WorldWideScience

Sample records for bottlenecks population differentiation

  1. Bottlenecks, population differentiation and apparent selection at microsatellite loci in Australian Drosophila buzzatii

    DEFF Research Database (Denmark)

    Barker, J.S.F.; Frydenberg, Jane; González, J.; Davies, H.I.; Ruiz, A; Sørensen, Jesper Givskov; Loeschcke, Volker

    2009-01-01

    original population simply due to genetic drift. Disentangling the effects of founder drift and selection after colonization is crucial to understanding the adaptive process. Drosophila buzzatii colonized Australia some 600-700 generations ago, and spread rapidly over a wide geographical range. Genetic......Species colonizing new areas disjunct from their original habitat may be subject to novel selection pressures, and exhibit adaptive genetic changes. However, if colonization occurs through a small number of founders, the genetic composition of the colonized population may differ from that of the...

  2. Genetic variability and bottleneck detection of four Tricholoma matsutake populations from northeastern and southwestern China.

    Science.gov (United States)

    Zeng, Dong-Fang; Chen, Bin

    2015-08-01

    The excessive commercial collection of matsutake mushrooms can lead to extreme reduction of population size, which may cause genetic bottleneck and decrease genetic diversity of Tricholoma matsutake. Here, six polymorphic microsatellite loci markers were used to examine the genetic diversity of four natural T. matsutake populations from two main producing regions of China. The minimum combinations of four loci were able to discriminate total 86 sampled individuals with distinctive multilocus genotypes. Our analysis of molecular variance (AMOVA) revealed that about 80% and 20% of the overall genetic variation were respectively partitioned within and among populations. The principal-coordinate analyses (PCA) distinguished the four tested populations into three genetic clusters, each of which was correlated with respective endemic host plants on a geographical basis. The AMOVA, PCA and pairwise population FST estimates consistently displayed the same genetic divergence patterns and spatial structure of T. matsutake mediated by host plants in China. The significant heterozygosity excesses demonstrated that a recent genetic bottleneck occurred in each population tested. The complementary M-ratio test indicated past genetic bottleneck events over longer periods. Only four individuals were identified as putative first generation migrants within northeastern China, which implies restricted interpopulation gene flow in T. matsutake. We discuss that the significant genetic differentiation among populations of T. matsutake is most likely a function of host adaptation, host specificity, genetic bottleneck, limited dispersal and habitat fragmentation. PMID:25682708

  3. Size of genetic bottlenecks leading to virus fitness loss is determined by mean initial population fitness.

    OpenAIRE

    Novella, I S; Elena, S F; Moya, A.; Domingo, E; Holland, J J

    1995-01-01

    Genetic bottlenecks are important events in the genetic diversification of organisms and colonization of new ecological niches. Repeated bottlenecking of RNA viruses often leads to fitness losses due to the operation of Muller's ratchet. Herein we use vesicular stomatitis virus to determine the transmission population size which leads to fitness decreases of virus populations. Remarkably, the effective size of a genetic bottleneck associated with fitness loss is greater when the fitness of th...

  4. Divergent evolution peaks under intermediate population bottlenecks during bacterial experimental evolution.

    Science.gov (United States)

    Vogwill, Tom; Phillips, Robyn L; Gifford, Danna R; MacLean, R Craig

    2016-07-27

    There is growing evidence that parallel molecular evolution is common, but its causes remain poorly understood. Demographic parameters such as population bottlenecks are predicted to be major determinants of parallelism. Here, we test the hypothesis that bottleneck intensity shapes parallel evolution by elucidating the genomic basis of adaptation to antibiotic-supplemented media in hundreds of populations of the bacterium Pseudomonas fluorescens Pf0-1. As expected, bottlenecking decreased the rate of phenotypic and molecular adaptation. Surprisingly, bottlenecking had no impact on the likelihood of parallel adaptive molecular evolution at a genome-wide scale. However, bottlenecking had a profound impact on the genes involved in antibiotic resistance. Specifically, under either intense or weak bottlenecking, resistance predominantly evolved by strongly beneficial mutations which provide high levels of antibiotic resistance. In contrast with intermediate bottlenecking regimes, resistance evolved by a greater diversity of genetic mechanisms, significantly reducing the observed levels of parallel genetic evolution. Our results demonstrate that population bottlenecking can be a major predictor of parallel evolution, but precisely how may be more complex than many simple theoretical predictions. PMID:27466449

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

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    Mariette Stéphanie

    2010-08-01

    Full Text Available Abstract 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.

  6. Population Bottlenecks Increase Additive Genetic Variance But Do Not Break a Selection Limit in Rainforest Drosophila

    DEFF Research Database (Denmark)

    van Heerwaarden, Belinda; Willi, Yvonne; Kristensen, Torsten N; Hoffmann, Ary A

    2008-01-01

    desiccation resistance in the rain forest-restricted fly Drosophila bunnanda. After one generation of single-pair mating, additive genetic variance for desiccation resistance increased to a significant level, on average higher than for the control lines. Line crosses revealed that both dominance and epistatic......According to neutral quantitative genetic theory, population bottlenecks are expected to decrease standing levels of additive genetic variance of quantitative traits. However, some empirical and theoretical results suggest that, if nonadditive genetic effects influence the trait, bottlenecks may...... actually increase additive genetic variance. This has been an important issue in conservation genetics where it has been suggested that small population size might actually experience an increase rather than a decrease in the rate of adaptation. Here we test if bottlenecks can break a selection limit for...

  7. On the prospect of identifying adaptive loci in recently bottlenecked populations.

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    Yu-Ping Poh

    Full Text Available Identifying adaptively important loci in recently bottlenecked populations - be it natural selection acting on a population following the colonization of novel habitats in the wild, or artificial selection during the domestication of a breed - remains a major challenge. Here we report the results of a simulation study examining the performance of available population-genetic tools for identifying genomic regions under selection. To illustrate our findings, we examined the interplay between selection and demography in two species of Peromyscus mice, for which we have independent evidence of selection acting on phenotype as well as functional evidence identifying the underlying genotype. With this unusual information, we tested whether population-genetic-based approaches could have been utilized to identify the adaptive locus. Contrary to published claims, we conclude that the use of the background site frequency spectrum as a null model is largely ineffective in bottlenecked populations. Results are quantified both for site frequency spectrum and linkage disequilibrium-based predictions, and are found to hold true across a large parameter space that encompasses many species and populations currently under study. These results suggest that the genomic footprint left by selection on both new and standing variation in strongly bottlenecked populations will be difficult, if not impossible, to find using current approaches.

  8. Circulating virus load determines the size of bottlenecks in viral populations progressing within a host.

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    Serafín Gutiérrez

    Full Text Available For any organism, population size, and fluctuations thereof, are of primary importance in determining the forces driving its evolution. This is particularly true for viruses--rapidly evolving entities that form populations with transient and explosive expansions alternating with phases of migration, resulting in strong population bottlenecks and associated founder effects that increase genetic drift. A typical illustration of this pattern is the progression of viral disease within a eukaryotic host, where such demographic fluctuations are a key factor in the emergence of new variants with altered virulence. Viruses initiate replication in one or only a few infection foci, then move through the vasculature to seed secondary infection sites and so invade distant organs and tissues. Founder effects during this within-host colonization might depend on the concentration of infectious units accumulating and circulating in the vasculature, as this represents the infection dose reaching new organs or "territories". Surprisingly, whether or not the easily measurable circulating (plasma virus load directly drives the size of population bottlenecks during host colonization has not been documented in animal viruses, while in plants the virus load within the sap has never been estimated. Here, we address this important question by monitoring both the virus concentration flowing in host plant sap, and the number of viral genomes founding the population in each successive new leaf. Our results clearly indicate that the concentration of circulating viruses directly determines the size of bottlenecks, which hence controls founder effects and effective population size during disease progression within a host.

  9. Anatomy of a bottleneck: diagnosing factors limiting population growth in the Puerto Rican parrot

    Science.gov (United States)

    Beissenger, S.R.; Wunderle, J.M., Jr.; Meyers, J.M.; Saether, B.-E.; Engen, S.

    2008-01-01

    The relative importance of genetic, demographic, environmental, and catastrophic processes that maintain population bottlenecks has received little consideration. We evaluate the role of these factors in maintaining the Puerto Rican Parrot (Amazona vittata) in a prolonged bottleneck from 1973 through 2000 despite intensive conservation efforts. We first conduct a risk analysis, then examine evidence for the importance of specific processes maintaining the bottleneck using the multiple competing hypotheses approach, and finally integrate these results through a sensitivity analysis of a demographic model using life-stage simulation analysis (LSA) to determine the relative importance of genetic, demographic, environmental, and catastrophic processes on population growth. Annual population growth has been slow and variable (1.0 6 5.2 parrots per year, or an average k?1.05 6 0.19) from 16 parrots (1973) to a high of 40-42 birds (1997-1998). A risk analysis based on population prediction intervals (PPI) indicates great risk and large uncertainty, with a range of 22?83 birds in the 90% PPI only five years into the future. Four primary factors (reduced hatching success due to inbreeding, failure of adults to nest, nest failure due to nongenetic causes, and reduced survival of adults and juveniles) were responsible for maintaining the bottleneck. Egghatchability rates were low (70.6% per egg and 76.8% per pair), and hatchability increased after mate changes, suggesting inbreeding effects. Only an average of 34% of the population nested annually, which was well below the percentage of adults that should have reached an age of first breeding (41-56%). This chronic failure to nest appears to have been caused primarily by environmental and/or behavioral factors, and not by nest-site scarcity or a skewed sex ratio. Nest failure rates from nongenetic causes (i.e., predation, parasitism, and wet cavities) were low (29%) due to active management (protecting nests and fostering

  10. Population aging and migrant workers: bottlenecks in tuberculosis control in rural China.

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    Sumedh Bele

    Full Text Available BACKGROUND: Tuberculosis is a serious global health problem. Its paradigms are shifting through time, especially in rapidly developing countries such as China. Health providers in China are at the forefront of the battle against tuberculosis; however, there are few empirical studies on health providers' perspectives on the challenges they face in tuberculosis control at the county level in China. This study was conducted among health providers to explore their experiences with tuberculosis control in order to identify bottlenecks and emerging challenges in controlling tuberculosis in rural China. METHODS: A qualitative approach was used. Semi-structured, in-depth interviews were conducted with 17 health providers working in various positions within the health system of one rural county (ZJG of China. Data were analyzed based on thematic content analysis using MAXQDA 10 qualitative data analysis software. RESULTS: Health providers reported several problems in tuberculosis control in ZJG county. Migrant workers and the elderly were repeatedly documented as the main obstacles in effective tuberculosis control in the county. At a personal level, doctors showed their frustration with the lack of new drugs for treating tuberculosis patients, and their opinions varied regarding incentives for referring patients. CONCLUSION: The results suggest that several problems still remain for controlling tuberculosis in rural China. Tuberculosis control efforts need to make reaching the most vulnerable populations a priority and encourage local health providers to adopt innovative practices in the local context based on national guidelines to achieve the best results. Considerable changes in China's National Tuberculosis Control Program are needed to tackle these emerging challenges faced by health workers at the county level.

  11. Limited population structure, genetic drift and bottlenecks characterise an endangered bird species in a dynamic, fire-prone ecosystem.

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    Sarah M Brown

    Full Text Available Fire is a major disturbance process in many ecosystems world-wide, resulting in spatially and temporally dynamic landscapes. For populations occupying such environments, fire-induced landscape change is likely to influence population processes, and genetic patterns and structure among populations. The Mallee Emu-wren Stipiturus mallee is an endangered passerine whose global distribution is confined to fire-prone, semi-arid mallee shrublands in south-eastern Australia. This species, with poor capacity for dispersal, has undergone a precipitous reduction in distribution and numbers in recent decades. We used genetic analyses of 11 length-variable, nuclear loci to examine population structure and processes within this species, across its global range. Populations of the Mallee Emu-wren exhibited a low to moderate level of genetic diversity, and evidence of bottlenecks and genetic drift. Bayesian clustering methods revealed weak genetic population structure across the species' range. The direct effects of large fires, together with associated changes in the spatial and temporal patterns of suitable habitat, have the potential to cause population bottlenecks, serial local extinctions and subsequent recolonisation, all of which may interact to erode and homogenise genetic diversity in this species. Movement among temporally and spatially shifting habitat, appears to maintain long-term genetic connectivity. A plausible explanation for the observed genetic patterns is that, following extensive fires, recolonisation exceeds in-situ survival as the primary driver of population recovery in this species. These findings suggest that dynamic, fire-dominated landscapes can drive genetic homogenisation of populations of species with low-mobility and specialised habitat that otherwise would be expected to show strongly structured populations. Such effects must be considered when formulating management actions to conserve species in fire-prone systems.

  12. Meta-Analysis of Mitochondrial DNA Reveals Several Population Bottlenecks during Worldwide Migrations of Cattle

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    Johannes A. Lenstra

    2014-03-01

    Full Text Available Several studies have investigated the differentiation of mitochondrial DNA in Eurasian, African and American cattle as well as archaeological bovine material. A global survey of these studies shows that haplogroup distributions are more stable in time than in space. All major migrations of cattle have shifted the haplogroup distributions considerably with a reduction of the number of haplogroups and/or an expansion of haplotypes that are rare or absent in the ancestral populations. The most extreme case is the almost exclusive colonization of Africa by the T1 haplogroup, which is rare in Southwest Asian cattle. In contrast, ancient samples invariably show continuity with present-day cattle from the same location. These findings indicate strong maternal founder effects followed by limited maternal gene flow when new territories are colonized. However, effects of adaptation to new environments may also play a role.

  13. Genetic Evidence of a Population Bottleneck and Inbreeding in the Endangered New Zealand Sea Lion, Phocarctos hookeri.

    Science.gov (United States)

    Osborne, Amy J; Negro, Sandra S; Chilvers, B Louise; Robertson, Bruce C; Kennedy, Martin A; Gemmell, Neil J

    2016-09-01

    The New Zealand sea lion (NZSL) is of high conservation concern due to its limited distribution and its declining population size. Historically, it occupied most of coastal New Zealand, but is now restricted to a few coastal sites in southern mainland New Zealand and the sub-Antarctic Islands. NZSLs have experienced a recent reduction in population size due to sealing in the 1900s, which is expected to have resulted in increased inbreeding and a loss of genetic variation, potentially reducing the evolutionary capacity of the species and negatively impacting on its long-term prospects for survival. We used 17 microsatellite loci, previously shown to have cross-species applications in pinnipeds, to determine locus- and population-specific statistics for 1205 NZSLs from 7 consecutive breeding seasons. We show that the NZSL population has a moderate level of genetic diversity in comparison to other pinnipeds. We provide genetic evidence for a population reduction, likely caused by historical sealing, and a measure of allele sharing/parental relatedness (internal relatedness) that is suggestive of increased inbreeding in pups that died during recent epizootic episodes. We hypothesize that population bottlenecks and nonrandom mating have impacted on the population genetic architecture of NZSLs, affecting its population recovery. PMID:26995741

  14. Narrow bottlenecks affect Pea seedborne mosaic virus populations during vertical seed transmission but not during leaf colonization.

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    Frédéric Fabre

    2014-01-01

    Full Text Available The effective size of populations (Ne determines whether selection or genetic drift is the predominant force shaping their genetic structure and evolution. Populations having high Ne adapt faster, as selection acts more intensely, than populations having low Ne, where random effects of genetic drift dominate. Estimating Ne for various steps of plant virus life cycle has been the focus of several studies in the last decade, but no estimates are available for the vertical transmission of plant viruses, although virus seed transmission is economically significant in at least 18% of plant viruses in at least one plant species. Here we study the co-dynamics of two variants of Pea seedborne mosaic virus (PSbMV colonizing leaves of pea plants (Pisum sativum L. during the whole flowering period, and their subsequent transmission to plant progeny through seeds. Whereas classical estimators of Ne could be used for leaf infection at the systemic level, as virus variants were equally competitive, dedicated stochastic models were needed to estimate Ne during vertical transmission. Very little genetic drift was observed during the infection of apical leaves, with Ne values ranging from 59 to 216. In contrast, a very drastic genetic drift was observed during vertical transmission, with an average number of infectious virus particles contributing to the infection of a seedling from an infected mother plant close to one. A simple model of vertical transmission, assuming a cumulative action of virus infectious particles and a virus density threshold required for vertical transmission to occur fitted the experimental data very satisfactorily. This study reveals that vertically-transmitted viruses endure bottlenecks as narrow as those imposed by horizontal transmission. These bottlenecks are likely to slow down virus adaptation and could decrease virus fitness and virulence.

  15. Meta-Analysis of mitochondrial DNA reveals several population bottlenecks during worldwide migrations of cattle

    NARCIS (Netherlands)

    Lenstra, Johannes A.; Ajmone-Marsan, Paolo; Beja-Pereira, Albano; Bollongino, Ruth; Bradley, Daniel G.; Colli, Licia; De Gaetano, Anna; Edwards, Ceiridwen J.; Felius, Marleen; Ferretti, Luca; Ginja, Catarina; Hristov, Peter; Kantanen, Juha; Lirón, Juan Pedro; Magee, David A.; Negrini, Riccardo; Radoslavov, Georgi A.

    2014-01-01

    Several studies have investigated the differentiation of mitochondrial DNA in Eurasian, African and American cattle as well as archaeological bovine material. A global survey of these studies shows that haplogroup distributions are more stable in time than in space. All major migrations of cattle ha

  16. Logistics bottlenecks

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2010-09-15

    Many of the vulnerabilities to Energy Access, Energy Security, and Environmental Sustainability result from impediments to reaching a global demand-supply balance, as well as local balances, for various energy sources and carriers. Vulnerabilities result from multiple reasons: regional imbalances of energy production and consumption, the bulky character of the majority of energy fuels, the virtual necessity of electricity consumption following its production, among others. To detect and prioritize respective 'bottlenecks' across energy carriers, they have to be measured. In this report, production, consumption, exports, and imports were measured across all major energy carriers for seven key regions of the world for three time frames-2008, 2020, and 2050. Imbalances between production and consumption form bottlenecks in each region.

  17. Demographic and genetic factors in the recovery or demise of ex situ populations following a severe bottleneck in fifteen species of Hawaiian tree snails.

    Science.gov (United States)

    Price, Melissa R; Sischo, David; Pascua, Mark-Anthony; Hadfield, Michael G

    2015-01-01

    Wild populations of endangered Hawaiian tree snails have declined precipitously over the last century due to introduced predators and other human impacts. Life history traits, such as very low fecundity (species were collected from the wild to initiate captive-reared populations as a hedge against extinction. This small number of founders resulted in a severe bottleneck in each of the captive-reared populations. We identified key demographic parameters that predicted population recovery from this bottleneck. Species with captive populations that produced between two and four offspring per adult per year and had 20-50% of those offspring survive to maturity recovered to numbers above 100 individuals, and maintained viable populations following a decline that occurred between 2009 and 2014. Those populations that had less than two offspring per adult per year and less than 20% survival to maturity did not reach 100 individuals in captivity, and many of these populations died out during the recent decline. We suggest that small reductions in fitness may contribute to extirpation in taxa with inherently low fecundity, by keeping populations below a threshold number essential to long-term recovery. Future ex situ populations should be founded with no less than 15 adults, and maintained in conditions closely approximating the temperature and humidity of source locations to optimize fitness. Permanent translocations of wild populations for conservation purposes will be more likely to succeed with greater than 100 adults, and should be limited to locations with a similar climate to source locations. PMID:26587358

  18. Maintenance of genetic diversity in an introduced island population of guanacos after seven decades and two severe demographic bottlenecks: implications for camelid conservation.

    Science.gov (United States)

    González, Benito A; Orozco-Terwengel, Pablo; von Borries, Rainer; Johnson, Warren E; Franklin, William L; Marín, Juan C

    2014-01-01

    Fifteen guanacos were introduced to Staats Island in the Falklands/Malvinas archipelago from Patagonia in the 1930s. Twenty five years later, the population was culled from 300 to 10-20 individuals, but quickly rebounded to a population of almost 400 animals that today retain the genetic signature of the founding event and later bottleneck. The goals of this study were to (i) make a genetic assessment of this island population through comparisons with mainland populations and simulations, and (ii) assess the likely source-population of the introduced guanacos. Genetic variation was estimated from 513 bp of mitochondrial DNA sequence and 15 microsatellite loci among 154 guanacos collected from eight localities, including the adjacent mainland and the islands of Tierra del Fuego and Staats Island. Of the 23 haplotypes observed among our samples, the Staats Island population only contained three haplotypes, all of which were shared with the coastal Monte Leon population in southern Patagonia. Mitochondrial DNA and microsatellite variations on Staats Island were comparable to most mainland populations and greater than those observed on Tierra del Fuego. Patterns of genetic structure suggest that the Staats Island guanaco population was founded with animals from southern Patagonia (as opposed to northern Patagonia or Tierra del Fuego), but that effective reductions in population size lasted only a few generations and that surviving animals were a random sample of the pre-bottleneck genetic variation. PMID:24663026

  19. Hurry Up and Wait: Differential Impacts of Congestion, Bottleneck Pressure, and Predictability on Patient Length of Stay

    OpenAIRE

    Berry Jaeker, Jillian Alexandra; Tucker, Anita Lynn

    2012-01-01

    High work load, from high inventory levels, impacts unit processing times, but prior operations management studies have found conflicting results regarding direction. Thus, it is difficult to predict inventory’s effects on productivity a priori, inhibiting effective capacity management in high load systems. We categorize load into in-process inventory (congestion) and incoming inventory, decomposing the latter into its levels of bottleneck (BN) pressure and predictability, and quantify the ma...

  20. Ancient and contemporary DNA reveal a pre-human decline but no population bottleneck associated with recent human persecution in the kea (Nestor notabilis).

    Science.gov (United States)

    Dussex, Nicolas; Rawlence, Nicolas J; Robertson, Bruce C

    2015-01-01

    The impact of population bottlenecks is an important factor to consider when assessing species survival. Population declines can considerably limit the evolutionary potential of species and make them more susceptible to stochastic events. New Zealand has a well documented history of decline of endemic avifauna related to human colonization. Here, we investigate the genetic effects of a recent population decline in the endangered kea (Nestor notabilis). Kea have undergone a long-lasting persecution between the late 1800s to 1970s where an estimated 150,000 kea were culled under a governmental bounty scheme. Kea now number 1,000-5,000 individuals in the wild and it is likely that the recent population decline may have reduced the genetic diversity of the species. Comparison of contemporary (n = 410), historical (n = 15) and fossil samples (n = 4) showed a loss of mitochondrial diversity since the end of the last glaciation (Otiran Glacial) but no loss of overall genetic diversity associated with the cull. Microsatellite data indicated a recent bottleneck for only one population and a range-wide decline in Ne dating back some 300 - 6,000 years ago, a period predating European arrival in NZ. These results suggest that despite a recent human persecution, kea might have experienced a large population decline before stabilizing in numbers prior to human settlement of New Zealand in response to Holocene changes in habitat distribution. Our study therefore highlights the need to understand the respective effects of climate change and human activities on endangered species dynamics when proposing conservation guidelines. PMID:25719752

  1. Ancient and contemporary DNA reveal a pre-human decline but no population bottleneck associated with recent human persecution in the kea (Nestor notabilis.

    Directory of Open Access Journals (Sweden)

    Nicolas Dussex

    Full Text Available The impact of population bottlenecks is an important factor to consider when assessing species survival. Population declines can considerably limit the evolutionary potential of species and make them more susceptible to stochastic events. New Zealand has a well documented history of decline of endemic avifauna related to human colonization. Here, we investigate the genetic effects of a recent population decline in the endangered kea (Nestor notabilis. Kea have undergone a long-lasting persecution between the late 1800s to 1970s where an estimated 150,000 kea were culled under a governmental bounty scheme. Kea now number 1,000-5,000 individuals in the wild and it is likely that the recent population decline may have reduced the genetic diversity of the species. Comparison of contemporary (n = 410, historical (n = 15 and fossil samples (n = 4 showed a loss of mitochondrial diversity since the end of the last glaciation (Otiran Glacial but no loss of overall genetic diversity associated with the cull. Microsatellite data indicated a recent bottleneck for only one population and a range-wide decline in Ne dating back some 300 - 6,000 years ago, a period predating European arrival in NZ. These results suggest that despite a recent human persecution, kea might have experienced a large population decline before stabilizing in numbers prior to human settlement of New Zealand in response to Holocene changes in habitat distribution. Our study therefore highlights the need to understand the respective effects of climate change and human activities on endangered species dynamics when proposing conservation guidelines.

  2. Demographic changes and marker properties affect detection of human population differentiation

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    Sanichwankul Kittipong

    2007-05-01

    Full Text Available Abstract Background Differentiating genetically between populations is valuable for admixture and population stratification detection and in understanding population history. This is easy to achieve for major continental populations, but not for closely related populations. It has been claimed that a large marker panel is necessary to reliably distinguish populations within a continent. We investigated whether empirical genetic differentiation could be accomplished efficiently among three Asian populations (Hmong, Thai, and Chinese using a small set of highly variable markers (15 tetranucleotide and 17 dinucleotide repeats. Results Hmong could be differentiated from Thai and Chinese based on multi-locus genotypes, but Thai and Chinese were indistinguishable from each other. We found significant evidence for a recent population bottleneck followed by expansion in the Hmong that was not present in the Thai or Chinese. Tetranucleotide repeats were less useful than dinucleotide repeat markers in distinguishing between major continental populations (Asian, European, and African while both successfully distinguished Hmong from Thai and Chinese. Conclusion Demographic history contributes significantly to robust detection of intracontinental population structure. Populations having experienced a rapid size reduction may be reliably distinguished as a result of a genetic drift -driven redistribution of population allele frequencies. Tetranucleotide markers, which differ from dinucleotide markers in mutation mechanism and rate, are similar in information content to dinucleotide markers in this situation. These factors should be considered when identifying populations suitable for gene mapping studies and when interpreting interpopulation relationships based on microsatellite markers.

  3. A Structured Population Model of Cell Differentiation

    CERN Document Server

    Doumic, Marie; Perthame, Benoit; Zubelli, Jorge P

    2010-01-01

    We introduce and analyze several aspects of a new model for cell differentiation. It assumes that differentiation of progenitor cells is a continuous process. From the mathematical point of view, it is based on partial differential equations of transport type. Specifically, it consists of a structured population equation with a nonlinear feedback loop. This models the signaling process due to cytokines, which regulate the differentiation and proliferation process. We compare the continuous model to its discrete counterpart, a multi-compartmental model of a discrete collection of cell subpopulations recently proposed by Marciniak-Czochra et al. in 2009 to investigate the dynamics of the hematopoietic system. We obtain uniform bounds for the solutions, characterize steady state solutions, and analyze their linearized stability. We show how persistence or extinction might occur according to values of parameters that characterize the stem cells self-renewal. We also perform numerical simulations and discuss the q...

  4. The Mouse-colored Tyrannulet (Phaeomyias murina) is a species complex that includes the Cocos Flycatcher (Nesotriccus ridgwayi), an island form that underwent a population bottleneck.

    Science.gov (United States)

    Zucker, Marc R; Harvey, Michael G; Oswald, Jessica A; Cuervo, Andrés; Derryberry, Elizabeth; Brumfield, Robb T

    2016-08-01

    Simultaneous examination of evolutionary history in island forms and closely related mainland relatives can provide reciprocal insight into the evolution of island and mainland faunas. The Cocos Flycatcher (Nesotriccus ridgwayi) is a small tyrant flycatcher (Tyrannidae) endemic to Cocos Island, an oceanic island in the eastern Pacific Ocean. We first established its close relationship to the mainland species Mouse-colored Tyrannulet (Phaeomyias murina) using a phylogeny from genome-wide ultraconserved elements and exons. We then used mitochondrial DNA to explore the relationships between Nesotriccus and Phaeomyias populations from across its distribution in Central and South America. We found that Nesotriccus is nested within the Phaeomyias evolutionary tree, and that Phaeomyias represents a complex of at least four evolutionarily distinct species that differ in plumage, voice, and habitat association. Nesotriccus underwent a population bottleneck subsequent to its divergence from Central American and northern South American Phaeomyias populations in the middle Pleistocene. The 46 UCE loci containing alleles that are fixed between the two species are widely distributed across the genome, which suggests that selective or neutral processes responsible for divergence have occurred genome-wide. Overall, our simultaneous examination of Phaeomyias and Nesotriccus revealed divergent levels of genetic diversity and evolutionary histories between island and mainland forms. PMID:27126184

  5. When is a bottleneck a bottleneck?

    CERN Document Server

    Schadschneider, Andreas; Popkov, Vladislav

    2015-01-01

    Bottlenecks, i.e. local reductions of capacity, are one of the most relevant scenarios of traffic systems. The asymmetric simple exclusion process (ASEP) with a defect is a minimal model for such a bottleneck scenario. One crucial question is "What is the critical strength of the defect that is required to create global effects, i.e. traffic jams localized at the defect position". Intuitively one would expect that already an arbitrarily small bottleneck strength leads to global effects in the system, e.g. a reduction of the maximal current. Therefore it came as a surprise when, based on computer simulations, it was claimed that the reaction of the system depends in non-continuous way on the defect strength and weak defects do not have a global influence on the system. Here we reconcile intuition and simulations by showing that indeed the critical defect strength is zero. We discuss the implications for the analysis of empirical and numerical data.

  6. Phylogeography of postglacial range expansion in Juglans mandshurica (Juglandaceae) reveals no evidence of bottleneck, loss of genetic diversity, or isolation by distance in the leading-edge populations.

    Science.gov (United States)

    Wang, Wen-Ting; Xu, Bing; Zhang, Da-Yong; Bai, Wei-Ning

    2016-09-01

    The past studies of postglacial recolonization patterns in high latitude regions have revealed a significant role of dispersal capacity in shaping the genetic diversity and population structure of temperate trees. However, most of these studies have focused on species with long-distance dispersal followed by exponential population growth and were therefore unable to reveal the patterns in the case of a gradual expansion. Here we studied the impacts of postglacial range expansions on the distribution of genetic diversity in the Manchurian walnut (Juglans mandshurica), a common tree of East Asian cool-temperate deciduous forests that apparently lacks long-distance seed dispersal ability. The genetic diversity and structure of 19 natural walnut populations in Northeast China and the Korean Peninsula were examined using 17 nuclear simple sequence repeat (SSR) loci. Potential habitats under current and past climatic conditions were predicted using the ecological niche modelling (ENM) method. Bayesian clustering analysis revealed three groups, which were inferred to have diverged through multiple glacial-interglacial cycles in multiple refugia during the Quaternary Period. ENM estimated a southward range shift at the LGM, but high suitability scores still occurred in the western parts of the Changbai Mountains (Northeast China), the Korean peninsula and the exposed seafloor of the Yellow Sea. In contrast to most other cool-temperate trees co-occurring in the same region, the Manchurian walnut did not show any evidence of a population bottleneck, loss of genetic diversity or isolation by distance during the postglacial expansion. Our study clearly indicates that current northern populations originated from one glacial lineage and recolonization via a gradually advancing front due to the lack of a long-distance seed dispersal mechanism led to no latitudinal decrease in genetic diversity. PMID:27346642

  7. Microsatellite genetic diversity and differentiation of native and introduced grass carp populations in three continents

    Science.gov (United States)

    Chapman, Duane C.; Chen, Qin; Wang, Chenghui; Zhao, Jinlian; Lu, Guoqing; Zsigmond, Jeney; Li, Sifa

    2012-01-01

    Grass carp (Ctenopharyngodon idella), a freshwater species native to China, has been introduced to about 100 countries/regions and poses both biological and environmental challenges to the receiving ecosystems. In this study, we analyzed genetic variation in grass carp from three introduced river systems (Mississippi River Basin in US, Danube River in Hungary, and Tone River in Japan) as well as its native ranges (Yangtze, Pearl, and Amur Rivers) in China using 21 novel microsatellite loci. The allelic richness, observed heterozygosity, and within-population gene diversity were found to be lower in the introduced populations than in the native populations, presumably due to the small founder population size of the former. Significant genetic differentiation was found between all pairwise populations from different rivers. Both principal component analysis and Bayesian clustering analysis revealed obvious genetic distinction between the native and introduced populations. Interestingly, genetic bottlenecks were detected in the Hungarian and Japanese grass carp populations, but not in the North American population, suggesting that the Mississippi River Basin grass carp has experienced rapid population expansion with potential genetic diversification during the half-century since its introduction. Consequently, the combined forces of the founder effect, introduction history, and rapid population expansion help explaining the observed patterns of genetic diversity within and among both native and introduced populations of the grass carp.

  8. Genetic Differentiation between Geographically Distant Populations of DROSOPHILA MELANOGASTER

    OpenAIRE

    Rama S Singh; Hickey, Donal A; David, Jean

    1982-01-01

    We have studied allozyme variation at 26 gene loci in nine populations of Drosophila melanogaster originating on five different continents. The distant populations show significant genetic differentiation. However, only half of the loci studied have contributed to this differentiation; the other half show identical patterns in all populations. The genetic differentiation in North American, European and African populations is correlated with the major climatic differences between north and sou...

  9. Economic analysis of production bottlenecks

    Directory of Open Access Journals (Sweden)

    Lawrence Stephen R.

    1995-01-01

    Full Text Available The management of bottlenecks has become a central topic in the planning and control of production systems. In this paper, we critically analyze bottlenecks from an economic perspective. Using a queueing network model, we demonstrate that bottlenecks are inevitable when there are differences in job arrival rates, processing rates, or costs of productive resources. These differences naturally lead to the creation of bottlenecks both for facilities design and demand planning problems. To evaluate bottlenecks from an economic perspective, we develop the notion of an “economic bottleneck,” which defines resources as bottlenecks based on economic, rather than physical, characteristics.

  10. Different level of population differentiation among human genes

    Directory of Open Access Journals (Sweden)

    Zhang Ya-Ping

    2011-01-01

    Full Text Available Abstract Background During the colonization of the world, after dispersal out of African, modern humans encountered changeable environments and substantial phenotypic variations that involve diverse behaviors, lifestyles and cultures, were generated among the different modern human populations. Results Here, we study the level of population differentiation among different populations of human genes. Intriguingly, genes involved in osteoblast development were identified as being enriched with higher FST SNPs, a result consistent with the proposed role of the skeletal system in accounting for variation among human populations. Genes involved in the development of hair follicles, where hair is produced, were also found to have higher levels of population differentiation, consistent with hair morphology being a distinctive trait among human populations. Other genes that showed higher levels of population differentiation include those involved in pigmentation, spermatid, nervous system and organ development, and some metabolic pathways, but few involved with the immune system. Disease-related genes demonstrate excessive SNPs with lower levels of population differentiation, probably due to purifying selection. Surprisingly, we find that Mendelian-disease genes appear to have a significant excessive of SNPs with high levels of population differentiation, possibly because the incidence and susceptibility of these diseases show differences among populations. As expected, microRNA regulated genes show lower levels of population differentiation due to purifying selection. Conclusion Our analysis demonstrates different level of population differentiation among human populations for different gene groups.

  11. Uncorking the bottleneck

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2003-10-01

    CoeClerici Logistics' floating terminals have helped clients all over the world overcome a variety of infrastructure bottlenecks including limited draft or insufficient storage capacity. The vessel 'Bulk Irony' is a self-propelled 13,000 dwt transhipper built for Lucchini Steel's mill at Piombino, Italy for import of coal, coke and ores and export of steel products. The large 'Bulk Wayuu' coal terminal in the Lake of Maracaibo, Venezuela serves Carbones del Guasare, Venezuela's largest coal producer.

  12. Population Size, Structural Differentiation, and Human Behavior

    Science.gov (United States)

    Sadalla, Edward K.

    1978-01-01

    Reviews evidence which indicates that the sheer size of an urban center has important social and psychological consequences. Available literature suggests that size combined with structural differentiation is related to psychological and behavioral variables such as anomymity, deindividuation, deviance, personality development, and…

  13. Differential cold-shock resistance among acclimated European mussel populations

    NARCIS (Netherlands)

    Jansen, J.M.; Wendelaar Bonga, S.; Hummel, H.

    2007-01-01

    To study differential cold-shock resistance of marine mussel populations (Mytilus spp.) from different climatic regions in Europe, we sampled 12 populations, ranging from 43 to 58 degrees N. Minimum critical temperatures for aerobic metabolism (CTmin) were determined before and after 3 months of com

  14. Differential cold-shock resistance among acclimated European mussel populations

    NARCIS (Netherlands)

    Jansen, J.M.; Wendelaar Bonga, S.E.; Hummel, H.

    2007-01-01

    To study differential cold-shock resistance of marine mussel populations (Mytilus spp.) from different climatic regions in Europe, we sampled 12 populations, ranging from 43 to 58°N. Minimum critical temperatures for aerobic metabolism (CTmin) were determined before and after 3 months of common accl

  15. Differential cold-shock resistance among acclimated European mussel populations

    NARCIS (Netherlands)

    Jansen, J.M.; Wendelaar Bonga, S.E.; Hummel, H.

    2007-01-01

    To study differential cold-shock resistance of marine mussel populations (Mytilus spp.) from different climatic regions in Europe, we sampled 12 populations, ranging from 43 to 58_N. Minimum critical temperatures for aerobic metabolism (CTmin) were determined before and after 3 months of common accl

  16. Analysis of Microsatellite DNA Markers Reveals no Genetic Differentiation between Wild and Hatchery Populations of Pacific Threadfin in Hawaii

    Directory of Open Access Journals (Sweden)

    Gang Pan, Jinzeng Yang

    2010-01-01

    Full Text Available Pacific threadfin, Polydactylus sexfilis, is popular fish in recreational fishing, as well as aquaculture in Hawaii. Its natural population has been continuously declining in the past several decades. Microsatellite DNA markers are useful DNA-based tool for monitoring Pacific threadfin populations. In this study, fifteen Microsatellite (MS DNA markers were identified from a partial genomic Pacific threadfin DNA library enriched in CA repeats, and six highly-polymorphic microsatellite loci were employed to analyze genetic similarity and differences between the wild population and hatchery population in Oahu Island. A total of 37 alleles were detected at the six MS loci in the two populations. Statistical analysis of fixation index (FST and analysis of molecular variance (AMOVA showed no genetic differentiation between the wild and hatchery populations (FST=0.001, CI95%= -0.01-0.021. Both high genetic diversity (Ho=0.664-0.674 and He=0.710-0.715 and Hardy-Weinberg equilibrium were observed in the wild and hatchery populations. Results of genetic bottleneck analysis indicated that the hatchery was founded with sufficient numbers of brooders as inbreeding coefficient is very low (FIS=0.052-0.072 in both wild and hatchery populations. Further studies are needed for comprehensive determinations of genetic varieties of primary founder broodstocks and successive offspring of the hatchery and wild populations with increased number of Pacific threadfin sample collections.

  17. Impacts of genetic bottlenecks on soybean genome diversity

    OpenAIRE

    Hyten, David L; Song, Qijian; Zhu, Youlin; Choi, Ik-Young; Nelson, Randall L.; Costa, Jose M.; Specht, James E; Shoemaker, Randy C.; Cregan, Perry B

    2006-01-01

    Soybean has undergone several genetic bottlenecks. These include domestication in Asia to produce numerous Asian landraces, introduction of relatively few landraces to North America, and then selective breeding over the past 75 years. It is presumed that these three human-mediated events have reduced genetic diversity. We sequenced 111 fragments from 102 genes in four soybean populations representing the populations before and after genetic bottlenecks. We show that soybean has lost many rare...

  18. The Constrained Bottleneck Transportation Problem

    OpenAIRE

    Peerayuth Charnsethikul; Saeree Svetasreni

    2007-01-01

    Two classes of the bottleneck transportation problem with an additional budget constraint are introduced. An exact approach was proposed to solve both problem classes with proofs of correctness and complexity. Moreover, the approach was extended to solve a class of multi-commodity transportation network with a special case of the multi-period constrained bottleneck assignment problem.

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

    Science.gov (United States)

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

    2013-01-01

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

  20. Transcriptome sequencing from diverse human populations reveals differentiated regulatory architecture.

    Directory of Open Access Journals (Sweden)

    Alicia R Martin

    2014-08-01

    Full Text Available Large-scale sequencing efforts have documented extensive genetic variation within the human genome. However, our understanding of the origins, global distribution, and functional consequences of this variation is far from complete. While regulatory variation influencing gene expression has been studied within a handful of populations, the breadth of transcriptome differences across diverse human populations has not been systematically analyzed. To better understand the spectrum of gene expression variation, alternative splicing, and the population genetics of regulatory variation in humans, we have sequenced the genomes, exomes, and transcriptomes of EBV transformed lymphoblastoid cell lines derived from 45 individuals in the Human Genome Diversity Panel (HGDP. The populations sampled span the geographic breadth of human migration history and include Namibian San, Mbuti Pygmies of the Democratic Republic of Congo, Algerian Mozabites, Pathan of Pakistan, Cambodians of East Asia, Yakut of Siberia, and Mayans of Mexico. We discover that approximately 25.0% of the variation in gene expression found amongst individuals can be attributed to population differences. However, we find few genes that are systematically differentially expressed among populations. Of this population-specific variation, 75.5% is due to expression rather than splicing variability, and we find few genes with strong evidence for differential splicing across populations. Allelic expression analyses indicate that previously mapped common regulatory variants identified in eight populations from the International Haplotype Map Phase 3 project have similar effects in our seven sampled HGDP populations, suggesting that the cellular effects of common variants are shared across diverse populations. Together, these results provide a resource for studies analyzing functional differences across populations by estimating the degree of shared gene expression, alternative splicing, and

  1. Periodic solutions of nonautonomous differential systems modeling obesity population

    Energy Technology Data Exchange (ETDEWEB)

    Arenas, Abraham J. [Departamento de Matematicas y Estadistica, Universidad de Cordoba Monteria (Colombia)], E-mail: aarenas@sinu.unicordoba.edu.co; Gonzalez-Parra, Gilberto [Departamento de Calculo, Universidad de los Andes, Merida (Venezuela, Bolivarian Republic of)], E-mail: gcarlos@ula.ve; Jodar, Lucas [Instituto de Matematica Multidisciplinar, Universidad Politecnica de Valencia Edificio 8G, 2o, 46022 Valencia (Spain)], E-mail: ljodar@imm.upv.es

    2009-10-30

    In this paper we study the periodic behaviour of the solutions of a nonautonomous model for obesity population. The mathematical model represented by a nonautonomous system of nonlinear ordinary differential equations is used to model the dynamics of obese populations. Numerical simulations suggest periodic behaviour of subpopulations solutions. Sufficient conditions which guarantee the existence of a periodic positive solution are obtained using a continuation theorem based on coincidence degree theory.

  2. Genetic differentiation between Atlantic salmon populations in the Windermere catchment

    OpenAIRE

    Hartley, S.E.; Pickering, A.D.

    1994-01-01

    Genetic analysis, using single locus probes for genomic DNA, revealed that the juvenile Atlantic salmon populations in the Rivers Leven, Rothay and Troutbeck were related but genetically distinct. This genetic differentiation is greater than might be expected (by comparison with other salmon populations in the UK) and it is recommended that no action is taken which might promote genetic exchange between the three rivers. Thus, future fisheries management practices should treat the salmon from...

  3. Parameter Estimates in Differential Equation Models for Population Growth

    Science.gov (United States)

    Winkel, Brian J.

    2011-01-01

    We estimate the parameters present in several differential equation models of population growth, specifically logistic growth models and two-species competition models. We discuss student-evolved strategies and offer "Mathematica" code for a gradient search approach. We use historical (1930s) data from microbial studies of the Russian biologist,…

  4. Genetic diversity and population differentiation of natural populations of Sclerotinia sclerotiorum on lentils in eastern Washington.

    Science.gov (United States)

    Genetic diversity and population differentiation of natural populations of Sclerotinia sclerotiorum on lentils in eastern Washington. X. Wang and W. Chen. Washington State University, Pullman, WA, and USDA-ARS, Pullman, WA 99163 Sclerotinia sclerotiorum is the causal agent of white mold on lentils....

  5. Where do they come from? Flow connectivity detects landscape bottlenecks

    Directory of Open Access Journals (Sweden)

    Alessandro Ferrarini

    2015-03-01

    Full Text Available In this paper, bottleneck flow connectivity is first introduced. A landscape bottleneck is defined here as the portion of an arbitrary study area which inevitably tunnels a specimen towards the point where it has been detected in situ. In other words, a bottleneck delimits the portion of the study area which forces the specimen to pass through the detected point of presence with, at most, a tolerance distance equal to an a priori defined uncertainty. There is one precise reason for the introduction of bottleneck flow connectivity: when a specimen is detected through in situ observations or GPS devices, it should be possible to derive the portion of the landscape where it can come from. In fact, the detected specimen is usually just one individual of an entire population that is moving somewhere in the landscape. Hence, such specimen can work as a tracker of the whole population if we have the proper methodological tools to turn its detected position into a map where the landscape bottleneck of the detected location is delineated. In case of a species of conservation interest, the application of bottleneck flow connectivity is useful for the individuation and then the conservation of such population. In case of an exotic undesired species, bottleneck flow connectivity can help individuate the location of the population that should be eradicated, starting from few field observations. An applicative example for wolf in the Ceno Valley (Italy is provided. Bottleneck flow connectivity has thus interesting implications both for the conservation of species of interest, but also for the management of undesired exotic species.

  6. Genetic diversity and bottleneck studies in the Marwari horse breed

    Indian Academy of Sciences (India)

    A. K. Gupta; M. Chauhan; S. N. Tandon; Sonia

    2005-12-01

    Genetic diversity within the Marwari breed of horses was evaluated using 26 different microsatellite pairs with 48 DNA samples from unrelated horses. This molecular characterisation was undertaken to evaluate the problem of genetic bottlenecks also, if any, in this breed. The estimated mean (± s.e.) allelic diversity was 5.9 (± 2.24), with a total of 133 alleles. A high level of genetic variability within this breed was observed in terms of high values of mean (± s.e.) effective number of alleles (3.3 ± 1.27), observed heterozygosity (0.5306 ± 0.22), expected Levene’s heterozygosity (0.6612 ± 0.15), expected Nei’s heterozygosity (0.6535 ± 0.14), and polymorphism information content (0.6120 ± 0.03). Low values of Wright’s fixation index, $F_{\\text{IS}}$ (0.2433 ± 0.05) indicated low levels of inbreeding. This basic study indicated the existence of substantial genetic diversity in the Marwari horse population. No significant genotypic linkage disequilibrium was detected across the population, suggesting no evidence of linkage between loci. A normal ‘L’ shaped distribution of mode–shift test, non-significant heterozygote excess on the basis of different models, as revealed from Sign, Standardized differences and Wilcoxon sign rank tests as well as non-significant ratio value suggested that there was no recent bottleneck in the existing Marwari breed population, which is important information for equine breeders. This study also revealed that the Marwari breed can be differentiated from some other exotic breeds of horses on the basis of three microsatellite primers.

  7. A recent bottleneck in the warthog and elephant populations of Queen Elizabeth National Park, revealed by a comparative study of four mammalian species in Uganda national parks

    DEFF Research Database (Denmark)

    Muwanika, Vincent B.; Siegismund, Hans Redlef; Okello, John Bosco A.;

    2003-01-01

    varied in the different parks across different animal species. We have investigated the genetic effects of these reductions in four mammalian species (the common warthog, African savannah elephant, savannah buffalo and common river hippopotamus) from the three major parks of Uganda using both...... elephant (mean He 0.68-0.72). We interpret these results in terms of varying poaching pressure in the different parks, susceptibility of different species to poaching and differences in effective population sizes at the mitochondrial and nuclear loci....

  8. Insect population differentiation in response to enviromental thermal stress

    Institute of Scientific and Technical Information of China (English)

    CHEN Bing; KANG Le

    2005-01-01

    Numerous studies reported the adaptation strategies adopted by ecthotherms to survive under environmental thermal stress. Geographic and seasonal variations in the thermal stress tolerance, which is closely associated with species' climatic adaptation and allopatric speciation, have been extensively investigated in insects. The variation patterns suggest directional selection for species' adaptive straits, and are used to predict the origin, distribution and dynamics of insect populations. These studies are becoming more and more important in the context of global warming. This paper discusses the process of adaptation to environmental thermal stress and the mechanisms underlying the differentiation in related adaptive straits of insect populations.

  9. Analysis of pharmacogenomic variants associated with population differentiation.

    Directory of Open Access Journals (Sweden)

    Bora Yeon

    Full Text Available In the present study, we systematically investigated population differentiation of drug-related (DR genes in order to identify common genetic features underlying population-specific responses to drugs. To do so, we used the International HapMap project release 27 Data and Pharmacogenomics Knowledge Base (PharmGKB database. First, we compared four measures for assessing population differentiation: the chi-square test, the analysis of variance (ANOVA F-test, Fst, and Nearest Shrunken Centroid Method (NSCM. Fst showed high sensitivity with stable specificity among varying sample sizes; thus, we selected Fst for determining population differentiation. Second, we divided DR genes from PharmGKB into two groups based on the degree of population differentiation as assessed by Fst: genes with a high level of differentiation (HD gene group and genes with a low level of differentiation (LD gene group. Last, we conducted a gene ontology (GO analysis and pathway analysis. Using all genes in the human genome as the background, the GO analysis and pathway analysis of the HD genes identified terms related to cell communication. "Cell communication" and "cell-cell signaling" had the lowest Benjamini-Hochberg's q-values (0.0002 and 0.0006, respectively, and "drug binding" was highly enriched (16.51 despite its relatively high q-value (0.0142. Among the 17 genes related to cell communication identified in the HD gene group, five genes (STX4, PPARD, DCK, GRIK4, and DRD3 contained single nucleotide polymorphisms with Fst values greater than 0.5. Specifically, the Fst values for rs10871454, rs6922548, rs3775289, rs1954787, and rs167771 were 0.682, 0.620, 0.573, 0.531, and 0.510, respectively. In the analysis using DR genes as the background, the HD gene group contained six significant terms. Five were related to reproduction, and one was "Wnt signaling pathway," which has been implicated in cancer. Our analysis suggests that the HD gene group from PharmGKB is

  10. Effects of Bottlenecks in Vehicle Traffic

    CERN Document Server

    Yamamoto, S; Tadaki, S; Yamamoto, Syohei; Hieida, Yasuhiro; Tadaki, Shin-ichi

    2006-01-01

    Traffic congestion is usually observed at the upper streams of bottlenecks like tunnels. Congestion appears as stop-and-go waves and high density uniform flow. We perform simulations of traffic flow with a bottleneck using the coupled map optimal velocity model. The bottleneck is expressed as a road segment with speed reduction. The emergence of stop-and-go waves depends on the speed reduction in the bottleneck. A phenomenological theory of bottleneck effects is constructed.

  11. Effects of Bottlenecks on Vehicle Traffic

    OpenAIRE

    Yamamoto, Syohei; Hieida, Yasuhiro; Tadaki, Shin-ichi

    2006-01-01

    Traffic congestion is usually observed at the upper streams of bottlenecks such as tunnels. Congestion appears as stop-and-go waves and high density uniform flow. We perform simulations of traffic flow with a bottleneck using the coupled map optimal velocity model. The bottleneck is expressed as a road segment with speed reduction. The speed reduction in the bottleneck controls the emergence of stop-and-go waves. A phenomenological theory of bottleneck effects is constructed.

  12. Bottlenecks to coral recovery in the Seychelles

    Science.gov (United States)

    Chong-Seng, K. M.; Graham, N. A. J.; Pratchett, M. S.

    2014-06-01

    Processes that affect recovery of coral assemblages require investigation because coral reefs are experiencing a diverse array of more frequent disturbances. Potential bottlenecks to coral recovery include limited larval supply, low rates of settlement, and high mortality of new recruits or juvenile corals. We investigated spatial variation in local abundance of scleractinian corals in the Seychelles at three distinct life history stages (recruits, juveniles, and adults) on reefs with differing benthic conditions. Following widespread coral loss due to the 1998 bleaching event, some reefs are recovering (i.e., relatively high scleractinian coral cover: `coral-dominated'), some reefs have low cover of living macrobenthos and unconsolidated rubble substrates (`rubble-dominated'), and some reefs have high cover of macroalgae (`macroalgal-dominated'). Rates of coral recruitment to artificial settlement tiles were similar across all reef conditions, suggesting that larval supply does not explain differential coral recovery across the three reef types. However, acroporid recruits were absent on macroalgal-dominated reefs (0.0 ± 0.0 recruits tile-1) in comparison to coral-dominated reefs (5.2 ± 1.6 recruits tile-1). Juvenile coral colony density was significantly lower on macroalgal-dominated reefs (2.4 ± 1.1 colonies m-2), compared to coral-dominated reefs (16.8 ± 2.4 m-2) and rubble-dominated reefs (33.1 ± 7.3 m-2), suggesting that macroalgal-dominated reefs have either a bottleneck to successful settlement on the natural substrates or a high post-settlement mortality bottleneck. Rubble-dominated reefs had very low cover of adult corals (10.0 ± 1.7 %) compared to coral-dominated reefs (33.4 ± 3.6 %) despite no statistical difference in their juvenile coral densities. A bottleneck caused by low juvenile colony survivorship on unconsolidated rubble-dominated reefs is possible, or alternatively, recruitment to rubble-dominated reefs has only recently begun. This

  13. Narrower bottlenecks could be more efficient for concentrating choanoflagellates

    Science.gov (United States)

    Sparacino, J.; Miño, G.; Koehl, M. A. R.; King, N.; Stocker, R.; Banchio, A. J.; Marconi, V. I.

    2015-11-01

    In evolutionary biology choanoflagellates are broadly investigated as the closest living relatives of the animal ancestors. Under diverse environmental cues, choanoflagellate Salpingoeca rosetta can differentiate in two types of solitary swimming cells: slow and fast microswimmers. Here we present a first phenomenological 2D-model for the choanoflagellates dynamics confined into a flat device divided by a wall of asymmetric microconstrictions. The model allow us to optimize the geometry of the microchannels for directing and concentrating cell populations under strict control. We solve our set of dynamical equations using Langevin dynamics. Experimental parameters for the motility of the slow and fast cells were measured and used for our numerical estimations of the directed transport efficiency, otherwise we have no adjustable parameters. We find remarkable differences in the rectification results for slow and fast choanoflagellates, which give us a strategy to develop a suitable microfluidic sorting device. For a given population velocity, narrower bottlenecks, of similar size to the cell dimension, show to be more efficient as concentrator of populations. Experiments and simulations are in good agreement.

  14. Nomenclature for clusters of differentiation (CD) of antigens defined on human leukocyte populations*

    OpenAIRE

    1984-01-01

    Evaluation of 139 monoclonal antibodies detecting human leukocyte differentiation antigens during the First International Workshop on Human Leucocyte Differentiation Antigens in 1982 permitted the designation of a nomenclature for the Clusters of Differentiation of antigens defined on human leukocyte populations.

  15. Geographical structure and differential natural selection among North European populations

    DEFF Research Database (Denmark)

    McEvoy, Brian P; Montgomery, Grant W; McRae, Allan F;

    2009-01-01

    from F(ST)-based analysis of genic and nongenic SNPs that differential positive selection has operated across these populations despite their short divergence time and relatively similar geographic and environmental range. The pressure appears to have been focused on genes involved in immunity, perhaps...... reflecting response to infectious disease epidemic. Such an event may explain a striking selective sweep centered on the rs2508049-G allele, close to the HLA-G gene on chromosome 6. Evidence of the sweep extends over a 8-Mb/3.5-cM region. Overall, the results illustrate the power of dense genotype and sample...

  16. Quantifying population genetic differentiation from next-generation sequencing data

    DEFF Research Database (Denmark)

    Fumagalli, Matteo; Vieira, Filipe G.; Korneliussen, Thorfinn Sand;

    2013-01-01

    method for quantifying population genetic differentiation from next-generation sequencing data. In addition, we present a strategy to investigate population structure via Principal Components Analysis. Through extensive simulations, we compare the new method herein proposed to approaches based......Over the last few years, new high-throughput DNA sequencing technologies have dramatically increased speed and reduced sequencing costs. However, the use of these sequencing technologies is often challenged by errors and biases associated with the bioinformatical methods used for analyzing the data....... In particular, the use of naïve methods to identify polymorphic sites and infer genotypes can inflate downstream analyses. Recently, explicit modeling of genotype probability distributions has been proposed as a method for taking genotype call uncertainty into account. Based on this idea, we propose a novel...

  17. Genetic diversity and differentiation of Mongolian indigenous cattle populations

    International Nuclear Information System (INIS)

    and relationship of Mongolian cattle populations with breeds from neighboring countries and exotic breeds, data from the ILRI cattle genotyping database were included. More particularly, we used previously obtained data from Asian taurine (Hanwoo, Yanbian and Japanese Black), two European taurine (Friesian and Charolais), two African taurine (Baoule and N'Dama) and two zebu breeds (Sahiwal and Ongole). For each breed, observed (Ho) and expected (He) heterozygosities as well as the mean number of alleles (MNA) across the nine loci were calculated between pairs of populations were also estimated and a UPGMA tree was constructed. The heterozygosities (Ho and He) in Mongolian cattle populations are similar to those obtained in Northeast Asian taurine breeds but the values are higher compared to the ones obtained for the European and African taurine breeds. The Mongol cattle in North Hangay has the highest corrected MNA value (all animals or 28 animals only). The UPGMA tree, built with the Reynolds' genetic distances, shows all six Northeast Asian cattle populations clustering into one group linked to the two European taurine breed. Interestingly, the two populations of the Mongol cattle are not closely related to each other. However, bootstrap values between the Northeast Asian taurine breeds, with the exception of the bootstrap value between Yanbian and Hanwoo, are relatively low, therefore the relationship between the Northeast Asian populations should be taken with caution. Fst values between the three Mongolian cattle populations are significant (P < 0.01), with the Govi Altay population being more differentiated from the North Hangay population than from the Khalkhun Golun breed (data not shown). Our data suggest that the traditional classification of Govi Altay and North Hangay populations as one breed, the Mongol cattle, should be revisited

  18. Genetic diversity and differentiation of masu salmon (Oncorhynchus masou masou) between and within cultured populations inferred from microsatellite DNA analysis

    Institute of Scientific and Technical Information of China (English)

    Zhiying JIA; Yuyong ZHANG; Shuqiang CHEN; Lianyu SHI

    2012-01-01

    Masu salmon,Oncorhynchus masou masou,is one of the most valuable fishery species that has been introduced to China,though to date no studies on the genetic diversity and genetic relationship among hatchery populations has been performed with molecular markers.We undertook such a study and sampled 120 individuals from three hatchery stocks and analyzed 20 microsatellite loci.All loci were polymorphic and a total of 91 alleles were detected.A relatively low level of genetic diversity was revealed with effective number of allele of 3.1094,3.3299 and 3.1894 and expected heterozygosity of 0.6600,0.6648 and 0.6638 in the three stocks,respectively.Deviations from Hardy-Weinberg equilibrium were found due to heterozygote deficit.Accordingly,evidence of genetic bottlenecks were found in the three stocks.An individual assignment test demonstrated that 85% of individuals were correctly assigned into their original stocks.Pairwise Fst revealed that significant differentiation occurred between these three stocks.The results of the study indicated that disequilibrium of genetic structure and differentiation has occurred in all three stocks.This information collectively provides a basis for measures to avoid of loss of genetic diversity and introgression in Chinese aquaculture.

  19. MODIFIED BOTTLENECK-BASED PROCEDURE FOR LARGE-SCALE FLOW-SHOP SCHEDULING PROBLEMS WITH BOTTLENECK

    Institute of Scientific and Technical Information of China (English)

    ZUO Yan; GU Hanyu; XI Yugeng

    2006-01-01

    A new bottleneck-based heuristic for large-scale flow-shop scheduling problems with a bottleneck is proposed, which is simpler but more tailored than the shifting bottleneck (SB)procedure. In this algorithm, a schedule for the bottleneck machine is first constructed optimally and then the non-bottleneck machines are scheduled around the bottleneck schedule by some effective dispatching rules. Computational results show that the modified bottleneck-based procedure can achieve a tradeoff between solution quality and computational time comparing with SB procedure for medium-size problems. Furthermore it can obtain a good solution in quite short time for large-scale scheduling problems.

  20. Dynamic Prediction Method of Production Logistics Bottleneck Based on Bottleneck Index

    Institute of Scientific and Technical Information of China (English)

    LIU Mingzhou; TANG Juan; GE Maogen; JIANG Zengqiang; HU Jing; LING Lin

    2009-01-01

    In modern manufacturing pattern, there are many uncertain factors in the modern manufacturing process, such as changes of product attribute, changes of manufacturing resources' state, and so on, which cause production logistics bottleneck frequently shift, and make decisions of production planning and control based on formed bottleneck deviated from practical production process. Considering these factors, present researches mainly apply afterwards control to optimize production process to passively adapt to bottleneck changes. If the direction of bottleneck shifting can be accurately forecasted, the transition from afterwards control of chasing bottleneck to beforehand control can be realized. Therefore, aiming at the phenomenon of production logistics bottleneck shifting under uncertain manufacturing circumstances, this paper starts off with dynamic property of capability and requirement and then builds the concepts of bottleneck degree and bottleneck index to describe dynamic bottleneck characteristic of production unit;taken production capability, production load and quality assurance capability into consideration, mathematical model of bottleneck index is established to measure bottleneck degree accurately, consequently, quantitative research on mechanism of production logistics shifting is achieved. Based on bottleneck index, the prediction model of production logistics bottleneck is founded to predict dynamic change of bottleneck accurately. Finally, an example of forecasting and monitoring the production logistics bottleneck in one manufacturing shop is given to testify the validation and practicability of the prediction method.

  1. A range-wide genetic bottleneck overwhelms contemporary landscape factors and local abundance in shaping genetic patterns of an alpine butterfly (Lepidoptera: Pieridae: Colias behrii).

    Science.gov (United States)

    Schoville, Sean D; Lam, Athena W; Roderick, George K

    2012-09-01

    Spatial and environmental heterogeneity are major factors in structuring species distributions in alpine landscapes. These landscapes have also been affected by glacial advances and retreats, causing alpine taxa to undergo range shifts and demographic changes. These nonequilibrium population dynamics have the potential to obscure the effects of environmental factors on the distribution of genetic variation. Here, we investigate how demographic change and environmental factors influence genetic variation in the alpine butterfly Colias behrii. Data from 14 microsatellite loci provide evidence of bottlenecks in all population samples. We test several alternative models of demography using approximate Bayesian computation (ABC), with the results favouring a model in which a recent bottleneck precedes rapid population growth. Applying independent calibrations to microsatellite loci and a nuclear gene, we estimate that this bottleneck affected both northern and southern populations 531-281 years ago, coinciding with a period of global cooling. Using regression approaches, we attempt to separate the effects of population structure, geographical distance and landscape on patterns of population genetic differentiation. Only 40% of the variation in F(ST) is explained by these models, with geographical distance and least-cost distance among meadow patches selected as the best predictors. Various measures of genetic diversity within populations are also decoupled from estimates of local abundance and habitat patch characteristics. Our results demonstrate that demographic change can have a disproportionate influence on genetic diversity in alpine species, contrasting with other studies that suggest landscape features control contemporary demographic processes in high-elevation environments. PMID:22849440

  2. Hyperbolic partial differential equations populations, reactors, tides and waves theory and applications

    CERN Document Server

    Witten, Matthew

    1983-01-01

    Hyperbolic Partial Differential Equations, Volume 1: Population, Reactors, Tides and Waves: Theory and Applications covers three general areas of hyperbolic partial differential equation applications. These areas include problems related to the McKendrick/Von Foerster population equations, other hyperbolic form equations, and the numerical solution.This text is composed of 15 chapters and begins with surveys of age specific population interactions, populations models of diffusion, nonlinear age dependent population growth with harvesting, local and global stability for the nonlinear renewal eq

  3. Global population structure and migration patterns suggest significant population differentiation among isolates of Pyrenophora tritici-repentis.

    Science.gov (United States)

    Gurung, S; Short, D P G; Adhikari, T B

    2013-03-01

    The global population structure and migration patterns of foliar wheat pathogen Pyrenophora tritici-repentis (PTR) were determined using 12 microsatellite loci. Analysis of 439 single-spore isolates of PTR from five continents (18 wheat-producing countries) showed high level of genetic diversity, and moderate to high population differentiation between continents. A high level of gene diversity (H(S)=0.31 to 0.56) was observed within each population. Allelic richness indicated the European and the North American population have a high effective population size. Bayesian analyses showed five clusters where the inferred clusters did not represent geographical populations. Corrected standardized fixation index (G(ST)(″)) estimates ranged from 0.042 to 0.265 between populations, indicating low to high genetic differentiation exists between populations. We found migration (gene flow) between old world (Europe) and new world (Americas) population; however, little migration was observed among other continents. The European population was the major source of immigrants for the North American, South American, Australian and the Asian populations. Significant (PAustralian and the South American populations. In contrast, non-significant (P<0.001) LD values were observed in the Asian, European and the North American populations. Overall, our findings demonstrate the population differentiation exits among the global populations and strict quarantine measures should be applied to prevent the accelerated global spread of this pathogen. PMID:23376549

  4. BOTTLENECKS IN PRODUCTION NETWORKS: AN OVERVIEW

    Institute of Scientific and Technical Information of China (English)

    Yongcai WANG; Qianchuan ZHAO; Dazhong ZHENG

    2005-01-01

    Bottlenecks, the key ingredients for improving the performances of the production networks,have been profoundly studied during the last decade. Yet, because of the complexity of the research results, there is still a significant gap between theory and practice. In this paper, we review various bottleneck definitions, detection methods and the asymptotic results and provide a practical guidance for recognizing and utilizing the bottlenecks in production networks. Queueing theory works as the mathematical foundation in our study. Various definitions of the bottlenecks are classified as either Performance in Processing (PIP) based or sensitivity based definitions, which reflect the preferences of the managers. Detection methods are surveyed closely based on the definitions. These methods are used to recognize the bottlenecks and to provide diagnosis results to managers. Comparisons show that different detection methods may lead to vastly different conclusions. The recognition of the bottlenecks has another advantage: the ultimate phenomena of the bottlenecks can greatly reduce the computation complexity in calculating the system performances. Bottlenecks based approximation and asymptotic results are studied to exhibit the contribution of bottlenecks in performance estimation and theoretical analysis.

  5. Relevant genetic differentiation among Brazilian populations of Anastrepha fraterculus (Diptera, Tephritidae)

    Science.gov (United States)

    Manni, Mosè; Lima, Kátia Manuela; Guglielmino, Carmela Rosalba; Lanzavecchia, Silvia Beatriz; Juri, Marianela; Vera, Teresa; Cladera, Jorge; Scolari, Francesca; Gomulski, Ludvik; Bonizzoni, Mariangela; Gasperi, Giuliano; Silva, Janisete Gomes; Malacrida, Anna Rodolfa

    2015-01-01

    Abstract We used a population genetic approach to detect the presence of genetic diversity among six populations of Anastrepha fraterculus across Brazil. To this aim, we used Simple Sequence Repeat (SSR) markers, which may capture the presence of differentiative processes across the genome in distinct populations. Spatial analyses of molecular variance were used to identify groups of populations that are both genetically and geographically homogeneous while also being maximally differentiated from each other. The spatial analysis of genetic diversity indicates that the levels of diversity among the six populations vary significantly on an eco-geographical basis. Particularly, altitude seems to represent a differentiating adaptation, as the main genetic differentiation is detected between the two populations present at higher altitudes and the other four populations at sea level. The data, together with the outcomes from different cluster analyses, identify a genetic diversity pattern that overlaps with the distribution of the known morphotypes in the Brazilian area. PMID:26798258

  6. Genetic diversity and genetic differentiation of natural populations of Pinus kesiya var. Langbinanensis

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Genetic diversity and genetic differentiation of natural populations of Pinus kesiya var. Langbinanensis were examined by means of electrophoresis technique. Analysis of 9 enzyme systems including 16 loci showed that all the three natural populations of the pine were high in genetic diversity but low in inter -population genetic differentiation. The proportion of polymorphic loci is 0.667 , with eachlocus holding 2.13 alleles, averagely. The average expected and obse rved heterozygosity was 0.288 and 0.197, respectively. The gene differentiation among populations was 0.052, but the mean genetic distance was only 0.015.

  7. Phenotypic plasticity and population differentiation in an ongoing species invasion.

    Directory of Open Access Journals (Sweden)

    Silvia Matesanz

    Full Text Available The ability to succeed in diverse conditions is a key factor allowing introduced species to successfully invade and spread across new areas. Two non-exclusive factors have been suggested to promote this ability: adaptive phenotypic plasticity of individuals, and the evolution of locally adapted populations in the new range. We investigated these individual and population-level factors in Polygonum cespitosum, an Asian annual that has recently become invasive in northeastern North America. We characterized individual fitness, life-history, and functional plasticity in response to two contrasting glasshouse habitat treatments (full sun/dry soil and understory shade/moist soil in 165 genotypes sampled from nine geographically separate populations representing the range of light and soil moisture conditions the species inhabits in this region. Polygonum cespitosum genotypes from these introduced-range populations expressed broadly similar plasticity patterns. In response to full sun, dry conditions, genotypes from all populations increased photosynthetic rate, water use efficiency, and allocation to root tissues, dramatically increasing reproductive fitness compared to phenotypes expressed in simulated understory shade. Although there were subtle among-population differences in mean trait values as well as in the slope of plastic responses, these population differences did not reflect local adaptation to environmental conditions measured at the population sites of origin. Instead, certain populations expressed higher fitness in both glasshouse habitat treatments. We also compared the introduced-range populations to a single population from the native Asian range, and found that the native population had delayed phenology, limited functional plasticity, and lower fitness in both experimental environments compared with the introduced-range populations. Our results indicate that the future spread of P. cespitosum in its introduced range will likely be

  8. Population Genomics of Early Events in the Ecological Differentiation of Bacteria

    OpenAIRE

    Shapiro, B. Jesse; Friedman, Jonathan; Cordero, Otto X.; Preheim, Sarah P.; Timberlake, Sonia C.; Szabó, Gitta; Polz, Martin F.; Alm, Eric J.

    2011-01-01

    Genetic exchange is common among bacteria, but its effect on population diversity during ecological differentiation remains controversial. A fundamental question is whether advantageous mutations lead to selection of clonal genomes or, as in sexual eukaryotes, sweep through populations on their own. Here we show that in two recently diverged populations of ocean bacteria, ecological differentiation has occurred akin to a sexual mechanism: a few genome regions have swept through subpopulations...

  9. Exposure to a novel environment in conjunction with serial bottlenecks increases phenotypic and additive variation of a quantitative trait

    Directory of Open Access Journals (Sweden)

    T.E. Callicrate

    2012-09-01

    Full Text Available Demographic bottlenecks were replicated in laboratory conditions using Tribolium castaneum in order to determine how additive genetic variance, and therefore adaptive potential, may be affected by a novel environment. A two-level bottleneck was imposed. The first level was a 100-individual bottleneck (five replicates. After three generations at population size 100, the second bottleneck consisted of a single mating pair (15 sub-replicates stemming from each first-level replicate. Two growth media (environments, standard (wheat flour or novel (wheat bran, were used in the sub-replicates to simulate translocation to an environment with a different foraging substrate. Sub-replicates were managed for slow population growth during six generations to population size 50 and were thus maintained for nine additional generations. Variance in pupa weight in generation 16 was affected by drift from the first and second-level bottlenecks (flour: N=382, bran: N=470 pupae, both P < 0.0001 at each bottleneck level. Total phenotypic variance was determined from the progeny of the single pair matings and was larger for bottlenecks occurring in bran than in flour, P < 0.01 (F469,381 = 1.29. Additive variance was also larger in bran than flour bottlenecks, P < 0.01 (F469,381 = 1.38. These results indicate that bottlenecks occurring in a novel environment could potentially increase the effectiveness of selection by bolstering additive variance.

  10. Analytical approach to continuous and intermittent bottleneck flows

    DEFF Research Database (Denmark)

    Helbing, D.; Johansson, A.; Mathiesen, Joachim Kaj; Jensen, M.H.; Hansen, A.

    2006-01-01

    Many-particle-inspired theory, Continuous and Intermittent Bottleneck Flows Udgivelsesdato: Oct. 20......Many-particle-inspired theory, Continuous and Intermittent Bottleneck Flows Udgivelsesdato: Oct. 20...

  11. Cloud Technology May Widen Genomic Bottleneck - TCGA

    Science.gov (United States)

    Computational biologist Dr. Ilya Shmulevich suggests that renting cloud computing power might widen the bottleneck for analyzing genomic data. Learn more about his experience with the Cloud in this TCGA in Action Case Study.

  12. Differential response of two sourgrass populations to glyphosate

    Directory of Open Access Journals (Sweden)

    São Paulo State University, Jaboticabal, SP, Brazil

    2013-02-01

    Full Text Available The repetitive use of glyphosate may cause increase on the resistance of sourgrass (Digitaria insularis through mechanisms of natural selection. The aim of this study was to verify the response of two populations of sourgrass (one collected from nonagricultural area and the other one from area suspected of glyphosate resistance to increasing doses of glyphosate. The experimental design was completely randomized with four repetitions. For both populations, glyphosate was sprayed at 10 doses (0D, D/16, D/8, D/4, D/2, D, 2D, 4D, 8D, and 16D; so that D is the dose of 1.08 kg e.a. ha-1. The treatments were sprayed when the plants had shown 3-5 tillers. The population collected in the nonagricultural area was slightly more sensible to the herbicide glyphosate than the population originated from an area where the herbicide application is common, not indicating glyphosate resistance.

  13. Differential drought tolerance in tree populations from contrasting elevations

    OpenAIRE

    Ma, Fei; Xu, Ting Ting; Ji, Ming Fei; Zhao, Chang Ming

    2014-01-01

    To predict the ecological consequences of climate change for a widely distributed tree species, it is essential to develop a deep understanding of the ecophysiological responses of populations from contrasting climates to varied soil water availabilities. In the present study, we focused on Pinus tabuliformis, one of the most economically and ecologically important tree species in China. In a greenhouse experiment, we exposed trees from high-elevation (HP) and low-elevation (LP) populations t...

  14. The bottleneck of second language acquisition

    OpenAIRE

    Slabakova, Roumyana

    2014-01-01

    Explaining why some linguistic features and constructions are easy or difficult to acquire in a second language has become a prominent current concern in generative second language acquisition (SLA) research. Based on a comparison of findings on the L2 acquisition of functional morphology, syntax, semantics and pragmatics, the Bottleneck Hypothesis argues that functional morphemes and their features are the bottleneck of L2 acquisition; acquisition of universal syntax, semantics and pragmatic...

  15. MMOD: an R library for the calculation of population differentiation statistics.

    Science.gov (United States)

    Winter, David J

    2012-11-01

    MMOD is a library for the R programming language that allows the calculation of the population differentiation measures D(est), G″(ST) and φ'(ST). R provides a powerful environment in which to conduct and record population genetic analyses but, at present, no R libraries provide functions for the calculation of these statistics from standard population genetic files. In addition to the calculation of differentiation measures, mmod can produce parametric bootstrap and jackknife samples of data sets for further analysis. By integrating with and complimenting the existing libraries adegenet and pegas, mmod extends the power of R as a population genetic platform. PMID:22883857

  16. Genetic Differentiation of Different Geographical Populations of Bemisia tabaci (Gennadius) Complex

    Institute of Scientific and Technical Information of China (English)

    CHU Dong; LIU Guo-xia; FAN Zhong-xue; TAO Yun-li; ZHANG You-jun

    2007-01-01

    Bemisia tabaci (Gennadius) is a species complex, which includes different geographical populations with genetic differentiation. The recent progress on the genetic differentiation of various geographical populations of B. tabaci complex was introduced. The genetic differentiation was further analyzed on the basis of the sequences of mtDNA COI and rDNA ITSl recorded in the world's GenBank. Five groups are defined on the basis of mtDNA COI and rDNA ITS1, including the Asia group, America group, Africa group, Australia group, and Biotype B/Mediterranean/Middle East/ Northern Africa/Biotype Ms group. There are several ungrouped geographical classifications, such as the Uganda population, Ivory Coast population, and Taiwan population. Geographical isolation may be the most important factor that contributed to the genetic differentiation of various geographical populations of B. tabaci. Many populations with biological advantages invaded new regions and caused severe economic losses within human activity. It is necessary to strengthen the research of B. tabaci biotype to prevent the spread of invaded populations and the invasion of potentially dangerous populations.

  17. Population genetic structure of Bombus terrestris in Europe: Isolation and genetic differentiation of Irish and British populations.

    Science.gov (United States)

    Moreira, António S; Horgan, Finbarr G; Murray, Tomás E; Kakouli-Duarte, Thomais

    2015-07-01

    The genetic structure of the earth bumblebee (Bombus terrestris L.) was examined across 22 wild populations and two commercially reared populations using eight microsatellite loci and two mitochondrial genes. Our study included wild bumblebee samples from six populations in Ireland, one from the Isle of Man, four from Britain and 11 from mainland Europe. A further sample was acquired from New Zealand. Observed levels of genetic variability and heterozygosity were low in Ireland and the Isle of Man, but relatively high in continental Europe and among commercial populations. Estimates of Fst revealed significant genetic differentiation among populations. Bayesian cluster analysis indicated that Irish populations were highly differentiated from British and continental populations, the latter two showing higher levels of admixture. The data suggest that the Irish Sea and prevailing south westerly winds act as a considerable geographical barrier to gene flow between populations in Ireland and Britain; however, some immigration from the Isle of Man to Ireland was detected. The results are discussed in the context of the recent commercialization of bumblebees for the European horticultural industry. PMID:25958977

  18. Differentiation of Effector CD4 T Cell Populations*

    OpenAIRE

    Zhu, Jinfang; Yamane, Hidehiro; Paul, William E.

    2010-01-01

    CD4 T cells play critical roles in mediating adaptive immunity to a variety of pathogens. They are also involved in autoimmunity, asthma, and allergic responses as well as in tumor immunity. During TCR activation in a particular cytokine milieu, naive CD4 T cells may differentiate into one of several lineages of T helper (Th) cells, including Th1, Th2, Th17, and iTreg, as defined by their pattern of cytokine production and function. In this review, we summarize the discovery, functions, and r...

  19. Genetic and phenotypic differentiation of an Andean intermediate altitude population

    OpenAIRE

    Eichstaedt, Christina A; Antão, Tiago; Cardona, Alexia; Pagani, Luca; Kivisild, Toomas; Mormina, Maru

    2015-01-01

    Highland populations living permanently under hypobaric hypoxia have been subject of extensive research because of the relevance of their physiological adaptations for the understanding of human health and disease. In this context, what is considered high altitude is a matter of interpretation and while the adaptive processes at high altitude (above 3000 m) are well documented, the effects of moderate altitude (below 3000 m) on the phenotype are less well established. In this study, we compar...

  20. Tracing Road Network Bottleneck by Data Driven Approach

    Science.gov (United States)

    Qi, Hongsheng; Liu, Meiqi; Zhang, Lihui; Wang, Dianhai

    2016-01-01

    Urban road congestions change both temporally and spatially. They are essentially caused by network bottlenecks. Therefore, understanding bottleneck dynamics is critical in the goal of reasonably allocating transportation resources. In general, a typical bottleneck experiences the stages of formation, propagation and dispersion. In order to understand the three stages of a bottle neck and how the bottleneck moves on a road network, traffic flow data can be used to reconstruct these dynamics. However, raw traffic flow data is usually flawed in many ways. For instance some portion of data may be missing due to the failure of data collection devices, or some random factors in the data make it hard to identify real bottlenecks. In this paper a “user voting method” is proposed to deal with such raw-data-related issues. In this method, road links are ranked according to the weighed sum of certain performance measures and the links that are ranked relatively high are regarded as recurrent bottlenecks in a network, and several bottlenecks form a bottleneck area. A series of bottleneck parameters can be defined based on the identified bottleneck areas, such as bottleneck coverage, bottleneck link length, etc. Identifying bottleneck areas and calculating the bottleneck parameters for each time interval can reflect the evolution of the bottlenecks and also help trace how the bottlenecks move. PMID:27228150

  1. Tracing Road Network Bottleneck by Data Driven Approach.

    Science.gov (United States)

    Qi, Hongsheng; Liu, Meiqi; Zhang, Lihui; Wang, Dianhai

    2016-01-01

    Urban road congestions change both temporally and spatially. They are essentially caused by network bottlenecks. Therefore, understanding bottleneck dynamics is critical in the goal of reasonably allocating transportation resources. In general, a typical bottleneck experiences the stages of formation, propagation and dispersion. In order to understand the three stages of a bottle neck and how the bottleneck moves on a road network, traffic flow data can be used to reconstruct these dynamics. However, raw traffic flow data is usually flawed in many ways. For instance some portion of data may be missing due to the failure of data collection devices, or some random factors in the data make it hard to identify real bottlenecks. In this paper a "user voting method" is proposed to deal with such raw-data-related issues. In this method, road links are ranked according to the weighed sum of certain performance measures and the links that are ranked relatively high are regarded as recurrent bottlenecks in a network, and several bottlenecks form a bottleneck area. A series of bottleneck parameters can be defined based on the identified bottleneck areas, such as bottleneck coverage, bottleneck link length, etc. Identifying bottleneck areas and calculating the bottleneck parameters for each time interval can reflect the evolution of the bottlenecks and also help trace how the bottlenecks move. PMID:27228150

  2. Tracing Road Network Bottleneck by Data Driven Approach.

    Directory of Open Access Journals (Sweden)

    Hongsheng Qi

    Full Text Available Urban road congestions change both temporally and spatially. They are essentially caused by network bottlenecks. Therefore, understanding bottleneck dynamics is critical in the goal of reasonably allocating transportation resources. In general, a typical bottleneck experiences the stages of formation, propagation and dispersion. In order to understand the three stages of a bottle neck and how the bottleneck moves on a road network, traffic flow data can be used to reconstruct these dynamics. However, raw traffic flow data is usually flawed in many ways. For instance some portion of data may be missing due to the failure of data collection devices, or some random factors in the data make it hard to identify real bottlenecks. In this paper a "user voting method" is proposed to deal with such raw-data-related issues. In this method, road links are ranked according to the weighed sum of certain performance measures and the links that are ranked relatively high are regarded as recurrent bottlenecks in a network, and several bottlenecks form a bottleneck area. A series of bottleneck parameters can be defined based on the identified bottleneck areas, such as bottleneck coverage, bottleneck link length, etc. Identifying bottleneck areas and calculating the bottleneck parameters for each time interval can reflect the evolution of the bottlenecks and also help trace how the bottlenecks move.

  3. Geographic After-Tax Real Income Differentials and Population Growth Rates

    OpenAIRE

    Alexander, Gigi; Cebula, Richard; Koch, James

    1989-01-01

    This empirical note investigates the impact of geographic after-tax real, as opposed to nominal, income differentials on geographic population growth rates. The focus is on Florida's 67 counties and the 1980-88 time period. The empirical results imply that the population growth rate in Florida counties was of after-tax real income.

  4. Differential stress resistance and metabolic traits underlie coexistence in a sympatrically evolved bacterial population

    NARCIS (Netherlands)

    Puentes Tellez, Pilar; van Elsas, Jan Dirk

    2015-01-01

    Following intermittent batch growth in Luria-Bertani (LB) broth for about 1000 generations, differentially evolved forms were found in a population of Escherichia coli cells. Studies on this population revealed the emergence of key polymorphisms, as evidenced by analysis of both whole genome sequenc

  5. Patterns of genetic and reproductive traits differentiation in Mainland vs. Corsican populations of bumblebees.

    Directory of Open Access Journals (Sweden)

    Thomas Lecocq

    Full Text Available Populations on islands often exhibit lower levels of genetic variation and ecomorphological divergence compared to their mainland relatives. While phenotypic differentiation in characters, such as size or shape among insular organisms, has been well studied, insular differentiation in quantitative reproductive traits involved in chemical communication has received very little attention to date. Here, we investigated the impact of insularity on two syntopic bumblebee species pairs: one including species that are phylogenetically related (Bombus terrestris and B. lucorum, and the other including species that interact ecologically (B. terrestris and its specific nest inquiline B. vestalis. For each bumblebee species, we characterized the patterns of variation and differentiation of insular (Corsican vs. mainland (European populations (i with four genes (nuclear and mitochondrial, 3781 bp and (ii in the chemical composition of male marking secretions (MMS, a key trait for mate attraction in bumblebees, by gas chromatography-mass spectrometry (GC-MS. Our results provide evidence for genetic differentiation in Corsican bumblebees and show that, contrary to theoretical expectations, island populations of bumblebees exhibit levels of genetic variation similar to the mainland populations. Likewise, our comparative chemical analyses of MMS indicate that Corsican populations of bumblebees are significantly differentiated from the mainland yet they hold comparative levels of within-population MMS variability compared to the mainland. Therefore, insularity has led Corsican populations to diverge both genetically and chemically from their mainland relatives, presumably through genetic drift, but without a decrease of genetic diversity in island populations. We hypothesize that MMS divergence in Corsican bumblebees was driven by a persistent lack of gene flow with mainland populations and reinforced by the preference of Corsican females for sympatric (Corsican

  6. Molecular and Quantitative Genetic Differentiation in European Populations of Silene latifolia (Caryophyllaceae)

    OpenAIRE

    Jolivet, Céline; Bernasconi, Giorgina

    2009-01-01

    Background and Aims: Among-population differentiation in phenotypic traits and allelic variation is expected as a consequence of isolation, drift, founder effects and local selection. Therefore, investigating molecular and quantitative genetic divergence is a pre-requisite for studies of local adaptation in response to selection under variable environmental conditions. Methods: Among- and within-population variation were investigated in six geographically separated European populations of t...

  7. Identification and optimization of traffic bottleneck with signal timing

    OpenAIRE

    Shaoxin Yuan; Xiangmo Zhao; Yisheng An

    2014-01-01

    In urban transportation network, traffic congestion is likely to occur at traffic bottlenecks. The signal timing at intersections together with static properties of left-turn and straight-through lanes of roads are two significant factors causing traffic bottlenecks. A discrete-time model of traffic bottleneck is hence developed to analyze these two factors, and a bottleneck indicator is introduced to estimate the comprehensive bottleneck degree of individual road in regional transportation n...

  8. Potential performance bottleneck in Linux TCP

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Wenji; Crawford, Matt; /Fermilab

    2006-12-01

    TCP is the most widely used transport protocol on the Internet today. Over the years, especially recently, due to requirements of high bandwidth transmission, various approaches have been proposed to improve TCP performance. The Linux 2.6 kernel is now preemptible. It can be interrupted mid-task, making the system more responsive and interactive. However, we have noticed that Linux kernel preemption can interact badly with the performance of the networking subsystem. In this paper we investigate the performance bottleneck in Linux TCP. We systematically describe the trip of a TCP packet from its ingress into a Linux network end system to its final delivery to the application; we study the performance bottleneck in Linux TCP through mathematical modeling and practical experiments; finally we propose and test one possible solution to resolve this performance bottleneck in Linux TCP.

  9. New insights into pedestrian flow through bottlenecks

    CERN Document Server

    Seyfried, A; Klingsch, W; Passon, O; Rupprecht, T; Steffen, B; Boltes, Maik; Klingsch, Wolfram; Passon, Oliver; Rupprecht, Tobias; Seyfried, Armin; Steffen, Bernhard

    2007-01-01

    Capacity estimation is an important tool for the design and dimensioning of pedestrian facilities. The literature contains different procedures and specifications which show considerable differences with respect to the estimated flow values. Moreover do new experimental data indicate a stepwise growing of the capacity with the width and thus challenge the validity of the specific flow concept. To resolve these differences we have studied experimentally the unidirectional pedestrian flow through bottlenecks under laboratory conditions. The time development of quantities like individual velocities, density and individual time gaps in bottlenecks of different width is presented. The data show a linear growth of the flow with the width. The comparison of the results with experimental data of other authors indicates that the basic assumption of the capacity estimation for bottlenecks has to be revised. In contradiction with most planning guidelines our main result is, that a jam occurs even if the incoming flow do...

  10. Gene variation, population differentiation, and sociogenetic structure of nests of Partamona seridoensis (Hymenoptera: Apidae, Meliponini).

    Science.gov (United States)

    Fernandes, Carlo Rivero Moura; Martins, Celso Feitosa; Ferreira, Kátia Maria; Del Lama, Marco Antonio

    2012-06-01

    Gene variation and the differentiation of two populations of Partamona seridoensis (Hymenoptera: Apidae: Meliponini) from the Caatinga biome, a semiarid ecosystem unique to Brazil, were estimated through allozymic and microsatellite analyses. These populations exhibited similar low degrees of enzyme gene variation. Observed genotype frequencies at the allozyme and microsatellite loci were in accordance with Hardy-Weinberg equilibrium in the two populations. Both markers demonstrated that the two populations are not genetically homogeneous and must be considered distinct populations. The occurrence of private alleles at the allozyme and microsatellite loci corroborates this differentiation, sustaining the hypothesis of a low level of interpopulation gene flow. The phenotypic segregations clearly demonstrated that the progeny inside each nest were the result of mating between the queen of the colony and only one male. PMID:21938561

  11. Rapid differentiation of sexual signals in invasive toads: call variation among populations.

    Science.gov (United States)

    Yasumiba, Kiyomi; Duffy, Richard L; Parsons, Scott A; Alford, Ross A; Schwarzkopf, Lin

    2016-01-01

    Advertisement calls tend to differ among populations, based on morphological and environmental factors, or simply geographic distance, in many taxa. Invasive cane toads (Rhinella marina) were introduced to Australia in 1935 and their distribution has expanded at increasing rates over time. Rapid evolution occurred in morphological and behavioural characters that accelerate dispersal, but the effects of rapid expansion on sexual signals have not been examined. We collected advertisement calls from four populations of different ages since invasion, and analysed the geographic differentiation of seven call parameters. Our comparisons indicate that the calls of R. marina differ among Australian populations. The signal variation was not simply clinal with respect to population age, climate, or morphological differentiation. We suggest that selection on signalling among populations has been idiosyncratic and may reflect local female preferences or adaptation to environmental factors that are not clinal such as energy availability. PMID:27328666

  12. Genetic bottlenecks during systemic movement of Cucumber mosaic virus vary in different host plants

    International Nuclear Information System (INIS)

    Genetic bottlenecks are stochastic events that narrow variation in a population. We compared bottlenecks during the systemic infection of Cucumber mosaic virus (CMV) in four host plants. We mechanically inoculated an artificial population of twelve CMV mutants to young leaves of tomato, pepper, Nicotiana benthamiana, and squash. The inoculated leaves and primary and secondary systemically infected leaves were sampled at 2, 10, and 15 days post-inoculation. All twelve mutants were detected in all of the inoculated leaves. The number of mutants recovered from the systemically infected leaves of all host species was reduced significantly, indicating bottlenecks in systemic movement. The recovery frequencies of a few of the mutants were significantly different in each host probably due to host-specific selective forces. These results have implications for the differences in virus population variation that is seen in different host plants.

  13. Differential effects of chronic monocyte depletion on macrophage populations

    International Nuclear Information System (INIS)

    The administration of the bone-seeking isotope, 89Sr, to mice results in severe monocytopenia without any apparent effect on the numbers of resident peritoneal macrophages (M luminal diameter). An explanation for this dichotomy was sought by determining whether the residual blood monocytes were still an effective source of M luminal diameter after 89Sr treatment. Stem cell enumeration showed that a 90% fall in bone marrow macrophage colony-forming cells after 89Sr was accompanied by a 10-fold rise in splenic M-CFC. Splenectomy performed before 89Sr treatment, however, resulted in little additional monocytopenia and had no affect on the numbers of resident peritoneal M luminal diameter even when sampling was extended to 31 days, an interval beyond the accepted half-time for peritoneal M luminal diameter. Intraperitoneal injections of thioglycollate or Corynebacterium parvum elicited few or no monocyte-M luminal diameter during respective intervals of 4 and 7 days. Elicitation with thioglycollate was attempted in tritiated thymidine-labeled mice 26 days after 89Sr. Four days later only a 2-fold increase in labeled peritoneal M luminal diameter was found in the 89Sr-treated mice compared with a 150-fold increase in the controls. Studies of the ectoenzymes 5'-nucleotidase, alkaline phosphodiesterase I, and leucine aminopeptidase in such elicitation experiments suggested that the observed changes in activities reflected the direct stimulation of resident M luminal diameter rather than monocyte immigration. Overall, the results indicate that treatment with 89Sr distinguishes two large populations of M luminal diameter on the basis of their dependence on bone marrow. M luminal diameter of inflammation reflect the monocytopenia and are severely and rapidly depleted by such treatment

  14. Shear bands as bottlenecks in force transmission

    Science.gov (United States)

    Tordesillas, Antoinette; Pucilowski, Sebastian; Tobin, Steven; Kuhn, Matthew R.; Andò, Edward; Viggiani, Gioacchino; Druckrey, Andrew; Alshibli, Khalid

    2015-06-01

    The formation of shear bands is a key attribute of degradation and failure in soil, rocks, and many other forms of amorphous and crystalline materials. Previous studies of dense sand under triaxial compression and two-dimensional analogues from simulations have shown that the ultimate shear band pattern may be detected in the nascent stages of loading, well before the band's known nucleation point (i.e., around peak stress ratio), as reported in the published literature. Here we construct a network flow model of force transmission to identify the bottlenecks in the contact networks of dense granular media: triaxial compression of Caicos ooid and Ottawa sand and a discrete element simulation of simple shear. The bottlenecks localise in the nascent stages of loading —in the location where the persistent shear band ultimately forms. This corroborates recent findings on vortices that suggest localised failure is a progressive process of degradation, initiating early in the loading history at sites spanning the full extent, yet confined to a subregion, of the sample. Bottlenecks are governed by the local and global properties of the sample fabric and the grain kinematics. Grains with large rotations and/or contacts having minimal load-bearing capacities per se do not identify the bottlenecks early in the loading history.

  15. Population genomic footprints of fine-scale differentiation between habitats in Mediterranean blue tits.

    Science.gov (United States)

    Szulkin, M; Gagnaire, P-A; Bierne, N; Charmantier, A

    2016-01-01

    Linking population genetic variation to the spatial heterogeneity of the environment is of fundamental interest to evolutionary biology and ecology, in particular when phenotypic differences between populations are observed at biologically small spatial scales. Here, we applied restriction-site associated DNA sequencing (RAD-Seq) to test whether phenotypically differentiated populations of wild blue tits (Cyanistes caeruleus) breeding in a highly heterogeneous environment exhibit genetic structure related to habitat type. Using 12 106 SNPs in 197 individuals from deciduous and evergreen oak woodlands, we applied complementary population genomic analyses, which revealed that genetic variation is influenced by both geographical distance and habitat type. A fine-scale genetic differentiation supported by genome- and transcriptome-wide analyses was found within Corsica, between two adjacent habitats where blue tits exhibit marked differences in breeding time while nesting < 6 km apart. Using redundancy analysis (RDA), we show that genomic variation remains associated with habitat type when controlling for spatial and temporal effects. Finally, our results suggest that the observed patterns of genomic differentiation were not driven by a small proportion of highly differentiated loci, but rather emerged through a process such as habitat choice, which reduces gene flow between habitats across the entire genome. The pattern of genomic isolation-by-environment closely matches differentiation observed at the phenotypic level, thereby offering significant potential for future inference of phenotype-genotype associations in a heterogeneous environment. PMID:26800038

  16. Genetic diversity and differentiation of mud crab Scylla serrata populations from southeastern China

    Institute of Scientific and Technical Information of China (English)

    LI Zhongbao; LI Shaojing; WANG Guizhong

    2004-01-01

    The genetic diversity and differentiation of 6 mud crab Scylla serrata populations from southeastern China are investigated using allozyme electrophoresis. The mean number of alleles per locus population is 1.3 ± 0.1; the percentage of polymorphic loci per population is 27.3; the observed heterozygosity ranges from ( 0.195 ± 0.083)to ( 0.241 ± 0.090) and the expected heterozygosity ranges from ( 0.105 ± 0.043 ) to ( 0.131 ± 0.047 ). The coefficient of gene differentiation among populations is low (Fst =0.032), indicating that only 3.2 % of the total genetic diversity comes from inter-population, while the remaining 96.8 % comes from intra-population differences.The genetic distance among populations is 0.000~0.008 (the average is 0.002). Gene flow among the populations is large (Nm= 7.56).Genetic structure is very similar among 6 Scylla serrata populations.

  17. Breaking the biomass bottleneck of the fossil free society

    DEFF Research Database (Denmark)

    Wenzel, Henrik

    for heat and power services as well as for transportation fuels and as feedstock for chemicals and materials – i.e. in practice all sectors today being dependant on fossil fuels. At the same time, unfortunately, the food sector is also in growing demand for agricultural crops. World population is still...... demand on food prices, namely the food crisis in 2007 – 2008. During this period, market prices on food and feed crops increased by almost a factor of 2, and the part of the world population suffering from hunger and starvation increased from 800 million to 900 million people. The amount of biomass...... resources, the food sector and the poorest part of the world population. We can, however, break this bottleneck. First of all, we must seek further energy savings. Secondly, we need to look for ways to de-carbonize society. There is a growing consensus among energy scientists and energy planners...

  18. Analysis of the genetic diversity and differentiation of Fenneropenaeus penicillatus populations using AFLP technology

    Institute of Scientific and Technical Information of China (English)

    ZHANG Guiling; CAO Yuanyu; LI Zhongbao; CHEN Jin; ZHAO Binli; LEI Guanggao; WANG Zhanlin

    2012-01-01

    Fenneropenaeus penicillatus (redtail shrimp) is an important marine commercial animal in China.Recently,its resources have been depleted rapidly as a result of,for example,over-exploitation and environmental degradation of spawning grounds.Therefore,we analyzed the genetic diversity and differentiation of nine wild populations of F.penicillatus of China (Ningde,Lianjiang,Putian,Xiamen,Quanzhou,Zhangpu,Dongshan,Nanao,and Shenzhen populations) by amplified fragment length polymorphism (AFLP) technology,to provide genetic information necessary for resource protection,rejuvenation,artificial breeding,and sustainable use of the resource.Eight AFLP primer pairs were used for amplification,and 508 bands were detected among the populations.The results show that the percentage of polymorphic loci (P) ranged from 41.34% to 63.58%; the Nei's gene diversity (H) of the populations was 0.119 4-0.230 5; and Sharnon's Information Index (I) was 0.184 1-0.342 5.These genetic data indicate that the genetic diversity of F.penicillatus was high.The genetic differentiation coefficient (Gsr=0.216 2) and gene flow (Nm=1.812 4) show that there was a high level of genetic differentiation and a moderate level of gene flow among populations.More studies on the genetic differentiation mechanism of F.penicillatus along the south-eastern coast of China need to be conducted to find more effective scientific protection strategies for the conservation ofF.penicillatus genetic resources.

  19. Microgeographic and Temporal Genetic Differentiation in Natural Populations of DROSOPHILA SUBOBSCURA

    OpenAIRE

    Cabrera, V M; González, A M; M Hernández; Larruga, J. M.; Martell, M

    1985-01-01

    Evidence of microgeographic and temporal genetic differentiation in natural populations of Drosophila subobscura is presented. The alcohol dehydrogenease locus was used as a genetic marker. Behavioral differences among the sexes and genotypes may explain these observations, although the molecular basis remains obscure.

  20. Molecular differentiation of commercial varieties and feral populations of oilseed rape (Brassica napus L.

    Directory of Open Access Journals (Sweden)

    Glössl Josef

    2010-03-01

    Full Text Available Abstract Background For assessing the risk of escape of transgenes from cultivation, the persistence of feral populations of crop plants is an important aspect. Feral populations of oilseed rape, Brassica napus, are well known, but only scarce information is available on their population dynamics, particularly in Central Europe. To investigate genetic diversity, origin and persistence of feral oilseed rape in Austria, we compared variation at nine polymorphic microsatellite loci in eight feral populations with 19 commercial varieties. Results Overall, commercial varieties and feral populations showed a similar pattern of genetic variation and a similar level of observed heterozygosity. The two groups, however, shared less than 50% of the alleles and no multilocus genotype. A significant among-group (commercial varieties versus feral populations component of genetic variation was observed (AMOVA: FCT = 0.132. Pairwise comparisons between varieties and feral populations showed moderate to very high genetic differentiation (FST = 0.209 - 0.900. The software STRUCTURE also demonstrated a clear separation between commercial varieties and feral samples: out of 17 identified genetic clusters, only one comprised plants from both a commercial variety and feral sites. Conclusions The results suggest that feral oilseed rape is able to maintain persistent populations. The feral populations may have derived from older cultivars that were not included in our analyses or perhaps have already hybridised with related crops or wild relatives. Feral populations therefore have to be considered in ecological risk assessment and future coexistence measures as a potential hybridisation partner of transgenic oilseed rape.

  1. Performance Bottlenecks in Digital Movie Systems

    OpenAIRE

    Keller, Ralf; Effelsberg, Wolfgang; Lamparter, Bernd

    1993-01-01

    Digital movie systems offer great perspectives for multimedia applications. But the large amounts of data involved and the demand for isochronous transmission and playback are also great challenges for the designers of a new generation of file systems, database systems, operating systems, window systems, video encoder/decoder and networks. Today's research prototypes of digital movie systems suffer from severe performance bottlenecks, resulting in small movie windows, low frame rates or bad i...

  2. Teleworking and Congestion: A Dynamic Bottleneck Analysis

    OpenAIRE

    Gubins, Sergejs; Verhoef, Erik T.

    2011-01-01

    We analyze the welfare effects of part-day teleworking on road traffic congestion in the context of Vickrey's dynamic bottleneck model. Endogenous decisions to become equipped with a teleworking-enabling technology change the scheduling of arrival times at work for equipped drivers and, due to congestion externalities, affects travel costs of all drivers. We show that even costless teleworking might be marginally welfare reducing, after reaching the optimal penetration level, as an equipped d...

  3. Individual Microscopic Results Of Bottleneck Experiments

    CERN Document Server

    Bukáček, Marek; Krbálek, Milan

    2016-01-01

    This contribution provides microscopic experimental study of pedestrian motion in front of the bottleneck, explains the high variance of individual travel time by the statistical analysis of trajectories. The analysis shows that this heterogeneity increases with increasing occupancy. Some participants were able to reach lower travel time due more efficient path selection and more aggressive behavior within the crowd. Based on this observations, linear model predicting travel time with respect to the aggressiveness of pedestrian is proposed.

  4. DYNAMIC BOTTLENECKS IN HANDLING AND STORAGE SYSTEMS

    OpenAIRE

    PANOVA YULIA; HILMOLA OLLI-PEKKA

    2015-01-01

    The development of industrial engineering and production systems is manifested under the demand of Russian customers in the current economic and political situation, e.g. deprivation from several import markets. In these circumstances, issues related to the formation of process systems are gaining their importance. The article considers the objective of reaching the smooth and continuous material flow in the handling and storage system of the plant, as well as the problems of bottlenecks opti...

  5. Deep Bottleneck Feature for Image Classification

    OpenAIRE

    Song, Yan; McLoughlin, Ian Vince; Dai, Lirong

    2015-01-01

    Effective image representation plays an important role for image classification and retrieval. Bag-of-Features (BoF) is well known as an effective and robust visual representation. However, on large datasets, convolutional neural networks (CNN) tend to perform much better, aided by the availability of large amounts of training data. In this paper, we propose a bag of Deep Bottleneck Features (DBF) for image classification, effectively combining the strengths of a CNN within a BoF framework. T...

  6. Ecological differentiation of Lemna minor L. and Spirodela polyrrhiza (L. Schleiden populations

    Directory of Open Access Journals (Sweden)

    Hanna Wożakowska-Natkaniec

    2015-05-01

    Full Text Available The subject of thep resent study are 19 natural, ecological populations of Lemna minor and Spirodela polyrrhiza coming from sixteen habitats in Lower Silesia. The study showed the essential differences between ecological populations of both species, conditioned on chemistry (pH, level N, P, K, Ca, Mg and Fe and the natural water radioactivity. It was shown experimentally that these populations, in nature, establish a set of ecotypes or ecophene variability. Ecotypic differentiation of populations of Lemna minor and Spirodela polyrrhiza is based upon individual features and population characteristics such as: shape and size of plants, plant frequency of two, three, and four fronds, the ratio of right- to left-handed plants, and the dynamics of growth and biomass production.

  7. Nucleotide diversity and population differentiation of the Melanocortin 1 Receptor gene, MC1R

    Directory of Open Access Journals (Sweden)

    Peris Ketty

    2008-04-01

    Full Text Available Abstract Background The melanocortin 1 receptor gene (MC1R is responsible for normal pigment variation in humans and is highly polymorphic with numerous population-specific alleles. Some MC1R variants have been associated with skin cancer risk. Results Allele frequency data were compiled on 55 single nucleotide polymorphisms from seven geographically distinct human populations (n = 2306 individuals. MC1R nucleotide diversity, π, was much higher (10.1 × 10-4 than in other genes for all subjects. A large degree of population differentiation, determined by FST, was also present, particularly between Asia and all other populations, due to the p.R163Q (c.488 G>A polymorphism. The least amount of differentiation was between the United States, Northern Europe, and Southern Europe. Tajima's D statistic suggested the presence of positive selection in individuals from Europe. Conclusion This study further quantifies the degree of population-specific genetic variation and suggests that positive selection may be present in European populations in MC1R.

  8. Local environment but not genetic differentiation influences biparental care in ten plover populations.

    Directory of Open Access Journals (Sweden)

    Orsolya Vincze

    Full Text Available Social behaviours are highly variable between species, populations and individuals. However, it is contentious whether behavioural variations are primarily moulded by the environment, caused by genetic differences, or a combination of both. Here we establish that biparental care, a complex social behaviour that involves rearing of young by both parents, differs between closely related populations, and then test two potential sources of variation in parental behaviour between populations: ambient environment and genetic differentiation. We use 2904 hours behavioural data from 10 geographically distinct Kentish (Charadrius alexandrinus and snowy plover (C. nivosus populations in America, Europe, the Middle East and North Africa to test these two sources of behavioural variation. We show that local ambient temperature has a significant influence on parental care: with extreme heat (above 40 °C total incubation (i.e. % of time the male or female incubated the nest increased, and female share (% female share of incubation decreased. By contrast, neither genetic differences between populations, nor geographic distances predicted total incubation or female's share of incubation. These results suggest that the local environment has a stronger influence on a social behaviour than genetic differentiation, at least between populations of closely related species.

  9. Population based model of human embryonic stem cell (hESC differentiation during endoderm induction.

    Directory of Open Access Journals (Sweden)

    Keith Task

    Full Text Available The mechanisms by which human embryonic stem cells (hESC differentiate to endodermal lineage have not been extensively studied. Mathematical models can aid in the identification of mechanistic information. In this work we use a population-based modeling approach to understand the mechanism of endoderm induction in hESC, performed experimentally with exposure to Activin A and Activin A supplemented with growth factors (basic fibroblast growth factor (FGF2 and bone morphogenetic protein 4 (BMP4. The differentiating cell population is analyzed daily for cellular growth, cell death, and expression of the endoderm proteins Sox17 and CXCR4. The stochastic model starts with a population of undifferentiated cells, wherefrom it evolves in time by assigning each cell a propensity to proliferate, die and differentiate using certain user defined rules. Twelve alternate mechanisms which might describe the observed dynamics were simulated, and an ensemble parameter estimation was performed on each mechanism. A comparison of the quality of agreement of experimental data with simulations for several competing mechanisms led to the identification of one which adequately describes the observed dynamics under both induction conditions. The results indicate that hESC commitment to endoderm occurs through an intermediate mesendoderm germ layer which further differentiates into mesoderm and endoderm, and that during induction proliferation of the endoderm germ layer is promoted. Furthermore, our model suggests that CXCR4 is expressed in mesendoderm and endoderm, but is not expressed in mesoderm. Comparison between the two induction conditions indicates that supplementing FGF2 and BMP4 to Activin A enhances the kinetics of differentiation than Activin A alone. This mechanistic information can aid in the derivation of functional, mature cells from their progenitors. While applied to initial endoderm commitment of hESC, the model is general enough to be applicable

  10. A theory of traffic congestion at moving bottlenecks

    Science.gov (United States)

    Kerner, Boris S.; Klenov, Sergey L.

    2010-10-01

    The physics of traffic congestion occurring at a moving bottleneck on a multi-lane road is revealed based on the numerical analyses of vehicular traffic with a discrete stochastic traffic flow model in the framework of three-phase traffic theory. We find that there is a critical speed of a moving bottleneck at which traffic breakdown, i.e. a first-order phase transition from free flow to synchronized flow, occurs spontaneously at the moving bottleneck, if the flow rate upstream of the bottleneck is great enough. The greater the flow rate, the higher the critical speed of the moving bottleneck. A diagram of congested traffic patterns at the moving bottleneck is found, which shows regions in the flow-rate-moving-bottleneck-speed plane in which congested patterns emerge spontaneously or can be induced through large enough disturbances in an initial free flow. A comparison of features of traffic breakdown and resulting congested patterns at the moving bottleneck with known ones at an on-ramp (and other motionless) bottleneck is made. Nonlinear features of complex interactions and transformations of congested traffic patterns occurring at on- and off-ramp bottlenecks due to the existence of the moving bottleneck are found. The physics of the phenomenon of traffic congestion due to 'elephant racing' on a multi-lane road is revealed.

  11. A theory of traffic congestion at moving bottlenecks

    International Nuclear Information System (INIS)

    The physics of traffic congestion occurring at a moving bottleneck on a multi-lane road is revealed based on the numerical analyses of vehicular traffic with a discrete stochastic traffic flow model in the framework of three-phase traffic theory. We find that there is a critical speed of a moving bottleneck at which traffic breakdown, i.e. a first-order phase transition from free flow to synchronized flow, occurs spontaneously at the moving bottleneck, if the flow rate upstream of the bottleneck is great enough. The greater the flow rate, the higher the critical speed of the moving bottleneck. A diagram of congested traffic patterns at the moving bottleneck is found, which shows regions in the flow-rate-moving-bottleneck-speed plane in which congested patterns emerge spontaneously or can be induced through large enough disturbances in an initial free flow. A comparison of features of traffic breakdown and resulting congested patterns at the moving bottleneck with known ones at an on-ramp (and other motionless) bottleneck is made. Nonlinear features of complex interactions and transformations of congested traffic patterns occurring at on- and off-ramp bottlenecks due to the existence of the moving bottleneck are found. The physics of the phenomenon of traffic congestion due to 'elephant racing' on a multi-lane road is revealed.

  12. A recent bottleneck of Y chromosome diversity coincides with a global change in culture

    KAUST Repository

    Karmin, Monika

    2015-04-30

    It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50–100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192–307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47–52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.

  13. Low genetic differentiation in a sedentary bird: house sparrow population genetics in a contiguous landscape

    OpenAIRE

    Kekkonen, J; Seppä, P.; Hanski, I K; Jensen, H; Väisänen, R A; Brommer, J. E.

    2010-01-01

    The house sparrow Passer domesticus has been declining in abundance in many localities, including Finland. We studied the genetic diversity and differentiation of the house sparrow populations across Finland in the 1980s, at the onset of the species' decline in abundance. We genotyped 472 adult males (the less dispersive sex) from 13 locations in Finland (covering a range of 400 × 800 km) and one in Sweden (Stockholm) for 13 polymorphic microsatellite markers. Our analysis of Finnish ringing ...

  14. Differential Exploitation of Atlantic Salmon Populations by a Rod Fishery on the River Spey, Scotland

    OpenAIRE

    Thorley, Joseph L.; Youngson, Alan F.; Laughton, Robert

    2004-01-01

    Due to heritable population differences in run-timing, Atlantic salmon (Salmo salar) enter Scottish rivers throughout the year. Maintenance of this diversity is vital for the continued commercial and recreational value of the associated rod fisheries, which extend on most rivers from February to September. However, as the data we present demonstrate, management of the rod fishery on the River Spey, Scotland, is complicated by differential exploitation of the Atlantic salmon from the various r...

  15. Analysis of bottleneck motion using Voronoi diagrams

    CERN Document Server

    Liddle, Jack; Steffen, Bernhard

    2010-01-01

    Standard definitions of the density exhibit large fluctuations when the size of the measurement area is comparable with the size of a pedestrian. An alternative measurement method exists where a personal space, calculated through the Voronoi diagram, is assigned to each pedestrian. In this contribution this method is applied to an experiment studying motion through a bottleneck and the reduced fluctuations demonstrated. The integrated density also permits examination on much smaller spatial scales than the standard definition, the insights into the pedestrian motion this provides are discussed.

  16. Differentiation of population income and poverty problem (based on the data of Tyumen region

    Directory of Open Access Journals (Sweden)

    Aleksandr Anatolyevich Kuklin

    2011-03-01

    Full Text Available The results of differentiation analysis of money income in the Tyumen region are presented in this paper. Analysis of differentiation was performed using Foster-Greer-Torbeke class indicators by areas included in Tyumen region: autonomous areas (Khanty-Mansiysk and Yamal-Nenets and the southern part of the region. It is shown that, along with increasing interterritorial income differentiation, income differentiation within these regions is also growing. Based on the results of an assessment carried out during the last ten years in the social policy, the package of measures aimed at improving the situation of the poor population is proposed. Thus, it is shown that the advancement of the poor population may be the result of a comprehensive social policy aimed at reducing income inequality by eliminating the strain distribution in the relationship. The emphasis of the regional authorities should be given to programs that go beyond the narrow definition of social protection: programs to improve labour market efficiency, quality of workforce and education etc.

  17. Microsatellite variability reveals high genetic diversity and low genetic differentiation in a critical giant panda population

    Institute of Scientific and Technical Information of China (English)

    Jiandong YANG; Zhihe ZHANG; Fujun SHEN; Xuyu YANG; Liang ZHANG; Limin CHEN; Wenping ZHANG; Qing ZHU; Rong HOU

    2011-01-01

    Understanding present patterns of genetic diversity is critical in order to design effective conservation and management strategies for endangered species.Tangjiahe Nature Reserve (NR) is one of the most important national reserves for giant pandas Ailuropoda melanoleuca in China.Previous studies have shown that giant pandas in Tangjiahe NR may be threatened by population decline and fragmentation.Here we used 10 microsatellite DNA markers to assess the genetic variability in the Tangjiahe population.The results indicate a low level of genetic differentiation between the Hongshihe and Motianling subpopulations in the reserve.Assignment tests using the Bayesian clustering method in STRUCTURE identified one genetic cluster from 42 individuals of the two subpopulations.All individuals from the same subpopulation were assigned to one cluster.This indicates high gene flow between subpopulations.F statistic analyses revealed a low Fls-value of 0.024 in the total population and implies a randomly mating population in Tangjiahe NR.Additionally,our data show a high level of genetic diversity for the Tangjiahe population.Mean allele number (A),Allelic richness (AR) and mean expected heterozygosity (HE) for the Tangiiahe population was 5.9,5.173 and 0.703,respectively.This wild giant panda population can be restored through concerted effort [Current Zoology 57 (6):717-724,2011].

  18. Low genetic differentiation across three major ocean populations of the whale shark, Rhincodon typus.

    Directory of Open Access Journals (Sweden)

    Jennifer V Schmidt

    Full Text Available BACKGROUND: Whale sharks are a declining species for which little biological data is available. While these animals are protected in many parts of their range, they are fished legally and illegally in some countries. Baseline biological and ecological data are needed to allow the formulation of an effective conservation plan for whale sharks. It is not known, for example, whether the whale shark is represented by a single worldwide panmictic population or by numerous, reproductively isolated populations. Genetic analysis of population structure is one essential component of the baseline data required for whale shark conservation. METHODOLOGY/PRINCIPAL FINDINGS: We have identified 8 polymorphic microsatellites in the whale shark and used these markers to assess genetic variation and population structure in a panel of whale sharks covering a broad geographic region. This is the first record of microsatellite loci in the whale shark, which displayed an average of 9 alleles per locus and mean H(o = 0.66 and H(e = 0.69. All but one of the eight loci meet the expectations of Hardy-Weinberg equilibrium. Analysis of these loci in whale sharks representing three major portions of their range, the Pacific (P, Caribbean (C, and Indian (I Oceans, determined that there is little population differentiation between animals sampled in different geographic regions, indicating historical gene flow between populations. F(ST values for inter-ocean comparisons were low (PxC = 0.0387, CxI = 0.0296 and PxI = -0.0022, and only CxI approached statistical significance (p = 0.0495. CONCLUSIONS/SIGNIFICANCE: We have shown only low levels of genetic differentiation between geographically distinct whale shark populations. Existing satellite tracking data have revealed both regional and long-range migration of whale sharks throughout their range, which supports the finding of gene flow between populations. Whale sharks traverse geographic and political boundaries during their

  19. Where do they come from? Flow connectivity detects landscape bottlenecks

    OpenAIRE

    Alessandro Ferrarini

    2015-01-01

    In this paper, bottleneck flow connectivity is first introduced. A landscape bottleneck is defined here as the portion of an arbitrary study area which inevitably tunnels a specimen towards the point where it has been detected in situ. In other words, a bottleneck delimits the portion of the study area which forces the specimen to pass through the detected point of presence with, at most, a tolerance distance equal to an a priori defined uncertainty. There is one precise reason for the introd...

  20. Population genetic structure of wild and farmed rusa deer (Cervus timorensis russa) in New-Caledonia inferred from polymorphic microsatellite loci

    OpenAIRE

    Garine-Wichatitsky de, M.; De Meeûs, Thierry; Chevillon, Christine; BERTHIER, D.; Barre, N.; Thevenon, S.; Maillard, J.C.

    2009-01-01

    Historical records indicate that 12 rusa deer (Cervus timorensis russa) were introduced in New-Caledonia during the 1870s. We used eight polymorphic microsatellite DNA loci to assess the genetic differentiation and diversity of farmed and wild deer populations. Past genetic bottlenecks were detected in both sub-populations, although higher genetic diversity was maintained in farmed populations, probably due to the regular introduction of reproducers from wild populations and from other farms....

  1. Herbivory at marginal populations: Consequences for maternal fitness and vegetative differentiation

    Science.gov (United States)

    Castilla, Antonio R.; Alonso, Conchita; Herrera, Carlos M.

    2013-05-01

    Margins of distribution of plant species constitute natural areas where the impact of the antagonistic interactions is expected to be higher and where changes in the dynamics of plant-herbivore coevolution could promote intraspecific differentiation in (co)evolving plant traits. In the present study, we investigated how differences in the average herbivory level affect maternal fitness in core continuous and marginal disjunct populations of Daphne laureola in an effort to assess the role of herbivores limiting plant distribution. Furthermore, we investigated intraspecific differentiation in vegetative traits and their potential connection to divergent selection by herbivores in both groups of populations. Our results did not support increased herbivory at the species margin but did support a difference in the effect of herbivory on maternal fitness between core continuous and marginal disjunct populations of D. laureola. In addition, herbivores did not exert phenotypic selection consistent with the geographic variation in studied plant traits. Therefore, the geographic variation of vegetative traits of D. laureola seems to be consequence of environmental heterogeneity more than result of geographically divergent selection by herbivores.

  2. Modified bottleneck-based heuristic for large-scale job-shop scheduling problems with a single bottleneck

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    A modified bottleneck-based (MB) heuristic for large-scale job-shop scheduling problems with a welldefined bottleneck is suggested,which is simpler but more tailored than the shifting bottleneck (SB) procedure.In this algorithm,the bottleneck is first scheduled optimally while the non-bottleneck machines are subordinated around the solutions of the bottleneck schedule by some effective dispatching rules.Computational results indicate that the MB heuristic can achieve a better tradeoff between solution quality and computational time compared to SB procedure for medium-size problems.Furthermore,it can obtain a good solution in a short time for large-scale job-shop scheduling problems.

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

    Science.gov (United States)

    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.

  4. A differential equation with state-dependent delay from cell population biology

    Science.gov (United States)

    Getto, Philipp; Waurick, Marcus

    2016-04-01

    We analyze a differential equation, describing the maturation of a stem cell population, with a state-dependent delay, which is implicitly defined via the solution of an ODE. We elaborate smoothness conditions for the model ingredients, in particular vital rates, that guarantee the existence of a local semiflow and allow to specify the linear variational equation. The proofs are based on theoretical results of Hartung et al. combined with implicit function arguments in infinite dimensions. Moreover we elaborate a criterion for global existence for differential equations with state-dependent delay. To prove the result we adapt a theorem by Hale and Lunel to the C1-topology and use a result on metric spaces from Diekmann et al.

  5. Genetic variability in four Alouatta species measured by means of nine DNA microsatellite markers: genetic structure and recent bottlenecks.

    Science.gov (United States)

    Ruiz-Garcia, M; Escobar-Armel, P; Alvarez, D; Mudry, M; Ascunce, M; Gutierrez-Espeleta, G; Shostell, J M

    2007-01-01

    We used microsatellite DNA to study the population genetics of 4 Alouatta species from Central and South America. Our main findings include the following: (1) A. seniculus had the highest level of microsatellite variability while A. caraya and A. palliata had the lowest mean number of alleles per locus and the lowest expected heterozygosity, respectively; (2) the samples of A. seniculus and A. palliata came from different regions and were not in Hardy-Weinberg equilibrium (HWE) which may indicate a Wahlund effect and differentiated gene pools -- in contrast, A. macconnelli and A. caraya were in HWE; (3) the microsatellite genetic heterogeneity of the 4 Alouatta species was similar to the karyotype divergence found among these Alouatta species; the species pair with the lowest level of heterogeneity (genetic differentiation) was A. seniculus/A. caraya, while the Central American species, A. palliata, was highly differentiated from the other 3 South American species; (4) we recommend the establishment of a conservation plan to help protect A. caraya because the Cornuet and Luikart procedure demonstrated a recent bottleneck for this species. PMID:17303937

  6. The strength and timing of the mitochondrial bottleneck in salmon suggests a conserved mechanism in vertebrates.

    Directory of Open Access Journals (Sweden)

    Jonci N Wolff

    Full Text Available In most species mitochondrial DNA (mtDNA is inherited maternally in an apparently clonal fashion, although how this is achieved remains uncertain. Population genetic studies show not only that individuals can harbor more than one type of mtDNA (heteroplasmy but that heteroplasmy is common and widespread across a diversity of taxa. Females harboring a mixture of mtDNAs may transmit varying proportions of each mtDNA type (haplotype to their offspring. However, mtDNA variants are also observed to segregate rapidly between generations despite the high mtDNA copy number in the oocyte, which suggests a genetic bottleneck acts during mtDNA transmission. Understanding the size and timing of this bottleneck is important for interpreting population genetic relationships and for predicting the inheritance of mtDNA based disease, but despite its importance the underlying mechanisms remain unclear. Empirical studies, restricted to mice, have shown that the mtDNA bottleneck could act either at embryogenesis, oogenesis or both. To investigate whether the size and timing of the mitochondrial bottleneck is conserved between distant vertebrates, we measured the genetic variance in mtDNA heteroplasmy at three developmental stages (female, ova and fry in chinook salmon and applied a new mathematical model to estimate the number of segregating units (N(e of the mitochondrial bottleneck between each stage. Using these data we estimate values for mtDNA Ne of 88.3 for oogenesis, and 80.3 for embryogenesis. Our results confirm the presence of a mitochondrial bottleneck in fish, and show that segregation of mtDNA variation is effectively complete by the end of oogenesis. Considering the extensive differences in reproductive physiology between fish and mammals, our results suggest the mechanism underlying the mtDNA bottleneck is conserved in these distant vertebrates both in terms of it magnitude and timing. This finding may lead to improvements in our understanding of

  7. Genetic Differentiation between Sympatric Populations of Bacillus cereus and Bacillus thuringiensis

    Science.gov (United States)

    Vilas-Boas, Gislayne; Sanchis, Vincent; Lereclus, Didier; Lemos, Manoel Victor F.; Bourguet, Denis

    2002-01-01

    Little is known about genetic exchanges in natural populations of bacteria of the spore-forming Bacillus cereus group, because no population genetics studies have been performed with local sympatric populations. We isolated strains of Bacillus thuringiensis and B. cereus from small samples of soil collected at the same time from two separate geographical sites, one within the forest and the other at the edge of the forest. A total of 100 B. cereus and 98 B. thuringiensis strains were isolated and characterized by electrophoresis to determine allelic composition at nine enzymatic loci. We observed genetic differentiation between populations of B. cereus and B. thuringiensis. Populations of a given Bacillus species—B. thuringiensis or B. cereus—were genetically more similar to each other than to populations of the other Bacillus species. Hemolytic activity provided further evidence of this genetic divergence, which remained evident even if putative clones were removed from the data set. Our results suggest that the rate of gene flow was higher between strains of the same species, but that exchanges between B. cereus and B. thuringiensis were nonetheless possible. Linkage disequilibrium analysis revealed sufficient recombination for B. cereus populations to be considered panmictic units. In B. thuringiensis, the balance between clonal proliferation and recombination seemed to depend on location. Overall, our data indicate that it is not important for risk assessment purposes to determine whether B. cereus and B. thuringiensis belong to a single or two species. Assessment of the biosafety of pest control based on B. thuringiensis requires evaluation of the extent of genetic exchange between strains in realistic natural conditions. PMID:11872495

  8. Mechanisms of population differentiation in marbled murrelets: historical versus contemporary processes.

    Science.gov (United States)

    Congdon, B C; Piatt, J F; Martin, K; Friesen, V L

    2000-06-01

    Mechanisms of population differentiation in highly vagile species such as seabirds are poorly understood. Previous studies of marbled murrelets (Brachyramphus marmoratus; Charadriiformes: Alcidae) found significant population genetic structure, but could not determine whether this structure is due to historical vicariance (e.g., due to Pleistocene glaciers), isolation by distance, drift or selection in peripheral populations, or nesting habitat selection. To discriminate among these possibilities, we analyzed sequence variation in nine nuclear introns from 120 marbled murrelets sampled from British Columbia to the western Aleutian Islands. Mismatch distributions indicated that murrelets underwent at least one population expansion during the Pleistocene and probably are not in genetic equilibrium. Maximum-likelihood analysis of allele frequencies suggested that murrelets from "mainland" sites (from the Alaskan Peninsula east) are genetically different from those in the Aleutians and that these two lineages diverged prior to the last glaciation. Analyses of molecular variance, as well as estimates of gene flow derived using coalescent theory, indicate that population genetic structure is best explained by peripheral isolation of murrelets in the Aleutian Islands, rather than by selection associated with different nesting habitats. No isolation-by-distance effects could be detected. Our results are consistent with a rapid expansion of murrelets from a single refugium during the early-mid Pleistocene, subsequent isolation and divergence in two or more refugia during the final Pleistocene glacial advance, and secondary contact following retreat of the ice sheets. Population genetic structure now appears to be maintained by distance effects combined with small populations and a highly fragmented habitat in the Aleutian Islands. PMID:10937270

  9. Microsatellite data suggest significant population structure and differentiation within the malaria vector Anopheles darlingi in Central and South America

    Directory of Open Access Journals (Sweden)

    Achee Nicole L

    2008-03-01

    Full Text Available Abstract Background Anopheles darlingi is the most important malaria vector in the Neotropics. An understanding of A. darlingi's population structure and contemporary gene flow patterns is necessary if vector populations are to be successfully controlled. We assessed population genetic structure and levels of differentiation based on 1,376 samples from 31 localities throughout the Peruvian and Brazilian Amazon and Central America using 5–8 microsatellite loci. Results We found high levels of polymorphism for all of the Amazonian populations (mean RS = 7.62, mean HO = 0.742, and low levels for the Belize and Guatemalan populations (mean RS = 4.3, mean HO = 0.457. The Bayesian clustering analysis revealed five population clusters: northeastern Amazonian Brazil, southeastern and central Amazonian Brazil, western and central Amazonian Brazil, Peruvian Amazon, and the Central American populations. Within Central America there was low non-significant differentiation, except for between the populations separated by the Maya Mountains. Within Amazonia there was a moderate level of significant differentiation attributed to isolation by distance. Within Peru there was no significant population structure and low differentiation, and some evidence of a population expansion. The pairwise estimates of genetic differentiation between Central America and Amazonian populations were all very high and highly significant (FST = 0.1859 – 0.3901, P DA and FST distance-based trees illustrated the main division to be between Central America and Amazonia. Conclusion We detected a large amount of population structure in Amazonia, with three population clusters within Brazil and one including the Peru populations. The considerable differences in Ne among the populations may have contributed to the observed genetic differentiation. All of the data suggest that the primary division within A. darlingi corresponds to two white gene genotypes between Amazonia (genotype 1

  10. Pronounced population genetic differentiation in the rock bream Oplegnathus fasciatus inferred from mitochondrial DNA sequences.

    Science.gov (United States)

    Xiao, Yongshuang; Li, Jun; Ren, Guijing; Ma, Daoyuan; Wang, Yanfeng; Xiao, ZhiZhong; Xu, Shihong

    2016-05-01

    The population genetic structure of the rock bream (Oplegnathus fasciatus) along the coastal waters of China was estimated based on three mtDNA fragments (D-loop, COI, and Cytb). A total of 112 polymorphic sites were checked, which defined 63 haplotypes. A pattern with high levels of haplotype diversity (hCOI = 0.886 ± 0.034, hCytb = 0.874 ± 0.023) and low levels of nucleotide diversity (лCOI = 0.009 ± 0.005, лCytb = 0.006 ± 0.003) was detected based on the COI and Cytb fragments, and high levels of genetic diversity (hD-loop = 0.995 ± 0.007, лD-loop = 0.021 ± 0.011) were detected from the mtDNA D-loop. The population genetic diversity of O. fasciatus in south China was significantly higher than those of north China. Three genealogical clades were checked in the O. fasciatus populations based on the NJ and MST analyses of mtDNA COI gene sequence, and the genetic distances among the clades ranged from 0.018 to 0.025. Significant population genetic differentiation was also checked based on the Fst (0.331, p = 0.000) and exact p (0.000) test analyses. No significant population differentiations were checked based on mtDNA D-loop and Cytb fragments. Using a variety of phylogenetic methods, coalescent reasoning, and molecular dating interpreted in conjunction with paleoclimatic and physiographic evidences, we inferred that the genetic make-up of extant populations of O. fasciatus was shaped by Pleistocene environmental impacts on the historical demography of this species. Coalescent analyses (neutrality tests, mismatch distribution analysis, and Bayesian skyline analyses) showed that the species along coastline of China has experienced population expansions originated in its most recent history at about 169-175 kya before present. PMID:25427804

  11. Genetic differentiation of the Cabo Verde archipelago population analysed by STR polymorphisms.

    Science.gov (United States)

    Fernandes, A T; Velosa, R; Jesus, J; Carracedo, A; Brehm, A

    2003-07-01

    Allele frequencies for 17 STR loci were analyzed in a sample of unrelated males from the Cabo Verde Archipelago. The samples were gathered in such a way that the origin of the subjects was perfectly identified, and they could be included in one of the leeward or windward groups of islands. This study reveals that there are significant differences between both groups of islands, and between Cabo Verdeans and other populations from sub-Sahara Africa including the Guineans, the most probable source population for Cabo Verdeans. This study confirms mtDNA data and, together with HLA and Y chromosome data already published, shows that the Cabo Verde population is sub-structured and atypical, diverging substantially from mainland sub-Saharan populations. Overall these differences are most probably due to admixture between sub-Saharan slaves brought into the islands and other settlers of European origin. In the absence of a clear indication of a different ethnic composition of the first sub-Saharan settlers of Cabo Verde, the differentiation exhibited in both groups of islands can be most probably be attributed to genetic drift. PMID:12914568

  12. Differential fertilization success between two populations of eastern oyster, Crassostrea virginica.

    Science.gov (United States)

    Zhang, Haibin; Scarpa, John; Hare, Matthew P

    2010-10-01

    Identification of mechanisms promoting prezygotic reproductive isolation and their prevalence are key goals in evolutionary biology because of their potential role in speciation. In marine broadcast-spawning species, molecular interactions between gamete surface proteins are more important than mating behavior for determining reproductive compatibility. Evidence for differential fertilization capacity has been reported from experiments utilizing competing sperm from two males sampled within populations and between species, but to our knowledge conspecific populations that might have diverged in allopatry have never been tested on the basis of sperm competition. In the present study, the gametic compatibility and embryo survivorship from matings between two allopatric populations of Crassostrea virginica, the eastern oyster, on either side of a genetic step cline were investigated. Fertilization success, embryo survival, and paternity data all indicated an absence of strong reproductive barriers between the two oyster populations, implicating other mechanisms for maintenance of the cline step. Sperm from northern male oysters showed a tendency to produce more larvae than expected when competing with sperm from southern male oysters. Although the northern male advantage was not strong, the trend implies that long-distance dispersal across the step cline might more successfully result in north-to-south gene flow than the reverse, providing a mechanistic hypothesis explaining the asymmetric cline shape. PMID:20972259

  13. Evidence of ecotypic differentiation between populations of the tree species Parapiptadenia rigida due to flooding.

    Science.gov (United States)

    Silva, D C G; Carvalho, M C C G; Ruas, P M; Ruas, C F; Medri, M E

    2010-01-01

    The tree species Parapiptadenia rigida, native to southern South America, is frequently used in reforestation of riverbanks in Brazil. This tree is also a source of gums, tannins and essential oils, and it has some medicinal uses. We investigated flooding tolerance and genetic diversity in two populations of P. rigida; one of them was naturally exposed to flooding. Plants derived from seeds collected from each population were submitted to variable periods of experimental waterlogging and submergence. Waterlogging promoted a decrease in biomass and structural adjustments, such as superficial roots with aerenchyma and hypertrophied lenticels, that contribute to increase atmospheric oxygen intake. Plants that were submerged had an even greater reduction in biomass and a high mortality rate (40%). The two populations varied significantly in their RAPD marker profiles, in their ability to produce aerenchyma when waterlogged and to survive when submerged, suggesting ecotypic differentiation between them. Hence, the seasonal flooding that has been challenging the tropical riparian forest appears to be genetically modifying the P. rigida populations exposed to it by selecting individuals with increased ability to live under this condition. PMID:20449813

  14. Life history trait differentiation and local adaptation in invasive populations of Ambrosia artemisiifolia in China.

    Science.gov (United States)

    Li, Xiao-Meng; She, Deng-Ying; Zhang, Da-Yong; Liao, Wan-Jin

    2015-03-01

    Local adaptation has been suggested to play an important role in range expansion, particularly among invasive species. However, the extent to which local adaptation affects the success of an invasive species and the factors that contribute to local adaptation are still unclear. This study aimed to investigate a case of population divergence that may have contributed to the local adaptation of invasive populations of Ambrosia artemisiifolia in China. Common garden experiments in seven populations indicated clinal variations along latitudinal gradients, with plants from higher latitudes exhibiting earlier flowering and smaller sizes at flowering. In reciprocal transplant experiments, plants of a northern Beijing origin produced more seeds at their home site than plants of a southern Wuhan origin, and the Wuhan-origin plants had grown taller at flowering than the Beijing-origin plants in Wuhan, which is believed to facilitate pollen dispersal. These results suggest that plants of Beijing origin may be locally adapted through female fitness and plants from Wuhan possibly locally adapted through male fitness. Selection and path analysis suggested that the phenological and growth traits of both populations have been influenced by natural selection and that flowering time has played an important role through its direct and indirect effects on the relative fitness of each individual. This study evidences the life history trait differentiation and local adaptation during range expansion of invasive A. artemisiifolia in China. PMID:25362583

  15. The role of selection and historical factors in driving population differentiation along an elevational gradient in an island bird.

    Science.gov (United States)

    Bertrand, J A M; Delahaie, B; Bourgeois, Y X C; Duval, T; García-Jiménez, R; Cornuault, J; Pujol, B; Thébaud, C; Milá, B

    2016-04-01

    Adaptation to local environmental conditions and the range dynamics of populations can influence evolutionary divergence along environmental gradients. Thus, it is important to investigate patterns of both phenotypic and genetic variations among populations to reveal the respective roles of these two types of factors in driving population differentiation. Here, we test for evidence of phenotypic and genetic structure across populations of a passerine bird (Zosterops borbonicus) distributed along a steep elevational gradient on the island of Réunion. Using 11 microsatellite loci screened in 401 individuals from 18 localities distributed along the gradient, we found that genetic differentiation occurred at two spatial levels: (i) between two main population groups corresponding to highland and lowland areas, respectively, and (ii) within each of these two groups. In contrast, several morphological traits varied gradually along the gradient. Comparison of neutral genetic differentiation (FST ) and phenotypic differentiation (PST ) showed that PST largely exceeds FST at several morphological traits, which is consistent with a role for local adaptation in driving morphological divergence along the gradient. Overall, our results revealed an area of secondary contact midway up the gradient between two major, cryptic, population groups likely diverged in allopatry. Remarkably, local adaptation has shaped phenotypic differentiation irrespective of population history, resulting in different patterns of variation along the elevational gradient. Our findings underscore the importance of understanding both historical and selective factors when trying to explain variation along environmental gradients. PMID:26779843

  16. Genetic differentiation of Arthrobacter population from heavy metal-contaminated environment

    Institute of Scientific and Technical Information of China (English)

    ZHANG Hanbo; REN Weimin; SHAO Qiyong; DUAN Changqun

    2007-01-01

    Six samples containing extremely high concentration of Pb,Zn,and Cd were obtained from the layers of 5-10 cm and 25-30 cm three tailing piles,with ages of about 10,20 and more than 80 years,respectively.Then,48 bacterial strains were obtained from these samples,and subsequently their phylogenetic positions were determined by analysis on the partial sequence of 16S rRNA gene (fragment length ranging from 474 to 708 bp).These isolates were members of the Arthrobacter genus,phylogenetically close to A.keyseri and A.ureafaciens,with sequence ranging from 99.1%to 100%.Furthermore,genetic variation between subpopulations from different samples was revealed by analysis on their randomly amplified polymorphic DNA profile.Nei genetic distance showed that the greatest differentiation occurred between subpopulation A and C.Notably,either genetic distance between subpopulations from the layers of 5-10 cm and 25-30 cm of each tailing pile or between same layers of different tailing pile increased with the history of tailings.Moreover,correlation analysis showed that soluble Pb has a significantly negative relationship with Nei'gene diversity of subpopulation.It was assumed that soluble Pb may be responsible for the reduced genetic diversity of the Arthrobacter population.Our data provided evidence that genetic differentiation of microbial populations was consistent with the changes of environmental factors,particularly heavy metals.

  17. Genetic structure and differentiation of Psathyrostachys huashanica populations detected with RAPD markers

    Institute of Scientific and Technical Information of China (English)

    WANG Li; YANG Juan; GUO Jing; ZHAO Guifang

    2007-01-01

    Psathyrostachys huashanica Keng is a perennial grass and belongs to genus Psathyrostachys under Triticeae.sathyrostachys is found in the center of Middle Asia and the Caucasus Mountain,while P.huashanica,a species endemic to China,is only located in Mt.Hua in the Shaanxi province,China.At present,the population of this species is decreasing,and reaching the edge of extinction.Due to the limitation in distribution and the importance as breeding material for germplasm storage,it has been considered as first class among the national protected rare plants.For this reason,the present study is significant in probing plant flora,origin and evolution of Triticeae,and crop breeding.Randomly amplified polymorphic DNA (RAPD)markers were used to analyze the genetic structure and differentiation of P.huashanica populations sampled in three valleys (Huangpu,Xian,and Huashan Valleys)in Mr.Hua.One hundred and twenty-two RAPDfragments were obtained in all 266 individuals with 20 primers with a mean of 6.1 (2-10)fragments per primer.The percentage of polymorphic loci (PPB)was 60.66%in Huangpu Valley,90.98%in Xian Valley,95.08%in Huashan Valley,and the total PPB was 95.08%,which indicated a highly genetic variability of P.huashanica.The Shannon's Information index and GST were 0.3306 and 0.3263,respectively,indicating that there were more genetic variations within the subpopulations than those among the subpopulations.The gene flow among the subpopulations of P.huashanica (Nm=1.0322)was much less than that of the common anemophytes (Nm=5.24).Mean genetic distance is 0.1571(range:0.0022-0.2901).The highest value of genetic distance was found between the subpopulation (hp1)of Huangpu Valley and the highest altitude subpopulation (h8)of Huashan Valley.Correlation analysis detected significant correlation between genetic distance and vertical distance of altitude.Clustering analysis and principal coordinate analysis revealed the genetic differentiation among the populations of P.huashanica.Differentiation

  18. Laboratory colonisation and genetic bottlenecks in the tsetse fly Glossina pallidipes.

    Directory of Open Access Journals (Sweden)

    Marc Ciosi

    2014-02-01

    Full Text Available BACKGROUND: The IAEA colony is the only one available for mass rearing of Glossina pallidipes, a vector of human and animal African trypanosomiasis in eastern Africa. This colony is the source for Sterile Insect Technique (SIT programs in East Africa. The source population of this colony is unclear and its genetic diversity has not previously been evaluated and compared to field populations. METHODOLOGY/PRINCIPAL FINDINGS: We examined the genetic variation within and between the IAEA colony and its potential source populations in north Zimbabwe and the Kenya/Uganda border at 9 microsatellites loci to retrace the demographic history of the IAEA colony. We performed classical population genetics analyses and also combined historical and genetic data in a quantitative analysis using Approximate Bayesian Computation (ABC. There is no evidence of introgression from the north Zimbabwean population into the IAEA colony. Moreover, the ABC analyses revealed that the foundation and establishment of the colony was associated with a genetic bottleneck that has resulted in a loss of 35.7% of alleles and 54% of expected heterozygosity compared to its source population. Also, we show that tsetse control carried out in the 1990's is likely reduced the effective population size of the Kenya/Uganda border population. CONCLUSIONS/SIGNIFICANCE: All the analyses indicate that the area of origin of the IAEA colony is the Kenya/Uganda border and that a genetic bottleneck was associated with the foundation and establishment of the colony. Genetic diversity associated with traits that are important for SIT may potentially have been lost during this genetic bottleneck which could lead to a suboptimal competitiveness of the colony males in the field. The genetic diversity of the colony is lower than that of field populations and so, studies using colony flies should be interpreted with caution when drawing general conclusions about G. pallidipes biology.

  19. Bimodal mesoporous silica with bottleneck pores.

    Science.gov (United States)

    Reber, M J; Brühwiler, D

    2015-11-01

    Bimodal mesoporous silica consisting of two sets of well-defined mesopores is synthesized by a partial pseudomorphic transformation of an ordered mesoporous starting material (SBA-15 type). The introduction of a second set of smaller mesopores (MCM-41 type) establishes a pore system with bottlenecks that restricts the access to the core of the bimodal mesoporous silica particles. The particle size and shape of the starting material are retained, but micropores present in the starting material disappear during the transformation, leading to a true bimodal mesoporous product. A varying degree of transformation allows the adjustment of the pore volume contribution of the two mesopore domains. Information on the accessibility of the mesopores is obtained by the adsorption of fluorescence-labeled poly(amidoamine) dendrimers and imaging by confocal laser scanning microscopy. This information is correlated with nitrogen sorption data to provide insights regarding the spatial distribution of the two mesopore domains. The bimodal mesoporous materials are excellent model systems for the investigation of cavitation effects in nitrogen desorption isotherms. PMID:26399172

  20. Bottleneck Management in Discrete Batch Production

    Directory of Open Access Journals (Sweden)

    Ferenčíková Denisa

    2012-06-01

    Full Text Available Today, production planning and scheduling becomes very important part of production management because companies have to react to dynamic market conditions and rising customers´ requirements for shorter delivery times, lower prices and better quality and services. They can use a lot of sophisticated methods and approaches to make their planning processes more efficient and thus meet growing customers´ requirements. However, using these new approaches is not so easy in all types of production systems. This paper deals with production planning and scheduling in discrete batch production that is just an example of very complicated production system. This type of production process is susceptible to demand fluctuation and facility exceptions and this implies bottleneck shifting. Therefore it is quite difficult to implement methods such as Theory of Constraints (TOC for production planning improvement in the standard way. One part of this paper is a case study wherecurrent production planning and scheduling in real factory is improved just through the use TOC principles.

  1. The Limited Utility of Multiunit Data in Differentiating Neuronal Population Activity.

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    Corey J Keller

    Full Text Available To date, single neuron recordings remain the gold standard for monitoring the activity of neuronal populations. Since obtaining single neuron recordings is not always possible, high frequency or 'multiunit activity' (MUA is often used as a surrogate. Although MUA recordings allow one to monitor the activity of a large number of neurons, they do not allow identification of specific neuronal subtypes, the knowledge of which is often critical for understanding electrophysiological processes. Here, we explored whether prior knowledge of the single unit waveform of specific neuron types is sufficient to permit the use of MUA to monitor and distinguish differential activity of individual neuron types. We used an experimental and modeling approach to determine if components of the MUA can monitor medium spiny neurons (MSNs and fast-spiking interneurons (FSIs in the mouse dorsal striatum. We demonstrate that when well-isolated spikes are recorded, the MUA at frequencies greater than 100Hz is correlated with single unit spiking, highly dependent on the waveform of each neuron type, and accurately reflects the timing and spectral signature of each neuron. However, in the absence of well-isolated spikes (the norm in most MUA recordings, the MUA did not typically contain sufficient information to permit accurate prediction of the respective population activity of MSNs and FSIs. Thus, even under ideal conditions for the MUA to reliably predict the moment-to-moment activity of specific local neuronal ensembles, knowledge of the spike waveform of the underlying neuronal populations is necessary, but not sufficient.

  2. Disparities in allele frequencies and population differentiation for 101 disease-associated single nucleotide polymorphisms between Puerto Ricans and non-Hispanic whites

    Science.gov (United States)

    Background: Variations in gene allele frequencies can contribute to differences in the prevalence of some common complex diseases among populations. Natural selection modulates the balance in allele frequencies across populations. Population differentiation (FST) can evidence environmental selection...

  3. Endothelial Progenitor Cell Fraction Contained in Bone Marrow-Derived Mesenchymal Stem Cell Populations Impairs Osteogenic Differentiation

    Directory of Open Access Journals (Sweden)

    Fabian Duttenhoefer

    2015-01-01

    Full Text Available In bone tissue engineering (TE endothelial cell-osteoblast cocultures are known to induce synergies of cell differentiation and activity. Bone marrow mononucleated cells (BMCs are a rich source of mesenchymal stem cells (MSCs able to develop an osteogenic phenotype. Endothelial progenitor cells (EPCs are also present within BMC. In this study we investigate the effect of EPCs present in the BMC population on MSCs osteogenic differentiation. Human BMCs were isolated and separated into two populations. The MSC population was selected through plastic adhesion capacity. EPCs (CD34+ and CD133+ were removed from the BMC population and the resulting population was named depleted MSCs. Both populations were cultured over 28 days in osteogenic medium (Dex+ or medium containing platelet lysate (PL. MSC population grew faster than depleted MSCs in both media, and PL containing medium accelerated the proliferation for both populations. Cell differentiation was much higher in Dex+ medium in both cases. Real-time RT-PCR revealed upregulation of osteogenic marker genes in depleted MSCs. Higher values of ALP activity and matrix mineralization analyses confirmed these results. Our study advocates that absence of EPCs in the MSC population enables higher osteogenic gene expression and matrix mineralization and therefore may lead to advanced bone neoformation necessary for TE constructs.

  4. A theory of traffic congestion at heavy bottlenecks

    International Nuclear Information System (INIS)

    Spatiotemporal features and physics of vehicular traffic congestion occurring due to heavy highway bottlenecks caused for example by bad weather conditions or accidents are found based on simulations in the framework of three-phase traffic theory. A model of a heavy bottleneck is presented. Under a continuous non-limited increase in bottleneck strength, i.e., when the average flow rate within a congested pattern allowed by the heavy bottleneck decreases continuously up to zero, the evolution of the traffic phases in congested traffic, synchronized flow and wide moving jams, is studied. It is found that at a small enough flow rate within the congested pattern, the pattern exhibits a non-regular structure: a pinch region of synchronized flow within the pattern disappears and appears randomly over time; wide moving jams upstream of the pinch region exhibit a complex non-regular dynamics in which the jams appear and disappear randomly. At greater bottleneck strengths, wide moving jams merge onto a mega-wide moving jam (mega-jam) within which low-speed patterns with a complex non-regular spatiotemporal dynamics occur. We show that when the bottleneck strength is great enough, only the mega-jam survives and synchronized flow remains only within its downstream front separating free flow and congested traffic. Theoretical results presented can explain why no sequence of wide moving jams can often be distinguished in non-homogeneous traffic congestion measured at very heavy bottlenecks caused by bad weather conditions or accidents

  5. Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon

    DEFF Research Database (Denmark)

    Tartally, András; Kelager, Andreas; Fürst, Matthias A.;

    2016-01-01

    The rare socially parasitic butterfly Maculinea alcon occurs in two forms, which are characteristic of hygric or xeric habitats and which exploit different host plants and host ants. The status of these two forms has been the subject of considerable controversy. Populations of the two forms are...... usually spatially distinct, but at R€scruci in Romania both forms occur on the same site (syntopically). We examined the genetic differentiation between the two forms using eight microsatellite markers, and compared with a nearby hygric site, fiardu. Our results showed that while the two forms are...... different host plants, each with a distinct flowering phenology, providing a temporal rather than spatial barrier to gene flow....

  6. Lack of population genetic differentiation of a marine ovoviviparous fish Sebastes schlegelii in Northwestern Pacific.

    Science.gov (United States)

    Zhang, Hui; Yanagimoto, Takashi; Zhang, Xiumei; Song, Na; Gao, Tianxiang

    2016-05-01

    Sebastes schlegelii is one of the fishes that aggregate around drifting seaweed during early development. To examine the population genetic structure of S. schlegelii, a 452-bp fragment of the mtDNA control region was sequenced and used to interpret life history characteristics and larval dispersal strategy. Two-hundred and twenty-one individuals from 13 sites across the entire range of S. schlegelii in China, Japan and Korea were analyzed. A neighbor-joining tree and network showed that there were no significant genealogical structures corresponding to sampling locations. AMOVA, pair-wise FST and exact test revealed no significant genetic differentiation among locations. The migration rate among locations was high based on the result of LAMARC. We conclude that larval dispersal with drifting seaweed and the current environmental factors may play an important role in shaping the contemporary phylogeographic pattern and genetic homogeneity of S. schlegelii. PMID:25269000

  7. Deep bottleneck features for spoken language identification.

    Directory of Open Access Journals (Sweden)

    Bing Jiang

    Full Text Available A key problem in spoken language identification (LID is to design effective representations which are specific to language information. For example, in recent years, representations based on both phonotactic and acoustic features have proven their effectiveness for LID. Although advances in machine learning have led to significant improvements, LID performance is still lacking, especially for short duration speech utterances. With the hypothesis that language information is weak and represented only latently in speech, and is largely dependent on the statistical properties of the speech content, existing representations may be insufficient. Furthermore they may be susceptible to the variations caused by different speakers, specific content of the speech segments, and background noise. To address this, we propose using Deep Bottleneck Features (DBF for spoken LID, motivated by the success of Deep Neural Networks (DNN in speech recognition. We show that DBFs can form a low-dimensional compact representation of the original inputs with a powerful descriptive and discriminative capability. To evaluate the effectiveness of this, we design two acoustic models, termed DBF-TV and parallel DBF-TV (PDBF-TV, using a DBF based i-vector representation for each speech utterance. Results on NIST language recognition evaluation 2009 (LRE09 show significant improvements over state-of-the-art systems. By fusing the output of phonotactic and acoustic approaches, we achieve an EER of 1.08%, 1.89% and 7.01% for 30 s, 10 s and 3 s test utterances respectively. Furthermore, various DBF configurations have been extensively evaluated, and an optimal system proposed.

  8. Ecological differentiation in planktonic and sediment-associated chemotrophic microbial populations in Yellowstone hot springs.

    Science.gov (United States)

    Colman, Daniel R; Feyhl-Buska, Jayme; Robinson, Kirtland J; Fecteau, Kristopher M; Xu, Huifang; Shock, Everett L; Boyd, Eric S

    2016-09-01

    Chemosynthetic sediment and planktonic community composition and sizes, aqueous geochemistry and sediment mineralogy were determined in 15 non-photosynthetic hot springs in Yellowstone National Park (YNP). These data were used to evaluate the hypothesis that differences in the availability of dissolved or mineral substrates in the bulk fluids or sediments within springs coincides with ecologically differentiated microbial communities and their populations. Planktonic and sediment-associated communities exhibited differing ecological characteristics including community sizes, evenness and richness. pH and temperature influenced microbial community composition among springs, but within-spring partitioning of taxa into sediment or planktonic communities was widespread, statistically supported (P < 0.05) and could be best explained by the inferred metabolic strategies of the partitioned taxa. Microaerophilic genera of the Aquificales predominated in many of the planktonic communities. In contrast, taxa capable of mineral-based metabolism such as S(o) oxidation/reduction or Fe-oxide reduction predominated in sediment communities. These results indicate that ecological differentiation within thermal spring habitats is common across a range of spring geochemistry and is influenced by the availability of dissolved nutrients and minerals that can be used in metabolism. PMID:27306555

  9. Genetic variation and differentiation in wide ranging populations of razor clam ( Sinonovacula constricta) inferred from AFLP markers

    Science.gov (United States)

    Wang, Jingbo; Li, Qi; Kong, Lingfeng

    2010-09-01

    The genetic variation and differentiation of the razor clam Sinonovacula constricta distributed along the coast of China were studied through amplified fragment length polymorphism (AFLP) analysis. Six primer combinations generated 193 fragments. The H e values varied from 0.322 to 0.463 and the percentage of polymorphic loci ranged from 74.1% to 98.4%, which indicates a high level of genetic diversity. Cluster analysis by Nei’s pairwise distance grouped all specimens by geographical origins. AMOVA consistently showed that genetic variation among populations was 8.71%, and most of the variation came from the genetic variation within populations (91.29%). Genetic differentiation among the six populations was moderate; pairwise F ST ranged from 0.0282 to 0.1480, which indicated that S. constricta populations along the coast of China are genetically connected. Among all the six populations, the Beihai population is the mostly differentiated from the others, suggesting that Hainan Island and Leizhou Peninsula act as barriers to gene flow. All populations abide isolation by distance model as indicated by Mantel test, except for ZS (Zhoushan) and YQ (Yueqing) populations. Information obtained in this study will provide guidelines for conservation and fishery management of this species in the future.

  10. [Genetic diversity and differentiation between populations of Glyptothorax zanaensis in the middle and lower reaches of the Nujiang River].

    Science.gov (United States)

    Liu, Shao-Ping; Wang, Ke; Yuan, Xi-Ping; Wang, Deng-Qiang; Yue, Xing-Jian; Chen, Da-Qing

    2010-03-01

    The development of hydroelectricity in the Nujiang River would have adverse impacts on the populations of Glyptothorax zanaensis. In order to assess the genetic diversity and differentiation of this species, we sequenced the cytochrome b gene of the mitochondria in 102 individuals of the fish collected from 6 sampling sites (Gongshan, Gudeng and Lushui in the Nujiang Prefectural District and Daojie, Mengnuo and Mucheng in the Baoshan Municipal District). A total of 87 variation sites were detected in the fragment of 1 137 bp in length, with which the 102 samples were defined as 36 haplotypes. The haplotype diversity (h) and the nucleotide diversity (pi) of total samples were 0.851+/-0.028 and 0.01356+/-0.0008, respectively. Therefore, the genetic diversity of G. zanaensis was relatively low. However, the genetic diversity of the Nujiang population was significantly higher than that of the Baoshan population. The pairwise Fst value between the populations (0.475-0.846) was higher than that within the population (0.002-0.108), which implied that the Fst value was positively related to geographic distance. Analysis of molecular variance (AMOVA) showed that the genetic differentiation between the populations and within the populations were 53.65% and 46.35%, respectively. The fixation index (Fst value) was 0.5365, indicating that there existed significant differentiation between the Nujiang population and the Baoshan population. The phylogentic tree and networks of the haplotypes of G. zanaensis showed that there were two separate lineages: the Nujiang lineage and the Baoshan lineage. Each lineage represents at least one separated management unit, or belongs to an evolutionary significant unit. It was suggested that in the construction of hydroelectric projects the measures for protecting G. zanaensis should be adopted in fully considering the populations of G. zanaensis and the status quo of their population structure to avoid the occurrence of gene exchange among

  11. Karyotype differentiation and reproductive isolation among natural populations of Drosophila lacertosa

    Institute of Scientific and Technical Information of China (English)

    LI PING HE; HIDE AKI WATABE; YA PING ZHANG; TADASHI AOTSUKA

    2003-01-01

    Drosophila lacertosa is widely distributed from northern India to Far East of Russia throughout China.We have studied geographical distributions of three kinds of chromosomal karyotypes,type D(2n=10,4 pairs of V-shaped metacentric chromosomes and a pair of micro-chromosomes),type L(2n= 10,5V with a pair of large-sized heterochromatic autosomes)and type M(2n=10,5V with middle-sized ones).Type D was found exclusively in local populations of D.lacertosa distributed in Yun-Gui Plateau,southwestern China.Both type L and M have a wide range of distribution,and the former occurred in subtropical regions of China including Taiwan Island,whereas the latter in cool temperate regions of East Asia covering Far East of Russia,Korea and the Japan Islands.A strong premating isolation was detected between flies with type D and those with type L or M.These data demonstrate that genetic differentiation leading to cryptic speciation might have occurred in natural populations of Drosophila lacertosa.

  12. Celebrity Suicides and Their Differential Influence on Suicides in the General Population: A National Population-Based Study in Korea

    OpenAIRE

    Myung, Woojae; Won, Hong-Hee; Fava, Maurizio; Mischoulon, David; Yeung, Albert; Lee, Dongsoo; Kim, Doh Kwan; Jeon, Hong Jin

    2015-01-01

    Objective: Although evidence suggests that there is an increase in suicide rates in the general population following celebrity suicide, the rates are heterogeneous across celebrities and countries. It is unclear which is the more vulnerable population according to the effect sizes of celebrity suicides to general population. Methods: All suicide victims in the general population verified by the Korea National Statistical Office and suicides of celebrity in South Korea were included for 7 year...

  13. Mapping enteroendocrine cell populations in transgenic mice reveals an unexpected degree of complexity in cellular differentiation within the gastrointestinal tract

    OpenAIRE

    1990-01-01

    The gastrointestinal tract is lined with a monolayer of cells that undergo perpetual and rapid renewal. Four principal, terminally differentiated cell types populate the monolayer, enterocytes, goblet cells, Paneth cells, and enteroendocrine cells. This epithelium exhibits complex patterns of regional differentiation, both from crypt- to-villus and from duodenum-to-colon. The "liver" fatty acid binding protein (L-FABP) gene represents a useful model for analyzing the molecular basis for intes...

  14. Systemic administration of RANKL overcomes the bottleneck of oral vaccine delivery through microfold cells in ileum.

    Science.gov (United States)

    Maharjan, Sushila; Singh, Bijay; Jiang, Tao; Yoon, So-Yeon; Li, Hui-Shan; Kim, Girak; Gu, Min Jeong; Kim, Soo Ji; Park, Ok-Jin; Han, Seung Hyun; Kang, Sang-Kee; Yun, Cheol-Heui; Choi, Yun-Jaie; Cho, Chong-Su

    2016-04-01

    A successful delivery of antigen through oral route requires to overcome several barriers, such as enzymatic barrier of gastrointestinal tract and epithelial barrier that constitutes of microfold cells (M cells) for antigen uptake. Although each barrier represents a critical step in determining the final efficiency of antigen delivery, the transcytosis of antigen by M cells in the follicle-associated epithelium (FAE) to Peyer's patches appears to be a major bottleneck. Considering the systemic administration of receptor activator of nuclear factor (NF)-ĸB ligand (RANKL) induces differentiation of receptor activator of nuclear factor (NF)-ĸB (RANK)-expressing enterocytes into M cells, here, we illustrated a promising approach of antigen delivery using full length transmembrane RANKL (mRANKL). The results showed that the intraperitoneal injection of mRANKL increased the population of dendritic cells and macrophages in mesenteric lymph nodes and spleen. Subsequently, systemic administration of mRANKL resulted in significantly higher number of functional GP2(+) M cells leading higher transcytosis of fluorescent beads through them. To corroborate the effect of mRANKL in antigen delivery through M cells, we orally delivered microparticulate antigen to mice treated with mRANKL. Oral immunization induced strong protective IgA and systemic IgG antibody responses against orally delivered antigen in mRANKL-treated mice. The higher antibody responses are attributed to the higher transcytosis of antigens through M cells. Ultimately, the higher memory B cells and effector memory CD4 T cells after oral immunization in RANKL-treated mice confirmed potency of RANKL-mediated antigen delivery. To the best of our knowledge, this is the first study to demonstrate significant induction of mucosal and humoral immune responses to M cell targeted oral vaccines after the systemic administration of RANKL. PMID:26851393

  15. Gene variation and genetic differentiation among populations of the solitary mud dauber wasp Trypoxylon (Trypargilum albitarse Fabricius 1804 (Hymenoptera, Crabronidae

    Directory of Open Access Journals (Sweden)

    Antonio C.B. Bergamaschi

    2015-01-01

    Full Text Available Abstract Trypoxylon is a genus of solitary crabronid wasps whose population genetics is poorly known. The purpose of the present study was to investigate the genetic variation and differentiation among five populations of Trypoxylon albitarse, a species widely distributed throughout the Neotropics, with records from Panama to northern Argentina. Eight species-specific microsatellite loci were used for genotyping 96 adult wasps (one female per nest sampled at five sites in Brazil. The analysis of allelic richness and private alleles indicated high genetic diversity in the populations sampled. Pairwise comparisons using the Fst and Dest indices revealed significant differentiation for all, but one pair of populations. Fst, Dest, AMOVA and assignment test values pointed to inter-population differentiation. Additionally, the analysis of population structure using Bayesian and PCA methods characterized two alternative genetic groups. The Mantel test indicated no correlation between genetic and geographic distances. Despite evidence of considerable dispersal capacity for T. albitarse, the data indicate low to moderate population structuring in this species.

  16. Bottleneck management in the German and European electricity supply

    International Nuclear Information System (INIS)

    This publication describes how bottlenecks in the German and European electricity supply pose a danger to the realization of the European internal market in electricity, the transition to electricity production from renewable resources and to the safeguarding of grid availability and security of supply. Bottlenecks at cross-border interconnectors between member states of the European Union are hampering cross-border trade in electricity, posing an impediment to EU-wide competition among electricity production and electricity trading companies. Grid bottlenecks at cross-border interconnectors isolate national markets from one another, with the result that it is not always possible in the European Union to have the most competitive power plant produce electricity. This amounts to a loss of welfare compared with what it would be in the case of an electricity supply without bottlenecks. Furthermore, bottlenecks make it impossible for green electricity that would be eligible for promotion for reasons of climate and environmental protection to be transmitted unimpeded from the most suitable site to the consumer regions. Thus the transmission of electricity produced from wind power in Northern Germany to the industrial centres in Southern Germany is impeded by bottlenecks along the north-south lines of the national transmission network. Today some of the German electricity supply networks already have to be operated near the limits of their capacity, especially during high wind episodes. This poses a growing danger to network availability and security of supply. Since the installation, expansion and conversion of electricity supply networks in Germany and other member states of the European Union is no longer progressing at the required speed, growing importance attaches to the management of bottlenecks. The goal of bottleneck management is to resolve conflicts over network use such as can occur in overload situations with as little discrimination and as little

  17. Optimizing Database Architecture for the New Bottleneck: Memory Access

    OpenAIRE

    Manegold, Stefan; Boncz, Peter; Kersten, Martin

    2000-01-01

    In the past decade, advances in speed of commodity CPUs have far out-paced advances in memory latency. Main-memory access is therefore increasingly a performance bottleneck for many computer applications, including database systems. In this article, we use a simple scan test to show the severe impact of this bottleneck. The insights gained are translated into guidelines for database architecture; in terms of both data structures and algorithms. We discuss how vertically fragmented data struct...

  18. Database architecture optimized for the new bottleneck: Memory access

    OpenAIRE

    Boncz, Peter; Manegold, Stefan; Kersten, Martin

    1999-01-01

    In the past decade, advances in speed of commodity CPUs have far out-paced advances in memory latency. Main-memory access is therefore increasingly a performance bottleneck for many computer applications, including database systems. In this article, we use a simple scan test to show the severe impact of this bottleneck. The insights gained are translated into guidelines for database architecture; in terms of both data structures and algorithms. We discuss how vertically fragmented data struct...

  19. Genetic diversity and differentiation of central European freshwater pearl mussel (Margaritifera margaritifera L.) populations: implications for conservation and management.

    Science.gov (United States)

    Geist, Juergen; Kuehn, Ralph

    2005-02-01

    Despite the fact that mollusc species play an important role in many aquatic ecosystems, little is known about their biodiversity and conservation genetics. Freshwater pearl mussel (Margaritifera margaritifera L.) populations are seriously declining all over Europe and a variety of conservation programs are being established to support the remaining endangered central European populations. In order to provide guidelines for conservation strategies and management programs, we investigated the genetic structure of 24 freshwater pearl mussel populations originating from five major central European drainages including Elbe, Danube, Rhine, Maas and Weser, representing the last and most important populations in this area. We present a nondestructive sampling method of haemolymph for DNA analyses, which is applicable for endangered bivalves. The analyses of nine microsatellite loci with different levels of polymorphism revealed a high degree of fragmented population structure and very different levels of genetic diversity within populations. These patterns can be explained by historical and demographic effects and have been enforced by anthropogenic activities. Even within drainages, distinct conservation units were detected, as revealed from high F(ST) values, private alleles and genetic distance measures. Populations sampled close to contact zones between main drainage systems showed lowest levels of correct assignment to present-day drainage systems. Populations with high priority for conservation should not only be selected by means of census population size and geographical distance to other populations. Instead, detailed genetic analyses are mandatory for revealing differentiation and diversity parameters, which should be combined with ecological criteria for sustainable conservation and recovery programs. PMID:15660935

  20. Multiple and differentiated contributions to the male gene pool of pastoral and farmer populations of the African Sahel.

    Science.gov (United States)

    Bučková, Jana; Cerný, Viktor; Novelletto, Andrea

    2013-05-01

    The African Sahel is conducive to studies of divergence/admixture genetic events as a result of its population history being so closely related with past climatic changes. Today, it is a place of the co-existence of two differing food-producing subsistence systems, i.e., that of sedentary farmers and nomadic pastoralists, whose populations have likely been formed from several dispersed indigenous hunter-gatherer groups. Using new methodology, we show here that the male gene pool of the extant populations of the African Sahel harbors signatures of multiple and differentiated contributions from different genetic sources. We also show that even if the Fulani pastoralists and their neighboring farmers share high frequencies of four Y chromosome subhaplogroups of E, they have drawn on molecularly differentiated subgroups at different times. These findings, based on combinations of SNP and STR polymorphisms, add to our previous knowledge and highlight the role of differences in the demographic history and displacements of the Sahelian populations as a major factor in the segregation of the Y chromosome lineages in Africa. Interestingly, within the Fulani pastoralist population as a whole, a differentiation of the groups from Niger is characterized by their high presence of R1b-M343 and E1b1b1-M35. Moreover, the R1b-M343 is represented in our dataset exclusively in the Fulani group and our analyses infer a north-to-south African migration route during a recent past. PMID:23460272

  1. Genetic differentiation and recombination among geographic populations of the fungal pathogen Colletotrichum truncatum from chili peppers in China.

    Science.gov (United States)

    Diao, Yongzhao; Zhang, Can; Xu, Jianping; Lin, Dong; Liu, Li; Mtung'e, Olivo G; Liu, Xili

    2015-01-01

    Colletotrichum truncatum is an extremely important fungal pathogen. It can cause diseases both in humans and in over 460 plant species. However, little is known about its genetic diversity within and among populations. One of the major plant hosts of C. truncatum is pepper, and China is one of the main pepper-producing countries in the world. Here, we propose the hypotheses that geography has a major influence on the relationships among populations of C. truncatum in China and that infections in different populations need to be managed differently. To test these hypotheses, we obtained and analyzed 266 C. truncatum isolates from 13 regions representing the main pepper-growing areas throughout China. The analysis based on nine microsatellite markers identified high intrapopulation genetic diversity, evidence of sexual recombination, and geographic differentiation. The genetic differentiation was positively correlated with geographic distance, with the southern and northern China populations grouped in two distinct clusters. Interestingly, isolates collected from the pepper-breeding center harbored the most private alleles. The results suggest that the geographic populations of C. truncatum on peppers in China are genetically differentiated and should be managed accordingly. Our study also provides a solid foundation from which to further explore the global genetic epidemiology of C. truncatum in both plants and humans. PMID:25667606

  2. Genetic differentiation among populations of the beetle Bolitophagus reticulatus (Coleoptera: tenebrionidae) in a fragmented and a continuous landscape.

    Science.gov (United States)

    Knutsen, H; Rukke, B A; Jorde, P E; Ims, R A

    2000-06-01

    The effect of habitat fragmentation on genetic differentiation among local populations of the fungivorous beetle Bolitophagus reticulatus (Coleoptera: Tenebrionidae) was studied in two contrasting landscapes: one heavily fragmented with forest fragments of variable size surrounded by inhabitable agricultural fields, the other an old forest providing a continuous habitat. The genetic structure of the beetle within each of the two contrasting areas was investigated by means of protein electrophoresis, screening four polymorphic loci in 20 populations from each area. In both areas there were significant genetic differences among local populations, but on average differentiation in the fragmented area was three times greater than in the continuous one, strongly indicating a genetic isolation effect of habitat fragmentation. These genetic results are in accordance with previous studies on dispersal in this species. PMID:10886382

  3. Genetic analysis of scattered populations of the Indian eri silkworm, Samia cynthia ricini Donovan: Differentiation of subpopulations.

    Science.gov (United States)

    Pradeep, Appukuttannair R; Jingade, Anuradha H; Singh, Choba K; Awasthi, Aravind K; Kumar, Vikas; Rao, Guruprasad C; Prakash, N B Vijaya

    2011-07-01

    Deforestation and exploitation has led to the fragmentation of habitats and scattering of populations of the economically important eri silkworm, Samia cynthia ricini, in north-east India. Genetic analysis of 15 eri populations, using ISSR markers, showed 98% inter-population, and 23% to 58% intra-population polymorphism. Nei's genetic distance between populations increased significantly with altitude (R(2) = 0.71) and geographic distance (R(2) = 0.78). On the dendrogram, the lower and upper Assam populations were clustered separately, with intermediate grouping of those from Barpathar and Chuchuyimlang, consistent with geographical distribution. The Nei's gene diversity index was 0.350 in total populations and 0.121 in subpopulations. The genetic differentiation estimate (Gst) was 0.276 among scattered populations. Neutrality tests showed deviation of 118 loci from Hardy-Weinberg equilibrium. The number of loci that deviated from neutrality increased with altitude (R(2) = 0.63). Test of linkage disequilibrium showed greater contribution of variance among eri subpopulations to total variance. D('2)IS exceeded D('2)ST, showed significant contribution of random genetic drift to the increase in variance of disequilibrium in subpopulations. In the Lakhimpur population, the peripheral part was separated from the core by a genetic distance of 0.260. Patchy habitats promoted low genetic variability, high linkage disequilibrium and colonization by new subpopulations. Increased gene flow and habitat-area expansion are required to maintain higher genetic variability and conservation of the original S. c. ricini gene pool. PMID:21931526

  4. Genetic Diversity and Differentiation in Urban and Indigenous Populations of Mexico: Patterns of Mitochondrial DNA and Y-Chromosome Lineages.

    Science.gov (United States)

    González-Sobrino, Blanca Z; Pintado-Cortina, Ana P; Sebastián-Medina, Leticia; Morales-Mandujano, Fabiola; Contreras, Alejandra V; Aguilar, Yasnaya E; Chávez-Benavides, Juan; Carrillo-Rodríguez, Aurelio; Silva-Zolezzi, Irma; Medrano-González, Luis

    2016-01-01

    Aside from the admixture between indigenous people and people from overseas, populations in Mexico changed drastically after the Spanish conquest of the sixteenth century, forming an intricate history that has been underutilized in understanding the genetic population structure of Mexicans. To infer historical processes of isolation, dispersal, and assimilation, we examined the phylogeography of mitochondrial (mt) DNA and Y-chromosome lineages in 3,026 individuals from 10 urban and nine indigenous populations by identifying single nucleotide polymorphisms. A geographic array with a predominance of Amerindian lineages was observed for mtDNA, with northern indigenous populations being divergent from the central and southern indigenous populations; urban populations showed low differentiation with isolation by distance. Y-chromosome variation distinguished urban and indigenous populations through the Amerindian haplogroup Q frequency. The MtDNA and the Y-chromosome together primarily distinguished urban and indigenous populations, with different geographic arrays for both. Gene flow across geographical distance and between the urban and indigenous realms appears to have altered the pre-Hispanic phylogeography in central and southern Mexico, mainly by displacement of women, while maintaining the indigenous isolation in the north, southeast, and Zapotec regions. Most Amerindian mtDNA diversity currently occurs in urban populations and appears to be reduced among indigenous people. PMID:27050033

  5. Steady State of Pedestrian Flow in Bottleneck Experiments

    CERN Document Server

    Liao, Weichen; Seyfried, Armin; Chraibi, Mohcine; Drzycimski, Kevin; Zheng, Xiaoping; Zhao, Ying

    2015-01-01

    Experiments with pedestrians could depend strongly on initial conditions. Comparisons of the results of such experiments require to distinguish carefully between transient state and steady state. In this work, a feasible algorithm - Cumulative Sum Control Chart - is proposed and improved to automatically detect steady states from density and speed time series of bottleneck experiments. The threshold of the detection parameter in the algorithm is calibrated using an autoregressive model. Comparing the detected steady states with previous manually selected ones, the modified algorithm gives more reproducible results. For the applications, three groups of bottleneck experiments are analysed and the steady states are detected. The study about pedestrian flow shows that the difference between the flows in all states and in steady state mainly depends on the ratio of pedestrian number to bottleneck width. When the ratio is higher than a critical value (approximately 115 persons/m), the flow in all states is almost ...

  6. Research of Cruise Industry Development Bottlenecks In China

    Directory of Open Access Journals (Sweden)

    Ping Zhou

    2014-08-01

    Full Text Available Cruise industry is a comprehensive new industry, which has a strong impetus to the development of other industries. In recent years, as the explosive growth in cruise market, China has become a global rapidly-growing emerging cruise market. The cruise industry has begun transiting from infancy to the development phase, in all likelihood facing a number of bottlenecks problem. In this paper, the development trend of the cruise industry is first analyzed, then the bottlenecks of cruise industry are studied and finally some reasonable countermeasures and suggestions are put forward. By perfecting policy and legal, expanding industrial chain, diversifying investment mode, cultivating the market of consumer subjects, and establishing a scientific talents training mode of enterprise, the bottlenecks of cruise industry can be solved. This will consequently promote healthy and rapid development in cruise tourism industry, and give full play to the role of joint economy.

  7. Isoenzymatic differentiation in putative hybrid swarm population (Pinus mugo Turra x P. sylvestris L. from "Torfowisko Zieleniec" peat-bog

    Directory of Open Access Journals (Sweden)

    Anna Siedlewska

    2014-02-01

    Full Text Available Isoenzyme variability of eight groups of individuals from different parts of putative hybrid swarm population (P. mugo Turra x P. sylvestris L. from "Torfowisko Zieleniec" peat-bog complex was studied at ten enzymatic loci. Differences in allelic frequencies distribution among particular samples of the Zieleniec population were statistically significant at 9 loci, as shown by G2- statistics. Chi-square test indicated that in each of studied subpopulations frequencies of alleles at some loci (2-5 differed significantly from frequencies expected for a homogeneous population. Heterozygosity values and also a genotypic polymorphism in studied population confirmed the existence of large genetic variation. Wright's fixation indices (F showed some excess of homozygotes in majority studied groups of individuals, notably higher in some subpopulations. Gene diversity coefficient for 8 subpopulations was high (GST=9.4%. However, when MDH C locus was excluded from the calculation, its value decreased to 2.8%. Presented data demonstrated notable differentiation of subpopulations within studied pine population, comparable with the differentiation among different populations of coniferous species.

  8. Bottleneck Paths and Trees and Deterministic Graphical Games

    OpenAIRE

    Chechik, Shiri; Kaplan, Haim; Thorup, Mikkel; Zamir, Or; Zwick, Uri

    2016-01-01

    Gabow and Tarjan showed that the Bottleneck Path (BP) problem, i.e., finding a path between a given source and a given target in a weighted directed graph whose largest edge weight is minimized, as well as the Bottleneck spanning tree (BST) problem, i.e., finding a directed spanning tree rooted at a given vertex whose largest edge weight is minimized, can both be solved deterministically in O(m * log^*(n)) time, where m is the number of edges and n is the number of vertices in the graph. We p...

  9. The "Bottleneck" Behaviours in Linear FNNCs and Their Breakthrough

    Institute of Scientific and Technical Information of China (English)

    HUANG Deshuang

    1999-01-01

    The classification mechanisms of linear feed forward neural network classifiers (FNNC), whose hidden layer performs the Fisher lineartrans formation of the input patterns, under the supervision of outer-supervised signals are investigated. The "bottleneck" behavioursin linear FNNCs are observed and analyzed. In addition, the structure stabilities of the linear FNNCs are also discussed. It is pointed out that the key point to break through the "bottleneck" behaviours forlinear FNNCs is to change linear hidden neurons into nonlinear hiddenones. Finally, the experimental results, taking the parity 3 problem asexample, are given.

  10. Fast Approximation Algorithm for Restricted Euclidean Bottleneck Steiner Tree Problem

    Directory of Open Access Journals (Sweden)

    Zimao Li

    2014-04-01

    Full Text Available Bottleneck Steiner tree problem asks to find a Steiner tree for n terminals with at most k Steiner points such that the length of the longest edge in the tree is minimized. The problem has applications in the design of wireless communication networks. In this paper we study a restricted version of the bottleneck Steiner tree problem in the Euclidean plane which requires that only degree-2 Steiner points are possibly adjacent in the optimal solution. We first show that the problem is NP-hard and cannot be approximated within unless P=NP, and provide a fast polynomial time deterministic approximation algorithm with performance ratio .

  11. GENETIC DIFFERENTIATION BETWEEN NOBLE CRAYFISH, ASTACUS ASTACUS (L., POPULATIONS DETECTED BY MICROSATELLITE LENGTH VARIATION IN THE RDNA ITS1 REGION

    Directory of Open Access Journals (Sweden)

    EDSMAN L.

    2002-07-01

    Full Text Available The Internal Transcribed Spacer (ITS region of the nuclear ribosomal repeat was investigated in the search for a suitable genetic marker for population studies of the noble crayfish Astacus astacus (L.. DNA sequencing revealed the presence of two microsatellite insertions in ITS1. By designing highly specific PCR primers, adjacent to one of the insertions, we were able to use fragment analysis to explore the variation of the insertion in 642 specimens from 17 populations of crayfish from Sweden and former Yugoslavia. A new statistical test, the Population Divergence Test, was developed to assess statistical significance of divergence between populations. This test does not assume Mendelian inheritance. Our results demonstrate that different populations often produce characteristic fragment patterns, and that most, but not all, populations are genetically distinct, with high significance. The populations that cannot be significantly differentiated are situated in close geographic proximity to each other and belong to the same main river system, probably reflecting that these populations have had recent contact and that gene flow has occurred.

  12. Demographic history and asynchronous spawning shape genetic differentiation among populations of the hard coral Acropora tenuis in Western Australia.

    Science.gov (United States)

    Rosser, Natalie L

    2016-05-01

    Genetic subdivision within populations can ultimately lead to the evolution of new species, and in populations of broadcast-spawners a potential facilitator of genetic subdivision is asynchronous reproduction. However, the factors that shape genetic variation in marine systems are complex and ambiguous, and ecological genetic structure may be influenced by the overriding signature of past demographic events. Here, the relative roles of the timing of reproduction and historical geography on the partitioning of genetic variation were examined in seven populations of the broadcast-spawning coral Acropora tenuis over 12° of latitude. The analysis of multiple loci (mitochondrial control region, two nuclear introns and six microsatellites) revealed significant genetic division between the most northern reef and all other reefs, suggesting that WA reefs were re-colonized from two different sources after the Pleistocene glaciation. Accompanying this pattern was significant genetic differentiation associated with different breeding seasons (spring and autumn), which was greatest in PaxC, in which there were two divergent lineages (ΦST=0.98). This is the second study to find divergent clades of PaxC associated with spring and autumn spawners, strengthening the suggestion of some selective connection to timing of reproduction in corals. This study reiterates the need to incorporate reproductive timing into population genetic studies of corals because it facilitates genetic differentiation; however, careful analysis of population genetic data is required to separate ecological and evolutionary processes. PMID:26876640

  13. Effect of anthropogenic landscape features on population genetic differentiation of Przewalski's gazelle: main role of human settlement.

    Directory of Open Access Journals (Sweden)

    Ji Yang

    Full Text Available Anthropogenic landscapes influence evolutionary processes such as population genetic differentiation, however, not every type of landscape features exert the same effect on a species, hence it is necessary to estimate their relative effect for species management and conservation. Przewalski's gazelle (Procapra przewalskii, which inhabits a human-altered area on Qinghai-Tibet Plateau, is one of the most endangered antelope species in the world. Here, we report a landscape genetic study on Przewalski's gazelle. We used skin and fecal samples of 169 wild gazelles collected from nine populations and thirteen microsatellite markers to assess the genetic effect of anthropogenic landscape features on this species. For comparison, the genetic effect of geographical distance and topography were also evaluated. We found significant genetic differentiation, six genetic groups and restricted dispersal pattern in Przewalski's gazelle. Topography, human settlement and road appear to be responsible for observed genetic differentiation as they were significantly correlated with both genetic distance measures [F(ST/(1-F(ST and F'(ST/(1-F'(ST] in Mantel tests. IBD (isolation by distance was also inferred as a significant factor in Mantel tests when genetic distance was measured as F(ST/(1-F(ST. However, using partial Mantel tests, AIC(c calculations, causal modeling and AMOVA analysis, we found that human settlement was the main factor shaping current genetic differentiation among those tested. Altogether, our results reveal the relative influence of geographical distance, topography and three anthropogenic landscape-type on population genetic differentiation of Przewalski's gazelle and provide useful information for conservation measures on this endangered species.

  14. The Case for a Gaian Bottleneck: The Biology of Habitability.

    Science.gov (United States)

    Chopra, Aditya; Lineweaver, Charles H

    2016-01-01

    The prerequisites and ingredients for life seem to be abundantly available in the Universe. However, the Universe does not seem to be teeming with life. The most common explanation for this is a low probability for the emergence of life (an emergence bottleneck), notionally due to the intricacies of the molecular recipe. Here, we present an alternative Gaian bottleneck explanation: If life emerges on a planet, it only rarely evolves quickly enough to regulate greenhouse gases and albedo, thereby maintaining surface temperatures compatible with liquid water and habitability. Such a Gaian bottleneck suggests that (i) extinction is the cosmic default for most life that has ever emerged on the surfaces of wet rocky planets in the Universe and (ii) rocky planets need to be inhabited to remain habitable. In the Gaian bottleneck model, the maintenance of planetary habitability is a property more associated with an unusually rapid evolution of biological regulation of surface volatiles than with the luminosity and distance to the host star. PMID:26789354

  15. The bottleneck may be the solution, not the problem.

    Science.gov (United States)

    Lotem, Arnon; Kolodny, Oren; Halpern, Joseph Y; Onnis, Luca; Edelman, Shimon

    2016-01-01

    As a highly consequential biological trait, a memory "bottleneck" cannot escape selection pressures. It must therefore co-evolve with other cognitive mechanisms rather than act as an independent constraint. Recent theory and an implemented model of language acquisition suggest that a limit on working memory may evolve to help learning. Furthermore, it need not hamper the use of language for communication. PMID:27562516

  16. Differential marking, investigation and motor activity in presence of conspecific odours differing on their population of origin in bank voles

    Directory of Open Access Journals (Sweden)

    Geraldine Verplancke

    2011-06-01

    Full Text Available Odours emitted by rodent species convey cues about their overall body conditions and provide valuable information intervening in many aspects of their social relationships such as territorial and mating activities. Although bank vole is one of the primary models for studying chemical communication in wild rodents, literature is scarce about its reactivity to odours of conspecifics from its population compared to those of conspecifics from a different population. Here we tested the effect of the population of origin on the behaviour of wild bank voles (Myodes glareolus through 30min tests in laboratory. We observed both males and females differential marking (i.e. by urine or glandular secretions, motor activity and investigation (i.e. sniffing events in presence of conspecific whole body odours coming from either the Same Population of Origin (SPO or from a Different Population of Origin (DPO. Our results showed that both male and female bank voles react differently to odours of conspecifics according to the population of origin of the latter. Both motor activity and marking were more important when voles were confronted to odours from DPO donors than SPO ones. These effects were independent of the sex of the subjects. Moreover, male subjects tended to investigate more odours from DPO conspecifics than odours from SPO ones. Causes underlying apparent between-populations differences in the bank voles' body odours are discussed.

  17. High genetic differentiation of Aegla longirostri (Crustacea, Decapoda, Anomura) populations in southern Brazil revealed by multi-loci microsatellite analysis.

    Science.gov (United States)

    Bartholomei-Santos, M L; Roratto, P A; Santos, S

    2011-01-01

    Species with a broad distribution rarely have the same genetic make-up throughout their entire range. In some cases, they may constitute a cryptic complex consisting of a few species, each with a narrow distribution, instead of a single-, widely distributed species. These differences can have profound impacts for biodiversity conservation planning. The genetic differentiation of four populations of Aegla longirostri, a freshwater crab found in two geographically isolated basins in Rio Grande do Sul State, Brazil, was investigated by analyzing pentanucleotide multi-loci microsatellites in a heteroduplex assay. Although no morphological differences were evident, we found significant genetic differentiation among the four populations, based on F(ST) values and clustering analysis. This high level of differentiation may be indicative of cryptic species in these populations. If this hypothesis is correct, then the species occurring in the Ibicuí-Mirim River, at the southern limit of the Atlantic Rain Forest, would be under threat, considering its very restricted distribution. PMID:22179994

  18. Population differentiation in a Mediterranean relict shrub: the potential role of local adaptation for coping with climate change.

    Science.gov (United States)

    Lázaro-Nogal, Ana; Matesanz, Silvia; Hallik, Lea; Krasnova, Alisa; Traveset, Anna; Valladares, Fernando

    2016-04-01

    Plants can respond to climate change by either migrating, adapting to the new conditions or going extinct. Relict plant species of limited distribution can be especially vulnerable as they are usually composed of small and isolated populations, which may reduce their ability to cope with rapidly changing environmental conditions. The aim of this study was to assess the vulnerability of Cneorum tricoccon L. (Cneoraceae), a Mediterranean relict shrub of limited distribution, to a future drier climate. We evaluated population differentiation in functional traits related to drought tolerance across seven representative populations of the species' range. We measured morphological and physiological traits in both the field and the greenhouse under three water availability levels. Large phenotypic differences among populations were found under field conditions. All populations responded plastically to simulated drought, but they differed in mean trait values as well as in the slope of the phenotypic response. Particularly, dry-edge populations exhibited multiple functional traits that favored drought tolerance, such as more sclerophyllous leaves, strong stomatal control but high photosynthetic rates, which increases water use efficiency (iWUE), and an enhanced ability to accumulate sugars as osmolytes. Although drought decreased RGR in all populations, this reduction was smaller for populations from the dry edge. Our results suggest that dry-edge populations of this relict species are well adapted to drought, which could potentially mitigate the species' extinction risk under drier scenarios. Dry-edge populations not only have a great conservation value but can also change expectations from current species' distribution models. PMID:26662734

  19. Significant genetic differentiation among populations of Anomalocardia brasiliana (Gmelin, 1791: a bivalve with planktonic larval dispersion

    Directory of Open Access Journals (Sweden)

    Cinthya Cristina Bulhões Arruda

    2009-01-01

    Full Text Available Four Brazilian populations of Anomalocardia brasiliana were tested for mutual genetic homogeneity, using data from 123 sequences of the mtDNA cytochrome oxidase c subunit I gene. A total of 36 haplotypes were identified, those shared being H3 (Canela Island, Prainha and Acupe and both H5 and H9 (Prainha and Acupe. Haplotype diversity values were high, except for the Camurupim population, whereas nucleotide values were low in all the populations, except for that of Acupe. Only the Prainha population showed a deviation from neutrality and the SSD test did not reject the demographic expansion hypothesis. Fst values showed that the Prainha and Acupe populations represent a single stock, whereas in both the Canela Island and Camurupim stocks, population structures are different and independent. The observed structure at Canela Island may be due to the geographic distance between this population and the remainder. The Camurupim population does not share any haplotype with the remaining populations in northeastern Brazil. The apparent isolation could be due to the rocky barrier located facing the mouth of the Mamanguape River. The results highlight the importance of wide-scale studies to identify and conserve local genetic diversity, especially where migration is restricted.

  20. Population stochastic modelling (PSM)--an R package for mixed-effects models based on stochastic differential equations.

    Science.gov (United States)

    Klim, Søren; Mortensen, Stig Bousgaard; Kristensen, Niels Rode; Overgaard, Rune Viig; Madsen, Henrik

    2009-06-01

    The extension from ordinary to stochastic differential equations (SDEs) in pharmacokinetic and pharmacodynamic (PK/PD) modelling is an emerging field and has been motivated in a number of articles [N.R. Kristensen, H. Madsen, S.H. Ingwersen, Using stochastic differential equations for PK/PD model development, J. Pharmacokinet. Pharmacodyn. 32 (February(1)) (2005) 109-141; C.W. Tornøe, R.V. Overgaard, H. Agersø, H.A. Nielsen, H. Madsen, E.N. Jonsson, Stochastic differential equations in NONMEM: implementation, application, and comparison with ordinary differential equations, Pharm. Res. 22 (August(8)) (2005) 1247-1258; R.V. Overgaard, N. Jonsson, C.W. Tornøe, H. Madsen, Non-linear mixed-effects models with stochastic differential equations: implementation of an estimation algorithm, J. Pharmacokinet. Pharmacodyn. 32 (February(1)) (2005) 85-107; U. Picchini, S. Ditlevsen, A. De Gaetano, Maximum likelihood estimation of a time-inhomogeneous stochastic differential model of glucose dynamics, Math. Med. Biol. 25 (June(2)) (2008) 141-155]. PK/PD models are traditionally based ordinary differential equations (ODEs) with an observation link that incorporates noise. This state-space formulation only allows for observation noise and not for system noise. Extending to SDEs allows for a Wiener noise component in the system equations. This additional noise component enables handling of autocorrelated residuals originating from natural variation or systematic model error. Autocorrelated residuals are often partly ignored in PK/PD modelling although violating the hypothesis for many standard statistical tests. This article presents a package for the statistical program R that is able to handle SDEs in a mixed-effects setting. The estimation method implemented is the FOCE(1) approximation to the population likelihood which is generated from the individual likelihoods that are approximated using the Extended Kalman Filter's one-step predictions. PMID:19268387

  1. Genetic differentiation in red-bellied piranha populations (Pygocentrus nattereri, Kner, 1858) from the Solimões-Amazonas River.

    Science.gov (United States)

    Dos Santos, Carlos Henrique Dos A; de Sá Leitão, Carolina S; Paula-Silva, Maria de N; Almeida-Val, Vera Maria F

    2016-06-01

    Red-bellied piranhas (Pygocentrus nattereri) are widely caught with different intensities throughout the region of Solimões-Amazonas River by local fishermen. Thus, the management of this resource is performed in the absence of any information on its genetic stock. P. nattereri is a voracious predator and widely distributed in the Neotropical region, and it is found in other regions of American continent. However, information about genetic variability and structure of wild populations of red-bellied piranha is unavailable. Here, we describe the levels of genetic diversity and genetic structure of red-bellied piranha populations collected at different locations of Solimões-Amazonas River system. We collected 234 red-bellied piranhas and analyzed throughout eight microsatellite markers. We identified high genetic diversity within populations, although the populations of lakes ANA, ARA, and MAR have shown some decrease in their genetic variability, indicating overfishing at these communities. Was identified the existence of two biological populations when the analysis was taken altogether at the lakes of Solimões-Amazonas River system, with significant genetic differentiation between them. The red-bellied piranha populations presented limited gene flow between two groups of populations, which were explained by geographical distance between these lakes. However, high level of gene flow was observed between the lakes within of the biological populations. We have identified high divergence between the Catalão subpopulation and all other subpopulations. We suggest the creation of sustainable reserve for lakes near the city of Manaus to better manage and protect this species, whose populations suffer from both extractive and sport fishing. PMID:27516875

  2. Genome size differentiates co-occurring populations of the planktonic diatom Ditylum brightwellii (Bacillariophyta

    Directory of Open Access Journals (Sweden)

    von Dassow Peter

    2010-01-01

    Full Text Available Abstract Background Diatoms are one of the most species-rich groups of eukaryotic microbes known. Diatoms are also the only group of eukaryotic micro-algae with a diplontic life history, suggesting that the ancestral diatom switched to a life history dominated by a duplicated genome. A key mechanism of speciation among diatoms could be a propensity for additional stable genome duplications. Across eukaryotic taxa, genome size is directly correlated to cell size and inversely correlated to physiological rates. Differences in relative genome size, cell size, and acclimated growth rates were analyzed in isolates of the diatom Ditylum brightwellii. Ditylum brightwellii consists of two main populations with identical 18s rDNA sequences; one population is distributed globally at temperate latitudes and the second appears to be localized to the Pacific Northwest coast of the USA. These two populations co-occur within the Puget Sound estuary of WA, USA, although their peak abundances differ depending on local conditions. Results All isolates from the more regionally-localized population (population 2 possessed 1.94 ± 0.74 times the amount of DNA, grew more slowly, and were generally larger than isolates from the more globally distributed population (population 1. The ITS1 sequences, cell sizes, and genome sizes of isolates from New Zealand were the same as population 1 isolates from Puget Sound, but their growth rates were within the range of the slower-growing population 2 isolates. Importantly, the observed genome size difference between isolates from the two populations was stable regardless of time in culture or the changes in cell size that accompany the diatom life history. Conclusions The observed two-fold difference in genome size between the D. brightwellii populations suggests that whole genome duplication occurred within cells of population 1 ultimately giving rise to population 2 cells. The apparent regional localization of population 2 is

  3. Locally adapted fish populations maintain small-scale genetic differentiation despite perturbation by a catastrophic flood event

    Directory of Open Access Journals (Sweden)

    Plath Martin

    2010-08-01

    Full Text Available Abstract Background Local adaptation to divergent environmental conditions can promote population genetic differentiation even in the absence of geographic barriers and hence, lead to speciation. Perturbations by catastrophic events, however, can distort such parapatric ecological speciation processes. Here, we asked whether an exceptionally strong flood led to homogenization of gene pools among locally adapted populations of the Atlantic molly (Poecilia mexicana, Poeciliidae in the Cueva del Azufre system in southern Mexico, where two strong environmental selection factors (darkness within caves and/or presence of toxic H2S in sulfidic springs drive the diversification of P. mexicana. Nine nuclear microsatellites as well as heritable female life history traits (both as a proxy for quantitative genetics and for trait divergence were used as markers to compare genetic differentiation, genetic diversity, and especially population mixing (immigration and emigration before and after the flood. Results Habitat type (i.e., non-sulfidic surface, sulfidic surface, or sulfidic cave, but not geographic distance was the major predictor of genetic differentiation. Before and after the flood, each habitat type harbored a genetically distinct population. Only a weak signal of individual dislocation among ecologically divergent habitat types was uncovered (with the exception of slightly increased dislocation from the Cueva del Azufre into the sulfidic creek, El Azufre. By contrast, several lines of evidence are indicative of increased flood-induced dislocation within the same habitat type, e.g., between different cave chambers of the Cueva del Azufre. Conclusions The virtual absence of individual dislocation among ecologically different habitat types indicates strong natural selection against migrants. Thus, our current study exemplifies that ecological speciation in this and other systems, in which extreme environmental factors drive speciation, may be little

  4. Reproductive Allochrony in Seasonally Sympatric Populations Maintained by Differential Response to Photoperiod: Implications for Population Divergence and Response to Climate Change.

    Science.gov (United States)

    Fudickar, Adam M; Greives, Timothy J; Atwell, Jonathan W; Stricker, Craig A; Ketterson, Ellen D

    2016-04-01

    Reproductive allochrony presents a potential barrier to gene flow and is common in seasonally sympatric migratory and sedentary birds. Mechanisms mediating reproductive allochrony can influence population divergence and the capacity of populations to respond to environmental change. We asked whether reproductive allochrony in seasonally sympatric birds results from a difference in response to supplementary or photoperiodic cues and whether the response varies in relation to the distance separating breeding and wintering locations as measured by stable isotopes. We held seasonally sympatric migratory and sedentary male dark-eyed juncos (Junco hyemalis) in a common garden in early spring under simulated natural changes in photoperiod and made measurements of reproductive and migratory physiology. On the same dates and photoperiods, sedentary juncos had higher testosterone (initial and gonadotropin-releasing hormone induced), more developed cloacal protuberances, and larger testes than migrants. In contrast, migratory juncos had larger fat reserves (fuel for migration). We found a negative relationship between testis mass and feather hydrogen isotope ratios, indicating that testis growth was more delayed in migrants making longer migrations. We conclude that reproductive allochrony in seasonally sympatric migratory and sedentary birds can result from a differential response to photoperiodic cues in a common garden, and as a result, gene flow between migrants and residents may be reduced by photoperiodic control of reproductive development. Further, earlier breeding in response to future climate change may currently be constrained by differential response to photoperiodic cues. PMID:27028072

  5. Low biochemical variability in European fallow deer (Dama dama L.): natural bottlenecks and the effects of domestication.

    Science.gov (United States)

    Randi, E; Apollonio, M

    1988-12-01

    Tissue and blood samples from 180 fallow deer (Dama dama L.) belonging to an Italian free-ranging population were studied for biochemical variability by means of cellulose acetate and polyacrylamide gel electrophoresis. The 51 putative genetic loci successfully resolved showed a very low level of variability (P = 0.020, H = 0.006) in accordance with previously reported data on British and West German populations. That low biochemical polymorphism in European fallow deer populations is discussed taking into account the effects of natural bottlenecks and of domestication. PMID:3230030

  6. Genomic diversity and differentiation of a managed island wild boar population

    DEFF Research Database (Denmark)

    Iacolina, Laura; Scandura, Massimo; J. Goedbloed, Daniel;

    2016-01-01

    The evolution of island populations in natural systems is driven by local adaptation and genetic drift. However, evolutionary pathways may be altered by humans in several ways. The wild boar (WB) (Sus scrofa) is an iconic game species occurring in several islands, where it has been strongly managed...... (small ROHs) and recent population substructuring (highly homozygous individuals). The observed effect of a non-random selection of Sardinian individuals on diversity, FST and ROH estimates, stressed the importance of sampling design in the study of structured or introgressed populations. Our results...

  7. A novel population of local pericyte precursor cells in tumor stroma that require Notch signaling for differentiation.

    Science.gov (United States)

    Patenaude, Alexandre; Woerher, Stefan; Umlandt, Patricia; Wong, Fred; Ibrahim, Rawa; Kyle, Alastair; Unger, Sandy; Fuller, Megan; Parker, Jeremy; Minchinton, Andrew; Eaves, Connie J; Karsan, Aly

    2015-09-01

    Pericytes are perivascular support cells, the origin of which in tumor tissue is not clear. Recently, we identified a Tie1(+) precursor cell that differentiates into vascular smooth muscle, in a Notch-dependent manner. To understand the involvement of Notch in the ontogeny of tumor pericytes we used a novel flow immunophenotyping strategy to define CD146(+)/CD45(-)/CD31(-/lo) pericytes in the tumor stroma. This strategy combined with ex vivo co-culture experiments identified a novel pericyte progenitor cell population defined as Sca1(hi)/CD146(-)/CD45(-)/CD31(-). The differentiation of these progenitor cells was stimulated by co-culture with endothelial cells. Overexpression of the Notch ligand Jagged1 in endothelial cells further stimulated the differentiation of Sca1(hi)/CD146(-)/CD45(-)/CD31(-) cells into pericytes, while inhibition of Notch signaling with a γ-secretase inhibitor reduced this differentiation. However, Notch inhibition specifically in Tie1-expressing cells did not change the abundance of pericytes in tumors, suggesting that the pericyte precursor is distinct from the vascular smooth muscle cell precursor. Transplant experiments showed that the bone marrow contributes minimally to tumor pericytes. Immunophenotyping revealed that Sca1(hi)/CD146(-)/CD45(-)/CD31(-) cells have greater potential to differentiate into pericytes and have increased expression of classic mesenchymal stem cell markers (CD13, CD44, Nt5e and Thy-1) compared to Sca1(-/lo)/CD146(-)/CD45(-)/CD31(-) cells. Our results suggest that a local Sca1(hi)/CD146(-)/CD45(-)/CD31(-) pericyte progenitor resides in the tumor microenvironment and requires Notch signaling for differentiation into mature pericytes. PMID:26092680

  8. Population differentiation of the Chagas disease vector Triatoma maculata (Erichson, 1848) from Colombia and Venezuela.

    Science.gov (United States)

    Monsalve, Yoman; Panzera, Francisco; Herrera, Leidi; Triana-Chávez, Omar; Gómez-Palacio, Andrés

    2016-06-01

    The emerging vector of Chagas disease, Triatoma maculata (Hemiptera, Reduviidae), is one of the most widely distributed Triatoma species in northern South America. Despite its increasing relevance as a vector, no consistent picture of the magnitude of genetic and phenetic diversity has yet been developed. Here, several populations of T. maculata from eleven Colombia and Venezuela localities were analyzed based on the morphometry of wings and the mitochondrial NADH dehydrogenase subunit 4 (ND4) gene sequences. Our results showed clear morphometric and genetic differences among Colombian and Venezuelan populations, indicating high intraspecific diversity. Inter-population divergence is suggested related to East Cordillera in Colombia. Analyses of other populations from Colombia, Venezuela, and Brazil from distinct eco-geographic regions are still needed to understand its systematics and phylogeography as well as its actual role as a vector of Chagas disease. PMID:27232127

  9. [Genetic Differentiation of Populations of Baikal Endemic Sergentia baicalensis Tshern. (Diptera, Chironomidae)].

    Science.gov (United States)

    Kravtsova, L S; Bukin, Yu S; Peretolchina, T E; Shcherbakov, D Yu

    2015-07-01

    The population structure of endemic species Sergentia baicalensis (Diptera, Chironomidae) from Lake Baikal was studied using the first subunit of the cytochrome C oxidase mitochondrial gene (Col). Two populations inhabiting different basins of this lake, the southern-central and northern, were detected. It was confirmed that the divergence time of this species was dated to Late Miocene (9.53 ± 3.9 Mya), during the period when geographically separated basins existed in the Baikal rift zone. PMID:26410937

  10. Aging and differentiation in yeast populations: elders with different properties and functions

    Czech Academy of Sciences Publication Activity Database

    Palková, Z.; Wilkinson, D.; Váchová, Libuše

    2014-01-01

    Roč. 14, č. 1 (2014), s. 96-108. ISSN 1567-1356 R&D Projects: GA ČR GA13-08605S Institutional support: RVO:61388971 Keywords : yeast colonies * stationary-phase liquid cultures * comparison of differentiated cell subpopulations Subject RIV: EE - Microbiology, Virology Impact factor: 2.818, year: 2014

  11. Building the mammalian testis: origins, differentiation, and assembly of the component cell populations

    OpenAIRE

    Svingen, Terje; Koopman, Peter

    2013-01-01

    Testis development in the mammalian embryo requires the formation and assembly of several cell types that allow these organs to achieve their roles in male reproduction and endocrine regulation. In this review, Svingen and Koopman focus on the issues of cell differentiation and development of the testis architecture and highlight the questions that remain to be explored.

  12. Towards a microscopic understanding of the phonon bottleneck

    Science.gov (United States)

    Garanin, D. A.

    2007-03-01

    The problem of the phonon bottleneck in the relaxation of two-level systems (spins) to a narrow group of resonant phonons via emission-absorption processes is investigated from first principles. It is shown that the kinetic approach based on the Pauli master equation is invalid because of the narrow distribution of the phonons exchanging their energy with the spins. This results in a long-memory effect that can be best taken into account by introducing an additional dynamical variable corresponding to the nondiagonal matrix elements responsible for spin-phonon correlation. The resulting system of dynamical equations describes the phonon-bottleneck plateau in the spin excitation, as well as a gap in the spin-phonon spectrum, for any finite concentration of spins. On the other hand, it does not accurately render the line shape of emitted phonons and still needs improving.

  13. Nearly Optimal Solution for Restricted Euclidean Bottleneck Steiner Tree Problem

    Directory of Open Access Journals (Sweden)

    Zimao Li

    2014-04-01

    Full Text Available A variation of the traditional Steiner tree problem, the bottleneck Steiner tree problem is considered in this paper, which asks to find a Steiner tree for n terminals with at most k Steiner points such that the length of the longest edge in the tree is minimized. The problem has applications in the design of WDM optical networks, design of wireless communication networks and reconstruction of phylogenetic tree in biology. We study a restricted version of the bottleneck Steiner tree problem in the Euclidean plane which requires that only degree-2 Steiner points are possibly adjacent in the optimal solution. The problem is known to be MAX-SNP hard and cannot be approximated within unless P=NP, we propose a nearly optimal randomized polynomial time approximation algorithm with performance ratio +e, where e is a positive number.

  14. Bottleneck Non-Crossing Matching in the Plane

    CERN Document Server

    Abu-Affash, A Karim; Katz, Matthew J; Trabelsi, Yohai

    2012-01-01

    Let $P$ be a set of $2n$ points in the plane, and let $M_{\\rm C}$ (resp., $M_{\\rm NC}$) denote a bottleneck matching (resp., a bottleneck non-crossing matching) of $P$. We study the problem of computing $M_{\\rm NC}$. We first prove that the problem is NP-hard and does not admit a PTAS. Then, we present an $O(n^{1.5}\\log^{0.5} n)$-time algorithm that computes a non-crossing matching $M$ of $P$, such that $bn(M) \\le 2\\sqrt{10} \\cdot bn(M_{\\rm NC})$, where $bn(M)$ is the length of a longest edge in $M$. An interesting implication of our construction is that $bn(M_{\\rm NC})/bn(M_{\\rm C}) \\le 2\\sqrt{10}$.

  15. Label-free detection of neuronal differentiation in cell populations using high-throughput live-cell imaging of PC12 cells.

    Directory of Open Access Journals (Sweden)

    Sebastian Weber

    Full Text Available Detection of neuronal cell differentiation is essential to study cell fate decisions under various stimuli and/or environmental conditions. Many tools exist that quantify differentiation by neurite length measurements of single cells. However, quantification of differentiation in whole cell populations remains elusive so far. Because such populations can consist of both proliferating and differentiating cells, the task to assess the overall differentiation status is not trivial and requires a high-throughput, fully automated approach to analyze sufficient data for a statistically significant discrimination to determine cell differentiation. We address the problem of detecting differentiation in a mixed population of proliferating and differentiating cells over time by supervised classification. Using nerve growth factor induced differentiation of PC12 cells, we monitor the changes in cell morphology over 6 days by phase-contrast live-cell imaging. For general applicability, the classification procedure starts out with many features to identify those that maximize discrimination of differentiated and undifferentiated cells and to eliminate features sensitive to systematic measurement artifacts. The resulting image analysis determines the optimal post treatment day for training and achieves a near perfect classification of differentiation, which we confirmed in technically and biologically independent as well as differently designed experiments. Our approach allows to monitor neuronal cell populations repeatedly over days without any interference. It requires only an initial calibration and training step and is thereafter capable to discriminate further experiments. In conclusion, this enables long-term, large-scale studies of cell populations with minimized costs and efforts for detecting effects of external manipulation of neuronal cell differentiation.

  16. Energetic bottlenecks and other design constraints in avian annual cycles

    OpenAIRE

    Piersma, T

    2002-01-01

    The flexible phenotypes of birds and mammals often appear to represent adjustments to alleviate some energetic bottleneck or another. By increasing the size of the organs involved in digestion and assimilation of nutrients (gut and liver), an individual bird can increase its ability to process nutrients, for example to quickly store fuel for onward flight. Similarly, an increase in the exercise organs (pectoral muscles and heart) enables a bird to increase its metabolic power for sustained fl...

  17. Health Care Reform and the Primary Care Workforce Bottleneck

    OpenAIRE

    Schwartz, Mark D

    2011-01-01

    To establish and sustain the high-performing health care system envisioned in the Affordable Care Act (ACA), current provisions in the law to strengthen the primary care workforce must be funded, implemented, and tested. However, the United States is heading towards a severe primary care workforce bottleneck due to ballooning demand and vanishing supply. Demand will be fueled by the “silver tsunami” of 80 million Americans retiring over the next 20 years and the expanded insurance coverage fo...

  18. Metaheuristic procedures for the lexicographic bottleneck assembly line balancing problem

    OpenAIRE

    Pastor Moreno, Rafael; García Villoria, Alberto; Laguna, Manuel; Martí Cunquero, Rafael

    2015-01-01

    The goal of this work is to develop an improved procedure for the solution of the lexicographic bottleneck variant of the assembly line balancing problem (LB-ALBP). The objective of the LB-ALBP is to minimize the workload of the most heavily loaded workstation, followed by the workload of the second most heavily loaded workstation and so on. This problem-recently introduced to the literature (Pastor, 2011)-has practical relevance to manufacturing facilities. We design, implement and fine-tune...

  19. Congestion costs in bottleneck equilibrium with stochastic capacity and demand

    OpenAIRE

    Fosgerau, Mogens

    2008-01-01

    I analyse congestion costs in the Vickrey bottleneck model of a congestible facility with a peak load in demand. The shape of the peak is endogenous, being the sum of individual scheduling decisions. Capacity and demand are random, which introduces uncertainty into the individual scheduling choices. These are essential features of actual peak loads. Based on work by Arnott, de Palma and Lindsey, I derive the expected marginal and total congestion costs and compare to the case with fixed capac...

  20. Linguistics, cognitive psychology, and the Now-or-Never bottleneck.

    Science.gov (United States)

    Endress, Ansgar D; Katzir, Roni

    2016-01-01

    Christiansen & Chater (C&C)'s key premise is that "if linguistic information is not processed rapidly, that information is lost for good" (sect. 1, para. 1). From this "Now-or-Never bottleneck" (NNB), C&C derive "wide-reaching and fundamental implications for language processing, acquisition and change as well as for the structure of language itself" (sect. 2, para. 10). We question both the premise and the consequentiality of its purported implications. PMID:27561603

  1. Bottleneck on Supply Chain of Organic Agricultural Products and Countermeasures

    Institute of Scientific and Technical Information of China (English)

    ZHANG Xin-min

    2012-01-01

    Organic agriculture is one of successful models of low-carbon agriculture, and plays an important role in alleviating and adapting to climate change. However, the development of supply chain of organic agricultural products lags behind, which seriously restricts development of organic agricultural product market. In this paper, major models and bottleneck of supply chain of organic agricultural products are analyzed, and finally countermeasures are put forward.

  2. Time minimizing transportation problem with fractional bottleneck objective function

    OpenAIRE

    Jain Madhuri; Saksena P.K.

    2012-01-01

    This paper is aimed at studying the Time Minimizing Transportation Problem with Fractional Bottleneck Objective Function (TMTP-FBOF). TMTP-FBOF is related to a Lexicographic Fractional Time Minimizing Transportation Problem (LFTMTP), which will be solved by a lexicographic primal code. An algorithm is also developed to determine an initial efficient basic solution to this TMTP-FBOF. The developed TMTP-FBOF Algorithm is supported by a real life example of Military Transportation Problem ...

  3. Restricted Dynamic Programming Heuristic for Precedence Constrained Bottleneck Generalized TSP

    OpenAIRE

    Salii, Y.

    2015-01-01

    We develop a restricted dynamical programming heuristic for a complicated traveling salesman problem: a) cities are grouped into clusters, resp. Generalized TSP; b) precedence constraints are imposed on the order of visiting the clusters, resp. Precedence Constrained TSP; c) the costs of moving to the next cluster and doing the required job inside one are aggregated in a minimax manner, resp. Bottleneck TSP; d) all the costs may depend on the sequence of previously visited clusters, resp. Seq...

  4. Clogging transition of many-particle systems flowing through bottlenecks

    OpenAIRE

    Iker Zuriguel; Daniel Ricardo Parisi; Raúl Cruz Hidalgo; Celia Lozano; Alvaro Janda; Paula Alejandra Gago; Juan Pablo Peralta; Luis Miguel Ferrer; Luis Ariel Pugnaloni; Eric Clément; Diego Maza; Ignacio Pagonabarraga; Angel Garcimartín

    2014-01-01

    When a large set of discrete bodies passes through a bottleneck, the flow may become intermittent due to the development of clogs that obstruct the constriction. Clogging is observed, for instance, in colloidal suspensions, granular materials and crowd swarming, where consequences may be dramatic. Despite its ubiquity, a general framework embracing research in such a wide variety of scenarios is still lacking. We show that in systems of very different nature and scale -including sheep herds, ...

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

    Directory of Open Access Journals (Sweden)

    Thomas Meredith M

    2009-10-01

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

  6. Physiological basis of differential zinc and copper tolerance of Verbascum populations from metal-contaminated and uncontaminated areas.

    Science.gov (United States)

    Morina, Filis; Jovanović, Ljubinko; Prokić, Ljiljana; Veljović-Jovanović, Sonja

    2016-05-01

    Metal contamination represents a strong selective pressure favoring tolerant genotypes and leading to differentiation between plant populations. We investigated the adaptive capacity of early-colonizer species of Verbascum recently exposed to Zn- and Cu-contaminated soils (10-20 years). Two Verbascum thapsus L. populations from uncontaminated sites (NMET1, NMET2), one V. thapsus from a zinc-contaminated site (MET1), and a Verbascum lychnitis population from an open-cast copper mine (MET2) were exposed to elevated Zn or Cu in hydroponic culture under glasshouse conditions. MET populations showed considerably higher tolerance to both Zn and Cu than NMET populations as assessed by measurements of growth and net photosynthesis, yet they accumulated higher tissue Zn concentrations in the shoot. Abscisic acid (ABA) concentration increased with Zn and Cu treatment in the NMET populations, which was correlated to stomatal closure, decrease of net photosynthesis, and nutritional imbalance, indicative of interference with xylem loading and divalent-cation homeostasis. At the cellular level, the sensitivity of NMET2 to Zn and Cu was reflected in significant metal-induced ROS accumulation and ion leakage from roots as well as strong induction of peroxidase activity (POD, EC 1.11.1.7), while Zn had no significant effect on ABA concentration and POD activity in MET1. Interestingly, MET2 had constitutively higher root ABA concentration and POD activity. We propose that ABA distribution between shoots and roots could represent an adaptive mechanism for maintaining low ABA levels and unaffected stomatal conductance. The results show that metal tolerance can occur in Verbascum populations after relatively short time of exposure to metal-contaminated soil, indicating their potential use for phytostabilization. PMID:26865485

  7. The analysis of genetic diversity and differentiation of six Chinese cattle populations using microsatellite markers

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    A total of 321 individuals from six cattle populations of four species in a bovine subfamily in China were studied using 12 pairs of microsatellite markers. The genetic diversities within and between populations were calculated. The phylogenetic trees were constructed by(δμ)2 and DA distances, and the divergence times between populations were estimated by (δμ)2. Altogether, 144 microsatellite alleles were detected including 24 private alleles and nine shared alleles. Chinese Holstein had the largest number of private alleles (10), whereas,Bohai black and Buffalo had the smallest number of private alleles (2). Chinese Holstein showed the highest genetic variability. Its observed number of alleles (Na), mean effective number of alleles (MNA), and mean heterozygosity (He) were 7.7500, 4.9722, and 0.7719,respectively, whereas, the Buffalo and Yak showed low genetic variability. In the phylogenetic trees, Luxi and Holstein grouped first,followed by Bohai and Minnan. Yak branched next and buffalo emerged as the most divergent population from other cattle populations.Luxi and Bohai were estimated to have diverged 0.039-0.105 million years ago (MYA), however, buffalo and Holstein diverged 0.501-1.337 MYA. The divergence time of Yak versus Minnan, Holstein and buffalo was 0.136-0.363, 0.273-0.729, and 0.326-0.600MYA, respectively.

  8. Genetic Differentiations among the Populations of Salvia japonica (Lamiaceae and Its Related Species

    Directory of Open Access Journals (Sweden)

    SUDARMONO

    2008-03-01

    Full Text Available Morphological and genetic variations within Salvia japonica (Lamiaceae and its related species in Japan were analyzed for clarifying their taxonomic significance. The genetic variations were explored through chloroplast and nuclear ribosomal DNA sequences and allozyme polymorphisms. Since chromosome numbers characterized the genus of Salvia, we also examined whether the karyotypes were different. We examined 58 populations of S. japonica and 14 populations of others species of Salvia. Among the populations of S. japonica represented four forms (f. japonica, f. longipes, f. lanuginosa and f. albiflora. The size of chromosomes were various among Salvia spp. Based on the allozyme as well as the DNA sequence, the populations of S. japonica separated from the others Salvia species. The populations of S. japonica exhibited four combinations of the morphological characters. However, these combinations did not correlate to the four forms of S. japonica. In addition, the morphological variations did not correlate to the allozyme and DNA sequences. It is suggested that the four morphological variations as well as the four form of S. japonica should not considered to be a taxonomic unit; accordingly, S. japonica were considered to be still at the early stage of speciation process.

  9. Phylogeography and population dynamics of the white-sided dolphin (Lagenorhynchus acutus) in the North Atlantic

    KAUST Repository

    Banguera-Hinestroza, E.

    2014-02-27

    Highly mobile species in the marine environment may be expected to show little differentiation at the population level, but this is often not the case. Instead cryptic population structure is common, and effective conservation will require an understanding of how these patterns evolve. Here we present an assessment from both sides of the North Atlantic of differentiation among populations of a dolphin species that inhabits mainly pelagic waters, the Atlantic white-sided dolphin. We compare eleven putative populations in the western and eastern North Atlantic at mtDNA and microsatellite DNA loci and find reduced nucleotide diversity and signals for historical bottlenecks and post-bottleneck expansions in all regions. We calculate expansion times to have occurred during the early Holocene, following the last glacial maximum (LGM). We find evidence for connectivity among populations from either side of the North Atlantic, and differentiation between putative populations in the far northeast compared with all other areas sampled. Some data suggest the possibility of separate refugia during the LGM explaining this pattern, although ongoing ecological processes may also be a factor. We discuss the implications for developing effective programs of conservation and management in the context of ongoing anthropogenic impact. © 2014 Springer Science+Business Media Dordrecht.

  10. Populism

    OpenAIRE

    Abts, Koenraad; van Kessel, Stijn

    2015-01-01

    Populism is a concept applied to a wide range of political movements and actors across the globe. There is, at the same time, considerable confusion about the attributes and manifestation of populism, as well as its impact on democracy. This contribution identifies the defining elements of the populist ideology and discusses the varieties in which populism manifests itself, for instance as a component of certain party families. We finally discuss various normative interpretations of populism,...

  11. Differentiation of ovarian development and the evolution of fecundity in rapidly diverging exotic beetle populations.

    Science.gov (United States)

    Macagno, Anna L M; Beckers, Oliver M; Moczek, Armin P

    2015-11-01

    Fecundity is a fundamental determinant of fitness, yet the proximate developmental and physiological mechanisms that enable its often rapid evolution in natural populations are poorly understood. Here, we investigated two populations of the dung beetle Onthophagus taurus that were established in exotic ranges in the early 1970s. These populations are subject to drastically different levels of resource competition in the field, and have diverged dramatically in female fecundity. Specifically, Western Australian O. taurus experience high levels of resource competition, and exhibit greatly elevated reproductive output compared to beetles from the Eastern US, where resource competition is minimal and female fecundity is low. We compared patterns of ovarian maturation, relative investment into and timing of egg production, and potential trade-offs between ovarian investment and the duration of larval development and adult body size between populations representative of both exotic ranges. We found that the rapid divergence in fecundity between exotic populations is associated with striking differences in several aspects of ovarian development: (1) Western Australian females exhibit accelerated ovarian development, (2) produce more eggs, (3) bigger eggs, and (4) start laying eggs earlier compared to their Eastern US counterparts. At the same time, divergence in ovarian maturation patterns occurred alongside changes in (5) larval developmental time, and (6) adult body size, and (7) mass. Western Australian females take longer to complete larval development and, surprisingly, emerge into smaller yet heavier adults than size-matched Eastern US females. We discuss our results in the context of the evolutionary developmental biology of fecundity in exotic populations. PMID:26300520

  12. Whole genome distribution and ethnic differentiation of copy number variation in Caucasian and Asian populations.

    Directory of Open Access Journals (Sweden)

    Jian Li

    Full Text Available Although copy number variation (CNV has recently received much attention as a form of structure variation within the human genome, knowledge is still inadequate on fundamental CNV characteristics such as occurrence rate, genomic distribution and ethnic differentiation. In the present study, we used the Affymetrix GeneChip(R Mapping 500K Array to discover and characterize CNVs in the human genome and to study ethnic differences of CNVs between Caucasians and Asians. Three thousand and nineteen CNVs, including 2381 CNVs in autosomes and 638 CNVs in X chromosome, from 985 Caucasian and 692 Asian individuals were identified, with a mean length of 296 kb. Among these CNVs, 190 had frequencies greater than 1% in at least one ethnic group, and 109 showed significant ethnic differences in frequencies (p<0.01. After merging overlapping CNVs, 1135 copy number variation regions (CNVRs, covering approximately 439 Mb (14.3% of the human genome, were obtained. Our findings of ethnic differentiation of CNVs, along with the newly constructed CNV genomic map, extend our knowledge on the structural variation in the human genome and may furnish a basis for understanding the genomic differentiation of complex traits across ethnic groups.

  13. Identification of a unique hepatocellular carcinoma line, Li-7, with CD13(+) cancer stem cells hierarchy and population change upon its differentiation during culture and effects of sorafenib

    OpenAIRE

    Yamada, Takeshi; Abei, Masato; Danjoh, Inaho; Shirota, Ryoko; Yamashita, Taro; Hyodo, Ichinosuke; Nakamura, Yukio

    2015-01-01

    Backgrounds Cancer stem cell (CSC) research has highlighted the necessity of developing drugs targeting CSCs. We investigated a hepatocellular carcinoma (HCC) cell line that not only has CSC hierarchy but also shows phenotypic changes (population changes) upon differentiation of CSC during culture and can be used for screening drugs targeting CSC. Methods Based on a hypothesis that the CSC proportion should decrease upon its differentiation into progenitors (population change), we tested HCC ...

  14. Population genetic differentiation of height and body mass index across Europe

    DEFF Research Database (Denmark)

    Robinson, Matthew R.; Hemani, Gibran; Medina-Gomez, Carolina; Mezzavilla, Massimo; Esko, Tonu; Shakhbazov, Konstantin; Powell, Joseph E.; Vinkhuyzen, Anna; Berndt, Sonja I.; Gustafsson, Stefan; Pers, Tune Hannes; Werge, Thomas M.

    2015-01-01

    Across-nation differences in the mean values for complex traits are common(1-8), but the reasons for these differences are unknown. Here we find that many independent loci contribute to population genetic differences in height and body mass index (BMI) in 9,416 individuals across 14 European...

  15. Genetic diversity of native Turkish cattle breeds: Mantel, AMOVA and bottleneck analysis

    Directory of Open Access Journals (Sweden)

    Yusuf Özşensoy

    2014-09-01

    Full Text Available This study was conducted to evaluate potential extinction risk of Turkish native cattle breeds using Mantel and AMOVA tests and Bottleneck analysis. A total of 271 DNA samples were isolated from Anatolian Black, Anatolian Grey, South Anatolian Red, Native Southern Anatolian Yellow, East Anatolian Red, and Zavot cattle. In this study, genotypes of 20 microsatellites were determined by capillary electrophoresis and fragment analysis. A total of 269 different alleles were detected. The maximum and minimum numbers of total alleles were observed in TGLA122 (n=26 and INRA005 (n=7 loci, respectively. The highest average observed and expected heterozygosity values were determined as 0.619–0.852 and 0.669–0.877, respectively. The average FIS value was 0.068. Results of AMOVA and Mantel tests illustrated statistically significant differences in populations (p<0.001 and correlation (p<0.01. Bottleneck analysis revealed a normal distribution of L–shaped curve indicating that there was no recent risk of extinction for these breeds.

  16. Genetic differentiation among Parastichopus regalis populations from Western Mediterranean Sea: potential effects of its fishery and current connectivity.

    Directory of Open Access Journals (Sweden)

    C. MAGGI

    2015-11-01

    Full Text Available Parastichopus regalis (Cuvier, 1817 is the most expensive seafood product on the catalonian market (NE Spain, with prices around 130 €/Kg (fresh weight. Despite its ecological and economic importance, biological and genetic information on this sea cucumber species is scarce. We provided the first insight on the genetic structure of P. regalis using sequences of cytochrome oxidase I (COI and 16S genes, as well as a morphological description of its populations. Individuals were collected in six locations along the Spanish Mediterranean coast, including an area under fishery pressure (Catalonia. We found high haplotype diversity and low nucleotide diversity for both genes, with higher levels of genetic diversity observed on COI gene. Population pairwise fixation index (FST, AMOVA and correspondence analysis (CA based on COI, revealed significant genetic differentiation among some locations. However, further analysis using nuclear markers (e.g. microsatellites would be necessary to corroborate these results. Moreover, the genetic and morphological data may indicate fishery effects on the Catalonian population with decrease of the size and weight average and lower genetic diversity compared to locations without fishery pressure. For an appropriate management of this species, we suggest: 1 an accurate assessment of the stocks status along the Spanish coasts; 2 the study of the reproductive cycle of this target species and the establishment of a closed fishery season according to it; 3 the founding of protected areas (i.e. not take zones to conserve healthy populations and favour the recruitment on the nearby areas.

  17. Investigating population differentiation in a major African agricultural pest: evidence from geometric morphometrics and connectivity suggests high invasion potential.

    Science.gov (United States)

    Karsten, M; Addison, P; Jansen van Vuuren, B; Terblanche, J S

    2016-07-01

    The distribution, spatial pattern and population dynamics of a species can be influenced by differences in the environment across its range. Spatial variation in climatic conditions can cause local populations to undergo disruptive selection and ultimately result in local adaptation. However, local adaptation can be constrained by gene flow and may favour resident individuals over migrants-both are factors critical to the assessment of invasion potential. The Natal fruit fly (Ceratitis rosa) is a major agricultural pest in Africa with a history of island invasions, although its range is largely restricted to south east Africa. Across Africa, C. rosa is genetically structured into two clusters (R1 and R2), with these clusters occurring sympatrically in the north of South Africa. The spatial distribution of these genotypic clusters remains unexamined despite their importance for understanding the pest's invasion potential. Here, C. rosa, sampled from 22 South African locations, were genotyped at 11 polymorphic microsatellite loci and assessed morphologically using geometric morphometric wing shape analyses to investigate patterns of population structure and determine connectedness of pest-occupied sites. Our results show little to no intraspecific (population) differentiation, high population connectivity, high effective population sizes and only one morphological type (R2) within South Africa. The absence of the R1 morphotype at sites where it was previously found may be a consequence of differences in thermal niches of the two morphotypes. Overall, our results suggest high invasion potential of this species, that area-wide pest management should be undertaken on a country-wide scale, and that border control is critical to preventing further invasions. PMID:27085997

  18. Are all intertidal wetlands naturally created equal? Bottlenecks, thresholds and knowledge gaps to mangrove and saltmarsh ecosystems

    Science.gov (United States)

    Friess, Daniel A.; Krauss, Ken W.; Horstman, Erik M.; Balke, Thorsten; Bouma, Tjeerd J.; Galli, Demis; Webb, Edward L.

    2011-01-01

    Intertidal wetlands such as saltmarshes and mangroves provide numerous important ecological functions, though they are in rapid and global decline. To better conserve and restore these wetland ecosystems, we need an understanding of the fundamental natural bottlenecks and thresholds to their establishment and long-term ecological maintenance. Despite inhabiting similar intertidal positions, the biological traits of these systems differ markedly in structure, phenology, life history, phylogeny and dispersal, suggesting large differences in biophysical interactions. By providing the first systematic comparison between saltmarshes and mangroves, we unravel how the interplay between species-specific life-history traits, biophysical interactions and biogeomorphological feedback processes determine where, when and what wetland can establish, the thresholds to long-term ecosystem stability, and constraints to genetic connectivity between intertidal wetland populations at the landscape level. To understand these process interactions, research into the constraints to wetland development, and biological adaptations to overcome these critical bottlenecks and thresholds requires a truly interdisciplinary approach.

  19. The impact of share wave elastography in differentiation of hepatic hemangioma from malignant liver tumors in pediatric population

    International Nuclear Information System (INIS)

    Highlights: • We evaluated the impact of share wave elastography technique in differentiation hepatic hemangiomas from malignant liver tumors in pediatric population. • Share wave technique can increase the diagnostic capability of conventional ultrasonography in the differential diagnosis of liver tumors in children. • Share wave elastography is a potential adjunctive diagnostic technique for pediatric liver tumors. - Abstract: Objective: In children it is crucial to differentiate malignant liver tumors from the most common benign tumor, hepatic hemangiomas since the treatment strategies are quite different. We aimed to evaluate the efficiency of shear wave elastography (SWE) technique in differentiation of malignant hepatic tumors and hepatic hemangiomas. Methods: Twenty patients with hepatic tumor were included in our study. Two radiologists performed SWE for 13 patients with malignant hepatic tumors including hepatoblastoma (n = 7), hepatocellular carcinoma (n = 3), metastasis (n = 2), embryonal sarcoma (n = 1) and 7 patients with hepatic hemangioma. All of our patients were between the age of 1 and 192 months (mean age: 56.88 months). Receiver operating characteristic analysis was achieved to evaluate the diagnostic accuracy of SWE and to determine the optimal cut-off value in differentiation hepatic hemangioma from malignant hepatic tumors. Results: The mean SWE values (in kPa) for the first observer were 46.94 (13.8–145) and 22.38 (6.6–49.6) and those for the second observer were 57.91 (11–237) and 23.87 (6.4–57.5), respectively for malignant hepatic tumors and hepatic hemangiomas. The SWE values of malignant hepatic tumors were significantly higher than those of hepatic hemangioma (p = 0.02). The inter-observer agreement was almost perfect (0.81). The area under the receiver operating characteristic curve of SWE for differentiating the hepatic hemangioma from malignant hepatic tumors was 0.77 with a sensitivity of 72.7% and a specificity of 66

  20. SSR Marker Analysis on indica-japonica Differentiation of Natural Population of Oryza rufipogon in Yuanjiang, Yunnan Province

    Institute of Scientific and Technical Information of China (English)

    LI Ya-li; YANG Xiao-xi; ZHAO Feng-ping; XU Ming-hui

    2006-01-01

    By using 19 pairs of primers that could identify two subspecies (indica and japonica) of cultivated rice (Oryza sativa L.), the indica-japonica differentiation of 56 individuals from the natural population of common wild rice (Oryza rufipogon Griff.) in Yuanjiang was analyzed by SSR (microsatellite DNAs, or simple sequence repeat). Of the 19 pairs of primers, 17 pairs (89.47%) could amplify only one kind of band type among ail of the individuals, but primers RM251 and RM18 could amplify polymorphic band types. The bands amplified by 16 pairs of primers (84.21%) were identical to the indica-japonica diagnostic bands of relevant locus in cultivated rice, including 11 japonica-like loci and 4 indica-like loci. The bands amplified by the other three pairs of primers (RM18, RM202,RM205) were different from indica or japonica diagnostic bands of cultivated rice. The results showed that according to 19 loci analyzed, 84.21% of SSR loci in genomic DNA of common wild rice in Yuanjiang displayed indica-japonica differentiation and 13.79% of the loci still kept primitive, and most of the detected loci were homogenetic in the natural population.

  1. Explicative Factors for Entrepreneurial Intention in Women: Gender Differentials Amongst the University Population

    Directory of Open Access Journals (Sweden)

    María José Quero Gervilla

    2013-01-01

    Full Text Available The aim of this research project is to shed some light on the reasons why women are less likely to get involved in the processes of setting up businesses. To do this, a structural equations model has been developed, identifying a series of variables that can explain entrepreneurial intention amongst the potentially entrepreneurial population. The model has been validated by carrying out a survey amongst 1,222 students studying 12 different degree courses at the University of Malaga, Spain. In applying the model to both the male and female populations, significant differences have been found in the patterns of behaviour of the two sexes, with women undergoing a more complex process than men, and requiring external support.

  2. Genetic Differentiation among Populations and Color Variants of Sea Cucumbers (Stichopus Japonicus) from Korea and China

    OpenAIRE

    Kang, Jung-Ha; Kim, Yi-Kyong; Kim, Mi-Jung; Park, Jung-Yeon; An, Chul-Min; Kim, Bong-Seok; Jun, Je-Cheon; Kim, Sang-Kyu

    2011-01-01

    The Far Eastern sea cucumber, Stichopus japonicus, is a favored food in Eastern Asia, including Korea, Japan, and China. Aquaculture production of this species has increased because of recent declines in natural stocks and government-operated stock release programs are ongoing. Therefore, the analyses of genetic structure in wild and hatchery populations are necessary to maintain the genetic diversity of this valuable marine resource. In addition, given that sea cucumber color affects market ...

  3. Fmr1 KO and Fenobam Treatment Differentially Impact Distinct Synapse Populations of Mouse Neocortex

    OpenAIRE

    Wang, Gordon X.; Smith, Stephen J.; MOURRAIN, PHILIPPE

    2014-01-01

    Cognitive deficits in fragile X syndrome (FXS) are attributed to molecular abnormalities of the brain’s vast and heterogeneous synapse populations. Unfortunately, the density of synapses coupled with their molecular heterogeneity presents formidable challenges in understanding the specific contribution of synapse changes in FXS. We demonstrate powerful new methods for the large-scale molecular analysis of individual synapses that allow quantification of numerous specific changes in synapse po...

  4. Microbial Population Differentials between Mucosal and Submucosal Intestinal Tissues in Advanced Crohn's Disease of the Ileum.

    Directory of Open Access Journals (Sweden)

    Rodrick J Chiodini

    Full Text Available Since Crohn's disease is a transmural disease, we hypothesized that examination of deep submucosal tissues directly involved in the inflammatory disease process may provide unique insights into bacterial populations transgressing intestinal barriers and bacterial populations more representative of the causes and agents of the disease. We performed deep 16s microbiota sequencing on isolated ilea mucosal and submucosal tissues on 20 patients with Crohn's disease and 15 non-inflammatory bowel disease controls with a depth of coverage averaging 81,500 sequences in each of the 70 DNA samples yielding an overall resolution down to 0.0001% of the bacterial population. Of the 4,802,328 total sequences generated, 98.9% or 4,749,183 sequences aligned with the Kingdom Bacteria that clustered into 8545 unique sequences with <3% divergence or operational taxonomic units enabling the identification of 401 genera and 698 tentative bacterial species. There were significant differences in all taxonomic levels between the submucosal microbiota in Crohn's disease compared to controls, including organisms of the Order Desulfovibrionales that were present within the submucosal tissues of most Crohn's disease patients but absent in the control group. A variety of organisms of the Phylum Firmicutes were increased in the subjacent submucosa as compared to the parallel mucosal tissue including Ruminococcus spp., Oscillospira spp., Pseudobutyrivibrio spp., and Tumebacillus spp. In addition, Propionibacterium spp. and Cloacibacterium spp. were increased as well as large increases in Proteobacteria including Parasutterella spp. and Methylobacterium spp. This is the first study to examine the microbial populations within submucosal tissues of patients with Crohn's disease and to compare microbial communities found deep within the submucosal tissues with those present on mucosal surfaces. Our data demonstrate the existence of a distinct submucosal microbiome and ecosystem

  5. Education, Elderly Health, and Differential Population Aging in South Korea: A Demographic Approach

    OpenAIRE

    Bongoh Kye; Erika Arenas; Graciela Teruel; Luis Rubalcava

    2014-01-01

    Background: Population aging proceeds with other socioeconomic developments, including educational expansion. Improvements in educational attainment lead to changes in demographic behaviors such as assortative mating, fertility, and the intergenerational transmission of education, which change the health of the elderly and the education of their offspring generation. Objective: We examine such a jointly-changing process in South Korea. Methods: We apply a recursive demographic model (Ma...

  6. Genome-wide patterns of latitudinal differentiation among populations of Drosophila melanogaster from North America

    OpenAIRE

    Fabian, Daniel K; Kapun, Martin; Nolte, Viola; Kofler, Robert; Schmidt, Paul S; Schlötterer, Christian; Flatt, Thomas

    2012-01-01

    Abstract Understanding the genetic underpinnings of adaptive change is a fundamental but largely unresolved problem in evolutionary biology. Drosophila melanogaster, an ancestrally tropical insect that has spread to temperate regions and become cosmopolitan, offers a powerful opportunity for identifying the molecular polymorphisms underlying clinal adaptation. Here, we use genome-wide next-generation sequencing of DNA pools ('pool-seq') from three populations collected along the North America...

  7. Rapid differentiation of sexual signals in invasive toads: call variation among populations

    OpenAIRE

    Kiyomi Yasumiba; Duffy, Richard L.; Parsons, Scott A.; Ross A Alford; Lin Schwarzkopf

    2016-01-01

    Advertisement calls tend to differ among populations, based on morphological and environmental factors, or simply geographic distance, in many taxa. Invasive cane toads (Rhinella marina) were introduced to Australia in 1935 and their distribution has expanded at increasing rates over time. Rapid evolution occurred in morphological and behavioural characters that accelerate dispersal, but the effects of rapid expansion on sexual signals have not been examined. We collected advertisement calls ...

  8. Low Genetic Differentiation across Three Major Ocean Populations of the Whale Shark, Rhincodon typus

    OpenAIRE

    Schmidt, Jennifer V.; Claudia L Schmidt; Fusun Ozer; Robin E Ernst; Feldheim, Kevin A; Ashley, Mary V.; Marie Levine

    2009-01-01

    BACKGROUND: Whale sharks are a declining species for which little biological data is available. While these animals are protected in many parts of their range, they are fished legally and illegally in some countries. Baseline biological and ecological data are needed to allow the formulation of an effective conservation plan for whale sharks. It is not known, for example, whether the whale shark is represented by a single worldwide panmictic population or by numerous, reproductively isolated ...

  9. The differential effects of increasing frequency and magnitude of extreme events on coral populations

    OpenAIRE

    Fabina, NS; Baskett, ML; Gross, K.

    2015-01-01

    © 2015 by the Ecological Society of America. Extreme events, which have profound ecological consequences, are changing in both frequency and magnitude with climate change. Because extreme temperatures induce coral bleaching, we can explore the relative impacts of changes in frequency and magnitude of high temperature events on coral reefs. Here, we combined climate projections and a dynamic population model to determine how changing bleaching regimes influence coral persistence. We additional...

  10. Juvenile Myelomonocytic Leukemia (JMML Cells Spontaneously Differentiate into Dendritic-Cell Like Populations in vitro

    Directory of Open Access Journals (Sweden)

    Parviz Shayan

    2008-09-01

    Full Text Available Objective: Juvenile myelomonocytic leukemia (JMML is a rare myelodysplastic/ myeloproliferative malignancy of early childhood, characterized by monocytosis, hepatosplenomegaly and an aggressive clinical course. Methods: In semi-solid culture JMML progenitor cells proliferate spontaneously into colony forming units. In order to study the mechanisms of proliferation and differentiation of JMML cells we developed a suspension culture system without additional exogenous growth factor supplement. Mononuclear cells (MNC from peripheral blood, bone marrow or spleen of 14 patients with JMML and 24 controls were studied. Findings: JMML cells expressed higher levels of the proliferation marker Ki67 (median 24% [7-39%] vs a median of 3.5% in controls. 90% of JMML cells were CD68-positive (vs 35% in controls and by day 7 all JMML samples contained CD1a- positive cells. Electron microscopy demonstrated cytoplasmic vesicular structures resembling multilamellar MHC II compare­timents, which together with the expression of CD1a - support a dendritic cell (DC-phenotype. Conclusion: Differentiation into CD1a-positive DC seems to be a frequent phenomenon in cultured JMML MNC, which in vivo may contribute to clinical characteristics such as skin and organ infiltration.

  11. Time matters: Some interesting properties of the population differentiation measures GST and D overlooked in the equilibrium perspective

    Institute of Scientific and Technical Information of China (English)

    Liang LENG; De-Xing ZHANG

    2013-01-01

    Genetic differentiation of populations has been traditionally quantified by Wright's F-statistics,typically assuming mutation-migration-drift equilibrium.However,the equilibrium perspective can be unrealistic as many natural populations are likely not yet in equilibrium.Therefore,understanding the behaviors,robustness,and power of the differentiation indexes under non-equilibrium conditions has important implications.Here,we report an extensive examination of the properties of two major indexes GsT and D under non-equilibrium conditions by theoretical deduction under the infinite allele model (IAM) and simulation under the stepwise mutation model (SMM).Several properties of GST and D valid under both SMM and IAM,which have not been recognized under the equilibrium perspective,were unveiled.First,ifgene flow is very weak (e.g.,m < 10 4),GsT,like D,also takes a fairly long time to reach equilibrium if mutation rate is not very large.When GST (D) is in equilibrium depends on when Hs and HT are both in equilibrium.Under IAM and complete isolation,this is determined by the product ofμ and t:GsT will not approach equilibrium as long as μt < 1.Under SMM,10-4 appears to be the rough threshold migration rate; when m < 10-4,GsT approaches equilibrium much slower and later than Hs,whereas the opposite is true when m > 10 4.Second,contrary to the popular belief,μ < m is neither an obligatory request for GST to be an effective differentiation measure nor a sufficient condition for using GST to estimate gene flow level (Nm),if GST is not yet approaching equilibrium.Third,under SMM (but not IAM) and complete isolation,when population size is large (e.g.,> 1000),mutation rate shows a great impact on GST but only a mild influence on D; hence D can be much less sensitive to mutation rate heterogeneity than GST in certain situations.Fourth,whatever the level of gene flow,drift plays a dominant role on GST,whereas gene flow appears to have a stronger influence on D when

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

    DEFF Research Database (Denmark)

    Nyakaana, Silvester; Stothard, J. Russell; Nalugwa, Allen;

    2013-01-01

    characterized and quantified using FST statistics and Bayesian clustering algorithms. The four loci used in this study contained sufficient statistical power to detect low levels of population genetic differentiation and were highly polymorphic with the number of alleles per locus across populations ranging...

  13. Genetic Differentiation of Archachatina marginata Populations from Three Vegetation Zones Using Radom Amplified Polymorphic DNA Polymerase Chain Reaction

    Directory of Open Access Journals (Sweden)

    Comfort O. AFOLAYAN

    2015-09-01

    Full Text Available The genetic differentiation of Archachatina marginata populations from three different zones of Nigeria was studied with a view to delimiting them into sub-species. One hundred and nineteen (119 snail specimens were collected, comprising of forty (40 specimens from Yenagoa (Mangrove forest and from Kabba (Guinea Savanna and thirty nine (39 specimens were from Ile-Ife (Rainforest. Eight parameters of the shell specimens of A. marginata which included height of shell, width of shell, aperture height, aperture width, spire length, spire width, penultimate whorl length and first whorl length were subjected to Principal Component Analysis (PCA and Canonical Variates Analysis (CVA to delimit the populations into sub-species. DNA of the various populations was extracted from the foot muscle using CTAB (Cetyl Trimethyl Ammonium Bromide method, which was subjected to RAPD analysis. The RAPD studies employed five (5 oligonucleotide primers (OPB – 17, OPH – 12, OPH – 17, OPI – 06 and OPU – 14 to amplify DNA from 27 samples of A. marginata selected. All five primers produced different band patterns, and the number of fragments amplified per primer varied. Among them, OPB- 17 gave DNA profiles with more numerous bands than the others primers. Both PCA and CVA produced overlapped clusters of A. marginata specimens from the three vegetation zones. The height of shell was observed to be the most variable feature and preferably the most suitable parameter for population grouping. Analysis of the proportions of polymorphic loci and band sharing based on similarity indices for A. marginata samples indicated a relatively high level of genetic variation in the populations from the three areas.

  14. Conservation genetics of extremely isolated urban populations of the northern dusky salamander (Desmognathus fuscus in New York City

    Directory of Open Access Journals (Sweden)

    Jason Munshi-South

    2013-04-01

    Full Text Available Urbanization is a major cause of amphibian decline. Stream-dwelling plethodontid salamanders are particularly susceptible to urbanization due to declining water quality and hydrological changes, but few studies have examined these taxa in cities. The northern dusky salamander (Desmognathus fuscus was once common in the New York City metropolitan area, but has substantially declined throughout the region in recent decades. We used five tetranucleotide microsatellite loci to examine population differentiation, genetic variation, and bottlenecks among five remnant urban populations of dusky salamanders in NYC. These genetic measures provide information on isolation, prevalence of inbreeding, long-term prospects for population persistence, and potential for evolutionary responses to future environmental change. All populations were genetically differentiated from each other, and the most isolated populations in Manhattan have maintained very little genetic variation (i.e. <20% heterozygosity. A majority of the populations also exhibited evidence of genetic bottlenecks. These findings contrast with published estimates of high genetic variation within and lack of structure between populations of other desmognathine salamanders sampled over similar or larger spatial scales. Declines in genetic variation likely resulted from population extirpations and the degradation of stream and terrestrial paths for dispersal in NYC. Loss of genetic variability in populations isolated by human development may be an underappreciated cause and/or consequence of the decline of this species in urbanized areas of the northeast USA.

  15. Differential Estimates of Southern Flying Squirrel (Glaucomys volans) Population Structure Based on Capture Method.

    Energy Technology Data Exchange (ETDEWEB)

    Laves, Kevin S.; Loeb, Susan C.

    2006-01-01

    ABSTRACT.—It is commonly assumed that population estimates derived from trapping small mammals are accurate and unbiased or that estimates derived from different capture methods are comparable. We captured southern flying squirrels (Glaucomys volans) using two methods to study their effect on red-cockaded woodpecker (Picoides borealis) reproductive success. Southern flying squirrels were captured at and removed from 30 red-cockaded woodpecker cluster sites during March to July 1994 and 1995 using Sherman traps placed in a grid encompassing a red-cockaded woodpecker nest tree and by hand from red-cockaded woodpecker cavities. Totals of 195 (1994) and 190 (1995) red-cockaded woodpecker cavities were examined at least three times each year. Trappability of southern flying squirrels in Sherman traps was significantly greater in 1995 (1.18%; 22,384 trap nights) than in 1994 (0.42%; 20,384 trap nights), and capture rate of southern flying squirrels in cavities was significantly greater in 1994 (22.7%; 502 cavity inspections) than in 1995 (10.8%; 555 cavity inspections). However, more southern flying squirrels were captured per cavity inspection than per Sherman trap night in both years. Male southern flying squirrels were more likely to be captured from cavities than in Sherman traps in 1994, but not in 1995. Both male and female juveniles were more likely to be captured in cavities than in traps in both years. In 1994 males in reproductive condition were more likely to be captured in cavities than in traps and in 1995 we captured significantly more reproductive females in cavities than in traps. Our data suggest that population estimates based solely on one trapping method may not represent true population size or structure of southern flying squirrels.

  16. The bottleneck effect in three-dimensional turbulence simulations

    CERN Document Server

    Dobler, W; Yousef, T A; Brandenburg, A; Dobler, Wolfgang; Haugen, Nils Erland L.; Yousef, Tarek A.; Brandenburg, Axel

    2003-01-01

    At numerical resolutions around $512^3$ and above, three-dimensional energy spectra from turbulence simulations begin to show noticeably shallower spectra than $k^{-5/3}$ near the Kolmogorov dissipation wavenumber (`bottleneck effect'). This effect is shown to be significantly weaker in one-dimensional spectra like those obtained in wind tunnel turbulence. The difference can be understood in terms of the transformation between one-dimensional and three-dimensional energy spectra under the assumption that the turbulent velocity field is isotropic. Transversal and longitudinal energy spectra are similar and can both accurately be computed from the full three-dimensional spectra.

  17. A lexisearch Algorithm for the Bottleneck Traveling Salesman Problem

    Directory of Open Access Journals (Sweden)

    Zakir H. Ahmed

    2010-02-01

    Full Text Available The Bottleneck Traveling Salesman Problem (BTSP is a variation of the well-known Traveling Salesman Problem in which the objective is to minimize the maximum lap (arc length in the tour of the salesman. In this paper, a lexisearch algorithm using adjacency representation for a tour has been developed for obtaining exact optimal solution to the problem. Then a comparative study has been carried out to show the efficiency of the algorithm as against existing exact algorithm for some randomly generated and TSPLIB instances of different sizes.

  18. Give or take? Rewards vs. Charges for a Congested Bottleneck

    OpenAIRE

    Rouwendal, Jan; Erik T. Verhoef; Knockaert, Jasper

    2010-01-01

    This discussion paper resulted in a publication in 'Regional Science and Urban Economics', 42(1-2), 166-76.This paper analyzes the possibilities to relieve congestion using rewards instead of taxes, as well as combinations of rewards and taxes. The model considers a Vickrey-ADL model of bottleneck congestion with endogenous scheduling. With inelastic demand, a fine (time-varying) reward is equivalent to a fine toll, and to a continuum of combinations of time-varying tolls and rewards (includi...

  19. Bottlenecks in molecular testing for rare genetic diseases.

    Science.gov (United States)

    Willems, Patrick J

    2008-06-01

    Despite the impressive progress in our understanding of the genetic causes of genetic diseases over the past decade, molecular diagnosis for rare genetic disorders is still in its infancy, being slow, expensive, unreliable, insufficient, and ill-organized in many countries. This leaves the gap between the hype of the current genomic research and the hope for a simple genetic diagnosis too large for patients and families affected with genetic disease. The bottlenecks in the molecular testing for rare genetic disorders are discussed below. PMID:18412107

  20. Orphan drug development across Europe: bottlenecks and opportunities.

    Science.gov (United States)

    Heemstra, Harald E; de Vrueh, Remco L A; van Weely, Sonja; Büller, Hans A; Leufkens, Hubert G M

    2008-08-01

    With the assignment of the 500th European Union orphan drug designation in 2007, the Regulation on Orphan Medicinal Products truly begins to show its potential for delivering new medicines to patients with rare diseases. Here, we analysed European orphan drug development at a national level and unveil a strong relationship between orphan drug development and pharmaceutical innovation performance in Europe. Moreover, we identify gaps in transition from science into orphan drug development as important bottlenecks that exist in several European countries. Our findings underline the importance of innovation-based policies to enhance the development of orphan drugs in Europe. PMID:18583178

  1. Asymmetric exclusion processes on a closed network with bottlenecks

    International Nuclear Information System (INIS)

    We study the generic nonequilibrium steady states in asymmetric exclusion processes on a closed network with bottlenecks. To this end we propose and study closed simple networks with multiple-connected non-identical junctions. Depending upon the parameters that define the network junctions and the particle number density, the models display phase transitions with both static and moving density inhomogeneities. The currents in the models can be tuned by the junction parameters. Our models highlight how extended and point defects may affect the density profiles in a closed directed network. Phenomenological implications of our results are discussed. (paper)

  2. Genetic differentiation of water buffalo (Bubalus bubalis) populations in China, Nepal and south-east Asia: inferences on the region of domestication of the swamp buffalo.

    Science.gov (United States)

    Zhang, Y; Vankan, D; Zhang, Y; Barker, J S F

    2011-08-01

    Data from three published studies of genetic variation at 18 microsatellite loci in water buffalo populations in China (18 swamp type, two river type), Nepal (one wild, one domestic river, one hybrid) and south-east Asia (eight swamp, three river) were combined so as to gain a broader understanding of genetic relationships among the populations and their demographic history. Mean numbers of alleles and expected heterozygosities were significantly different among populations. Estimates of θ (a measure of population differentiation) were significant among the swamp populations for all loci and among the river populations for most loci. Differentiation among the Chinese swamp populations (which was due primarily to just one population) was much less than among the south-east Asian. The Nepal wild animals, phenotypically swamp type but genetically like river type, are significantly different from all the domestic river populations and presumably represent the ancestral Bubalus arnee (possibly with some river-type introgression). Relationships among the swamp populations (D(A) genetic distances, principal component analysis and structure analyses) show the south-east Asian populations separated into two groups by the Chinese populations. Given these relationships and the patterns of genetic variability, we postulate that the swamp buffalo was domesticated in the region of the far south of China, northern Thailand and Indochina. Following domestication, it spread south through peninsular Malaysia to Sumatra, Java and Sulawesi, and north through China, and then to Taiwan, the Philippines and Borneo. PMID:21749419

  3. Conservation genetics of the alligator snapping turtle: cytonuclear evidence of range-wide bottleneck effects and unusually pronounced geographic structure

    Science.gov (United States)

    Echelle, A.A.; Hackler, J.C.; Lack, Justin B.; Ballard, S. R.; Roman, J.; Fox, S. F.; Leslie,, David M., Jr.; Van Den Bussche, Ronald A.

    2010-01-01

    A previous mtDNA study indicated that female-mediated gene flow was extremely rare among alligator snapping turtle populations in different drainages of the Gulf of Mexico. In this study, we used variation at seven microsatellite DNA loci to assess the possibility of male-mediated gene flow, we augmented the mtDNA survey with additional sampling of the large Mississippi River System, and we evaluated the hypothesis that the consistently low within-population mtDNA diversity reflects past population bottlenecks. The results show that dispersal between drainages of the Gulf of Mexico is rare (F STmsat  = 0.43, ΦSTmtDNA = 0.98). Past range-wide bottlenecks are indicated by several genetic signals, including low diversity for microsatellites (1.1–3.9 alleles/locus; H e = 0.06–0.53) and mtDNA (h = 0.00 for most drainages; π = 0.000–0.001). Microsatellite data reinforce the conclusion from mtDNA that the Suwannee River population might eventually be recognized as a distinct taxonomic unit. It was the only population showing fixation or near fixation for otherwise rare microsatellite alleles. Six evolutionarily significant units are recommended on the basis of reciprocal mtDNA monophyly and high levels of microsatellite DNA divergence.

  4. Sex-differentiated migration patterns, protandry and phenology in North European songbird populations

    DEFF Research Database (Denmark)

    Tøttrup, Anders Peter; Thorup, Kasper

    2008-01-01

    This study aims to investigate causes and mechanisms controlling protandrous migration patterns (the earlier breeding area arrival of males relative to females) and inter-sexual differences in timing of migration in relation to the recent climate-driven changes in phenology. Using standardised...... all studied species. Males show more synchronous migration patterns compared to females and, hence, first arriving females followed males more closely than later arriving individuals. However, we found no inter-sexual differences in arrival trends as both sexes advance spring arrival over time with...... climatic changes may influence subsequent mating decisions, with subsequent feedbacks on population dynamics such as reproductive success and individual fitness. However, during decades of consistent earlier spring arrival in all phases of migration we found no evidence of inter-sexual phenological...

  5. Application of ILO classification to a population without industrial exposure: findings to be differentiated from pneumoconiosis

    International Nuclear Information System (INIS)

    The International Labour Office (ILO) classification for radiographs of pneumoconiosis is a standard means of assessing the presence or absence of pneumoconiosis in workers exposed to mineral dusts. Using this classification, 200 admission chest radiographs were reviewed on hospitalized patients in an urban university medical center to determine the prevalence and possible significance of ''small opacities'' in a population without known industrial exposure. Seventy-one men and 129 women were screened with the mean age of 44.2 years (range, 15-84). Thirty-six (18%) of the 200 patients had small opacities at profusion level 1/0 or greater, and this constituted the ''positive radiographs'' group. Twenty-two patients (11%) with positive radiographs had no documentable dust exposure or other specific medical etiology that would explain the presence of their lung opacities. The high prevalence of small opacities in ''normal'' older individuals has important implications in the assessment of patients with suspected pneumoconiosis

  6. Genetic Differentiation among Populations and Color Variants of Sea Cucumbers (Stichopus Japonicus from Korea and China

    Directory of Open Access Journals (Sweden)

    Jung-Ha Kang, Yi-Kyong Kim, Mi-Jung Kim, Jung-Yeon Park, Chul-Min An, Bong-Seok Kim, Je-Cheon Jun, Sang-Kyu Kim

    2011-01-01

    Full Text Available The Far Eastern sea cucumber, Stichopus japonicus, is a favored food in Eastern Asia, including Korea, Japan, and China. Aquaculture production of this species has increased because of recent declines in natural stocks and government-operated stock release programs are ongoing. Therefore, the analyses of genetic structure in wild and hatchery populations are necessary to maintain the genetic diversity of this valuable marine resource. In addition, given that sea cucumber color affects market price, with the rare, possibly reproductively isolated, red type being the most valuable, an understanding of the genetic structure and diversity in color variation of green and red types is necessary. We analyzed the genetic structure of wild and hatchery-produced green type S. japonicus from Korea and China, and wild red type from Korea using 9 microsatellite makers. The number of alleles per locus ranged from 11 to 29 across all populations. The mean allele numbers of the green types from Korea (10.6 and China (10.1 were similar, but differed slightly from that of the red type (9.1. Pairwise multilocus FST and genetic distance estimations showed no significant differences between the green types from Korea and China, whereas the differences between the green and red types were significant. This was clearly illustrated by a UPGMA dendrogram, in which the two close subclusters of green types were completely separated from the red type. In addition, the allele frequencies of the green and red types were significantly different. Assignment tests correctly assigned 100% (quality index 99.97% of individuals to their original color types and demonstrated the feasibility of microsatellite analysis for discrimination between color types.

  7. Larval Environment Alters Amphibian Immune Defenses Differentially across Life Stages and Populations.

    Directory of Open Access Journals (Sweden)

    Katherine L Krynak

    Full Text Available Recent global declines, extirpations and extinctions of wildlife caused by newly emergent diseases highlight the need to improve our knowledge of common environmental factors that affect the strength of immune defense traits. To achieve this goal, we examined the influence of acidification and shading of the larval environment on amphibian skin-associated innate immune defense traits, pre and post-metamorphosis, across two populations of American Bullfrogs (Rana catesbeiana, a species known for its wide-ranging environmental tolerance and introduced global distribution. We assessed treatment effects on 1 skin-associated microbial communities and 2 post-metamorphic antimicrobial peptide (AMP production and 3 AMP bioactivity against the fungal pathogen Batrachochytrium dendrobatidis (Bd. While habitat acidification did not affect survival, time to metamorphosis or juvenile mass, we found that a change in average pH from 7 to 6 caused a significant shift in the larval skin microbial community, an effect which disappeared after metamorphosis. Additionally, we found shifts in skin-associated microbial communities across life stages suggesting they are affected by the physiological or ecological changes associated with amphibian metamorphosis. Moreover, we found that post-metamorphic AMP production and bioactivity were significantly affected by the interactions between pH and shade treatments and interactive effects differed across populations. In contrast, there were no significant interactions between treatments on post-metamorphic microbial community structure suggesting that variation in AMPs did not affect microbial community structure within our study. Our findings indicate that commonly encountered variation in the larval environment (i.e. pond pH and degree of shading can have both immediate and long-term effects on the amphibian innate immune defense traits. Our work suggests that the susceptibility of amphibians to emerging diseases could be

  8. A bottleneck model of set-specific capture.

    Directory of Open Access Journals (Sweden)

    Katherine Sledge Moore

    Full Text Available Set-specific contingent attentional capture is a particularly strong form of capture that occurs when multiple attentional sets guide visual search (e.g., "search for green letters" and "search for orange letters". In this type of capture, a potential target that matches one attentional set (e.g. a green stimulus impairs the ability to identify a temporally proximal target that matches another attentional set (e.g. an orange stimulus. In the present study, we investigated whether set-specific capture stems from a bottleneck in working memory or from a depletion of limited resources that are distributed across multiple attentional sets. In each trial, participants searched a rapid serial visual presentation (RSVP stream for up to three target letters (T1-T3 that could appear in any of three target colors (orange, green, or lavender. The most revealing findings came from trials in which T1 and T2 matched different attentional sets and were both identified. In these trials, T3 accuracy was lower when it did not match T1's set than when it did match, but only when participants failed to identify T2. These findings support a bottleneck model of set-specific capture in which a limited-capacity mechanism in working memory enhances only one attentional set at a time, rather than a resource model in which processing capacity is simultaneously distributed across multiple attentional sets.

  9. Efficacy of sorafenib in advanced differentiated and medullary thyroid cancer: experience in a Turkish population

    Science.gov (United States)

    Benekli, Mustafa; Yalcin, Suayib; Ozkan, Metin; Elkiran, Emin Tamer; Sevinc, Alper; Cabuk, Devrim; Coskun, Hasan Senol; Oksuzoglu, Berna; Bayar, Banu; Akbulat, Akif; Ozet, Ahmet

    2015-01-01

    Background Antivascular endothelial growth factor tyrosine kinase inhibitors have been used recently in the treatment of advanced differentiated thyroid cancer (DTC) and medullary thyroid cancer (MTC). Off-label sorafenib is used in Turkey with special permission by the Ministry of Health for this indication. Patients and methods Patients with advanced DTC and MTC were retrospectively identified from the Turkish Ministry of Health database. Data on these patients were prospectively collected before permission is granted to use sorafenib. Results Thirty patients with complete data were analyzed: 14 DTC (papillary number [n] =10; follicular n=4) and 16 MTC. The median age of the patients was 57 years (range: 28–79 years), and there were 18 males and 12 females. All DTC patients were iodine refractory and had received a median three doses of radioactive iodine (range: 1–7 doses). Sorafenib was used for a median of 12 months (range: 1–49 months). The overall response rate was 20%, all partial responses, with no complete response. The overall response rate was 14% in DTC and 25% in MTC patients. The median progression-free survival (PFS) was 17.1 months (95% confidence interval [CI]: 7.3–26.8) and overall survival (OS) was not reached. The 2-year PFS and OS were 39% and 68%, respectively. DTC and MTC patients had similar survival outcomes: median PFS of 21.3 months (95% CI: 5.8–36.7) versus 14.5 months (95% CI: 3.7–25.2), respectively (P=0.36), with the median OS not reached in either group (P=0.17). Tumor marker levels did not have any prognostic or predictive role. The toxicity profile was similar to that of other sorafenib trials. Conclusion Sorafenib is an effective and well-tolerated treatment in advanced thyroid cancers. PMID:25548522

  10. Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus.

    Directory of Open Access Journals (Sweden)

    Damien C Tully

    2016-05-01

    Full Text Available Due to the stringent population bottleneck that occurs during sexual HIV-1 transmission, systemic infection is typically established by a limited number of founder viruses. Elucidation of the precise forces influencing the selection of founder viruses may reveal key vulnerabilities that could aid in the development of a vaccine or other clinical interventions. Here, we utilize deep sequencing data and apply a genetic distance-based method to investigate whether the mode of sexual transmission shapes the nascent founder viral genome. Analysis of 74 acute and early HIV-1 infected subjects revealed that 83% of men who have sex with men (MSM exhibit a single founder virus, levels similar to those previously observed in heterosexual (HSX transmission. In a metadata analysis of a total of 354 subjects, including HSX, MSM and injecting drug users (IDU, we also observed no significant differences in the frequency of single founder virus infections between HSX and MSM transmissions. However, comparison of HIV-1 envelope sequences revealed that HSX founder viruses exhibited a greater number of codon sites under positive selection, as well as stronger transmission indices possibly reflective of higher fitness variants. Moreover, specific genetic "signatures" within MSM and HSX founder viruses were identified, with single polymorphisms within gp41 enriched among HSX viruses while more complex patterns, including clustered polymorphisms surrounding the CD4 binding site, were enriched in MSM viruses. While our findings do not support an influence of the mode of sexual transmission on the number of founder viruses, they do demonstrate that there are marked differences in the selection bottleneck that can significantly shape their genetic composition. This study illustrates the complex dynamics of the transmission bottleneck and reveals that distinct genetic bottleneck processes exist dependent upon the mode of HIV-1 transmission.

  11. Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus

    Science.gov (United States)

    Tully, Damien C.; Ogilvie, Colin B.; Batorsky, Rebecca E.; Bean, David J.; Power, Karen A.; Ghebremichael, Musie; Bedard, Hunter E.; Gladden, Adrianne D.; Seese, Aaron M.; Amero, Molly A.; Lane, Kimberly; McGrath, Graham; Bazner, Suzane B.; Tinsley, Jake; Lennon, Niall J.; Henn, Matthew R.; Brumme, Zabrina L.; Norris, Philip J.; Rosenberg, Eric S.; Mayer, Kenneth H.; Jessen, Heiko; Kosakovsky Pond, Sergei L.; Walker, Bruce D.; Altfeld, Marcus; Carlson, Jonathan M.; Allen, Todd M.

    2016-01-01

    Due to the stringent population bottleneck that occurs during sexual HIV-1 transmission, systemic infection is typically established by a limited number of founder viruses. Elucidation of the precise forces influencing the selection of founder viruses may reveal key vulnerabilities that could aid in the development of a vaccine or other clinical interventions. Here, we utilize deep sequencing data and apply a genetic distance-based method to investigate whether the mode of sexual transmission shapes the nascent founder viral genome. Analysis of 74 acute and early HIV-1 infected subjects revealed that 83% of men who have sex with men (MSM) exhibit a single founder virus, levels similar to those previously observed in heterosexual (HSX) transmission. In a metadata analysis of a total of 354 subjects, including HSX, MSM and injecting drug users (IDU), we also observed no significant differences in the frequency of single founder virus infections between HSX and MSM transmissions. However, comparison of HIV-1 envelope sequences revealed that HSX founder viruses exhibited a greater number of codon sites under positive selection, as well as stronger transmission indices possibly reflective of higher fitness variants. Moreover, specific genetic “signatures” within MSM and HSX founder viruses were identified, with single polymorphisms within gp41 enriched among HSX viruses while more complex patterns, including clustered polymorphisms surrounding the CD4 binding site, were enriched in MSM viruses. While our findings do not support an influence of the mode of sexual transmission on the number of founder viruses, they do demonstrate that there are marked differences in the selection bottleneck that can significantly shape their genetic composition. This study illustrates the complex dynamics of the transmission bottleneck and reveals that distinct genetic bottleneck processes exist dependent upon the mode of HIV-1 transmission. PMID:27163788

  12. Tracing early stages of species differentiation: Ecological, morphological and genetic divergence of Galápagos sea lion populations

    Directory of Open Access Journals (Sweden)

    Brunner Sylvia

    2008-05-01

    Full Text Available Abstract Background Oceans are high gene flow environments that are traditionally believed to hamper the build-up of genetic divergence. Despite this, divergence appears to occur occasionally at surprisingly small scales. The Galápagos archipelago provides an ideal opportunity to examine the evolutionary processes of local divergence in an isolated marine environment. Galápagos sea lions (Zalophus wollebaeki are top predators in this unique setting and have an essentially unlimited dispersal capacity across the entire species range. In theory, this should oppose any genetic differentiation. Results We find significant ecological, morphological and genetic divergence between the western colonies and colonies from the central region of the archipelago that are exposed to different ecological conditions. Stable isotope analyses indicate that western animals use different food sources than those from the central area. This is likely due to niche partitioning with the second Galápagos eared seal species, the Galápagos fur seal (Arctocephalus galapagoensis that exclusively dwells in the west. Stable isotope patterns correlate with significant differences in foraging-related skull morphology. Analyses of mitochondrial sequences as well as microsatellites reveal signs of initial genetic differentiation. Conclusion Our results suggest a key role of intra- as well as inter-specific niche segregation in the evolution of genetic structure among populations of a highly mobile species under conditions of free movement. Given the monophyletic arrival of the sea lions on the archipelago, our study challenges the view that geographical barriers are strictly needed for the build-up of genetic divergence. The study further raises the interesting prospect that in social, colonially breeding mammals additional forces, such as social structure or feeding traditions, might bear on the genetic partitioning of populations.

  13. The differential effects of increasing frequency and magnitude of extreme events on coral populations.

    Science.gov (United States)

    Fabina, Nicholas S; Baskett, Marissa L; Gross, Kevin

    2015-09-01

    Extreme events, which have profound ecological consequences, are changing in both frequency and magnitude with climate change. Because extreme temperatures induce coral bleaching, we can explore the relative impacts of changes in frequency and magnitude of high temperature events on coral reefs. Here, we combined climate projections and a dynamic population model to determine how changing bleaching regimes influence coral persistence. We additionally explored how coral traits and competition with macroalgae mediate changes in bleaching regimes. Our results predict that severe bleaching events reduce coral persistence more than frequent bleaching. Corals with low adult mortality and high growth rates are successful when bleaching is mild, but bleaching resistance is necessary to persist when bleaching is severe, regardless of frequency. The existence of macroalgae-dominated stable states reduces coral persistence and changes the relative importance of coral traits. Building on previous studies, our results predict that management efforts may need to prioritize protection of "weaker" corals with high adult mortality when bleaching is mild, and protection of "stronger" corals with high bleaching resistance when bleaching is severe. In summary, future reef projections and conservation targets depend on both local bleaching regimes and biodiversity. PMID:26552262

  14. Comparative physiology of radish populations with differential sensitivity to O3 and SO2

    International Nuclear Information System (INIS)

    Radish plants (Raphanus sativus L. cv Cherry Belle) were exposed to 0.10 μl l-1 ozone (O3) or 0.50 μl l-1 sulfur dioxide (SO2) for 4 h d-1, 3 d wk-1 for 3 weeks. From these fumigated plants, individuals were selected that were resistant or sensitive to these pollutants. The selected plants were used as parental material in a breeding program to produce lines differing in resistance to O3 and SO2. Non-selected (NS) plants from the original populations served as controls. Plants selected for O3 resistance (O3R) weighed significantly more than either plants selected for sensitivity to O3 (O3S) or NS plants when exposed to either O3 or SO2. Plants selected for resistance or sensitivity to SO2 generally had biomass production similar to that of NS plants. Ozone fumigations tended to decrease free sugar concentrations in leaves at early stages of growth in both O3R and O3S plants, and caused some accumulations of carbohydrates during late stages of growth in O3S plants. Allocation of 14C was significantly lower to hypocotyls and roots of O3 fumigated O3S plants. Allocation to hypocotyls of O3R plants was not affected, although both O3R and O3S plant groups had lower photosynthetic rates due to O3 fumigation. Ozone did not significantly affect chlorophyll concentrations in leaves of either sensitive or resistant plants, nor was the time of new leaf production affected by fumigation

  15. A methodology for determining and controlling the buffers before floating bottlenecks in heavy machinery production

    Directory of Open Access Journals (Sweden)

    R. Lenort

    2013-07-01

    Full Text Available Heavy machinery industry is characterized by a number of specific features that cause significant variations in the processing time of products in the individual workplaces and frequent occurrence of floating bottlenecks, which change their positions. Depending on the product range being processed, a given workplace is the bottleneck only for some period of time. When the bottleneck moves to another workplace, it leads to unnecessary loss of capacity of the floating bottleneck. To maximize the utilization, it is necessary to protect those bottlenecks by creating special buffers. The objective of this article is to design a methodology used for the determination and control of buffers that are going to protect the floating bottlenecks from operating capacity losses caused by transfer of the constrain to another workplace. These buffers are referred to as „power buffers“. The designed methodology has been verified in the process of forged pieces machining.

  16. Whole-body MRI in generalized cystic lymphangiomatosis in the pediatric population: diagnosis, differential diagnoses, and follow-up

    International Nuclear Information System (INIS)

    Generalized cystic lymphangiomatosis is a particularly rare disease with variable involvement of skeletal and extraskeletal sites. The key role of imaging in the diagnosis of this disease is no longer in doubt. The aim of our study was to demonstrate the contribution of whole-body magnetic resonance imaging (WB-MRI) at the diagnostic stage and during the follow-up in the pediatric population. Three children were included from 2008. The inclusion criteria were radiological images (conventional radiographs, computed tomography, and MRI) compatible with histological confirmation. Each child included received WB-MRI at the diagnosis stage and during follow-up. WB-MRI detected multiple hypointense T1 and hyperintense T2-STIR cystic bony lesions. One unnoticed mass in the retroperitoneum on computed tomography was easily detected by MRI. Mediastinal involvement was observed in one asymptomatic case. Histology was contributory in all cases. Preventive intramedullary nailings was done in one case. Follow-up WB-MRI detected new asymptomatic lesions in all cases. One child presented a third episode of lymphangitis of the right thigh during follow-up. Due to its high sensitivity to diagnose, ability to eliminate differential diagnoses and make exhaustive lesions assessment, and its non-radiating character for long-term follow-up, WB-MRI is highly recommended for generalized cystic lymphangiomatosis in the pediatric population. (orig.)

  17. Community differentiation and population enrichment of Sargasso Sea bacterioplankton in the euphotic zone of a mesoscale mode-water eddy.

    Science.gov (United States)

    Nelson, Craig E; Carlson, Craig A; Ewart, Courtney S; Halewood, Elisa R

    2014-03-01

    Eddies are mesoscale oceanographic features (∼ 200 km diameter) that can cause transient blooms of phytoplankton by shifting density isoclines in relation to light and nutrient resources. To better understand how bacterioplankton respond to eddies, we examined depth-resolved distributions of bacterial populations across an anticyclonic mode-water eddy in the Sargasso Sea. Previous work on this eddy has documented elevated phytoplankton productivity and diatom abundance within the eddy centre with coincident bacterial productivity and biomass maxima. We illustrate bacterial community shifts within the eddy centre, differentiating populations uplifted along isopycnals from those enriched or depleted at horizons of enhanced bacterial and primary productivity. Phylotypes belonging to the Roseobacter, OCS116 and marine Actinobacteria clades were enriched in the eddy core and were highly correlated with pigment-based indicators of diatom abundance, supporting developing hypotheses that members of these clades associate with phytoplankton blooms. Typical mesopelagic clades (SAR202, SAR324, SAR406 and SAR11 IIb) were uplifted within the eddy centre, increasing bacterial diversity in the lower euphotic zone. Typical surface oligotrophic clades (SAR116, OM75, Prochlorococcus and SAR11 Ia) were relatively depleted in the eddy centre. The biogeochemical context of a bloom-inducing eddy provides insight into the ecology of the diverse uncultured bacterioplankton dominating the oligotrophic oceans. PMID:24589288

  18. Whole-body MRI in generalized cystic lymphangiomatosis in the pediatric population: diagnosis, differential diagnoses, and follow-up

    Energy Technology Data Exchange (ETDEWEB)

    Herruela-Suffee, Cecile; Warin, Mathilde; Castier-Amouyel, Melody; Dallery, Florine; Bonnaire, Bruno; Constans, Jean-Marc [CHU Amiens-Picardie, Service de Radiologie, Amiens Cedex 1 (France)

    2016-02-15

    Generalized cystic lymphangiomatosis is a particularly rare disease with variable involvement of skeletal and extraskeletal sites. The key role of imaging in the diagnosis of this disease is no longer in doubt. The aim of our study was to demonstrate the contribution of whole-body magnetic resonance imaging (WB-MRI) at the diagnostic stage and during the follow-up in the pediatric population. Three children were included from 2008. The inclusion criteria were radiological images (conventional radiographs, computed tomography, and MRI) compatible with histological confirmation. Each child included received WB-MRI at the diagnosis stage and during follow-up. WB-MRI detected multiple hypointense T1 and hyperintense T2-STIR cystic bony lesions. One unnoticed mass in the retroperitoneum on computed tomography was easily detected by MRI. Mediastinal involvement was observed in one asymptomatic case. Histology was contributory in all cases. Preventive intramedullary nailings was done in one case. Follow-up WB-MRI detected new asymptomatic lesions in all cases. One child presented a third episode of lymphangitis of the right thigh during follow-up. Due to its high sensitivity to diagnose, ability to eliminate differential diagnoses and make exhaustive lesions assessment, and its non-radiating character for long-term follow-up, WB-MRI is highly recommended for generalized cystic lymphangiomatosis in the pediatric population. (orig.)

  19. Efficacy of sorafenib in advanced differentiated and medullary thyroid cancer: experience in a Turkish population

    Directory of Open Access Journals (Sweden)

    Benekli M

    2014-12-01

    Full Text Available Mustafa Benekli,1 Suayib Yalcin,2 Metin Ozkan,3 Emin Tamer Elkiran,4 Alper Sevinc,5 Devrim Cabuk,6 Hasan Senol Coskun,7 Berna Oksuzoglu,8 Banu Bayar,9 Akif Akbulat,9 Ahmet Ozet1 On behalf of Turkish Thyroid Cancer Study Group 1Department of Medical Oncology, Gazi University Faculty of Medicine, Ankara, 2Department of Medical Oncology, Hacettepe University Faculty of Medicine, Ankara, 3Department of Medical Oncology, Erciyes University Faculty of Medicine, Kayseri, 4Department of Medical Oncology, Inonu University Faculty of Medicine, Malatya, 5Department of Medical Oncology, Gaziantep University Faculty of Medicine, Gaziantep, 6Department of Medical Oncology, Kocaeli University Faculty of Medicine, Kocaeli, 7Department of Medical Oncology, Akdeniz University Faculty of Medicine, Antalya, 8Department of Medical Oncology, Ankara Oncology Training and Research Hospital, Ankara, 9Ministry of Health of Turkey, General Directorate of Pharmaceuticals and Medical Devices, Ankara, Turkey Background: Antivascular endothelial growth factor tyrosine kinase inhibitors have been used recently in the treatment of advanced differentiated thyroid cancer (DTC and medullary thyroid cancer (MTC. Off-label sorafenib is used in Turkey with special permission by the Ministry of Health for this indication. Patients and methods: Patients with advanced DTC and MTC were retrospectively identified from the Turkish Ministry of Health database. Data on these patients were prospectively collected before permission is granted to use sorafenib. Results: Thirty patients with complete data were analyzed: 14 DTC (papillary number [n] =10; follicular n=4 and 16 MTC. The median age of the patients was 57 years (range: 28–79 years, and there were 18 males and 12 females. All DTC patients were iodine refractory and had received a median three doses of radioactive iodine (range: 1–7 doses. Sorafenib was used for a median of 12 months (range: 1–49 months. The overall response rate

  20. Relationship between hierarchic - spatial differentiation of social structure and population size of municipalities in turkey: Evidence from the election case of local administration in 2004

    Directory of Open Access Journals (Sweden)

    Murat Çiftçi

    2011-07-01

    Full Text Available Turkey, whose population is young and dynamic, is a country where social change has a high acceleration. This circumstance has led to a spatial heterogeneity of social structure in the scale of campuses. Almost all the municipalities differ significantly from each other. In results of statistical applications, it was possible to conclude that there is a relationship between spatial differentiation of social structure indicators (PDI, PIDI and population sizes in municipalities. This relationship also supports that there was a differentiation of graded spatial social structure among municipalities in the Turkey of 2004. It is possible to make contact with this to the spatial differentiation that moves in parallel with population size and is in transition degree from a community to a society.

  1. Down-regulation of the Fetal Stem Cell Factor SOX17 by H33342: A MECHANISM RESPONSIBLE FOR DIFFERENTIAL GENE EXPRESSION IN BREAST CANCER SIDE POPULATION CELLS

    OpenAIRE

    Christgen, Matthias; Geffers, Robert; Ballmaier, Matthias; Christgen, Henriette; Poczkaj, Janette; Krech, Till; Kreipe, Hans; Lehmann, Ulrich

    2009-01-01

    Human solid tumors contain rare cancer side population (SP) cells, which expel the fluorescent dye Hoechst 33342 (H33342) and display cancer stem cell characteristics. Transcriptional profiling of cancer SP cells isolated by H33342 fluorescence analysis is a newly emerging approach to discover cancer stem cell markers and aberrant differentiation pathways. Using Affymetrix expression microarrays and quantitative reverse transcription-PCR, we investigated differential gene expression between S...

  2. Secreted protein gene derived-single nucleotide polymorphisms (SP-SNPs) reveal population diversity and differentiation of Puccinia striiformis f. sp. tritici in the United States.

    Science.gov (United States)

    Xia, Chongjing; Wan, Anmin; Wang, Meinan; Jiwan, Derick A; See, Deven R; Chen, Xianming

    2016-05-01

    Single nucleotide polymorphism (SNP) is a powerful molecular marker technique that has been widely used in population genetics and molecular mapping studies for various organisms. However, the technique has not been used for studying Puccinia striiformis f. sp. tritici (Pst), the wheat stripe rust pathogen. In this study, we developed over a hundred secreted protein gene-derived SNP (SP-SNP) markers and used 92 markers to study the population structure of Pst. From 352 isolates collected in the United States, we identified 242 multi-locus genotypes. The SP-SNP genotypes had a moderate, but significant correlation with the virulence phenotype data. Clustering of the multi-locus genotypes was consistent by various analyses, revealing distinct genetic groups. Analysis of molecular variance detected significant differences between the eastern and western US Pst populations. High heterozygosity was found in the US population with significant differences identified among epidemiological regions. Analysis of population differentiation revealed that populations between the eastern and western US were highly differentiated while moderate differentiation was found in populations within the western or eastern US. Isolates from the western US were more diverse than isolates from the eastern US. The information is useful for guiding the disease management in different epidemiological regions. PMID:27109369

  3. Client-server computer architecture saves costs and eliminates bottlenecks

    International Nuclear Information System (INIS)

    This paper reports that workstation, client-server architecture saved costs and eliminated bottlenecks that BP Exploration (Alaska) Inc. experienced with mainframe computer systems. In 1991, BP embarked on an ambitious project to change technical computing for its Prudhoe Bay, Endicott, and Kuparuk operations on Alaska's North Slope. This project promised substantial rewards, but also involved considerable risk. The project plan called for reservoir simulations (which historically had run on a Cray Research Inc. X-MP supercomputer in the company's Houston data center) to be run on small computer workstations. Additionally, large Prudhoe Bay, Endicott, and Kuparuk production and reservoir engineering data bases and related applications also would be moved to workstations, replacing a Digital Equipment Corp. VAX cluster in Anchorage

  4. Queuing model of a traffic bottleneck with bimodal arrival rate

    Science.gov (United States)

    Woelki, Marko

    2016-06-01

    This paper revisits the problem of tuning the density in a traffic bottleneck by reduction of the arrival rate when the queue length exceeds a certain threshold, studied recently for variants of totally asymmetric simple exclusion process (TASEP) and Burgers equation. In the present approach, a simple finite queuing system is considered and its contrasting “phase diagram” is derived. One can observe one jammed region, one low-density region and one region where the queue length is equilibrated around the threshold. Despite the simplicity of the model the physics is in accordance with the previous approach: The density is tuned at the threshold if the exit rate lies in between the two arrival rates.

  5. Traffic Flow States in a Freeway with Bottleneck

    Institute of Scientific and Technical Information of China (English)

    PENG Zi-Hui; SUN Gang; ZHU Jing-Yi

    2009-01-01

    The system of mixture of single lane and double lane is studied by a cellular automata model, which is developed by us based on the Nagel and Schreckenberg's models. We justify that the model can reach a stable states quickly. The density distributions of the stable state is presented for several cases, which illustrate the manner of the congestion. The relationship between the outflow rate and the total number of vehicles and that between the outflow rate and the density just before the bottleneck are both given. Comparing with the relationship that occurring in the granular flow, we conclude that the transition from the free traffic flow to the congested traffic flow can also be attributed to the abrupt variation through unstable flow state, which can naturally explain the discontinuities and the complex time variation behavior observed in the traffic flow experiments.

  6. Adaptation in isolated populations: when does it happen and when can we tell?

    Science.gov (United States)

    Crisci, Jessica L; Dean, Matthew D; Ralph, Peter

    2016-08-01

    Isolated populations with novel phenotypes present an exciting opportunity to uncover the genetic basis of ecologically significant adaptation, and genomic scans have often, but not always, led to candidate genes directly related to an adaptive phenotype. However, in many cases these populations were established by a severe bottleneck, which can make identifying targets of selection problematic. Here, we simulate severe bottlenecks and subsequent selection on standing variation, mimicking adaptation after establishment of a new small population, such as an island or an artificial selection experiment. Using simulations of single loci under positive selection and population genetics theory, we examine how population size and age of the population isolate affect the ability of outlier scans for selection to identify adaptive alleles using both single-site measures and haplotype structure. We find and explain an optimal combination of selection strength, starting frequency, and age of the adaptive allele, which we refer to as a Goldilocks zone, where adaptation is likely to occur and yet the adaptive variants are most likely to derive from a single ancestor (a 'hard' selective sweep); in this zone, four commonly used statistics detect selection with high power. Real-world examples of both island colonization and experimental evolution studies are discussed. Our study provides concrete considerations to be made before embarking on whole-genome sequencing of differentiated populations. PMID:27297514

  7. Automatic Differentiation Variational Inference

    OpenAIRE

    Kucukelbir, Alp; Tran, Dustin; Ranganath, Rajesh; Gelman, Andrew; Blei, David M.

    2016-01-01

    Probabilistic modeling is iterative. A scientist posits a simple model, fits it to her data, refines it according to her analysis, and repeats. However, fitting complex models to large data is a bottleneck in this process. Deriving algorithms for new models can be both mathematically and computationally challenging, which makes it difficult to efficiently cycle through the steps. To this end, we develop automatic differentiation variational inference (ADVI). Using our method, the scientist on...

  8. Genetic variation of mini- and microsatellites and a clonal structure in Enterocytozoon bieneusi population in foxes and raccoon dogs and population differentiation of the parasite between fur animals and humans.

    Science.gov (United States)

    Li, Wei; Wan, Qiang; Yu, Qinlei; Yang, Yuqi; Tao, Wei; Jiang, Yanxue; Xiao, Lihua

    2016-07-01

    Enterocytozoon bieneusi is an obligate intracellular protozoan parasite that infects a wide range of mammal hosts and birds. Previous genotypic surveys were limited to measure the polymorphisms at the ribosomal internal transcribed spacer (ITS) that evolved slowly. Data on population structure are available only on E. bieneusi isolates from primates. This study explored the genotypic and phylogenetic characteristics of four mini- and microsatellites and performed a population genetic analysis in 39 E. bieneusi isolates of potentially zoonotic ITS genotype D from farmed foxes and raccoon dogs in China. Sequence polymorphisms facilitated determination of six, two, four, and five genotypes at markers MS1, MS3, MS4, and MS7, respectively. Patterns of phylogeny revealed different levels of diversity within and among the genetic markers. Clear genotypic and phylogenetic divergences between E. bieneusi isolates of ITS genotype D from fur animals and humans were observed at individual markers. Complete linkage disequilibrium and very limited recombination in subsequent population genetic analysis supported a clonal structure for E. bieneusi population from fur animals (FID). Phylogenetic analysis, genetic network, and measures of F ST and gene flow demonstrated population differentiation of FID from two known human E. bieneusi populations HID (with a clonal structure) and HIA (with an epidemic structure). The data indicated an ideal resolving power of MLST compared to the previously widely used ITS genotyping and confirmed the clonal nature and population differentiation of E. bieneusi in various hosts. PMID:27095568

  9. Bottlenecks of motion processing during a visual glance: the leaky flask model.

    Directory of Open Access Journals (Sweden)

    Haluk Öğmen

    Full Text Available Where do the bottlenecks for information and attention lie when our visual system processes incoming stimuli? The human visual system encodes the incoming stimulus and transfers its contents into three major memory systems with increasing time scales, viz., sensory (or iconic memory, visual short-term memory (VSTM, and long-term memory (LTM. It is commonly believed that the major bottleneck of information processing resides in VSTM. In contrast to this view, we show major bottlenecks for motion processing prior to VSTM. In the first experiment, we examined bottlenecks at the stimulus encoding stage through a partial-report technique by delivering the cue immediately at the end of the stimulus presentation. In the second experiment, we varied the cue delay to investigate sensory memory and VSTM. Performance decayed exponentially as a function of cue delay and we used the time-constant of the exponential-decay to demarcate sensory memory from VSTM. We then decomposed performance in terms of quality and quantity measures to analyze bottlenecks along these dimensions. In terms of the quality of information, two thirds to three quarters of the motion-processing bottleneck occurs in stimulus encoding rather than memory stages. In terms of the quantity of information, the motion-processing bottleneck is distributed, with the stimulus-encoding stage accounting for one third of the bottleneck. The bottleneck for the stimulus-encoding stage is dominated by the selection compared to the filtering function of attention. We also found that the filtering function of attention is operating mainly at the sensory memory stage in a specific manner, i.e., influencing only quantity and sparing quality. These results provide a novel and more complete understanding of information processing and storage bottlenecks for motion processing.

  10. Effect of host plant chemistry on genetic differentiation and reduction of gene flow among Anastrepha fraterculus (Diptera: Tephritidae) populations exploiting sympatric, synchronic hosts.

    Science.gov (United States)

    Oroño, Luis; Paulin, Laura; Alberti, Andrea C; Hilal, Mirna; Ovruski, Sergio; Vilardi, Juan C; Rull, Juan; Aluja, Martin

    2013-08-01

    Herbivore host specialization includes changes in behavior, driven by locally induced adaptations to specific plants. These adaptations often result in sexual isolation that can be gauged through detection of reduced gene flow between host associated populations. Hypothetically, reduced gene flow can be mediated both by differential response to specific plant kairomones and by the influence of larval diet on some adult traits such as pheromone composition. These hypotheses could serve as a model to explain rapid radiation of phytophagous tephritid fruit flies, a group that includes several complexes of cryptic species. The South American Fruit Fly Anastrepha fraterculus (Wiedemann) is a complex of at least seven cryptic species among which pheromone mediated sexual isolation resulted in rapid differentiation. Cryptic species also exhibit differences in host affiliation. In search of a model explaining rapid radiation in this group, we studied host plant chemical composition and genetic structure of three host associated sympatric populations of A. fraterculus. Chemical composition among host plant fruit varied widely both for nutrient and potentially toxic secondary metabolite content. Adaptation to plant chemistry appears to have produced population differentiation. We found host mediated differentiation to be stronger between populations exploiting sympatric synchronic hosts differing in chemical composition, than between populations that exploit hosts that fruit in succession. Gene flow among such host associated populations was extremely low. We propose as a working hypothesis for future research, that for those differences to persist over time, isolating mechanisms such as male produced sex pheromones and female preferences resulting from adaptation to different larval diets should evolve. PMID:23905743

  11. Analysis of registered CDM projects: potential removal of evidenced bottlenecks

    Energy Technology Data Exchange (ETDEWEB)

    Agosto, D.; Bombard, P.; Gostinelli, F.

    2007-07-01

    The Clean Development Mechanism (CDM) has developed during its first period of implementation, a distinctive set of patterns. The authors thought of concentrating on the CDM analysis in order to highlight potential remedies or reasons for given bottlenecks. In order to establish a sort of extensive SWOT analysis for CDMs, all the 356 projects actually (November 2006) registered at UNFCCC were examined, together with all the about 1000 PDDs presented to the UNFCCC but not registered yet. The CDM projects have been studied trying to cluster projects according to relevant characteristics, both from a technical and an economic point of view. Chosen indicators are meant to identify: more convenient/more diffused energy system for a CDM; reasons for a geographical distribution of different types of projects; potentials for a future exploitation of lower used technologies in CDM. Conclusions are drawn and appropriate tables and graphs presented. (1) the Baseline Emission Factor, combined to economic patterns, is the pivotal factor that characterizes both choices of host country and technology; (2) some technologies can exploit appropriately CDM scheme, whilst other technologies, are constrained by it. (3) there are still some important weak points: grouping of non Annex I countries; crediting period; criteria for the evaluation of sustainable development. (auth)

  12. Photonic ADC: overcoming the bottleneck of electronic jitter.

    Science.gov (United States)

    Khilo, Anatol; Spector, Steven J; Grein, Matthew E; Nejadmalayeri, Amir H; Holzwarth, Charles W; Sander, Michelle Y; Dahlem, Marcus S; Peng, Michael Y; Geis, Michael W; DiLello, Nicole A; Yoon, Jung U; Motamedi, Ali; Orcutt, Jason S; Wang, Jade P; Sorace-Agaskar, Cheryl M; Popović, Miloš A; Sun, Jie; Zhou, Gui-Rong; Byun, Hyunil; Chen, Jian; Hoyt, Judy L; Smith, Henry I; Ram, Rajeev J; Perrott, Michael; Lyszczarz, Theodore M; Ippen, Erich P; Kärtner, Franz X

    2012-02-13

    Accurate conversion of wideband multi-GHz analog signals into the digital domain has long been a target of analog-to-digital converter (ADC) developers, driven by applications in radar systems, software radio, medical imaging, and communication systems. Aperture jitter has been a major bottleneck on the way towards higher speeds and better accuracy. Photonic ADCs, which perform sampling using ultra-stable optical pulse trains generated by mode-locked lasers, have been investigated for many years as a promising approach to overcome the jitter problem and bring ADC performance to new levels. This work demonstrates that the photonic approach can deliver on its promise by digitizing a 41 GHz signal with 7.0 effective bits using a photonic ADC built from discrete components. This accuracy corresponds to a timing jitter of 15 fs - a 4-5 times improvement over the performance of the best electronic ADCs which exist today. On the way towards an integrated photonic ADC, a silicon photonic chip with core photonic components was fabricated and used to digitize a 10 GHz signal with 3.5 effective bits. In these experiments, two wavelength channels were implemented, providing the overall sampling rate of 2.1 GSa/s. To show that photonic ADCs with larger channel counts are possible, a dual 20-channel silicon filter bank has been demonstrated. PMID:22418205

  13. Information bottleneck based incremental fuzzy clustering for large biomedical data.

    Science.gov (United States)

    Liu, Yongli; Wan, Xing

    2016-08-01

    Incremental fuzzy clustering combines advantages of fuzzy clustering and incremental clustering, and therefore is important in classifying large biomedical literature. Conventional algorithms, suffering from data sparsity and high-dimensionality, often fail to produce reasonable results and may even assign all the objects to a single cluster. In this paper, we propose two incremental algorithms based on information bottleneck, Single-Pass fuzzy c-means (spFCM-IB) and Online fuzzy c-means (oFCM-IB). These two algorithms modify conventional algorithms by considering different weights for each centroid and object and scoring mutual information loss to measure the distance between centroids and objects. spFCM-IB and oFCM-IB are used to group a collection of biomedical text abstracts from Medline database. Experimental results show that clustering performances of our approaches are better than such prominent counterparts as spFCM, spHFCM, oFCM and oHFCM, in terms of accuracy. PMID:27260783

  14. HIV/AIDS: global trends, global funds and delivery bottlenecks

    Directory of Open Access Journals (Sweden)

    Hadingham Jacqui

    2005-08-01

    Full Text Available Abstract Globalisation affects all facets of human life, including health and well being. The HIV/AIDS epidemic has highlighted the global nature of human health and welfare and globalisation has given rise to a trend toward finding common solutions to global health challenges. Numerous international funds have been set up in recent times to address global health challenges such as HIV. However, despite increasingly large amounts of funding for health initiatives being made available to poorer regions of the world, HIV infection rates and prevalence continue to increase world wide. As a result, the AIDS epidemic is expanding and intensifying globally. Worst affected are undoubtedly the poorer regions of the world as combinations of poverty, disease, famine, political and economic instability and weak health infrastructure exacerbate the severe and far-reaching impacts of the epidemic. One of the major reasons for the apparent ineffectiveness of global interventions is historical weaknesses in the health systems of underdeveloped countries, which contribute to bottlenecks in the distribution and utilisation of funds. Strengthening these health systems, although a vital component in addressing the global epidemic, must however be accompanied by mitigation of other determinants as well. These are intrinsically complex and include social and environmental factors, sexual behaviour, issues of human rights and biological factors, all of which contribute to HIV transmission, progression and mortality. An equally important factor is ensuring an equitable balance between prevention and treatment programmes in order to holistically address the challenges presented by the epidemic.

  15. Overcoming bottlenecks in the membrane protein structural biology pipeline.

    Science.gov (United States)

    Hardy, David; Bill, Roslyn M; Jawhari, Anass; Rothnie, Alice J

    2016-06-15

    Membrane proteins account for a third of the eukaryotic proteome, but are greatly under-represented in the Protein Data Bank. Unfortunately, recent technological advances in X-ray crystallography and EM cannot account for the poor solubility and stability of membrane protein samples. A limitation of conventional detergent-based methods is that detergent molecules destabilize membrane proteins, leading to their aggregation. The use of orthologues, mutants and fusion tags has helped improve protein stability, but at the expense of not working with the sequence of interest. Novel detergents such as glucose neopentyl glycol (GNG), maltose neopentyl glycol (MNG) and calixarene-based detergents can improve protein stability without compromising their solubilizing properties. Styrene maleic acid lipid particles (SMALPs) focus on retaining the native lipid bilayer of a membrane protein during purification and biophysical analysis. Overcoming bottlenecks in the membrane protein structural biology pipeline, primarily by maintaining protein stability, will facilitate the elucidation of many more membrane protein structures in the near future. PMID:27284049

  16. Clogging transition of many-particle systems flowing through bottlenecks

    Science.gov (United States)

    Zuriguel, Iker; Parisi, Daniel Ricardo; Hidalgo, Raúl Cruz; Lozano, Celia; Janda, Alvaro; Gago, Paula Alejandra; Peralta, Juan Pablo; Ferrer, Luis Miguel; Pugnaloni, Luis Ariel; Clément, Eric; Maza, Diego; Pagonabarraga, Ignacio; Garcimartín, Angel

    2014-12-01

    When a large set of discrete bodies passes through a bottleneck, the flow may become intermittent due to the development of clogs that obstruct the constriction. Clogging is observed, for instance, in colloidal suspensions, granular materials and crowd swarming, where consequences may be dramatic. Despite its ubiquity, a general framework embracing research in such a wide variety of scenarios is still lacking. We show that in systems of very different nature and scale -including sheep herds, pedestrian crowds, assemblies of grains, and colloids- the probability distribution of time lapses between the passages of consecutive bodies exhibits a power-law tail with an exponent that depends on the system condition. Consequently, we identify the transition to clogging in terms of the divergence of the average time lapse. Such a unified description allows us to put forward a qualitative clogging state diagram whose most conspicuous feature is the presence of a length scale qualitatively related to the presence of a finite size orifice. This approach helps to understand paradoxical phenomena, such as the faster-is-slower effect predicted for pedestrians evacuating a room and might become a starting point for researchers working in a wide variety of situations where clogging represents a hindrance.

  17. Population genomics of the Anthropocene: urbanization is negatively associated with genome-wide variation in white-footed mouse populations.

    Science.gov (United States)

    Munshi-South, Jason; Zolnik, Christine P; Harris, Stephen E

    2016-04-01

    Urbanization results in pervasive habitat fragmentation and reduces standing genetic variation through bottlenecks and drift. Loss of genomewide variation may ultimately reduce the evolutionary potential of animal populations experiencing rapidly changing conditions. In this study, we examined genomewide variation among 23 white-footed mouse (Peromyscus leucopus) populations sampled along an urbanization gradient in the New York City metropolitan area. Genomewide variation was estimated as a proxy for evolutionary potential using more than 10 000 single nucleotide polymorphism (SNP) markers generated by ddRAD-Seq. We found that genomewide variation is inversely related to urbanization as measured by percent impervious surface cover, and to a lesser extent, human population density. We also report that urbanization results in enhanced genomewide differentiation between populations in cities. There was no pattern of isolation by distance among these populations, but an isolation by resistance model based on impervious surface significantly explained patterns of genetic differentiation. Isolation by environment modeling also indicated that urban populations deviate much more strongly from global allele frequencies than suburban or rural populations. This study is the first to examine loss of genomewide SNP variation along an urban-to-rural gradient and quantify urbanization as a driver of population genomic patterns. PMID:27099621

  18. Allozyme variation in Czech populations of the invasive spiny-cheek crayfish Orconectes limosus (Cambaridae

    Directory of Open Access Journals (Sweden)

    L. Filipová

    2009-01-01

    Full Text Available The North American spiny-cheek crayfish, Orconectes limosus, was most probably introduced into Europe only once, in 1890. The size of the founding population was just 90 individuals. Low genetic variability resulting from a bottleneck effect during introduction might therefore be supposed in European spiny-cheek crayfish populations. On the other hand, the fast spread of O. limosus in Europe and colonisation of various habitats suggest that this species does not suffer from inbreeding depression due to an introduction bottleneck. We analysed 14 O. limosus populations from the Czech Republic using allozyme electrophoresis to evaluate the level of intra- and among-population genetic variation. Out of eight well-scoring allozyme loci chosen for detailed analysis, six were variable in studied populations, suggesting that sufficient variability was maintained during the introduction. Genetic differentiation of Czech populations of the spiny-cheek crayfish was relatively low and did not show any clear geographic pattern, probably due to long-range translocations by humans.

  19. Inducible nitric oxide synthase polymorphism is associated with the increased risk of differentiated gastric cancer in a Japanese population

    Institute of Scientific and Technical Information of China (English)

    Yasuyuki Goto; Takafumi Ando; Mariko Naito; Hidemi Goto; Nobuyuki Hamajima

    2006-01-01

    AIM: To examine the association of inducible nitric oxide synthase (iNOS) C150T polymorphism with gastric cancer, as well as with gastric atrophy and H pylori seropositivity.METHODS: A single nucleotide polymorphism of iNOS C150T was examined for 454 Japanese health checkup examinees (126 males and 328 females) aged 35 to 85 years without a history of cancer and 202 gastric cancer patients (134 males and 68 females) aged 33 to 94 years with pathologically confirmed diagnosis of gastric adenocarcinoma.RESULTS: The iNOS C150T polymorphism was not associated with gastric atrophy or with H pylori seropositivity. The odds ratio (OR) of the C/T +T/T for gastric cancer was increased without statistical significance (OR=1.19, 95% confidence interval (CI):0.68-2.08). In the differentiated subgroup (n = 113),however, the OR of the C/T genotype for gastric cancer was significant (OR = 2.02, 95% CI: 1.04-3.92) relative to the C/C genotype. In addition, considering the location of gastric cancer (n = 105), there were significant differences between the controls and non-cardia group with the OR of 2.13 (95% CI: 1.08-4.18) for C/T and 1.94(95% CI: 1.00-3.78) for C/T + T/T.CONCLUSION: The iNOS C150T polymorphism is associated with the risk of H pylori-related gastric cancer in a Japanese population. This polymorphism may play an important role in increasing the risk of gastric cancer in Asian countires with the highest rates of gastric cancer.

  20. Childhood osteomyelitis-incidence and differentiation from other acute onset musculoskeletal features in a population-based study

    Directory of Open Access Journals (Sweden)

    Reiseter Tor

    2008-10-01

    Full Text Available Abstract Background Osteomyelitis can be difficult to diagnose and there has previously not been a prospective approach to identify all children in a defined geographic area. The aim of this study was to assess the annual incidence of osteomyelitis in children, describe the patient and disease characteristics in those with acute ( Methods In a population-based Norwegian study physicians were asked to refer all children with suspected osteomyelitis. Children with osteomyelitis received follow-up at six weeks, six months and thereafter as long as clinically needed. Results The total annual incidence rate of osteomyelitis was 13 per 100 000 (acute osteomyelitis 8 and subacute osteomyelitis 5 per 100 000. The incidence was higher in patients under the age of 3 than in older children (OR 2.9, 95%: CI 2.3–3.7. The incidence of non-vertebral osteomyelitis was higher than the incidence of vertebral osteomyelitis (10 vs. 3 per 100 000; p = .002. Vertebral osteomyelitis was more frequent in girls than in boys (OR 7.0, 95%: CI 3.3–14.7. ESR ≥ 40 mm/hr had the highest positive predictive laboratory value to identify osteomyelitis patients at 26% and MRI had a positive predictive value of 85%. Long-bone infection was found in 16 (43% patients. ESR, CRP, white blood cell count, neutrophils and platelet count were higher for patients with acute osteomyelitis than for patients with subacute osteomyelitis. Subacute findings on MRI and doctor's delay were more common in subacute osteomyelitis than in acute osteomyelitis patients. Blood culture was positive in 26% of the acute osteomyelitis patients and was negative in all the subacute osteomyelitis patients. Conclusion The annual incidence of osteomyelitis in Norway remains high. ESR values and MRI scan may help to identify osteomyelitis patients and differentiate acute and subacute osteomyelitis.

  1. Genetic differentiation of hypothalamus parentally biased transcripts in populations of the house mouse implicate the Prader-Willi syndrome imprinted region as a possible source of behavioral divergence.

    Science.gov (United States)

    Lorenc, Anna; Linnenbrink, Miriam; Montero, Inka; Schilhabel, Markus B; Tautz, Diethard

    2014-12-01

    Parentally biased expression of transcripts (genomic imprinting) in adult tissues, including the brain, can influence and possibly drive the evolution of behavioral traits. We have previously found that paternally determined cues are involved in population-specific mate choice decisions between two populations of the Western house mouse (Mus musculus domesticus). Here, we ask whether this could be mediated by genomically imprinted transcripts that are subject to fast differentiation between these populations. We focus on three organs that are of special relevance for mate choice and behavior: The vomeronasal organ (VNO), the hypothalamus, and the liver. To first identify candidate transcripts at a genome-wide scale, we used reciprocal crosses between M. m. domesticus and M. m. musculus inbred strains and RNA sequencing of the respective tissues. Using a false discovery cutoff derived from mock reciprocal cross comparisons, we find a total of 66 imprinted transcripts, 13 of which have previously not been described as imprinted. The largest number of imprinted transcripts were found in the hypothalamus; fewer were found in the VNO, and the least were found in the liver. To assess molecular differentiation and imprinting in the wild-derived M. m. domesticus populations, we sequenced the RNA of the hypothalamus from individuals of these populations. This confirmed the presence of the above identified transcripts also in wild populations and allowed us to search for those that show a high genetic differentiation between these populations. Our results identify the Ube3a-Snrpn imprinted region on chromosome 7 as a region that encompasses the largest number of previously not described transcripts with paternal expression bias, several of which are at the same time highly differentiated. For four of these, we confirmed their imprinting status via single nucleotide polymorphism-specific pyrosequencing assays with RNA from reciprocal crosses. In addition, we find the

  2. Spatial and temporal population genetic variation and structure of Nothotsuga longibracteata (Pinaceae, a relic conifer species endemic to subtropical China

    Directory of Open Access Journals (Sweden)

    Yingjun Qiu

    2013-01-01

    Full Text Available Nothotsuga longibracteata, a relic and endangered conifer species endemic to subtropical China, was studied for examining the spatial-temporal population genetic variation and structure to understand the historical biogeographical processes underlying the present geographical distribution. Ten populations were sampled over the entire natural range of the species for spatial analysis, while three key populations with large population sizes and varied age structure were selected for temporal analyses using both nuclear microsatellites (nSSR and chloroplast microsatellites (cpSSR. A recent bottleneck was detected in the natural populations of N. longibracteata. The spatial genetic analysis showed significant population genetic differentiation across its total geographical range. Notwithstanding, the temporal genetic analysis revealed that the level of genetic diversity between different age class subpopulations remained constant over time. Eleven refugia of the Last Glacial Maximum were identified, which deserve particular attention for conservation management.

  3. Genetic diversity of and differentiation among five populations of blunt snout bream (Megalobrama amblycephala revealed by SRAP markers: implications for conservation and management.

    Directory of Open Access Journals (Sweden)

    Wei Ji

    Full Text Available The blunt snout bream (Megalobrama amblycephala is an important freshwater aquaculture fish throughout China. Because of widespread introductions of this species to many regions, the genetic diversity of wild and natural populations is now threatened. In the present study, SRAP (sequence-related amplified polymorphism markers were used to assess genetic diversity of blunt snout bream. Three natural populations (Liangzi Lake, Poyang Lake and Yuni Lake, one cultured population (Nanxian and one genetic strain ('Pujiang No. 1' of blunt snout bream were screened with 88 SRAP primer combinations, of which 13 primer pairs produced stable and reproducible amplification patterns. In total, 172 bands were produced, of which 132 bands were polymorphic. Nei's gene diversity (h and Shannon's information index (I values provided evidence of differences in genetic diversity among the five populations (Poyang Lake>Liangzi Lake>Nanxian>'Pujiang No. 1'>Yuni Lake. Based on cluster analysis conducted on genetic distance values, the five blunt snout bream populations were divided into three groups, Poyang Lake and Liangzi Lake (natural populations, Nanxian and 'Pujiang No. 1' (cultured population and genetically selected strain, and Yuni Lake (natural population. Significant genetic differentiation was found among the five populations using analysis of molecular variance (AMOVA, with more genetic divergence existing among populations (55.49%, than within populations (44.51%. This molecular marker technique is a simple and efficient method to quantify genetic diversity within and among fish populations, and is employed here to help manage and conserve germplasm variability of blunt snout bream and to support the ongoing selective breeding programme for this fish.

  4. Genetic differentiation and trade among populations of peach palm ( Bactris gasipaes Kunth) in the Peruvian Amazon-implications for genetic resource management.

    Science.gov (United States)

    Adin, A; Weber, J C; Sotelo Montes, C; Vidaurre, H; Vosman, B; Smulders, M J M

    2004-05-01

    Peach palm ( Bactris gasipaes Kunth) is cultivated for fruit and 'heart of palm', and is an important component of agroforestry systems in the Peruvian Amazon. In this study, AFLP was used to compare genetic diversity among domesticated populations along the Paranapura and Cuiparillo rivers, which are managed by indigenous and colonist farming communities, respectively. Gene diversity was 0.2629 for the populations in indigenous communities and 0.2534 in colonist communities. Genetic differentiation among populations ( G(st)) was 0.0377-0.0416 ( P<0.01) among populations along both rivers. There was no relation between genetic differentiation and the geographical location of populations along the rivers. Since natural seed dispersal by birds and rodents is thought to occur only across relatively short distances (100-200 m), it is likely that exchange of material by farmers and commercial traders is responsible for most of the 'long-distance' (over more than 20 km) gene flow among populations along the two rivers studied. This exchange of material may be important to counteract the effects of selection as well as genetic drift in small groups of trees in farmers' fields, much as in a metapopulation, and may account for the weak genetic differentiation between the two rivers ( G(st)=0.0249, P<0.01). A comparison with samples from other landraces in Peru and Brazil showed the existence of an isolation-by-distance structure up to 3,000 km, consistent with gene flow on a regional scale, likely mediated by trade in the Amazon Basin. Results are discussed with regard to practical implications for the management of genetic resources with farming communities. PMID:14985969

  5. Genetic variation and population differentiation of Michelia formosana (Magnoliaceae) based on cpDNA variation and RAPD fingerprints: relevance to post-Pleistocene recolonization.

    Science.gov (United States)

    Lu, Sheng-You; Hong, Kuo-Hsiang; Liu, Show-Ling; Cheng, Yu-Pin; Wu, Wen-Luan; Chiang, Tzen-Yuh

    2002-06-01

    We used sequence variation of the atpB- rbcL intergenic spacer of cpDNA and nested clade analysis to assess the phylogeographic pattern of Michelia formosana, a species restricted to Taiwan and the Ryukyus. In total, 31 haplotypes were identified and clustered into four major chlorotypes. Genetic composition of nearly all populations was heterogeneous and paraphyletic phylogenetically. Although the apportionment of cpDNA variation hardly revealed a geographic pattern due to the coancestry of dominant sequences, some chlorotypes were restrictedly distributed. According to the patterns of clade dispersion and displacement, a reconstructed minimum spanning network revealed that historical events of past fragmentation and range expansion, associated with glaciation, may have shaped the phylogeographic patterns of M. formosana. Four possible refugia were identified: the Iriomote and Ishigaki Islands (the southern Ryukyus), Wulai (northern Taiwan), and Nanjen (southern Taiwan), on the basis of the interior positions of their haplotypes in the network and the high level of nucleotide diversity. Given insufficient time for coalescence at the cpDNA locus since the late Pleistocene recolonization, lineage sorting led to low levels of genetic differentiation among populations. In contrast, hierarchical examination of the random amplified polymorphic DNA (RAPD) data scored from six populations across three geographical regions, using an analysis of molecular variance (AMOVA), indicated high genetic differentiation both among populations (Phi(ST) = 0.471) and among regions (Phi(CT) = 0.368). An unweighted pair group method with arithmetic mean (UPGMA) tree of the RAPD fingerprints revealed that populations of two offshore islands of eastern Taiwan ( M. formosana var. kotoensis) were clustered with geographically remote populations of the Ryukyus instead of those in southern Taiwan, suggesting some historical division due to geographic barriers of the central mountain range. In

  6. Only adding stationary storage to vaccine supply chains may create and worsen transport bottlenecks.

    Science.gov (United States)

    Haidari, Leila A; Connor, Diana L; Wateska, Angela R; Brown, Shawn T; Mueller, Leslie E; Norman, Bryan A; Schmitz, Michelle M; Paul, Proma; Rajgopal, Jayant; Welling, Joel S; Leonard, Jim; Claypool, Erin G; Weng, Yu-Ting; Chen, Sheng-I; Lee, Bruce Y

    2013-01-01

    Although vaccine supply chains in many countries require additional stationary storage and transport capacity to meet current and future needs, international donors tend to donate stationary storage devices far more often than transport equipment. To investigate the impact of only adding stationary storage equipment on the capacity requirements of transport devices and vehicles, we used HERMES (Highly Extensible Resource for Modeling Supply Chains) to construct a discrete event simulation model of the Niger vaccine supply chain. We measured the transport capacity requirement for each mode of transport used in the Niger vaccine cold chain, both before and after adding cold rooms and refrigerators to relieve all stationary storage constraints in the system. With the addition of necessary stationary storage, the average transport capacity requirement increased from 88% to 144% for cold trucks, from 101% to 197% for pickup trucks, and from 366% to 420% for vaccine carriers. Therefore, adding stationary storage alone may worsen or create new transport bottlenecks as more vaccines flow through the system, preventing many vaccines from reaching their target populations. Dynamic modeling can reveal such relationships between stationary storage capacity and transport constraints. PMID:23903398

  7. Genetic architecture and bottleneck analyses of Salem Black goat breed based on microsatellite markers

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    A. K. Thiruvenkadan

    2014-09-01

    Full Text Available Aim: The present study was undertaken in Salem Black goat population for genetic analysis at molecular level to exploit the breed for planning sustainable improvement, conservation and utilization, which subsequently can improve the livelihood of its stakeholders. Materials and Methods: Genomic DNA was isolated from blood samples of 50 unrelated Salem Black goats with typical phenotypic features in several villages in the breeding tract and the genetic characterization and bottleneck analysis in Salem Black goat was done using 25 microsatellite markers as recommended by the Food and Agricultural Organization, Rome, Italy. The basic measures of genetic variation were computed using bioinformatic software. To evaluate the Salem Black goats for mutation drift equilibrium, three tests were performed under three different mutation models, viz., infinite allele model (IAM, stepwise mutation model (SMM and two-phase model (TPM and the observed gene diversity (He and expected equilibrium gene diversity (Heq were estimated under different models of microsatellite evolution. Results: The study revealed that the observed number of alleles ranged from 4 (ETH10, ILSTS008 to 17 (BM64444 with a total of 213 alleles and mean of 10.14±0.83 alleles across loci. The overall observed heterozygosity, expected heterozygosity, inbreeding estimate and polymorphism information content values were 0.631±0.041, 0.820±0.024, 0.233±0.044 and 0.786±0.023 respectively indicating high genetic diversity. The average observed gene diversities (He pooled over different markers was 0.829±0.024 and the average expected gene diversities under IAM, TPM and SMM models were 0.769±0.026, 0.808±0.024 and 0.837±0.020 respectively. The number of loci found to exhibit gene diversity excess under IAM, TPM and SMM models were 18, 17 and 12 respectively. Conclusion: All the three statistical tests, viz., sign test, standardized differences test and Wilcoxon sign rank test, revealed

  8. A genetic association study between growth differentiation factor 5 (GDF 5 polymorphism and knee osteoarthritis in Thai population

    Directory of Open Access Journals (Sweden)

    Sura Thanyachai

    2011-09-01

    Full Text Available Abstract Objective Osteoarthritis (OA is a multi-factorial disease and genetic factor is one of the important etiologic risk factors. Various genetic polymorphisms have been elucidated that they might be associated with OA. Recently, several studies have shown an association between Growth Differentiation Factor 5(GDF5 polymorphism and knee OA. However, the role of genetic predisposing factor in each ethnic group cannot be replicated to all, with conflicting data in the literatures. Therefore, the aim of this study was to investigate the association between GDF5 polymorphism and knee OA in Thai population. Materials and Methods One hundred and ninety three patients aged 54-88 years who attended Ramathibodi Hospital were enrolled. Ninety cases with knee OA according to American College of Rheumatology criteria and one hundred and three cases in control group gave informed consent. Blood sample (5 ml were collected for identification of GDF5 (rs143383 single nucleotide polymorphism by PCR/RFLP according to a standard protocol. This study protocol was approved by the Ethics Committee on human experimentation of Ramathibodi Hospital Faculty of Medicine, Mahidol University. Odds ratios (OR and 95% confidence intervals were calculated for the risk of knee OA by genotype (TT, TC and CC and allele (T/C analyses. Results The baseline characteristics between two groups including job, smoking and activity were not different, except age and BMI. The entire cases and controls were in Hardy-Weinberg equilibrium (p > 0.05. The OA knee group (n = 90 had genotypic figure which has shown by TT 42.2% (n = 38, TC 45.6% (n = 41 and CC 12% (n = 11, whereas the control group (n = 103 revealed TT 32% (n = 33, TC 45.6% (n = 47, and CC 22.3% (n = 23, respectively. Genotypic TT increased risk of knee OA as compared to CC [OR = 2.41 (P = 0.04, 95%CI = 1.02-5.67]. In the allele analysis, the T allele was found to be significantly associated with knee OA [OR = 1.53 (P = 0

  9. Genetic Differentiation within the Puccinia triticina Population in South America and Comparison with the North American Population Suggests Common Ancestry and Intercontinental Migration

    Science.gov (United States)

    Leaf rust, caused by Puccinia triticina is the most prevalent and widespread disease of wheat in South America. The objective of this study was to determine the number of genetically differentiated groups of P. triticina that are currently present in South America, and to compare the South American ...

  10. Differentiation of muscle, fat, cartilage, and bone from progenitor cells present in a bone-derived clonal cell population: effect of dexamethasone

    OpenAIRE

    1988-01-01

    RCJ 3.1, a clonally derived cell population isolated from 21-d fetal rat calvaria, expresses the osteoblast-associated characteristics of polygonal morphology, a cAMP response to parathyroid hormone, synthesis of predominantly type I collagen, and the presence of 1,25- dihydroxyvitamin D3-regulated alkaline phosphatase activity. When cultured in the presence of ascorbic acid, sodium beta- glycerophosphate, and the synthetic glucocorticoid dexamethasone, this clone differentiated in a time-dep...

  11. Lexical Access and Dual-Task Performance: Determining the Locus of the Bottleneck

    Science.gov (United States)

    Allen, Phil

    2004-01-01

    During the two years of funding for NASA Grant "NCC21325, Lexical access and dual-task performance: Determining the locus of the bottleneck," we completed three experiments involving the psychological refractory period (PRP) and word frequency.

  12. Processing bottlenecks in dual-task performance: structural limitation or strategic postponement?

    Science.gov (United States)

    Ruthruff, E.; Pashler, H. E.; Klaassen, A.

    2001-01-01

    Recent evidence indicates that a central bottleneck causes much of the slowing that occurs when two tasks are performed at the same time. This bottleneck might reflect a structural limitation inherent in the cognitive architecture. Alternatively, the bottleneck might reflect strategic (i.e., voluntary) postponement, induced by instructions to emphasize one task over the other. To distinguish structural limitations from strategic postponement, we examine a new paradigm in which subjects are told to place equal emphasis on both tasks and to emit both responses at about the same time. An experiment using this paradigm demonstrated patterns of interference that cannot easily be attributed to strategic postponement, preparation effects, or conflicts in response production. The data conform closely to the predictions of structural central bottleneck models.

  13. Is Dementia Differentially Distributed? A Study on the Prevalence of Dementia in Migrant, Urban, Rural, and Tribal Elderly Population of Himalayan Region in Northern India

    Directory of Open Access Journals (Sweden)

    Sunil Kumar Raina

    2014-01-01

    Full Text Available Background: Throughout the world, a large number of surveys have been carried out to find the prevalence of dementia with variable results. Aims: This study was to generate data on the prevalence of dementia and to generate a hypothesis on the differential distribution across populations. Materials and Methods: Four settings identified for the purpose of this study included a migrant, urban, rural, and tribal. The study was conducted in two phases: 1 A screening phase and 2 a clinical phase, on 2,000 individuals above 60 years of age. To complete the required sample of 2,000 elderly individuals, 500 individuals were approached from each site. Nobody refused to participate. Results: A total of 32/2,000 (1.6% elderly individuals were classified as demented. No case of dementia was reported from tribal population. A look at sex differential reveals that majority (21/32; 66% of individuals identified as demented were females. As age advanced scores on cognitive screen decreased with elders above 80 years of age showing lowest scores. Out of 32, 18 (56% of patients classified as demented were more than 80 years of age. Conclusion: The findings of this study are in agreement with previous studies which point towards differential distribution of dementia across populations.

  14. Teacher Diversity in Canada: Leaky Pipelines, Bottlenecks, and Glass Ceilings

    Science.gov (United States)

    Ryan, James; Pollock, Katina; Antonelli, Fab

    2009-01-01

    This article examines the racial diversity of the teacher population in Canada. In particular, we compare the number of teachers of colour in Canadian elementary and secondary schools from the 2001 and 2006 Census data with the diversity of the student and general populations. We also explore ways to understand the gap between the proportion of…

  15. Circuit model for spin-bottleneck resistance in magnetic-tunnel-junction devices

    OpenAIRE

    Jungwirth, T.; MacDonald, A. H.

    1998-01-01

    Spin-bottlenecks are created in magnetic-tunnel-junction devices by spatial inhomogeneity in the relative resistances for up and down spins. We propose a simple electrical circuit model for these devices which incorporates spin-bottleneck effects and can be used to calculate their overall resistance and magnetoresistance. The model permits a simple understanding of the dependence of device magnetoresistance on spin diffusion lengths, tunneling magnetoresistance, and majority and minority spin...

  16. A Framework for Accelerating Bottlenecks in GPU Execution with Assist Warps

    OpenAIRE

    Vijaykumar, Nandita; Pekhimenko, Gennady; Jog, Adwait; Ghose, Saugata; Bhowmick, Abhishek; Ausavarangnirun, Rachata; Das, Chita; Kandemir, Mahmut; Mowry, Todd C.; Mutlu, Onur

    2016-01-01

    Modern Graphics Processing Units (GPUs) are well provisioned to support the concurrent execution of thousands of threads. Unfortunately, different bottlenecks during execution and heterogeneous application requirements create imbalances in utilization of resources in the cores. For example, when a GPU is bottlenecked by the available off-chip memory bandwidth, its computational resources are often overwhelmingly idle, waiting for data from memory to arrive. This work describes the Core-Assist...

  17. BOTTLENECK ANALYSIS AND STRATEGIC PLANNING ON CHILDHOOD DIARRHEA MANAGEMENT IN 6 HIGH PRIORITY DISTRICTS OF GUJARAT

    OpenAIRE

    Rupani Mihir

    2015-01-01

    Introduction:Bottleneck Analysis and Strategic Planning exercise was carried out in 6 High Priority Districts (HPDs), under Call-to-Action for RMNCH+A strategy.Rationale: In spite of continued efforts, India is still lagging behind in its MDG goals.Objectives: To identify gaps in childhood diarrhea management and propose strategic options for the same.Materials and Methods: Bottleneck analysis exercisewas carried out based on the Tanahashi model, desk review and focused group discussions betw...

  18. Bottleneck Problem Solution using Biological Models of Attention in High Resolution Tracking Sensors

    OpenAIRE

    Fish, Alexander; Yadid-Pecht, Orly

    2005-01-01

    Every high resolution imaging system suffers from the bottleneck problem. This problem relates to the huge amount of data transmission from the sensor array to a digital signal processing (DSP) and to bottleneck in performance, caused by the requirement to process a large amount of information in parallel. The same problem exists in biological vision systems, where the information, sensed by many millions of receptors should be transmitted and processed in real time. Models, descr...

  19. Analysis of the pedestrian arching at bottleneck based on a bypassing behavior model

    Science.gov (United States)

    Tang, Ming; Jia, Hongfei; Ran, Bin; Li, Jun

    2016-07-01

    A bypassing behavior model was proposed, in which the local optimal decision behavior in the strategy level was modeled in velocity-time domain, to describe how pedestrians bypass the local obstacles considering the relative speed. The model contains (1) pedestrian visual and contact information acquisition; (2) motion state prediction of the local obstacles based on the visual and contact information; (3) pedestrian bypass strategy modeling in the velocity-time domain; (4) moving and overlapping solution. In the numerical solution, velocity domain was divided into n equal angle, the value of n ranges from 2 to infinity, the Manhattan space was refined gradually to Euclid Space accordingly, in which the movement of pedestrians was described. The model was applied to the analysis of pedestrian arching at the bottleneck in the emergent evacuation situation. (1) The results showed that the formation of the pedestrian arching at the bottleneck was deformation pressure, because many pedestrians try to pass through the bottleneck simultaneously, even in the absence of friction, the pedestrian arching still occurs; (2) In the emergent situation, we are more concerned about the bottleneck attribution of resistance to form the arching, the calculation and simulation results showed that the probability of an arching and the bottleneck width is an exponential function relationship, so when the stampede occurs in the middle of the bottleneck, the probability of arching will increase exponentially.

  20. The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics.

    Science.gov (United States)

    Yu, Haiyuan; Kim, Philip M; Sprecher, Emmett; Trifonov, Valery; Gerstein, Mark

    2007-04-20

    It has been a long-standing goal in systems biology to find relations between the topological properties and functional features of protein networks. However, most of the focus in network studies has been on highly connected proteins ("hubs"). As a complementary notion, it is possible to define bottlenecks as proteins with a high betweenness centrality (i.e., network nodes that have many "shortest paths" going through them, analogous to major bridges and tunnels on a highway map). Bottlenecks are, in fact, key connector proteins with surprising functional and dynamic properties. In particular, they are more likely to be essential proteins. In fact, in regulatory and other directed networks, betweenness (i.e., "bottleneck-ness") is a much more significant indicator of essentiality than degree (i.e., "hub-ness"). Furthermore, bottlenecks correspond to the dynamic components of the interaction network-they are significantly less well coexpressed with their neighbors than non-bottlenecks, implying that expression dynamics is wired into the network topology. PMID:17447836

  1. Population dynamics of a natural red deer population over 200 years detected via substantial changes of genetic variation.

    Science.gov (United States)

    Hoffmann, Gunther Sebastian; Johannesen, Jes; Griebeler, Eva Maria

    2016-05-01

    Most large mammals have constantly been exposed to anthropogenic influence over decades or even centuries. Because of their long generation times and lack of sampling material, inferences of past population genetic dynamics, including anthropogenic impacts, have only relied on the analysis of the structure of extant populations. Here, we investigate for the first time the change in the genetic constitution of a natural red deer population over two centuries, using up to 200-year-old antlers (30 generations) stored in trophy collections. To the best of our knowledge, this is the oldest DNA source ever used for microsatellite population genetic analyses. We demonstrate that government policy and hunting laws may have strong impacts on populations that can lead to unexpectedly rapid changes in the genetic constitution of a large mammal population. A high ancestral individual polymorphism seen in an outbreeding population (1813-1861) was strongly reduced in descendants (1923-1940) during the mid-19th and early 20th century by genetic bottlenecks. Today (2011), individual polymorphism and variance among individuals is increasing in a constant-sized (managed) population. Differentiation was high among periods (F ST > ***); consequently, assignment tests assigned individuals to their own period with >85% probability. In contrast to the high variance observed at nuclear microsatellite loci, mtDNA (D-loop) was monomorphic through time, suggesting that male immigration dominates the genetic evolution in this population. PMID:27096075

  2. Epigeic earthworms exert a bottleneck effect on microbial communities through gut associated processes.

    Directory of Open Access Journals (Sweden)

    María Gómez-Brandón

    Full Text Available BACKGROUND: Earthworms play a critical role in organic matter decomposition because of the interactions they establish with microorganisms. The ingestion, digestion, assimilation of organic material in the gut and then casting is the first step in earthworm-microorganism interactions. The current knowledge of these direct effects is still limited for epigeic earthworm species, mainly those living in man-made environments. Here we tested whether and to what extent the earthworm Eisenia andrei is capable of altering the microbiological properties of fresh organic matter through gut associated processes; and if these direct effects are related to the earthworm diet. METHODOLOGY: To address these questions we determined the microbial community structure (phospholipid fatty acid profiles and microbial activity (fluorescein diacetate hydrolysis in the earthworm casts derived from three types of animal manure (cow, horse and pig manure, which differed in microbial composition. PRINCIPAL FINDINGS: The passage of the organic material through the gut of E. andrei reduced the total microbial biomass irrespective of the type of manure, and resulted in a decrease in bacterial biomass in all the manures; whilst leaving the fungi unaffected in the egested materials. However, unlike the microbial biomass, no such reduction was detected in the total microbial activity of cast samples derived from the pig manure. Moreover, no differences were found between cast samples derived from the different types of manure with regards to microbial community structure, which provides strong evidence for a bottleneck effect of worm digestion on microbial populations of the original material consumed. CONCLUSIONS/SIGNIFICANCE: Our data reveal that earthworm gut is a major shaper of microbial communities, thereby favouring the existence of a reduced but more active microbial population in the egested materials, which is of great importance to understand how biotic interactions

  3. Thermodynamic modelling predicts energetic bottleneck for seabirds wintering in the northwest Atlantic.

    Science.gov (United States)

    Fort, Jérôme; Porter, Warren P; Grémillet, David

    2009-08-01

    Studying the energetics of marine top predators such as seabirds is essential to understand processes underlying adult winter survival and its impact on population dynamics. Winter survival is believed to be the single most important life-history trait in long-lived species but its determinants are largely unknown. Seabirds are inaccessible during this season, so conventional metabolic studies are extremely challenging and new approaches are needed. This paper describes and uses a state-of-the-art mechanistic model, Niche Mapper, to predict energy expenditure and food requirements of the two main seabird species wintering in the northwest Atlantic. We found that energy demand increased throughout the winter phase in both species. Across this period, mean estimated daily energy requirements were 1306 kJ day(-1) for Brünnich's guillemots (Uria lomvia) and 430 kJ day(-1) for little auks (Alle alle) wintering off Greenland and Newfoundland. Mean estimated daily food requirements were 547 g wet food day(-1) for Brünnich's guillemots, and 289 g wet food day(-1) for little auks. For both species and both wintering sites, our model predicts a sharp increase in energy expenditure between November and December, primarily driven by climatic factors such as air temperature and wind speed. These findings strongly suggest the existence of an energetic bottleneck for North Atlantic seabirds towards the end of the year, a challenging energetic phase which might explain recurrent events of winter mass-mortality, so called 'seabird winter wrecks'. Our study therefore emphasizes the relevance of thermodynamics/biophysical modelling for investigating the energy balance of wintering marine top predators and its interplay with survival and population dynamics in the context of global change. PMID:19617442

  4. Stocking impact and temporal stability of genetic composition in a brackish northern pike population ( Esox lucius L.), assessed using microsatellite DNA analysis of historical and contemporary samples

    DEFF Research Database (Denmark)

    Larsen, Peter Foged; Hansen, Michael Møller; Eg Nielsen, Einar;

    2005-01-01

    three populations used for stocking. Despite large numbers of stocked fry, the results from both individual and population level admixture analyses demonstrated extremely poor performance and 250), but there were indications of bottlenecks in all samples and populations. We ascribe this finding to...... historical rather than recent bottlenecks, possibly dating back to founder events associated with postglacial recolonisation....

  5. Extensive sampling of polar bears (Ursus maritimus) in the Northwest Passage (Canadian Arctic Archipelago) reveals population differentiation across multiple spatial and temporal scales.

    Science.gov (United States)

    Campagna, Leonardo; Van Coeverden de Groot, Peter J; Saunders, Brenda L; Atkinson, Stephen N; Weber, Diana S; Dyck, Markus G; Boag, Peter T; Lougheed, Stephen C

    2013-09-01

    As global warming accelerates the melting of Arctic sea ice, polar bears (Ursus maritimus) must adapt to a rapidly changing landscape. This process will necessarily alter the species distribution together with population dynamics and structure. Detailed knowledge of these changes is crucial to delineating conservation priorities. Here, we sampled 361 polar bears from across the center of the Canadian Arctic Archipelago spanning the Gulf of Boothia (GB) and M'Clintock Channel (MC). We use DNA microsatellites and mitochondrial control region sequences to quantify genetic differentiation, estimate gene flow, and infer population history. Two populations, roughly coincident with GB and MC, are significantly differentiated at both nuclear (F ST = 0.01) and mitochondrial (ΦST = 0.47; F ST = 0.29) loci, allowing Bayesian clustering analyses to assign individuals to either group. Our data imply that the causes of the mitochondrial and nuclear genetic patterns differ. Analysis of mtDNA reveals the matrilineal structure dates at least to the Holocene, and is common to individuals throughout the species' range. These mtDNA differences probably reflect both genetic drift and historical colonization dynamics. In contrast, the differentiation inferred from microsatellites is only on the scale of hundreds of years, possibly reflecting contemporary impediments to gene flow. Taken together, our data suggest that gene flow is insufficient to homogenize the GB and MC populations and support the designation of GB and MC as separate polar bear conservation units. Our study also provide a striking example of how nuclear DNA and mtDNA capture different aspects of a species demographic history. PMID:24102001

  6. Impact of population structure, effective bottleneck time, and allele frequency on linkage disequilibrium maps

    OpenAIRE

    Zhang, Weihua; Collins, Andrew; Gibson, Jane; Tapper, William J; Hunt, Sarah; Deloukas, Panos; Bentley, David R.; Morton, Newton E.

    2004-01-01

    Genetic maps in linkage disequilibrium (LD) units play the same role for association mapping as maps in centimorgans provide at much lower resolution for linkage mapping. Association mapping of genes determining disease susceptibility and other phenotypes is based on the theory of LD, here applied to relations with three phenomena. To test the theory, markers at high density along a 10-Mb continuous segment of chromosome 20q were studied in African-American, Asian, and Caucasian samples. Popu...

  7. Population Bottlenecks during the Infectious Cycle of the Lyme Disease Spirochete Borrelia burgdorferi

    Czech Academy of Sciences Publication Activity Database

    Rego, Ryan O. M.; Bestor, A.; Štefka, Jan; Rosa, P. A.

    2014-01-01

    Roč. 9, č. 6 (2014), e101009. E-ISSN 1932-6203 Institutional support: RVO:60077344 Keywords : sensu stricto * mammalian host * peromyscus-leucopus * Ixodes ricinus * ticks * mice * transmission * dissemination * diversity * North America Subject RIV: GJ - Animal Vermins ; Diseases, Veterinary Medicine Impact factor: 3.234, year: 2014

  8. Population Aging and Migrant Workers: Bottlenecks in Tuberculosis Control in Rural China

    OpenAIRE

    Bele, Sumedh; Jiang, Wei; Lu, Hui; You, Hua; Fan, Hong; Huang, Lifang; Wang, Qungang; Shen, Hongbing; Wang, Jianming

    2014-01-01

    Background Tuberculosis is a serious global health problem. Its paradigms are shifting through time, especially in rapidly developing countries such as China. Health providers in China are at the forefront of the battle against tuberculosis; however, there are few empirical studies on health providers' perspectives on the challenges they face in tuberculosis control at the county level in China. This study was conducted among health providers to explore their experiences with tuberculosis con...

  9. Raptor mortality in wind farms of southern Spain: mitigation measures on a major migration bottleneck area

    Energy Technology Data Exchange (ETDEWEB)

    Gallego, Antonio-Roman Munoz; Lucas, Manuela De; Casado, Eva; Ferrer, Miguel

    2011-07-01

    Full text: To assess and monitor the impact of wind farms on fauna is crucial if we want to achieve ecologically sustainable development of this renewable energy resource. Today there are clear evidences that the probability of raptor collision depends critically on species behaviour and weather conditions, and the topographic factors related to each windmill. In our study area EIA were not able to predict this differential risk and in these circumstances mitigating the causes of bird mortality becomes a task of major importance, especially to those wind farms located in the Strait of Gibraltar, a water crossing of 14 km at its shortest distance acting as a major migration bottleneck for Paleo-African soaring migrants. We collected all available information on raptor collision from 1992, when the first wind farm was installed, and from 2005 until present a total of 262 turbines, grouped into 20 wind farms, were surveyed in a daily basis through a surveillance program with the main goal of register the actual mortality of birds. A total of 1291 raptors of 19 species were found of which 78.5% correspond to two species, the griffon vulture (Gyps fulvus) and the kestrel (Falco tinnunculus). In order to mitigate the impact on raptors, and particularly on the griffon vulture, in 2007 a program based on selective stopping of turbines was imposed, in collaboration with the environmental competent authority, on new approved projects. During 2008 there was a reduction in mortality by 48%, which remained in 2009 with a remarkably lower economic cost. An analysis of the temporal collision patterns will be presented and discussed, with special attention to those species suffering higher mortality rate, and to those who have some degree of threat. (Author)

  10. [Genetic variability and differentiation of three Russian populations of yellow potato cyst nematode Globodera rostochiensis as revealed by nuclear markers].

    Science.gov (United States)

    Khrisanfova, G G; Kharchevnikov, D A; Popov, I O; Zinov'eva, S V; Semenova, S K

    2008-05-01

    Genetic variability of yellow potato cyst nematode G. rostochiensis from three Russian populations (Karelia, Vladimir oblast, and Moscow oblast) was investigated using two types of nuclear markers. Using RAPD markers identified with the help of six random primers (P-29, OPA-10, OPT-14, OPA-11, OPB-11, and OPH-20), it was possible to distinguish Karelian population from the group consisting of the populations from two adjacent regions (Moscow oblast and Vladimir oblast). Based on the combined matrix, containing 294 RAPD fragments, dendrogram of genetic differences was constructed, and the indices of genetic divergence and partition (P, H, and G(st)), as well as the gene flow indices N(m) between the nematode samples examined, were calculated. The dendrogram structure, genetic diversity indices, and variations of genetic distances between single individuals in each population from Karelia and Central Russia pointed to genetic isolation and higher genetic diversity of the nematodes from Karelia. Based on polymorphism of rDNA first intergenic spacer ITS1, attribution of all populations examined to the species G. rostochiensis was proved. Small variations of the ITS1 sequence in different geographic populations of nematodes from different regions of the species world range did not allow isolation of separate groups within the species. Possible factors (including interregional transportations of seed potato) affecting nematode population structure in Russia are discussed. PMID:18672794

  11. p -State Luminescence in CdSe Nanoplatelets: Role of Lateral Confinement and a Longitudinal Optical Phonon Bottleneck

    Science.gov (United States)

    Achtstein, Alexander W.; Scott, Riccardo; Kickhöfel, Sebastian; Jagsch, Stefan T.; Christodoulou, Sotirios; Bertrand, Guillaume H. V.; Prudnikau, Anatol V.; Antanovich, Artsiom; Artemyev, Mikhail; Moreels, Iwan; Schliwa, Andrei; Woggon, Ulrike

    2016-03-01

    We evidence excited state emission from p states well below ground state saturation in CdSe nanoplatelets. Size-dependent exciton ground and excited state energies and population dynamics are determined by four independent methods: time-resolved PL, time-integrated PL, rate equation modeling, and Hartree renormalized k .p calculations—all in very good agreement. The ground state-excited state energy spacing strongly increases with the lateral platelet quantization. Depending on its detuning to the LO phonon energy, the PL decay of CdSe platelets is governed by a size tunable LO phonon bottleneck, related to the low exciton-phonon coupling, very large oscillator strength, and energy spacing of both states. This is, for instance, ideal to tune lasing properties. CdSe platelets are perfectly suited to control the exciton-phonon interaction by changing their lateral size while the optical transition energy is determined by their thickness.

  12. Diversity and stability of Aleutian mink disease virus during bottleneck transitions resulting from eradication in domestic mink in Denmark

    DEFF Research Database (Denmark)

    Christensen, Laurids Siig; Hansen, Lene Gram; Chriél, Mariann;

    2011-01-01

    Aleutian mink disease (plasmacytosis) virus (AMDV) in domestic mink (Neovison vison) has been subject to eradication in Denmark since 1976. In 2001, approximately 5% of Danish mink farms were still infected and all were located in the northern part of the peninsula of Jutland. In the present study...... cluster compared with Swedish, Finnish and Dutch isolates and seem to represent a minor fraction of the genetic diversity previously found in Denmark. Stability of nucleoide deviations reveals that the purifying selection of bottlenecks imposed on the AMDV population in Denmark by the stamping out policy...... was a predisposing risk parameter for disease outbreak at a farm, and strain identity substantiates the suggestion that inadequate disinfection is involved in the recurrence of outbreaks. In cases of new introductions to farms it is indicated that contact including transport between farms played a...

  13. Central as well as peripheral attentional bottlenecks in dual-task performance activate lateral prefrontal cortices

    Directory of Open Access Journals (Sweden)

    Andre J Szameitat

    2016-03-01

    Full Text Available Human information processing suffers from severe limitations in parallel processing. In particular, when required to respond to two stimuli in rapid succession, processing bottlenecks may appear at central and peripheral stages of task processing. Importantly, it has been suggested that executive functions are needed to resolve the interference arising at such bottlenecks. The aims of the present study were to test whether central attentional limitations (i.e., bottleneck at the decisional response selection stage as well as peripheral limitations (i.e., bottleneck at response initiation both demand executive functions located in the lateral prefrontal cortex. For this, we re-analysed two previous studies, in which a total of 33 participants performed a dual-task according to the paradigm of the psychological refractory period (PRP during fMRI. In one study (N=17, the PRP task consisted of two two-choice response tasks known to suffer from a central bottleneck (CB group. In the other study (N=16, the PRP task consisted of two simple-response tasks known to suffer from a peripheral bottleneck (PB group. Both groups showed considerable dual-task costs in form of slowing of the second response in the dual-task (PRP effect. Imaging results are based on the subtraction of both single-tasks from the dual-task within each group. In the CB group, the bilateral middle frontal gyri and inferior frontal gyri were activated. Higher activation in these areas was associated with lower dual-task costs. In the PB group, the right middle frontal and inferior frontal gyrus were activated. Here, higher activation was associated with higher dual-task costs. In conclusion we suggest that central and peripheral bottlenecks both demand executive functions located in lateral prefrontal cortices. Differences between the CB and PB groups with respect to the exact prefrontal areas activated and the correlational patterns suggest that the executive functions resolving

  14. Phylogeography of two parthenogenetic sawfly species (Hymenoptera: Tenthredinidae): relationship of population genetic differentiation to host plant distribution

    NARCIS (Netherlands)

    Müller, C.; Barker, A.; Boevé, J.L.; Jong, de P.W.; Vos, de H.; Brakefield, P.M.

    2004-01-01

    This study compares the population genetic structure of two obligate parthenogenetic sawfly species, Aneugmenus padi (L.) Zhelochovtsev and Eurhadinoceraea ventralis (Panzer) Enslin (Hymenoptera: Tenthredinidae). Allozymes were used to detect genetic differences in larvae collected at different site

  15. Genetic population structure of European sprat (Sprattus sprattus L.): differentiation across a steep environmental gradient in a small pelagic fish

    DEFF Research Database (Denmark)

    Limborg, Morten; Pedersen, Jes S.; Hansen, Jakob Hemmer; Tomkiewicz, Jonna; Bekkevold, Dorte

    2009-01-01

    population structure resembles that of most other marine fishes studied in the North/Baltic Sea areas. Nevertheless, spatially explicit differences are observed among species, likely reflecting specific life-histories. Such fine-scale population structure should be taken into account, e.g. in ecosystem......Factors such as oceanographic retention, isolation by distance and secondary contact zones have, among others, been suggested to explain the low, but statistically significant, neutral population structure observed in many marine fishes. European sprat Sprattus sprattus is not known to display...... philopatric spawning behaviour or to exhibit local retention of eggs and larvae. It thus constitutes a good model for studying population structure in a characteristic small pelagic fish with high dispersal potential and an opportunistic life history. We analysed 931 specimens of sprat from nine spawning...

  16. Isoenzymatic differentiation in putative hybrid swarm population (Pinus mugo Turra x P. sylvestris L.) from "Torfowisko Zieleniec" peat-bog

    OpenAIRE

    Anna Siedlewska

    2014-01-01

    Isoenzyme variability of eight groups of individuals from different parts of putative hybrid swarm population (P. mugo Turra x P. sylvestris L.) from "Torfowisko Zieleniec" peat-bog complex was studied at ten enzymatic loci. Differences in allelic frequencies distribution among particular samples of the Zieleniec population were statistically significant at 9 loci, as shown by G2- statistics. Chi-square test indicated that in each of studied subpopulations frequencies of alleles at some loci ...

  17. Water-Price Differential and the Efficient Population Size and Urban-Rural Composition of a Distant, Large, Arid Island

    OpenAIRE

    Levy, Amnon; Zamani, Reza

    2004-01-01

    A low population density and a large distance from civilization centres present a high degree of isolation to the island's residents. Immigration can reduce the mental and material costs of isolation for the veteran residents, but at the expense of cultural and national cohesion and social harmony; and, in the case of an arid land, also at the expense of the amount and price of water allocated to agriculture. An expected-net-benefit-maximisation model for determining population size and its e...

  18. Temporal differentiation across a West-European Y-chromosomal cline: genealogy as a tool in human population genetics

    OpenAIRE

    Larmuseau, Maarten HD; Ottoni, Claudio; Raeymaekers, Joost AM; Vanderheyden, Nancy; Larmuseau, Hendrik FM; Decorte, Ronny

    2011-01-01

    The pattern of population genetic variation and allele frequencies within a species are unstable and are changing over time according to different evolutionary factors. For humans, it is possible to combine detailed patrilineal genealogical records with deep Y-chromosome (Y-chr) genotyping to disentangle signals of historical population genetic structures because of the exponential increase in genetic genealogical data. To test this approach, we studied the temporal pattern of the ‘autochthon...

  19. Genome-wide SNPs reveal fine-scale differentiation among wingless alpine stonefly populations and introgression between winged and wingless forms.

    Science.gov (United States)

    Dussex, Nicolas; Chuah, Aaron; Waters, Jonathan M

    2016-01-01

    Insect flight loss is a repeated phenomenon in alpine habitats, where wing reduction is thought to enhance local recruitment and increase fecundity. One predicted consequence of flight loss is reduced dispersal ability, which should lead to population genetic differentiation and perhaps ultimately to speciation. Using a dataset of 15,123 SNP loci, we present comparative analyses of fine-scale population structure in codistributed Zelandoperla stonefly species, across three parallel altitudinal transects in New Zealand's Rock and Pillar mountain range. We find that winged populations (altitude 200-500 m; Zelandoperla decorata) show no genetic structuring within or among streams, suggesting substantial dispersal mediated by flight. By contrast, wingless populations (Zelandoperla fenestrata; altitude 200-1100 m) exhibit distinct genetic clusters associated with each stream, and additional evidence of isolation by distance within streams. Our data support the hypothesis that wing-loss can initiate diversification in alpine insect populations over small spatial scales. The often deep phylogenetic placement of lowland Z. fenestrata within their stream-specific clades suggests the possibility of independent alpine colonization events for each stream. Additionally, the detection of winged, interspecific hybrid individuals raises the intriguing possibility that a previously flightless lineage could reacquire flight via introgression. PMID:26614689

  20. Population differentiation and hybridisation of Australian snubfin (Orcaella heinsohni and Indo-Pacific humpback (Sousa chinensis dolphins in north-western Australia.

    Directory of Open Access Journals (Sweden)

    Alexander M Brown

    Full Text Available Little is known about the Australian snubfin (Orcaella heinsohni and Indo-Pacific humpback (Sousa chinensis dolphins ('snubfin' and 'humpback dolphins', hereafter of north-western Australia. While both species are listed as 'near threatened' by the IUCN, data deficiencies are impeding rigorous assessment of their conservation status across Australia. Understanding the genetic structure of populations, including levels of gene flow among populations, is important for the assessment of conservation status and the effective management of a species. Using nuclear and mitochondrial DNA markers, we assessed population genetic diversity and differentiation between snubfin dolphins from Cygnet (n = 32 and Roebuck Bays (n = 25, and humpback dolphins from the Dampier Archipelago (n = 19 and the North West Cape (n = 18. All sampling locations were separated by geographic distances >200 km. For each species, we found significant genetic differentiation between sampling locations based on 12 (for snubfin dolphins and 13 (for humpback dolphins microsatellite loci (FST = 0.05-0.09; P<0.001 and a 422 bp sequence of the mitochondrial control region (FST = 0.50-0.70; P<0.001. The estimated proportion of migrants in a population ranged from 0.01 (95% CI 0.00-0.06 to 0.13 (0.03-0.24. These are the first estimates of genetic diversity and differentiation for snubfin and humpback dolphins in Western Australia, providing valuable information towards the assessment of their conservation status in this rapidly developing region. Our results suggest that north-western Australian snubfin and humpback dolphins may exist as metapopulations of small, largely isolated population fragments, and should be managed accordingly. Management plans should seek to maintain effective population size and gene flow. Additionally, while interactions of a socio-sexual nature between these two species have been observed previously, here we provide strong evidence for

  1. Population genetic structure of the blue-fronted Amazon (Amazona aestiva, Psittacidae: Aves) based on nuclear microsatellite loci: implications for conservation.

    Science.gov (United States)

    Leite, K C E; Seixas, G H F; Berkunsky, I; Collevatti, R G; Caparroz, R

    2008-01-01

    The blue-fronted Amazon (Amazona aestiva) is a widely distributed Neotropical parrot and one of the most captured parrots in nature to supply the illegal trade of wild animals. The objectives of the present study were to analyze the genetic structure of A. aestiva to identify management units and support conservation planning and to verified if A. aestiva populations have undergone a recent bottleneck due to habitat loss and capture for the pet trade. The genetic structure was accessed by analyzing six microsatellite loci in 74 individuals of A. aestiva, including samples from the two subspecies (A. a. aestiva and A. a. xanthopteryx), from five populations: four in Brazil and one in Argentina. A significant genetic differentiation (theta = 0.007, p = 0.005) could be detected only between the most distant populations, Tocantins and Argentina, localized at the northeast and southwest limits of the sample sites, respectively. There was no evidence of inbreeding within or between populations, suggesting random mating among individuals. These results suggest a clinal distribution of genetic variability, as observed for variation in plumage color of the two A. aestiva subspecies. Bottleneck analysis did not show a recent reduction in population size. Thus, for the management and conservation of the species, the populations from Argentina and Tocantins should be considered as different management units, and the other populations from the center of the geographical distribution as another management unit. PMID:18949701

  2. How Population Growth Affects Linkage Disequilibrium

    OpenAIRE

    Alan R Rogers

    2014-01-01

    The “LD curve” relates the linkage disequilibrium (LD) between pairs of nucleotide sites to the distance that separates them along the chromosome. The shape of this curve reflects natural selection, admixture between populations, and the history of population size. This article derives new results about the last of these effects. When a population expands in size, the LD curve grows steeper, and this effect is especially pronounced following a bottleneck in population size. When a population ...

  3. Automatic Stress Testing of Multi-tier Systems by Dynamic Bottleneck Switch Generation

    Science.gov (United States)

    Casale, Giuliano; Kalbasi, Amir; Krishnamurthy, Diwakar; Rolia, Jerry

    The performance of multi-tier systems is known to be significantly degraded by workloads that place bursty service demands on system resources. Burstiness can cause queueing delays, oversubscribe limited threading resources, and even cause dynamic bottleneck switches between resources. Thus, there is need for a methodology to create benchmarks with controlled burstiness and bottleneck switches to evaluate their impact on system performance. We tackle this problem using a model-based technique for the automatic and controlled generation of bursty benchmarks. Markov models are constructed in an automated manner to model the distribution of service demands placed by sessions of a given system on various system resources. The models are then used to derive session submission policies that result in user-specified levels of service demand burstiness for resources at the different tiers in a system. Our approach can also predict under what conditions these policies can create dynamic bottleneck switching among resources. A case study using a three-tier TPC-W testbed shows that our method is able to control and predict burstiness for session service demands. Further, results from the study demonstrate that our approach was able to inject controlled bottleneck switches. Experiments show that these bottleneck switches cause dramatic latency and throughput degradations that are not shown by the same session mix with non-bursty conditions.

  4. IDENTIFYING BOTTLENECKS FOR APPROPRIATE INFANT FEEDING IN URBAN SLUMS, ALIGARH CITY.

    Directory of Open Access Journals (Sweden)

    Saira Mehnaz

    2012-04-01

    Full Text Available Introduction: Urban population is increasing rapidly. Majority of these families are poor or landless farmers and labourers, who settle down in peri-urban areas, creating slums. Urban slums are thus growing at an alarming rate. The present study was carried out with the general objective of identifying factors which prevent access to health services. Objectives: 1. To determine the prevalence of stunting, wasting, and underweight in infants and young children. 2. To determine presence of certain micro-environmental and socioeconomic factors associated with poor nutritional status of infants and children. Methodology: Baseline study was carried out in Oct –Nov 2009 (as a part of another ongoing study and data was collected in 110 Mothers who had delivered children during the last one month. In Oct 2010 these families were visited again the infants were followed up. 39 families had shifted to another location or emigrated back to their parent state or village mostly in search of seasonal employment as reported by neighbours. One family refused to cooperate. . Two infants had died. Remaining 68 Mothers were interviewed in friendly informal manner after taking consent for study. Results: (35.4% study subjects had migrated to other areas, as reported by neighbours. Of the 68 mothers interviewed during follow up visit, previous baseline record showed that a majority were 20-30 years of age. , only 2 mothers (2.9% had exclusively breastfed for 6 months. 46 (67.6% said they had not been contacted by any health worker during the last 3 months. All 68 children were malnourished. Immunization status was poor and 94.1% children had suffered from some illness in the last one month. Conclusion: Migration is a problem which makes it difficult for providers to give continuity of care. Capacity building of the community can reduce the the bottlenecks leading to marginalization and exclusion of slum mothers from the mainstream urban health services.

  5. Genetic variation and geographic differentiation among populations of the nonmigratory agricultural pest Oedaleus infernalis (Orthoptera: Acridoidea) in China.

    Science.gov (United States)

    Sun, Wei; Dong, Hui; Gao, Yue-Bo; Su, Qian-Fu; Qian, Hai-Tao; Bai, Hong-Yan; Zhang, Zhu-Ting; Cong, Bin

    2015-01-01

    The nonmigratory grasshopper Oedaleus infernalis Saussure (Orthoptera : Acridoidea) is an agricultural pest to crops and forage grasses over a wide natural geographical distribution in China. The genetic diversity and genetic variation among 10 geographically separated populations of O. infernalis was assessed using polymerase chain reaction-based molecular markers, including the intersimple sequence repeat and mitochondrial cytochrome oxidase sequences. A high level of genetic diversity was detected among these populations from the intersimple sequence repeat (H: 0.2628, I: 0.4129, Hs: 0.2130) and cytochrome oxidase analyses (Hd: 0.653). There was no obvious geographical structure based on an unweighted pair group method analysis and median-joining network. The values of FST, θ(II), and Gst estimated in this study are low, and the gene flow is high (Nm > 4). Analysis of the molecular variance suggested that most of the genetic variation occurs within populations, whereas only a small variation takes place between populations. No significant correlation was found between the genetic distance and geographical distance. Overall, our results suggest that the geographical distance plays an unimpeded role in the gene flow among O. infernalis populations. PMID:26496789

  6. Selectivity of fish ladders: a bottleneck in Neotropical fish movement

    Directory of Open Access Journals (Sweden)

    Carlos Sérgio Agostinho

    2007-01-01

    their proportions in the downriver stretch: fish samples in the ladder were clearly dominated by a few species, including some that do not need to be translocated. Thus, selectivity constitutes an important bottleneck to initiatives for translocating fish aimed at conserving their stocks or biodiversity. It is urgent to review the decision-making process for the construction of fish passages and to evaluate the functioning of those already operating.Dezenas de escadas de peixes foram construídas em barragens de reservatórios brasileiros, mas são raros os estudos acerca de suas eficiências como instrumentos de conservação da ictiofauna Neotropical, em especial de espécies migradoras. Neste contexto, o presente estudo teve como objetivo avaliar a seletividade específica no ingresso e ascensão de peixes na escada localizada junto à barragem de Lajeado (UHE Luis Eduardo Magalhães, rio Tocantins. Amostragens foram realizadas mensalmente de novembro de 2002 a outubro de 2003 nos tanques de descanso da escada, utilizando tarrafas, e no trecho a jusante, utilizando redes de espera. A avaliação da seletividade no ingresso da escada foi realizada através da comparação da ocorrência, abundância relativa, dominância e congruência dos ranks de abundância de espécies migradoras e não migradoras na escada e no trecho imediatamente a jusante. A riqueza e abundância específica nos diferentes tanques de descanso foram utilizadas para avaliar a seletividade ao longo da escada. Os efeitos das variações temporais do nível hidrométrico de jusante e da velocidade de fluxo na seletividade foram também analisados. Das 130 espécies registradas a jusante, 63,2% foram capturadas na escada, com claro favorecimento das espécies migradoras. Entretanto, mais de 2/3 das capturas pertenceram a apenas três espécies (Rhaphiodon vulpinus, Psectrogaster amazonica e Oxydoras niger. Embora a maioria das espécies que ingressa na escada possa alcançar seu topo, constatou

  7. Population genetic structure of gray wolves (Canis lupus) in a marine archipelago suggests island-mainland differentiation consistent with dietary niche

    DEFF Research Database (Denmark)

    Stronen, Astrid Vik; Navid, Erin L; Quinn, Michael S;

    2014-01-01

    Background Emerging evidence suggests that ecological heterogeneity across space can influence the genetic structure of populations, including that of long-distance dispersers such as large carnivores. On the central coast of British Columbia, Canada, wolf (Canis lupus L., 1758) dietary niche and...... parasite prevalence data indicate strong ecological divergence between marine-oriented wolves inhabiting islands and individuals on the coastal mainland that interact primarily with terrestrial prey. Local holders of traditional ecological knowledge, who distinguish between mainland and island wolf forms......) might contribute to genetic differentiation. Accordingly, this working hypothesis presents an exciting avenue for future research where marine resources or other components of ecological heterogeneity are present....

  8. Predictive performance for population models using stochastic differential equations applied on data from an oral glucose tolerance test

    DEFF Research Database (Denmark)

    Møller, Jonas Bech; Overgaard, R.V.; Madsen, Henrik;

    2010-01-01

    Several articles have investigated stochastic differential equations (SDEs) in PK/PD models, but few have quantitatively investigated the benefits to predictive performance of models based on real data. Estimation of first phase insulin secretion which reflects beta-cell function using models of ...... obtained from the glucose tolerance tests. Since, the estimation time of extended models was not heavily increased compared to basic models, the applied method is concluded to have high relevance not only in theory but also in practice....

  9. Genetic differentiation and recombination among geographic populations of the fungal pathogen Colletotrichum truncatum from chili peppers in China

    OpenAIRE

    Diao, Yongzhao; Zhang, Can; Xu, Jianping; Lin, Dong; Liu, Li; Mtung'e, Olivo G; Liu, Xili

    2014-01-01

    Colletotrichum truncatum is an extremely important fungal pathogen. It can cause diseases both in humans and in over 460 plant species. However, little is known about its genetic diversity within and among populations. One of the major plant hosts of C. truncatum is pepper, and China is one of the main pepper-producing countries in the world. Here, we propose the hypotheses that geography has a major influence on the relationships among populations of C. truncatum in China and that infections...

  10. Distribution and differentiation of wild, feral, and cultivated populations of perennial upland cotton (Gossypium hirsutum L. in Mesoamerica and the Caribbean.

    Directory of Open Access Journals (Sweden)

    Geo Coppens d'Eeckenbrugge

    Full Text Available Perennial forms of Gossypium hirsutum are classified under seven races. Five Mesoamerican races would have been derived from the wild race 'yucatanense' from northern Yucatán. 'Marie-Galante', the main race in the Caribbean, would have developed from introgression with G. barbadense. The racial status of coastal populations from the Caribbean has not been clearly defined. We combined Ecological Niche Modeling with an analysis of SSR marker diversity, to elucidate the relationships among cultivated, feral and wild populations of perennial cottons. Out of 954 records of occurrence in Mesoamerica and the Caribbean, 630 were classified into four categories cultivated, feral (disturbed and secondary habitats, wild/feral (protected habitats, and truly wild cotton (TWC populations. The widely distributed three first categories cannot be differentiated on ecological grounds, indicating they mostly belong to the domesticated pool. In contrast, TWC are restricted to the driest and hottest littoral habitats, in northern Yucatán and in the Caribbean (from Venezuela to Florida, as confirmed by their climatic envelope in the factorial analysis. Extrapolating this TWC climatic model to South America and the Pacific Ocean points towards places where other wild representatives of tetraploid Gossypium species have been encountered. The genetic analysis sample comprised 42 TWC accessions from 12 sites and 68 feral accessions from 18 sites; at nine sites, wild and feral accessions were collected in close vicinity. Principal coordinate analysis, neighbor joining, and STRUCTURE consistently showed a primary divergence between TWC and feral cottons, and a secondary divergence separating 'Marie-Galante' from all other feral accessions. This strong genetic structure contrasts strikingly with the absence of geographic differentiation. Our results show that TWC populations of Mesoamerica and the Caribbean constitute a homogenous gene pool. Furthermore, the relatively

  11. Stem cell-like differentiation potentials of endometrial side population cells as revealed by a newly developed in vivo endometrial stem cell assay.

    Directory of Open Access Journals (Sweden)

    Kaoru Miyazaki

    Full Text Available BACKGROUND: Endometrial stem/progenitor cells contribute to the cyclical regeneration of human endometrium throughout a woman's reproductive life. Although the candidate cell populations have been extensively studied, no consensus exists regarding which endometrial population represents the stem/progenitor cell fraction in terms of in vivo stem cell activity. We have previously reported that human endometrial side population cells (ESP, but not endometrial main population cells (EMP, exhibit stem cell-like properties, including in vivo reconstitution of endometrium-like tissues when xenotransplanted into immunodeficient mice. The reconstitution efficiency, however, was low presumably because ESP cells alone could not provide a sufficient microenvironment (niche to support their stem cell activity. The objective of this study was to establish a novel in vivo endometrial stem cell assay employing cell tracking and tissue reconstitution systems and to examine the stem cell properties of ESP through use of this assay. METHODOLOGY/PRINCIPAL FINDINGS: ESP and EMP cells isolated from whole endometrial cells were infected with lentivirus to express tandem Tomato (TdTom, a red fluorescent protein. They were mixed with unlabeled whole endometrial cells and then transplanted under the kidney capsule of ovariectomized immunodeficient mice. These mice were treated with estradiol and progesterone for eight weeks and nephrectomized. All of the grafts reconstituted endometrium-like tissues under the kidney capsules. Immunofluorescence revealed that TdTom-positive cells were significantly more abundant in the glandular, stromal, and endothelial cells of the reconstituted endometrium in mice transplanted with TdTom-labeled ESP cells than those with TdTom-labeled EMP cells. CONCLUSIONS/SIGNIFICANCE: We have established a novel in vivo endometrial stem cell assay in which multi-potential differentiation can be identified through cell tracking during in vivo

  12. Population structure of African buffalo inferred from mtDNA sequences and microsatellite loci: high variation but low differentiation

    DEFF Research Database (Denmark)

    Simonsen, Bo Thisted; Siegismund, H R; Arctander, P

    1998-01-01

    mtDNA and microsatellite data were found to be congruent, disagreeing with the alleged male-biased dispersal. We propose that the observed pattern of the distribution of genetic variation between buffalo populations at the regional level can be caused by fragmentation of a previous panmictic...

  13. Bucking the trend: genetic analysis reveals high diversity, large population size and low differentiation in a deep ocean cetacean.

    Science.gov (United States)

    Thompson, K F; Patel, S; Baker, C S; Constantine, R; Millar, C D

    2016-03-01

    Understanding the genetic structure of a population is essential to its conservation and management. We report the level of genetic diversity and determine the population structure of a cryptic deep ocean cetacean, the Gray's beaked whale (Mesoplodon grayi). We analysed 530 bp of mitochondrial control region and 12 microsatellite loci from 94 individuals stranded around New Zealand and Australia. The samples cover a large area of the species distribution (~6000 km) and were collected over a 22-year period. We show high genetic diversity (h=0.933-0.987, π=0.763-0.996% and Rs=4.22-4.37, He=0.624-0.675), and, in contrast to other cetaceans, we found a complete lack of genetic structure in both maternally and biparentally inherited markers. The oceanic habitats around New Zealand are diverse with extremely deep waters, seamounts and submarine canyons that are suitable for Gray's beaked whales and their prey. We propose that the abundance of this rich habitat has promoted genetic homogeneity in this species. Furthermore, it has been suggested that the lack of beaked whale sightings is the result of their low abundance, but this is in contrast to our estimates of female effective population size based on mitochondrial data. In conclusion, the high diversity and lack of genetic structure can be explained by a historically large population size, in combination with no known exploitation, few apparent behavioural barriers and abundant habitat. PMID:26626574

  14. A double-blind, randomized quantitative comparison of calcitriol ointment and calcipotriol ointment on epidermal cell populations, proliferation and differentiation.

    NARCIS (Netherlands)

    Korver, J.E.M.; Vissers, W.H.P.M.; Rens, D.W.A. van; Pasch, M.C.; Erp, P.E.J. van; Boezeman, J.B.M.; Kerkhof, P.C.M. van de

    2007-01-01

    BACKGROUND: Calcitriol and calcipotriol are widely used in the topical treatment of psoriasis. However, studies comparing both treatment modalities are scarce. Especially, there are almost no studies comparing the effects on epidermal cell populations in a quantitative manner. OBJECTIVES: The aim of

  15. A size-structured simulation model for evaluating management strategies in gillnet fisheries exploiting spatially differentiated populations.

    NARCIS (Netherlands)

    Pet, J.S.; Machiels, M.A.M.; Densen, van W.L.T.

    1996-01-01

    A length-structured simulation model is presented as a tool in decision making for gillnet fisheries management. The analytical model simulates the fish population dynamics and impact of the fisheries, taking into account size-dependent spatial distribution patterns and migration of the fish. The da

  16. Memory bottlenecks and memory contention in multi-core Monte Carlo transport codes

    International Nuclear Information System (INIS)

    Highlights: • The performance of nuclear reactor Monte Carlo transport applications is examined. • A “proxy-application” (XSBench) is presented representing the key kernel. • In-depth performance analyses reveal the algorithm is bottlenecked by bandwidth. • Strategies are discussed to improve scalability on next generation HPC systems. - Abstract: We have extracted a kernel that executes only the most computationally expensive steps of the Monte Carlo particle transport algorithm – the calculation of macroscopic cross sections – in an effort to expose bottlenecks within multi-core, shared memory architectures

  17. Reducing the Analytical Bottleneck for Domain Scientists: Lessons from a Climate Data Visualization Case Study

    Energy Technology Data Exchange (ETDEWEB)

    Dasgupta, Aritra; Poco, Jorge; Bertini, Enrico; Silva, Claudio T.

    2016-01-31

    The gap between large-scale data production rate and the rate of generation of data-driven scientific insights has led to an analytical bottleneck in scientific domains like climate, biology, etc. This is primarily due to the lack of innovative analytical tools that can help scientists efficiently analyze and explore alternative hypotheses about the data, and communicate their findings effectively to a broad audience. In this paper, by reflecting on a set of successful collaborative research efforts between with a group of climate scientists and visualization researchers, we introspect how interactive visualization can help reduce the analytical bottleneck for domain scientists.

  18. Genetic structure and population differentiation of the Mediterranean pioneer spiny broom Calicotome villosa across the Strait of Gibraltar

    DEFF Research Database (Denmark)

    Arroyo, Juan; Aparicio, Abelardo; Albadalejo, Rafael G.;

    2008-01-01

    The region around the Strait of Gibraltar is considered to be one of the most relevant ‘hot spots’ of biodiversity in the Mediterranean Basin due to its historical, biogeographical, and ecological features. Prominent among these is its role as a land bridge for the migration and differentiation of...... species during the Pleistocene, as a consequence of the lowering of sea level and climate changes associated with the Ice Ages. In the present study, we report a multilevel hierarchical investigation of the genetic diversity of Calicotome villosa, a common pioneer legume shrub, at the regional scale. The...

  19. Population stochastic modelling (PSM)-An R package for mixed-effects models based on stochastic differential equations

    DEFF Research Database (Denmark)

    Klim, Søren; Mortensen, Stig Bousgaard; Kristensen, Niels Rode;

    2009-01-01

    are often partly ignored in PK/PD modelling although violating the hypothesis for many standard statistical tests. This article presents a package for the statistical program R that is able to handle SDEs in a mixed-effects setting. The estimation method implemented is the FOCE1 approximation......)) (2005) 1247-1258; R.V. Overgaard, N. Jonsson, C.W. Tornoe, H. Madsen, Non-linear mixed-effects models with stochastic differential equations: implementation of an estimation algorithm, J. Pharmacokinet. Pharmacodyn. 32 (February(1)) (2005) 85-107; U. Picchini, S. Ditlevsen, A. De Gaetano, Maximum...

  20. A population of human brain cells expressing phenotypic markers of more than one lineage can be induced in vitro to differentiate into mesenchymal cells

    International Nuclear Information System (INIS)

    Proliferating astrocytic cells from germinal, as well as mature areas of brain parenchyma, have the characteristics of neural stem/progenitor cells and are capable of generating both neurons and glia. We previously reported that primary fetal human brain cells, designated as Normal Human Astrocytes (NHA), expressed, in addition to GFAP, Vimentin and Nestin, low levels of βIII-Tubulin, an early neuronal marker, and differentiated into neurons and astrocytes in vitro. Here, we showed that primary NHA cells co-express low levels of mesenchymal markers Fibronectin and Collagen-1 in culture. These cells transitioned into mesenchymal-like cells when cultured in adherent conditions in serum containing media. The mesenchymal-like derivatives of these cells were characterized based on their morphological changes, high expression of Vimentin and extracellular matrix (ECM) proteins, Collagen-1 and Fibronectin, and decline of neural markers. When incubated in osteogenic and adipogenic induction media, the mesenchymal-like cells differentiated into osteoblasts and adipocytes. Furthermore, NHA cells express markers of neural crest cells, SOX-10 and p75. These data support the idea of ectoderm-derived mesenchymal lineages. These findings suggest that a population of primitive fetal brain cells with neural/neural crest/mesenchymal phenotype, resembles the remarkable phenotypic plasticity of neural crest cells, and differentiates into adipocytes and osteocytes under the influence of environmental factors

  1. Herbivory Differentially Affects Plant Fitness in Three Populations of the Perennial Herb Lythrum salicaria along a Latitudinal Gradient

    OpenAIRE

    Lina Lehndal; Jon Ågren

    2015-01-01

    Herbivory can negatively and selectively affect plant fitness by reducing growth, survival and reproductive output, thereby influencing plant population dynamics and evolution. Latitudinal variation in intensity of herbivory is common, but the extent to which it translates into corresponding variation in effects on plant performance is still poorly known. We tested the hypothesis that variation in the fitness-consequences of herbivory mirror differences in intensity of herbivory among three n...

  2. 16S partial gene mitochondrial DNA and internal transcribed spacers ribosomal DNA as differential markers of Trichuris discolor populations.

    Science.gov (United States)

    Callejón, R; Halajian, A; de Rojas, M; Marrugal, A; Guevara, D; Cutillas, C

    2012-05-25

    Comparative morphological, biometrical and molecular studies of Trichuris discolor isolated from Bos taurus from Spain and Iran was carried out. Furthermore, Trichuris ovis isolated from B. taurus and Capra hircus from Spain has been, molecularly, analyzed. Morphological studies revealed clear differences between T. ovis and T. discolor isolated from B. taurus but differences were not observed between populations of T. discolor isolated from different geographical regions. Nevertheless, the molecular studies based on the amplification and sequencing of the internal transcribed spacers 1 and 2 ribosomal DNA and 16S partial gene mitochondrial DNA showed clear differences between both populations of T. discolor from Spain and Iran suggesting two cryptic species. Phylogenetic studies corroborated these data. Thus, phylogenetic trees based on ITS1, ITS2 and 16S partial gene sequences showed that individuals of T. discolor from B. taurus from Iran clustered together and separated, with high bootstrap values, of T. discolor isolated from B. taurus from Spain, while populations of T. ovis from B. taurus and C. hircus from Spain clustered together but separated with high bootstrap values of both populations of T. discolor. Furthermore, a comparative phylogenetic study has been carried out with the ITS1and ITS2 sequences of Trichuris species from different hosts. Three clades were observed: the first clustered all the species of Trichuris parasitizing herbivores (T. discolor, T. ovis, Trichuris leporis and Trichuris skrjabini), the second clustered all the species of Trichuris parasitizing omnivores (Trichuris trichiura and Trichuris suis) and finally, the third clustered species of Trichuris parasitizing carnivores (Trichuris muris, Trichuris arvicolae and Trichuris vulpis). PMID:22136768

  3. The spatial genetic differentiation of the legume pod borer, Maruca vitrata F. (Lepidoptera: Crambidae) populations in West Africa

    KAUST Repository

    Agunbiade, Tolulope A.

    2012-04-17

    The legume pod borer, Maruca vitrata, is an endemic insect pest that causes significant yield loss to the cowpea crop in West Africa. The application of population genetic tools is important in the management of insect pests but such data on M. vitrata is lacking. We applied a set of six microsatellite markers to assess the population structure of M. vitrata collected at five sites from Burkina Faso, Niger and Nigeria. Observed polymorphisms ranged from one (marker 3393) to eight (marker 32008) alleles per locus. Observed and expected heterozygosities ranged from 0.0 to 0.8 and 0.0 to 0.6, respectively. Three of the loci in samples from Nigeria and Burkina Faso deviated significantly from Hardy-Weinberg Equilibrium (HWE), whereas no loci deviated significantly in samples from Niger. Analysis of molecular variance (AMOVA) indicated that 67.3% level of the genetic variation was within individuals compared to 17.3% among populations. A global estimate of F ST=0.1 (ENA corrected F ST=0.1) was significant (Pa=0.05) and corroborated by pairwise F ST values that were significant among all possible comparisons. A significant correlation was predicted between genetic divergence and geographic distance between subpopulations (R2=0.6, P=0.04), and cluster analysis by the program STRUCTURE predicted that co-ancestry of genotypes were indicative of three distinct populations. The spatial genetic variance among M. vitrata in West Africa may be due to limited gene flow, south-north seasonal movement pattern or other reproductive barriers. This information is important for the cultural, chemical and biological control strategies for managing M. vitrata. Copyright © 2012 Cambridge University Press.

  4. Skull and limb morphology differentially track population history and environmental factors in the transition to agriculture in Europe

    OpenAIRE

    von Cramon-Taubadel, N.; Stock, J. T.; Pinhasi, R.

    2013-01-01

    The Neolithic transition in Europe was a complex mosaic spatio-temporal process, involving both demic diffusion from the Near East and the cultural adoption of farming practices by indigenous hunter–gatherers. Previous analyses of Mesolithic hunter–gatherers and Early Neolithic farmers suggest that cranial shape variation preserves the population history signature of the Neolithic transition. However, the extent to which these same demographic processes are discernible in the postcranium is p...

  5. Genetic diversity and population structure of Sitodiplosis mosellana in Northern China.

    Directory of Open Access Journals (Sweden)

    Yun Duan

    Full Text Available The wheat midge, Sitodiplosis mosellana, is an important pest in Northern China. We tested the hypothesis that the population structure of this species arises during a range expansion over the past 30 years. This study used microsatellite and mitochondrial loci to conduct population genetic analysis of S. mosellana across its distribution range in China. We found strong genetic structure among the 16 studied populations, including two genetically distinct groups (the eastern and western groups, broadly consistent with the geography and habitat fragmentation. These results underline the importance of natural barriers in impeding dispersal and gene flow of S. mosellana populations. Low to moderate genetic diversity among the populations and moderate genetic differentiation (F ST = 0.117 between the two groups were also found. The populations in the western group had lower genetic diversity, higher genetic differentiation and lower gene flow (F ST = 0.116, Nm = 1.89 than those in the eastern group (F ST = 0.049, Nm = 4.91. Genetic distance between populations was positively and significantly correlated with geographic distance (r = 0.56, P<0.001. The population history of this species provided no evidence for population expansion or bottlenecks in any of these populations. Our data suggest that the distribution of genetic diversity, genetic differentiation and population structure of S. mosellana have resulted from a historical event, reflecting its adaptation to diverse habitats and forming two different gene pools. These results may be the outcome of a combination of restricted gene flow due to geographical and environmental factors, population history, random processes of genetic drift and individual dispersal patterns. Given the current risk status of this species in China, this study can offer useful information for forecasting outbreaks and designing effective pest management programs.

  6. Differentiation of Tetragenococcus populations occurring in products and manufacturing processes of puffer fish ovaries fermented with rice-bran.

    Science.gov (United States)

    Kobayashi, T; Kimura, B; Fujii, T

    2000-06-01

    Tetragenococcus strains isolated from the manufacturing process of Japanese puffer fish ovaries fermented with rice-bran were characterized and differentiated phenotypically and genotypically. A total of 413 Tetragenococcus isolates were evaluated. On the basis of five representative substrates, the isolates were grouped into seven groups. An RFLP (restriction fragment length polymorphisms) analysis of the 16S rRNA gene of representative strains of major groups revealed that they could be grouped into two groups: one was identified as the most prominent halophilic lactic acid coccus, Tetragenococcus halophilus, and the other as T. muriaticus, which has recently been added to the genus Tetragenococcus as a new species. Physiologically, the major differences between the two groups were found in the ability to grow in medium not supplemented with NaCl and the fermentation of L-arabinose, sucrose and D-mannitol, and several other carbohydrates. PMID:10857547

  7. Divergence in morphology, but not habitat use, despite low genetic differentiation among insular populations of the lizard Anolis lemurinus in Honduras

    Science.gov (United States)

    Logan, M.L.; Montgomery, Chad E.; Boback, Scott M.; Reed, R.N.; Campbell, J.A.

    2012-01-01

    Studies of recently isolated populations are useful because observed differences can often be attributed to current environmental variation. Two populations of the lizard Anolis lemurinus have been isolated on the islands of Cayo Menor and Cayo Mayor in the Cayos Cochinos Archipelago of Honduras for less than 15 000 y. We measured 12 morphometric and 10 habitat-use variables on 220 lizards across these islands in 2 y, 2008 and 2009. The goals of our study were (1) to explore patterns of sexual dimorphism, and (2) to test the hypothesis that differences in environment among islands may have driven divergence in morphology and habitat use despite genetic homogeneity among populations. Although we found no differences among sexes in habitat use, males had narrower pelvic girdles and longer toe pads on both islands. Between islands, males differed in morphology, but neither males nor females differed in habitat use. Our data suggest that either recent selection has operated differentially on males despite low genetic dill'erentiation, or that they display phenotypic plasticity in response to environmental variation. We suggest that patterns may be driven by variation in intrapopulation density or differences in predator diversity among islands.

  8. Temperature dependence of the polariton relaxation bottleneck in a GaN microcavity

    Energy Technology Data Exchange (ETDEWEB)

    Stokker-Cheregi, F. [LENS and Department of Physics, University of Florence (Italy); NILPRP, Lasers Department, Magurele, Bucharest (Romania); Vinattieri, A.; Colocci, M.; Gurioli, M. [LENS and Department of Physics, University of Florence (Italy); Semond, F.; Leroux, M.; Massies, J. [CRHEA-CNRS, Valbonne (France); Sellers, I.R. [CRHEA-CNRS, Valbonne (France); Department of Physics, University of Buffalo, NY (United States)

    2008-07-01

    We present an experimental study aimed to investigate discuss the possible presence of a phonon bottleneck in a GaN bulk microcavity. Clear anticrossing between the lower (LP) and upper polariton (UP) branches has been observed up to room temperature in photoluminescence (PL) by angular measurements with a Rabi splitting of the order of 30 meV. In order to determine the presence of a relaxation bottleneck, angular PL measurements have been performed at different temperatures for negative detuning. At low T the PL shows a clear maximum, at the angle corresponding to the resonance between the exciton and the photon modes, which is an experimental demonstration of the presence of a relaxation bottleneck. The PL enhancement in resonance condition is suppressed with increasing T and it almost disappears at room temperature. We therefore demonstrate that the exciton-phonon interaction washes out the polariton bottleneck in GaN MCs at room temperature. (copyright 2008 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  9. Identifikasi Bottleneck pada Hasil Ekstraksi Proses Bisnis ERP dengan Membandingkan Algoritma Alpha++ dan Heuristics Miner

    Directory of Open Access Journals (Sweden)

    Laeila Mardhatillah

    2012-09-01

    Full Text Available Saat ini banyak perusahaan menggunakan sistem informasi untuk menunjang proses bisnis. Namun kenyataannya hanya beberapa perusahaan yang melakukan evaluasi untuk proses bisnis pada sistem informasi tersebut. Evaluasi ini didapat dari data Event log yang merupakan hasil proses ekstrasi ERP. Cara melakukan evaluasi yaitu dengan process mining. Process mining berfungsi untuk menggali proses transaksi sehingga terbentuk suatu workflow proses bisnis yang actual. Workflow proses bisnis ini akan digambarkan dalam bentuk Petri Net, selanjutnya dari Petri Net inilah akan dilakukan analisis untuk mengidentifikasi adanya BottleneckBottleneck merupakan peristiwa pada suatu transaksi yang memiliki waktu tunggu yang lebih lama dibandingkan transaksi lainnya dalam suatu proses bisnis. Dengan adanya PROM Tools maka penggambaran mengenai proses bisnis ERP dapat terbentuk. Penggambaran model tersebut menggunakan dua algoritma, yaitu Algoritma Alpha ++ dan Heuristics Miner. Kedua algoritma ini digunakan untuk mencari perbedaan bottleneck yang terjadi. Dari penelitian didapatkan  hasil bahwa algoritma sangat mempengaruhi letak bottleneck. Letak tersebut didasarkan pada perhitungan waktu token yang ada pada place (tempat antara dua transisi atau dua transaksi saat terbentuk model.

  10. Consequences of the Now-or-Never bottleneck for signed versus spoken languages.

    Science.gov (United States)

    Emmorey, Karen

    2016-01-01

    Signed and spoken languages emerge, change, are acquired, and are processed under distinct perceptual, motor, and memory constraints. Therefore, the Now-or-Never bottleneck has different ramifications for these languages, which are highlighted in this commentary. The extent to which typological differences in linguistic structure can be traced to processing differences provides unique evidence for the claim that structure is processing. PMID:27562833

  11. South West Georgia: an important bottleneck for raptor migration during autumn

    NARCIS (Netherlands)

    B. Verhelst; J. Jansen; W. Vansteelant

    2011-01-01

    Counts of migrating raptors at Batumi, Georgia, revealed the eastern Black Sea coast to form one of the most important bottlenecks for raptor migration during autumn in the Eurasian-African migration system. Totals for 10 species (European Honey-buzzard Pernis apivorus, Steppe Buzzard Buteo buteo vu

  12. Achievements & bottlenecks in humanitarian demining EU-funded research: Final results from the EC DELVE project

    NARCIS (Netherlands)

    Sahli, H.; Bruschini, C.; Kempen, L. van; Schleijpen, H.M.A.; Breejen, E. den

    2008-01-01

    The EC DELVE Support Action project has analyzed the bottlenecks in the transfer of Humanitarian Demining (HD) technology from technology development to the use in the field, and drawn some lessons learned, basing itself on the assessment of the European Humanitarian Demining Research and Technology

  13. Y-chromosome descent clusters and male differential reproductive success: young lineage expansions dominate Asian pastoral nomadic populations.

    Science.gov (United States)

    Balaresque, Patricia; Poulet, Nicolas; Cussat-Blanc, Sylvain; Gerard, Patrice; Quintana-Murci, Lluis; Heyer, Evelyne; Jobling, Mark A

    2015-10-01

    High-frequency microsatellite haplotypes of the male-specific Y-chromosome can signal past episodes of high reproductive success of particular men and their patrilineal descendants. Previously, two examples of such successful Y-lineages have been described in Asia, both associated with Altaic-speaking pastoral nomadic societies, and putatively linked to dynasties descending, respectively, from Genghis Khan and Giocangga. Here we surveyed a total of 5321 Y-chromosomes from 127 Asian populations, including novel Y-SNP and microsatellite data on 461 Central Asian males, to ask whether additional lineage expansions could be identified. Based on the most frequent eight-microsatellite haplotypes, we objectively defined 11 descent clusters (DCs), each within a specific haplogroup, that represent likely past instances of high male reproductive success, including the two previously identified cases. Analysis of the geographical patterns and ages of these DCs and their associated cultural characteristics showed that the most successful lineages are found both among sedentary agriculturalists and pastoral nomads, and expanded between 2100 BCE and 1100 CE. However, those with recent origins in the historical period are almost exclusively found in Altaic-speaking pastoral nomadic populations, which may reflect a shift in political organisation in pastoralist economies and a greater ease of transmission of Y-chromosomes through time and space facilitated by the use of horses. PMID:25585703

  14. Age, differential growth and mortality rates in unexploited populations of Florida gar, an apex predator in the Florida Everglades

    Science.gov (United States)

    Murie, D.J.; Parkyn, D.C.; Nico, L.G.; Herod, J.J.; Loftus, W.F.

    2009-01-01

    Florida gar, Lepisosteus platyrhincus DeKay, were sampled in two canal systems in south Florida during 2000-2001 to estimate age, growth and mortality as part of the Everglades ecosystem-restoration effort. Tamiami (C-4) and L-31W canal systems had direct connections to natural wetlands of the Everglades and harboured large Florida gar populations. Of 476 fish aged, maximum ages were 19 and 10years for females and males, respectively. Maximum sizes were also larger for females compared with males (817 vs 602 mm total length). Overall, female Florida gar from both Tamiami and L-31W were larger at age than males from L-31W that, in turn, were larger at any given age than males from Tamiami. Females also had lower rates of annual mortality (Z = 0.21) than males from L-31W (Z = 0.31) or males from Tamiami (Z = 0.54). As a large and long-lived apex predator in the Everglades, Florida gar may structure lower trophic levels. Regional- and sex-specific population parameters for Florida gar will contribute to the simulation models designed to evaluate Everglades restoration alternatives. ?? 2009 Blackwell Publishing Ltd.

  15. Hierarchical genetic analysis of German cockroach (Blattella germanica populations from within buildings to across continents.

    Directory of Open Access Journals (Sweden)

    Edward L Vargo

    Full Text Available Understanding the population structure of species that disperse primarily by human transport is essential to predicting and controlling human-mediated spread of invasive species. The German cockroach (Blattella germanica is a widespread urban invader that can actively disperse within buildings but is spread solely by human-mediated dispersal over longer distances; however, its population structure is poorly understood. Using microsatellite markers we investigated population structure at several spatial scales, from populations within single apartment buildings to populations from several cities across the U.S. and Eurasia. Both traditional measures of genetic differentiation and Bayesian clustering methods revealed increasing levels of genetic differentiation at greater geographic scales. Our results are consistent with active dispersal of cockroaches largely limited to movement within a building. Their low levels of genetic differentiation, yet limited active spread between buildings, suggests a greater likelihood of human-mediated dispersal at more local scales (within a city than at larger spatial scales (within and between continents. About half the populations from across the U.S. clustered together with other U.S. populations, and isolation by distance was evident across the U.S. Levels of genetic differentiation among Eurasian cities were greater than those in the U.S. and greater than those between the U.S. and Eurasia, but no clear pattern of structure at the continent level was detected. MtDNA sequence variation was low and failed to reveal any geographical structure. The weak genetic structure detected here is likely due to a combination of historical admixture among populations and periodic population bottlenecks and founder events, but more extensive studies are needed to determine whether signatures of global movement may be present in this species.

  16. Hierarchical genetic analysis of German cockroach (Blattella germanica) populations from within buildings to across continents.

    Science.gov (United States)

    Vargo, Edward L; Crissman, Jonathan R; Booth, Warren; Santangelo, Richard G; Mukha, Dmitry V; Schal, Coby

    2014-01-01

    Understanding the population structure of species that disperse primarily by human transport is essential to predicting and controlling human-mediated spread of invasive species. The German cockroach (Blattella germanica) is a widespread urban invader that can actively disperse within buildings but is spread solely by human-mediated dispersal over longer distances; however, its population structure is poorly understood. Using microsatellite markers we investigated population structure at several spatial scales, from populations within single apartment buildings to populations from several cities across the U.S. and Eurasia. Both traditional measures of genetic differentiation and Bayesian clustering methods revealed increasing levels of genetic differentiation at greater geographic scales. Our results are consistent with active dispersal of cockroaches largely limited to movement within a building. Their low levels of genetic differentiation, yet limited active spread between buildings, suggests a greater likelihood of human-mediated dispersal at more local scales (within a city) than at larger spatial scales (within and between continents). About half the populations from across the U.S. clustered together with other U.S. populations, and isolation by distance was evident across the U.S. Levels of genetic differentiation among Eurasian cities were greater than those in the U.S. and greater than those between the U.S. and Eurasia, but no clear pattern of structure at the continent level was detected. MtDNA sequence variation was low and failed to reveal any geographical structure. The weak genetic structure detected here is likely due to a combination of historical admixture among populations and periodic population bottlenecks and founder events, but more extensive studies are needed to determine whether signatures of global movement may be present in this species. PMID:25020136

  17. A low-density SNP array for analyzing differential selection in freshwater and marine populations of threespine stickleback (Gasterosteus aculeatus)

    DEFF Research Database (Denmark)

    Ferchaud, Anne-Laure; Pedersen, Susanne H.; Bekkevold, Dorte;

    2014-01-01

    for rapid and cost efficient analysis of genetic divergence between freshwater and marine sticklebacks, we generated a low-density SNP (Single Nucleotide Polymorphism) array encompassing markers of chromosome regions under putative directional selection, along with neutral markers for background....... Results: RAD (Restriction site Associated DNA) sequencing of sixty individuals representing two freshwater and one marine population led to the identification of 33,993 SNP markers. Ninety-six of these were chosen for the low-density SNP array, among which 70 represented SNPs under putatively directional...... selection in freshwater vs. marine environments, whereas 26 SNPs were assumed to be neutral. Annotation of these regions revealed several genes that are candidates for affecting stickleback phenotypic variation, some of which have been observed in previous studies whereas others are new. Conclusions: We...

  18. Modest genetic differentiation among North American populations of Sarcocystic neurona may reflect expansion in its geographic range

    Science.gov (United States)

    Sundar, N.; Asmundsson, I.M.; Thomas, N.J.; Samuel, M.D.; Dubey, J.P.; Rosenthal, B.M.

    2008-01-01

    Sarcocystis neurona is an important cause of neurological disease in horses (equine protozoal myeloencephalitis, EPM) and sea otters in the United States. In addition, EPM-like disease has been diagnosed in several other land and marine mammals. Opossums are its only definitive hosts. Little genetic diversity among isolates of S. neurona from different hosts has been reported. Here, we used 11 microsatellites to characterize S. neurona DNA isolated from natural infections in 22 sea otters (Enhydra lutris) from California and Washington and in 11 raccoons (Procyon lotor) and 1 striped skunk (Mephitis mephitis) from Wisconsin. By jointly analyzing these 34 isolates with 26 isolates previously reported, we determined that geographic barriers may limit S. neurona dispersal and that only a limited subset of possible parasite genotypes may have been introduced to recently established opossum populations. Moreover, our study confirms that diverse intermediate hosts share a common infection source, the opossum (Didelphis virginiana).

  19. Differential effects of drugs targeting cancer stem cell (CSC and non-CSC populations on lung primary tumors and metastasis.

    Directory of Open Access Journals (Sweden)

    Leyre Larzabal

    Full Text Available Cancer stem cells (CSCs are thought to be responsible for tumor initiation and recurrence after chemotherapy. Targeting CSCs and non-CSCs with specific compounds may be an effective approach to reduce lung cancer growth and metastasis. The aim of this study was to investigate the effect of salinomycin, a selective inhibitor of CSCs, with or without combination with paclitaxel, in a metastatic model. To evaluate the effect of these drugs in metastasis and tumor microenvironment we took advantage of the immunocompetent and highly metastatic LLC mouse model. Aldefluor assays were used to analyze the ALDH+/- populations in murine LLC and human H460 and H1299 lung cancer cells. Salinomycin reduced the proportion of ALDH+ CSCs in LLC cells, whereas paclitaxel increased such population. The same effect was observed for the H460 and H1299 cell lines. Salinomycin reduced the tumorsphere formation capacity of LLC by more than 7-fold, but paclitaxel showed no effect. In in vivo experiments, paclitaxel reduced primary tumor volume but increased the number of metastatic nodules (p<0.05, whereas salinomycin had no effect on primary tumors but reduced lung metastasis (p<0.05. Combination of both drugs did not improve the effect of single therapies. ALDH1A1, SOX2, CXCR4 and SDF-1 mRNA levels were higher in metastatic lesions than in primary tumors, and were significantly elevated in both locations by paclitaxel treatment. On the contrary, such levels were reduced (or in some cases did not change when mice were administered with salinomycin. The number of F4/80+ and CD11b+ cells was also reduced upon administration of both drugs, but particularly in metastasis. These results show that salinomycin targets ALDH+ lung CSCs, which has important therapeutic effects in vivo by reducing metastatic lesions. In contrast, paclitaxel (although reducing primary tumor growth promotes the selection of ALDH+ cells that likely modify the lung microenvironment to foster

  20. Differential effects of drugs targeting cancer stem cell (CSC) and non-CSC populations on lung primary tumors and metastasis.

    Science.gov (United States)

    Larzabal, Leyre; El-Nikhely, Nefertiti; Redrado, Miriam; Seeger, Werner; Savai, Rajkumar; Calvo, Alfonso

    2013-01-01

    Cancer stem cells (CSCs) are thought to be responsible for tumor initiation and recurrence after chemotherapy. Targeting CSCs and non-CSCs with specific compounds may be an effective approach to reduce lung cancer growth and metastasis. The aim of this study was to investigate the effect of salinomycin, a selective inhibitor of CSCs, with or without combination with paclitaxel, in a metastatic model. To evaluate the effect of these drugs in metastasis and tumor microenvironment we took advantage of the immunocompetent and highly metastatic LLC mouse model. Aldefluor assays were used to analyze the ALDH+/- populations in murine LLC and human H460 and H1299 lung cancer cells. Salinomycin reduced the proportion of ALDH+ CSCs in LLC cells, whereas paclitaxel increased such population. The same effect was observed for the H460 and H1299 cell lines. Salinomycin reduced the tumorsphere formation capacity of LLC by more than 7-fold, but paclitaxel showed no effect. In in vivo experiments, paclitaxel reduced primary tumor volume but increased the number of metastatic nodules (p<0.05), whereas salinomycin had no effect on primary tumors but reduced lung metastasis (p<0.05). Combination of both drugs did not improve the effect of single therapies. ALDH1A1, SOX2, CXCR4 and SDF-1 mRNA levels were higher in metastatic lesions than in primary tumors, and were significantly elevated in both locations by paclitaxel treatment. On the contrary, such levels were reduced (or in some cases did not change) when mice were administered with salinomycin. The number of F4/80+ and CD11b+ cells was also reduced upon administration of both drugs, but particularly in metastasis. These results show that salinomycin targets ALDH+ lung CSCs, which has important therapeutic effects in vivo by reducing metastatic lesions. In contrast, paclitaxel (although reducing primary tumor growth) promotes the selection of ALDH+ cells that likely modify the lung microenvironment to foster metastasis. PMID

  1. Dual-task performance with ideomotor-compatible tasks: is the central processing bottleneck intact, bypassed, or shifted in locus?

    Science.gov (United States)

    Lien, Mei-Ching; McCann, Robert S.; Ruthruff, Eric; Proctor, Robert W.

    2005-01-01

    The present study examined whether the central bottleneck, assumed to be primarily responsible for the psychological refractory period (PRP) effect, is intact, bypassed, or shifted in locus with ideomotor (IM)-compatible tasks. In 4 experiments, factorial combinations of IM- and non-IM-compatible tasks were used for Task 1 and Task 2. All experiments showed substantial PRP effects, with a strong dependency between Task 1 and Task 2 response times. These findings, along with model-based simulations, indicate that the processing bottleneck was not bypassed, even with two IM-compatible tasks. Nevertheless, systematic changes in the PRP and correspondence effects across experiments suggest that IM compatibility shifted the locus of the bottleneck. The findings favor an engage-bottleneck-later hypothesis, whereby parallelism between tasks occurs deeper into the processing stream for IM- than for non-IM-compatible tasks, without the bottleneck being actually eliminated.

  2. HIF-1alpha and HIF-2alpha are differentially activated in distinct cell populations in retinal ischaemia.

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    Freya M Mowat

    Full Text Available BACKGROUND: Hypoxia plays a key role in ischaemic and neovascular disorders of the retina. Cellular responses to oxygen are mediated by hypoxia-inducible transcription factors (HIFs that are stabilised in hypoxia and induce the expression of a diverse range of genes. The purpose of this study was to define the cellular specificities of HIF-1alpha and HIF-2alpha in retinal ischaemia, and to determine their correlation with the pattern of retinal hypoxia and the expression profiles of induced molecular mediators. METHODOLOGY/PRINCIPAL FINDINGS: We investigated the tissue distribution of retinal hypoxia during oxygen-induced retinopathy (OIR in mice using the bio-reductive drug pimonidazole. We measured the levels of HIF-1alpha and HIF-2alpha proteins by Western blotting and determined their cellular distribution by immunohistochemistry during the development of OIR. We measured the temporal expression profiles of two downstream mediators, vascular endothelial growth factor (VEGF and erythropoietin (Epo by ELISA. Pimonidazole labelling was evident specifically in the inner retina. Labelling peaked at 2 hours after the onset of hypoxia and gradually declined thereafter. Marked binding to Müller glia was evident during the early hypoxic stages of OIR. Both HIF-1alpha and HIF-2alpha protein levels were significantly increased during retinal hypoxia but were evident in distinct cellular distributions; HIF-1alpha stabilisation was evident in neuronal cells throughout the inner retinal layers whereas HIF-2alpha was restricted to Müller glia and astrocytes. Hypoxia and HIF-alpha stabilisation in the retina were closely followed by upregulated expression of the downstream mediators VEGF and EPO. CONCLUSIONS/SIGNIFICANCE: Both HIF-1alpha and HIF-2alpha are activated in close correlation with retinal hypoxia but have contrasting cell specificities, consistent with differential roles in retinal ischaemia. Our findings suggest that HIF-2alpha activation

  3. Chromosome mapping of 5S rRNA genes differentiates Brazilian populations of Leporellus vittatus (Anostomidae, Characiformes

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    Cecilia Teixeira de Aguilar

    2008-01-01

    Full Text Available Among the anostomid fishes, the genus Leporellus is represented by only three species: L. nattereri, endemic of the Amazon River, L. retropinnis, endemic of the Piracicaba River, and L. vittatus, widely distributed in rivers from Peru, Colombia, Guianas, and different major hydrographic basins of Brazil. A cytogenetic study carried out on specimens of Leporellus vittatus from three major Brazilian hydrographic basins evidenced a karyotype of 54 metacentric and submetacentric chromosomes. C-banding analysis revealed the presence of large pericentromeric heterochromatic segments in all chromosomes and a telomeric block coincident with the NOR sites. Ag, CMA3 or MM staining, and FISH with ribosomal probes located the 45S ribosomal genes on the terminal region of the long arm of the 12th chromosome pair of all populations. Nevertheless, in the specimens from the Paraná and São Francisco Basins the 5S rDNA clusters were interstitially located by FISH on the long arm of the 2nd chromosome pair, while in the specimens from the Tocantins-Araguaia Basin these sites were observed on the long arm of the 9th chromosome pair and on the short arm of the 17th chromosome pair. These data suggest that the species currently named Leporellus vittatus may comprise a complex of cryptic species.

  4. The effects of differential reddening and stellar rotation on the appearance of multiple populations in star clusters: the case of Trumpler 20

    CERN Document Server

    Platais, I; Quinn, S N; Clem, J L; de Mink, S E; Dotter, A; Kozhurina-Platais, V; Latham, D W; Bellini, A

    2012-01-01

    We present a detailed analysis of the upper main sequence of the 1.3 Gyr old open cluster Trumpler 20. High accuracy BV photometry combined with the Very Large Telescope/FLAMES medium-resolution spectroscopy of 954 stars is essential to understanding the unusual appearance of the color-magnitude diagram (CMD), initially suggesting multiple populations in Trumpler 20. We show that differential reddening is a dominant contributor to the apparent splitting/widening of the main-sequence turnoff region. At its extreme, the excess differential reddening reaches Delta(B-V)=0.1 while the adopted minimum reddening for the cluster is E(B-V)=0.36. A unique sample of measured projected rotational velocities indicates that stellar rotation is high near the main-sequence turnoff, reaching vsin i=180 km/s. By dividing the upper main-sequence stars into equal groups of slow and fast rotators, we find that fast rotators have a marginal blueshift of delta(V-I)=-0.01, corresponding to a difference in the median vsin i of 60 km/...

  5. Interlimb coupling from the arms to legs is differentially specified for populations of motor units comprising the compound H-reflex during "reduced" human locomotion.

    Science.gov (United States)

    Mezzarane, Rinaldo A; Klimstra, Marc; Lewis, Allen; Hundza, Sandra R; Zehr, E Paul

    2011-01-01

    Recent experiments have identified neuromechanical interactions between the arms and legs during human locomotor movement. Previous work reported that during the rhythmic movement of all four limbs, the influence of the arms on reflex expression in the legs was superimposed on the dominant effect of the legs. This evidence was based upon studies using cutaneous and H-reflex modulation as indices of neuronal activity related to locomotion. The earlier H-reflex study was restricted to one phase of movement and to only a fixed H-reflex amplitude. Also, all four limbs were actively engaged in locomotor movement, and this led to the speculation that the effect from the arms could be underestimated by "swamping" of the conditioning during movement of the test limb. Work from the cat suggests that descending locomotor drive may be differentially specified for different motor unit populations in the hindlimb. Accordingly, details of interlimb coordination between the arms and legs in humans require further characterization and an examination of different populations of motor units as can be obtained from H-reflex recruitment curve (RC) parameters. Using modulation of H-reflex amplitudes across the entire ascending limb as neural probes for interlimb coupling, the present study evaluated the separated influences of rhythmic activity of the arms and leg on neuronal excitability of a stationary "test leg". This three-limb "reduced" locomotion approach was applied using a stepping ergometer during the performance of three rhythmic movement tasks: arms (A); contralateral leg (L); and arms and contralateral leg (AL). Data were sampled at four different phases of the stepping cycle (using the moving leg as reference): start power (SP); end power (EP); start recovery (SR); and end recovery (ER). The main result was a large and significant influence of rhythmic AL activity on RC parameters of the H-reflex at EP and SP phases. However, the parameters (and thus motor unit populations

  6. "Use of Random Amplified Polymorphic DNA Polymerase Chain Reaction (RAPD-PCR and ITS2 PCR assays for differentiation of populations and putative sibling species of Anopheles fluviatilis (Diptera: Culicidae in Iran"

    Directory of Open Access Journals (Sweden)

    SR Naddaf Dezfouli

    2002-09-01

    Full Text Available Anopheles fluviatilis complex is known to be a vector of malaria in Iran. Since mosquitoes of this species cover a wide geographical range in Iran, they might have evolved into different separated populations. Random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR assay was used to differentiate geographic populations of this species. DNA was extracted from individual mosquitoes from 8 localities in 4 south and southeast provinces and amplified in PCR reactions using 18 single primers of arbitrary nucleotide sequence. Results of RAPD-PCR showed that Kazeroun populations could simply be differentiated from other populations using a diagnostic fragment amplified with primer UBC-306. But other populations could not be differentiated either visually or by means of statistical analysis. Moreover ITS2 fragments of some selected specimens were amplified using a pair of universal primer and sequenced as a key standard for detection of putative sibling species. Sequence analysis of the ITS2 fragments revealed a very high (100% homology among the populations. These findings are crucial in epidemiological studies concerning relatedness of geographic populations and vector movement in the region. Results of RAPD-PCR and ITS2 analysis suggest that this taxon in Iran comprises of only one species with a low genetic variation among geographic populations.

  7. Population genetic structure of wild and farmed rusa deer (Cervus timorensis russa) in New-Caledonia inferred from polymorphic microsatellite loci.

    Science.gov (United States)

    de Garine-Wichatitsky, M; de Meeûs, T; Chevillon, C; Berthier, D; Barré, N; Thévenon, S; Maillard, J-C

    2009-12-01

    Historical records indicate that 12 rusa deer (Cervus timorensis russa) were introduced in New-Caledonia during the 1870s. We used eight polymorphic microsatellite DNA loci to assess the genetic differentiation and diversity of farmed and wild deer populations. Past genetic bottlenecks were detected in both sub-populations, although higher genetic diversity was maintained in farmed populations, probably due to the regular introduction of reproducers from wild populations and from other farms. The genetic structure of farmed and wild populations differed significantly. There was a significant isolation by distance for wild populations, whereas farmed populations were significantly differentiated between farms independently from their geographical proximity. Wild rusa deer consisted of small populations (with effective population sizes ranging between 7 and 19 individuals depending on the methods used), with a low parent-offspring dispersion range (0.20-2.02 km). Genetic tools and direct observations provided congruent estimates of dispersion and population sizes. We discuss the relevance of our results for management purposes. PMID:19680748

  8. Population genetic differences along a latitudinal cline between original and recently colonized habitat in a butterfly.

    Directory of Open Access Journals (Sweden)

    Sofie Vandewoestijne

    Full Text Available BACKGROUND: Past and current range or spatial expansions have important consequences on population genetic structure. Habitat-use expansion, i.e. changing habitat associations, may also influence genetic population parameters, but has been less studied. Here we examined the genetic population structure of a Palaeartic woodland butterfly Pararge aegeria (Nymphalidae which has recently colonized agricultural landscapes in NW-Europe. Butterflies from woodland and agricultural landscapes differ in several phenotypic traits (including morphology, behavior and life history. We investigated whether phenotypic divergence is accompanied by genetic divergence between populations of different landscapes along a 700 km latitudinal gradient. METHODOLOGY/PRINCIPAL FINDINGS: Populations (23 along the latitudinal gradient in both landscape types were analyzed using microsatellite and allozyme markers. A general decrease in genetic diversity with latitude was detected, likely due to post-glacial colonization effects. Contrary to expectations, agricultural landscapes were not less diverse and no significant bottlenecks were detected. Nonetheless, a genetic signature of recent colonization is reflected in the absence of clinal genetic differentiation within the agricultural landscape, significantly lower gene flow between agricultural populations (3.494 than between woodland populations (4.183, and significantly higher genetic differentiation between agricultural (0.050 than woodland (0.034 pairwise comparisons, likely due to multiple founder events. Globally, the genetic data suggest multiple long distance dispersal/colonization events and subsequent high intra- and inter-landscape gene flow in this species. Phosphoglucomutase deviated from other enzymes and microsatellite markers, and hence may be under selection along the latitudinal gradient but not between landscape types. Phenotypic divergence was greater than genetic divergence, indicating directional

  9. Human migration through bottlenecks from Southeast Asia into East Asia during Last Glacial Maximum revealed by Y chromosomes.

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    Xiaoyun Cai

    Full Text Available Molecular anthropological studies of the populations in and around East Asia have resulted in the discovery that most of the Y-chromosome lineages of East Asians came from Southeast Asia. However, very few Southeast Asian populations had been investigated, and therefore, little was known about the purported migrations from Southeast Asia into East Asia and their roles in shaping the genetic structure of East Asian populations. Here, we present the Y-chromosome data from 1,652 individuals belonging to 47 Mon-Khmer (MK and Hmong-Mien (HM speaking populations that are distributed primarily across Southeast Asia and extend into East Asia. Haplogroup O3a3b-M7, which appears mainly in MK and HM, indicates a strong tie between the two groups. The short tandem repeat network of O3a3b-M7 displayed a hierarchical expansion structure (annual ring shape, with MK haplotypes being located at the original point, and the HM and the Tibeto-Burman haplotypes distributed further away from core of the network. Moreover, the East Asian dominant haplogroup O3a3c1-M117 shows a network structure similar to that of O3a3b-M7. These patterns indicate an early unidirectional diffusion from Southeast Asia into East Asia, which might have resulted from the genetic drift of East Asian ancestors carrying these two haplogroups through many small bottle-necks formed by the complicated landscape between Southeast Asia and East Asia. The ages of O3a3b-M7 and O3a3c1-M117 were estimated to be approximately 19 thousand years, followed by the emergence of the ancestors of HM lineages out of MK and the unidirectional northward migrations into East Asia.

  10. Association with Spontaneous Hepatitis C Viral Clearance and Genetic Differentiation of IL28B/IFNL4 Haplotypes in Populations from Mexico

    Science.gov (United States)

    Gonzalez-Aldaco, Karina; Rebello Pinho, João R.; Roman, Sonia; Gleyzer, Ketti; Fierro, Nora A.; Oyakawa, Leticia; Ramos-Lopez, Omar; Ferraz Santana, Rubia A.; Sitnik, Roberta; Panduro, Arturo

    2016-01-01

    Aim To analyze the genetic heterogeneity of the Amerindian and admixed population (Mestizos) based on the IL28B (rs12979860, rs8099917) and IFNL4 (rs368234815) haplotypes, and their association with spontaneous clearance (SC) and liver damage in patients with hepatitis C infection from West Mexico. Methods A total of 711 subjects from West Mexico (181 Amerindians and 530 Mestizos) were studied for the prevalence of IL28B (rs12979860C/T, rs8099917G/T) and IFNL4 (rs368234815∆G/TT) genotypes. A case-control study was performed in 234 treatment-naïve HCV Mestizos (149 chronic hepatitis C and 85 with SC) for the association of haplotypes with SC and liver damage. A real-time PCR assay was used for genotyping, and transitional elastography staged liver damage. Results Significant Fst-values indicated differentiation between the studied populations. The frequencies of the protective C, T, TT alleles were significantly lower in the Amerindians than in Mestizos (p<0.05). The r2 measure of linkage disequilibrium was significant for all variants and the T/G/ΔG risk haplotype predominated in Amerindians and secondly in Mestizos. The protective C/T/TT haplotype was associated with SC (OR = 0.46, 95% IC 0.22–0.95, p = 0.03) and less liver damage (OR = 0.32, 95% IC 0.10–0.97, p = 0.04) in chronic patients. The Structure software analysis demonstrated no significant differences in ancestry among SC and chronic patients. Conclusions West Mexico´s population is genetically heterogeneous at the IL28B/IFNL4 polymorphisms. The T/G/ΔG high-risk haplotype predominated in Amerindians and the beneficial alternative haplotype in Mestizos. The C/T/TT haplotype was associated with SC and less liver damage in chronically infected Mestizo patients. PMID:26741362

  11. Note: Inhibiting bottleneck corrosion in electrical calcium tests for ultra-barrier measurements

    Science.gov (United States)

    Nehm, F.; Müller-Meskamp, L.; Klumbies, H.; Leo, K.

    2015-12-01

    A major failure mechanism is identified in electrical calcium corrosion tests for quality assessment of high-end application moisture barriers. Accelerated calcium corrosion is found at the calcium/electrode junction, leading to an electrical bottleneck. This causes test failure not related to overall calcium loss. The likely cause is a difference in electrochemical potential between the aluminum electrodes and the calcium sensor, resulting in a corrosion element. As a solution, a thin, full-area copper layer is introduced below the calcium, shifting the corrosion element to the calcium/copper junction and inhibiting bottleneck degradation. Using the copper layer improves the level of sensitivity for the water vapor transmission rate (WVTR) by over one order of magnitude. Thin-film encapsulated samples with 20 nm of atomic layer deposited alumina barriers this way exhibit WVTRs of 6 × 10-5 g(H2O)/m2/d at 38 °C, 90% relative humidity.

  12. Note: Inhibiting bottleneck corrosion in electrical calcium tests for ultra-barrier measurements

    International Nuclear Information System (INIS)

    A major failure mechanism is identified in electrical calcium corrosion tests for quality assessment of high-end application moisture barriers. Accelerated calcium corrosion is found at the calcium/electrode junction, leading to an electrical bottleneck. This causes test failure not related to overall calcium loss. The likely cause is a difference in electrochemical potential between the aluminum electrodes and the calcium sensor, resulting in a corrosion element. As a solution, a thin, full-area copper layer is introduced below the calcium, shifting the corrosion element to the calcium/copper junction and inhibiting bottleneck degradation. Using the copper layer improves the level of sensitivity for the water vapor transmission rate (WVTR) by over one order of magnitude. Thin-film encapsulated samples with 20 nm of atomic layer deposited alumina barriers this way exhibit WVTRs of 6 × 10−5 g(H2O)/m2/d at 38 °C, 90% relative humidity

  13. Understanding of empty container movement: A study on a bottleneck at an off-dock depot

    Science.gov (United States)

    Zain, Rosmaizura Mohd; Rahman, Mohd Nizam Ab; Nopiah, Zulkifli Mohd; Saibani, Nizaroyani

    2014-09-01

    Port not only function as connections between marine and land transportation but also as core business areas. In a port terminal, available space is limited, but the influx of container is growing. The off-dock depot is one of the key supply chain players that hold empty containers in the inventory. Therefore, this paper aims to identify the main factors of bottlenecks or congestion that hinder the rapid movement of empty containers from the off-dock depot to the customers. Thirty interviews were conducted with individuals who are key players in the container supply chain. The data were analyzed using Atlas.ti software and the analytic hierarchy process to rank the priority factors of bottlenecks. Findings show that several pertinent factors act as barriers to the key players in the container movement in the day-to-day operations. In future studies, strategies to overcome fragmentation in the container supply chain and logistics must be determined.

  14. Zero-temperature quantum annealing bottlenecks in the spin-glass phase

    Science.gov (United States)

    Knysh, Sergey

    2016-08-01

    A promising approach to solving hard binary optimization problems is quantum adiabatic annealing in a transverse magnetic field. An instantaneous ground state--initially a symmetric superposition of all possible assignments of N qubits--is closely tracked as it becomes more and more localized near the global minimum of the classical energy. Regions where the energy gap to excited states is small (for instance at the phase transition) are the algorithm's bottlenecks. Here I show how for large problems the complexity becomes dominated by O(log N) bottlenecks inside the spin-glass phase, where the gap scales as a stretched exponential. For smaller N, only the gap at the critical point is relevant, where it scales polynomially, as long as the phase transition is second order. This phenomenon is demonstrated rigorously for the two-pattern Gaussian Hopfield model. Qualitative comparison with the Sherrington-Kirkpatrick model leads to similar conclusions.

  15. Defining population structure and genetic signatures of decline in the giant garter snake (Thamnophis gigas): implications for conserving threatened species within highly altered landscapes

    Science.gov (United States)

    Wood, Dustin A.; Halstead, Brian J.; Casazza, Michael L.; Hansen, Eric C.; Wylie, Glenn D.; Vandergast, Amy

    2015-01-01

    Anthropogenic habitat fragmentation can disrupt the ability of species to disperse across landscapes, which can alter the levels and distribution of genetic diversity within populations and negatively impact long-term viability. The giant gartersnake (Thamnophis gigas) is a state and federally threatened species that historically occurred in the wetland habitats of California’s Great Central Valley. Despite the loss of 93 % of historic wetlands throughout the Central Valley, giant gartersnakes continue to persist in relatively small, isolated patches of highly modified agricultural wetlands. Gathering information regarding genetic diversity and effective population size represents an essential component for conservation management programs aimed at this species. Previous mitochondrial sequence studies have revealed historical patterns of differentiation, yet little is known about contemporary population structure and diversity. On the basis of 15 microsatellite loci, we estimate population structure and compare indices of genetic diversity among populations spanning seven drainage basins within the Central Valley. We sought to understand how habitat loss may have affected genetic differentiation, genetic diversity and effective population size, and what these patterns suggest in terms of management and restoration actions. We recovered five genetic clusters that were consistent with regional drainage basins, although three northern basins within the Sacramento Valley formed a single genetic cluster. Our results show that northern drainage basin populations have higher connectivity than among central and southern basins populations, and that greater differentiation exists among the more geographically isolated populations in the central and southern portion of the species’ range. Genetic diversity measures among basins were significantly different, and were generally lower in southern basin populations. Levels of inbreeding and evidence of population

  16. Microsatellite analysis reveals genetically distinct populations of red pine (Pinus resinosa, Pinaceae).

    Science.gov (United States)

    Boys, Jacquelyn; Cherry, Marilyn; Dayanandan, Selvadurai

    2005-05-01

    Red pine (Pinus resinosa Ait.) is an ecologically and economically important forest tree species of northeastern North America and is considered one of the most genetically depauperate conifer species in the region. We have isolated and characterized 13 nuclear microsatellite loci by screening a partial genomic library with di-, tri-, and tetranucleotide repeat oligonucleotide probes. In an analysis of over 500 individuals representing 17 red pine populations from Manitoba through Newfoundland, five polymorphic microsatellite loci with an average of nine alleles per locus were identified. The mean expected and observed heterozygosity values were 0.508 and 0.185, respectively. Significant departures from Hardy-Weinberg equilibrium with excess homozygosity indicating high levels of inbreeding were evident in all populations studied. The population differentiation was high with 28-35% of genetic variation partitioned among populations. The genetic distance analysis showed that three northeastern (two Newfoundland and one New Brunswick) populations are genetically distinct from the remaining populations. The coalescence-based analysis suggests that "northeastern" and "main" populations likely became isolated during the most recent Pleistocene glacial period, and severe population bottlenecks may have led to the evolution of a highly selfing mating system in red pine. PMID:21652464

  17. Phonon bottleneck in GaAs/AlxGa1−xAs quantum dots

    International Nuclear Information System (INIS)

    We report low-temperature photoluminescence measurements on highly-uniform GaAs/AlxGa1−xAs quantum dots grown by droplet epitaxy. Recombination between confined electrons and holes bound to carbon acceptors in the dots allow us to determine the energies of the confined states in the system, as confirmed by effective mass calculations. The presence of acceptor-bound holes in the quantum dots gives rise to a striking observation of the phonon-bottleneck effect

  18. CO2 capture enhancement in InOF-1 via the bottleneck effect of confined ethanol.

    Science.gov (United States)

    Peralta, Ricardo A; Campos-Reales-Pineda, Alberto; Pfeiffer, Heriberto; Álvarez, J Raziel; Zárate, J Antonio; Balmaseda, Jorge; González-Zamora, Eduardo; Martínez, Ana; Martínez-Otero, Diego; Jancik, Vojtech; Ibarra, Ilich A

    2016-08-11

    CO2 capture of InOF-1 was enhanced 3.6-fold, at 1 bar and 30 °C, by confining EtOH within its pores. Direct visualisation by single crystal X-ray diffraction revealed that EtOH divides InOF-1 channels in wide sections separated by "bottlenecks" caused by EtOH molecules bonded to the μ2-OH functional groups of InOF-1. PMID:27469274

  19. Why don’t we see changes?: The role of attentional bottlenecks and limited visual memory

    OpenAIRE

    Jeremy M Wolfe; Reinecke, Andrea; BRAWN, PETER

    2006-01-01

    Seven experiments explore the role of bottlenecks in selective attention and access to visual short-term memory in the failure of observers to identify clearly visible changes in otherwise stable visual displays. Experiment One shows that observers fail to register a color change in an object even if they are cued to the location of the object by a transient at that location as the change is occurring. Experiment Two shows the same for orientation change. In Experiments Three and Four, attent...

  20. Germline Bottlenecks, Biparental Inheritance and Selection on Mitochondrial Variants: A Two-Level Selection Model

    OpenAIRE

    Roze, Denis; Rousset, François; Michalakis, Yannis

    2005-01-01

    Selection on mitochondrial mutations potentially occurs at different levels: at the mitochondria, cell, and organism levels. Several factors affect the strength of selection at these different levels; in particular, mitochondrial bottlenecks during germline development and reduced paternal transmission decrease the genetic variance within cells, while they increase the variance between cells and between organisms, thus decreasing the strength of selection within cells and increasing the stren...

  1. An assessment of The Capacity Drops at The Bottleneck Segments: A review on the existing methodologies

    Directory of Open Access Journals (Sweden)

    Sugiarto Sugiarto

    2015-08-01

    Full Text Available The term of capacity is very useful to quantify the ability of transport facilities in terms of carrying traffic. The capacity of the road is an essential ingredient in the planning, design, and operation of roadways. It is desirable for traffic analyst to be able to predict the time and places where congestion will occur and the volumes to be expected. Most of urbanized areas have been experiencing of traffic congestion problems particularly at urban arterial systems. High traffic demand and limited supply of roadways are always the main factors produced traffic congestion. However, there are other sources of local and temporal congestion, such as uncontrolled access point, median opening and on-street parking activities, which are caused a reduction of roadway capacity during peak operations. Those locations could result in reduction of travel speed and road, as known as hidden bottlenecks. This is bottleneck which is without any changes in geometric of the segments. The Indonesian Highway Capacity Manual (IHCM, 1997 is used to assess urban arterial systems till current days. IHCM provides a static method for examining the capacityand does not systematically take into account of bottleneck activities. However, bottleneck activities create interruption smooth traffic flow along arterial streets, which in turns stimulate related problems, such as, excessive air pollution, additional energy consumption and driver’s frustration due to traffic jammed. This condition could happen simultaneously; mostly repetitive and predictable in same peak hour demands. Therefore, this paper carefully summarize on the existing methodologies considering required data, handled data processing and expected output of each proposed of analysis. We further notice that dynamic approach could be more appropriated for analyzing temporal congestion segments (median opening, on street parking, etc.. Method of oblique cumulative plot seems to be more applicable in terms of

  2. Emerging from the bottleneck: Benefits of the comparative approach to modern neuroscience

    OpenAIRE

    Brenowitz, Eliot A.; Zakon, Harold H.

    2015-01-01

    Neuroscience historically exploited a wide diversity of animal taxa. Recently, however, research focused increasingly on a few model species. This trend accelerated with the genetic revolution, as genomic sequences and genetic tools became available for a few species, which formed a bottleneck. This coalescence on a small set of model species comes with several costs often not considered, especially in the current drive to use mice explicitly as models for human diseases. Comparative studies ...

  3. Bottlenecks and opportunities for quality improvement in fresh pineapple supply chains in Benin

    OpenAIRE

    Fassinou Hotegni, V.N.; Lommen, W.J.M.; Vorst, van de, GAL Alfred; Agbossou, E.K.; Struik, P.C.

    2014-01-01

    This study mapped and diagnosed the fresh pineapple supply chains in Benin to identify bottlenecks in pineapple quality improvement for different markets. A research framework was defined that comprised all relevant aspects to be researched. After 54 semi-structured interviews with key informants, 173 structured interviews were held with actor groups. The chain diagnosis showed there was no concordance between actor groups in which quality attribute they valued most. Moreover, pineapple quali...

  4. Potential and bottlenecks of the carbon market: The case of a developing country, Nepal

    International Nuclear Information System (INIS)

    The majority of clean development mechanism (CDM) projects are confined to a few countries. For many developing nations, entry into the carbon market, either through CDM or others, has been difficult. Thus, rationalizing CDM projects and the carbon market as a tool for sustainable development is often questioned. Many developing countries, such as Nepal, lack a quantification of CO2 reduction potential and an assessment of bottlenecks necessary for the carbon market. In this context, this paper assesses the potential emission reductions from major sectors of Nepal and the accompanying bottlenecks of the carbon market. The analyses provide indications of the type and scale of the carbon mitigation opportunities in key sectors such as waste management, biogas utilization, promotion of electric vehicles, rice cultivation, bio-energy utilization, brick making, hydropower development and a few others. These might be helpful to decision-makers in Nepal as well as to the process of re-orienting CDM and other carbon markets to better understand the bottlenecks of developing countries.

  5. Empirical Features of Spontaneous and Induced Traffic Breakdowns in Free Flow at Highway Bottlenecks

    CERN Document Server

    Kerner, Boris S; Klenov, Sergey L; Rehborn, Hubert; Leibel, Michael

    2015-01-01

    Based on an empirical study of real field traffic data measured in 1996--2014 through road detectors installed on German freeways, we reveal physical features of empirical nuclei for spontaneous traffic breakdown in free flow at highway bottlenecks. It is shown that the source of a nucleus for traffic breakdown is the solely difference between empirical spontaneous and induced traffic breakdowns at a highway bottleneck. Microscopic traffic simulations with a stochastic traffic flow model in the framework of three-phase theory explain the empirical findings. It turns out that in the most cases, a nucleus for empirical spontaneous traffic breakdown occurs through an interaction of one of waves in free flow with an empirical permanent speed disturbance localized at a highway bottleneck. The wave is a localized structure in free flow, in which the total flow rate is larger and the speed averaged across the highway is smaller than outside the wave. The waves in free flow appear due to oscilations in the percentage...

  6. Incident and Traffic-Bottleneck Detection Algorithm in High-Resolution Remote Sensing Imagery

    Directory of Open Access Journals (Sweden)

    S.M.M. Kahaki

    2012-09-01

    Full Text Available One of the most important methods to solve traffic congestion is to detect the incident state of a roadway. This paper describes the development of a method for road traffic monitoring aimed at the acquisition and analysis of remote sensing imagery. We propose a strategy for road extraction, vehicle detection and incident detection from remote sensing imagery using techniques based on neural networks, Radon transform for angle detection and traffic-flow measurements. Traffic-bottleneck detection is another method that is proposed for recognizing incidents in both offline and real-time mode. Traffic flows and incidents are extracted from aerial images of bottleneck zones. The results show that the proposed approach has a reasonable detection performance compared to other methods. The best performance of the learning system was a detection rate of 87% and a false alarm rate of less than 18% on 45 aerial images of roadways. The performance of the traffic-bottleneck detection method had a detection rate of 87.5%.

  7. Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA

    DEFF Research Database (Denmark)

    Rebolledo-Jaramillo, Boris; Su, Marcia Shu-Wei; Stoler, Nicholas;

    2014-01-01

    The manifestation of mitochondrial DNA (mtDNA) diseases depends on the frequency of heteroplasmy (the presence of several alleles in an individual), yet its transmission across generations cannot be readily predicted owing to a lack of data on the size of the mtDNA bottleneck during oogenesis. For...... deleterious heteroplasmies, a severe bottleneck may abruptly transform a benign (low) frequency in a mother into a disease-causing (high) frequency in her child. Here we present a high-resolution study of heteroplasmy transmission conducted on blood and buccal mtDNA of 39 healthy mother-child pairs of...... generations and estimated the effective size of the germ-line mtDNA bottleneck at only ∼30-35 (interquartile range from 9 to 141). Accounting for heteroplasmies, we estimated the mtDNA germ-line mutation rate at 1.3 × 10(-8) (interquartile range from 4.2 × 10(-9) to 4.1 × 10(-8)) mutations per site per year...

  8. Lagrangian-averaged model for magnetohydrodynamic turbulence and the absence of bottlenecks.

    Science.gov (United States)

    Pietarila Graham, Jonathan; Mininni, Pablo D; Pouquet, Annick

    2009-07-01

    We demonstrate that, for the case of quasiequipartition between the velocity and the magnetic field, the Lagrangian-averaged magnetohydrodynamics (LAMHD) alpha model reproduces well both the large-scale and the small-scale properties of turbulent flows; in particular, it displays no increased (superfilter) bottleneck effect with its ensuing enhanced energy spectrum at the onset of the subfilter scales. This is in contrast to the case of the neutral fluid in which the Lagrangian-averaged Navier-Stokes alpha model is somewhat limited in its applications because of the formation of spatial regions with no internal degrees of freedom and subsequent contamination of superfilter-scale spectral properties. We argue that, as the Lorentz force breaks the conservation of circulation and enables spectrally nonlocal energy transfer (associated with Alfvén waves), it is responsible for the absence of a viscous bottleneck in magnetohydrodynamics (MHD), as compared to the fluid case. As LAMHD preserves Alfvén waves and the circulation properties of MHD, there is also no (superfilter) bottleneck found in LAMHD, making this method capable of large reductions in required numerical degrees of freedom; specifically, we find a reduction factor of approximately 200 when compared to a direct numerical simulation on a large grid of 1536;{3} points at the same Reynolds number. PMID:19658812

  9. Modeling the Impact of Border Crossing Bottlenecks on Supply Chain Disruption Risk

    Directory of Open Access Journals (Sweden)

    Shaheen Sardar

    2015-04-01

    Full Text Available In order to remain competitive, companies outsource the manufacturing process to global markets. Globalization requires shipping of goods across borders. Cross border movement of goods faces diverse difficulties and creates bottlenecks in the supply chain. Complex products involve numerous parts and complications in the assembly process, resulting in multiple border-crossings with varying level of complexity across multiple countries before reaching to the customers. This activity contributes to the supply chain disruption risk. Border crossing is unavoidable in global supply chains, and how to integrate border crossing complexity in supply chain models is an unresolved issue. This paper suggests an approach to quantify the border crossing complexity and its impact on the supply chain disruption risk in the global outsourcing environment. Results show that key factors which contribute to border crossing complexity include product complexity, trade procedures, and various bottlenecks at each bordercrossing. Based on results drawn from the quantitative analysis, we propose several strategies to manage the impact of border crossing bottlenecks. The focus of this research is the manufacturing companies which are involved in managing the global supply chains.

  10. Range-wide distribution of genetic diversity in the North American tree Juglans cinerea: a product of range shifts, not ecological marginality or recent population decline.

    Science.gov (United States)

    Hoban, Sean M; Borkowski, Daniel S; Brosi, Sunshine L; McCleary, Tim S; Thompson, Laura M; McLachlan, Jason S; Pereira, Marie A; Schlarbaum, Scott E; Romero-Severson, Jeanne

    2010-11-01

    The spatial distribution of genetic diversity is a product of recent and historical ecological processes, as well as anthropogenic activities. A current challenge in population and conservation genetics is to disentangle the relative effects of these processes, as a first step in predicting population response to future environmental change. In this investigation, we compare the influence of contemporary population decline, contemporary ecological marginality and postglacial range shifts. Using classical model comparison procedures and Bayesian methods, we have identified postglacial range shift as the clear determinant of genetic diversity, differentiation and bottlenecks in 29 populations of butternut, Juglans cinerea L., a North American outcrossing forest tree. Although butternut has experienced dramatic 20th century decline because of an introduced fungal pathogen, our analysis indicates that recent population decline has had less genetic impact than postglacial recolonization history. Location within the range edge vs. the range core also failed to account for the observed patterns of diversity and differentiation. Our results suggest that the genetic impact of large-scale recent population losses in forest trees should be considered in the light of Pleistocene-era large-scale range shifts that may have had long-term genetic consequences. The data also suggest that the population dynamics and life history of wind-pollinated forest trees may provide a buffer against steep population declines of short duration, a result having important implications for habitat management efforts, ex situ conservation sampling and population viability analysis. PMID:21040046

  11. Effects of changes in food supply at the time of sex differentiation on the gonadal transcriptome of juvenile fish. Implications for natural and farmed populations.

    Directory of Open Access Journals (Sweden)

    Noelia Díaz

    Full Text Available Food supply is a major factor influencing growth rates in animals. This has important implications for both natural and farmed fish populations, since food restriction may difficult reproduction. However, a study on the effects of food supply on the development of juvenile gonads has never been transcriptionally described in fish.This study investigated the consequences of growth on gonadal transcriptome of European sea bass in: 1 4-month-old sexually undifferentiated fish, comparing the gonads of fish with the highest vs. the lowest growth, to explore a possible link between transcriptome and future sex, and 2 testis from 11-month-old juveniles where growth had been manipulated through changes in food supply. The four groups used were: i sustained fast growth, ii sustained slow growth, iii accelerated growth, iv decelerated growth. The transcriptome of undifferentiated gonads was not drastically affected by initial natural differences in growth. Further, changes in the expression of genes associated with protein turnover were seen, favoring catabolism in slow-growing fish and anabolism in fast-growing fish. Moreover, while fast-growing fish took energy from glucose, as deduced from the pathways affected and the analysis of protein-protein interactions examined, in slow-growing fish lipid metabolism and gluconeogenesis was favored. Interestingly, the highest transcriptomic differences were found when forcing initially fast-growing fish to decelerate their growth, while accelerating growth of initially slow-growing fish resulted in full transcriptomic convergence with sustained fast-growing fish.Food availability during sex differentiation shapes the juvenile testis transcriptome, as evidenced by adaptations to different energy balances. Remarkably, this occurs in absence of major histological changes in the testis. Thus, fish are able to recover transcriptionally their testes if they are provided with enough food supply during sex

  12. Meta-population structure in a coral reef fish demonstrated by genetic data on patterns of migration, extinction and re-colonisation

    Directory of Open Access Journals (Sweden)

    Bay Line K

    2008-09-01

    Full Text Available Abstract Background Management strategies for coral reefs are dependant on information about the spatial population structure and connectivity of reef organisms. Genetic tools can reveal important information about population structure, however, this information is lacking for many reef species. We used a mitochondrial molecular marker to examine the population genetic structure and the potential for meta-population dynamics in a direct developing coral reef fish using 283 individuals from 15 reefs on the Great Barrier Reef, Australia. We employed a hierarchical sampling design to test genetic models of population structure at multiple geographical scales including among regions, among shelf position and reefs within regions. Predictions from island, isolation-by-distance and meta-population models, including the potential for asymmetric migration, local extinction and patterns of re-colonisation were examined. Results Acanthochromis polyacanthus displayed strong genetic structure among regions (ΦST = 0.81, P ST = 0.31, P ST values indicated overall strong but variable genetic structure (mean ΦST among reefs within regions = 0.28, 0.38, 0.41, and asymmetric migration rates among reefs with low genetic structure. Genetic differentiation among younger reefs was greater than among older reefs supporting a meta-population propagule-pool colonisation model. Variation in genetic diversities, demographic expansion and population growth estimates indicated more frequent genetic bottlenecks/founder effects and subsequent population expansion in the central and southern regions compared to the northern one. Conclusion Our findings provide genetic evidence for meta-population dynamics in a direct developing coral reef fish and we reject the equilibrium island and isolation-by distance models at local spatial scales. Instead, strong non-equilibrium genetic structure appears to be generated by genetic bottlenecks/founder effects associated with population

  13. The effect of recurrent floods on genetic composition of marble trout populations.

    Directory of Open Access Journals (Sweden)

    José Martin Pujolar

    Full Text Available A changing global climate can threaten the diversity of species and ecosystems. We explore the consequences of catastrophic disturbances in determining the evolutionary and demographic histories of secluded marble trout populations in Slovenian streams subjected to weather extremes, in particular recurrent flash floods and debris flows causing massive mortalities. Using microsatellite data, a pattern of extreme genetic differentiation was found among populations (global F(ST of 0.716, which exceeds the highest values reported in freshwater fish. All locations showed low levels of genetic diversity as evidenced by low heterozygosities and a mean of only 2 alleles per locus, with few or no rare alleles. Many loci showed a discontinuous allele distribution, with missing alleles across the allele size range, suggestive of a population contraction. Accordingly, bottleneck episodes were inferred for all samples with a reduction in population size of 3-4 orders of magnitude. The reduced level of genetic diversity observed in all populations implies a strong impact of genetic drift, and suggests that along with limited gene flow, genetic differentiation might have been exacerbated by recurrent mortalities likely caused by flash flood and debris flows. Due to its low evolutionary potential the species might fail to cope with an intensification and altered frequency of flash flood events predicted to occur with climate change.

  14. Population structure of Squatina guggenheim (Squatiniformes, Squatinidae) from the south-western Atlantic Ocean.

    Science.gov (United States)

    Garcia, G; Pereyra, S; Gutierrez, V; Oviedo, S; Miller, P; Domingo, A

    2015-01-01

    Population genetic analyses based on both mitochondrial cytochrome b and the internal transcribed spacer 2 of recombinant (r)DNA genes were implemented to examine hypotheses of population differentiation in the angular angel shark Squatina guggenheim, one of the four most-widespread endemic species inhabiting coastal ecosystems in the south-western Atlantic Ocean. A total of 82 individuals of S. guggenheim from 10 sampling sites throughout the Río de la Plata mouth, its maritime front, the outer shelf at the subtropical confluence and the coastal areas of the south-west Atlantic Ocean, were included. The analysis of molecular variance (AMOVA) based on the second internal transcribed spacer (its-2) region supports that the samples from the outer shelf represent an isolated group from other sites. Historical gene flow in a coalescent-based approach revealed significant immigration and emigration asymmetry between sampling sites. Based on the low level of genetic diversity, the existence of a long-term population decline or a past recent population expansion following a population bottleneck could be proposed in S. guggenheim. This demographic differentiation suggests a degree of vulnerability to overexploitation in this endemic and endangered south-west Atlantic Ocean shark, given its longevity and low reproductive potential. PMID:25424738

  15. Genome-wide view of genetic diversity reveals paths of selection and cultivar differentiation in peach domestication.

    Science.gov (United States)

    Akagi, Takashi; Hanada, Toshio; Yaegaki, Hideaki; Gradziel, Thomas M; Tao, Ryutaro

    2016-06-01

    Domestication and cultivar differentiation are requisite processes for establishing cultivated crops. These processes inherently involve substantial changes in population structure, including those from artificial selection of key genes. In this study, accessions of peach (Prunus persica) and its wild relatives were analysed genome-wide to identify changes in genetic structures and gene selections associated with their differentiation. Analysis of genome-wide informative single-nucleotide polymorphism loci revealed distinct changes in genetic structures and delineations among domesticated peach and its wild relatives and among peach landraces and modern fruit (F) and modern ornamental (O-A) cultivars. Indications of distinct changes in linkage disequilibrium extension/decay and of strong population bottlenecks or inbreeding were identified. Site frequency spectrum- and extended haplotype homozygosity-based evaluation of genome-wide genetic diversities supported selective sweeps distinguishing the domesticated peach from its wild relatives and each F/O-A cluster from the landrace clusters. The regions with strong selective sweeps harboured promising candidates for genes subjected to selection. Further sequence-based evaluation further defined the candidates and revealed their characteristics. All results suggest opportunities for identifying critical genes associated with each differentiation by analysing genome-wide genetic diversity in currently established populations. This approach obviates the special development of genetic populations, which is particularly difficult for long-lived tree crops. PMID:27085183

  16. Genome-wide view of genetic diversity reveals paths of selection and cultivar differentiation in peach domestication

    Science.gov (United States)

    Akagi, Takashi; Hanada, Toshio; Yaegaki, Hideaki; Gradziel, Thomas M.; Tao, Ryutaro

    2016-01-01

    Domestication and cultivar differentiation are requisite processes for establishing cultivated crops. These processes inherently involve substantial changes in population structure, including those from artificial selection of key genes. In this study, accessions of peach (Prunus persica) and its wild relatives were analysed genome-wide to identify changes in genetic structures and gene selections associated with their differentiation. Analysis of genome-wide informative single-nucleotide polymorphism loci revealed distinct changes in genetic structures and delineations among domesticated peach and its wild relatives and among peach landraces and modern fruit (F) and modern ornamental (O-A) cultivars. Indications of distinct changes in linkage disequilibrium extension/decay and of strong population bottlenecks or inbreeding were identified. Site frequency spectrum- and extended haplotype homozygosity-based evaluation of genome-wide genetic diversities supported selective sweeps distinguishing the domesticated peach from its wild relatives and each F/O-A cluster from the landrace clusters. The regions with strong selective sweeps harboured promising candidates for genes subjected to selection. Further sequence-based evaluation further defined the candidates and revealed their characteristics. All results suggest opportunities for identifying critical genes associated with each differentiation by analysing genome-wide genetic diversity in currently established populations. This approach obviates the special development of genetic populations, which is particularly difficult for long-lived tree crops. PMID:27085183

  17. BOTTLENECK ANALYSIS AND STRATEGIC PLANNING ON CHILDHOOD DIARRHEA MANAGEMENT IN 6 HIGH PRIORITY DISTRICTS OF GUJARAT

    Directory of Open Access Journals (Sweden)

    Rupani Mihir

    2015-01-01

    Full Text Available Introduction:Bottleneck Analysis and Strategic Planning exercise was carried out in 6 High Priority Districts (HPDs, under Call-to-Action for RMNCH+A strategy.Rationale: In spite of continued efforts, India is still lagging behind in its MDG goals.Objectives: To identify gaps in childhood diarrhea management and propose strategic options for the same.Materials and Methods: Bottleneck analysis exercisewas carried out based on the Tanahashi model, desk review and focused group discussions between district officials, front-line workers and UNICEF officials. These bottlenecks were pertaining to the availability, accessibility, utilization of services and quality of services being provided by the health department.Elaborating the Tanahashi model for the 6 HPDs, 94% of the front-line workers (FLWs had stock of Zinc-ORS; 88% FLWs were trained in diarrhea management; 98% villages had at least one FLW trained in diarrhea management; health care seeking for diarrhea cases was 17%; 5.1% diarrhea cases received Zinc-ORS from health worker and 2.4% care takers prepared Zinc-ORS in safe drinking water.Results: The major bottlenecks identified for Childhood Diarrhea management in the 6 High Priority Districts were poor demand generation, unsafe drinking water, poor access to improved sanitation facility and lack of equitable distribution of Zinc-ORS till the front-line worker level. The main strategic options that were suggested for relieving these bottlenecks were Zinc-ORS roll out in scale-up districts, develop IEC/BCC plan for childhood diarrhea management at state/district level, use of Drug Logistics Information Management System (DLIMS software for supply chain management of Zinc-ORS, strengthening of chlorination activity at household level, monitoring implementation of Nirmal Bharat Abhiyaan (NBA for constructing improved sanitation facilities at household level and to develop an IEC/BCC plan for hygiene promotion and usage of sanitary latrines

  18. Gas to Power in China. Gas-fired Power in China. Clearing the policy bottleneck

    International Nuclear Information System (INIS)

    -to-be-defined elusive competitive power pooling system. This makes it difficult for gas-fired power plants to fulfil their obligations with the gas suppliers under the long-term take-or-pay gas sales contracts. It also increases the perceived risks of the Chinese market. Last but not least, gas-fired power is such a new phenomenon in the coal-dominated market that power sector professionals have a limited understanding of the gas economics. This led them to treat gas-fired power simply as fossil-fuel based generation source. In addition to the difficulties in sourcing LNG for the proposed LNG projects, lack of a clear supportive policy for gas-fired power at the initial stage of China's gas market development also casts serious doubts about the country's ambitious gas market development plans. To resolve those conflicting issues facing gas-fired power, the Chinese government needs to make a policy pronouncement on gas-fired power in the context of the overall national energy strategies and policies. The key may lie with a differentiated and flexible approach that recognises both the difficulties of the power reform process and the urgency of clearing the policy bottleneck on gas-fired power

  19. 1. Fertility differentials by incidence of marriage and their reproductive wastage in a Muslim population from rural north-east India

    Directory of Open Access Journals (Sweden)

    Anjali Haloi

    2014-01-01

    Full Text Available :The study strives to assess the fertility differentials by women's present age, influence of incidence of marriage (whether once or more than once married /consanguineous or non-consanguineous marriage, their reproductive wastage and the effect of socio-economic factors on reproductive wastage of women in a rural Muslim population of North-East India. Data for the present study were collected on 1034 married women (15-49 years through structured schedule by cross sectional method and then presented in terms of percentage, mean, and standard error. Student's t-test and ANOVA test were also applied to see the significant difference. The multiple regression analysis was used to predict whether or not reproductive wastage depends on some other independent variables. . The present study reveals that mean live births (fertility are directly proportional to the advancement of age of women, which is probably due to the fact that higher number of pregnancies in older women results from a lack of education and antenatal care leading to concomitant miscarriages and stillbirths. Marriage among the Assamese Muslims was found to be very 'stable' as only 12 females (1.17% of all married individuals reportedly changed their mates. There are 23.73% women, whose marriage is consanguineous while 77.27% women have non-consanguineous marriage. In the former group, 38 (3.7% women have given birth to physically deformed children while not a single case of physically deformed children was reported among the mothers of the latter group. The frequency of reproductive wastage, of all the pregnancies considered in this study, was found to be 14.32%. Further the study shows that women's age, maternal education, type of family, household income and antenatal care are important factors in regulating the fertility and reproductive wastage of a population.

  20. Local time stepping on high performance computing architectures: mitigating CFL bottlenecks for large-scale wave propagation

    OpenAIRE

    Rietmann, Max; Schenk, Olaf

    2015-01-01

    Modeling problems that require the simulation of hyperbolic PDEs (wave equations) on large heterogeneous domains have potentially many bottlenecks. We attack this problem through two techniques: the massively parallel capabilities of graphics processors (GPUs) and local time stepping (LTS) to mitigate any CFL bottlenecks on a multiscale mesh. Many modern supercomputing centers are installing GPUs due to their high performance, and extending existing seismic wave-propagation software to ...

  1. Genetic polymorphism analyses of 30 InDels in Chinese Xibe ethnic group and its population genetic differentiations with other groups.

    Science.gov (United States)

    Meng, Hao-Tian; Zhang, Yu-Dang; Shen, Chun-Mei; Yuan, Guo-Lian; Yang, Chun-Hua; Jin, Rui; Yan, Jiang-Wei; Wang, Hong-Dan; Liu, Wen-Juan; Jing, Hang; Zhu, Bo-Feng

    2015-01-01

    In the present study, we obtained population genetic data and forensic parameters of 30 InDel loci in Chinese Xibe ethnic group from northwestern China and studied the genetic relationships between the studied Xibe group and other reference groups. The observed heterozygosities ranged from 0.1704 at HLD118 locus to 0.5247 at HLD92 locus while the expected heterozygosities ranged from 0.1559 at HLD118 locus to 0.4997 at HLD101 locus. The cumulative power of exclusion and total probability of discrimination power in the studied group were 0.9867 and 0.9999999999902 for the 30 loci, respectively. Analyses of structure, PCA, interpopulation differentiations and phylogenetic tree revealed that the Xibe group had close genetic relationships with South Korean, Beijing Han and Guangdong Han groups. The results indicated that these 30 loci should only be used as a complement for autosomal STRs in paternity cases but could provide an acceptable level of discrimination in forensic identification cases in the studied Xibe group. Further studies should be conducted for better understanding of the Xibe genetic background. PMID:25651970

  2. Using Genome-Wide SNP Discovery and Genotyping to Reveal the Main Source of Population Differentiation in Nothofagus dombeyi (Mirb.) Oerst. in Chile

    Science.gov (United States)

    González, Jorge; Fuentes, Glenda; Alarcón, Diego; Ruiz, Eduardo

    2016-01-01

    Within a woody plant species, environmental heterogeneity has the potential to influence the distribution of genetic variation among populations through several evolutionary processes. In some species, a relationship between environmental characteristics and the distribution of genotypes can be detected, showing the importance of natural selection as the main source of differentiation. Nothofagus dombeyi (Mirb.) Oerst. (Nothofagaceae) is an endemic tree species occurring both in Chile and in Argentina temperate forests. Postglacial history has been studied with chloroplast DNA and evolutionary forces shaping genetic variation patterns have been analysed with isozymes but fine-scale genetic diversity studies are needed. The study of demographic and selection histories in Nothofagus dombeyi requires more informative markers such as single nucleotide polymorphisms (SNP). Genotyping-by-Sequencing tools now allow studying thousands of SNP markers at reasonable prices in nonmodel species. We investigated more than 10 K SNP loci for signatures of local adaptation and showed that interrogation of genomic resources can identify shifts in genetic diversity and putative adaptive signals in this nonmodel woody species. PMID:27446942

  3. Genetic analysis of a Sicilian population using 15 short tandem repeats.

    Science.gov (United States)

    Calò, C M; Garofano, L; Mameli, A; Pizzamiglio, M; Vona, G

    2003-04-01

    The genetic structure of the population of Alia (Sicily, Italy) was analyzed using 15 short tandem repeats: TPOX, D2S1338, D3S1358, FIBRA, D5S818, CSF1PO, D7S820, D8S1179, TH01, VWA, D13S317, D16S539, D18S51, D19S433, and D21S11. Two of these markers, D2S1338 and D19S433, have never before been used in research on population genetics and only recently have they been put to use in forensic medicine. Results of the analysis underline the genetic isolation of the Alia population and show it to be a recent bottleneck as a consequence of a cholera epidemic in 1837. While comparing the Alia population with other populations from Sicily, a genetic heterogeneity within Sicily was uncovered, thus confirming previous results obtained from the analysis of classical markers. This heterogeneity underlines the existence of genetic boundaries within the island. Comparisons with other Italian, Mediterranean, and European populations highlight the differentiation of the Sicilian population, reflecting the presence of a genetic boundary that separates Sicily from northern and central Italy and from the western Mediterranean basin. PMID:12943156

  4. Genetic Variability and Structuring of Arctic Charr (Salvelinus alpinus Populations in Northern Fennoscandia.

    Directory of Open Access Journals (Sweden)

    Takahito Shikano

    Full Text Available Variation in presumably neutral genetic markers can inform us about evolvability, historical effective population sizes and phylogeographic history of contemporary populations. We studied genetic variability in 15 microsatellite loci in six native landlocked Arctic charr (Salvelinus alpinus populations in northern Fennoscandia, where this species is considered near threatened. We discovered that all populations were genetically highly (mean FST ≈ 0.26 differentiated and isolated from each other. Evidence was found for historical, but not for recent population size bottlenecks. Estimates of contemporary effective population size (Ne ranged from seven to 228 and were significantly correlated with those of historical Ne but not with lake size. A census size (NC was estimated to be approximately 300 individuals in a pond (0.14 ha, which exhibited the smallest Ne (i.e. Ne/NC = 0.02. Genetic variability in this pond and a connected lake is severely reduced, and both genetic and empirical estimates of migration rates indicate a lack of gene flow between them. Hence, albeit currently thriving, some northern Fennoscandian populations appear to be vulnerable to further loss of genetic variability and are likely to have limited capacity to adapt if selection pressures change.

  5. [Genetic variability in captive populations of Crocodylus moreletii (Crocodylia: Crocodylidae) using microsatellites markers].

    Science.gov (United States)

    Serna-Lagunes, Ricardo; González, Dolores; Díaz-Rivera, Pablo

    2012-03-01

    Crocodylus moreletii, an extinction threatened species, represents an emblem for tropical ecosystems in Mexico. Surprisingly, there is a lack of information about their genetic constitution, which should be evaluated for a proper management ex situ and for making decisions on the release of crocodiles into natural habitats. The aim of this study was to characterize and compare the genetic variability of four populations of C. moreletii (two wild versus two born ex situ). Through PCR were amplified seven microsatellite polymorphic loci, however a heterozygote deficit, diminished by the presence of null alleles, was found in the populations (average Ho=0.02). The AMOVA indicated that the highest proportion of genetic variability is within populations, and a limited genetic differentiation among populations (average F(ST)=0.03), probably due to high inbreeding index (average F(IS)=0.97). When comparing the genetic variability between and within other crocodilian species, we found that in C. moreletii is well below those reported. We concluded that the limited genetic variability in ex situ born populations is probably due to a founder effect derived from the social structure of their progenitors, and by the bottleneck effect, inferred by the limited effective population size, that historically characterizes their natural distribution in wild populations. PMID:22458236

  6. Population genetic structure of the malaria vector Anopheles funestus, in a recently re-colonized area of the Senegal River basin and human-induced environmental changes

    Directory of Open Access Journals (Sweden)

    Samb Badara

    2012-09-01

    Full Text Available Abstract Background Anopheles funestus is one of the major malaria vectors in tropical Africa. Because of several cycles of drought events that occurred during the 1970s, this species had disappeared from many parts of sahelian Africa, including the Senegal River basin. However, this zone has been re-colonized during the last decade by An. funestus, following the implementation of two dams on the Senegal River. Previous studies in that area revealed heterogeneity at the biological and chromosomal level among these recent populations. Methods Here, we studied the genetic structure of the newly established mosquito populations using eleven microsatellite markers in four villages of the Senegal River basin and compared it to another An. funestus population located in the sudanian domain. Results Our results presume Hardy Weinberg equilibrium in each An. funestus population, suggesting a situation of panmixia. Moreover, no signal from bottleneck or population expansion was detected across populations. The tests of genetic differentiation between sites revealed a slight but significant division into three distinct genetic entities. Genetic distance between populations from the Senegal River basin and sudanian domain was correlated to geographical distance. In contrast, sub-division into the Senegal River basin was not correlated to geographic distance, rather to local adaptation. Conclusions The high genetic diversity among populations from Senegal River basin coupled with no evidence of bottleneck and with a gene flow with southern population suggests that the re-colonization was likely carried out by a massive and repeated stepping-stone dispersion starting from the neighboring areas where An. funestus endured.

  7. Population panmixia and the Pleistocene demographic expansion of spotty belly greenling Hexagrammos agrammus in the East Sea and Northwest Pacific

    Science.gov (United States)

    Habib, Kazi Ahsan; Jeong, Dageum; Myoung, Jung-Goo; Lee, Youn-Ho

    2015-06-01

    The population genetic structure and historical demography of spotty belly greenling, Hexagrammos agrammus, which has limited distribution in the Northwest Pacific, was assessed with partial sequences of the mitochondrial DNA (mtDNA) cytochrome b and the control region (D-loop). A total of 103 individuals were collected from four sites located at the Korea Strait (Southern coast of Korea) and the East coast of Korea and two places in the Pacific coast of Japan. For all the populations, nucleotide diversities were low (0.006-0.009) while the haplotype diversities were as high as 0.92 to 0.97, indicating that the fish has undergone a recent population expansion after experiencing bottleneck. Star-shaped patterns of haplotype networks as well as the significant negative values of Tajima's D and Fu's F S corroborate the recent population expansion. Mismatch distribution analysis reveals that the demographic expansion of the species started during the 2nd half of the Middle Pleistocene Series approximately 141,000-406,000 years ago. Hierarchical analysis of molecular variance (AMOVA), the pairwise population statistics ( F ST), and the exact test of haplotype differentiation demonstrate no significant genetic differentiation among populations investigated, suggesting that spotty belly greenling is panmictic in the East Sea and the Pacific coast of Japan.

  8. Genetic structuring among silverside fish (Atherinella brasiliensis) populations from different Brazilian regions

    Science.gov (United States)

    da Silva Cortinhas, Maria Cristina; Kersanach, Ralf; Proietti, Maíra; Dumont, Luiz Felipe Cestari; D'Incao, Fernando; Lacerda, Ana Luzia F.; Prata, Pedro Sanmartin; Matoso, Daniele Aparecida; Noleto, Rafael Bueno; Ramsdorf, Wanessa; Boni, Talge Aiex; Prioli, Alberto José; Cestari, Marta Margarete

    2016-09-01

    Estuaries are dynamic environments, key for the survival of innumerous ecologically or economically important fish species. Among these species are Neotropical silversides (Atherinella brasiliensis), which are resident and abundant in Brazilian estuaries and used as a complementary source of income and food for local communities. To better understand silverside populations in Brazil, we evaluated the genetic diversity, structure and demography of fish sampled at six estuaries from the northeastern to the southern coast, using Random Amplified Polymorphic DNA and mitochondrial DNA (D-loop) markers. High haplotype diversities (h ranging from 0.75 to 0.99) were found in all populations except Carapebus, located in Southeast Brazil (h = 0.54). A total of 69 mtDNA haplotypes were found, with Itaparica (Northeast Brazil) and Carapebus presenting only exclusive haplotypes, while some were shared among populations in the South. Strong regional structure was observed, with very high differentiation between Itaparica and Carapebus, as well as among these two populations and the ones from the Southern region (Paranaguá, Conceição, Camacho and Patos). Among southern areas, low/moderate structure was detected. Most populations showed unimodal mismatch distributions indicating recent demographic expansion, while Carapebus presented a multimodal distribution characteristic of a stable or bottlenecked population. Times since possible population expansion were highest in Itaparica (32,500 ya) and Carapebus (29,540 ya), while in the Southern region longest time was observed at Conceição (25,540 ya) and shortest at Patos (9720 ya). In a general manner, haplotype diversities were directly related to times since population expansions; again, Carapebus was the exception, displaying long time since expansion but low diversity, possibly due to a recent bottleneck caused by the isolation and human impacts this lagoon is subject to. Isolation by Distance was significant for Itaparica

  9. Bottleneck analysis and strategic planning using Tanahashi model for childhood diarrhea management in Gujarat, Western India.

    Science.gov (United States)

    Rupani, Mihir Prafulbhai; Gaonkar, Narayan T; Bhatt, Gneyaa S

    2016-10-01

    In spite of continued efforts, India is still lagging behind in achieving its MDG goals. The objectives of this study were to identify stake-holders who have a role to play in childhood diarrhea management, to identify gaps in childhood diarrhea management and to propose strategic options for relieving these gaps. Bottleneck analysis exercise was carried out based on the Tanahashi model in six High Priority Districts (HPDs) of Gujarat in period between July-November 2013. The major bottlenecks identified for Childhood Diarrhea management were poor demand generation, unsafe drinking water, poor access to improved sanitation facility and lack of equitable distribution and replenishment mechanisms for Oral Rehydration Solution (ORS) packets and Zinc tablets till the front-line worker level. The main strategic options that were suggested for relieving these bottlenecks were Zinc-ORS roll out in scale-up districts, develop Information Education Communication/Behaviour Change Communication (IEC/BCC) plan for childhood diarrhea management at state/district level, use of Drug Logistics Information Management System (DLIMS) software for supply chain management of Zinc-ORS, strengthening of chlorination activity at household level, monitoring implementation of Nirmal Bharat Abhiyaan (NBA) for constructing improved sanitation facilities at household level and to develop an IEC/BCC plan for hygiene promotion and usage of sanitary latrines. Use of Zinc tablets need to be intensified through an effective scale-up. Adequate demand generation activity is needed. There is need to address safe drinking water and improved sanitation measures at household levels. Multi-sectoral engagements and ownership of Zinc-ORS program is the need of the hour. PMID:27340871

  10. Bottle-neck type of neural network as a mapping device towards food specifications.

    Science.gov (United States)

    Novic, Marjana; Groselj, Neva

    2009-09-01

    A novel methodology is proposed for food specifications associated with the origin of food. The methodology was tested on honey samples collected within the TRACE EU project. The data were sampled in various regions in Europe and analysed for the trace elements content. The sampling sites were characterized by different geological origins, such as limestone, shale, or magmatic. We have chosen 14 elements, B, Na, Mg, A, K, Ca, Mn, Co, Ni, Cu, Zn, Rb, Sr, and Ba, due to their influence on the separation of samples regarding the geology of the sampling sites. A special architecture of an error back-propagation neural network, so called bottle-neck type of neural network was used to project the data into a 2D plane. The data were fed into the 14-nodes input layer and then transferred through the 2-nodes hidden layer (compared to a bottle-neck) to the 14-nodes output layer. The two hidden nodes representing the two coordinates of the projection plane enable us to map the samples used for training of the bottle-neck network. With the knowledge about the classes of individual samples we determine the clusters in the projection plane and consequently obtain the coordinates of the centroid (gravity point) of a particular cluster. The clusters are characterized with an ellipse shape borders spanning the length of up to 3sigma in each dimension. Since the data were classified as regard to the geology, three main clusters were sought: (i) limestone, (ii) shale/mudstone/clay/loess, and (iii) acid-magmatic origin of honey samples. The novel methodology proposed for food specifications was demonstrated on a reduced set of samples, which shows good clustering of all three classes in the projection plane, and on the third class of the original data set. PMID:19664464

  11. Direct structural mapping of organic field-effect transistors reveals bottlenecks to carrier transport

    KAUST Repository

    Li, Ruipeng

    2012-08-10

    X-ray microbeam scattering is used to map the microstructure of the organic semiconductor along the channel length of solution-processed bottom-contact OFET devices. Contact-induced nucleation is known to influence the crystallization behavior within the channel. We find that microstructural inhomogeneities in the center of the channel act as a bottleneck to charge transport. This problem can be overcome by controlling crystallization of the preferable texture, thus favoring more efficient charge transport throughout the channel. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Breaking CFD Bottlenecks in Gas-Turbine Flow-Path Design

    Science.gov (United States)

    Davis, Roger L.; Dannenhoffer, John F., III; Clark, John P.

    2010-01-01

    New ideas are forthcoming to break existing bottlenecks in using CFD during design. CAD-based automated grid generation. Multi-disciplinary use of embedded, overset grids to eliminate complex gridding problems. Use of time-averaged detached-eddy simulations as norm instead of "steady" RANS to include effects of self-excited unsteadiness. Combined GPU/Core parallel computing to provide over an order of magnitude increase in performance/price ratio. Gas-turbine applications are shown here but these ideas can be used for other Air Force, Navy, and NASA applications.

  13. A WEIGHTED INVERSE MINIMUM CUT PROBLEM UNDER THE BOTTLENECK TYPE HAMMING DISTANCE

    OpenAIRE

    LONGCHENG LIU; ENYU YAO

    2007-01-01

    An inverse optimization problem is defined as follows. Let S denote the set of feasible solutions of an optimization problem P, let c be a specified cost (capacity) vector, and x0 ∈ S. We want to perturb the cost (capacity) vector c to d so that x0 is an optimal solution of P with respect to the cost (capacity) vector d, and to minimize some objective function. In this paper, we consider the weighted inverse minimum cut problem under the bottleneck type Hamming distance. For the general case,...

  14. Phonon bottleneck in GaAs/AlxGa1−xAs quantum dots

    Directory of Open Access Journals (Sweden)

    Y. C. Chang

    2015-06-01

    Full Text Available We report low-temperature photoluminescence measurements on highly-uniform GaAs/AlxGa1−xAs quantum dots grown by droplet epitaxy. Recombination between confined electrons and holes bound to carbon acceptors in the dots allow us to determine the energies of the confined states in the system, as confirmed by effective mass calculations. The presence of acceptor-bound holes in the quantum dots gives rise to a striking observation of the phonon-bottleneck effect.

  15. Genetic diversity and population structure of Plasmodium falciparum over space and time in an African archipelago.

    Science.gov (United States)

    Salgueiro, Patrícia; Vicente, José Luís; Figueiredo, Rita Carrilho; Pinto, João

    2016-09-01

    The archipelago of São Tomé and Principe (STP), West Africa, has suffered the heavy burden of malaria since the 16th century. Until the last decade, when after a successful control program STP has become a low transmission country and one of the few nations with decreases of more than 90% in malaria admission and death rates. We carried out a longitudinal study to determine the genetic structure of STP parasite populations over time and space. Twelve microsatellite loci were genotyped in Plasmodium falciparum samples from two islands collected in 1997, 2000 and 2004. Analysis was performed on proportions of mixed genotype infections, allelic diversity, population differentiation, effective population size and bottleneck effects. We have found high levels of genetic diversity and minimal inter-population genetic differentiation typical of African continental regions with intense and stable malaria transmission. We detected significant differences between the years, with special emphasis for 1997 that showed the highest proportion of samples infected with P. falciparum and the highest mean number of haplotypes per isolate. This study establishes a comprehensive genetic data baseline of a pre-intervention scenario for future studies; taking into account the most recent and successful control intervention on the territory. PMID:27262356

  16. Lack of Population Genetic Structuring in Ocelots (Leopardus pardalis in a Fragmented Landscape

    Directory of Open Access Journals (Sweden)

    Marina G. Figueiredo

    2015-07-01

    Full Text Available Habitat fragmentation can promote patches of small and isolated populations, gene flow disruption between those populations, and reduction of local and total genetic variation. As a consequence, these small populations may go extinct in the long-term. The ocelot (Leopardus pardalis, originally distributed from Texas to southern Brazil and northern Argentina, has been impacted by habitat fragmentation throughout much of its range. To test whether habitat fragmentation has already induced genetic differentiation in an area where this process has been documented for a larger felid (jaguars, we analyzed molecular variation in ocelots inhabiting two Atlantic Forest fragments, Morro do Diabo (MD and Iguaçu Region (IR. Analyses using nine microsatellites revealed mean observed and expected heterozygosity of 0.68 and 0.70, respectively. The MD sampled population showed evidence of a genetic bottleneck under two mutational models (TPM = 0.03711 and SMM = 0.04883. Estimates of genetic structure (FST = 0.027; best fit of k = 1 with STRUCTURE revealed no meaningful differentiation between these populations. Thus, our results indicate that the ocelot populations sampled in these fragments are still not significantly different genetically, a pattern that strongly contrasts with that previously observed in jaguars for the same comparisons. This observation is likely due to a combination of two factors: (i larger effective population size of ocelots (relative to jaguars in each fragment, implying a slower effect of drift-induced differentiation; and (ii potentially some remaining permeability of the anthropogenic matrix for ocelots, as opposed to the observed lack of permeability for jaguars. The persistence of ocelot gene flow between these areas must be prioritized in long-term conservation planning on behalf of these felids.

  17. Evolution of Fitness in Experimental Populations of Vesicular Stomatitis Virus

    OpenAIRE

    Elena, S F; Gonzalez-Candelas, F.; Novella, I S; Duarte, E A; Clarke, D. K.; Domingo, E; Holland, J J; Moya, A.

    1996-01-01

    The evolution of fitness in experimental clonal populations of vesicular stomatitis virus (VSV) has been compared under different genetic (fitness of initial clone) and demographic (population dynamics) regimes. In spite of the high genetic heterogeneity among replicates within experiments, there is a clear effect of population dynamics on the evolution of fitness. Those populations that went through strong periodic bottlenecks showed a decreased fitness in competition experiments with wild t...

  18. Identification and Validation of Ifit1 as an Important Innate Immune Bottleneck

    Energy Technology Data Exchange (ETDEWEB)

    McDermott, Jason E.; Vartanian, Keri B.; Mitchell, Hugh D.; Stevens, S.L.; Sanfilippo, Antonio P.; Stenzel-Poore, Mary

    2012-06-20

    The innate immune system plays important roles in a number of disparate processes. Foremost, innate immunity is a first responder to invasion by pathogens and triggers early defensive responses and recruits the adaptive immune system. The innate immune system also responds to endogenous damage signals that arise from tissue injury. Recently it has been found that innate immunity plays an important role in neuroprotection against ischemic stroke through the activation of the primary innate immune receptors, Toll-like receptors (TLRs). Using several large-scale transcriptomic data sets from mouse and mouse macrophage studies we identified targets predicted to be important in controlling innate immune processes initiated by TLR activation. Targets were identified as genes with high betweenness centrality, so-called bottlenecks, in networks inferred from statistical associations between gene expression patterns. A small set of putative bottlenecks were identified in each of the data sets investigated including interferon-stimulated genes (Ifit1, Ifi47, Tgtp and Oasl2) as well as genes uncharacterized in immune responses (Axud1 and Ppp1r15a). We further validated one of these targets, Ifit1, in mouse macrophages by showing that silencing it suppresses induction of predicted downstream genes by lipopolysaccharide (LPS)-mediated TLR4 activation through an unknown direct or indirect mechanism. Our study demonstrates the utility of network analysis for identification of interesting targets related to innate immune function, and highlights that Ifit1 can exert a positive regulatory effect on downstream genes.

  19. The physics of empirical nuclei for spontaneous traffic breakdown in free flow at highway bottlenecks

    Science.gov (United States)

    Kerner, Boris S.; Koller, Micha; Klenov, Sergey L.; Rehborn, Hubert; Leibel, Michael

    2015-11-01

    Based on an empirical study of real field traffic data measured in 1996-2014 through road detectors installed on German freeways, we reveal physical features of empirical nuclei for spontaneous traffic breakdown in free flow at highway bottlenecks. A microscopic stochastic three-phase traffic model of the nucleation of spontaneous traffic breakdown presented in the article explains the empirical findings. It turns out that in the most cases a nucleus for the breakdown occurs through an interaction of one of waves in free flow with an empirical permanent speed disturbance localized at a highway bottleneck. The wave is a localized structure in free flow, in which the total flow rate is larger and the speed averaged across the highway is smaller than outside the wave. The waves in free flow appear due to oscillations in the percentage of slow vehicles; these waves propagate with the average speed of slow vehicles in free flow. Any of the empirical waves exhibits a two-dimensional asymmetric spatiotemporal structure: Wave's characteristics are different in different highway lanes.

  20. Note: Inhibiting bottleneck corrosion in electrical calcium tests for ultra-barrier measurements

    Energy Technology Data Exchange (ETDEWEB)

    Nehm, F., E-mail: frederik.nehm@iapp.de; Müller-Meskamp, L.; Klumbies, H.; Leo, K. [Institut für Angewandte Photophysik, Technische Universität Dresden, George-Bähr-Straße 1, 01069 Dresden (Germany)

    2015-12-15

    A major failure mechanism is identified in electrical calcium corrosion tests for quality assessment of high-end application moisture barriers. Accelerated calcium corrosion is found at the calcium/electrode junction, leading to an electrical bottleneck. This causes test failure not related to overall calcium loss. The likely cause is a difference in electrochemical potential between the aluminum electrodes and the calcium sensor, resulting in a corrosion element. As a solution, a thin, full-area copper layer is introduced below the calcium, shifting the corrosion element to the calcium/copper junction and inhibiting bottleneck degradation. Using the copper layer improves the level of sensitivity for the water vapor transmission rate (WVTR) by over one order of magnitude. Thin-film encapsulated samples with 20 nm of atomic layer deposited alumina barriers this way exhibit WVTRs of 6 × 10{sup −5} g(H{sub 2}O)/m{sup 2}/d at 38 °C, 90% relative humidity.

  1. [Bottlenecks in the provision of inpatient care--caused by the Hospital Funding Act].

    Science.gov (United States)

    Jansen, Christoph

    2010-01-01

    The responsibility of the state for ensuring the provision of hospital care services to its citizens derives from the welfare state principle laid down in Sect. 20 para. 1 GG (Grundgesetz, i.e., the German constitutional law). The state fulfils this responsibility by means of planning and funding regulations in the Hospital Funding Act (KHG), the Hospital Remuneration Act (KHEntG), the National Ordinance on Hospital Rates (BPflV), the Hospital Laws of the German federal states and other supplementary legislation. The funding of hospitals is based on a dual funding system, meaning that hospital investment costs generally need to be borne by the German federal states as required, while operating costs will have to be funded through the remuneration for hospital treatments. Because of the tight budget situation of the German federal states a considerable backlog of investment has built up. After a transition period (between 2005 and 2009) operating costs are now funded on the basis of the so-called DRG system (DRG=Diagnosis Related Groups)--irrespective of the actual costs incurred by each individual hospital, which has led to a commodification of hospital care services. Whether this commodification avoids bottlenecks in the provision of health services to hospital patients or creates additional bottlenecks, is a controversial issue. PMID:20870488

  2. Topological-based bottleneck analysis and improvement strategies for traffic networks

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    A method is proposed to find key components of traffic networks with homogenous and heterogeneous topologies, in which heavier traffic flow is transported. One component, called the skeleton, is the minimum spanning tree (MST) based on the zero flow cost (ZCMST). The other component is the infinite incipient percolation cluster (IIC) which represents the spine of the traffic network. Then, a new method to analysis the property of the bottleneck in a large scale traffic network is given from a macroscopic and statistical viewpoint. Moreover, three effective strategies are proposed to alleviate traffic congestion. The significance of the findings is that one can significantly improve the global transport by enhancing the capacity in the ZCMST with a few links, while for improving the local traffic property, improving a tiny fraction of the traffic network in the IIC is effective. The result can be used to help traffic managers prevent and alleviate traffic congestion in time, guard against the formation of congestion bottleneck, and make appropriate policies for traffic demand management. Meanwhile, the method has very important theoretical significance and practical worthiness in optimizing traffic organization, traffic control, and disposal of emergency.

  3. Optimal design of future electricity supply systems. An analysis of potential bottlenecks in NW-Europe

    International Nuclear Information System (INIS)

    This paper analyses the potential bottlenecks that might emerge in the North-western European electricity supply system as a result of a number of (autonomous) long-term developments. The main long-term developments we identify are 1) a continuing increase in the demand for electricity, 2) a gradual shift from conventional electricity generation towards unconventional (green) generation, 3) a gradual shift from centralized generation towards decentralized generation and 4) a shift from national self-sufficient electricity supply systems towards a pan-European electricity system. Although it has been recognized that these developments might cause certain problems in some or more elements of the electricity supply chain, a coherent and comprehensive framework for the identification of these problems is lacking. More specific, governments and regulators seem to focus on certain parts of the electricity supply system separately, whereas certain interdependencies in the system have received relatively little attention. This paper presents such a framework and identifies some potential bottlenecks that receive relatively little attention from policy makers. These are 1) the increasing penetration of distributed generation, 2) an increasingly important role for demand response and 3) the lack of locational signals in the electricity supply system. The potential role of governments and markets in these issues is briefly explored. (Author)

  4. Characteristics of forensic imaging performance--an analysis of forensic imaging bottlenecks.

    Science.gov (United States)

    Branigan, Steven

    2013-05-01

    Disk imaging involves copying all of the data from a source disk drive to a target. Typically, the target for the copy is another disk drive. Forensic processes developed years ago do not appear to be adequate for current storage technology. For example, with disk drive capacities now exceeding 1 Terabyte, a typical disk imaging can take over 8 hours at typical rates. With disk drive capacities increasing, forensic copying is expected to take even longer. Along with increase in disk capacity, the industry has also seen an increase in data transfer rates. In many cases, forensic imaging is taking longer than necessary. To identify the bottlenecks, an examination of different methods used to transfer data from a source disk was performed. Factors considered were differing disk access technologies. One finding is that the USB disk access technology (version 2.0 and earlier) is a significant bottleneck for data transfer rates, especially when the USB device is a write-blocker. Other factors that contribute to the efficiency of a forensic copy are the file system used to write a forensic image and the data transfer size used when reading from a disk drive. Optimal parameters for performing a forensic acquisition from a disk drive are identified. PMID:23458238

  5. Flagella-Driven Flows Circumvent Diffusive Bottlenecks that Inhibit Metabolite Exchange

    Science.gov (United States)

    Short, Martin; Solari, Cristian; Ganguly, Sujoy; Kessler, John; Goldstein, Raymond; Powers, Thomas

    2006-03-01

    The evolution of single cells to large and multicellular organisms requires matching the organisms' needs to the rate of exchange of metabolites with the environment. This logistic problem can be a severe constraint on development. For organisms with a body plan that approximates a spherical shell, such as colonies of the volvocine green algae, the required current of metabolites grows quadratically with colony radius whereas the rate at which diffusion can exchange metabolites grows only linearly with radius. Hence, there is a bottleneck radius beyond which the diffusive current cannot keep up with metabolic demands. Using Volvox carteri as a model organism, we examine experimentally and theoretically the role that advection of fluid by surface-mounted flagella plays in enhancing nutrient uptake. We show that fluid flow driven by the coordinated beating of flagella produces a convective boundary layer in the concentration of a diffusing solute which in turn renders the metabolite exchange rate quadratic in the colony radius. This enhanced transport circumvents the diffusive bottleneck, allowing increase in size and thus evolutionary transitions to multicellularity in the Volvocales.

  6. Greater Genetic Diversity in Spatially Restricted Coral Reef Fishes Suggests Secondary Contact among Differentiated Lineages

    Directory of Open Access Journals (Sweden)

    M. Julian Caley

    2011-09-01

    Full Text Available The maintenance of genetic diversity is a central goal of conservation. It is the raw material for evolutionary change and if lost, can accelerate extinction of species. According to theory, total genetic diversity should be less in species with restricted ranges and in populations on the margins of distributional ranges, making such species or populations more vulnerable to environmental perturbations. Using mtDNA and nuclear Inter Simple Sequence Repeat (ISSR data we investigated how the genetic diversity and structure of three con-generic species pairs of coral reef fishes (Pomacentridae was related to species’ range size and position of populations within these ranges. Estimates of genetic structure did not differ significantly among species, but mtDNA and nucDNA genetic diversities were up to 10 times greater in spatially restricted species compared to their widespread congeners. In two of the three species pairs, the distribution of genetic variation indicated secondary contact among differentiated lineages in the spatially restricted species. In contrast, the widespread species displayed a typical signature of population expansion suggesting recent genetic bottlenecks, possibly associated with the (re colonization of the Great Barrier Reef. These results indicate that historical processes, involving hybridization and founder effects, possibly associated with Pleistocene sea level fluctuations, have differentially influenced the widespread and spatially restricted coral reef damselfish species studied here.

  7. A replication study confirmed the EDAR gene to be a major contributor to population differentiation regarding head hair thickness in Asia

    OpenAIRE

    Fujimoto, Akihiro; Ohashi, Jun; Nishida, Nao; Miyagawa, Taku; Morishita, Yasuyuki; Tsunoda, Tatsuhiko; Kimura, Ryosuke; Tokunaga, Katsushi

    2008-01-01

    Hair morphology is a highly divergent phenotype among human populations. We recently reported that a nonsynonymous SNP in the ectodysplasin A receptor (EDAR 1540T/C) is associated with head hair fiber thickness in an ethnic group in Thailand (Thai-Mai) and an Indonesian population. However, these Southeast Asian populations are genetically and geographically close, and thus the genetic contribution of EDAR to hair morphological variation in the other Asian populations has remained unclear. In...

  8. Do hatchery-reared sea urchins pose a threat to genetic diversity in wild populations?

    Science.gov (United States)

    Segovia-Viadero, M; Serrão, E A; Canteras-Jordana, J C; Gonzalez-Wangüemert, M

    2016-04-01

    In salmonids, the release of hatchery-reared fish has been shown to cause irreversible genetic impacts on wild populations. However, although responsible practices for producing and releasing genetically diverse, hatchery-reared juveniles have been published widely, they are rarely implemented. Here, we investigated genetic differences between wild and early-generation hatchery-reared populations of the purple sea urchin Paracentrotus lividus (a commercially important species in Europe) to assess whether hatcheries were able to maintain natural levels of genetic diversity. To test the hypothesis that hatchery rearing would cause bottleneck effects (that is, a substantial reduction in genetic diversity and differentiation from wild populations), we compared the levels and patterns of genetic variation between two hatcheries and four nearby wild populations, using samples from both Spain and Ireland. We found that hatchery-reared populations were less diverse and had diverged significantly from the wild populations, with a very small effective population size and a high degree of relatedness between individuals. These results raise a number of concerns about the genetic impacts of their release into wild populations, particularly when such a degree of differentiation can occur in a single generation of hatchery rearing. Consequently, we suggest that caution should be taken when using hatchery-reared individuals to augment fisheries, even for marine species with high dispersal capacity, and we provide some recommendations to improve hatchery rearing and release practices. Our results further highlight the need to consider the genetic risks of releasing hatchery-reared juveniles into the wild during the establishment of restocking, stock enhancement and sea ranching programs. PMID:26758187

  9. The PPARgamma-selective ligand BRL-49653 differentially regulates the fate choices of rat calvaria versus rat bone marrow stromal cell populations

    Directory of Open Access Journals (Sweden)

    Yoshiko Yuji

    2008-07-01

    Full Text Available Abstract Background Osteoblasts and adipocytes are derived from a common mesenchymal progenitor and an inverse relationship between expression of the two lineages is seen with certain experimental manipulations and in certain diseases, i.e., osteoporosis, but the cellular pathway(s and developmental stages underlying the inverse relationship is still under active investigation. To determine which precursor mesenchymal cell types can differentiate into adipocytes, we compared the effects of BRL-49653 (BRL, a selective ligand for peroxisome proliferators-activated receptor (PPARγ, a master transcription factor of adipogenesis, on osteo/adipogeneis in two different osteoblast culture models: the rat bone marrow (RBM versus the fetal rat calvaria (RC cell system. Results BRL increased the number of adipocytes and corresponding marker expression, such as lipoprotein lipase, fatty acid-binding protein (aP2, and adipsin, in both culture models, but affected osteoblastogenesis only in RBM cultures, where a reciprocal decrease in bone nodule formation and osteoblast markers, e.g., osteopontin, alkaline phosphatase (ALP, bone sialoprotein, and osteocalcin was seen, and not in RC cell cultures. Even though adipocytes were histologically undetectable in RC cultures not treated with BRL, RC cells expressed PPAR and CCAAT/enhancer binding protein (C/EBP mRNAs throughout osteoblast development and their expression was increased by BRL. Some single cell-derived BRL-treated osteogenic RC colonies were stained not only with ALP/von Kossa but also with oil red O and co-expressed the mature adipocyte marker adipsin and the mature osteoblast marker OCN, as well as PPAR and C/EBP mRNAs. Conclusion The data show that there are clear differences in the capacity of BRL to alter the fate choices of precursor cells in stromal (RBM versus calvarial (RC cell populations and that recruitment of adipocytes can occur from multiple precursor cell pools (committed preadipocyte

  10. Asymmetric effect of route-length difference and bottleneck on route choice in two-route traffic system

    Science.gov (United States)

    Hino, Yuki; Nagatani, Takashi

    2015-06-01

    We study the traffic behavior in the asymmetric two-route traffic system with real-time information. In the asymmetric two-route system, the length on route A is different from that on route B and there exists a bottleneck on route A. We extend the symmetric two-route dynamic model to the asymmetric case. We investigate the asymmetric effects of the route-length difference and bottleneck on the route choice with real-time information. The travel time on each route depends on the road length, bottleneck, and vehicular density. We derive the dependence of the travel time and mean density on the route-length ratio. We show where, when, and how the congestion occurs by the route choice in the asymmetric two-route system. We clarify the effect of the route-length ratio on the traffic behavior in the route choice.

  11. Genetic diversity and differentiation of the rhesus macaque (Macaca mulatta) population in western Sichuan, China, based on the second exon of the major histocompatibility complex class II DQB (MhcMamu-DQB1) alleles

    OpenAIRE

    Yao, Yong-Fang; Dai, Qiu-Xia; Li, Jing; Ni, Qing-Yong; Zhang, Ming-Wang; Xu, Huai-Liang

    2014-01-01

    Abstracts Background Rhesus macaques living in western Sichuan, China, have been separated into several isolated populations due to habitat fragmentation. Previous studies based on the neutral or nearly neutral markers (mitochondrial DNA or microsatellites) showed high levels of genetic diversity and moderate genetic differentiation in the Sichuan rhesus macaques. Variation at the major histocompatibility complex (MHC) loci is widely accepted as being maintained by balancing selection, even w...

  12. Population Genetic Structure in Hyacinth Macaws (Anodorhynchus hyacinthinus) and Identification of the Probable Origin of Confiscated Individuals.

    Science.gov (United States)

    Presti, Flavia T; Guedes, Neiva M R; Antas, Paulo T Z; Miyaki, Cristina Y

    2015-01-01

    Understanding the intraspecific genetic composition of populations in different geographic locations is important for the conservation of species. If genetic variability is structured, conservation strategies should seek to preserve the diversity of units. Also, origin of individuals can be determined, which is important for guiding actions against animal trafficking. The hyacinth macaw (Anodorhynchus hyacinthinus) is located in allopatric regions, vulnerable to extinction and suffering animal trafficking pressure. Therefore, we characterized its population genetic structure based on 10 microsatellites from 98 individuals and 2123bp of mitochondrial sequence (ND5, cytochrome b, and ND2) from 80 individuals. Moderate to high levels of differentiation were observed among 3 geographic regions of Brazil: the north/northeast of the country, the north Pantanal, and the south Pantanal. Differentiation between the 2 regions within the Pantanal was not expected, as they are relatively close and there is no known barrier to macaw movement between these regions. These genetically differentiated groups were estimated to have diverged 16000 to 42000 years ago. The low genetic variability observed seems not to be the result of past bottlenecks, although a star-shaped haplotype network and the mismatch distribution suggest that there was recent demographic expansion in the north and northeast. Environmental changes in the Holocene could have caused this expansion. Given the genetic structure observed, the most probable regions of origin of 24 confiscated individuals were identified. Thus, these data helped to trace illegal traffic routes and identify natural populations that are being illegally harvested. PMID:26245784

  13. Country planning bottlenecks for the Integral Program Wind power (IPW) projects and the importance of knowledge transfer

    International Nuclear Information System (INIS)

    Most bottlenecks in realizing the aims of the Dutch title project concern problems with the site selection and administrative or juridical problems. The attitude of municipalities towards wind turbines is reserved, their policies not uniform, and the possibility to participate in the licensing procedures has been frequently used. If the energy policy of the Dutch government to produce 1000 MW in the year 2000 should be realized, initiatives must be developed to clear these planning bottlenecks. Some propositions are made with regard to government standards for noise pollution, safety, nature values, agreements with dike managers, regulations for land acquisition, transfer of information, and a manual for municipalities. 2 figs., 5 refs

  14. Quantification of bottlenecks to fast charging of lithium-ion-insertion cells for electric vehicles

    Science.gov (United States)

    Chandrasekaran, Rajeswari

    2014-12-01

    In this work, an isothermal, physics-based, dual lithium-ion insertion cell sandwich model is used for simulating the galvanostatic charge performance of a graphite (LixC6)/liquid electrolyte/Liy(NiaCobMnc)O2 at room temperature at various current densities. The modeling results are compared with experimental cell potential vs. capacity data. The validated model is used to identify the bottlenecks to fast charging by quantification of the various contributions to the cell overpotential. Lithium plating at the negative electrode is shown to be thermodynamically feasible during galvanostatic charging at 2C rate and above. This work will aid in research and development activities to overcome the hurdles to fast charging of advance electric vehicle batteries.

  15. Algorithm Based on Taboo Search and Shifting Bottleneck for Job Shop Scheduling

    Institute of Scientific and Technical Information of China (English)

    Wen-Qi Huang; Zhi Huang

    2004-01-01

    In this paper, a computational effective heuristic method for solving the minimum makespan problem of job shop scheduling is presented. It is based on taboo search procedure and on the shifting bottleneck procedure used to jump out of the trap of the taboo search procedure. A key point of the algorithm is that in the taboo search procedure two taboo lists are used to forbid two kinds of reversals of arcs, which is a new and effective way in taboo search methods for job shop scheduling. Computational experiments on a set of benchmark problem instances show that, in several cases, the approach, in reasonable time, yields better solutions than the other heuristic procedures discussed in the literature.

  16. Engineering oilseeds for sustainable production of industrial and nutritional feedstocks: solving bottlenecks in fatty acid flux.

    Science.gov (United States)

    Cahoon, Edgar B; Shockey, Jay M; Dietrich, Charles R; Gidda, Satinder K; Mullen, Robert T; Dyer, John M

    2007-06-01

    Oilseeds provide a unique platform for the production of high-value fatty acids that can replace non-sustainable petroleum and oceanic sources of specialty chemicals and aquaculture feed. However, recent efforts to engineer the seeds of crop and model plant species to produce new types of fatty acids, including hydroxy and conjugated fatty acids for industrial uses and long-chain omega-3 polyunsaturated fatty acids for farmed fish feed, have met with only modest success. The collective results from these studies point to metabolic 'bottlenecks' in the engineered plant seeds that substantially limit the efficient or selective flux of unusual fatty acids between different substrate pools and ultimately into storage triacylglycerol. Evidence is emerging that diacylglycerol acyltransferase 2, which catalyzes the final step in triacylglycerol assembly, is an important contributor to the synthesis of unusual fatty acid-containing oils, and is likely to be a key target for future oilseed metabolic engineering efforts. PMID:17434788

  17. Metabolic engineering of yeast to produce fatty acid-derived biofuels: bottlenecks and solutions.

    Science.gov (United States)

    Sheng, Jiayuan; Feng, Xueyang

    2015-01-01

    Fatty acid-derived biofuels can be a better solution than bioethanol to replace petroleum fuel, since they have similar energy content and combustion properties as current transportation fuels. The environmentally friendly microbial fermentation process has been used to synthesize advanced biofuels from renewable feedstock. Due to their robustness as well as the high tolerance to fermentation inhibitors and phage contamination, yeast strains such as Saccharomyces cerevisiae and Yarrowia lipolytica have attracted tremendous attention in recent studies regarding the production of fatty acid-derived biofuels, including fatty acids, fatty acid ethyl esters, fatty alcohols, and fatty alkanes. However, the native yeast strains cannot produce fatty acids and fatty acid-derived biofuels in large quantities. To this end, we have summarized recent publications in this review on metabolic engineering of yeast strains to improve the production of fatty acid-derived biofuels, identified the bottlenecks that limit the productivity of biofuels, and categorized the appropriate approaches to overcome these obstacles. PMID:26106371

  18. Piecewise Function Feedback Strategy in Intelligent Traffic Systems with a Speed Limit Bottleneck

    Science.gov (United States)

    Chen, Bokui; Sun, Xiaoyan; Wei, Hua; Dong, Chuanfei; Wang, Binghong

    The road capacity can be greatly improved if an appropriate and effective information feedback strategy is adopted in the traffic system. In this paper, a strategy called piecewise function feedback strategy (PFFS) is introduced and applied into an asymmetrical two-route scenario with a speed limit bottleneck in which the dynamic information can be generated and displayed on the information board to guide road users to make a choice. Meanwhile, the velocity-dependent randomization (VDR) mechanism is adopted which can better reflect the dynamic behavior of vehicles in the system than NS mechanism. Simulation results adopting PFFS have demonstrated high efficiency in controlling spatial distribution of traffic patterns compared with the previous strategies.

  19. Phonon bottleneck in p-type Ge/Si quantum dots

    Energy Technology Data Exchange (ETDEWEB)

    Yakimov, A. I., E-mail: yakimov@isp.nsc.ru [Rzhanov Institute of Semiconductor Physics, Siberian Branch of the Russian Academy of Science, 630090 Novosibirsk (Russian Federation); Tomsk State University, 634050 Tomsk (Russian Federation); Kirienko, V. V.; Armbrister, V. A. [Rzhanov Institute of Semiconductor Physics, Siberian Branch of the Russian Academy of Science, 630090 Novosibirsk (Russian Federation); Bloshkin, A. A.; Dvurechenskii, A. V. [Rzhanov Institute of Semiconductor Physics, Siberian Branch of the Russian Academy of Science, 630090 Novosibirsk (Russian Federation); Novosibirsk State University, 630090 Novosibirsk (Russian Federation)

    2015-11-23

    We study the effect of quantum dot size on the mid-infrared photo- and dark current, photoconductive gain, and hole capture probability in ten-period p-type Ge/Si quantum dot heterostructures. The dot dimensions are varied by changing the Ge coverage and the growth temperature during molecular beam epitaxy of Ge/Si(001) system in the Stranski-Krastanov growth mode. In all samples, we observed the general tendency: with decreasing the size of the dots, the dark current and hole capture probability are reduced, while the photoconductive gain and photoresponse are enhanced. Suppression of the hole capture probability in small-sized quantum dots is attributed to a quenched electron-phonon scattering due to phonon bottleneck.

  20. Allometric body shape changes and morphological differentiation of Shemaya, Alburnus chalcoides (Guldenstadf, 1772, populations in the southern part of Caspian Sea using Elliptic Fourier analysis

    Directory of Open Access Journals (Sweden)

    Mohammad Mohadasi

    2014-09-01

    Full Text Available Study of phenotypic diversity among populations can help better understanding of diversification of species within ecosystems and intraspecific diversification in fishes. A geometric morphometric study was carried out using the Elliptic Fourier analysis to demonstrate the effect of habitat type on morphological features of shemaya (Alburnus chalcoides populations. Populations were sampled from three rivers and one lagoon, from the southern part of Caspian Sea. Significant differences in body shape were found among the populations. Differences in shapes of the riverine populations were minute compared to those of lagoon one in terms of size and shape. Shemaya is an anaderemus fish and its populations have a common origin, therefore, observed differences could be as result of environmental factors. In addition, this study suggest that the amount of curvature i.e. fusiform body shape of this species could be independent form environmental condition.

  1. Sequential Markov coalescent algorithms for population models with demographic structure

    OpenAIRE

    A. Eriksson; Mahjani, B.; Mehlig, B.

    2009-01-01

    We analyse sequential Markov coalescent algorithms for populations with demographic structure: for a bottleneck model, a population-divergence model, and for a two-island model with migration. The sequential Markov coalescent method is an approximation to the coalescent suggested by McVean and Cardin, and Marjoram and Wall. Within this algorithm we compute, for two individuals randomly sampled from the population, the correlation between times to the most recent common ancestor and the linkag...

  2. Oscillating hydrogel based bioreactors for chondrogenic differentiation of mesenchymal stem cells

    OpenAIRE

    Neiman, Veronica Juliet

    2010-01-01

    Harnessing the differentiative potential of stem cells for use in tissue repair could be a powerful therapy for debilitating diseases. However, one of the bottlenecks of stem cell based therapeutics and tissue engineering is inefficient and homogeneous stem cell differentiation. Various physico-chemical cues such as mechanical strain, chemical components, and soluble factors have been shown to direct stem cell differentiation. This study developed a multifunctional polymer-based artificial EC...

  3. To an optimal electricity supply system. Possible bottlenecks in the development to an optimal electricity supply system in northwest Europe

    International Nuclear Information System (INIS)

    It is uncertain how the electricity system in Europe, and in particular northwest Europe and the Netherlands, will develop in the next fifteen years. The main objective of this report is to identify possible bottlenecks that may hamper the northwest European electricity system to develop into an optimal system in the long term (until 2020). Subsequently, based on the identified bottlenecks, the report attempts to indicate relevant market response and policy options. To be able to identify possible bottlenecks in the development to an optimal electricity system, an analytical framework has been set up with the aim to identify possible (future) problems in a structured way. The segments generation, network, demand, balancing, and policy and regulation are analysed, as well as the interactions between these segments. Each identified bottleneck is assessed on the criteria reliability, sustainability and affordability. Three bottlenecks are analysed in more detail: (1) The increasing penetration of distributed generation (DG) and its interaction with the electricity network. Dutch policy could be aimed at: (a) Gaining more insight in the costs and benefits that result from the increasing penetration of DG; (b) Creating possibilities for DSOs to experiment with innovative (network management) concepts; (c) Introducing locational signals; and (d) Further analyse the possibility of ownership unbundling; (2) The problem of intermittency and its implications for balancing the electricity system. Dutch policy could be aimed at: (a) Creating the environment in which the market is able to respond in an efficient way; (b) Monitoring market responses; (c) Market coupling; and (d) Discussing the timing of the gate closure; and (3) Interconnection and congestion issues in combination with generation. Dutch policy could be aimed at: (a) Using the existing interconnection capacity as efficient as possible; (b) Identifying the causes behind price differences; and (c) Harmonise market

  4. Smart-pixel-based free-space interconnects: solving the high-speed multichip packaging bottleneck

    Science.gov (United States)

    Haney, Michael W.; Christensen, Marc P.; Milojkovic, Predrag; McFadden, Michael J.

    2001-11-01

    As IC densities grow to 100's of millions of devices per chip and beyond, the inter-chip link bandwidth becomes a critical performance-limiting bottleneck in many applications. Electronic packaging technology has not kept pace with the growth of IC I/O requirements. Recent advances in smart pixel technology, however, offer the potential to use 3-D optical interconnects to overcome the inter-chip I/O bottleneck by linking dense arrays of Vertical Cavity Surface Emitting Lasers (VCSELs) and photodetectors, which are directly integrated onto electronic IC circuits. Many switching and parallel computing applications demand multi-chip interconnection fabrics that achieve high-density global I/O across an array of chips. Such global interconnections require a high degree of space-variance in the interconnection fabric, in addition to high inter-chip throughput capacity. This paper reviews the architectural and optical design issues associated with global interconnections among arrays of chips. The emphasis is on progress made in the design and implementation of the second generation Free-space Accelerator for Switching Terabit Networks (FAST-Net) prototype. The FAST-Net prototype uses a macro-optical lens array and mirror to effect a global (fully connected) fabric across a 4 X 4 array of smart pixel chips. Clusters of VCSELs and photodetectors are imaged onto corresponding clusters on other chips, creating a high- density bi-directional data path between every pair of smart pixel chips on a multi-chip module. The combination of programmable intra-chip electronic routing and the fixed global inter-chip optical interconnection pattern of the FAST- Net architecture has been shown to provide a low latency, minimum complexity fabric, that can effect an arbitrary interconnection pattern across the chip array. Recent experimental results show that the narrow beam characteristics of VCSELs can be exploited in an efficient optical design for the FAST-Net optical interconnection

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

    Science.gov (United States)

    Hull, Joshua M; Keane, John J; Savage, Wesley K; Godwin, Steven A; Shafer, Jo Ann; Jepsen, Eric P; Gerhardt, Rick; Stermer, Chris; Ernest, Holly B

    2010-07-01

    Investigations of regional genetic differentiation are essential for describing phylogeographic patterns and informing management efforts for species of conservation concern. In this context, we investigated genetic diversity and evolutionary relationships among great gray owl (Strix nebulosa) populations in western North America, which includes an allopatric range in the southern Sierra Nevada in California. Based on a total dataset consisting of 30 nuclear microsatellite DNA loci and 1938-base pairs of mitochondrial DNA, we found that Pacific Northwest sampling groups were recovered by frequency and Bayesian analyses of microsatellite data and each population sampled, except for western Canada, showed evidence of recent population bottlenecks and low effective sizes. Bayesian and maximum likelihood phylogenetic analyses of sequence data indicated that the allopatric Sierra Nevada population is also a distinct lineage with respect to the larger species range in North America; we suggest a subspecies designation for this lineage should be considered (Strix nebulosa yosemitensis). Our study underscores the importance of phylogeographic studies for identifying lineages of conservation concern, as well as the important role of Pleistocene glaciation events in driving genetic differentiation of avian fauna. PMID:20193768

  6. Photodegradation alleviates the lignin bottleneck for carbon turnover in terrestrial ecosystems.

    Science.gov (United States)

    Austin, Amy T; Méndez, M Soledad; Ballaré, Carlos L

    2016-04-19

    A mechanistic understanding of the controls on carbon storage and losses is essential for our capacity to predict and mitigate human impacts on the global carbon cycle. Plant litter decomposition is an important first step for carbon and nutrient turnover, and litter inputs and losses are essential in determining soil organic matter pools and the carbon balance in terrestrial ecosystems. Photodegradation, the photochemical mineralization of organic matter, has been recently identified as a mechanism for previously unexplained high rates of litter mass loss in arid lands; however, the global significance of this process as a control on carbon cycling in terrestrial ecosystems is not known. Here we show that, across a wide range of plant species, photodegradation enhanced subsequent biotic degradation of leaf litter. Moreover, we demonstrate that the mechanism for this enhancement involves increased accessibility to plant litter carbohydrates for microbial enzymes. Photodegradation of plant litter, driven by UV radiation, and especially visible (blue-green) light, reduced the structural and chemical bottleneck imposed by lignin in secondary cell walls. In leaf litter from woody species, specific interactions with UV radiation obscured facilitative effects of solar radiation on biotic decomposition. The generalized effect of sunlight exposure on subsequent microbial activity, mediated by increased accessibility to cell wall polysaccharides, suggests that photodegradation is quantitatively important in determining rates of mass loss, nutrient release, and the carbon balance in a broad range of terrestrial ecosystems. PMID:27044070

  7. Metabolic Engineering of Yeast to Produce Fatty Acid-derived Biofuels: Bottlenecks and Solutions

    Directory of Open Access Journals (Sweden)

    Jiayuan eSheng

    2015-06-01

    Full Text Available Fatty acid-derived biofuels can be a better solution than bioethanol to replace petroleum fuel, since they have similar energy content and combustion properties as current transportation fuels. The environmentally friendly microbial fermentation process has been used to synthesize advanced biofuels from renewable feedstock. Due to their robustness as well as the high tolerance to fermentation inhibitors and phage contamination, yeast strains such as Saccharomyces cerevisiae and Yarrowia lipolytica have attracted tremendous attention in recent studies regarding the production of fatty acid-derived biofuels, including fatty acids, fatty acid ethyl esters, fatty alcohols, and fatty alkanes. However, the native yeast strains cannot produce fatty acids and fatty acid-derived biofuels in large quantities. To this end, we have summarized recent publications in this review on metabolic engineering of yeast strains to improve the production of fatty acid-derived biofuels, identified the bottlenecks that limit the productivity of biofuels, and categorized the appropriate approaches to overcome these obstacles.

  8. Development and bottlenecks of renewable electricity generation in China: a critical review.

    Science.gov (United States)

    Hu, Yuanan; Cheng, Hefa

    2013-04-01

    This review provides an overview on the development and status of electricity generation from renewable energy sources, namely hydropower, wind power, solar power, biomass energy, and geothermal energy, and discusses the technology, policy, and finance bottlenecks limiting growth of the renewable energy industry in China. Renewable energy, dominated by hydropower, currently accounts for more than 25% of the total electricity generation capacity. China is the world's largest generator of both hydropower and wind power, and also the largest manufacturer and exporter of photovoltaic cells. Electricity production from solar and biomass energy is at the early stages of development in China, while geothermal power generation has received little attention recently. The spatial mismatch in renewable energy supply and electricity demand requires construction of long-distance transmission networks, while the intermittence of renewable energy poses significant technical problems for feeding the generated electricity into the power grid. Besides greater investment in research and technology development, effective policies and financial measures should also be developed and improved to better support the healthy and sustained growth of renewable electricity generation. Meanwhile, attention should be paid to the potential impacts on the local environment from renewable energy development, despite the wider benefits for climate change. PMID:23445126

  9. Policy redesign for solving the financial bottleneck in demand side management (DSM) in China

    International Nuclear Information System (INIS)

    DSM is one of the best and most practical policy tools for China to balance environmental protection and economic growth. However, the bottleneck lies in the lack of long-term, stable, sufficient and gradually increasing funds to flow into DSM projects. The author redesigns the practical 'system benefit charge (SBC)' policy, which will provide long-term and stable funding for DSM, the policy to facilitate the financial support from banking sector and capital market, and investigates the possibility of DSM funding from CDM projects. SBC is the best way to boost long-term stable and sufficient funding for DSM at present in China. The current low inflation rate and natural resource price are favored to expedite the implementation of SBC and DSM developments. With regard to the uneven development, China needs to design relative policies to offset the impact in different areas, such as tax reduction and fiscal subsides. It is time for China to develop a definite and clear target and timetable to implement DSM, which will give the public and enterprises a definite and clear expectation for the future. The government should publicize a clear and integrated DSM development plan and relative policy outline in the near, medium, and long term. (author)

  10. Fluctuating bottleneck model studies on kinetics of DNA escape from α-hemolysin nanopores.

    Science.gov (United States)

    Bian, Yukun; Wang, Zilin; Chen, Anpu; Zhao, Nanrong

    2015-11-14

    We have proposed a fluctuation bottleneck (FB) model to investigate the non-exponential kinetics of DNA escape from nanometer-scale pores. The basic idea is that the escape rate is proportional to the fluctuating cross-sectional area of DNA escape channel, the radius r of which undergoes a subdiffusion dynamics subjected to fractional Gaussian noise with power-law memory kernel. Such a FB model facilitates us to obtain the analytical result of the averaged survival probability as a function of time, which can be directly compared to experimental results. Particularly, we have applied our theory to address the escape kinetics of DNA through α-hemolysin nanopores. We find that our theoretical framework can reproduce the experimental results very well in the whole time range with quite reasonable estimation for the intrinsic parameters of the kinetics processes. We believe that FB model has caught some key features regarding the long time kinetics of DNA escape through a nanopore and it might provide a sound starting point to study much wider problems involving anomalous dynamics in confined fluctuating channels. PMID:26567685

  11. End-Devonian extinction and a bottleneck in the early evolution of modern jawed vertebrates.

    Science.gov (United States)

    Sallan, Lauren Cole; Coates, Michael I

    2010-06-01

    The Devonian marks a critical stage in the early evolution of vertebrates: It opens with an unprecedented diversity of fishes and closes with the earliest evidence of limbed tetrapods. However, the latter part of the Devonian has also been characterized as a period of global biotic crisis marked by two large extinction pulses: a "Big Five" mass extinction event at the Frasnian-Famennian stage boundary (374 Ma) and the less well-documented Hangenberg event some 15 million years later at the Devonian-Carboniferous boundary (359 Ma). Here, we report the results of a wide-ranging analysis of the impact of these events on early vertebrate evolution, which was obtained from a database of vertebrate occurrences sampling over 1,250 taxa from 66 localities spanning Givetian to Serpukhovian stages (391 to 318 Ma). We show that major vertebrate clades suffered acute and systematic effects centered on the Hangenberg extinction involving long-term losses of over 50% of diversity and the restructuring of vertebrate ecosystems worldwide. Marine and nonmarine faunas were equally affected, precluding the existence of environmental refugia. The subsequent recovery of previously diverse groups (including placoderms, sarcopterygian fish, and acanthodians) was minimal. Tetrapods, actinopterygians, and chondrichthyans, all scarce within the Devonian, undergo large diversification events in the aftermath of the extinction, dominating all subsequent faunas. The Hangenberg event represents a previously unrecognized bottleneck in the evolutionary history of vertebrates as a whole and a historical contingency that shaped the roots of modern biodiversity. PMID:20479258

  12. Neutron capture cross section of $^{90}$Zr Bottleneck in the s-process reaction flow

    CERN Document Server

    Tagliente, G; Milazzo, P M; Moreau, C; Aerts, G; Abbondanno, U; Alvarez, H; Alvarez-Velarde, F; Andriamonje, Samuel A; Andrzejewski, J; Assimakopoulos, Panayiotis; Audouin, L; Badurek, G; Baumann, P; Bečvář, F; Berthoumieux, E; Bisterzo, S; Calviño, F; Calviani, M; Cano-Ott, D; Capote, R; Carrapiço, C; Cennini, P; Chepel, V; Chiaveri, Enrico; Colonna, N; Cortés, G; Couture, A; Cox, J; Dahlfors, M; David, S; Dillman, I; Domingo-Pardo, C; Dridi, W; Durán, I; Eleftheriadis, C; Embid-Segura, M; Ferrant, L; Ferrari, A; Ferreira-Marques, R; Furman, W; Gallino, R; Gonçalves, I; Gonzalez-Romero, E; Gramegna, F; Guerrero, C; Gunsing, F; Haas, B; Haight, R; Heil, M; Herrera-Martínez, A; Igashira, M; Jericha, E; Käppeler, F; Kadi, Y; Karadimos, D; Karamanis, D; Kerveno, M; Köhler, P; Kossionides, E; Krtička, M; Lamboudis, C; Leeb, H; Lindote, A; Lopes, I; Lozano, M; Lukic, S; Marganiec, J; Marrone, S; Martínez, T; Massimi, C; Mastinu, P; Mengoni, A; Mosconi, M; Neves, F; Oberhummer, Heinz; O'Brien, S; Pancin, J; Papachristodoulou, C; Papadopoulos, C; Paradela, C; Patronis, N; Pavlik, A; Pavlopoulos, P; Perrot, L; Pigni, M T; Plag, R; Plompen, A; Plukis, A; Poch, A; Praena, J; Pretel, C; Quesada, J; Rauscher, T; Reifarth, R; Rubbia, Carlo; Rudolf, G; Rullhusen, P; Salgado, J; Santos, J; Sarchiapone, L; Savvidis, I; Stéphan, C; Taín, J L; Tassan-Got, L; Tavora, L; Terlizzi, R; Vannini, G; Vaz, P; Ventura, A; Villamarín, D; Vincente, M, C; Vlachoudis, V; Vlastou, R; Voss, F; Walter, S; Wendler, H; Wiescher, M; Wisshak, K

    2008-01-01

    The neutron capture cross sections of the Zr isotopes have important implications in nuclear astrophysics and for reactor design. The small cross section of the neutron magic nucleus 90Zr, which accounts for more than 50% of natural zirconium represents one of the key isotopes for the stellar s-process, because it acts as a bottleneck in the neutron capture chain between the Fe seed and the heavier isotopes. The same element, Zr, also is an important component of the structural materials used in traditional and advanced nuclear reactors. The (n,γ) cross section has been measured at CERN, using the n_TOF spallation neutron source. In total, 45 resonances could be resolved in the neutron energy range below 70 keV, 10 being observed for the first time thanks to the high resolution and low backgrounds at n_TOF. On average, the Γγ widths obtained in resonance analyses with the R-matrix code SAMMY were 15% smaller than reported previously. By these results, the accuracy of the Maxwellian averaged cross section f...

  13. Observation of a hot-phonon bottleneck in lead-iodide perovskites

    Science.gov (United States)

    Yang, Ye; Ostrowski, David P.; France, Ryan M.; Zhu, Kai; van de Lagemaat, Jao; Luther, Joseph M.; Beard, Matthew C.

    2016-01-01

    We study the carrier dynamics in planar methyl ammonium lead iodide perovskite films using broadband transient absorption spectroscopy. We show that the sharp optical absorption onset is due to an exciton transition that is inhomogeneously broadened with a binding energy of 9 meV. We fully characterize the transient absorption spectrum by free-carrier-induced bleaching of the exciton transition, quasi-Fermi energy, carrier temperature and bandgap renormalization constant. The photo-induced carrier temperature is extracted from the transient absorption spectra and monitored as a function of delay time for different excitation wavelengths and photon fluences. We find an efficient hot-phonon bottleneck that slows down cooling of hot carriers by three to four orders of magnitude in time above a critical injection carrier density of ˜5 × 1017 cm-3. Compared with molecular beam epitaxially grown GaAs, the critical density is an order of magnitude lower and the relaxation time is approximately three orders of magnitude longer.

  14. Regular bottlenecks and restrictions to somatic fusion prevent the accumulation of mitochondrial defects in Neurospora.

    Science.gov (United States)

    Bastiaans, E; Aanen, D K; Debets, A J M; Hoekstra, R F; Lestrade, B; Maas, M F P M

    2014-07-01

    The replication and segregation of multi-copy mitochondrial DNA (mtDNA) are not under strict control of the nuclear DNA. Within-cell selection may thus favour variants with an intracellular selective advantage but a detrimental effect on cell fitness. High relatedness among the mtDNA variants of an individual is predicted to disfavour such deleterious selfish genetic elements, but experimental evidence for this hypothesis is scarce. We studied the effect of mtDNA relatedness on the opportunities for suppressive mtDNA variants in the fungus Neurospora carrying the mitochondrial mutator plasmid pKALILO. During growth, this plasmid integrates into the mitochondrial genome, generating suppressive mtDNA variants. These mtDNA variants gradually replace the wild-type mtDNA, ultimately culminating in growth arrest and death. We show that regular sequestration of mtDNA variation is required for effective selection against suppressive mtDNA variants. First, bottlenecks in the number of mtDNA copies from which a 'Kalilo' culture started significantly increased the maximum lifespan and variation in lifespan among cultures. Second, restrictions to somatic fusion among fungal individuals, either by using anastomosis-deficient mutants or by generating allotype diversity, prevented the accumulation of suppressive mtDNA variants. We discuss the implications of these results for the somatic accumulation of mitochondrial defects during ageing. PMID:24864316

  15. Fluctuating bottleneck model studies on kinetics of DNA escape from α-hemolysin nanopores

    Science.gov (United States)

    Bian, Yukun; Wang, Zilin; Chen, Anpu; Zhao, Nanrong

    2015-11-01

    We have proposed a fluctuation bottleneck (FB) model to investigate the non-exponential kinetics of DNA escape from nanometer-scale pores. The basic idea is that the escape rate is proportional to the fluctuating cross-sectional area of DNA escape channel, the radius r of which undergoes a subdiffusion dynamics subjected to fractional Gaussian noise with power-law memory kernel. Such a FB model facilitates us to obtain the analytical result of the averaged survival probability as a function of time, which can be directly compared to experimental results. Particularly, we have applied our theory to address the escape kinetics of DNA through α-hemolysin nanopores. We find that our theoretical framework can reproduce the experimental results very well in the whole time range with quite reasonable estimation for the intrinsic parameters of the kinetics processes. We believe that FB model has caught some key features regarding the long time kinetics of DNA escape through a nanopore and it might provide a sound starting point to study much wider problems involving anomalous dynamics in confined fluctuating channels.

  16. Controlling Population with Pollution

    Science.gov (United States)

    Browne, Joseph

    2010-01-01

    Population models are often discussed in algebra, calculus, and differential equations courses. In this article we will use the human population of the world as our application. After quick looks at two common models we'll investigate more deeply a model which incorporates the negative effect that accumulated pollution may have on population.

  17. Population differentiation in tree-ring growth response of white fir (Abies concolor) to climate: Implications for predicting forest responses to climate change

    Energy Technology Data Exchange (ETDEWEB)

    Jensen, D.B.

    1993-10-01

    Forest succession models and correlative models have predicted 200--650 kilometer shifts in the geographic range of temperate forests and forest species as one response to global climate change. Few studies have investigated whether population differences may effect the response of forest species to climate change. This study examines differences in tree-ring growth, and in the phenotypic plasticity of tree-ring growth in 16-year old white fir, Abies concolor, from ten populations grown in four common gardens in the Sierra Nevada of California. For each population, tree-ring growth was modelled as a function of precipitation and degree-day sums. Tree-ring growth under three scenarios of doubled C0{sub 2} climates was estimated.

  18. Genetic differentiation and trade among populations of Peach Palm (Bactris gasipaes Kunth) in the Peruvian Amazon - implications for genetic resource management

    NARCIS (Netherlands)

    Adin, A.; Weber, J.C.; Sotelo Montes, C.; Vidaurre, H.; Vosman, B.J.; Smulders, M.J.M.

    2004-01-01

    Peach palm (Bactris gasipaes Kunth) is cultivated for fruit and 'heart of palm', and is an important component of agroforestry systems in the Peruvian Amazon. In this study, AFLP was used to compare genetic diversity among domesticated populations along the Paranapura and Cuiparillo rivers, which ar

  19. The anthropometric factors in the risk of differentiated cancer of the thyroid in French Polynesia: study of witness-cases in population

    International Nuclear Information System (INIS)

    A weight, a size and a high body mass index were associated to an increased risk by cancer of the thyroid in this study, confirming the importance of the anthropometric factors in the risk of this cancer in the populations of the Pacific Islands. (N.C.)

  20. Disparity in population differentiation of sex-linked and autosomal variation in sibling species of the Jaera albifrons (Isopoda) complex

    DEFF Research Database (Denmark)

    Siegismund, H R

    2003-01-01

    The genetic variation at four enzyme loci is described for 22 populations of three Jaera species--J. albifrons, J. ischiosetosa, and J. praehirsuta--in the J. albifrons complex (Crustacea, Isopoda) in Denmark. The variation at three of the loci is similar, with the allele frequency spectra close to...

  1. The Eating Disorder Diagnostic Scale: psychometric features within a clinical population and a cut-off point to differentiate clinical patients from healthy controls

    NARCIS (Netherlands)

    Krabbenborg, M.A.M.; Danner, U.N.; Larsen, J.K.; Veer, N. van der; Elburg, A.A. van; Ridder, D.T. de; Evers, C.; Stice, E.; Engels, R.C.E.M.

    2012-01-01

    The Eating Disorder Diagnostic Scale (EDDS) is a brief self-report measure for diagnosing anorexia nervosa, bulimia nervosa and binge eating disorder. Research has provided evidence of the reliability and validity of this scale in non-clinical populations. Our study is the first to examine the psych

  2. Statistical guidelines for detecting past population shifts using ancient DNA

    DEFF Research Database (Denmark)

    Mourier, Tobias; Ho, Simon; Gilbert, M Thomas P;

    2012-01-01

    Populations carry a genetic signal of their demographic past, providing an opportunity for investigating the processes that shaped their evolution. Our ability to infer population histories can be enhanced by including ancient DNA data. Using serial-coalescent simulations and a range of both...... quantitative and temporal sampling schemes, we test the power of ancient mitochondrial sequences and nuclear single-nucleotide polymorphisms (SNPs) to detect past population bottlenecks. Within our simulated framework, mitochondrial sequences have only limited power to detect subtle bottlenecks and/or fast...... results provide useful guidelines for scaling sampling schemes and for optimizing our ability to infer past population dynamics. In addition, our results suggest that many ancient DNA studies may face power issues in detecting moderate demographic collapses and/or highly dynamic demographic shifts when...

  3. A New Wireless Packet Scheduling Algorithm Based on EDF and Its Application in Multi-bottleneck Networks

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Most of current wireless packet scheduling algorithms aim at resource allocation as fairly as possible or maximizing throughput. This paper proposed a new packet scheduling algorithm that aims at satisfying delay requirement and is the improvement of earliest due first (EDF) algorithm in wired networks. The main idea is to classify the packets based on their delay bound, scheduling the most "urgent" class of user and the users that have the best channel condition with higher priority. This algorithm can easily integrate with common buffer management algorithms, when buffer management algorithm cannot accept new arrival packets, try to modify scheduling policy. Packet scheduling algorithms in multiple bottleneck wireless networks were also discussed. A new variable multi-hop factor was defined to estimate the congestion situation (including channel condition) of future hops.Multi-hop factor can be integrated into packet scheduling algorithms as assistant and supplement to improve its performance in multi-bottleneck wireless networks.

  4. Retinoic Acid and Polyriboinosinic:Polyribocytidylic Acid Stimulate Robust Anti-Tetanus Antibody Production while Differentially Regulating Type 1/Type 2 Cytokines and Lymphocyte Populations1

    OpenAIRE

    Ma, Yifan; Chen, Qiuyan; Ross, A. Catharine

    2005-01-01

    Retinoic acid (RA), a bioactive retinoid, and polyriboinosinic:polyribocytidylic acid (PIC) are known to promote immunity in vitamin A-deficient animals. In this study, we hypothesized that RA, PIC, and the combination can provide significant immunoadjuvant activity even in the vitamin A-adequate state. Six-week-old C57BL/6 mice were immunized with tetanus toxoid (TT) and treated with RA and/or PIC at priming in three independent studies of short and long duration. RA and PIC differentially r...

  5. Circular trimers of gelatinase B/matrix metalloproteinase-9 constitute a distinct population of functional enzyme molecules differentially regulated by tissue inhibitor of metalloproteinases-1

    DEFF Research Database (Denmark)

    Vandooren, Jennifer; Born, Benjamin; Solomonov, Inna;

    2015-01-01

    knowledge about the overall structure of proMMP-9 monomers and multimers is limited. We investigated biochemical, biophysical and functional characteristics of zymogen and activated forms of MMP-9 monomers and multimers. In contrast with a conventional notion of a dimeric nature of MMP-9 homomultimers, we...... in a higher extent of TIMP-1 inhibition of angiogenesis induced by trimers compared with monomers. Our results show that proMMP-9 trimers constitute a novel structural and functional entity that is differentially regulated by TIMP-1....

  6. 基于双种群小生境差分进化算法的动态经济调度%Dynamic Economic Dispatching Based on Dual Population Niche Differential Evolution Algorithm

    Institute of Scientific and Technical Information of China (English)

    赖文海; 陈贤阳; 明国锋; 李芳玲

    2016-01-01

    When considering valve-point effect and ramp-rate limit,the problem of dynamic economic dispatching (DED) shows characteristics of non-convex,non-smooth and non-linear. In allusion to this complex problem of engineering optimi-zation,this paper presents to combine niche technology and differential evolution (DE)algorithm and use niche sharing mechanism and dual population evolution strategy to increase diversity of population so as to avoid premature of DE algo-rithm. Dual population niche DE (NDE)algorithm is applied in NDE typical model of 1 0 units with 24 hours test system and compared with particle swarm optimization (PSO),standard DE algorithm,enhanced self-adaptive PSO algorithm,im-proved DE algorithm,chaos differential swarm optimization algorithm,basic biogeography optimization algorithm,space expansion algorithm. Simulation results prove effectiveness and feasibility of NDE algorithm which could provide a new idea for solving DED problem.%当计及阀点效应和爬坡率后,动态经济调度(dynamic economic dispatch,DED)问题呈现出非凸、非平滑、非线性等特性。针对此类复杂的工程优化问题,提出将小生境技术与差分进化(differential evolution,DE)算法相结合,利用小生境共享机制和双种群进化策略增加种群的多样性,从而避免了 DE 算法的早熟现象。将双种群小生境DE算法(niche differential evolution,NDE)应用到10机组24时段的 DED 经典模型中,并与粒子群算法(particle swarm optimization,PSO)、标准DE算法、增强自适应 PSO算法、改进DE算法、混沌差分蜂群优化算法、基本生物地理学优化算法、空间扩张算法进行对比,仿真结果证明 NDE 算法的有效性和可行性,为解决DED问题提供了一种新思路。

  7. Oracle Database Common Bottleneck Issues Analysis%Oracle数据库常见的瓶颈问题分析

    Institute of Scientific and Technical Information of China (English)

    李文鹏

    2011-01-01

    Oracle database as the world's largest database companies at home and abroad has been applied widely.Article on the current Oracle database common bottleneck issues analyzed and discussed.%Oracle数据库作为全球第一大数据库厂商,在国内外获得了广泛应用。文章对目前Oracle数据库常见的瓶颈问题进行了分析探讨。

  8. Combinatorial Sec pathway analysis for improved heterologous protein secretion in Bacillus subtilis: identification of bottlenecks by systematic gene overexpression

    OpenAIRE

    Chen, Jingqi; Fu, Gang; Gai, Yuanming; Zheng, Ping; Zhang, Dawei; Wen, Jianping

    2015-01-01

    Background Secretory expression of valuable proteins by B. subtilis and its related species has attracted intensive work over the past three decades. Although very high yields can be achieved with homologous proteins, production of heterologous proteins by B. subtilis is unfortunately not the straight forward. The Sec pathway is the major route for protein secretion in B. subtilis. Therefore, the aim of this work was to identify the bottlenecks of the Sec pathway and improve the secretion of ...

  9. Differential population studies using asteroseismology: Solar-like oscillating giants in CoRoT fields LRc01 and LRa01

    Directory of Open Access Journals (Sweden)

    Casagrande L.

    2013-03-01

    Full Text Available Solar-like oscillating giants observed by the space-borne satellites CoRoT and Kepler can be used as key tracers of stellar populations in the Milky Way. When combined with additional photometric/spectroscopic constraints, the pulsation spectra of solar-like oscillating giant stars not only reveal their radii, and hence distances, but also provide well-constrained estimates of their masses, which can be used as proxies for the ages of these evolved stars. In this contribution we provide supplementary material to the comparison we presented in Miglio et al. (2013 between populations of giants observed by CoRoT in the fields designated LRc01 and LRa01.

  10. Brown trout population dynamics versus long term habitat history

    OpenAIRE

    Capra, H.; Souchon, Y.; Lamouroux, N.

    2004-01-01

    The influence of stream discharge and habitat suitability history was investigated over 12 years on three natural brown trout (Salmo trutta) population dynamics. Discharge and habitat (described by Weighted Usable Area, WUA) variability during three "bottleneck" periods of population dynamics (spawning, fry, and summer) were used to explain variability of trout age-class densities (young of the year, juveniles, and adults). Discharge and WUA variability for each period was described with mean...

  11. Analysis of talent bottleneck of chain retailing business%连锁零售企业人才瓶颈问题浅析

    Institute of Scientific and Technical Information of China (English)

    赵根良

    2012-01-01

    In the chain retailing business operation and management, talent is the foundation of its success and continuous development. With the rapid expansion of chain retailing business, chain retailing business in China has relatively serious talent bottleneck problem. Based on the analysis of the situation and reasons of Chinese chain retailing business talent bottleneck, this article puts forward counter- measures and suggestions to solve Chinese chain retailing business talent bottleneck problem.%在分析了我国连锁零售企业人才瓶颈的现状和原因的基础上,提出了解决这一问题的对策和建议。

  12. Associations of social and material deprivation with tobacco, alcohol, and psychotropic drug use, and gender differentials: a population-based study

    OpenAIRE

    Baumann, Michèle; Spitz, Elisabeth; Guillemin, F.; Ravaud, J. F.; Choquet, M.; Falissard, B; Chau, N.

    2007-01-01

    The aim was to assess the relationships between social and material deprivation and the use of tobacco, excessive alcohol and psychotropic drugs by both sexes and in various age groups. Greater knowledge concerning these issues may help public health policy-makers design more effective means of preventing substance abuse. Methods: The sample comprised 6,216 people aged ≥ 15 years randomly selected from the population in northeastern France. Subjects completed a post-mailed questionnaire cover...

  13. Genetic and morphological population differentiation in the rock-dwelling and specialized shrimp-feeding cichlid fish species Altolamprologus compressiceps from Lake Tanganyika, East Africa

    OpenAIRE

    Spreitzer, Maria Luise; Mautner, Selma; Makasa, Lawrence; Sturmbauer, Christian

    2011-01-01

    With about 250 endemic species, Lake Tanganyika contains an extraordinarily diverse cichlid fish fauna, and thus represents an ideal model system for the study of pathways and processes of speciation. The Lamprologini form the most species-rich tribe in Lake Tanganyika comprising about 100 species in seven genera, most of which are endemic to the lake. They are territorial substrate-breeders and represent a monophyletic tribe. By combined analysis of population genetics and geometric morphome...

  14. Genetic structure of the date palm (Phoenix dactylifera) in the Old World reveals a strong differentiation between eastern and western populations

    OpenAIRE

    Zehdi-Azouzi, Salwa; Cherif, Emira; Moussouni, Souhila; Gros-Balthazard, Muriel; Abbas Naqvi, Summar; Ludeña, Bertha; Castillo, Karina; Chabrillange, Nathalie; Bouguedoura, Nadia; Bennaceur, Malika; Si-Dehbi, Farida; Abdoulkader, Sabira; Daher, Abdourahman; Terral, Jean-Frederic; Santoni, Sylvain

    2015-01-01

    Background and Aims Date palms (Phoenix dactylifera, Arecaceae) are of great economic and ecological value to the oasis agriculture of arid and semi-arid areas. However, despite the availability of a large date palm germplasm spreading from the Atlantic shores to Southern Asia, improvement of the species is being hampered by a lack of information on global genetic diversity and population structure. In order to contribute to the varietal improvement of date palms and to provide new insights o...

  15. Lack of global population genetic differentiation in thearbuscular mycorrhizal fungus Glomus mosseae suggestsa recent range expansion which may have coincided withthe spread of agriculture

    DEFF Research Database (Denmark)

    Rosendahl, Søren; McGee, Peter; Morton, Joseph B

    2009-01-01

    The arbuscular mycorrhizal fungus Glomus mosseae is commonly found in agricultural fields. The cosmopolitan species is found in Africa, Europe, America, Asia and Australia. Three hypotheses may explain this worldwide distribution: First, speciation occurred before the continents separated 120 Ma;...... happened much later than continental spread and that human activity may have had a major impact on the dispersal and the population structure of the fungus....

  16. Sea Star Wasting Disease in the Keystone Predator Pisaster ochraceus in Oregon: Insights into Differential Population Impacts, Recovery, Predation Rate, and Temperature Effects from Long-Term Research

    OpenAIRE

    Bruce A Menge; Cerny-Chipman, Elizabeth B.; Johnson, Angela; Sullivan, Jenna; Gravem, Sarah; Chan, Francis

    2016-01-01

    Sea star wasting disease (SSWD) first appeared in Oregon in April 2014, and by June had spread to most of the coast. Although delayed compared to areas to the north and south, SSWD was initially most intense in north and central Oregon and spread southward. Up to 90% of individuals showed signs of disease from June-August 2014. In rocky intertidal habitats, populations of the dominant sea star Pisaster ochraceus were rapidly depleted, with magnitudes of decline in density among sites ranging ...

  17. Quantification and Localization of Watermelon Chlorotic Stunt Virus and Tomato Yellow Leaf Curl Virus (Geminiviridae) in Populations of Bemisia tabaci (Hemiptera, Aleyrodidae) with Differential Virus Transmission Characteristics

    OpenAIRE

    Mario Kollenberg; Stephan Winter; Monika Götz

    2014-01-01

    Bemisia tabaci (Gennadius) is one of the economically most damaging insects to crops in tropical and subtropical regions. Severe damage is caused by feeding and more seriously by transmitting viruses. Those of the genus begomovirus (Geminiviridae) cause the most significant crop diseases and are transmitted by B. tabaci in a persistent circulative mode, a process which is largely unknown. To analyze the translocation and to identify critical determinants for transmission, two populations of B...

  18. Population heterogeneity of trait anger and differential associations of trait anger facets with borderline personality features, neuroticism, depression, Attention Deficit Hyperactivity Disorder (ADHD), and alcohol problems.

    Science.gov (United States)

    Lubke, Gitta H; Ouwens, Klaasjan G; de Moor, Marleen H M; Trull, Timothy J; Boomsma, Dorret I

    2015-12-15

    Anger is an emotion consisting of feelings of variable intensity ranging from mild irritation to intense fury. High levels of trait anger are associated with a range of psychiatric, interpersonal, and health problems. The objectives of this study were to explore heterogeneity of anger as measured by the Spielberger Trait Anger Scale (STAS), and to assess the association of the different anger facets with a selection of psychiatric disorders covering externalizing and internalizing problems, personality disorders, and substance use. Factor mixture models differentiated between a high and low scoring class (28% vs. 72%), and between three factors (anger-temperament, anger-reaction, and immediacy of an anger response). Whereas all psychiatric scales correlated significantly with the STAS total score, regressing the three STAS factors on psychiatric behaviors model showed a more detailed pattern. Only borderline affect instability and depression were significantly associated with all three factors in both classes whereas other problem behaviors were associated only with 1 or 2 of the factors. Alcohol problems were associated with immediacy only in the high scoring class, indicating a non-linear relation in the total sample. Taking into account these more specific associations is likely to be beneficial when investigating differential treatment strategies. PMID:26454404

  19. The effect of dried thyroid gland pretreatment upon survival, formation of endogenous spleen colonies and differentiation of haemopoietic cell populations in X-irradiated mice

    International Nuclear Information System (INIS)

    Experiments on non-inbred H-strain male mice confirmed that their radioresistance could be increased by a stimulatory action of thyroid hormones applied for three weeks preceding radiation It was found that the 30-day survival after 750 R increased between the 1st and the 5th days after the end of pre-treatment. The highest degree of radioresistance was observed when the radiation exposure fell into a phase of the gradual recession of an increased metabolic rate. The relevant experimental groups showed a higher frequency of endogenous spleen colonies and an increased granulocytic differentiation of haemopoietic stem cells. A higher colony-forming activity was also found in animals irradiated immediately after the termination of pre-treatment with the thyroid, but without an increase in survival. The lack of radioprotective effect under those circumstances could be explained by a persisting hypermetabolic effect of the thyroid, and by the fact that an increased proportion of haemopoietic stem cells underwent differentiation into the erythroid line. (author)

  20. Contact transmission of influenza virus between ferrets imposes a looser bottleneck than respiratory droplet transmission allowing propagation of antiviral resistance.

    Science.gov (United States)

    Frise, Rebecca; Bradley, Konrad; van Doremalen, Neeltje; Galiano, Monica; Elderfield, Ruth A; Stilwell, Peter; Ashcroft, Jonathan W; Fernandez-Alonso, Mirian; Miah, Shahjahan; Lackenby, Angie; Roberts, Kim L; Donnelly, Christl A; Barclay, Wendy S

    2016-01-01

    Influenza viruses cause annual seasonal epidemics and occasional pandemics. It is important to elucidate the stringency of bottlenecks during transmission to shed light on mechanisms that underlie the evolution and propagation of antigenic drift, host range switching or drug resistance. The virus spreads between people by different routes, including through the air in droplets and aerosols, and by direct contact. By housing ferrets under different conditions, it is possible to mimic various routes of transmission. Here, we inoculated donor animals with a mixture of two viruses whose genomes differed by one or two reverse engineered synonymous mutations, and measured the transmission of the mixture to exposed sentinel animals. Transmission through the air imposed a tight bottleneck since most recipient animals became infected by only one virus. In contrast, a direct contact transmission chain propagated a mixture of viruses suggesting the dose transferred by this route was higher. From animals with a mixed infection of viruses that were resistant and sensitive to the antiviral drug oseltamivir, resistance was propagated through contact transmission but not by air. These data imply that transmission events with a looser bottleneck can propagate minority variants and may be an important route for influenza evolution. PMID:27430528

  1. A carrier relaxation bottleneck probed in single InGaAs quantum dots using integrated superconducting single photon detectors

    International Nuclear Information System (INIS)

    Using integrated superconducting single photon detectors, we probe ultra-slow exciton capture and relaxation dynamics in single self-assembled InGaAs quantum dots embedded in a GaAs ridge waveguide. Time-resolved luminescence measurements performed with on- and off-chip detection reveal a continuous decrease in the carrier relaxation time from 1.22 ± 0.07 ns to 0.10 ± 0.07 ns upon increasing the number of non-resonantly injected carriers. By comparing off-chip time-resolved spectroscopy with spectrally integrated on-chip measurements, we identify the observed dynamics in the rise time (τr) as arising from a relaxation bottleneck at low excitation levels. From the comparison with the temporal dynamics of the single exciton transition with the on-chip emission signal, we conclude that the relaxation bottleneck is circumvented by the presence of charge carriers occupying states in the bulk material and the two-dimensional wetting layer continuum. A characteristic τr ∝ P−2∕3 power law dependence is observed suggesting Auger-type scattering between carriers trapped in the quantum dot and the two-dimensional wetting layer continuum which circumvents the phonon relaxation bottleneck.

  2. Childhood leukemia genetic bottleneck phenomenon related to TEL-AML1: the postulation by a mathematical model

    Institute of Scientific and Technical Information of China (English)

    Petar Ivanovski; Ivan Ivanovski; Dimitrije Nikoli(c); Ivana Jovanovi(c)

    2012-01-01

    Childhood leukemia bottleneck phenomenon is the most mysterious corollary of the prenatal origin discovery of leukemogenic chromosome translocations.The bottleneck is evidence that leukemia initiation,by in utero acquired chromosome translocations that generate functional fusion genes,is far more common than the incidence rate of corresponding leukemia.For childhood TEL-AML1+ acute lymphoblastic leukemia (ALL) this equates to approximately 100 times.Practically this means that among a hundred children born with TEL-AML1 fusion gene,only one child will later in its life develop ALL.The key data necessary for unraveling of this mystery were discovered in 2002.It was the level of TEL-AML1 + cells' frequency.The bottleneck is caused by the very low body TEL-AML1 + cell count.Only one out of a thousand B cells carries TEL-AML1 fusion gene.TEL-AML1+ body cell count is low because TEL-AML1 fusion is generated at cell level of 10a to 10-4 just during the late fetal lymphopoiesis i.e.after the 36th gestational week.

  3. Chromosomal differentiation between populations of Oligosarcus hepsetus (Teleostei, Characidae from small tributaries at opposite margins of the Paraíba do Sul river (Brazil

    Directory of Open Access Journals (Sweden)

    Liano Centofante

    2006-11-01

    Full Text Available Cytogenetic analyses were carried out in two populations of Oligosarcus hepsetus from tributaries at opposite margins of the Paraíba do Sul river. The same diploid number was observed in both populations (2n=50, but they showed remarkable differences related to karyotype formula and distribution of rDNA sites as revealed by silver nitrate staining and in situ hybridization with 18S probes. The results suggested that the main channel of the Paraíba do Sul river acted as barrier to gene flow between populations.Análises citogenéticas foram realizadas em duas populações de Oligosarcus hepsetus provenientes de riachos de margens opostas do rio Paraíba do Sul. O número diplóide foi o mesmo para ambas as populações (2n=50, porém diferenças significativas foram observadas com relação à fórmula cariotípica e distribuição dos sítios de DNAr detectados pela impregnação por prata e pela hibridação "in situ" com sonda 18S. Estes resultados sugerem que a calha principal do rio Paraíba do Sul estaria atuando como uma barreira para o fluxo gênico entre essas populações.

  4. Effective population size dynamics and the demographic collapse of Bornean orang-utans.

    Directory of Open Access Journals (Sweden)

    Reeta Sharma

    Full Text Available Bornean orang-utans experienced a major demographic decline and local extirpations during the Pleistocene and Holocene due to climate change, the arrival of modern humans, of farmers and recent commercially-driven habitat loss and fragmentation. The recent loss of habitat and its dramatic fragmentation has affected the patterns of genetic variability and differentiation among the remaining populations and increased the extinction risk of the most isolated ones. However, the contribution of recent demographic events to such genetic patterns is still not fully clear. Indeed, it can be difficult to separate the effects of recent anthropogenic fragmentation from the genetic signature of prehistoric demographic events. Here, we investigated the genetic structure and population size dynamics of orang-utans from different sites. Altogether 126 individuals were analyzed and a full-likelihood Bayesian approach was applied. All sites exhibited clear signals of population decline. Population structure is known to generate spurious bottleneck signals and we found that it does indeed contribute to the signals observed. However, population structure alone does not easily explain the observed patterns. The dating of the population decline varied across sites but was always within the 200-2000 years period. This suggests that in some sites at least, orang-utan populations were affected by demographic events that started before the recent anthropogenic effects that occurred in Borneo. These results do not mean that the recent forest exploitation did not leave its genetic mark on orang-utans but suggests that the genetic pool of orang-utans is also impacted by more ancient events. While we cannot identify the main cause for this decline, our results suggests that the decline may be related to the arrival of the first farmers or climatic events, and that more theoretical work is needed to understand how multiple demographic events impact the genome of species and

  5. Trap and corral: a two-step approach for constructing and constraining dynamic cell contact events in differentiating progenitor cell populations

    International Nuclear Information System (INIS)

    Cells are constantly subjected to a host of external signals which can influence their state, phenotype and behavior. Mammalian cells are dependent on signals from surrounding cells to maintain viability, proliferate and coordinate their actions. During developmental and regenerative processes, these lateral signals between cells provide instructive cues informing stem cells how, when and where to differentiate. Moreover, differentiating cells often experience cell–cell contact events interspersed with bouts of motility, process extension and multi-cell agglomeration (Gage 2000 Science 287 1433–8) processes which are not easily recapitulated in existing cell capture devices. Here, we present a two-step process involving microwells to trap cells with high efficiency followed by the alignment of a PDMS mesh around the cells to corral them after the trapping. The microwells trap single cells and paired cells with up to 90% and 80% efficiencies, respectively. After seeding, the PDMS mesh is aligned with the seeded wells to create a 150 µm × 150 µm corral around each trap, allowing cells to interact in a larger arena. The corralling must be done in liquid after seeding because the seeding requires high cell densities to achieve near-full occupancy in the wells. Low-density seeding of the PDMS corrals alone can result in two cells being trapped in each well, but in those conditions, the two cells often engage in very little contact or none at all (and seeding obeys a non-desirable Poisson distribution). Interestingly, trapping cells in proximity and then corralling them elicits much higher contact times than simply seeding into corrals

  6. Two gut intraepithelial CD8+ lymphocyte populations with different T cell receptors: a role for the gut epithelium in T cell differentiation

    OpenAIRE

    1991-01-01

    Mouse gut intraepithelial lymphocytes (IEL) consist mainly (90%) of two populations of CD8+ T cells. One bears heterodimeric alpha/beta CD8 chains (Lyt-2+, Lyt-3+), a T cell receptor (TCR) made of alpha/beta chains, and is Thy-1+; it represents the progeny of T blasts elicited in Peyer's patches by antigenic stimulation. The other bears homodimeric alpha/alpha CD8+ chains, contains no beta chain mRNA, and is mostly Thy-1- and TCR-gamma/delta + or -alpha/beta +; it is thymo- independent and do...

  7. Genetic Structure and Effective Population Sizes in European Red Deer (Cervus elaphus) at a Continental Scale: Insights from Microsatellite DNA.

    Science.gov (United States)

    Zachos, Frank E; Frantz, Alain C; Kuehn, Ralph; Bertouille, Sabine; Colyn, Marc; Niedziałkowska, Magdalena; Pérez-González, Javier; Skog, Anna; Sprĕm, Nikica; Flamand, Marie-Christine

    2016-07-01

    We analyzed more than 600 red deer (Cervus elaphus) from large parts of its European distribution range at 13 microsatellite loci, presenting the first continent-wide study of this species using nuclear markers. Populations were clearly differentiated (overall F ST = 0.166, Jost's D est = 0.385), and the BAPS clustering algorithm yielded mainly geographically limited and adjacent genetic units. When forced into only 3 genetic clusters our data set produced a very similar geographic pattern as previously found in mtDNA phylogeographic studies: a western group from Iberia to central and parts of Eastern Europe, an eastern group from the Balkans to Eastern Europe, and a third group including the threatened relict populations from Sardinia and Mesola in Italy. This result was also confirmed by a multivariate approach to analyzing our data set, a discriminant analysis of principal components. Calculations of genetic diversity and effective population sizes (linkage disequilibrium approach) yielded the lowest results for Italian (Sardinia, Mesola; N e between 2 and 8) and Scandinavian red deer, in line with known bottlenecks in these populations. Our study is the first to present comparative nuclear genetic data in red deer across Europe and may serve as a baseline for future analyses of genetic diversity and structuring in this widespread ungulate. PMID:26912909

  8. Transcriptomic Analysis of Paeonia delavayi Wild Population Flowers to Identify Differentially Expressed Genes Involved in Purple-Red and Yellow Petal Pigmentation.

    Science.gov (United States)

    Shi, Qianqian; Zhou, Lin; Wang, Yan; Li, Kui; Zheng, Baoqiang; Miao, Kun

    2015-01-01

    Tree peony (Paeonia suffruticosa Andrews) is a very famous traditional ornamental plant in China. P. delavayi is a species endemic to Southwest China that has aroused great interest from researchers as a precious genetic resource for flower color breeding. However, the current understanding of the molecular mechanisms of flower pigmentation in this plant is limited, hindering the genetic engineering of novel flower color in tree peonies. In this study, we conducted a large-scale transcriptome analysis based on Illumina HiSeq sequencing of cDNA libraries generated from yellow and purple-red P. delavayi petals. A total of 90,202 unigenes were obtained by de novo assembly, with an average length of 721 nt. Using Blastx, 44,811 unigenes (49.68%) were found to have significant similarity to accessions in the NR, NT, and Swiss-Prot databases. We also examined COG, GO and KEGG annotations to better understand the functions of these unigenes. Further analysis of the two digital transcriptomes revealed that 6,855 unigenes were differentially expressed between yellow and purple-red flower petals, with 3,430 up-regulated and 3,425 down-regulated. According to the RNA-Seq data and qRT-PCR analysis, we proposed that four up-regulated key structural genes, including F3H, DFR, ANS and 3GT, might play an important role in purple-red petal pigmentation, while high co-expression of THC2'GT, CHI and FNS II ensures the accumulation of pigments contributing to the yellow color. We also found 50 differentially expressed transcription factors that might be involved in flavonoid biosynthesis. This study is the first to report genetic information for P. delavayi. The large number of gene sequences produced by transcriptome sequencing and the candidate genes identified using pathway mapping and expression profiles will provide a valuable resource for future association studies aimed at better understanding the molecular mechanisms underlying flower pigmentation in tree peonies. PMID

  9. Transcriptomic Analysis of Paeonia delavayi Wild Population Flowers to Identify Differentially Expressed Genes Involved in Purple-Red and Yellow Petal Pigmentation.

    Directory of Open Access Journals (Sweden)

    Qianqian Shi

    Full Text Available Tree peony (Paeonia suffruticosa Andrews is a very famous traditional ornamental plant in China. P. delavayi is a species endemic to Southwest China that has aroused great interest from researchers as a precious genetic resource for flower color breeding. However, the current understanding of the molecular mechanisms of flower pigmentation in this plant is limited, hindering the genetic engineering of novel flower color in tree peonies. In this study, we conducted a large-scale transcriptome analysis based on Illumina HiSeq sequencing of cDNA libraries generated from yellow and purple-red P. delavayi petals. A total of 90,202 unigenes were obtained by de novo assembly, with an average length of 721 nt. Using Blastx, 44,811 unigenes (49.68% were found to have significant similarity to accessions in the NR, NT, and Swiss-Prot databases. We also examined COG, GO and KEGG annotations to better understand the functions of these unigenes. Further analysis of the two digital transcriptomes revealed that 6,855 unigenes were differentially expressed between yellow and purple-red flower petals, with 3,430 up-regulated and 3,425 down-regulated. According to the RNA-Seq data and qRT-PCR analysis, we proposed that four up-regulated key structural genes, including F3H, DFR, ANS and 3GT, might play an important role in purple-red petal pigmentation, while high co-expression of THC2'GT, CHI and FNS II ensures the accumulation of pigments contributing to the yellow color. We also found 50 differentially expressed transcription factors that might be involved in flavonoid biosynthesis. This study is the first to report genetic information for P. delavayi. The large number of gene sequences produced by transcriptome sequencing and the candidate genes identified using pathway mapping and expression profiles will provide a valuable resource for future association studies aimed at better understanding the molecular mechanisms underlying flower pigmentation in tree

  10. Effect of Driver Behavior on Spatiotemporal Congested Traffic Patterns at Highway Bottlenecks in the Framework of Three-Phase Traffic Theory

    OpenAIRE

    Kerner, Boris S.

    2010-01-01

    We present results of numerical simulations of the effect of driver behavior on spatiotemporal congested traffic patterns that result from traffic breakdown at an on-ramp bottleneck. The simulations are made with the Kerner-Klenov stochastic traffic flow model in the framework of three-phase traffic theory. Different diagrams of congested patterns at the bottleneck associated with different driver behavioral characteristics are found and compared each other. An adaptive cruise control (ACC) i...

  11. Differential impact of statin on new-onset diabetes in different age groups: a population-based case-control study in women from an asian country.

    Directory of Open Access Journals (Sweden)

    Chih-Wei Chen

    Full Text Available BACKGROUND: Statins reduce cardiovascular risks but increase the risk of new-onset diabetes (NOD. The aim of this study is to determine what effect, if any, statins have on the risk of NOD events in a population-based case-control study. An evaluation of the relationship between age and statin-exposure on NOD risks was further examined in a female Asian population. METHOD: In a nationwide case-controlled study, the authors assessed 1065 female NOD patients and 10650 controls with matching ages, genders and physician visit dates. The impact of statin-exposure on NOD was examined through multiple logistic regression models. Subgroup analysis for exploring the risk of NOD and statin-exposure in different age groups was performed. RESULTS: Statin-exposure was statistically significantly associated with increased new-onset diabetes risks using multivariate analysis. Interaction effect between age and statin-exposure on NOD risk was noted. For atorvastatin, the risk of cDDDs>60 was highest among the 55-64 year-olds (adjusted odds ratio [OR], 8.0; 95% confidence interval [CI], 2.57-24.90. For rosuvastatin, the risk of cDDDs>60 was highest among the 40-54 year-olds (adjusted OR, 14.8; 95% CI, 2.27-96.15. For simvastatin, the risk of cDDDs>60 was highest among the 55-64 year-olds (adjusted OR, 15.8; 95% CI, 5.77-43.26. For pravastatin, the risk of cDDDs>60 was highest among the 55-64 year-olds (adjusted OR, 14.0; 95% CI, 1.56-125.18. CONCLUSIONS: This population-based study found that statin use is associated with an increased risk of NOD in women. The risk of statin-related NOD was more evident for women aged 40-64 years compared to women aged 65 or more, and was cumulative-dose dependent. The use of statins should always be determined by weighing the clinical benefits and potential risks for NOD, and the patients should be continuously monitored for adverse effects.

  12. Comparative abundance and population structure of sympatric Afrotropical tortoises in six rainforest areas: the differential effects of ``traditional veneration'' and of ``subsistence hunting'' by local people

    Science.gov (United States)

    Luiselli, Luca

    2003-07-01

    Hinge-back tortoises are actively hunted by human populations in sub-Saharan Africa, and are currently threatened in wide areas of their ranges. The wide wetlands and moist rainforests of the Niger Delta (southeastern Nigeria, west Africa) house three sympatric species of hinge-back tortoises: Kinixys erosa, K. homeana, and K. belliana nogueyi. These tortoises are subjected to strong hunting pressure for several reasons (mainly domestic consumption), but in a few places in Bayelsa and Rivers States (eastern axis of the Niger Delta), they are traditionally venerated as "holy animals" bringing happiness. These few places may represent ideal laboratories for monitoring the effects of hundreds of years of "traditional conservation" on the wild populations of a tropical reptile. Here, I compare the apparent abundance, sex ratio, body sizes, microhabitats, and seasonal occurrence of free-ranging Kinixys populations inhabiting three of these "traditional sanctuaries" with the same ecological aspects of conspecifics from three neighbouring areas where the tortoises are actively hunted. K. homeana was the most common species at all sites, followed by K. erosa, whereas K. belliana was extremely rare. Adult sex ratio did not depart significantly from equality both in K. erosa and in K. homeana, and was not influenced by locality or by type of "management" (veneration or harvesting). The frequency of juveniles of K. homeana was significantly higher in areas with traditional veneration than in areas of harvesting, but the same pattern was not observed in K. erosa. There was a significant decrease in terms of the number of observed specimens between areas of traditional protection and areas of usual harvesting in all species, and this trend was more obvious in K. homeana than in K. erosa. The ratio "number of observed erosa/number of observed homeana" was not dependent on the presence of traditional veneration. Mean body sizes were not different in harvest areas and in

  13. Disentangling the developmental and neurobehavioural effects of perinatal exposure to a chemical mixture found in blood of Arctic populations: differential toxicity of mixture components

    Energy Technology Data Exchange (ETDEWEB)

    Bowers, W.; Nakai, J.; Yagminas, A.; Chu, I.; Moir, D. [Health Canada (Canada)

    2004-09-15

    The current study was designed to evaluate the neurobehavioral effects of perinatal exposure to a chemical mixture that is based on relative concentrations of persistent organic pollutants found in the blood of Canadian Arctic populations and contains 14 PCB congeners, 12 organochlorine pesticides and methyl mercury. This study compared the effects of the complete mixture with the effects of three major components of the mixture (the PCB component, the organochlorine pesticide component, and the methyl mercury component). By examining a range of neurobehavioural functions over development we also determine if specific neurobehavioural disturbances produced by the mixture can be attributed to components of the mixture and if neurobehavioural effects produced by components of the mixture are altered by concurrent exposure to other components in the mixture. Ninety-two nulliparious female Sprague-Dawley rats served as subjects.

  14. Two gut intraepithelial CD8+ lymphocyte populations with different T cell receptors: A role for the gut epithelium in T cell differentiation

    International Nuclear Information System (INIS)

    Mouse gut intraepithelial lymphocytes (IEL) consist mainly (90%) of two populations of CD8+ T cells. One bears heterodimeric alpha/beta CD8 chains (Lyt-2+, Lyt-3+), a T cell receptor (TCR) made of alpha/beta chains, and is Thy-1+; it represents the progeny of T blasts elicited in Peyer's patches by antigenic stimulation. The other bears homodimeric alpha/alpha CD8+ chains, contains no beta chain mRNA, and is mostly Thy-1- and TCR-gamma/delta + or -alpha/beta +; it is thymo-independent and does not require antigenic stimulation, as shown by its presence: (a) in nude and scid mice; (b) in irradiated and thymectomized mice repopulated by T-depleted bone marrow cells bearing an identifiable marker; (c) in thymectomized mice treated by injections of monoclonal anti-CD8 antibody, which lead to total depletion of peripheral CD8+ T lymphocytes; and (d) in germ-free mice and in suckling mice. In young nude mice, alpha/alpha CD8 chains, CD3-TCR complexes, and TCR mRNAs (first gamma/delta) are found on IEL, while they are not detectable on or in peripheral or circulating lymphocytes or bone marrow cells. IEL, in contrast to mature T cells, contain mRNA for the RAG protein, which is required for the rearrangement of TCR and Ig genes. We propose that the gut epithelium (an endoderm derivative, as the thymic epithelium) has an inductive property, attracting progenitors of bone marrow origin, and triggering their TCR rearrangement and alpha/alpha CD8 chains expression, thus giving rise to a T cell population that appears to belong to the same lineage as gamma/delta thymocytes and to recognize an antigenic repertoire different from that of alpha/beta CD8+ IEL

  15. Genetic differentiation among Maruca vitrata F. (Lepidoptera: Crambidae populations on cultivated cowpea and wild host plants: implications for insect resistance management and biological control strategies.

    Directory of Open Access Journals (Sweden)

    Tolulope A Agunbiade

    Full Text Available Maruca vitrata Fabricius (Lepidoptera: Crambidae is a polyphagous insect pest that feeds on a variety of leguminous plants in the tropics and subtropics. The contribution of host-associated genetic variation on population structure was investigated using analysis of mitochondrial cytochrome oxidase 1 (cox1 sequence and microsatellite marker data from M. vitrata collected from cultivated cowpea (Vigna unguiculata L. Walp., and alternative host plants Pueraria phaseoloides (Roxb. Benth. var. javanica (Benth. Baker, Loncocarpus sericeus (Poir, and Tephrosia candida (Roxb.. Analyses of microsatellite data revealed a significant global FST estimate of 0.05 (P≤0.001. The program STRUCTURE estimated 2 genotypic clusters (co-ancestries on the four host plants across 3 geographic locations, but little geographic variation was predicted among genotypes from different geographic locations using analysis of molecular variance (AMOVA; among group variation -0.68% or F-statistics (FSTLoc = -0.01; P = 0.62. These results were corroborated by mitochondrial haplotype data (φSTLoc = 0.05; P = 0.92. In contrast, genotypes obtained from different host plants showed low but significant levels of genetic variation (FSTHost = 0.04; P = 0.01, which accounted for 4.08% of the total genetic variation, but was not congruent with mitochondrial haplotype analyses (φSTHost = 0.06; P = 0.27. Variation among host plants at a location and host plants among locations showed no consistent evidence for M. vitrata population subdivision. These results suggest that host plants do not significantly influence the genetic structure of M. vitrata, and this has implications for biocontrol agent releases as well as insecticide resistance management (IRM for M. vitrata in West Africa.

  16. Comparison of differential renal function using technetium-99m mercaptoacetyltriglycine (MAG3) and technetium-99m dimercaptosuccinic acid (DMSA) renography in a paediatric population

    International Nuclear Information System (INIS)

    In children who have undergone both 99mTc-DMSA and 99mTc-MAG3 studies for the assessment of differential renal function (DRF) and drainage, respectively, we have noticed good agreement between the calculated DRF values, and hypothesized that there is no significant difference in DRF values calculated from these tests. Therefore, both tests may not always be necessary. To determine whether there is a statistically significant difference between DRF values calculated using 99mTc-DMSA and those calculated using 99mTc-MAG3. We retrospectively identified children imaged with 99mTc-DMSA and 99mTc-MAG3. We recorded DRF values, age, indication, and renal pelvis diameter. For the 99mTc-DMSA studies we recorded the imaging time after injection. For the 99mTc-MAG3 studies we recorded the delay between injection and data acquisition, diuretic use and evidence of delayed drainage or reflux. We identified 100 episodes in 92 children where both 99mTc-DMSA and 99mTc-MAG3 scans had been performed within a few days. The commonest indication was urinary tract infection or pelviureteric junction obstruction. The mean age of the children was 6.96 years. A significant but clinically acceptable trend was seen between abnormal DRF and difference between tests. A significant link was found with the difference between tests and the time of imaging after DMSA injection, and also with scarring. No significant effect was caused by renal pelvis dilatation, delayed drainage, frusemide administration, or delayed 99mTc-MAG3 imaging. If a 99mTc-MAG3 study has been performed then a 99mTc-DMSA study is unnecessary provided DRF is normal on the 99mTc-MAG3 study and there is no scarring. A change in practice would lead to considerable savings in time, cost and radiation burden. (orig.)

  17. Sea Star Wasting Disease in the Keystone Predator Pisaster ochraceus in Oregon: Insights into Differential Population Impacts, Recovery, Predation Rate, and Temperature Effects from Long-Term Research

    Science.gov (United States)

    Menge, Bruce A.; Cerny-Chipman, Elizabeth B.; Johnson, Angela; Sullivan, Jenna; Gravem, Sarah; Chan, Francis

    2016-01-01

    Sea star wasting disease (SSWD) first appeared in Oregon in April 2014, and by June had spread to most of the coast. Although delayed compared to areas to the north and south, SSWD was initially most intense in north and central Oregon and spread southward. Up to 90% of individuals showed signs of disease from June-August 2014. In rocky intertidal habitats, populations of the dominant sea star Pisaster ochraceus were rapidly depleted, with magnitudes of decline in density among sites ranging from -2x to -9x (59 to 84%) and of biomass from -2.6x to -15.8x (60 to 90%) by September 2014. The frequency of symptomatic individuals declined over winter and persisted at a low rate through the spring and summer 2015 (~5–15%, at most sites) and into fall 2015. Disease expression included six symptoms: initially with twisting arms, then deflation and/or lesions, lost arms, losing grip on substrate, and final disintegration. SSWD was disproportionally higher in orange individuals, and higher in tidepools. Although historically P. ochraceus recruitment has been low, from fall 2014 to spring 2015 an unprecedented surge of sea star recruitment occurred at all sites, ranging from ~7x to 300x greater than in 2014. The loss of adult and juvenile individuals in 2014 led to a dramatic decline in predation rate on mussels compared to the previous two decades. A proximate cause of wasting was likely the “Sea Star associated Densovirus” (SSaDV), but the ultimate factors triggering the epidemic, if any, remain unclear. Although warm temperature has been proposed as a possible trigger, SSWD in Oregon populations increased with cool temperatures. Since P. ochraceus is a keystone predator that can strongly influence the biodiversity and community structure of the intertidal community, major community-level responses to the disease are expected. However, predicting the specific impacts and time course of change across west coast meta-communities is difficult, suggesting the need for

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

    Science.gov (United States)

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

    2012-07-01

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

  19. Linking Diversity and Differentiation

    Directory of Open Access Journals (Sweden)

    Hans-Rolf Gregorius

    2010-03-01

    Full Text Available Generally speaking, the term differentiation refers to differences between collections for the distribution of specified traits of their members, while diversity deals with (effective numbers of trait states (types. Counting numbers of types implies discrete traits such as alleles and genotypes in population genetics or species and taxa in ecology. Comparisons between the concepts of differentiation and diversity therefore primarily refer to discrete traits. Diversity is related to differentiation through the idea that the total diversity of a subdivided collection should be composed of the diversity within the subcollections and a complement called “diversity between subcollections”. The idea goes back to the perception that the mixing of differentiated collections increases diversity. Several existing concepts of “diversity between subcollections” are based on this idea. Among them, β-diversity and fixation (inadvertently called differentiation are the most prominent in ecology and in population genetics, respectively. The pertaining measures are shown to quantify the effect of differentiation in terms of diversity components, though from a dual perspective: the classical perspective of differentiation between collections for their type compositions, and the reverse perspective of differentiation between types for their collection affiliations. A series of measures of diversity-oriented differentiation is presented that consider this dual perspective at two levels of diversity partitioning: the overall type or subcollection diversity and the joint type-subcollection diversity. It turns out that, in contrast with common notions, the measures of fixation (such as FST or GST refer to the perspective of type rather than subcollection differentiation. This unexpected observation strongly suggests that the popular interpretations of fixation measures must be reconsidered.

  20. Morphological and genetic differentiation among Chilean populations of Bufo spinulosus (Anura: Bufonidae Diferenciación morfológica y genética entre poblaciones chilenas de Bufo spinulosus (Anura: Bufonidae

    Directory of Open Access Journals (Sweden)

    Marco A. Méndez

    2004-09-01

    Full Text Available Bufo spinulosus has a wide and fragmented range distribution in Chile (18° to 33° S along altitudinal and latitudinal gradients. Genetic variation was estimated using RAPD (Random Amplified Polymorphic DNA markers in 10 populations from northern and central Chile. Morphometric and genetic information was analyzed as a function of geographical origin. The correlation between genetic and morphometric differentiation was analyzed by the Mantel test. An increase in body size as a function of latitude was observed. Specimens from El Tatio had the smallest body size and the greatest morphometric divergence. The AMOVA applied to genetic data indicated that 57.85 % of the variance is explained by interregional differences and that 30.12 % of the variance is found within populations. Low levels of within-regions genetic differentiation was observed in northern populations while higher levels of genetic differentiation was found in populations from central Chile. Mantel tests revealed a significant, positive correlation between genetic variation and geographic distance. When we excluded El Tatio population, Mantel test analyses showed significant correlations between morphological distance and genetic and geographic distances. We discuss whether water temperature could explain the morphological divergence observed in individuals from El TatioBufo spinulosus presenta una amplia y fragmentada distribución en Chile (18º a 33º S a lo largo de gradientes altitudinales y latitudinales. La variación genética fue estimada utilizando marcadores RAPD ("Random Amplified Polymorphic DNA" en diez poblaciones del norte y centro de Chile. La información morfométrica y genética fue analizada en función de la procedencia geográfica. La correlación entre diferenciación genética y morfométrica fue analizada utilizando la prueba de Mantel. Se observó un incremento en el tamaño corporal en función de la latitud. Los individuos de El Tatio mostraron el tama