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. Antimicrobial activity in the egg wax of the African cattle tick Amblyomma hebraeum (Acari: Ixodidae) [Download]

    Title: Antimicrobial activity in the egg wax of the African cattle tick Amblyomma hebraeum (Acari: Ixodidae)
    Creator: Arrieta, M. C.
    Description: Abstract: Eggs of the tick Amblyomma hebraeum Koch (Acari: Ixodidae) inhibited the growth of Escherichia coli and Serratia marcescens (Gram-negative bacteria) in solid culture, but not the growth of Staphylococcus epidermidis, and only marginally the growth of Bacillus subtilis (Gram-positive bacteria). When egg wax was extracted with chloroform/methanol (2:1), the extract contained antibacterial activity, but the denuded eggs did not. When assayed against bacteria in liquid culture, the aqueous phase inhibited the growth of S. epidermidis. However, the activity against E. coli was lost during extraction. The antimicrobial component of the aqueous phase was heat stable (100 degrees C for 10 min), resistant to proteinase K (15 min at 55 degrees C) and to pronase (30 min at 37 degrees C). The antibacterial activity in the aqueous phase increased the permeability of the cell membrane of susceptible bacterial cells within 30 min. However, lysis of the cells was detected by optical density measurements (OD600 nm) only after 1.5 h. The most evident cytological changes observed by transmission electron microscopy were a thickening of the cell wall and the appearance of numerous electron lucent areas within the cytoplasm of treated bacteria. Gene's organ, the egg-waxing organ in ticks, grew enormously during the first 16 days post-engorgement, and gained antimicrobial activity by day 10 (when oviposition began). This suggests that Gene's organ is the major source of the antibacterial substance in the egg wax. The vitellogenic hormone in A. hebraeum, 20-hydroxyecdysone, when injected into recently engorged females, did not stimulate growth of Gene's organ or precocious secretion of antimicrobial activity.
    Subjects: Egg wax, Antimicrobial activity, Gené's organ, Ixodid ticks, Amblyomma hebraeum
    Date Created: 2006
  10. Structural and Biochemical Changes in Loblolly Pine (Pinus taeda L.) Seeds During Germination and Early-Seedling Growth. I. Storage Protein Reserves [Download]

    Title: Structural and Biochemical Changes in Loblolly Pine (Pinus taeda L.) Seeds During Germination and Early-Seedling Growth. I. Storage Protein Reserves
    Creator: Stone, S. L.
    Description: Abstract: Quantitative and qualitative changes in the storage proteins of loblolly pine (Pinus taeda L.) seeds were followed during germination and early-seedling growth and were correlated with light-microscopic observations. In both the megagametophyte and the embryo, the cells of tissues from fully stratified seeds appeared very similar to the cells of tissues from mature desiccated seeds. A change in the appearance of protein vacuoles. resulting from the hydrolysis of storage proteins, occurred in the seedling prior to the completion of germination (denoted by radicle emergence from the seed coat) and continued during early-seedling growth. Within the seedling, storage proteins were mobilized more rapidly in the root pole, including the hypocotyl and radicle, than in the shoot pole, including the cotyledonary whorl, and shoot apex or epicotyl. In both parts of the seedling, protein hydrolysis was first observed in the procambial and epidermal tissue. In contrast to the seedling, changes in the appearance of protein vacuoles were not evident in the megagametophyte until after germination was completed. Changes in protein vacuoles in the megagametophyte occurred in two directional waves, relative to corrosion cavity proximity.
    Subjects: Stratification, Megagametophyte, Postfertilization, Localization, Dormancy, Metabolism, Monticola, Zygotic embryo, Deposition, Cotyledons, Body-composition
    Date Created: 1997