ERA

Journal Articles (Biological Sciences)

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  1. The Genomes of Oryza sativa: A History of Duplications [Download]

    Title: The Genomes of Oryza sativa: A History of Duplications
    Creator: Yu, Jun
    Subjects: Biological Sciences , Genetics, Cell Biology , Evolutionary Biology , genomes
  2. Ankylosaurid dinosaur tail clubs evolved through stepwise acquisition of key features [Download]

    Title: Ankylosaurid dinosaur tail clubs evolved through stepwise acquisition of key features
    Creator: Arbour, Victoria M.
    Description: Ankylosaurid ankylosaurs were quadrupedal, herbivorous dinosaurs with abundant dermal ossifications. They are best known for their distinctive tail club composed of stiff, interlocking vertebrae (the handle) and large, bulbous osteoderms (the knob), which may have been used as a weapon. However, tail clubs appear relatively late in the evolution of ankylosaurids, and seemed to have been present only in a derived clade of ankylosaurids during the last 20 million years of the Mesozoic Era. New evidence from mid Cretaceous fossils from China suggests that the evolution of the tail club occurred at least 40 million years earlier, and in a stepwise manner, with early ankylosaurids evolving handle-like vertebrae before the distal osteoderms enlarged and coossified to form a knob.
    Subjects: Ankylosauria, Ankylosauridae, Cretaceous, Dinosauria
  3. Identifying non-invasible habitats for marine copepods using temperature-dependent R0. [Download]

    Title: Identifying non-invasible habitats for marine copepods using temperature-dependent R0.
    Creator: Rajakaruna, H.
    Description: If a non-indigenous species is to thrive and become invasive it must first persist under its new set of environmental conditions. Net reproductive rate (R 0) represents the average number of female offspring produced by a female over its lifetime, and has been used as a metric of population persistence. We modeled R 0 as a function of ambient water temperature (T) for the invasive marine calanoid copepod Pseudodiaptomus marinus, which is introduced to west coast of North America from East Asia by ship ballast water. The model was based on temperature-dependent stage-structured population dynamics given by a system of ordinary differential equations. We proposed a methodology to identify habitats that are non-invasible for P. marinus using the threshold of R 0(T) < 1 in order to identify potentially invasible habitats. We parameterized the model using published data on P. marinus and applied R 0(T) to identify the range of non-invasible habitats in a global scale based on sea surface temperature data. The model predictions matched the field evidence of species occurrences well.
    Subjects: stage-structured population models, marine copepods, net reproductive rate, ordinary differential equations, temperature, Pseudodiaptomus marinus, habitat suitability, ecological modeling, habitat invasibility, invasive species
  4. Allozyme survey and relationships of Limnoporus Stal species (Heteroptera: Gerridae) [Download]

    Title: Allozyme survey and relationships of Limnoporus Stal species (Heteroptera: Gerridae)
    Creator: Sperling, F. A. H.
    Description: Five species of Limnoporus Stål (L. canaliculatus [Say], L. dissortis [Drake and Harris], L. nearcticus [Kelton], L. notabilis [Drake and Hottes], and L. rufoscutellatus [Latreille]) were each sampled at 20 electrophoretic loci. Twofold differences among species in mean heterozygosity appear to be unrelated to presence of wing dimorphism. Low heterozygosity in some populations within species may reflect geographic isolation. There were substantial differences in allele frequency among, but not within, species. Limnoporus rufoscutellatus from western Europe and L. nearcticus from Alaska were the most similar pair of species, with a Nei’s standard genetic identity that is generally found only between populations of the same species. Limnoporus canaliculatus was the most divergent species, and the relationship among L. dissortis, L. notabilis, and the L. rufoscutellatus – L. nearcticus pair is resolved as a trichotomy.
    Subjects: Allozyme survery, Limnoporus Stal
  5. Palaeoenvironment and palaeoecology of three Cretaceous snakes: Pachyophis, Pachyrhachis, and Dinilysia [Download]

    Title: Palaeoenvironment and palaeoecology of three Cretaceous snakes: Pachyophis, Pachyrhachis, and Dinilysia
    Creator: Caldwell, M. W.
    Description: The palaeoecology of three Late Cretaceous snakes is evaluated. Pachyophis woodwardi Nopcsa, 1923 and Pachyrhachis problematicus Haas, 1979, are Cenomanian in age and are found in carbonate rocks deposited in marine inter-reef basin environments of the European and African Tethys Sea. Dinilysia patagonica Woodward, 1901, Coniacian in age, is considered closely allied to Living anilioid snakes, and is found in clastic rocks deposited in a terrestrial inter-dune basin environment in northern Patagonia, Argentina. All three snakes are known from well preserved and articulated specimens found in sediments where detailed sedimentological and taphonomic analyses are possible. Pachyophis and Pachyrhachis were laterally compressed, have pachyostotic ribs and vertebrae, and small, narrow heads. These two snakes are interpreted as aquatic predators living in and around the margins of reef mounds on a shallow water carbonate platform. Dinilysia was a large bodied snake with a relatively large head, and is interpreted here as a terrestrial predator that lived in a dry, interdune basin environment dominated by aeolian sedimentation. Sedimentary units preserve ichnological evidence of burrowing insects and rooting plants.
    Subjects: Dinilysia, Pachyrhachis, Pachyophis, Snakes, Phylogeny, Palaeoecology, Palaeobiogeography, Palaeoenvironment, Cretaceous
  6. Proteomic analysis of opsins and thyroid hormone-induced retinal development using isotope-coded affinity tags (ICAT) and mass spectrometry [Download]

    Title: Proteomic analysis of opsins and thyroid hormone-induced retinal development using isotope-coded affinity tags (ICAT) and mass spectrometry
    Creator: Allison, W. Ted
    Description: Purpose: Analyses that reveal the relative abundance of proteins are informative in elucidating mechanisms of retinal development and disease progression. However, popular high-throughput proteomic methods do not reliably detect opsin protein abundance, which serve as markers of photoreceptor differentiation. We utilized thyroid-hormone (TH) treatment of rainbow trout (Oncorhynchus mykiss) as a model of cone apoptosis and cone regeneration. We used this model to investigate if emerging proteomic technology allows effective analysis of retinal development and opsin protein abundance. We also sought to begin a characterization of proteomic changes in the retina occurring with TH treatment and address whether TH affects proliferation or photoreceptor differentiation. Methods: Retinal homogenates were prepared from control and TH-treated fish. Peptides from control and treated homogenates were differentially labeled, using isotope-code affinity tags (ICAT) and analyzed using capillary liquid chromatography-electrospray ionization-tandem mass spectrometry (capLC-ESI-MS/MS). This method identifies proteins and quantifies their relative abundance between two samples. Results: The relative abundance of many retinal proteins changed during TH treatment. These included proteins from every functional class. We detected 1,684 different peptides, and our quantification suggests that 94 increased and 146 decreased in abundance more than 50% during TH treatment. Cell-cycle proteins appear to be increased, consistent with TH-inducing cell proliferation, similar to its effect in Xenopus. Other proteins associated with retinal development, such as ΔA and tubulins, changed in abundance during TH treatment. Rod opsin and three cone opsins were identified and the relative abundance of each changed with TH treatment. Conclusions: ICAT and capLC-ESI-MS/MS are an effective complement to other molecular approaches that investigate the mechanisms of retinal development. Unlike other proteomic techniques, this approach does not require development of species- or tissue-specific methodology, such as characterizing two dimensional (2D) gels or antibodies, in order to be practical as a high-throughput approach. Importantly, this technology was able to assess the relative abundance of opsin proteins. These findings represent the first high-throughput proteomic analysis of the retina and demonstrate the technique’s ability to provide useful information in retinal development.
    Subjects: rainbow trout, thyroid-hormone treatment, retinal development, protein analysis
  7. SilkDB: A knowledgebase for silkworm biology and genomic [Download]

    Title: SilkDB: A knowledgebase for silkworm biology and genomic
    Creator: Wang, J.
    Description: The Silkworm Knowledgebase (SilkDB) is a web-based repository for the curation, integration and study of silkworm genetic and genomic data. With the recent accomplishment of a ~6X draft genome sequence of the domestic silkworm (Bombyx mori ), SilkDB provides an integrated representation of the large-scale, genome-wide sequence assembly, cDNAs, clusters of expressed sequence tags (ESTs), transposable elements (TEs), mutants, single nucleotide polymorphisms (SNPs) and functional annotations of genes with assignments to InterPro domains and Gene Ontology (GO) terms. SilkDB also hosts a set of ESTs from Bombyx mandarina, a wild progenitor of B.mori, and a collection of genes from other Lepidoptera.Comparative analysis results between the domestic and wild silkworm, between B.mori and other Lepidoptera, and between B.mori and the two sequenced insects, fruitfly and mosquito, are displayed by using B.mori genome sequence as a reference framework. Designed as a basic platform, SilkDB strives to provide a comprehensive knowledgebase about the silkworm and present the silkworm genome and related information in systematic and graphical ways for the convenience of in-depth comparative studies. SilkDB is publicly accessible at  http://silkworm.genomics.org.cn
    .
    Subjects: DNA, resources, Bombyx-mori, databases, sequences
  8. Congruence Versus Phylogenetic Accuracy: Revisiting the Incongruence Length Difference Test [Download]

    Title: Congruence Versus Phylogenetic Accuracy: Revisiting the Incongruence Length Difference Test
    Creator: Hipp, A.L.
    Subjects: evolution, origin, parismony, inference, data sets, trees, DNA, combining data, topologies
  9. Diversity and acyl-homoserine lactone production among subtidal biofilm-forming bacteria [Download]

    Title: Diversity and acyl-homoserine lactone production among subtidal biofilm-forming bacteria
    Creator: Huang, Yi-Li
    Description: Bacteria isolated from subtidal biofilms were identified via 16S rRNA gene sequencing and screened for acyl-homoserine lactone (AHL) production. In total, 68 strains were isolated from 1 to 9 d-old subtidal biofilms developed at a coastal fish farm. Identification based on partial 16S rRNA gene sequencing revealed that these isolates were distributed among 3 phylogenetic groups (4 Bacteroidetes, 13 α-Proteobacteria and 51 γ-Proteobacteria), with most isolates belonging to the family Rhodobacteraceae and the genera Thalassomonas, Alteromonas, Pseudoalteromonas, Shewanella and Vibrio. AHL screening was performed using 2 AHL reporter strains, Agrobacterium tumefaciens A136 and Chromobacterium violaceum CV026. Results showed that 21 strains (31%) produced AHLs, including 3 Bacteroidetes, 5 α-Proteobacteria and 13 γ-Proteobacteria. All the AHL-producing α-Proteobacteria belonged to the family Rhodobacteraceae, whereas the AHL-producing γ-Proteobacteria consisted of 6 Pseudoalteromonas spp., 6 Vibrio spp. and 1 Thalassomonas sp. This is the first report of AHL-producing marine bacteria in the genera Flammeovirga, Pseudoalteromonas and Thalassomonas. The family Rhodobacteraceae (11 isolates) and the genera Vibrio (15 isolates) and Pseudoalteromonas (17 isolates) had the greatest number of AHL-producing isolates. AHL profiling of the AHL-producing isolates was performed by GC-MS. Most AHL-producing isolates produced several different AHLs, many of which were long-chain- and 3-oxo-AHLs. The widespread occurrence of AHL-producing bacteria in subtidal biofilms suggests that AHLs may play a role in the community development in this environment.
    Subjects: marine bacteria, acyl-homoserine lactone, AHL, subtidal biofilm
    Date Created: 2008
  10. R0 Analysis of a Spatiotemporal Model for a Stream Population [Download]

    Title: R0 Analysis of a Spatiotemporal Model for a Stream Population
    Creator: McKenzie, H.W.
    Description: Water resources worldwide require management to meet industrial, agricultural, and urban consumption needs. Management actions change the natural flow regime, which impacts the river ecosystem. Water managers are tasked with meeting water needs while mitigating ecosystem impacts. We develop process-oriented advection-diffusion-reaction equations that couple hydraulic flow to population growth, and we analyze them to assess the effect of water flow on population persistence. We present a new mathematical framework, based on the net reproductive rate R0 for advection-diffusion-reaction equations and on related measures. We apply the measures to population persistence in rivers under various flow regimes. This work lays the groundwork for connecting R0 to more complex models of spatially structured and interacting populations, as well as more detailed habitat and hydrological data.
    Subjects: instream flow needs, next generation operator, drift paradox, positive operator, net reproductive rate, spectral radius
    Date Created: 2011