PSAT: A web tool to compare genomic neighborhoods of multiple prokaryotic genomes

<p>Abstract</p> <p>Background</p> <p>The conservation of gene order among prokaryotic genomes can provide valuable insight into gene function, protein interactions, or events by which genomes have evolved. Although some tools are available for visualizing and comparing the order of genes between genomes of study, few support an efficient and organized analysis between large numbers of genomes. The Prokaryotic Sequence homology Analysis Tool (PSAT) is a web tool for comparing gene neighborhoods among multiple prokaryotic genomes.</p> <p>Results</p> <p>PSAT utilizes a database that is preloaded with gene annotation, BLAST hit results, and gene-clustering scores designed to help identify regions of conserved gene order. Researchers use the PSAT web interface to find a gene of interest in a reference genome and efficiently retrieve the sequence homologs found in other bacterial genomes. The tool generates a graphic of the genomic neighborhood surrounding the selected gene and the corresponding regions for its homologs in each comparison genome. Homologs in each region are color coded to assist users with analyzing gene order among various genomes. In contrast to common comparative analysis methods that filter sequence homolog data based on alignment score cutoffs, PSAT leverages gene context information for homologs, including those with weak alignment scores, enabling a more sensitive analysis. Features for constraining or ordering results are designed to help researchers browse results from large numbers of comparison genomes in an organized manner. PSAT has been demonstrated to be useful for helping to identify gene orthologs and potential functional gene clusters, and detecting genome modifications that may result in loss of function.</p> <p>Conclusion</p> <p>PSAT allows researchers to investigate the order of genes within local genomic neighborhoods of multiple genomes. A PSAT web server for public use is available for performing analyses on a growing set of reference genomes through any web browser with no client side software setup or installation required. Source code is freely available to researchers interested in setting up a local version of PSAT for analysis of genomes not available through the public server. Access to the public web server and instructions for obtaining source code can be found at <url>http://www.nwrce.org/psat</url>.</p

15N MAS NMR studies of Cph1 phytochrome:chromophore dynamics and intramolecular signal transduction

Solid state NMR/Biophysical Organic Chemistr

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Uluslararası Bakalorya Programı, A1 dersi Türk Dili ve Edebiyatı alanında ele alınan bu tezde, Orhan Kemal'in Gurbet Kuşları adlı yapıtında göç olgusu nedenleri ve sonuçlarıyla beraber incelenmiştir. Göç olgusuyla değişen toplumsal yapı, ekonomik ve kültürel farklılıklar çerçevesinde değerlendirilmiştir. Bu tezin amacı, göç olgusunun toplumsal yapıda alt sınıf ve üst sınıflardaki bireyler üzerindeki etkilerini ortaya koymaktır. Üç ana bölümden oluşan tezin ilk bölümünde yapıta adını veren Gurbet Kuşları kavramı üzerinde durulmuştur. Köylülerin aidiyetsizliği ve uyum sorunu bu bölümde aktarılmıştır. Tezin ikinci bölümünde ise köylülerin köyden kente göç sürecinde yaşadıkları kadın ve erkek figürler üzerinden neden ve sonuçlarıyla işlenmiştir. Tezin üçüncü bölümünde şehirliler başlığı altından genel olarak şehirde – İstanbul – yaşayan insanların göç sürecinde köylülerle yaşadıkları uyumsuzluk ve çatışmalara yer verilmektedir. Çalışmada göç sürecinde şehre yerleşen figürlerin şehirlilerle aralarındaki ekonomik ve kültürel farklılıkların sınıflar arasında geçişe olanak tanımadığı sonucuna varılmıştır

Autistic people’s perspectives on stereotypes: An interpretative phenomenological analysis

Autism stereotypes can often portray autistic people in a negative way. However, few studies have looked at how autistic people think they are perceived by others, and none have specifically asked autistic people what they think the autistic stereotypes are. Semi-structured interviews with twelve autistic adults (aged between 20-63 years) were conducted. Using Interpretative Phenomenological Analysis, three main themes emerged from the data. These were: (1) primary stereotype is that autistic people are ‘weird’; (2) autistic stereotypes have negative effects and consequences; (3) autistic people are heterogeneous. This study makes an important and novel contribution to understanding the experience of being autistic in several ways by exploring how autistic people feel they are perceived by others and identifying some of the ways in which negative stereotypes are believed to have negative consequences for autistic people

A Francisella Mutant in Lipid A Carbohydrate Modification Elicits Protective Immunity

Francisella tularensis (Ft) is a highly infectious Gram-negative bacterium and the causative agent of the human disease tularemia. Ft is designated a class A select agent by the Centers for Disease Control and Prevention. Human clinical isolates of Ft produce lipid A of similar structure to Ft subspecies novicida (Fn), a pathogen of mice. We identified three enzymes required for Fn lipid A carbohydrate modifications, specifically the presence of mannose (flmF1), galactosamine (flmF2), or both carbohydrates (flmK). Mutants lacking either galactosamine (flmF2) or galactosamine/mannose (flmK) addition to their lipid A were attenuated in mice by both pulmonary and subcutaneous routes of infection. In addition, aerosolization of the mutants (flmF2 and flmK) provided protection against challenge with wild-type (WT) Fn, whereas subcutaneous administration of only the flmK mutant provided protection from challenge with WT Fn. Furthermore, infection of an alveolar macrophage cell line by the flmK mutant induced higher levels of tumor necrosis factor-α (TNF-α) and macrophage inhibitory protein-2 (MIP-2) when compared to infection with WT Fn. Bone marrow–derived macrophages (BMMø) from Toll-like receptor 4 (TLR4) and TLR2/4 knockout mice infected with the flmK mutant also produced significantly higher amounts of interleukin-6 (IL-6) and MIP-2 than BMMø infected with WT Fn. However, production of IL-6 and MIP-2 was undetectable in BMMø from MyD88−/− mice infected with either strain. MyD88−/− mice were also susceptible to flmK mutant infection. We hypothesize that the ability of the flmK mutant to activate pro-inflammatory cytokine/chemokine production and innate immune responses mediated by the MyD88 signaling pathway may be responsible for its attenuation, leading to the induction of protective immunity by this mutant

Uncertainties in shoreline projections to 2100 at Truc Vert Beach (France): Role of sea‐level rise and equilibrium model assumptions

Sandy shorelines morphodynamics responds to a myriad of processes interacting at different spatial and temporal scales, making shoreline predictions challenging. Shoreline modeling inherits uncertainties from the primary driver boundary conditions (e.g., sea-level rise and wave forcing) as well as uncertainties related to model assumptions and/or misspecifications of the physics. This study presents an analysis of the uncertainties associated with future shoreline evolution at the cross-shore transport dominated sandy beach of Truc Vert (France) over the 21st century. We explicitly resolve wave-driven shoreline change using two different equilibrium modeling approaches to provide new insight into the contributions of sea-level rise, and free model parameters uncertainties on future shoreline change in the frame of climate change. Based on a Global Sensitivity Analysis, shoreline response during the first half of the century is found to be mainly sensitive to the equilibrium model parameters, with the influence of sea-level rise emerging in the second half of the century (∼2050 or later), under several simulated scenarios. The results reveal that the seasonal and interannual variability of the predicted shoreline position is sensitive to the choice of the wave-driven equilibrium-based model. Finally, we discuss the importance of the chronology of wave events in future shoreline change, calling for more continuous wave projection time series to further address uncertainties in future wave conditions. Our contribution demonstrates that unmitigated climate change can result in shoreline retreat of several tens of meters by 2100, even for sectors that have been stable or slightly accreting over the last century

A case of non-Hodgkin's lymphoma associated with hypercalcemia.

A patient with a diffuse, small cleaved cell, non-Hodgkin's lymphoma associated with marked hypecalcemia was described. Antibody to the adult T-cell leukemia-lymphoma virus was absent. Although bone marrow was infiltrated by lymphoma cells, destructive or lytic bone lesions could not be detected. The serum level of immunoreactive parathyroid hormone C-terminal (PTH-C) was normal. The serum level of 1, 25-dihydroxyvitamin D was lower than normal. This case suggests that other humoral substances produced by lymphoma cells may be responsible for hypercalcemia.&#60;/P&#62;</p

Non-smooth developable geometry for interactively animating paper crumpling

International audienceWe present the first method to animate sheets of paper at interactive rates, while automatically generating a plausible set of sharp features when the sheet is crumpled. The key idea is to interleave standard physically-based simulation steps with procedural generation of a piecewise continuous developable surface. The resulting hybrid surface model captures new singular points dynamically appearing during the crumpling process, mimicking the effect of paper fiber fracture. Although the model evolves over time to take these irreversible damages into account, the mesh used for simulation is kept coarse throughout the animation, leading to efficient computations. Meanwhile, the geometric layer ensures that the surface stays almost isometric to its original 2D pattern. We validate our model through measurements and visual comparison with real paper manipulation, and show results on a variety of crumpled paper configurations