from temperate, tropical, and subtropical public breeding programs. A total of 1229 informative SNPs and 1749 haplotypes within 327 loci was used to estimate the genetic diversity, population structure, and familial relatedness. Population structure identified tropical and temperate subgroups, and complex familial relationships were identified within the global collection. Linkage disequilibrium (LD) was measured overall and within chromosomes, allelic frequency groups, subgroups related by geographic origin, and subgroups of different sample sizes. The LD decay distance differed among chromosomes and ranged between 1 to 10 kb. The LD distance increased with the increase of minor allelic frequency (MAF), and with smaller sample sizes, encouraging caution when using too few lines in a study. The LD decay distance was much higher in temperate than in tropical and subtropical lines, because tropical and subtropical lines are more diverse and contain more rare alleles than temperate lines. A core set of inbreds was defined based on haplotypes, and 60 lines capture 90% of the haplotype diversity of the entire panel. The defined core sets and the entire collection can be used widely for different research targets. PMID:20041112

  19. The parameter optimization in the inverse distance method by genetic algorithm for estimating precipitation.

    PubMed

    Chang, Chia-Ling; Lo, Shang-Lien; Yu, Shaw-L

    2006-06-01

    The inverse distance method, one of the commonly used methods for analyzing spatial variation of rainfall, is flexible if the order of distances in the method is adjustable. By applying the genetic algorithm (GA), the optimal order of distances can be found to minimize the difference between estimated and measured precipitation data. A case study of the Feitsui reservoir watershed in Taiwan is described in the present paper. The results show that the variability of the order of distances is small when the topography of rainfall stations is uniform. Moreover, when rainfall characteristic is uniform, the horizontal distance between rainfall stations and interpolated locations is the major factor influencing the order of distances. The results also verify that the variable-order inverse distance method is more suitable than the arithmetic average method and the Thiessen Polygons method in describing the spatial variation of rainfall. The efficiency and reliability of hydrologic modeling and hence of general water resource management can be significantly improved by more accurate rainfall data interpolated by the variable-order inverse distance method. PMID:16917704

  20. Short communication: Multi-trait estimation of genetic parameters for milk protein composition in the Danish Holstein.

    PubMed

    Gebreyesus, G; Lund, M S; Janss, L; Poulsen, N A; Larsen, L B; Bovenhuis, H; Buitenhuis, A J

    2016-04-01

    Genetic parameters were estimated for the major milk proteins using bivariate and multi-trait models based on genomic relationships between animals. The analyses included, apart from total protein percentage, αS1-casein (CN), αS2-CN, β-CN, κ-CN, α-lactalbumin, and β-lactoglobulin, as well as the posttranslational sub-forms of glycosylated κ-CN and αS1-CN-8P (phosphorylated). Standard errors of the estimates were used to compare the models. In total, 650 Danish Holstein cows across 4 parities and days in milk ranging from 9 to 481d were selected from 21 herds. The multi-trait model generally resulted in lower standard errors of heritability estimates, suggesting that genetic parameters can be estimated with high accuracy using multi-trait analyses with genomic relationships for scarcely recorded traits. The heritability estimates from the multi-trait model ranged from low (0.05 for β-CN) to high (0.78 for κ-CN). Genetic correlations between the milk proteins and the total milk protein percentage were generally low, suggesting the possibility to alter protein composition through selective breeding with little effect on total milk protein percentage. PMID:26805988

  1. Mechanisms and genetic control of interspecific crossing barriers in lycopersicon. Progress report, First year, August 1, 1992

    SciTech Connect

    Mutschler, M.A.; McCormick, S.

    1992-12-31

    The goal of this program is to use Lycopersica esculentum and L. pennellii as a model system to study the interspecific reproductive barriers unilateral incongruity (UI), hybrid breakdown and interspecific aberrant ratio syndrome (IARS). Specifically we seek to determine the functional basis of UI including the timing of the failure of incongruous crosses, the developmental step(s) interrupted by UI, the tissue and genomes involved in UI.

  2. Estimating the risks of cancer mortality and genetic defects resulting from exposures to low levels of ionizing radiation

    SciTech Connect

    Buhl, T.E.; Hansen, W.R.

    1984-05-01

    Estimators for calculating the risk of cancer and genetic disorders induced by exposure to ionizing radiation have been recommended by the US National Academy of Sciences Committee on the Biological Effects of Ionizing Radiations, the UN Scientific Committee on the Effects of Atomic Radiation, and the International Committee on Radiological Protection. These groups have also considered the risks of somatic effects other than cancer. The US National Council on Radiation Protection and Measurements has discussed risk estimate procedures for radiation-induced health effects. The recommendations of these national and international advisory committees are summarized and compared in this report. Based on this review, two procedures for risk estimation are presented for use in radiological assessments performed by the US Department of Energy under the National Environmental Policy Act of 1969 (NEPA). In the first procedure, age- and sex-averaged risk estimators calculated with US average demographic statistics would be used with estimates of radiation dose to calculate the projected risk of cancer and genetic disorders that would result from the operation being reviewed under NEPA. If more site-specific risk estimators are needed, and the demographic information is available, a second procedure is described that would involve direct calculation of the risk estimators using recommended risk-rate factors. The computer program REPCAL has been written to perform this calculation and is described in this report. 25 references, 16 tables.

  3. A method to estimate the contribution of regional genetic associations to complex traits from summary association statistics

    PubMed Central

    Pare, Guillaume; Mao, Shihong; Deng, Wei Q.

    2016-01-01

    Despite considerable efforts, known genetic associations only explain a small fraction of predicted heritability. Regional associations combine information from multiple contiguous genetic variants and can improve variance explained at established association loci. However, regional associations are not easily amenable to estimation using summary association statistics because of sensitivity to linkage disequilibrium (LD). We now propose a novel method, LD Adjusted Regional Genetic Variance (LARGV), to estimate phenotypic variance explained by regional associations using summary statistics while accounting for LD. Our method is asymptotically equivalent to a multiple linear regression model when no interaction or haplotype effects are present. It has several applications, such as ranking of genetic regions according to variance explained or comparison of variance explained by two or more regions. Using height and BMI data from the Health Retirement Study (N = 7,776), we show that most genetic variance lies in a small proportion of the genome and that previously identified linkage peaks have higher than expected regional variance. PMID:27273519

  4. Comparison of estimates of hip dysplasia genetic parameters in Estrela Mountain Dog using linear and threshold models.

    PubMed

    Silvestre, A M; Ginja, M M D; Ferreira, A J A; Colaço, J

    2007-08-01

    Genetic parameters, breeding values, and genetic trends of hip dysplasia in Estrela Mountain Dogs were estimated using a linear model (LM) and a threshold model (TM). A database with 313 animals was used. Right and left hip joints were individually scored, according to the Fédération Cynologic Internationale grading rules of the canine hip dysplasia system, as normal (1), borderline (2), slight (3), moderate (4), and severe (5 and 6). The estimate of repeatability was lower in LM (0.86) than in TM (0.90). The same tendency was verified with the heritability because its estimate in LM was 0.38 and in TM was 0.43. However, these results did not establish any statistical differences between the models. The genetic trend of canine hip dysplasia for LM and TM showed a similarity in shape, but considerable individual differences were found in the EBV ranking lists. Therefore, the selection of breeding animals would not be the same with the 2 methodologies. To select the best method for genetic evaluation of hip dysplasia, further studies using more data and other dog breeds are required. PMID:17468417

  5. Genome-Enabled Estimates of Additive and Nonadditive Genetic Variances and Prediction of Apple Phenotypes Across Environments

    PubMed Central

    Kumar, Satish; Molloy, Claire; Muñoz, Patricio; Daetwyler, Hans; Chagné, David; Volz, Richard

    2015-01-01

    The nonadditive genetic effects may have an important contribution to total genetic variation of phenotypes, so estimates of both the additive and nonadditive effects are desirable for breeding and selection purposes. Our main objectives were to: estimate additive, dominance and epistatic variances of apple (Malus × domestica Borkh.) phenotypes using relationship matrices constructed from genome-wide dense single nucleotide polymorphism (SNP) markers; and compare the accuracy of genomic predictions using genomic best linear unbiased prediction models with or without including nonadditive genetic effects. A set of 247 clonally replicated individuals was assessed for six fruit quality traits at two sites, and also genotyped using an Illumina 8K SNP array. Across several fruit quality traits, the additive, dominance, and epistatic effects contributed about 30%, 16%, and 19%, respectively, to the total phenotypic variance. Models ignoring nonadditive components yielded upwardly biased estimates of additive variance (heritability) for all traits in this study. The accuracy of genomic predicted genetic values (GEGV) varied from about 0.15 to 0.35 for various traits, and these were almost identical for models with or without including nonadditive effects. However, models including nonadditive genetic effects further reduced the bias of GEGV. Between-site genotypic correlations were high (>0.85) for all traits, and genotype-site interaction accounted for <10% of the phenotypic variability. The accuracy of prediction, when the validation set was present only at one site, was generally similar for both sites, and varied from about 0.50 to 0.85. The prediction accuracies were strongly influenced by trait heritability, and genetic relatedness between the training and validation families. PMID:26497141

  6. Integrating Genetic Studies of Nicotine Addiction into Public Health Practice: Stakeholder Views on Challenges, Barriers and Opportunities

    PubMed Central

    Dingel, M.J.; Hicks, A.D.; Robinson, M.E.; Koenig, B.A.

    2011-01-01

    Objective: Will emerging genetic research strengthen tobacco control programs? In this empirical study, we interview stakeholders in tobacco control to illuminate debates about the role of genomics in public health. Methods: The authors performed open-ended interviews with 86 stakeholders from 5 areas of tobacco control: basic scientists, clinicians, tobacco prevention specialists, health payers, and pharmaceutical industry employees. Interviews were qualitatively analyzed using standard techniques. Results: The central tension is between the hope that an expanding genomic knowledge base will improve prevention and smoking cessation therapies and the fear that genetic research might siphon resources away from traditional and proven public health programs. While showing strong support for traditional public health approaches to tobacco control, stakeholders recognize weaknesses, specifically the difficulty of countering the powerful voice of the tobacco industry when mounting public campaigns and the problem of individuals who are resistant to treatment and continue smoking. Conclusions: In order for genetic research to be effectively translated into efforts to minimize the harm of smoking-related disease, the views of key stakeholders must be voiced and disagreements reconciled. Effective translation requires honest evaluation of both the strengths and limitations of genetic approaches. PMID:21757875

  7. QTL mapping reveals the genetic architecture of loci affecting pre- and post-zygotic isolating barriers in Louisiana Iris

    PubMed Central

    2012-01-01

    Background Hybridization among Louisiana Irises has been well established and the genetic architecture of reproductive isolation is known to affect the potential for and the directionality of introgression between taxa. Here we use co-dominant markers to identify regions where QTL are located both within and between backcross maps to compare the genetic architecture of reproductive isolation and fitness traits across treatments and years. Results QTL mapping was used to elucidate the genetic architecture of reproductive isolation between Iris fulva and Iris brevicaulis. Homologous co-dominant EST-SSR markers scored in two backcross populations between I. fulva and I. brevicaulis were used to generate genetic linkage maps. These were used as the framework for mapping QTL associated with variation in 11 phenotypic traits likely responsible for reproductive isolation and fitness. QTL were dispersed throughout the genome, with the exception of one region of a single linkage group (LG) where QTL for flowering time, sterility, and fruit production clustered. In most cases, homologous QTL were not identified in both backcross populations, however, homologous QTL for flowering time, number of growth points per rhizome, number of nodes per inflorescence, and number of flowers per node were identified on several linkage groups. Conclusions Two different traits affecting reproductive isolation, flowering time and sterility, exhibit different genetic architectures, with numerous QTL across the Iris genome controlling flowering time and fewer, less distributed QTL affecting sterility. QTL for traits affecting fitness are largely distributed across the genome with occasional overlap, especially on LG 4, where several QTL increasing fitness and decreasing sterility cluster. Given the distribution and effect direction of QTL affecting reproductive isolation and fitness, we have predicted genomic regions where introgression may be more likely to occur (those regions associated with

  8. Estimating Genetic and Maternal Effects Determining Variation in Immune Function of a Mixed-Mating Snail

    PubMed Central

    Seppälä, Otto; Langeloh, Laura

    2016-01-01

    Evolution of host defenses such as immune function requires heritable genetic variation in them. However, also non-genetic maternal effects can contribute to phenotypic variation, thus being an alternative target for natural selection. We investigated the role of individuals’ genetic background and maternal effects in determining immune defense traits (phenoloxidase and antibacterial activity of hemolymph), as well as in survival and growth, in the simultaneously hermaphroditic snail Lymnaea stagnalis. We utilized the mixed mating system of this species by producing full-sib families in which each parental snail had produced offspring as both a dam and as a sire, and tested whether genetic background (family) and non-genetic maternal effects (dam nested within family) explain trait variation. Immune defense traits and growth were affected solely by individuals’ genetic background. Survival of snails did not show family-level variation. Additionally, some snails were produced through self-fertilization. They showed reduced growth and survival suggesting recessive load or overdominance. Immune defense traits did not respond to inbreeding. Our results suggest that the variation in snail immune function and growth was due to genetic differences. Since immune traits did not respond to inbreeding, this variation is most likely due to additive or epistatic genetic variance. PMID:27551822

  9. Genetic diversity in three natural populations of Pitcairnia flammea (l.) John (Bromeliaceae) estimated by ISSR markers.

    PubMed

    Souza-Sobreira, F B; Souza, G B; Rosado, C C G; Miranda, F D; Soares, T C B; Gontijo, A B P L

    2015-01-01

    Bromeliads are greatly represented in the Atlantic Forest, although many species are threatened with extinction owing to habitat fragmentation and intense extraction for ornamental purposes. Therefore, it is necessary to conduct studies generating knowledge about genetic diversity and the distribution of this diversity among and within natural populations to establish conservation strategies. These studies can be performed with the use of molecular markers. Molecular markers are advantageous for studies of natural populations, for conservation programs, and to aid in properly classifying plant species. This study aimed to evaluate the genetic diversity among and within natural populations of Pitcairnia flammea, occurring in three fragments of the Atlantic Forest in the southern State of Espírito Santo through the use of inter-simple sequence repeat (ISSR) markers. DNA samples from 55 individuals were amplified with 18 ISSR primers, generating 180 bands, 159 of which were polymorphic. The Shannon genetic diversity index ranged from 0.348 to 0.465, with an average of 0.412. The Bayesian approach for the molecular data indicated the existence of two genetic groups. Analysis of molecular variance indicated the existence of 90.3% diversity within the population and 9.74% among populations. The amount of genetic differentiation of populations was moderate (0.0974), indicating that gene flow rates may be enough to counteract the effects of genetic drift. Greater genetic variability found in population B indicates that this area is an important source of genetic variability. PMID:26634557

  10. Estimating Genetic and Maternal Effects Determining Variation in Immune Function of a Mixed-Mating Snail.

    PubMed

    Seppälä, Otto; Langeloh, Laura

    2016-01-01

    Evolution of host defenses such as immune function requires heritable genetic variation in them. However, also non-genetic maternal effects can contribute to phenotypic variation, thus being an alternative target for natural selection. We investigated the role of individuals' genetic background and maternal effects in determining immune defense traits (phenoloxidase and antibacterial activity of hemolymph), as well as in survival and growth, in the simultaneously hermaphroditic snail Lymnaea stagnalis. We utilized the mixed mating system of this species by producing full-sib families in which each parental snail had produced offspring as both a dam and as a sire, and tested whether genetic background (family) and non-genetic maternal effects (dam nested within family) explain trait variation. Immune defense traits and growth were affected solely by individuals' genetic background. Survival of snails did not show family-level variation. Additionally, some snails were produced through self-fertilization. They showed reduced growth and survival suggesting recessive load or overdominance. Immune defense traits did not respond to inbreeding. Our results suggest that the variation in snail immune function and growth was due to genetic differences. Since immune traits did not respond to inbreeding, this variation is most likely due to additive or epistatic genetic variance. PMID:27551822

  11. Impact of marker ascertainment bias on genomic selection accuracy and estimates of genetic diversity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genome-wide molecular markers are readily being applied to evaluate genetic diversity in germplasm collections and for making genomic selections in breeding programs. To accurately predict phenotypes and assay genetic diversity, molecular markers should assay a representative sample of the polymorp...

  12. Estimation and interpretation of genetic effects with epistasis using the NOIA model.

    PubMed

    Alvarez-Castro, José M; Carlborg, Orjan; Rönnegård, Lars

    2012-01-01

    We introduce this communication with a brief outline of the historical landmarks in genetic modeling, especially concerning epistasis. Then, we present methods for the use of genetic modeling in QTL analyses. In particular, we summarize the essential expressions of the natural and orthogonal interactions (NOIA) model of genetic effects. Our motivation for reviewing that theory here is twofold. First, this review presents a digest of the expressions for the application of the NOIA model, which are often mixed with intermediate and additional formulae in the original articles. Second, we make the required theory handy for the reader to relate the genetic concepts to the particular mathematical expressions underlying them. We illustrate those relations by providing graphical interpretations and a diagram summarizing the key features for applying genetic modeling with epistasis in comprehensive QTL analyses. Finally, we briefly review some examples of the application of NOIA to real data and the way it improves the interpretability of the results. PMID:22565838

  13. Do island plant populations really have lower genetic variation than mainland populations? Effects of selection and distribution range on genetic diversity estimates.

    PubMed

    García-Verdugo, C; Sajeva, M; La Mantia, T; Harrouni, C; Msanda, F; Caujapé-Castells, J

    2015-02-01

    Ecological and evolutionary studies largely assume that island populations display low levels of neutral genetic variation. However, this notion has only been formally tested in a few cases involving plant taxa, and the confounding effect of selection on genetic diversity (GD) estimates based on putatively neutral markers has typically been overlooked. Here, we generated nuclear microsatellite and plastid DNA sequence data in Periploca laevigata, a plant taxon with an island-mainland distribution area, to (i) investigate whether selection affects GD estimates of populations across contrasting habitats; and (ii) test the long-standing idea that island populations have lower GD than their mainland counterparts. Plastid data showed that colonization of the Canary Islands promoted strong lineage divergence within P. laevigata, which was accompanied by selective sweeps at several nuclear microsatellite loci. Inclusion of loci affected by strong divergent selection produced a significant downward bias in the GD estimates of the mainland lineage, but such underestimates were substantial (>14%) only when more than one loci under selection were included in the computations. When loci affected by selection were removed, we did not find evidence that insular Periploca populations have less GD than their mainland counterparts. The analysis of data obtained from a comprehensive literature survey reinforced this result, as overall comparisons of GD estimates between island and mainland populations were not significant across plant taxa (N = 66), with the only exception of island endemics with narrow distributions. This study suggests that identification and removal of markers potentially affected by selection should be routinely implemented in estimates of GD, particularly if different lineages are compared. Furthermore, it provides compelling evidence that the expectation of low GD cannot be generalized to island plant populations. PMID:25580539

  14. A population genetic assessment of coral recovery on highly disturbed reefs of the Keppel Island archipelago in the southern Great Barrier Reef

    PubMed Central

    Lukoschek, Vimoksalehi; Berkelmans, Ray; Peplow, Lesa M.; Jones, Alison M.

    2015-01-01

    Coral reefs surrounding the islands lying close to the coast are unique to the Great Barrier Reef (GBR) in that they are frequently exposed to disturbance events including floods caused by cyclonic rainfall, strong winds and occasional periods of prolonged above-average temperatures during summer. In one such group of islands in the southern GBR, the Keppel Island archipelago, climate-driven disturbances frequently result in major coral mortality. Whilst these island reefs have clearly survived such dramatic disturbances in the past, the consequences of extreme mortality events may include the loss of genetic diversity, and hence adaptive potential, and a reduction in fitness due to inbreeding, especially if new recruitment from external sources is limited. Here we examined the level of isolation of the Keppel Island group as well as patterns of gene flow within the Keppel Islands using 10 microsatellite markers in nine populations of the coral, Acropora millepora. Bayesian cluster analysis and assignment tests indicated gene flow is restricted, but not absent, between the outer and inner Keppel Island groups, and that extensive gene flow exists within each of these island groups. Comparison of the Keppel Island data with results from a previous GBR-wide study that included a single Keppel Island population, confirmed that A. millepora in the Keppel Islands is genetically distinct from populations elsewhere on the GBR, with exception of the nearby inshore High Peak Reef just north of the Keppel Islands. We compared patterns of genetic diversity in the Keppel Island populations with those from other GBR populations and found them to be slightly, but significantly lower, consistent with the archipelago being geographically isolated, but there was no evidence for recent bottlenecks or deviation from mutation-drift equilibrium. A high incidence of private alleles in the Keppel Islands, particularly in the outer islands, supports their relative isolation and contributes

  15. A population genetic assessment of coral recovery on highly disturbed reefs of the Keppel Island archipelago in the southern Great Barrier Reef.

    PubMed

    van Oppen, Madeleine J H; Lukoschek, Vimoksalehi; Berkelmans, Ray; Peplow, Lesa M; Jones, Alison M

    2015-01-01

    Coral reefs surrounding the islands lying close to the coast are unique to the Great Barrier Reef (GBR) in that they are frequently exposed to disturbance events including floods caused by cyclonic rainfall, strong winds and occasional periods of prolonged above-average temperatures during summer. In one such group of islands in the southern GBR, the Keppel Island archipelago, climate-driven disturbances frequently result in major coral mortality. Whilst these island reefs have clearly survived such dramatic disturbances in the past, the consequences of extreme mortality events may include the loss of genetic diversity, and hence adaptive potential, and a reduction in fitness due to inbreeding, especially if new recruitment from external sources is limited. Here we examined the level of isolation of the Keppel Island group as well as patterns of gene flow within the Keppel Islands using 10 microsatellite markers in nine populations of the coral, Acropora millepora. Bayesian cluster analysis and assignment tests indicated gene flow is restricted, but not absent, between the outer and inner Keppel Island groups, and that extensive gene flow exists within each of these island groups. Comparison of the Keppel Island data with results from a previous GBR-wide study that included a single Keppel Island population, confirmed that A. millepora in the Keppel Islands is genetically distinct from populations elsewhere on the GBR, with exception of the nearby inshore High Peak Reef just north of the Keppel Islands. We compared patterns of genetic diversity in the Keppel Island populations with those from other GBR populations and found them to be slightly, but significantly lower, consistent with the archipelago being geographically isolated, but there was no evidence for recent bottlenecks or deviation from mutation-drift equilibrium. A high incidence of private alleles in the Keppel Islands, particularly in the outer islands, supports their relative isolation and contributes

  16. Genetic diversity analysis in Tunisian perennial ryegrass germplasm as estimated by RAPD, ISSR, and morpho-agronomical markers.

    PubMed

    Ghariani, S; Elazreg, H; Chtourou-Ghorbel, N; Chakroun, M; Trifi-Farah, N

    2015-01-01

    Tunisia is rich in diverse forage and pasture species including perennial ryegrass. In order to enhance forage production and improve agronomic performance of this local germplasm, a molecular analysis was undertaken. Random amplified polymorphic DNA (RAPD), inter simple sequence repeats (ISSR) and morpho-agronomical traits markers were used for genetic diversity estimation of ryegrass germplasm after screening 20 spontaneous accessions, including a local and an introduced cultivars. Same mean polymorphism information content values were obtained (0.37) for RAPD and ISSR suggesting that both marker systems were equally effective in determining polymorphisms. The average pairwise genetic distance values were 0.57 (morpho-agronomical traits), 0.68 (RAPD), and 0.51 (ISSR) markers data sets. A higher Shannon diversity index was obtained with ISSR marker (0.57) than for RAPD (0.54) and morpho-agronomical traits (0.36). The Mantel test based on genetic distances of a combination of molecular markers and morpho-agronomical data exhibited a significant correlation between RAPD and ISSR data, suggesting that the use of a combination of molecular techniques was a highly efficient method of estimating genetic variability levels among Tunisian ryegrass germplasm. In summary, results showed that combining molecular and morpho-agronomical markers is an efficient way in assessing the genetic variability among Tunisian ryegrass genotypes. In addition, the combined analysis provided an exhaustive coverage for the analyzed diversity and helped us to identify suitable accessions showed by Beja and Jendouba localities, which present large similarities with cultivated forms and can be exploited for designing breeding programmes, conservation of germplasm and management of ryegrass genetic resources. PMID:26782500

  17. Estimates of genetic parameters for stayability and their associations with traits of economic interest in Gir dairy cows.

    PubMed

    Silva, R M O; Boligon, A A; Fernandes, A R; Vercesi Filho, A E; El Faro, L; Tonhati, H; Albuquerque, L G; Fraga, A B

    2016-01-01

    The objective of the present study was to estimate genetic parameters for stayability at 60 months of age (STAY60) and its association with first lactation cumulative milk yield (P305), age at first calving (AFC), and first calving interval (FCI), in order to adopt these traits as selection criteria for longevity in Gir dairy cattle. Records for 2770 cows born between 1982 and 2008 from six herds in the Brazilian states of Minas Gerais, São Paulo, and Paraíba were analyzed. The (co)variance components were estimated by a Bayesian approach using bivariate animal models. The heritability estimates were 0.37 ± 0.09, 0.23 ± 0.04, 0.26 ± 0.06, and 0.07 ± 0.03 for STAY60, P305, AFC, and FCI, respectively. The genetic correlations of STAY60 with P305, AFC, and FCI were moderate to high, with values of 0.61 (0.17), -0.44 (0.23), and 0.88 (0.13), respectively. STAY60, P305, and AFC exhibited additive genetic variability, and these traits should be considered in selection indices. The indirect selection for longevity through the correlated responses of early-expression traits, such as milk production at first lactation, could be used to improve the ability of animals to remain in the herd. PMID:26909978

  18. Estimates for Genetic Variance Components in Reciprocal Recurrent Selection in Populations Derived from Maize Single-Cross Hybrids

    PubMed Central

    dos Reis, Matheus Costa; Pádua, José Maria Villela; Abreu, Guilherme Barbosa; Guedes, Fernando Lisboa; Balbi, Rodrigo Vieira; de Souza, João Cândido

    2014-01-01

    This study was carried out to obtain the estimates of genetic variance and covariance components related to intra- and interpopulation in the original populations (C0) and in the third cycle (C3) of reciprocal recurrent selection (RRS) which allows breeders to define the best breeding strategy. For that purpose, the half-sib progenies of intrapopulation (P11 and P22) and interpopulation (P12 and P21) from populations 1 and 2 derived from single-cross hybrids in the 0 and 3 cycles of the reciprocal recurrent selection program were used. The intra- and interpopulation progenies were evaluated in a 10 × 10 triple lattice design in two separate locations. The data for unhusked ear weight (ear weight without husk) and plant height were collected. All genetic variance and covariance components were estimated from the expected mean squares. The breakdown of additive variance into intrapopulation and interpopulation additive deviations (στ2) and the covariance between these and their intrapopulation additive effects (CovAτ) found predominance of the dominance effect for unhusked ear weight. Plant height for these components shows that the intrapopulation additive effect explains most of the variation. Estimates for intrapopulation and interpopulation additive genetic variances confirm that populations derived from single-cross hybrids have potential for recurrent selection programs. PMID:25009831

  19. Simulation analysis to test the influence of model adequacy and data structure on the estimation of genetic parameters for traits with direct and maternal effects

    PubMed Central

    Clément, Virginie; Bibé, Bernard; Verrier, Étienne; Elsen, Jean-Michel; Manfredi, Eduardo; Bouix, Jacques; Hanocq, Éric

    2001-01-01

    Simulations were used to study the influence of model adequacy and data structure on the estimation of genetic parameters for traits governed by direct and maternal effects. To test model adequacy, several data sets were simulated according to different underlying genetic assumptions and analysed by comparing the correct and incorrect models. Results showed that omission of one of the random effects leads to an incorrect decomposition of the other components. If maternal genetic effects exist but are neglected, direct heritability is overestimated, and sometimes more than double. The bias depends on the value of the genetic correlation between direct and maternal effects. To study the influence of data structure on the estimation of genetic parameters, several populations were simulated, with different degrees of known paternity and different levels of genetic connectedness between flocks. Results showed that the lack of connectedness affects estimates when flocks have different genetic means because no distinction can be made between genetic and environmental differences between flocks. In this case, direct and maternal heritabilities are under-estimated, whereas maternal environmental effects are overestimated. The insufficiency of pedigree leads to biased estimates of genetic parameters. PMID:11563370

  20. NeEstimator v2: re-implementation of software for the estimation of contemporary effective population size (Ne ) from genetic data.

    PubMed

    Do, C; Waples, R S; Peel, D; Macbeth, G M; Tillett, B J; Ovenden, J R

    2014-01-01

    NeEstimator v2 is a completely revised and updated implementation of software that produces estimates of contemporary effective population size, using several different methods and a single input file. NeEstimator v2 includes three single-sample estimators (updated versions of the linkage disequilibrium and heterozygote-excess methods, and a new method based on molecular coancestry), as well as the two-sample (moment-based temporal) method. New features include the following: (i) an improved method for accounting for missing data; (ii) options for screening out rare alleles; (iii) confidence intervals for all methods; (iv) the ability to analyse data sets with large numbers of genetic markers (10 000 or more); (v) options for batch processing large numbers of different data sets, which will facilitate cross-method comparisons using simulated data; and (vi) correction for temporal estimates when individuals sampled are not removed from the population (Plan I sampling). The user is given considerable control over input data and composition, and format of output files. The freely available software has a new JAVA interface and runs under MacOS, Linux and Windows. PMID:23992227

  1. Multiple-trait estimates of genetic parameters for metabolic disease traits, fertility disorders, and their predictors in Canadian Holsteins.

    PubMed

    Jamrozik, J; Koeck, A; Kistemaker, G J; Miglior, F

    2016-03-01

    Producer-recorded health data for metabolic disease traits and fertility disorders on 35,575 Canadian Holstein cows were jointly analyzed with selected indicator traits. Metabolic diseases included clinical ketosis (KET) and displaced abomasum (DA); fertility disorders were metritis (MET) and retained placenta (RP); and disease indicators were fat-to-protein ratio, milk β-hydroxybutyrate, and body condition score (BCS) in the first lactation. Traits in first and later (up to fifth) lactations were treated as correlated in the multiple-trait (13 traits in total) animal linear model. Bayesian methods with Gibbs sampling were implemented for the analysis. Estimates of heritability for disease incidence were low, up to 0.06 for DA in first lactation. Among disease traits, the environmental herd-year variance constituted 4% of the total variance for KET and less for other traits. First- and later-lactation disease traits were genetically correlated (from 0.66 to 0.72) across all traits, indicating different genetic backgrounds for first and later lactations. Genetic correlations between KET and DA were relatively strong and positive (up to 0.79) in both first- and later-lactation cows. Genetic correlations between fertility disorders were slightly lower. Metritis was strongly genetically correlated with both metabolic disease traits in the first lactation only. All other genetic correlations between metabolic and fertility diseases were statistically nonsignificant. First-lactation KET and MET were strongly positively correlated with later-lactation performance for these traits due to the environmental herd-year effect. Indicator traits were moderately genetically correlated (from 0.30 to 0.63 in absolute values) with both metabolic disease traits in the first lactation. Smaller and mostly nonsignificant genetic correlations were among indicators and metabolic diseases in later lactations. The only significant genetic correlations between indicators and fertility

  2. Estimating blood-brain barrier opening in a rat model of hemorrhagic transformation with Patlak plots of Gd-DTPA contrast-enhanced MRI.

    PubMed

    Fenstermacher, J D; Knight, R A; Ewing, J R; Nagaraja, T; Nagesh, V; Yee, J S; Arniego, P A

    2003-01-01

    Patlak plot processing of Gd-shifted T1 relaxation-time images from a rat model of hemorrhagic transformation yielded estimates and maps of the blood-to-brain influx rate constant of Gd-DTPA (K1). The Patlak plots also produced a heretofore unrecognized parameter, the distribution space of the intravascular-Gd-shifted protons (Vp), an index of blood-to-tissue transfer of water. The K1 values for Gd-DTPA were very high for the regions of blood-brain barrier (BBB) opening and were similar to those of 14C-sucrose concurrently obtained by quantitative autoradiographic (QAR) analysis. In these same ROI's, Vp was five-fold greater than normal, which suggests that the permeability of the BBB to water was also increased. The 14C-sucrose space of distribution in the ischemic ROI's was around 8%, thus indicating a sizable interstitial space. The spatial resolving power of Gd-DTPA-deltaT1 imaging was rather good, although no match for 14C-sucrose-QAR. This study shows that quantitative deltaT1-MRI estimates of regional blood-brain transfer constants of Gd-DTPA and water distribution are possible when Patlak plots are employed to process the data. This approach may be useful for tracking the time-course of BBB barrier function in both animals and humans. PMID:14753399

  3. Genetic deviation in geographically close populations of the dengue vector Aedes aegypti (Diptera: Culicidae): influence of environmental barriers in South India.

    PubMed

    Vadivalagan, Chithravel; Karthika, Pushparaj; Murugan, Kadarkarai; Panneerselvam, Chellasamy; Paulpandi, Manickam; Madhiyazhagan, Pari; Wei, Hui; Aziz, Al Thabiani; Alsalhi, Mohamad Saleh; Devanesan, Sandhanasamy; Nicoletti, Marcello; Paramasivan, Rajaiah; Dinesh, Devakumar; Benelli, Giovanni

    2016-03-01

    Mosquitoes are vectors of devastating pathogens and parasites, causing millions of deaths every year. Dengue is a mosquito-borne viral infection found in tropical and subtropical regions around the world. Recently, dengue transmission has strongly increased in urban and semiurban areas, becoming a major international public health concern. Aedes aegypti (Diptera: Culicidae) is a primary vector of dengue. Shedding light on genetic deviation in A. aegypti populations is of crucial importance to fully understand their molecular ecology and evolution. In this research, haplotype and genetic analyses were conducted using individuals of A. aegypti from 31 localities in the north, southeast, northeast and central regions of Tamil Nadu (South India). The mitochondrial DNA region of cytochrome c oxidase 1 (CO1) gene was used as marker for the analyses. Thirty-one haplotypes sequences were submitted to GenBank and authenticated. The complete haplotype set included 64 haplotypes from various geographical regions clustered into three groups (lineages) separated by three fixed mutational steps, suggesting that the South Indian Ae. aegypti populations were pooled and are linked with West Africa, Columbian and Southeast Asian lineages. The genetic and haplotype diversity was low, indicating reduced gene flow among close populations of the vector, due to geographical barriers such as water bodies. Lastly, the negative values for neutrality tests indicated a bottle-neck effect and supported for low frequency of polymorphism among the haplotypes. Overall, our results add basic knowledge to molecular ecology of the dengue vector A. aegypti, providing the first evidence for multiple introductions of Ae. aegypti populations from Columbia and West Africa in South India. PMID:26627691

  4. Genetics

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  5. Genetics

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  6. Contrasting demographic and genetic estimates of dispersal in the endangered Coahuilan box turtle: a contemporary approach to conservation.

    PubMed

    Howeth, Jennifer G; McGaugh, Suzanne E; Hendrickson, Dean A

    2008-10-01

    The evolutionary viability of an endangered species depends upon gene flow among subpopulations and the degree of habitat patch connectivity. Contrasting population connectivity over ecological and evolutionary timescales may provide novel insight into what maintains genetic diversity within threatened species. We employed this integrative approach to evaluating dispersal in the critically endangered Coahuilan box turtle (Terrapene coahuila) that inhabits isolated wetlands in the desert-spring ecosystem of Cuatro Ciénegas, Mexico. Recent wetland habitat loss has altered the spatial distribution and connectivity of habitat patches; and we therefore predicted that T. coahuila would exhibit limited movement relative to estimates of historic gene flow. To evaluate contemporary dispersal patterns, we employed mark-recapture techniques at both local (wetland complex) and regional (intercomplex) spatial scales. Gene flow estimates were obtained by surveying genetic variation at nine microsatellite loci in seven subpopulations located across the species' geographical range. The mark-recapture results at the local spatial scale reveal frequent movement among wetlands that was unaffected by interwetland distance. At the regional spatial scale, dispersal events were relatively less frequent between wetland complexes. The complementary analysis of population genetic substructure indicates strong historic gene flow (global F(ST) = 0.01). However, a relationship of genetic isolation by distance across the geographical range suggests that dispersal limitation exists at the regional scale. Our approach of contrasting direct and indirect estimates of dispersal at multiple spatial scales in T. coahuila conveys a sustainable evolutionary trajectory of the species pending preservation of threatened wetland habitats and a range-wide network of corridors. PMID:19378401

  7. Estimating heritabilities and genetic correlations: comparing the 'animal model' with parent-offspring regression using data from a natural population.

    PubMed

    Akesson, Mikael; Bensch, Staffan; Hasselquist, Dennis; Tarka, Maja; Hansson, Bengt

    2008-01-01

    Quantitative genetic parameters are nowadays more frequently estimated with restricted maximum likelihood using the 'animal model' than with traditional methods such as parent-offspring regressions. These methods have however rarely been evaluated using equivalent data sets. We compare heritabilities and genetic correlations from animal model and parent-offspring analyses, respectively, using data on eight morphological traits in the great reed warbler (Acrocephalus arundinaceus). Animal models were run using either mean trait values or individual repeated measurements to be able to separate between effects of including more extended pedigree information and effects of replicated sampling from the same individuals. We show that the inclusion of more pedigree information by the use of mean traits animal models had limited effect on the standard error and magnitude of heritabilities. In contrast, the use of repeated measures animal model generally had a positive effect on the sampling accuracy and resulted in lower heritabilities; the latter due to lower additive variance and higher phenotypic variance. For most trait combinations, both animal model methods gave genetic correlations that were lower than the parent-offspring estimates, whereas the standard errors were lower only for the mean traits animal model. We conclude that differences in heritabilities between the animal model and parent-offspring regressions were mostly due to the inclusion of individual replicates to the animal model rather than the inclusion of more extended pedigree information. Genetic correlations were, on the other hand, primarily affected by the inclusion of more pedigree information. This study is to our knowledge the most comprehensive empirical evaluation of the performance of the animal model in relation to parent-offspring regressions in a wild population. Our conclusions should be valuable for reconciliation of data obtained in earlier studies as well as for future meta

  8. Limitations to estimating bacterial cross-species transmission using genetic and genomic markers: inferences from simulation modeling

    PubMed Central

    Benavides, Julio A; Cross, Paul C; Luikart, Gordon; Creel, Scott

    2014-01-01

    Cross-species transmission (CST) of bacterial pathogens has major implications for human health, livestock, and wildlife management because it determines whether control actions in one species may have subsequent effects on other potential host species. The study of bacterial transmission has benefitted from methods measuring two types of genetic variation: variable number of tandem repeats (VNTRs) and single nucleotide polymorphisms (SNPs). However, it is unclear whether these data can distinguish between different epidemiological scenarios. We used a simulation model with two host species and known transmission rates (within and between species) to evaluate the utility of these markers for inferring CST. We found that CST estimates are biased for a wide range of parameters when based on VNTRs and a most parsimonious reconstructed phylogeny. However, estimations of CST rates lower than 5% can be achieved with relatively low bias using as low as 250 SNPs. CST estimates are sensitive to several parameters, including the number of mutations accumulated since introduction, stochasticity, the genetic difference of strains introduced, and the sampling effort. Our results suggest that, even with whole-genome sequences, unbiased estimates of CST will be difficult when sampling is limited, mutation rates are low, or for pathogens that were recently introduced. PMID:25469159

  9. Estimation of Genetic Parameters for Real-time Ultrasound Measurements for Hanwoo Cows at Different Ages and Pregnancy Status

    PubMed Central

    Lee, J. H.; Lee, Y. M.; Oh, S.-H.; Son, H. J.; Jeong, D. J.; Whitley, Niki; Kim, J. J.

    2014-01-01

    The purpose of this study was to estimate genetic parameters of ultrasound measurements for longissimus dorsi muscle area (LMA), backfat thickness (BFT), and marbling score (MS) in Hanwoo cows (N = 3,062) at the ages between 18 and 42 months. Data were collected from 100 Hanwoo breeding farms in Gyeongbuk province, Korea, in 2007 and 2008. The cows were classified into four different age groups, i.e. 18 to 22 months (the first pregnancy period), 23 to 27 (the first parturition), 28 to 32 (the second pregnancy), and 33 to 42 (the second parturition), respectively. For each age group, a multi-trait animal model was used to estimate variance components and heritabilities of the three traits. The averages of LMA, BFT, and MS measurements across the cows of all age groups were 50.1 cm2, 4.62 mm, and 3.04, respectively and heritability estimates were 0.09, 0.10, and 0.08 for the respective traits. However, when the data were analyzed in different age groups, heritability estimates of LMA and BFT were 0.24 and 0.47, respectively, for the cows of 18 to 22 months of age, and 0.21 for MS in the 28 to 32 months old cows. When the cows of all age groups were used, the estimates of genetic (phenotypic) correlations were 0.43 (0.35), −0.06 (0.34) and 0.21 (0.32) between LMA and BFT, LMA and MS, and BFT and MS, respectively. However, in the cow age group between 28 and 32 (18 and 22) months, the estimates of genetic (phenotypic) correlations were 0.05 (0.29), −0.15 (0.24) and 0.38 (0.24), for the respective pairs of traits. These results suggest that genetic, environmental, and phenotypic variations differ depending on cow age, such that care must be taken when ultrasound measurements are applied to selection of cows for meat quality. PMID:25049938

  10. Technical Note: Calculation of standard errors of estimates of genetic parameters with the multiple-trait derivative-free restricted maximal likelihood programs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The MTDFREML (Boldman et al., 1995) set of programs was written to handle partially missing data in an expedient manner. When estimating (co)variance components and genetic parameters for multiple trait models, the programs have not been able to estimate standard errors of those estimates for multi...

  11. Genetic parameters for test-day yield of milk, fat and protein in buffaloes estimated by random regression models.

    PubMed

    Aspilcueta-Borquis, Rúsbel R; Araujo Neto, Francisco R; Baldi, Fernando; Santos, Daniel J A; Albuquerque, Lucia G; Tonhati, Humberto

    2012-08-01

    The test-day yields of milk, fat and protein were analysed from 1433 first lactations of buffaloes of the Murrah breed, daughters of 113 sires from 12 herds in the state of São Paulo, Brazil, born between 1985 and 2007. For the test-day yields, 10 monthly classes of lactation days were considered. The contemporary groups were defined as the herd-year-month of the test day. Random additive genetic, permanent environmental and residual effects were included in the model. The fixed effects considered were the contemporary group, number of milkings (1 or 2 milkings), linear and quadratic effects of the covariable cow age at calving and the mean lactation curve of the population (modelled by third-order Legendre orthogonal polynomials). The random additive genetic and permanent environmental effects were estimated by means of regression on third- to sixth-order Legendre orthogonal polynomials. The residual variances were modelled with a homogenous structure and various heterogeneous classes. According to the likelihood-ratio test, the best model for milk and fat production was that with four residual variance classes, while a third-order Legendre polynomial was best for the additive genetic effect for milk and fat yield, a fourth-order polynomial was best for the permanent environmental effect for milk production and a fifth-order polynomial was best for fat production. For protein yield, the best model was that with three residual variance classes and third- and fourth-order Legendre polynomials were best for the additive genetic and permanent environmental effects, respectively. The heritability estimates for the characteristics analysed were moderate, varying from 0·16±0·05 to 0·29±0·05 for milk yield, 0·20±0·05 to 0·30±0·08 for fat yield and 0·18±0·06 to 0·27±0·08 for protein yield. The estimates of the genetic correlations between the tests varied from 0·18±0·120 to 0·99±0·002; from 0·44±0·080 to 0·99±0·004; and from 0·41±0·080 to

  12. [Estimating genetic distance and phylogenetic tree of HPA-1-3, 5, and 15 in different populations].

    PubMed

    Feng, Ming-Liang; Huang, Hui; Shen, Tong; Zhang, Xi; Yin, Biao; Yang, Jian-Hao; Liu, Da-Zhuang

    2008-07-01

    According to the human platelet alloantigens (HPA) polymorphisms in five systems, the distributions of HPA-1 -3, 5, and 15 systems in 1 000 Chinese donors were carried out by using a polymerase chain reaction with sequence-specific primers (PCR-SSP) method. The genetic distance and phylogenetic tree between Chinese Hans and other populations were estimated by using DISPAN and PHYLIP software. As presented by the phylogenetic tree, Asian had a convergence with European first, and grouped together with African. Beninese which came from Africa was on the top of dendrogram. Indian was located between Asian and European. Brazilian was converged with other Europe populations. Oceanian Polynexiya had been shown specifically to cluster with Asia populations. These results proved the "out of Africa theory" from one side, and it also confirmed that early migration of Asian is from south to southeast, and east Asia., thus it is probable that Europeans are migrated from south to north, and west Europe. As genetic distance was estimated effectively by HPA systems, HPA systems could serve as the genetic marker in human migration and evolution research. PMID:18779125

  13. A Model Framework to Estimate Impact and Cost of Genetics-Based Sterile Insect Methods for Dengue Vector Control

    PubMed Central

    Alphey, Nina; Alphey, Luke; Bonsall, Michael B.

    2011-01-01

    Vector-borne diseases impose enormous health and economic burdens and additional methods to control vector populations are clearly needed. The Sterile Insect Technique (SIT) has been successful against agricultural pests, but is not in large-scale use for suppressing or eliminating mosquito populations. Genetic RIDL technology (Release of Insects carrying a Dominant Lethal) is a proposed modification that involves releasing insects that are homozygous for a repressible dominant lethal genetic construct rather than being sterilized by irradiation, and could potentially overcome some technical difficulties with the conventional SIT technology. Using the arboviral disease dengue as an example, we combine vector population dynamics and epidemiological models to explore the effect of a program of RIDL releases on disease transmission. We use these to derive a preliminary estimate of the potential cost-effectiveness of vector control by applying estimates of the costs of SIT. We predict that this genetic control strategy could eliminate dengue rapidly from a human community, and at lower expense (approximately US$ 2∼30 per case averted) than the direct and indirect costs of disease (mean US$ 86–190 per case of dengue). The theoretical framework has wider potential use; by appropriately adapting or replacing each component of the framework (entomological, epidemiological, vector control bio-economics and health economics), it could be applied to other vector-borne diseases or vector control strategies and extended to include other health interventions. PMID:21998654

  14. Testing the effect of transient Plio-Pleistocene barriers in monsoonal Australo-Papua: did mangrove habitats maintain genetic connectivity in the Black Butcherbird?

    PubMed

    Kearns, Anna M; Joseph, Leo; Omland, Kevin E; Cook, Lyn G

    2011-12-01

    Changes in climate and sea level are hypothesized to have promoted the diversification of biota in monsoonal Australia and New Guinea by causing repeated range disjunctions and restricting gene flow between isolated populations. Using a multilocus (one mtDNA locus, five nuclear introns) phylogeographic approach, we test whether populations of the mangrove and rainforest restricted Black Butcherbird (Cracticus quoyi) have diverged across several geographic barriers defined a priori for this region. Phylogeographic structure and estimates of divergence times revealed Plio-Pleistocene divergences and long-term restricted gene flow of populations on either side of four major geographic barriers between and within Australia and New Guinea. Overall, our data are consistent with the hypothesis that mesic-adapted species did not disperse across the open dry woodlands and grasslands that dominated the transient palaeo-landbridges during the Plio-Pleistocene despite the presence of mangrove forests that might have acted as dispersal corridors for mesic-adapted species. Our study offers one of the first multilocus perspectives on the impact of changes in climate and sea level on the population history of widespread species with disjunct ranges in Australia and New Guinea. PMID:22060632

  15. Random regression models for the estimation of genetic and environmental covariance functions for growth traits in Santa Ines sheep.

    PubMed

    Sarmento, J L R; Torres, R A; Sousa, W H; Lôbo, R N B; Albuquerque, L G; Lopes, P S; Santos, N P S; Bignard, A B

    2016-01-01

    Polynomial functions of different orders were used to model random effects associated with weight of Santa Ines sheep from birth to 196 days. Fixed effects included in the models were contemporary groups, age of ewe at lambing, and fourth-order Legendre polynomials for age to represent the average growth curve. In the random part, functions of different orders were included to model variances associated with direct additive and maternal genetic effects and with permanent environmental effects of the animal and mother. Residual variance was fitted by a sixth-order ordinary polynomial for age. The higher the order of the functions, the better the model fit the data. According to the Akaike information criterion and likelihood ratio test, a continuous function of order, five, five, seven, and three for direct additive genetic, maternal genetic, animal permanent environmental, and maternal permanent environmental effects (k = 5573), respectively, was sufficient to model changes in (co)variances with age. However, a more parsimonious model of order three, three, five, and three (k = 3353) was suggested based on Schwarz's Bayesian information criterion for the same effects. Since it was a more flexible model, model k = 5573 provided inconsistent genetic parameter estimates when compared to the biologically expected result. Predicted breeding values obtained with models k = 3353 and k = 5573 differed, especially at young ages. Model k = 3353 adequately fit changes in variances and covariances with time, and may be used to describe changes in variances with age in the Santa Ines sheep studied. PMID:27323203

  16. Differing impact of a major biogeographic barrier on genetic structure in two large kangaroos from the monsoon tropics of Northern Australia

    PubMed Central

    Eldridge, Mark D B; Potter, Sally; Johnson, Christopher N; Ritchie, Euan G

    2014-01-01

    Tropical savannas cover 20–30% of the world's land surface and exhibit high levels of regional endemism, but the evolutionary histories of their biota remain poorly studied. The most extensive and unmodified tropical savannas occur in Northern Australia, and recent studies suggest this region supports high levels of previously undetected genetic diversity. To examine the importance of barriers to gene flow and the environmental history of Northern Australia in influencing patterns of diversity, we investigated the phylogeography of two closely related, large, vagile macropodid marsupials, the antilopine wallaroo (Macropus antilopinus; n = 78), and the common wallaroo (Macropus robustus; n = 21). Both species are widespread across the tropical savannas of Australia except across the Carpentarian Barrier (CB) where there is a break in the distribution of M. antilopinus. We determined sequence variation in the hypervariable Domain I of the mitochondrial DNA control region and genotyped individuals at 12 polymorphic microsatellite loci to assess the historical and contemporary influence of the CB on these species. Surprisingly, we detected only limited differentiation between the disjunct Northern Territory and QueenslandM. antilopinus populations. In contrast, the continuously distributedM. robustus was highly divergent across the CB. Although unexpected, these contrasting responses appear related to minor differences in species biology. Our results suggest that vicariance may not explain well the phylogeographic patterns in Australia's dynamic monsoonal environments. This is because Quaternary environmental changes in this region have been complex, and diverse individual species’ biologies have resulted in less predictable and idiosyncratic responses. PMID:25035797

  17. Genetic and phenotypic parameter estimates for feed intake and other traits in growing beef cattle, and opportunities for selection.

    PubMed

    Rolfe, K M; Snelling, W M; Nielsen, M K; Freetly, H C; Ferrell, C L; Jenkins, T G

    2011-11-01

    Growth, feed intake, and temperament indicator data, collected over 5 yr on a total of 1,141 to 1,183 mixed-breed steers, were used to estimate genetic and phenotypic parameters. All steers had a portion of Hereford, Angus, or both as well as varying percentages of Simmental, Charolais, Limousin, Gelbvieh, Red Angus, and MARC III composite. Because the steers were slaughtered on various dates each year and the animals thus varied in days on feed, BW and feed data were adjusted to a 140-d feeding period basis. Adjustment of measures of feed efficiency [G:F or residual feed intake (RFI), intake adjusted for metabolic body size, and BW gain] for body fatness recorded at slaughter had little effect on the results of analyses. Average daily gain was less heritable (0.26) than was midtest BW (MBW; 0.35). Measures of feed intake had greater estimates of heritability, with 140-d DMI at 0.40 and RFI at 0.52; the heritability estimate for G:F was 0.27. Flight speed (FS), as an indicator of temperament, had an estimated heritability of 0.34 and a repeatability of 0.63. As expected, a strong genetic (0.86) correlation was estimated between ADG and MBW; genetic correlations were less strong between DMI and ADG or MBW (0.56 and 0.71). Residual feed intake and DMI had a genetic correlation of 0.66. Indexes for phenotypic RFI and genotypically restricted RFI (no correlation with BW gain) were compared with simple economic indexes incorporating feed intake and growth to elucidate expected selection responses under different criteria. In general, few breed differences were detected across the various measurements. Heterosis contributed to greater DMI, RFI, and MBW, but it did not significantly affect ADG, G:F, or FS. Balancing output (growth) with input costs (feed) is needed in practicing selection, and FS would not be recommended as an indicator trait for selection to change feed efficiency. An index including BW gain and RFI produced the best economic outcome. PMID:21622877

  18. Assessment of the value of a genetic risk score in improving the estimation of coronary risk

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The American Heart Association has established criteria for the evaluation of novel markers of cardiovascular risk. In accordance with these criteria, we assessed the association between a multi-locus genetic risk score (GRS) and incident coronary heart disease (CHD), and evaluated whether this GRS ...

  19. Estimation of the Proportion of Variation Accounted for by DNA Tests. I: Genetic Variance

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The proportion of genetic variation accounted for (Rg2) is an important characteristic of a DNA test. For each of 3 levels of narrow sense heritability of the observed trait (h2gy) and 4 levels of Rg2, 500 independent replicates of an observed trait and a molecular breeding value (MBV) for 1000 offs...

  20. Estimating interaction between genetic and environmental risk factors efficiency of sampling designs within a cohort

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Large prospective cohorts originally assembled to study environmental risk factors are increasingly exploited to study gene-environment interactions. Given the cost of genetic studies in large numbers of subjects, being able to select a sub-sample for genotyping that contains most of the information...

  1. ESTIMATES OF GENETIC PARAMETERS USING RANDOM REGRESSION MODELS FOR GASTROINTESTINAL HELMINTHOID DATA IN ANGUS CATTLE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic evaluation of livestock is based on appropriate modeling of phenotypic measurements. In ruminants, fecal egg count (FEC) is commonly used to measure resistance to nematodes. A series of repeated FEC measurements may provide information about the population dynamics. A total of 6,378 FEC mea...

  2. PRELIMINARY INVESTIGATION OF THE PARALLELOGRAM CONCEPT IN GENETIC MONITORING AND RISK ESTIMATION

    EPA Science Inventory

    The main objective of genetic monitoring in human health surveillance is to prevent excessive exposure to genotoxic agents and to ensure the safety of the exposed or potentially-exposed populace. To attain fully this objective one must understand low dose exposure and associated ...

  3. Yield estimation in commercial cranberry systems using physiological, environmental, and genetic variables

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study sought to improve the current understanding of yield by measuring the effects of genetic, physiological, and environmental variables on yield. Sixty-six variables representing ‘Stevens’ and ‘Ben Lear’ cultivars were evaluated from samples collected from eight commercial cranberry marshes ...

  4. Genetic diversity of mango cultivars estimated using Start Codon Targeted (SCoT) markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Diversity and genetic relationships among 23 mango germplasm accessions, collected from different locations in Guangxi province in China, were analyzed by using a novel and simple gene targeted DNA marker: Start Codon Targeted (SCoT) markers. This technique uses a single, 18-mer primer PCR amplifica...

  5. Loss of genetic diversity in farmed populations of Colossoma macropomum estimated by microsatellites.

    PubMed

    Santos, C H A; Santana, G X; Sá Leitão, C S; Paula-Silva, M N; Almeida-Val, V M F

    2016-06-01

    The genetic variability of four Colossoma macropomum broodstocks, three from fish farms in different regions and one from the natural environment in Brazil, was analyzed using microsatellite markers. The wild progeny (n = 30) were caught in the Solimões-Amazonas River, at the varzea lakes; this location is used to mature the fish from larvae to juveniles. The three fish farms were selected according to the age of their lineages and broodstock availability: DNOCS (n = 21) is located in the Ceará State, representing the oldest lineage of cultivated tambaqui in Brazil; Balbina (n = 30) is located in the Amazonas State, representing the youngest stocks of tambaqui farmed in Brazil (approximately 15 years); and UFRPE (n = 30) is located in the Pernambuco State and is considered to be a mixed stock formed from the DNOCS and Balbina lineages. The analysis of 13 microsatellite loci indicated the occurrence of a variability reduction in the farmed populations; the UFRPE stock was the population with the highest diversity level. Low values of molecular coancestry were found in these populations. Additionally, significant differences in the RST values among the populations were detected, as was the occurrence of genetic structure. The genetic loss found in these populations may have been influenced by the founder effect. Because no breeding programs were during the entire production period and no pedigree records were kept for these broodstocks, we suggest that a wild population might be used as an important genetic resource to increase the genetic diversity of renewal stock lineages. PMID:26970241

  6. Cathode Formed by Thermal Evaporation of Ba:Al Alloy and Estimations of Barrier Height in an Organic LED

    NASA Astrophysics Data System (ADS)

    Ding, Lei; Zhang, Fang-Hui

    2011-06-01

    It is demonstrated that barium and aluminum alloy synthesized by melting in a glass tube under low vacuum is applicable for organic laser emitting diodes (LEDs) as a thin film cathode. The alloy film obtained by the thermal evaporation of pre-synthesized alloy is used in a single-boat organic LED device with the structure: indium tin oxide (ITO)/4,4'-bis[N-(1-naphthyl)-N-phenylamino]biphenyl(NPB)/tris-(8-hydroxyquinoline) aluminum(Alq3)/barium:aluminum alloy. The experimental results show that devices with this alloy film cathode exhibit better current density-voltage-luminance characteristics than those with a conventional pure Al cathode, and more weight of barium in aluminum leads to better performance of the devices. Characteristics of current density versus voltage for the electron-only devices are fitted by the Richardson—Schottky emission model, indicating that the electron injection barrier has a decrease of about 0.3 eV by this alloy cathode.

  7. Estimates of epistatic and pleiotropic effects of casein alpha s1 (CSN1S1) and thyroglobulin (TG) genetic markers on beef heifer performance traits enhanced by selection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic marker effects and type of inheritance are estimated with poor precision when minor marker allele frequencies are low. A stable composite population (MARC II) was subjected to marker assisted selection for two years to equalize CSN1S1 and TG genetic marker frequencies to evaluate the epista...

  8. History of expansion and anthropogenic collapse in a top marine predator of the Black Sea estimated from genetic data.

    PubMed

    Fontaine, Michaël C; Snirc, Alodie; Frantzis, Alexandros; Koutrakis, Emmanuil; Oztürk, Bayram; Oztürk, Ayaka A; Austerlitz, Fréderic

    2012-09-18

    Two major ecological transitions marked the history of the Black Sea after the last Ice Age. The first was the postglacial transition from a brackish-water to a marine ecosystem dominated by porpoises and dolphins once this basin was reconnected back to the Mediterranean Sea (ca. 8,000 y B.P.). The second occurred during the past decades, when overfishing and hunting activities brought these predators close to extinction, having a deep impact on the structure and dynamics of the ecosystem. Estimating the extent of this decimation is essential for characterizing this ecosystem's dynamics and for formulating restoration plans. However, this extent is poorly documented in historical records. We addressed this issue for one of the main Black Sea predators, the harbor porpoise, using a population genetics approach. Analyzing its genetic diversity using an approximate Bayesian computation approach, we show that only a demographic expansion (at most 5,000 y ago) followed by a contemporaneous population collapse can explain the observed genetic data. We demonstrate that both the postglacial settlement of harbor porpoises in the Black Sea and the recent anthropogenic activities have left a clear footprint on their genetic diversity. Specifically, we infer a strong population reduction (~90%) that occurred within the past 5 decades, which can therefore clearly be related to the recent massive killing of small cetaceans and to the continuing incidental catches in commercial fisheries. Our study thus provides a quantitative assessment of these demographically catastrophic events, also showing that two separate historical events can be inferred from contemporary genetic data. PMID:22949646

  9. Risk estimations, risk factors, and genetic variants associated with Alzheimer's disease in selected publications from the Framingham Heart Study.

    PubMed

    Weinstein, Galit; Wolf, Philip A; Beiser, Alexa S; Au, Rhoda; Seshadri, Sudha

    2013-01-01

    The study of Alzheimer's disease (AD) in the Framingham Heart Study (FHS), a multi-generational, community-based population study, began nearly four decades ago. In this overview, we highlight findings from seven prior publications that examined lifetime risk estimates for AD, environmental risk factors for AD, circulating and imaging markers of aging-related brain injury, and explorations on the genetics underlying AD. First, we describe estimations of the lifetime risk of AD. These estimates are distinguished from other measures of disease burden and have substantial public health implications. We then describe prospective studies of environmental AD risk factors: one examined the association between plasma levels of omega-3 fatty-acid and risk of incident AD, the other explored the association of diabetes to this risk in subsamples with specific characteristics. With evidence of inflammation as an underlying mechanism, we also describe findings from a study that compared the effects of serum cytokines and spontaneous production of peripheral blood mononuclear cell cytokines on AD risk. Investigating AD related endophenotypes increases sensitivity in identifying risk factors and can be used to explore pathophysiologic pathways between a risk factor and the disease. We describe findings of an association between large volume of white matter hyperintensities and a specific pattern of cognitive deficits in non-demented participants. Finally, we summarize our findings from two genetic studies: The first used genome-wide association (GWA) and family-based association methods to explore the genetic basis of cognitive and structural brain traits. The second is a large meta-analysis GWA study of AD, in which novel loci of AD susceptibility were found. Together, these findings demonstrate the FHS multi-directional efforts in investigating dementia and AD. PMID:22796871

  10. Estimation of indirect genetic effects in group-housed mink (Neovison vison) should account for systematic interactions either due to kin or sex.

    PubMed

    Alemu, S W; Berg, P; Janss, L; Bijma, P

    2016-02-01

    Social interactions among individuals are abundant, both in wild and in domestic populations. With social interactions, the genes of an individual may affect the trait values of other individuals, a phenomenon known as indirect genetic effects (IGEs). IGEs can be estimated using linear mixed models. Most IGE models assume that individuals interact equally to all group mates irrespective of relatedness. Kin selection theory, however, predicts that an individual will interact differently with family members versus non-family members. Here, we investigate kin- and sex-specific non-genetic social interactions in group-housed mink. Furthermore, we investigated whether systematic non-genetic interactions between kin or individuals of the same sex influence the estimates of genetic parameters. As a second objective, we clarify the relationship between estimates of the traditional IGE model and a family-based IGE model proposed in a previous study. Our results indicate that male siblings in mink show different non-genetic interactions than female siblings in mink and that this may impact the estimation of genetic parameters. Moreover, we have shown how estimates from a family-based IGE model can be translated to the ordinary direct-indirect model and vice versa. We find no evidence for genetic differences in interactions among related versus unrelated mink. PMID:25900536

  11. Samples from subdivided populations yield biased estimates of effective size that overestimate the rate of loss of genetic variation

    PubMed Central

    Ryman, Nils; Allendorf, Fred W; Jorde, Per Erik; Laikre, Linda; Hössjer, Ola

    2014-01-01

    Many empirical studies estimating effective population size apply the temporal method that provides an estimate of the variance effective size through the amount of temporal allele frequency change under the assumption that the study population is completely isolated. This assumption is frequently violated, and the magnitude of the resulting bias is generally unknown. We studied how gene flow affects estimates of effective size obtained by the temporal method when sampling from a population system and provide analytical expressions for the expected estimate under an island model of migration. We show that the temporal method tends to systematically underestimate both local and global effective size when populations are connected by gene flow, and the bias is sometimes dramatic. The problem is particularly likely to occur when sampling from a subdivided population where high levels of gene flow obscure identification of subpopulation boundaries. In such situations, sampling in a manner that prevents biased estimates can be difficult. This phenomenon might partially explain the frequently reported unexpectedly low effective population sizes of marine populations that have raised concern regarding the genetic vulnerability of even exceptionally large populations. PMID:24034449

  12. Estimation of genetic associations between reproduction and production traits based on a sire and dam line with common ancestry.

    PubMed

    Kapell, D N R G; Ashworth, C J; Walling, G A; Lawrence, A B; Edwards, S A; Roehe, R

    2009-10-01

    Genetic parameters for survival, reproduction and production traits were estimated for a sire and dam line, originating from one Large White breed separated more than 25 years ago. The change in parameters due to different selection pressure on reproduction and production traits in both lines was also examined. Data collected between 1990 and 2007 were available for the analysis of reproduction traits in 4713 litters (sire line) and 14836 litters (dam line) and for the production traits in 58329 pigs (sire line) and 108912 pigs (dam line). Genetic parameters were estimated using a Bayesian approach. Average phenotypic differences between lines were substantial with 1.5 more piglets born in the dam line and 1.7 mm less backfat thickness (BF) in the sire line. Based on a multiple trait analysis which included both reproduction and production traits, heritabilities for survival and litter size traits in the sire (or dam) line were estimated at 0.03 ± 0.01 (0.06 ± 0.01) for percentage of stillborn piglets (SB), 0.10 ± 0.03 (0.11 ± 0.01) for total number of piglets born (NBT) and 0.09 ± 0.03 (0.09 ± 0.01) for number of piglets born alive. Heritabilities for production traits were estimated at 0.29 ± 0.01 (0.29 ± 0.01) for average daily gain, 0.50 ± 0.01 (0.42 ± 0.01) for BF and 0.41 ± 0.01 for muscle depth. Selection pressure on litter size in the dam line resulted in a slightly unfavourable correlation for SB-NBT (0.21 ± 0.11), which was only marginally unfavourable in the sire line (0.06 ± 0.24). Selection pressure on BF in the sire line may have resulted in the moderately undesirable correlation with SB (-0.46 ± 0.15), which was not significant in the dam line (-0.08 ± 0.06). Changing the base population in the dam line to animals born since the year 2000 indicated that selection pressure on different traits has altered the heritabilities and correlations of the traits within the line. The undesirable correlations between survival at birth and

  13. Estimation of a genetically viable population for multigenerational interstellar voyaging: Review and data for project Hyperion

    NASA Astrophysics Data System (ADS)

    Smith, Cameron M.

    2014-04-01

    Designing interstellar starships for human migration to exoplanets requires establishing the starship population, which factors into many variables including closed-ecosystem design, architecture, mass and propulsion. I review the central issues of population genetics (effects of mutation, migration, selection and drift) for human populations on such voyages, specifically referencing a roughly 5-generation (c. 150-year) voyage currently in the realm of thought among Icarus Interstellar's Project Hyperion research group. I present several formulae as well as concrete numbers that can be used to help determine populations that could survive such journeys in good health. I find that previously proposed such populations, on the order of a few hundred individuals, are significantly too low to consider based on current understanding of vertebrate (including human) genetics and population dynamics. Population genetics theory, calculations and computer modeling determine that a properly screened and age- and sex-structured total founding population (Nc) of anywhere from roughly 14,000 to 44,000 people would be sufficient to survive such journeys in good health. A safe and well-considered Nc figure is 40,000, an Interstellar Migrant Population (IMP) composed of an Effective Population [Ne] of 23,400 reproductive males and females, the rest being pre- or post-reproductive individuals. This number would maintain good health over five generations despite (a) increased inbreeding resulting from a relatively small human population, (b) depressed genetic diversity due to the founder effect, (c) demographic change through time and (d) expectation of at least one severe population catastrophe over the 5-generation voyage.

  14. Genetic diversity of Forest and Savannah chicken populations of Ghana as estimated by microsatellite markers.

    PubMed

    Osei-Amponsah, Richard; Kayang, Boniface B; Naazie, Augustine; Osei, Yaa D; Youssao, Issaka A K; Yapi-Gnaore, Valentine C; Tixier-Boichard, Michèle; Rognon, Xavier

    2010-06-01

    The characterization of indigenous animal genetic resources is a requisite step in providing needed information for the conservation of useful genotypes against future needs. Thus, in this study, 22 microsatellite markers were used to genotype 114 local chickens from the Forest (n = 59) and Savannah (n = 55) eco-zones of Ghana and the results compared to those of the ancestral red junglefowl (n = 15) and two European commercial chicken populations--a broiler (n = 25) and white leghorn (n = 25). A total of 171 alleles were observed, with an average of 7.8 alleles per locus. The local Ghanaian chickens showed higher diversity in terms of the observed number of alleles per locus (6.6) and observed heterozygosity (0.568) compared with the combined control populations (6.0 and 0.458, respectively). However, Wright's F-statistics revealed negligible genetic differentiation (F(ST)) in local Ghanaian chicken populations. In addition, 65% of the Savannah chickens were inferred to be more likely from the Forest, suggesting a south-north dispersal of chickens from their probable original location in the Forest zone to the Savannah areas. It is concluded that the Forest and Savannah chickens of Ghana are a single, randomly mating unselected population, characterized by high genetic diversity and constitute a valuable resource for conservation and improvement. PMID:20597885

  15. Acceptance of, inclination for, and barriers in genetic testing for gene mutations that increase the risk of breast and ovarian cancers among female residents of Warsaw

    PubMed Central

    Dera, Paulina; Religioni, Urszula; Duda-Zalewska, Aneta; Deptała, Andrzej

    2016-01-01

    Aim of the study To check the degree of acceptance of, inclination for, and barriers in genetic testing for gene mutations that increase the risk of breast and ovarian cancers among female residents of Warsaw Material and methods This study involved 562 women between 20 and 77 years of age, all of whom were patients visiting gynaecologists practising in clinics in the City of Warsaw. The studied population was divided into six age categories. The study method was a diagnostic poll conducted with the use of an original questionnaire containing 10 multiple-choice questions. Results Nearly 70% of the women showed an interest in taking a test to detect predispositions to develop breast and ovarian cancer. More than 10% did not want to take such a test, while every fifth women was undecided. No statistically significant differences between the respondents’ willingness to pay and education were found (p = 0.05). The most frequent answer given by women in all groups was that the amount to pay was too high. Such an answer was given by 52.17% of women with primary education, 65.22% of women with vocational education, 58.61% of women with secondary education, and 41.62% of women with higher education. Conclusions Women with a confirmed increased risk of developing breast and/or ovarian cancer due to inter alia the presence of BRCA1 and BRCA2 gene mutations should pay particular attention to 1st and 2nd level prophylaxis. PMID:27095945

  16. Low genetic structuring among Pericharax heteroraphis (Porifera: Calcarea) populations from the Great Barrier Reef (Australia), revealed by analysis of nrDNA and nuclear intron sequences

    NASA Astrophysics Data System (ADS)

    Bentlage, B.; Wörheide, G.

    2007-12-01

    A new nuclear marker system for sponges, the second intron of the nuclear ATP synthetase beta subunit gene (ATPSbeta-iII), was analysed together with nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) sequences aiming to uncover phylogeographic patterns of the coral reef sponge Pericharax heteroraphis in the south-west Pacific, focussing on the Great Barrier Reef (GBR). Variation among ITS sequences was low (<1.1% p-distance), in contrast to ATPSbeta-iII (<8.3% p-distance). Single-Stranded Conformation Polymorphism (SSCP) analysis proved to be an effective tool for phasing ATPSbeta-iII alleles of 292 bp length. Although sample sizes were limited for most populations and these results await corroboration by an extended sampling regime, a past population subdivision with subsequent range expansion was indicated by a ‘dumb-bell’ shaped statistical parsimony network of GBR ATPSbeta-iII alleles. Although no clear phylogeographic break was discovered on the GBR, the northern GBR was genetically differentiated from the central/southern GBR and Queensland Plateau, based on significant pairwise F st values (0.137-0.275 and p ≤ 0.05) of pooled regional populations. The ATPSbeta-iII used in this study outperformed the frequently employed nrDNA ITS and might also turn out to be useful for phylogeographic studies of other coral reef taxa.

  17. Identical twins in forensic genetics - Epidemiology and risk based estimation of weight of evidence.

    PubMed

    Tvedebrink, Torben; Morling, Niels

    2015-12-01

    The increase in the number of forensic genetic loci used for identification purposes results in infinitesimal random match probabilities. These probabilities are computed under assumptions made for rather simple population genetic models. Often, the forensic expert reports likelihood ratios, where the alternative hypothesis is assumed not to encompass close relatives. However, this approach implies that important factors present in real human populations are discarded. This approach may be very unfavourable to the defendant. In this paper, we discuss some important aspects concerning the closest familial relationship, i.e., identical (monozygotic) twins, when reporting the weight of evidence. This can be done even when the suspect has no knowledge of an identical twin or when official records hold no twin information about the suspect. The derived expressions are not original as several authors previously have published results accounting for close familial relationships. However, we revisit the discussion to increase the awareness among forensic genetic practitioners and include new information on medical and societal factors to assess the risk of not considering a monozygotic twin as the true perpetrator. If accounting for a monozygotic twin in the weight of evidence, it implies that the likelihood ratio is truncated at a maximal value depending on the prevalence of monozygotic twins and the societal efficiency of recognising a monozygotic twin. If a monozygotic twin is considered as an alternative proposition, then data relevant for the Danish society suggests that the threshold of likelihood ratios should approximately be between 150,000 and 2,000,000 in order to take the risk of an unrecognised identical, monozygotic twin into consideration. In other societies, the threshold of the likelihood ratio in crime cases may reach other, often lower, values depending on the recognition of monozygotic twins and the age of the suspect. In general, more strictly kept

  18. Genetic Algorithm for Optimization: Preprocessing with n Dimensional Bisection and Error Estimation

    NASA Technical Reports Server (NTRS)

    Sen, S. K.; Shaykhian, Gholam Ali

    2006-01-01

    A knowledge of the appropriate values of the parameters of a genetic algorithm (GA) such as the population size, the shrunk search space containing the solution, crossover and mutation probabilities is not available a priori for a general optimization problem. Recommended here is a polynomial-time preprocessing scheme that includes an n-dimensional bisection and that determines the foregoing parameters before deciding upon an appropriate GA for all problems of similar nature and type. Such a preprocessing is not only fast but also enables us to get the global optimal solution and its reasonably narrow error bounds with a high degree of confidence.

  19. Estimates of epistatic and pleiotropic effects of () and () genetic markers on beef heifer performance traits enhanced by selection.

    PubMed

    Tait, R G; Cushman, R A; McNeel, A K; Casas, E; Smith, T P L; Freetly, H C; Bennett, G L

    2016-03-01

    Genetic marker effects and type of inheritance are estimated with poor precision when minor marker allele frequencies are low. A stable composite population (MARC II) was subjected to marker assisted selection for 2 yr to equalize and genetic marker frequencies to evaluate the epistatic and pleiotropic effects of these markers on BW, reproduction, and first calf performance traits in replacement beef females ( = 171) managed under 2 postweaning development protocols. Traits evaluated on the heifers were birth BW, weaning BW, 11-mo BW, 12-mo BW, 13-mo BW, first breeding season pregnancy evaluation BW, first calving season BW, 11-mo puberty, 12-mo puberty, 13-mo puberty, first breeding season pregnancy, and first calf weaning rate. Additionally, heifer's first calf performance traits of ordinal calving date, first calf birth BW, and first calf weaning BW (with and without age adjustment) were analyzed. Selection to increase minor allele frequencies and balanced sampling across genotype classes enhanced the ability to detect all genetic effects except dominance × dominance epistasis. The × genotype effect was significant ( < 0.05) for 11-mo BW and 12-mo BW and tended to be significant ( = 0.08) for 13-mo BW. Consistently, for all 3 traits, the most significant effect among epistatic × genotype effects was the additive effect, with the G allele decreasing BW. There were no associations between × genotype and fertility related traits ( ≥ 0.46) in this study. Additionally, there were no × genotype associations with first progeny performance traits ( ≥ 0.14). The large effect of the additive × additive interaction on first calf weaning BW was imprecisely estimated, which may warrant further investigation. PMID:27065254

  20. A twin study of self-regulatory eating in early childhood: Estimates of genetic and environmental influence, and measurement considerations

    PubMed Central

    Faith, Myles S.; Pietrobelli, Angelo; Heo, Moonseong; Johnson, Susan L.; Keller, Kathleen L.; Heymsfield, Steven B.; Allison, David B.

    2016-01-01

    Objective Children differ greatly in their ability to self-regulate food intake for reasons that are poorly understood. This laboratory-based twin study tested genetic and environmental contributions to self-regulatory eating and body fat in early childhood. Methods Sixty-nine 4 to 7 year-old same-sex twin pairs, including 40 monozygotic (MZ) and 29 dizygotic (DZ) pairs, were studied. Self-regulatory eating was operationalized as the percentage compensation index (COMPX%), assessed by a “preload” challenge in which lunch intake was measured following a low- (3 kcal) or high-calorie (159 kcal) drink. Body fat indexes also were measured. The familial association for COMPX% was estimated by an intraclass correlation, and biometric analyses estimated heritability. Results Children ate more at lunch following the low- compared to high-energy preload (p< 0.001), although variability in COMPX% was considerable. Compensation was significantly poorer among African American and Hispanic compared to European American children, and among girls compared to boys. There was a familial association for self-regulatory eating (ρ= 0.23, p= 0.03) but no significant genetic component. Twenty two percent of the variance in COMPX% was due to shared environmental (‘household’) factors, with the remaining variance attributable to child-specific (‘unique’ or ‘random’) environments. Poorer self-regulatory eating was associated with greater percent body fat (r= −0.21, p= 0.04). Conclusions Self-regulatory eating was influenced by environmental factors, especially those differing among siblings. The absence of a significant genetic effect may reflect age of the sample or could be artifactual due to measurement issues that need to be considered in future studies. PMID:22249227

  1. Improving pollutant source characterization by better estimating wind direction with a genetic algorithm

    NASA Astrophysics Data System (ADS)

    Allen, Christopher T.; Young, George S.; Haupt, Sue Ellen

    In homeland security applications, it is often necessary to characterize the source location and strength of a potentially harmful contaminant. Correct source characterization requires accurate meteorological data such as wind direction. Unfortunately, available meteorological data is often inaccurate or unrepresentative, having insufficient spatial and temporal resolution for precise modeling of pollutant dispersion. To address this issue, a method is presented that simultaneously determines the surface wind direction and the pollutant source characteristics. This method compares monitored receptor data to pollutant dispersion model output and uses a genetic algorithm (GA) to find the combination of source location, source strength, and surface wind direction that best matches the dispersion model output to the receptor data. A GA optimizes variables using principles from genetics and evolution. The approach is validated with an identical twin experiment using synthetic receptor data and a Gaussian plume equation as the dispersion model. Given sufficient receptor data, the GA is able to reproduce the wind direction, source location, and source strength. Additional runs incorporating white noise into the receptor data to simulate real-world variability demonstrate that the GA is still capable of computing the correct solution, as long as the magnitude of the noise does not exceed that of the receptor data.

  2. A general framework for estimating the relative pathogenicity of human genetic variants

    PubMed Central

    Kircher, Martin; Witten, Daniela M.; Jain, Preti; O’Roak, Brian J.; Cooper, Gregory M.; Shendure, Jay

    2014-01-01

    Our capacity to sequence human genomes has exceeded our ability to interpret genetic variation. Current genomic annotations tend to exploit a single information type (e.g. conservation) and/or are restricted in scope (e.g. to missense changes). Here, we describe Combined Annotation Dependent Depletion (CADD), a framework that objectively integrates many diverse annotations into a single, quantitative score. We implement CADD as a support vector machine trained to differentiate 14.7 million high-frequency human derived alleles from 14.7 million simulated variants. We pre-compute “C-scores” for all 8.6 billion possible human single nucleotide variants and enable scoring of short insertions/deletions. C-scores correlate with allelic diversity, annotations of functionality, pathogenicity, disease severity, experimentally measured regulatory effects, and complex trait associations, and highly rank known pathogenic variants within individual genomes. The ability of CADD to prioritize functional, deleterious, and pathogenic variants across many functional categories, effect sizes and genetic architectures is unmatched by any current annotation. PMID:24487276

  3. Estimation of genetic parameters for average daily gain using models with competition effects

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Components of variance for ADG with models including competition effects were estimated from data provided by Pig Improvement Company on 11,235 pigs from 4 selected lines of swine. Fifteen pigs with average age of 71 d were randomly assigned to a pen by line and sex and taken off test after approxi...

  4. ESTIMATION OF GENETIC PARAMETERS IN SELECTED LINES OF SWINE USING MODELS WITH COMPETITION EFFECTS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Components of variance for average daily gain (ADG, g) were estimated from data provided by PIC on 11,235 pigs from 4 lines. Pigs with average age of 71 d were randomly assigned to pens of size 15 by line and sex and taken off test after approximately 89 days (weights ranged from 61 to 158 kg). Mode...

  5. Estimation of Current Breed Differences in Multibreed Genetic Evaluations Using Quantitative and Molecular Approaches

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objectives of this presentation were to review methods used in multibreed approaches in national cattle evaluation, suggest guidelines for utilizing information for research estimates of breed differences, describe the design of the multibreed research program (germplasm evaluation; GPE) at the ...

  6. Estimation of genetic marker effects for CAPN1, CAST, and GHR on carcass quality traits in Angus cattle selected to increase minor marker frequencies

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic marker effects and interactions cannot be accurately estimated when minor marker allele frequencies (MAF) are low. To increase the accuracy of estimation for three marker systems in commercial use, an Angus population at USMARC was subjected to marker assisted-selection for multiple years t...

  7. Using a hybrid Monte Carlo/ Slip Estimator-Genetic Algorithm (MCSE-GA) to produce high resolution estimates of paleoearthquakes from geodetic data

    NASA Astrophysics Data System (ADS)

    Lindsay, Anthony; McCloskey, John; Simão, Nuno; Murphy, Shane; Bhloscaidh, Mairead Nic

    2014-05-01

    Identifying fault sections where slip deficits have accumulated may provide a means for understanding sequences of large megathrust earthquakes. Stress accumulated during the interseismic period on an active megathrust is stored as potential slip, referred to as slip deficit, along locked sections of the fault. Analysis of the spatial distribution of slip during antecedent events along the fault will show where the locked plate has spent its stored slip. Areas of unreleased slip indicate where the potential for large events remain. The location of recent earthquakes and their distribution of slip can be estimated from instrumentally recorded seismic and geodetic data. However, long-term slip-deficit modelling requires detailed information on the size and distribution of slip for pre-instrumental events over hundreds of years covering more than one 'seismic cycle'. This requires the exploitation of proxy sources of data. Coral microatolls, growing in the intertidal zone of the outer island arc of the Sunda trench, present the possibility of reconstructing slip for a number of pre-instrumental earthquakes. Their growth is influenced by tectonic flexing of the continental plate beneath them; they act as long term recorders of the vertical component of deformation. However, the sparse distribution of data available using coral geodesy results in a under determined problem with non-unique solutions. Rather than accepting any one realisation as the definite model satisfying the coral displacement data, a Monte Carlo approach identifies a suite of models consistent with the observations. Using a Genetic Algorithm to accelerate the identification of desirable models, we have developed a Monte Carlo Slip Estimator- Genetic Algorithm (MCSE-GA) which exploits the full range of uncertainty associated with the displacements. Each iteration of the MCSE-GA samples different values from within the spread of uncertainties associated with each coral displacement. The Genetic

  8. Models for Estimating Genetic Parameters of Milk Production Traits Using Random Regression Models in Korean Holstein Cattle

    PubMed Central

    Cho, C. I.; Alam, M.; Choi, T. J.; Choy, Y. H.; Choi, J. G.; Lee, S. S.; Cho, K. H.

    2016-01-01

    The objectives of the study were to estimate genetic parameters for milk production traits of Holstein cattle using random regression models (RRMs), and to compare the goodness of fit of various RRMs with homogeneous and heterogeneous residual variances. A total of 126,980 test-day milk production records of the first parity Holstein cows between 2007 and 2014 from the Dairy Cattle Improvement Center of National Agricultural Cooperative Federation in South Korea were used. These records included milk yield (MILK), fat yield (FAT), protein yield (PROT), and solids-not-fat yield (SNF). The statistical models included random effects of genetic and permanent environments using Legendre polynomials (LP) of the third to fifth order (L3–L5), fixed effects of herd-test day, year-season at calving, and a fixed regression for the test-day record (third to fifth order). The residual variances in the models were either homogeneous (HOM) or heterogeneous (15 classes, HET15; 60 classes, HET60). A total of nine models (3 orders of polynomials×3 types of residual variance) including L3-HOM, L3-HET15, L3-HET60, L4-HOM, L4-HET15, L4-HET60, L5-HOM, L5-HET15, and L5-HET60 were compared using Akaike information criteria (AIC) and/or Schwarz Bayesian information criteria (BIC) statistics to identify the model(s) of best fit for their respective traits. The lowest BIC value was observed for the models L5-HET15 (MILK; PROT; SNF) and L4-HET15 (FAT), which fit the best. In general, the BIC values of HET15 models for a particular polynomial order was lower than that of the HET60 model in most cases. This implies that the orders of LP and types of residual variances affect the goodness of models. Also, the heterogeneity of residual variances should be considered for the test-day analysis. The heritability estimates of from the best fitted models ranged from 0.08 to 0.15 for MILK, 0.06 to 0.14 for FAT, 0.08 to 0.12 for PROT, and 0.07 to 0.13 for SNF according to days in milk of first

  9. Models for Estimating Genetic Parameters of Milk Production Traits Using Random Regression Models in Korean Holstein Cattle.

    PubMed

    Cho, C I; Alam, M; Choi, T J; Choy, Y H; Choi, J G; Lee, S S; Cho, K H

    2016-05-01

    The objectives of the study were to estimate genetic parameters for milk production traits of Holstein cattle using random regression models (RRMs), and to compare the goodness of fit of various RRMs with homogeneous and heterogeneous residual variances. A total of 126,980 test-day milk production records of the first parity Holstein cows between 2007 and 2014 from the Dairy Cattle Improvement Center of National Agricultural Cooperative Federation in South Korea were used. These records included milk yield (MILK), fat yield (FAT), protein yield (PROT), and solids-not-fat yield (SNF). The statistical models included random effects of genetic and permanent environments using Legendre polynomials (LP) of the third to fifth order (L3-L5), fixed effects of herd-test day, year-season at calving, and a fixed regression for the test-day record (third to fifth order). The residual variances in the models were either homogeneous (HOM) or heterogeneous (15 classes, HET15; 60 classes, HET60). A total of nine models (3 orders of polynomials×3 types of residual variance) including L3-HOM, L3-HET15, L3-HET60, L4-HOM, L4-HET15, L4-HET60, L5-HOM, L5-HET15, and L5-HET60 were compared using Akaike information criteria (AIC) and/or Schwarz Bayesian information criteria (BIC) statistics to identify the model(s) of best fit for their respective traits. The lowest BIC value was observed for the models L5-HET15 (MILK; PROT; SNF) and L4-HET15 (FAT), which fit the best. In general, the BIC values of HET15 models for a particular polynomial order was lower than that of the HET60 model in most cases. This implies that the orders of LP and types of residual variances affect the goodness of models. Also, the heterogeneity of residual variances should be considered for the test-day analysis. The heritability estimates of from the best fitted models ranged from 0.08 to 0.15 for MILK, 0.06 to 0.14 for FAT, 0.08 to 0.12 for PROT, and 0.07 to 0.13 for SNF according to days in milk of first

  10. Nest-site fidelity and dispersal of Gyrfalcons estimated by noninvasive genetic sampling

    USGS Publications Warehouse

    Booms, T.L.; Talbot, S.L.; Sage, G.K.; McCaffery, B.J.; McCracken, K.G.; Schempf, P.F.

    2011-01-01

    We used feathers from adult Gyrfalcons (Falco rusticolus) molted in breeding territories and blood samples from nestlings to document nest-site fidelity and dispersal of breeding adults and juveniles at three areas 100- 350 km apart in Yukon Delta National Wildlife Refuge, Alaska, 2003-2007. We used genotypes from seven polymorphic microsatellite loci that provided a mean probability of identity of 0.91 ??10 -5. Breeding Gyrfalcons were highly faithful to study area and territory; we documented no dispersals of breeding birds among study areas and only one dispersal between territories. But their fidelity to nest sites was low; 22% of birds returned to the same nest site the following year. Distance among alternate nests within a territory averaged 750 m and was similar for both sexes. Mean tenure in a territory was 2.8 years, similar for both sexes, and distributed bimodally with peaks at 1 and 4 years. Mean annual turnover rate at the Ingakslugwat Hills (Volcanoes) study area was 20%. We detected three young that established breeding territories at distances ranging from 0 to 254 km from their natal territory, representing 2.5% apparent recruitment. Gyrfalcons in the Askinuk Mountains study area were slightly but statistically significantly differentiated genetically from those in the Volcanoes and Kilbuck Mountain study areas. These data are the first published on the nest-site fidelity, breeding dispersal, and natal dispersal of the Gyrfalcon in North America and demonstrate the utility of noninvasive genetic sampling to greatly improve our understanding of avian dispersal and its underlying mechanisms. ?? The Cooper Ornithological Society 2011.

  11. Tumor location, but not H3.3K27M, significantly influences the blood-brain-barrier permeability in a genetic mouse model of pediatric high-grade glioma.

    PubMed

    Subashi, Ergys; Cordero, Francisco J; Halvorson, Kyle G; Qi, Yi; Nouls, John C; Becher, Oren J; Johnson, G Allan

    2016-01-01

    Pediatric high-grade gliomas (pHGGs) occur with strikingly different frequencies in infratentorial and supratentorial regions. Although histologically these malignancies appear similar, they represent distinct diseases. Recent genomic studies have identified histone K27M H3.3/H3.1 mutations in the majority of brainstem pHGGs; these mutations are rarely encountered in pHGGs that arise in the cerebral cortex. Previous research in brainstem pHGGs suggests a restricted permeability of the blood-brain-barrier (BBB). In this work, we use dynamic contrast-enhanced (DCE) MRI to evaluate BBB permeability in a genetic mouse model of pHGG as a function of location (cortex vs. brainstem, n = 8 mice/group) and histone mutation (mutant H3.3K27M vs. wild-type H3.3, n = 8 mice/group). The pHGG models are induced either in the brainstem or the cerebral cortex and are driven by PDGF signaling and p53 loss with either H3.3K27M or wild-type H3.3. T2-weighted MRI was used to determine tumor location/extent followed by 4D DCE-MRI for estimating the rate constant (K (trans) ) for tracer exchange across the barrier. BBB permeability was 67 % higher in cortical pHGGs relative to brainstem pHGGs (t test, p = 0.012) but was not significantly affected by the expression of mutant H3.3K27M versus wild-type H3.3 (t-test, p = 0.78). Although mice became symptomatic at approximately the same time, the mean volume of cortical tumors was 3.6 times higher than the mean volume of brainstem tumors. The difference between the mean volume of gliomas with wild-type and mutant H3.3 was insignificant. Mean K (trans) was significantly correlated to glioma volume. These results present a possible explanation for the poor response of brainstem pHGGs to systemic therapy. Our findings illustrate a potential role played by the microenvironment in shaping tumor growth and BBB permeability. PMID:26511492

  12. Estimating grizzly and black bear population abundance and trend in Banff National Park using noninvasive genetic sampling.

    PubMed

    Sawaya, Michael A; Stetz, Jeffrey B; Clevenger, Anthony P; Gibeau, Michael L; Kalinowski, Steven T

    2012-01-01

    We evaluated the potential of two noninvasive genetic sampling methods, hair traps and bear rub surveys, to estimate population abundance and trend of grizzly (Ursus arctos) and black bear (U. americanus) populations in Banff National Park, Alberta, Canada. Using Huggins closed population mark-recapture models, we obtained the first precise abundance estimates for grizzly bears (N= 73.5, 95% CI = 64-94 in 2006; N= 50.4, 95% CI = 49-59 in 2008) and black bears (N= 62.6, 95% CI = 51-89 in 2006; N= 81.8, 95% CI = 72-102 in 2008) in the Bow Valley. Hair traps had high detection rates for female grizzlies, and male and female black bears, but extremely low detection rates for male grizzlies. Conversely, bear rubs had high detection rates for male and female grizzlies, but low rates for black bears. We estimated realized population growth rates, lambda, for grizzly bear males (λ= 0.93, 95% CI = 0.74-1.17) and females (λ= 0.90, 95% CI = 0.67-1.20) using Pradel open population models with three years of bear rub data. Lambda estimates are supported by abundance estimates from combined hair trap/bear rub closed population models and are consistent with a system that is likely driven by high levels of human-caused mortality. Our results suggest that bear rub surveys would provide an efficient and powerful means to inventory and monitor grizzly bear populations in the Central Canadian Rocky Mountains. PMID:22567089

  13. Estimation of genetic effects on BMI during adolescence in an ethnically diverse cohort: The National Longitudinal Study of Adolescent Health

    PubMed Central

    Graff, M; North, K E; Mohlke, K L; Lange, L A; Luo, J; Harris, K M; Young, K L; Richardson, A S; Lange, E M; Gordon-Larsen, P

    2012-01-01

    Objective: The contribution of genetic variants to body mass index (BMI) during adolescence across multiethnic samples is largely unknown. We selected genetic loci associated with BMI or obesity in European-descent samples and examined them in a multiethnic adolescent sample. Design and Sample: In 5103 European American (EA), 1748 African American (AfA), 1304 Hispanic American (HA) and 439 Asian American (AsA) participants of the National Longitudinal Study of Adolescent Health (Add Health; ages 12–21 years, 47.5% male), we assessed the association between 41 established obesity-related single-nucleotide polymorphisms (SNPs) with BMI using additive genetic models, stratified by race/ethnicity, and in a pooled meta-analysis sample. We also compared the magnitude of effect for BMI–SNP associations in EA and AfA adolescents to comparable effect estimates from 11 861 EA and AfA adults in the Atherosclerosis Risk in Communities study (ages 45–64 years, 43.2% male). Results: Thirty-five of 41 BMI–SNP associations were directionally consistent with published studies in European populations, 18 achieved nominal significance (P<0.05; effect sizes from 0.19 to 0.71 kg m−2 increase in BMI per effect allele), while 4 (FTO, TMEM18, TFAP2B, MC4R) remained significant after Bonferroni correction (P<0.0015). Of 41 BMI–SNP associations in AfA, HA and AsA adolescents, nine, three and five, respectively, were directionally consistent and nominally significant. In the pooled meta-analysis, 36 of 41 effect estimates were directionally consistent and 21 of 36 were nominally significant. In EA adolescents, BMI effect estimates were larger (P<0.05) for variants near TMEM18, PTER and MC4R and smaller for variants near MTIF3 and NRXN3 compared with EA adults. Conclusion: Our findings suggest that obesity susceptibility loci may have a comparatively stronger role during adolescence than during adulthood, with variation across race/ethnic subpopulation. PMID:23168566

  14. Likelihood-based genetic mark-recapture estimates when genotype samples are incomplete and contain typing errors.

    PubMed

    Macbeth, Gilbert M; Broderick, Damien; Ovenden, Jennifer R; Buckworth, Rik C

    2011-11-01

    Genotypes produced from samples collected non-invasively in harsh field conditions often lack the full complement of data from the selected microsatellite loci. The application to genetic mark-recapture methodology in wildlife species can therefore be prone to misidentifications leading to both 'true non-recaptures' being falsely accepted as recaptures (Type I errors) and 'true recaptures' being undetected (Type II errors). Here we present a new likelihood method that allows every pairwise genotype comparison to be evaluated independently. We apply this method to determine the total number of recaptures by estimating and optimising the balance between Type I errors and Type II errors. We show through simulation that the standard error of recapture estimates can be minimised through our algorithms. Interestingly, the precision of our recapture estimates actually improved when we included individuals with missing genotypes, as this increased the number of pairwise comparisons potentially uncovering more recaptures. Simulations suggest that the method is tolerant to per locus error rates of up to 5% per locus and can theoretically work in datasets with as little as 60% of loci genotyped. Our methods can be implemented in datasets where standard mismatch analyses fail to distinguish recaptures. Finally, we show that by assigning a low Type I error rate to our matching algorithms we can generate a dataset of individuals of known capture histories that is suitable for the downstream analysis with traditional mark-recapture methods. PMID:21763337

  15. aCGH Analysis to Estimate Genetic Variations among Domesticated Chickens.

    PubMed

    Komiyama, Tomoyoshi; Lin, Mengjie; Ogura, Atsushi

    2016-01-01

    Chickens have been familiar to humans since ancient times and have been used not only for culinary purposes but also for cultural purposes including ritual ceremonies and traditional entertainment. The various chicken breeds developed for these purposes often display distinct morphological and/or behavioural traits. For example, the Japanese Shamo is larger and more aggressive than other domesticated chickens, reflecting its role as a fighting cock breed, whereas Japanese Naganakidori breeds, which have long-crowing behaviour, were bred instead for their entertaining and aesthetic qualities. However, the genetic backgrounds of these distinct morphological and behavioural traits remain unclear. Therefore, the question arises as to which genomic regions in these chickens were acted upon by selective pressures through breeding. We compared the entire genomes of six chicken breeds domesticated for various cultural purposes by utilizing array comparative genomic hybridization. From these analyses, we identified 782 regions that underwent insertions, deletions, or mutations, representing man-made selection pressure in these chickens. Furthermore, we found that a number of genes diversified in domesticated chickens bred for cultural or entertainment purposes were different from those diversified in chickens bred for food, such as broilers and layers. PMID:27525263

  16. aCGH Analysis to Estimate Genetic Variations among Domesticated Chickens

    PubMed Central

    Lin, Mengjie

    2016-01-01

    Chickens have been familiar to humans since ancient times and have been used not only for culinary purposes but also for cultural purposes including ritual ceremonies and traditional entertainment. The various chicken breeds developed for these purposes often display distinct morphological and/or behavioural traits. For example, the Japanese Shamo is larger and more aggressive than other domesticated chickens, reflecting its role as a fighting cock breed, whereas Japanese Naganakidori breeds, which have long-crowing behaviour, were bred instead for their entertaining and aesthetic qualities. However, the genetic backgrounds of these distinct morphological and behavioural traits remain unclear. Therefore, the question arises as to which genomic regions in these chickens were acted upon by selective pressures through breeding. We compared the entire genomes of six chicken breeds domesticated for various cultural purposes by utilizing array comparative genomic hybridization. From these analyses, we identified 782 regions that underwent insertions, deletions, or mutations, representing man-made selection pressure in these chickens. Furthermore, we found that a number of genes diversified in domesticated chickens bred for cultural or entertainment purposes were different from those diversified in chickens bred for food, such as broilers and layers. PMID:27525263

  17. Population structure and genetic bottleneck in sweet cherry estimated with SSRs and the gametophytic self-incompatibility locus

    PubMed Central

    2010-01-01

    Background Domestication and breeding involve the selection of particular phenotypes, limiting the genomic diversity of the population and creating a bottleneck. These effects can be precisely estimated when the location of domestication is established. Few analyses have focused on understanding the genetic consequences of domestication and breeding in fruit trees. In this study, we aimed to analyse genetic structure and changes in the diversity in sweet cherry Prunus avium L. Results Three subgroups were detected in sweet cherry, with one group of landraces genetically very close to the analysed wild cherry population. A limited number of SSR markers displayed deviations from the frequencies expected under neutrality. After the removal of these markers from the analysis, a very limited bottleneck was detected between wild cherries and sweet cherry landraces, with a much more pronounced bottleneck between sweet cherry landraces and modern sweet cherry varieties. The loss of diversity between wild cherries and sweet cherry landraces at the S-locus was more significant than that for microsatellites. Particularly high levels of differentiation were observed for some S-alleles. Conclusions Several domestication events may have happened in sweet cherry or/and intense gene flow from local wild cherry was probably maintained along the evolutionary history of the species. A marked bottleneck due to breeding was detected, with all markers, in the modern sweet cherry gene pool. The microsatellites did not detect the bottleneck due to domestication in the analysed sample. The vegetative propagation specific to some fruit trees may account for the differences in diversity observed at the S-locus. Our study provides insights into domestication events of cherry, however, requires confirmation on a larger sampling scheme for both sweet cherry landraces and wild cherry. PMID:20727153

  18. Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference.

    PubMed

    Mastretta-Yanes, A; Arrigo, N; Alvarez, N; Jorgensen, T H; Piñero, D; Emerson, B C

    2015-01-01

    Restriction site-associated DNA sequencing (RADseq) provides researchers with the ability to record genetic polymorphism across thousands of loci for nonmodel organisms, potentially revolutionizing the field of molecular ecology. However, as with other genotyping methods, RADseq is prone to a number of sources of error that may have consequential effects for population genetic inferences, and these have received only limited attention in terms of the estimation and reporting of genotyping error rates. Here we use individual sample replicates, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome. We then use sample replicates to (i) optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci; and (ii) quantify error rates for loci, alleles and single-nucleotide polymorphisms. As an empirical example, we use a double-digest RAD data set of a nonmodel plant species, Berberis alpina, collected from high-altitude mountains in Mexico. PMID:24916682

  19. Influence of genetic composition of test-animal populations on chronic toxicity studies used for risk estimation.

    PubMed

    Littlefield, N A; Wolff, G L; Nelson, C J

    1985-01-01

    A lifespan exposure of mice to benzidine dihydrochloride was conducted for 33 m using both sexes of two populations of mice with the same gene pool. One population was the genetically homogeneous F1 hybrid produced by crossing BALB/cStCrlC3Hf/Nctr males with C57BL/6jfC3Hf/Nctr females. The second population consisted of genetically heterogenous monohybrid cross (MC) offspring produced by mating the F1 hybrids inter se. Data comparisons were made to determine if gene distribution among members of a population affects the response to a toxic insult. Endpoints tested consisted of mortality, liver tumor incidence and time of tumor onset, mortality from reticulum-cell sarcoma, and body weights. In most instances it was noted that among animals not dosed (controls), the F1 population had lower background incidence of lesions and lived longer than the MC population. However, among the dosed animals, the F1 mice were generally more susceptible to the toxic agent and developed higher incidences of the chemically induced lesions than did the MC population. The F1 hybrid population gave a more conservative estimate of risk than did the MC population. The calculation of the liver tumor risk for these two populations showed that lifespan exposure to benzidine would be predicted to result in a larger number (higher risk) when using the F1 data. A 4.5-fold difference in the toxic response was observed between the F1 females and the MC males. This emphasizes the importance of gene distribution in risk estimation studies. PMID:4032486

  20. Influence of genetic composition of test-animal populations on chronic toxicity studies used for risk estimation

    SciTech Connect

    Littlefield, N.A.; Wolff, G.L.; Nelson, C.J.

    1985-01-01

    A lifespan exposure of mice to benzidine dihydrochloride was conducted for 33 m using both sexes of two populations of mice with the same gene pool. One population was the genetically homogeneous F/sub 1/ hybrid produced by crossing BALB/cStCrlC3Hf/Nctr males with C57BL/6JfC3Hf/Nctr females. The second population consisted of genetically heterogenous monohybrid cross (MC) offspring produced by mating the F/sub 1/ hybrids inter se. Data comparisons were made to determine if gene distribution among members of a population affects the response to a toxic insult. Endpoints tested consisted of mortality, liver tumor incidence and time of tumor onset, mortality from reticulum-cell sarcoma, and body weights. In most instances it was noted that among animals not dosed (controls), the F/sub 1/ population has lower background incidence of lesions and lived longer than the MC population. However, among the dosed animals, the F/sub 1/ mice were generally more susceptible to the toxic agent and developed higher incidences of the chemically induced lesions than did the MC population. The F/sub 1/ hybrid population gave a more conservative estimate of risk than did the MC population. The calculation of the liver tumor risk for these two populations showed that lifespan, exposure to benzidine would be predicted to result in a larger number (higher risk) when using the F/sub 1/ data. A 4.5-fold difference in the toxic response was observed between the F/sub 1/ females and the MC males. This emphasizes the importance of gene distribution in risk estimation studies.

  1. Diffusion barriers

    NASA Technical Reports Server (NTRS)

    Nicolet, M. A.

    1983-01-01

    The choice of the metallic film for the contact to a semiconductor device is discussed. One way to try to stabilize a contact is by interposing a thin film of a material that has low diffusivity for the atoms in question. This thin film application is known as a diffusion barrier. Three types of barriers can be distinguished. The stuffed barrier derives its low atomic diffusivity to impurities that concentrate along the extended defects of a polycrystalline layer. Sacrificial barriers exploit the fact that some (elemental) thin films react in a laterally uniform and reproducible fashion. Sacrificial barriers have the advantage that the point of their failure is predictable. Passive barriers are those most closely approximating an ideal barrier. The most-studied case is that of sputtered TiN films. Stuffed barriers may be viewed as passive barriers whose low diffusivity material extends along the defects of the polycrystalline host.

  2. Experimental design for estimating unknown groundwater pumping using genetic algorithm and reduced order model

    NASA Astrophysics Data System (ADS)

    Ushijima, Timothy T.; Yeh, William W.-G.

    2013-10-01

    An optimal experimental design algorithm is developed to select locations for a network of observation wells that provide maximum information about unknown groundwater pumping in a confined, anisotropic aquifer. The design uses a maximal information criterion that chooses, among competing designs, the design that maximizes the sum of squared sensitivities while conforming to specified design constraints. The formulated optimization problem is non-convex and contains integer variables necessitating a combinatorial search. Given a realistic large-scale model, the size of the combinatorial search required can make the problem difficult, if not impossible, to solve using traditional mathematical programming techniques. Genetic algorithms (GAs) can be used to perform the global search; however, because a GA requires a large number of calls to a groundwater model, the formulated optimization problem still may be infeasible to solve. As a result, proper orthogonal decomposition (POD) is applied to the groundwater model to reduce its dimensionality. Then, the information matrix in the full model space can be searched without solving the full model. Results from a small-scale test case show identical optimal solutions among the GA, integer programming, and exhaustive search methods. This demonstrates the GA's ability to determine the optimal solution. In addition, the results show that a GA with POD model reduction is several orders of magnitude faster in finding the optimal solution than a GA using the full model. The proposed experimental design algorithm is applied to a realistic, two-dimensional, large-scale groundwater problem. The GA converged to a solution for this large-scale problem.

  3. Associating optical measurements and estimating orbits of geocentric objects with a Genetic Algorithm: performance limitations.

    NASA Astrophysics Data System (ADS)

    Zittersteijn, Michiel; Schildknecht, Thomas; Vananti, Alessandro; Dolado Perez, Juan Carlos; Martinot, Vincent

    2016-07-01

    Currently several thousands of objects are being tracked in the MEO and GEO regions through optical means. With the advent of improved sensors and a heightened interest in the problem of space debris, it is expected that the number of tracked objects will grow by an order of magnitude in the near future. This research aims to provide a method that can treat the correlation and orbit determination problems simultaneously, and is able to efficiently process large data sets with minimal manual intervention. This problem is also known as the Multiple Target Tracking (MTT) problem. The complexity of the MTT problem is defined by its dimension S. Current research tends to focus on the S = 2 MTT problem. The reason for this is that for S = 2 the problem has a P-complexity. However, with S = 2 the decision to associate a set of observations is based on the minimum amount of information, in ambiguous situations (e.g. satellite clusters) this will lead to incorrect associations. The S > 2 MTT problem is an NP-hard combinatorial optimization problem. In previous work an Elitist Genetic Algorithm (EGA) was proposed as a method to approximately solve this problem. It was shown that the EGA is able to find a good approximate solution with a polynomial time complexity. The EGA relies on solving the Lambert problem in order to perform the necessary orbit determinations. This means that the algorithm is restricted to orbits that are described by Keplerian motion. The work presented in this paper focuses on the impact that this restriction has on the algorithm performance.

  4. Divergence of East Asians and Europeans Estimated Using Male- and Female-Specific Genetic Markers

    PubMed Central

    Tateno, Yoshio; Komiyama, Tomoyoshi; Katoh, Toru; Munkhbat, Batmunkh; Oka, Akira; Haida, Yuko; Kobayashi, Hiroyuki; Tamiya, Gen; Inoko, Hidetoshi

    2014-01-01

    To study the male and female lineages of East Asian and European humans, we have sequenced 25 short tandem repeat markers on 453 Y-chromosomes and collected sequences of 72 complete mitochondrial genomes to construct independent phylogenetic trees for male and female lineages. The results indicate that East Asian individuals fall into two clades, one that includes East Asian individuals only and a second that contains East Asian and European individuals. Surprisingly, the European individuals did not form an independent clade, but branched within in the East Asians. We then estimated the divergence time of the root of the European clade as ∼41,000 years ago. These data indicate that, contrary to traditional views, Europeans diverged from East Asians around that time. We also address the origin of the Ainu lineage in northern Japan. PMID:24589501

  5. Breed effects, retained heterosis, and estimates of genetic and phenotypic parameters for carcass and meat traits of beef cattle.

    PubMed

    Gregory, K E; Cundiff, L V; Koch, R M; Dikeman, M E; Koohmaraie, M

    1994-05-01

    Retained heterosis for meat traits was estimated in F3 generation castrate males in three composite populations of beef cattle finished on two levels of dietary energy density (2.82 Mcal of ME and 3.07 Mcal of ME and 11.50% CP) and serially slaughtered at four end points at intervals of 20 to 22 d. Breed effects were evaluated in nine parental breeds (Red Poll [R], Hereford [H], Angus [A], Limousin [L], Braunvieh [B], Pinzgauer [P], Gelbvieh [G], Simmental [S], and Charolais [C]) that contributed to the three composite populations (MARC I = 1/4 B, 1/4 C, 1/4 L, 1/8 H, 1/8 A; MARC II = 1/4 G, 1/4 S, 1/4 H, 1/4 A; and MARC III = 1/4 R, 1/4 P, 1/4 H, and 1/4 A). Breed effects were important (P < .01) for all carcass and meat traits evaluated. Dietary energy density and slaughter group affected (P < .05) most traits evaluated. The effects of retained heterosis were not consistent among composites. For the mean of the three composites, retained heterosis was significant only for percentage of 9-10-11th rib fat and for percentage of retail product. Phenotypic correlations indicated that marbling score was a poor predictor of palatability attributes of individual carcasses. Estimates of heritability were intermediate to high for measures of fatness but were generally low for palatability attributes. The high negative genetic correlation (-.56) between percentage of retail product and marbling score and the relatively low genetic correlations between percentage of retail product and palatability attributes suggests the need for simultaneous attention to percentage of retail product and palatability attributes rather than to marbling score. Correlations among breed group means were generally high for measures of fatness with palatability attributes and were high and negative for percentage of retail product with marbling score and with other measures of fatness. Limited opportunity exists for selecting among breeds to achieve high levels of marbling in the longissimus

  6. Three-dimensional motion estimation using genetic algorithms from image sequence in an active stereo vision system

    NASA Astrophysics Data System (ADS)

    Dipanda, Albert; Ajot, Jerome; Woo, Sanghyuk

    2003-06-01

    This paper proposes a method for estimating 3D rigid motion parameters from an image sequence of a moving object. The 3D surface measurement is achieved using an active stereovision system composed of a camera and a light projector, which illuminates objects to be analyzed by a pyramid-shaped laser beam. By associating the laser rays and the spots in the 2D image, the 3D points corresponding to these spots are reconstructed. Each image of the sequence provides a set of 3D points, which is modeled by a B-spline surface. Therefore, estimating the motion between two images of the sequence boils down to matching two B-spline surfaces. We consider the matching environment as an optimization problem and find the optimal solution using Genetic Algorithms. A chromosome is encoded by concatenating six binary coded parameters, the three angles of rotation and the x-axis, y-axis and z-axis translations. We have defined an original fitness function to calculate the similarity measure between two surfaces. The matching process is performed iteratively: the number of points to be matched grows as the process advances and results are refined until convergence. Experimental results with a real image sequence are presented to show the effectiveness of the method.

  7. The children of parents exposed to atomic bombs: Estimates of the genetic doubling dose of radiation for humans

    SciTech Connect

    Neel, J.V.; Schull, W.J.; Awa, A.A.; Satoh, C.; Kato, H.; Otake, M.; Yoshimoto, Y. )

    1990-06-01

    The data collected in Hiroshima and Nagasaki during the past 40 years on the children of survivors of the atomic bombings and on the children of a suitable control population are analyzed on the basis of the newly revised estimates of radiation doses. No statistically significant effects emerge with respect to eight different indicators. Since, however, it may confidently be assumed some mutations were induced, we have taken the data at face value and calculated the minimal gametic doubling doses of acute radiation for the individual indicators at various probability levels. An effort has also been made to calculate the most probable doubling dose for the indicators combined. The latter value is between 1.7 and 2.2 Sv. It is suggested the appropriate figure for chronic radiation would be between 3.4 and 4.5 Sv. These estimates suggest humans are less sensitive to the genetic effects of radiation than has been assumed on the basis of past extrapolations from experiments with mice.

  8. Anabolic implant effects on visceral organ mass, chemical body composition, and estimated energetic efficiency in cloned (genetically identical) beef steers.

    PubMed

    Hutcheson, J P; Johnson, D E; Gerken, C L; Morgan, J B; Tatum, J D

    1997-10-01

    Six sets of four genetically identical Brangus steers (n = 24; X BW 409 kg) were used to determine the effect of different anabolic implants on visceral organ mass, chemical body composition, estimated tissue deposition, and energetic efficiency. Steers within a clone set were randomly assigned to one of the following implant treatments: C, no implant; E, estrogenic; A, androgenic, or AE, androgenic + estrogenic. Steers were slaughtered 112 d after implanting; visceral organs were weighed and final body composition determined by mechanical grinding and chemical analysis of the empty body. Mass of the empty gastrointestinal tract (GIT) was reduced approximately 9% (P < .10) in steers implanted with estrogen alone or in combination with an androgen. Liver mass was increased (P < .10) from 6 to 14% by implants. Steers implanted with the AE combination had greater (P < .10) daily protein accretion (163.4 g/d) than either E (128.8 g/d) or A (137.1 g/d), and, because the combination improved gain above C (101.1 g/d), this demonstrates the additive effects of a combination implant on protein deposition. Anabolic implants did not alter (P > .10) the efficiency of ME utilization. In general, estrogenic implants decreased GIT, androgenic implants increased liver, and all implants increased hide mass. Steers implanted with an AE combination had additive effects on protein deposition compared with either implant alone. The NEg requirements for body gain are estimated to be reduced 19% by estrogenic or combination implants. PMID:9331863

  9. The children of parents exposed to atomic bombs: estimates of the genetic doubling dose of radiation for humans.

    PubMed

    Neel, J V; Schull, W J; Awa, A A; Satoh, C; Kato, H; Otake, M; Yoshimoto, Y

    1990-06-01

    The data collected in Hiroshima and Nagasaki during the past 40 years on the children of survivors of the atomic bombings and on the children of a suitable control population are analyzed on the basis of the newly revised estimates of radiation doses. No statistically significant effects emerge with respect to eight different indicators. Since, however, it may confidently be assumed some mutations were induced, we have taken the data at face value and calculated the minimal gametic doubling doses of acute radiation for the individual indicators at various probability levels. An effort has also been made to calculate the most probable doubling dose for the indicators combined. The latter value is between 1.7 and 2.2 Sv. It is suggested the appropriate figure for chronic radiation would be between 3.4 and 4.5 Sv. These estimates suggest humans are less sensitive to the genetic effects of radiation than has been assumed on the basis of past extrapolations from experiments with mice. PMID:2339701

  10. Estimation of genetic parameters for productive life, reproduction, and milk-production traits in US dairy goats.

    PubMed

    Castañeda-Bustos, V J; Montaldo, H H; Torres-Hernández, G; Pérez-Elizalde, S; Valencia-Posadas, M; Hernández-Mendo, O; Shepard, L

    2014-01-01

    Heritabilities and correlations for milk yield (MY), fat yield (FY), protein yield (PY), combined fat and protein yield (FPY), fat percentage (F%), protein percentage (P%), age at first kidding (AFK), interval between the first and second kidding (KI), and real and functional productive life at 72mo (FPL72) of 33,725 US dairy goats, were estimated using animal models. Productive life was defined as the total days in production until 72mo of age (PL72) for goats having the opportunity to express the trait. Functional productive life was obtained by correcting PL72 for MY, FY, PY, and final type score (FS). Six selection indexes were used, including or excluding PL72, with 6 groups of different economic weights, to estimate the responses to selection considering MY, FY, PY, and PL72 as selection criteria. The main criteria that determined the culling of a goat from the herd were low FS, MY, and FY per lactation. Heritability estimates were 0.22, 0.17, 0.37, 0.37, 0.38, 0.39, 0.54, 0.64, 0.09, and 0.16 for PL72, FPL72, MY, FY, PY, FPY, F%, P%, KI, and AFK, respectively. Most genetic correlations between the evaluated traits and PL72 or FPL72 were positive, except for F% (-0.04 and -0.06, respectively), P% (-0.002 and -0.03, respectively), and AFK (-0.03 and -0.01, respectively). The highest genetic correlations were between FPL72 and MY (0.39) and between PL72 and MY (0.33). Most phenotypic correlations between the traits evaluated and FPL72 and PL72 were positive (>0.23 and >0.26, respectively), except for F% (-0.004 and -0.02, respectively), P% (-0.05 and -0.02), KI (-0.01 and -0.07), and AFK (-0.08 and -0.08). The direct selection for PL72 increased it by 102.28d per generation. The use of MY, FY, PY, KI, or AFK as selection criteria increased PL72 by 39.21, 27.33, 35.90, -8.28, or 2.77d per generation, respectively. The inclusion of PL72 as selection criterion increased the expected response per generation from 0.15 to 17.35% in all selection indices studied. PMID

  11. Seismic velocity estimation from well log data with genetic algorithms in comparison to neural networks and multilinear approaches

    NASA Astrophysics Data System (ADS)

    Aleardi, Mattia

    2015-06-01

    Predicting missing log data is a useful capability for geophysicists. Geophysical measurements in boreholes are frequently affected by gaps in the recording of one or more logs. In particular, sonic and shear sonic logs are often recorded over limited intervals along the well path, but the information these logs contain is crucial for many geophysical applications. Estimating missing log intervals from a set of recorded logs is therefore of great interest. In this work, I propose to estimate the data in missing parts of velocity logs using a genetic algorithm (GA) optimisation and I demonstrate that this method is capable of extracting linear or exponential relations that link the velocity to other available logs. The technique was tested on different sets of logs (gamma ray, resistivity, density, neutron, sonic and shear sonic) from three wells drilled in different geological settings and through different lithologies (sedimentary and intrusive rocks). The effectiveness of this methodology is demonstrated by a series of blind tests and by evaluating the correlation coefficients between the true versus predicted velocity values. The combination of GA optimisation with a Gibbs sampler (GS) and subsequent Monte Carlo simulations allows the uncertainties in the final predicted velocities to be reliably quantified. The GA method is also compared with the neural networks (NN) approach and classical multilinear regression. The comparisons show that the GA, NN and multilinear methods provide velocity estimates with the same predictive capability when the relation between the input logs and the seismic velocity is approximately linear. The GA and NN approaches are more robust when the relations are non-linear. However, in all cases, the main advantages of the GA optimisation procedure over the NN approach is that it directly provides an interpretable and simple equation that relates the input and predicted logs. Moreover, the GA method is not affected by the disadvantages

  12. Snow Depth Estimation Using Time Series Passive Microwave Imagery via Genetically Support Vector Regression (case Study Urmia Lake Basin)

    NASA Astrophysics Data System (ADS)

    Zahir, N.; Mahdi, H.

    2015-12-01

    Lake Urmia is one of the most important ecosystems of the country which is on the verge of elimination. Many factors contribute to this crisis among them is the precipitation, paly important roll. Precipitation has many forms one of them is in the form of snow. The snow on Sahand Mountain is one of the main and important sources of the Lake Urmia's water. Snow Depth (SD) is vital parameters for estimating water balance for future year. In this regards, this study is focused on SD parameter using Special Sensor Microwave/Imager (SSM/I) instruments on board the Defence Meteorological Satellite Program (DMSP) F16. The usual statistical methods for retrieving SD include linear and non-linear ones. These methods used least square procedure to estimate SD model. Recently, kernel base methods widely used for modelling statistical problem. From these methods, the support vector regression (SVR) is achieved the high performance for modelling the statistical problem. Examination of the obtained data shows the existence of outlier in them. For omitting these outliers, wavelet denoising method is applied. After the omission of the outliers it is needed to select the optimum bands and parameters for SVR. To overcome these issues, feature selection methods have shown a direct effect on improving the regression performance. We used genetic algorithm (GA) for selecting suitable features of the SSMI bands in order to estimate SD model. The results for the training and testing data in Sahand mountain is [R²_TEST=0.9049 and RMSE= 6.9654] that show the high SVR performance.

  13. Estimation of soil cation exchange capacity using Genetic Expression Programming (GEP) and Multivariate Adaptive Regression Splines (MARS)

    NASA Astrophysics Data System (ADS)

    Emamgolizadeh, S.; Bateni, S. M.; Shahsavani, D.; Ashrafi, T.; Ghorbani, H.

    2015-10-01

    The soil cation exchange capacity (CEC) is one of the main soil chemical properties, which is required in various fields such as environmental and agricultural engineering as well as soil science. In situ measurement of CEC is time consuming and costly. Hence, numerous studies have used traditional regression-based techniques to estimate CEC from more easily measurable soil parameters (e.g., soil texture, organic matter (OM), and pH). However, these models may not be able to adequately capture the complex and highly nonlinear relationship between CEC and its influential soil variables. In this study, Genetic Expression Programming (GEP) and Multivariate Adaptive Regression Splines (MARS) were employed to estimate CEC from more readily measurable soil physical and chemical variables (e.g., OM, clay, and pH) by developing functional relations. The GEP- and MARS-based functional relations were tested at two field sites in Iran. Results showed that GEP and MARS can provide reliable estimates of CEC. Also, it was found that the MARS model (with root-mean-square-error (RMSE) of 0.318 Cmol+ kg-1 and correlation coefficient (R2) of 0.864) generated slightly better results than the GEP model (with RMSE of 0.270 Cmol+ kg-1 and R2 of 0.807). The performance of GEP and MARS models was compared with two existing approaches, namely artificial neural network (ANN) and multiple linear regression (MLR). The comparison indicated that MARS and GEP outperformed the MLP model, but they did not perform as good as ANN. Finally, a sensitivity analysis was conducted to determine the most and the least influential variables affecting CEC. It was found that OM and pH have the most and least significant effect on CEC, respectively.

  14. A stochastic dynamic simulation model including multi-trait genetics to estimate genetic, technical and financial consequences of dairy farm reproduction and selection strategies

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this study was to develop a daily stochastic dynamic dairy simulation model which included multi-trait genetics, and to evaluate the effects of various reproduction and selection strategies on the genetic, technical and financial performance of a dairy herd. The 12 correlated geneti...

  15. Estimation of Genetic Parameters for First Lactation Monthly Test-day Milk Yields using Random Regression Test Day Model in Karan Fries Cattle.

    PubMed

    Singh, Ajay; Singh, Avtar; Singh, Manvendra; Prakash, Ved; Ambhore, G S; Sahoo, S K; Dash, Soumya

    2016-06-01

    A single trait linear mixed random regression test-day model was applied for the first time for analyzing the first lactation monthly test-day milk yield records in Karan Fries cattle. The test-day milk yield data was modeled using a random regression model (RRM) considering different order of Legendre polynomial for the additive genetic effect (4th order) and the permanent environmental effect (5th order). Data pertaining to 1,583 lactation records spread over a period of 30 years were recorded and analyzed in the study. The variance component, heritability and genetic correlations among test-day milk yields were estimated using RRM. RRM heritability estimates of test-day milk yield varied from 0.11 to 0.22 in different test-day records. The estimates of genetic correlations between different test-day milk yields ranged 0.01 (test-day 1 [TD-1] and TD-11) to 0.99 (TD-4 and TD-5). The magnitudes of genetic correlations between test-day milk yields decreased as the interval between test-days increased and adjacent test-day had higher correlations. Additive genetic and permanent environment variances were higher for test-day milk yields at both ends of lactation. The residual variance was observed to be lower than the permanent environment variance for all the test-day milk yields. PMID:26954137

  16. Estimation of Genetic Parameters for First Lactation Monthly Test-day Milk Yields using Random Regression Test Day Model in Karan Fries Cattle

    PubMed Central

    Singh, Ajay; Singh, Avtar; Singh, Manvendra; Prakash, Ved; Ambhore, G. S.; Sahoo, S. K.; Dash, Soumya

    2016-01-01

    A single trait linear mixed random regression test-day model was applied for the first time for analyzing the first lactation monthly test-day milk yield records in Karan Fries cattle. The test-day milk yield data was modeled using a random regression model (RRM) considering different order of Legendre polynomial for the additive genetic effect (4th order) and the permanent environmental effect (5th order). Data pertaining to 1,583 lactation records spread over a period of 30 years were recorded and analyzed in the study. The variance component, heritability and genetic correlations among test-day milk yields were estimated using RRM. RRM heritability estimates of test-day milk yield varied from 0.11 to 0.22 in different test-day records. The estimates of genetic correlations between different test-day milk yields ranged 0.01 (test-day 1 [TD-1] and TD-11) to 0.99 (TD-4 and TD-5). The magnitudes of genetic correlations between test-day milk yields decreased as the interval between test-days increased and adjacent test-day had higher correlations. Additive genetic and permanent environment variances were higher for test-day milk yields at both ends of lactation. The residual variance was observed to be lower than the permanent environment variance for all the test-day milk yields. PMID:26954137

  17. Shared spatial effects on quantitative genetic parameters: accounting for spatial autocorrelation and home range overlap reduces estimates of heritability in wild red deer.

    PubMed

    Stopher, Katie V; Walling, Craig A; Morris, Alison; Guinness, Fiona E; Clutton-Brock, Tim H; Pemberton, Josephine M; Nussey, Daniel H

    2012-08-01

    Social structure, limited dispersal, and spatial heterogeneity in resources are ubiquitous in wild vertebrate populations. As a result, relatives share environments as well as genes, and environmental and genetic sources of similarity between individuals are potentially confounded. Quantitative genetic studies in the wild therefore typically account for easily captured shared environmental effects (e.g., parent, nest, or region). Fine-scale spatial effects are likely to be just as important in wild vertebrates, but have been largely ignored. We used data from wild red deer to build "animal models" to estimate additive genetic variance and heritability in four female traits (spring and rut home range size, offspring birth weight, and lifetime breeding success). We then, separately, incorporated spatial autocorrelation and a matrix of home range overlap into these models to estimate the effect of location or shared habitat on phenotypic variation. These terms explained a substantial amount of variation in all traits and their inclusion resulted in reductions in heritability estimates, up to an order of magnitude up for home range size. Our results highlight the potential of multiple covariance matrices to dissect environmental, social, and genetic contributions to phenotypic variation, and the importance of considering fine-scale spatial processes in quantitative genetic studies. PMID:22834741

  18. Using a hybrid Monte Carlo/Genetic Algorithm Slip Estimator to produce high resolution models of paleoearthquakes from geodetic data

    NASA Astrophysics Data System (ADS)

    Lindsay, A.; McCloskey, J.; Nalbant, S. S.; Simao, N.; Murphy, S.; NicBhloscaidh, M.; Steacy, S.

    2013-12-01

    Identifying fault sections where slip deficits have accumulated may provide a means for understanding sequences of large megathrust earthquakes. Stress accumulated during the interseismic period on locked sections of an active fault is stored as potential slip. Where this potential slip remains unreleased during earthquakes, a slip deficit can be said to have accrued. Analysis of the spatial distribution of slip during antecedent events along the fault will show where the locked plate has spent its stored slip and indicate where the potential for large events remains. The location of recent earthquakes and their distribution of slip can be estimated instrumentally. To develop the idea of long-term slip-deficit modelling it is necessary to constrain the size and distribution of slip for pre-instrumental events dating back hundreds of years covering more than one ';seismic cycle'. This requires the exploitation of proxy sources of data. Coral microatolls, growing in the intertidal zone of the outer island arc of the Sunda trench, present the possibility of producing high resolution reconstructions of slip for a number of pre-instrumental earthquakes. Their growth is influenced by tectonic flexing of the continental plate beneath them allows them to act as long term geodetic recorders. However, the sparse distribution of data available using coral geodesy results in a under determined problem with non-unique solutions. Instead of producing one definite model satisfying the observed corals displacements, a Monte Carlo Slip Estimator based on a Genetic Algorithm (MCSE-GA) accelerating the rate of convergence is used to identify a suite of models consistent with the data. Successive iterations of the MCSE-GA sample different displacements at each coral location, from within the spread of associated uncertainties, producing a catalog of models from the full range of possibilities. The suite of best slip distributions are weighted according to their fitness and stacked to

  19. Range-Wide Genetic Analysis of Little Brown Bat (Myotis lucifugus) Populations: Estimating the Risk of Spread of White-Nose Syndrome

    PubMed Central

    Vonhof, Maarten J.; Russell, Amy L.; Miller-Butterworth, Cassandra M.

    2015-01-01

    The little brown bat (Myotis lucifugus) is one of the most widespread bat species in North America and is experiencing severe population declines because of an emerging fungal disease, white-nose syndrome (WNS). To manage and conserve this species effectively it is important to understand patterns of gene flow and population connectivity to identify possible barriers to disease transmission. However, little is known about the population genetic structure of little brown bats, and to date, no studies have investigated population structure across their entire range. We examined mitochondrial DNA and nuclear microsatellites in 637 little brown bats (including all currently recognized subspecific lineages) from 29 locations across North America, to assess levels of genetic variation and population differentiation across the range of the species, including areas affected by WNS and those currently unaffected. We identified considerable spatial variation in patterns of female dispersal and significant genetic variation between populations in eastern versus western portions of the range. Overall levels of nuclear genetic differentiation were low, and there is no evidence for any major barriers to gene flow across their range. However, patterns of mtDNA differentiation are highly variable, with high ΦST values between most sample pairs (including between all western samples, between western and eastern samples, and between some eastern samples), while low mitochondrial differentiation was observed within two groups of samples found in central and eastern regions of North America. Furthermore, the Alaskan population was highly differentiated from all others, and western populations were characterized by isolation by distance while eastern populations were not. These data raise the possibility that the current patterns of spread of WNS observed in eastern North America may not apply to the entire range and that there may be broad-scale spatial variation in the risk of WNS

  20. Range-Wide Genetic Analysis of Little Brown Bat (Myotis lucifugus) Populations: Estimating the Risk of Spread of White-Nose Syndrome.

    PubMed

    Vonhof, Maarten J; Russell, Amy L; Miller-Butterworth, Cassandra M

    2015-01-01

    The little brown bat (Myotis lucifugus) is one of the most widespread bat species in North America and is experiencing severe population declines because of an emerging fungal disease, white-nose syndrome (WNS). To manage and conserve this species effectively it is important to understand patterns of gene flow and population connectivity to identify possible barriers to disease transmission. However, little is known about the population genetic structure of little brown bats, and to date, no studies have investigated population structure across their entire range. We examined mitochondrial DNA and nuclear microsatellites in 637 little brown bats (including all currently recognized subspecific lineages) from 29 locations across North America, to assess levels of genetic variation and population differentiation across the range of the species, including areas affected by WNS and those currently unaffected. We identified considerable spatial variation in patterns of female dispersal and significant genetic variation between populations in eastern versus western portions of the range. Overall levels of nuclear genetic differentiation were low, and there is no evidence for any major barriers to gene flow across their range. However, patterns of mtDNA differentiation are highly variable, with high ΦST values between most sample pairs (including between all western samples, between western and eastern samples, and between some eastern samples), while low mitochondrial differentiation was observed within two groups of samples found in central and eastern regions of North America. Furthermore, the Alaskan population was highly differentiated from all others, and western populations were characterized by isolation by distance while eastern populations were not. These data raise the possibility that the current patterns of spread of WNS observed in eastern North America may not apply to the entire range and that there may be broad-scale spatial variation in the risk of WNS

  1. Building genetic networks using relatedness information: a novel approach for the estimation of dispersal and characterization of group structure in social animals.

    PubMed

    Rollins, Lee Ann; Browning, Lucy E; Holleley, Clare E; Savage, James L; Russell, Andrew F; Griffith, Simon C

    2012-04-01

    Natal dispersal is an important life history trait driving variation in individual fitness, and therefore, a proper understanding of the factors underlying dispersal behaviour is critical to many fields including population dynamics, behavioural ecology and conservation biology. However, individual dispersal patterns remain difficult to quantify despite many years of research using direct and indirect methods. Here, we quantify dispersal in a single intensively studied population of the cooperatively breeding chestnut-crowned babbler (Pomatostomus ruficeps) using genetic networks created from the combination of pairwise relatedness data and social networking methods and compare this to dispersal estimates from re-sighting data. This novel approach not only identifies movements between social groups within our study sites but also provides an estimation of immigration rates of individuals originating outside the study site. Both genetic and re-sighting data indicated that dispersal was strongly female biased, but the magnitude of dispersal estimates was much greater using genetic data. This suggests that many previous studies relying on mark-recapture data may have significantly underestimated dispersal. An analysis of spatial genetic structure within the sampled population also supports the idea that females are more dispersive, with females having no structure beyond the bounds of their own social group, while male genetic structure expands for 750 m from their social group. Although the genetic network approach we have used is an excellent tool for visualizing the social and genetic microstructure of social animals and identifying dispersers, our results also indicate the importance of applying them in parallel with behavioural and life history data. PMID:22335253

  2. Estimating the predictive ability of genetic risk models in simulated data based on published results from genome-wide association studies

    PubMed Central

    Kundu, Suman; Mihaescu, Raluca; Meijer, Catherina M. C.; Bakker, Rachel; Janssens, A. Cecile J. W.

    2014-01-01

    Background: There is increasing interest in investigating genetic risk models in empirical studies, but such studies are premature when the expected predictive ability of the risk model is low. We assessed how accurately the predictive ability of genetic risk models can be estimated in simulated data that are created based on the odds ratios (ORs) and frequencies of single-nucleotide polymorphisms (SNPs) obtained from genome-wide association studies (GWASs). Methods: We aimed to replicate published prediction studies that reported the area under the receiver operating characteristic curve (AUC) as a measure of predictive ability. We searched GWAS articles for all SNPs included in these models and extracted ORs and risk allele frequencies to construct genotypes and disease status for a hypothetical population. Using these hypothetical data, we reconstructed the published genetic risk models and compared their AUC values to those reported in the original articles. Results: The accuracy of the AUC values varied with the method used for the construction of the risk models. When logistic regression analysis was used to construct the genetic risk model, AUC values estimated by the simulation method were similar to the published values with a median absolute difference of 0.02 [range: 0.00, 0.04]. This difference was 0.03 [range: 0.01, 0.06] and 0.05 [range: 0.01, 0.08] for unweighted and weighted risk scores. Conclusions: The predictive ability of genetic risk models can be estimated using simulated data based on results from GWASs. Simulation methods can be useful to estimate the predictive ability in the absence of empirical data and to decide whether empirical investigation of genetic risk models is warranted. PMID:24982668

  3. Plasmacytoid dendritic cells are short-lived: reappraising the influence of migration, genetic factors and activation on estimation of lifespan.

    PubMed

    Zhan, Yifan; Chow, Kevin V; Soo, Priscilla; Xu, Zhen; Brady, Jamie L; Lawlor, Kate E; Masters, Seth L; O'keeffe, Meredith; Shortman, Ken; Zhang, Jian-Guo; Lew, Andrew M

    2016-01-01

    Plasmacytoid dendritic cells (pDCs) play an important role in immunity to certain pathogens and immunopathology in some autoimmune diseases. They are thought to have a longer lifespan than conventional DCs (cDCs), largely based on a slower rate of BrdU labeling by splenic pDCs. Here we demonstrated that pDC expansion and therefore BrdU labeling by pDCs occurs in bone marrow (BM). The rate of labeling was similar between BM pDCs and spleen cDCs. Therefore, slower BrdU labeling of spleen pDCs likely reflects the "migration time" (∼2 days) for BrdU labeled pDCs to traffic to the spleen, not necessarily reflecting longer life span. Tracking the decay of differentiated DCs showed that splenic pDCs and cDCs decayed at a similar rate. We suggest that spleen pDCs have a shorter in vivo lifespan than estimated utilizing some of the previous approaches. Nevertheless, pDC lifespan varies between mouse strains. pDCs from lupus-prone NZB mice survived longer than C57BL/6 pDCs. We also demonstrated that activation either positively or negatively impacted on the survival of pDCs via different cell-death mechanisms. Thus, pDCs are also short-lived. However, the pDC lifespan is regulated by genetic and environmental factors that may have pathological consequence. PMID:27112985

  4. Tuning of Kalman Filter Parameters via Genetic Algorithm for State-of-Charge Estimation in Battery Management System

    PubMed Central

    Ting, T. O.; Lim, Eng Gee

    2014-01-01

    In this work, a state-space battery model is derived mathematically to estimate the state-of-charge (SoC) of a battery system. Subsequently, Kalman filter (KF) is applied to predict the dynamical behavior of the battery model. Results show an accurate prediction as the accumulated error, in terms of root-mean-square (RMS), is a very small value. From this work, it is found that different sets of Q and R values (KF's parameters) can be applied for better performance and hence lower RMS error. This is the motivation for the application of a metaheuristic algorithm. Hence, the result is further improved by applying a genetic algorithm (GA) to tune Q and R parameters of the KF. In an online application, a GA can be applied to obtain the optimal parameters of the KF before its application to a real plant (system). This simply means that the instantaneous response of the KF is not affected by the time consuming GA as this approach is applied only once to obtain the optimal parameters. The relevant workable MATLAB source codes are given in the appendix to ease future work and analysis in this area. PMID:25162041

  5. Plasmacytoid dendritic cells are short-lived: reappraising the influence of migration, genetic factors and activation on estimation of lifespan

    PubMed Central

    Zhan, Yifan; Chow, Kevin V.; Soo, Priscilla; Xu, Zhen; Brady, Jamie L.; Lawlor, Kate E.; Masters, Seth L.; O’keeffe, Meredith; Shortman, Ken; Zhang, Jian-Guo; Lew, Andrew M.

    2016-01-01

    Plasmacytoid dendritic cells (pDCs) play an important role in immunity to certain pathogens and immunopathology in some autoimmune diseases. They are thought to have a longer lifespan than conventional DCs (cDCs), largely based on a slower rate of BrdU labeling by splenic pDCs. Here we demonstrated that pDC expansion and therefore BrdU labeling by pDCs occurs in bone marrow (BM). The rate of labeling was similar between BM pDCs and spleen cDCs. Therefore, slower BrdU labeling of spleen pDCs likely reflects the “migration time” (∼2 days) for BrdU labeled pDCs to traffic to the spleen, not necessarily reflecting longer life span. Tracking the decay of differentiated DCs showed that splenic pDCs and cDCs decayed at a similar rate. We suggest that spleen pDCs have a shorter in vivo lifespan than estimated utilizing some of the previous approaches. Nevertheless, pDC lifespan varies between mouse strains. pDCs from lupus-prone NZB mice survived longer than C57BL/6 pDCs. We also demonstrated that activation either positively or negatively impacted on the survival of pDCs via different cell-death mechanisms. Thus, pDCs are also short-lived. However, the pDC lifespan is regulated by genetic and environmental factors that may have pathological consequence. PMID:27112985

  6. Estimation of the minimum uncertainty of DNA concentration in a genetically modified maize sample candidate certified reference material.

    PubMed

    Prokisch, J; Zeleny, R; Trapmann, S; Le Guern, L; Schimmel, H; Kramer, G N; Pauwels, J

    2001-08-01

    Homogeneity testing and the determination of minimum sample mass are an important part of the certification of reference materials. The smallest theoretically achievable uncertainty of certified concentration values is limited by the concentration distribution of analyte in the different particle size fractions of powdered biological samples. This might be of special importance if the reference material is prepared by dry mixing, a dilution technique which is used for the production of the new and third generation of genetically modified (GMO) plant certified reference materials. For the production of dry mixed PMON 810 maize reference material a computer program was developed to calculate the theoretically smallest uncertainty for a selected sample intake. This model was used to compare three differently milled maize samples, and the effect of dilution on the uncertainty of the DNA content of GMO maize was estimated as well. In the case of a 50-mg sample mass the lowest achievable standard deviation was 2% for the sample containing 0.1% GMO and the minimum deviation was less than 0.5% for the sample containing 5% GMO. PMID:11569879

  7. Vehicle barrier

    DOEpatents

    Hirsh, Robert A.

    1991-01-01

    A vehicle security barrier which can be conveniently placed across a gate opening as well as readily removed from the gate opening to allow for easy passage. The security barrier includes a barrier gate in the form of a cable/gate member in combination with laterally attached pipe sections fixed by way of the cable to the gate member and lateral, security fixed vertical pipe posts. The security barrier of the present invention provides for the use of cable restraints across gate openings to provide necessary security while at the same time allowing for quick opening and closing of the gate areas without compromising security.

  8. Is Pairing with a Relative Heritable? Estimating Female and Male Genetic Contributions to the Degree of Biparental Inbreeding in Song Sparrows (Melospiza melodia).

    PubMed

    Wolak, Matthew E; Reid, Jane M

    2016-06-01

    The degree of inbreeding expressed within populations can profoundly shape evolutionary dynamics. The degree to which individuals inbreed is frequently assumed to evolve in response to selection, for example, resulting from inbreeding depression. Such evolutionary responses require additive genetic variance (VA) in the degree to which individuals inbreed. However, the magnitude of VA in the degree of biparental inbreeding has never been estimated. We devised a quantitative genetic model to estimate sex-specific VA in the degree to which individuals inbreed while accounting for effects of individuals' own coefficients of inbreeding and genetic effects stemming from immigration. We applied this model to the degree of inbreeding expressed through social pairing in free-living song sparrows (Melospiza melodia). Estimates of VA for both sexes appreciably exceeded 0 and the cross-sex genetic covariance was strongly positive, creating substantial total VA in the degree of inbreeding. Our analyses also revealed inbreeding depression in the degree of inbreeding, such that more inbred individuals paired with closer relatives, and immigrant effects, such that individuals with greater genomic contributions from immigrants paired with more distant relatives. We thereby demonstrate that the degree of biparental inbreeding can show substantial VA in nature and might consequently evolve in response to selection. PMID:27172593

  9. Estimates of effective population size and inbreeding in South African indigenous chicken populations: implications for the conservation of unique genetic resources.

    PubMed

    Mtileni, Bohani; Dzama, Kennedy; Nephawe, Khathutshelo; Rhode, Clint

    2016-06-01

    Conservation of locally adapted indigenous livestock breeds has become an important objective in sustainable animal breeding, as these breeds represent a unique genetic resource. Therefore, the Agricultural Research Council of South Africa initiated a conservation programme for four South African indigenous chicken breeds. The evaluation and monitoring of the genetic constitution of these conservation flocks is important for proper management of the conservation programme. Using molecular genetic analyses, the effective population sizes and relatedness of these conservation flocks were compared to village (field) chicken populations from which they were derived. Genetic diversity within and between these populations are further discussed within the context of population size. The conservation flocks for the respective breeds had relatively small effective population sizes (point estimate range 38.6-78.6) in comparison to the field populations (point estimate range 118.9-580.0). Furthermore, evidence supports a transient heterozygous excess, generally associated with the occurrence of a recent population bottleneck. Genetic diversity, as measured by the number of alleles, heterozygosity and information index, was also significantly reduced in the conservation flocks. The average relatedness amongst the conservation flocks was high, whilst it remained low for the field populations. There was also significant evidence for population differentiation between field and conservation populations. F st estimates for conservation flocks were moderate to high with a maximum reached between VD_C and VD_F (0.285). However, F st estimates for field population were excessively low between the NN_C and EC_F (0.007) and between EC_F and OV_F (0.009). The significant population differentiation of the conservation flocks from their geographically correlated field populations of origin is further supported by the analysis of molecular variance (AMOVA), with 10.51 % of genetic

  10. Ionizing radiation and genetic risks. VIII. The concept of mutation component and its use in risk estimation for multifactorial diseases.

    PubMed

    Denniston, C; Chakraborty, R; Sankaranarayanan, K

    1998-08-31

    Multifactorial diseases, which include the common congenital abnormalities (incidence: 6%) and chronic diseases with onset predominantly in adults (population prevalence: 65%), contribute substantially to human morbidity and mortality. Their transmission patterns do not conform to Mendelian expectations. The model most frequently used to explain their inheritance and to estimate risks to relatives is a Multifactorial Threshold Model (MTM) of disease liability. The MTM assumes that: (i) the disease is due to the joint action of a large number of genetic and environmental factors, each of which contributing a small amount of liability, (ii) the distribution of liability in the population is Gaussian and (iii) individuals whose liability exceeds a certain threshold value are affected by the disease. For most of these diseases, the number of genes involved or the environmental factors are not fully known. In the context of radiation exposures of the population, the question of the extent to which induced mutations will cause an increase in the frequencies of these diseases has remained unanswered. In this paper, we address this problem by using a modified version of MTM which incorporates mutation and selection as two additional parameters. The model assumes a finite number of gene loci and threshold of liability (hence, the designation, Finite-Locus Threshold Model or FLTM). The FLTM permits one to examine the relationship between broad-sense heritability of disease liability and mutation component (MC), the responsiveness of the disease to a change in mutation rate. Through the use of a computer program (in which mutation rate, selection, threshold, recombination rate and environmental variance are input parameters and MC and heritability of liability are output estimates), we studied the MC-heritability relationship for (i) a permanent increase in mutation rate (e.g., when the population sustains radiation exposure in every generation) and (ii) a one-time increase

  11. Estimation of genetic variability and selection response for clutch length in dwarf brown-egg layers carrying or not the naked neck gene.

    PubMed

    Chen, Chih-Feng; Tixier-Boichard, Michèle

    2003-01-01

    In order to investigate the possibility of using the dwarf gene for egg production, two dwarf brown-egg laying lines were selected for 16 generations on average clutch length; one line (L1) was normally feathered and the other (L2) was homozygous for the naked neck gene NA. A control line from the same base population, dwarf and segregating for the NA gene, was maintained during the selection experiment under random mating. The average clutch length was normalized using a Box-Cox transformation. Genetic variability and selection response were estimated either with the mixed model methodology, or with the classical methods for calculating genetic gain, as the deviation from the control line, and the realized heritability, as the ratio of the selection response on cumulative selection differentials. Heritability of average clutch length was estimated to be 0.42 +/- 0.02, with a multiple trait animal model, whereas the estimates of the realized heritability were lower, being 0.28 and 0.22 in lines L1 and L2, respectively. REML estimates of heritability were found to decline with generations of selection, suggesting a departure from the infinitesimal model, either because a limited number of genes was involved, or their frequencies were changed. The yearly genetic gains in average clutch length, after normalization, were estimated to be 0.37 +/- 0.02 and 0.33 +/- 0.04 with the classical methods, 0.46 +/- 0.02 and 0.43 +/- 0.01 with animal model methodology, for lines L1 and L2 respectively, which represented about 30% of the genetic standard deviation on the transformed scale. Selection response appeared to be faster in line L2, homozygous for the NA gene, but the final cumulated selection response for clutch length was not different between the L1 and L2 lines at generation 16. PMID:12633534

  12. Geographically weighted regression as a generalized Wombling to detect barriers to gene flow.

    PubMed

    Diniz-Filho, José Alexandre Felizola; Soares, Thannya Nascimento; de Campos Telles, Mariana Pires

    2016-08-01

    Barriers to gene flow play an important role in structuring populations, especially in human-modified landscapes, and several methods have been proposed to detect such barriers. However, most applications of these methods require a relative large number of individuals or populations distributed in space, connected by vertices from Delaunay or Gabriel networks. Here we show, using both simulated and empirical data, a new application of geographically weighted regression (GWR) to detect such barriers, modeling the genetic variation as a "local" linear function of geographic coordinates (latitude and longitude). In the GWR, standard regression statistics, such as R(2) and slopes, are estimated for each sampling unit and thus are mapped. Peaks in these local statistics are then expected close to the barriers if genetic discontinuities exist, capturing a higher rate of population differentiation among neighboring populations. Isolation-by-Distance simulations on a longitudinally warped lattice revealed that higher local slopes from GWR coincide with the barrier detected with Monmonier algorithm. Even with a relatively small effect of the barrier, the power of local GWR in detecting the east-west barriers was higher than 95 %. We also analyzed empirical data of genetic differentiation among tree populations of Dipteryx alata and Eugenia dysenterica Brazilian Cerrado. GWR was applied to the principal coordinate of the pairwise FST matrix based on microsatellite loci. In both simulated and empirical data, the GWR results were consistent with discontinuities detected by Monmonier algorithm, as well as with previous explanations for the spatial patterns of genetic differentiation for the two species. Our analyses reveal how this new application of GWR can viewed as a generalized Wombling in a continuous space and be a useful approach to detect barriers and discontinuities to gene flow. PMID:27353234

  13. Application of the genetic algorithm to estimate the parameters related to the kinetics of the reduction of the iron ore, coal mixture

    SciTech Connect

    Kumar, A.; Roy, G.G.

    2005-12-01

    A novel methodology has been developed to calculate the kinetic parameters associated with reduction of ore-coal composite mixtures and to describe the time course of reduction of hematite to iron. The empirical parameters, namely, the three sets of activation energies and frequency factors, have been estimated by employing an evolutionary optimization tool, the genetic algorithm (GA). The model prediction matches well with the experimental literature data. The estimated activation energies are higher than the corresponding intrinsic values, indicating the role of heat transfer in the process.

  14. Estimates of genetic parameters for 320-day pelvic measurements of males and females and calving ease of 2-year-old females.

    PubMed

    Kriese, L A; Van Vleck, L D; Gregory, K E; Boldman, K G; Cundiff, L V; Koch, R M

    1994-08-01

    Records from 12 breed groups collected from 1983 to 1991, included in the Germ Plasm Utilization project at the U.S. Meat Animal Research Center, were analyzed separately by breed group and combined to estimate heritabilities and genetic correlations for 320-d male and female pelvic width, height, and area, and for 320-d male pelvic and female 2-yr-old calving ease. Calving ease was analyzed as a trait of the dam using 1) actual and 2) binary scale calving ease scores with a covariate of calf birth weight. A bivariate animal model and derivative-free REML incorporating sparse matrix techniques were used. When breed groups were analyzed separately, heritability estimates of male and female 320-d pelvic traits varied by breed group and sex. Average genetic correlations between male and female 320-d pelvic width, pelvic height, and pelvic area were large and positive. When breed groups were combined (n = 26,071), heritability estimates for 320-d pelvic traits were moderate in size. Genetic correlations of .68, .48, and .61, between male and female 320-d pelvic width, height, and area, respectively, suggest male and female pelvic traits are largely under the same genetic control but are correlated traits rather than the same trait. Heritability estimates for actual calving ease in 2-yr-olds ranged from .00 to .49 in separate breed group analyses, and from .00 to .37 for binary measures. When breed groups were combined, heritability was .11 for actual calving ease and was .09 on the binary scale.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7982822

  15. A genetic method for dating ancient genomes provides a direct estimate of human generation interval in the last 45,000 years.

    PubMed

    Moorjani, Priya; Sankararaman, Sriram; Fu, Qiaomei; Przeworski, Molly; Patterson, Nick; Reich, David

    2016-05-17

    The study of human evolution has been revolutionized by inferences from ancient DNA analyses. Key to these studies is the reliable estimation of the age of ancient specimens. High-resolution age estimates can often be obtained using radiocarbon dating, and, while precise and powerful, this method has some biases, making it of interest to directly use genetic data to infer a date for samples that have been sequenced. Here, we report a genetic method that uses the recombination clock. The idea is that an ancient genome has evolved less than the genomes of present-day individuals and thus has experienced fewer recombination events since the common ancestor. To implement this idea, we take advantage of the insight that all non-Africans have a common heritage of Neanderthal gene flow into their ancestors. Thus, we can estimate the date since Neanderthal admixture for present-day and ancient samples simultaneously and use the difference as a direct estimate of the ancient specimen's age. We apply our method to date five Upper Paleolithic Eurasian genomes with radiocarbon dates between 12,000 and 45,000 y ago and show an excellent correlation of the genetic and (14)C dates. By considering the slope of the correlation between the genetic dates, which are in units of generations, and the (14)C dates, which are in units of years, we infer that the mean generation interval in humans over this period has been 26-30 y. Extensions of this methodology that use older shared events may be applicable for dating beyond the radiocarbon frontier. PMID:27140627

  16. A Preliminary Study of Genetic Variation in Populations of Monstera adansonii var. klotzschiana (Araceae) from North-East Brazil, Estimated with AFLP Molecular Markers

    PubMed Central

    Andrade, I. M.; Mayo, S. J.; van den Berg, C.; Fay, M. F.; Chester, M.; Lexer, C.; Kirkup, D.

    2007-01-01

    Background and Aims This study sought genetic evidence of long-term isolation in populations of Monstera adansonii var. klotzschiana (Araceae), a herbaceous, probably outbreeding, humid forest hemi-epiphyte, in the brejo forests of Ceará (north-east Brazil), and clarification of their relationships with populations in Amazonia and the Atlantic forest of Brazil. Methods Within-population genetic diversity and between-population dissimilarity were estimated using AFLP molecular markers in 75 individuals from eight populations located in Ceará, the Brazilian Atlantic Forest and Amazonia. Key Results The populations showed a clinal pattern of weak genetic differentiation over a large geographical region (FST = 0·1896). A strong correlation between genetic and geographical distance (Mantel test: r = 0·6903, P = 0·002) suggests a historical pattern of isolation by distance. Genetic structure analysis revealed at least two distinct gene pools in the data. The two isolated Ceará populations are significantly different from each other (pairwise ΦPT = 0·137, P = 0·003) and as diverse (Nei's gene diversity, average He = 0·1832, 0·1706) as those in the Atlantic and Amazon forest regions. The population in southern Brazil is less diverse (Nei's gene diversity, average He = 0·127) than the rest. The Ceará populations are related to those of the Atlantic forest rather than those from Amazonia (AMOVA, among-groups variation = 11·95 %, P = 0·037). Conclusions The gene pools detected within an overall pattern of clinal variation suggest distinct episodes of gene flow, possibly correlated with past humid forest expansions. The Ceará populations show no evidence of erosion of genetic diversity, although this was expected because of their isolation. Their genetic differentiation and relatively high diversity reinforce the importance of conserving the endangered brejo forests. PMID:17823112

  17. Estimation of genetic trends from 1977 to 1998 for farrowing characteristics in the French Large White breed using frozen semen.

    PubMed

    Canario, L; Rydhmer, L; Gogué, J; Tribout, T; Bidanel, J P

    2007-08-01

    The objective of the study was to estimate genetic trends from 1977 to 1998 in the French Large White (LW) breed for stillbirth and associated traits measured at farrowing using frozen semen. Two groups of pigs (G77 and G98) were obtained by inseminating LW sows with semen from LW boars born either in 1977 or in 1998. A second generation was produced by inter se mating in each group. Farrowing was thoroughly supervised through both direct observations and video recording all long farrowing on a total of 137 first- and second-parity litters produced by sows from this second generation (68 G77 and 69 G98 litters, respectively). Measurements included birth time, weight and birth characteristics (including orientation, presence of cyanosis or oedema, membrane obstruction, umbilical cord length/content) of each piglet, as well as sow traits (weight and backfat thickness, farrowing duration, litter size and within-litter variation of weights at birth). The data were analysed using linear or generalised linear mixed models, according to the definition of the trait (continuous or binary data). The importance of several effects to piglet probability of stillbirth was then quantified by computing the reduction of variance associated with the addition of each effect in the model. Litter size did not significantly differ in first parity, but was higher in G98 second-parity sows: the differences for global (including pre partum dead piglets) and total numbers of piglets born per litter were +2.3 ± 1.1 and +1.3 ± 0.6, respectively. G98 sows also had a higher number of stillbirths in both parities (+0.7 ± 0.3 stillborn per litter). Piglets from G98 litters were heavier at birth (+130 ± 40 g for birth weight adjusted for litter size), without any increase in within-litter heterogeneity of birth weight. No significant difference was detected between G77 and G88 groups for farrowing length and the distribution of time interval between piglet births. G98 stillborn piglets had

  18. [Individual identification of Amur leopards (Panthera pardus orientalis) using molecular-genetic methods and estimation of the population].

    PubMed

    Rozhnov, V V; Sorokin, P A; Lukarevskiĭ, V S; Naĭdenko, S V; Ernandes-Blanko, Kh A; Lukarevskiĭ, S V

    2013-01-01

    For the first time, the genetic structure of a population of Amur leopards (Panthera pardus orientalis) in southwest Primorie was analyzed in detail. In 2010-2012, 23 individuals were identified individually. It was shown that the studied microsatellite markers are suitable for individual identification of leopards, monitoring the population numbers, and creating a unified database of genetic profiles of this species to solve research and nature-preserving tasks. PMID:23789419

  19. Comparison between morphological and genetic data to estimate biological relationship: the case of the Egyin Gol necropolis (Mongolia).

    PubMed

    Ricaut, François-X; Auriol, Vincent; von Cramon-Taubadel, Noreen; Keyser, Christine; Murail, Pascal; Ludes, Bertrand; Crubézy, Eric

    2010-11-01

    Osseous and dental nonmetric (discrete) traits have long been used to assess population variability and affinity in anthropological and archaeological contexts. However, the full extent to which nonmetric traits can reliably be used as a proxy for genetic data when assessing close or familial relationships is currently poorly understood. This study represents the unique opportunity to directly compare genetic and nonmetric data for the same individuals excavated from the Egyin Gol necropolis, Mongolia. These data were analyzed to consider the general efficacy of nonmetric traits for detecting familial groupings in the absence of available genetic data. The results showed that the Egyin Gol population is quite homogenous both metrically and genetically confirming a previous suggestion that the same people occupied the necropolis throughout the five centuries of its existence. Kinship analysis detected the presence of potential family burials in the necropolis. Moreover, individuals buried in one sector of the necropolis were differentiated from other sectors on the basis of nonmetric data. This separation is likely due to an outside Turkish influence in the paternal line, as indicated by the results of Y-chromosome analysis. Affinity matrices based on nonmetric and genetic data were correlated demonstrating the potential of nonmetric traits for detecting relationships in the absence of genetic data. However, the strengths of the correlations were relatively low, cautioning against the use of nonmetric traits when the resolution of the familial relationships is low. PMID:20949608

  20. [Hyper spectral estimation method for soil alkali hydrolysable nitrogen content based on discrete wavelet transform and genetic algorithm in combining with partial least squares DWT-GA-PLS)].

    PubMed

    Chen, Hong-Yan; Zhao, Geng-Xing; Li, Xi-Can; Wang, Xiang-Feng; Li, Yu-Ling

    2013-11-01

    Taking the Qihe County in Shandong Province of East China as the study area, soil samples were collected from the field, and based on the hyperspectral reflectance measurement of the soil samples and the transformation with the first deviation, the spectra were denoised and compressed by discrete wavelet transform (DWT), the variables for the soil alkali hydrolysable nitrogen quantitative estimation models were selected by genetic algorithms (GA), and the estimation models for the soil alkali hydrolysable nitrogen content were built by using partial least squares (PLS) regression. The discrete wavelet transform and genetic algorithm in combining with partial least squares (DWT-GA-PLS) could not only compress the spectrum variables and reduce the model variables, but also improve the quantitative estimation accuracy of soil alkali hydrolysable nitrogen content. Based on the 1-2 levels low frequency coefficients of discrete wavelet transform, and under the condition of large scale decrement of spectrum variables, the calibration models could achieve the higher or the same prediction accuracy as the soil full spectra. The model based on the second level low frequency coefficients had the highest precision, with the model predicting R2 being 0.85, the RMSE being 8.11 mg x kg(-1), and RPD being 2.53, indicating the effectiveness of DWT-GA-PLS method in estimating soil alkali hydrolysable nitrogen content. PMID:24564148

  1. Genetic admixture, self-reported ethnicity, self-estimated admixture, and skin pigmentation among Hispanics and Native Americans.

    PubMed

    Klimentidis, Yann C; Miller, Geoffrey F; Shriver, Mark D

    2009-04-01

    The relationship between ethnicity and biology is of interest to anthropologists, biomedical scientists, and historians in understanding how human groups are constructed. Ethnic self-identification in recently admixed groups such as Hispanics, African Americans, and Native Americans (NA) is likely to be complex due to the heterogeneity in individual admixture proportions and social environments within these groups. This study examines the relationships between self-identified ethnicity, self-estimated admixture proportions, skin pigmentation, and genetic marker estimated admixture proportions. These measures were assessed using questionnaires, skin color measurements, and genotyping of a panel of 76 ancestry informative markers, among 170 Hispanics and NAs from New Mexico, a state known for its complex history of interactions between people of NA and European (EU) ancestry. Results reveal that NAs underestimate their degree of EU admixture, and that Hispanics underestimate their degree of NA admixture. Within Hispanics, genetic-marker estimated admixture is better predicted by forehead skin pigmentation than by self-estimated admixture. We also find that Hispanic individuals self-identified as "half-White, half Hispanic" and "Spanish" have lower levels of NA admixture than those self-identified as "Mexican" and "Mexican American." Such results highlight the interplay between culture and biology in how individuals identify and view themselves, and have implications for how ethnicity and disease risk are assessed in a medical setting. PMID:18951390

  2. Potential of Start Codon Targeted (SCoT) markers to estimate genetic diversity and relationships among Chinese Elymus sibiricus accessions.

    PubMed

    Zhang, Junchao; Xie, Wengang; Wang, Yanrong; Zhao, Xuhong

    2015-01-01

    Elymus sibiricus as an important forage grass and gene pool for improving cereal crops, that is widely distributed in West and North China. Information on its genetic diversity and relationships is limited but necessary for germplasm collection, conservation and future breeding. Start Codon Targeted (SCoT) markers were used for studying the genetic diversity and relationships among 53 E. sibiricus accessions from its primary distribution area in China. A total of 173 bands were generated from 16 SCoT primers, 159 bands of which were polymorphic with the percentage of polymorphic bands (PPB) of 91.91%. Based upon population structure analysis five groups were formed. The cluster analysis separated the accessions into two major clusters and three sub-clusters, similar to results of principal coordinate analysis (PCoA). The molecular variance analysis (AMOVA) showed that genetic variation was greater within geographical regions (50.99%) than between them (49.01%). Furthermore, the study also suggested that collecting and evaluating E. sibiricus germplasm for major geographic regions and special environments broadens the available genetic base and illustrates the range of variation. The results of the present study showed that SCoT markers were efficient in assessing the genetic diversity among E. sibiricus accessions. PMID:25853316

  3. Application of multivariate heavy-tailed distributions to residuals in the estimation of genetic parameters of growth traits in beef cattle.

    PubMed

    Peters, S O; Kizilkaya, K; Garrick, D J; Fernando, R L; Pollak, E J; De Donato, M; Hussain, T; Imumorin, I G

    2013-04-01

    Assumptions of normality in most animal breeding applications may make inferences vulnerable to the presence of outliers. Heavy-tail densities are viable alternatives to normal distributions and provide robustness against unusual or outlying observations when used to model the densities of residual effects. Our objective is to compare estimates of genetic parameters by fitting multivariate normal (MN) or heavy-tail distributions [multivariate Student's t (MSt) and multivariate slash (MS)] for residuals in data of body birth weight (BBW), weaning (WW), and yearling (YW) weight traits in beef cattle. A total of 17,019 weight records for BBW, WW, and YW from 1998 through 2010 from a large commercial cow/calf operation in the sand hills of Nebraska were analyzed. Models included fixed effects of contemporary group and sire breed whereas animal and maternal effects were random and the degrees of freedom (v) was treated as unknown for MSt and MS. Model comparisons using deviance information criteria (DIC) favored MSt over MS and MN models, respectively. The posterior means [and 95% posterior probability intervals (PPI)] of v for the MSt and MS models were 5.28 (4.80, 5.85) and 1.88 (1.76, 2.00), respectively. Smaller values of posterior densities of v for MSt and MS models confirm that the assumption of normally distributed residuals is not adequate for the analysis of BBW, WW, and YW datasets. Posterior mean (PM) and posterior median (PD) estimates of direct and maternal genetic variances were the same and posterior densities of these parameters were found to be symmetric. The 95% PPI estimates from MN and MSt models for BBW did not overlap, which indicates significant difference between PM estimates from MN or MSt models. The observed antagonistic relationship between additive direct and additive maternal effects indicated that genetic evaluation and selection strategies will be sensitive to the assumed model for residuals. PMID:23408820

  4. Implications of the Hiroshima-Nagasaki genetic studies for the estimation of the human "doubling dose" of radiation.

    PubMed

    Neel, J V; Schull, W J; Awa, A A; Satoh, C; Otake, M; Kato, H; Yoshimoto, Y

    1989-01-01

    Since 1946 a continuous effort to evaluate the potential genetic effects of the atomic bombs has been sustained. Observations on children born in Hiroshima and Nagasaki include sex ratio, congenital malformations, stillbirths, survival of liveborn infants, chromosomal abnormalities (sex chromosomal abnormalities and balanced chromosomal rearrangements), mutations altering protein structure or activity, and physical growth and development. There are no statistically significant differences between the children of parents who received increased amounts of radiation at the time of the bombings and those whose parents did not. However, the difference between the two sets of children is consistent with the hypothesis of a genetic effect of the exposure, but its magnitude suggests humans are not as sensitive to the genetic effects of radiation as projected from the mouse paradigm. PMID:2698842

  5. Estimating Genetic Relationships Among Semi-Dormant and Nondormant Alfalfa Cultivars with Sequence Related Amplified Polymorphisms (SRAPs)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of the present study was to assess the utility of molecular marker data generated by Sequence Related Amplified Polymorphisms (SRAPs) to assess genetic relationships among semi-dormant and non-dormant modern alfalfa cultivars using bulked DNAs. Marker data was also used to examine rel...

  6. The accuracies of DNA-based estimates of genetic merit derived from Angus or multibreed beef cattle training populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Several organizations have developed prediction models for molecular breeding values (MBV) for quantitative growth and carcass traits in beef cattle using BovineSNP50 genotypes and phenotypic or EBV data. MBV for Angus cattle have been developed by IGENITY, Pfizer Animal Genetics, and a collaboratio...

  7. Development of single nucleotide polymorphism (SNP) markers from the mango (Mangiferaindica) transcriptome for mapping and estimation of genetic diversity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The development of resources for genomic studies in Mangifera indica (mango) will allow marker-assisted selection and identification of genetically diverse germplasm, greatly aiding mango breeding programs. We report here a first step in developing such resources, our identification of thousands una...

  8. Genetic Diversity and Population Structure of Tetraploid Wheats (Triticum turgidum L.) Estimated by SSR, DArT and Pedigree Data

    PubMed Central

    Laidò, Giovanni; Mangini, Giacomo; Taranto, Francesca; Gadaleta, Agata; Blanco, Antonio; Cattivelli, Luigi; Marone, Daniela; Mastrangelo, Anna M.; Papa, Roberto; De Vita, Pasquale

    2013-01-01

    Levels of genetic diversity and population genetic structure of a collection of 230 accessions of seven tetraploid Triticum turgidum L. subspecies were investigated using six morphological, nine seed storage protein loci, 26 SSRs and 970 DArT markers. The genetic diversity of the morphological traits and seed storage proteins was always lower in the durum wheat compared to the wild and domesticated emmer. Using Bayesian clustering (K = 2), both of the sets of molecular markers distinguished the durum wheat cultivars from the other tetraploid subspecies, and two distinct subgroups were detected within the durum wheat subspecies, which is in agreement with their origin and year of release. The genetic diversity of morphological traits and seed storage proteins was always lower in the improved durum cultivars registered after 1990, than in the intermediate and older ones. This marked effect on diversity was not observed for molecular markers, where there was only a weak reduction. At K >2, the SSR markers showed a greater degree of resolution than for DArT, with their identification of a greater number of groups within each subspecies. Analysis of DArT marker differentiation between the wheat subspecies indicated outlier loci that are potentially linked to genes controlling some important agronomic traits. Among the 211 loci identified under selection, 109 markers were recently mapped, and some of these markers were clustered into specific regions on chromosome arms 2BL, 3BS and 4AL, where several genes/quantitative trait loci (QTLs) are involved in the domestication of tetraploid wheats, such as the tenacious glumes (Tg) and brittle rachis (Br) characteristics. On the basis of these results, it can be assumed that the population structure of the tetraploid wheat collection partially reflects the evolutionary history of Triticum turgidum L. subspecies and the genetic potential of landraces and wild accessions for the detection of unexplored alleles. PMID:23826256

  9. Genetic parameters estimated at receiving for circulating cortisol, immunoglobulin G, interleukin 8, and incidence of bovine respiratory disease in feedlot beef steers.

    PubMed

    Cockrum, R R; Speidel, S E; Salak-Johnson, J L; Chase, C C L; Peel, R K; Weaber, R L; Loneagan, G H; Wagner, J J; Boddhireddy, P; Thomas, M G; Prayaga, K; DeNise, S; Enns, R M

    2016-07-01

    Bovine respiratory disease complex (i.e., shipping fever and bacterial bronchopneumonia) is a multifaceted respiratory illness influenced by numerous environmental factors and microorganisms. Bovine respiratory disease (BRD) is just one component of BRD complex. Because BRD is moderately heritable, it may be possible to reduce the incidence of BRD through genetic selection. The objectives of this study were to determine the heritability and associative genetic relationships among immune system traits (i.e., cortisol, total IgG, IgG isotypes, and IL-8) in cattle monitored for BRD incidence. At an average of 83 d after weaning (219 d age and mean = 221.7 kg [SD 4.34]), crossbred steer calves ( = 2,869) were received at a commercial feedlot in southeastern Colorado over a 2-yr period. At receiving, jugular blood samples were collected at 212 (yr 1) and 226 d (yr 2) of age for immune trait analyses. The BRD phenotype was defined as a binomial variable (0 = no and 1 = yes) and compared with immune system traits measured at receiving (prior to illness onset). An animal identified as BRD positive exhibited ≥ 2 clinical signs (i.e., eye or nasal discharge, cough, lethargy, rapid breathing, acute interstitial pneumonia, or acute upper respiratory syndrome and/or a rectal temperature > 39.7°C). Heritability and genetic correlation estimates for categorical variable BRD, cortisol, IgG, IgG1, IgG2, and IL-8 were estimated from a sire model using ASREML. Heritability estimates were low to moderate for BRD (0.17 ± 0.08), cortisol (0.13 ± 0.05), IgG (0.15 ± 0.05), IgG1 (0.11 ± 0.05), IgG2 (0.24 ± 0.06), and IL-8 (0.30 ± 0.06). A moderate negative genetic correlation was determined between BRD and cortisol ( = -0.19 ± 0.32). Moderate positive correlations were found between BRD with IgG (0.42 ± 0.28), IgG1 (0.36 ± 0.32), and IL-8 ( = 0.26 ± 0.26). Variation in the BRD phenotype and immune system traits suggested herd health improvement may be achieved through genetic

  10. Estimation of Genetic Parameters and Trends for Length of Productive Life and Lifetime Production Traits in a Commercial Landrace and Yorkshire Swine Population in Northern Thailand

    PubMed Central

    Noppibool, Udomsak; Elzo, Mauricio A.; Koonawootrittriron, Skorn; Suwanasopee, Thanathip

    2016-01-01

    The objective of this research was to estimate genetic parameters and trends for length of productive life (LPL), lifetime number of piglets born alive (LBA), lifetime number of piglets weaned (LPW), lifetime litter birth weight (LBW), and lifetime litter weaning weight (LWW) in a commercial swine farm in Northern Thailand. Data were gathered during a 24-year period from July 1989 to August 2013. A total of 3,109 phenotypic records from 2,271 Landrace (L) and 838 Yorkshire sows (Y) were analyzed. Variance and covariance components, heritabilities and correlations were estimated using an Average Information Restricted Maximum Likelihood (AIREML) procedure. The 5-trait animal model contained the fixed effects of first farrowing year-season, breed group, and age at first farrowing. Random effects were sow and residual. Estimates of heritabilities were medium for all five traits (0.17±0.04 for LPL and LBA to 0.20±0.04 for LPW). Genetic correlations among these traits were high, positive, and favorable (p<0.05), ranging from 0.93±0.02 (LPL-LWW) to 0.99±0.02 (LPL-LPW). Sow genetic trends were non-significant for LPL and all lifetime production traits. Sire genetic trends were negative and significant for LPL (−2.54±0.65 d/yr; p = 0.0007), LBA (−0.12±0.04 piglets/yr; p = 0.0073), LPW (−0.14±0.04 piglets/yr; p = 0.0037), LBW (−0.13±0.06 kg/yr; p = 0.0487), and LWW (−0.69±0.31 kg/yr; p = 0.0365). Dam genetic trends were positive, small and significant for all traits (1.04±0.42 d/yr for LPL, p = 0.0217; 0.16±0.03 piglets/yr for LBA, p<0.0001; 0.12±0.03 piglets/yr for LPW, p = 0.0002; 0.29±0.04 kg/yr for LBW, p<0.0001 and 1.23±0.19 kg/yr for LWW, p<0.0001). Thus, the selection program in this commercial herd managed to improve both LPL and lifetime productive traits in sires and dams. It was ineffective to improve LPL and lifetime productive traits in sows. PMID:26954115

  11. Risk estimation and value-of-information analysis for three proposed genetic screening programs for chronic beryllium disease prevention

    SciTech Connect

    Bartell, S.M.; Ponce, R.A.; Takaro, T.K.; Zerbe, R.O.; Omenn, G.S.; Faustman, E.M.

    2000-02-01

    Genetic differences (polymorphisms) among members of a population are thought to influence susceptibility to various environmental exposures. In practice, however, this information is rarely incorporated into quantitative risk assessment and risk management. The authors describe an analytic framework for predicting the risk reduction and value-of-information (VOI) resulting from specific risk management applications of genetic biomarkers, and they apply the framework to the example of occupational chronic beryllium disease (CBD), an immune-mediated pulmonary granulomatous disease. One described Human Leukocyte Antigen gene variant, HLA-DP{beta}1*0201, contains a substitution of glutamate for lysine at position 69 that appears to have high sensitivity ({approximately}94%) but low specificity ({approximately}70%) with respect to CBD among individuals occupationally exposed to respirable beryllium. The expected postintervention CBD prevalence rates for using the genetic variant (1) as a required job placement screen, (2) as a medical screen for semiannual in place of annual lymphocyte proliferation testing, or (3) as a voluntary job placement screen are 0.08%, 0.8%, and 0.6%, respectively, in a hypothetical cohort with 1% baseline CBD prevalence. VOI analysis is used to examine the reduction in total social cost, calculated as the net value of disease reduction and financial expenditures, expected for proposed CBD intervention programs based on the genetic susceptibility test. For the example cohort the expected net VOI per beryllium worker for genetically based testing and intervention is $13,000, $1,800, and $5,100, respectively, based on a health valuation of $1.45 million per CBD case avoided. VOI results for alternative CBD valuations are also presented. Despite large parameter uncertainty, probabilistic analysis predicts generally positive utility for each of the three evaluated programs when avoidance of a CBD case is valued at $1 million or higher. Although

  12. Language barriers

    PubMed Central

    Ngwakongnwi, Emmanuel; Hemmelgarn, Brenda R.; Musto, Richard; King-Shier, Kathryn M.; Quan, Hude

    2012-01-01

    Abstract Objective To assess use of regular medical doctors (RMDs), as well as awareness and use of telephone health lines or telehealth services, by official language minorities (OLMs) in Canada. Design Analysis of data from the 2006 postcensal survey on the vitality of OLMs. Setting Canada. Participants In total, 7691 English speakers in Quebec and 12 376 French speakers outside Quebec, grouped into those who experienced language barriers and those with no language barriers. Main outcome measures Health services utilization (HSU) by the presence of language barriers; HSU measures included having an RMD, use of an RMD’s services, and awareness of and use of telephone health lines or telehealth services. Multivariable models examined the associations between HSU and language barriers. Results After adjusting for age and sex, English speakers residing in Quebec with limited proficiency in French were less likely to have RMDs (adjusted odds ratio [AOR] 0.66, 95% CI 0.50 to 0.87) and to use the services of their RMDs (AOR 0.65, 95% CI 0.50 to 0.86), but were more likely to be aware of the existence of (AOR 1.50, 95% CI 1.16 to 1.93) and to use (AOR 1.43, 95% CI 0.97 to 2.11) telephone health lines or telehealth services. This pattern of having and using RMDs and telehealth services was not observed for French speakers residing outside of Quebec. Conclusion Overall we found variation in HSU among the language barrier populations, with lower use observed in Quebec. Age older than 45 years, male sex, being married or in common-law relationships, and higher income were associated with having RMDs for OLMs. PMID:23242902

  13. Linkage disequilibrium estimates of contemporary N e using highly variable genetic markers: a largely untapped resource for applied conservation and evolution.

    PubMed

    Waples, Robin S; Do, Chi

    2010-05-01

    Genetic methods are routinely used to estimate contemporary effective population size (N e) in natural populations, but the vast majority of applications have used only the temporal (two-sample) method. We use simulated data to evaluate how highly polymorphic molecular markers affect precision and bias in the single-sample method based on linkage disequilibrium (LD). Results of this study are as follows: (1) Low-frequency alleles upwardly bias [Formula: see text], but a simple rule can reduce bias to estimates can be obtained for relatively small populations (N e < 200), and small populations are not likely to be mistaken for large ones. However, it is very difficult to obtain reliable estimates for large populations. (3) With 'microsatellite' data, the LD method has greater precision than the temporal method, unless the latter is based on samples taken many generations apart. Our results indicate the LD method has widespread applicability to conservation (which typically focuses on small populations) and the study of evolutionary processes in local populations. Considerable opportunity exists to extract more information about N e in nature by wider use of single-sample estimators and by combining estimates from different methods. PMID:25567922

  14. High levels of fish oil enhance neutrophil development and activation and influence colon mucus barrier function in a genetically susceptible mouse model.

    PubMed

    Duriancik, David M; Comstock, Sarah S; Langohr, Ingeborg M; Fenton, Jenifer I

    2015-11-01

    Dietary fatty acids influence immunologic homeostasis, but their effect on initiation of colitis, an immune-mediated disease, is not well established. Previously, our laboratory demonstrated that high doses of dietary fish oil (FO) increased colon inflammation and dysplasia in a model of infection-induced colitis. In the current study, we assessed the effects of high-dose dietary FO, 6% by weight, on colon inflammation, neutrophil recruitment and function, and mucus layer integrity in a genetically susceptible, colitis-prone mouse model in the absence of infection. FO-fed SMAD3(-/-) mice had increased colon inflammation evidenced by increased numbers of systemic and local neutrophils and increased neutrophil chemoattractant and inflammatory cytokine gene expression in the colon. Mucus layer thickness in the cecum and goblet cell numbers in the cecum and colon in FO-fed mice were reduced compared to control. FO consumption affected colitis in male and female mice differently. Compared to female control mice, neutrophils from FO-fed female mice had reduced reactive oxygen species (ROS) upon ex vivo stimulation with phorbol myristate acetate while FO-fed male mice produced increased ROS compared to control-fed male mice. In summary, dietary FO impaired mucus layer integrity and was associated with colon inflammation characterized by increased neutrophil numbers and altered neutrophil function. High-dose FO may have detrimental effects in populations genetically susceptible for inflammatory bowel disease and these effects may differ between males and females. PMID:26297475

  15. ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data

    PubMed Central

    2011-01-01

    Background With next-generation sequencing technologies, experiments that were considered prohibitive only a few years ago are now possible. However, while these technologies have the ability to produce enormous volumes of data, the sequence reads are prone to error. This poses fundamental hurdles when genetic diversity is investigated. Results We developed ShoRAH, a computational method for quantifying genetic diversity in a mixed sample and for identifying the individual clones in the population, while accounting for sequencing errors. The software was run on simulated data and on real data obtained in wet lab experiments to assess its reliability. Conclusions ShoRAH is implemented in C++, Python, and Perl and has been tested under Linux and Mac OS X. Source code is available under the GNU General Public License at http://www.cbg.ethz.ch/software/shorah. PMID:21521499

  16. Genetic Diversity of Arabica Coffee (Coffea arabica L.) in Nicaragua as Estimated by Simple Sequence Repeat Markers

    PubMed Central

    Geleta, Mulatu; Herrera, Isabel; Monzón, Arnulfo; Bryngelsson, Tomas

    2012-01-01

    Coffea arabica L. (arabica coffee), the only tetraploid species in the genus Coffea, represents the majority of the world's coffee production and has a significant contribution to Nicaragua's economy. The present paper was conducted to determine the genetic diversity of arabica coffee in Nicaragua for its conservation and breeding values. Twenty-six populations that represent eight varieties in Nicaragua were investigated using simple sequence repeat (SSR) markers. A total of 24 alleles were obtained from the 12 loci investigated across 260 individual plants. The total Nei's gene diversity (HT) and the within-population gene diversity (HS) were 0.35 and 0.29, respectively, which is comparable with that previously reported from other countries and regions. Among the varieties, the highest diversity was recorded in the variety Catimor. Analysis of variance (AMOVA) revealed that about 87% of the total genetic variation was found within populations and the remaining 13% differentiate the populations (FST = 0.13; P < 0.001). The variation among the varieties was also significant. The genetic variation in Nicaraguan coffee is significant enough to be used in the breeding programs, and most of this variation can be conserved through ex situ conservation of a low number of populations from each variety. PMID:22701376

  17. Estimate of the optimum weight ratio in zero-valent iron/pumice granular mixtures used in permeable reactive barriers for the remediation of nickel contaminated groundwater.

    PubMed

    Calabrò, P S; Moraci, N; Suraci, P

    2012-03-15

    This paper presents the results of laboratory column tests aimed at defining the optimum weight ratio of zero-valent iron (ZVI)/pumice granular mixtures to be used in permeable reactive barriers (PRBs) for the removal of nickel from contaminated groundwater. The tests were carried out feeding the columns with aqueous solutions of nickel nitrate at concentrations of 5 and 50 mg/l using three ZVI/pumice granular mixtures at various weight ratios (10/90, 30/70 and 50/50), for a total of six column tests; two additional tests were carried out using ZVI alone. The most successful compromise between reactivity (higher ZVI content) and long-term hydraulic performance (higher Pumice content) seems to be given by the ZVI/pumice granular mixture with a 30/70 weight ratio. PMID:21885195

  18. Sand and nest temperatures and an estimate of hatchling sex ratio from the Heron Island green turtle ( Chelonia mydas) rookery, Southern Great Barrier Reef

    NASA Astrophysics Data System (ADS)

    Booth, David T.; Freeman, Candida

    2006-11-01

    Sand and nest temperatures were monitored during the 2002-2003 nesting season of the green turtle, Chelonia mydas, at Heron Island, Great Barrier Reef, Australia. Sand temperatures increased from ˜ 24°C early in the season to 27-29°C in the middle, before decreasing again. Beach orientation affected sand temperature at nest depth throughout the season; the north facing beach remained 0.7°C warmer than the east, which was 0.9°C warmer than the south, but monitored nest temperatures were similar across all beaches. Sand temperature at 100 cm depth was cooler than at 40 cm early in the season, but this reversed at the end. Nest temperatures increased 2-4°C above sand temperatures during the later half of incubation due to metabolic heating. Hatchling sex ratio inferred from nest temperature profiles indicated a strong female bias.

  19. Genetic structuring across marine biogeographic boundaries in rocky shore invertebrates.

    PubMed

    Villamor, Adriana; Costantini, Federica; Abbiati, Marco

    2014-01-01

    Biogeography investigates spatial patterns of species distribution. Discontinuities in species distribution are identified as boundaries between biogeographic areas. Do these boundaries affect genetic connectivity? To address this question, a multifactorial hierarchical sampling design, across three of the major marine biogeographic boundaries in the central Mediterranean Sea (Ligurian-Tyrrhenian, Tyrrhenian-Ionian and Ionian-Adriatic) was carried out. Mitochondrial COI sequence polymorphism of seven species of Mediterranean benthic invertebrates was analysed. Two species showed significant genetic structure across the Tyrrhenian-Ionian boundary, as well as two other species across the Ionian Sea, a previously unknown phylogeographic barrier. The hypothesized barrier in the Ligurian-Tyrrhenian cannot be detected in the genetic structure of the investigated species. Connectivity patterns across species at distances up to 800 km apart confirmed that estimates of pelagic larval dispersal were poor predictors of the genetic structure. The detected genetic discontinuities seem more related to the effect of past historical events, though maintained by present day oceanographic processes. Multivariate statistical tools were used to test the consistency of the patterns across species, providing a conceptual framework for across-species barrier locations and strengths. Additional sequences retrieved from public databases supported our findings. Heterogeneity of phylogeographic patterns shown by the 7 investigated species is relevant to the understanding of the genetic diversity, and carry implications for conservation biology. PMID:24983738

  20. Genetic Structuring across Marine Biogeographic Boundaries in Rocky Shore Invertebrates

    PubMed Central

    Villamor, Adriana; Costantini, Federica; Abbiati, Marco

    2014-01-01

    Biogeography investigates spatial patterns of species distribution. Discontinuities in species distribution are identified as boundaries between biogeographic areas. Do these boundaries affect genetic connectivity? To address this question, a multifactorial hierarchical sampling design, across three of the major marine biogeographic boundaries in the central Mediterranean Sea (Ligurian-Tyrrhenian, Tyrrhenian-Ionian and Ionian-Adriatic) was carried out. Mitochondrial COI sequence polymorphism of seven species of Mediterranean benthic invertebrates was analysed. Two species showed significant genetic structure across the Tyrrhenian-Ionian boundary, as well as two other species across the Ionian Sea, a previously unknown phylogeographic barrier. The hypothesized barrier in the Ligurian-Tyrrhenian cannot be detected in the genetic structure of the investigated species. Connectivity patterns across species at distances up to 800 km apart confirmed that estimates of pelagic larval dispersal were poor predictors of the genetic structure. The detected genetic discontinuities seem more related to the effect of past historical events, though maintained by present day oceanographic processes. Multivariate statistical tools were used to test the consistency of the patterns across species, providing a conceptual framework for across-species barrier locations and strengths. Additional sequences retrieved from public databases supported our findings. Heterogeneity of phylogeographic patterns shown by the 7 investigated species is relevant to the understanding of the genetic diversity, and carry implications for conservation biology. PMID:24983738

  1. Annual recapture and survival rates of two non-breeding adult populations of Roseate Terns Stema dougallii captured on the Great Barrier Reef, Australia, and estimates of their population sizes

    USGS Publications Warehouse

    O'Neill, P.; Minton, C.D.T.; Nisbet, I.C.T.; Hines, J.E.

    2008-01-01

    Capture-recapture data from two disparate breeding populations of Roseate Terns (Sterna dougallii) captured together as non-breeding individuals from 2002 to 2007 in the southern Great Barrier Reef. Australia were analyzed for both survival rate and recapture rate. The average annual survival rate for the birds from the Asian population (S. d. bangsi) (0.901) is higher than that of the other population of unknown breeding origin (0.819). There was large variability in survival in both populations among years, but the average survival rate of 0.85 is similar to estimates for the same species in North America. The Cormack-Jolly-Seber models used in program MARK to estimate survival rates also produced estimated of recapture probabilities and population sizes. These estimates of population size were 29,000 for S. D. bangsi and 8,300 for the study area and much larger than the documented numbers in the likely breeding areas, suggesting that many breeding sites are currently unknown.

  2. Bayesian systems-based genetic association analysis with effect strength estimation and omic wide interpretation: a case study in rheumatoid arthritis.

    PubMed

    Hullám, Gábor; Gézsi, András; Millinghoffer, András; Sárközy, Péter; Bolgár, Bence; Srivastava, Sanjeev K; Pál, Zsuzsanna; Buzás, Edit I; Antal, Péter

    2014-01-01

    Rich dependency structures are often formed in genetic association studies between the phenotypic, clinical, and environmental descriptors. These descriptors may not be standardized, and may encompass various disease definitions and clinical endpoints which are only weakly influenced by various (e.g., genetic) factors. Such loosely defined complex intermediate clinical phenotypes are typically used in follow-up candidate gene association studies, e.g., after genome-wide analysis, to deepen the understanding of the associations and to estimate effect strength. This chapter discusses a solid methodology, which is useful in such a scenario, by using probabilistic graphical models, namely, Bayesian networks in the Bayesian statistical framework. This method offers systematically scalable, comprehensive hierarchical hypotheses about multivariate relevance. We discuss its workflow: from data engineering to semantic publication of the results. We overview the construction, visualization, and interpretation of complex hypotheses related to the structural analysis of relevance. Furthermore, we illustrate the use of a dependency model-based relevance measure, which takes into account the structural properties of the model, for quantifying the effect strength. Finally, we discuss the "interpretational" or translational challenge of a genetic association study, with a focus on the fusion of heterogeneous omic knowledge to reintegrate the results into a genome-wide context. PMID:24706282

  3. Medical genetics and genetic counseling in Chile.

    PubMed

    Margarit, Sonia B; Alvarado, Mónica; Alvarez, Karin; Lay-Son, Guillermo

    2013-12-01

    In the South American Republic of Chile genetic counseling is not currently recognized as an independent clinical discipline, and in general is provided by physicians with training in clinical genetics. At present only one genetic counselor and 28 clinical geneticists practice in this country of over 16 million inhabitants. Pediatric dysmorphology constitutes the primary area of practice in clinical genetics. Although the country has a universal health care system and an adequate level of health care, genetic conditions are not considered a health care priority and there is a lack of clinical and laboratory resources designated for clinical genetics services. Multiple educational, cultural and financial barriers exist to the growth and development of genetic counseling services in Chile. However, during the last 10 years increased awareness of the importance of identifying individuals at risk for inherited cancer syndromes led to growing interest in the practice of cancer genetics. PMID:23744184

  4. Fusion barrier distribution described by above-barrier resonances

    NASA Astrophysics Data System (ADS)

    Sahu, B.; Agarwalla, S. K.; Shastry, C. S.

    2003-01-01

    We have constructed an analytically solvable, smooth, short-ranged, realistic and composite barrier potential with parameters controlling the flatness at the top, the range and the asymmetry of the barrier. When certain condition on flatness is obeyed, the transmission coefficient (T) across this barrier is found to be oscillatory in the above-barrier region of energy representing above-barrier resonances (ABR). Using this T with proper dependence on angular momentum, we estimate the results of fusion cross section σ f and the distribution function {d2(Eσ f) }/{dE 2} in the cases of two best studied examples namely 16O +144Sm and 16O +208Pb systems. On comparison with the corresponding experimental data we find good explanations of these fusion data. The asymmetry in the composite barrier addresses the problem of sub-barrier enhancement of σ f data. On the other hand, for the first time, the oscillatory structure in the results of {d2(Eσ f) }/{dE 2} is proved to be the manifestation of ABR sustained by the composite barrier by virtue of its flatness at the top.

  5. Estimation of Pairwise Identity by Descent From Dense Genetic Marker Data in a Population Sample of Haplotypes

    PubMed Central

    Browning, Sharon R.

    2008-01-01

    I present a new approach for calculating probabilities of identity by descent for pairs of haplotypes. The approach is based on a joint hidden Markov model for haplotype frequencies and identity by descent (IBD). This model allows for linkage disequilibrium, and the method can be applied to very dense marker data. The method has high power for detecting IBD tracts of genetic length of 1 cM, with the use of sufficiently dense markers. This enables detection of pairwise IBD between haplotypes from individuals whose most recent common ancestor lived up to 50 generations ago. PMID:18430938

  6. Unraveling the Limits of Mitochondrial Control Region to Estimate the Fine Scale Population Genetic Differentiation in Anadromous Fish Tenualosa ilisha

    PubMed Central

    Verma, Rashmi; Singh, Mahender; Kumar, Sudhir

    2016-01-01

    The mitochondrial control region has been the first choice for examining the population structure but hypervariability and homoplasy have reduced its suitability. We analysed eight populations using control region for examining the population structure of Hilsa. Although the control region analysis revealed broad structuring between the Arabian Sea and Bay of Bengal (FST  0.0441, p < 0.001) it was unable to detect structure among riverine populations. These results suggest that the markers used must be able to distinguish populations and control region has led to an underestimation of genetic differentiation among populations of Hilsa. PMID:27313951

  7. Unraveling the Limits of Mitochondrial Control Region to Estimate the Fine Scale Population Genetic Differentiation in Anadromous Fish Tenualosa ilisha.

    PubMed

    Verma, Rashmi; Singh, Mahender; Kumar, Sudhir

    2016-01-01

    The mitochondrial control region has been the first choice for examining the population structure but hypervariability and homoplasy have reduced its suitability. We analysed eight populations using control region for examining the population structure of Hilsa. Although the control region analysis revealed broad structuring between the Arabian Sea and Bay of Bengal (F ST  0.0441, p < 0.001) it was unable to detect structure among riverine populations. These results suggest that the markers used must be able to distinguish populations and control region has led to an underestimation of genetic differentiation among populations of Hilsa. PMID:27313951

  8. Contrasting population genetic structure among freshwater-resident and anadromous lampreys: the role of demographic history, differential dispersal and anthropogenic barriers to movement

    PubMed Central

    Bracken, Fiona S A; Hoelzel, A Rus; Hume, John B; Lucas, Martyn C

    2015-01-01

    The tendency of many species to abandon migration remains a poorly understood aspect of evolutionary biology that may play an important role in promoting species radiation by both allopatric and sympatric mechanisms. Anadromy inherently offers an opportunity for the colonization of freshwater environments, and the shift from an anadromous to a wholly freshwater life history has occurred in many families of fishes. Freshwater-resident forms have arisen repeatedly among lampreys (within the Petromyzontidae and Mordaciidae), and there has been much debate as to whether anadromous lampreys, and their derived freshwater-resident analogues, constitute distinct species or are divergent ecotypes of polymorphic species. Samples of 543 European river lamprey Lampetra fluviatilis (mostly from anadromous populations) and freshwater European brook lamprey Lampetra planeri from across 18 sites, primarily in the British Isles, were investigated for 13 polymorphic microsatellite DNA loci, and 108 samples from six of these sites were sequenced for 829 bp of mitochondrial DNA (mtDNA). We found contrasting patterns of population structure for mtDNA and microsatellite DNA markers, such that low diversity and little structure were seen for all populations for mtDNA (consistent with a recent founder expansion event), while fine-scale structuring was evident for nuclear markers. Strong differentiation for microsatellite DNA loci was seen among freshwater-resident L. planeri populations and between L. fluviatilis and L. planeri in most cases, but little structure was evident among anadromous L. fluviatilis populations. We conclude that postglacial colonization founded multiple freshwater-resident populations with strong habitat fidelity and limited dispersal tendencies that became highly differentiated, a pattern that was likely intensified by anthropogenic barriers. PMID:25689694

  9. Contrasting population genetic structure among freshwater-resident and anadromous lampreys: the role of demographic history, differential dispersal and anthropogenic barriers to movement.

    PubMed

    Bracken, Fiona S A; Hoelzel, A Rus; Hume, John B; Lucas, Martyn C

    2015-03-01

    The tendency of many species to abandon migration remains a poorly understood aspect of evolutionary biology that may play an important role in promoting species radiation by both allopatric and sympatric mechanisms. Anadromy inherently offers an opportunity for the colonization of freshwater environments, and the shift from an anadromous to a wholly freshwater life history has occurred in many families of fishes. Freshwater-resident forms have arisen repeatedly among lampreys (within the Petromyzontidae and Mordaciidae), and there has been much debate as to whether anadromous lampreys, and their derived freshwater-resident analogues, constitute distinct species or are divergent ecotypes of polymorphic species. Samples of 543 European river lamprey Lampetra fluviatilis (mostly from anadromous populations) and freshwater European brook lamprey Lampetra planeri from across 18 sites, primarily in the British Isles, were investigated for 13 polymorphic microsatellite DNA loci, and 108 samples from six of these sites were sequenced for 829 bp of mitochondrial DNA (mtDNA). We found contrasting patterns of population structure for mtDNA and microsatellite DNA markers, such that low diversity and little structure were seen for all populations for mtDNA (consistent with a recent founder expansion event), while fine-scale structuring was evident for nuclear markers. Strong differentiation for microsatellite DNA loci was seen among freshwater-resident L. planeri populations and between L. fluviatilis and L. planeri in most cases, but little structure was evident among anadromous L. fluviatilis populations. We conclude that postglacial colonization founded multiple freshwater-resident populations with strong habitat fidelity and limited dispersal tendencies that became highly differentiated, a pattern that was likely intensified by anthropogenic barriers. PMID:25689694

  10. An estimate of chinook salmon (Oncorhynchus tshawytscha) spawning habitat and redd capacity upstream of a migration barrier in the upper Columbia River

    SciTech Connect

    Hanrahan, Timothy P.; Dauble, Dennis D.; Geist, David R.

    2004-02-01

    Chief Joseph Dam on the Columbia River is the upstream terminus for anadromous fish, due to its lack of fish passage facilities. Management agencies are currently evaluating the feasibility of reintroducing anadromous fish upriver of Chief Joseph Dam. We evaluated the physical characteristics of potential fall chinook salmon (Oncorhynchus tshawytscha) spawning habitat in the upper section of Chief Joseph Reservoir. The objective of this study was to estimate the quantity and location of potential spawning habitat, and secondly to determine the redd capacity of the area based on spawning habitat characteristics. We used a geomorphic approach to first identify specific segments with the highest potential for spawning. The suitability of these segments for spawning was then estimated through the use of empirical physical data and modeled hydraulic data. We estimated 5% (48.7 ha) of the study area contains potentially suitable fall chinook salmon spawning habitat. Potential spawning habitat is primarily limited by water too deep and secondly by water velocities too low, the combination of which results in 20% (9.6 ha) of the potential spawning habitat being characterized as high quality. Estimates of redd capacity within potential spawning habitat range from 207? 1599 redds, based on proportional use of potential habitat and varying amounts of channelbed used by spawning salmon. The results of our study provide fisheries managers significant insight into one component of the complex issue of reintroducing anadromous fish to the Columbia River upstream of Chief Joseph Dam.

  11. Making (up) the grade? estimating the genetic and environmental influences of discrepancies between self-reported grades and official GPA scores.

    PubMed

    Schwartz, Joseph A; Beaver, Kevin M

    2015-05-01

    Academic achievement has been found to have a pervasive and substantial impact on a wide range of developmental outcomes and has also been implicated in the critical transition from adolescence into early adulthood. Previous research has revealed that self-reported grades tend to diverge from official transcript grade point average (GPA) scores, with students being more likely to report inflated scores. Making use of a sample of monozygotic twin (N = 282 pairs), dizygotic twin (N = 441 pairs), and full sibling (N = 1,757 pairs) pairs from the National Longitudinal Study of Adolescent Health (Add Health; 65 % White; 50 % male; mean age = 16.14), the current study is the first to investigate the role that genetic and environmental factors play in misreporting grade information. A comparison between self-reported GPA (mean score of 2.86) and official transcript GPA scores (mean score of 2.44) revealed that self-reported scores were approximately one-half letter grade greater than official scores. Liability threshold models revealed that additive genetic influences explained between 40 and 63 % of the variance in reporting inflated grades and correctly reporting GPA, with the remaining variance explained by the nonshared environment. Conversely, 100 % of the variance in reporting deflated grade information was explained by nonshared environmental influences. In an effort to identify specific nonshared environmental influences on reporting accuracy, multivariate models that adequately control for genetic influences were estimated and revealed that siblings with lower transcript GPA scores were significantly less likely to correctly report their GPA and significantly more likely to report inflated GPA scores. Additional analyses revealed that verbal IQ and self-control were not significantly associated with self-reported GPA accuracy after controlling for genetic influences. These findings indicate that previous studies that implicate verbal IQ and self

  12. Overcoming Barriers.

    PubMed

    Neal-Boylan, Leslie; Schmidt, Kari L

    2015-01-01

    Dr. Neal-Boylan's program of scholarship has always focused on nurse workforce issues. She recently published two books related to how nurses work. One (The Nurse's Reality Gap: Overcoming Barriers Between Academic Achievement and Clinical Success; Neal-Boylan, 2013) focused on the experience of new graduates from baccalaureate, master's, and doctoral programs. The second book, The Nurse's Reality Shift: Using Our History to Transform Our Future (Neal-Boylan, 2014), focuses on the problems nursing continues to face throughout our history and has failed to correct. PMID:26200309

  13. Sea surface temperature as a tracer to estimate cross-shelf turbulent diffusivity and flushing time in the Great Barrier Reef lagoon

    NASA Astrophysics Data System (ADS)

    Mao, Yadan; Ridd, Peter V.

    2015-06-01

    Accurate parameterization of spatially variable diffusivity in complex shelf regions such as the Great Barrier Reef (GBR) lagoon is an unresolved issue for hydrodynamic models. This leads to large uncertainties to the flushing time derived from them and to the evaluation of ecosystem resilience to terrestrially derived pollution. In fact, numerical hydrodynamic models and analytical cross-shore diffusion models have predicted very different flushing times for the GBR lagoon. Nevertheless, scarcity of in situ measurements used previously in the latter method prevents derivation of detailed diffusivity profiles. Here detailed cross-shore profiles of diffusivity were calculated explicitly in a closed form for the first time from the steady state transects of sea surface temperature for different sections of the GBR lagoon. We find that diffusivity remains relatively constant within the inner lagoon (<˜20 km) where tidal current is weak, and increases linearly with sufficiently large tidal amplitude in reef-devoid regions, but increases dramatically where the reef matrixes start and fluctuates with reef size and density. The cross-shelf profile of steady state salinity calculated using the derived diffusivity values agrees well with field measurements. The calculated diffusivity values are also consistent with values derived from satellite-tracked drifters. Flushing time by offshore diffusion is of the order of 1 month, suggesting the important role of turbulent diffusion in flushing the lagoon, especially in reef-distributed regions. The results imply that previous very large residence times predicted by numerical hydrodynamic models may result from underestimation of diffusivity. Our findings can guide parameterization of diffusivity in hydrodynamic modeling.

  14. Estimation of free energy barriers in the cytoplasmic and mitochondrial aspartate aminotransferase reactions probed by hydrogen-exchange kinetics of C alpha-labeled amino acids with solvent

    SciTech Connect

    Julin, D.A.; Wiesinger, H.; Toney, M.D.; Kirsch, J.F. )

    1989-05-02

    The existence of the postulated quinonoid intermediate in the cytoplasmic aspartate amino-transferase catalyzed transamination of aspartate to oxaloacetate was probed by determining the extent of transfer of tritium from the C alpha position of tritiated L-aspartate to pyridoxamine 5'-phosphate in single turnover experiments in which washout from the back-reaction was obviated by product trapping. The maximum amount of transferred tritium observed was 0.7%, consistent either with a mechanism in which a fraction of the net transamination reaction proceeds through a quinonoid intermediate or with a mechanism in which this intermediate is formed off the main reaction pathway. It is shown that transfer of labeled hydrogen from the amino acid to cofactor cannot be used to differentiate a stepwise from a concerted transamination mechanism. The amount of tritium transferred is a function of the rate constant for torsional equilibration about the epsilon-amino group of Lys-258, the presumptive abstractor of the C alpha proton; the relative rate constants for hydrogen exchange with solvent versus cofactor protonation; and the tritium isotope effect on this ratio. The free energy barriers facing the covalent intermediate between aldimine and keto acid product (i.e., ketimine and possibly quinonoid) were evaluated relatively by comparing the rates of C alpha-hydrogen exchange in starting amino acid with the rates of keto acid formation. The value of theta (= kexge/kprod) was found to be 2.6 for the reaction of cytoplasmic isozyme with aspartate and ca. 0.5 for that of the mitochondrial form with glutamate.

  15. Barrier Formation

    PubMed Central

    Lyaruu, D.M.; Medina, J.F.; Sarvide, S.; Bervoets, T.J.M.; Everts, V.; DenBesten, P.; Smith, C.E.; Bronckers, A.L.J.J.

    2014-01-01

    Enamel fluorosis is an irreversible structural enamel defect following exposure to supraoptimal levels of fluoride during amelogenesis. We hypothesized that fluorosis is associated with excess release of protons during formation of hypermineralized lines in the mineralizing enamel matrix. We tested this concept by analyzing fluorotic enamel defects in wild-type mice and mice deficient in anion exchanger-2a,b (Ae2a,b), a transmembrane protein in maturation ameloblasts that exchanges extracellular Cl− for bicarbonate. Defects were more pronounced in fluorotic Ae2a,b−/− mice than in fluorotic heterozygous or wild-type mice. Phenotypes included a hypermineralized surface, extensive subsurface hypomineralization, and multiple hypermineralized lines in deeper enamel. Mineral content decreased in all fluoride-exposed and Ae2a,b−/− mice and was strongly correlated with Cl−. Exposure of enamel surfaces underlying maturation-stage ameloblasts to pH indicator dyes suggested the presence of diffusion barriers in fluorotic enamel. These results support the concept that fluoride stimulates hypermineralization at the mineralization front. This causes increased release of protons, which ameloblasts respond to by secreting more bicarbonates at the expense of Cl− levels in enamel. The fluoride-induced hypermineralized lines may form barriers that impede diffusion of proteins and mineral ions into the subsurface layers, thereby delaying biomineralization and causing retention of enamel matrix proteins. PMID:24170372

  16. Genetic heterogeneity, modes of inheritance, and risk estimates for a joint study of caucasians with insulin-dependent diabetes mellitus

    PubMed Central

    Thomson, Glenys; Robinson, Wendy P.; Kuhner, Mary K.; Joe, Sharon; MacDonald, Michael J.; Gottschall, Jerome L.; Barbosa, Jose; Rich, Stephen S.; Bertrams, Jörg; Baur, Max P.; Partanen, Jukka; Tait, Brian D.; Schober, Edith; Mayr, Wolfgang R.; Ludvigsson, Johnny; Lindblom, Bertil; Farid, Nadir R.; Thompson, Christine; Deschamps, Ingeborg

    1988-01-01

    From 11 studies, a total of 1,792 Caucasian probands with insulin-dependent diabetes mellitus (IDDM) are analyzed. Antigen genotype frequencies in patients, transmission from affected parents to affected children, and the relative frequencies of HLA-DR3 and -DR4 homozygous patients all indicate that DR3 predisposes in a “recessive”-like and DR4 in a “dominant”-like or “intermediate” fashion, after allowing for the DR3/DR4 synergistic effect. Removal of DR3 and DR4 reveals an overall protective effect of DR2, predisposing effects of DR1 and DRw8, and a slight protective effect of DR5 and a predisposing effect of DRw6. Analysis of affected-parent-to-affected-child data indicates that a subset of DR2 may predispose. The non-DR3, non-DR4 antigens are not independently associated with DR3 and DR4; the largest effect is a deficiency of DR2, followed by excesses of DR1, DRw8, and DRw6, in DR4 individuals, as compared with DR3 individuals. HLA-B locus distributions on patient haplotypes indicate that only subsets of both DR3 and DR4 are predisposing. The presence or absence of Asp at position 57 of the DQβ gene, recently implicated in IDDM predisposition, is not by itself sufficient to explain the inheritance of IDDM. At a minimum, the distinguishing features of the DR3-associated and DR4-associated predisposition remain to be identified at the molecular level. Risk estimates for sibs of probands are calculated based on an overall sibling risk of 6%; estimates for those sharing two, one, or zero haplotypes are 12.9%, 4.5%, and 1.8%, respectively. Risk estimates subdivided by the DR type of the proband are also calculated, the highest being 19.2% for sibs sharing two haplotypes with a DR3/DR4 proband. PMID:3057885

  17. Admixture patterns and genetic differentiation in negrito groups from West Malaysia estimated from genome-wide SNP data.

    PubMed

    Jinam, Timothy A; Phipps, Maude E; Saitou, Naruya

    2013-01-01

    Southeast Asia houses various culturally and linguistically diverse ethnic groups. In Malaysia, where the Malay, Chinese, and Indian ethnic groups form the majority, there exist minority groups such as the "negritos" who are believed to be descendants of the earliest settlers of Southeast Asia. Here we report patterns of genetic substructure and admixture in two Malaysian negrito populations (Jehai and Kensiu), using ~50,000 genome-wide single-nucleotide polymorphism (SNP) data. We found traces of recent admixture in both the negrito populations, particularly in the Jehai, with the Malay through principal component analysis and STRUCTURE analysis software, which suggested that the admixture was as recent as one generation ago. We also identified significantly differentiated nonsynonymous SNPs and haplotype blocks related to intracellular transport, metabolic processes, and detection of stimulus. These results highlight the different levels of admixture experienced by the two Malaysian negritos. Delineating admixture and differentiated genomic regions should be of importance in designing and interpretation of molecular anthropology and disease association studies. PMID:24297225

  18. Experimental Design for Estimating Unknown Hydraulic Conductivity in a Confined Aquifer using a Genetic Algorithm and a Reduced Order Model

    NASA Astrophysics Data System (ADS)

    Ushijima, T.; Yeh, W.

    2013-12-01

    An optimal experimental design algorithm is developed to select locations for a network of observation wells that provides the maximum information about unknown hydraulic conductivity in a confined, anisotropic aquifer. The design employs a maximal information criterion that chooses, among competing designs, the design that maximizes the sum of squared sensitivities while conforming to specified design constraints. Because that the formulated problem is non-convex and contains integer variables (necessitating a combinatorial search), for a realistically-scaled model, the problem may be difficult, if not impossible, to solve through traditional mathematical programming techniques. Genetic Algorithms (GAs) are designed to search out the global optimum; however because a GA requires a large number of calls to a groundwater model, the formulated optimization problem may still be infeasible to solve. To overcome this, Proper Orthogonal Decomposition (POD) is applied to the groundwater model to reduce its dimension. The information matrix in the full model space can then be searched without solving the full model.

  19. Experimental design for estimating unknown hydraulic conductivity in an aquifer using a genetic algorithm and reduced order model

    NASA Astrophysics Data System (ADS)

    Ushijima, Timothy T.; Yeh, William W.-G.

    2015-12-01

    We develop an experimental design algorithm to select locations for a network of observation wells that provide the maximum robust information about unknown hydraulic conductivity in a confined, anisotropic aquifer. Since the information that a design provides is dependent on an aquifer's hydraulic conductivity, a robust design is one that provides the maximum information in the worst-case scenario. The design can be formulated as a max-min optimization problem. The problem is generally non-convex, non-differentiable, and contains integer variables. We use a Genetic Algorithm (GA) to perform the combinatorial search. We employ proper orthogonal decomposition (POD) to reduce the dimension of the groundwater model, thereby reducing the computational burden posed by employing a GA. The GA algorithm exhaustively searches for the robust design across a set of hydraulic conductivities and finds an approximate design (called the High Frequency Observation Well Design) through a Monte Carlo-type search. The results from a small-scale 1-D test case validate the proposed methodology. We then apply the methodology to a realistically-scaled 2-D test case.

  20. Estimating genetic potential of biofuel forest hardwoods to withstand metal toxicity in industrial effluent under dry tropical conditions.

    PubMed

    Manzoor, S A; Mirza, S N; Zubair, M; Nouman, W; Hussain, S B; Mehmood, S; Irshad, A; Sarwar, N; Ammar, A; Iqbal, M F; Asim, A; Chattha, M U; Chattha, M B; Zafar, A; Abid, R

    2015-01-01

    Biofuel tree species are recognized as a promising alternative source of fuel to conventional forms. Additionally, these tree species are also effective in accumulating toxic heavy metals present in some industrial effluents. In developing countries such as Pakistan, the use of biofuel tree species is gaining popularity not only for harvesting economical and environmentally friendly biofuel, but also to sequester poisonous heavy metals from industrial wastewater. This study was aimed at evaluating the genetic potential of two biofuel species, namely, Jatropha curcas and Pongamia pinnata, to grow when irrigated with industrial effluent from the Pak-Arab Fertilizer Factory Multan, Southern Punjab, Pakistan. The growth performances of one-year-old seedlings of both species were compared in soil with adverse physiochemical properties. It was found that J. curcas was better able to withstand the toxicity of the heavy metals present in the fertilizer factory effluent. J. curcas showed maximum gain in height, diameter, and biomass production in soil irrigated with 75% concentrated industrial effluent. In contrast, P. pinnata showed a significant reduction in growth in soil irrigated with more than 50% concentrated industrial effluent, indicating that this species is less tolerant to higher toxicity levels of industrial effluent. This study identifies J. curcas as a promising biofuel tree species that can be grown using industrial wastewater. PMID:26345887

  1. Source-sink estimates of genetic introgression show influence of hatchery strays on wild chum salmon populations in Prince William Sound, Alaska.

    PubMed

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

    2013-01-01

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

  2. Using Genetic Markers to Directly Estimate Gene Flow and Reproductive Success Parameters in Plants on the Basis of Naturally Regenerated Seedlings

    PubMed Central

    Burczyk, J.; Adams, W. T.; Birkes, D. S.; Chybicki, I. J.

    2006-01-01

    Estimating seed and pollen gene flow in plants on the basis of samples of naturally regenerated seedlings can provide much needed information about “realized gene flow,” but seems to be one of the greatest challenges in plant population biology. Traditional parentage methods, because of their inability to discriminate between male and female parentage of seedlings, unless supported by uniparentally inherited markers, are not capable of precisely describing seed and pollen aspects of gene flow realized in seedlings. Here, we describe a maximum-likelihood method for modeling female and male parentage in a local plant population on the basis of genotypic data from naturally established seedlings and when the location and genotypes of all potential parents within the population are known. The method models female and male reproductive success of individuals as a function of factors likely to influence reproductive success (e.g., distance of seed dispersal, distance between mates, and relative fecundity–i.e., female and male selection gradients). The method is designed to account for levels of seed and pollen gene flow into the local population from unsampled adults; therefore, it is well suited to isolated, but also wide-spread natural populations, where extensive seed and pollen dispersal complicates traditional parentage analyses. Computer simulations were performed to evaluate the utility and robustness of the model and estimation procedure and to assess how the exclusion power of genetic markers (isozymes or microsatellites) affects the accuracy of the parameter estimation. In addition, the method was applied to genotypic data collected in Scots pine (isozymes) and oak (microsatellites) populations to obtain preliminary estimates of long-distance seed and pollen gene flow and the patterns of local seed and pollen dispersal in these species. PMID:16489237

  3. Estimating the capability of microalgae to physiological acclimatization and genetic adaptation to petroleum and diesel oil contamination.

    PubMed

    Romero-Lopez, Julia; Lopez-Rodas, Victoria; Costas, Eduardo

    2012-11-15

    There is increasing scientific interest in how phytoplankton reacts to petroleum contamination, since crude oil and its derivatives are generating extensive contamination of aquatic environments. However, toxic effects of short-term petroleum exposure are more widely known than the adaptation of phytoplankton to long-term petroleum exposure. An analysis of short-term and long-term effects of petroleum exposure was done using experimental populations of freshwater (Scenedesmus intermedius and Microcystis aeruginosa) and marine (Dunaliella tertiolecta) microalgae isolated from pristine sites without crude oil product contamination. These strains were exposed to increased levels of petroleum and diesel oil. Short-term exposure to petroleum or diesel oil revealed a rapid inhibition of photosynthetic performance and cell proliferation in freshwater and marine phytoplankton species. A broad degree of inter-specific variation in lethal contamination level was observed. When different strains were exposed to petroleum or diesel oil over the long-term, the cultures showed massive destruction of the sensitive cells. Nonetheless, after further incubation, some cultures were able to grow again due to cells that were resistant to the toxins. By means of a fluctuation analysis, discrimination between cells that had become resistant due to physiological acclimatization and resistant cells arising from rare spontaneous mutations was accomplished. In addition, an analysis was done as to the maximum capacity of adaptation to a gradual contamination process. An experimental ratchet protocol was used, which maintains a strong selection pressure in a temporal scale up to several months over very large experimental populations of microalgae. Microalgae are able to survive to petroleum contamination as a result of physiological acclimatization without genetic changes. However, when petroleum concentration exceeds the physiological limits, survival depends exclusively on the occurrence on

  4. In Estimated Good Prognosis Patients Could Unexpected "Hyporesponse" to Controlled Ovarian Stimulation be Related to Genetic Polymorphisms of FSH Receptor?

    PubMed

    Alviggi, Carlo; Conforti, Alessandro; Caprio, Francesca; Gizzo, Salvatore; Noventa, Marco; Strina, Ida; Pagano, Tiziana; De Rosa, Pasquale; Carbone, Floriana; Colacurci, Nicola; De Placido, Giuseppe

    2016-08-01

    It has been reported that 10% to 15% of young normogonadotrophic women show suboptimal response to standard gonadotropin-releasing hormone-a long protocol. These patients require higher doses of exogenous follicle-stimulating hormone (FSH). This phenomenon could be associated with genetic characteristics. In this study, FSH receptor polymorphism was retrospectively evaluated in 42 normoresponder young women undergoing an in vitro fertilization/intracytoplasmic sperm injection cycle; patients were stratified according to recombinant human FSH (r-hFSH) consumption. We selected 17 normoresponder young patients who required a cumulative dose of recombinant FSH (rFSH) >2500 UI (group A). A control group was randomly selected among patients who required a cumulative dose of rFSH <2500 UI (group B). Follicle-stimulating hormone receptor (FSH-R) 307Ala and 680Ser variants were analyzed in all our patients. Our results show that the mean number of rFSH vials (36.3 ± 7.5 vs 28.6 ± 4.5, P = .0001) and days of stimulation (12.7 ± 2.4 vs 10.8 ± 2.8, P = .03) were significantly lower in group B, whereas the number of oocytes retrieved (7.1 ± 1.5 vs 9.6 ± 2.4; P = .0005) and the average number of embryos transferred (2.1 ± 0.7 vs 2.7 ± 0.4; P = .001) were significantly lower in group A. Estradiol serum levels on the human chorionic gonadotrophin day were significantly lower in group A (997.8 ± 384.9 pg/mL vs 1749.1 ± 644.4; P = .0001). The incidence of the Ser/Ser genotype was higher in patients with higher r-hFSH consumption (group A; P = .02). Based on our results, we hypothesize an association between the FSH-R polymorphisms and a "hyporesponse" to exogenous FSH. PMID:26902430

  5. On the genetic parameter determining the efficiency of purging: an estimate for Drosophila egg-to-pupae viability.

    PubMed

    Bersabé, D; García-Dorado, A

    2013-02-01

    The consequences of inbreeding on fitness can be crucial in evolutionary and conservation grounds and depend upon the efficiency of purging against deleterious recessive alleles. Recently, analytical expressions have been derived to predict the evolution of mean fitness, taking into account both inbreeding and purging, which depend on an 'effective purging coefficient (d(e) )'. Here, we explore the validity of that predictive approach and assay the strength of purging by estimating d(e) for egg-to-pupae viability (EPV) after a drastic reduction in population size in a recently captured base population of Drosophila melanogaster. For this purpose, we first obtained estimates of the inbreeding depression rate (δ) for EPV in the base population, and we found that about 40% was due to segregating recessive lethals. Then, two sets of lines were founded from this base population and were maintained with different effective size throughout the rest of the experiment (N = 6; N = 12), their mean EPV being assayed at different generations. Due to purging, the reductions in mean EPV experienced by these lines were considerably smaller than the corresponding neutral predictions. For the 60% of δ attributable to nonlethal deleterious alleles, our results suggest an effective purging coefficient d(e) > 0.02. Similarly, we obtain that d(e) > 0.09 is required to roughly account for purging against the pooled inbreeding depression from lethal and nonlethal deleterious alleles. This implies that purging should be efficient for population sizes of the order of a few tens and larger, but might be inefficient against nonlethal deleterious alleles in smaller populations. PMID:23199278

  6. Genetic Drift, Purifying Selection and Vector Genotype Shape Dengue Virus Intra-host Genetic Diversity in Mosquitoes

    PubMed Central

    Fontaine, Albin; Ar Gouilh, Meriadeg; Moltini-Conclois, Isabelle

    2016-01-01

    Due to their error-prone replication, RNA viruses typically exist as a diverse population of closely related genomes, which is considered critical for their fitness and adaptive potential. Intra-host demographic fluctuations that stochastically reduce the effective size of viral populations are a challenge to maintaining genetic diversity during systemic host infection. Arthropod-borne viruses (arboviruses) traverse several anatomical barriers during infection of their arthropod vectors that are believed to impose population bottlenecks. These anatomical barriers have been associated with both maintenance of arboviral genetic diversity and alteration of the variant repertoire. Whether these patterns result from stochastic sampling (genetic drift) rather than natural selection, and/or from the influence of vector genetic heterogeneity has not been elucidated. Here, we used deep sequencing of full-length viral genomes to monitor the intra-host evolution of a wild-type dengue virus isolate during infection of several mosquito genetic backgrounds. We estimated a bottleneck size ranging from 5 to 42 founding viral genomes at initial midgut infection, irrespective of mosquito genotype, resulting in stochastic reshuffling of the variant repertoire. The observed level of genetic diversity increased following initial midgut infection but significantly differed between mosquito genetic backgrounds despite a similar initial bottleneck size. Natural selection was predominantly negative (purifying) during viral population expansion. Taken together, our results indicate that dengue virus intra-host genetic diversity in the mosquito vector is shaped by genetic drift and purifying selection, and point to a novel role for vector genetic factors in the genetic breadth of virus populations during infection. Identifying the evolutionary forces acting on arboviral populations within their arthropod vector provides novel insights into arbovirus evolution. PMID:27304978

  7. Genetic Drift, Purifying Selection and Vector Genotype Shape Dengue Virus Intra-host Genetic Diversity in Mosquitoes.

    PubMed

    Lequime, Sebastian; Fontaine, Albin; Ar Gouilh, Meriadeg; Moltini-Conclois, Isabelle; Lambrechts, Louis

    2016-06-01

    Due to their error-prone replication, RNA viruses typically exist as a diverse population of closely related genomes, which is considered critical for their fitness and adaptive potential. Intra-host demographic fluctuations that stochastically reduce the effective size of viral populations are a challenge to maintaining genetic diversity during systemic host infection. Arthropod-borne viruses (arboviruses) traverse several anatomical barriers during infection of their arthropod vectors that are believed to impose population bottlenecks. These anatomical barriers have been associated with both maintenance of arboviral genetic diversity and alteration of the variant repertoire. Whether these patterns result from stochastic sampling (genetic drift) rather than natural selection, and/or from the influence of vector genetic heterogeneity has not been elucidated. Here, we used deep sequencing of full-length viral genomes to monitor the intra-host evolution of a wild-type dengue virus isolate during infection of several mosquito genetic backgrounds. We estimated a bottleneck size ranging from 5 to 42 founding viral genomes at initial midgut infection, irrespective of mosquito genotype, resulting in stochastic reshuffling of the variant repertoire. The observed level of genetic diversity increased following initial midgut infection but significantly differed between mosquito genetic backgrounds despite a similar initial bottleneck size. Natural selection was predominantly negative (purifying) during viral population expansion. Taken together, our results indicate that dengue virus intra-host genetic diversity in the mosquito vector is shaped by genetic drift and purifying selection, and point to a novel role for vector genetic factors in the genetic breadth of virus populations during infection. Identifying the evolutionary forces acting on arboviral populations within their arthropod vector provides novel insights into arbovirus evolution. PMID:27304978

  8. The Combination of Grazoprevir, a Hepatitis C Virus (HCV) NS3/4A Protease Inhibitor, and Elbasvir, an HCV NS5A Inhibitor, Demonstrates a High Genetic Barrier to Resistance in HCV Genotype 1a Replicons.

    PubMed

    Lahser, Frederick C; Bystol, Karin; Curry, Stephanie; McMonagle, Patricia; Xia, Ellen; Ingravallo, Paul; Chase, Robert; Liu, Rong; Black, Todd; Hazuda, Daria; Howe, Anita Y M; Asante-Appiah, Ernest

    2016-05-01

    The selection of resistance-associated variants (RAVs) against single agents administered to patients chronically infected with hepatitis C virus (HCV) necessitates that direct-acting antiviral agents (DAAs) targeting multiple viral proteins be developed to overcome failure resulting from emergence of resistance. The combination of grazoprevir (formerly MK-5172), an NS3/4A protease inhibitor, and elbasvir (formerly MK-8742), an NS5A inhibitor, was therefore studied in genotype 1a (GT1a) replicon cells. Both compounds were independently highly potent in GT1a wild-type replicon cells, with 90% effective concentration (EC90) values of 0.9 nM and 0.006 nM for grazoprevir and elbasvir, respectively. No cross-resistance was observed when clinically relevant NS5A and NS3 RAVs were profiled against grazoprevir and elbasvir, respectively. Kinetic analyses of HCV RNA reduction over 14 days showed that grazoprevir and elbasvir inhibited prototypic NS5A Y93H and NS3 R155K RAVs, respectively, with kinetics comparable to those for the wild-type GT1a replicon. In combination, grazoprevir and elbasvir interacted additively in GT1a replicon cells. Colony formation assays with a 10-fold multiple of the EC90 values of the grazoprevir-elbasvir inhibitor combination suppressed emergence of resistant colonies, compared to a 100-fold multiple for the independent agents. The selected resistant colonies with the combination harbored RAVs that required two or more nucleotide changes in the codons. Mutations in the cognate gene caused greater potency losses for elbasvir than for grazoprevir. Replicons bearing RAVs identified from resistant colonies showed reduced fitness for several cell lines and may contribute to the activity of the combination. These studies demonstrate that the combination of grazoprevir and elbasvir exerts a potent effect on HCV RNA replication and presents a high genetic barrier to resistance. The combination of grazoprevir and elbasvir is currently approved for

  9. Penetration through the Skin Barrier.

    PubMed

    Nielsen, Jesper Bo; Benfeldt, Eva; Holmgaard, Rikke

    2016-01-01

    The skin is a strong and flexible organ with barrier properties essential for maintaining homeostasis and thereby human life. Characterizing this barrier is the ability to prevent some chemicals from crossing the barrier while allowing others, including medicinal products, to pass at varying rates. During recent decades, the latter has received increased attention as a route for intentionally delivering drugs to patients. This has stimulated research in methods for sampling, measuring and predicting percutaneous penetration. Previous chapters have described how different endogenous, genetic and exogenous factors may affect barrier characteristics. The present chapter introduces the theory for barrier penetration (Fick's law), and describes and discusses different methods for measuring the kinetics of percutaneous penetration of chemicals, including in vitro methods (static and flow-through diffusion cells) as well as in vivo methods (microdialysis and microperfusion). Then follows a discussion with examples of how different characteristics of the skin (age, site and integrity) and of the penetrants (size, solubility, ionization, logPow and vehicles) affect the kinetics of percutaneous penetration. Finally, a short discussion of the advantages and challenges of each method is provided, which will hopefully allow the reader to improve decision making and treatment planning, as well as the evaluation of experimental studies of percutaneous penetration of chemicals. PMID:26844902

  10. Genetic counseling.

    PubMed

    Fraser, F C

    1974-09-01

    A workshop was sponsored by the National Genetics Foundation to evaluate and make recommendations about the status of genetic counseling, its goals, nature, achievements, and needs. The process of genetic workup and counseling is divided into 5 stages: validation of the diagnosis; obtaining family history; estimation of the risk of recurrence; helping the family make a decision and take appropriate action; and extending counseling to other members of the family. Counseling can be directed at individuals or at special groups with the potential of carrying such diseases as sickle cell amenia or Tay-Sachs. No consensus exists on an optimal counseling approach. Genetic counseling is regarded as a team effort, requiring, in addition to the counselor, laboratory facilities and a variety of specialists. The source of payment for genetic counseling services is regarded as a problem of increasing concern. Generally, the fee paid rarely covers the cost of the many procedures and it is suggested that the cost, like that of other public health services, should be subsidized by the state. Considerable argument exists over whether a genetic counselor must have a M.D. degree or whether a Ph. D. in medical genetics is suitable enough. The quality of much genetic counseling, which is often done in the office of doctors unskilled in the field, would be increased if better training in genetics were offered to medical students and if physicians were informed of the existence of counseling centers. Further, there is a growing feeling that some sort of accreditation of genetic counselors is desirable. PMID:4609197

  11. Sprache als Barriere (Language as a Barrier)

    ERIC Educational Resources Information Center

    Mattheier, Klaus

    1974-01-01

    The concept of language barrier has its derivations in the fields of dialectology, sociology and psychology. In contemporary usage however, the concept has two meanings i.e. regional-cultural barrier and socio-cultural barrier. (Text is in German.) (DS)

  12. Efficiency of single noise barriers

    NASA Astrophysics Data System (ADS)

    Hothersall, D. C.; Chandler-Wilde, S. N.; Hajmirzae, M. N.

    1991-04-01

    A numerical model is described which enables the sound field in the region of outdoor noise barriers to be calculated by using the boundary element method. The non-uniqueness of solution of the method, producing unreliable results in some conditions, is discussed. The model can be applied to barriers of arbitrary cross-sectional shape and arbitrary distribution of surface cover. The model is two-dimensional, but results are shown to agree well with those obtained for the three-dimensional problem of propagation from a point source over a noise barrier of infinite length. The model is used to compare the efficiency of a wide range of constructions of single noise barriers of different height, cross-sectional shape and surface cover. The effects of the ground cover are also considered. Comparison is made by examining spectra of the insertion loss of the barriers, and also broadband insertion losses for a source with a characteristic A-weighted road traffic noise spectrum. Single-figure estimates are presented of the relative efficiency, in terms of insertion loss, in the deep shadow zone, of a wide range of barrier configurations.

  13. Fine-scale estimation of carbon monoxide and fine particulate matter concentrations in proximity to a road intersection by using wavelet neural network with genetic algorithm

    NASA Astrophysics Data System (ADS)

    Wang, Zhanyong; Lu, Feng; He, Hong-di; Lu, Qing-Chang; Wang, Dongsheng; Peng, Zhong-Ren

    2015-03-01

    At road intersections, vehicles frequently stop with idling engines during the red-light period and speed up rapidly in the green-light period, which generates higher velocity fluctuation and thus higher emission rates. Additionally, the frequent changes of wind direction further add the highly variable dispersion of pollutants at the street scale. It is, therefore, very difficult to estimate the distribution of pollutant concentrations using conventional deterministic causal models. For this reason, a hybrid model combining wavelet neural network and genetic algorithm (GA-WNN) is proposed for predicting 5-min series of carbon monoxide (CO) and fine particulate matter (PM2.5) concentrations in proximity to an intersection. The proposed model is examined based on the measured data under two situations. As the measured pollutant concentrations are found to be dependent on the distance to the intersection, the model is evaluated in three locations respectively, i.e. 110 m, 330 m and 500 m. Due to the different variation of pollutant concentrations on varied time, the model is also evaluated in peak and off-peak traffic time periods separately. Additionally, the proposed model, together with the back-propagation neural network (BPNN), is examined with the measured data in these situations. The proposed model is found to perform better in predictability and precision for both CO and PM2.5 than BPNN does, implying that the hybrid model can be an effective tool to improve the accuracy of estimating pollutants' distribution pattern at intersections. The outputs of these findings demonstrate the potential of the proposed model to be applicable to forecast the distribution pattern of air pollution in real-time in proximity to road intersection.

  14. Short communication: Genotyping of cows to speed up availability of genomic estimated breeding values for direct health traits in Austrian Fleckvieh (Simmental) cattle--genetic and economic aspects.

    PubMed

    Egger-Danner, C; Schwarzenbacher, H; Willam, A

    2014-07-01

    The aim of this study was to quantify the impact of genotyping cows with reliable phenotypes for direct health traits on annual monetary genetic gain (AMGG) and discounted profit. The calculations were based on a deterministic approach using ZPLAN software (University of Hohenheim, Stuttgart, Germany). It was assumed that increases in reliability of the total merit index (TMI) of 5, 15, and 25 percentage points were achieved through genotyping 5,000, 25,000, and 50,000 cows, respectively. Costs for phenotyping, genotyping, and genomic estimated breeding values vary between €150 and €20 per cow. The gain in genotyping cows for traits with medium to high heritability is more than for direct health traits with low heritability. The AMGG is increased by 1.5% if the reliability of TMI is 5 percentage points higher (i.e., 5,000 cows genotyped) and 6.53% higher AMGG can be expected when the reliability of TMI is increased by 25 percentage points (i.e., 50,000 cows genotyped). The discounted profit depends not only on the costs of genotyping but also on the population size. This study indicates that genotyping cows with reliable phenotypes is feasible to speed up the availability of genomic estimated breeding values for direct health traits. But, because of the huge amount of valid phenotypes and genotypes needed to establish an efficient genomic evaluation, it is likely that financial constraints will be the main limiting factor for implementation into breeding program such as Fleckvieh Austria. PMID:24835973

  15. Epidermal Permeability Barrier Defects and Barrier Repair Therapy in Atopic Dermatitis

    PubMed Central

    Lee, Hae-Jin

    2014-01-01

    Atopic dermatitis (AD) is a multifactorial inflammatory skin disease perpetuated by gene-environmental interactions and which is characterized by genetic barrier defects and allergic inflammation. Recent studies demonstrate an important role for the epidermal permeability barrier in AD that is closely related to chronic immune activation in the skin during systemic allergic reactions. Moreover, acquired stressors (e.g., Staphylococcus aureus infection) to the skin barrier may also initiate inflammation in AD. Many studies involving patients with AD revealed that defective skin barriers combined with abnormal immune responses might contribute to the pathophysiology of AD, supporting the outside-inside hypothesis. In this review, we discuss the recent advances in human and animal models, focusing on the defects of the epidermal permeability barrier, its immunologic role and barrier repair therapy in AD. PMID:24991450

  16. Mathematical modeling and application of genetic algorithm to parameter estimation in signal transduction: trafficking and promiscuous coupling of G-protein coupled receptors.

    PubMed

    Modchang, Charin; Triampo, Wannapong; Lenbury, Yongwimon

    2008-05-01

    G-protein-coupled receptors (GPCRs) constitute a large and diverse family of proteins whose primary function is to transduce extracellular stimuli into intracellular signals. These receptors play a critical role in signal transduction, and are among the most important pharmacological drug targets. Upon binding of extracellular ligands, these receptor molecules couple to one or several subtypes of G-protein which reside at the intracellular side of the plasma membrane to trigger intracellular signaling events. The question of how GPCRs select and activate a single or multiple G-protein subtype(s) has been the topic of intense investigations. Evidence is also accumulating; however, that certain GPCRs can be internalized via lipid rafts and caveolae. In many cases, the mechanisms responsible for this still remain to be elucidated. In this work, we extend the mathematical model proposed by Chen et al. [Modelling of signalling via G-protein coupled receptors: pathway-dependent agonist potency and efficacy, Bull. Math. Biol. 65 (5) (2003) 933-958] to take into account internalization, recycling, degradation and synthesis of the receptors. In constructing the model, we assume that the receptors can exist in multiple conformational states allowing for a multiple effecter pathways. As data on kinetic reaction rates in the signalling processes measured in reliable in vivo and in vitro experiments is currently limited to a small number of known values. In this paper, we also apply a genetic algorithm (GA) to estimate the parameter values in our model. PMID:18367158

  17. Temporal sampling helps unravel the genetic structure of naturally occurring populations of a phytoparasitic nematode. 1. Insights from the estimation of effective population sizes.

    PubMed

    Jan, Pierre-Loup; Gracianne, Cécile; Fournet, Sylvain; Olivier, Eric; Arnaud, Jean-François; Porte, Catherine; Bardou-Valette, Sylvie; Denis, Marie-Christine; Petit, Eric J

    2016-03-01

    The sustainability of modern agriculture relies on strategies that can control the ability of pathogens to overcome chemicals or genetic resistances through natural selection. This evolutionary potential, which depends partly on effective population size (N e ), is greatly influenced by human activities. In this context, wild pathogen populations can provide valuable information for assessing the long-term risk associated with crop pests. In this study, we estimated the effective population size of the beet cyst nematode, Heterodera schachtii, by sampling 34 populations infecting the sea beet Beta vulgaris spp. maritima twice within a one-year period. Only 20 populations produced enough generations to analyze the variation in allele frequencies, with the remaining populations showing a high mortality rate of the host plant after only 1 year. The 20 analyzed populations showed surprisingly low effective population sizes, with most having N e close to 85 individuals. We attribute these low values to the variation in population size through time, systematic inbreeding, and unbalanced sex-ratios. Our results suggest that H. schachtii has low evolutionary potential in natural environments. Pest control strategies in which populations on crops mimic wild populations may help prevent parasite adaptation to host resistance. PMID:26989440

  18. Thermal barrier research

    SciTech Connect

    Moses, K.G.

    1990-03-07

    The thermal barrier region in the TARA device is a complex arrangement combining ion-plugging by sloshing ions with an ECRH-generated thermal barrier plasma. An axisymmetric, high-mirror-ratio magnetic field, adjacent to the central cell, provides the confinement of the thermal barrier plasma and sloshing ions. This paper discusses research being done in this thermal barrier region.

  19. Strong selection barriers explain microgeographic adaptation in wild salamander populations.

    PubMed

    Richardson, Jonathan L; Urban, Mark C

    2013-06-01

    Microgeographic adaptation occurs when populations evolve divergent fitness advantages across the spatial scales at which focal organisms regularly disperse. Although an increasing number of studies find evidence for microgeographic adaptation, the underlying causes often remain unknown. Adaptive divergence requires some combination of limited gene flow and strong divergent natural selection among populations. In this study, we estimated the relative influence of selection, gene flow, and the spatial arrangement of populations in shaping patterns of adaptive divergence in natural populations of the spotted salamander (Ambystoma maculatum). Within the study region, A. maculatum co-occur with the predatory marbled salamander (Ambystoma opacum) in some ponds, and past studies have established a link between predation risk and adaptive trait variation in A. maculatum. Using 14 microsatellite loci, we found a significant pattern of genetic divergence among A. maculatum populations corresponding to levels of A. opacum predation risk. Additionally, A. maculatum foraging rate was strongly associated with predation risk, genetic divergence, and the spatial relationship of ponds on the landscape. Our results indicate the sorting of adaptive genotypes by selection regime and strongly suggest that substantial selective barriers operate against gene flow. This outcome suggests that microgeographic adaptation in A. maculatum is possible because strong antagonistic selection quickly eliminates maladapted phenotypes despite ongoing and substantial immigration. Increasing evidence for microgeographic adaptation suggests a strong role for selective barriers in counteracting the homogenizing influence of gene flow. PMID:23730765

  20. Parameter estimation by genetic algorithms

    SciTech Connect

    Reese, G.M.

    1993-11-01

    Test/Analysis correlation, or structural identification, is a process of reconciling differences in the structural dynamic models constructed analytically (using the finite element (FE) method) and experimentally (from modal test). This is a methodology for assessing the reliability of the computational model, and is very important in building models of high integrity, which may be used as predictive tools in design. Both the analytic and experimental models evaluate the same quantities: the natural frequencies (or eigenvalues, ({omega}{sub i}), and the mode shapes (or eigenvectors, {var_phi}). In this paper, selected frequencies are reconciled in the two models by modifying physical parameters in the FE model. A variety of parameters may be modified such as the stiffness of a joint member or the thickness of a plate. Engineering judgement is required to identify important frequencies, and to characterize the uncertainty of the model design parameters.

  1. Heterogeneous road networks have no apparent effect on the genetic structure of small mammal populations.

    PubMed

    Grilo, Clara; Del Cerro, Irene; Centeno-Cuadros, Alejandro; Ramiro, Victor; Román, Jacinto; Molina-Vacas, Guillem; Fernández-Aguilar, Xavier; Rodríguez, Juan; Porto-Peter, Flávia; Fonseca, Carlos; Revilla, Eloy; Godoy, José A

    2016-09-15

    Roads are widely recognized to represent a barrier to individual movements and, conversely, verges can act as potential corridors for the dispersal of many small mammals. Both barrier and corridor effects should generate a clear spatial pattern in genetic structure. Nevertheless, the effect of roads on the genetic structure of small mammal populations still remains unclear. In this study, we examine the barrier effect that different road types (4-lane highway, 2-lane roads and single-lane unpaved roads) may have on the population genetic structure of three species differing in relevant life history traits: southern water vole Arvicola sapidus, the Mediterranean pine vole Microtus duodecimcostatus and the Algerian mouse Mus spretus. We also examine the corridor effect of highway verges on the Mediterranean pine vole and the Algerian mouse. We analysed the population structure through pairwise estimates of FST among subpopulations bisected by roads, identified genetic clusters through Bayesian assignment approaches, and used simple and partial Mantel tests to evaluate the relative barrier or corridor effect of roads. No strong evidences were found for an effect of roads on population structure of these three species. The barrier effect of roads seems to be site-specific and no corridor effect of verges was found for the pine vole and Algerian mouse populations. The lack of consistent results among species and for each road type lead us to believe that the ability of individual dispersers to use those crossing structures or the habitat quality in the highway verges may have a relatively higher influence on gene flow among populations than the presence of crossing structures per se. Further research should include microhabitat analysis and the estimates of species abundance to understand the mechanisms that underlie the genetic structure observed at some sites. PMID:27219505

  2. The role of genetically engineered pigs in xenotransplantation research.

    PubMed

    Cooper, David K C; Ekser, Burcin; Ramsoondar, Jagdeece; Phelps, Carol; Ayares, David

    2016-01-01

    There is a critical shortage in the number of deceased human organs that become available for the purposes of clinical transplantation. This problem might be resolved by the transplantation of organs from pigs genetically engineered to protect them from the human immune response. The pathobiological barriers to successful pig organ transplantation in primates include activation of the innate and adaptive immune systems, coagulation dysregulation and inflammation. Genetic engineering of the pig as an organ source has increased the survival of the transplanted pig heart, kidney, islet and corneal graft in non-human primates (NHPs) from minutes to months or occasionally years. Genetic engineering may also contribute to any physiological barriers that might be identified, as well as to reducing the risks of transfer of a potentially infectious micro-organism with the organ. There are now an estimated 40 or more genetic alterations that have been carried out in pigs, with some pigs expressing five or six manipulations. With the new technology now available, it will become increasingly common for a pig to express even more genetic manipulations, and these could be tested in the pig-to-NHP models to assess their efficacy and benefit. It is therefore likely that clinical trials of pig kidney, heart and islet transplantation will become feasible in the near future. PMID:26365762

  3. Immunobiological barriers to xenotransplantation.

    PubMed

    Cooper, David K C; Ekser, Burcin; Tector, A Joseph

    2015-11-01

    Binding of natural anti-pig antibodies in humans and nonhuman primates to carbohydrate antigens expressed on the transplanted pig organ, the most important of which is galactose-α1,3-galactose (Gal), activate the complement cascade, which results in destruction of the graft within minutes or hours, known as hyperacute rejection. Even if antibody is removed from the recipient's blood by plasmapheresis, recovery of antibody is associated with acute humoral xenograft rejection. If immunosuppressive therapy is inadequate, the development of high levels of T cell-dependent elicited anti-pig IgG similarly results in graft destruction, though classical acute cellular rejection is rarely seen. Vascular endothelial activation by low levels of anti-nonGal antibody, coupled with dysregulation of the coagulation-anticoagulation systems between pigs and primates, leads to a thrombotic microangiopathy in the graft that may be associated with a consumptive coagulopathy in the recipient. The most successful approach to overcoming these barriers is by genetically-engineering the pig to provide it with resistance to the human humoral and cellular immune responses and to correct the coagulation discrepancies between the two species. Organs and cells from pigs that (i) do not express the important Gal antigen, (ii) express a human complement-regulatory protein, and (iii) express a human coagulation-regulatory protein, when combined with an effective immunosuppressive regimen, have been associated with prolonged pig graft survival in nonhuman primates. PMID:26159291

  4. Puncture detecting barrier materials

    DOEpatents

    Hermes, Robert E.; Ramsey, David R.; Stampfer, Joseph F.; Macdonald, John M.

    1998-01-01

    A method and apparatus for continuous real-time monitoring of the integrity of protective barrier materials, particularly protective barriers against toxic, radioactive and biologically hazardous materials has been developed. Conductivity, resistivity or capacitance between conductive layers in the multilayer protective materials is measured by using leads connected to electrically conductive layers in the protective barrier material. The measured conductivity, resistivity or capacitance significantly changes upon a physical breach of the protective barrier material.

  5. Puncture detecting barrier materials

    DOEpatents

    Hermes, R.E.; Ramsey, D.R.; Stampfer, J.F.; Macdonald, J.M.

    1998-03-31

    A method and apparatus for continuous real-time monitoring of the integrity of protective barrier materials, particularly protective barriers against toxic, radioactive and biologically hazardous materials has been developed. Conductivity, resistivity or capacitance between conductive layers in the multilayer protective materials is measured by using leads connected to electrically conductive layers in the protective barrier material. The measured conductivity, resistivity or capacitance significantly changes upon a physical breach of the protective barrier material. 4 figs.

  6. Intestinal inflammation and mucosal barrier function.

    PubMed

    Sánchez de Medina, Fermín; Romero-Calvo, Isabel; Mascaraque, Cristina; Martínez-Augustin, Olga

    2014-12-01

    Intestinal mucosal barrier function is the capacity of the intestine to provide adequate containment of luminal microorganisms and molecules while preserving the ability to absorb nutrients. The central element is the epithelial layer, which physically separates the lumen and the internal milieu and is in charge of vectorial transport of ions, nutrients, and other substances. The secretion of mucus-forming mucins, sIgA, and antimicrobial peptides reinforces the mucosal barrier on the extraepithelial side, while a variety of immune cells contributes to mucosal defense in the inner side. Thus, the mucosal barrier is of physical, biochemical, and immune nature. In addition, the microbiota may be viewed as part of this system because of the mutual influence occurring between the host and the luminal microorganisms. Alteration of the mucosal barrier function with accompanying increased permeability and/or bacterial translocation has been linked with a variety of conditions, including inflammatory bowel disease. Genetic and environmental factors may converge to evoke a defective function of the barrier, which in turn may lead to overt inflammation of the intestine as a result of an exacerbated immune reaction toward the microbiota. According to this hypothesis, inflammatory bowel disease may be both precipitated and treated by either stimulation or downregulation of the different elements of the mucosal barrier, with the outcome depending on timing, the cell type affected, and other factors. In this review, we cover briefly the elements of the barrier and their involvement in functional defects and the resulting phenotype. PMID:25222662

  7. Mountains and refuges: Genetic structure and evolutionary history in closely related, endemic Centaurea in continental Greece.

    PubMed

    López-Vinyallonga, Sara; López-Pujol, Jordi; Constantinidis, Theophanis; Susanna, Alfonso; Garcia-Jacas, Núria

    2015-11-01

    Mountains of continental Greece are one of the main Mediterranean biodiversity hotspots, very rich in endemic species. The speciation in this area might have resulted from two main factors: a complex orography and its role as a refugium during past glaciations. We have investigated genetic diversity and population structure for a group of narrow endemics of Centaurea subsect. Phalolepis, with three main goals: to investigate population structure of these narrow endemics, to check whether patterns of genetic variation are in agreement with recognized species boundaries, and to get insights into the process of diversification within this group. Fifteen populations belonging to seven species were genotyped using cpDNA (rpl32-trnL region) sequences and nuclear microsatellites (eight loci). SSR were used to assess genetic variability, to analyse molecular variance, to identify genetic barriers, to estimate recent and historical gene flow, and to carry out a model-based Bayesian clustering. Analysis of cpDNA was used to construct a haplotype network. Despite being narrow endemics, all the studied species show moderate to high SSR genetic diversity. Genetic isolation of populations is very high, with no current gene flow among them. Patterns of genetic structure indicate that there are more genetic clusters than there are currently recognized taxa. Genetic data suggest that isolation in mountain ranges and subsequent allopatric speciation would be the main driver of diversification in the group; the refugial nature of the mountains of continental Greece has allowed the maintenance of high within-population genetic diversity. PMID:26151220

  8. Planar doped barrier subharmonic mixers

    NASA Technical Reports Server (NTRS)

    Lee, T. H.; East, J. R.; Haddad, G. I.

    1992-01-01

    The Planar Doped Barrier (PDB) diode is a device consisting of a p(+) doping spike between two intrinsic layers and n(+) ohmic contacts. This device has the advantages of controllable barrier height, diode capacitance and forward to reverse current ratio. A symmetrically designed PDB has an anti-symmetric current vs. voltage characteristic and is ideal for use as millimeter wave subharmonic mixers. We have fabricated such devices with barrier heights of 0.3, 0.5 and 0.7 volts from GaAs and InGaAs using a multijunction honeycomb structure with junction diameters between one and ten microns. Initial RF measurements are encouraging. The 0.7 volt barrier height 4 micron GaAs devices were tested as subharmonic mixers at 202 GHz with an IF frequency of 1 GHz and had 18 dB of conversion loss. The estimated mismatch loss was 7 dB and was due to higher diode capacitance. The LO frequency was 100.5 GHz and the pump power was 8 mW.

  9. Permeability Barrier Generation in the Martian Lithosphere

    NASA Astrophysics Data System (ADS)

    Schools, Joe; Montési, Laurent

    2015-11-01

    Permeability barriers develop when a magma produced in the interior of a planet rises into the cooler lithosphere and crystallizes more rapidly than the lithosphere can deform (Sparks and Parmentier, 1991). Crystallization products may then clog the porous network in which melt is propagating, reducing the permeability to almost zero, i.e., forming a permeability barrier. Subsequent melts cannot cross the barrier. Permeability barriers have been useful to explain variations in crustal thickness at mid-ocean ridges on Earth (Magde et al., 1997; Hebert and Montési, 2011; Montési et al., 2011). We explore here under what conditions permeability barriers may form on Mars.We use the MELTS thermodynamic calculator (Ghiorso and Sack, 1995; Ghiorso et al., 2002; Asimow et al., 2004) in conjunction with estimated Martian mantle compositions (Morgan and Anders, 1979; Wänke and Dreibus, 1994; Lodders and Fegley, 1997; Sanloup et al., 1999; Taylor 2013) to model the formation of permeability barriers in the lithosphere of Mars. In order to represent potential past and present conditions of Mars, we vary the lithospheric thickness, mantle potential temperature (heat flux), oxygen fugacity, and water content.Our results show that permeability layers can develop in the thermal boundary layer of the simulated Martian lithosphere if the mantle potential temperature is higher than ~1500°C. The various Martian mantle compositions yield barriers in the same locations, under matching variable conditions. There is no significant difference in barrier location over the range of accepted Martian oxygen fugacity values. Water content is the most significant influence on barrier development as it reduces the temperature of crystallization, allowing melt to rise further into the lithosphere. Our lower temperature and thicker lithosphere model runs, which are likely the most similar to modern Mars, show no permeability barrier generation. Losing the possibility of having a permeability

  10. Comparing barrier algorithms

    NASA Technical Reports Server (NTRS)

    Arenstorf, Norbert S.; Jordan, Harry F.

    1987-01-01

    A barrier is a method for synchronizing a large number of concurrent computer processes. After considering some basic synchronization mechanisms, a collection of barrier algorithms with either linear or logarithmic depth are presented. A graphical model is described that profiles the execution of the barriers and other parallel programming constructs. This model shows how the interaction between the barrier algorithms and the work that they synchronize can impact their performance. One result is that logarithmic tree structured barriers show good performance when synchronizing fixed length work, while linear self-scheduled barriers show better performance when synchronizing fixed length work with an imbedded critical section. The linear barriers are better able to exploit the process skew associated with critical sections. Timing experiments, performed on an eighteen processor Flex/32 shared memory multiprocessor, that support these conclusions are detailed.

  11. Comparing barrier algorithms

    NASA Technical Reports Server (NTRS)

    Arenstorf, Norbert S.; Jordan, Harry F.

    1989-01-01

    A barrier is a method for synchronizing a large number of concurrent computer processes. After considering some basic synchronization mechanisms, a collection of barrier algorithms with either linear or logarithmic depth are presented. A graphical model is described that profiles the execution of the barriers and other parallel programming constructs. This model shows how the interaction between the barrier algorithms and the work that they synchronize can impact their performance. One result is that logarithmic tree structured barriers show good performance when synchronizing fixed length work, while linear self-scheduled barriers show better performance when synchronizing fixed length work with an imbedded critical section. The linear barriers are better able to exploit the process skew associated with critical sections. Timing experiments, performed on an eighteen processor Flex/32 shared memory multiprocessor that support these conclusions, are detailed.

  12. SPECIATION IN MAMMALS AND THE GENETIC SPECIES CONCEPT.

    PubMed

    Baker, Robert J; Bradley, Robert D

    2006-08-01

    We define a genetic species as a group of genetically compatible interbreeding natural populations that is genetically isolated from other such groups. This focus on genetic isolation rather than reproductive isolation distinguishes the Genetic Species Concept from the Biological Species Concept. Recognition of species that are genetically isolated (but not reproductively isolated) results in an enhanced understanding of biodiversity and the nature of speciation as well as speciation-based issues and evolution of mammals. We review criteria and methods for recognizing species of mammals and explore a theoretical scenario, the Bateson-Dobzhansky-Muller (BDM) model, for understanding and predicting genetic diversity and speciation in mammals. If the BDM model is operating in mammals, then genetically defined phylogroups would be predicted to occur within species defined by morphology, and phylogroups experiencing stabilizing selection will evolve genetic isolation without concomitant morphological diversification. Such species will be undetectable using classical skin and skull morphology (Morphological Species Concept). Using cytochrome-b data from sister species of mammals recognized by classical morphological studies, we estimated the number of phylogroups that exist within mammalian species and hypothesize that there will be >2,000 currently unrecognized species of mammals. Such an underestimation significantly affects conclusions on the nature of speciation in mammals, barriers associated with evolution of genetic isolation, estimates of biodiversity, design of conservation initiatives, zoonoses, and so on. A paradigm shift relative to this and other speciation-based issues will be needed. Data that will be effective in detecting these "morphologically cryptic genetic species" are genetic, especially DNA-sequence data. Application of the Genetic Species Concept uses genetic data from mitochondrial and nuclear genomes to identify species and species boundaries

  13. Understanding the Spatial Scale of Genetic Connectivity at Sea: Unique Insights from a Land Fish and a Meta-Analysis.

    PubMed

    Cooke, Georgina M; Schlub, Timothy E; Sherwin, William B; Ord, Terry J

    2016-01-01

    Quantifying the spatial scale of population connectivity is important for understanding the evolutionary potential of ecologically divergent populations and for designing conservation strategies to preserve those populations. For marine organisms like fish, the spatial scale of connectivity is generally set by a pelagic larval phase. This has complicated past estimates of connectivity because detailed information on larval movements are difficult to obtain. Genetic approaches provide a tractable alternative and have the added benefit of estimating directly the reproductive isolation of populations. In this study, we leveraged empirical estimates of genetic differentiation among populations with simulations and a meta-analysis to provide a general estimate of the spatial scale of genetic connectivity in marine environments. We used neutral genetic markers to first quantify the genetic differentiation of ecologically-isolated adult populations of a land dwelling fish, the Pacific leaping blenny (Alticus arnoldorum), where marine larval dispersal is the only probable means of connectivity among populations. We then compared these estimates to simulations of a range of marine dispersal scenarios and to collated FST and distance data from the literature for marine fish across diverse spatial scales. We found genetic connectivity at sea was extensive among marine populations and in the case of A. arnoldorum, apparently little affected by the presence of ecological barriers. We estimated that ~5000 km (with broad confidence intervals ranging from 810-11,692 km) was the spatial scale at which evolutionarily meaningful barriers to gene flow start to occur at sea, although substantially shorter distances are also possible for some taxa. In general, however, such a large estimate of connectivity has important implications for the evolutionary and conservation potential of many marine fish communities. PMID:27195493

  14. Understanding the Spatial Scale of Genetic Connectivity at Sea: Unique Insights from a Land Fish and a Meta-Analysis

    PubMed Central

    Cooke, Georgina M.; Schlub, Timothy E.; Sherwin, William B.; Ord, Terry J.

    2016-01-01

    Quantifying the spatial scale of population connectivity is important for understanding the evolutionary potential of ecologically divergent populations and for designing conservation strategies to preserve those populations. For marine organisms like fish, the spatial scale of connectivity is generally set by a pelagic larval phase. This has complicated past estimates of connectivity because detailed information on larval movements are difficult to obtain. Genetic approaches provide a tractable alternative and have the added benefit of estimating directly the reproductive isolation of populations. In this study, we leveraged empirical estimates of genetic differentiation among populations with simulations and a meta-analysis to provide a general estimate of the spatial scale of genetic connectivity in marine environments. We used neutral genetic markers to first quantify the genetic differentiation of ecologically-isolated adult populations of a land dwelling fish, the Pacific leaping blenny (Alticus arnoldorum), where marine larval dispersal is the only probable means of connectivity among populations. We then compared these estimates to simulations of a range of marine dispersal scenarios and to collated FST and distance data from the literature for marine fish across diverse spatial scales. We found genetic connectivity at sea was extensive among marine populations and in the case of A. arnoldorum, apparently little affected by the presence of ecological barriers. We estimated that ~5000 km (with broad confidence intervals ranging from 810–11,692 km) was the spatial scale at which evolutionarily meaningful barriers to gene flow start to occur at sea, although substantially shorter distances are also possible for some taxa. In general, however, such a large estimate of connectivity has important implications for the evolutionary and conservation potential of many marine fish communities. PMID:27195493

  15. [Genetics and genetic counseling].

    PubMed

    Izzi, Claudia; Liut, Francesca; Dallera, Nadia; Mazza, Cinzia; Magistroni, Riccardo; Savoldi, Gianfranco; Scolari, Francesco

    2016-01-01

    Autosomal Dominant Polycystic Kidney Disease (ADPKD) is the most frequent genetic disease, characterized by progressive development of bilateral renal cysts. Two causative genes have been identified: PKD1 and PKD2. ADPKD phenotype is highly variable. Typically, ADPKD is an adult onset disease. However, occasionally, ADPKD manifests as very early onset disease. The phenotypic variability of ADPKD can be explained at three genetic levels: genic, allelic and gene modifier effects. Recent advances in molecular screening for PKD gene mutations and the introduction of the new next generation sequencing (NGS)- based genotyping approach have generated considerable improvement regarding the knowledge of genetic basis of ADPKD. The purpose of this article is to provide a comprehensive review of the genetics of ADPKD, focusing on new insights in genotype-phenotype correlation and exploring novel clinical approach to genetic testing. Evaluation of these new genetic information requires a multidisciplinary approach involving a nephrologist and a clinical geneticist. PMID:27067213

  16. Multilayer moisture barrier

    DOEpatents

    Pankow, Joel W; Jorgensen, Gary J; Terwilliger, Kent M; Glick, Stephen H; Isomaki, Nora; Harkonen, Kari; Turkulainen, Tommy

    2015-04-21

    A moisture barrier, device or product having a moisture barrier or a method of fabricating a moisture barrier having at least a polymer layer, and interfacial layer, and a barrier layer. The polymer layer may be fabricated from any suitable polymer including, but not limited to, fluoropolymers such as polyethylene terephthalate (PET) or polyethylene naphthalate (PEN), or ethylene-tetrafluoroethylene (ETFE). The interfacial layer may be formed by atomic layer deposition (ALD). In embodiments featuring an ALD interfacial layer, the deposited interfacial substance may be, but is not limited to, Al.sub.2O.sub.3, AlSiO.sub.x, TiO.sub.2, and an Al.sub.2O.sub.3/TiO.sub.2 laminate. The barrier layer associated with the interfacial layer may be deposited by plasma enhanced chemical vapor deposition (PECVD). The barrier layer may be a SiO.sub.xN.sub.y film.

  17. Bulk-barrier transistor

    NASA Astrophysics Data System (ADS)

    Mader, H.; Mueller, R.; Beinvogl, W.

    1983-10-01

    Experimental and theoretical results are presented on a bulk-barrier transistor (BBT). In this device the charge-carrier transportation is determined by an energy barrier, which is located inside a semiconductor. The barrier is the result of a space-charge region in a three-layered n-p-n or p-n-p structure with a very thin middle layer. The height of the energy barrier, which is adjustable by technological parameters, can be controlled by an external voltage.

  18. Immigrant inviability produces a strong barrier to gene flow between parapatric ecotypes of Senecio lautus.

    PubMed

    Richards, Thomas J; Ortiz-Barrientos, Daniel

    2016-06-01

    Speciation proceeds when gene exchange is prevented between populations. Determining the different barriers preventing gene flow can therefore give insights into the factors driving and maintaining species boundaries. These reproductive barriers may result from intrinsic genetic incompatibilities between populations, from extrinsic environmental differences between populations, or a combination of both mechanisms. We investigated the potential barriers to gene exchange between three adjacent ecotypes of an Australian wildflower to determine the strength of individual barriers and the degree of overall isolation between populations. We found almost complete isolation between the three populations mainly due to premating extrinsic barriers. Intrinsic genetic barriers were weak and variable among populations. There were asymmetries in some intrinsic barriers due to the origin of cytoplasm in hybrids. Overall, these results suggest that reproductive isolation between these three populations is almost complete despite the absence of geographic barriers, and that the main drivers of this isolation are ecologically based, consistent with the mechanisms underlying ecological speciation. PMID:27159252

  19. Estimates of Spatial Genetic Structure within and among Clones of Wild Lowbush Blueberry in Maine using EST-PCR Molecular Markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Using recently developed EST-PCR markers, several levels of spatial genetic structure of wild lowbush blueberry, Vaccinium angustifolium Ait., were investigated. Knowledge of this structure (or lack of it) is a prerequisite to testing hypotheses regarding the dramatic yield variation among individu...

  20. Determination of epigenetic inheritance, genetic inheritance, and estimation of genome DNA methylation in a full-sib family of Cupressus sempervirens L.

    PubMed

    Avramidou, Evangelia V; Doulis, Andreas G; Aravanopoulos, Filippos A

    2015-05-15

    Genetic inheritance and epigenetic inheritance are significant determinants of plant evolution, adaptation and plasticity. We studied inheritance of restriction site polymorphisms by the f-AFLP method and epigenetic DNA cytosine methylation inheritance by the f-MSAP technique. The study involved parents and 190 progeny of a Cupressus sempervirens L. full-sib family. Results from AFLP genetic data revealed that 71.8% of the fragments studied are under Mendelian genetic control, whereas faithful Mendelian inheritance for the MSAP fragments was low (4.29%). Further, MSAP fragment analysis showed that total methylation presented a mean of 28.2%, which was higher than the midparent value, while maternal inheritance was higher (5.65%) than paternal (3.01%). Interestingly de novo methylation in the progeny was high (19.65%) compared to parental methylation. Genetic and epigenetic distances for parents and offspring were not correlated (R(2)=0.0005). Furthermore, we studied correlation of total relative methylation and CG methylation with growth (height, diameter). We found CG/CNG methylation (N: A, C, T) to be positively correlated with height and diameter, while total relative methylation and CG methylation were positively correlated with height. Results are discussed in light of further research needed and of their potential application in breeding. PMID:25726917

  1. Medical genetics

    SciTech Connect

    Nora, J.J.; Fraser, F.C.

    1989-01-01

    This book presents a discussion of medical genetics for the practitioner treating or counseling patients with genetic disease. It includes a discussion of the relationship of heredity and diseases, the chromosomal basis for heredity, gene frequencies, and genetics of development and maldevelopment. The authors also focus on teratology, somatic cell genetics, genetics and cancer, genetics of behavior.

  2. Recognizing Andean Uplift and the Growth of Continuous Topographic Barriers

    NASA Astrophysics Data System (ADS)

    Horton, B. K.

    2014-12-01

    Although long debated, the timing of Andean uplift and establishment of a continuous topographic barrier along western South America remains critical to biogeographic assessments of the influence of mountain uplift and erosion on Neotropical biodiversity. Recent methodological advances allow independent geologic estimates of barrier uplift and river drainage shifts that can be compared with molecular-clock calculations of genetic divergence times for various Andean and Amazonian populations. Emerging results from U-Pb geochronology and stable-isotope paleoaltimetry suggest a nearly continuous western barrier since the late Eocene-Oligocene and a complex yet decipherable Miocene-Quaternary history of eastward advancing Andean deformation, upper-crustal erosion, and foreland-directed fluvial transport. In the central Andes, U-Pb ages for detrital zircon minerals from multiple sedimentary basins suggest continuous contributions of Cenozoic-age volcanic detritus from the Western Cordillera since late Eocene-Oligocene time. Hydrogen stable isotopic signatures from volcanic glasses further suggest that the long-lived Western Cordillera magmatic arc attained modern elevations by 19-16 Ma in southern Peru. In the northern Andes, major shifts in detrital age signatures, sandstone compositions, and sediment dispersal for hinterland basins of southern Colombia and Ecuador record punctuated 12-6 Ma uplift of the Eastern Cordillera fold-thrust belt. This eastward advance of deformation helped establish the modern Amazon, Magdalena, and Orinoco river drainage systems, terminating any significant west-directed sediment transport and likely explaining late Miocene vicariance events among taxa of the northern Andes, western forearc slope, and Amazonian foreland basin.

  3. Assessing barriers to immunization.

    PubMed

    Niederhauser, Victoria; Ferris, Catherine

    2016-05-01

    Parental barriers to childhood immunizations vary among countries, states and communities. There is a plethora of studies that exist to examine barriers to immunizations including many intervention studies designed to improve immunization rates in children. Often, intervention studies designed to minimize barriers and increase immunization uptake among children lack the inclusion of a standardized instrument to measure accurately parental barriers to childhood immunizations before and after interventions. The Searching for Hardships and Obstacles To Shots (SHOTS) survey is a standardized survey instrument to measure parental barriers to childhood immunizations. In several studies, the SHOTS survey has demonstrated consistent reliability and has been validated in diverse populations. The inclusion of the SHOTS survey instrument in studies to examine barriers to childhood immunization will provide researchers and clinicians with a better understanding of parents' individualized barriers to immunizations. Furthermore, use of the SHOTS survey instrument to collect information about parental barriers to immunizations can lead to targeted interventions to minimize these obstacles at the individual and community level and to help us to achieve our national, state and community childhood immunization goals. PMID:26810618

  4. Penetration resistant barrier

    DOEpatents

    Hoover, William R.; Mead, Keith E.; Street, Henry K.

    1977-01-01

    The disclosure relates to a barrier for resisting penetration by such as hand tools and oxy-acetylene cutting torches. The barrier comprises a layer of firebrick, which is preferably epoxy impregnated sandwiched between inner and outer layers of steel. Between the firebrick and steel are layers of resilient rubber-like filler.

  5. Liquid metal hydrogen barriers

    DOEpatents

    Grover, George M.; Frank, Thurman G.; Keddy, Edward S.

    1976-01-01

    Hydrogen barriers which comprise liquid metals in which the solubility of hydrogen is low and which have good thermal conductivities at operating temperatures of interest. Such barriers are useful in nuclear fuel elements containing a metal hydride moderator which has a substantial hydrogen dissociation pressure at reactor operating temperatures.

  6. Test plan for hydrologic modeling of protective barriers

    SciTech Connect

    Fayer, M.J.

    1990-03-01

    Pacific Northwest Laboratory prepared this test plan for the Model Applications and Validation Task of the Hanford Protective Barriers Program, which is managed by Westinghouse Hanford Company. The objectives of this plan are to outline the conceptual hydrologic model of protective barriers, discuss the available computer codes, describe the interrelationships between the modeling task and the other tasks of the Protective Barriers Program, present the barrier modeling tests, and estimate the schedule and costs of the hydrologic modeling task for planning purposes by the Protective Barriers Program. The purpose of the tests is to validate models that will be used to confirm the long-term performance of the barrier in minimizing drainage. A second purpose of the tests is to provide information to other parts of the Protective Barriers Program that require such information. 26 refs., 2 figs., 3 tabs.

  7. Assessing performance of single-sample molecular genetic methods to estimate effective population size: empirical evidence from the endangered Gochu Asturcelta pig breed.

    PubMed

    Menéndez, Juan; Álvarez, Isabel; Fernandez, Iván; Menéndez-Arias, Nuria A; Goyache, Félix

    2016-07-01

    Estimating effective population size (N e ) using linkage disequilibrium (LD) information (N e( LD ) ) has the operational advantage of using a single sample. However, N e( LD ) estimates assume discrete generations and its performance are constrained by demographic issues. However, such concerns have received little empirical attention so far. The pedigree of the endangered Gochu Asturcelta pig breed includes individuals classified into discrete filial generations and individuals with generations overlap. Up to 780 individuals were typed with a set of 17 microsatellites. Performance of N e( LD ) was compared with N e estimates obtained using genealogical information, molecular coancestry (N e(M) ) and a temporal (two-sample) method (N e( JR ) ). Molecular-based estimates of N e exceeded those obtained using pedigree data. Estimates of N e( LD ) for filial generations F3 and F4 (17.0 and 17.3, respectively) were lower and steadier than those obtained using yearly or biannual samplings. N e( LD ) estimated for samples including generations overlap could only be compared with those obtained for the discrete filial generations when sampling span approached a generation interval and demographic correction for bias was applied. Single-sample N e(M) estimates were lower than their N e( LD ) counterparts. N e(M) estimates are likely to partially reflect the number of founders rather than population size. In any case, estimates of LD and molecular coancestry tend to covary and, therefore, N e(M) and N e( LD ) can hardly be considered independent. Demographically adjusted estimates of N e( JR ) and N e( LD ) took comparable values when: (1) the two samples used for the former were separated by one equivalent to discrete generations in the pedigree and (2) sampling span used for the latter approached a generation interval. Overall, the empirical evidence given in this study suggested that the advantage of using single-sample methods to obtain molecular-based estimates of N e

  8. Catalytic thermal barrier coatings

    DOEpatents

    Kulkarni, Anand A.; Campbell, Christian X.; Subramanian, Ramesh

    2009-06-02

    A catalyst element (30) for high temperature applications such as a gas turbine engine. The catalyst element includes a metal substrate such as a tube (32) having a layer of ceramic thermal barrier coating material (34) disposed on the substrate for thermally insulating the metal substrate from a high temperature fuel/air mixture. The ceramic thermal barrier coating material is formed of a crystal structure populated with base elements but with selected sites of the crystal structure being populated by substitute ions selected to allow the ceramic thermal barrier coating material to catalytically react the fuel-air mixture at a higher rate than would the base compound without the ionic substitutions. Precious metal crystallites may be disposed within the crystal structure to allow the ceramic thermal barrier coating material to catalytically react the fuel-air mixture at a lower light-off temperature than would the ceramic thermal barrier coating material without the precious metal crystallites.

  9. Challenges and complexities in estimating both the functional impact and the disease risk associated with the extensive genetic variation in human DNA repair genes.

    PubMed

    Mohrenweiser, Harvey W; Wilson, David M; Jones, Irene M

    2003-05-15

    Individual risk and the population incidence of disease result from the interaction of genetic susceptibility and exposure. DNA repair is an example of a cellular process where genetic variation in families with extreme predisposition is documented to be associated with high disease likelihood, including syndromes of premature aging and cancer. Although the identification and characterization of new genes or variants in cancer families continues to be important, the focus of this paper is the current status of efforts to define the impact of polymorphic amino acid substitutions in DNA repair genes on individual and population cancer risk. There is increasing evidence that mild reductions in DNA repair capacity, assumed to be the consequence of common genetic variation, affect cancer predisposition. The extensive variation being found in the coding regions of DNA repair genes and the large number of genes in each of the major repair pathways results in complex genotypes with potential to impact cancer risk in the general population. The implications of this complexity for molecular epidemiology studies, as well as concepts that may make these challenges more manageable, are discussed. The concepts include both experimental and computational approaches that could be employed to develop predictors of disease susceptibility based on DNA repair genotype, focusing initially on studies to assess functional impact on individual proteins and pathways and then on molecular epidemiology studies to assess exposure-dependent health risk. In closing, we raise some of the non-technical challenges to the utilization of the full richness of the genetic variation to reduce disease occurrence and ultimately improve health care. PMID:12714187

  10. Development and validation of RP-HPLC method for the quantitative estimation of αs1-genetic variants in goat milk.

    PubMed

    Montalbano, Maria; Tortorici, Lina; Mastrangelo, Salvatore; Sardina, Maria Teresa; Portolano, Baldassare

    2014-08-01

    A high-performance liquid chromatographic (HPLC) method was developed and validated for separation and quantification of the most common genetic variants of αs1-casein in goat's milk, to evaluate the effect of αs1-casein polymorphisms on casein content. Chromatography was carried out by binary gradient technique on a reversed-phase C8 Zorbax column and the detection was made at a wavelength of 214nm. The procedure was developed using individual raw milk samples of Girgentana goats. For calibration experiments, pure genetic variants were extracted from individual milk samples of animals with known genotypes, considering that commercial standards for goat genetic variants were not available. The data obtained for Girgentana goat breed showed that A, B, F variants were alleles associated with a content of αs1-casein in milk of 3.2±0.4, 5.4±0.5 and 0.7±0.1g/L, respectively, whereas N variant was a 'null' allele associated with the absence of αs1-casein in milk. PMID:24629953

  11. Regressive and transgressive barrier islands on the North-Central Gulf Coast — Contrasts in evolution, sediment delivery, and island vulnerability

    NASA Astrophysics Data System (ADS)

    Otvos, Ervin G.; Carter, Gregory A.

    2013-09-01

    Basic differences between non-deltaic regressive and deltaic transgressive barrier islands reflect major contrasts in geological settings and sediment sources. Two island groups on the N. Gulf of Mexico provide unique perspectives of genetic and geomorphic contrasts applicable in a worldwide context. The near-extinction of the deltaic transgressive Chandeleur barriers and reduction of the sturdier prograded Mississippi-Alabama (MS-AL) chain are related to differences in sediment sources, storm, and anthropogenic impact. 160 years of documentary evidence points to contrasting geological settings, development history, sediment sources, and island morphology as responsible for different island erodibility and life spans. The non-deltaic chain received larger volumes of coarser, less erodible medium sand from the NE Gulf coast. Onshore sand flux from reworked delta deposits received from the retreating delta shoreface initiated the fragile, thin, and isolated transgressive Chandeleur islands. Fine-grained sand from unconsolidated muds of abandoned Mississippi-St. Bernard delta lobes maintained two distinct transgressive barrier island categories. In the absence of quantitative data on cross-shore transport, discrepancies between estimated littoral drift volumes and sand reserves for nourishment remain unexplained. Medium-sandy MS-AL barriers have resisted storm events far better than delta barriers. However, even the former chain did undergo 26 to 53% area reduction since 1848. Anthropogenic intervention stymied island growth. Emerging intertidal berm-basins formed on sandy shoal platforms in storm-eliminated sectors have contributed to partial island recovery. Delta attrition by wave erosion, tectonic, and compactional subsidence had accelerated delta lobe and barrier island decay. Intensive storm erosion culminating in and following Hurricane Katrina came close to eradicate the highly vulnerable Chandeleur barrier chain. Lacking adequate nourishment, after

  12. Using population genetic tools to develop a control strategy for feral cats (Felis catus) in Hawai'i

    USGS Publications Warehouse

    Hansen, H.; Hess, S.C.; Cole, D.; Banko, P.C.

    2007-01-01

    Population genetics can provide information about the demographics and dynamics of invasive species that is beneficial for developing effective control strategies. We studied the population genetics of feral cats on Hawai'i Island by microsatellite analysis to evaluate genetic diversity and population structure, assess gene flow and connectivity among three populations, identify potential source populations, characterise population dynamics, and evaluate sex-biased dispersal. High genetic diversity, low structure, and high number of migrants per generation supported high gene flow that was not limited spatially. Migration rates revealed that most migration occurred out of West Mauna Kea. Effective population size estimates indicated increasing cat populations despite control efforts. Despite high gene flow, relatedness estimates declined significantly with increased geographic distance and Bayesian assignment tests revealed the presence of three population clusters. Genetic structure and relatedness estimates indicated male-biased dispersal, primarily from Mauna Kea, suggesting that this population should be targeted for control. However, recolonisation seems likely, given the great dispersal ability that may not be inhibited by barriers such as lava flows. Genetic monitoring will be necessary to assess the effectiveness of future control efforts. Management of other invasive species may benefit by employing these population genetic tools. ?? CSIRO 2007.

  13. Complementary Barrier Infrared Detector

    NASA Technical Reports Server (NTRS)

    Ting, David Z.; Bandara, Sumith V.; Hill, Cory J.; Gunapala, Sarath D.

    2009-01-01

    The complementary barrier infrared detector (CBIRD) is designed to eliminate the major dark current sources in the superlattice infrared detector. The concept can also be applied to bulk semiconductor- based infrared detectors. CBIRD uses two different types of specially designed barriers: an electron barrier that blocks electrons but not holes, and a hole barrier that blocks holes but not electrons. The CBIRD structure consists of an n-contact, a hole barrier, an absorber, an electron barrier, and a p-contact. The barriers are placed at the contact-absorber junctions where, in a conventional p-i-n detector structure, there normally are depletion regions that produce generation-recombination (GR) dark currents due to Shockley-Read- Hall (SRH) processes. The wider-bandgap complementary barriers suppress G-R dark current. The barriers also block diffusion dark currents generated in the diffusion wings in the neutral regions. In addition, the wider gap barriers serve to reduce tunneling dark currents. In the case of a superlattice-based absorber, the superlattice itself can be designed to suppress dark currents due to Auger processes. At the same time, the barriers actually help to enhance the collection of photo-generated carriers by deflecting the photo-carriers that are diffusing in the wrong direction (i.e., away from collectors) and redirecting them toward the collecting contacts. The contact layers are made from materials with narrower bandgaps than the barriers. This allows good ohmic contacts to be made, resulting in lower contact resistances. Previously, THALES Research and Technology (France) demonstrated detectors with bulk InAsSb (specifically InAs0.91Sb0.09) absorber lattice-matched to GaSb substrates. The absorber is surrounded by two wider bandgap layers designed to minimize impedance to photocurrent flow. The wide bandgap materials also serve as contacts. The cutoff wavelength of the InAsSb absorber is fixed. CBIRD may be considered as a modified

  14. Vehicle barrier systems

    SciTech Connect

    Sena, P.A.

    1986-01-01

    The ground vehicle is one of the most effective tools available to an adversary force. Vehicles can be used to penetrate many types of perimeter barriers, transport equipment and personnel rapidly over long distances, and deliver large amounts of explosives directly to facilities in suicide missions. The function of a vehicle barrier system is to detain or disable a defined threat vehicle at a selected distance from a protected facility. Numerous facilities are installing, or planning to install, vehicle barrier systems and many of these facilities are requesting guidance to do so adequately. Therefore, vehicle barriers are being evaluated to determine their stopping capabilities so that systems can be designed that are both balanced and capable of providing a desired degree of protection. Equally important, many of the considerations that should be taken into account when establishing a vehicle barrier system have been identified. These considerations which pertain to site preparation, barrier selection, system integration and operation, and vehicle/barrier interaction, are discussed in this paper. 2 tabs.

  15. Vehicle barrier systems

    SciTech Connect

    Sena, P.A.

    1986-01-01

    The ground vehicle is one of the most effective tools available to an adversary force. Vehicles can be used to penetrate many types of perimeter barriers, transport equipment, and personnel rapidly over long distances, and deliver large amounts of explosives directly to facilities in suicide missions. The function of a vehicle barrier system is to detain or disable a defined threat vehicle at a selected distance from a protected facility. Numerous facilities are installing, or planning to install, vehicle barrier systems and many of these facilities are requesting guidance to do so adequately. Therefore, vehicle barriers are being evaluated to determine their stopping capabilities so that systems can be designed that are both balanced and capable of providing a desired degree of protection. Equally important, many of the considerations that should be taken into account when establishing a vehicle barrier system have been identified. These considerations which pertain to site preparation, barrier selection, system integration and operation, and vehicle/barrier interaction, are discussed in this paper.

  16. Vehicle barrier systems

    SciTech Connect

    Sena, P.A.

    1986-01-01

    The ground vehicle is one of the most effective tools available to an adversary force. Vehicles can be used to penetrate many types of perimeter barriers, transport equipment and personnel rapidly over long distances, and deliver large amounts of explosives directly to facilities in suicide missions. The function of a vehicle barrier system is to detain or disable a defined threat vehicle at a selected distance from a protected facility. Numerous facilities are installing, or planning to install, vehicle barrier systems and many of these facilities are requesting guidance to do so adequately. Therefore, vehicle barriers are being evaluated to determine their stopping capabilities so that systems can be designed that are both balanced and capable of providing a desired degree of protection. Equally important, many of the considerations that should be taken into account when establishing a vehicle barrier system have been identified. These considerations which pertain to site preparation, barrier selection, system integration and operation, and vehicle/barrier interaction, are discussed in this paper.

  17. Retractable barrier strip

    DOEpatents

    Marts, Donna J.; Barker, Stacey G.; Wowczuk, Andrew; Vellenoweth, Thomas E.

    2002-01-01

    A portable barrier strip having retractable tire-puncture spikes for puncturing a vehicle tire. The tire-puncture spikes have an armed position for puncturing a tire and a retracted position for not puncturing a tire. The strip comprises a plurality of barrier blocks having the tire-puncture spikes removably disposed in a shaft that is rotatably disposed in each barrier block. The plurality of barrier blocks hare hingedly interconnected by complementary hinges integrally formed into the side of each barrier block which allow the strip to be rolled for easy storage and retrieval, but which prevent irregular or back bending of the strip. The shafts of adjacent barrier blocks are pivotally interconnected via a double hinged universal joint to accommodate irregularities in a roadway surface and to transmit torsional motion of the shaft from block to block. A single flexshaft cable is connected to the shaft of an end block to allow a user to selectively cause the shafts of a plurality of adjacently connected barrier blocks to rotate the tire-puncture spikes to the armed position for puncturing a vehicle tire, and to the retracted position for not puncturing the tire. The flexshaft is provided with a resiliently biased retracting mechanism, and a release latch for allowing the spikes to be quickly retracted after the intended vehicle tire is punctured.

  18. Highway noise barrier perceived benefit

    NASA Astrophysics Data System (ADS)

    May, D. N.; Osman, M. M.

    1980-05-01

    A laboratory experiment was performed in which 82 subjects judged the benefit of a noise barrier by listening to tape recordings of before-barrier and after-barrier traffic noise. These perceived benefit judgments were related by regression analysis to the barrier attenuation, the before-barrier traffic sound level, and a music background level, all of which were varied over the course of the experiment. Prediction equations were developed for barrier benefit in terms of these sound levels, their purpose being to provide a model for barrier benefit that can be used in barrier site selection and design. An unexpected finding was that barrier benefit was highest when before-barrier sound levels were lowest: i.e., subjects preferred a noise barrier that solved a moderate noise problem over an equally-attenuating barrier that only partially solved a more severe noise problem.

  19. Complementary barrier infrared detector (CBIRD)

    NASA Technical Reports Server (NTRS)

    Ting, David Z. (Inventor); Bandara, Sumith V. (Inventor); Hill, Cory J. (Inventor); Gunapala, Sarath D. (Inventor)

    2013-01-01

    An infrared detector having a hole barrier region adjacent to one side of an absorber region, an electron barrier region adjacent to the other side of the absorber region, and a semiconductor adjacent to the electron barrier.

  20. Native fishes in the Truckee River: Are in-stream structures and patterns of population genetic structure related?

    PubMed

    Peacock, Mary M; Gustin, Mae S; Kirchoff, Veronica S; Robinson, Morgan L; Hekkala, Evon; Pizzarro-Barraza, Claudia; Loux, Tim

    2016-09-01

    In-stream structures are recognized as significant impediments to movement for freshwater fishes. Apex predators such as salmonids have been the focus of much research on the impacts of such barriers to population dynamics and population viability however much less research has focused on native fishes, where in-stream structures may have a greater impact on long term population viability of these smaller, less mobile species. Patterns of genetic structure on a riverscape can provide information on which structures represent real barriers to movement for fish species and under what specific flow conditions. Here we characterize the impact of 41 dam and diversion structures on movement dynamics under varying flow conditions for a suite of six native fishes found in the Truckee River of California and Nevada. Microsatellite loci were used to estimate total allelic diversity, effective population size and assess genetic population structure. Although there is spatial overlap among species within the river there are clear differences in species distributions within the watershed. Observed population genetic structure was associated with in-stream structures, but only under low flow conditions. High total discharge in 2006 allowed fish to move over potential barriers resulting in no observed population genetic structure for any species in 2007. The efficacy of in-stream structures to impede movement and isolate fish emerged only after multiple years of low flow conditions. Our results suggest that restricted movement of fish species, as a result of in-stream barriers, can be mitigated by flow management. However, as flow dynamics are likely to be altered under global climate change, fragmentation due to barriers could isolate stream fishes into small subpopulations susceptible to both demographic losses and losses of genetic variation. PMID:27135585

  1. Modeling genetic connectivity in sticklebacks as a guideline for river restoration.

    PubMed

    Raeymaekers, Joost A M; Maes, Gregory E; Geldof, Sarah; Hontis, Ingrid; Nackaerts, Kris; Volckaert, Filip A M

    2008-08-01

    Estimating genetic connectivity in disturbed riverine landscapes is of key importance for river restoration. However, few species of the disturbed riverine fauna may provide a detailed and basin-wide picture of the human impact on the population genetics of riverine organisms. Here we used the most abundant native fish, the three-spined stickleback (Gasterosteus aculeatus L.), to detect the geographical determinants of genetic connectivity in the eastern part of the Scheldt basin in Belgium. Anthropogenic structures came out as the strongest determinant of population structure, when evaluated against a geographically well-documented baseline model accounting for natural effects. These barriers not only affected genetic diversity, but they also controlled the balance between gene flow and genetic drift, and therefore may crucially disrupt the population structure of sticklebacks. Landscape models explained a high percentage of variation (allelic richness: adjusted R (2) = 0.78; pairwise F ST: adjusted R (2) = 0.60), and likely apply to other species as well. River restoration and conservation genetics may highly benefit from riverine landscape genetics, including model building, the detection of outlier populations, and a specific test for the geographical factors controlling the balance between gene flow and genetic drift. PMID:25567729

  2. Modeling genetic connectivity in sticklebacks as a guideline for river restoration

    PubMed Central

    Raeymaekers, Joost A M; Maes, Gregory E; Geldof, Sarah; Hontis, Ingrid; Nackaerts, Kris; Volckaert, Filip A M

    2008-01-01

    Estimating genetic connectivity in disturbed riverine landscapes is of key importance for river restoration. However, few species of the disturbed riverine fauna may provide a detailed and basin-wide picture of the human impact on the population genetics of riverine organisms. Here we used the most abundant native fish, the three-spined stickleback (Gasterosteus aculeatus L.), to detect the geographical determinants of genetic connectivity in the eastern part of the Scheldt basin in Belgium. Anthropogenic structures came out as the strongest determinant of population structure, when evaluated against a geographically well-documented baseline model accounting for natural effects. These barriers not only affected genetic diversity, but they also controlled the balance between gene flow and genetic drift, and therefore may crucially disrupt the population structure of sticklebacks. Landscape models explained a high percentage of variation (allelic richness: adjusted R2 = 0.78; pairwise FST: adjusted R2 = 0.60), and likely apply to other species as well. River restoration and conservation genetics may highly benefit from riverine landscape genetics, including model building, the detection of outlier populations, and a specific test for the geographical factors controlling the balance between gene flow and genetic drift. PMID:25567729

  3. Recycler barrier RF buckets

    SciTech Connect

    Bhat, C.M.; /Fermilab

    2011-03-01

    The Recycler Ring at Fermilab uses a barrier rf systems for all of its rf manipulations. In this paper, I will give an overview of historical perspective on barrier rf system, the longitudinal beam dynamics issues, aspects of rf linearization to produce long flat bunches and methods used for emittance measurements of the beam in the RR barrier rf buckets. Current rf manipulation schemes used for antiproton beam stacking and longitudinal momentum mining of the RR beam for the Tevatron collider operation are explained along with their importance in spectacular success of the Tevatron luminosity performance.

  4. Thermal Barrier Coatings

    NASA Technical Reports Server (NTRS)

    1993-01-01

    In order to reduce heat transfer between a hot gas heat source and a metallic engine component, a thermal insulating layer of material is placed between them. This thermal barrier coating is applied by plasma spray processing the thin films. The coating has been successfully employed in aerospace applications for many years. Lewis Research Center, a leader in the development engine components coating technology, has assisted Caterpillar, Inc. in applying ceramic thermal barrier coatings on engines. Because these large engines use heavy fuels containing vanadium, engine valve life is sharply decreased. The barrier coating controls temperatures, extends valve life and reduces operating cost. Additional applications are currently under development.

  5. Medical genetics

    SciTech Connect

    Jorde, L.B.; Carey, J.C.; White, R.L.

    1995-10-01

    This book on the subject of medical genetics is a textbook aimed at a very broad audience: principally, medical students, nursing students, graduate, and undergraduate students. The book is actually a primer of general genetics as applied to humans and provides a well-balanced introduction to the scientific and clinical basis of human genetics. The twelve chapters include: Introduction, Basic Cell Biology, Genetic Variation, Autosomal Dominant and Recessive Inheritance, Sex-linked and Mitochondrial Inheritance, Clinical Cytogenetics, Gene Mapping, Immunogenetics, Cancer Genetics, Multifactorial Inheritance and Common Disease, Genetic Screening, Genetic Diagnosis and Gene Therapy, and Clinical Genetics and Genetic Counseling.

  6. Genetic algorithms

    NASA Technical Reports Server (NTRS)

    Wang, Lui; Bayer, Steven E.

    1991-01-01

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

  7. Dissecting gene expression at the blood-brain barrier

    PubMed Central

    Huntley, Melanie A.; Bien-Ly, Nga; Daneman, Richard; Watts, Ryan J.

    2014-01-01

    The availability of genome-wide expression data for the blood-brain barrier is an invaluable resource that has recently enabled the discovery of several genes and pathways involved in the development and maintenance of the blood-brain barrier, particularly in rodent models. The broad distribution of published data sets represents a viable starting point for the molecular dissection of the blood-brain barrier and will further direct the discovery of novel mechanisms of blood-brain barrier formation and function. Technical advances in purifying brain endothelial cells, the key cell that forms the critical barrier, have allowed for greater specificity in gene expression comparisons with other central nervous system cell types, and more systematic characterizations of the molecular composition of the blood-brain barrier. Nevertheless, our understanding of how the blood-brain barrier changes during aging and disease is underrepresented. Blood-brain barrier data sets from a wider range of experimental paradigms and species, including invertebrates and primates, would be invaluable for investigating the function and evolution of the blood-brain barrier. Newer technologies in gene expression profiling, such as RNA-sequencing, now allow for finer resolution of transcriptomic changes, including isoform specificity and RNA-editing. As our field continues to utilize more advanced expression profiling in its ongoing efforts to elucidate the blood-brain barrier, including in disease and drug delivery, we will continue to see rapid advances in our understanding of the molecular mediators of barrier biology. We predict that the recently published data sets, combined with forthcoming genomic and proteomic blood-brain barrier data sets, will continue to fuel the molecular genetic revolution of blood-brain barrier biology. PMID:25414634

  8. Estimating the Roles of Genetic Risk, Perinatal Risk, and Marital Hostility on Early Childhood Adjustment: Medical Records and Self-Reports.

    PubMed

    Neiderhiser, Jenae M; Marceau, Kristine; De Araujo-Greecher, Marielena; Ganiban, Jody M; Mayes, Linda C; Shaw, Daniel S; Reiss, David; Leve, Leslie D

    2016-05-01

    A wide variety of perinatal risk factors have been linked to later developmental outcomes in children. Much of this work has relied on either birth/medical records or mothers' self-reports collected after delivery, and there has been an ongoing debate about which strategy provides the most accurate and reliable data. This report uses a parent-offspring adoption design (N = 561 families) to (1) examine the correspondence between medical record data and self-report data, (2) examine how perinatal risk factors may influence child internalizing and externalizing behavior at age 4.5 years, and (3) explore interactions among genetic, perinatal risk, and rearing environment on child internalizing and externalizing behavior during early childhood. The agreement of self-reports and medical records data was relatively high (51-100 %), although there was some variation based on the construct. There were few main effects of perinatal risk on child outcomes; however, there were several 2- and 3-way interactions suggesting that the combined influences of genetic, perinatal, and rearing environmental risks are important, particularly for predicting whether children exhibit internalizing versus externalizing symptoms at age 4.5 years. PMID:27075497

  9. Estimation of BDNF gene polymorphism and predisposition to dependence development for selected psychoactive compounds: genetic aspects of addiction with the selected drugs, amphetamine, tetrahydrocannabinol and opiates.

    PubMed

    Biskupska, J; Borowiak, K S; Karlin-Grazewicz, K; Janus, T; Waloszczyk, P; Potocka-Banas, B; Machoy-Mokrzynska, A; Ossowski, A; Ciechanowicz, A

    2013-03-01

    The etiology of drug addiction, a central nervous system (CNS) disease, is not fully known. This complex problem is believed to be connected with concurrently affecting genetic, psychological and environmental factors. The development of addiction is connected with CNS reinforcement system and dopaminergic neurotransmission. Molecular processes are postulated to be of universal character and allow to presume a similar mechanism of dependence for both ethanol and other substances. Therefore, elements of dopaminergic transmission become excellent candidates for the examination of genetic influence on the development of addiction. A relationship between alcoholic disease and the presence of TaqIA1 and DRD2 alleles permits to initiate another investigation of gene-coding DRD2 dopamine receptor. The latest results indicate the importance of brain-derived neurotrophic factor (BDNF) in the regulation of dopaminergic route. The purpose of this research was to reveal the relationship between the Val66Met BDNF gene polymorphism and dependence of psychoactive agent. The examinations were performed with the Local Research Ethics Committee approval and patient's consent. The study group consisted of 100 patients (88 men and 12 women) aged 18-52 years, qualified for research program according to the International Classification of Diseases, Tenth Revision (ICD-10) requirements, medical examination and detailed questionnaire. PMID:23111884

  10. The genetic backburn: using rapid evolution to halt invasions.

    PubMed

    Phillips, Ben L; Shine, Richard; Tingley, Reid

    2016-02-24

    The impact of an invasive species depends upon the extent of area across which it ultimately spreads. A powerful strategy for limiting impact, then, is to limit spread, and this can most easily be achieved by managing or reinforcing natural barriers to spread. Using a simulation model, we show that rapid evolutionary increases in dispersal can render permeable an otherwise effective barrier. On the other hand, we also show that, once the barrier is reached, and if it holds, resultant evolutionary decreases in dispersal rapidly make the barrier more effective. Finally, we sketch a strategy--the genetic backburn--in which low-dispersal individuals from the range core are translocated to the nearside of the barrier ahead of the oncoming invasion. We find that the genetic backburn--by preventing invasion front genotypes reaching the barrier, and hastening the evolutionary decrease in dispersal--can make barriers substantially more effective. In our simulations, the genetic backburn never reduced barrier strength, however, the improvement to barrier strength was negligible when there was substantial long-distance dispersal, or when there was no genetic variation for dispersal distance. The improvement in barrier strength also depended on the trade-off between dispersal and competitive ability, with a stronger trade-off conferring greater power to the genetic backburn. PMID:26911962

  11. Economic evaluation of closure cap barrier materials study

    SciTech Connect

    Serrato, M.G.; Bhutani, J.S.; Mead, S.M.

    1993-09-01

    Volume II of the Economic Evaluation of the Closure Cap Barrier Materials, Revision I contains detailed cost estimates for closure cap barrier materials. The cost estimates incorporate the life cycle costs for a generic hazardous waste seepage basin closure cap under the RCRA Post Closure Period of thirty years. The economic evaluation assessed six barrier material categories. Each of these categories consists of several composite cover system configurations, which were used to develop individual cost estimates. The information contained in this report is not intended to be used as a cost estimating manual. This information provides the decision makers with the ability to screen barrier materials, cover system configurations, and identify cost-effective materials for further consideration.

  12. Information barriers and authentication.

    SciTech Connect

    MacArthur, D. W.; Wolford, J. K.

    2001-01-01

    Acceptance of nuclear materials into a monitoring regime is complicated if the materials are in classified shapes or have classified composition. An attribute measurement system with an information barrier can be emplo,yed to generate an unclassified display from classified measurements. This information barrier must meet two criteria: (1) classified information cannot be released to the monitoring party, and (2) the monitoring party must be convinced that the unclassified output accurately represents the classified input. Criterion 1 is critical to the host country to protect the classified information. Criterion 2 is critical to the monitoring party and is often termed the 'authentication problem.' Thus, the necessity for authentication of a measurement system with an information barrier stems directly from the description of a useful information barrier. Authentication issues must be continually addressed during the entire development lifecycle of the measurement system as opposed to being applied only after the system is built.

  13. Barrier Island Hazard Mapping.

    ERIC Educational Resources Information Center

    Pilkey, Orrin H.; Neal, William J.

    1980-01-01

    Describes efforts to evaluate and map the susceptibility of barrier islands to damage from storms, erosion, rising sea levels and other natural phenomena. Presented are criteria for assessing the safety and hazard potential of island developments. (WB)

  14. Optimistic barrier synchronization

    NASA Technical Reports Server (NTRS)

    Nicol, David M.

    1992-01-01

    Barrier synchronization is fundamental operation in parallel computation. In many contexts, at the point a processor enters a barrier it knows that it has already processed all the work required of it prior to synchronization. The alternative case, when a processor cannot enter a barrier with the assurance that it has already performed all the necessary pre-synchronization computation, is treated. The problem arises when the number of pre-sychronization messages to be received by a processor is unkown, for example, in a parallel discrete simulation or any other computation that is largely driven by an unpredictable exchange of messages. We describe an optimistic O(log sup 2 P) barrier algorithm for such problems, study its performance on a large-scale parallel system, and consider extensions to general associative reductions as well as associative parallel prefix computations.

  15. New Genetics

    MedlinePlus

    ... human genome, behavioral genetics, pharmacogenetics, drug resistance, biofilms, computer modeling. » more Chapter 5: 21st-Century Genetics Covers systems biology, GFP, genetic testing, privacy concerns, DNA forensics, ...

  16. Genetic Counseling

    MedlinePlus

    ... Articles Genetic Counseling Information For... Media Policy Makers Genetic Counseling Language: English Español (Spanish) Recommend on Facebook ... informed decisions about testing and treatment. Reasons for Genetic Counseling There are many reasons that people go ...

  17. Retractable barrier strip

    DOEpatents

    Marts, Donna J.; Barker, Stacey G.; McQueen, Miles A.

    1996-01-01

    A portable barrier strip having retractable tire-puncture means for puncturing a vehicle tire. The tire-puncture means, such as spikes, have an armed position for puncturing a tire and a retracted position for not puncturing a tire. The strip comprises a plurality of barrier blocks having the tire-puncture means removably disposed in a shaft that is rotatably disposed in each barrier block. The shaft removably and pivotally interconnects the plurality of barrier blocks. Actuation cables cause the shaft to rotate the tire-puncture means to the armed position for puncturing a vehicle tire and to the retracted position for not puncturing the tire. Each tire-puncture means is received in a hollow-bed portion of its respective barrier block when in the retracted position. The barrier strip rests stable in its deployed position and substantially motionless as a tire rolls thereon and over. The strip is rolled up for retrieval, portability, and storage purposes, and extended and unrolled in its deployed position for use.

  18. Retractable barrier strip

    DOEpatents

    Marts, D.J.; Barker, S.G.; McQueen, M.A.

    1996-04-16

    A portable barrier strip is described having retractable tire-puncture means for puncturing a vehicle tire. The tire-puncture means, such as spikes, have an armed position for puncturing a tire and a retracted position for not puncturing a tire. The strip comprises a plurality of barrier blocks having the tire-puncture means removably disposed in a shaft that is rotatably disposed in each barrier block. The shaft removably and pivotally interconnects the plurality of barrier blocks. Actuation cables cause the shaft to rotate the tire-puncture means to the armed position for puncturing a vehicle tire and to the retracted position for not puncturing the tire. Each tire-puncture means is received in a hollow-bed portion of its respective barrier block when in the retracted position. The barrier strip rests in its deployed position and substantially motionless as a tire rolls thereon and over. The strip is rolled up for retrieval, portability, and storage purposes, and extended and unrolled in its deployed position for use. 13 figs.

  19. MetaPIGA v2.0: maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics

    PubMed Central

    2010-01-01

    Background The development, in the last decade, of stochastic heuristics implemented in robust application softwares has made large phylogeny inference a key step in most comparative studies involving molecular sequences. Still, the choice of a phylogeny inference software is often dictated by a combination of parameters not related to the raw performance of the implemented algorithm(s) but rather by practical issues such as ergonomics and/or the availability of specific functionalities. Results Here, we present MetaPIGA v2.0, a robust implementation of several stochastic heuristics for large phylogeny inference (under maximum likelihood), including a Simulated Annealing algorithm, a classical Genetic Algorithm, and the Metapopulation Genetic Algorithm (metaGA) together with complex substitution models, discrete Gamma rate heterogeneity, and the possibility to partition data. MetaPIGA v2.0 also implements the Likelihood Ratio Test, the Akaike Information Criterion, and the Bayesian Information Criterion for automated selection of substitution models that best fit the data. Heuristics and substitution models are highly customizable through manual batch files and command line processing. However, MetaPIGA v2.0 also offers an extensive graphical user interface for parameters setting, generating and running batch files, following run progress, and manipulating result trees. MetaPIGA v2.0 uses standard formats for data sets and trees, is platform independent, runs in 32 and 64-bits systems, and takes advantage of multiprocessor and multicore computers. Conclusions The metaGA resolves the major problem inherent to classical Genetic Algorithms by maintaining high inter-population variation even under strong intra-population selection. Implementation of the metaGA together with additional stochastic heuristics into a single software will allow rigorous optimization of each heuristic as well as a meaningful comparison of performances among these algorithms. MetaPIGA v2

  20. Epidermal Differentiation in Barrier Maintenance and Wound Healing.

    PubMed

    Wikramanayake, Tongyu Cao; Stojadinovic, Olivera; Tomic-Canic, Marjana

    2014-03-01

    Significance: The epidermal barrier prevents water loss and serves as the body's first line of defense against toxins, chemicals, and infectious microbes. Disruption of the barrier, either through congenital disorders of barrier formation or through wounds, puts the individual at risk for dehydration, hypersensitivity, infection, and prolonged inflammation. Epidermal barrier disorders affect millions of patients in the United States, causing loss of productivity and diminished quality of life for patients and their families, and represent a burden to the health-care system and society. Recent Advances: The genetic basis of many congenital barrier disorders has been identified in recent years, and great advances have been made in the molecular mechanisms of the formation and homeostasis of epidermal barrier, as well as acute and chronic wound healing. Progress in stem cell (SC) biology, particularly in induced pluripotent stem cells (iPSCs) and allogeneic mesenchymal stem cells (MSCs), has opened new doors for cell-based therapy of chronic wounds. Critical Issues: Understanding of the molecular mechanisms of barrier homeostasis in health and disease, as well as contributions of iPSCs and allogeneic MSCs to wound healing, will lead to the identification of novel targets for developing therapeutics for congenital barrier and wound healing disorders. Future Directions: Future studies should focus on better understanding of molecular mechanisms leading to disrupted homeostasis of epidermal barrier to identify potential therapeutic targets to combat its associated diseases. PMID:24669361

  1. Genetic characterisation of the rabies virus vaccine strains used for oral immunization of foxes in Poland to estimate the effectiveness of vaccination.

    PubMed

    Orłowska, Anna; Żmudziński, Jan Franciszek

    2015-02-01

    The main reservoir of rabies virus in Poland has been the red fox. To control rabies in wildlife, oral immunization of foxes was introduced in 1993. The vaccine is effective when it confers immunity against the virus circulating in the environment. To assess the above issue, a study of the molecular characteristics of 570-bp fragments of the N and G genes of vaccine strains SAD B19 and SAD Bern against street virus strains was performed. The results confirmed the similarity of the vaccine strains and rabies virus strains circulating in the environment and also demonstrate the genetic stability of vaccine strains that have been distributed in Poland for 20 years. PMID:25408374

  2. Estimation of the proportion of genetically unbalanced spermatozoa in the semen of boars carrying chromosomal rearrangements using FISH on sperm nuclei

    PubMed Central

    Pinton, Alain; Ducos, Alain; Yerle, Martine

    2004-01-01

    Many chromosomal rearrangements are detected each year in France on young boars candidates for reproduction. The possible use of these animals requires a good knowledge of the potential effect of the rearrangements on the prolificacy of their mates. This effect can be estimated by an accurate determination of the rate of unbalanced spermatozoa in the semen of boars which carry the rearrangements. Indeed, these spermatozoa exhibiting normal fertilizing ability are responsible for an early embryonic mortality, and then, for a decrease of the litter sizes. The "spermFISH" technique, i.e. fluorescent in situ hybridization on decondensed sperm heads, has been used on several occasions in Man, in this perspective. In livestock species, this method was formerly used mainly for semen sexing purposes. We used it, for the first time, to estimate the rates of imbalance in the semen of four boars carrying chromosomal rearrangements: two reciprocal translocations, rcp(3;15)(q27;q13) and rcp(12;14)(q13;q21), as well as two independent cases of trisomy 18 mosaicism. The rates of unbalanced gametes were relatively high for the two reciprocal translocations (47.83% and 24.33%, respectively). These values differed from the apparent effects of the rearrangements estimated using a limited number of litters: a decrease in prolificacy of 23% (estimation obtained using the results of 6 litters) and 39% (57 litters), respectively for the 3/15 and 12/14 translocations. The imbalance rates were much lower for the trisomy mosaics (0.58% and 1.13%), suggesting a very moderate effect of this special kind of chromosomal rearrangement. PMID:14713414

  3. Genetic Manipulation in Pigs

    PubMed Central

    Sachs, David H.; Galli, Cesare

    2009-01-01

    Purpose of Review Recent developments in the field of genetic engineering have made it possible to add, delete or exchange genes from one species to another. This technology has special relevance to the field of xenotransplantation, in which the elimination of a species-specific disparity could make the difference between success or failure of an organ transplant. This review focuses on developments in both the techniques and applications of genetically modified animals. Recent Findings Advances have been made using existing techniques for genetic modifications of swine and in the development of new, emerging technologies, including enzymatic engineering and the use of siRNA. Applications of the modified animals have provided evidence that genetically modified swine have the potential to overcome both physiologic and immunologic barriers that have previously impeded this field. Use of GalT-KO animals as donors have shown marked improvements in xenograft survivals. Summary Techniques for genetic engineering of swine have been directed toward avoiding naturally existing cellular and antibody responses to species-specific antigens. Organs from genetically engineered animals have enjoyed markedly improved survivals in non-human primates, especially in protocols directed toward the induction of tolerance, presumably by avoiding immunization to new antigens. PMID:19469029

  4. Vacuum barrier for excimer lasers

    DOEpatents

    Shurter, Roger P.

    1992-01-01

    A barrier for separating the vacuum area of a diode from the pressurized gas area of an excimer laser. The barrier is a composite material comprising layers of a metal such as copper, along with layers of polyimide, and a matrix of graphite fiber yarns impregnated with epoxy. The barrier is stronger than conventional foil barriers, and allows greater electron throughput.

  5. Vacuum barrier for excimer lasers

    DOEpatents

    Shurter, R.P.

    1992-09-15

    A barrier for separating the vacuum area of a diode from the pressurized gas area of an excimer laser. The barrier is a composite material comprising layers of a metal such as copper, along with layers of polyimide, and a matrix of graphite fiber yarns impregnated with epoxy. The barrier is stronger than conventional foil barriers, and allows greater electron throughput. 3 figs.

  6. Effectiveness of cable barriers, guardrails, and concrete barrier walls in reducing the risk of injury.

    PubMed

    Zou, Yaotian; Tarko, Andrew P; Chen, Erdong; Romero, Mario A

    2014-11-01

    Roadway departure crashes tend to be severe, especially when the roadside exposes the occupants of errant vehicles to excessive injury hazards. As a cost-effective method when the clear zone width is insufficient, road barriers are often installed to prevent errant vehicles from colliding with dangerous obstacles or traversing steep slopes. This paper focuses on the safety performance of road barriers in Indiana in reducing the risk of injury. The objective of the study presented here is to compare the risk of injury among different hazardous events faced by an occupant in a single-vehicle crash. The studied hazardous events include rolling over, striking three types of barriers (guardrails, concrete barrier walls, and cable barriers) with different barrier offsets to the edge of the travelled way, and striking various roadside objects. A total of 2124 single-vehicle crashes (3257 occupants) that occurred between 2008 and 2012 on 517 pair-matched homogeneous barrier and non-barrier segments were analyzed. A binary logistic regression model with mixed effects was estimated for vehicle occupants. The segment pairing process and the use of random effects were able to handle the commonality within the same segment pair as well as the heterogeneity across segment pairs. The modeling results revealed that hitting a barrier is associated with lower risk of injury than a high-hazard event (hitting a pole, rollover, etc.). The odds of injury are reduced by 39% for median concrete barrier walls offset 15-18ft from the travelled way, reduced by 65% for a guardrail face offset 5-55ft, reduced by 85% for near-side median cable barriers (offset between 10ft and 29ft), and reduced by 78% with far-side median cable barriers (offset at least 30ft). Comparing different types of barriers is useful where some types of barriers can be used alternatively. This study found that the odds of injury are 43% lower when striking a guardrail instead of a median concrete barrier offset 15-18ft

  7. Numerical valuation of discrete double barrier options

    NASA Astrophysics Data System (ADS)

    Milev, Mariyan; Tagliani, Aldo

    2010-03-01

    In the present paper we explore the problem for pricing discrete barrier options utilizing the Black-Scholes model for the random movement of the asset price. We postulate the problem as a path integral calculation by choosing approach that is similar to the quadrature method. Thus, the problem is reduced to the estimation of a multi-dimensional integral whose dimension corresponds to the number of the monitoring dates. We propose a fast and accurate numerical algorithm for its valuation. Our results for pricing discretely monitored one and double barrier options are in agreement with those obtained by other numerical and analytical methods in Finance and literature. A desired level of accuracy is very fast achieved for values of the underlying asset close to the strike price or the barriers. The method has a simple computer implementation and it permits observing the entire life of the option.

  8. Micro heat barrier

    DOEpatents

    Marshall, Albert C.; Kravitz, Stanley H.; Tigges, Chris P.; Vawter, Gregory A.

    2003-08-12

    A highly effective, micron-scale micro heat barrier structure and process for manufacturing a micro heat barrier based on semiconductor and/or MEMS fabrication techniques. The micro heat barrier has an array of non-metallic, freestanding microsupports with a height less than 100 microns, attached to a substrate. An infrared reflective membrane (e.g., 1 micron gold) can be supported by the array of microsupports to provide radiation shielding. The micro heat barrier can be evacuated to eliminate gas phase heat conduction and convection. Semi-isotropic, reactive ion plasma etching can be used to create a microspike having a cusp-like shape with a sharp, pointed tip (<0.1 micron), to minimize the tip's contact area. A heat source can be placed directly on the microspikes. The micro heat barrier can have an apparent thermal conductivity in the range of 10.sup.-6 to 10.sup.-7 W/m-K. Multiple layers of reflective membranes can be used to increase thermal resistance.

  9. Method of installing subsurface barrier

    DOEpatents

    Nickelson, Reva A.; Richardson, John G.; Kostelnik, Kevin M.; Sloan, Paul A.

    2007-10-09

    Systems, components, and methods relating to subterranean containment barriers. Laterally adjacent tubular casings having male interlock structures and multiple female interlock structures defining recesses for receiving a male interlock structure are used to create subterranean barriers for containing and treating buried waste and its effluents. The multiple female interlock structures enable the barriers to be varied around subsurface objects and to form barrier sidewalls. The barrier may be used for treating and monitoring a zone of interest.

  10. Broad and fine-scale genetic analysis of white-tailed deer populations: estimating the relative risk of chronic wasting disease spread

    PubMed Central

    Cullingham, Catherine I; Merrill, Evelyn H; Pybus, Margo J; Bollinger, Trent K; Wilson, Gregory A; Coltman, David W

    2011-01-01

    Chronic wasting disease is a transmissible spongiform encephalopathy of cervids, similar to sheep scrapie that has only recently been detected in wild populations of white-tailed deer (Odocoileus virginianus) and mule deer (Odocoileus hemionus hemionus) in western Canada. Relatively little is known about local transmission dynamics of the disease or the potential for long-distance spread. We analysed the population genetic structure of over 2000 white-tailed deer sampled from Alberta, British Columbia, and Saskatchewan using microsatellite profiles and mtDNA sequencing to assess the relative risk of disease spread. There was very little differentiation among subpopulations and a weak trend of increasing differentiation with geographic distance. This suggests that the potential for long-distance disease spread through the dispersal of infected individuals is possible, yet the risk of spread should gradually diminish with distance from infection foci. Within subpopulations, females were more related than expected by chance (R > 0) within a radius of approximately 500 m. Sex-biased philopatry and social interactions among related females may facilitate local disease transmission within social groups. Local herd reduction may therefore be an effective tool for reducing the disease prevalence when implemented at the appropriate spatial scale. PMID:25567957

  11. Coulomb explosion in dicationic noble gas clusters: A genetic algorithm-based approach to critical size estimation for the suppression of Coulomb explosion and prediction of dissociation channels

    NASA Astrophysics Data System (ADS)

    Nandy, Subhajit; Chaudhury, Pinaki; Bhattacharyya, S. P.

    2010-06-01

    We present a genetic algorithm based investigation of structural fragmentation in dicationic noble gas clusters, Arn+2, Krn+2, and Xen+2, where n denotes the size of the cluster. Dications are predicted to be stable above a threshold size of the cluster when positive charges are assumed to remain localized on two noble gas atoms and the Lennard-Jones potential along with bare Coulomb and ion-induced dipole interactions are taken into account for describing the potential energy surface. Our cutoff values are close to those obtained experimentally [P. Scheier and T. D. Mark, J. Chem. Phys. 11, 3056 (1987)] and theoretically [J. G. Gay and B. J. Berne, Phys. Rev. Lett. 49, 194 (1982)]. When the charges are allowed to be equally distributed over four noble gas atoms in the cluster and the nonpolarization interaction terms are allowed to remain unchanged, our method successfully identifies the size threshold for stability as well as the nature of the channels of dissociation as function of cluster size. In Arn2+, for example, fissionlike fragmentation is predicted for n =55 while for n =43, the predicted outcome is nonfission fragmentation in complete agreement with earlier work [Golberg et al., J. Chem. Phys. 100, 8277 (1994)].

  12. Comparison of Control Approaches in Genetic Regulatory Networks by Using Stochastic Master Equation Models, Probabilistic Boolean Network Models and Differential Equation Models and Estimated Error Analyzes

    NASA Astrophysics Data System (ADS)

    Caglar, Mehmet Umut; Pal, Ranadip

    2011-03-01

    Central dogma of molecular biology states that ``information cannot be transferred back from protein to either protein or nucleic acid''. However, this assumption is not exactly correct in most of the cases. There are a lot of feedback loops and interactions between different levels of systems. These types of interactions are hard to analyze due to the lack of cell level data and probabilistic - nonlinear nature of interactions. Several models widely used to analyze and simulate these types of nonlinear interactions. Stochastic Master Equation (SME) models give probabilistic nature of the interactions in a detailed manner, with a high calculation cost. On the other hand Probabilistic Boolean Network (PBN) models give a coarse scale picture of the stochastic processes, with a less calculation cost. Differential Equation (DE) models give the time evolution of mean values of processes in a highly cost effective way. The understanding of the relations between the predictions of these models is important to understand the reliability of the simulations of genetic regulatory networks. In this work the success of the mapping between SME, PBN and DE models is analyzed and the accuracy and affectivity of the control policies generated by using PBN and DE models is compared.

  13. Demography and genetic structure of a recovering grizzly bear population

    USGS Publications Warehouse

    Kendall, K.C.; Stetz, J.B.; Boulanger, J.; Macleod, A.C.; Paetkau, David; White, Gary C.

    2009-01-01

    Grizzly bears (brown bears; Ursus arctos) are imperiled in the southern extent of their range worldwide. The threatened population in northwestern Montana, USA, has been managed for recovery since 1975; yet, no rigorous data were available to monitor program success. We used data from a large noninvasive genetic sampling effort conducted in 2004 and 33 years of physical captures to assess abundance, distribution, and genetic health of this population. We combined data from our 3 sampling methods (hair trap, bear rub, and physical capture) to construct individual bear encounter histories for use in Huggins-Pledger closed mark-recapture models. Our population estimate, N?? = 765 (95% CI = 715-831) was more than double the existing estimate derived from sightings of females with young. Based on our results, the estimated known, human-caused mortality rate in 2004 was 4.6% (95% CI = 4.2-4.9%), slightly above the 4% considered sustainable; however, the high proportion of female mortalities raises concern. We used location data from telemetry, confirmed sightings, and genetic sampling to estimate occupied habitat. We found that grizzly bears occupied 33,480 km2 in the Northern Continental Divide Ecosystem (NCDE) during 1994-2007, including 10,340 km beyond the Recovery Zone. We used factorial correspondence analysis to identify potential barriers to gene flow within this population. Our results suggested that genetic interchange recently increased in areas with low gene flow in the past; however, we also detected evidence of incipient fragmentation across the major transportation corridor in this ecosystem. Our results suggest that the NCDE population is faring better than previously thought, and they highlight the need for a more rigorous monitoring program.

  14. Barriers to Gene Flow in the Marine Environment: Insights from Two Common Intertidal Limpet Species of the Atlantic and Mediterranean

    PubMed Central

    Sá-Pinto, Alexandra; Branco, Madalena S.; Alexandrino, Paulo B.; Fontaine, Michaël C.; Baird, Stuart J. E.

    2012-01-01

    Knowledge of the scale of dispersal and the mechanisms governing gene flow in marine environments remains fragmentary despite being essential for understanding evolution of marine biota and to design management plans. We use the limpets Patella ulyssiponensis and Patella rustica as models for identifying factors affecting gene flow in marine organisms across the North-East Atlantic and the Mediterranean Sea. A set of allozyme loci and a fragment of the mitochondrial gene cytochrome C oxidase subunit I were screened for genetic variation through starch gel electrophoresis and DNA sequencing, respectively. An approach combining clustering algorithms with clinal analyses was used to test for the existence of barriers to gene flow and estimate their geographic location and abruptness. Sharp breaks in the genetic composition of individuals were observed in the transitions between the Atlantic and the Mediterranean and across southern Italian shores. An additional break within the Atlantic cluster separates samples from the Alboran Sea and Atlantic African shores from those of the Iberian Atlantic shores. The geographic congruence of the genetic breaks detected in these two limpet species strongly supports the existence of transpecific barriers to gene flow in the Mediterranean Sea and Northeastern Atlantic. This leads to testable hypotheses regarding factors restricting gene flow across the study area. PMID:23239977

  15. Thermal barrier coating system

    NASA Technical Reports Server (NTRS)

    Stecura, S. (Inventor)

    1984-01-01

    A high temperature oxidation resistant, thermal barrier coating system is disclosed for a nickel cobalt, or iron base alloy substrate. An inner metal bond coating contacts the substrate, and a thermal barrier coating covers the bond coating. NiCrAlR, FeCrAlR, and CoCrAlR alloys are satisfactory as bond coating compositions where R=Y or Yb. These alloys contain, by weight, 24.9-36.7% chromium, 5.4-18.5% aluminum, and 0.05 to 1.55% yttrium or 0.05 to 0.53% ytterbium. The coatings containing ytterbium are preferred over those containing yttrium. An outer thermal barrier coating of partial stabilized zirconium oxide (zirconia) which is between 6% and 8%, by weight, of yttrium oxide (yttria) covers the bond coating. Partial stabilization provi