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Sample records for gene flow marine

  1. Dispersal and gene flow in free-living marine nematodes.

    PubMed

    Derycke, Sofie; Backeljau, Thierry; Moens, Tom

    2013-01-01

    Dispersal and gene flow determine connectivity among populations, and can be studied through population genetics and phylogeography. We here review the results of such a framework for free-living marine nematodes. Although field experiments have illustrated substantial dispersal in nematodes at ecological time scales, analysis of the genetic diversity illustrated the importance of priority effects, founder effects and genetic bottlenecks for population structuring between patches <1 km apart. In contrast, only little genetic structuring was observed within an estuary (<50 km), indicating that these small scale fluctuations in genetic differentiation are stabilized over deeper time scales through extensive gene flow. Interestingly, nematode species with contrasting life histories (extreme colonizers vs persisters) or with different habitat preferences (algae vs sediment) show similar, low genetic structuring. Finally, historical events have shaped the genetic pattern of marine nematodes and show that gene flow is restricted at large geographical scales. We also discuss the presence of substantial cryptic diversity in marine nematodes, and end with highlighting future important steps to further unravel nematode evolution and diversity. PMID:23356547

  2. Dispersal and gene flow in free-living marine nematodes

    PubMed Central

    2013-01-01

    Dispersal and gene flow determine connectivity among populations, and can be studied through population genetics and phylogeography. We here review the results of such a framework for free-living marine nematodes. Although field experiments have illustrated substantial dispersal in nematodes at ecological time scales, analysis of the genetic diversity illustrated the importance of priority effects, founder effects and genetic bottlenecks for population structuring between patches <1 km apart. In contrast, only little genetic structuring was observed within an estuary (<50 km), indicating that these small scale fluctuations in genetic differentiation are stabilized over deeper time scales through extensive gene flow. Interestingly, nematode species with contrasting life histories (extreme colonizers vs persisters) or with different habitat preferences (algae vs sediment) show similar, low genetic structuring. Finally, historical events have shaped the genetic pattern of marine nematodes and show that gene flow is restricted at large geographical scales. We also discuss the presence of substantial cryptic diversity in marine nematodes, and end with highlighting future important steps to further unravel nematode evolution and diversity. PMID:23356547

  3. Barriers to Gene Flow in the Marine Environment: Insights from Two Common Intertidal Limpet Species of the Atlantic and Mediterranean

    PubMed Central

    Sá-Pinto, Alexandra; Branco, Madalena S.; Alexandrino, Paulo B.; Fontaine, Michaël C.; Baird, Stuart J. E.

    2012-01-01

    Knowledge of the scale of dispersal and the mechanisms governing gene flow in marine environments remains fragmentary despite being essential for understanding evolution of marine biota and to design management plans. We use the limpets Patella ulyssiponensis and Patella rustica as models for identifying factors affecting gene flow in marine organisms across the North-East Atlantic and the Mediterranean Sea. A set of allozyme loci and a fragment of the mitochondrial gene cytochrome C oxidase subunit I were screened for genetic variation through starch gel electrophoresis and DNA sequencing, respectively. An approach combining clustering algorithms with clinal analyses was used to test for the existence of barriers to gene flow and estimate their geographic location and abruptness. Sharp breaks in the genetic composition of individuals were observed in the transitions between the Atlantic and the Mediterranean and across southern Italian shores. An additional break within the Atlantic cluster separates samples from the Alboran Sea and Atlantic African shores from those of the Iberian Atlantic shores. The geographic congruence of the genetic breaks detected in these two limpet species strongly supports the existence of transpecific barriers to gene flow in the Mediterranean Sea and Northeastern Atlantic. This leads to testable hypotheses regarding factors restricting gene flow across the study area. PMID:23239977

  4. Conservation, Spillover and Gene Flow within a Network of Northern European Marine Protected Areas

    PubMed Central

    Huserbråten, Mats Brockstedt Olsen; Moland, Even; Knutsen, Halvor; Olsen, Esben Moland; André, Carl; Stenseth, Nils Chr.

    2013-01-01

    To ensure that marine protected areas (MPAs) benefit conservation and fisheries, the effectiveness of MPA designs has to be evaluated in field studies. Using an interdisciplinary approach, we empirically assessed the design of a network of northern MPAs where fishing for European lobster (Homarusgammarus) is prohibited. First, we demonstrate a high level of residency and survival (50%) for almost a year (363 days) within MPAs, despite small MPA sizes (0.5-1 km2). Second, we demonstrate limited export (4.7%) of lobsters tagged within MPAs (N = 1810) to neighbouring fished areas, over a median distance of 1.6 km out to maximum 21 km away from MPA centres. In comparison, median movement distance of lobsters recaptured within MPAs was 164 m, and recapture rate was high (40%). Third, we demonstrate a high level of gene flow within the study region, with an estimated FST of less than 0.0001 over a ≈ 400 km coastline. Thus, the restricted movement of older life stages, combined with a high level of gene flow suggests that connectivity is primarily driven by larval drift. Larval export from the MPAs can most likely affect areas far beyond their borders. Our findings are of high importance for the design of MPA networks for sedentary species with pelagic early life stages. PMID:24039927

  5. Southern hospitality: a latitudinal gradient in gene flow in the marine environment.

    PubMed

    Kelly, Ryan P; Eernisse, Douglas J

    2007-03-01

    In recent years population genetics and phylogeographic studies have become increasingly valuable tools for inferring both historical and present-day genetic patterns within marine species. Here, we take a comparative approach to population-level study, analyzing original mitochondrial DNA data from 969 individuals representing 28 chiton (Mollusca: Polyplacophora) species to uncover large-scale genetic patterns along the Pacific coast of North America. The data reveal a distinct latitudinal connectivity gradient among chitons: species that exist at lower latitudes tend to have more isolated populations. This trend appears to be a product of between-species differences; within species, no significant gradient in connectivity is observed. Lower average annual sea surface temperatures are hypothesized to contribute to longer larval duration (and by extension, greater connectivity) among lecithotrophic species, providing a mechanism for the observed positive correlation between gene flow and latitude. Because increased isolation among populations may lead to speciation, a latitudinal trend in gene flow may contribute to the increased species diversity observed at lower latitudes. PMID:17348933

  6. Evidence for extensive gene flow and Thermotoga subpopulations in subsurface and marine environments

    PubMed Central

    Nesbø, Camilla L; S Swithers, Kristen; Dahle, Håkon; Haverkamp, Thomas HA; Birkeland, Nils-Kåre; Sokolova, Tatiana; Kublanov, Ilya; Zhaxybayeva, Olga

    2015-01-01

    Oil reservoirs represent a nutrient-rich ecological niche of the deep biosphere. Although most oil reservoirs are occupied by microbial populations, when and how the microbes colonized these environments remains unanswered. To address this question, we compared 11 genomes of Thermotoga maritima-like hyperthermophilic bacteria from two environment types: subsurface oil reservoirs in the North Sea and Japan, and marine sites located in the Kuril Islands, Italy and the Azores. We complemented our genomes with Thermotoga DNA from publicly available subsurface metagenomes from North America and Australia. Our analysis revealed complex non-bifurcating evolutionary history of the isolates' genomes, suggesting high amounts of gene flow across all sampled locations, a conjecture supported by numerous recombination events. Genomes from the same type of environment tend to be more similar, and have exchanged more genes with each other than with geographically close isolates from different types of environments. Hence, Thermotoga populations of oil reservoirs do not appear isolated, a requirement of the ‘burial and isolation' hypothesis, under which reservoir bacteria are descendants of the isolated communities buried with sediments that over time became oil reservoirs. Instead, our analysis supports a more complex view, where bacteria from subsurface and marine populations have been continuously migrating into the oil reservoirs and influencing their genetic composition. The Thermotoga spp. in the oil reservoirs in the North Sea and Japan probably entered the reservoirs shortly after they were formed. An Australian oil reservoir, on the other hand, was likely colonized very recently, perhaps during human reservoir development. PMID:25500512

  7. Genomic signatures of local directional selection in a high gene flow marine organism; the Atlantic cod (Gadus morhua)

    PubMed Central

    2009-01-01

    Background Marine fishes have been shown to display low levels of genetic structuring and associated high levels of gene flow, suggesting shallow evolutionary trajectories and, possibly, limited or lacking adaptive divergence among local populations. We investigated variation in 98 gene-associated single nucleotide polymorphisms (SNPs) for evidence of selection in local populations of Atlantic cod (Gadus morhua L.) across the species distribution. Results Our global genome scan analysis identified eight outlier gene loci with very high statistical support, likely to be subject to directional selection in local demes, or closely linked to loci under selection. Likewise, on a regional south/north transect of central and eastern Atlantic populations, seven loci displayed strongly elevated levels of genetic differentiation. Selection patterns among populations appeared to be relatively widespread and complex, i.e. outlier loci were generally not only associated with one of a few divergent local populations. Even on a limited geographical scale between the proximate North Sea and Baltic Sea populations four loci displayed evidence of adaptive evolution. Temporal genome scan analysis applied to DNA from archived otoliths from a Faeroese population demonstrated stability of the intra-population variation over 24 years. An exploratory landscape genetic analysis was used to elucidate potential effects of the most likely environmental factors responsible for the signatures of local adaptation. We found that genetic variation at several of the outlier loci was better correlated with temperature and/or salinity conditions at spawning grounds at spawning time than with geographic distance per se. Conclusion These findings illustrate that adaptive population divergence may indeed be prevalent despite seemingly high levels of gene flow, as found in most marine fishes. Thus, results have important implications for our understanding of the interplay of evolutionary forces in

  8. Population Structure and Adaptive Divergence in a High Gene Flow Marine Fish: The Small Yellow Croaker (Larimichthys polyactis)

    PubMed Central

    Xue, Dong-Xiu; Gao, Tian-Xiang; Liu, Jin-Xian

    2016-01-01

    The spatial distribution of genetic diversity has been long considered as a key component of policy development for management and conservation of marine fishes. However, unraveling the population genetic structure of migratory fish species is challenging due to high potential for gene flow. Despite the shallow population differentiation revealed by putatively neutral loci, the higher genetic differentiation with panels of putatively adaptive loci could provide greater resolution for stock identification. Here, patterns of population differentiation of small yellow croaker (Larimichthys polyactis) were investigated by genotyping 15 highly polymorphic microsatellites in 337 individuals of 15 geographic populations collected from both spawning and overwintering grounds. Outlier analyses indicated that the locus Lpol03 might be under directional selection, which showed a strong homology with Grid2 gene encoding the glutamate receptor δ2 protein (GluRδ2). Based on Lpol03, two distinct clusters were identified by both STRUCTURE and PCoA analyses, suggesting that there were two overwintering aggregations of L. polyactis. A novel migration pattern was suggested for L. polyactis, which was inconsistent with results of previous studies based on historical fishing yield statistics. These results provided new perspectives on the population genetic structure and migratory routes of L. polyactis, which could have significant implications for sustainable management and utilization of this important fishery resource. PMID:27100462

  9. Population Structure and Adaptive Divergence in a High Gene Flow Marine Fish: The Small Yellow Croaker (Larimichthys polyactis).

    PubMed

    Liu, Bing-Jian; Zhang, Bai-Dong; Xue, Dong-Xiu; Gao, Tian-Xiang; Liu, Jin-Xian

    2016-01-01

    The spatial distribution of genetic diversity has been long considered as a key component of policy development for management and conservation of marine fishes. However, unraveling the population genetic structure of migratory fish species is challenging due to high potential for gene flow. Despite the shallow population differentiation revealed by putatively neutral loci, the higher genetic differentiation with panels of putatively adaptive loci could provide greater resolution for stock identification. Here, patterns of population differentiation of small yellow croaker (Larimichthys polyactis) were investigated by genotyping 15 highly polymorphic microsatellites in 337 individuals of 15 geographic populations collected from both spawning and overwintering grounds. Outlier analyses indicated that the locus Lpol03 might be under directional selection, which showed a strong homology with Grid2 gene encoding the glutamate receptor δ2 protein (GluRδ2). Based on Lpol03, two distinct clusters were identified by both STRUCTURE and PCoA analyses, suggesting that there were two overwintering aggregations of L. polyactis. A novel migration pattern was suggested for L. polyactis, which was inconsistent with results of previous studies based on historical fishing yield statistics. These results provided new perspectives on the population genetic structure and migratory routes of L. polyactis, which could have significant implications for sustainable management and utilization of this important fishery resource. PMID:27100462

  10. Progressive colonization and restricted gene flow shape island-dependent population structure in Galápagos marine iguanas (Amblyrhynchus cristatus)

    PubMed Central

    2009-01-01

    Background Marine iguanas (Amblyrhynchus cristatus) inhabit the coastlines of large and small islands throughout the Galápagos archipelago, providing a rich system to study the spatial and temporal factors influencing the phylogeographic distribution and population structure of a species. Here, we analyze the microevolution of marine iguanas using the complete mitochondrial control region (CR) as well as 13 microsatellite loci representing more than 1200 individuals from 13 islands. Results CR data show that marine iguanas occupy three general clades: one that is widely distributed across the northern archipelago, and likely spread from east to west by way of the South Equatorial current, a second that is found mostly on the older eastern and central islands, and a third that is limited to the younger northern and western islands. Generally, the CR haplotype distribution pattern supports the colonization of the archipelago from the older, eastern islands to the younger, western islands. However, there are also signatures of recurrent, historical gene flow between islands after population establishment. Bayesian cluster analysis of microsatellite genotypes indicates the existence of twenty distinct genetic clusters generally following a one-cluster-per-island pattern. However, two well-differentiated clusters were found on the easternmost island of San Cristóbal, while nine distinct and highly intermixed clusters were found on youngest, westernmost islands of Isabela and Fernandina. High mtDNA and microsatellite genetic diversity were observed for populations on Isabela and Fernandina that may be the result of a recent population expansion and founder events from multiple sources. Conclusions While a past genetic study based on pure FST analysis suggested that marine iguana populations display high levels of nuclear (but not mitochondrial) gene flow due to male-biased dispersal, the results of our sex-biased dispersal tests and the finding of strong genetic

  11. Gene flow and bacterial transformation

    SciTech Connect

    Dixon, B.

    1993-07-01

    It is common knowledge that Salmonella which should be removed during the processing of sewage can persist is sewage sludge that is sprayed as agricultural fertilizer. Currently, researchers have found that Salmonella may become nonculturable by conventional means, while remaining viable. The issue raised by this article is the knowledge of lateral gene flow as secure as scientist suppose The author sites several research papers that suggest that intergeneric transformation can and does take place in marine environments such as tropical and subtropical estuaries.

  12. High abundance of virulence gene homologues in marine bacteria

    PubMed Central

    Persson, Olof P; Pinhassi, Jarone; Riemann, Lasse; Marklund, Britt-Inger; Rhen, Mikael; Normark, Staffan; González, José M; Hagström, Åke

    2009-01-01

    Marine bacteria can cause harm to single-celled and multicellular eukaryotes. However, relatively little is known about the underlying genetic basis for marine bacterial interactions with higher organisms. We examined whole-genome sequences from a large number of marine bacteria for the prevalence of homologues to virulence genes and pathogenicity islands known from bacteria that are pathogenic to terrestrial animals and plants. As many as 60 out of 119 genomes of marine bacteria, with no known association to infectious disease, harboured genes of virulence-associated types III, IV, V and VI protein secretion systems. Type III secretion was relatively uncommon, while type IV was widespread among alphaproteobacteria (particularly among roseobacters) and type VI was primarily found among gammaproteobacteria. Other examples included homologues of the Yersinia murine toxin and a phage-related ‘antifeeding’ island. Analysis of the Global Ocean Sampling metagenomic data indicated that virulence genes were present in up to 8% of the planktonic bacteria, with highest values in productive waters. From a marine ecology perspective, expression of these widely distributed genes would indicate that some bacteria infect or even consume live cells, that is, generate a previously unrecognized flow of organic matter and nutrients directly from eukaryotes to bacteria. PMID:19207573

  13. Behavior of Settling Marine Larvae in Flow

    NASA Astrophysics Data System (ADS)

    Hernandez, J.; Koehl, M. A.

    2012-12-01

    Many bottom-dwelling marine animals produce microscopic larvae that are dispersed by ambient water currents. These larvae can only recruit to habitats on which they have landed if they can resist being washed away by ambient water flow. We found that larvae on marine surfaces do not experience steady water flow, but rather are exposed to brief pulses of water movement as turbulent eddies sweep across them. We made video recordings of larvae of the tube worm, Hydroides elegans, (important members of the community of organisms growing on docks and ships) on surfaces subjected to measured realistic flow pulses to study factors that might affect their dislodgement from surfaces in nature. We found that the response of a larva of H. elegans to a realistic pulse of water flow depended on its behavior at the time of the pulse and on its recent history of exposure to flow pulses, and that stationary larvae were less likely than locomoting larvae to be blown away when hit by the first pulse of water flow.; ;

  14. A New U.S. Marine Heat Flow Capability

    NASA Astrophysics Data System (ADS)

    Harris, R. N.; Fisher, A. T.

    2009-12-01

    Marine heat flow observations provide critical information on physical, chemical and biological processes occurring near and below the seafloor. Renewed interest in the collection and application of marine heat flow data to a broad range of scientific purposes is indicated by a renaissance in heat flow studies and publications over the last 10-15 years, as documented by a recent NSF-sponsored workshop and report on the Future of Marine Heat Flow [Harris et al., 2007]. Fundamental questions of geodynamics, global mass and energy fluxes across the seafloor, marine hydrogeology, gas hydrates, marine microbiology, sedimentary processes and other topics are addressed in recent heat flow studies. To facilitate these measurements we are establishing a marine heat flow capability for use by U.S. academic researchers on standard UNOLS vessels in collaboration with the Oregon State University coring capability. This capability includes two main sets of instruments: 1) A multipenetration probe that allows multiple measurements of heat flow, the product of the thermal gradient and thermal conductivity, with a single instrument transit to the seafloor; and 2) an outrigger probe system that allows measurements at a single location when a gravity or piston core is collected. A thermal conductivity needle probe system for use on recovered core samples will complete the determination of heat flow using outrigger probes, and supplement in-situ measurements from the multipenetration probe. This capability is available to U.S. scientists for an initial five-year period through funding from the National Science Foundation. Researchers wishing to include measurements of marine heat flow as part of a field program can request access to equipment, software, and technical support through the UNOLS ship time request system, and should consult early in the cruise planning process with US heat flow capability personnel to determine specific needs and capabilities. More information is

  15. Targeted gene flow for conservation.

    PubMed

    Kelly, Ella; Phillips, Ben L

    2016-04-01

    Anthropogenic threats often impose strong selection on affected populations, causing rapid evolutionary responses. Unfortunately, these adaptive responses are rarely harnessed for conservation. We suggest that conservation managers pay close attention to adaptive processes and geographic variation, with an eye to using them for conservation goals. Translocating pre-adapted individuals into recipient populations is currently considered a potentially important management tool in the face of climate change. Targeted gene flow, which involves moving individuals with favorable traits to areas where these traits would have a conservation benefit, could have a much broader application in conservation. Across a species' range there may be long-standing geographic variation in traits or variation may have rapidly developed in response to a threatening process. Targeted gene flow could be used to promote natural resistance to threats to increase species resilience. We suggest that targeted gene flow is a currently underappreciated strategy in conservation that has applications ranging from the management of invasive species and their impacts to controlling the impact and virulence of pathogens. PMID:26332195

  16. Gene flow and population history in high dispersal marine invertebrates: mitochondrial DNA analysis of Holothuria nobilis (Echinodermata: Holothuroidea) populations from the Indo-Pacific.

    PubMed

    Uthicke, S; Benzie, J A H

    2003-10-01

    The sea cucumber, Holothuria nobilis, has a long-lived planktotrophic larvae, and previous allozyme surveys have suggested that high dispersal is realized. In contrast, recent ecological studies indicate that dispersal is low. To reconcile these data, and to investigate the evolution of this Indo-Pacific species, we screened geographical variation in 559 bp of a mitochondrial gene (COI) in 360 samples from the Australasian region and La Réunion. Sequences from La Réunion differed by > 7% from others and may constitute another species. Haplotype diversity in other samples was high (0.942, SD = 0.007), but haplotypes were closely related (mean nucleotide diversity: 0.0075, SD = 0.0041). AMOVA, pairwise FST values and exact tests did not detect significant population structure. Nested clade analysis showed that one of two main clades was over-represented in west Australia, whereas the other was more common in the northern Great Barrier Reef. Isolation-by-distance was identified as the main determinant of population structure at several clade levels. Contiguous range expansion was inferred for evolutionary older clade levels and this may correspond to a late Pleistocene (88 000-193 000 years ago) population expansion inferred from haplotype mismatch distributions. Thus, the population genetic structures detected are likely to be formed prior to the last ice age, with some indications for high dispersal on shorter time scales. PMID:12969467

  17. Diversity and Detection of Nitrate Assimilation Genes in Marine Bacteria

    PubMed Central

    Allen, Andrew E.; Booth, Melissa G.; Frischer, Marc E.; Verity, Peter G.; Zehr, Jonathan P.; Zani, Sabino

    2001-01-01

    A PCR approach was used to construct a database of nasA genes (called narB genes in cyanobacteria) and to detect the genetic potential for heterotrophic bacterial nitrate utilization in marine environments. A nasA-specific PCR primer set that could be used to selectively amplify the nasA gene from heterotrophic bacteria was designed. Using seawater DNA extracts obtained from microbial communities in the South Atlantic Bight, the Barents Sea, and the North Pacific Gyre, we PCR amplified and sequenced nasA genes. Our results indicate that several groups of heterotrophic bacterial nasA genes are common and widely distributed in oceanic environments. PMID:11679368

  18. Gene flow from glyphosate-resistant crops.

    PubMed

    Mallory-Smith, Carol; Zapiola, Maria

    2008-04-01

    Gene flow from transgenic glyphosate-resistant crops can result in the adventitious presence of the transgene, which may negatively impact markets. Gene flow can also produce glyphosate-resistant plants that may interfere with weed management systems. The objective of this article is to review the gene flow literature as it pertains to glyphosate-resistant crops. Gene flow is a natural phenomenon not unique to transgenic crops and can occur via pollen, seed and, in some cases, vegetative propagules. Gene flow via pollen can occur in all crops, even those that are considered to be self-pollinated, because all have low levels of outcrossing. Gene flow via seed or vegetative propagules occurs when they are moved naturally or by humans during crop production and commercialization. There are many factors that influence gene flow; therefore, it is difficult to prevent or predict. Gene flow via pollen and seed from glyphosate-resistant canola and creeping bentgrass fields has been documented. The adventitious presence of the transgene responsible for glyphosate resistance has been found in commercial seed lots of canola, corn and soybeans. In general, the glyphosate-resistant trait is not considered to provide an ecological advantage. However, regulators should consider the examples of gene flow from glyphosate-resistant crops when formulating rules for the release of crops with traits that could negatively impact the environment or human health. PMID:18181145

  19. Gene Flow in Seed Alfalfa: A Summary of Recent Research

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Gene flow is the mechanism by which a gene from one population becomes established in another population. There are two types of gene flow: pollen-mediated gene flow and seed-mediated gene flow. Pollen-mediated gene flow results from the movement of pollen from one location to another resulting in f...

  20. Effective gene collection from the metatranscriptome of marine microorganisms

    PubMed Central

    2011-01-01

    Background Metagenomic studies, accelerated by the evolution of sequencing technologies and the rapid development of genomic analysis methods, can reveal genetic diversity and biodiversity in various samples including those of uncultured or unknown species. This approach, however, cannot be used to identify active functional genes under actual environmental conditions. Metatranscriptomics, which is similar in approach to metagenomics except that it utilizes RNA samples, is a powerful tool for the transcriptomic study of environmental samples. Unlike metagenomic studies, metatranscriptomic studies have not been popular to date due to problems with reliability, repeatability, redundancy and cost performance. Here, we propose a normalized metatranscriptomic method that is suitable for the collection of genes from samples as a platform for comparative transcriptomics. Results We constructed two libraries, one non-normalized and the other normalized library, from samples of marine microorganisms taken during daylight hours from Hiroshima bay in Japan. We sequenced 0.6M reads for each sample on a Roche GS FLX, and obtained 0.2M genes after quality control and assembly. A comparison of the two libraries showed that the number of unique genes was larger in the normalized library than in the non-normalized library. Functional analysis of genes revealed that a small number of gene groups, ribosomal RNA genes and chloroplast genes, were dominant in both libraries. Taxonomic distribution analysis of the libraries suggests that Stramenopiles form a major taxon that includes diatoms. The normalization technique thus increases unique genes, functional categories of genes, and taxonomic richness. Conclusions Normalization of the marine metatranscriptome could be useful in increasing the number of genes collected, and in reducing redundancies among highly expressed genes. Gene collection through the normalization method was effective in providing a foundation for comparative

  1. GenePattern flow cytometry suite

    PubMed Central

    2013-01-01

    Background Traditional flow cytometry data analysis is largely based on interactive and time consuming analysis of series two dimensional representations of up to 20 dimensional data. Recent technological advances have increased the amount of data generated by the technology and outpaced the development of data analysis approaches. While there are advanced tools available, including many R/BioConductor packages, these are only accessible programmatically and therefore out of reach for most experimentalists. GenePattern is a powerful genomic analysis platform with over 200 tools for analysis of gene expression, proteomics, and other data. A web-based interface provides easy access to these tools and allows the creation of automated analysis pipelines enabling reproducible research. Results In order to bring advanced flow cytometry data analysis tools to experimentalists without programmatic skills, we developed the GenePattern Flow Cytometry Suite. It contains 34 open source GenePattern flow cytometry modules covering methods from basic processing of flow cytometry standard (i.e., FCS) files to advanced algorithms for automated identification of cell populations, normalization and quality assessment. Internally, these modules leverage from functionality developed in R/BioConductor. Using the GenePattern web-based interface, they can be connected to build analytical pipelines. Conclusions GenePattern Flow Cytometry Suite brings advanced flow cytometry data analysis capabilities to users with minimal computer skills. Functionality previously available only to skilled bioinformaticians is now easily accessible from a web browser. PMID:23822732

  2. Cloning of a marine cyanobacterial promoter for foreign gene expression using a promoter probe vector

    SciTech Connect

    Sode, Koji; Hatano, Naoaki; Tatara, Masahiro

    1996-06-01

    A marine cyanobacterial promoter was cloned to allow efficient foreign gene expression. This was carried out using chloramphenicol acetyl transferase (CAT) as a marker protein. For rapid and simple measurement of CAT activity, a method based on a fluorescently labeled substrate was improved by utilizing HPLC equipped with a flow-through fluorescent spectrophotometer. This method was used in conjunction with a newly constructed promoter probe vector. Cyanobacterial transformants, harboring plasmid containing a cloned 2-kbp marine cyanobacterial genomic fragment, showed a 10-fold higher CAT activity, compared with that achieved using the kanamycin-resistant gene promoter. From the sequence analysis of the cloned fragment, a putative promoter region was found. 20 refs., 7 figs., 2 tabs.

  3. Estimation of Male Gene Flow: Use Caution.

    PubMed

    Hedrick, Philip W; Singh, Sujeet; Aspi, Jouni

    2015-01-01

    Because male gene flow cannot easily be estimated directly in many organisms, Hedrick et al. (2013) provided an approach to estimate male gene flow given estimates of diploid nuclear and female differentiation. This approach appears to work well when there is lower female than male gene flow. However, in a tiger data set there was less female differentiation observed as estimated by mitochondrial DNA than expected given the observed overall nuclear diploid differentiation. To analyze these data, we suggest an alternative approach which allows incorporation of sex-specific gene flow and sex-specific effective population size. We find that the pattern of differentiation observed in tigers was consistent with a lower male than female effective population size using this alternative approach. Further, this finding is consistent with observed data in tigers where the male effective population size was 33% that of the female effective population size. PMID:26464090

  4. Numerical simulation of a cross flow Marine Hydrokinetic turbine.

    NASA Astrophysics Data System (ADS)

    Hall, Taylor; Aliseda, Alberto

    2011-11-01

    In the search for alternative sources of energy, the kinetic energy of water currents in oceans, rivers and estuaries is being explored as predictable and environmentally benign. We are investigating the flow past a cross flow turbine in which a helical blade under hydrodynamic forces turns around a shaft perpendicular to the free stream. This type of turbine, while very different from the classical horizontal axis turbine commonly used in the wind energy field, presents advantages for stacking in very narrow constricted channels where the water currents are consistently high and therefore turbine installation may be economically feasible. We use a model of a helical four-bladed turbine in cross flow to investigate the efficiency of the energy capture and the dynamics of the turbulent wake. Scale model experiments in a flume are used to validate the numerical results on a stationary configuration as an initial step towards creating an accurate numerical model of the turbine. The simulation of the rotating turbine provides a full perspective on the effect of angular position on flow detachment and vortex shedding from the blade, as well as on the fluctuations of the shaft torque produced (a problematic feature of this type of turbine). The results are analyzed in terms of hydrodynamic optimization of the blade and its structural loading. Supported by DOE through the Northwest National Marine Renewable Energy Center.

  5. Plant introductions, hybridization and gene flow.

    PubMed Central

    Abbott, Richard J; James, Juliet K; Milne, Richard I; Gillies, Amanda C M

    2003-01-01

    Many regional floras contain a high proportion of recently introduced plant species. Occasionally, hybridization between an introduced species and another species (introduced or native) can result in interspecific gene flow. This may occur even in instances where the F(1) hybrid shows very high sterility, but occasionally produces a few viable gametes. We provide examples of gene flow occurring between some rhododendrons recently introduced to the British flora, and between an introduced and native Senecio species. Neutral molecular markers have normally been employed to obtain evidence of interspecific gene flow, but the challenge now is to isolate and characterize functional introgressed genes and to determine how they affect the fitness of introgressants and whether they improve adaptation to novel habitats allowing introgressants to expand the range of a species. We outline a candidate gene approach for isolating and characterizing an allele of the RAY gene in Senecio vulgaris, which is believed to have introgressed from S. squalidus, and which causes the production of ray florets in flower heads. We discuss the effects of this introgressed allele on individual fitness, including those that originate directly from the production of ray florets plus those that may arise from pleiotropy and/or linkage. PMID:12831478

  6. Device for passive flow control around vertical axis marine turbine

    NASA Astrophysics Data System (ADS)

    Coşoiu, C. I.; Georgescu, A. M.; Degeratu, M.; Haşegan, L.; Hlevca, D.

    2012-11-01

    The power supplied by a turbine with the rotor placed in a free stream flow may be increased by augmenting the velocity in the rotor area. The energy of the free flow is dispersed and it may be concentrated by placing a profiled structure around the bare turbine in order to concentrate more energy in the rotor zone. At the Aerodynamic and Wind Engineering Laboratory (LAIV) of the Technical University of Civil Engineering of Bucharest (UTCB) it was developed a concentrating housing to be used for hydro or aeolian horizontal axis wind turbines, in order to increase the available energy in the active section of turbine rotor. The shape of the concentrating housing results by superposing several aero/hydro dynamic effects, the most important being the one generated by the passive flow control devices that were included in the housing structure. Those concentrating housings may be also adapted for hydro or aeolian turbines with vertical axis. The present paper details the numerical research effectuated at the LAIV to determine the performances of a vertical axis marine turbine equipped with such a concentrating device, in order to increase the energy quantity extracted from the main flow. The turbine is a Darrieus type one with three vertical straight blades, symmetric with respect to the axis of rotation, generated using a NACA4518 airfoil. The global performances of the turbine equipped with the concentrating housing were compared to the same characteristics of the bare turbine. In order to validate the numerical approach used in this paper, test cases from the literature resulting from experimental and numerical simulations for similar situations, were used.

  7. Methanesulfonate (MSA) Catabolic Genes from Marine and Estuarine Bacteria.

    PubMed

    Henriques, Ana C; De Marco, Paolo

    2015-01-01

    Quantitatively, methanesulfonate (MSA) is a very relevant compound in the global biogeochemical sulfur cycle. Its utilization by bacteria as a source of carbon and energy has been described and a specific enzyme, methanesulfonate monooxygenase (MSAMO), has been found to perform the first catabolic step of its oxidation. Other proteins seemingly involved in the import of MSA into bacterial cells have been reported. In this study, we obtained novel sequences of genes msmA and msmE from marine, estuary and soil MSA-degraders (encoding the large subunit of the MSAMO enzyme and the periplasmic component of the import system, respectively). We also obtained whole-genome sequences of two novel marine Filomicrobium strains, Y and W, and annotated two full msm operons in these genomes. Furthermore, msmA and msmE sequences were amplified from North Atlantic seawater and analyzed. Good conservation of the MsmA deduced protein sequence was observed in both cultured strains and metagenomic clones. A long spacer sequence in the Rieske-type [2Fe-2S] cluster-binding motif within MsmA was found to be conserved in all instances, supporting the hypothesis that this feature is specific to the large (α) subunit of the MSAMO enzyme. The msmE gene was more difficult to amplify, from both cultivated isolates and marine metagenomic DNA. However, 3 novel msmE sequences were obtained from isolated strains and one directly from seawater. With both genes, our results combined with previous metagenomic analyses seem to imply that moderate to high-GC strains are somehow favored during enrichment and isolation of MSA-utilizing bacteria, while the majority of msm genes obtained by cultivation-independent methods have low levels of GC%, which is a clear example of the misrepresentation of natural populations that culturing, more often than not, entails. Nevertheless, the data obtained in this work show that MSA-degrading bacteria are abundant in surface seawater, which suggests ecological

  8. Coalescent and biophysical models of stepping-stone gene flow in neritid snails.

    PubMed

    Crandall, Eric D; Treml, Eric A; Barber, Paul H

    2012-11-01

    Marine species in the Indo-Pacific have ranges that can span thousands of kilometres, yet studies increasingly suggest that mean larval dispersal distances are less than historically assumed. Gene flow across these ranges must therefore rely to some extent on larval dispersal among intermediate 'stepping-stone' populations in combination with long-distance dispersal far beyond the mean of the dispersal kernel. We evaluate the strength of stepping-stone dynamics by employing a spatially explicit biophysical model of larval dispersal in the tropical Pacific to construct hypotheses for dispersal pathways. We evaluate these hypotheses with coalescent models of gene flow among high-island archipelagos in four neritid gastropod species. Two of the species live in the marine intertidal, while the other two are amphidromous, living in fresh water but retaining pelagic dispersal. Dispersal pathways predicted by the biophysical model were strongly favoured in 16 of 18 tests against alternate hypotheses. In regions where connectivity among high-island archipelagos was predicted as direct, there was no difference in gene flow between marine and amphidromous species. In regions where connectivity was predicted through stepping-stone atolls only accessible to marine species, gene flow estimates between high-island archipelagos were significantly higher in marine species. Moreover, one of the marine species showed a significant pattern of isolation by distance consistent with stepping-stone dynamics. While our results support stepping-stone dynamics in Indo-Pacific species, we also see evidence for nonequilibrium processes such as range expansions or rare long-distance dispersal events. This study couples population genetic and biophysical models to help to shed light on larval dispersal pathways. PMID:23050562

  9. Detection of photoactive siderophore biosynthetic genes in the marine environment.

    PubMed

    Gärdes, Astrid; Triana, Christopher; Amin, Shady A; Green, David H; Romano, Ariel; Trimble, Lyndsay; Carrano, Carl J

    2013-06-01

    Iron is an essential element for oceanic microbial life but its low bioavailability limits microorganisms in large areas of the oceans. To acquire this metal many marine bacteria produce organic chelates that bind and transport iron (siderophores). While it has been hypothesized that the global production of siderophores by heterotrophic bacteria and some cyanobacteria constitutes the bulk of organic ligands binding iron in the ocean because stability constants of siderophores and these organic ligands are similar, and because ligand concentrations rise sharply in response to iron fertilization events, direct evidence for this proposal is lacking. This lack is due to the difficulty in characterizing these ligands due both to their extremely low concentrations and their highly heterogeneous nature. The situation for characterizing photoactive siderophores in situ is more problematic because of their expected short lifetimes in the photic zone. An alternative approach is to make use of high sensitivity molecular technology (qPCR) to search for siderophore biosynthesis genes related to the production of photoactive siderophores. In this way one can access their "biochemical potential" and utilize this information as a proxy for the presence of these siderophores in the marine environment. Here we show, using qPCR primers designed to detect biosynthetic genes for the siderophores vibrioferrin, petrobactin and aerobactin that such genes are widespread and based on their abundance, the "biochemical potential" for photoactive siderophore production is significant. Concurrently we also briefly examine the microbial biodiversity responsible for such production as a function of depth and location across a North Atlantic transect. PMID:23700243

  10. Unique marine derived cyanobacterial biosynthetic genes for chemical diversity.

    PubMed

    Kleigrewe, Karin; Gerwick, Lena; Sherman, David H; Gerwick, William H

    2016-02-01

    Cyanobacteria are a prolific source of structurally unique and biologically active natural products that derive from intriguing biochemical pathways. Advancements in genome sequencing have accelerated the identification of unique modular biosynthetic gene clusters in cyanobacteria and reveal a wealth of unusual enzymatic reactions involved in their construction. This article examines several interesting mechanistic transformations involved in cyanobacterial secondary metabolite biosynthesis with a particular focus on marine derived modular polyketide synthases (PKS), nonribosomal peptide synthetases (NRPS) and combinations thereof to form hybrid natural products. Further, we focus on the cyanobacterial genus Moorea and the co-evolution of its enzyme cassettes that create metabolic diversity. Progress in the development of heterologous expression systems for cyanobacterial gene clusters along with chemoenzymatic synthesis makes it possible to create new analogs. Additionally, phylum-wide genome sequencing projects have enhanced the discovery rate of new natural products and their distinctive enzymatic reactions. Summarizing, cyanobacterial biosynthetic gene clusters encode for a large toolbox of novel enzymes that catalyze unique chemical reactions, some of which may be useful in synthetic biology. PMID:26758451

  11. Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing.

    PubMed Central

    Schmidt, T M; DeLong, E F; Pace, N R

    1991-01-01

    The phylogenetic diversity of an oligotrophic marine picoplankton community was examined by analyzing the sequences of cloned ribosomal genes. This strategy does not rely on cultivation of the resident microorganisms. Bulk genomic DNA was isolated from picoplankton collected in the north central Pacific Ocean by tangential flow filtration. The mixed-population DNA was fragmented, size fractionated, and cloned into bacteriophage lambda. Thirty-eight clones containing 16S rRNA genes were identified in a screen of 3.2 x 10(4) recombinant phage, and portions of the rRNA gene were amplified by polymerase chain reaction and sequenced. The resulting sequences were used to establish the identities of the picoplankton by comparison with an established data base of rRNA sequences. Fifteen unique eubacterial sequences were obtained, including four from cyanobacteria and eleven from proteobacteria. A single eucaryote related to dinoflagellates was identified; no archaebacterial sequences were detected. The cyanobacterial sequences are all closely related to sequences from cultivated marine Synechococcus strains and with cyanobacterial sequences obtained from the Atlantic Ocean (Sargasso Sea). Several sequences were related to common marine isolates of the gamma subdivision of proteobacteria. In addition to sequences closely related to those of described bacteria, sequences were obtained from two phylogenetic groups of organisms that are not closely related to any known rRNA sequences from cultivated organisms. Both of these novel phylogenetic clusters are proteobacteria, one group within the alpha subdivision and the other distinct from known proteobacterial subdivisions. The rRNA sequences of the alpha-related group are nearly identical to those of some Sargasso Sea picoplankton, suggesting a global distribution of these organisms. Images PMID:2066334

  12. Characterization of SNAP-25 gene from marine teleostean, Lateolabrax japonicus

    NASA Astrophysics Data System (ADS)

    Chen, Kui; Huang, Xiaohang; Chai, Yingmei; Gaisano, Herbert Y.

    2007-10-01

    The t-SNARE protein SNAP-25 (synaptosome-associated protein of 25 kDa) plays an essential role in regulating fusion between the vesicle and plasma membranes during exocytosis. To clone and characterize SNAP-25 gene, the first step in the functional study of SNARE proteins in marine teleostean, was to obtain the cDNA of sea perch SNAP-25 (SPsn25) by RT-PCR and RACE-PCR amplification of a Japanese sea perch. The full-length cDNA of 831bp contains a CDS of 615 bp, coding 204 amino acid residues, and a 5 UTR of 219bp. Bioinformatic analysis revealed that SPsn25 corresponds with SNAP-25a isoform and shares 91.1% identity with SNAP-25a of a goldfish and a zebrafish. The SPsn25 expression in both mRNA and protein levels in the Japanese sea perch had been identified through semi-quantitative RT-PCR and Western Blot assay. Together, these data again confirmed the nerve tissue specificity of the fish SNAP-25 gene expression.

  13. The impact of selection, gene flow and demographic history on heterogeneous genomic divergence: three-spine sticklebacks in divergent environments.

    PubMed

    Ferchaud, Anne-Laure; Hansen, Michael M

    2016-01-01

    Heterogeneous genomic divergence between populations may reflect selection, but should also be seen in conjunction with gene flow and drift, particularly population bottlenecks. Marine and freshwater three-spine stickleback (Gasterosteus aculeatus) populations often exhibit different lateral armour plate morphs. Moreover, strikingly parallel genomic footprints across different marine-freshwater population pairs are interpreted as parallel evolution and gene reuse. Nevertheless, in some geographic regions like the North Sea and Baltic Sea, different patterns are observed. Freshwater populations in coastal regions are often dominated by marine morphs, suggesting that gene flow overwhelms selection, and genomic parallelism may also be less pronounced. We used RAD sequencing for analysing 28 888 SNPs in two marine and seven freshwater populations in Denmark, Europe. Freshwater populations represented a variety of environments: river populations accessible to gene flow from marine sticklebacks and large and small isolated lakes with and without fish predators. Sticklebacks in an accessible river environment showed minimal morphological and genomewide divergence from marine populations, supporting the hypothesis of gene flow overriding selection. Allele frequency spectra suggested bottlenecks in all freshwater populations, and particularly two small lake populations. However, genomic footprints ascribed to selection could nevertheless be identified. No genomic regions were consistent freshwater-marine outliers, and parallelism was much lower than in other comparable studies. Two genomic regions previously described to be under divergent selection in freshwater and marine populations were outliers between different freshwater populations. We ascribe these patterns to stronger environmental heterogeneity among freshwater populations in our study as compared to most other studies, although the demographic history involving bottlenecks should also be considered in the

  14. Flow Cytometric Analysis of Marine Bacteria with Hoechst 33342 †

    PubMed Central

    Monger, Bruce C.; Landry, Michael R.

    1993-01-01

    We investigated the accuracy and precision of flow cytometric (FCM) estimates of bacterial abundances using 4′, 6-diamidino-2-phenylindole (DAPI) and Hoechst 33342 (HO342, a bisbenzamide derivative) on paraformaldehyde-fixed seawater samples collected from two stations near Oahu, Hawaii. The accuracy of FCM estimates was assessed against direct counts by using epifluorescence microscopy. DAPI and HO342 differ in two aspects of their chemistry that make HO342 better suited for staining marine heterotrophic bacteria for FCM analysis. These differences are most important in studies of open-ocean ecosystems that require dual-beam FCM analysis to clearly separate heterotrophic bacterial populations from populations of photosynthetic Prochlorococcus spp. Bacterial populations were easier to distinguish from background fluorescence when stained with HO342 than when stained with DAPI, because HO342 has a higher relative fluorescence quantum yield. A substantially higher coefficient of variation of blue fluorescence, which was probably due to fluorescent complexes formed by DAPI with double-stranded RNA, was observed for DAPI-stained populations. FCM estimates averaged 2.0 and 12% higher than corresponding epifluorescence microscopy direct counts for HO342 and DAPI-stained samples, respectively. A paired-sample t test between FCM estimates and direct counts found no significant difference for HO342-stained samples but a significant difference for DAPI-stained samples. Coefficients of variation of replicate FCM abundance estimates ranged from 0.63 to 2.9% (average, 1.5%) for natural bacterial concentrations of 6 × 105 to 15 × 105 cells ml-1. PMID:16348898

  15. Element flows associated with marine shore mine tailings deposits.

    PubMed

    Dold, Bernhard

    2006-02-01

    From 1938 until 1975, flotation tailings from the Potrerillos--El Salvador mining district (porphyry copper deposits) were discharged into the El Salado valley and transported in suspension to the sea at Chaliaral Bay, Atacama Desert, northern Chile. Over 220 Mt of tailings, averaging 0.8 +/- 0.25 wt % of pyrite, were deposited into the bay, resulting in over a 1 kilometer seaward displacement of the shoreline and an estimated 10-15 m thick tailings accumulation covering a approximately 4 km2 surface area. The Chaniaral case was classified by the United Nations Environmental Programme (UNEP) in 1983 as one of the most serious cases of marine contamination in the Pacific area. Since 1975, the tailings have been exposed to oxidation, resulting in a 70-188 cm thick low-pH (2.6-4) oxidation zone at the top with liberation of divalent metal cations, such as Cu2+, Ni2+, and Zn2+ (up to 2265 mg/L, 18.1 mg/L, and 20.3 mg/ L, respectively). Evaporation-induced transport capillarity led to metal enrichment atthe tailings surface (e.g. up to 2.4% Cu) in the form of secondary chlorides and/or sulfates (dominated by eriochalcite [CuCl.H2O] and halite). These, mainly water-soluble, secondary minerals were exposed to eolian transport in the direction of the Village of Chañaral by the predominant W-SW winds. Two element-flow directions (toward the tailings surface, via capillarity, and toward the sea) and two element groups with different geochemical behaviors (cations such as Cu, Zn, Ni, and oxyanions such as As and Mo) could be distinguished. It can be postulated, that the sea is mainly affected by the following: As, Mo, Cu, and Zn contamination, which were liberated from the oxidation zone from the tailings and mobilized through the tidal cycle, and by Cu and Zn from the subsurface waters flowing in the El Salado valley (up to 19 mg/L and 12 mg/L Zn, respectively), transported as chloro complexes at neutral pH. PMID:16509314

  16. A Continuous Method for Gene Flow

    PubMed Central

    Palczewski, Michal; Beerli, Peter

    2013-01-01

    Most modern population genetics inference methods are based on the coalescence framework. Methods that allow estimating parameters of structured populations commonly insert migration events into the genealogies. For these methods the calculation of the coalescence probability density of a genealogy requires a product over all time periods between events. Data sets that contain populations with high rates of gene flow among them require an enormous number of calculations. A new method, transition probability-structured coalescence (TPSC), replaces the discrete migration events with probability statements. Because the speed of calculation is independent of the amount of gene flow, this method allows calculating the coalescence densities efficiently. The current implementation of TPSC uses an approximation simplifying the interaction among lineages. Simulations and coverage comparisons of TPSC vs. MIGRATE show that TPSC allows estimation of high migration rates more precisely, but because of the approximation the estimation of low migration rates is biased. The implementation of TPSC into programs that calculate quantities on phylogenetic tree structures is straightforward, so the TPSC approach will facilitate more general inferences in many computer programs. PMID:23666937

  17. Gene flow from transgenic common beans expressing the bar gene.

    PubMed

    Faria, Josias C; Carneiro, Geraldo E S; Aragão, Francisco J L

    2010-01-01

    Gene flow is a common phenomenon even in self-pollinated plant species. With the advent of genetically modified plants this subject has become of the utmost importance due to the need for controlling the spread of transgenes. This study was conducted to determine the occurrence and intensity of outcrossing in transgenic common beans. In order to evaluate the outcross rates, four experiments were conducted in Santo Antonio de Goiás (GO, Brazil) and one in Londrina (PR, Brazil), using transgenic cultivars resistant to the herbicide glufosinate ammonium and their conventional counterparts as recipients of the transgene. Experiments with cv. Olathe Pinto and the transgenic line Olathe M1/4 were conducted in a completely randomized design with ten replications for three years in one location, whereas the experiments with cv. Pérola and the transgenic line Pérola M1/4 were conducted at two locations for one year, with the transgenic cultivar surrounded on all sides by the conventional counterpart. The outcross occurred at a negligible rate of 0.00741% in cv. Pérola, while none was observed (0.0%) in cv. Olathe Pinto. The frequency of gene flow was cultivar dependent and most of the observed outcross was within 2.5 m from the edge of the pollen source. Index terms: Phaseolus vulgaris, outcross, glufosinate ammonium. PMID:21865877

  18. Separating underwater ambient noise from flow noise recorded on stereo acoustic tags attached to marine mammals.

    PubMed

    von Benda-Beckmann, Alexander M; Wensveen, Paul J; Samarra, Filipa I P; Beerens, S Peter; Miller, Patrick J O

    2016-08-01

    Sound-recording acoustic tags attached to marine animals are commonly used in behavioural studies. Measuring ambient noise is of interest to efforts to understand responses of marine mammals to anthropogenic underwater sound, or to assess their communication space. Noise of water flowing around the tag reflects the speed of the animal, but hinders ambient noise measurement. Here, we describe a correlation-based method for stereo acoustic tags to separate the relative contributions of flow and ambient noise. The uncorrelated part of the noise measured in digital acoustic recording tag (DTAG) recordings related well to swim speed of a humpback whale (Megaptera novaeangliae), thus providing a robust measure of flow noise over a wide frequency bandwidth. By removing measurements affected by flow noise, consistent ambient noise estimates were made for two killer whales (Orcinus orca) with DTAGs attached simultaneously. The method is applicable to any multi-channel acoustic tag, enabling application to a wide range of marine species. PMID:27229472

  19. Gene Flow in Genetically Modified Wheat

    PubMed Central

    Rieben, Silvan; Kalinina, Olena; Schmid, Bernhard; Zeller, Simon L.

    2011-01-01

    Understanding gene flow in genetically modified (GM) crops is critical to answering questions regarding risk-assessment and the coexistence of GM and non-GM crops. In two field experiments, we tested whether rates of cross-pollination differed between GM and non-GM lines of the predominantly self-pollinating wheat Triticum aestivum. In the first experiment, outcrossing was studied within the field by planting “phytometers” of one line into stands of another line. In the second experiment, outcrossing was studied over distances of 0.5–2.5 m from a central patch of pollen donors to adjacent patches of pollen recipients. Cross-pollination and outcrossing was detected when offspring of a pollen recipient without a particular transgene contained this transgene in heterozygous condition. The GM lines had been produced from the varieties Bobwhite or Frisal and contained Pm3b or chitinase/glucanase transgenes, respectively, in homozygous condition. These transgenes increase plant resistance against pathogenic fungi. Although the overall outcrossing rate in the first experiment was only 3.4%, Bobwhite GM lines containing the Pm3b transgene were six times more likely than non-GM control lines to produce outcrossed offspring. There was additional variation in outcrossing rate among the four GM-lines, presumably due to the different transgene insertion events. Among the pollen donors, the Frisal GM line expressing a chitinase transgene caused more outcrossing than the GM line expressing both a chitinase and a glucanase transgene. In the second experiment, outcrossing after cross-pollination declined from 0.7–0.03% over the test distances of 0.5–2.5 m. Our results suggest that pollen-mediated gene flow between GM and non-GM wheat might only be a concern if it occurs within fields, e.g. due to seed contamination. Methodologically our study demonstrates that outcrossing rates between transgenic and other lines within crops can be assessed using a phytometer approach and

  20. Laccase activity and putative laccase genes in marine-derived basidiomycetes.

    PubMed

    Bonugli-santos, Rafaella C; Durrant, Lucia R; Sette, Lara D

    2010-10-01

    Studies of laccases from marine-derived fungi are limited. In the present work, putative laccase genes from three marine-derived basidiomycetes and their laccase activities were evaluated. High amounts of laccase were produced by the fungal strains Marasmiellus sp. CBMAI 1062 (971.2UL⁻¹) and Peniophora sp. CBMAI 1063 (709.03UL⁻¹) when grown for 21d at 28°C in MA2ASW medium prepared with artificial seawater. Marine-derived basidiomycetes produced multiple distinct laccase sequences of about 200bp with 73-90% similarity to terrestrial basidiomycete laccases. Marasmiellus sp. CBMAI 1062 and Tinctoporellus sp. CBMAI 1061 showed the greatest laccase gene diversity with three and four distinct putative laccase sequences, respectively. This is the first report of laccase genes from marine-derived fungi, and our results revealed new putative laccases produced by three basidiomycetes. PMID:20943196

  1. Hundreds of Genes Experienced Convergent Shifts in Selective Pressure in Marine Mammals.

    PubMed

    Chikina, Maria; Robinson, Joseph D; Clark, Nathan L

    2016-09-01

    Mammal species have made the transition to the marine environment several times, and their lineages represent one of the classical examples of convergent evolution in morphological and physiological traits. Nevertheless, the genetic mechanisms of their phenotypic transition are poorly understood, and investigations into convergence at the molecular level have been inconclusive. While past studies have searched for convergent changes at specific amino acid sites, we propose an alternative strategy to identify those genes that experienced convergent changes in their selective pressures, visible as changes in evolutionary rate specifically in the marine lineages. We present evidence of widespread convergence at the gene level by identifying parallel shifts in evolutionary rate during three independent episodes of mammalian adaptation to the marine environment. Hundreds of genes accelerated their evolutionary rates in all three marine mammal lineages during their transition to aquatic life. These marine-accelerated genes are highly enriched for pathways that control recognized functional adaptations in marine mammals, including muscle physiology, lipid-metabolism, sensory systems, and skin and connective tissue. The accelerations resulted from both adaptive evolution as seen in skin and lung genes, and loss of function as in gustatory and olfactory genes. In regard to sensory systems, this finding provides further evidence that reduced senses of taste and smell are ubiquitous in marine mammals. Our analysis demonstrates the feasibility of identifying genes underlying convergent organism-level characteristics on a genome-wide scale and without prior knowledge of adaptations, and provides a powerful approach for investigating the physiological functions of mammalian genes. PMID:27329977

  2. Numerical analysis for cavitation flow of marine propeller

    NASA Astrophysics Data System (ADS)

    Tauviqirrahman, Mohammad; Muchammad, Ismail, Rifky; Jamari, J.

    2015-12-01

    Concerning the environmental issue and the increase of fuel price, optimizing the fuel consumption has been recently an important subject in all industries. In marine industries one of the ways to decrease the energy consumption was by reducing the presence of cavitation on marine propeller blades. This will give a higher propulsive efficiency. This paper provides an investigation into the influence of the cavitation on a hydrodynamic performance around the propeller based on numerical method. Hydrofoil representing the blade form of propeller was of particular of interest. Two types of cavitation model were investigated with respect to the accuracy of the result and the effectiveness of the method. The results include the hydrodynamic characteristics of cavitation phenomenon like lift/drag variation with respect to the cavity extent. It was found that a high accuracy and low computational time is achieved when the cavitation model of Zwart-Gerber-Belamri is used. The interesting outcome of this study is that the results can be used as a good evaluation tool for high marine propeller performance.

  3. Estimation of the annual flow and stock of marine debris in South Korea for management purposes.

    PubMed

    Jang, Yong Chang; Lee, Jongmyoung; Hong, Sunwook; Mok, Jin Yong; Kim, Kyoung Shin; Lee, Yun Jeong; Choi, Hyun-Woo; Kang, Hongmook; Lee, Sukhui

    2014-09-15

    The annual flow and stock of marine debris in the Sea of Korea was estimated by summarizing previous survey results and integrating them with other relevant information to underpin the national marine debris management plan. The annual inflow of marine debris was estimated to be 91,195 tons [32,825 tons (36% of the total) from sources on land and 58,370 tons (64%) from ocean sources]. As of the end of 2012, the total stock of marine debris on all South Korean coasts (12,029 tons), the seabed (137,761 tons), and in the water column (2451 tons) was estimated to be 152,241 tons. In 2012, 42,595 tons of marine debris was collected from coasts, seabeds, and the water column. This is a very rare case study that estimated the amount of marine debris at a national level, the results of which provide essential information for the development of efficient marine debris management policies. PMID:25038983

  4. Inconsistency of Species Tree Methods under Gene Flow.

    PubMed

    Solís-Lemus, Claudia; Yang, Mengyao; Ané, Cécile

    2016-09-01

    Coalescent-based methods are now broadly used to infer evolutionary relationships between groups of organisms under the assumption that incomplete lineage sorting (ILS) is the only source of gene tree discordance. Many of these methods are known to consistently estimate the species tree when all their assumptions are met. Nonetheless, little work has been done to test the robustness of such methods to violations of their assumptions. Here, we study the performance of two of the most efficient coalescent-based methods, ASTRAL and NJst, in the presence of gene flow. Gene flow violates the assumption that ILS is the sole source of gene tree conflict. We find anomalous gene trees on three-taxon rooted trees and on four-taxon unrooted trees. These anomalous trees do not exist under ILS only, but appear because of gene flow. Our simulations show that species tree methods (and concatenation) may reconstruct the wrong evolutionary history, even from a very large number of well-reconstructed gene trees. In other words, species tree methods can be inconsistent under gene flow. Our results underline the need for methods like PhyloNet, to account simultaneously for ILS and gene flow in a unified framework. Although much slower, PhyloNet had better accuracy and remained consistent at high levels of gene flow. PMID:27151419

  5. Gene flow in Antarctic fishes: the role of oceanography and life history

    NASA Astrophysics Data System (ADS)

    Young, Emma; Rock, Jenny; Carvalho, Gary; Murphy, Eugene; Meredith, Michael; Hutchinson, Bill

    2010-05-01

    Marine organisms with pelagic larvae are generally assumed to experience high gene flow and low levels of population differentiation. However, variability in life history and environmental characteristics, in particular oceanographic flow fields, can significantly influence dispersal, and their relative effects are frequently unclear. Our research examines the influence of oceanographic and life history variability on gene flow in two species of Antarctic fish: Champsocephalus gunnari and Notothenia rossii. These species are broadly sympatric in their distribution, but differ in aspects of life history that are expected to strongly affect their dispersal capabilities. Our research has used two complementary techniques. Genetic analyses, specifically mtDNA and microsatellite markers, have been used to examine historic and contemporary gene flow and thus describe patterns of population differentiation at the circumpolar scale. These analyses have been compared with predicted larval transport from a global oceanographic model (OCCAM) combined with individual based particle tracking models. In using these complementary techniques, the relative influences of early life history and oceanographic variability can be elucidated. Here we present the key findings of our research, including evidence for inter-specific variation in mitochondrial gene flow at the circumpolar level and a limited degree of genetic structuring within the Scotia Sea.

  6. Antibiotic resistance genes detected in the marine sponge Petromica citrina from Brazilian coast.

    PubMed

    Laport, Marinella Silva; Pontes, Paula Veronesi Marinho; Dos Santos, Daniela Silva; Santos-Gandelman, Juliana de Fátima; Muricy, Guilherme; Bauwens, Mathieu; Giambiagi-deMarval, Marcia; George, Isabelle

    2016-01-01

    Although antibiotic-resistant pathogens pose a significant threat to human health, the environmental reservoirs of the resistance determinants are still poorly understood. This study reports the detection of resistance genes (ermB, mecA, mupA, qnrA, qnrB and tetL) to antibiotics among certain culturable and unculturable bacteria associated with the marine sponge Petromica citrina. The antimicrobial activities elicited by P. citrina and its associated bacteria are also described. The results indicate that the marine environment could play an important role in the development of antibiotic resistance and the dissemination of resistance genes among bacteria. PMID:27287338

  7. Calanoid Copepod Behavior in Thin Layer Shear Flows: Freshwater Versus Marine

    NASA Astrophysics Data System (ADS)

    Skipper, A. N.; Webster, D. R.; Yen, J.

    2015-11-01

    Marine copepods have been shown to behaviorally respond to vertical gradients of horizontal velocity and aggregate around thin layers. The current study addresses whether a freshwater copepod from an alpine lake demonstrates similar behavior response. Hesperodiaptomus shoshone is often the greatest biomass in alpine lakes and is the dominant zooplankton predator within its environment. The hypothesis is that H. shoshone responds to vertical gradients of horizontal velocity, which are associated with river outflows from alpine lakes, with fine-scale changes in swimming kinematics. The two calanoid copepods studied here, H. shoshone (freshwater) and Calanus finmarchicus(marine), are of similar size (2 - 4 mm), have similar morphologies, and utilize cruising as their primary swimming mode. The two animals differ not only in environment, but also in diet; H. shoshone is a carnivore, whereas C. finmarchicusis an herbivore. A laminar, planar jet (Bickley) was used in the laboratory to simulate a free shear flow. Particle image velocimetry (PIV) quantified the flow field. The marine species changed its swimming behavior significantly (increased swimming speed and turning frequency) and spent more time in the layer (40% vs. 70%) from control to treatment. In contrast, the freshwater species exhibited very few changes in either swimming behavior or residence time. Swimming kinematics and residence time results were also similar between males and females. Unlike the marine copepod, the results suggest the environmental flow structure is unimportant to the freshwater species.

  8. Application of community phylogenetic approaches to understand gene expression: differential exploration of venom gene space in predatory marine gastropods

    PubMed Central

    2014-01-01

    Background Predatory marine gastropods of the genus Conus exhibit substantial variation in venom composition both within and among species. Apart from mechanisms associated with extensive turnover of gene families and rapid evolution of genes that encode venom components (‘conotoxins’), the evolution of distinct conotoxin expression patterns is an additional source of variation that may drive interspecific differences in the utilization of species’ ‘venom gene space’. To determine the evolution of expression patterns of venom genes of Conus species, we evaluated the expression of A-superfamily conotoxin genes of a set of closely related Conus species by comparing recovered transcripts of A-superfamily genes that were previously identified from the genomes of these species. We modified community phylogenetics approaches to incorporate phylogenetic history and disparity of genes and their expression profiles to determine patterns of venom gene space utilization. Results Less than half of the A-superfamily gene repertoire of these species is expressed, and only a few orthologous genes are coexpressed among species. Species exhibit substantially distinct expression strategies, with some expressing sets of closely related loci (‘under-dispersed’ expression of available genes) while others express sets of more disparate genes (‘over-dispersed’ expression). In addition, expressed genes show higher dN/dS values than either unexpressed or ancestral genes; this implies that expression exposes genes to selection and facilitates rapid evolution of these genes. Few recent lineage-specific gene duplicates are expressed simultaneously, suggesting that expression divergence among redundant gene copies may be established shortly after gene duplication. Conclusions Our study demonstrates that venom gene space is explored differentially by Conus species, a process that effectively permits the independent and rapid evolution of venoms in these species. PMID:24903151

  9. Cyanobacterial assimilatory nitrate reductase gene diversity in coastal and oligotrophic marine environments.

    PubMed

    Jenkins, Bethany D; Zehr, Jonathan P; Gibson, Angela; Campbell, Lisa

    2006-12-01

    Cyanobacteria are important primary producers in many marine ecosystems and their abundances and growth rates depend on their ability to assimilate various nitrogen sources. To examine the diversity of nitrate-utilizing marine cyanobacteria, we developed PCR primers specific for cyanobacterial assimilatory nitrate reductase (narB) genes. We obtained amplification products from diverse strains of cultivated cyanobacteria and from several marine environments. Phylogenetic trees constructed with the narB gene are congruent with those based on ribosomal RNA genes and RNA polymerase genes. Analysis of sequence library data from coastal and oligotrophic marine environments shows distinct groups of Synechococcus sp. in each environment; some of which are represented by sequences from cultivated organisms and others that are unrelated to known sequences and likely represent novel phylogenetic groups. We observed spatial differences in the distribution of sequences between two sites in Monterey Bay and differences in the vertical distribution of sequence types at the Hawai'i Ocean Time-series Station ALOHA, suggesting that nitrogen assimilation in Synechococcus living in different ecological niches can be followed with the nitrate reductase gene. PMID:17107550

  10. Current knowledge of gene flow in plants: implications for transgene flow.

    PubMed Central

    Ellstrand, Norman C

    2003-01-01

    Plant evolutionary biologists' view of gene flow and hybridization has undergone a revolution. Twenty-five years ago, both were considered rare and largely inconsequential. Now gene flow and hybridization are known to be idiosyncratic, varying with the specific populations involved. Gene flow typically occurs at evolutionarily significant rates and at significant distances. Spontaneous hybridization occasionally has important applied consequences, such as stimulating the evolution of more aggressive invasives and increasing the extinction risk for rare species. The same problems have occurred for spontaneous hybridization between crops and their wild relatives. These new data have implications for transgenic crops: (i) for most crops, gene flow can act to introduce engineered genes into wild populations; (ii) depending on the specific engineered gene(s) and populations involved, gene flow may have the same negative impacts as those observed for traditionally improved crops; (iii) gene flow's idiosyncratic nature may frustrate management and monitoring attempts; and (iv) intercrop transgene flow, although rarely discussed, is equally worthy of study. PMID:12831483

  11. Application of alkaline elution, Fast Micromethod and flow cytometry in detection of marine contamination.

    PubMed

    Bihari, Nevenka; Hamer, Bojan; Jaksić, Zeljko; Fafandel, Maja; Micić, Milena; Batel, Renato

    2002-06-01

    DNA damage is an inescapable aspect of life in the biosphere. The presented investigations were an attempt to examine the response of a DNA damage as a biomarker of environmental quality in the mussels Mytilus galloprovincialis sampled at differently contaminated areas of Istrian coast, Northern Adriatic. The investigations were performed in order to get information about the genotoxic risk for marine organisms exposed to mixed environmental pollution, as well as the information about the presence of unknown mixture of genotoxic contaminants in the marine environment. Types of DNA damage detected are alkali-labile sites and single-strand breaks measured by Fast Micromethod, interstrand cross-links and DNA protein cross-links by alkaline filter elution and cell cycle disturbation by flow cytometry. The applicability of all three methods for marine quality control is discussed. PMID:12064444

  12. Interior flow and near-nozzle spray development in a marine-engine diesel fuel injector

    NASA Astrophysics Data System (ADS)

    Hult, J.; Simmank, P.; Matlok, S.; Mayer, S.; Falgout, Z.; Linne, M.

    2016-04-01

    A consolidated effort at optically characterising flow patterns, in-nozzle cavitation, and near-nozzle jet structure of a marine diesel fuel injector is presented. A combination of several optical techniques was employed to fully transparent injector models, compound metal-glass and full metal injectors. They were all based on a common real-scale dual nozzle hole geometry for a marine two-stroke diesel engine. In a stationary flow rig, flow velocities in the sac-volume and nozzle holes were measured using PIV, and in-nozzle cavitation visualized using high-resolution shadowgraphs. The effect of varying cavitation number was studied and results compared to CFD predictions. In-nozzle cavitation and near-nozzle jet structure during transient operation were visualized simultaneously, using high-speed imaging in an atmospheric pressure spray rig. Near-nozzle spray formation was investigated using ballistic imaging. Finally, the injector geometry was tested on a full-scale marine diesel engine, where the dynamics of near-nozzle jet development was visualized using high-speed shadowgraphy. The range of studies focused on a single common geometry allows a comprehensive survey of phenomena ranging from first inception of cavitation under well-controlled flow conditions to fuel jet structure at real engine conditions.

  13. Novel aromatic ring-hydroxylating dioxygenase genes from coastal marine sediments of Patagonia

    PubMed Central

    Lozada, Mariana; Riva Mercadal, Juan P; Guerrero, Leandro D; Di Marzio, Walter D; Ferrero, Marcela A; Dionisi, Hebe M

    2008-01-01

    Background Polycyclic aromatic hydrocarbons (PAHs), widespread pollutants in the marine environment, can produce adverse effects in marine organisms and can be transferred to humans through seafood. Our knowledge of PAH-degrading bacterial populations in the marine environment is still very limited, and mainly originates from studies of cultured bacteria. In this work, genes coding catabolic enzymes from PAH-biodegradation pathways were characterized in coastal sediments of Patagonia with different levels of PAH contamination. Results Genes encoding for the catalytic alpha subunit of aromatic ring-hydroxylating dioxygenases (ARHDs) were amplified from intertidal sediment samples using two different primer sets. Products were cloned and screened by restriction fragment length polymorphism analysis. Clones representing each restriction pattern were selected in each library for sequencing. A total of 500 clones were screened in 9 gene libraries, and 193 clones were sequenced. Libraries contained one to five different ARHD gene types, and this number was correlated with the number of PAHs found in the samples above the quantification limit (r = 0.834, p < 0.05). Overall, eight different ARHD gene types were detected in the sediments. In five of them, their deduced amino acid sequences formed deeply rooted branches with previously described ARHD peptide sequences, exhibiting less than 70% identity to them. They contain consensus sequences of the Rieske type [2Fe-2S] cluster binding site, suggesting that these gene fragments encode for ARHDs. On the other hand, three gene types were closely related to previously described ARHDs: archetypical nahAc-like genes, phnAc-like genes as identified in Alcaligenes faecalis AFK2, and phnA1-like genes from marine PAH-degraders from the genus Cycloclasticus. Conclusion These results show the presence of hitherto unidentified ARHD genes in this sub-Antarctic marine environment exposed to anthropogenic contamination. This information

  14. DNA capture reveals transoceanic gene flow in endangered river sharks

    PubMed Central

    Li, Chenhong; Corrigan, Shannon; Yang, Lei; Straube, Nicolas; Harris, Mark; Hofreiter, Michael; White, William T.; Naylor, Gavin J. P.

    2015-01-01

    For over a hundred years, the “river sharks” of the genus Glyphis were only known from the type specimens of species that had been collected in the 19th century. They were widely considered extinct until populations of Glyphis-like sharks were rediscovered in remote regions of Borneo and Northern Australia at the end of the 20th century. However, the genetic affinities between the newly discovered Glyphis-like populations and the poorly preserved, original museum-type specimens have never been established. Here, we present the first (to our knowledge) fully resolved, complete phylogeny of Glyphis that includes both archival-type specimens and modern material. We used a sensitive DNA hybridization capture method to obtain complete mitochondrial genomes from all of our samples and show that three of the five described river shark species are probably conspecific and widely distributed in Southeast Asia. Furthermore we show that there has been recent gene flow between locations that are separated by large oceanic expanses. Our data strongly suggest marine dispersal in these species, overturning the widely held notion that river sharks are restricted to freshwater. It seems that species in the genus Glyphis are euryhaline with an ecology similar to the bull shark, in which adult individuals live in the ocean while the young grow up in river habitats with reduced predation pressure. Finally, we discovered a previously unidentified species within the genus Glyphis that is deeply divergent from all other lineages, underscoring the current lack of knowledge about the biodiversity and ecology of these mysterious sharks. PMID:26460025

  15. DNA capture reveals transoceanic gene flow in endangered river sharks.

    PubMed

    Li, Chenhong; Corrigan, Shannon; Yang, Lei; Straube, Nicolas; Harris, Mark; Hofreiter, Michael; White, William T; Naylor, Gavin J P

    2015-10-27

    For over a hundred years, the "river sharks" of the genus Glyphis were only known from the type specimens of species that had been collected in the 19th century. They were widely considered extinct until populations of Glyphis-like sharks were rediscovered in remote regions of Borneo and Northern Australia at the end of the 20th century. However, the genetic affinities between the newly discovered Glyphis-like populations and the poorly preserved, original museum-type specimens have never been established. Here, we present the first (to our knowledge) fully resolved, complete phylogeny of Glyphis that includes both archival-type specimens and modern material. We used a sensitive DNA hybridization capture method to obtain complete mitochondrial genomes from all of our samples and show that three of the five described river shark species are probably conspecific and widely distributed in Southeast Asia. Furthermore we show that there has been recent gene flow between locations that are separated by large oceanic expanses. Our data strongly suggest marine dispersal in these species, overturning the widely held notion that river sharks are restricted to freshwater. It seems that species in the genus Glyphis are euryhaline with an ecology similar to the bull shark, in which adult individuals live in the ocean while the young grow up in river habitats with reduced predation pressure. Finally, we discovered a previously unidentified species within the genus Glyphis that is deeply divergent from all other lineages, underscoring the current lack of knowledge about the biodiversity and ecology of these mysterious sharks. PMID:26460025

  16. Actinorhodopsins: proteorhodopsin-like gene sequences found predominantly in non-marine environments.

    PubMed

    Sharma, Adrian K; Zhaxybayeva, Olga; Papke, R Thane; Doolittle, W Ford

    2008-04-01

    Proteorhodopsins are light-energy-harvesting transmembrane proteins encoded by genes recently discovered in the surface waters of the world's oceans. Metagenomic data from the Global Ocean Sampling expedition (GOS) recovered 2674 proteorhodopsin-related sequences from 51 aquatic samples. Four of these samples were from non-marine environments, specifically, Lake Gatun within the Panama Canal, Delaware Bay and Chesapeake Bay and the Punta Cormorant Lagoon in Ecuador. Rhodopsins related to but phylogenetically distinct from most sequences designated proteorhodopsins were present at all four of these non-marine sites and comprised three different clades that were almost completely absent from marine samples. Phylogenomic analyses of genes adjacent to those encoding these novel rhodopsins suggest affiliation to the Actinobacteria, and hence we propose to name these divergent, non-marine rhodopsins 'actinorhodopsins'. Actinorhodopsins conserve the acidic amino acid residues critical for proton pumping and their genes lack genomic association with those encoding photo-sensory transducer proteins, thus supporting a putative ion pumping function. The ratio of recA and radA to rhodopsin genes in the different environment types sampled within the GOS indicates that rhodopsins of one type or another are abundant in microbial communities in freshwater, estuarine and lagoon ecosystems, supporting an important role for these photosystems in all aquatic environments influenced by sunlight. PMID:18218036

  17. Demographic history and gene flow during silkworm domestication

    PubMed Central

    2014-01-01

    Background Gene flow plays an important role in domestication history of domesticated species. However, little is known about the demographic history of domesticated silkworm involving gene flow with its wild relative. Results In this study, four model-based evolutionary scenarios to describe the demographic history of B. mori were hypothesized. Using Approximate Bayesian Computation method and DNA sequence data from 29 nuclear loci, we found that the gene flow at bottleneck model is the most likely scenario for silkworm domestication. The starting time of silkworm domestication was estimated to be approximate 7,500 years ago; the time of domestication termination was 3,984 years ago. Using coalescent simulation analysis, we also found that bi-directional gene flow occurred during silkworm domestication. Conclusions Estimates of silkworm domestication time are nearly consistent with the archeological evidence and our previous results. Importantly, we found that the bi-directional gene flow might occur during silkworm domestication. Our findings add a dimension to highlight the important role of gene flow in domestication of crops and animals. PMID:25123546

  18. Development of phoH as a Novel Signature Gene for Assessing Marine Phage Diversity▿

    PubMed Central

    Goldsmith, Dawn B.; Crosti, Giuseppe; Dwivedi, Bhakti; McDaniel, Lauren D.; Varsani, Arvind; Suttle, Curtis A.; Weinbauer, Markus G.; Sandaa, Ruth-Anne; Breitbart, Mya

    2011-01-01

    Phages play a key role in the marine environment by regulating the transfer of energy between trophic levels and influencing global carbon and nutrient cycles. The diversity of marine phage communities remains difficult to characterize because of the lack of a signature gene common to all phages. Recent studies have demonstrated the presence of host-derived auxiliary metabolic genes in phage genomes, such as those belonging to the Pho regulon, which regulates phosphate uptake and metabolism under low-phosphate conditions. Among the completely sequenced phage genomes in GenBank, this study identified Pho regulon genes in nearly 40% of the marine phage genomes, while only 4% of nonmarine phage genomes contained these genes. While several Pho regulon genes were identified, phoH was the most prevalent, appearing in 42 out of 602 completely sequenced phage genomes. Phylogenetic analysis demonstrated that phage phoH sequences formed a cluster distinct from those of their bacterial hosts. PCR primers designed to amplify a region of the phoH gene were used to determine the diversity of phage phoH sequences throughout a depth profile in the Sargasso Sea and at six locations worldwide. phoH was present at all sites examined, and a high diversity of phoH sequences was recovered. Most phoH sequences belonged to clusters without any cultured representatives. Each depth and geographic location had a distinct phoH composition, although most phoH clusters were recovered from multiple sites. Overall, phoH is an effective signature gene for examining phage diversity in the marine environment. PMID:21926220

  19. Development of phoH as a novel signature gene for assessing marine phage diversity.

    PubMed

    Goldsmith, Dawn B; Crosti, Giuseppe; Dwivedi, Bhakti; McDaniel, Lauren D; Varsani, Arvind; Suttle, Curtis A; Weinbauer, Markus G; Sandaa, Ruth-Anne; Breitbart, Mya

    2011-11-01

    Phages play a key role in the marine environment by regulating the transfer of energy between trophic levels and influencing global carbon and nutrient cycles. The diversity of marine phage communities remains difficult to characterize because of the lack of a signature gene common to all phages. Recent studies have demonstrated the presence of host-derived auxiliary metabolic genes in phage genomes, such as those belonging to the Pho regulon, which regulates phosphate uptake and metabolism under low-phosphate conditions. Among the completely sequenced phage genomes in GenBank, this study identified Pho regulon genes in nearly 40% of the marine phage genomes, while only 4% of nonmarine phage genomes contained these genes. While several Pho regulon genes were identified, phoH was the most prevalent, appearing in 42 out of 602 completely sequenced phage genomes. Phylogenetic analysis demonstrated that phage phoH sequences formed a cluster distinct from those of their bacterial hosts. PCR primers designed to amplify a region of the phoH gene were used to determine the diversity of phage phoH sequences throughout a depth profile in the Sargasso Sea and at six locations worldwide. phoH was present at all sites examined, and a high diversity of phoH sequences was recovered. Most phoH sequences belonged to clusters without any cultured representatives. Each depth and geographic location had a distinct phoH composition, although most phoH clusters were recovered from multiple sites. Overall, phoH is an effective signature gene for examining phage diversity in the marine environment. PMID:21926220

  20. A novel halotolerant xylanase from marine isolate Bacillus subtilis cho40: gene cloning and sequencing.

    PubMed

    Khandeparker, Rakhee; Verma, Preeti; Deobagkar, Deepti

    2011-10-01

    Although several xylanases have been studied, only few xylanases from marine micro-organisms have been reported. We report here a novel halotolerant xylanase from marine bacterium Bacillus subtilis cho40 isolated from Chorao island of mandovi estuary Goa, India. Extracellular xylanase was produced by using agricultural residue such as wheat bran as carbon source under solid-state fermentation (SSF). The optimal pH and temperature of xylanase were reported to be 6.0 and 60°C, respectively. Xyn40 was highly salt-tolerant, and showed highest activity at 0.5M NaCl. Xylanase activity was greatly induced (140%) when pre-incubated with 0.5M NaCl for 4h. The xylanase gene, xyn40, from marine bacterium B. subtilis cho40 was cloned, and expressed in Escherichia coli. The xylanase gene was 645 bp long and had a 215 amino acid ORF protein with a molecular mass of 22.9 kDa. It had all features of xylanase enzyme and showed homology to xylanases reported from B. subtilis. It differs from the earlier reported xylanase sequences by the presence of more serine residues compared to threonine and also by the presence of polar (hydrophilic) amino acids in higher abundance (61%) than non-polar amino acids (39%). The novel xylanase, reported in this study is a halotolerant enzyme from marine isolate and can play a very important role in bioethanol production from marine seaweeds. PMID:21890005

  1. Speciation with gene flow on Lord Howe Island

    PubMed Central

    Papadopulos, Alexander S. T.; Baker, William J.; Crayn, Darren; Butlin, Roger K.; Kynast, Ralf G.; Hutton, Ian; Savolainen, Vincent

    2011-01-01

    Understanding the processes underlying the origin of species is a fundamental goal of biology. It is widely accepted that speciation requires an interruption of gene flow between populations: ongoing gene exchange is considered a major hindrance to population divergence and, ultimately, to the evolution of new species. Where a geographic barrier to reproductive isolation is lacking, a biological mechanism for speciation is required to counterbalance the homogenizing effect of gene flow. Speciation with initially strong gene flow is thought to be extremely rare, and few convincing empirical examples have been published. However, using phylogenetic, karyological, and ecological data for the flora of a minute oceanic island (Lord Howe Island, LHI), we demonstrate that speciation with gene flow may, in fact, be frequent in some instances and could account for one in five of the endemic plant species of LHI. We present 11 potential instances of species divergence with gene flow, including an in situ radiation of five species of Coprosma (Rubiaceae, the coffee family). These results, together with the speciation of Howea palms on LHI, challenge current views on the origin of species diversity. PMID:21730151

  2. Compact test apparatus for evaluation of flow erosion of marine coatings

    NASA Astrophysics Data System (ADS)

    Debowski, M. A.; Quintana, R.; Lee, H. P.

    2015-10-01

    An apparatus designed and manufactured for evaluation of flow erosion of coatings or layers is presented in this paper. The setup was primarily designed for coatings intended to perform in dynamic marine environments but can be also used for evaluation using fresh water. The concept is based on an in-line flow test cell and modular design allowing good flexibility of varying testing parameters. The flow rate that can be achieved depends on the flow cell geometry and can reach 28 km/h (15 kn) with the presented setup. Temperature may be adjusted between 15 and 35 °C. Particle and metal ion filters are parts of this setup. The dimensions of the apparatus including all components do not exceed 2 m × 2 m × 2 m. The use of the apparatus is illustrated with the results of evaluation of self-polishing anti-fouling coatings and model, silicon wafer grafted layers.

  3. Compact test apparatus for evaluation of flow erosion of marine coatings.

    PubMed

    Dębowski, M A; Quintana, R; Lee, H P

    2015-10-01

    An apparatus designed and manufactured for evaluation of flow erosion of coatings or layers is presented in this paper. The setup was primarily designed for coatings intended to perform in dynamic marine environments but can be also used for evaluation using fresh water. The concept is based on an in-line flow test cell and modular design allowing good flexibility of varying testing parameters. The flow rate that can be achieved depends on the flow cell geometry and can reach 28 km/h (15 kn) with the presented setup. Temperature may be adjusted between 15 and 35 °C. Particle and metal ion filters are parts of this setup. The dimensions of the apparatus including all components do not exceed 2 m × 2 m × 2 m. The use of the apparatus is illustrated with the results of evaluation of self-polishing anti-fouling coatings and model, silicon wafer grafted layers. PMID:26520992

  4. Trends in International Flow of Holstein Genes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Holstein genes spread from Europe to much of the world through live cattle more than 100 yr ago. By the advent of artificial insemination, selection emphasis in North America had led to a specialized dairy strain that was in demand internationally. From 1995, genetic evaluations through Interbull mo...

  5. Response of marine bacterioplankton pH homeostasis gene expression to elevated CO2

    NASA Astrophysics Data System (ADS)

    Bunse, Carina; Lundin, Daniel; Karlsson, Christofer M. G.; Akram, Neelam; Vila-Costa, Maria; Palovaara, Joakim; Svensson, Lovisa; Holmfeldt, Karin; González, José M.; Calvo, Eva; Pelejero, Carles; Marrasé, Cèlia; Dopson, Mark; Gasol, Josep M.; Pinhassi, Jarone

    2016-05-01

    Human-induced ocean acidification impacts marine life. Marine bacteria are major drivers of biogeochemical nutrient cycles and energy fluxes; hence, understanding their performance under projected climate change scenarios is crucial for assessing ecosystem functioning. Whereas genetic and physiological responses of phytoplankton to ocean acidification are being disentangled, corresponding functional responses of bacterioplankton to pH reduction from elevated CO2 are essentially unknown. Here we show, from metatranscriptome analyses of a phytoplankton bloom mesocosm experiment, that marine bacteria responded to lowered pH by enhancing the expression of genes encoding proton pumps, such as respiration complexes, proteorhodopsin and membrane transporters. Moreover, taxonomic transcript analysis showed that distinct bacterial groups expressed different pH homeostasis genes in response to elevated CO2. These responses were substantial for numerous pH homeostasis genes under low-chlorophyll conditions (chlorophyll a <2.5 μg l-1) however, the changes in gene expression under high-chlorophyll conditions (chlorophyll a >20 μg l-1) were low. Given that proton expulsion through pH homeostasis mechanisms is energetically costly, these findings suggest that bacterioplankton adaptation to ocean acidification could have long-term effects on the economy of ocean ecosystems.

  6. Isolation and expression of two aquaporin-encoding genes from the marine phanerogam Posidonia oceanica.

    PubMed

    Maestrini, Pierluigi; Giordani, Tommaso; Lunardi, Andrea; Cavallini, Andrea; Natali, Lucia

    2004-12-01

    Seagrasses such as Posidonia oceanica (L.) Delile are marine phanerogams, widespread in various seas, where they form large prairies representing dynamic substrates exceeding the area of the sediment surface several times over and allowing settlement of epiphyte organisms. Studying mechanisms involved in water transport in marine plants, we isolated two aquaporin-encoding genes, PoPIP1;1 and PoTIP1;1, showing high similarity to plasma membrane- and tonoplast-intrinsic protein-encoding genes, respectively. PoPIP1;1 is unique in the genome of P. oceanica, while PoTIP1;1 belongs to an aquaporin subfamily of at least four members. PoPIP1;1 and PoTIP1;1 encode functional proteins, as indicated by expression experiments in Xenopus oocytes. Both genes are constitutively expressed in the leaves, with higher levels of transcripts in young than in differentiated leaf tissues. Variations of salt concentration in aquarium determined different PoPIP1;1 and PoTIP1;1 transcript accumulation, indicating the existence of adaptation mechanisms related to gene expression also in marine plants, i.e. adapted to very high salt concentrations. Hyposalinity induced lower levels of PIP1 transcripts, while hypersalinity determined more PIP1 transcripts than normal salinity. TIP1 transcripts increased in response to both hypo- and hypersalinity after 2 days of treatment and went back to control levels after 5 d. PMID:15653802

  7. Historical divergence and gene flow in the genus Zea.

    PubMed

    Ross-Ibarra, Jeffrey; Tenaillon, Maud; Gaut, Brandon S

    2009-04-01

    Gene flow plays a fundamental role in plant evolutionary history, yet its role in population divergence--and ultimately speciation--remains poorly understood. We investigated gene flow and the modalities of divergence in the domesticated Zea mays ssp. mays and three wild Zea taxa using sequence polymorphism data from 26 nuclear loci. We described diversity across loci and assessed evidence for adaptive and purifying selection at nonsynonymous sites. For each of three divergence events in the history of these taxa, we used approximate Bayesian simulation to estimate population sizes and divergence times and explicitly compare among alternative models of divergence. Our estimates of divergence times are surprisingly consistent with previous data from other markers and suggest rapid diversification of lineages within Zea in the last approximately 150,000 years. We found widespread evidence of historical gene flow, including evidence for divergence in the face of gene flow. We speculate that cultivated maize may serve as a bridge for gene flow among otherwise allopatric wild taxa. PMID:19153259

  8. Historical Divergence and Gene Flow in the Genus Zea

    PubMed Central

    Ross-Ibarra, Jeffrey; Tenaillon, Maud; Gaut, Brandon S.

    2009-01-01

    Gene flow plays a fundamental role in plant evolutionary history, yet its role in population divergence—and ultimately speciation—remains poorly understood. We investigated gene flow and the modalities of divergence in the domesticate Zea mays ssp. mays and three wild Zea taxa using sequence polymorphism data from 26 nuclear loci. We described diversity across loci and assessed evidence for adaptive and purifying selection at nonsynonymous sites. For each of three divergence events in the history of these taxa, we used approximate Bayesian simulation to estimate population sizes and divergence times and explicitly compare among alternative models of divergence. Our estimates of divergence times are surprisingly consistent with previous data from other markers and suggest rapid diversification of lineages within Zea in the last ∼150,000 years. We found widespread evidence of historical gene flow, including evidence for divergence in the face of gene flow. We speculate that cultivated maize may serve as a bridge for gene flow among otherwise allopatric wild taxa. PMID:19153259

  9. Analyzing gene expression from marine microbial communities using environmental transcriptomics.

    PubMed

    Poretsky, Rachel S; Gifford, Scott; Rinta-Kanto, Johanna; Vila-Costa, Maria; Moran, Mary Ann

    2009-01-01

    Analogous to metagenomics, environmental transcriptomics (metatranscriptomics) retrieves and sequences environmental mRNAs from a microbial assemblage without prior knowledge of what genes the community might be expressing. Thus it provides the most unbiased perspective on community gene expression in situ. Environmental transcriptomics protocols are technically difficult since prokaryotic mRNAs generally lack the poly(A) tails that make isolation of eukaryotic messages relatively straightforward (1) and because of the relatively short half lives of mRNAs (2). In addition, mRNAs are much less abundant than rRNAs in total RNA extracts, thus an rRNA background often overwhelms mRNA signals. However, techniques for overcoming some of these difficulties have recently been developed. A procedure for analyzing environmental transcriptomes by creating clone libraries using random primers to reverse-transcribe and amplify environmental mRNAs was recently described was successful in two different natural environments, but results were biased by selection of the random primers used to initiate cDNA synthesis (3). Advances in linear amplification of mRNA obviate the need for random primers in the amplification step and make it possible to use less starting material decreasing the collection and processing time of samples and thereby minimizing RNA degradation (4). In vitro transcription methods for amplifying mRNA involve polyadenylating the mRNA and incorporating a T7 promoter onto the 3' end of the transcript. Amplified RNA (aRNA) can then be converted to double stranded cDNA using random hexamers and directly sequenced by pyrosequencing (5). A first use of this method at Station ALOHA demonstrated its utility for characterizing microbial community gene expression (6). PMID:19229184

  10. Numerical predictions of the turbulent cavitating flow around a marine propeller and an axial turbine

    NASA Astrophysics Data System (ADS)

    Morgut, M.; Jošt, D.; Nobile, E.; Škerlavaj, A.

    2015-12-01

    The numerical predictions of cavitating flow around a marine propeller working in non-uniform inflow and an axial turbine are presented. The cavitating flow is modelled using the homogeneous (mixture) model. Time-dependent simulations are performed for the marine propeller case using OpenFOAM. Three calibrated mass transfer models are alternatively used to model the mass transfer rate due to cavitation and the two-equation SST (Shear Stress Transport) turbulence model is employed to close the system of the governing equations. The predictions of the cavitating flow in an axial turbine are carried out with ANSYS-CFX, where only the native mass transfer model with tuned parameters is used. Steady-state simulations are performed in combination with the SST turbulence model, while time-dependent results are obtained with the more advanced SAS (Scale Adaptive Simulation) SST model. The numerical results agree well with the available experimental measurements, and the simulations performed with the three different calibrated mass transfer models are close to each other for the propeller flow. Regarding the axial turbine the effect of the cavitation on the machine efficiency is well reproduced only by the time dependent simulations.

  11. Discrepancies in the Estimation of Gene Flow in Partula

    PubMed Central

    Johnson, M. S.; Clarke, B.; Murray, J.

    1988-01-01

    Methods for estimating gene flow (Nm) from genetic data should provide important insights into the dynamics of natural populations. If they are to be used with confidence, however, the methods must be shown to produce valid results. Estimates of Nm have been obtained for the snails Partula taeniata and Partula suturalis, based on F(ST) and on the frequencies of private alleles, p(1). Jackknifing was used to reduce the bias of estimates and to obtain confidence limits. The estimates derived from F(ST) are consistent with the low vagility of snails, and with direct field studies of gene flow in P. taeniata. In contrast, the estimates derived from p(1) were up to seven times as large, less precise and less consistent. Although the underlying causes of these discrepancies are not clear, the results suggest that F(ST) is the more reliable indirect estimator of gene flow, at least for Partula. PMID:17246477

  12. Convergent evolution of marine mammals is associated with distinct substitutions in common genes

    PubMed Central

    Zhou, Xuming; Seim, Inge; Gladyshev, Vadim N.

    2015-01-01

    Phenotypic convergence is thought to be driven by parallel substitutions coupled with natural selection at the sequence level. Multiple independent evolutionary transitions of mammals to an aquatic environment offer an opportunity to test this thesis. Here, whole genome alignment of coding sequences identified widespread parallel amino acid substitutions in marine mammals; however, the majority of these changes were not unique to these animals. Conversely, we report that candidate aquatic adaptation genes, identified by signatures of likelihood convergence and/or elevated ratio of nonsynonymous to synonymous nucleotide substitution rate, are characterized by very few parallel substitutions and exhibit distinct sequence changes in each group. Moreover, no significant positive correlation was found between likelihood convergence and positive selection in all three marine lineages. These results suggest that convergence in protein coding genes associated with aquatic lifestyle is mainly characterized by independent substitutions and relaxed negative selection. PMID:26549748

  13. Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears

    PubMed Central

    Cahill, James A; Stirling, Ian; Kistler, Logan; Salamzade, Rauf; Ersmark, Erik; Fulton, Tara L; Stiller, Mathias; Green, Richard E; Shapiro, Beth

    2015-01-01

    Polar bears are an arctic, marine adapted species that is closely related to brown bears. Genome analyses have shown that polar bears are distinct and genetically homogeneous in comparison to brown bears. However, these analyses have also revealed a remarkable episode of polar bear gene flow into the population of brown bears that colonized the Admiralty, Baranof and Chichagof islands (ABC islands) of Alaska. Here, we present an analysis of data from a large panel of polar bear and brown bear genomes that includes brown bears from the ABC islands, the Alaskan mainland and Europe. Our results provide clear evidence that gene flow between the two species had a geographically wide impact, with polar bear DNA found within the genomes of brown bears living both on the ABC islands and in the Alaskan mainland. Intriguingly, while brown bear genomes contain up to 8.8% polar bear ancestry, polar bear genomes appear to be devoid of brown bear ancestry, suggesting the presence of a barrier to gene flow in that direction. PMID:25490862

  14. Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears.

    PubMed

    Cahill, James A; Stirling, Ian; Kistler, Logan; Salamzade, Rauf; Ersmark, Erik; Fulton, Tara L; Stiller, Mathias; Green, Richard E; Shapiro, Beth

    2015-03-01

    Polar bears are an arctic, marine adapted species that is closely related to brown bears. Genome analyses have shown that polar bears are distinct and genetically homogeneous in comparison to brown bears. However, these analyses have also revealed a remarkable episode of polar bear gene flow into the population of brown bears that colonized the Admiralty, Baranof and Chichagof islands (ABC islands) of Alaska. Here, we present an analysis of data from a large panel of polar bear and brown bear genomes that includes brown bears from the ABC islands, the Alaskan mainland and Europe. Our results provide clear evidence that gene flow between the two species had a geographically wide impact, with polar bear DNA found within the genomes of brown bears living both on the ABC islands and in the Alaskan mainland. Intriguingly, while brown bear genomes contain up to 8.8% polar bear ancestry, polar bear genomes appear to be devoid of brown bear ancestry, suggesting the presence of a barrier to gene flow in that direction. PMID:25490862

  15. A CRISPR/Cas9 system adapted for gene editing in marine algae

    PubMed Central

    Nymark, Marianne; Sharma, Amit Kumar; Sparstad, Torfinn; Bones, Atle M.; Winge, Per

    2016-01-01

    Here we report that the CRISPR/Cas9 technology can be used to efficiently generate stable targeted gene mutations in microalgae, using the marine diatom Phaeodactylum tricornutum as a model species. Our vector design opens for rapid and easy adaption of the construct to the target chosen. To screen for CRISPR/Cas9 mutants we employed high resolution melting based PCR assays, mutants were confirmed by sequencing and further validated by functional analyses. PMID:27108533

  16. A CRISPR/Cas9 system adapted for gene editing in marine algae.

    PubMed

    Nymark, Marianne; Sharma, Amit Kumar; Sparstad, Torfinn; Bones, Atle M; Winge, Per

    2016-01-01

    Here we report that the CRISPR/Cas9 technology can be used to efficiently generate stable targeted gene mutations in microalgae, using the marine diatom Phaeodactylum tricornutum as a model species. Our vector design opens for rapid and easy adaption of the construct to the target chosen. To screen for CRISPR/Cas9 mutants we employed high resolution melting based PCR assays, mutants were confirmed by sequencing and further validated by functional analyses. PMID:27108533

  17. Long Serial Analysis of Gene Expression for Gene Discovery and Transcriptome Profiling in the Widespread Marine Coccolithophore Emiliania huxleyi†

    PubMed Central

    Dyhrman, Sonya T.; Haley, Sheean T.; Birkeland, Shanda R.; Wurch, Louie L.; Cipriano, Michael J.; McArthur, Andrew G.

    2006-01-01

    The abundant and widespread coccolithophore Emiliania huxleyi plays an important role in mediating CO2 exchange between the ocean and the atmosphere through its impact on marine photosynthesis and calcification. Here, we use long serial analysis of gene expression (SAGE) to identify E. huxleyi genes responsive to nitrogen (N) or phosphorus (P) starvation. Long SAGE is an elegant approach for examining quantitative and comprehensive gene expression patterns without a priori knowledge of gene sequences via the detection of 21-bp nucleotide sequence tags. E. huxleyi appears to have a robust transcriptional-level response to macronutrient deficiency, with 42 tags uniquely present or up-regulated twofold or greater in the N-starved library and 128 tags uniquely present or up-regulated twofold or greater in the P-starved library. The expression patterns of several tags were validated with reverse transcriptase PCR. Roughly 48% of these differentially expressed tags could be mapped to publicly available genomic or expressed sequence tag (EST) sequence data. For example, in the P-starved library a number of the tags mapped to genes with a role in P scavenging, including a putative phosphate-repressible permease and a putative polyphosphate synthetase. In short, the long SAGE analyses have (i) identified many new differentially regulated gene sequences, (ii) assigned regulation data to EST sequences with no database homology and unknown function, and (iii) highlighted previously uncharacterized aspects of E. huxleyi N and P physiology. To this end, our long SAGE libraries provide a new public resource for gene discovery and transcriptional analysis in this biogeochemically important marine organism. PMID:16391051

  18. Consequences of recurrent gene flow from crops to wild relatives.

    PubMed

    Haygood, Ralph; Ives, Anthony R; Andow, David A

    2003-09-22

    Concern about gene flow from crops to wild relatives has become widespread with the increasing cultivation of transgenic crops. Possible consequences of such gene flow include genetic assimilation, wherein crop genes replace wild ones, and demographic swamping, wherein hybrids are less fertile than their wild parents, and wild populations shrink. Using mathematical models of a wild population recurrently receiving pollen from a genetically fixed crop, we find that the conditions for genetic assimilation are not stringent, and progress towards replacement can be fast, even for disfavoured crop genes. Demographic swamping and genetic drift relax the conditions for genetic assimilation and speed progress towards replacement. Genetic assimilation can involve thresholds and hysteresis, such that a small increase in immigration can lead to fixation of a disfavoured crop gene that had been maintained at a moderate frequency, even if the increase in immigration is cancelled before the gene fixes. Demographic swamping can give rise to 'migrational meltdown', such that a small increase in immigration can lead to not only fixation of a disfavoured crop gene but also drastic shrinkage of the wild population. These findings suggest that the spread of crop genes in wild populations should be monitored more closely. PMID:14561300

  19. Consequences of recurrent gene flow from crops to wild relatives.

    PubMed Central

    Haygood, Ralph; Ives, Anthony R; Andow, David A

    2003-01-01

    Concern about gene flow from crops to wild relatives has become widespread with the increasing cultivation of transgenic crops. Possible consequences of such gene flow include genetic assimilation, wherein crop genes replace wild ones, and demographic swamping, wherein hybrids are less fertile than their wild parents, and wild populations shrink. Using mathematical models of a wild population recurrently receiving pollen from a genetically fixed crop, we find that the conditions for genetic assimilation are not stringent, and progress towards replacement can be fast, even for disfavoured crop genes. Demographic swamping and genetic drift relax the conditions for genetic assimilation and speed progress towards replacement. Genetic assimilation can involve thresholds and hysteresis, such that a small increase in immigration can lead to fixation of a disfavoured crop gene that had been maintained at a moderate frequency, even if the increase in immigration is cancelled before the gene fixes. Demographic swamping can give rise to 'migrational meltdown', such that a small increase in immigration can lead to not only fixation of a disfavoured crop gene but also drastic shrinkage of the wild population. These findings suggest that the spread of crop genes in wild populations should be monitored more closely. PMID:14561300

  20. Speciation with gene flow and the genetics of habitat transitions.

    PubMed

    Cristescu, Melania E; Constantin, Anna; Bock, Dan G; Cáceres, Carla E; Crease, Teresa J

    2012-03-01

    Whether speciation can advance to completion in the face of initially high levels of gene flow is a very controversial topic in evolutionary biology. Extensive gene exchange is generally considered to homogenize populations and counteract divergence. Moreover, the role of introgressive hybridization in evolution remains largely unexplored in animals, particularly in freshwater zooplankton in which allopatric speciation is considered to be the norm. Our work investigates the genetic structure of two young ecological species: the pond species, Daphnia pulex and the lake species, Daphnia pulicaria. Phylogenetic and population genetics analyses were conducted on mitochondrial NADH dehydrogenase 5 (ND5) gene, the nuclear Lactate dehydrogenase (Ldh) gene and 21 nuclear microsatellite markers in 416 individuals from habitats with various degrees of permanence. The strong and consistent phylogenetic discordance between nuclear and mitochondrial markers suggests a complex evolutionary history of multiple independent habitat transition events that involved hybridization and introgression between lake and pond Daphnia. On the other hand, the low level of contemporary gene flow between adjacent populations indicates the presence of effective habitat isolating barriers. The Daphnia system provides strong evidence for a divergence-with-gene flow speciation model that involves multiple habitat transition events. PMID:22269101

  1. Correlating carbon monoxide oxidation with cox genes in the abundant Marine Roseobacter Clade

    PubMed Central

    Cunliffe, Michael

    2011-01-01

    The Marine Roseobacter Clade (MRC) is a numerically and biogeochemically significant component of the bacterioplankton. Annotation of multiple MRC genomes has revealed that an abundance of carbon monoxide dehydrogenase (CODH) cox genes are present, subsequently implying a role for the MRC in marine CO cycling. The cox genes fall into two distinct forms based on sequence analysis of the coxL gene; forms I and II. The two forms are unevenly distributed across the MRC genomes. Most (18/29) of the MRC genomes contain only the putative form II coxL gene. Only 10 of the 29 MRC genomes analysed have both the putative form II and the definitive form I coxL. None have only the form I coxL. Genes previously shown to be required for post-translational maturation of the form I CODH enzyme are absent from the MRC genomes containing only form II. Subsequent analyses of a subset of nine MRC strains revealed that only MRC strains with both coxL forms are able to oxidise CO. PMID:21068776

  2. A Gene Island with Two Possible Configurations Is Involved in Chromatic Acclimation in Marine Synechococcus

    PubMed Central

    Humily, Florian; Partensky, Frédéric; Six, Christophe; Farrant, Gregory K.; Ratin, Morgane; Marie, Dominique; Garczarek, Laurence

    2013-01-01

    Synechococcus, the second most abundant oxygenic phototroph in the marine environment, harbors the largest pigment diversity known within a single genus of cyanobacteria, allowing it to exploit a wide range of light niches. Some strains are capable of Type IV chromatic acclimation (CA4), a process by which cells can match the phycobilin content of their phycobilisomes to the ambient light quality. Here, we performed extensive genomic comparisons to explore the diversity of this process within the marine Synechococcus radiation. A specific gene island was identified in all CA4-performing strains, containing two genes (fciA/b) coding for possible transcriptional regulators and one gene coding for a phycobilin lyase. However, two distinct configurations of this cluster were observed, depending on the lineage. CA4-A islands contain the mpeZ gene, encoding a recently characterized phycoerythrobilin lyase-isomerase, and a third, small, possible regulator called fciC. In CA4-B islands, the lyase gene encodes an uncharacterized relative of MpeZ, called MpeW. While mpeZ is expressed more in blue light than green light, this is the reverse for mpeW, although only small phenotypic differences were found among chromatic acclimaters possessing either CA4 island type. This study provides novel insights into understanding both diversity and evolution of the CA4 process. PMID:24391958

  3. Experimental simulation of hydrodynamic flow noises in an autonomous marine laboratory

    NASA Astrophysics Data System (ADS)

    Kudashev, E. B.; Kolyshnitsyn, V. A.; Marshov, V. P.; Tkachenko, V. M.; Tsvetkov, A. M.

    2013-03-01

    The spectral characteristics of turbulent pressure pulsations arising from the flow around an autonomous marine laboratory have been measured. The autonomous marine laboratory is an upgraded Dolphin buoyant device, equipped with modern digital facilities for autonomous recording, which extends the frequency range of the signals under study up to 50-60 kHz. The power spectra and cross spectra of turbulent pressure pulsations have been measured at different points of the measuring section by point pressure transducers 1.3 or 20 mm in diameter at a speed of the autonomous marine laboratory of 8-22 m/s. The measurements have revealed unexpected behavioral features of the spectra (their inflection points) at high frequencies. An analysis is performed to explain these features. In particular, it is shown that the correction function based on the more complex cross spectrum model (in comparison with the Corcos cross spectrum model) developed by Smol'yakov in 2006 predicts a monotonic (without inflection points) decrease in the spectral levels at high frequencies for reconstructed (corrected) spectra.

  4. Phosphate transporters in marine phytoplankton and their viruses: cross-domain commonalities in viral-host gene exchanges.

    PubMed

    Monier, Adam; Welsh, Rory M; Gentemann, Chelle; Weinstock, George; Sodergren, Erica; Armbrust, E Virginia; Eisen, Jonathan A; Worden, Alexandra Z

    2012-01-01

    Phosphate (PO(4)) is an important limiting nutrient in marine environments. Marine cyanobacteria scavenge PO(4) using the high-affinity periplasmic phosphate binding protein PstS. The pstS gene has recently been identified in genomes of cyanobacterial viruses as well. Here, we analyse genes encoding transporters in genomes from viruses that infect eukaryotic phytoplankton. We identified inorganic PO(4) transporter-encoding genes from the PHO4 superfamily in several virus genomes, along with other transporter-encoding genes. Homologues of the viral pho4 genes were also identified in genome sequences from the genera that these viruses infect. Genome sequences were available from host genera of all the phytoplankton viruses analysed except the host genus Bathycoccus. Pho4 was recovered from Bathycoccus by sequencing a targeted metagenome from an uncultured Atlantic Ocean population. Phylogenetic reconstruction showed that pho4 genes from pelagophytes, haptophytes and infecting viruses were more closely related to homologues in prasinophytes than to those in what, at the species level, are considered to be closer relatives (e.g. diatoms). We also identified PHO4 superfamily members in ocean metagenomes, including new metagenomes from the Pacific Ocean. The environmental sequences grouped with pelagophytes, haptophytes, prasinophytes and viruses as well as bacteria. The analyses suggest that multiple independent pho4 gene transfer events have occurred between marine viruses and both eukaryotic and bacterial hosts. Additionally, pho4 genes were identified in available genomes from viruses that infect marine eukaryotes but not those that infect terrestrial hosts. Commonalities in marine host-virus gene exchanges indicate that manipulation of host-PO(4) uptake is an important adaptation for viral proliferation in marine systems. Our findings suggest that PO(4) -availability may not serve as a simple bottom-up control of marine phytoplankton. PMID:21914098

  5. Phosphate transporters in marine phytoplankton and their viruses: cross-domain commonalities in viral-host gene exchanges

    PubMed Central

    Monier, Adam; Welsh, Rory M; Gentemann, Chelle; Weinstock, George; Sodergren, Erica; Armbrust, E Virginia; Eisen, Jonathan A; Worden, Alexandra Z

    2012-01-01

    Phosphate (PO4) is an important limiting nutrient in marine environments. Marine cyanobacteria scavenge PO4 using the high-affinity periplasmic phosphate binding protein PstS. The pstS gene has recently been identified in genomes of cyanobacterial viruses as well. Here, we analyse genes encoding transporters in genomes from viruses that infect eukaryotic phytoplankton. We identified inorganic PO4 transporter-encoding genes from the PHO4 superfamily in several virus genomes, along with other transporter-encoding genes. Homologues of the viral pho4 genes were also identified in genome sequences from the genera that these viruses infect. Genome sequences were available from host genera of all the phytoplankton viruses analysed except the host genus Bathycoccus. Pho4 was recovered from Bathycoccus by sequencing a targeted metagenome from an uncultured Atlantic Ocean population. Phylogenetic reconstruction showed that pho4 genes from pelagophytes, haptophytes and infecting viruses were more closely related to homologues in prasinophytes than to those in what, at the species level, are considered to be closer relatives (e.g. diatoms). We also identified PHO4 superfamily members in ocean metagenomes, including new metagenomes from the Pacific Ocean. The environmental sequences grouped with pelagophytes, haptophytes, prasinophytes and viruses as well as bacteria. The analyses suggest that multiple independent pho4 gene transfer events have occurred between marine viruses and both eukaryotic and bacterial hosts. Additionally, pho4 genes were identified in available genomes from viruses that infect marine eukaryotes but not those that infect terrestrial hosts. Commonalities in marine host-virus gene exchanges indicate that manipulation of host-PO4 uptake is an important adaptation for viral proliferation in marine systems. Our findings suggest that PO4-availability may not serve as a simple bottom-up control of marine phytoplankton. PMID:21914098

  6. Gene flow in genetically altered crops helps progress transgenic turfgrass.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Numerous useful traits are being imparted into transgenic and non-transgenic plants. Gene flow as indicated in a recent publication from the Council for Agricultural Science and Technology (CAST 2007) is the successful transfer of genetic information between different individuals, populations, and g...

  7. LONG DISTANCE POLLEN-MEDIATED GENE FLOW FROM CREEPING BENTGRASS

    EPA Science Inventory

    Researchers from USEPA WED have measured gene flow from experimental fields of Roundup? herbicide resistant genetically modified (GM) creeping bentgrass a grass used primarily on golf courses, to compatible non-crop relatives. Using a sampling design based on the estimated time ...

  8. Gene flow networks among American Aedes aegypti populations

    PubMed Central

    Gonçalves da Silva, Anders; Cunha, Ivana C L; Santos, Walter S; Luz, Sérgio L B; Ribolla, Paulo E M; Abad-Franch, Fernando

    2012-01-01

    The mosquito Aedes aegypti, the dengue virus vector, has spread throughout the tropics in historical times. While this suggests man-mediated dispersal, estimating contemporary connectivity among populations has remained elusive. Here, we use a large mtDNA dataset and a Bayesian coalescent framework to test a set of hypotheses about gene flow among American Ae. aegypti populations. We assessed gene flow patterns at the continental and subregional (Amazon basin) scales. For the Americas, our data favor a stepping-stone model in which gene flow is higher among adjacent populations but in which, at the same time, North American and southeastern Brazilian populations are directly connected, likely via sea trade. Within Amazonia, the model with highest support suggests extensive gene flow among major cities; Manaus, located at the center of the subregional transport network, emerges as a potentially important connecting hub. Our results suggest substantial connectivity across Ae. aegypti populations in the Americas. As long-distance active dispersal has not been observed in this species, our data support man-mediated dispersal as a major determinant of the genetic structure of American Ae. aegypti populations. The inferred topology of interpopulation connectivity can inform network models of Ae. aegypti and dengue spread. PMID:23144654

  9. Development of a gene cloning system for the hydrogen-producing marine photosynthetic bacterium Rhodopseudomonas sp.

    PubMed Central

    Matsunaga, T; Matsunaga, N; Tsubaki, K; Tanaka, T

    1986-01-01

    Seventy-six strains of marine photosynthetic bacteria were analyzed by agarose gel electrophoresis for plasmid DNA content. Among these strains, 12 carried two to four different plasmids with sizes ranging from 3.1 to 11.0 megadaltons. The marine photosynthetic bacterium Rhodopseudomonas sp. NKPB002106 had two plasmids, pRD06S and pRD06L. The smaller plasmid, pRD06S, had a molecular weight of 3.8 megadaltons and was cut at a single site by restriction endonucleases SalI, SmaI, PstI, XhoI, and BglII. Moreover, the marine photosynthetic bacterium Rhodopseudomonas sp. NKPB002106 containing plasmid pRD06 had a satisfactory growth rate (doubling time, 7.5 h), a hydrogen-producing rate of 0.96 mumol/mg (dry weight) of cells per h, and nitrogen fixation capability. Plasmid pRD06S, however, had neither drug resistance nor heavy-metal resistance, and its copy number was less than 10. Therefore, a recombinant plasmid consisting of pRD06S and Escherichia coli cloning vector pUC13 was constructed and cloned in E. coli. The recombinant plasmid was transformed into Rhodopseudomonas sp. NKPB002106. As a result, Rhodopseudomonas sp. NKPB002106 developed ampicillin resistance. Thus, a shuttle vector for gene transfer was constructed for marine photosynthetic bacteria. PMID:3020006

  10. Genetic Population Structure and Gene Flow in the Atlantic Cod Gadus Morhua: A Comparison of Allozyme and Nuclear RFLP Loci

    PubMed Central

    Pogson, G. H.; Mesa, K. A.; Boutilier, R. G.

    1995-01-01

    High levels of gene flow have been implicated in producing uniform patterns of allozyme variation among populations of many marine fish species. We have examined whether gene flow is responsible for the limited population structure in the Atlantic cod, Gadus morhua L., by comparing the previously published patterns of variation at 10 allozyme loci to 17 nuclear restriction fragment length polymorphism (RFLP) loci scored by 11 anonymous cDNA clones. Unlike the allozyme loci, highly significant differences were observed among all populations at the DNA markers in a pattern consistent with an isolation-by-distance model of population structure. The magnitude of allele frequency variation at the nuclear RFLP loci significantly exceeded that observed at the protein loci (χ(2) = 24.6, d.f. = 5, P < 0.001). Estimates of gene flow from the private alleles method were similar for the allozymes and nuclear RFLPs. From the infinite island model, however, estimates of gene flow from the DNA markers were fivefold lower than indicated by the proteins. The discrepancy between gene flow estimates, combined with the observation of a large excess of rare RFLP alleles, suggests that the Atlantic cod has undergone a recent expansion in population size and that populations are significantly displaced from equilibrium. Because gene flow is a process that affects all loci equally, the heterogeneity observed among populations at the DNA level eliminates gene flow as the explanation for the homogeneous allozyme patterns. Our results suggest that a recent origin of cod populations has acted to constrain the extent of population differentiation observed at weakly polymorphic loci and implicate a role for selection in affecting the distribution of protein variation among natural populations in this species. PMID:7705638

  11. Giant virus with a remarkable complement of genes infects marine zooplankton

    PubMed Central

    Fischer, Matthias G.; Allen, Michael J.; Wilson, William H.; Suttle, Curtis A.

    2010-01-01

    As major consumers of heterotrophic bacteria and phytoplankton, microzooplankton are a critical link in aquatic foodwebs. Here, we show that a major marine microflagellate grazer is infected by a giant virus, Cafeteria roenbergensis virus (CroV), which has the largest genome of any described marine virus (≈730 kb of double-stranded DNA). The central 618-kb coding part of this AT-rich genome contains 544 predicted protein-coding genes; putative early and late promoter motifs have been detected and assigned to 191 and 72 of them, respectively, and at least 274 genes were expressed during infection. The diverse coding potential of CroV includes predicted translation factors, DNA repair enzymes such as DNA mismatch repair protein MutS and two photolyases, multiple ubiquitin pathway components, four intein elements, and 22 tRNAs. Many genes including isoleucyl-tRNA synthetase, eIF-2γ, and an Elp3-like histone acetyltransferase are usually not found in viruses. We also discovered a 38-kb genomic region of putative bacterial origin, which encodes several predicted carbohydrate metabolizing enzymes, including an entire pathway for the biosynthesis of 3-deoxy-d-manno-octulosonate, a key component of the outer membrane in Gram-negative bacteria. Phylogenetic analysis indicates that CroV is a nucleocytoplasmic large DNA virus, with Acanthamoeba polyphaga mimivirus as its closest relative, although less than one-third of the genes of CroV have homologs in Mimivirus. CroV is a highly complex marine virus and the only virus studied in genetic detail that infects one of the major groups of predators in the oceans. PMID:20974979

  12. Giant virus with a remarkable complement of genes infects marine zooplankton.

    PubMed

    Fischer, Matthias G; Allen, Michael J; Wilson, William H; Suttle, Curtis A

    2010-11-01

    As major consumers of heterotrophic bacteria and phytoplankton, microzooplankton are a critical link in aquatic foodwebs. Here, we show that a major marine microflagellate grazer is infected by a giant virus, Cafeteria roenbergensis virus (CroV), which has the largest genome of any described marine virus (≈730 kb of double-stranded DNA). The central 618-kb coding part of this AT-rich genome contains 544 predicted protein-coding genes; putative early and late promoter motifs have been detected and assigned to 191 and 72 of them, respectively, and at least 274 genes were expressed during infection. The diverse coding potential of CroV includes predicted translation factors, DNA repair enzymes such as DNA mismatch repair protein MutS and two photolyases, multiple ubiquitin pathway components, four intein elements, and 22 tRNAs. Many genes including isoleucyl-tRNA synthetase, eIF-2γ, and an Elp3-like histone acetyltransferase are usually not found in viruses. We also discovered a 38-kb genomic region of putative bacterial origin, which encodes several predicted carbohydrate metabolizing enzymes, including an entire pathway for the biosynthesis of 3-deoxy-d-manno-octulosonate, a key component of the outer membrane in Gram-negative bacteria. Phylogenetic analysis indicates that CroV is a nucleocytoplasmic large DNA virus, with Acanthamoeba polyphaga mimivirus as its closest relative, although less than one-third of the genes of CroV have homologs in Mimivirus. CroV is a highly complex marine virus and the only virus studied in genetic detail that infects one of the major groups of predators in the oceans. PMID:20974979

  13. Diversity of Nonribosomal Peptide Synthetase Genes in the Microbial Metagenomes of Marine Sponges

    PubMed Central

    Pimentel-Elardo, Sheila Marie; Grozdanov, Lubomir; Proksch, Sebastian; Hentschel, Ute

    2012-01-01

    Genomic mining revealed one major nonribosomal peptide synthetase (NRPS) phylogenetic cluster in 12 marine sponge species, one ascidian, an actinobacterial isolate and seawater. Phylogenetic analysis predicts its taxonomic affiliation to the actinomycetes and hydroxy-phenyl-glycine as a likely substrate. Additionally, a phylogenetically distinct NRPS gene cluster was discovered in the microbial metagenome of the sponge Aplysina aerophoba, which shows highest similarities to NRPS genes that were previously assigned, by ways of single cell genomics, to a Chloroflexi sponge symbiont. Genomic mining studies such as the one presented here for NRPS genes, contribute to on-going efforts to characterize the genomic potential of sponge-associated microbiota for secondary metabolite biosynthesis. PMID:22822366

  14. Diversity of nonribosomal peptide synthetase genes in the microbial metagenomes of marine sponges.

    PubMed

    Pimentel-Elardo, Sheila Marie; Grozdanov, Lubomir; Proksch, Sebastian; Hentschel, Ute

    2012-06-01

    Genomic mining revealed one major nonribosomal peptide synthetase (NRPS) phylogenetic cluster in 12 marine sponge species, one ascidian, an actinobacterial isolate and seawater. Phylogenetic analysis predicts its taxonomic affiliation to the actinomycetes and hydroxy-phenyl-glycine as a likely substrate. Additionally, a phylogenetically distinct NRPS gene cluster was discovered in the microbial metagenome of the sponge Aplysina aerophoba, which shows highest similarities to NRPS genes that were previously assigned, by ways of single cell genomics, to a Chloroflexi sponge symbiont. Genomic mining studies such as the one presented here for NRPS genes, contribute to on-going efforts to characterize the genomic potential of sponge-associated microbiota for secondary metabolite biosynthesis. PMID:22822366

  15. The Sound of Silence: Activating Silent Biosynthetic Gene Clusters in Marine Microorganisms.

    PubMed

    Reen, F Jerry; Romano, Stefano; Dobson, Alan D W; O'Gara, Fergal

    2015-08-01

    Unlocking the rich harvest of marine microbial ecosystems has the potential to both safeguard the existence of our species for the future, while also presenting significant lifestyle benefits for commercial gain. However, while significant advances have been made in the field of marine biodiscovery, leading to the introduction of new classes of therapeutics for clinical medicine, cosmetics and industrial products, much of what this natural ecosystem has to offer is locked in, and essentially hidden from our screening methods. Releasing this silent potential represents a significant technological challenge, the key to which is a comprehensive understanding of what controls these systems. Heterologous expression systems have been successful in awakening a number of these cryptic marine biosynthetic gene clusters (BGCs). However, this approach is limited by the typically large size of the encoding sequences. More recently, focus has shifted to the regulatory proteins associated with each BGC, many of which are signal responsive raising the possibility of exogenous activation. Abundant among these are the LysR-type family of transcriptional regulators, which are known to control production of microbial aromatic systems. Although the environmental signals that activate these regulatory systems remain unknown, it offers the exciting possibility of evoking mimic molecules and synthetic expression systems to drive production of potentially novel natural products in microorganisms. Success in this field has the potential to provide a quantum leap forward in medical and industrial bio-product development. To achieve these new endpoints, it is clear that the integrated efforts of bioinformaticians and natural product chemists will be required as we strive to uncover new and potentially unique structures from silent or cryptic marine gene clusters. PMID:26264003

  16. The Sound of Silence: Activating Silent Biosynthetic Gene Clusters in Marine Microorganisms

    PubMed Central

    Reen, F. Jerry; Romano, Stefano; Dobson, Alan D.W.; O’Gara, Fergal

    2015-01-01

    Unlocking the rich harvest of marine microbial ecosystems has the potential to both safeguard the existence of our species for the future, while also presenting significant lifestyle benefits for commercial gain. However, while significant advances have been made in the field of marine biodiscovery, leading to the introduction of new classes of therapeutics for clinical medicine, cosmetics and industrial products, much of what this natural ecosystem has to offer is locked in, and essentially hidden from our screening methods. Releasing this silent potential represents a significant technological challenge, the key to which is a comprehensive understanding of what controls these systems. Heterologous expression systems have been successful in awakening a number of these cryptic marine biosynthetic gene clusters (BGCs). However, this approach is limited by the typically large size of the encoding sequences. More recently, focus has shifted to the regulatory proteins associated with each BGC, many of which are signal responsive raising the possibility of exogenous activation. Abundant among these are the LysR-type family of transcriptional regulators, which are known to control production of microbial aromatic systems. Although the environmental signals that activate these regulatory systems remain unknown, it offers the exciting possibility of evoking mimic molecules and synthetic expression systems to drive production of potentially novel natural products in microorganisms. Success in this field has the potential to provide a quantum leap forward in medical and industrial bio-product development. To achieve these new endpoints, it is clear that the integrated efforts of bioinformaticians and natural product chemists will be required as we strive to uncover new and potentially unique structures from silent or cryptic marine gene clusters. PMID:26264003

  17. Maintenance of Species Boundaries Despite Ongoing Gene Flow in Ragworts.

    PubMed

    Osborne, Owen G; Chapman, Mark A; Nevado, Bruno; Filatov, Dmitry A

    2016-01-01

    The role of hybridization between diversifying species has been the focus of a huge amount of recent evolutionary research. While gene flow can prevent speciation or initiate species collapse, it can also generate new hybrid species. Similarly, while adaptive divergence can be wiped out by gene flow, new adaptive variation can be introduced via introgression. The relative frequency of these outcomes, and indeed the frequency of hybridization and introgression in general are largely unknown. One group of closely-related species with several documented cases of hybridization is the Mediterranean ragwort (genus: Senecio) species-complex. Examples of both polyploid and homoploid hybrid speciation are known in the clade, although their evolutionary relationships and the general frequency of introgressive hybridization among them remain unknown. Using a whole genome gene-space dataset comprising eight Senecio species we fully resolve the phylogeny of these species for the first time despite phylogenetic incongruence across the genome. Using a D-statistic approach, we demonstrate previously unknown cases of introgressive hybridization between multiple pairs of taxa across the species tree. This is an important step in establishing these species as a study system for diversification with gene flow, and suggests that introgressive hybridization may be a widespread and important process in plant evolution. PMID:26979797

  18. Blockage effects on the hydrodynamic performance of a marine cross-flow turbine.

    PubMed

    Consul, Claudio A; Willden, Richard H J; McIntosh, Simon C

    2013-02-28

    This paper explores the influence of blockage and free-surface deformation on the hydrodynamic performance of a generic marine cross-flow turbine. Flows through a three-bladed turbine with solidity 0.125 are simulated at field-test blade Reynolds numbers, O(10(5)-10(6)), for three different cross-stream blockages: 12.5, 25 and 50 per cent. Two representations of the free-surface boundary are considered: rigid lid and deformable free surface. Increasing the blockage is observed to lead to substantial increases in the power coefficient; the highest power coefficient computed is 1.23. Only small differences are observed between the two free-surface representations, with the deforming free-surface turbine out-performing the rigid lid turbine by 6.7 per cent in power at the highest blockage considered. This difference is attributed to the increase in effective blockage owing to the deformation of the free surface. Hydrodynamic efficiency, the ratio of useful power generated to overall power removed from the flow, is found to increase with blockage, which is consistent with the presence of a higher flow velocity through the core of the turbine at higher blockage ratios. Froude number is found to have little effect on thrust and power coefficients, but significant influence on surface elevation drop across the turbine. PMID:23319712

  19. Integration of flow studies for robust selection of mechanoresponsive genes.

    PubMed

    Maimari, Nataly; Pedrigi, Ryan M; Russo, Alessandra; Broda, Krysia; Krams, Rob

    2016-03-01

    Blood flow is an essential contributor to plaque growth, composition and initiation. It is sensed by endothelial cells, which react to blood flow by expressing > 1000 genes. The sheer number of genes implies that one needs genomic techniques to unravel their response in disease. Individual genomic studies have been performed but lack sufficient power to identify subtle changes in gene expression. In this study, we investigated whether a systematic meta-analysis of available microarray studies can improve their consistency. We identified 17 studies using microarrays, of which six were performed in vivo and 11 in vitro. The in vivo studies were disregarded due to the lack of the shear profile. Of the in vitro studies, a cross-platform integration of human studies (HUVECs in flow cells) showed high concordance (> 90 %). The human data set identified > 1600 genes to be shear responsive, more than any other study and in this gene set all known mechanosensitive genes and pathways were present. A detailed network analysis indicated a power distribution (e. g. the presence of hubs), without a hierarchical organisation. The average cluster coefficient was high and further analysis indicated an aggregation of 3 and 4 element motifs, indicating a high prevalence of feedback and feed forward loops, similar to prokaryotic cells. In conclusion, this initial study presented a novel method to integrate human-based mechanosensitive studies to increase its power. The robust network was large, contained all known mechanosensitive pathways and its structure revealed hubs, and a large aggregate of feedback and feed forward loops. PMID:26842798

  20. Do Major Roads Reduce Gene Flow in Urban Bird Populations?

    PubMed Central

    Zhang, Shuping; Suo, Mingli; Liu, Shenglin; Liang, Wei

    2013-01-01

    Background Although the negative effects of roads on the genetics of animal populations have been extensively reported, the question of whether roads reduce gene flow in volant, urban bird populations has so far not been addressed. In this study, we assess whether highways decreased gene flow and genetic variation in a small passerine bird, the tree sparrow (Passer montanus). Methodology We assessed genetic differences among tree sparrows (Passer montanus) sampled at 19 sites within Beijing Municipality, China, using 7 DNA microsatellites as genetic markers. Results AMOVA showed that genetic variation between sites, between urban and rural populations, and between opposite sides of the same highway, were very weak. Mantel tests on all samples, and on urban samples only, indicated that the age and number of highways, and the number of ordinary roads, were uncorrelated with genetic differences (FST) among tree sparrows from different urban sites. Birds sampled at urban sites had similar levels of genetic diversity to those at rural sites. There was, however, evidence of some weak genetic structure between urban sites. Firstly, there were significant genetic differences (FST) between birds from opposite sides of the same highway, but no significant FST values between those from sites that were not separated by highways. Secondly, birds from eleven urban sites had loci that significantly deviated from the Hardy–Weinberg equilibrium but no such deviation was found in birds from rural sites. Conclusion We cannot, therefore, conclusively reject the hypothesis that highways have no effect on the gene flow of tree sparrow populations. Furthermore, since the significance of these results may increase with time, we suggested that research on the influence of highways on gene flow in urban bird populations needs to be conducted over several decades. PMID:24204724

  1. Illegal gene flow from transgenic creeping bentgrass: the saga continues.

    PubMed

    Snow, Allison A

    2012-10-01

    Ecologists have paid close attention to environmental effects that fitness-enhancing transgenes might have following crop-to-wild gene flow (e.g. Snow et al. 2003). For some crops, gene flow also can lead to legal problems,especially when government agencies have not approved transgenic events for unrestricted environmental release.Creeping bentgrass (Agrostis stolonifera), a common turf grass used in golf courses, is the focus of both areas of concern. In 2002, prior to expected deregulation (still pending), The Scotts Company planted creeping bentgrass with transgenic resistance to the herbicide glyphosate,also known as RoundUp, on 162 ha in a designated control area in central Oregon (Fig. 1).Despite efforts to restrict gene flow, wind-dispersed pollen carried transgenes to florets of local A. stolonifera and A. gigantea as far as 14 km away, and to sentinel plants placed as far as 21 km away (Watrud et al. 2004).Then, in August 2003, a strong wind event moved transgenic seeds from wind rows of cut bentgrass into nearby areas. The company’s efforts to kill all transgenic survivors in the area failed: feral glyphosate-resistant populations of A. stolonifera were found by Reichman et al.(2006), and 62% of 585 bentgrass plants had the telltale CP4 EPSPS transgene in 2006 (Zapiola et al. 2008; Fig. 2).Now, in this issue, the story gets even more interesting as Zapiola & Mallory-Smith (2012) describe a transgenic,intergeneric hybrid produced on a feral, transgenic creeping bentgrass plant that received pollen from Polypogon monspeliensis (rabbitfoot grass). Their finding raises a host of new questions about the prevalence and fitness of intergeneric hybrids, as well as how to evaluate the full extent of gene flow from transgenic crops. PMID:23009646

  2. Identification of Carbohydrate Metabolism Genes in the Metagenome of a Marine Biofilm Community Shown to Be Dominated by Gammaproteobacteria, Bacteroidetes

    PubMed Central

    Edwards, Jennifer L.; Smith, Darren L.; Connolly, John; McDonald, James E.; Cox, Michael J.; Joint, Ian; Edwards, Clive; McCarthy, Alan J.

    2010-01-01

    Polysaccharides are an important source of organic carbon in the marine environment, degradation of the insoluble, globally abundant cellulose is a major component of the marine carbon cycle. Although a number of species of cultured bacteria are known to degrade crystalline cellulose, little is known of the polysaccharide hydrolases expressed by cellulose-degrading microbial communities, particularly in the marine environment. Next generation 454 Pyrosequencing was applied to analyze the microbial community that colonizes, degrades insoluble polysaccharides in situ in the Irish Sea. The bioinformatics tool MG-RAST was used to examine the randomly sampled data for taxonomic markers, functional genes,, showed that the community was dominated by members of the Gammaproteobacteria, Bacteroidetes. Furthermore, the identification of 211 gene sequences matched to a custom-made database comprising the members of nine glycoside hydrolase families revealed an extensive repertoire of functional genes predicted to be involved in cellulose utilization. This demonstrates that the use of an in situ cellulose baiting method yielded a marine microbial metagenome considerably enriched in functional genes involved in polysaccharide degradation. The research reported here is the first designed to specifically address the bacterial communities that colonize, degrade cellulose in the marine environment, to evaluate the glycoside hydrolase (cellulase, chitinase) gene repertoire of that community, in the absence of the biases associated with PCR-based molecular techniques. PMID:24710093

  3. Cautions on direct gene flow estimation in plant populations.

    PubMed

    Burczyk, Jaroslaw; Chybicki, Igor J

    2004-05-01

    Through simulations we have investigated the statistical properties of two of the main approaches for directly estimating pollen gene flow (m) in plant populations: genotypic exclusion and mating models. When the assumptions about accurately known background pollen pool allelic frequencies are met, both methods provide unbiased results with comparable variances across a range of true m values. However, when presumed allelic frequencies differ from actual ones, which is more likely in research practice, both estimators are biased. We demonstrate that the extent and direction of bias largely depend on the difference (measured as genetic distance) between the presumed and actual pollen pools, and on the degree of genetic differentiation between the local population and the actual background pollen sources. However, one feature of the mating model is its ability to estimate pollen gene flow simultaneously with background pollen pool allelic frequencies. We have found that this approach gives nearly unbiased pollen gene flow estimates, and is practical because it eliminates the necessity of providing independent estimates of background pollen pool allelic frequencies. Violations of the mating model assumptions of random mating within local population affect the precision of the estimates only to a limited degree. PMID:15212377

  4. Maintenance of Species Boundaries Despite Ongoing Gene Flow in Ragworts

    PubMed Central

    Osborne, Owen G.; Chapman, Mark A.; Nevado, Bruno; Filatov, Dmitry A.

    2016-01-01

    The role of hybridization between diversifying species has been the focus of a huge amount of recent evolutionary research. While gene flow can prevent speciation or initiate species collapse, it can also generate new hybrid species. Similarly, while adaptive divergence can be wiped out by gene flow, new adaptive variation can be introduced via introgression. The relative frequency of these outcomes, and indeed the frequency of hybridization and introgression in general are largely unknown. One group of closely-related species with several documented cases of hybridization is the Mediterranean ragwort (genus: Senecio) species-complex. Examples of both polyploid and homoploid hybrid speciation are known in the clade, although their evolutionary relationships and the general frequency of introgressive hybridization among them remain unknown. Using a whole genome gene–space dataset comprising eight Senecio species we fully resolve the phylogeny of these species for the first time despite phylogenetic incongruence across the genome. Using a D-statistic approach, we demonstrate previously unknown cases of introgressive hybridization between multiple pairs of taxa across the species tree. This is an important step in establishing these species as a study system for diversification with gene flow, and suggests that introgressive hybridization may be a widespread and important process in plant evolution. PMID:26979797

  5. Extremely reduced dispersal and gene flow in an island bird

    PubMed Central

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

    2014-01-01

    The Réunion grey white-eye, Zosterops borbonicus, a passerine bird endemic to Réunion Island in the Mascarene archipelago, represents an extreme case of microgeographical plumage colour variation in birds, with four distinct colour forms occupying different parts of this small island (2512 km2). To understand whether such population differentiation may reflect low levels of dispersal and gene flow at a very small spatial scale, we examined population structure and gene flow by analysing variation at 11 microsatellite loci among four geographically close localities (<26 km apart) sampled within the distribution range of one of the colour forms, the brown-headed brown form. Our results revealed levels of genetic differentiation that are exceptionally high for birds at such a small spatial scale. This strong population structure appears to reflect low levels of historical and contemporary gene flow among populations, unless very close geographically (<10 km). Thus, we suggest that the Réunion grey white-eye shows an extremely reduced propensity to disperse, which is likely to be related to behavioural processes. PMID:24084644

  6. Large-eddy simulation of 3D turbulent flow past a complete marine hydrokinetic turbine

    NASA Astrophysics Data System (ADS)

    Kang, S.; Sotiropoulos, F.

    2011-12-01

    A high-resolution computational framework was recently developed by Kang et al (Adv. Water Resour., submitted) for simulating three-dimensional (3D), turbulent flow past real-life, complete marine hydrokinetic (MHK) turbine configurations. In this model the complex turbine geometry is resolved by employing the curvilinear immersed boundary (CURVIB) method, which solves the 3D unsteady incompressible Navier-Stokes equations in generalized curvilinear domains with embedded arbitrarily complex, moving and/or stationary immersed boundaries (Ge and Sotiropoulos, 2007). Turbulence is simulated using the large-eddy simulation (LES) approach adapted in the context of the CURVIB method, with a wall model based on solving the simplified boundary layer equations used to reconstruct boundary conditions near all solid surfaces (Kang et al., 2011). The model can resolve the flow patterns generated by the rotor and all stationary components of the turbine as well as the interactions of the flow structures with the channel bed. We apply this model to carry out LES of the flow past the model-size hydrokinetic turbine deployed in the St. Anthony Falls Laboratory main channel. The mean velocities and second-order turbulence statistics measured in the downstream wake using acoustic Doppler velocimetry (ADV) are compared with the LES results. The comparisons show that the computed mean velocities and turbulent stresses are in good agreement with the measurements. The high-resolution LES data are used to explore physically important downstream flow characteristics such as the time-averaged wake structure, recovery of cross-sectionally averaged power potential, near-bed scour potential, etc. This work is supported by Verdant Power.

  7. Tracking Pollinator Movement with Protein Markers to Enhance Gene Flow Evaluations.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tracking polinator movement is an important component of gene flow. In recent years, understanding pollen-mediated gene flow has received much attention in the development of strategies to manage gene flow between transgenic and conventional crops. Using a modified Mark-Recapture technique, foragin...

  8. The Genes and Enzymes of Phosphonate Metabolism by Bacteria, and Their Distribution in the Marine Environment

    PubMed Central

    Villarreal-Chiu, Juan F.; Quinn, John P.; McGrath, John W.

    2011-01-01

    Phosphonates are compounds that contain the chemically stable carbon–phosphorus (C–P) bond. They are widely distributed amongst more primitive life forms including many marine invertebrates and constitute a significant component of the dissolved organic phosphorus reservoir in the oceans. Virtually all biogenic C–P compounds are synthesized by a pathway in which the key step is the intramolecular rearrangement of phosphoenolpyruvate to phosphonopyruvate. However C–P bond cleavage by degradative microorganisms is catalyzed by a number of enzymes – C–P lyases, C–P hydrolases, and others of as-yet-uncharacterized mechanism. Expression of some of the pathways of phosphonate catabolism is controlled by ambient levels of inorganic P (Pi) but for others it is Pi-independent. In this report we review the enzymology of C–P bond metabolism in bacteria, and also present the results of an in silico investigation of the distribution of the genes that encode the pathways responsible, in both bacterial genomes and in marine metagenomic libraries, and their likely modes of regulation. Interrogation of currently available whole-genome bacterial sequences indicates that some 10% contain genes encoding putative pathways of phosphonate biosynthesis while ∼40% encode one or more pathways of phosphonate catabolism. Analysis of metagenomic data from the global ocean survey suggests that some 10 and 30%, respectively, of bacterial genomes across the sites sampled encode these pathways. Catabolic routes involving phosphonoacetate hydrolase, C–P lyase(s), and an uncharacterized 2-aminoethylphosphonate degradative sequence were predominant, and it is likely that both substrate-inducible and Pi-repressible mechanisms are involved in their regulation. The data we present indicate the likely importance of phosphonate-P in global biogeochemical P cycling, and by extension its role in marine productivity and in carbon and nitrogen dynamics in the oceans. PMID:22303297

  9. Think laterally: horizontal gene transfer from symbiotic microbes may extend the phenotype of marine sessile hosts

    PubMed Central

    Degnan, Sandie M.

    2014-01-01

    Since the origin of the animal kingdom, marine animals have lived in association with viruses, prokaryotes and unicellular eukaryotes, often as symbionts. This long and continuous interaction has provided ample opportunity not only for the evolution of intimate interactions such as sharing of metabolic pathways, but also for horizontal gene transfer (HGT) of non-metazoan genes into metazoan genomes. The number of demonstrated cases of inter-kingdom HGT is currently small, such that it is not yet widely appreciated as a significant player in animal evolution. Sessile marine invertebrates that vertically inherit bacterial symbionts, that have no dedicated germ line, or that bud or excise pluripotent somatic cells during their life history may be particularly receptive to HGT from their symbionts. Closer scrutiny of the growing number of genomes being accrued for these animals may thus reveal HGT as a regular source of novel variation that can function to extend the host phenotype metabolically, morphologically, or even behaviorally. Taxonomic identification of symbionts will help to address the intriguing question of whether past HGT events may constrain contemporary symbioses. PMID:25477875

  10. Speciation with gene flow in equids despite extensive chromosomal plasticity.

    PubMed

    Jónsson, Hákon; Schubert, Mikkel; Seguin-Orlando, Andaine; Ginolhac, Aurélien; Petersen, Lillian; Fumagalli, Matteo; Albrechtsen, Anders; Petersen, Bent; Korneliussen, Thorfinn S; Vilstrup, Julia T; Lear, Teri; Myka, Jennifer Leigh; Lundquist, Judith; Miller, Donald C; Alfarhan, Ahmed H; Alquraishi, Saleh A; Al-Rasheid, Khaled A S; Stagegaard, Julia; Strauss, Günter; Bertelsen, Mads Frost; Sicheritz-Ponten, Thomas; Antczak, Douglas F; Bailey, Ernest; Nielsen, Rasmus; Willerslev, Eske; Orlando, Ludovic

    2014-12-30

    Horses, asses, and zebras belong to a single genus, Equus, which emerged 4.0-4.5 Mya. Although the equine fossil record represents a textbook example of evolution, the succession of events that gave rise to the diversity of species existing today remains unclear. Here we present six genomes from each living species of asses and zebras. This completes the set of genomes available for all extant species in the genus, which was hitherto represented only by the horse and the domestic donkey. In addition, we used a museum specimen to characterize the genome of the quagga zebra, which was driven to extinction in the early 1900s. We scan the genomes for lineage-specific adaptations and identify 48 genes that have evolved under positive selection and are involved in olfaction, immune response, development, locomotion, and behavior. Our extensive genome dataset reveals a highly dynamic demographic history with synchronous expansions and collapses on different continents during the last 400 ky after major climatic events. We show that the earliest speciation occurred with gene flow in Northern America, and that the ancestor of present-day asses and zebras dispersed into the Old World 2.1-3.4 Mya. Strikingly, we also find evidence for gene flow involving three contemporary equine species despite chromosomal numbers varying from 16 pairs to 31 pairs. These findings challenge the claim that the accumulation of chromosomal rearrangements drive complete reproductive isolation, and promote equids as a fundamental model for understanding the interplay between chromosomal structure, gene flow, and, ultimately, speciation. PMID:25453089

  11. Selected Chitinase Genes in Cultured and Uncultured Marine Bacteria in the α- and γ-Subclasses of the Proteobacteria

    PubMed Central

    Cottrell, Matthew T.; Wood, Daniel N.; Yu, Liying; Kirchman, David L.

    2000-01-01

    PCR primers were patterned after chitinase genes in four γ-proteobacteria in the families Alteromonadaceae and Enterobacteriaceae (group I chitinases) and used to explore the occurrence and diversity of these chitinase genes in cultured and uncultured marine bacteria. The PCR results from 104 bacterial strains indicated that this type of chitinase gene occurs in two major groups of marine bacteria, α- and γ-proteobacteria, but not the Cytophaga-Flavobacter group. Group I chitinase genes also occur in some viruses infecting arthropods. Phylogenetic analysis indicated that similar group I chitinase genes occur in taxonomically related bacteria. However, the overall phylogeny of chitinase genes did not correspond to the phylogeny of 16S rRNA genes, possibly due to lateral transfer of chitinase genes between groups of bacteria, but other mechanisms, such as gene duplication, cannot be ruled out. Clone libraries of chitinase gene fragments amplified from coastal Pacific Ocean and estuarine Delaware Bay bacterioplankton revealed similarities and differences between cultured and uncultured bacteria. We had hypothesized that cultured and uncultured chitin-degrading bacteria would be very different, but in fact, clones having nucleotide sequences identical to those of chitinase genes of cultured α-proteobacteria dominated both libraries. The other clones were similar but not identical to genes in cultured γ-proteobacteria, including vibrios and alteromonads. Our results suggest that a closer examination of chitin degradation by α-proteobacteria will lead to a better understanding of chitin degradation in the ocean. PMID:10698791

  12. Tools for Gene-Regulatory Analyses in the Marine Annelid Platynereis dumerilii

    PubMed Central

    Kirchmaier, Stephan; Tessmar-Raible, Kristin; Raible, Florian

    2014-01-01

    The advent of high-throughput sequencing technology facilitates the exploration of a variety of reference species outside the few established molecular genetic model systems. Bioinformatic and gene expression analyses provide new ways for comparative analyses between species, for instance, in the field of evolution and development. Despite these advances, a critical bottleneck for the exploration of new model species remains the establishment of functional tools, such as the ability to experimentally express genes in specific cells of an organism. We recently established a first transgenic strain of the annelid Platynereis, using a Tc1/mariner-type Mos1 transposon vector. Here, we compare Mos1 with Tol2, a member of the hAT family of transposons. In Platynereis, Tol2-based constructs showed a higher frequency of nuclear genome insertion and sustained gene expression in the G0 generation. However, in contrast to Mos1-mediated transgenes, Tol2-mediated insertions failed to retain fluorescence in the G1 generation, suggesting a germ line-based silencing mechanism. Furthermore, we present three novel expression constructs that were generated by a simple fusion-PCR approach and allow either ubiquitous or cell-specific expression of a reporter gene. Our study indicates the versatility of Tol2 for transient transgenesis, and provides a template for transgenesis work in other emerging reference species. PMID:24714200

  13. Tools for gene-regulatory analyses in the marine annelid Platynereis dumerilii.

    PubMed

    Backfisch, Benjamin; Kozin, Vitaly V; Kirchmaier, Stephan; Tessmar-Raible, Kristin; Raible, Florian

    2014-01-01

    The advent of high-throughput sequencing technology facilitates the exploration of a variety of reference species outside the few established molecular genetic model systems. Bioinformatic and gene expression analyses provide new ways for comparative analyses between species, for instance, in the field of evolution and development. Despite these advances, a critical bottleneck for the exploration of new model species remains the establishment of functional tools, such as the ability to experimentally express genes in specific cells of an organism. We recently established a first transgenic strain of the annelid Platynereis, using a Tc1/mariner-type Mos1 transposon vector. Here, we compare Mos1 with Tol2, a member of the hAT family of transposons. In Platynereis, Tol2-based constructs showed a higher frequency of nuclear genome insertion and sustained gene expression in the G0 generation. However, in contrast to Mos1-mediated transgenes, Tol2-mediated insertions failed to retain fluorescence in the G1 generation, suggesting a germ line-based silencing mechanism. Furthermore, we present three novel expression constructs that were generated by a simple fusion-PCR approach and allow either ubiquitous or cell-specific expression of a reporter gene. Our study indicates the versatility of Tol2 for transient transgenesis, and provides a template for transgenesis work in other emerging reference species. PMID:24714200

  14. PKS and NRPS gene clusters from microbial symbiont cells of marine sponges by whole genome amplification.

    PubMed

    Siegl, Alexander; Hentschel, Ute

    2010-08-01

    Whole genome amplification (WGA) approaches provide genomic information on single microbial cells and hold great promise for the field of environmental microbiology. Here, the microbial consortia of the marine sponge Aplysina aerophoba were sorted by fluorescence-activated cell sorting (FACS) and then subjected to WGA. A cosmid library was constructed from the WGA product of a sample containing two bacterial cells, one a member of the candidate phylum Poribacteria and one of a sponge-specific clade of Chloroflexi. Library screening led to the genomic characterization of three cosmid clones, encoding a polyketide synthase (PKS), a non-ribosomal peptide synthetase (NRPS) and the Chloroflexi 16S rRNA gene. PCR screening of WGA products from additional, FACS-sorted single bacterial symbiont cells supports the assignment of the Sup-PKS gene to the Poribacteria and the novel NRPS gene to the Chloroflexi. This promising single-cell genomics approach has permitted cloning of entire gene clusters from single microbial cells of known phylogenetic origin and thus provides a sought-after link between phylogeny and function. PMID:23766222

  15. Regulation of iron transport related genes by boron in the marine bacterium Marinobacter algicola DG893.

    PubMed

    Romano, Ariel; Trimble, Lyndsay; Hobusch, Ashtian R; Schroeder, Kristine J; Amin, Shady A; Hartnett, Andrej D; Barker, Ryan A; Crumbliss, Alvin L; Carrano, Carl J

    2013-08-01

    While there has been extensive interest in the use of boron isotope ratios as a surrogate of pH in paleoclimate studies in the context of climate change-related questions, the high (0.4 mM) concentration and the depth-independent (conservative or non-nutrient-like) concentration profile of this element have led to boron being neglected as a potentially biologically relevant element in the modern ocean. Here we report that boron affects the expression of a number of protein and genes in the "algal-associated" Gram-negative marine bacterium Marinobacter algicola DG893. Most intriguingly, a number of these proteins and genes are related to iron uptake. In a recent separate publication we have shown that boron regulates one such iron transport related protein, i.e. the periplasmic iron binding protein FbpA via a direct interaction of the metalloid with this protein. Here we show that a number of other iron uptake related genes are also affected by boron but in the opposite way i.e. they are up-regulated. We propose that the differential effect of boron on FbpA expression relative to other iron transport related genes is a result of an interaction between boron and the global iron regulatory protein Fur. PMID:23775459

  16. Marine heat flow measurements across subsea permafrost limit in the eastern Mackenzie Trough, Canadian Beaufort Sea

    NASA Astrophysics Data System (ADS)

    Kim, Y. G.; Hong, J. K.; Jin, Y. K.; Riedel, M.; Melling, H.; Kang, S. G.; Dallimore, S.

    2015-12-01

    Marine heat flow measurements using a 5 m-long Ewing-type heat probe were made during Korean icebreaker R/V Araon's Arctic expeditions (ARA04C in 2013 and ARA05B in 2014) to better know the shallow subsurface thermal structure in the eastern slope of Mackenzie Trough, the Canadian Beaufort Sea, in which associative geological processes of permafrost degradation and gas hydrate dissociation occur because of long-term warming since the Last Glacial Maximum. Heat flow in the continental slope was collected for the first time and is rather higher than those from deep boreholes (up to a few km below the seafloor) in the continental shelf. However, the smaller geothermal gradient and thermal conductivity were observed from sites along a transect line across permafrost limit on the eastern slope of the trough. It is noted that geothermal gradients are relatively constant in the vicinity of permafrost limit but are much smaller (even minus) only at deeper depths with positive bottom water temperature. Reason for such distribution is unclear yet. Based on observed geothermal gradient and bottom water temperature, permafrost table shown in subbottom profile seems to be controlled not by temperature. On the other hand, our finding of permafrost evidence on the other subbottom profile located landward may support that permafrost limit in the trough is along with ~100 m isobath.

  17. Gene flow and demographic history of the mangrove crab Neosarmatium meinerti: A case study from the western Indian Ocean

    NASA Astrophysics Data System (ADS)

    Ragionieri, Lapo; Cannicci, Stefano; Schubart, Christoph D.; Fratini, Sara

    2010-01-01

    Most marine organisms are characterized by at least one planktonic phase during their life history, potentially allowing interconnection of populations separated by several hundred kilometers. For many years, the idea that marine species are genetically homogenous throughout their range of distribution, due to passive larval transport, has been a paradigm. Nowadays, a growing number of studies underline the existence of boundaries in the marine realm and highlight how larval dispersal is a complex process depending on biotic as well as abiotic factors. Marine fragmented habitats, such as atolls, mangroves and estuaries, are optimal systems for investigating the marine dispersion process under a metapopulation approach, since populations can be geographically defined a priori as opposed to those occupying open marine environments. Within this frame, the present paper investigates the population genetic structure and the demographic history of the mangrove crab Neosarmatium meinerti within the western Indian Ocean by partial sequences of the mitochondrial DNA cytochrome oxidase subunit I. A total of 167 specimens were sampled from six mangrove sites distributed along the East African coast, from Kenya to South Africa, also including a mangrove forest located on Mahé Island, Seychelles. A sharp genetic break between the mainland and the Seychelles is recorded, revealing the existence of two historically distinct groups that can be defined as independent evolutionary units. Gene flow along the East African coast appears to be high enough to form a single metapopulation, probably by means of stepping stone populations. Otherwise, this mainland metapopulation is currently under expansion through a gradual moving front from the subtropical toward the equatorial populations.

  18. Tracing carbon flow in an arctic marine food web using fatty acid-stable isotope analysis.

    PubMed

    Budge, S M; Wooller, M J; Springer, A M; Iverson, S J; McRoy, C P; Divoky, G J

    2008-08-01

    Global warming and the loss of sea ice threaten to alter patterns of productivity in arctic marine ecosystems because of a likely decline in primary productivity by sea ice algae. Estimates of the contribution of ice algae to total primary production range widely, from just 3 to >50%, and the importance of ice algae to higher trophic levels remains unknown. To help answer this question, we investigated a novel approach to food web studies by combining the two established methods of stable isotope analysis and fatty acid (FA) analysis--we determined the C isotopic composition of individual diatom FA and traced these biomarkers in consumers. Samples were collected near Barrow, Alaska and included ice algae, pelagic phytoplankton, zooplankton, fish, seabirds, pinnipeds and cetaceans. Ice algae and pelagic phytoplankton had distinctive overall FA signatures and clear differences in delta(13)C for two specific diatom FA biomarkers: 16:4n-1 (-24.0+/-2.4 and -30.7+/-0.8 per thousand, respectively) and 20:5n-3 (-18.3+/-2.0 and -26.9+/-0.7 per thousand, respectively). Nearly all delta(13)C values of these two FA in consumers fell between the two stable isotopic end members. A mass balance equation indicated that FA material derived from ice algae, compared to pelagic diatoms, averaged 71% (44-107%) in consumers based on delta(13)C values of 16:4n-1, but only 24% (0-61%) based on 20:5n-3. Our estimates derived from 16:4n-1, which is produced only by diatoms, probably best represented the contribution of ice algae relative to pelagic diatoms. However, many types of algae produce 20:5n-3, so the lower value derived from it likely represented a more realistic estimate of the proportion of ice algae material relative to all other types of phytoplankton. These preliminary results demonstrate the potential value of compound-specific isotope analysis of marine lipids to trace C flow through marine food webs and provide a foundation for future work. PMID:18481094

  19. A transcriptomic scan for positively selected genes in two closely related marine fishes: Sebastes caurinus and S. rastrelliger.

    PubMed

    Heras, Joseph; Koop, Ben F; Aguilar, Andres

    2011-06-01

    Comparative genomic analyses can provide valuable insight into functional evolutionary divergence among closely related species. Here we employ a comparative evolutionary analysis of expressed sequence tags (ESTs) from two closely related species of marine fishes (genus Sebastes--rockfish). Sebastes is a highly diverse group of marine fishes that inhabit a wide array of marine habitats and the study of this group can provide insights into speciation in the marine environment. ESTs were developed for S. caurinus (23,668 from brain, kidney, and spleen tissues) and S. rastrelliger (11,207 from brain and pituitary tissues). Following assembly we were able to identify, with high confidence, 257 orthologous sequence pairs between the two species through a reciprocal best hit blast search. An analysis of functional divergence between orthologs revealed that 19.46% had Ka/Ks values greater than 0.5 and 8.17% had Ka/Ks values greater than one, identifying a large pool of candidate genes to further study adaptive divergence in the group. Genes with elevated Ka/Ks values belonged to the following functional categories: immune function, metabolism, longevity, and reproductive behavior, indicating that adaptive divergence in these functional groups may be important in the diversification of this group of fishes. This study provides the ground work to better understand the molecular evolution of genes involved in a radiation of marine fishes. PMID:21620330

  20. Numerical simulation of 3D flow past a real-life marine hydrokinetic turbine

    NASA Astrophysics Data System (ADS)

    Kang, Seokkoo; Borazjani, Iman; Colby, Jonathan A.; Sotiropoulos, Fotis

    2012-04-01

    We simulate three-dimensional, turbulent flow past an axial-flow marine hydrokinetic (MHK) turbine mounted on the bed of a rectangular open channel by adapting a computational framework developed for carrying out high-resolution large-eddy simulation (LES) in arbitrarily complex domains involving moving or stationary boundaries. The complex turbine geometry, including the rotor and all stationary components, is handled by employing the curvilinear immersed boundary (CURVIB) method [1,2]. Velocity boundary conditions near all solid surfaces are reconstructed using a wall model based on solving the simplified boundary layer equations [2]. To demonstrate the capabilities of the model we apply it to simulate the flow past a Gen4 axial flow MHK turbine developed by Verdant Power for the Roosevelt Island Tidal Energy (RITE) project in the East River in New York City, USA. We carry out systematic grid refinement studies, using grids with up to 185 million nodes, for only the turbine rotor placed in an infinite free stream to show that the computed torque converges to a grid insensitive value, which is in good agreement with field measurements. We also carry out LES for the complete turbine configuration, including the pylon, nacelle and rotor, mounted on the bed of a straight rectangular open channel. The computed results illustrate the complexity of the flow and show that the power output of the complete turbine is primarily dependent on the rotor geometry and tip speed ratio, and is not affected by the stationary components of the turbine and the presence of the channel bed. The complete turbine simulation also reveals that the downstream wake of the turbine consists of three main regions: (1) the outer layer with the spiral blade tip vortices rotating in the same direction as the blades; (2) the counter-rotating inner layer surrounded by the spiral tip vortices; and (3) the core layer co-rotating with respect to the tip vortices. This study is the first to report the

  1. Comparative Analysis and Distribution of Omega-3 lcPUFA Biosynthesis Genes in Marine Molluscs

    PubMed Central

    Surm, Joachim M.; Prentis, Peter J.; Pavasovic, Ana

    2015-01-01

    Recent research has identified marine molluscs as an excellent source of omega-3 long-chain polyunsaturated fatty acids (lcPUFAs), based on their potential for endogenous synthesis of lcPUFAs. In this study we generated a representative list of fatty acyl desaturase (Fad) and elongation of very long-chain fatty acid (Elovl) genes from major orders of Phylum Mollusca, through the interrogation of transcriptome and genome sequences, and various publicly available databases. We have identified novel and uncharacterised Fad and Elovl sequences in the following species: Anadara trapezia, Nerita albicilla, Nerita melanotragus, Crassostrea gigas, Lottia gigantea, Aplysia californica, Loligo pealeii and Chlamys farreri. Based on alignments of translated protein sequences of Fad and Elovl genes, the haeme binding motif and histidine boxes of Fad proteins, and the histidine box and seventeen important amino acids in Elovl proteins, were highly conserved. Phylogenetic analysis of aligned reference sequences was used to reconstruct the evolutionary relationships for Fad and Elovl genes separately. Multiple, well resolved clades for both the Fad and Elovl sequences were observed, suggesting that repeated rounds of gene duplication best explain the distribution of Fad and Elovl proteins across the major orders of molluscs. For Elovl sequences, one clade contained the functionally characterised Elovl5 proteins, while another clade contained proteins hypothesised to have Elovl4 function. Additional well resolved clades consisted only of uncharacterised Elovl sequences. One clade from the Fad phylogeny contained only uncharacterised proteins, while the other clade contained functionally characterised delta-5 desaturase proteins. The discovery of an uncharacterised Fad clade is particularly interesting as these divergent proteins may have novel functions. Overall, this paper presents a number of novel Fad and Elovl genes suggesting that many mollusc groups possess most of the

  2. Detection of genes involved in fatty acid elongation and desaturation in thraustochytrid marine eukaryotes.

    PubMed

    Nagano, Naoki; Sakaguchi, Keishi; Taoka, Yousuke; Okita, Yuji; Honda, Daiske; Ito, Makoto; Hayashi, Masahiro

    2011-01-01

    Heterotrophic marine protists known as thraustochytrids can synthesize polyunsaturated fatty acids (PUFAs) such as docosahexaenoic acid (DHA). The biosynthetic pathways of PUFAs in thraustochytrids are poorly understood, however. In this study, we attempted to reveal the enzymes involved in DHA synthesis in thraustochytrids. Nine thraustochytrid strains representing 3 genera (Aurantiochytrium, Schizochytrium, and Thraustochytrium) were used for PCR-based detection of the genes encoding Δ5-elongase and Δ4-desaturase and for fatty acid analysis. The degenerate primers were designed to amplify the Δ5-elongase and Δ4-desaturase genes, and the partial sequences of the enzymes were obtained from the genera Thraustochytrium and Schizochytrium. These fragments were identical to those of known Δ5-elongase and Δ4-desaturase. Neither Δ5-elongase nor Δ4-desaturase was detected in the strains belonging to the genus Aurantiochytrium, however, suggesting that this group likely synthesizes DHA not via the elongation/desaturation pathway but via an alternate pathway such as the polyketide synthase pathway. The fatty acid profiles of thraustochytrids were consistent with the presence of genes involved in PUFA biosynthesis in thraustochytrid genera. Thus, our findings suggest that two biosynthetic pathways for PUFAs exist in these organisms. PMID:21852747

  3. Cloning, expression and characterization of a new agarase-encoding gene from marine Pseudoalteromonas sp.

    PubMed

    Lu, Xinzhi; Chu, Yan; Wu, Qianqian; Gu, Yuchao; Han, Feng; Yu, Wengong

    2009-10-01

    The beta-agarase gene agaA, cloned from a marine bacterium, Pseudoalteromonas sp. CY24, consists of 1,359 nucleotides encoding 453 amino acids in a sequence corresponding to a catalytic domain of glycosyl hydrolase family 16 (GH16) and a carbohydrate-binding module type 13 (CBM13). The recombinant enzyme is an endo-type agarase that hydrolyzes beta-1,4-linkages of agarose, yielding neoagarotetraose and neoagarohexaose as the predominant products. In two cleavage patterns, AgaA digested the smallest substrate, neoagarooctaose, into neoagarobiose, neoagarotetraose and neoagarohexaose. Site directed mutation was performed to investigate the differences between AgaA and AgaD of Vibrio sp. PO-303, identifying residues V(109)VTS(112) as playing a key role in the enzyme reaction. PMID:19504047

  4. Development of Ecogenomic Sensors for Remote Detection of Marine Microbes, Their Genes and Gene Products

    NASA Astrophysics Data System (ADS)

    Scholin, C.; Preston, C.; Harris, A.; Birch, J.; Marin, R.; Jensen, S.; Roman, B.; Everlove, C.; Makarewicz, A.; Riot, V.; Hadley, D.; Benett, W.; Dzenitis, J.

    2008-12-01

    An internet search using the phrase "ecogenomic sensor" will return numerous references that speak broadly to the idea of detecting molecular markers indicative of specific organisms, genes or other biomarkers within an environmental context. However, a strict and unified definition of "ecogenomic sensor" is lacking and the phrase may be used for laboratory-based tools and techniques as well as semi or fully autonomous systems that can be deployed outside of laboratory. We are exploring development of an ecogenomic sensor from the perspective of a field-portable device applied towards oceanographic research and water quality monitoring. The device is known as the Environmental Sample Processor, or ESP. The ESP employs wet chemistry molecular analytical techniques to autonomously assess the presence and abundance of specific organisms, their genes and/or metabolites in near real-time. Current detection chemistries rely on low- density DNA probe and protein arrays. This presentation will emphasize results from 2007-8 field trials when the ESP was moored in Monterey Bay, CA, as well as current engineering activities for improving analytical capacity of the instrument. Changes in microbial community structure at the rRNA level were observed remotely in accordance with changing chemical and physical oceanographic conditions. Current developments include incorporation of a reusable solid phase extraction column for purifying nucleic acids and a 4-channel real-time PCR module. Users can configure this system to support a variety of PCR master mixes, primer/probe combinations and control templates. An update on progress towards fielding a PCR- enabled ESP will be given along with an outline of plans for its use in coastal and oligotrophic oceanic regimes.

  5. Gene invasion in distant eukaryotic lineages: discovery of mutually exclusive genetic elements reveals marine biodiversity.

    PubMed

    Monier, Adam; Sudek, Sebastian; Fast, Naomi M; Worden, Alexandra Z

    2013-09-01

    Inteins are rare, translated genetic parasites mainly found in bacteria and archaea, while spliceosomal introns are distinctly eukaryotic features abundant in most nuclear genomes. Using targeted metagenomics, we discovered an intein in an Atlantic population of the photosynthetic eukaryote, Bathycoccus, harbored by the essential spliceosomal protein PRP8 (processing factor 8 protein). Although previously thought exclusive to fungi, we also identified PRP8 inteins in parasitic (Capsaspora) and predatory (Salpingoeca) protists. Most new PRP8 inteins were at novel insertion sites that, surprisingly, were not in the most conserved regions of the gene. Evolutionarily, Dikarya fungal inteins at PRP8 insertion site a appeared more related to the Bathycoccus intein at a unique insertion site, than to other fungal and opisthokont inteins. Strikingly, independent analyses of Pacific and Atlantic samples revealed an intron at the same codon as the Bathycoccus PRP8 intein. The two elements are mutually exclusive and neither was found in cultured Bathycoccus or other picoprasinophyte genomes. Thus, wild Bathycoccus contain one of few non-fungal eukaryotic inteins known and a rare polymorphic intron. Our data indicate at least two Bathycoccus ecotypes exist, associated respectively with oceanic or mesotrophic environments. We hypothesize that intein propagation is facilitated by marine viruses; and, while intron gain is still poorly understood, presence of a spliceosomal intron where a locus lacks an intein raises the possibility of new, intein-primed mechanisms for intron gain. The discovery of nucleus-encoded inteins and associated sequence polymorphisms in uncultivated marine eukaryotes highlights their diversity and reveals potential sexual boundaries between populations indistinguishable by common marker genes. PMID:23635865

  6. Gene invasion in distant eukaryotic lineages: discovery of mutually exclusive genetic elements reveals marine biodiversity

    PubMed Central

    Monier, Adam; Sudek, Sebastian; Fast, Naomi M; Worden, Alexandra Z

    2013-01-01

    Inteins are rare, translated genetic parasites mainly found in bacteria and archaea, while spliceosomal introns are distinctly eukaryotic features abundant in most nuclear genomes. Using targeted metagenomics, we discovered an intein in an Atlantic population of the photosynthetic eukaryote, Bathycoccus, harbored by the essential spliceosomal protein PRP8 (processing factor 8 protein). Although previously thought exclusive to fungi, we also identified PRP8 inteins in parasitic (Capsaspora) and predatory (Salpingoeca) protists. Most new PRP8 inteins were at novel insertion sites that, surprisingly, were not in the most conserved regions of the gene. Evolutionarily, Dikarya fungal inteins at PRP8 insertion site a appeared more related to the Bathycoccus intein at a unique insertion site, than to other fungal and opisthokont inteins. Strikingly, independent analyses of Pacific and Atlantic samples revealed an intron at the same codon as the Bathycoccus PRP8 intein. The two elements are mutually exclusive and neither was found in cultured Bathycoccus or other picoprasinophyte genomes. Thus, wild Bathycoccus contain one of few non-fungal eukaryotic inteins known and a rare polymorphic intron. Our data indicate at least two Bathycoccus ecotypes exist, associated respectively with oceanic or mesotrophic environments. We hypothesize that intein propagation is facilitated by marine viruses; and, while intron gain is still poorly understood, presence of a spliceosomal intron where a locus lacks an intein raises the possibility of new, intein-primed mechanisms for intron gain. The discovery of nucleus-encoded inteins and associated sequence polymorphisms in uncultivated marine eukaryotes highlights their diversity and reveals potential sexual boundaries between populations indistinguishable by common marker genes. PMID:23635865

  7. Divergence with gene flow within the recent chipmunk radiation (Tamias)

    PubMed Central

    Sullivan, J; Demboski, J R; Bell, K C; Hird, S; Sarver, B; Reid, N; Good, J M

    2014-01-01

    Increasing data have supported the importance of divergence with gene flow (DGF) in the generation of biological diversity. In such cases, lineage divergence occurs on a shorter timescale than does the completion of reproductive isolation. Although it is critical to explore the mechanisms driving divergence and preventing homogenization by hybridization, it is equally important to document cases of DGF in nature. Here we synthesize data that have accumulated over the last dozen or so years on DGF in the chipmunk (Tamias) radiation with new data that quantify very high rates of mitochondrial DNA (mtDNA) introgression among para- and sympatric species in the T. quadrivittatus group in the central and southern Rocky Mountains. These new data (188 cytochrome b sequences) bring the total number of sequences up to 1871; roughly 16% (298) of the chipmunks we have sequenced exhibit introgressed mtDNA. This includes ongoing introgression between subspecies and between both closely related and distantly related taxa. In addition, we have identified several taxa that are apparently fixed for ancient introgressions and in which there is no evidence of ongoing introgression. A recurrent observation is that these introgressions occur between ecologically and morphologically diverged, sometimes non-sister taxa that engage in well-documented niche partitioning. Thus, the chipmunk radiation in western North America represents an excellent mammalian example of speciation in the face of recurrent gene flow among lineages and where biogeography, habitat differentiation and mating systems suggest important roles for both ecological and sexual selection. PMID:24781803

  8. Divergence with gene flow within the recent chipmunk radiation (Tamias).

    PubMed

    Sullivan, J; Demboski, J R; Bell, K C; Hird, S; Sarver, B; Reid, N; Good, J M

    2014-09-01

    Increasing data have supported the importance of divergence with gene flow (DGF) in the generation of biological diversity. In such cases, lineage divergence occurs on a shorter timescale than does the completion of reproductive isolation. Although it is critical to explore the mechanisms driving divergence and preventing homogenization by hybridization, it is equally important to document cases of DGF in nature. Here we synthesize data that have accumulated over the last dozen or so years on DGF in the chipmunk (Tamias) radiation with new data that quantify very high rates of mitochondrial DNA (mtDNA) introgression among para- and sympatric species in the T. quadrivittatus group in the central and southern Rocky Mountains. These new data (188 cytochrome b sequences) bring the total number of sequences up to 1871; roughly 16% (298) of the chipmunks we have sequenced exhibit introgressed mtDNA. This includes ongoing introgression between subspecies and between both closely related and distantly related taxa. In addition, we have identified several taxa that are apparently fixed for ancient introgressions and in which there is no evidence of ongoing introgression. A recurrent observation is that these introgressions occur between ecologically and morphologically diverged, sometimes non-sister taxa that engage in well-documented niche partitioning. Thus, the chipmunk radiation in western North America represents an excellent mammalian example of speciation in the face of recurrent gene flow among lineages and where biogeography, habitat differentiation and mating systems suggest important roles for both ecological and sexual selection. PMID:24781803

  9. Time to get moving: assisted gene flow of forest trees.

    PubMed

    Aitken, Sally N; Bemmels, Jordan B

    2016-01-01

    Geographic variation in trees has been investigated since the mid-18th century. Similar patterns of clinal variation have been observed along latitudinal and elevational gradients in common garden experiments for many temperate and boreal species. These studies convinced forest managers that a 'local is best' seed source policy was usually safest for reforestation. In recent decades, experimental design, phenotyping methods, climatic data and statistical analyses have improved greatly and refined but not radically changed knowledge of clines. The maintenance of local adaptation despite high gene flow suggests selection for local adaptation to climate is strong. Concerns over maladaptation resulting from climate change have motivated many new genecological and population genomics studies; however, few jurisdictions have implemented assisted gene flow (AGF), the translocation of pre-adapted individuals to facilitate adaptation of planted forests to climate change. Here, we provide evidence that temperate tree species show clines along climatic gradients sufficiently similar for average patterns or climate models to guide AGF in the absence of species-specific knowledge. Composite provenancing of multiple seed sources can be used to increase diversity and buffer against future climate uncertainty. New knowledge will continue to refine and improve AGF as climates warm further. PMID:27087852

  10. Passive rafting is a powerful driver of transoceanic gene flow

    PubMed Central

    Nikula, Raisa; Spencer, Hamish G.; Waters, Jonathan M.

    2013-01-01

    Dispersal by passive oceanic rafting is considered important for the assembly of biotic communities on islands. However, not much is known about levels of population genetic connectivity maintained by rafting over transoceanic distances. We assess the evolutionary impact of kelp-rafting by estimating population genetic differentiation in three kelp-associated invertebrate species across a system of islands isolated by oceanic gaps for over 5 million years, using mtDNA and AFLP markers. The species occur throughout New Zealand's subantarctic islands, but lack pelagic stages and any opportunity for anthropogenic transportation, and hence must rely on passive rafting for long-distance dispersal. They all have been directly observed to survive transoceanic kelp-rafting journeys in this region. Our analyses indicate that regular gene flow occurs among populations of all three species between all of the islands, especially those on either side of the subtropical front oceanographic boundary. Notwithstanding its perceived sporadic nature, long-distance kelp-rafting appears to enable significant gene flow among island populations separated by hundreds of kilometres of open ocean. PMID:23134782

  11. Inteins as indicators of gene flow in the halobacteria

    PubMed Central

    Soucy, Shannon M.; Fullmer, Matthew S.; Papke, R. Thane; Gogarten, Johann Peter

    2014-01-01

    This research uses inteins, a type of mobile genetic element, to infer patterns of gene transfer within the Halobacteria. We surveyed 118 genomes representing 26 genera of Halobacteria for intein sequences. We then used the presence-absence profile, sequence similarity and phylogenies from the inteins recovered to explore how intein distribution can provide insight on the dynamics of gene flow between closely related and divergent organisms. We identified 24 proteins in the Halobacteria that have been invaded by inteins at some point in their evolutionary history, including two proteins not previously reported to contain an intein. Furthermore, the size of an intein is used as a heuristic for the phase of the intein's life cycle. Larger size inteins are assumed to be the canonical two domain inteins, consisting of self-splicing and homing endonuclease domains (HEN); smaller sizes are assumed to have lost the HEN domain. For many halobacterial groups the consensus phylogenetic signal derived from intein sequences is compatible with vertical inheritance or with a strong gene transfer bias creating these clusters. Regardless, the coexistence of intein-free and intein-containing alleles reveal ongoing transfer and loss of inteins within these groups. Inteins were frequently shared with other Euryarchaeota and among the Bacteria, with members of the Cyanobacteria (Cyanothece, Anabaena), Bacteriodetes (Salinibacter), Betaproteobacteria (Delftia, Acidovorax), Firmicutes (Halanaerobium), Actinobacteria (Longispora), and Deinococcus-Thermus-group. PMID:25018750

  12. Genetics, Gene Flow, and Glaciation: The Case of the South American Limpet Nacella mytilina.

    PubMed

    González-Wevar, Claudio A; Rosenfeld, Sebastián; Segovia, Nicolás I; Hüne, Mathias; Gérard, Karin; Ojeda, Jaime; Mansilla, Andrés; Brickle, Paul; Díaz, Angie; Poulin, Elie

    2016-01-01

    Glacial episodes of the Quaternary, and particularly the Last Glacial Maximum (LGM) drastically altered the distribution of the Southern-Hemisphere biota, principally at higher latitudes. The irregular coastline of Patagonia expanding for more than 84.000 km constitutes a remarkable area to evaluate the effect of Quaternary landscape and seascape shifts over the demography of near-shore marine benthic organisms. Few studies describing the biogeographic responses of marine species to the LGM have been conducted in Patagonia, but existing data from coastal marine species have demonstrated marked genetic signatures of post-LGM recolonization and expansion. The kelp-dweller limpet Nacella mytilina is broadly distributed along the southern tip of South America and at the Falkland/Malvinas Islands. Considering its distribution, abundance, and narrow bathymetry, N. mytilina represents an appropriate model to infer how historical and contemporary processes affected the distribution of intraspecific genetic diversity and structure along the southern tip of South America. At the same time, it will be possible to determine how life history traits and the ecology of the species are responsible for the current pattern of gene flow and connectivity across the study area. We conducted phylogeographic and demographic inference analyses in N. mytilina from 12 localities along Pacific Patagonia (PP) and one population from the Falkland/Malvinas Islands (FI). Analyses of the mitochondrial gene COI in 300 individuals of N. mytilina revealed low levels of genetic polymorphism and the absence of genetic differentiation along PP. In contrast, FI showed a strong and significant differentiation from Pacific Patagonian populations. Higher levels of genetic diversity were also recorded in the FI population, together with a more expanded genealogy supporting the hypothesis of glacial persistence of the species in these islands. Haplotype genealogy, and mismatch analyses in the FI population

  13. Natural selection on marine carnivores elaborated a diverse family of classical MHC class I genes exhibiting haplotypic gene content variation and allelic polymorphism.

    PubMed

    Hammond, John A; Guethlein, Lisbeth A; Norman, Paul J; Parham, Peter

    2012-12-01

    Pinnipeds, marine carnivores, diverged from terrestrial carnivores ~45 million years ago, before their adaptation to marine environments. This lifestyle change exposed pinnipeds to different microbiota and pathogens, with probable impact on their MHC class I genes. Investigating this question, genomic sequences were determined for 71 MHC class I variants: 27 from harbor seal and 44 from gray seal. These variants form three MHC class I gene lineages, one comprising a pseudogene. The second, a candidate nonclassical MHC class I gene, comprises a nonpolymorphic transcribed gene related to dog DLA-79 and giant panda Aime-1906. The third is the diversity lineage, which includes 62 of the 71 seal MHC class I variants. All are transcribed, and they minimally represent six harbor and 12 gray seal MHC class I genes. Besides species-specific differences in gene number, seal MHC class I haplotypes exhibit gene content variation and allelic polymorphism. Patterns of sequence variation, and of positions for positively selected sites, indicate the diversity lineage genes are the seals' classical MHC class I genes. Evidence that expansion of diversity lineage genes began before gray and harbor seals diverged is the presence in both species of two distinctive sublineages of diversity lineage genes. Pointing to further expansion following the divergence are the presence of species-specific genes and greater MHC class I diversity in gray seals than harbor seals. The elaboration of a complex variable family of classical MHC class I genes in pinnipeds contrasts with the single, highly polymorphic classical MHC class I gene of dog and giant panda, terrestrial carnivores. PMID:23001684

  14. Natural selection on marine carnivores elaborated a diverse family of classical MHC class I genes exhibiting haplotypic gene content variation and allelic polymorphism

    PubMed Central

    Norman, Paul J.; Parham, Peter

    2012-01-01

    Pinnipeds, marine carnivores, diverged from terrestrial carnivores ~45 million years ago, before their adaptation to marine environments. This lifestyle change exposed pinnipeds to different microbiota and pathogens, with probable impact on their MHC class I genes. Investigating this question, genomic sequences were determined for 71 MHC class I variants: 27 from harbor seal and 44 from gray seal. These variants form three MHC class I gene lineages, one comprising a pseudogene. The second, a candidate nonclassical MHC class I gene, comprises a nonpolymorphic transcribed gene related to dog DLA-79 and giant panda Aime-1906. The third is the diversity lineage, which includes 62 of the 71 seal MHC class I variants. All are transcribed, and they minimally represent six harbor and 12 gray seal MHC class I genes. Besides species-specific differences in gene number, seal MHC class I haplotypes exhibit gene content variation and allelic polymorphism. Patterns of sequence variation, and of positions for positively selected sites, indicate the diversity lineage genes are the seals’ classical MHC class I genes. Evidence that expansion of diversity lineage genes began before gray and harbor seals diverged is the presence in both species of two distinctive sublineages of diversity lineage genes. Pointing to further expansion following the divergence are the presence of species-specific genes and greater MHC class I diversity in gray seals than harbor seals. The elaboration of a complex variable family of classical MHC class I genes in pinnipeds contrasts with the single, highly polymorphic classical MHC class I gene of dog and giant panda, terrestrial carnivores. PMID:23001684

  15. Observations of the atmospheric boundary layer height under marine upstream flow conditions at a coastal site

    NASA Astrophysics Data System (ADS)

    PeñA, A.; Gryning, S.-E.; Hahmann, A. N.

    2013-02-01

    AbstractWe investigate several lidar-type instruments and methodologies for boundary layer height (BLH) estimation during 2 days at a coastal site for winds that experience <span class="hlt">marine</span> upstream <span class="hlt">flow</span> conditions. Wavelet and profile fitting procedures on the aerosol backscatter signals from a ceilometer and an aerosol lidar reveal similar BLHs, but their agreement depends on the presence of clouds and the instrument signal, among others. BLHs derived by a threshold on the carrier-to-noise profiles of a wind lidar agree well with those derived by using a threshold on the backscatter profile of the ceilometer and are used as reference for a 10 day BLH intercomparison. Furthermore, the BLHs from the aerosol analysis are comparable to those derived from wind speed and direction profiles from combined mast/wind lidar measurements. The BLH derived from simulations performed with the Weather Research and Forecasting (WRF) model shows similar behavior compared to the lidar observations. The seasonal diurnal variation of the BLH for 2010, derived from the wind lidar and ceilometer thresholds, shows similar BLHs but generally higher values compared to that from WRF. No clear BLH diurnal variation is observed neither from the observations nor from the WRF model outputs, except in summer for the latter. Both observations and WRF model simulations reveal higher BLHs during autumn compared to spring time. These BLHs are used to evaluate the intra-annual variation and show high peaks in September, November, and February.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2013APS..DFDE13005S','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2013APS..DFDE13005S"><span id="translatedtitle">Simulation of <span class="hlt">Marine</span> Hydrokinetic Turbines in Unsteady <span class="hlt">Flow</span> using Vortex Particle Method</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Sale, Danny; Aliseda, Alberto</p> <p>2013-11-01</p> <p>A vortex particle method has been developed to study the performance and wake characteristics of <span class="hlt">Marine</span> Hydrokinetic turbines. The goals are to understand mean <span class="hlt">flow</span> and turbulent eddy effects on wake evolution, and the unsteady loading on the rotor and support structures. The vorticity-velocity formulation of the Navier-Stokes equations are solved using a hybrid Lagrangian-Eulerian method involving both vortex particle and spatial mesh discretizations. Particle strengths are modified by vortex stretching, diffusion, and body forces; these terms in the vorticity transport equation involve differential operators and are computed more efficiently on a Cartesian mesh using finite differences. High-order and moment-conserving interpolations allow the particles and mesh to exchange field quantities and particle strengths. An immersed boundary method which introduces a penalization term in the vorticity transport equations provides an efficient way to satisfy the no-slip boundary condition on solid boundaries. To provide further computational speedup, we investigate the use of multicore processors and graphics processing units using the OpenMP and OpenCL interfaces within the Parallel Particle-Mesh Library.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/20936320','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/20936320"><span id="translatedtitle">Identification of copper-induced <span class="hlt">genes</span> in the <span class="hlt">marine</span> alga Ulva compressa (Chlorophyta).</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Contreras-Porcia, Loretto; Dennett, Geraldine; González, Alberto; Vergara, Eva; Medina, Cristóbal; Correa, Juan A; Moenne, Alejandra</p> <p>2011-06-01</p> <p>In order to identify <span class="hlt">genes</span>/proteins involved in copper tolerance, the <span class="hlt">marine</span> alga Ulva compressa was cultivated with 10 μM copper for 3 days. The activities of antioxidant enzymes ascorbate peroxidase (AP), peroxiredoxin (PRX), thioredoxin (TRX), and glutathione-S-transferase (GST) and the level of lipoperoxides were determined in the alga cultivated with and without copper addition. Antioxidant enzyme activities and lipoperoxides level increased in response to copper excess, indicating that the alga was under oxidative stress. A cDNA library was prepared using U. compressa cultivated with 10 μM copper for 3 days. A total of 3 × 10(4) clones were isolated and 480 clones were sequenced, resulting in 235 non-redundant ESTs, of which 104 encode proteins with known functions. Among them, we identified proteins involved in (1) antioxidant metabolism such as AP, PRX, TRX, GST, and metalothionein (MET), (2) signal transduction, such as calmodulin (CAM), (3) calcium-dependent protein kinase (CDPK) and nucleoside diphosphate kinase (NDK), (4) <span class="hlt">gene</span> expression, (5) protein synthesis and degradation, and (6) chloroplast and mitochondria electron transport chains. Half of the identified proteins are potentially localized in organelles. The relative level of 18 <span class="hlt">genes</span>, including those coding for AP, PRX, TRX, GST, MET, CAM, CDPK, and NDK were determined by quantitative RT-PCR in the alga cultivated with 10 μM copper for 0 to 7 days. Transcript levels increased in response to copper stress and most of them reached a maximum at days 3 and 5. Thus, the selected <span class="hlt">genes</span> are induced by copper stress and they are probably involved in copper acclimation and tolerance. PMID:20936320</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3718166','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3718166"><span id="translatedtitle">Role of a Microcin-C–like biosynthetic <span class="hlt">gene</span> cluster in allelopathic interactions in <span class="hlt">marine</span> Synechococcus</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Paz-Yepes, Javier; Brahamsha, Bianca; Palenik, Brian</p> <p>2013-01-01</p> <p>Competition between phytoplankton species for nutrients and light has been studied for many years, but allelopathic interactions between them have been more difficult to characterize. We used liquid and plate assays to determine whether these interactions occur between <span class="hlt">marine</span> unicellular cyanobacteria of the genus Synechococcus. We have found a clear growth impairment of Synechococcus sp. CC9311 and Synechococcus sp. WH8102 when they are cultured in the presence of Synechococcus sp. CC9605. The genome of CC9605 contains a region showing homology to <span class="hlt">genes</span> of the Escherichia coli Microcin C (McC) biosynthetic pathway. McC is a ribosome-synthesized peptide that inhibits translation in susceptible strains. We show that the CC9605 McC <span class="hlt">gene</span> cluster is expressed and that three <span class="hlt">genes</span> (mccD, mccA, and mccB) are further induced by coculture with CC9311. CC9605 was resistant to McC purified from E. coli, whereas strains CC9311 and WH8102 were sensitive. Cloning the CC9605 McC biosynthetic <span class="hlt">gene</span> cluster into sensitive CC9311 led this strain to become resistant to both purified E. coli McC and Synechococcus sp. CC9605. A CC9605 mutant lacking mccA1, mccA2, and the N-terminal domain of mccB did not inhibit CC9311 growth, whereas the inhibition of WH8102 was reduced. Our results suggest that an McC-like molecule is involved in the allelopathic interactions with CC9605. PMID:23818639</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2823876','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2823876"><span id="translatedtitle"><span class="hlt">Flow</span> enhances photosynthesis in <span class="hlt">marine</span> benthic autotrophs by increasing the efflux of oxygen from the organism to the water</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Mass, Tali; Genin, Amatzia; Shavit, Uri; Grinstein, Mor; Tchernov, Dan</p> <p>2010-01-01</p> <p>Worldwide, many <span class="hlt">marine</span> coastal habitats are facing rapid deterioration due in part to human-driven changes in habitat characteristics, including changes in <span class="hlt">flow</span> patterns, a factor known to greatly affect primary production in corals, algae, and seagrasses. The effect of <span class="hlt">flow</span> traditionally is attributed to enhanced influx of nutrients and dissolved inorganic carbon (DIC) across the benthic boundary layer from the water to the organism however, here we report that the organism’s photosynthetic response to changes in the <span class="hlt">flow</span> is nearly instantaneous, and that neither nutrients nor DIC limits this rapid response. Using microelectrodes, dual-pulse amplitude-modulated fluorometry, particle image velocimetry, and real time mass-spectrometry with the common scleractinian coral Favia veroni, the alga Gracilaria cornea, and the seagrass Halophila stipulacea, we show that this augmented photosynthesis is due to <span class="hlt">flow</span>-driven enhancement of oxygen efflux from the organism to the water, which increases the affinity of the RuBisCO to CO2. No augmentation of photosynthesis was found in the absence of <span class="hlt">flow</span> or when <span class="hlt">flow</span> occurred, but the ambient concentration of oxygen was artificially elevated. We suggest that water motion should be considered a fundamental factor, equivalent to light and nutrients, in determining photosynthesis rates in <span class="hlt">marine</span> benthic autotrophs. PMID:20133799</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/1041485','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/1041485"><span id="translatedtitle">Extensive <span class="hlt">gene</span> <span class="hlt">flow</span> over Europe and possible speciation</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>VINCENOT, Dr. LUCIE; NARA, Dr. KAZUHIDE; STHULTZ, CHRISTOPHER; Labbe, Jessy L; DUBOIS, MARIE-PIERRE; TEDERSOO, LEHO; Martin, Francis; SELOSSE, Dr. MARC-ANDRE</p> <p>2012-01-01</p> <p>Biogeographical patterns and large-scale genetic structure have been little studied in ectomycorrhizal (EM) fungi, despite the ecological and economic importance of EM symbioses. We coupled population genetics and phylogenetic approaches to understand spatial structure in fungal populations on a continental scale. Using nine microsatellite markers, we characterized <span class="hlt">gene</span> <span class="hlt">flow</span> among 16 populations of the widespread EM basidiomycete Laccaria amethystina over Europe (i.e. over 2900 km). We also widened our scope to two additional populations from Japan (104 km away) and compared them with European populations through microsatellite markers and multilocus phylogenies, using three nuclear <span class="hlt">genes</span> (NAR, G6PD and ribosomal DNA) and two mitochondrial ribosomal <span class="hlt">genes</span>. European L. amethystina populations displayed limited differentiation (average FST = 0.041) and very weak isolation by distance (IBD). This panmictic European pattern may result from effective aerial dispersal of spores, high genetic diversity in populations and mutualistic interactions with multiple hosts that all facilitate migration. The multilocus phylogeny based on nuclear <span class="hlt">genes</span> confirmed that Japanese and European specimens were closely related but clustered on a geographical basis. By using microsatellite markers, we found that Japanese populations were strongly differentiated from the European populations (FST = 0.416), more than expected by extrapolating the European pattern of IBD. Population structure analyses clearly separated the populations into two clusters, i.e. European and Japanese clusters. We discuss the possibility of IBD in a continuous population (considering some evidence for a ring species over the Northern Hemisphere) vs. an allopatric speciation over Eurasia, making L. amethystina a promising model of intercontinental species for future studies.</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_5");'>5</a></li> <li><a href="#" onclick='return showDiv("page_6");'>6</a></li> <li class="active"><span>7</span></li> <li><a href="#" onclick='return showDiv("page_8");'>8</a></li> <li><a href="#" onclick='return showDiv("page_9");'>9</a></li> <li><a href="#" onclick='return showDiv("page_13");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_7 --> <div id="page_8" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_6");'>6</a></li> <li><a href="#" onclick='return showDiv("page_7");'>7</a></li> <li class="active"><span>8</span></li> <li><a href="#" onclick='return showDiv("page_9");'>9</a></li> <li><a href="#" onclick='return showDiv("page_10");'>10</a></li> <li><a href="#" onclick='return showDiv("page_13");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="141"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/26613339','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/26613339"><span id="translatedtitle">Reverse transcriptase <span class="hlt">genes</span> are highly abundant and transcriptionally active in <span class="hlt">marine</span> plankton assemblages.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Lescot, Magali; Hingamp, Pascal; Kojima, Kenji K; Villar, Emilie; Romac, Sarah; Veluchamy, Alaguraj; Boccara, Martine; Jaillon, Olivier; Iudicone, Daniele; Bowler, Chris; Wincker, Patrick; Claverie, Jean-Michel; Ogata, Hiroyuki</p> <p>2016-05-01</p> <p><span class="hlt">Genes</span> encoding reverse transcriptases (RTs) are found in most eukaryotes, often as a component of retrotransposons, as well as in retroviruses and in prokaryotic retroelements. We investigated the abundance, classification and transcriptional status of RTs based on Tara Oceans <span class="hlt">marine</span> metagenomes and metatranscriptomes encompassing a wide organism size range. Our analyses revealed that RTs predominate large-size fraction metagenomes (>5 μm), where they reached a maximum of 13.5% of the total <span class="hlt">gene</span> abundance. Metagenomic RTs were widely distributed across the phylogeny of known RTs, but many belonged to previously uncharacterized clades. Metatranscriptomic RTs showed distinct abundance patterns across samples compared with metagenomic RTs. The relative abundances of viral and bacterial RTs among identified RT sequences were higher in metatranscriptomes than in metagenomes and these sequences were detected in all metatranscriptome size fractions. Overall, these observations suggest an active proliferation of various RT-assisted elements, which could be involved in genome evolution or adaptive processes of plankton assemblage. PMID:26613339</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=168073','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=168073"><span id="translatedtitle">Genetic diversity in <span class="hlt">marine</span> algal virus communities as revealed by sequence analysis of DNA polymerase <span class="hlt">genes</span>.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Chen, F; Suttle, C A; Short, S M</p> <p>1996-01-01</p> <p>Algal-virus-specific PCR primers were used to amplify DNA polymerase <span class="hlt">gene</span> (pol) fragments (683 to 689 bp) from the virus-sized fraction (0.02 to 0.2 microns) concentrated from inshore and offshore water samples collected from the Gulf of Mexico. Algal-virus-like DNA pol <span class="hlt">genes</span> were detected in five samples collected from the surface and deep chlorophyll maximum. PCR products from an offshore station were cloned, and the genetic diversity of 33 fragments was examined by restriction fragment length polymorphism and sequence analysis. The five different genotypes or operational taxonomic units (OTUs) that were identified on the basis of restriction fragment length polymorphism banding patterns were present in different relative abundances (9 to 34%). One clone from each OTU was sequenced, and phylogenetic analysis showed that all of the OTUs fell within the family Phycodnaviridae. Four of the OTUs fell within a group of viruses (MpV) which infect the photosynthetic picoplankter Micromonas pusilla. The genetic diversity among these genotypes was as large as that previously found for MpV isolates from different oceans. The remaining genotype formed its own clade between viruses which infect M. pusilla and Chrysochromulina brevifilum. These results imply that <span class="hlt">marine</span> virus communities contain a diverse assemblage of MpV-like viruses, as well as other unknown members of the Phycodnaviridae. PMID:8702280</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4315400','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4315400"><span id="translatedtitle">Ubiquity and Diversity of Heterotrophic Bacterial nasA <span class="hlt">Genes</span> in Diverse <span class="hlt">Marine</span> Environments</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Jiang, Xuexia; Dang, Hongyue; Jiao, Nianzhi</p> <p>2015-01-01</p> <p>Nitrate uptake by heterotrophic bacteria plays an important role in <span class="hlt">marine</span> N cycling. However, few studies have investigated the diversity of environmental nitrate assimilating bacteria (NAB). In this study, the diversity and biogeographical distribution of NAB in several global oceans and particularly in the western Pacific marginal seas were investigated using both cultivation and culture-independent molecular approaches. Phylogenetic analyses based on 16S rRNA and nasA (encoding the large subunit of the assimilatory nitrate reductase) <span class="hlt">gene</span> sequences indicated that the cultivable NAB in South China Sea belonged to the α-Proteobacteria, γ-Proteobacteria and CFB (Cytophaga-Flavobacteria-Bacteroides) bacterial groups. In all the environmental samples of the present study, α-Proteobacteria, γ-Proteobacteria and Bacteroidetes were found to be the dominant nasA-harboring bacteria. Almost all of the α-Proteobacteria OTUs were classified into three Roseobacter-like groups (I to III). Clone library analysis revealed previously underestimated nasA diversity; e.g. the nasA <span class="hlt">gene</span> sequences affiliated with β-Proteobacteria, ε-Proteobacteria and Lentisphaerae were observed in the field investigation for the first time, to the best of our knowledge. The geographical and vertical distributions of seawater nasA-harboring bacteria indicated that NAB were highly diverse and ubiquitously distributed in the studied marginal seas and world oceans. Niche adaptation and separation and/or limited dispersal might mediate the NAB composition and community structure in different water bodies. In the shallow-water Kueishantao hydrothermal vent environment, chemolithoautotrophic sulfur-oxidizing bacteria were the primary NAB, indicating a unique nitrate-assimilating community in this extreme environment. In the coastal water of the East China Sea, the relative abundance of Alteromonas and Roseobacter-like nasA <span class="hlt">gene</span> sequences responded closely to algal blooms, indicating that NAB may be</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25647610','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25647610"><span id="translatedtitle">Ubiquity and diversity of heterotrophic bacterial nasA <span class="hlt">genes</span> in diverse <span class="hlt">marine</span> environments.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Jiang, Xuexia; Dang, Hongyue; Jiao, Nianzhi</p> <p>2015-01-01</p> <p>Nitrate uptake by heterotrophic bacteria plays an important role in <span class="hlt">marine</span> N cycling. However, few studies have investigated the diversity of environmental nitrate assimilating bacteria (NAB). In this study, the diversity and biogeographical distribution of NAB in several global oceans and particularly in the western Pacific marginal seas were investigated using both cultivation and culture-independent molecular approaches. Phylogenetic analyses based on 16S rRNA and nasA (encoding the large subunit of the assimilatory nitrate reductase) <span class="hlt">gene</span> sequences indicated that the cultivable NAB in South China Sea belonged to the α-Proteobacteria, γ-Proteobacteria and CFB (Cytophaga-Flavobacteria-Bacteroides) bacterial groups. In all the environmental samples of the present study, α-Proteobacteria, γ-Proteobacteria and Bacteroidetes were found to be the dominant nasA-harboring bacteria. Almost all of the α-Proteobacteria OTUs were classified into three Roseobacter-like groups (I to III). Clone library analysis revealed previously underestimated nasA diversity; e.g. the nasA <span class="hlt">gene</span> sequences affiliated with β-Proteobacteria, ε-Proteobacteria and Lentisphaerae were observed in the field investigation for the first time, to the best of our knowledge. The geographical and vertical distributions of seawater nasA-harboring bacteria indicated that NAB were highly diverse and ubiquitously distributed in the studied marginal seas and world oceans. Niche adaptation and separation and/or limited dispersal might mediate the NAB composition and community structure in different water bodies. In the shallow-water Kueishantao hydrothermal vent environment, chemolithoautotrophic sulfur-oxidizing bacteria were the primary NAB, indicating a unique nitrate-assimilating community in this extreme environment. In the coastal water of the East China Sea, the relative abundance of Alteromonas and Roseobacter-like nasA <span class="hlt">gene</span> sequences responded closely to algal blooms, indicating that NAB may be</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2011AGUFMOS52A..03W','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2011AGUFMOS52A..03W"><span id="translatedtitle">Experimental Investigation of Cross-<span class="hlt">Flow</span> Axis <span class="hlt">Marine</span> Hydrokinetic Turbines, Including Effects of Waves and Turbulence</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Wosnik, M.; Bachant, P.</p> <p>2011-12-01</p> <p>A new test bed for <span class="hlt">Marine</span> Hydrokinetic (MHK) turbines at the Center for Ocean Renewable Energy at the University of New Hampshire (UNH-CORE) was used to evaluate the performance of different cross-<span class="hlt">flow</span> axis hydrokinetic turbines, and investigate the effects of waves and turbulence on these devices. The test bed was designed and built to operate in the UNH tow and wave tank, which has a cross section of 3.67m (width) x 2.44m (depth). In the present configuration, tow speeds of up to 3 m/s can be achieved for smaller turbine models, and up to 1.5 m/s for large turbine models with low gear ratio. It features a flap style wave maker at one end that is capable of producing waves with 1-5 s periods up to 0.4 m wave height. Turbine thrust (drag) and mechanical power output (torque, angular velocity) were measured at tow speeds of 0.6-1.5 m/s for two cross-<span class="hlt">flow</span> axis MHK turbines: a Gorlov Helical Turbine (GHT) and a Lucid spherical turbine (LST). Both were provided by Lucid Energy Technologies, LLP, and have frontal areas of 1.3 (GHT) and 1.0 (LST) square meters, respectively. GHT performance was also measured in progressive waves of various periods, grid turbulence, and in the wake of a cylinder, installed upstream at various cross-stream locations. Overall, the GHT performs with higher power and thrust (drag) coefficients than the LST. A 2nd law efficiency, or kinetic exergy efficiency, was defined to calculate what fraction of the kinetic energy removed from the <span class="hlt">flow</span> is converted to usable shaft work by each turbine. The exergy efficiency varies with tip speed ratio but approaches 90% for the optimum operating conditions for each turbine. The fraction of kinetic energy removed from the fluid that is not converted to shaft work is redistributed into turbulent kinetic energy in the wake. Quantifying the kinetic energy <span class="hlt">flowing</span> out of the turbine is important for modeling of environmental transport processes and for predicting performance when turbines are used in arrays</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25363522','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25363522"><span id="translatedtitle">Locally adapted traits maintained in the face of high <span class="hlt">gene</span> <span class="hlt">flow</span>.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Fitzpatrick, S W; Gerberich, J C; Kronenberger, J A; Angeloni, L M; Funk, W C</p> <p>2015-01-01</p> <p><span class="hlt">Gene</span> <span class="hlt">flow</span> between phenotypically divergent populations can disrupt local adaptation or, alternatively, may stimulate adaptive evolution by increasing genetic variation. We capitalised on historical Trinidadian guppy transplant experiments to test the phenotypic effects of increased <span class="hlt">gene</span> <span class="hlt">flow</span> caused by replicated introductions of adaptively divergent guppies, which were translocated from high- to low-predation environments. We sampled two native populations prior to the onset of <span class="hlt">gene</span> <span class="hlt">flow</span>, six historic introduction sites, introduction sources and multiple downstream points in each basin. Extensive <span class="hlt">gene</span> <span class="hlt">flow</span> from introductions occurred in all streams, yet adaptive phenotypic divergence across a gradient in predation level was maintained. Descendants of guppies from a high-predation source site showed high phenotypic similarity with native low-predation guppies in as few as ~12 generations after <span class="hlt">gene</span> <span class="hlt">flow</span>, likely through a combination of adaptive evolution and phenotypic plasticity. Our results demonstrate that locally adapted phenotypes can be maintained despite extensive <span class="hlt">gene</span> <span class="hlt">flow</span> from divergent populations. PMID:25363522</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/21681483','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/21681483"><span id="translatedtitle">Impact of <span class="hlt">gene</span> stacking on <span class="hlt">gene</span> <span class="hlt">flow</span>: the case of maize.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Paul, Lénaïc; Angevin, Frédérique; Collonnier, Cécile; Messéan, Antoine</p> <p>2012-04-01</p> <p>To respect the European labelling threshold for the adventitious presence of genetically modified organisms (GMOs) in food and feed, stakeholders mainly rely on real-time PCR analysis, which provides a measurement expressed as a percentage of GM-DNA. However, this measurement veils the complexity of <span class="hlt">gene</span> <span class="hlt">flow</span>, especially in the case of <span class="hlt">gene</span> stacking. We have investigated the impact of <span class="hlt">gene</span> stacking on adventitious GM presence due to pollen <span class="hlt">flow</span> and seed admixture as well as its translation in terms of the percentage of GM-DNA in a non-GM maize harvest. In the case of varieties bearing one to four stacked events, we established a set of relationships between the percentage of GM kernels and the percentage of GM-DNA in a non-GM harvest as well as a set of relationships between the rate of seed admixture and the percentages of GM material in a non-GM harvest. Thanks to these relationships, and based on simulations with a <span class="hlt">gene</span> <span class="hlt">flow</span> model, we have been able to demonstrate that the number of events and the stacking structure of the emitting fields impact the ability of a non-GM maize producer to comply with given GM kernel or GM-DNA thresholds. We also show that a great variability in the rates of GM kernels, embryos and DNA results from seed admixture. Finally, the choice of a unit of measurement for a GM threshold in seed lots can have opposite effects on the ability of farmers to comply with a given threshold depending on whether they are crop or seed producers. PMID:21681483</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4745443','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4745443"><span id="translatedtitle">Phylogenetic Framework and Biosurfactant <span class="hlt">Gene</span> Expression Analysis of <span class="hlt">Marine</span> Bacillus spp. of Eastern Coastal Plain of Tamil Nadu</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Swaathy, Sreethar; Kavitha, Varadharajan; Sahaya Pravin, Arockiasamy; Sekaran, Ganesan; Gnanamani, Arumugam</p> <p>2014-01-01</p> <p>The present study emphasizes the diversity assessment of <span class="hlt">marine</span> Bacillus species with special reference to biosurfactant production, respective <span class="hlt">gene</span> expression, and discrimination among Bacillus licheniformis and Bacillus subtilis. Among the 200 individual species of eastern coastal plain of Tamil Nadu screened, five biosurfactant producing potential bacterial species with entirely different morphology were selected. Biochemical and 16S rRNA <span class="hlt">gene</span> sequence analysis suggested that all the said five species belong to Bacillus genera but differ in species levels. Biosurfactant of all the five species fluctuates in greater levels with respect to activity as well as to constituents but showed partial similarity to the commercially available surfactin. The expression of srf <span class="hlt">gene</span> was realized in all of the five species. However, the sfp <span class="hlt">gene</span> expression was observed only in three species. In conclusion, both B. licheniformis and B. subtilis demonstrate srf <span class="hlt">gene</span>; nevertheless, sfp <span class="hlt">gene</span> was expressed only by Bacillus subtilis. PMID:26904741</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/11048786','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/11048786"><span id="translatedtitle">Latitude-correlated genetic polymorphisms: selection or <span class="hlt">gene</span> <span class="hlt">flow</span>?</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Ciminelli, B M; Jodice, C; Scozzari, R; Corbo, R M; Nahum, M; Pompei, F; Santachiara-Benerecetti, S A; Santolamazza, C; Morpurgo, G P; Modiano, G</p> <p>2000-08-01</p> <p>Latitude-correlated polymorphisms can be due to either selection-driven evolution or <span class="hlt">gene</span> <span class="hlt">flow</span>. To discriminate between them, we propose an approach that studies subpopulations springing from a single population that have lived for generations at different latitudes and have had a low genetic admixture. These requirements are fulfilled to a large extent by Ashkenazi and Sephardi Jews. The original population lived at a latitude of 35 degrees N, where the Sephardis still live. The Ashkenazis, however, moved to a latitude of 50 degrees N, starting about 10 centuries ago. The present study examines 3 latitude-correlated polymorphisms: PGP, PGM1, and AHSG. We found that PGP*2 and AHSG*2 alleles most likely underwent selection-driven evolution, but that PGM1*ts allele was not similarly affected. Since temperature might have been considered a reasonable selective factor, we also studied a population living at >800 m above sea level from Aosta Valley (Italy). PMID:11048786</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/21709253','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/21709253"><span id="translatedtitle"><span class="hlt">Gene</span> <span class="hlt">flow</span> increases fitness at the warm edge of a species' range.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Sexton, Jason P; Strauss, Sharon Y; Rice, Kevin J</p> <p>2011-07-12</p> <p>According to theory, <span class="hlt">gene</span> <span class="hlt">flow</span> to marginal populations may stall or aid adaptation at range limits by swamping peripheral populations with maladaptive <span class="hlt">gene</span> <span class="hlt">flow</span> or by enhancing genetic variability and reducing inbreeding depression, respectively. We tested these contrasting predictions by manipulating patterns of <span class="hlt">gene</span> <span class="hlt">flow</span> of the annual plant, Mimulus laciniatus, at its warm range limit. <span class="hlt">Gene</span> <span class="hlt">flow</span> was experimentally applied by using crosses within warm-limit populations (selfed and outcrossed), between warm-limit populations, and between warm-limit and central range populations across two elevational transects. We measured the fitness of offspring in a common garden at the warm-edge species range limit. All sources of <span class="hlt">gene</span> <span class="hlt">flow</span> increased seedling emergence at the range limit, suggesting local inbreeding depression at both range limit populations; however, lifetime reproductive success only increased significantly when pollen originated from another warm-limit population. Center-to-warm-edge <span class="hlt">gene</span> <span class="hlt">flow</span> was maladaptive by delaying time to development at this warm, fast-drying range limit, whereas edge-to-edge <span class="hlt">gene</span> <span class="hlt">flow</span> hastened emergence time and time to reproduction. By empirically testing theory on the effects of <span class="hlt">gene</span> <span class="hlt">flow</span> on the formation of geographic range limits, we find benefits of <span class="hlt">gene</span> <span class="hlt">flow</span> among populations to be greatest when <span class="hlt">gene</span> <span class="hlt">flow</span> is between populations occupying the same range limit. Our results emphasize the overlooked importance of <span class="hlt">gene</span> <span class="hlt">flow</span> among populations occurring near the same range limit and highlight the potential for prescriptive <span class="hlt">gene</span> <span class="hlt">flow</span> as a conservation option for populations at risk from climate change. PMID:21709253</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/23580401','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/23580401"><span id="translatedtitle">The Himalayas: barrier and conduit for <span class="hlt">gene</span> <span class="hlt">flow</span>.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Gayden, Tenzin; Perez, Annabel; Persad, Patrice J; Bukhari, Areej; Chennakrishnaiah, Shilpa; Simms, Tanya; Maloney, Trisha; Rodriguez, Kristina; Herrera, Rene J</p> <p>2013-06-01</p> <p>The Himalayan mountain range is strategically located at the crossroads of the major cultural centers in Asia, the Middle East and Europe. Although previous Y-chromosome studies indicate that the Himalayas served as a natural barrier for <span class="hlt">gene</span> <span class="hlt">flow</span> from the south to the Tibetan plateau, this region is believed to have played an important role as a corridor for human migrations between East and West Eurasia along the ancient Silk Road. To evaluate the effects of the Himalayan mountain range in shaping the maternal lineages of populations residing on either side of the cordillera, we analyzed mitochondrial DNA variation in 344 samples from three Nepalese collections (Newar, Kathmandu and Tamang) and a general population of Tibet. Our results revealed a predominantly East Asian-specific component in Tibet and Tamang, whereas Newar and Kathmandu are both characterized by a combination of East and South Central Asian lineages. Interestingly, Newar and Kathmandu harbor several deep-rooted Indian lineages, including M2, R5, and U2, whose coalescent times from this study (U2, >40 kya) and previous reports (M2 and R5, >50 kya) suggest that Nepal was inhabited during the initial peopling of South Central Asia. Comparisons with our previous Y-chromosome data indicate sex-biased migrations in Tamang and a founder effect and/or genetic drift in Tamang and Newar. Altogether, our results confirm that while the Himalayas acted as a geographic barrier for human movement from the Indian subcontinent to the Tibetan highland, it also served as a conduit for <span class="hlt">gene</span> <span class="hlt">flow</span> between Central and East Asia. PMID:23580401</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4494067','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4494067"><span id="translatedtitle">Molecular Diversity and <span class="hlt">Gene</span> Evolution of the Venom Arsenal of Terebridae Predatory <span class="hlt">Marine</span> Snails</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Gorson, Juliette; Ramrattan, Girish; Verdes, Aida; Wright, Elizabeth M.; Kantor, Yuri; Rajaram Srinivasan, Ramakrishnan; Musunuri, Raj; Packer, Daniel; Albano, Gabriel; Qiu, Wei-Gang; Holford, Mandë</p> <p>2015-01-01</p> <p>Venom peptides from predatory organisms are a resource for investigating evolutionary processes such as adaptive radiation or diversification, and exemplify promising targets for biomedical drug development. Terebridae are an understudied lineage of conoidean snails, which also includes cone snails and turrids. Characterization of cone snail venom peptides, conotoxins, has revealed a cocktail of bioactive compounds used to investigate physiological cellular function, predator-prey interactions, and to develop novel therapeutics. However, venom diversity of other conoidean snails remains poorly understood. The present research applies a venomics approach to characterize novel terebrid venom peptides, teretoxins, from the venom gland transcriptomes of Triplostephanus anilis and Terebra subulata. Next-generation sequencing and de novo assembly identified 139 putative teretoxins that were analyzed for the presence of canonical peptide features as identified in conotoxins. To meet the challenges of de novo assembly, multiple approaches for cross validation of findings were performed to achieve reliable assemblies of venom duct transcriptomes and to obtain a robust portrait of Terebridae venom. Phylogenetic methodology was used to identify 14 teretoxin <span class="hlt">gene</span> superfamilies for the first time, 13 of which are unique to the Terebridae. Additionally, basic local algorithm search tool homology-based searches to venom-related <span class="hlt">genes</span> and posttranslational modification enzymes identified a convergence of certain venom proteins, such as actinoporin, commonly found in venoms. This research provides novel insights into venom evolution and recruitment in Conoidean predatory <span class="hlt">marine</span> snails and identifies a plethora of terebrid venom peptides that can be used to investigate fundamental questions pertaining to <span class="hlt">gene</span> evolution. PMID:26025559</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/26380680','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/26380680"><span id="translatedtitle">Contrasting demographic history and <span class="hlt">gene</span> <span class="hlt">flow</span> patterns of two mangrove species on either side of the Central American Isthmus.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Cerón-Souza, Ivania; Gonzalez, Elena G; Schwarzbach, Andrea E; Salas-Leiva, Dayana E; Rivera-Ocasio, Elsie; Toro-Perea, Nelson; Bermingham, Eldredge; McMillan, W Owen</p> <p>2015-08-01</p> <p>Comparative phylogeography offers a unique opportunity to understand the interplay between past environmental events and life-history traits on diversification of unrelated but co-distributed species. Here, we examined the effects of the quaternary climate fluctuations and palaeomarine currents and present-day <span class="hlt">marine</span> currents on the extant patterns of genetic diversity in the two most conspicuous mangrove species of the Neotropics. The black (Avicennia germinans, Avicenniaceae) and the red (Rhizophora mangle, Rhizophoraceae) mangroves have similar geographic ranges but are very distantly related and show striking differences on their life-history traits. We sampled 18 Atlantic and 26 Pacific locations for A. germinans (N = 292) and R. mangle (N = 422). We performed coalescence simulations using microsatellite diversity to test for evidence of population change associated with quaternary climate fluctuations. In addition, we examined whether patterns of genetic variation were consistent with the directions of major <span class="hlt">marine</span> (historical and present day) currents in the region. Our demographic analysis was grounded within a phylogeographic framework provided by the sequence analysis of two chloroplasts and one flanking microsatellite region in a subsample of individuals. The two mangrove species shared similar biogeographic histories including: (1) strong genetic breaks between Atlantic and Pacific ocean basins associated with the final closure of the Central American Isthmus (CAI), (2) evidence for simultaneous population declines between the mid-Pleistocene and early Holocene, (3) asymmetric historical migration with higher <span class="hlt">gene</span> <span class="hlt">flow</span> from the Atlantic to the Pacific oceans following the direction of the palaeomarine current, and (4) contemporary <span class="hlt">gene</span> <span class="hlt">flow</span> between West Africa and South America following the major Atlantic Ocean currents. Despite the remarkable differences in life-history traits of mangrove species, which should have had a strong influence on seed</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4569042','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4569042"><span id="translatedtitle">Contrasting demographic history and <span class="hlt">gene</span> <span class="hlt">flow</span> patterns of two mangrove species on either side of the Central American Isthmus</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Cerón-Souza, Ivania; Gonzalez, Elena G; Schwarzbach, Andrea E; Salas-Leiva, Dayana E; Rivera-Ocasio, Elsie; Toro-Perea, Nelson; Bermingham, Eldredge; McMillan, W Owen</p> <p>2015-01-01</p> <p>Comparative phylogeography offers a unique opportunity to understand the interplay between past environmental events and life-history traits on diversification of unrelated but co-distributed species. Here, we examined the effects of the quaternary climate fluctuations and palaeomarine currents and present-day <span class="hlt">marine</span> currents on the extant patterns of genetic diversity in the two most conspicuous mangrove species of the Neotropics. The black (Avicennia germinans, Avicenniaceae) and the red (Rhizophora mangle, Rhizophoraceae) mangroves have similar geographic ranges but are very distantly related and show striking differences on their life-history traits. We sampled 18 Atlantic and 26 Pacific locations for A. germinans (N = 292) and R. mangle (N = 422). We performed coalescence simulations using microsatellite diversity to test for evidence of population change associated with quaternary climate fluctuations. In addition, we examined whether patterns of genetic variation were consistent with the directions of major <span class="hlt">marine</span> (historical and present day) currents in the region. Our demographic analysis was grounded within a phylogeographic framework provided by the sequence analysis of two chloroplasts and one flanking microsatellite region in a subsample of individuals. The two mangrove species shared similar biogeographic histories including: (1) strong genetic breaks between Atlantic and Pacific ocean basins associated with the final closure of the Central American Isthmus (CAI), (2) evidence for simultaneous population declines between the mid-Pleistocene and early Holocene, (3) asymmetric historical migration with higher <span class="hlt">gene</span> <span class="hlt">flow</span> from the Atlantic to the Pacific oceans following the direction of the palaeomarine current, and (4) contemporary <span class="hlt">gene</span> <span class="hlt">flow</span> between West Africa and South America following the major Atlantic Ocean currents. Despite the remarkable differences in life-history traits of mangrove species, which should have had a strong influence on seed</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2391162','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2391162"><span id="translatedtitle"><span class="hlt">Gene</span> <span class="hlt">flow</span> and the genealogical history of Heliconius heurippa</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p></p> <p>2008-01-01</p> <p>Background The neotropical butterfly Heliconius heurippa has a hybrid colour pattern, which also contributes to reproductive isolation, making it a likely example of hybrid speciation. Here we used phylogenetic and coalescent-based analyses of multilocus sequence data to investigate the origin of H. heurippa. Results We sequenced a mitochondrial region (CoI and CoII), a sex-linked locus (Tpi) and two autosomal loci (w and sd) from H. heurippa and the putative parental species, H. cydno and H. melpomene. These were analysed in combination with data from two previously sequenced autosomal loci, Dll and Inv. H. heurippa was monophyletic at mtDNA and Tpi, but showed a shared distribution of alleles derived from both parental lineages at all four autosomal loci. Estimates of genetic differentiation showed that H. heurippa is closer to H. cydno at mtDNA and three autosomal loci, intermediate at Tpi, and closer to H. melpomene at Dll. Using coalescent simulations with the Isolation-Migration model (IM), we attempted to establish the incidence of <span class="hlt">gene</span> <span class="hlt">flow</span> in the origin of H. heurippa. This analysis suggested that ongoing introgression is frequent between all three species and variable in extent between loci. Conclusion Introgression, which is a necessary precursor of hybrid speciation, seems to have also blurred the coalescent history of these species. The origin of Heliconius heurippa may have been restricted to introgression of few colour pattern <span class="hlt">genes</span> from H. melpomene into the H. cydno genome, with little evidence of genomic mosaicism. PMID:18454858</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4771337','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4771337"><span id="translatedtitle">Ultrafiltration and Microarray for Detection of Microbial Source Tracking Marker and Pathogen <span class="hlt">Genes</span> in Riverine and <span class="hlt">Marine</span> Systems</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Li, Xiang; Harwood, Valerie J.; Nayak, Bina</p> <p>2016-01-01</p> <p>Pathogen identification and microbial source tracking (MST) to identify sources of fecal pollution improve evaluation of water quality. They contribute to improved assessment of human health risks and remediation of pollution sources. An MST microarray was used to simultaneously detect <span class="hlt">genes</span> for multiple pathogens and indicators of fecal pollution in freshwater, <span class="hlt">marine</span> water, sewage-contaminated freshwater and <span class="hlt">marine</span> water, and treated wastewater. Dead-end ultrafiltration (DEUF) was used to concentrate organisms from water samples, yielding a recovery efficiency of >95% for Escherichia coli and human polyomavirus. Whole-genome amplification (WGA) increased <span class="hlt">gene</span> copies from ultrafiltered samples and increased the sensitivity of the microarray. Viruses (adenovirus, bocavirus, hepatitis A virus, and human polyomaviruses) were detected in sewage-contaminated samples. Pathogens such as Legionella pneumophila, Shigella flexneri, and Campylobacter fetus were detected along with <span class="hlt">genes</span> conferring resistance to aminoglycosides, beta-lactams, and tetracycline. Nonmetric dimensional analysis of MST marker <span class="hlt">genes</span> grouped sewage-spiked freshwater and <span class="hlt">marine</span> samples with sewage and apart from other fecal sources. The sensitivity (percent true positives) of the microarray probes for <span class="hlt">gene</span> targets anticipated in sewage was 51 to 57% and was lower than the specificity (percent true negatives; 79 to 81%). A linear relationship between <span class="hlt">gene</span> copies determined by quantitative PCR and microarray fluorescence was found, indicating the semiquantitative nature of the MST microarray. These results indicate that ultrafiltration coupled with WGA provides sufficient nucleic acids for detection of viruses, bacteria, protozoa, and antibiotic resistance <span class="hlt">genes</span> by the microarray in applications ranging from beach monitoring to risk assessment. PMID:26729716</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/26729716','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/26729716"><span id="translatedtitle">Ultrafiltration and Microarray for Detection of Microbial Source Tracking Marker and Pathogen <span class="hlt">Genes</span> in Riverine and <span class="hlt">Marine</span> Systems.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Li, Xiang; Harwood, Valerie J; Nayak, Bina; Weidhaas, Jennifer L</p> <p>2016-03-01</p> <p>Pathogen identification and microbial source tracking (MST) to identify sources of fecal pollution improve evaluation of water quality. They contribute to improved assessment of human health risks and remediation of pollution sources. An MST microarray was used to simultaneously detect <span class="hlt">genes</span> for multiple pathogens and indicators of fecal pollution in freshwater, <span class="hlt">marine</span> water, sewage-contaminated freshwater and <span class="hlt">marine</span> water, and treated wastewater. Dead-end ultrafiltration (DEUF) was used to concentrate organisms from water samples, yielding a recovery efficiency of >95% for Escherichia coli and human polyomavirus. Whole-genome amplification (WGA) increased <span class="hlt">gene</span> copies from ultrafiltered samples and increased the sensitivity of the microarray. Viruses (adenovirus, bocavirus, hepatitis A virus, and human polyomaviruses) were detected in sewage-contaminated samples. Pathogens such as Legionella pneumophila, Shigella flexneri, and Campylobacter fetus were detected along with <span class="hlt">genes</span> conferring resistance to aminoglycosides, beta-lactams, and tetracycline. Nonmetric dimensional analysis of MST marker <span class="hlt">genes</span> grouped sewage-spiked freshwater and <span class="hlt">marine</span> samples with sewage and apart from other fecal sources. The sensitivity (percent true positives) of the microarray probes for <span class="hlt">gene</span> targets anticipated in sewage was 51 to 57% and was lower than the specificity (percent true negatives; 79 to 81%). A linear relationship between <span class="hlt">gene</span> copies determined by quantitative PCR and microarray fluorescence was found, indicating the semiquantitative nature of the MST microarray. These results indicate that ultrafiltration coupled with WGA provides sufficient nucleic acids for detection of viruses, bacteria, protozoa, and antibiotic resistance <span class="hlt">genes</span> by the microarray in applications ranging from beach monitoring to risk assessment. PMID:26729716</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://pubs.er.usgs.gov/publication/70131494','USGSPUBS'); return false;" href="http://pubs.er.usgs.gov/publication/70131494"><span id="translatedtitle">Sex-biased <span class="hlt">gene</span> <span class="hlt">flow</span> among elk in the greater Yellowstone ecosystem</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>, Brian K. Hand; , Shanyuan Chen; , N. Anderson; , A. Beja-Pereira; Cross, Paul C.; , M. Ebinger; , H. Edwards; , R.A. Garrott; , M.D. Kardos; Kauffman, Matthew J.; , E.L. Landguth; , A. Middleton; , B. Scurlock; , P.J. White; , P. Zager; , M.K. Schwartz; , G. Luikart</p> <p>2014-01-01</p> <p>We quantified patterns of population genetic structure to help understand <span class="hlt">gene</span> <span class="hlt">flow</span> among elk populations across the Greater Yellowstone Ecosystem. We sequenced 596 base pairs of the mitochondrial control region of 380 elk from eight populations. Analysis revealed high mitochondrial DNA variation within populations, averaging 13.0 haplotypes with high mean <span class="hlt">gene</span> diversity (0.85). The genetic differentiation among populations for mitochondrial DNA was relatively high (FST = 0.161; P = 0.001) compared to genetic differentiation for nuclear microsatellite data (FST = 0.002; P = 0.332), which suggested relatively low female <span class="hlt">gene</span> <span class="hlt">flow</span> among populations. The estimated ratio of male to female <span class="hlt">gene</span> <span class="hlt">flow</span> (mm/mf = 46) was among the highest we have seen reported for large mammals. Genetic distance (for mitochondrial DNA pairwise FST) was not significantly correlated with geographic (Euclidean) distance between populations (Mantel’s r = 0.274, P = 0.168). Large mitochondrial DNA genetic distances (e.g., FST > 0.2) between some of the geographically closest populations (<65 km) suggested behavioral factors and/or landscape features might shape female <span class="hlt">gene</span> <span class="hlt">flow</span> patterns. Given the strong sex-biased <span class="hlt">gene</span> <span class="hlt">flow</span>, future research and conservation efforts should consider the sexes separately when modeling corridors of <span class="hlt">gene</span> <span class="hlt">flow</span> or predicting spread of maternally transmitted diseases. The growing availability of genetic data to compare male vs. female <span class="hlt">gene</span> <span class="hlt">flow</span> provides many exciting opportunities to explore the magnitude, causes, and implications of sex-biased <span class="hlt">gene</span> <span class="hlt">flow</span> likely to occur in many species</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/11351409','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/11351409"><span id="translatedtitle">Potential multidrug resistance <span class="hlt">gene</span> POHL: an ecologically relevant indicator in <span class="hlt">marine</span> sponges.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Krasko, A; Kurelec, B; Batel, R; Müller, I M; Müller, W E</p> <p>2001-01-01</p> <p> correlated with the level of expression of the potential multidrug resistance <span class="hlt">gene</span> POHL in G. cydonium. This report demonstrates that the detoxification POH pathway, here mediated by the G. cydonium GCPOHL <span class="hlt">gene</span>, is an additional marker for the assessment of the environmental load in a given <span class="hlt">marine</span> area. PMID:11351409</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://pubs.er.usgs.gov/publication/70162429','USGSPUBS'); return false;" href="http://pubs.er.usgs.gov/publication/70162429"><span id="translatedtitle">Analysis of the nucleoprotein <span class="hlt">gene</span> identifies three distinct lineages of viral haemorrhagic septicemia virus (VHSV) within the European <span class="hlt">marine</span> environment</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Snow, M.; Cunningham, C.O.; Melvin, W.T.; Kurath, G.</p> <p>1999-01-01</p> <p>A ribonuclease (RNase) protection assay (RPA) has been used to detect nucleotide sequence variation within the nucleoprotein <span class="hlt">gene</span> of 39 viral haemorrhagic septicaemia virus (VHSV) isolates of European <span class="hlt">marine</span> origin. The classification of VHSV isolates based on RPA cleavage patterns permitted the identification of ten distinct groups of viruses based on differences at the molecular level. The nucleotide sequence of representatives of each of these groupings was determined and subjected to phylogenetic analysis. This revealed grouping of the European <span class="hlt">marine</span> isolates of VHSV into three genotypes circulating within distinct geographic areas. A fourth genotype was identified comprising isolates originating from North America. Phylogenetic analyses indicated that VHSV isolates recovered from wild caught fish around the British Isles were genetically related to isolates responsible for losses in farmed turbot. Furthermore, a relationship between naturally occurring <span class="hlt">marine</span> isolates and VHSV isolates causing mortality among rainbow trout in continental Europe was demonstrated. Analysis of the nucleoprotein <span class="hlt">gene</span> identifies distinct lineages of viral haemorrhagic septicaemia virus within the European <span class="hlt">marine</span> environment. Virus Res. 63, 35-44. Available from: </p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_6");'>6</a></li> <li><a href="#" onclick='return showDiv("page_7");'>7</a></li> <li class="active"><span>8</span></li> <li><a href="#" onclick='return showDiv("page_9");'>9</a></li> <li><a href="#" onclick='return showDiv("page_10");'>10</a></li> <li><a href="#" onclick='return showDiv("page_13");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_8 --> <div id="page_9" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_7");'>7</a></li> <li><a href="#" onclick='return showDiv("page_8");'>8</a></li> <li class="active"><span>9</span></li> <li><a href="#" onclick='return showDiv("page_10");'>10</a></li> <li><a href="#" onclick='return showDiv("page_11");'>11</a></li> <li><a href="#" onclick='return showDiv("page_13");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="161"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2016GML....36...25S','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2016GML....36...25S"><span id="translatedtitle">Conductive heat <span class="hlt">flow</span> and nonlinear geothermal gradients in <span class="hlt">marine</span> sediments—observations from Ocean Drilling Program boreholes</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Stranne, Christian; O'Regan, Matt</p> <p>2016-02-01</p> <p>A basic premise in <span class="hlt">marine</span> heat <span class="hlt">flow</span> studies is that the temperature gradient varies with depth as a function of the bulk thermal conductivity of the sediments. As sediments become more deeply buried, compaction reduces the porosity and causes an increase in the bulk thermal conductivity. Therefore, while the heat <span class="hlt">flow</span> may remain constant with depth, the thermal gradient is not necessarily linear. However, it has been argued that measurements showing increased sediment thermal conductivity with burial depth may be caused by a horizontal measurement bias generated by increasing anisotropy in sediments during consolidation. This study reanalyses a synthesis of Ocean Drilling Program data from 186 boreholes, and investigates the occurrence of nonlinear geothermal gradients in <span class="hlt">marine</span> sediments. The aim is to identify whether observed downhole changes in thermal conductivity influence the measured temperature gradient, and to investigate potential errors in the prediction of in-situ temperatures derived from the extrapolation of near-surface thermal gradients. The results indicate that the measured thermal conductivity does influence the geothermal gradient. Furthermore, comparisons between shallow measurements (<10 m) from surface heat <span class="hlt">flow</span> surveys and the deeply constrained temperature data from 98 ODP boreholes indicate that the shallow gradients are consistently higher by on average 19 °C km-1. This is consistent with higher porosity and generally lower thermal conductivity in near-seafloor sediments, and highlights the need to develop robust porosity-thermal conductivity models to accurately predict temperatures at depth from shallow heat <span class="hlt">flow</span> surveys.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2014EGUGA..16.4814K','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2014EGUGA..16.4814K"><span id="translatedtitle">Preliminary results of <span class="hlt">marine</span> heat <span class="hlt">flow</span> measurements in the Canadian Beaufort Sea and its implications for intermittent methane fluid expulsion</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Kim, Young-Gyun; Jin, Young Keun; Kuk Hong, Jong; Riedel, Michael; Lee, Sang-Mook</p> <p>2014-05-01</p> <p><span class="hlt">Marine</span> heat <span class="hlt">flow</span> measured at subsurface interval of a few meters using a heat probe is one of useful approaches to show the status of fluid circulation within the <span class="hlt">marine</span> sediments, even though it can show only a snapshot of long-term variation caused by the fluid circulation. Expedition ARA04C using IBRV Araon was carried out in the Canadian Beaufort Sea during 6-24 September 2013 as Korea/Canada/USA international cooperative research. During the expedition, multidisciplinary programs including multichannel seismic survey, sediment coring, water sampling, atmospheric observation, and heat <span class="hlt">flow</span> measurement were carried out over the continental shelf and slope area. In particular, Beaufort Shelf, one of regions experiencing fast ocean warming in the past several decades, shows characteristic features associated with degradation of permafrost reaching at the continental shelf. In this context, 8 sites for <span class="hlt">marine</span> heat <span class="hlt">flow</span> measurements were chosen: 1) in/outside of the flat-topped mud volcano located in the continental slope as one of fluid expulsion features, 2) along a transect line on the eastern slope of MacKenzie Trough where degradation of permafrost may occur, and 3) at a site closed to IODP pre-proposal #753 as reference. Unfortunately, attempts to measure in-situ thermal conductivity of sediments were failed due to instrument problem. Geothermal gradient observed on the mud volcano flat-top is much higher than ones from the reference site and outside of the volcano, indicating that there occur intermittent fluid expulsions restricted within the volcano. High methane concentration detected in bottom water column by 10 meters above the volcano top is indicative of methane fluid expulsion. Further detailed heat <span class="hlt">flow</span> study in association with analysis of physical properties of sediment cores through all sites would increase our understanding of nature of methane expulsion emitted from sediments in linkage with degradation of permafrost over the arctic shelf.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/23980394','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/23980394"><span id="translatedtitle">Hominin evolution and <span class="hlt">gene</span> <span class="hlt">flow</span> in the Pleistocene Africa.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Ovchinnikov, Igor V</p> <p>2013-01-01</p> <p>Africa demonstrates a complex process of the hominin evolution with a series of adaptive radiations during several millions of years that led to diverse morphological forms. Recently, Hammer et al. (2011) and Harvati et al. (2011) provided integrated morphological and genetic evidence of interbreeding between modern humans and unknown archaic hominins in Africa as recently as 35,000 years ago. However, a genetic evidence of hybridization between hominin lineages during the Lower and Middle Pleistocene epochs is unknown and the direct retrieval of DNA from extinct lineages of African hominins remains elusive. The availability of both nuclear and mitochondrial genome sequences from modern humans, Neanderthals, and Denisovans allows collecting nuclear DNA sequences of mitochondrial origin (numts) inserted into the nuclear genome of the ancestral hominin lineages and drawing conclusions about the hominin evolution in the remote past. The mtDNA and numt analysis uncovered a deep division of mtDNA lineages that existed in African hominins in the Middle Pleistocene. The first cluster included the human and Neanderthal-like mtDNA sequences while the second consisted of DNA sequences that are known today as mtAncestor-1, a nuclear fossil of the mtDNA, and the Denisova mtDNA isolated from a bone and a tooth found in southern Siberia. The two groups initially diverged 610,000-1,110,000 years ago. Approximately 220,000 years after the primary split, the Denisova - mtAncestor-1 mtDNA lineages mixed with the mtDNA pool of an ancestral population of Neanderthals and modern humans. This admixture after the profound division is demonstrated by the transposition of the Denisova-like mtDNA sequence into the nuclear genome of an ancestor of Neanderthals and modern humans. This finding suggests the matrilineal genetic structure among the Middle Pleistocene hominins as well as the existence of <span class="hlt">gene</span> <span class="hlt">flow</span> between African hominin lineages. Through paleogenomic analyses, it is impossible to</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/19457182','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/19457182"><span id="translatedtitle"><span class="hlt">Gene</span> <span class="hlt">flow</span> by larval dispersal in the Antarctic notothenioid fish Gobionotothen gibberifrons.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Matschiner, Michael; Hanel, Reinhold; Salzburger, Walter</p> <p>2009-06-01</p> <p>The diversification of the teleost suborder Notothenioidei (Perciformes) in Antarctic waters provides one of the most striking examples of a <span class="hlt">marine</span> adaptive radiation. Along with a number of adaptations to the cold environment, such as the evolution of antifreeze glycoproteins, notothenioids diversified into eight families and at least 130 species. Here, we investigate the genetic population structure of the humped rockcod (Gobionotothen gibberifrons), a benthic notothenioid fish. Six populations were sampled at different locations around the Scotia Sea, comprising a large part of the species' distribution range (N = 165). Our analyses based on mitochondrial DNA sequence data (352 bp) and eight microsatellite markers reveal a lack of genetic structuring over large geographic distances (Phi(ST) < or = 0.058, F(ST) < or = 0.005, P values nonsignificant). In order to test whether this was due to passive larval dispersal, we used GPS-tracked drifter trajectories, which approximate movement of passive surface particles with ocean currents. The drifter data indicate that the Antarctic Circumpolar Current (ACC) connects the sampling locations in one direction only (west-east), and that passive transport is possible within the 4-month larval period of G. gibberifrons. Indeed, when applying the isolation-with-migration model in IMA, strong unidirectional west-east migration rates are detected in the humped rockcod. This leads us to conclude that, in G. gibberifrons, genetic differentiation is prevented by <span class="hlt">gene</span> <span class="hlt">flow</span> via larval dispersal with the ACC. PMID:19457182</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/22097887','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/22097887"><span id="translatedtitle">Matching genetics with oceanography: directional <span class="hlt">gene</span> <span class="hlt">flow</span> in a Mediterranean fish species.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Schunter, C; Carreras-Carbonell, J; Macpherson, E; Tintoré, J; Vidal-Vijande, E; Pascual, A; Guidetti, P; Pascual, M</p> <p>2011-12-01</p> <p>Genetic connectivity and geographic fragmentation are two opposing mechanisms determining the population structure of species. While the first homogenizes the genetic background across populations the second one allows their differentiation. Therefore, knowledge of processes affecting dispersal of <span class="hlt">marine</span> organisms is crucial to understand their genetic distribution patterns and for the effective management of their populations. In this study, we use genetic analyses of eleven microsatellites in combination with oceanographic satellite and dispersal simulation data to determine distribution patterns for Serranus cabrilla, a ubiquitous demersal broadcast spawner, in the Mediterranean Sea. Pairwise population F(ST) values ranged between -0.003 and 0.135. Two genetically distinct clusters were identified, with a clear division located between the oceanographic discontinuities at the Ibiza Channel (IC) and the Almeria-Oran Front (AOF), revealing an admixed population in between. The Balearic Front (BF) also appeared to dictate population structure. Directional <span class="hlt">gene</span> <span class="hlt">flow</span> on the Spanish coast was observed as S. cabrilla dispersed from west to east over the AOF, from north to south on the IC and from south of the IC towards the Balearic Islands. Correlations between genetic and oceanographic data were highly significant. Seasonal changes in current patterns and the relationship between ocean circulation patterns and spawning season may also play an important role in population structure around oceanographic fronts. PMID:22097887</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/19967877','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/19967877"><span id="translatedtitle">Wolverine <span class="hlt">gene</span> <span class="hlt">flow</span> across a narrow climatic niche.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Schwartz, Michael K; Copeland, Jeffrey P; Anderson, Neil J; Squires, John R; Inman, Robert M; McKelvey, Kevin S; Pilgrim, Kristy L; Waits, Lisette P; Cushman, Samuel A</p> <p>2009-11-01</p> <p>Wolverines (Gulo gulo) are one of the rarest carnivores in the contiguous United States. Effective population sizes in Montana, Idaho, and Wyoming, where most of the wolverines in the contiguous United States exist, were calculated to be 35 (credible limits, 28 52) suggesting low abundance. Landscape features that influence wolverine population substructure and <span class="hlt">gene</span> <span class="hlt">flow</span> are largely unknown. Recent work has identified strong associations between areas with persistent spring snow and wolverine presence and range. We tested whether a dispersal model in which wolverines prefer to disperse through areas characterized by persistent spring snow cover produced least-cost paths among all individuals that correlated with genetic distance among individuals. Models simulating large preferences for dispersing within areas characterized by persistent spring snow explained the data better than a model based on Euclidean distance. Partial Mantel tests separating Euclidean distance from spring snow-cover-based effects indicated that Euclidean distance was not significant in describing patterns of genetic distance. Because these models indicated that successful dispersal paths followed areas characterized by spring snow cover, we used these understandings to derive empirically based least-cost corridor maps in the U.S. Rocky Mountains. These corridor maps largely explain previously published population subdivision patterns based on mitochondrial DNA and indicate that natural colonization of the southern Rocky Mountains by wolverines will be difficult but not impossible. PMID:19967877</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3640393','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3640393"><span id="translatedtitle">Cloning, Characterization and Heterologous Expression of the Indolocarbazole Biosynthetic <span class="hlt">Gene</span> Cluster from <span class="hlt">Marine</span>-Derived Streptomyces sanyensis FMA</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Li, Tong; Du, Yuanyuan; Cui, Qiu; Zhang, Jingtao; Zhu, Weiming; Hong, Kui; Li, Wenli</p> <p>2013-01-01</p> <p>The indolocarbazole (ICZ) alkaloids have attracted much attention due to their unique structures and potential therapeutic applications. A series of ICZs were recently isolated and identified from a <span class="hlt">marine</span>-derived actinomycete strain, Streptomyces sanyensis FMA. To elucidate the biosynthetic machinery associated with ICZs production in S. sanyensis FMA, PCR using degenerate primers was carried out to clone the FAD-dependent monooxygenase <span class="hlt">gene</span> fragment for ICZ ring formation, which was used as a probe to isolate the 34.6-kb DNA region containing the spc <span class="hlt">gene</span> cluster. Sequence analysis revealed <span class="hlt">genes</span> for ICZ ring formation (spcO, D, P, C), sugar unit formation (spcA, B, E, K, J, I), glycosylation (spcN, G), methylation (spcMA, MB), as well as regulation (spcR). Their involvement in ICZ biosynthesis was confirmed by <span class="hlt">gene</span> inactivation and heterologous expression in Streptomyces coelicolor M1152. This work represents the first cloning and characterization of an ICZ <span class="hlt">gene</span> cluster isolated from a <span class="hlt">marine</span>-derived actinomycete strain and would be helpful for thoroughly understanding the biosynthetic mechanism of ICZ glycosides. PMID:23389092</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1204880','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1204880"><span id="translatedtitle">Estimates of <span class="hlt">Gene</span> <span class="hlt">Flow</span> among Populations, Geographic Races, and Species in the Ipomopsis Aggregata Complex</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Wolf, P. G.; Soltis, P. S.</p> <p>1992-01-01</p> <p>Interpopulational <span class="hlt">gene</span> <span class="hlt">flow</span> within a species can reduce population differentiation due to genetic drift, whereas genetic exchange among taxa can impede speciation. We used allozyme data to estimate <span class="hlt">gene</span> <span class="hlt">flow</span> within and among geographic races and species of perennial herbs in the Ipomopsis aggregata complex (Polemoniaceae). Estimates of interpopulational <span class="hlt">gene</span> <span class="hlt">flow</span> within taxa from two methods (F statistics and private alleles) were correlated with one another. <span class="hlt">Gene</span> <span class="hlt">flow</span> among populations within each geographic race (subspecies) of I. aggregata was relatively high (Nm > ~1.0). <span class="hlt">Gene</span> <span class="hlt">flow</span> was also high among populations of I. arizonica and among four northern populations of I. tenuituba. However, <span class="hlt">gene</span> <span class="hlt">flow</span> was low (Nm < 1.0) for I. tenuituba when a population representing subsp. macrosiphon was included. This is consistent with previous findings that subsp. macrosiphon has had an independent origin and is reproductively, as well as geographically, isolated. A recently developed model, based on hierarchical F statistics, was employed to estimate genetic exchange among taxa. <span class="hlt">Gene</span> <span class="hlt">flow</span> estimates were generally high among races of I. aggregata (dNm(race) > 1.0) but were low among subspecies of I. tenuituba (dNm(race) < 1.0). Consistent with morphological evidence, estimates of interspecific <span class="hlt">gene</span> <span class="hlt">flow</span> were moderate between I. aggregata and I. tenuituba, which hybridize in several areas. However, contrary to morphological evidence, we estimated relatively high levels of interspecific <span class="hlt">gene</span> <span class="hlt">flow</span> involving I. arizonica. Our results suggest that I. arizonica has hybridized with other species without the transfer of morphological traits. In the I. aggregata complex, <span class="hlt">gene</span> <span class="hlt">flow</span> appears to be an important evolutionary force shaping geographic variation for allozymes within species, but is insufficient to prevent morphological divergence among taxa. PMID:1551582</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/servlets/purl/1241132','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/servlets/purl/1241132"><span id="translatedtitle">Genomic insights into the evolution of hybrid isoprenoid biosynthetic <span class="hlt">gene</span> clusters in the MAR4 <span class="hlt">marine</span> streptomycete clade</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Gallagher, Kelley A.; Jensen, Paul R.</p> <p>2015-11-17</p> <p>Background: Considerable advances have been made in our understanding of the molecular genetics of secondary metabolite biosynthesis. Coupled with increased access to genome sequence data, new insight can be gained into the diversity and distributions of secondary metabolite biosynthetic <span class="hlt">gene</span> clusters and the evolutionary processes that generate them. Here we examine the distribution of <span class="hlt">gene</span> clusters predicted to encode the biosynthesis of a structurally diverse class of molecules called hybrid isoprenoids (HIs) in the genus Streptomyces. These compounds are derived from a mixed biosynthetic origin that is characterized by the incorporation of a terpene moiety onto a variety of chemical scaffolds and include many potent antibiotic and cytotoxic agents. Results: One hundred and twenty Streptomyces genomes were searched for HI biosynthetic <span class="hlt">gene</span> clusters using ABBA prenyltransferases (PTases) as queries. These enzymes are responsible for a key step in HI biosynthesis. The strains included 12 that belong to the ‘MAR4’ clade, a largely <span class="hlt">marine</span>-derived lineage linked to the production of diverse HI secondary metabolites. We found ABBA PTase homologs in all of the MAR4 genomes, which averaged five copies per strain, compared with 21 % of the non-MAR4 genomes, which averaged one copy per strain. Phylogenetic analyses suggest that MAR4 PTase diversity has arisen by a combination of horizontal <span class="hlt">gene</span> transfer and <span class="hlt">gene</span> duplication. Furthermore, there is evidence that HI <span class="hlt">gene</span> cluster diversity is generated by the horizontal exchange of orthologous PTases among clusters. Many putative HI <span class="hlt">gene</span> clusters have not been linked to their secondary metabolic products, suggesting that MAR4 strains will yield additional new compounds in this structure class. Finally, we confirm that the mevalonate pathway is not always present in genomes that contain HI <span class="hlt">gene</span> clusters and thus is not a reliable query for identifying strains with the potential to produce HI secondary metabolites. In</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/pages/biblio/1241132-genomic-insights-evolution-hybrid-isoprenoid-biosynthetic-gene-clusters-mar4-marine-streptomycete-clade','SCIGOV-DOEP'); return false;" href="http://www.osti.gov/pages/biblio/1241132-genomic-insights-evolution-hybrid-isoprenoid-biosynthetic-gene-clusters-mar4-marine-streptomycete-clade"><span id="translatedtitle">Genomic insights into the evolution of hybrid isoprenoid biosynthetic <span class="hlt">gene</span> clusters in the MAR4 <span class="hlt">marine</span> streptomycete clade</span></a></p> <p><a target="_blank" href="http://www.osti.gov/pages">DOE PAGESBeta</a></p> <p>Gallagher, Kelley A.; Jensen, Paul R.</p> <p>2015-11-17</p> <p>Background: Considerable advances have been made in our understanding of the molecular genetics of secondary metabolite biosynthesis. Coupled with increased access to genome sequence data, new insight can be gained into the diversity and distributions of secondary metabolite biosynthetic <span class="hlt">gene</span> clusters and the evolutionary processes that generate them. Here we examine the distribution of <span class="hlt">gene</span> clusters predicted to encode the biosynthesis of a structurally diverse class of molecules called hybrid isoprenoids (HIs) in the genus Streptomyces. These compounds are derived from a mixed biosynthetic origin that is characterized by the incorporation of a terpene moiety onto a variety of chemicalmore » scaffolds and include many potent antibiotic and cytotoxic agents. Results: One hundred and twenty Streptomyces genomes were searched for HI biosynthetic <span class="hlt">gene</span> clusters using ABBA prenyltransferases (PTases) as queries. These enzymes are responsible for a key step in HI biosynthesis. The strains included 12 that belong to the ‘MAR4’ clade, a largely <span class="hlt">marine</span>-derived lineage linked to the production of diverse HI secondary metabolites. We found ABBA PTase homologs in all of the MAR4 genomes, which averaged five copies per strain, compared with 21 % of the non-MAR4 genomes, which averaged one copy per strain. Phylogenetic analyses suggest that MAR4 PTase diversity has arisen by a combination of horizontal <span class="hlt">gene</span> transfer and <span class="hlt">gene</span> duplication. Furthermore, there is evidence that HI <span class="hlt">gene</span> cluster diversity is generated by the horizontal exchange of orthologous PTases among clusters. Many putative HI <span class="hlt">gene</span> clusters have not been linked to their secondary metabolic products, suggesting that MAR4 strains will yield additional new compounds in this structure class. Finally, we confirm that the mevalonate pathway is not always present in genomes that contain HI <span class="hlt">gene</span> clusters and thus is not a reliable query for identifying strains with the potential to produce HI secondary metabolites</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4199086','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4199086"><span id="translatedtitle">Blood-Based <span class="hlt">Gene</span>-Expression Biomarkers of Post-Traumatic Stress Disorder among Deployed <span class="hlt">Marines</span>: A Pilot Study</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Tylee, Daniel S.; Chandler, Sharon D.; Nievergelt, Caroline M.; Liu, Xiaohua; Pazol, Joel; Woelk, Christopher H.; Lohr, James B.; Kremen, William S.; Baker, Dewleen G.; Glatt, Stephen J.; Tsuang, Ming T.</p> <p>2014-01-01</p> <p>The etiology of post-traumatic stress disorder (PTSD) likely involves the interaction of numerous <span class="hlt">genes</span> and environmental factors. Similarly, <span class="hlt">gene</span>-expression levels in peripheral blood are influenced by both <span class="hlt">genes</span> and environment, and expression levels of many <span class="hlt">genes</span> show good correspondence between peripheral blood and brain tissues. In that context, this pilot study sought to test the following hypotheses: 1) post-trauma expression levels of a <span class="hlt">gene</span> subset in peripheral blood would differ between <span class="hlt">Marines</span> with and without PTSD; 2) a diagnostic biomarker panel of PTSD among high-risk individuals could be developed based on <span class="hlt">gene</span> expression in readily assessable peripheral blood cells; and 3) a diagnostic panel based on expression of individual exons would surpass the accuracy of a model based on expression of full-length <span class="hlt">gene</span> transcripts. <span class="hlt">Gene</span>-expression levels in peripheral blood samples from 50 U.S. <span class="hlt">Marines</span> (25 PTSD cases and 25 non-PTSD comparison subjects) were determined by microarray following their return from deployment to war-zones in Iraq or Afghanistan. The original sample was carved into training and test subsets for construction of support vector machine classifiers. The panel of peripheral blood biomarkers achieved 80% prediction accuracy in the test subset based on the expression of just two full-length transcripts (GSTM1 and GSTM2). A biomarker panel based on 20 exons attained an improved 90% accuracy in the test subset. Though further refinement and replication of these biomarker profiles are required, these preliminary results provide proof-of-principle for the diagnostic utility of blood-based mRNA-expression in PTSD among trauma-exposed individuals. PMID:25311155</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2012IJNAO...4...58C','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2012IJNAO...4...58C"><span id="translatedtitle">Effect of bidirectional internal <span class="hlt">flow</span> on fluid-structure interaction dynamics of conveying <span class="hlt">marine</span> riser model subject to shear current</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Chen, Zheng-Shou; Kim, Wu-Joan</p> <p>2012-03-01</p> <p>This article presents a numerical investigation concerning the effect of two kinds of axially progressing internal <span class="hlt">flows</span> (namely, upward and downward) on fluid-structure interaction (FSI) dynamics about a <span class="hlt">marine</span> riser model which is subject to external shear current. The CAE technology behind the current research is a proposed FSI solution, which combines structural analysis software with CFD technology together. Efficiency validation for the CFD software was carried out first. It has been proved that the result from numerical simulations agrees well with the observation from relating model test cases in which the fluidity of internal <span class="hlt">flow</span> is ignorable. After verifying the numerical code accuracy, simulations are conducted to study the vibration response that attributes to the internal progressive <span class="hlt">flow</span>. It is found that the existence of internal <span class="hlt">flow</span> does play an important role in determining the vibration mode (/dominant frequency) and the magnitude of instantaneous vibration amplitude. Since asymmetric curvature along the riser span emerges in the case of external shear current, the centrifugal and Coriolis accelerations owing to up- and downward internal progressive <span class="hlt">flows</span> play different roles in determining the fluid-structure interaction response. The discrepancy between them becomes distinct, when the velocity ratio of internal <span class="hlt">flow</span> against external shear current is relatively high.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/27386093','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/27386093"><span id="translatedtitle">Genomic heterogeneity of historical <span class="hlt">gene</span> <span class="hlt">flow</span> between two species of newts inferred from transcriptome data.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Stuglik, Michał T; Babik, Wiesław</p> <p>2016-07-01</p> <p>The role of <span class="hlt">gene</span> <span class="hlt">flow</span> in species formation is a major unresolved issue in speciation biology. Progress in this area requires information on the long-term patterns of <span class="hlt">gene</span> <span class="hlt">flow</span> between diverging species. Here, we used thousands of single-nucleotide polymorphisms derived from transcriptome resequencing and a method modeling the joint frequency spectrum of these polymorphisms to reconstruct patterns of historical <span class="hlt">gene</span> <span class="hlt">flow</span> between two Lissotriton newts: L. vulgaris (Lv) and L. montandoni (Lm). We tested several models of divergence including complete isolation and various scenarios of historical <span class="hlt">gene</span> <span class="hlt">flow</span>. The model of secondary contact received the highest support. According to this model, the species split from their common ancestor ca. 5.5 million years (MY) ago, evolved in isolation for ca. 2 MY, and have been exchanging <span class="hlt">genes</span> for the last 3.5 MY Demographic changes have been inferred in both species, with the current effective population size of ca. 0.7 million in Lv and 0.2 million in Lm. The postdivergence <span class="hlt">gene</span> <span class="hlt">flow</span> resulted in two-directional introgression which affected the genomes of both species, but was more pronounced from Lv to Lm. Interestingly, we found evidence for genomic heterogeneity of interspecific <span class="hlt">gene</span> <span class="hlt">flow</span>. This study demonstrates the complexity of long-term <span class="hlt">gene</span> <span class="hlt">flow</span> between distinct but incompletely reproductively isolated taxa which divergence was initiated millions of years ago. PMID:27386093</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/17217345','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/17217345"><span id="translatedtitle">Pleistocene isolation and recent <span class="hlt">gene</span> <span class="hlt">flow</span> in Haliotis asinina, an Indo-Pacific vetigastropod with limited dispersal capacity.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Imron; Jeffrey, Benardine; Hale, Peter; Degnan, Bernard M; Degnan, Sandie M</p> <p>2007-01-01</p> <p>Haliotis asinina is a broadcast-spawning mollusc that inhabits Indo-Pacific coral reefs. This tropical abalone develops through a nonfeeding larval stage that is competent to settle on specific species of coralline algae after 3-4 days in the plankton. Failure to contact an inductive algae within 10 days of hatching usually results in death. These life cycle characteristics suggest a limited capacity for dispersal and thus <span class="hlt">gene</span> <span class="hlt">flow</span>. This makes H. asinina particularly suitable for elucidating phylogeographical structure throughout the Indo-Malay Archipelagoes, and eastern Indian and western Pacific Oceans, all regions of biogeographical complexity and high conservation value. We assayed 482 bp of the mitochondrial cytochrome oxidase II <span class="hlt">gene</span> in 206 abalone collected from 16 geographically discrete sites across the Indian and Pacific Oceans and Indo-Malay Archipelagoes. DNA sequence variation was analysed via population genetics and phylogenetics, and by nested clade analyses (NCA). Our data resolved clear phylogeographical breaks among major biogeographical regions, with sequence divergences ranging from a high of 3.7% and 3.0% between Indian and Pacific sites and Pacific and Indo-Malay sites, respectively, to a low of 1.1% between Indian and Indo-Malay sites. Despite the apparent limited dispersal capacity of H. asinina, no finer scale phylogeographical structure was resolved within the respective biogeographical regions. However, amova and NCA identified several significant associations between haplotypes and geographical distribution, most notably higher <span class="hlt">gene</span> <span class="hlt">flow</span> among geographical populations associated with major ocean currents. Our study provides further evidence that larval dispersal capacity alone is not a good predictor of population genetic structure in <span class="hlt">marine</span> invertebrates. We infer instead that a combination of historical events (long-term barriers followed by range expansion associated with Pleistocene sea level changes) and contemporary processes</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/530722','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/530722"><span id="translatedtitle">Diversity and depth-specific distribution of SAR11 cluster rRNA <span class="hlt">genes</span> from <span class="hlt">marine</span> planktonic bacteria</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Field, K.G.; Gordon, D.; Wright, T.</p> <p>1997-01-01</p> <p>Small-subunit (SSU) ribosomal DNA (rDNA) <span class="hlt">gene</span> clusters are phylogenetically related sets of SSU rRNA <span class="hlt">genes</span>, commonly encountered in <span class="hlt">genes</span> amplified from natural populations. Genetic variability in <span class="hlt">gene</span> clusters could result form artifacts (polymerase error or PCR chimera formation), microevolution (variation among rrn copies within strains), or macroevolution (genetic divergence correlated with long-term evolutionary divergence). To better understand <span class="hlt">gene</span> clusters, this study assessed genetic diversity and distribution of a single environmental SSU rDNA <span class="hlt">gene</span> cluster, the SAR11 cluster. SAR11 cluster <span class="hlt">genes</span>, from an uncultured group of the {alpha} subclass of the class Proteobacteria, have been recovered from coastal and midoceanic waters of the North Atlantic and Pacific. We cloned and bidirectionally sequenced 23 new SAR11 cluster 16S rRNA <span class="hlt">genes</span>, from 80 and 250 m im the Sargasso Sea and from surface coastal waters of the Atlantic and Pacific, and analyzed them with previously published sequences. Two SAR11 <span class="hlt">genes</span> were obviously PCR chimeras, but the biological (nonchimeric) origins of most subgroups within the cluster were confirmed by independent recovery from separate <span class="hlt">gene</span> libraries. Using group-specific oligonucleotide probes, we analyzed depth profiles of nucleic acids, targeting both amplified rDNAs and bulk RNAs. Two subgroups within the SAR11 cluster showed different highly depth-specific distributions. We conclude that some of the genetic diversity within the SAR11 <span class="hlt">gene</span> cluster represents macroevolutionary divergence correlated with niche specialization. Furthermore, we demonstrate the utility for <span class="hlt">marine</span> microbial ecology of oligonucleotide probes based on <span class="hlt">gene</span> sequences amplified from natural populations and show that a detailed knowledge of sequence variability may be needed to effectively design these probes. 48 refs., 7 figs., 3 tabs.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2007IJBm...51..493G','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2007IJBm...51..493G"><span id="translatedtitle"><span class="hlt">Gene</span> <span class="hlt">flow</span> in maize fields with different local pollen densities</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Goggi, A. Susana; Lopez-Sanchez, Higinio; Caragea, Petrutza; Westgate, Mark; Arritt, Raymond; Clark, Craig A.</p> <p>2007-08-01</p> <p>The development of maize ( Zea mays L.) varieties as factories of pharmaceutical and industrial compounds has renewed interest in controlling pollen dispersal. The objective of this study was to compare <span class="hlt">gene</span> <span class="hlt">flow</span> into maize fields of different local pollen densities under the same environmental conditions. Two fields of approximately 36 ha were planted with a nontransgenic, white hybrid, in Ankeny, Iowa, USA. In the center of both fields, a 1-ha plot of a yellow-seeded stacked RR/Bt transgenic hybrid was planted as a pollen source. Before flowering, the white receiver maize of one field was detasseled in a 4:1 ratio to reduce the local pollen density (RPD). The percentage of outcross in the field with RPD was 42.2%, 6.3%, and 1.3% at 1, 10, and 35 m from the central plot, respectively. The percentage of outcross in the white maize with normal pollen density (NPD) was 30.1%, 2.7%, and 0.4%, respectively, at these distances. At distances greater than 100 m, the outcross frequency decreased below 0.1 and 0.03% in the field with RPD and NPD, respectively. A statistical model was used to compare pollen dispersal based on observed outcross percentages. The likelihood ratio test confirmed that the models of outcrossing in the two fields were significantly different ( P is practically 0). Results indicated that when local pollen is low, the incoming pollen has a competitive advantage and the level of outcross is significantly greater than when the local pollen is abundant.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/16367829','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/16367829"><span id="translatedtitle">The relative influence of natural selection and geography on <span class="hlt">gene</span> <span class="hlt">flow</span> in guppies.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Crispo, Erika; Bentzen, Paul; Reznick, David N; Kinnison, Michael T; Hendry, Andrew P</p> <p>2006-01-01</p> <p>Two general processes may influence <span class="hlt">gene</span> <span class="hlt">flow</span> among populations. One involves divergent selection, wherein the maladaptation of immigrants and hybrids impedes <span class="hlt">gene</span> <span class="hlt">flow</span> between ecological environments (i.e. ecological speciation). The other involves geographic features that limit dispersal. We determined the relative influence of these two processes in natural populations of Trinidadian guppies (Poecilia reticulata). If selection is important, <span class="hlt">gene</span> <span class="hlt">flow</span> should be reduced between different selective environments. If geography is important, <span class="hlt">gene</span> <span class="hlt">flow</span> should be impeded by geographic distance and physical barriers. We examined how genetic divergence, long-term <span class="hlt">gene</span> <span class="hlt">flow</span>, and contemporary dispersal within a watershed were influenced by waterfalls, geographic distance, predation, and habitat features. We found that waterfalls and geographic distance increased genetic divergence and reduced dispersal and long-term <span class="hlt">gene</span> <span class="hlt">flow</span>. Differences in predation or habitat features did not influence genetic divergence or <span class="hlt">gene</span> <span class="hlt">flow</span>. In contrast, differences in predation did appear to reduce contemporary dispersal. We suggest that the standard predictions of ecological speciation may be heavily nuanced by the mating behaviour and life history strategies of guppies. PMID:16367829</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/17189914','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/17189914"><span id="translatedtitle">C-values of seven <span class="hlt">marine</span> mammal species determined by <span class="hlt">flow</span> cytometry.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Du, Bo; Wang, Ding</p> <p>2006-11-01</p> <p>C-values, which estimate genome size, have puzzled geneticists for years because they bear no relationship to organismal complexity. Though C-values have been estimated for thousands of species, considerably more data are required in order to better understanding genome evolution. This is particularly true for mammals, in which C-values are known for less than 8% of the total number of mammalian species. Among <span class="hlt">marine</span> mammals, a C-value has been estimated only for the bottlenose dolphin (Tursiops truncatus). Thus examination of additional species of <span class="hlt">marine</span> mammals is necessary for comparative purposes. It will enable a better understanding of <span class="hlt">marine</span> mammal genome evolution, and it is also relevant to conservation, because larger genome size has been linked to increased likelihood of extinction in some plant and animal groups. Our study presents C-values of seven <span class="hlt">marine</span> mammal species, including five cetacean species that are endangered to varying degrees. Similarly to the results for other groups, our results suggest that larger genome size in cetaceans is related to an increased likelihood of extinction. PMID:17189914</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25953647','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25953647"><span id="translatedtitle"><span class="hlt">Flow</span>-Dependent Epigenetic DNA Methylation in Endothelial <span class="hlt">Gene</span> Expression and Atherosclerosis.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Dunn, Jessilyn; Thabet, Salim; Jo, Hanjoong</p> <p>2015-07-01</p> <p>Epigenetic mechanisms that regulate endothelial cell <span class="hlt">gene</span> expression are now emerging. DNA methylation is the most stable epigenetic mark that confers persisting changes in <span class="hlt">gene</span> expression. Not only is DNA methylation important in rendering cell identity by regulating cell type-specific <span class="hlt">gene</span> expression throughout differentiation, but it is becoming clear that DNA methylation also plays a key role in maintaining endothelial cell homeostasis and in vascular disease development. Disturbed blood <span class="hlt">flow</span> causes atherosclerosis, whereas stable <span class="hlt">flow</span> protects against it by differentially regulating <span class="hlt">gene</span> expression in endothelial cells. Recently, we and others have shown that <span class="hlt">flow</span>-dependent <span class="hlt">gene</span> expression and atherosclerosis development are regulated by mechanisms dependent on DNA methyltransferases (1 and 3A). Disturbed blood <span class="hlt">flow</span> upregulates DNA methyltransferase expression both in vitro and in vivo, which leads to genome-wide DNA methylation alterations and global <span class="hlt">gene</span> expression changes in a DNA methyltransferase-dependent manner. These studies revealed several mechanosensitive <span class="hlt">genes</span>, such as HoxA5, Klf3, and Klf4, whose promoters were hypermethylated by disturbed blood <span class="hlt">flow</span>, but rescued by DNA methyltransferases inhibitors such as 5Aza-2-deoxycytidine. These findings provide new insight into the mechanism by which <span class="hlt">flow</span> controls epigenomic DNA methylation patterns, which in turn alters endothelial <span class="hlt">gene</span> expression, regulates vascular biology, and modulates atherosclerosis development. PMID:25953647</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4130427','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4130427"><span id="translatedtitle">Direct and reverse pollen-mediated <span class="hlt">gene</span> <span class="hlt">flow</span> between GM rice and red rice weed</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Serrat, X.; Esteban, R.; Peñas, G.; Català, M. M.; Melé, E.; Messeguer, J.</p> <p>2013-01-01</p> <p>Potential risks of genetically modified (GM) crops must be identified before their commercialization, as happens with all new technologies. One of the major concerns is the proper risk assessment of adventitious presence of transgenic material in rice fields due to cross-pollination. Several studies have been conducted in order to quantify pollen-mediated <span class="hlt">gene</span> <span class="hlt">flow</span> from transgenic rice (Oryza sativa) to both conventional rice and red rice weed (O. sativa f. spontanea) under field conditions. Some of these studies reported GM pollen-donor rice transferring GM traits to red rice. However, <span class="hlt">gene</span> <span class="hlt">flow</span> also occurs in the opposite direction, in a phenomenon that we have called reverse <span class="hlt">gene</span> <span class="hlt">flow</span>, resulting in transgenic seeds that have incorporated the traits of wild red rice. We quantified reverse <span class="hlt">gene</span> <span class="hlt">flow</span> using material from two field trials. A molecular analysis based on amplified fragment length polymorphisms was carried out, being complemented with a phenotypic identification of red rice traits. In both field trials, the reverse <span class="hlt">gene</span> <span class="hlt">flow</span> detected was greater than the direct <span class="hlt">gene</span> <span class="hlt">flow</span>. The rate of direct <span class="hlt">gene</span> <span class="hlt">flow</span> varied according to the relative proportions of the donor (GM rice) and receptor (red rice) plants and was influenced by wind direction. The ecological impact of reverse <span class="hlt">gene</span> <span class="hlt">flow</span> is limited in comparison with that of direct <span class="hlt">gene</span> <span class="hlt">flow</span> because non-shattered and non-dormant seeds would be obtained in the first generation. Hybrid seed would remain in the spike and therefore most of it would be removed during harvesting. Nevertheless, this phenomenon must be considered in fields used for elite seed production and in developing countries where farmers often keep some seed for planting the following year. In these cases, there is a higher risk of GM red rice weed infestation increasing from year to year and therefore a proper monitoring plan needs to be established.</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_7");'>7</a></li> <li><a href="#" onclick='return showDiv("page_8");'>8</a></li> <li class="active"><span>9</span></li> <li><a href="#" onclick='return showDiv("page_10");'>10</a></li> <li><a href="#" onclick='return showDiv("page_11");'>11</a></li> <li><a href="#" onclick='return showDiv("page_13");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_9 --> <div id="page_10" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_8");'>8</a></li> <li><a href="#" onclick='return showDiv("page_9");'>9</a></li> <li class="active"><span>10</span></li> <li><a href="#" onclick='return showDiv("page_11");'>11</a></li> <li><a href="#" onclick='return showDiv("page_12");'>12</a></li> <li><a href="#" onclick='return showDiv("page_13");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="181"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2011JSR....66..123R&link_type=ABSTRACT','NASAADS'); return false;" href="http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2011JSR....66..123R&link_type=ABSTRACT"><span id="translatedtitle">The Bolivar Channel Ecosystem of the Galapagos <span class="hlt">Marine</span> Reserve: Energy <span class="hlt">flow</span> structure and role of keystone groups</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Ruiz, Diego J.; Wolff, Matthias</p> <p>2011-08-01</p> <p>The Bolivar Channel Ecosystem (BCE) is among the most productive zones in the Galapagos <span class="hlt">Marine</span> Reserve (GMR). It is exposed to relatively cool, nutrient-rich waters of the Cromwell current, which are brought to the photic zone through topographic upwelling. The BCE is characterized by a heterogeneous rocky reef habitat covered by dense algae beds and inhabited by numerous invertebrate and fish species, which represent the food for higher predators including seals and sharks and exploited fish species. In addition, plankton and detritus based food chains channel large amounts of energy through the complex food web. Important emblematic species of the Galapagos archipelagos reside in this area such as the flightless cormorant, the Galapagos penguin and the <span class="hlt">marine</span> iguanas. A trophic model of BCE was constructed for the habitats < 30 m depth that fringe the west coast of Isabela and east coast of Fernandina islands covering 14% of the total BCE area (44 km 2). The model integrates data sets from sub tidal ecological monitoring and <span class="hlt">marine</span> vertebrate population monitoring (2004 to 2008) programs of the Charles Darwin Foundation and consists of 30 compartments, which are trophically linked through a diet matrix. Results reveal that the BCE is a large system in terms of <span class="hlt">flows</span> (38 695 t km - 2 yr - 1 ) comparable to Peruvian Bay Systems of the Humboldt upwelling system. A very large proportion of energy <span class="hlt">flows</span> from the primary producers (phytoplankton and macro-algae) to the second level and to the detritus pool. Catches are high (54.3 t km - 2 yr - 1 ) and are mainly derived from the second and third trophic levels (mean TL of catch = 2.45) making the fisheries gross efficiency high (0.3%). The system's degree of development seems rather low as indicated by a P/R ratio of 4.19, a low ascendency (37.4%) and a very low Finn's cycling index (1.29%). This is explained by the system's exposure to irregular changes in oceanographic conditions as related to the EL Niño Southern</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/17148333','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/17148333"><span id="translatedtitle">Local differentiation in the presence of <span class="hlt">gene</span> <span class="hlt">flow</span> in the citril finch Serinus citrinella.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Senar, Juan Carlos; Borras, Antoni; Cabrera, Josep; Cabrera, Toni; Björklund, Mats</p> <p>2006-03-22</p> <p>It is well known theoretically that <span class="hlt">gene</span> <span class="hlt">flow</span> can impede genetic differentiation between populations. In this study, we show that in a highly mobile bird species, where dispersal is well documented, there is a strong genetic and morphological differentiation over a very short geographical scale (less than 5 km). Allocation tests revealed that birds caught in one area were assigned genetically to the same area with a very high probability, in spite of current <span class="hlt">gene</span> <span class="hlt">flow</span>. Populations were also morphologically differentiated. The results suggest that the relationship between <span class="hlt">gene</span> <span class="hlt">flow</span> and differentiation can be rather complicated and non-intuitive. PMID:17148333</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3490371','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3490371"><span id="translatedtitle">Long-distance <span class="hlt">gene</span> <span class="hlt">flow</span> and adaptation of forest trees to rapid climate change</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Kremer, Antoine; Ronce, Ophélie; Robledo-Arnuncio, Juan J; Guillaume, Frédéric; Bohrer, Gil; Nathan, Ran; Bridle, Jon R; Gomulkiewicz, Richard; Klein, Etienne K; Ritland, Kermit; Kuparinen, Anna; Gerber, Sophie; Schueler, Silvio</p> <p>2012-01-01</p> <p>Forest trees are the dominant species in many parts of the world and predicting how they might respond to climate change is a vital global concern. Trees are capable of long-distance <span class="hlt">gene</span> <span class="hlt">flow</span>, which can promote adaptive evolution in novel environments by increasing genetic variation for fitness. It is unclear, however, if this can compensate for maladaptive effects of <span class="hlt">gene</span> <span class="hlt">flow</span> and for the long-generation times of trees. We critically review data on the extent of long-distance <span class="hlt">gene</span> <span class="hlt">flow</span> and summarise theory that allows us to predict evolutionary responses of trees to climate change. Estimates of long-distance <span class="hlt">gene</span> <span class="hlt">flow</span> based both on direct observations and on genetic methods provide evidence that <span class="hlt">genes</span> can move over spatial scales larger than habitat shifts predicted under climate change within one generation. Both theoretical and empirical data suggest that the positive effects of <span class="hlt">gene</span> <span class="hlt">flow</span> on adaptation may dominate in many instances. The balance of positive to negative consequences of <span class="hlt">gene</span> <span class="hlt">flow</span> may, however, differ for leading edge, core and rear sections of forest distributions. We propose future experimental and theoretical research that would better integrate dispersal biology with evolutionary quantitative genetics and improve predictions of tree responses to climate change. PMID:22372546</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/scitech/biblio/1184950','SCIGOV-STC'); return false;" href="http://www.osti.gov/scitech/biblio/1184950"><span id="translatedtitle">Numerical performance analysis of acoustic Doppler velocity profilers in the wake of an axial-<span class="hlt">flow</span> <span class="hlt">marine</span> hydrokinetic turbine</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Richmond, Marshall C.; Harding, Samuel F.; Romero Gomez, Pedro DJ</p> <p>2015-09-01</p> <p>The use of acoustic Doppler current profilers (ADCPs) for the characterization of <span class="hlt">flow</span> conditions in the vicinity of both experimental and full scale <span class="hlt">marine</span> hydrokinetic (MHK) turbines is becoming increasingly prevalent. The computation of a three dimensional velocity measurement from divergent acoustic beams requires the assumption that the <span class="hlt">flow</span> conditions are homogeneous between all beams at a particular axial distance from the instrument. In the near wake of MHK devices, the mean fluid motion is observed to be highly spatially dependent as a result of torque generation and energy extraction. This paper examines the performance of ADCP measurements in such scenarios through the modelling of a virtual ADCP (VADCP) instrument in the velocity field in the wake of an MHK turbine resolved using unsteady computational fluid dynamics (CFD). This is achieved by sampling the CFD velocity field at equivalent locations to the sample bins of an ADCP and performing the coordinate transformation from beam coordinates to instrument coordinates and finally to global coordinates. The error in the mean velocity calculated by the VADCP relative to the reference velocity along the instrument axis is calculated for a range of instrument locations and orientations. The stream-wise velocity deficit and tangential swirl velocity caused by the rotor rotation lead to significant misrepresentation of the true <span class="hlt">flow</span> velocity profiles by the VADCP, with the most significant errors in the transverse (cross-<span class="hlt">flow</span>) velocity direction.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015APS..DFD.R1001B','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015APS..DFD.R1001B"><span id="translatedtitle">Performance and Near-Wake <span class="hlt">Flow</span> field of A <span class="hlt">Marine</span> Hydrokinetic Turbine Operating in Free surface Proximity</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Banerjee, Arindam; Kolekar, Nitin</p> <p>2015-11-01</p> <p>The current experimental investigation aims at understanding the effect of free surface proximity and associated blockage on near-wake <span class="hlt">flow</span>-field and performance of a three bladed horizontal axis <span class="hlt">marine</span> hydrokinetic turbine. Experiments were conducted on a 0.14m radius, three bladed constant chord turbine in a 0.61m ×0.61m test section water channel. The turbine was subjected to various rotational speeds, <span class="hlt">flow</span> speeds and depths of immersion. Experimental data was acquired through a submerged in-line thrust-torque sensor that was corrected to an unblocked dataset with a blockage correction using measured thrust data. A detailed comparison is presented between blocked and unblocked datasets to identify influence of Reynolds number and free surface proximity on blockage effects. The percent change in Cp was found to be dependent on <span class="hlt">flow</span> velocity, rotational speed and free surface to blade tip clearance. Further, <span class="hlt">flow</span> visualization using a stereoscopic particle image velocimetry was carried out in the near-wake region of turbine to understand the mechanism responsible for variation of Cp with rotational speed and free surface proximity. Results revealed presence of slower wake at higher rotational velocities and increased asymmetry in the wake at high free surface proximity.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2014EGUGA..1616081C&link_type=ABSTRACT','NASAADS'); return false;" href="http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2014EGUGA..1616081C&link_type=ABSTRACT"><span id="translatedtitle">Mathematical simulation of boulder dislodgement by high-energy <span class="hlt">marine</span> <span class="hlt">flows</span> in the western coast of Portugal</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Canelas, Ricardo; Oliveira, Maria; Crespo, Alejandro; Neves, Ramiro; Costa, Pedro; Freitas, Conceição; Andrade, César; Ferreira, Rui</p> <p>2014-05-01</p> <p>The study of coastal boulder deposits related with <span class="hlt">marine</span> abrupt inundation events has been addressed by several authors using conventional numerical solutions that simulate particle transport by storm and tsunami, sometimes with contradictory results (Nandasena et al. 2011, Kain et al. 2012). The biggest challenge has been the differentiation of the events (storm or tsunami), and the reconstruction of wave parameters (e.g. wave height, length, direction) responsible for the entrainment and transport of these megaclasts. In this study we employ an inverse-problem strategy to determine the cause of dislodgement of megaclasts and to explain the pattern of deposition found in some locations of the Portuguese western coast, well above maximum records of sea level. It is envisaged that the causes are either <span class="hlt">flows</span> originated by wave breaking, typically associated to storms, which would impart large momentum in a short time interval (herein impulsive motion), or long waves such as a tsunamis, that would transport the clasts in a mode analogous to bedload (herein sustained motion). The geometry of the problem is idealized but represents the key features of overhanging layers related with fractures, bedding and differential erosion of sub-horizontal layers. In plan view, concave and convex coastline shapes are testes to assess the influence of <span class="hlt">flow</span> concentration. These geometrical features are representative of the western Portuguese coast. The fluid-solid model solves numerically the Navier-Stokes equations for the liquid phase and Newton's motion equations for solid bodies. The discretization of both fluid and solids is performed with Smooth Particle Hydrodynamics (SPH). The model is based DualSPHyics code (www.dual.sphysics.org) and represents an effort to avoid different discretization techniques for different phases in motion. This approach to boulder transport demonstrates that the ability of high-energy <span class="hlt">flow</span> events to entrain and transport large particles largely</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/22146392','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/22146392"><span id="translatedtitle">The evolution of sensory divergence in the context of limited <span class="hlt">gene</span> <span class="hlt">flow</span> in the bumblebee bat.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Puechmaille, Sébastien J; Gouilh, Meriadeg Ar; Piyapan, Piyathip; Yokubol, Medhi; Mie, Khin Mie; Bates, Paul J; Satasook, Chutamas; Nwe, Tin; Bu, Si Si Hla; Mackie, Iain J; Petit, Eric J; Teeling, Emma C</p> <p>2011-01-01</p> <p>The sensory drive theory of speciation predicts that populations of the same species inhabiting different environments can differ in sensory traits, and that this sensory difference can ultimately drive speciation. However, even in the best-known examples of sensory ecology driven speciation, it is uncertain whether the variation in sensory traits is the cause or the consequence of a reduction in levels of <span class="hlt">gene</span> <span class="hlt">flow</span>. Here we show strong genetic differentiation, no <span class="hlt">gene</span> <span class="hlt">flow</span> and large echolocation differences between the allopatric Myanmar and Thai populations of the world's smallest mammal, Craseonycteris thonglongyai, and suggest that geographic isolation most likely preceded sensory divergence. Within the geographically continuous Thai population, we show that geographic distance has a primary role in limiting <span class="hlt">gene</span> <span class="hlt">flow</span> rather than echolocation divergence. In line with sensory-driven speciation models, we suggest that in C. thonglongyai, limited <span class="hlt">gene</span> <span class="hlt">flow</span> creates the suitable conditions that favour the evolution of sensory divergence via local adaptation. PMID:22146392</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3247819','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3247819"><span id="translatedtitle">The evolution of sensory divergence in the context of limited <span class="hlt">gene</span> <span class="hlt">flow</span> in the bumblebee bat</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Puechmaille, Sébastien J.; Gouilh, Meriadeg Ar; Piyapan, Piyathip; Yokubol, Medhi; Mie, Khin Mie; Bates, Paul J.; Satasook, Chutamas; Nwe, Tin; Bu, Si Si Hla; Mackie, Iain J.; Petit, Eric J.; Teeling, Emma C.</p> <p>2011-01-01</p> <p>The sensory drive theory of speciation predicts that populations of the same species inhabiting different environments can differ in sensory traits, and that this sensory difference can ultimately drive speciation. However, even in the best-known examples of sensory ecology driven speciation, it is uncertain whether the variation in sensory traits is the cause or the consequence of a reduction in levels of <span class="hlt">gene</span> <span class="hlt">flow</span>. Here we show strong genetic differentiation, no <span class="hlt">gene</span> <span class="hlt">flow</span> and large echolocation differences between the allopatric Myanmar and Thai populations of the world's smallest mammal, Craseonycteris thonglongyai, and suggest that geographic isolation most likely preceded sensory divergence. Within the geographically continuous Thai population, we show that geographic distance has a primary role in limiting <span class="hlt">gene</span> <span class="hlt">flow</span> rather than echolocation divergence. In line with sensory-driven speciation models, we suggest that in C. thonglongyai, limited <span class="hlt">gene</span> <span class="hlt">flow</span> creates the suitable conditions that favour the evolution of sensory divergence via local adaptation. PMID:22146392</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2013BGeo...10.7279M','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2013BGeo...10.7279M"><span id="translatedtitle">Finding immune <span class="hlt">gene</span> expression differences induced by <span class="hlt">marine</span> bacterial pathogens in the Deep-sea hydrothermal vent mussel Bathymodiolus azoricus</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Martins, E.; Queiroz, A.; Serrão Santos, R.; Bettencourt, R.</p> <p>2013-11-01</p> <p>The deep-sea hydrothermal vent mussel Bathymodiolus azoricus lives in a natural environment characterised by extreme conditions of hydrostatic pressure, temperature, pH, high concentrations of heavy metals, methane and hydrogen sulphide. The deep-sea vent biological systems represent thus the opportunity to study and provide new insights into the basic physiological principles that govern the defense mechanisms in vent animals and to understand how they cope with microbial infections. Hence, the importance of understanding this animal's innate defense mechanisms, by examining its differential immune <span class="hlt">gene</span> expressions toward different pathogenic agents. In the present study, B. azoricus mussels were infected with single suspensions of <span class="hlt">marine</span> bacterial pathogens, consisting of Vibrio splendidus, Vibrio alginolyticus, or Vibrio anguillarum, and a pool of these Vibrio bacteria. Flavobacterium suspensions were also used as a non-pathogenic bacterium. <span class="hlt">Gene</span> expression analyses were carried out using gill samples from infected animals by means of quantitative-Polymerase Chain Reaction aimed at targeting several immune <span class="hlt">genes</span>. We also performed SDS-PAGE protein analyses from the same gill tissues. We concluded that there are different levels of immune <span class="hlt">gene</span> expression between the 12 h to 24 h exposure times to various bacterial suspensions. Our results from qPCR demonstrated a general pattern of <span class="hlt">gene</span> expression, decreasing from 12 h over 24 h post-infection. Among the bacteria tested, Flavobacterium is the bacterium inducing the highest <span class="hlt">gene</span> expression level in 12 h post-infections animals. The 24 h infected animals revealed, however, greater <span class="hlt">gene</span> expression levels, using V. splendidus as the infectious agent. The SDS-PAGE analysis also pointed at protein profile differences between 12 h and 24 h, particularly evident for proteins of 18-20 KDa molecular mass, where most dissimilarity was found. Multivariate analyses demonstrated that immune <span class="hlt">genes</span>, as well as experimental</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2013BGD....10.2675M','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2013BGD....10.2675M"><span id="translatedtitle">Finding immune <span class="hlt">gene</span> expression differences induced by <span class="hlt">marine</span> bacterial pathogens in the deep-sea hydrothermal vent mussel Bathymodiolus azoricus</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Martins, E.; Queiroz, A.; Serrão Santos, R.; Bettencourt, R.</p> <p>2013-02-01</p> <p>The deep-sea hydrothermal vent mussel Bathymodiolus azoricus lives in a natural environment characterized by extreme conditions of hydrostatic pressure, temperature, pH, high concentrations of heavy metals, methane and hydrogen sulphide. The deep-sea vent biological systems represent thus the opportunity to study and provide new insights into the basic physiological principles that govern the defense mechanisms in vent animals and to understand how they cope with microbial infections. Hence, the importance of understanding this animal's innate defense mechanisms, by examining its differential immune <span class="hlt">gene</span> expressions toward different pathogenic agents. In the present study, B. azoricus mussels were infected with single suspensions of <span class="hlt">marine</span> bacterial pathogens, consisting of Vibrio splendidus, Vibrio alginolyticus, or Vibrio anguillarum, and a pool of these Vibrio strains. Flavobacterium suspensions were also used as an irrelevant bacterium. <span class="hlt">Gene</span> expression analyses were carried out using gill samples from animals dissected at 12 h and 24 h post-infection times by means of quantitative-Polymerase Chain Reaction aimed at targeting several immune <span class="hlt">genes</span>. We also performed SDS-PAGE protein analyses from the same gill tissues. We concluded that there are different levels of immune <span class="hlt">gene</span> expression between the 12 h and 24 h exposure times to various bacterial suspensions. Our results from qPCR demonstrated a general pattern of <span class="hlt">gene</span> expression, decreasing from 12 h over 24 h post-infection. Among the bacteria tested, Flavobacterium is the microorganism species inducing the highest <span class="hlt">gene</span> expression level in 12 h post-infections animals. The 24 h infected animals revealed, however, greater <span class="hlt">gene</span> expression levels, using V. splendidus as the infectious agent. The SDS-PAGE analysis also pointed at protein profile differences between 12 h and 24 h, particularly around a protein area, of 18 KDa molecular mass, where most dissimilarities were found. Multivariate analyses</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25555812','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25555812"><span id="translatedtitle">Immune <span class="hlt">gene</span> expression profile of Penaeus monodon in response to <span class="hlt">marine</span> yeast glucan application and white spot syndrome virus challenge.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Wilson, Wilsy; Lowman, Douglas; Antony, Swapna P; Puthumana, Jayesh; Bright Singh, I S; Philip, Rosamma</p> <p>2015-04-01</p> <p>Immunostimulant potential of eight <span class="hlt">marine</span> yeast glucans (YG) from Candida parapsilosis R20, Hortaea werneckii R23, Candida spencermartinsiae R28, Candida haemulonii R63, Candida oceani R89, Debaryomyces fabryi R100, Debaryomyces nepalensis R305 and Meyerozyma guilliermondii R340 were tested against WSSV challenge in Penaeus monodon post larvae (PL). Structural characterization of these <span class="hlt">marine</span> yeast glucans by proton nuclear magnetic resonance (NMR) indicated structures containing (1-6)-branched (1-3)-β-D-glucan. PL were fed 0.2% glucan incorporated diet once in seven days for a period of 45 days and the animals were challenged with white spot syndrome virus (WSSV). The immunostimulatory activity of yeast glucans were assessed pre- and post-challenge WSSV by analysing the expression profile of six antimicrobial peptide (AMP) <span class="hlt">genes</span> viz., anti-lipopolysaccharide factor (ALF), crustin-1, crustin-2, crustin-3, penaeidin-3 and penaeidin-5 and 13 immune <span class="hlt">genes</span> viz., alpha-2-macroglobulin (α-2-M), astakine, caspase, catalase, glutathione peroxidase, glutathione-s-transferase, haemocyanin, peroxinectin, pmCathepsinC, prophenol oxidase (proPO), Rab-7, superoxide dismutase and transglutaminase. Expression of seven WSSV <span class="hlt">genes</span> viz., DNA polymerase, endonuclease, protein kinase, immediate early <span class="hlt">gene</span>, latency related <span class="hlt">gene</span>, thymidine kinase and VP28 were also analysed to detect the presence and intensity of viral infection in the experimental animals post-challenge. The study revealed that yeast glucans (YG) do possess immunostimulatory activity against WSSV and also supported higher survival (40-70 %) post-challenge WSSV. Among the various glucans tested, YG23 showed maximum survival (70.27%), followed by YG20 (66.66%), YG28 (60.97%), YG89 (58.53%), YG100 (54.05%), YG63 (48.64%), YG305 (45.7%) and YG340 (43.24%). PMID:25555812</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/22362031','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/22362031"><span id="translatedtitle">Population genetic structure of the striped silverside, Atherinomorus endrachtensis (Atherinidae, Atheriniformes, Teleostei), inhabiting <span class="hlt">marine</span> lakes and adjacent lagoons in Palau: <span class="hlt">marine</span> lakes are "Islands" for <span class="hlt">marine</span> species.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Gotoh, Ryo O; Chiba, Satoru N; Goto, Tadasuke V; Tamate, Hidetoshi B; Hanzawa, Naoto</p> <p>2011-01-01</p> <p>Although evidence for the evolution of terrestrial species on islands continues to rapidly accumulate, little is known about the evolution of <span class="hlt">marine</span> species in geographically isolated environments such as islands as ocean currents often facilitate <span class="hlt">gene</span> <span class="hlt">flow</span> among populations. In this study, we focused on <span class="hlt">marine</span> lakes of the Palau Islands, which are considered to be true analogues of terrestrial islands for <span class="hlt">marine</span> species. To examine evolutionary processes in <span class="hlt">marine</span> lakes, we conducted population genetic analyses on <span class="hlt">marine</span> lake and lagoon populations of the striped silverside, Atherinomorus endrachtensis, using two mitochondrial DNA markers differing in evolutionary rate, the cytochrome b <span class="hlt">gene</span> and the control region. The analyses revealed that the amount of genetic diversity of <span class="hlt">marine</span> lake populations is much lower than that of lagoon populations and high levels of genetic differentiation occur among <span class="hlt">marine</span> lake and lagoon populations. The present study has shown that <span class="hlt">marine</span> lake populations have been completely isolated and have differentiated from lagoon populations, and each <span class="hlt">marine</span> lake population is experiencing different evolutionary processes. These findings clearly demonstrate that <span class="hlt">marine</span> lakes are excellent environments for the evolutionary study of <span class="hlt">marine</span> species. PMID:22362031</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2008AGUFM.T44B..02G','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2008AGUFM.T44B..02G"><span id="translatedtitle"><span class="hlt">Marine</span> Heat <span class="hlt">flow</span> measurements from the submerged section of the North Anatolian Fault, in the Sea of Marmara</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Geli, L.; Henry, P.; Andre, C.; Zitter, T.; Cagatay, N.; Mercier de Lepinay, B.</p> <p>2008-12-01</p> <p>For the first time, <span class="hlt">marine</span> heat <span class="hlt">flow</span> data were collected in the Sea of Marmara, in 2007, during the MarNaut cruise of R/V L'Atalante. A total of 45 heat <span class="hlt">flow</span> measurements were carried out along three transects, respectively : the Tekirdag, the Central and the Cinarçik basins. The data were collected using 7 Micrel autonomous digital temperature probes fitted on a 10 cm-diameter gravity corer (the tube length was 10 m for the first 5 measurements ; 5 m for the remaining ones). The thermal profiles are linear, except near the very surface, where slight changes in water bottom temperature can be suspected. The measured heat <span class="hlt">flow</span> values range between about 15 and 55 mW.m-2, except at one single location near the northern Cinarcik Basin escarpment, where heat <span class="hlt">flow</span> reaches 120 mW.m-2, probably in response to deep, upward fluid <span class="hlt">flow</span>. The measured values are lower than the published regional heat <span class="hlt">flow</span> averages, which are of about 50 to 60 mW.m-2 and of about 100 mW.m-2 north and south of the Sea of Marmara, respectively. The lowest values correspond to the basins depocenters, where the syn-rift sediment cover is thickest, which suggests strong thermal sediment blanketing effects. Near the edges of the basins, effects resulting from basement topography are also suspected. Corrections are made to account for both effects, assuming different scenarii for the temporal and spatial evolution of the sedimentation rate. The computation results provide constraints to estimate the age of initiation of the North Anatolian Fault within what is now the Sea of Marmara.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2004AGUFM.B53A0976K','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2004AGUFM.B53A0976K"><span id="translatedtitle">Application of wireless sensor networks to study <span class="hlt">flow</span> over heterogeneous surfaces: <span class="hlt">flow</span> over an isolated mountain in the <span class="hlt">marine</span> atmosphere</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Kleissl, J.; Dziobak, M. P.; Honrath, R. E.</p> <p>2004-12-01</p> <p>A combination of standard meteorological equipment (3d sonic anemometer, energy balance sensors) and Crossbow MPR400 (Mica2) wireless motes and sensorboards were deployed along the slope of Pico mountain in the Azores, Portugal, between z = 1200 m and z = 2300 m MSL. The isolated location and uniform, conic shape make Pico mountain an ideal location to study orographic effects. This experiment focuses on upslope and downslope <span class="hlt">flow</span>. Cost effective wireless sensor technology allows for high density of observations in time and space as necessary for characterization of <span class="hlt">flows</span> over heterogeneous surfaces. Thus the features of upslope and downslope <span class="hlt">flows</span> (speed, location and duration) and their effect on atmospheric physics and chemistry (temperature, relative humidity) can be studied in great detail. Synchronous measurements of O3, CO, NOx, NOy and NMHC at the PICO-NARE observatory (Honrath et al. 2004) situated at the mountaintop give further clues on airmass origin and dispersion. Findings regarding the occurrence and impacts of upslope and downslope <span class="hlt">flow</span> and the advantages and disadvantages of wireless sensors relative to standard meteorological instruments will be presented. In particular, practical issues of wireless sensor deployment, such as durability in harsh conditions, power management, accuracy, and cost will be discussed.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3779095','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3779095"><span id="translatedtitle"><span class="hlt">Gene</span> <span class="hlt">flow</span> and demographic history of leopards (Panthera pardus) in the central Indian highlands</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Dutta, Trishna; Sharma, Sandeep; Maldonado, Jesús E; Wood, Thomas C; Panwar, Hemendra S; Seidensticker, John</p> <p>2013-01-01</p> <p><span class="hlt">Gene</span> <span class="hlt">flow</span> is a critical ecological process that must be maintained in order to counteract the detrimental effects of genetic drift in subdivided populations, with conservation benefits ranging from promoting the persistence of small populations to spreading adaptive traits in changing environments. We evaluated historical and contemporary <span class="hlt">gene</span> <span class="hlt">flow</span> and effective population sizes of leopards in a landscape in central India using noninvasive sampling. Despite the dramatic changes in land-use patterns in this landscape through recent times, we did not detect any signs that the leopard populations have been through a genetic bottleneck, and they appear to have maintained migration–drift equilibrium. We found that historical levels of <span class="hlt">gene</span> <span class="hlt">flow</span> (mean mh = 0.07) were significantly higher than contemporary levels (mean mc = 0.03), and populations with large effective population sizes (Satpura and Kanha Tiger Reserves) are the larger exporters of migrants at both timescales. The greatest decline in historical versus contemporary <span class="hlt">gene</span> <span class="hlt">flow</span> is between pairs of reserves that are currently not connected by forest corridors (i.e., Melghat-Pench mh − mc = 0.063; and Kanha-Satpura mh − mc = 0.054). We attribute this reduction in <span class="hlt">gene</span> <span class="hlt">flow</span> to accelerated fragmentation and habitat alteration in the landscape over the past few centuries, and suggest protection of forest corridors to maintain <span class="hlt">gene</span> <span class="hlt">flow</span> in this landscape. PMID:24062803</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4382708','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4382708"><span id="translatedtitle">Quantitating and Dating Recent <span class="hlt">Gene</span> <span class="hlt">Flow</span> between European and East Asian Populations</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Qin, Pengfei; Zhou, Ying; Lou, Haiyi; Lu, Dongsheng; Yang, Xiong; Wang, Yuchen; Jin, Li; Chung, Yeun-Jun; Xu, Shuhua</p> <p>2015-01-01</p> <p>Historical records indicate that extensive cultural, commercial and technological interaction occurred between European and Asian populations. What have been the biological consequences of these contacts in terms of <span class="hlt">gene</span> <span class="hlt">flow</span>? We systematically estimated <span class="hlt">gene</span> <span class="hlt">flow</span> between Eurasian groups using genome-wide polymorphisms from 34 populations representing Europeans, East Asians, and Central/South Asians. We identified recent <span class="hlt">gene</span> <span class="hlt">flow</span> between Europeans and Asians in most populations we studied, including East Asians and Northwestern Europeans, which are normally considered to be non-admixed populations. In addition we quantitatively estimated the extent of this <span class="hlt">gene</span> <span class="hlt">flow</span> using two statistical approaches, and dated admixture events based on admixture linkage disequilibrium. Our results indicate that most genetic admixtures occurred between 2,400 and 310 years ago and show the admixture proportions to be highly correlated with geographic locations, with the highest admixture proportions observed in Central Asia and the lowest in East Asia and Northwestern Europe. Interestingly, we observed a North-to-South decline of European <span class="hlt">gene</span> <span class="hlt">flow</span> in East Asians, suggesting a northern path of European <span class="hlt">gene</span> <span class="hlt">flow</span> diffusing into East Asian populations. Our findings contribute to an improved understanding of the history of human migration and the evolutionary mechanisms that have shaped the genetic structure of populations in Eurasia. PMID:25833680</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/24903145','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/24903145"><span id="translatedtitle">Bears in a forest of <span class="hlt">gene</span> trees: phylogenetic inference is complicated by incomplete lineage sorting and <span class="hlt">gene</span> <span class="hlt">flow</span>.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Kutschera, Verena E; Bidon, Tobias; Hailer, Frank; Rodi, Julia L; Fain, Steven R; Janke, Axel</p> <p>2014-08-01</p> <p>Ursine bears are a mammalian subfamily that comprises six morphologically and ecologically distinct extant species. Previous phylogenetic analyses of concatenated nuclear <span class="hlt">genes</span> could not resolve all relationships among bears, and appeared to conflict with the mitochondrial phylogeny. Evolutionary processes such as incomplete lineage sorting and introgression can cause <span class="hlt">gene</span> tree discordance and complicate phylogenetic inferences, but are not accounted for in phylogenetic analyses of concatenated data. We generated a high-resolution data set of autosomal introns from several individuals per species and of Y-chromosomal markers. Incorporating intraspecific variability in coalescence-based phylogenetic and <span class="hlt">gene</span> <span class="hlt">flow</span> estimation approaches, we traced the genealogical history of individual alleles. Considerable heterogeneity among nuclear loci and discordance between nuclear and mitochondrial phylogenies were found. A species tree with divergence time estimates indicated that ursine bears diversified within less than 2 My. Consistent with a complex branching order within a clade of Asian bear species, we identified unidirectional <span class="hlt">gene</span> <span class="hlt">flow</span> from Asian black into sloth bears. Moreover, <span class="hlt">gene</span> <span class="hlt">flow</span> detected from brown into American black bears can explain the conflicting placement of the American black bear in mitochondrial and nuclear phylogenies. These results highlight that both incomplete lineage sorting and introgression are prominent evolutionary forces even on time scales up to several million years. Complex evolutionary patterns are not adequately captured by strictly bifurcating models, and can only be fully understood when analyzing multiple independently inherited loci in a coalescence framework. Phylogenetic incongruence among <span class="hlt">gene</span> trees hence needs to be recognized as a biologically meaningful signal. PMID:24903145</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4104321','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4104321"><span id="translatedtitle">Bears in a Forest of <span class="hlt">Gene</span> Trees: Phylogenetic Inference Is Complicated by Incomplete Lineage Sorting and <span class="hlt">Gene</span> <span class="hlt">Flow</span></span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Kutschera, Verena E.; Bidon, Tobias; Hailer, Frank; Rodi, Julia L.; Fain, Steven R.; Janke, Axel</p> <p>2014-01-01</p> <p>Ursine bears are a mammalian subfamily that comprises six morphologically and ecologically distinct extant species. Previous phylogenetic analyses of concatenated nuclear <span class="hlt">genes</span> could not resolve all relationships among bears, and appeared to conflict with the mitochondrial phylogeny. Evolutionary processes such as incomplete lineage sorting and introgression can cause <span class="hlt">gene</span> tree discordance and complicate phylogenetic inferences, but are not accounted for in phylogenetic analyses of concatenated data. We generated a high-resolution data set of autosomal introns from several individuals per species and of Y-chromosomal markers. Incorporating intraspecific variability in coalescence-based phylogenetic and <span class="hlt">gene</span> <span class="hlt">flow</span> estimation approaches, we traced the genealogical history of individual alleles. Considerable heterogeneity among nuclear loci and discordance between nuclear and mitochondrial phylogenies were found. A species tree with divergence time estimates indicated that ursine bears diversified within less than 2 My. Consistent with a complex branching order within a clade of Asian bear species, we identified unidirectional <span class="hlt">gene</span> <span class="hlt">flow</span> from Asian black into sloth bears. Moreover, <span class="hlt">gene</span> <span class="hlt">flow</span> detected from brown into American black bears can explain the conflicting placement of the American black bear in mitochondrial and nuclear phylogenies. These results highlight that both incomplete lineage sorting and introgression are prominent evolutionary forces even on time scales up to several million years. Complex evolutionary patterns are not adequately captured by strictly bifurcating models, and can only be fully understood when analyzing multiple independently inherited loci in a coalescence framework. Phylogenetic incongruence among <span class="hlt">gene</span> trees hence needs to be recognized as a biologically meaningful signal. PMID:24903145</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25524569','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25524569"><span id="translatedtitle">Metagenomic-based study of the phylogenetic and functional <span class="hlt">gene</span> diversity in Galápagos land and <span class="hlt">marine</span> iguanas.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Hong, Pei-Ying; Mao, Yuejian; Ortiz-Kofoed, Shannon; Shah, Rushabh; Cann, Isaac; Mackie, Roderick I</p> <p>2015-02-01</p> <p>In this study, a metagenome-based analysis of the fecal samples from the macrophytic algae-consuming <span class="hlt">marine</span> iguana (MI; Amblyrhynchus cristatus) and terrestrial biomass-consuming land iguanas (LI; Conolophus spp.) was conducted. Phylogenetic affiliations of the fecal microbiome were more similar between both iguanas than to other mammalian herbivorous hosts. However, functional <span class="hlt">gene</span> diversities in both MI and LI iguana hosts differed in relation to the diet, where the MI fecal microbiota had a functional diversity that clustered apart from the other terrestrial-biomass consuming reptilian and mammalian hosts. A further examination of the carbohydrate-degrading <span class="hlt">genes</span> revealed that several of the prevalent glycosyl hydrolases (GH), glycosyl transferases (GT), carbohydrate binding modules (CBM), and carbohydrate esterases (CE) <span class="hlt">gene</span> classes were conserved among all examined herbivorous hosts, reiterating the important roles these <span class="hlt">genes</span> play in the breakdown and metabolism of herbivorous diets. <span class="hlt">Genes</span> encoding some classes of carbohydrate-degrading families, including GH2, GH13, GT2, GT4, CBM50, CBM48, CE4, and CE11, as well as <span class="hlt">genes</span> associated with sulfur metabolism and dehalogenation, were highly enriched or unique to the MI. In contrast, <span class="hlt">gene</span> sequences that relate to archaeal methanogenesis were detected only in LI fecal microbiome, and <span class="hlt">genes</span> coding for GH13, GH66, GT2, GT4, CBM50, CBM13, CE4, and CE8 carbohydrate active enzymes were highly abundant in the LI. Bacterial populations were enriched on various carbohydrates substrates (e.g., glucose, arabinose, xylose). The majority of the enriched bacterial populations belong to genera Clostridium spp. and Enterococcus spp. that likely accounted for the high prevalence of GH13 and GH2, as well as the GT families (e.g., GT2, GT4, GT28, GT35, and GT51) that were ubiquitously present in the fecal microbiota of all herbivorous hosts. PMID:25524569</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://eric.ed.gov/?q=pollen&pg=2&id=EJ339300','ERIC'); return false;" href="http://eric.ed.gov/?q=pollen&pg=2&id=EJ339300"><span id="translatedtitle"><span class="hlt">Gene</span> <span class="hlt">Flow</span> and the Measurement of Dispersal in Plant Populations.</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Nicholls, Marc S.</p> <p>1986-01-01</p> <p>Reviews methods of estimating pollen and seed dispersals and discusses the extent and frequency of <span class="hlt">gene</span> exchange within and between populations. Offers suggestions for designing exercises suitable for estimating dispersal distances in natural plant populations. (ML)</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_8");'>8</a></li> <li><a href="#" onclick='return showDiv("page_9");'>9</a></li> <li class="active"><span>10</span></li> <li><a href="#" onclick='return showDiv("page_11");'>11</a></li> <li><a href="#" onclick='return showDiv("page_12");'>12</a></li> <li><a href="#" onclick='return showDiv("page_13");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_10 --> <div id="page_11" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_9");'>9</a></li> <li><a href="#" onclick='return showDiv("page_10");'>10</a></li> <li class="active"><span>11</span></li> <li><a href="#" onclick='return showDiv("page_12");'>12</a></li> <li><a href="#" onclick='return showDiv("page_13");'>13</a></li> <li><a href="#" onclick='return showDiv("page_13");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="201"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ars.usda.gov/research/publications/publication/?seqNo115=331878','TEKTRAN'); return false;" href="http://www.ars.usda.gov/research/publications/publication/?seqNo115=331878"><span id="translatedtitle">Patterns of <span class="hlt">gene</span> <span class="hlt">flow</span> between crop and wild carrot, Daucus carota (Apiaceae) in the United States</span></a></p> <p><a target="_blank" href="http://www.ars.usda.gov/services/TekTran.htm">Technology Transfer Automated Retrieval System (TEKTRAN)</a></p> <p></p> <p></p> <p>Studies of <span class="hlt">gene</span> <span class="hlt">flow</span> between crops and their wild relatives have implications for both management practices for farming and breeding as well as understanding the risk of transgene escape. These types of studies may also yield insight into population dynamics and the evolutionary consequences of <span class="hlt">gene</span>...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ars.usda.gov/research/publications/Publications.htm?seq_no_115=269329','TEKTRAN'); return false;" href="http://www.ars.usda.gov/research/publications/Publications.htm?seq_no_115=269329"><span id="translatedtitle"><span class="hlt">Gene</span> <span class="hlt">flow</span> and herbicide resistance: Lessons learned from herbicide-resistant rice systems</span></a></p> <p><a target="_blank" href="http://www.ars.usda.gov/services/TekTran.htm">Technology Transfer Automated Retrieval System (TEKTRAN)</a></p> <p></p> <p></p> <p><span class="hlt">Gene</span> <span class="hlt">flow</span> in plants is a process whereby <span class="hlt">genes</span> are exchanged between members of the same or closely related species via pollen and become established in new populations. This natural process has long been an issue in breeding and the seed industry, but interest has increased since the deployment of ...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ars.usda.gov/research/publications/Publications.htm?seq_no_115=131261','TEKTRAN'); return false;" href="http://www.ars.usda.gov/research/publications/Publications.htm?seq_no_115=131261"><span id="translatedtitle">A TECHNIQUE TO REDUCE THE RISK OF <span class="hlt">GENE</span> <span class="hlt">FLOW</span> THROUGH SORGHUM POLLEN</span></a></p> <p><a target="_blank" href="http://www.ars.usda.gov/services/TekTran.htm">Technology Transfer Automated Retrieval System (TEKTRAN)</a></p> <p></p> <p></p> <p>A critical impediment to field testing and deployment of transgenic sorghum (Sorghum bicolor (L.) Moench) is the threat of <span class="hlt">gene</span> <span class="hlt">flow</span> to weedy relatives through pollen. A technique using sorghum with A3 cytoplasmic male sterility to control transgene <span class="hlt">flow</span> through pollen while using non- transgenic po...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3084246','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3084246"><span id="translatedtitle">Plastid 16S rRNA <span class="hlt">Gene</span> Diversity among Eukaryotic Picophytoplankton Sorted by <span class="hlt">Flow</span> Cytometry from the South Pacific Ocean</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Shi, Xiao Li; Lepère, Cécile; Scanlan, David J.; Vaulot, Daniel</p> <p>2011-01-01</p> <p>The genetic diversity of photosynthetic picoeukaryotes was investigated in the South East Pacific Ocean. Genetic libraries of the plastid 16S rRNA <span class="hlt">gene</span> were constructed on picoeukaryote populations sorted by <span class="hlt">flow</span> cytometry, using two different primer sets, OXY107F/OXY1313R commonly used to amplify oxygenic organisms, and PLA491F/OXY1313R, biased towards plastids of <span class="hlt">marine</span> algae. Surprisingly, the two sets revealed quite different photosynthetic picoeukaryote diversity patterns, which were moreover different from what we previously reported using the 18S rRNA nuclear <span class="hlt">gene</span> as a marker. The first 16S primer set revealed many sequences related to Pelagophyceae and Dictyochophyceae, the second 16S primer set was heavily biased toward Prymnesiophyceae, while 18S sequences were dominated by Prasinophyceae, Chrysophyceae and Haptophyta. Primer mismatches with major algal lineages is probably one reason behind this discrepancy. However, other reasons, such as DNA accessibility or <span class="hlt">gene</span> copy numbers, may be also critical. Based on plastid 16S rRNA <span class="hlt">gene</span> sequences, the structure of photosynthetic picoeukaryotes varied along the BIOSOPE transect vertically and horizontally. In oligotrophic regions, Pelagophyceae, Chrysophyceae, and Prymnesiophyceae dominated. Pelagophyceae were prevalent at the DCM depth and Chrysophyceae at the surface. In mesotrophic regions Pelagophyceae were still important but Chlorophyta contribution increased. Phylogenetic analysis revealed a new clade of Prasinophyceae (clade 16S-IX), which seems to be restricted to hyper-oligotrophic stations. Our data suggest that a single <span class="hlt">gene</span> marker, even as widely used as 18S rRNA, provides a biased view of eukaryotic communities and that the use of several markers is necessary to obtain a complete image. PMID:21552558</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015JPhCS.655a2052M','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015JPhCS.655a2052M"><span id="translatedtitle">Numerical investigation of the <span class="hlt">flow</span> in axial water turbines and <span class="hlt">marine</span> propellers with scale-resolving simulations</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Morgut, Mitja; Jošt, Dragica; Nobile, Enrico; Škerlavaj, Aljaž</p> <p>2015-11-01</p> <p>The accurate prediction of the performances of axial water turbines and naval propellers is a challenging task, of great practical relevance. In this paper a numerical prediction strategy, based on the combination of a trusted CFD solver and a calibrated mass transfer model, is applied to the turbulent <span class="hlt">flow</span> in axial turbines and around a model scale naval propeller, under non-cavitating and cavitating conditions. Some selected results for axial water turbines and a <span class="hlt">marine</span> propeller, and in particular the advantages, in terms of accuracy and fidelity, of ScaleResolving Simulations (SRS), like SAS (Scale Adaptive Simulation) and Zonal-LES (ZLES) compared to standard RANS approaches, are presented. Efficiency prediction for a Kaplan and a bulb turbine was significantly improved by use of the SAS SST model in combination with the ZLES in the draft tube. Size of cavitation cavity and sigma break curve for Kaplan turbine were successfully predicted with SAS model in combination with robust high resolution scheme, while for mass transfer the Zwart model with calibrated constants were used. The results obtained for a <span class="hlt">marine</span> propeller in non-uniform inflow, under cavitating conditions, compare well with available experimental measurements, and proved that a mass transfer model, previously calibrated for RANS (Reynolds Averaged Navier Stokes), can be successfully applied also within the SRS approaches.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25657838','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25657838"><span id="translatedtitle">Experimental and computational analysis of a novel <span class="hlt">flow</span> channel to assess the adhesion strength of sessile <span class="hlt">marine</span> organisms.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Dimartino, Simone; Mather, Anton V; Alestra, Tommaso; Nawada, Suhas; Haber, Meir</p> <p>2015-02-01</p> <p>Bioadhesives produced by <span class="hlt">marine</span> macroalgae represent a potential source of inspiration for the development of water-resistant adhesives. Assessing their adhesion strength, however, remains difficult owing to low volumes of adhesive material produced, low solubility and rapid curing time. These difficulties can be circumvented by testing the adhesion strength of macroalgae propagules attached to a substrate. In this paper, we present a simple, novel <span class="hlt">flow</span> channel used to test the adhesion strength of the germlings of the fucalean alga Hormosira banksii to four substrates of biomedical relevance (PMMA, agar, gelatin and gelatin + lipid). The adhesion strength of H. banksii germlings was found to increase in a time-dependent manner, with minimal adhesion success after a settlement period of 6 h and maximum adhesion strength achieved 24 h after initial settlement. Adhesion success increased most dramatically between 6 and 12 h settlement time, while no additional increase in adhesion strength was recorded for settlement times over 24 h. No significant difference in adhesion strength to the various substrates was observed. Computational fluid dynamics (CFD) was used to estimate the influence of fluid velocity and germling density on drag force acting on the settled organisms. CFD modelling showed that, on average, the drag force decreased with increasing germling number, suggesting that germlings would benefit from gregarious settlement behaviour. Collectively, our results contribute to a better understanding of the mechanisms allowing benthic <span class="hlt">marine</span> organisms to thrive in hydrodynamically stressful environments and provide useful insights for further investigations. PMID:25657838</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4275873','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4275873"><span id="translatedtitle">Experimental and computational analysis of a novel <span class="hlt">flow</span> channel to assess the adhesion strength of sessile <span class="hlt">marine</span> organisms</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Dimartino, Simone; Mather, Anton V.; Alestra, Tommaso; Nawada, Suhas; Haber, Meir</p> <p>2015-01-01</p> <p>Bioadhesives produced by <span class="hlt">marine</span> macroalgae represent a potential source of inspiration for the development of water-resistant adhesives. Assessing their adhesion strength, however, remains difficult owing to low volumes of adhesive material produced, low solubility and rapid curing time. These difficulties can be circumvented by testing the adhesion strength of macroalgae propagules attached to a substrate. In this paper, we present a simple, novel <span class="hlt">flow</span> channel used to test the adhesion strength of the germlings of the fucalean alga Hormosira banksii to four substrates of biomedical relevance (PMMA, agar, gelatin and gelatin + lipid). The adhesion strength of H. banksii germlings was found to increase in a time-dependent manner, with minimal adhesion success after a settlement period of 6 h and maximum adhesion strength achieved 24 h after initial settlement. Adhesion success increased most dramatically between 6 and 12 h settlement time, while no additional increase in adhesion strength was recorded for settlement times over 24 h. No significant difference in adhesion strength to the various substrates was observed. Computational fluid dynamics (CFD) was used to estimate the influence of fluid velocity and germling density on drag force acting on the settled organisms. CFD modelling showed that, on average, the drag force decreased with increasing germling number, suggesting that germlings would benefit from gregarious settlement behaviour. Collectively, our results contribute to a better understanding of the mechanisms allowing benthic <span class="hlt">marine</span> organisms to thrive in hydrodynamically stressful environments and provide useful insights for further investigations. PMID:25657838</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2013AIPC.1532..812J&link_type=ABSTRACT','NASAADS'); return false;" href="http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2013AIPC.1532..812J&link_type=ABSTRACT"><span id="translatedtitle">Study on the metal <span class="hlt">flow</span> of large <span class="hlt">marine</span> full-fiber crankshaft processed by TR bending-upsetting method</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Jia, Zhen; Xu, Bin; Sun, Ming-yue; Li, Dian-zhong; Deng, Jun-jiang; He, Ming-jiu</p> <p>2013-05-01</p> <p>Large <span class="hlt">marine</span> crankshaft is the heart of medium-speed diesel engine. The TR forming method used to obtain full-fiber workpiece is considerably complex. However, the metal <span class="hlt">flow</span> behavior during bending-upsetting process, which determines the forming quality, was seldom studied in previous works. In this study, a finite element model (FEM) was established using constitutive model of 42CrMo4 steel and specified boundary conditions. The simulated results has demonstrated that the early filled metal resists the following metal entering the upper cavity, thereby causing the flash on the upper edge and the unfilled defect on the lower edge of the crank-arm. Further analysis has indicated that larger initial angel of the elbow rod θ0 and a good lubrication condition between dies and workpiece can effectively decrease the volume of flash and eliminate the unfilled defect on the final product.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/27474849','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/27474849"><span id="translatedtitle">Evaluation of gemfibrozil effects on a <span class="hlt">marine</span> fish (Sparus aurata) combining <span class="hlt">gene</span> expression with conventional endocrine and biochemical endpoints.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Teles, M; Fierro-Castro, C; Na-Phatthalung, P; Tvarijonaviciute, A; Soares, A M V M; Tort, L; Oliveira, M</p> <p>2016-11-15</p> <p>The information on the potential hazardous effects of gemfibrozil (GEM) on <span class="hlt">marine</span> fish is extremely scarce. In the current study, molecular, endocrine and biochemical parameters were assessed in Sparus aurata after 96h waterborne exposure to a GEM concentration range. Hepatic mRNA levels of target <span class="hlt">genes</span> known to be regulated via peroxisome proliferator-activated receptor α (pparα) in mammals, such as apolipoprotein AI (apoa1) and lipoprotein (lpl) were significantly increased, without a concomitant activation of the ppar pathways. GEM (15μgL(-1)) induced an upregulation in mRNA levels of interleukin 1β (il1β), tumour necrosis factor-α (tnfα) and caspase 3 (casp3), suggesting an activation of proinflammatory processes in S. aurata liver. However, mRNA levels of <span class="hlt">genes</span> related with the antioxidant defence system and cell-tissue repair were unaltered under the tested experimental conditions. Higher levels of GEM induced a cortisol rise, an indication that it is recognized as a stressor by S. aurata. Cortisol levels and the mRNA levels of il1β, tnfα and casp3 may be suggested as potential biomarkers of GEM effects in <span class="hlt">marine</span> fish. PMID:27474849</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/17974346','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/17974346"><span id="translatedtitle">Effect of pollinator abundance on self-fertilization and <span class="hlt">gene</span> <span class="hlt">flow</span>: application to GM Canola.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Hoyle, Martin; Hayter, Katrina; Cresswell, James E</p> <p>2007-10-01</p> <p>Cross-pollination from fields of transgenic crops is of great public concern. Although cross-pollination in commercial canola (Brassica napus) fields has been empirically measured, field trials are expensive and do not identify the causes of cross-pollination. Therefore, theoretical models can be valuable because they can provide estimates of cross-pollination at any given site and time. We present a general analytical model of field-to-field <span class="hlt">gene</span> <span class="hlt">flow</span> due to the following competing mechanisms: the wind, bees, and autonomous pollination. We parameterize the model for the particular case of field-to-field cross-pollination of genetically modified (GM) canola via the wind and via bumble bees (Bombus spp.) and honey bees (Apis mellifera). We make extensive use of the large data set of bee densities collected during the recent U.K. Farm Scale Evaluations. We predict that canola approaches almost full seed set without pollinators and that autonomous pollination is responsible for > or = 25% of seed set, irrespective of pollinator abundance. We do not predict the relative contribution of bees vs. the wind in landscape-scale <span class="hlt">gene</span> <span class="hlt">flow</span> in canola. However, under model assumptions, we predict that the maximum field-to-field <span class="hlt">gene</span> <span class="hlt">flow</span> due to bumble bees is 0.04% and 0.13% below the current EU limit for adventitious GM presence for winter- and spring-sown canola, respectively. We predict that <span class="hlt">gene</span> <span class="hlt">flow</span> due to bees is approximately 3.1 times higher at 20% compared to 100% male-fertility, and due to the wind, 1.3 times higher at 20% compared to 100% male-fertility, for both winter- and spring-sown canola. Bumble bee-mediated <span class="hlt">gene</span> <span class="hlt">flow</span> is approximately 2.7 times higher and wind-mediated <span class="hlt">gene</span> <span class="hlt">flow</span> approximately 1.7 times lower in spring-sown than in winter-sown canola, regardless of the degree of male-sterility. The model of cross-pollination due to the wind most closely predicted three previously published observations: field-to-field <span class="hlt">gene</span> <span class="hlt">flow</span> is low; <span class="hlt">gene</span> <span class="hlt">flow</span> increases with</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015AGUFM.T14B..04A','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015AGUFM.T14B..04A"><span id="translatedtitle"><span class="hlt">Marine</span> Heat <span class="hlt">Flow</span> Measurements of the Northern and Southern Hikurangi Margin, New Zealand</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Antriasian, A. M.; Harris, R. N.; Trehu, A. M.; Henrys, S. A.; Gorman, A. R.; Lauer, R. M.; Phrampus, B. J.; Colella, H.; Baker, D.; Rocco, N.</p> <p>2015-12-01</p> <p>The 120 Ma Hikurangi Plateau, a large igneous province on the Pacific plate, is subducting below the Australian plate at the Hikurangi margin. Large along-strike variations in apparent interseismic coupling and in the depth range over which slow slip occurs provide the opportunity to better understand which factors affect the slip behavior along the megathrust. Prior to our heat <span class="hlt">flow</span> survey the thermal regime of the incoming Hikurangi Plateau was largely unknown. In May and June, 2015, we collected 196 seafloor heat <span class="hlt">flow</span> values in a series of transects consisting of closely-spaced measurements with a 3.5 m "violin-bow" type probe. Heat <span class="hlt">flow</span> measurements are located around the northern and southern Hikurangi margin and are collocated with seismic reflection lines. The background heat <span class="hlt">flow</span> on the incoming plate is 49 ± 7, and 52 ± 9, mW/m2 for the northern and southern areas, respectively. These values are consistent with cooling plate models for this age of oceanic crust and suggest no difference in the basal heat flux between these two areas. However, heat <span class="hlt">flow</span> transects in the northern Hikurangi trough show clear evidence for crustal fluid <span class="hlt">flow</span> associated with the basement relief, while heat <span class="hlt">flow</span> transects along the southern Hikurangi trough do not show evidence for crustal fluid <span class="hlt">flow</span>, which may be due to a lack of basement relief. We are developing a 2D thermal model for each region to understand the thermal and hydrologic regimes and their influence on clay diagenesis and modes of deformation.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2234187','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2234187"><span id="translatedtitle">Whole-genome expression profiling of the <span class="hlt">marine</span> diatom Thalassiosira pseudonana identifies <span class="hlt">genes</span> involved in silicon bioprocesses</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Mock, Thomas; Samanta, Manoj Pratim; Iverson, Vaughn; Berthiaume, Chris; Robison, Matthew; Holtermann, Karie; Durkin, Colleen; BonDurant, Sandra Splinter; Richmond, Kathryn; Rodesch, Matthew; Kallas, Toivo; Huttlin, Edward L.; Cerrina, Francesco; Sussman, Michael R.; Armbrust, E. Virginia</p> <p>2008-01-01</p> <p>Formation of complex inorganic structures is widespread in nature. Diatoms create intricately patterned cell walls of inorganic silicon that are a biomimetic model for design and generation of three-dimensional silica nanostructures. To date, only relatively simple silica structures can be generated in vitro through manipulation of known diatom phosphoproteins (silaffins) and long-chain polyamines. Here, we report the use of genome-wide transcriptome analyses of the <span class="hlt">marine</span> diatom Thalassiosira pseudonana to identify additional candidate <span class="hlt">gene</span> products involved in the biological manipulation of silicon. Whole-genome oligonucleotide tiling arrays and tandem mass spectrometry identified transcripts for >8,000 <span class="hlt">genes</span>, ≈3,000 of which were not previously described and included noncoding and antisense RNAs. <span class="hlt">Gene</span>-specific expression profiles detected a set of 75 <span class="hlt">genes</span> induced only under low concentrations of silicon but not under low concentrations of nitrogen or iron, alkaline pH, or low temperatures. Most of these induced <span class="hlt">gene</span> products were predicted to contain secretory signals and/or transmembrane domains but displayed no homology to known proteins. Over half of these <span class="hlt">genes</span> were newly discovered, identified only through the use of tiling arrays. Unexpectedly, a common set of 84 <span class="hlt">genes</span> were induced by both silicon and iron limitations, suggesting that biological manipulation of silicon may share pathways in common with iron or, alternatively, that iron may serve as a required cofactor for silicon processes. These results provide insights into the transcriptional and translational basis for the biological generation of elaborate silicon nanostructures by these ecologically important microbes. PMID:18212125</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25237766','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25237766"><span id="translatedtitle">Adaptive divergence with <span class="hlt">gene</span> <span class="hlt">flow</span> in incipient speciation of Miscanthus floridulus/sinensis complex (Poaceae).</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Huang, Chao-Li; Ho, Chuan-Wen; Chiang, Yu-Chung; Shigemoto, Yasumasa; Hsu, Tsai-Wen; Hwang, Chi-Chuan; Ge, Xue-Jun; Chen, Charles; Wu, Tai-Han; Chou, Chang-Hung; Huang, Hao-Jen; Gojobori, Takashi; Osada, Naoki; Chiang, Tzen-Yuh</p> <p>2014-12-01</p> <p>Young incipient species provide ideal materials for untangling the process of ecological speciation in the presence of <span class="hlt">gene</span> <span class="hlt">flow</span>. The Miscanthus floridulus/sinensis complex exhibits diverse phenotypic and ecological differences despite recent divergence (approximately 1.59 million years ago). To elucidate the process of genetic differentiation during early stages of ecological speciation, we analyzed genomic divergence in the Miscanthus complex using 72 randomly selected <span class="hlt">genes</span> from a newly assembled transcriptome. In this study, rampant <span class="hlt">gene</span> <span class="hlt">flow</span> was detected between species, estimated as M = 3.36 × 10(-9) to 1.20 × 10(-6) , resulting in contradicting phylogenies across loci. Nevertheless, beast analyses revealed the species identity and the effects of extrinsic cohesive forces that counteracted the non-stop introgression. As expected, early in speciation with <span class="hlt">gene</span> <span class="hlt">flow</span>, only 3-13 loci were highly diverged; two to five outliers (approximately 2.78-6.94% of the genome) were characterized by strong linkage disequilibrium, and asymmetrically distributed among ecotypes, indicating footprints of diversifying selection. In conclusion, ecological speciation of incipient species of Miscanthus probably followed the parapatric model, whereas allopatric speciation cannot be completely ruled out, especially between the geographically isolated northern and southern M. sinensis, for which no significant <span class="hlt">gene</span> <span class="hlt">flow</span> across oceanic barriers was detected. Divergence between local ecotypes in early-stage speciation began at a few genomic regions under the influence of natural selection and divergence hitchhiking that overcame <span class="hlt">gene</span> <span class="hlt">flow</span>. PMID:25237766</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4557025','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4557025"><span id="translatedtitle">Effect of an Introduced Phytoene Synthase <span class="hlt">Gene</span> Expression on Carotenoid Biosynthesis in the <span class="hlt">Marine</span> Diatom Phaeodactylum tricornutum</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Kadono, Takashi; Kira, Nozomu; Suzuki, Kengo; Iwata, Osamu; Ohama, Takeshi; Okada, Shigeru; Nishimura, Tomohiro; Akakabe, Mai; Tsuda, Masashi; Adachi, Masao</p> <p>2015-01-01</p> <p>Carotenoids exert beneficial effects on human health through their excellent antioxidant activity. To increase carotenoid productivity in the <span class="hlt">marine</span> Pennales Phaeodactylum tricornutum, we genetically engineered the phytoene synthase <span class="hlt">gene</span> (psy) to improve expression because RNA-sequencing analysis has suggested that the expression level of psy is lower than other enzyme-encoding <span class="hlt">genes</span> that are involved in the carotenoid biosynthetic pathway. We isolated psy from P. tricornutum, and this <span class="hlt">gene</span> was fused with the enhanced green fluorescent protein <span class="hlt">gene</span> to detect psy expression. After transformation using the microparticle bombardment technique, we obtained several P. tricornutum transformants and confirmed psy expression in their plastids. We investigated the amounts of PSY mRNA and carotenoids, such as fucoxanthin and β-carotene, at different growth phases. The introduction of psy increased the fucoxanthin content of a transformants by approximately 1.45-fold relative to the levels in the wild-type diatom. However, some transformants failed to show a significant increase in the carotenoid content relative to that of the wild-type diatom. We also found that the amount of PSY mRNA at log phase might contribute to the increase in carotenoids in the transformants at stationary phase. PMID:26308005</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/17293531','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/17293531"><span id="translatedtitle">Widespread occurrence and genomic context of unusually small polyketide synthase <span class="hlt">genes</span> in microbial consortia associated with <span class="hlt">marine</span> sponges.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Fieseler, Lars; Hentschel, Ute; Grozdanov, Lubomir; Schirmer, Andreas; Wen, Gaiping; Platzer, Matthias; Hrvatin, Sinisa; Butzke, Daniel; Zimmermann, Katrin; Piel, Jörn</p> <p>2007-04-01</p> <p>Numerous <span class="hlt">marine</span> sponges harbor enormous amounts of as-yet-uncultivated bacteria in their tissues. There is increasing evidence that these symbionts play an important role in the synthesis of protective metabolites, many of which are of great pharmacological interest. In this study, <span class="hlt">genes</span> for the biosynthesis of polyketides, one of the most important classes of bioactive natural products, were systematically investigated in 20 demosponge species from different oceans. Unexpectedly, the sponge metagenomes were dominated by a ubiquitously present, evolutionarily distinct, and highly sponge-specific group of polyketide synthases (PKSs). Open reading frames resembling animal fatty acid <span class="hlt">genes</span> were found on three corresponding DNA regions isolated from the metagenomes of Theonella swinhoei and Aplysina aerophoba. Their architecture suggests that methyl-branched fatty acids are the metabolic product. According to a phylogenetic analysis of housekeeping <span class="hlt">genes</span>, at least one of the PKSs belongs to a bacterium of the Deinococcus-Thermus phylum. The results provide new insights into the chemistry of sponge symbionts and allow inference of a detailed phylogeny of the diverse functional PKS types present in sponge metagenomes. Based on these qualitative and quantitative data, we propose a significantly simplified strategy for the targeted isolation of biomedically relevant PKS <span class="hlt">genes</span> from complex sponge-symbiont associations. PMID:17293531</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/26308005','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/26308005"><span id="translatedtitle">Effect of an Introduced Phytoene Synthase <span class="hlt">Gene</span> Expression on Carotenoid Biosynthesis in the <span class="hlt">Marine</span> Diatom Phaeodactylum tricornutum.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Kadono, Takashi; Kira, Nozomu; Suzuki, Kengo; Iwata, Osamu; Ohama, Takeshi; Okada, Shigeru; Nishimura, Tomohiro; Akakabe, Mai; Tsuda, Masashi; Adachi, Masao</p> <p>2015-08-01</p> <p>Carotenoids exert beneficial effects on human health through their excellent antioxidant activity. To increase carotenoid productivity in the <span class="hlt">marine</span> Pennales Phaeodactylum tricornutum, we genetically engineered the phytoene synthase <span class="hlt">gene</span> (psy) to improve expression because RNA-sequencing analysis has suggested that the expression level of psy is lower than other enzyme-encoding <span class="hlt">genes</span> that are involved in the carotenoid biosynthetic pathway. We isolated psy from P. tricornutum, and this <span class="hlt">gene</span> was fused with the enhanced green fluorescent protein <span class="hlt">gene</span> to detect psy expression. After transformation using the microparticle bombardment technique, we obtained several P. tricornutum transformants and confirmed psy expression in their plastids. We investigated the amounts of PSY mRNA and carotenoids, such as fucoxanthin and β-carotene, at different growth phases. The introduction of psy increased the fucoxanthin content of a transformants by approximately 1.45-fold relative to the levels in the wild-type diatom. However, some transformants failed to show a significant increase in the carotenoid content relative to that of the wild-type diatom. We also found that the amount of PSY mRNA at log phase might contribute to the increase in carotenoids in the transformants at stationary phase. PMID:26308005</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ars.usda.gov/research/publications/Publications.htm?seq_no_115=219451','TEKTRAN'); return false;" href="http://www.ars.usda.gov/research/publications/Publications.htm?seq_no_115=219451"><span id="translatedtitle">Impact of distinct insect pollinators on <span class="hlt">gene</span> <span class="hlt">flow</span></span></a></p> <p><a target="_blank" href="http://www.ars.usda.gov/services/TekTran.htm">Technology Transfer Automated Retrieval System (TEKTRAN)</a></p> <p></p> <p></p> <p>The vast majority of fruits and vegetables, together with some hay crops (alfalfa) and some oil-producing crops (canola) are pollinated by insects. However we have little information on how insect pollinators affect the movement of <span class="hlt">genes</span> via pollen and even less on how distinct insect pollinators ma...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ars.usda.gov/research/publications/Publications.htm?seq_no_115=272262','TEKTRAN'); return false;" href="http://www.ars.usda.gov/research/publications/Publications.htm?seq_no_115=272262"><span id="translatedtitle">Importance of <span class="hlt">gene</span> <span class="hlt">flow</span> to germplasm conservation and development</span></a></p> <p><a target="_blank" href="http://www.ars.usda.gov/services/TekTran.htm">Technology Transfer Automated Retrieval System (TEKTRAN)</a></p> <p></p> <p></p> <p><span class="hlt">Gene</span> banks conserve and make available valuable germplasm that scientists and plant breeders can deploy to develop useful traits. The USDA National Plant Germplasm System (NPGS) manages over 542,000 germplasm accessions. A large part of our work is regenerating accessions when seed numbers decline. ...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/26954487','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/26954487"><span id="translatedtitle">Individual differences in <span class="hlt">flow</span> proneness are linked to a dopamine D2 receptor <span class="hlt">gene</span> variant.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Gyurkovics, Mate; Kotyuk, Eszter; Katonai, Eniko Rozsa; Horvath, Erzsebet Zsofia; Vereczkei, Andrea; Szekely, Anna</p> <p>2016-05-01</p> <p><span class="hlt">Flow</span> is a special mental state characterized by deep concentration that occurs during the performance of optimally challenging tasks. In prior studies, proneness to experience <span class="hlt">flow</span> has been found to be moderately heritable. In the present study, we investigated whether individual differences in <span class="hlt">flow</span> proneness are related to a polymorphism of the dopamine D2 receptor coding <span class="hlt">gene</span> (DRD2 C957T rs6277). This polymorphism affects striatal D2 receptor availability, a factor that has been shown to be related to <span class="hlt">flow</span> proneness. To our knowledge, this is the first study to investigate the association between this trait and a specific <span class="hlt">gene</span> variant. In a sample of 236 healthy Hungarian adults, we found that CC homozygotes report higher <span class="hlt">flow</span> proneness than do T allele carriers, but only during mandatory activities (i.e., studying and working), not during leisure time. We discuss implications of this result, e.g., the potential mediators of the relationship. PMID:26954487</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3807425','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3807425"><span id="translatedtitle">Transposon Mutagenesis Identified Chromosomal and Plasmid <span class="hlt">Genes</span> Essential for Adaptation of the <span class="hlt">Marine</span> Bacterium Dinoroseobacter shibae to Anaerobic Conditions</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Ebert, Matthias; Laaß, Sebastian; Burghartz, Melanie; Petersen, Jörn; Koßmehl, Sebastian; Wöhlbrand, Lars; Rabus, Ralf; Wittmann, Christoph; Jahn, Dieter</p> <p>2013-01-01</p> <p>Anaerobic growth and survival are integral parts of the life cycle of many <span class="hlt">marine</span> bacteria. To identify <span class="hlt">genes</span> essential for the anoxic life of Dinoroseobacter shibae, a transposon library was screened for strains impaired in anaerobic denitrifying growth. Transposon insertions in 35 chromosomal and 18 plasmid <span class="hlt">genes</span> were detected. The essential contribution of plasmid <span class="hlt">genes</span> to anaerobic growth was confirmed with plasmid-cured D. shibae strains. A combined transcriptome and proteome approach identified oxygen tension-regulated <span class="hlt">genes</span>. Transposon insertion sites of a total of 1,527 mutants without an anaerobic growth phenotype were determined to identify anaerobically induced but not essential <span class="hlt">genes</span>. A surprisingly small overlap of only three <span class="hlt">genes</span> (napA, phaA, and the Na+/Pi antiporter <span class="hlt">gene</span> Dshi_0543) between anaerobically essential and induced <span class="hlt">genes</span> was found. Interestingly, transposon mutations in <span class="hlt">genes</span> involved in dissimilatory and assimilatory nitrate reduction (napA, nasA) and corresponding cofactor biosynthesis (genomic moaB, moeB, and dsbC and plasmid-carried dsbD and ccmH) were found to cause anaerobic growth defects. In contrast, mutation of anaerobically induced <span class="hlt">genes</span> encoding proteins required for the later denitrification steps (nirS, nirJ, nosD), dimethyl sulfoxide reduction (dmsA1), and fermentation (pdhB1, arcA, aceE, pta, acs) did not result in decreased anaerobic growth under the conditions tested. Additional essential components (ferredoxin, cccA) of the anaerobic electron transfer chain and central metabolism (pdhB) were identified. Another surprise was the importance of sodium gradient-dependent membrane processes and genomic rearrangements via viruses, transposons, and insertion sequence elements for anaerobic growth. These processes and the observed contributions of cell envelope restructuring (lysM, mipA, fadK), C4-dicarboxylate transport (dctM1, dctM3), and protease functions to anaerobic growth require further investigation to unravel the</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_9");'>9</a></li> <li><a href="#" onclick='return showDiv("page_10");'>10</a></li> <li class="active"><span>11</span></li> <li><a href="#" onclick='return showDiv("page_12");'>12</a></li> <li><a href="#" onclick='return showDiv("page_13");'>13</a></li> <li><a href="#" onclick='return showDiv("page_13");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_11 --> <div id="page_12" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_9");'>9</a></li> <li><a href="#" onclick='return showDiv("page_10");'>10</a></li> <li><a href="#" onclick='return showDiv("page_11");'>11</a></li> <li class="active"><span>12</span></li> <li><a href="#" onclick='return showDiv("page_13");'>13</a></li> <li><a href="#" onclick='return showDiv("page_13");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="221"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3832940','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3832940"><span id="translatedtitle"><span class="hlt">Gene</span> expression studies for the analysis of domoic acid production in the <span class="hlt">marine</span> diatom Pseudo-nitzschia multiseries</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p></p> <p>2013-01-01</p> <p>Background Pseudo-nitzschia multiseries Hasle (Hasle) (Ps-n) is distinctive among the ecologically important <span class="hlt">marine</span> diatoms because it produces the neurotoxin domoic acid. Although the biology of Ps-n has been investigated intensely, the characterization of the <span class="hlt">genes</span> and biochemical pathways leading to domoic acid biosynthesis has been limited. To identify transcripts whose levels correlate with domoic acid production, we analyzed Ps-n under conditions of high and low domoic acid production by cDNA microarray technology and reverse-transcription quantitative PCR (RT-qPCR) methods. Our goals included identifying and validating robust reference <span class="hlt">genes</span> for Ps-n RNA expression analysis under these conditions. Results Through microarray analysis of exponential- and stationary-phase cultures with low and high domoic acid production, respectively, we identified candidate reference <span class="hlt">genes</span> whose transcripts did not vary across conditions. We tested eleven potential reference <span class="hlt">genes</span> for stability using RT-qPCR and GeNorm analyses. Our results indicated that transcripts encoding JmjC, dynein, and histone H3 proteins were the most suitable for normalization of expression data under conditions of silicon-limitation, in late-exponential through stationary phase. The microarray studies identified a number of <span class="hlt">genes</span> that were up- and down-regulated under toxin-producing conditions. RT-qPCR analysis, using the validated controls, confirmed the up-regulation of transcripts predicted to encode a cycloisomerase, an SLC6 transporter, phosphoenolpyruvate carboxykinase, glutamate dehydrogenase, a small heat shock protein, and an aldo-keto reductase, as well as the down-regulation of a transcript encoding a fucoxanthin-chlorophyll a-c binding protein, under these conditions. Conclusion Our results provide a strong basis for further studies of RNA expression levels in Ps-n, which will contribute to our understanding of <span class="hlt">genes</span> involved in the production and release of domoic acid, an important</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3495768','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3495768"><span id="translatedtitle">Is <span class="hlt">Gene</span> <span class="hlt">Flow</span> Promoting the Reversal of Pleistocene Divergence in the Mountain Chickadee (Poecile gambeli)?</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Manthey, Joseph D.; Klicka, John; Spellman, Garth M.</p> <p>2012-01-01</p> <p>The Pleistocene glacial cycles left a genetic legacy on taxa throughout the world; however, the persistence of genetic lineages that diverged during these cycles is dependent upon levels of <span class="hlt">gene</span> <span class="hlt">flow</span> and introgression. The consequences of secondary contact among taxa may reveal new insights into the history of the Pleistocene’s genetic legacy. Here, we use phylogeographic methods, using 20 nuclear loci from regional populations, to infer the consequences of secondary contact following divergence in the Mountain Chickadee (Poecile gambeli). Analysis of nuclear data identified two geographically-structured genetic groups, largely concordant with results from a previous mitochondrial DNA (mtDNA) study. Additionally, the estimated multilocus divergence times indicate a Pleistocene divergence, and are highly concordant with mtDNA. The previous mtDNA study showed a paucity of sympatry between clades, while nuclear patterns of <span class="hlt">gene</span> <span class="hlt">flow</span> show highly varied patterns between populations. The observed pattern of <span class="hlt">gene</span> <span class="hlt">flow</span>, from coalescent-based analyses, indicates southern populations in both clades exhibit little <span class="hlt">gene</span> <span class="hlt">flow</span> within or between clades, while northern populations are experiencing higher <span class="hlt">gene</span> <span class="hlt">flow</span> within and between clades. If this pattern were to persist, it is possible the historical legacy of Pleistocene divergence may be preserved in the southern populations only, and the northern populations would become a genetically diverse hybrid species. PMID:23152877</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/27075252','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/27075252"><span id="translatedtitle">Pollinator sharing and <span class="hlt">gene</span> <span class="hlt">flow</span> among closely related sympatric dioecious fig taxa.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Wang, Gang; Cannon, Charles H; Chen, Jin</p> <p>2016-04-13</p> <p>Hybridization and insect pollination are widely believed to increase rates of plant diversification. The extreme diversity of figs (Ficus) and their obligate pollinators, fig wasps (Agaonidae), provides an opportunity to examine the possible role of pollinator-mediated hybridization in plant diversification. Increasing evidence suggests that pollinator sharing and hybridization occurs among fig taxa, despite relatively strict coevolution with the pollinating wasp. Using five sympatric dioecious fig taxa and their pollinators, we examine the degree of pollinator sharing and inter-taxa <span class="hlt">gene</span> <span class="hlt">flow</span>. We experimentally test pollinator preference for floral volatiles, the main host recognition signal, from different figs. All five fig taxa shared pollinators with other taxa, and <span class="hlt">gene</span> <span class="hlt">flow</span> occurred between fig taxa within and between sections. Floral volatiles of each taxon attracted more than one pollinator species. Floral volatiles were more similar between closely related figs, which experienced higher levels of pollinator sharing and inter-taxa <span class="hlt">gene</span> <span class="hlt">flow</span>. This study demonstrates that pollinator sharing and inter-taxa <span class="hlt">gene</span> <span class="hlt">flow</span> occurs among closely related sympatric dioecious fig taxa and that pollinators choose the floral volatiles of multiple fig taxa. The implications of pollinator sharing and inter-taxa <span class="hlt">gene</span> <span class="hlt">flow</span> on diversification, occurring even in this highly specialized obligate pollination system, require further study. PMID:27075252</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3735263','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3735263"><span id="translatedtitle">Forest corridors maintain historical <span class="hlt">gene</span> <span class="hlt">flow</span> in a tiger metapopulation in the highlands of central India</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Sharma, Sandeep; Dutta, Trishna; Maldonado, Jesús E.; Wood, Thomas C.; Panwar, Hemendra Singh; Seidensticker, John</p> <p>2013-01-01</p> <p>Understanding the patterns of <span class="hlt">gene</span> <span class="hlt">flow</span> of an endangered species metapopulation occupying a fragmented habitat is crucial for landscape-level conservation planning and devising effective conservation strategies. Tigers (Panthera tigris) are globally endangered and their populations are highly fragmented and exist in a few isolated metapopulations across their range. We used multi-locus genotypic data from 273 individual tigers (Panthera tigris tigris) from four tiger populations of the Satpura–Maikal landscape of central India to determine whether the corridors in this landscape are functional. This 45 000 km2 landscape contains 17% of India's tiger population and 12% of its tiger habitat. We applied Bayesian and coalescent-based analyses to estimate contemporary and historical <span class="hlt">gene</span> <span class="hlt">flow</span> among these populations and to infer their evolutionary history. We found that the tiger metapopulation in central India has high rates of historical and contemporary <span class="hlt">gene</span> <span class="hlt">flow</span>. The tests for population history reveal that tigers populated central India about 10 000 years ago. Their population subdivision began about 1000 years ago and accelerated about 200 years ago owing to habitat fragmentation, leading to four spatially separated populations. These four populations have been in migration–drift equilibrium maintained by high <span class="hlt">gene</span> <span class="hlt">flow</span>. We found the highest rates of contemporary <span class="hlt">gene</span> <span class="hlt">flow</span> in populations that are connected by forest corridors. This information is highly relevant to conservation practitioners and policy makers, because deforestation, road widening and mining are imminent threats to these corridors. PMID:23902910</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3144194','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3144194"><span id="translatedtitle">Cryptic Species? Patterns of Maternal and Paternal <span class="hlt">Gene</span> <span class="hlt">Flow</span> in Eight Neotropical Bats</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Clare, Elizabeth L.</p> <p>2011-01-01</p> <p>Levels of sequence divergence at mitochondrial loci are frequently used in phylogeographic analysis and species delimitation though single marker systems cannot assess bi-parental <span class="hlt">gene</span> <span class="hlt">flow</span>. In this investigation I compare the phylogeographic patterns revealed through the maternally inherited mitochondrial COI region and the paternally inherited 7th intron region of the Dby <span class="hlt">gene</span> on the Y-chromosome in eight common Neotropical bat species. These species are diverse and include members of two families from the feeding guilds of sanguivores, nectarivores, frugivores, carnivores and insectivores. In each case, the currently recognized taxon is comprised of distinct, substantially divergent intraspecific mitochondrial lineages suggesting cryptic species complexes. In Chrotopterus auritus, and Saccopteryx bilineata I observed congruent patterns of divergence in both genetic regions suggesting a cessation of <span class="hlt">gene</span> <span class="hlt">flow</span> between intraspecific groups. This evidence supports the existence of cryptic species complexes which meet the criteria of the genetic species concept. In Glossophaga soricina two intraspecific groups with largely sympatric South American ranges show evidence for incomplete lineage sorting or frequent hybridization while a third group with a Central American distribution appears to diverge congruently at both loci suggesting speciation. Within Desmodus rotundus and Trachops cirrhosus the paternally inherited region was monomorphic and thus does not support or refute the potential for cryptic speciation. In Uroderma bilobatum, Micronycteris megalotis and Platyrrhinus helleri the <span class="hlt">gene</span> regions show conflicting patterns of divergence and I cannot exclude ongoing <span class="hlt">gene</span> <span class="hlt">flow</span> between intraspecific groups. This analysis provides a comprehensive comparison across taxa and employs both maternally and paternally inherited <span class="hlt">gene</span> regions to validate patterns of <span class="hlt">gene</span> <span class="hlt">flow</span>. I present evidence for previously unrecognized species meeting the criteria of the genetic species</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25272969','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25272969"><span id="translatedtitle">Homologues of insecticidal toxin complex <span class="hlt">genes</span> within a genomic island in the <span class="hlt">marine</span> bacterium Vibrio parahaemolyticus.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Tang, Kathy F J; Lightner, Donald V</p> <p>2014-10-01</p> <p>Three insecticidal toxin complex (tc)-like <span class="hlt">genes</span> were identified in Vibrio parahaemolyticus 13-028/A3, which can cause acute hepatopancreatic necrosis disease in penaeid shrimp. The three <span class="hlt">genes</span> are a tcdA-like <span class="hlt">gene</span> (7710 bp), predicted to code for a 284-kDa protein; a tcdB-like <span class="hlt">gene</span> (4272 bp), predicted to code for a 158-kDa protein; and a tccC3-like <span class="hlt">gene</span> (2916 bp), predicted to encode a 107-kDa protein. All three predicted proteins contain conserved domains that are characteristic of their respective Tc proteins. By RT-PCR, all three tc-like <span class="hlt">genes</span> were found to be expressed in this bacterium. Through genome walking and the use of PCR to join contigs surrounding these three <span class="hlt">genes</span>, a genomic island (87 712 bp, named tc-GIvp) was found on chromosome II localized next to the tRNA Gly. The GC content of this island, which is not found in other Vibrio species, is 40%. The tc-GIvp is characterized to have 60 ORFs encoding regulatory or virulence factors. These include a type 6 secretion protein VgrG, EAL domain-containing proteins, fimbriae subunits and assembly proteins, invasin-like proteins, peptidoglycan-binding proteins, and Tc proteins. The tc-GIvp also contains 21 transposase <span class="hlt">genes</span>, suggesting that it was acquired through horizontal transfer from other organisms. PMID:25272969</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2012AGUFMOS21B1706S','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2012AGUFMOS21B1706S"><span id="translatedtitle">Remote Sensing of Salinity Profiles and Multi-sensor Profiler for <span class="hlt">Marine</span> Estuarine <span class="hlt">Flow</span>, Water Properties and Sediment Studies</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Sanford, T. B.</p> <p>2012-12-01</p> <p>Observing the numerous characteristics of <span class="hlt">flow</span> and water properties in <span class="hlt">marine</span> estuaries requires many sensors and systems. As a component of CMOP (Coastal Margin Observation and Prediction), an NSF Science and Technology Center, two innovative new instruments were developed and operated in the <span class="hlt">marine</span> estuary of the Columbia River. One determines the vertical profile of electrical conductivity (σ), which in the Columbia River can be converted to salinity. The goal of the Sigma Profiler is to provide a robust sensor for determining the salinity profile from the riverbed in a region of vessel traffic, fishing, debris and strong currents. The Sigma Profiler uses characteristics of deliberately emitted EM currents. Because the spatial attenuation of EM signals is proportional to the square root of signal frequency, the transmission of signals of many frequencies can determine the vertical structure of σ. Six frequencies between 270 Hz and 27.7 kHz are used. SP performance is determined with simultaneous CTD casts and the CMOP autonomous profiler at Saturn01. The observations are useful for comparison with numerical models simulations. The second instrument is a combination of many sensors on a tow body that is winched vertically. The sensors on the Winched Profiler include SonTek ADV, CTD, μσ, μT, dual shear probes, Wet Labs Triplet, LISST-100X, O2, acoustic altimeter, motion package, and magnetic compass. The various sensors on the Winched Profiler can be used to determine vertical eddy fluxes of salinity, mixing characteristics, dissipation rates of kinetic energy, internal waves, estuarine turbidity maxima (ETMs), terms in turbulent KE energy balance, BBL structure, turbidity, suspended sediment characteristic and transport and evaluate various turbulence closure schemes. The Winched Profiler has a real time display of 25 panels of sensor outputs and diagnostics. Results from the Sigma Profiler and Winched Profiler, which were operated extensively in May 2012</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/24356981','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/24356981"><span id="translatedtitle">Community structure and PAH ring-hydroxylating dioxygenase <span class="hlt">genes</span> of a <span class="hlt">marine</span> pyrene-degrading microbial consortium.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Gallego, Sara; Vila, Joaquim; Tauler, Margalida; Nieto, José María; Breugelmans, Philip; Springael, Dirk; Grifoll, Magdalena</p> <p>2014-07-01</p> <p><span class="hlt">Marine</span> microbial consortium UBF, enriched from a beach polluted by the Prestige oil spill and highly efficient in degrading this heavy fuel, was subcultured in pyrene minimal medium. The pyrene-degrading subpopulation (UBF-Py) mineralized 31 % of pyrene without accumulation of partially oxidized intermediates indicating the cooperation of different microbial components in substrate mineralization. The microbial community composition was characterized by culture dependent and PCR based methods (PCR-DGGE and clone libraries). Molecular analyses showed a highly stable community composed by Alphaproteobacteria (84 %, Breoghania, Thalassospira, Paracoccus, and Martelella) and Actinobacteria (16 %, Gordonia). The members of Thalasosspira and Gordonia were not recovered as pure cultures, but five additional strains, not detected in the molecular analysis, that classified within the genera Novosphingobium, Sphingopyxis, Aurantimonas (Alphaproteobacteria), Alcanivorax (Gammaproteobacteria) and Micrococcus (Actinobacteria), were isolated. None of the isolates degraded pyrene or other PAHs in pure culture. PCR amplification of Gram-positive and Gram-negative dioxygenase <span class="hlt">genes</span> did not produce results with any of the cultured strains. However, sequences related to the NidA3 pyrene dioxygenase present in mycobacterial strains were detected in UBF-Py consortium, suggesting the representative of Gordonia as the key pyrene degrader, which is consistent with a preeminent role of actinobacteria in pyrene removal in coastal environments affected by <span class="hlt">marine</span> oil spills. PMID:24356981</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/1998PhyA..259..457S','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/1998PhyA..259..457S"><span id="translatedtitle">Changes of a continuous character caused by <span class="hlt">gene</span> <span class="hlt">flow</span>. A Monte Carlo study</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Sznajd-Weron, Katarzyna; Pȩkalski, Andrzej</p> <p></p> <p>We introduce a model of a large, sexual, population in which partners for reproduction are chosen randomly, without any bias. This large population is composed of two groups of local populations living in different environments and being in contact. We propose a dynamic equation describing, like the existing one for the allele frequency, the temporal changes of a continuous character due to <span class="hlt">gene</span> <span class="hlt">flow</span>, i.e. the transfer of the allels resulting from migration of individuals between the populations, and natural selection. We show that the <span class="hlt">gene</span> <span class="hlt">flow</span> can be described by the linear term in the proposed equation and the natural selection by the nonlinear term. Additional killing rule introduces a random factor into our model. We discuss the role of both factors (<span class="hlt">gene</span> <span class="hlt">flow</span> and selection) on the structure of the population, i.e. spatial distribution of the considered character and the resulting from it existence of hybrid zones. We use the standard Monte Carlo simulations.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/26519802','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/26519802"><span id="translatedtitle">Characterization of the metabolic pathway and catabolic <span class="hlt">gene</span> expression in biphenyl degrading <span class="hlt">marine</span> bacterium Pseudomonas aeruginosa JP-11.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Chakraborty, Jaya; Das, Surajit</p> <p>2016-02-01</p> <p>Metabolic pathway of biphenyl assimilation and the catabolic <span class="hlt">gene</span> expression in a <span class="hlt">marine</span> bacterium Pseudomonas aeruginosa JP-11, isolated from the coastal sediments of Odisha, India have been studied. This strain utilized 98.86% ± 2.29% of biphenyl within 72 h when supplied as the sole source of carbon, however, preferential utilization of glucose was observed over catechol and biphenyl when grown in a complex medium. Combination of chromatographic and spectrophotometric techniques confirmed the catechol pathway and identified 2-Hydroxy-6-oxo-6-phenylhexa-2, 4-dienoate as the intermediate metabolic product. Assimilation of biphenyl was initiated by its dioxygenation, forming cis-2, 3-dihydro-2, 3-dihydroxybiphenyl subsequently transformed to 2-hydroxy-6-oxo-6-phenylhexa-2, 4-dienoate. In the lower pathway, cis-1, 6-dihydroxy-2, 4-cyclohexadiene-1-carboxylic acid was detected which formed catechol before entering into the Krebs cycle. Detection of key enzyme catechol-1, 2-dioxygenase in the cell-free extract of P. aeruginosa JP-11 supported the proposed degradation pathway. The primary enzyme for biphenyl assimilation, biphenyl dioxygenase encoded by bphA <span class="hlt">gene</span> was found in the genome of the isolate. On increasing biphenyl stress (50, 100, 150 and 200 mg L(-1)), bphA <span class="hlt">gene</span> showed a significant (P < 0.01) up-regulation upto 43.5 folds. Production of biosurfactant was confirmed and the rhamnolipid synthesizing <span class="hlt">gene</span> rhlAB was amplified. This <span class="hlt">gene</span> also showed a significant (P < 0.01) up-regulation upto 258 folds on increasing biphenyl stress. PMID:26519802</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2874808','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2874808"><span id="translatedtitle">Comparative <span class="hlt">gene</span> expression in toxic versus non-toxic strains of the <span class="hlt">marine</span> dinoflagellate Alexandrium minutum</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p></p> <p>2010-01-01</p> <p>Background The dinoflagellate Alexandrium minutum typically produces paralytic shellfish poisoning (PSP) toxins, which are known only from cyanobacteria and dinoflagellates. While a PSP toxin <span class="hlt">gene</span> cluster has recently been characterized in cyanobacteria, the genetic background of PSP toxin production in dinoflagellates remains elusive. Results We constructed and analysed an expressed sequence tag (EST) library of A. minutum, which contained 15,703 read sequences yielding a total of 4,320 unique expressed clusters. Of these clusters, 72% combined the forward-and reverse reads of at least one bacterial clone. This sequence resource was then used to construct an oligonucleotide microarray. We analysed the expression of all clusters in three different strains. While the cyanobacterial PSP toxin <span class="hlt">genes</span> were not found among the A. minutum sequences, 192 <span class="hlt">genes</span> were differentially expressed between toxic and non-toxic strains. Conclusions Based on this study and on the lack of identified PSP synthesis <span class="hlt">genes</span> in the two existent Alexandrium tamarense EST libraries, we propose that the PSP toxin <span class="hlt">genes</span> in dinoflagellates might be more different from their cyanobacterial counterparts than would be expected in the case of a recent <span class="hlt">gene</span> transfer. As a starting point to identify possible PSP toxin-associated <span class="hlt">genes</span> in dinoflagellates without relying on a priori sequence information, the sequences only present in mRNA pools of the toxic strain can be seen as putative candidates involved in toxin synthesis and regulation, or acclimation to intracellular PSP toxins. PMID:20403159</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/17683442','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/17683442"><span id="translatedtitle">Quantifying the constraining influence of <span class="hlt">gene</span> <span class="hlt">flow</span> on adaptive divergence in the lake-stream threespine stickleback system.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Moore, Jean-Sébastien; Gow, Jennifer L; Taylor, Eric B; Hendry, Andrew P</p> <p>2007-08-01</p> <p>The constraining effect of <span class="hlt">gene</span> <span class="hlt">flow</span> on adaptive divergence is often inferred but rarely quantified. We illustrate ways of doing so using stream populations of threespine stickleback (Gasterosteus aculeatus) that experience different levels of <span class="hlt">gene</span> <span class="hlt">flow</span> from a parapatric lake population. In the Misty Lake watershed (British Columbia, Canada), the inlet stream population is morphologically divergent from the lake population, and presumably experiences little <span class="hlt">gene</span> <span class="hlt">flow</span> from the lake. The outlet stream population, however, shows an intermediate phenotype and may experience more <span class="hlt">gene</span> <span class="hlt">flow</span> from the lake. We first used microsatellite data to demonstrate that <span class="hlt">gene</span> <span class="hlt">flow</span> from the lake is low into the inlet but high into the outlet, and that <span class="hlt">gene</span> <span class="hlt">flow</span> from the lake remains relatively constant with distance along the outlet. We next combined <span class="hlt">gene</span> <span class="hlt">flow</span> data with morphological and habitat data to quantify the effect of <span class="hlt">gene</span> <span class="hlt">flow</span> on morphological divergence. In one approach, we assumed that inlet stickleback manifest well-adapted phenotypic trait values not constrained by <span class="hlt">gene</span> <span class="hlt">flow</span>. We then calculated the deviation between the observed and expected phenotypes for a given habitat in the outlet. In a second approach, we parameterized a quantitative genetic model of adaptive divergence. Both approaches suggest a large impact of <span class="hlt">gene</span> <span class="hlt">flow</span>, constraining adaptation by 80-86% in the outlet (i.e., only 14-20% of the expected morphological divergence in the absence of <span class="hlt">gene</span> <span class="hlt">flow</span> was observed). Such approaches may be useful in other taxa to estimate how important <span class="hlt">gene</span> <span class="hlt">flow</span> is in constraining adaptive divergence in nature. PMID:17683442</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/20376102','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/20376102"><span id="translatedtitle">PtrA is required for coordinate regulation of <span class="hlt">gene</span> expression during phosphate stress in a <span class="hlt">marine</span> Synechococcus.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Ostrowski, Martin; Mazard, Sophie; Tetu, Sasha G; Phillippy, Katherine; Johnson, Aaron; Palenik, Brian; Paulsen, Ian T; Scanlan, Dave J</p> <p>2010-07-01</p> <p>Previous microarray analyses have shown a key role for the two-component system PhoBR (SYNW0947, SYNW0948) in the regulation of P transport and metabolism in the <span class="hlt">marine</span> cyanobacterium Synechococcus sp. WH8102. However, there is some evidence that another regulator, SYNW1019 (PtrA), probably under the control of PhoBR, is involved in the response to P depletion. PtrA is a member of the cAMP receptor protein transcriptional regulator family that shows homology to NtcA, the global nitrogen regulator in cyanobacteria. To define the role of this regulator, we constructed a mutant by insertional inactivation and compared the physiology of wild-type Synechcococcus sp. WH8102 with the ptrA mutant under P-replete and P-stress conditions. In response to P stress the ptrA mutant failed to upregulate phosphatase activity. Microarrays and quantitative RT-PCR indicate that a subset of the Pho regulon is controlled by PtrA, including two phosphatases, a predicted phytase and a <span class="hlt">gene</span> of unknown function psip1 (SYNW0165), all of which are highly upregulated during P limitation. Electrophoretic mobility shift assays indicate binding of overexpressed PtrA to promoter sequences upstream of the induced <span class="hlt">genes</span>. This work suggests a two-tiered response to P depletion in this strain, the first being PhoB-dependent induction of high-affinity PO(4) transporters, and the second the PtrA-dependent induction of phosphatases for scavenging organic P. The levels of numerous other transcripts are also directly or indirectly influenced by PtrA, including those involved in cell-surface modification, metal uptake, photosynthesis, stress responses and other metabolic processes, which may indicate a wider role for PtrA in cellular regulation in <span class="hlt">marine</span> picocyanobacteria. PMID:20376102</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3873393','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3873393"><span id="translatedtitle">Spread of a New Parasitic B Chromosome Variant Is Facilitated by High <span class="hlt">Gene</span> <span class="hlt">Flow</span></span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Manrique-Poyato, María Inmaculada; López-León, María Dolores; Cabrero, Josefa; Perfectti, Francisco; Camacho, Juan Pedro M.</p> <p>2013-01-01</p> <p>The B24 chromosome variant emerged several decades ago in a Spanish population of the grasshopper Eyprepocnemis plorans and is currently reaching adjacent populations. Here we report, for the first time, how a parasitic B chromosome (a strictly vertically transmitted parasite) expands its geographical range aided by high <span class="hlt">gene</span> <span class="hlt">flow</span> in the host species. For six years we analyzed B frequency in several populations to the east and west of the original population and found extensive spatial variation, but only a slight temporal trend. The highest B24 frequency was found in its original population (Torrox) and it decreased closer to both the eastern and the western populations. The analysis of Inter Simple Sequence Repeat (ISSR) markers showed the existence of a low but significant degree of population subdivision, as well as significant isolation by distance (IBD). Pairwise Nem estimates suggested the existence of high <span class="hlt">gene</span> <span class="hlt">flow</span> between the four populations located in the Torrox area, with higher values towards the east. No significant barriers to <span class="hlt">gene</span> <span class="hlt">flow</span> were found among these four populations, and we conclude that high <span class="hlt">gene</span> <span class="hlt">flow</span> is facilitating B24 diffusion both eastward and westward, with minor role for B24 drive due to the arrival of drive suppressor <span class="hlt">genes</span> which are also frequent in the donor population. PMID:24386259</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ars.usda.gov/research/publications/Publications.htm?seq_no_115=230333','TEKTRAN'); return false;" href="http://www.ars.usda.gov/research/publications/Publications.htm?seq_no_115=230333"><span id="translatedtitle">A Capsid <span class="hlt">Gene</span>-Based Real-Time Reverse Transcription Polymerase Chain Reaction Assay for the Detection of <span class="hlt">Marine</span> Vesiviruses in the Caliciviridae</span></a></p> <p><a target="_blank" href="http://www.ars.usda.gov/services/TekTran.htm">Technology Transfer Automated Retrieval System (TEKTRAN)</a></p> <p></p> <p></p> <p>A real-time reverse transcription polymerase chain reaction (rtRT-PCR) assay was developed for the identification of <span class="hlt">marine</span> vesiviruses. The primers were designed to target a 176-nucleotide fragment within a highly conserved region of the San Miguel sea lion viruses (SMSVs) capsid <span class="hlt">gene</span>. The assay de...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4059624','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4059624"><span id="translatedtitle"><span class="hlt">Gene</span> <span class="hlt">Flow</span> within and between Catchments in the Threatened Riparian Plant Myricaria germanica</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Werth, Silke; Scheidegger, Christoph</p> <p>2014-01-01</p> <p>One of the major distinctions of riparian habitats is their linearity. In linear habitats, <span class="hlt">gene</span> <span class="hlt">flow</span> is predicted to follow a one-dimensional stepping stone model, characterized by bidirectional <span class="hlt">gene</span> <span class="hlt">flow</span> between neighboring populations. Here, we studied the genetic structure of Myricaria germanica, a threatened riparian shrub which is capable of both wind and water dispersal. Our data led us to reject the ‘one catchment – one <span class="hlt">gene</span> pool’ hypothesis as we found support for two <span class="hlt">gene</span> pools, rather than four as expected in a study area including four catchments. This result also implies that in the history of the studied populations, dispersal across catchments has occurred. Two contemporary catchment-crossing migration events were detected, albeit between spatially proximate catchments. Allelic richness and inbreeding coefficients differed substantially between <span class="hlt">gene</span> pools. There was significant isolation by distance, and our data confirmed the one-dimensional stepping-stone model of <span class="hlt">gene</span> <span class="hlt">flow</span>. Contemporary migration was bidirectional within the studied catchments, implying that dispersal vectors other than water are important for M. germanica. PMID:24932520</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/10725393','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/10725393"><span id="translatedtitle">Multiplication of antenna <span class="hlt">genes</span> as a major adaptation to low light in a <span class="hlt">marine</span> prokaryote.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Garczarek, L; Hess, W R; Holtzendorff, J; van der Staay, G W; Partensky, F</p> <p>2000-04-11</p> <p>Two ecotypes of the prokaryote Prochlorococcus adapted to distinct light niches in the ocean have been described recently. These ecotypes are characterized by their different (divinyl-) chlorophyll (Chl) a to Chl b ratios and 16S rRNA <span class="hlt">gene</span> signatures, as well as by their significantly distinct irradiance optima for growth and photosynthesis [Moore, L. R., Rocap, G. & Chisholm, S. W. (1998) Nature (London) 393, 464-467]. However, the molecular basis of their physiological differences remained, so far, unexplained. In this paper, we show that the low-light-adapted Prochlorococcus strain SS120 possesses a <span class="hlt">gene</span> family of seven transcribed <span class="hlt">genes</span> encoding different Chl a/b-binding proteins (Pcbs). In contrast, Prochlorococcus sp. MED4, a high-light-adapted ecotype, possesses a single pcb <span class="hlt">gene</span>. The presence of multiple antenna <span class="hlt">genes</span> in another low-light ecotype (NATL2a), but not in another high-light ecotype (TAK9803-2), is demonstrated. Thus, the multiplication of pcb <span class="hlt">genes</span> appears as a key factor in the capacity of deep Prochlorococcus populations to survive at extremely low photon fluxes. PMID:10725393</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2016EGUGA..18...71R','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2016EGUGA..18...71R"><span id="translatedtitle">Metagenomic analysis of nitrogen metabolism <span class="hlt">genes</span> in the surface of <span class="hlt">marine</span> sediments</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Reyes, Carolina; Schneider, Dominik; Thürmer, Andrea; Dellwig, Olaf; Lipka, Marko; Daniel, Rolf; Böttcher, Michael E.; Friedrich, Michael W.</p> <p>2016-04-01</p> <p>In this study, we analysed metagenomes along with biogeochemical profiles from Skagerrak (North Sea) and Bothnian Bay (Baltic Sea) sediments, to trace the prevailing nitrogen pathways. NO3- was present in the top 5 cm below the sediment-water interface at both sites. NH4+ increased with depth below 5 cm where it overlapped with the NO3- zone. Steady state modelling of NO3- and NH4+ porewater profiles indicates zones of net nitrogen species transformations. Protease, peptidase, urease and deaminase ammonification <span class="hlt">genes</span> were detected in metagenomes. <span class="hlt">Genes</span> involved in ammonia oxidation (amo, hao), nitrite oxidation (nxr), denitrification (nar, nir, nor) and dissimilatory NO3- reduction to NH4+ (nap, nfr and otr) were also present. 16S rRNA <span class="hlt">gene</span> analysis showed that the nitrifying group Nitrosopumilales and other groups involved in nitrification and denitrification (Nitrobacter, Nitrosomonas, Nitrospira, Nitrosococcus, and Nitrosonomas) appeared less abundant in Skagerrak sediments compared to Bothnian Bay sediments. Beggiatoa and Thiothrix 16S rRNA <span class="hlt">genes</span> were also present suggesting chemolithoautotrophic NO3- reduction to NO2- or NH4+ as a possible pathway. Although anammox planctomycetes 16S rRNA <span class="hlt">genes</span> were present in metagenomes, anammox protein-coding <span class="hlt">genes</span> were not detected. Our results show the metabolic potential for ammonification, nitrification, NO3- reduction, and denitrification activities in Skagerrak and Bothnian Bay sediments.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/25820602','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/25820602"><span id="translatedtitle">Functional <span class="hlt">gene</span>-based discovery of phenazines from the actinobacteria associated with <span class="hlt">marine</span> sponges in the South China Sea.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Karuppiah, Valliappan; Li, Yingxin; Sun, Wei; Feng, Guofang; Li, Zhiyong</p> <p>2015-07-01</p> <p>Phenazines represent a large group of nitrogen-containing heterocyclic compounds produced by the diverse group of bacteria including actinobacteria. In this study, a total of 197 actinobacterial strains were isolated from seven different <span class="hlt">marine</span> sponge species in the South China Sea using five different culture media. Eighty-seven morphologically different actinobacterial strains were selected and grouped into 13 genera, including Actinoalloteichus, Kocuria, Micrococcus, Micromonospora, Mycobacterium, Nocardiopsis, Prauserella, Rhodococcus, Saccharopolyspora, Salinispora, Serinicoccus, and Streptomyces by the phylogenetic analysis of 16S rRNA <span class="hlt">gene</span>. Based on the screening of phzE <span class="hlt">genes</span>, ten strains, including five Streptomyces, two Nocardiopsis, one Salinispora, one Micrococcus, and one Serinicoccus were found to be potential for phenazine production. The level of phzE <span class="hlt">gene</span> expression was highly expressed in Nocardiopsis sp. 13-33-15, 13-12-13, and Serinicoccus sp. 13-12-4 on the fifth day of fermentation. Finally, 1,6-dihydroxy phenazine (1) from Nocardiopsis sp. 13-33-15 and 13-12-13, and 1,6-dimethoxy phenazine (2) from Nocardiopsis sp. 13-33-15 were isolated and identified successfully based on ESI-MS and NMR analysis. The compounds 1 and 2 showed antibacterial activity against Bacillus mycoides SJ14, Staphylococcus aureus SJ51, Escherichia coli SJ42, and Micrococcus luteus SJ47. This study suggests that the integrated approach of <span class="hlt">gene</span> screening and chemical analysis is an effective strategy to find the target compounds and lays the basis for the production of phenazine from the sponge-associated actinobacteria. PMID:25820602</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3623242','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3623242"><span id="translatedtitle">Thaumarchaeotal Signature <span class="hlt">Gene</span> Distribution in Sediments of the Northern South China Sea: an Indicator of the Metabolic Intersection of the <span class="hlt">Marine</span> Carbon, Nitrogen, and Phosphorus Cycles?</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Zhou, Haixia; Yang, Jinying; Ge, Huangmin; Jiao, Nianzhi; Luan, Xiwu; Klotz, Martin G.</p> <p>2013-01-01</p> <p>Thaumarchaeota are abundant and active in <span class="hlt">marine</span> waters, where they contribute to aerobic ammonia oxidation and light-independent carbon fixation. The ecological function of thaumarchaeota in <span class="hlt">marine</span> sediments, however, has rarely been investigated, even though <span class="hlt">marine</span> sediments constitute the majority of the Earth's surface. Thaumarchaeota in the upper layer of sediments may contribute significantly to the reservoir of nitrogen oxides in ocean waters and thus to productivity, including the assimilation of carbon. We tested this hypothesis in the northern South China Sea (nSCS), a section of a large oligotrophic marginal sea with limited influx of nutrients, including nitrogen, by investigating the diversity, abundance, community structure, and spatial distribution of thaumarchaeotal signatures in surface sediments. Quantitative real-time PCR using primers designed to detect 16S rRNA and amoA <span class="hlt">genes</span> in sediment community DNA revealed a significantly higher abundance of pertinent thaumarchaeotal than betaproteobacterial <span class="hlt">genes</span>. This finding correlates with high levels of hcd <span class="hlt">genes</span>, a signature of thaumarchaeotal autotrophic carbon fixation. Thaumarchaeol, a signature lipid biomarker for thaumarchaeota, constituted the majority of archaeal lipids in <span class="hlt">marine</span> sediments. Sediment temperature and organic P and silt contents were identified as key environmental factors shaping the community structure and distribution of the monitored thaumarchaeotal amoA <span class="hlt">genes</span>. When the pore water PO43− concentration was controlled for via partial-correlation analysis, thaumarchaeotal amoA <span class="hlt">gene</span> abundance significantly correlated with the sediment pore water NO2− concentration, suggesting that the amoA-bearing thaumarchaeota contribute to nitrite production. Statistical analyses also suggest that thaumarchaeotal metabolism could serve as a pivotal intersection of the carbon, nitrogen, and phosphorus cycles in <span class="hlt">marine</span> sediments. PMID:23335759</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_9");'>9</a></li> <li><a href="#" onclick='return showDiv("page_10");'>10</a></li> <li><a href="#" onclick='return showDiv("page_11");'>11</a></li> <li class="active"><span>12</span></li> <li><a href="#" onclick='return showDiv("page_13");'>13</a></li> <li><a href="#" onclick='return showDiv("page_13");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_12 --> <div id="page_13" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_9");'>9</a></li> <li><a href="#" onclick='return showDiv("page_10");'>10</a></li> <li><a href="#" onclick='return showDiv("page_11");'>11</a></li> <li><a href="#" onclick='return showDiv("page_12");'>12</a></li> <li class="active"><span>13</span></li> <li><a href="#" onclick='return showDiv("page_13");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="241"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3245544','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3245544"><span id="translatedtitle">Evolution and Functional Diversification of Fructose Bisphosphate Aldolase <span class="hlt">Genes</span> in Photosynthetic <span class="hlt">Marine</span> Diatoms</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Allen, Andrew E.; Moustafa, Ahmed; Montsant, Anton; Eckert, Angelika; Kroth, Peter G.; Bowler, Chris</p> <p>2012-01-01</p> <p>Diatoms and other chlorophyll-c containing, or chromalveolate, algae are among the most productive and diverse phytoplankton in the ocean. Evolutionarily, chlorophyll-c algae are linked through common, although not necessarily monophyletic, acquisition of plastid endosymbionts of red as well as most likely green algal origin. There is also strong evidence for a relatively high level of lineage-specific bacterial <span class="hlt">gene</span> acquisition within chromalveolates. Therefore, analyses of <span class="hlt">gene</span> content and derivation in chromalveolate taxa have indicated particularly diverse origins of their overall <span class="hlt">gene</span> repertoire. As a single group of functionally related enzymes spanning two distinct <span class="hlt">gene</span> families, fructose 1,6-bisphosphate aldolases (FBAs) illustrate the influence on core biochemical pathways of specific evolutionary associations among diatoms and other chromalveolates with various plastid-bearing and bacterial endosymbionts. Protein localization and activity, <span class="hlt">gene</span> expression, and phylogenetic analyses indicate that the pennate diatom Phaeodactylum tricornutum contains five FBA <span class="hlt">genes</span> with very little overall functional overlap. Three P. tricornutum FBAs, one class I and two class II, are plastid localized, and each appears to have a distinct evolutionary origin as well as function. Class I plastid FBA appears to have been acquired by chromalveolates from a red algal endosymbiont, whereas one copy of class II plastid FBA is likely to have originated from an ancient green algal endosymbiont. The other copy appears to be the result of a chromalveolate-specific <span class="hlt">gene</span> duplication. Plastid FBA I and chromalveolate-specific class II plastid FBA are localized in the pyrenoid region of the chloroplast where they are associated with β-carbonic anhydrase, which is known to play a significant role in regulation of the diatom carbon concentrating mechanism. The two pyrenoid-associated FBAs are distinguished by contrasting <span class="hlt">gene</span> expression profiles under nutrient limiting compared with</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4549332','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4549332"><span id="translatedtitle">Evaluation of Tangential <span class="hlt">Flow</span> Filtration for the Concentration and Separation of Bacteria and Viruses in Contrasting <span class="hlt">Marine</span> Environments</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Cai, Lanlan; Yang, Yunlan; Jiao, Nianzhi; Zhang, Rui</p> <p>2015-01-01</p> <p>Tangential <span class="hlt">flow</span> filtration (TFF), which has been widely adopted to concentrate a diverse array of microbes from water, is a promising method of microbial separation or removal. However, it is essential to select an optimal membrane suitable for the specific filtration application. This study evaluated two different scales of TFF systems for concentrating and separating microbes (including bacteria and viruses) from contrasting <span class="hlt">marine</span> waters. Among bacteria-size membranes, polyvinylidene difluoride (PVDF) membranes showed higher bacterial recovery, but lower viral permeation efficiencies than polyethersulfone (PES) membranes, regardless of environments and scales of TFF. Estuary samples showed significantly higher percentages of bacterial retention than nearshore and ocean samples. For virus-size membranes, a higher viral recovery and lower sorption was observed for regenerated cellulose membrane than PES membranes in the small-scale TFF. Similar viral recoveries were observed between PES membranes in the large-scale TFF, with higher viral concentrations being observed in estuary samples than in nearshore samples. Deep ocean samples showed the lowest recovery of viruses, which was consistent with observations of bacterial recovery. Synthetically, PVDF may be more suitable for the concentration of bacterial cells, while PES would be a better choice for the collection of viruses. When compared with the PES membrane, regenerated cellulose is better for viral concentration, while PES is recommended to obtain bacteria- and virus-free seawater. PMID:26305356</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3413404','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3413404"><span id="translatedtitle">Restricted <span class="hlt">Gene</span> <span class="hlt">Flow</span> among Hospital Subpopulations of Enterococcus faecium</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Willems, Rob J. L.; Top, Janetta; van Schaik, Willem; Leavis, Helen; Bonten, Marc; Sirén, Jukka; Hanage, William P.; Corander, Jukka</p> <p>2012-01-01</p> <p>ABSTRACT Enterococcus faecium has recently emerged as an important multiresistant nosocomial pathogen. Defining population structure in this species is required to provide insight into the existence, distribution, and dynamics of specific multiresistant or pathogenic lineages in particular environments, like the hospital. Here, we probe the population structure of E. faecium using Bayesian-based population genetic modeling implemented in Bayesian Analysis of Population Structure (BAPS) software. The analysis involved 1,720 isolates belonging to 519 sequence types (STs) (491 for E. faecium and 28 for Enterococcus faecalis). E. faecium isolates grouped into 13 BAPS (sub)groups, but the large majority (80%) of nosocomial isolates clustered in two subgroups (2-1 and 3-3). Phylogenetic and eBURST analysis of BAPS groups 2 and 3 confirmed the existence of three separate hospital lineages (17, 18, and 78), highlighting different evolutionary trajectories for BAPS 2-1 (lineage 78) and 3-3 (lineage 17 and lineage 18) isolates. Phylogenomic analysis of 29 E. faecium isolates showed agreement between BAPS assignment of STs and their relative positions in the phylogenetic tree. Odds ratio calculation confirmed the significant association between hospital isolates with BAPS 3-3 and lineages 17, 18, and 78. Admixture analysis showed a scarce number of recombination events between the different BAPS groups. For the E. faecium hospital population, we propose an evolutionary model in which strains with a high propensity to colonize and infect hospitalized patients arise through horizontal <span class="hlt">gene</span> transfer. Once adapted to the distinct hospital niche, this subpopulation becomes isolated, and recombination with other populations declines. PMID:22807567</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1218083','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1218083"><span id="translatedtitle">Structure and expression of a cluster of glutathione S-transferase <span class="hlt">genes</span> from a <span class="hlt">marine</span> fish, the plaice (Pleuronectes platessa).</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Leaver, M J; Wright, J; George, S G</p> <p>1997-01-01</p> <p>Glutathione S-transferases are involved in the detoxification of reactive electrophilic compounds, including intracellular metabolites, drugs, pollutants and pesticides. A cluster of three glutathione S-transferase <span class="hlt">genes</span>, designated GSTA, GSTA1 and GSTA2, was isolated from the <span class="hlt">marine</span> flatfish, plaice (Pleuronectes platessa). GSTA and GSTA1 code for protein products with 76% amino acid identity. GSTA2 appears to contain a single nucleotide deletion which would render any product non-functional. All of these <span class="hlt">genes</span> consist of six exons of similar sizes and greater than 70% nucleotide identity, and are interrupted by five introns of differing sizes. GSTA and GSTA1 mRNAs were present in a range of tissues, while GSTA2 mRNA was no detected. Expression of GSTA mRNA was increased in plaice intestine and spleen by pretreatment with beta-naphthoflavone, and expression of both GSTA and GSTA1 mRNAs was increased in plaice liver and gill by pretreatment with the peroxisome proliferating agent perfluoro-octanoic acid. PMID:9020873</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4231279','PMC'); return false;" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4231279"><span id="translatedtitle">Profiling <span class="hlt">gene</span> expression to distinguish the likely active diazotrophs from a sea of genetic potential in <span class="hlt">marine</span> sediments</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Brown, S M; Jenkins, B D</p> <p>2014-01-01</p> <p>Nitrogen (N) cycling microbial communities in <span class="hlt">marine</span> sediments are extremely diverse, and it is unknown whether this diversity reflects extensive functional redundancy. Sedimentary denitrifiers remove significant amounts of N from the coastal ocean and diazotrophs are typically regarded as inconsequential. Recently, N fixation has been shown to be a potentially important source of N in estuarine and continental shelf sediments. Analysis of expressed <span class="hlt">genes</span> for nitrite reductase (nirS) and a nitrogenase subunit (nifH) was used to identify the likely active denitrifiers and nitrogen fixers in surface sediments from different seasons in Narragansett Bay (Rhode Island, USA). The overall diversity of diazotrophs expressing nifH decreased along the estuarine gradient from the estuarine head to an offshore continental shelf site. Two groups of sequences related to anaerobic sulphur/iron reducers and sulphate reducers dominated libraries of expressed nifH <span class="hlt">genes</span>. Quantitative polymerase chain reaction (qPCR) and quantitative reverse transcription polymerase chain reaction (qRT-PCR) data shows the highest abundance of both groups at a mid bay site, and the highest nifH expression at the head of the estuary, regardless of season. Several potential environmental factors, including water temperature, oxygen concentration and metal contamination, may influence the abundance and nifH expression of these two bacterial groups. PMID:24447468</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ncbi.nlm.nih.gov/pubmed/19302361','PUBMED'); return false;" href="http://www.ncbi.nlm.nih.gov/pubmed/19302361"><span id="translatedtitle"><span class="hlt">Gene</span> <span class="hlt">flow</span> of Acanthaster planci (L.) in relation to ocean currents revealed by microsatellite analysis.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Yasuda, Nina; Nagai, Satoshi; Hamaguchi, Masami; Okaji, Ken; Gérard, Karin; Nadaoka, Kazuo</p> <p>2009-04-01</p> <p>Population outbreaks of the coral-eating starfish, Acanthaster planci, are hypothesized to spread to many localities in the Indo-Pacific Ocean through dispersal of planktonic larvae. To elucidate the <span class="hlt">gene</span> <span class="hlt">flow</span> of A. planci across the Indo-Pacific in relation to ocean currents and to test the larval dispersal hypothesis, the genetic structure among 23 samples over the Indo-Pacific was analysed using seven highly polymorphic microsatellite loci. The F-statistics and genetic admixture analysis detected genetically distinct groups in accordance with ocean current systems, that is, the Southeast African group (Kenya and Mayotte), the Northwestern Pacific group (the Philippines and Japan), Palau, the North Central Pacific group (Majuro and Pohnpei), the Great Barrier Reef, Fiji, and French Polynesia, with a large genetic break between the Indian and Pacific Oceans. A pattern of significant isolation by distance was observed among all samples (P = 0.001, r = 0.88, n = 253, Mantel test), indicating restricted <span class="hlt">gene</span> <span class="hlt">flow</span> among the samples in accordance with geographical distances. The data also indicated strong <span class="hlt">gene</span> <span class="hlt">flow</span> within the Southeast African, Northwestern Pacific, and Great Barrier Reef groups. These results suggest that the western boundary currents have strong influence on <span class="hlt">gene</span> <span class="hlt">flow</span> of this species and may trigger secondary outbreaks. PMID:19302361</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ars.usda.gov/research/publications/Publications.htm?seq_no_115=214436','TEKTRAN'); return false;" href="http://www.ars.usda.gov/research/publications/Publications.htm?seq_no_115=214436"><span id="translatedtitle">An empirically derived model of field-scale <span class="hlt">gene</span> <span class="hlt">flow</span> in winter wheat</span></a></p> <p><a target="_blank" href="http://www.ars.usda.gov/services/TekTran.htm">Technology Transfer Automated Retrieval System (TEKTRAN)</a></p> <p></p> <p></p> <p>The potential introduction of wheat (Triticum aestivum L.) cultivars with transgenic traits has generated increased interest in pollen-mediated <span class="hlt">gene</span> <span class="hlt">flow</span> (PMGF). The objectives of this study were to estimate wheat PMGF between commercial fields across multiple years and locations, and to compare est...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ars.usda.gov/research/publications/Publications.htm?seq_no_115=244888','TEKTRAN'); return false;" href="http://www.ars.usda.gov/research/publications/Publications.htm?seq_no_115=244888"><span id="translatedtitle">The Impact of Distinct Insect Species on Pollination and <span class="hlt">Gene</span> <span class="hlt">Flow</span> in Alfalfa</span></a></p> <p><a target="_blank" href="http://www.ars.usda.gov/services/TekTran.htm">Technology Transfer Automated Retrieval System (TEKTRAN)</a></p> <p></p> <p></p> <p>Pollinator species and plant density can influence pollination and <span class="hlt">gene</span> <span class="hlt">flow</span>. The efficacy of different floral visitors at tripping alfalfa flowers was examined in both low and high density patches to determine their potential role in pollination. In addition, for a subset of the floral visitors, th...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://dx.doi.org/10.1111/j.1365-294X.2012.05493.x','USGSPUBS'); return false;" href="http://dx.doi.org/10.1111/j.1365-294X.2012.05493.x"><span id="translatedtitle"><span class="hlt">Gene</span> <span class="hlt">flow</span> and pathogen transmission among bobcats (Lynx rufus) in a fragmented urban landscape</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Lee, Justin S.; Ruell, Emily W.; Boydston, Erin E.; Lyren, Lisa M.; Alonso, Robert S.; Troyer, Jennifer L.; Crooks, Kevin R.; VandeWoude, Sue</p> <p>2012-01-01</p> <p>Urbanization can result in the fragmentation of once contiguous natural landscapes into a patchy habitat interspersed within a growing urban matrix. Animals living in fragmented landscapes often have reduced movement among habitat patches because of avoidance of intervening human development, which potentially leads to both reduced <span class="hlt">gene</span> <span class="hlt">flow</span> and pathogen transmission between patches. Mammalian carnivores with large home ranges, such as bobcats (Lynx rufus), may be particularly sensitive to habitat fragmentation. We performed genetic analyses on bobcats and their directly transmitted viral pathogen, feline immunodeficiency virus (FIV), to investigate the effects of urbanization on bobcat movement. We predicted that urban development, including major freeways, would limit bobcat movement and result in genetically structured host and pathogen populations. We analysed molecular markers from 106 bobcats and 19 FIV isolates from seropositive animals in urban southern California. Our findings indicate that reduced <span class="hlt">gene</span> <span class="hlt">flow</span> between two primary habitat patches has resulted in genetically distinct bobcat subpopulations separated by urban development including a major highway. However, the distribution of genetic diversity among FIV isolates determined through phylogenetic analyses indicates that pathogen genotypes are less spatially structured--exhibiting a more even distribution between habitat fragments. We conclude that the types of movement and contact sufficient for disease transmission occur with enough frequency to preclude structuring among the viral population, but that the bobcat population is structured owing to low levels of effective bobcat migration resulting in <span class="hlt">gene</span> <span class="hlt">flow</span>. We illustrate the utility in using multiple molecular markers that differentially detect movement and <span class="hlt">gene</span> <span class="hlt">flow</span> between subpopulations when assessing connectivity.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://pubs.er.usgs.gov/publication/70162628','USGSPUBS'); return false;" href="http://pubs.er.usgs.gov/publication/70162628"><span id="translatedtitle">Elevational speciation in action? Restricted <span class="hlt">gene</span> <span class="hlt">flow</span> associated with adaptive divergence across an altitudinal gradient</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Funk, W. C.; Murphy, M.A.; Hoke, K. L.; Muths, Erin L.; Amburgey, Staci M.; Lemmon, Emily M.; Lemmon, A. R.</p> <p>2016-01-01</p> <p>Evolutionary theory predicts that divergent selection pressures across elevational gradients could cause adaptive divergence and reproductive isolation in the process of ecological speciation. Although there is substantial evidence for adaptive divergence across elevation, there is less evidence that this restricts <span class="hlt">gene</span> <span class="hlt">flow</span>. Previous work in the boreal chorus frog (Pseudacris maculata) has demonstrated adaptive divergence in morphological, life history and physiological traits across an elevational gradient from approximately 1500–3000 m in the Colorado Front Range, USA. We tested whether this adaptive divergence is associated with restricted <span class="hlt">gene</span> <span class="hlt">flow</span> across elevation – as would be expected if incipient speciation were occurring – and, if so, whether behavioural isolation contributes to reproductive isolation. Our analysis of 12 microsatellite loci in 797 frogs from 53 populations revealed restricted <span class="hlt">gene</span> <span class="hlt">flow</span> across elevation, even after controlling for geographic distance and topography. Calls also varied significantly across elevation in dominant frequency, pulse number and pulse duration, which was partly, but not entirely, due to variation in body size and temperature across elevation. However, call variation did not result in strong behavioural isolation: in phonotaxis experiments, low-elevation females tended to prefer an average low-elevation call over a high-elevation call, and vice versa for high-elevation females, but this trend was not statistically significant. In summary, our results show that adaptive divergence across elevation restricts <span class="hlt">gene</span> <span class="hlt">flow</span> in P. maculata, but the mechanisms for this potential incipient speciation remain open.</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_9");'>9</a></li> <li><a href="#" onclick='return showDiv("page_10");'>10</a></li> <li><a href="#" onclick='return showDiv("page_11");'>11</a></li> <li><a href="#" onclick='return showDiv("page_12");'>12</a></li> <li class="active"><span>13</span></li> <li><a href="#" onclick='return showDiv("page_13");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_13 --> <center> <div class="footer-extlink text-muted"><small>Some links on this page may take you to non-federal websites. 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