Impact Of Metazooplankton Filter Feeding On Escherichia Coli Under Variable Environmental Conditions,
2019
Smith College
Impact Of Metazooplankton Filter Feeding On Escherichia Coli Under Variable Environmental Conditions, Niveen S. Ismail, Brittney M. Blokker, Tyler R. Feeney, Ruby H. Kohn, Jingyi Liu, Vivian E. Nelson, Mariah C. Ollive, Sarah B. L. Price, Emma J. Underdaha
Engineering: Faculty Publications
The fecal indicator bacterial species Escherichia coli is an important measure of water quality and a leading cause of impaired surface waters. We investigated the impact of the filter-feeding metazooplankton Daphnia magna on the inactivation of E. coli. The E. coli clearance rates of these daphnids were calculated from a series of batch experiments conducted under variable environmental conditions. Batch system experiments of 24 to 48 h in duration were completed to test the impacts of bacterial concentration, organism density, temperature, and water type. The maximum clearance rate for adult D. magna organisms was 2 ml h1 organism1. Less than …
Deepep: A Deep Learning Framework For Identifying Essential Proteins,
2019
Old Dominion University
Deepep: A Deep Learning Framework For Identifying Essential Proteins, Min Zeng, Min Li, Fang-Xiang Wu, Yaohang Li, Yi Pan
Computer Science Faculty Publications
Background: Essential proteins are crucial for cellular life and thus, identification of essential proteins is an important topic and a challenging problem for researchers. Recently lots of computational approaches have been proposed to handle this problem. However, traditional centrality methods cannot fully represent the topological features of biological networks. In addition, identifying essential proteins is an imbalanced learning problem; but few current shallow machine learning-based methods are designed to handle the imbalanced characteristics. Results: We develop DeepEP based on a deep learning framework that uses the node2vec technique, multi-scale convolutional neural networks and a sampling technique to identify essential proteins. …
Use Of Uav Imagery And Nutrient Analyses For Estimation Of The Spatial And Temporal Contributions Of Cattle Dung To Nutrient Cycling In Grazed Ecosystems,
2019
University of Nebraska-Lincoln
Use Of Uav Imagery And Nutrient Analyses For Estimation Of The Spatial And Temporal Contributions Of Cattle Dung To Nutrient Cycling In Grazed Ecosystems, Amanda E. Shine
Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research
Nutrient inputs from cattle dung are crucial drivers of nutrient cycling processes in grazed ecosystems. These inputs are important both spatially and temporally and are affected by variables such as grazing strategy, water location, and the nutritional profile of forage being grazed. Past research has attempted to map dung deposition patterns in order to more accurately estimate nutrient input, but the large spatial extent of a typical pasture and the tedious nature of identifying and mapping individual dung pats has prohibited the development of a time- and cost-effective methodology. The first objective of this research was to develop and validate …
Species Richness And Ecological Diversity Of Myxomycetes And Myxomycete-Like Organisms In The Tropical Forests Of Brazil,
2019
University of Arkansas, Fayetteville
Species Richness And Ecological Diversity Of Myxomycetes And Myxomycete-Like Organisms In The Tropical Forests Of Brazil, Isadora Lima Coelho
Graduate Theses and Dissertations
Tropical rain forests cover less than two percent of Earth's surface, yet they sustain the greatest diversity of living organisms on the planet. Tropical rain forests cover nearly 73% of the Brazilian territory and besides harboring some of the most biodiverse ecosystems on the planet, this vast area also houses about 83% of the Brazilian population. Approximately 175 million people live in urban and rural areas with fragments of coverage of these biomes which contributes to the loss of biodiversity that rapidly increases over the years. Furthermore, the majority of the taxonomic and ecological efforts to describe and protect the …
The Effect Of Historic Shipwrecks On Sediment Microbiomes In The Northern Gulf Of Mexico,
2019
University of Southern Mississippi
The Effect Of Historic Shipwrecks On Sediment Microbiomes In The Northern Gulf Of Mexico, Melissa Brock
Master's Theses
Microorganisms are ubiquitously distributed across all aquatic habitats, but it is the environmental conditions of a habitat that determine which microorganisms can thrive in terms of abundance or metabolic activity. Habitats that experience consistent physical and chemical environmental conditions repeatedly favor specific taxonomic groups which may result in a microbial assemblage that is commonly associated with that habitat (i.e., a core microbiome). Core microbiomes have been identified for a variety of natural marine habitats including methane seeps, wood falls, octocoral, and deep-sea sediments. However, it was unknown if the presence of man-made structures on the seafloor, including historic shipwrecks, also …
Characterization Of Plasmids Harbored By Vibrio Cholerae Isolates Endemic To The Rio Grande Delta,
2019
The University of Texas Rio Grande Valley
Characterization Of Plasmids Harbored By Vibrio Cholerae Isolates Endemic To The Rio Grande Delta, Viviana Trevino
Theses and Dissertations
Cholera is a diarrheal disease responsible for considerable morbidity and mortality globally. Epidemics along the Rio Grande Delta were reported during the 1850s, and the etiological agent Vibrio cholerae, remains endemic, thus presenting a unique opportunity for a study of historical and biological relevance. V. cholerae strains were isolated from two locations: the Rio Grande River under a bridge linking Brownsville to Matamoros (site 21) and where the river empties into the Gulf of Mexico (site 42). Two strains from site 21, and one from site 42 were selected to isolate, subclone, sequence, assemble and annotate extra-chromosomal elements. Results …
Role Of Topoisomerase Ii Alpha In Dna Topology And T Cell Responses During Chronic Viral Infections,
2019
East Tennessee State University
Role Of Topoisomerase Ii Alpha In Dna Topology And T Cell Responses During Chronic Viral Infections, Stella Chinyere Ogbu
Electronic Theses and Dissertations
The clearance of viruses is largely dependent upon the activation of T cells to generate a robust immune response. However, host responses are suppressed during chronic viral infections. In this thesis, we explored the role of Top2α in DNA topology in individuals with chronic HBV, HCV, and HIV infections. We found that Top2α protein expression and activity were low in T cells derived from chronically virus-infected individuals compared to healthy subjects. Using CD4+ T cells treated with Top2α inhibitor or poisoner as a model, we demonstrated that Top2α inhibition disrupts the DNA topology, suppresses DNA repair kinase (ATM), and …
Cyclophilin A Enhances Hiv-1 Reverse Transcription In Human Microglial Cells,
2019
Missouri State University
Cyclophilin A Enhances Hiv-1 Reverse Transcription In Human Microglial Cells, Zachary Michael Ingram
Graduate Theses/Dissertations
Parenchymal microglia represent a susceptible cell type to HIV infection and contribute to HIV Associated Neurocognitive Disorders (HAND). Currently, HIV host-protein interactions in microglia are understudied, but relevant to the design of antiviral drugs. HIV replication events rely on host and viral proteins to evade an immune response while improve replication success. Post-fusion the HIV capsid is released into the cytoplasm and begins trafficking towards the nucleus. During transit viral RNA is transcribed to DNA through reverse transcription (RT). In addition, the HIV capsid that protects the reverse transcription complex disassembles in a step termed uncoating. Once the pre-integration complex …
Ppnac187 Enhances Lignin Synthesis In ‘Whangkeumbae’ Pear (Pyrus Pyrifolia) ‘Hard-End’ Fruit,
2019
Qingdao Agricultural University
Ppnac187 Enhances Lignin Synthesis In ‘Whangkeumbae’ Pear (Pyrus Pyrifolia) ‘Hard-End’ Fruit, Mingtong Li, Chenxia Cheng, Xinfu Zhang, Suping Zhou, Caihong Wang, Chunhui Ma, Shaolan Yang
Agricultural and Environmental Sciences Faculty Research
A disorder in pears that is known as ‘hard-end’ fruit affects the appearance, edible quality, and market value of pear fruit. RNA-Seq was carried out on the calyx end of ‘Whangkeumbae’ pear fruit with and without the hard-end symptom to explore the mechanism underlying the formation of hard-end. The results indicated that the genes in the phenylpropanoid pathway affecting lignification were up-regulated in hard-end fruit. An analysis of differentially expressed genes (DEGs) identified three NAC transcription factors, and RT-qPCR analysis of PpNAC138, PpNAC186, and PpNAC187 confirmed that PpNAC187 gene expression was correlated with the hard-end disorder in pear fruit. A …
The Role Of Multidrug Resistance Regulators Mara, Soxs, Rob And Rama In Regulating Virulence Traits In Salmonella Enterica,
2019
University of Missouri-St. Louis
The Role Of Multidrug Resistance Regulators Mara, Soxs, Rob And Rama In Regulating Virulence Traits In Salmonella Enterica, Srinivas Thota
Dissertations
Enteric pathogens sense numerous signals specific to the anatomical location in the intestine and integrate them with the complex regulatory networks to temporally and spatially regulate their virulence genes. MarA, SoxS, Rob and RamA are homologous transcription factors that belong to AraC family of proteins in Salmonella enterica that primarily were thought to be involved in rendering antibiotic resistance to bacteria by up regulating efflux pumps and down regulating outer membrane porins. The fact that these transcription factors respond to the same intestinal compounds that regulate virulence genes in Salmonella motivated us to look for other roles of these transcription …
The Role Of Secreted Proteases In Regulating Disease Progression In Staphylococcus Aureus,
2019
University of South Florida
The Role Of Secreted Proteases In Regulating Disease Progression In Staphylococcus Aureus, Brittney D. Gimza
USF Tampa Graduate Theses and Dissertations
Staphylococcus aureus is a highly successful pathogen capable of producing a wealth of virulence factors in the human host. Of note, ten extracellular proteases are produced alongside these virulence factors and play a multifaceted role during infection. They not only cleave host proteins to promote bacterial invasion, immune evasion and survival, but also control disease progression by modulating the stability of self-derived pathogenic determinants. The importance of the secreted proteases modulating virulence factor stability is evidenced by our groups previous finding that a protease-null strain has a substantially increased infectious capacity in a murine model of sepsis; resulting from the …
Genome-Wide Variation In Potyviruses,
2019
University of Nebraska-Lincoln
Genome-Wide Variation In Potyviruses, Deepti Nigam, Katherine Latourrette, Pedro F.N. Souza, Hernan Garcia Ruiz
Nebraska Center for Virology: Faculty Publications
Potyviruses (family Potyviridae, genus Potyvirus) are the result of an initial radiation event that occurred 6,600 years ago. The genus currently consists of 167 species that infect monocots or dicots, including domesticated and wild plants. Potyviruses are transmitted in a non-persistent way by more than 200 species of aphids. As indicated by their wide host range, worldwide distribution, and diversity of their vectors, potyviruses have an outstanding capacity to adapt to new hosts and environments. However, factors that confer adaptability are poorly understood. Viral RNA-dependent RNA polymerases introduce nucleotide substitutions that generate genetic diversity. We hypothesized that selection imposed by …
The Adaptations Of The Sulfur-Oxidizing, Gammaproteobacterium "Candidatus Endoriftia Persephone", Endosymbiont Of The Giant Tubeworm Riftia Pachyptila, To Hydrothermal Vent Habitat Heterogeneity,
2019
University of South Florida
The Adaptations Of The Sulfur-Oxidizing, Gammaproteobacterium "Candidatus Endoriftia Persephone", Endosymbiont Of The Giant Tubeworm Riftia Pachyptila, To Hydrothermal Vent Habitat Heterogeneity, Juliana M. Leonard
USF Tampa Graduate Theses and Dissertations
The siboglinid tubeworm Riftia pachyptila is a dominant member of the deep-sea megafauna where seawater and hydrothermal vent (HTV) effluent interface and mix. It is one of the fastest growing invertebrates on land or in the sea. It does not have a digestive tract (e.g. mouth, gut, or anus), and is completely dependent on its sulfur-oxidizing endosymbiont, the Gammaproteobacterium “Candidatus Endoriftia persephone” for its nutritional requirements. This association was the first and is the most well studied among chemolithoautotrophic symbioses. “Ca. E. persephone” is a chemolithoautotrophic bacterium that oxidizes sulfide as an electron donor for energy, reduces oxygen as a …
Targeting Bacterial Resistance And Cancer Metastasis: A Structure Based Approach,
2019
University of South Florida
Targeting Bacterial Resistance And Cancer Metastasis: A Structure Based Approach, Kyle Galen Kroeck
USF Tampa Graduate Theses and Dissertations
Current research in pharmaceutical development commonly utilizes a profusion of methods in molecular modeling in order to probe intricate biological problems. Many original and promising compounds have been identified and developed by integrating experimental and computational methods. Structural biology utilizes many different research techniques including x-ray crystallography, NMR, and electron microscopy in order to develop molecular models of macromolecules that are of biological interest. Such techniques can be used in conjunction with molecular docking, which utilizes those molecular models in order to target macromolecules of therapeutic interest by computationally analyzing the conformations adopted by ligands upon interaction with a desired …
Evaluating Volatile Organic Compounds For Contact-Independent Antagonism Of Pseudogymnoascus Destructans,
2019
Kennesaw State University
Evaluating Volatile Organic Compounds For Contact-Independent Antagonism Of Pseudogymnoascus Destructans
Symposium of Student Scholars
White-nose syndrome (WNS), a disease caused by the fungus Pseudogymnoascus destructans, is responsible for the extensive mortality of bats in the United States. In an effort to develop tools to reduce bat mortality attributed to WNS, an in vitro experiment was conducted to quantify the inhibitory effects of select volatile organic compounds (VOCs) as well as explore potential synergistic activities. The experiment involved exposing mycelial plugs of P. destructans to various concentrations of B23 as well as B23 and decanal together at equimolar ratios. Measurements of the plugs were taken over the course of the 13 day experiment allowing …
Macrophage-Associated Wound Healing Contributes To African Green Monkey Siv Pathogenesis Control,
2019
University of Washington & Uppsala University
Macrophage-Associated Wound Healing Contributes To African Green Monkey Siv Pathogenesis Control, Fredrik Barrenas, Kevin Raehtz, Cuiling Xu, Lynn Law, Richard R. Green, Guido Silvestri, Steven E. Bosinger, Andrew Nishida, Qingsheng Li, Wuxun Lu, Jianshui Zhang, Matthew J. Thomas, Jean Chang, Elise Smith, Jeffrey M. Weiss, Reem A. Dawoud, George H. Richter, Anita Trichel, Dongzhu Ma, Xinxia Peng, Jan Komorowski, Cristian Apetrei, Ivona Pandrea, Michael Gale Jr.
Nebraska Center for Virology: Faculty Publications
Natural hosts of simian immunodeficiency virus (SIV) avoid AIDS despite lifelong infection. Here, we examined how this outcome is achieved by comparing a natural SIV host, African green monkey (AGM) to an AIDS susceptible species, rhesus macaque (RM). To asses gene expression profiles from acutely SIV infected AGMs and RMs, we developed a systems biology approach termed Conserved Gene Signature Analysis (CGSA), which compared RNA sequencing data from rectal AGM and RM tissues to various other species. We found that AGMs rapidly activate, and then maintain, evolutionarily conserved regenerative wound healing mechanisms in mucosal tissue. The wound healing protein fibronectin …
Analysis Of The Cody Rnome Reveals Rsad As A Stress-Responsive Riboregulator Of Overflow Metabolism In Staphylococcus Aureus,
2019
Université de Rennes I
Analysis Of The Cody Rnome Reveals Rsad As A Stress-Responsive Riboregulator Of Overflow Metabolism In Staphylococcus Aureus, Yoann Augagneur, Alyssa N. King, Noëlla Germain-Amiot, Mohamed Sassi, John W. Fitzgerald, Gyan S. Sahukhal, Mohamed O. Elasri, Brice Felden, Shaun R. Brinsmade
Faculty Publications
In Staphylococcus aureus, the transcription factor CodY modulates the expression of hundreds of genes, including most virulence factors, in response to the availability of key nutrients like GTP and branched‐chain amino acids. Despite numerous studies examining how CodY controls gene expression directly or indirectly, virtually nothing is known about the extent to which CodY exerts its effect through small regulatory RNAs (sRNAs). Herein, we report the first set of sRNAs under the control of CodY. We reveal that staphylococcal sRNA RsaD is overexpressed >20‐fold in a CodY‐deficient strain in three S. aureus clinical isolates and in S. epidermidis. …
Effect Of Biosurfactant And Biochar On Ecosystem Functions And Oil Remediation In Crude Oil Contaminated Wetland Soils,
2019
Louisiana State University
Effect Of Biosurfactant And Biochar On Ecosystem Functions And Oil Remediation In Crude Oil Contaminated Wetland Soils, Zhuo Wei
LSU Doctoral Dissertations
Decontamination of oil spill from coastal wetland soils requires a delicate approach. Remediation strategies using biochar, biosurfactant, and nutrient additions have been proposed. However, there is little information on application of these with combination for treatment of crude oil-contaminated wetland soil. Therefore, incubation studies were carried out to investigate the impact of biochar and rhamnolipid (RL) biosurfactant along with nitrogen (N) application on petroleum hydrocarbon degradation in a Louisiana coastal saline marsh and their impacts on greenhouse gas (GHG) emission. Additionally, the toxicity of crude oil as well as remediation materials on coastal wetland ecosystem were assessed at three levels: …
Inferred Function And Dynamics Of Microbial Communities From The Northern Gulf Of Mexico,
2019
Nova Southeastern University
Inferred Function And Dynamics Of Microbial Communities From The Northern Gulf Of Mexico, Deepesh Tourani
HCNSO Student Theses and Dissertations
Microbial communities, or microbiomes, are the major drivers of global biogeochemical cycles, acting as primary producers and decomposers across the water column in the oceans. Thus, they reflect changes in physicochemical properties and nutrient composition of the ocean. However, this correlation between ecological changes and the function of marine microbiomes is poorly understood. Large-scale oceanic events such as the bottom-water oxygen-depleted zone (i.e., “dead zone”) and the Deepwater Horizon oil spill in the Gulf of Mexico (GoM) render the ecosystem fragile. These events decrease survival rates of pelagic and coastal macrofauna and affect the biodiversity of the region. As part …
Morphology, Molecular Characterization And Habitat Preference Of Harmful Benthic Dinoflagellate Gambierdiscus (Dinophyceae) In Malaysia,
2019
Universiti Malaya
Morphology, Molecular Characterization And Habitat Preference Of Harmful Benthic Dinoflagellate Gambierdiscus (Dinophyceae) In Malaysia, Nurin Izzati Mustapa
Student Works (2020-2029)
Ciguatera fish poisoning (CFP) is a type of illness that causes human intoxication after consuming contaminated coral fishes. The neurotoxins, ciguatoxins, are produced by species of Gambierdiscus, one of the harmful benthic dinoflagellates. Identification of harmful dinoflagellate species is important to gain further insights into the global dispersion. In this study, morphological characteristics of species in the genus Gambierdiscus and their habitat preferences were investigated. Field sampling was undertaken at Pulau Rawa, Terengganu and Pulau Sibu, Johor. Single cells of Gambierdiscus were isolated and clonal cultures were established. Morphology of Gambierdiscus was examined by using light and scanning electron microscopes. …
