Draft Genome Sequence of Bacillus velezensis CE2, Which Genetically Encodes a Novel Multicomponent Lantibiotic.

Bacillus velezensis CE2 produces potent antimicrobial compound(s). The draft genome sequence of the strain reported here is 4.1 Mb with a G+C content of 46.1%. Whole-genome sequencing revealed that the strain genetically encodes a novel multicomponent lantibiotic, velezensicidin

American Education Through Films and Documentaries

A social foundation of educatio

Occupational Responses of Older Adults Following Partner Loss

Spousal loss has been frequently identified as a life stressor that can greatly impede one’s ability to age at home. The purpose of this study is to identify the occupational changes that commonly result after this event and their impacts on one’s ability to age in place. This study utilized a qualitative phenomenological research design. Eight participants were recruited from an educational program for older adults and were interviewed using a semi-structured interview format. Researchers transcribed and coded all interviews to determine emergent themes. Two major categories of themes were found: occupational and intrinsic responses. The areas of occupation that were most commonly identified include: social participation, caregiving, activities of daily living, financial and household management, meal preparation, and leisure. Intrinsic responses were identified as autonomy, intrapersonal transition, and filling in time. Occupational and intrinsic responses occur transactionally and influence each other. Older adults may need to effectively address changes to both of these categories to facilitate successful aging in place after partner loss.https://scholar.dominican.edu/ug-student-posters/1085/thumbnail.jp

Review of Recent Legacy Airline Mergers in the U.S.: An Empirical Study from Investors’ Perspectives

Since the 2008 financial crisis, three legacy airline mergers have dramatically reshaped the landscape of the U.S. airline industry. Due to the lengthy process involved in an airline merger, it is important to understand whether the investors view the merger favorably. This study examined how investors reacted to the three recent legacy airline mergers in the U.S. by adopting a GARCH-EVT-Copula approach. Our empirical results revealed that positive dependencies between returns and trading volume changes were observed for each merger during various periods, indicating that investors were optimistic about the mergers. Accordingly, implications for future mergers are discussed

Roles of Candida albicans Mig1 and Mig2 in glucose repression, pathogenicity traits, and SNF1 essentiality.

Metabolic adaptation is linked to the ability of the opportunistic pathogen Candida albicans to colonize and cause infection in diverse host tissues. One way that C. albicans controls its metabolism is through the glucose repression pathway, where expression of alternative carbon source utilization genes is repressed in the presence of its preferred carbon source, glucose. Here we carry out genetic and gene expression studies that identify transcription factors Mig1 and Mig2 as mediators of glucose repression in C. albicans. The well-studied Mig1/2 orthologs ScMig1/2 mediate glucose repression in the yeast Saccharomyces cerevisiae; our data argue that C. albicans Mig1/2 function similarly as repressors of alternative carbon source utilization genes. However, Mig1/2 functions have several distinctive features in C. albicans. First, Mig1 and Mig2 have more co-equal roles in gene regulation than their S. cerevisiae orthologs. Second, Mig1 is regulated at the level of protein accumulation, more akin to ScMig2 than ScMig1. Third, Mig1 and Mig2 are together required for a unique aspect of C. albicans biology, the expression of several pathogenicity traits. Such Mig1/2-dependent traits include the abilities to form hyphae and biofilm, tolerance of cell wall inhibitors, and ability to damage macrophage-like cells and human endothelial cells. Finally, Mig1 is required for a puzzling feature of C. albicans biology that is not shared with S. cerevisiae: the essentiality of the Snf1 protein kinase, a central eukaryotic carbon metabolism regulator. Our results integrate Mig1 and Mig2 into the C. albicans glucose repression pathway and illuminate connections among carbon control, pathogenicity, and Snf1 essentiality

SteinerNet: a web server for integrating ‘omic’ data to discover hidden components of response pathways

High-throughput technologies including transcriptional profiling, proteomics and reverse genetics screens provide detailed molecular descriptions of cellular responses to perturbations. However, it is difficult to integrate these diverse data to reconstruct biologically meaningful signaling networks. Previously, we have established a framework for integrating transcriptional, proteomic and interactome data by searching for the solution to the prize-collecting Steiner tree problem. Here, we present a web server, SteinerNet, to make this method available in a user-friendly format for a broad range of users with data from any species. At a minimum, a user only needs to provide a set of experimentally detected proteins and/or genes and the server will search for connections among these data from the provided interactomes for yeast, human, mouse, Drosophila melanogaster and Caenorhabditis elegans. More advanced users can upload their own interactome data as well. The server provides interactive visualization of the resulting optimal network and downloadable files detailing the analysis and results. We believe that SteinerNet will be useful for researchers who would like to integrate their high-throughput data for a specific condition or cellular response and to find biologically meaningful pathways. SteinerNet is accessible at http://fraenkel.mit.edu/steinernet.National Institutes of Health (U.S.) (U54-CA112967)National Institutes of Health (U.S.) (R01-GM089903)National Science Foundation (Award Number DB1-0821391)National Institutes of Health (U.S.) (U54-CA112967

Are algal genes in nonphotosynthetic protists evidence of historical plastid endosymbioses?

<p>Abstract</p> <p>Background</p> <p>How photosynthetic organelles, or plastids, were acquired by diverse eukaryotes is among the most hotly debated topics in broad scale eukaryotic evolution. The history of plastid endosymbioses commonly is interpreted under the "chromalveolate" hypothesis, which requires numerous plastid losses from certain heterotrophic groups that now are entirely aplastidic. In this context, discoveries of putatively algal genes in plastid-lacking protists have been cited as evidence of gene transfer from a photosynthetic endosymbiont that subsequently was lost completely. Here we examine this evidence, as it pertains to the chromalveolate hypothesis, through genome-level statistical analyses of similarity scores from queries with two diatoms, <it>Phaeodactylum tricornutum </it>and <it>Thalassiosira pseudonana</it>, and two aplastidic sister taxa, <it>Phytophthora ramorum </it>and <it>P. sojae</it>.</p> <p>Results</p> <p>Contingency tests of specific predictions of the chromalveolate model find no evidence for an unusual red algal contribution to <it>Phytophthora </it>genomes, nor that putative cyanobacterial sequences that are present entered these genomes through a red algal endosymbiosis. Examination of genes unrelated to plastid function provide extraordinarily significant support for both of these predictions in diatoms, the control group where a red endosymbiosis is known to have occurred, but none of that support is present in genes specifically conserved between diatoms and oomycetes. In addition, we uncovered a strong association between overall sequence similarities among taxa and relative sizes of genomic data sets in numbers of genes.</p> <p>Conclusion</p> <p>Signal from "algal" genes in oomycete genomes is inconsistent with the chromalveolate hypothesis, and better explained by alternative models of sequence and genome evolution. Combined with the numerous sources of intragenomic phylogenetic conflict characterized previously, our results underscore the potential to be mislead by <it>a posteriori </it>interpretations of variable phylogenetic signals contained in complex genome-level data. They argue strongly for explicit testing of the different <it>a priori </it>assumptions inherent in competing evolutionary hypotheses.</p

A constraint optimization framework for discovery of cellular signaling and regulatory networks

Thesis (Ph. D.)--Massachusetts Institute of Technology, Computational and Systems Biology Program, 2011.Cataloged from PDF version of thesis.Includes bibliographical references.Cellular signaling and regulatory networks underlie fundamental biological processes such as growth, differentiation, and response to the environment. Although there are now various high-throughput methods for studying these processes, knowledge of them remains fragmentary. Typically, the majority of hits identified by transcriptional, proteomic, and genetic assays lie outside of the expected pathways. In addition, not all components in the regulatory networks can be exposed in one experiment because of systematic biases in the assays. These unexpected and hidden components of the cellular response are often the most interesting, because they can provide new insights into biological processes and potentially reveal new therapeutic approaches. However, they are also the most difficult to interpret. We present a technique, based on the Steiner tree problem, that uses a probabilistic protein-protein interaction network and high confidence measurement and prediction of protein-DNA interactions, to determine how these hits are organized into functionally coherent pathways, revealing many components of the cellular response that are not readily apparent in the original data. We report the results of applying this method to (1) phosphoproteomic and transcriptional data from the pheromone response in yeast, and (2) phosphoproteomic, DNaseI hypersensitivity sequencing and mRNA profiling data from the U87MG glioblastoma cell lines over-expressing the variant III mutant of the epidermal growth factor receptor (EGFRvIII). In both cases the method identifies changes in diverse cellular processes that extend far beyond the expected pathways. Analysis of the EGFRVIII network connectivity property and transcriptional regulators that link observed changes in protein phosphorylation and differential expression suggest a few intriguing hypotheses that may lead to improved therapeutic strategy for glioblastoma.by Shao-shan Carol Huang.Ph.D

A constitutive model for unsaturated cemented soils under cyclic loading

On the basis of plastic bounding surface model, the damage theory for structured soils and unsaturated soil mechanics, an elastoplastic model for unsaturated loessic soils under cyclic loading has been elaborated. Firstly, the description of bond degradation in a damage framework is given, linking the damage of soil's structure to the accumulated strain. The Barcelona Basic Model (BBM) was considered for the suction effects. The elastoplastic model is then integrated into a bounding surface plasticity framework in order to model strain accumulation along cyclic loading, even under small stress levels. The validation of the proposed model is conducted by comparing its predictions with the experimental results from multi-level cyclic triaxial tests performed on a natural loess sampled beside the Northern French railway for high speed train and about 140 km far from Paris. The comparisons show the capabilities of the model to describe the behaviour of unsaturated cemented soils under cyclic loading