Post-Breeding Season Migrations of a Top Predator, the Harbor Seal (Phoca vitulina richardii), from a Marine Protected Area in Alaska

Marine protected areas (MPAs) are increasingly being used as a conservation tool for highly mobile marine vertebrates and the focus is typically on protecting breeding areas where individuals are aggregated seasonally. Yet movements during the non-breeding season can overlap with threats that may be equally as important to population dynamics. Thus understanding habitat use and movements of species during the non-breeding periods is critical for conservation. Glacier Bay National Park, Alaska, is one of the largest marine mammal protected areas in the world and has the only enforceable protection measures for reducing disturbance to harbor seals in the United States. Yet harbor seals have declined by up to 11.5%/year from 1992 to 2009. We used satellite-linked transmitters that were attached to 37 female harbor seals to quantify the post-breeding season migrations of seals and the amount of time that seals spent inside vs. outside of the MPA of Glacier Bay. Harbor seals traveled extensively beyond the boundaries of the MPA of Glacier Bay during the post-breeding season, encompassing an area (25,325 km²) significantly larger than that used by seals during the breeding season (8,125 km²). These movements included the longest migration yet recorded for a harbor seal (3,411 km) and extended use (up to 23 days) of pelagic areas by some seals. Although the collective utilization distribution of harbor seals during the post-breeding season was quite expansive, there was a substantial degree of individual variability in the percentage of days that seals spent in the MPA. Nevertheless, harbor seals demonstrated a high degree of inter-annual site fidelity (93%) to Glacier Bay the following breeding season. Our results highlight the importance of understanding the threats that seals may interact with outside of the boundaries of the MPA of Glacier Bay for understanding population dynamics of seals in Glacier Bay

Linking marine predator diving behavior to local prey fields in contrasting habitats in a subarctic glacial fjord

Foraging theory predicts that animals will adjust their foraging behavior in order to maximize net energy intake and that trade-offs may exist that can influence their behavior. Although substantial advances have been made with respect to the foraging ecology of large marine predators, there is still a limited understanding of how predators respond to temporal and spatial variability in prey resources, primarily due to a lack of empirical studies that quantify foraging and diving behavior concurrently with characteristics of prey fields. Such information is important because changes in prey availability can influence the foraging success and ultimately fitness of marine predators. We assessed the diving behavior of juvenile female harbor seals (Phoca vitulina richardii) and prey fields near glacial ice and terrestrial haulout sites in Glacier Bay (58°40′N, −136°05′W), Alaska. Harbor seals captured at glacial ice sites dived deeper, had longer dive durations, lower percent bottom time, and generally traveled further to forage. The increased diving effort for seals from the glacial ice site corresponded to lower prey densities and prey at deeper depths at the glacial ice site. In contrast, seals captured at terrestrial sites dived shallower, had shorter dive durations, higher percent bottom time, and traveled shorter distances to access foraging areas with much higher prey densities at shallower depths. The increased diving effort for seals from glacial ice sites suggests that the lower relative availability of prey may be offset by other factors, such as the stability of the glacial ice as a resting platform and as a refuge from predation. We provide evidence of differences in prey accessibility for seals associated with glacial ice and terrestrial habitats and suggest that seals may balance trade-offs between the costs and benefits of using these habitats

Quantification and analysis of icebergs in a tidewater glacier fjord using an object-based approach

Tidewater glaciers are glaciers that terminate in, and calve icebergs into, the ocean. In addition to the influence that tidewater glaciers have on physical and chemical oceanography, floating icebergs serve as habitat for marine animals such as harbor seals (Phoca vitulina richardii). The availability and spatial distribution of glacier ice in the fjords is likely a key environmental variable that influences the abundance and distribution of selected marine mammals; however, the amount of ice and the fine-scale characteristics of ice in fjords have not been systematically quantified. Given the predicted changes in glacier habitat, there is a need for the development of methods that could be broadly applied to quantify changes in available ice habitat in tidewater glacier fjords. We present a case study to describe a novel method that uses object-based image analysis (OBIA) to classify floating glacier ice in a tidewater glacier fjord from high-resolution aerial digital imagery. Our objectives were to (i) develop workflows and rule sets to classify high spatial resolution airborne imagery of floating glacier ice; (ii) quantify the amount and fine-scale characteristics of floating glacier ice; (iii) and develop processes for automating the object-based analysis of floating glacier ice for large number of images from a representative survey day during June 2007 in Johns Hopkins Inlet (JHI), a tidewater glacier fjord in Glacier Bay National Park, southeastern Alaska. On 18 June 2007, JHI was comprised of brash ice ([Formula: see text] = 45.2%, SD = 41.5%), water ([Formula: see text] = 52.7%, SD = 42.3%), and icebergs ([Formula: see text] = 2.1%, SD = 1.4%). Average iceberg size per scene was 5.7 m2 (SD = 2.6 m2). We estimate the total area (± uncertainty) of iceberg habitat in the fjord to be 455,400 ± 123,000 m2. The method works well for classifying icebergs across scenes (classification accuracy of 75.6%); the largest classification errors occur in areas with densely-packed ice, low contrast between neighboring ice cover, or dark or sediment-covered ice, where icebergs may be misclassified as brash ice about 20% of the time. OBIA is a powerful image classification tool, and the method we present could be adapted and applied to other ice habitats, such as sea ice, to assess changes in ice characteristics and availability

Altered plasticity of the parasympathetic innervation in the recovering rat submandibular gland following extensive atrophy

Adult rat submandibular glands have a rich autonomic innervation, with parasympathetic and sympathetic nerves working in synergy rather than antagonistically. Ligation of the secretory duct rapidly causes atrophy and the loss of most acini, which are the main target cell for parasympathetic nerves. Following deligation, there is a recovery of gland structure and function, as assessed by autonomimetic stimulation. This study examines whether the parasympathetic nerves reattach to new target cells to form functional neuro-effector junctions. Under recovery anaesthesia, the submandibular duct of adult male rats was ligated via an intra-oral approach to avoid damaging the chorda-lingual nerve. Four weeks later, rats were either killed or anaesthetized and the ligation clip removed. Following a further 8 weeks, both submandibular ducts were cannulated under terminal anaesthesia. Salivary flows were then stimulated electrically (chorda-lingual nerve at 2, 5 and 10 Hz) and subsequently by methacholine (whole-body infusion at two doses). Glands were excised, weighed and divided for further in vitro studies or fixed for histological examination. Ligation of ducts caused 75% loss of gland weight, with the loss of most acinar cells. Of the remaining acini, only 50% were innervated despite unchanged choline acetyltransferase activity, suggesting few parasympathetic nerves had died. Following deligation, submandibular glands recovered half their weight and had normal morphology. Salivary flows from both glands (per unit of gland tissue) were similar when evoked by methacholine but greater from the deligated glands when evoked by nerve stimulation. This suggests that parasympathetic nerves had reattached to new target cells in the recovered glands at a greater ratio than normal, confirming reinnervation of the regenerating gland

GenomeBlast: a web tool for small genome comparison

BACKGROUND: Comparative genomics has become an essential approach for identifying homologous gene candidates and their functions, and for studying genome evolution. There are many tools available for genome comparisons. Unfortunately, most of them are not applicable for the identification of unique genes and the inference of phylogenetic relationships in a given set of genomes. RESULTS: GenomeBlast is a Web tool developed for comparative analysis of multiple small genomes. A new parameter called "coverage" was introduced and used along with sequence identity to evaluate global similarity between genes. With GenomeBlast, the following results can be obtained: (1) unique genes in each genome; (2) homologous gene candidates among compared genomes; (3) 2D plots of homologous gene candidates along the all pairwise genome comparisons; and (4) a table of gene presence/absence information and a genome phylogeny. We demonstrated the functions in GenomeBlast with an example of multiple herpesviral genome analysis and illustrated how GenomeBlast is useful for small genome comparison. CONCLUSION: We developed a Web tool for comparative analysis of small genomes, which allows the user not only to identify unique genes and homologous gene candidates among multiple genomes, but also to view their graphical distributions on genomes, and to reconstruct genome phylogeny. GenomeBlast runs on a Linux server with 4 CPUs and 4 GB memory. The online version of GenomeBlast is available to public by using a Web browser with the URL

Ancient, independent evolution and distinct molecular features of the novel human T-lymphotropic virus type 4

<p>Abstract</p> <p>Background</p> <p>Human T-lymphotropic virus type 4 (HTLV-4) is a new deltaretrovirus recently identified in a primate hunter in Cameroon. Limited sequence analysis previously showed that HTLV-4 may be distinct from HTLV-1, HTLV-2, and HTLV-3, and their simian counterparts, STLV-1, STLV-2, and STLV-3, respectively. Analysis of full-length genomes can provide basic information on the evolutionary history and replication and pathogenic potential of new viruses.</p> <p>Results</p> <p>We report here the first complete HTLV-4 sequence obtained by PCR-based genome walking using uncultured peripheral blood lymphocyte DNA from an HTLV-4-infected person. The HTLV-4(1863LE) genome is 8791-bp long and is equidistant from HTLV-1, HTLV-2, and HTLV-3 sharing only 62–71% nucleotide identity. HTLV-4 has a prototypic genomic structure with all enzymatic, regulatory, and structural proteins preserved. Like STLV-2, STLV-3, and HTLV-3, HTLV-4 is missing a third 21-bp transcription element found in the long terminal repeats of HTLV-1 and HTLV-2 but instead contains unique c-Myb and pre B-cell leukemic transcription factor binding sites. Like HTLV-2, the PDZ motif important for cellular signal transduction and transformation in HTLV-1 and HTLV-3 is missing in the C-terminus of the HTLV-4 Tax protein. A basic leucine zipper (b-ZIP) region located in the antisense strand of HTLV-1 and believed to play a role in viral replication and oncogenesis, was also found in the complementary strand of HTLV-4. Detailed phylogenetic analysis shows that HTLV-4 is clearly a monophyletic viral group. Dating using a relaxed molecular clock inferred that the most recent common ancestor of HTLV-4 and HTLV-2/STLV-2 occurred 49,800 to 378,000 years ago making this the oldest known PTLV lineage. Interestingly, this period coincides with the emergence of <it>Homo sapiens sapiens </it>during the Middle Pleistocene suggesting that early humans may have been susceptible hosts for the ancestral HTLV-4.</p> <p>Conclusion</p> <p>The inferred ancient origin of HTLV-4 coinciding with the appearance of <it>Homo sapiens</it>, the propensity of STLVs to cross-species into humans, the fact that HTLV-1 and -2 spread globally following migrations of ancient populations, all suggest that HTLV-4 may be prevalent. Expanded surveillance and clinical studies are needed to better define the epidemiology and public health importance of HTLV-4 infection.</p

Cosmological Parameters from the CERES Project

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Cosmological Parameters from the CERES Project

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Curation of viral genomes: challenges, applications and the way forward

BACKGROUND: Whole genome sequence data is a step towards generating the 'parts list' of life to understand the underlying principles of Biocomplexity. Genome sequencing initiatives of human and model organisms are targeted efforts towards understanding principles of evolution with an application envisaged to improve human health. These efforts culminated in the development of dedicated resources. Whereas a large number of viral genomes have been sequenced by groups or individuals with an interest to study antigenic variation amongst strains and species. These independent efforts enabled viruses to attain the status of 'best-represented taxa' with the highest number of genomes. However, due to lack of concerted efforts, viral genomic sequences merely remained as entries in the public repositories until recently. RESULTS: VirGen is a curated resource of viral genomes and their analyses. Since its first release, it has grown both in terms of coverage of viral families and development of new modules for annotation and analysis. The current release (2.0) includes data for twenty-five families with broad host range as against eight in the first release. The taxonomic description of viruses in VirGen is in accordance with the ICTV nomenclature. A well-characterised strain is identified as a 'representative entry' for every viral species. This non-redundant dataset is used for subsequent annotation and analyses using sequenced-based Bioinformatics approaches. VirGen archives precomputed data on genome and proteome comparisons. A new data module that provides structures of viral proteins available in PDB has been incorporated recently. One of the unique features of VirGen is predicted conformational and sequential epitopes of known antigenic proteins using in-house developed algorithms, a step towards reverse vaccinology. CONCLUSION: Structured organization of genomic data facilitates use of data mining tools, which provides opportunities for knowledge discovery. One of the approaches to achieve this goal is to carry out functional annotations using comparative genomics. VirGen, a comprehensive viral genome resource that serves as an annotation and analysis pipeline has been developed for the curation of public domain viral genome data . Various steps in the curation and annotation of the genomic data and applications of the value-added derived data are substantiated with case studies