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Full-Text Articles in Life Sciences

Mrub_3019 Casa Gene Is An Ortholog To E. Coli B2760, Kelsey Heiland, Dr. Lori Scott Feb 2019

Mrub_3019 Casa Gene Is An Ortholog To E. Coli B2760, Kelsey Heiland, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This research is part of the Meiothermus ruber genome annotation project which aims to predict gene function with various bioinformatics tools. We investigated the function of Mrub_3019, which encodes the CasA protein involved in the multi-subunit effector complex for the CRISPR-Cas immunity system and predicted it to be an ortholog of E. coli K12 MG1655 b2760 (casA). We predicted that Mrub_3019 encodes the protein CasA, which is involved in PAM recognition of CRISPR interference pathway. Foreign DNA will bind to CasA, which signals Cas3 for helicase-mediated DNA degradation. Our hypothesis is supported by low E-values for pairwise alignment in NCBI ...


Conservation And Divergence In Modules Of The Transcriptional Programs Of The Human And Mouse Immune Systems, Tal Shay, Vladimir Jojic, Broad Institute Of Mit And Harvard, Harvard Medical School, Stanford University, Immgen Consortium, Kavitha Narayan, Katelyn E. Sylvia, Joonso Kang May 2018

Conservation And Divergence In Modules Of The Transcriptional Programs Of The Human And Mouse Immune Systems, Tal Shay, Vladimir Jojic, Broad Institute Of Mit And Harvard, Harvard Medical School, Stanford University, Immgen Consortium, Kavitha Narayan, Katelyn E. Sylvia, Joonso Kang

University of Massachusetts Medical School Faculty Publications

Studies in mouse have shed important light on human hematopoietic differentiation and disease. However, substantial differences between the two species often limit the translation of findings from mouse to human. Here, we compare modules of co-expressed genes in human and mouse immune cells based on compendia of genome-wide profiles. We show that the overall modular organization of the transcriptional program is conserved. We highlight modules of co-expressed genes in one species that dissolve or split in the other species. Many of the associated regulatory mechanisms - as reflected by computationally inferred trans regulators, or enriched cis-regulatory elements - are conserved between the ...


Evolution Of Bordetella Pertussis Genome May Play A Role In The Increased Rate Of Whooping Cough Cases In The United States, Kevin Loftus May 2018

Evolution Of Bordetella Pertussis Genome May Play A Role In The Increased Rate Of Whooping Cough Cases In The United States, Kevin Loftus

Senior Honors Projects, 2010-current

Bordetella pertussis is the bacterium responsible for pertussis, a disease commonly referred to as whooping cough. Recently, pertussis has made a resurgence in the U.S. despite high-vaccination coverage. Possible causes of the increased number of pertussis cases include genetic evolution of B. pertussis, increased awareness of the disease, better laboratory diagnostics, and the switch from a whole-cellular (wP) vaccine to an acellular vaccine (aP) in the 1990s. Fortunately, just as B. pertussis is evolving, so is the arsenal of technologies used to understand and combat this pathogenic bacterium. Whole genome sequencing is one technology that helps researchers better understand ...


Cattle Infection Response Network And Its Functional Modules, Hamid Beiki, Abbas Pakdel, Ardeshir Nejati Javaremi, Ali Masoudi-Nejad, James M. Reecy Jan 2018

Cattle Infection Response Network And Its Functional Modules, Hamid Beiki, Abbas Pakdel, Ardeshir Nejati Javaremi, Ali Masoudi-Nejad, James M. Reecy

Animal Science Publications

Background: Weighted Gene Co-expression Network analysis, a powerful technique used to extract co-expressed gene pattern from mRNA expression data, was constructed to infer common immune strategies used by cattle in response to five different bacterial species (Escherichia coli, Mycobacterium avium, Mycobacterium bovis, Salmonella and Staphylococcus aureus) and a protozoa (Trypanosoma Congolense) using 604 publicly available gene expression microarrays from 12 cattle infection experiments.

Results: A total of 14,999 transcripts that were differentially expressed (DE) in at least three different infection experiments were consolidated into 15 modules that contained between 43 and 4441 transcripts. The high number of shared DE ...


Vaccination With Recombinant Cryptococcus Proteins In Glucan Particles Protects Mice Against Cryptococcosis In A Manner Dependent Upon Mouse Strain And Cryptococcal Species, Charles A. Specht, Chrono K. Lee, Haibin Huang, Maureen M. Hester, Jianhua Liu, Bridget A. Luckie, Melanie A. Torres Santana, Zeynep Mirza, Payam Khoshkenar, Ambily Abraham, Zu T. Shen, Ali Akalin, Gary R. Ostroff, Stuart M. Levitz Nov 2017

Vaccination With Recombinant Cryptococcus Proteins In Glucan Particles Protects Mice Against Cryptococcosis In A Manner Dependent Upon Mouse Strain And Cryptococcal Species, Charles A. Specht, Chrono K. Lee, Haibin Huang, Maureen M. Hester, Jianhua Liu, Bridget A. Luckie, Melanie A. Torres Santana, Zeynep Mirza, Payam Khoshkenar, Ambily Abraham, Zu T. Shen, Ali Akalin, Gary R. Ostroff, Stuart M. Levitz

Open Access Articles

Development of a vaccine to protect against cryptococcosis is a priority given the enormous global burden of disease in at-risk individuals. Using glucan particles (GPs) as a delivery system, we previously demonstrated that mice vaccinated with crude Cryptococcus-derived alkaline extracts were protected against lethal challenge with Cryptococcus neoformans and Cryptococcus gattii The goal of the present study was to identify protective protein antigens that could be used in a subunit vaccine. Using biased and unbiased approaches, six candidate antigens (Cda1, Cda2, Cda3, Fpd1, MP88, and Sod1) were selected, recombinantly expressed in Escherichia coli, purified, and loaded into GPs. Three mouse ...


Development Of An In Silico Kir Genotyping Algorithm And Its Application To Population And Cancer Immunogenetic Analyses, Howard Rosoff Aug 2016

Development Of An In Silico Kir Genotyping Algorithm And Its Application To Population And Cancer Immunogenetic Analyses, Howard Rosoff

UT GSBS Dissertations and Theses (Open Access)

Gene content determination and variant calling in the complex KIR genomic region are useful for immune system function analysis, pathogenesis and disease risk factor elucidation, immunotherapy development, evolutionary investigations, and human migration modeling. Sequence-specific oligonucleotide and sequence-specific primer PCR methods are the de facto standards for KIR presence/absence identification, but the current platforms are unsuitable for SNP calling, impractical for KIR typing large cohorts of DNA samples, and inapplicable for typing repositories in which sequence data, but not cells or cell analytes, are available. Alternative typing methods, such as in silico sequence-based typing, can address the problems associated with ...


Integrating Phage Therapy Into Western Medicine, Jacob B. Jaminet Jan 2014

Integrating Phage Therapy Into Western Medicine, Jacob B. Jaminet

Undergraduate Research Posters

The World Health Organization has described the rise of antibiotic use as a “global heath security emergency” (who.int). With the growing concern about antibiotic resistant bacteria, there has been an increased interest in bacteriophages. Bacteriophages are high-specific viruses that only infect bacteria. The use of bacteriophages medicinally to treat bacteria is called phage therapy. Research in phage therapy gained momentum until the introduction of antibiotics. While the USA and other Western countries accepted antibiotics, the Soviet Union and their satellite nations still continued to research phages. Since the funding for research was supplied by the Soviet military, the results ...


A Cluster-Based Approach For Biological Hypothesis Testing And Its Application, Ahmed Mustafa Jun 2012

A Cluster-Based Approach For Biological Hypothesis Testing And Its Application, Ahmed Mustafa

Ahmed Mustafa Dr.

No abstract provided.