P02. Production Of A Protein Subunit Vaccine For Mannheimia Haemolytica In Lettuce Chloroplasts, 2017 Western University
P02. Production Of A Protein Subunit Vaccine For Mannheimia Haemolytica In Lettuce Chloroplasts, Coby K. Martin
Western Research Forum
The cattle industry worldwide is ravaged by bovine respiratory disease (BRD), a bacterial disease caused by Mannheimia haemolytica. We have designed a chimeric protein subunit vaccine against M. haemolytica based on recent evidence demonstrating the protective potential of antigens against a virulence factor, leukotoxin, in addition to a surface lipoprotein. Plant-based production of this protein vaccine provides a safe and inexpensive alternative to traditional production methods. Plant-base production also supports the use of an edible vaccine that will deliver antigens to pharyngeal tissues to provide local immunization against M. haemolytica to prior to its progression into the lungs. Chloroplasts produce ...
Patterns Of Morphological And Molecular Evolution In The Antillean Tree Bat, Ardops Nichollsi (Chiroptera: Phyllostomidae), Roxanne J. Larsen, Peter A. Larsen, Caleb D. Phillips, Hugh H. Genoways, Gary G. Kwiecinski, Scott C. Pedersen, Carleton J. Phillips, Robert J. Baker
Mammalogy Papers: University of Nebraska State Museum
Species endemic to oceanic islands offer unique insights into the mechanisms underlying evolution and have served as model systems for decades. Often these species show phenotypic variation that is correlated with the ecosystems in which they occur and such correlations may be a product of genetic drift, natural selection, and/or environmental factors. We explore the morphologic and genetic variation within Ardops nichollsi, a species of phyllostomid bat endemic to the Lesser Antillean islands. Ardops nichollsi is an ideal taxon to investigate the tempo of evolution in Chiroptera, as it: is a recently derived genus in the family Phyllostomidae; contains ...
Draft Genome Sequences Of Three Closely Related Isolates Of The Purple Nonsulfur Bacterium Rhodovulum Sulfidophilum, 2017 Washington University in St. Louis
Draft Genome Sequences Of Three Closely Related Isolates Of The Purple Nonsulfur Bacterium Rhodovulum Sulfidophilum, Michael S. Guzman, Beau Mcginley, Natalia Santiago-Merced, Dinesh Gupta, Arpita Bose
Biology Faculty Publications & Presentations
We report here the draft genome sequences of three isolates of Rhodovulum sulfidophilum from a single population that will serve as a model system for understanding genomic traits that underlie metabolic variation within closely related marine purple nonsulfur bacteria in natural microbial communities.
Mhc Class Iiβ Diversity As A Correlate Of Neutral-Locus Similarity And Diversity, And A Predictor Of Overwinter Return, In Song Sparrows (Melospiza Melodia), 2017 The University of Western Ontario
Mhc Class Iiβ Diversity As A Correlate Of Neutral-Locus Similarity And Diversity, And A Predictor Of Overwinter Return, In Song Sparrows (Melospiza Melodia), Matthew J. Watson
Electronic Thesis and Dissertation Repository
The major histocompatibility complex (MHC) is a family of genes involved with recognizing pathogens and mounting an immune response. Parasite-mediated selection often favours heterozygosity at MHC because MHC-diverse individuals recognize a wider range of pathogens. Because migratory birds encounter many pathogens, I hypothesized that MHC diversity predicts overwinter and juvenile survivorship in song sparrows (Melospiza melodia). I found no correlation between MHC diversity and neutral-locus (microsatellite) heterozygosity, suggesting that measures of neutral and adaptive genetic diversity provide complementary rather than redundant information. However, pairwise similarity at MHC predicted pairwise similarity at microsatellite loci. In contrast to my hypothesis, MHC ...
Transcriptional And Post-Transcriptional Regulation Of Histone Variant H2a.Z During Sea Urchin Development, 2017 The Graduate Center, City University of New York
Transcriptional And Post-Transcriptional Regulation Of Histone Variant H2a.Z During Sea Urchin Development, Mihai Hajdu
All Graduate Works by Year: Dissertations, Theses, and Capstone Projects
Histone variant H2A.Z promotes chromatin accessibility at transcriptional regulatory elements and is developmentally regulated in metazoans. We characterize the transcriptional and post-transcriptional regulation of H2A.Z in the purple sea urchin Strongylocentrotus purpuratus. H2A.Z depletion by antisense translation-blocking morpholino oligonucleotides during early development causes developmental collapse, in agreement with its previously demonstrated general role in transcriptional multipotency. During H2A.Z peak expression in 24-h embryos, endogenous H2A.Z 3’ UTR sequences stabilize GFP mRNAs relative to those with SV40 3’ UTR sequences, although the 3’UTR of H2A.Z does not determine the spatial distribution of H2A.Z ...
Regulation Of The Drosophila Initiator Caspase Dronc Through Ubiquitylation, 2017 University of Massachusetts Medical School
Regulation Of The Drosophila Initiator Caspase Dronc Through Ubiquitylation, Hatem E. Kamber Kaya
GSBS Dissertations and Theses
Apoptosis is a programmed cell death mechanism that is evolutionary conserved from worms to humans. Apoptosis is mediated by initiator and effector caspases. The initiator caspases carry long pro-domains for their interaction with scaffolding proteins to form a cell-death platform, which is essential for their activation. Activated initiator caspases then cleave effector caspases that execute cell death through cleaving downstream targets. In addition to their apoptotic function, caspases also participate in events where caspase activity is not required for cell killing, but for regulating other functions, so-called non-apoptotic functions of caspases. The Drosophila initiator caspase Dronc, the ortholog of mammalian ...
Mrub_2642, Mrub_1054, And Mrub_1059 Genes Are Orthologs Of The Escherichia Coli Genes B2942, B0159, And B2687 Genes, Respectively, Which Code For Methionine Adenosyltransferase, Adenosylhomocysteine Nucleosidase, And S-Ribosylhomocysteine Lyase, 2017 Augustana College, Rock Island Illinois
Mrub_2642, Mrub_1054, And Mrub_1059 Genes Are Orthologs Of The Escherichia Coli Genes B2942, B0159, And B2687 Genes, Respectively, Which Code For Methionine Adenosyltransferase, Adenosylhomocysteine Nucleosidase, And S-Ribosylhomocysteine Lyase, Nicholas M. Orslini, Dr. Lori R. Scott
Meiothermus ruber Genome Analysis Project
This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of the genes Mrub_2642, Mrub_1054, and Mrub_1059.
We predict that Mrub_2642 encodes the enzyme methionine adenosyltransferase (DNA coordinates [2677251…2678426] on the reverse strand), the first step of the methionine degradation pathway (KEGG map number 00270). Methionine adenosyltransferase catalyzes the conversion of the substrates, ATP, L-methionine, and water, to yield the products S-adenosyl-L-methionine (SAM), inorganic phosphate, and diphosphate. Mrub_1054 encodes adenosylhomocysteine nucleosidase (DNA ...
Histone Deacetylase 3 Coordinates Heart Development Through Stage-Specific Roles In Cardiac Progenitor Cells, 2016 University of Massachusetts Medical School
Histone Deacetylase 3 Coordinates Heart Development Through Stage-Specific Roles In Cardiac Progenitor Cells, Sara L. Lewandowski
GSBS Dissertations and Theses
Disruptions in cardiac development cause congenital heart disease, the most prevalent and deadly congenital malformation. Genetic and environmental factors are thought to contribute to these defects, however molecular mechanisms remain largely undefined. Recent work highlighted potential roles of chromatin- modifying enzymes in congenital heart disease pathogenesis. Histone deacetylases, a class of chromatin-modifying enzymes, have developmental importance and recognized roles in the mature heart. This thesis aimed to characterize functions of Hdac3 in cardiac development. We found loss of Hdac3 in the primary heart field causes precocious progenitor cell differentiation, resulting in hypoplastic ventricular walls, ventricular septal defect, and mid- gestational ...
Functional Significance Of Branch Points In Mirtrons, 2016 The University of Southern Mississippi
Functional Significance Of Branch Points In Mirtrons, Britton A. Strickland
MicroRNAs are a heterogeneous group of small regulatory RNAs generated by many pathways. Mirtrons (miR) are a class of microRNAs produced by splicing, and some mirtrons contain a 3’ tail located downstream from the self-complementary hairpin. During RNA splicing, a loop-like “lariat” intermediate structure is created when the 5’ end of the RNA is attached to an adenine called the branch point. The goal of this project is to uncover the contribution of branch point location to the processing of tailed mirtrons into functional gene regulators. This project approaches this issue from two directions. First, branch points were identified by ...
Identification And Characterization Of Genes Involved In Metabolism Of N5 Monoene Precursors To N5 Anacardic Acids In The Trichomes Of Pelargonium X Hortorum., Richa A. Singhal
Electronic Theses and Dissertations
Unusual monoenoic fatty acids (UMFA’s) and specialized metabolites called anacardic acids (AnAc) are produced in glandular trichomes of Pelargonium ´ hortorum (geranium). The UMFA’s, 16:1∆11 and 18:1∆13 are precursors for the synthesis of unsaturated AnAc 22:1n5and 24:1n5 that contribute to pest resistance in geraniums. UMFAs and their derived AnAc metabolites not only provide a useful biological marker that differentiates the biosynthetic pathway for unusual mononenes from the common fatty acids (i.e. stearic, palmitic, oleic, linoleic and linolenic) but also have industrial, medical and agricultural applications. Fatty acid biosynthesis enzymes like acyl carrier ...
American Chestnut Sem Portfolio, 2016 SUNY College of Environmental Science and Forestry
American Chestnut Sem Portfolio, Dakota Matthews
N.C. Brown Center for Ultrastructure Studies
Scanning electron microscopy micrographs of transgenic american chestnut pollen and anthers. Chinkapin anthers and pollen imaged also.
Role Of Multicellular Aggregates In Biofilm Formation, 2016 University of Copenhagen
Role Of Multicellular Aggregates In Biofilm Formation, Kasper N. Kragh, Jaime B. Hutchison, Gavin Melaugh, Chris Rodesney, Aled E. L. Roberts, Yasuhiko Irie, Peter Ø. Jensen, Stephen P. Diggle, Rosalind J. Allen, Vernita Gordon, Thomas Bjarnsholt
In traditional models of in vitro biofilm development, individual bacterial cells seed a surface, multiply, and mature into multicellular, three-dimensional structures. Much research has been devoted to elucidating the mechanisms governing the initial attachment of single cells to surfaces. However, in natural environments and during infection, bacterial cells tend to clump as multicellular aggregates, and biofilms can also slough off aggregates as a part of the dispersal process. This makes it likely that biofilms are often seeded by aggregates and single cells, yet how these aggregates impact biofilm initiation and development is not known. Here we use a combination of ...
Chip-Seq And Rna-Seq Reveal An Amrz-Mediated Mechanism For Cyclic Di-Gmp Synthesis And Biofilm Development By Pseudomonas Aeruginosa, Christopher J. Jones, David Newsom, Benjamin Kelly, Yasuhiko Irie, Laura K. Jennings, Binjie Xu, Dominique H. Limoli, Joe J. Harrison, Matthew R. Parsek, Peter White, Daniel J. Wozniak
The transcription factor AmrZ regulates genes important for P. aeruginosa virulence, including type IV pili, extracellular polysaccharides, and the flagellum; however, the global effect of AmrZ on gene expression remains unknown, and therefore, AmrZ may directly regulate many additional genes that are crucial for infection. Compared to the wild type strain, a ΔamrZ mutant exhibits a rugose colony phenotype, which is commonly observed in variants that accumulate the intracellular second messenger cyclic diguanylate (c-di-GMP). Cyclic di-GMP is produced by diguanylate cyclases (DGC) and degraded by phosphodiesterases (PDE). We hypothesized that AmrZ limits the intracellular accumulation of c-di-GMP through transcriptional repression ...
The Cababc Operon Essential For Biofilm And Rugose Colony Development In Vibrio Vulnificus, 2016 Seoul National University
The Cababc Operon Essential For Biofilm And Rugose Colony Development In Vibrio Vulnificus, Jin Hwan Park, Youmi Jo, Song Yee Jang, Haenaem Kwon, Yasuhiko Irie, Matthew R. Parsek, Myung Hee Kim, Sang Ho Choi
A transcriptome analysis identified Vibrio vulnificus cabABC genes which were preferentially expressed in biofilms. The cabABC genes were transcribed as a single operon. The cabA gene was induced by elevated 3′,5′-cyclic diguanylic acid (c-di-GMP) and encoded a calcium-binding protein CabA. Comparison of the biofilms produced by the cabA mutant and its parent strain JN111 in microtiter plates using crystal-violet staining demonstrated that CabA contributed to biofilm formation in a calcium-dependent manner under elevated c-di-GMP conditions. Genetic and biochemical analyses revealed that CabA was secreted to the cell exterior through functional CabB and CabC, distributed throughout the biofilm matrix ...
Exploring Molecular Mechanisms Of Paradoxical Activation In The Braf Kinase Dimers: Atomistic Simulations Of Conformational Dynamics And Modeling Of Allosteric Communication Networks And Signaling Pathways, 2016 Chapman University
Exploring Molecular Mechanisms Of Paradoxical Activation In The Braf Kinase Dimers: Atomistic Simulations Of Conformational Dynamics And Modeling Of Allosteric Communication Networks And Signaling Pathways, Amanda Tse, Gennady M. Verkhivker
Mathematics, Physics, and Computer Science Faculty Articles and Research
The recent studies have revealed that most BRAF inhibitors can paradoxically induce kinase activation by promoting dimerization and enzyme transactivation. Despite rapidly growing number of structural and functional studies about the BRAF dimer complexes, the molecular basis of paradoxical activation phenomenon is poorly understood and remains largely hypothetical. In this work, we have explored the relationships between inhibitor binding, protein dynamics and allosteric signaling in the BRAF dimers using a network-centric approach. Using this theoretical framework, we have combined molecular dynamics simulations with coevolutionary analysis and modeling of the residue interaction networks to determine molecular determinants of paradoxical activation. We ...
Expression Of The Primary Carbohydrate Component Of The Bordetella Bronchiseptica Biofilm Matrix Is Dependent On Growth Phase But Independent Of Bvg Regulation, Yasuhiko Irie, Andrew Preston, Ming H. Yuk
We previously showed that the Bvg virulence control system regulates biofilm formation in Bordetella bronchiseptica (Y. Irie, S. Mattoo, and M. H. Yuk, J. Bacteriol. 186:5692-5698, 2004). Analyses of the extracellular components of B. bronchiseptica biofilm matrix revealed that the major sugar component in the matrix was xylose, and linkage analysis indicated a majority of it to be in a 4-linked polymeric form. The production of xylose was independent of Bvg regulation but instead was dependent on bacterial growth phase. In addition, N-acetyl-glucosamine in the matrix was found to be important for the initial development of the biofilm ...
Fluorescence-Based Reporter For Gauging Cyclic Di-Gmp Levels In Pseudomonas Aeruginosa, 2016 University of Copenhagen
Fluorescence-Based Reporter For Gauging Cyclic Di-Gmp Levels In Pseudomonas Aeruginosa, Morten T. Rybtke, Bradley R. Borlee, Keiji Murakami, Yasuhiko Irie, Morten Hentzer, Thomas E. Nielsen, Michael Givskov, Matthew R. Parsek, Tim Tolker-Nielsen
The increased tolerance toward the host immune system and antibiotics displayed by biofilm-forming Pseudomonas aeruginosa and other bacteria in chronic infections such as cystic fibrosis bronchopneumonia is of major concern. Targeting of biofilm formation is believed to be a key aspect in the development of novel antipathogenic drugs that can augment the effect of classic antibiotics by decreasing antimicrobial tolerance. The second messenger cyclic di-GMP is a positive regulator of biofilm formation, and cyclic di-GMP signaling is now regarded as a potential target for the development of antipathogenic compounds. Here we describe the development of fluorescent monitors that can gauge ...
Sequence Annotation & Designing Gene-Specific Qpcr Primers (Computational), 2016 email@example.com
Sequence Annotation & Designing Gene-Specific Qpcr Primers (Computational), Raymond A. Enke
Ray Enke Ph.D.
- Obtaining and annotating genomic DNA and mRNA sequence information
- Designing primers for quantitative PCR (qPCR) analysis of a cDNA library
Qpcr Primer Standard Curve Assay (Wet Lab) + Kegg Pathway Analysis (Computational), 2016 firstname.lastname@example.org
Qpcr Primer Standard Curve Assay (Wet Lab) + Kegg Pathway Analysis (Computational), Raymond A. Enke
Ray Enke Ph.D.
- analyzing qPCR standard curve data to determine primer efficiency
- analyzing differential gene expression experimental qPCR data
- applying KEGG pathway analysis of selected candidates genes
A Gene-Centered C. Elegans Protein-Dna Interaction Network Provides A Framework For Functional Predictions, 2016 University of Massachusetts Medical School
A Gene-Centered C. Elegans Protein-Dna Interaction Network Provides A Framework For Functional Predictions, Juan Fuxman Bass, Carles Pons, Lucie Kozlowski, John S. Reece-Hoyes, Shaleen Shrestha, Amy D. Holdorf, Akihiro Mori, Chad L. Myers, Albertha J. M. Walhout
Open Access Articles
Transcription factors (TFs) play a central role in controlling spatiotemporal gene expression and the response to environmental cues. A comprehensive understanding of gene regulation requires integrating physical protein-DNA interactions (PDIs) with TF regulatory activity, expression patterns, and phenotypic data. Although great progress has been made in mapping PDIs using chromatin immunoprecipitation, these studies have only characterized ~10% of TFs in any metazoan species. The nematode C. elegans has been widely used to study gene regulation due to its compact genome with short regulatory sequences. Here, we delineated the largest gene-centered metazoan PDI network to date by examining interactions between 90 ...