ERA

Journal Articles (Biological Sciences)

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  1. New specimens of the crested theropod dinosaur Elmisaurus rarus from Mongolia

    Title: New specimens of the crested theropod dinosaur Elmisaurus rarus from Mongolia
    Creator: Currie, Philip J.
    Subjects: Dinosauria, Theropoda, Oviraptorosauria, Caenagnathidae, Elmisaurinae, Upper Cretaceous, Mongolia
    Date Created: 2015/01/27
  2. MetaboMiner – semi-automated identification of metabolites from 2D NMR spectra of complex biofluids

    Title: MetaboMiner – semi-automated identification of metabolites from 2D NMR spectra of complex biofluids
    Creator: Xia, J.
    Description: Background One-dimensional (1D) 1H nuclear magnetic resonance (NMR) spectroscopy is widely used in metabolomic studies involving biofluids and tissue extracts. There are several software packages that support compound identification and quantification via 1D 1H NMR by spectral fitting techniques. Because 1D 1H NMR spectra are characterized by extensive peak overlap or spectral congestion, two-dimensional (2D) NMR, with its increased spectral resolution, could potentially improve and even automate compound identification or quantification. However, the lack of dedicated software for this purpose significantly restricts the application of 2D NMR methods to most metabolomic studies. Results We describe a standalone graphics software tool, called MetaboMiner, which can be used to automatically or semi-automatically identify metabolites in complex biofluids from 2D NMR spectra. MetaboMiner is able to handle both 1H-1H total correlation spectroscopy (TOCSY) and 1H-13C heteronuclear single quantum correlation (HSQC) data. It identifies compounds by comparing 2D spectral patterns in the NMR spectrum of the biofluid mixture with specially constructed libraries containing reference spectra of ~500 pure compounds. Tests using a variety of synthetic and real spectra of compound mixtures showed that MetaboMiner is able to identify >80% of detectable metabolites from good quality NMR spectra. Conclusion MetaboMiner is a freely available, easy-to-use, NMR-based metabolomics tool that facilitates automatic peak processing, rapid compound identification, and facile spectrum annotation from either 2D TOCSY or HSQC spectra. Using comprehensive reference libraries coupled with robust algorithms for peak matching and compound identification, the program greatly simplifies the process of metabolite identification in complex 2D NMR spectra.
    Subjects: tissues, C-13 NMR, metabonomics, H-1-NMR metabolomics, mixtures, toxicity, spectroscopy
  3. Effects of Heterogeneity on Spread and Persistence in Rivers

    Title: Effects of Heterogeneity on Spread and Persistence in Rivers
    Creator: Lutscher, F.
    Description: The question how aquatic populations persist in rivers when individuals are constantly lost due to downstream drift has been termed the “drift paradox.” Recent modeling approaches have revealed diffusion-mediated persistence as a solution. We study logistically growing populations with and without a benthic stage and consider spatially varying growth rates. We use idealized hydrodynamic equations to link river cross-sectional area to flow speed and assume heterogeneity in the form of alternating patches, i.e., piecewise constant conditions. We derive implicit formulae for the persistence boundary and for the dispersion relation of the wave speed. We explicitly discuss the influence of flow speed, cross-sectional area and benthic stage on both persistence and upstream invasion speed.
    Subjects: persistence, spatial heterogeneity, aquatic organisms, rivers, invasions, advection–diffusion equations
  4. Arboviral infections in Egyptian and Sardinian children and adults with aseptic meningitis and meningo-encephalitis

    Title: Arboviral infections in Egyptian and Sardinian children and adults with aseptic meningitis and meningo-encephalitis
    Creator: Venturi, Giulietta
    Subjects: Aseptic meningitis, meningo-encephalitis, Arboviral infections
  5. Allee effects may slow the spread of parasites in a coastal marine ecosystem

    Title: Allee effects may slow the spread of parasites in a coastal marine ecosystem
    Creator: Krkosek, M.
    Description: Allee effects are thought to mediate the dynamics of population colonization, particularly for invasive species. However, Allee effects acting on parasites have rarely been considered in the analogous process of infectious disease establishment and spread. We studied the colonization of uninfected wild juvenile Pacific salmon populations by ectoparasitic salmon lice (Lepeophtheirus salmonis) over a 4-year period. In a data set of 68, 376 fish, we observed 85 occurrences of precopular pair formation among 1, 259 preadult female and 613 adult male lice. The probability of pair formation was dependent on the local abundance of lice, but this mate limitation is likely offset somewhat by mate-searching dispersal of males among host fish. A mathematical model of macroparasite population dynamics that incorporates the empirical results suggest a high likelihood of a demographic Allee effect, which can cause the colonizing parasite populations to die out. These results may provide the first empirical evidence for Allee effects in a macroparasite. Furthermore, the data give a rare detailed view of Allee effects in colonization dynamics and suggest that Allee effects may dampen the spread of parasites in a coastal marine ecosystem.
    Subjects: Epidemiology, Fisheries, Convervation, Aquaculture, Ocean
    Date Created: 2012
  6. Wildlife disease elimination and density dependence.

    Title: Wildlife disease elimination and density dependence.
    Creator: Potapov, A.
    Description: Disease control by managers is a crucial response to emerging wildlife epidemics, yet the means of control may be limited by the method of disease transmission. In particular, it is widely held that population reduction, while effective for controlling diseases that are subject to density-dependent (DD) transmission, is ineffective for controlling diseases that are subject to frequency-dependent (FD) transmission. We investigate control for horizontally transmitted diseases with FD transmission where the control is via culling or harvest that is non-selective with respect to infection and the population can compensate through DD recruitment or survival. Using a mathematical model, we show that culling or harvesting can eradicate the disease, even when transmission dynamics are FD. Eradication can be achieved under FD transmission when DD birth or recruitment induces compensatory growth of new, healthy individuals, which has the net effect of reducing disease prevalence by dilution. We also show that if harvest is used simultaneously with vaccination, and there is high enough transmission coefficient, application of both controls may be less efficient than vaccination alone. We illustrate the effects of these control approaches on disease prevalence for chronic wasting disease in deer where the disease is transmitted directly among deer and through the environment.
    Subjects: frequency-dependent transmission, disease modelling, chronic wasting disease, disease management
    Date Created: 2012
  7. Evolutionary Dynamics of <i>Vibrio cholerae</i> O1 Following a Single-Source Introduction to Haiti

    Title: Evolutionary Dynamics of <i>Vibrio cholerae</i> O1 Following a Single-Source Introduction to Haiti
    Creator: Katz, Lee S.
    Description: Prior to the epidemic that emerged in Haiti in October of 2010, cholera had not been documented in this country. After its introduction, a strain of Vibrio cholerae O1 spread rapidly throughout Haiti, where it caused over 600,000 cases of disease and >7,500 deaths in the first two years of the epidemic. We applied whole-genome sequencing to a temporal series of V. cholerae isolates from Haiti to gain insight into the mode and tempo of evolution in this isolated population of V. cholerae O1. Phylogenetic and Bayesian analyses supported the hypothesis that all isolates in the sample set diverged from a common ancestor within a time frame that is consistent with epidemiological observations. A pangenome analysis showed nearly homogeneous genomic content, with no evidence of gene acquisition among Haiti isolates. Nine nearly closed genomes assembled from continuous-long-read data showed evidence of genome rearrangements and supported the observation of no gene acquisition among isolates. Thus, intrinsic mutational processes can account for virtually all of the observed genetic polymorphism, with no demonstrable contribution from horizontal gene transfer (HGT). Consistent with this, the 12 Haiti isolates tested by laboratory HGT assays were severely impaired for transformation, although unlike previously characterized noncompetent V. cholerae isolates, each expressed hapR and possessed a functional quorum-sensing system. Continued monitoring of V. cholerae in Haiti will illuminate the processes influencing the origin and fate of genome variants, which will facilitate interpretation of genetic variation in future epidemics.

    IMPORTANCE: Vibrio cholerae is the cause of substantial morbidity and mortality worldwide, with over three million cases of disease each year. An understanding of the mode and rate of evolutionary change is critical for proper interpretation of genome sequence data and attribution of outbreak sources. The Haiti epidemic provides an unprecedented opportunity to study an isolated, single-source outbreak of Vibrio cholerae O1 over an established time frame. By using multiple approaches to assay genetic variation, we found no evidence that the Haiti strain has acquired any genes by horizontal gene transfer, an observation that led us to discover that it is also poorly transformable. We have found no evidence that environmental strains have played a role in the evolution of the outbreak strain.
    Subjects: Haiti, Cholera, <i>Vibrio cholerae</i>
    Date Created: 2013
  8. Predicting local and nonlocal effects of resources on animal space use using a mechanistic step-selection function.

    Title: Predicting local and nonlocal effects of resources on animal space use using a mechanistic step-selection function.
    Creator: Potts, J.R.
    Description: Predicting space use patterns of animals from their interactions with the environment is fundamental for understanding the effect of habitat changes on ecosystem functioning. Recent attempts to address this problem have sought to unify resource selection analysis, where animal space use is derived from available habitat quality, and mechanistic movement models, where detailed movement processes of an animal are used to predict its emergent utilization distribution. Such models bias the animal's movement towards patches that are easily available and resource-rich, and the result is a predicted probability density at a given position being a function of the habitat quality at that position. However, in reality, the probability that an animal will use a patch of the terrain tends to be a function of the resource quality in both that patch and the surrounding habitat. We propose a mechanistic model where this non-local effect of resources naturally emerges from the local movement processes, by taking into account the relative utility of both the habitat where the animal currently resides and that of where it is moving. We give statistical techniques to parametrize the model from location data and demonstrate application of these techniques to GPS location data of caribou (Rangifer tarandus) in Newfoundland. Steady-state animal probability distributions arising from the model have complex patterns that cannot be expressed simply as a function of the local quality of the habitat. In particular, large areas of good habitat are used more intensively than smaller patches of equal quality habitat, whereas isolated patches are used less frequently. Both of these are real aspects of animal space use missing from previous mechanistic resource selection models. Whilst we focus on habitats in this study, our modelling framework can be readily used with any environmental covariates and therefore represents a unification of mechanistic modelling and step selection approaches to understanding animal space use.
    Subjects: mechanistic models, resource selection analysis, caribou, animal movement, step selection functions, master equation
    Date Created: 2013
  9. Polbase a repository of biochemical, genetic, and structural information about DNA polymerases.

    Title: Polbase a repository of biochemical, genetic, and structural information about DNA polymerases.
    Creator: Langhorst, B. S.
    Description: ABSTRACT Polbase ( http://polbase.neb.com
    ) is a freely accessible database of DNA polymerases and related references. It has been developed in a collaborative model with experts whose contributions reflect their varied backgrounds in genetics, structural biology and biochemistry. Polbase is designed to compile detailed results of polymerase experimentation, presenting them in a dynamic view to inform further research. After validation, results from references are displayed in context with relevant experimental details and are always traceable to their source publication. Polbase is connected to other resources, including PubMed, UniProt and the RCSB Protein Data Bank, to provide multi-faceted views of polymerase knowledge. In addition to a simple web interface, Polbase data is exposed for custom analysis by external software. With the contributions of many polymerase investigators, Polbase has become a powerful research tool covering most important aspects of polymerases, from sequence and structure to biochemistry.
    Subjects: Deoxyribonucleic-Acid, Revised Nomenclature
    Date Created: 2011
  10. High resolution mapping of community structure in three glass sponge reefs (Porifera, Hexactinellida)

    Title: High resolution mapping of community structure in three glass sponge reefs (Porifera, Hexactinellida)
    Creator: Chu, J.W.F.
    Description: Glass sponge reefs (Porifera, Hexactinellida) are unique to the Pacific coast of Canada. To date, the locations and extents of reefs have only been assessed by multibeam echosounders, a method that does not resolve where live, dead and buried sponges are within a reef. We performed fine-scale (25 and 12.5 m grids) photographic surveys using remote operated vehicles and carried out GIS and semivariogram analysis to produce high resolution maps of the spatial distribution and abundance of glass sponges among 3 reefs in the Strait of Georgia and also to determine the community structure of animals associated with the reefs. Within a reef, glass sponges are clustered in spatially dependent patches 35 to 72 m in diameter, which we interpret to result from growth and reproduction processes. Reefs occur within a narrow range of depths (30 to 50 m), which may be explained by suspension feeding requirements for flow, which is accelerated over the underlying elevated bedrock mounds and ridges. The local abundance of fish and crustaceans was significantly higher in the presence of glass sponges while significantly lower abundances of molluscs and other sponges were found within the reefs. Also, we determined that a dense population of reef sponges can process water at 83000 l s–1, removing carbon at a rate of 0.96 g C m–2 d–1. Our high resolution mapping establishes a biological baseline for 3 glass sponge reefs in the Strait of Georgia.
    Subjects: Semivariogram, Glass sponge reef, ROV, Hexactinellid sponges, GIS
    Date Created: 2010