Journal Articles (Biological Sciences)

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  1. 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
    Subjects: DNA, resources, Bombyx-mori, databases, sequences
  2. 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
  3. Seasonality, fasting endurance, and body size in mammals [Download]

    Title: Seasonality, fasting endurance, and body size in mammals
    Creator: Lindstedt, S. L.
    Subjects: Mammals, Seasonality, Body Size
    Date Created: 1985
  4. An Eocene Tar Spot on a Fossil Palm and Its Fungal Hyperparasite [Download]

    Title: An Eocene Tar Spot on a Fossil Palm and Its Fungal Hyperparasite
    Creator: Currah, R.S.
    Description: Two ascomycetes from the middle Eocene (48.7 million yr b.p.) Princeton chert are described. Palaeoserenomyces allenbyensis gen. et sp. nov. consists of long, loculate stromata of distinctive columnar cells beneath the epidermis of the extinct fan palm, Uhlia allenbyensis. The sporogenous locules are empty but stromatal features and locule shape are similar to extant Serenomyces, a genus in the Phyllachorales that forms leaf spots on coryphoid palms. The locules of P allenbyensis contain circular structures that are interpreted as intralocular ascomata of a mycoparasite, Cryptodidymosphaerites princetonensis gen. et sp. nov. Two-celled ascospores in uniseriate rows are similar to the genus Didymosphaeria of the Melanommatales. These fossils are compared to Didymosphaeria conoidea, an extant mycoparasite of stromatic ascomycetes. The large number of exquisitely preserved fungal structures on taxonomically defined hosts in the Princeton chert provides a unique opportunity for studying the diversity of microfungi in Tertiary paleoenvironments.
    Subjects: leaf spot fungi, Cryptodidymosphaerites, Serenomyces, Phyllachorales, Melanommatales, paleomycology, Paleoserenomyces, Didymosphaeria, mycoparasite
    Date Created: 1998
  5. 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
  6. 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
  7. The effect of dispersal patterns on stream populations [Download]

    Title: The effect of dispersal patterns on stream populations
    Creator: Lutscher, F.
    Description: Individuals in streams are constantly subject to predominantly unidirectional flow. The question of how these populations can persist in upper stream reaches is known as the “drift paradox.” We employ a general mechanistic movement-model framework and derive dispersal kernels for this situation. We derive thin- as well as fat-tailed kernels. We then introduce population dynamics and analyze the resultingin tegrodifferential equation. In particular, we study how the critical domain size and the invasion speed depend on the velocity of the stream flow. We give exact conditions under which a population can persist in a finite domain in the presence of stream flow, as well as conditions under which a population can spread against the direction of the flow. We find a critical stream velocity above which a population cannot persist in an arbitrarily large domain. At exactly the same stream velocity, the invasion speed against the flow becomes zero; for larger velocities, the population retreats with the flow.
    Subjects: critical domain size, spread speed, drift paradox, nonlocal dispersal
    Date Created: 2005
  8. Permineralized Flower From the Middle Eocene of British Columbia. [Download]

    Title: Permineralized Flower From the Middle Eocene of British Columbia.
    Creator: Stockey, R.A.
    Description: A permineralized flower bud, two stamen clusters and one isolated stamen of similar morphology have been found in the black cherts of the Middle Eocene Allenby Formation of Princeton, British Columbia. Specimens were studied using a modified cellulose acetate peel technique and hydrofluoric acid. The single flower specimen, 4.5 mm long and 4.0 mm in diameter, represents half of a relatively mature bud of a bisexual flower with a superior ovary. The two-loculate pistil is 2.5 mm long with a solid style and a lobed stigmatic surface. No ovules have been observed in attachment. Twenty-two to 24 stamens are borne in three whorls or a tight helix. Pollen sacs of the anther are elongate with a thin connective while filaments are laminar. Anther walls contain rectangular cells with dark contents that also can be identified in isolated stamens or stamen clusters. A bundant stephanocolpate (pentacolpate), psilate pollen grains 20 ,um in diameter have been isolated and examined using scanning and transmission electron microscopy. Grains are tectate, columellate with a broad foot layer that thins near the apertures, and an endexine of small platelets. The remains of four petals are surrounded by one large sepal, suggesting two in the whole flower. Morphological features of this flower are comparable to taxa of the Flacourtiaceae and Papaveraceae, but show closest similarities to the Eschscholziaeae of the Papaveraceae. Difficulties with reconciling the placement of this flower in the Eschscholziaeae and the known environment of deposition of the Princeton chert are discussed. The fossil material represents a new angiospermous taxon: Princetonia allenbyensis Stockey gen. et sp. nov., family Incertae sedis.
    Subjects: permineralized flowers, British Columbia, Allenby Formation, Middle Eocene
    Date Created: 1987
  9. Ecological characteristics of streams in the Barrenlands near Lac de Gras, NWT [Download]

    Title: Ecological characteristics of streams in the Barrenlands near Lac de Gras, NWT
    Creator: Jones, N.E.
    Description: We examined spatiotemporal variation in the physical, chemical, and biological characteristics of pristine streams that represent a range of conditions near Lac de Gras in the Barrenlands region of the Northwest Territories, Canada. Principal component analysis organized streams into four groups on the basis of seven physical characteristics. Despite broad differences among groups in physical characteristics, variation in chemical and biological characteristics was generally not large, with only pH and coarse particulate organic matter differing among the four groups. Nevertheless, several chemical and biological variables were correlated with physical characteristics, particularly measures of stream size (bankfull width and depth, drainage area, and stream discharge). Annual variability in climate affected stream temperature and discharge and influenced several biotic characteristics, particularly the growth of young-of-the-year arctic grayling (Thymallus arcticus). Barrenland streams share basic characteristics of Alaskan tundra streams, as a result of similar climatic regimes. Key differences between the two areas, however, appear related to the lake-outlet nature of the Barrenland streams, which may contribute to higher growth of young-of-the-year arctic grayling than would be expected from regional climate.
    Subjects: drift, Barrenlands, Thymallus arcticus, reference condition, spatiotemporal variation, tundra, arctic grayling, Lac de Gras, lake-outlet, streams, Northwest Territories
    Date Created: 2003
  10. An incident of polar bear infanticide and cannibalism on Phippsøya, Svalbard [Download]

    Title: An incident of polar bear infanticide and cannibalism on Phippsøya, Svalbard
    Creator: Stone, I.R.
    Description: A case of polar bear infanticide and cannibalism is reported from Phippsøya, Svalbard. In this instance, a cub of some 7 months was killed by an adult male bear, which was in poor condition, in the close proximity of the mother,which was also in poor condition. It seems probable that the attack was made for nutritional gain.
    Subjects: Ursus maritimus, trends, population ecology, Beaufort Sea
    Date Created: 2007