The Yeast Resource Center Public Data Repository

The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). The experimental data include large amounts of mass spectrometry results from protein co-purification experiments, yeast two-hybrid interaction experiments, fluorescence microscopy images and protein structure predictions. All of the data are accessible via searching by gene or protein name, and are available on the Web at http://www.yeastrc.org/pdr/

Biological and Biochemical Interactions Between Unicorn-Plant (Proboscidea Louisianica) and Cotton (Gossypium Hirsutum)

Crop Scienc

The Bible Story Producer App

The Bible Story Producer team at Cedarville University has been spending the past year on the Bible Story Producer app for Android. This app is a tool whose purpose is to facilitate the translation of Bible stories by bilingual laypersons in places where the Bible is unavailable in the vernacular. The aim of the app is to facilitate the oral translation of Bible stories transmitted as templates consisting of voice narration in a Language of Wider Communication (LWC). The narration is accompanied by a series of high-quality illustrations animated by the Ken Burns (pan and zoom) effect. An instance of oral translation may not involve writing down the translated words since some languages do not yet have an alphabet. Field testing has, so far, shown the controversial notion of oral translation to be effective. In our presentation, we will discuss the translation process that our client introduced to us as well as different implementation decisions that went into the making of the app

Superfamily Assignments for the Yeast Proteome through Integration of Structure Prediction with the Gene Ontology

Saccharomyces cerevisiae is one of the best-studied model organisms, yet the three-dimensional structure and molecular function of many yeast proteins remain unknown. Yeast proteins were parsed into 14,934 domains, and those lacking sequence similarity to proteins of known structure were folded using the Rosetta de novo structure prediction method on the World Community Grid. This structural data was integrated with process, component, and function annotations from the Saccharomyces Genome Database to assign yeast protein domains to SCOP superfamilies using a simple Bayesian approach. We have predicted the structure of 3,338 putative domains and assigned SCOP superfamily annotations to 581 of them. We have also assigned structural annotations to 7,094 predicted domains based on fold recognition and homology modeling methods. The domain predictions and structural information are available in an online database at http://rd.plos.org/10.1371_journal.pbio.0050076_01

The Yeast Resource Center Public Image Repository: A large database of fluorescence microscopy images

<p>Abstract</p> <p>Background</p> <p>There is increasing interest in the development of computational methods to analyze fluorescent microscopy images and enable automated large-scale analysis of the subcellular localization of proteins. Determining the subcellular localization is an integral part of identifying a protein's function, and the application of bioinformatics to this problem provides a valuable tool for the annotation of proteomes. Training and validating algorithms used in image analysis research typically rely on large sets of image data, and would benefit from a large, well-annotated and highly-available database of images and associated metadata.</p> <p>Description</p> <p>The Yeast Resource Center Public Image Repository (YRC PIR) is a large database of images depicting the subcellular localization and colocalization of proteins. Designed especially for computational biologists who need large numbers of images, the YRC PIR contains 532,182 TIFF images from nearly 85,000 separate experiments and their associated experimental data. All images and associated data are searchable, and the results browsable, through an intuitive web interface. Search results, experiments, individual images or the entire dataset may be downloaded as standards-compliant OME-TIFF data.</p> <p>Conclusions</p> <p>The YRC PIR is a powerful resource for researchers to find, view, and download many images and associated metadata depicting the subcellular localization and colocalization of proteins, or classes of proteins, in a standards-compliant format. The YRC PIR is freely available at <url>http://images.yeastrc.org/</url>.</p

Growth Phase Proteomics of the Heterotrophic Marine Bacterium \u3ci\u3eRuegeria pomeroyi\u3c/i\u3e

The heterotrophic marine bacterium, Ruegeria pomeroyi, was experimentally cultured under environmentally realistic carbon conditions and with a tracer-level addition of 13C-labeled leucine to track bacterial protein biosynthesis through growth phases. A combination of methods allowed observation of real-time bacterial protein production to understand metabolic priorities through the different growth phases. Over 2000 proteins were identified in each experimental culture from exponential and stationary growth phases. Within two hours of the 13C-labeled leucine addition, R. pomeroyi significantly assimilated the newly encountered substrate into new proteins. This dataset provides a fundamental baseline for understanding growth phase differences in molecular physiology of a cosmopolitan marine bacterium

MetaGOmics: A Web-Based Tool for Peptide-Centric Functional and Taxonomic Analysis of Metaproteomics Data

Metaproteomics is the characterization of all proteins being expressed by a community of organisms in a complex biological sample at a single point in time. Applications of metaproteomics range from the comparative analysis of environmental samples (such as ocean water and soil) to microbiome data from multicellular organisms (such as the human gut). Metaproteomics research is often focused on the quantitative functional makeup of the metaproteome and which organisms are making those proteins. That is: What are the functions of the currently expressed proteins? How much of the metaproteome is associated with those functions? And, which microorganisms are expressing the proteins that perform those functions? However, traditional protein-centric functional analysis is greatly complicated by the large size, redundancy, and lack of biological annotations for the protein sequences in the database used to search the data. To help address these issues, we have developed an algorithm and web application (dubbed MetaGOmics ) that automates the quantitative functional (using Gene Ontology) and taxonomic analysis of metaproteomics data and subsequent visualization of the results. MetaGOmics is designed to overcome the shortcomings of traditional proteomics analysis when used with metaproteomics data. It is easy to use, requires minimal input, and fully automates most steps of the analysis-including comparing the functional makeup between samples

Metaproteomics Reveal That Rapid Perturbations in Organic Matter Prioritize Functional Restructuring Over Taxonomy In Western Arctic Ocean Microbiomes

We examined metaproteome profiles from two Arctic microbiomes during 10-day shipboard incubations to directly track early functional and taxonomic responses to a simulated algal bloom and an oligotrophic control. Using a novel peptide-based enrichment analysis, significant changes (p-value \u3c 0.01) in biological and molecular functions associated with carbon and nitrogen recycling were observed. Within the first day under both organic matter conditions, Bering Strait surface microbiomes increased protein synthesis, carbohydrate degradation, and cellular redox processes while decreasing C1 metabolism. Taxonomic assignments revealed that the core microbiome collectively responded to algal substrates by assimilating carbon before select taxa utilize and metabolize nitrogen intracellularly. Incubations of Chukchi Sea bottom water microbiomes showed similar, but delayed functional responses to identical treatments. Although 24 functional terms were shared between experimental treatments, the timing, and degree of the remaining responses were highly variable, showing that organic matter perturbation directs community functionality prior to alterations to the taxonomic distribution at the microbiome class level. The dynamic responses of these two oceanic microbial communities have important implications for timing and magnitude of responses to organic perturbations within the Arctic Ocean and how community-level functions may forecast biogeochemical gradients in oceans

Effect of proton irradiation followed by hindlimb unloading on bone in mature mice: A model of long-duration spaceflight

Bone loss associated with microgravity unloading is well documented; however, the effects of spaceflight-relevant types and doses of radiation on the skeletal system are not well defined. In addition, the combined effect of unloading and radiation has not received much attention. In the present study, we investigated the effect of proton irradiation followed by mechanical unloading via hindlimb suspension (HLS) in mice. Sixteen-week-old female C57BL/6 mice were either exposed to 1 Gy of protons or a sham irradiation procedure (n=30/group). One day later, half of the mice in each group were subjected to four weeks of HLS or normal loading conditions. Radiation treatment alone (IRR) resulted in approximately 20% loss of trabecular bone volume fraction (BV/TV) in the tibia and femur, with no effect in the cortical bone compartment. Conversely, unloading induced substantially greater loss of both trabecular bone (60–70% loss of BV/TV) and cortical bone (approximately 20% loss of cortical bone volume) in both the tibia and femur, with corresponding decreases in cortical bone strength. Histological analyses and serum chemistry data demonstrated increased levels of osteoclast-mediated bone resorption in unloaded mice, but not IRR. HLS+IRR mice generally experienced greater loss of trabecular bone volume fraction, connectivity density, and trabecular number than either unloading or irradiation alone. Although the duration of unloading may have masked certain effects, the skeletal response to irradiation and unloading appears to be additive for certain parameters. Appropriate modeling of the environmental challenges of long duration spaceflight will allow for a better understanding of the underlying mechanisms mediating spaceflight-associated bone loss and for the development of effective countermeasures