Microbiology Commons^™

Anaplasma Phagocytophilum Modulates Mammalian And Arthropod Signaling For Its Survival And Transmission, Supreet Khanal

Biomedical Sciences Theses & Dissertations

Vector-borne diseases (VBDs) are illnesses transmitted to humans and other animals by arthropods such as ticks, mosquitoes, and fleas. These arthropod vectors transmit infectious pathogens such as viruses, bacteria, and protozoa, to humans during blood-feeding. We have very few control strategies to treat or control these diseases. Human anaplasmosis, caused by the bacterium Anaplasma phagocytophilum, is the second most common tick-borne disease in the United States. This work defines three studies elucidating Anaplasma phagocytophilum-mediated modulation of cell signaling in mammalian cells and arthropod vector Ixodes scapularis ticks.

The first study focused on mammalian PI3 kinases signaling in regulating …

Toward The Discovery Of Biological Functions Associated With The Mechanosensor Mtl1p Of Saccharomyces Cerevisiae Via Integrative Multi-Omics Analysis, Nelson Martínez-Matías, Nataliya Chorna, Sahily González-Crespo, Lilliam Villanueva, Ingrid Montes-Rodríguez, Loyda M. Melendez-Aponte, Abiel Roche-Lima, Kelvin Carrasquillo-Carrión, Ednalise Santiago-Cartagena, Brian C. Rymond, Mohan Babu, Igor Stagljar, José R. Rodríguez-Medina

Biology Faculty Publications

Functional analysis of the Mtl1 protein in Saccharomyces cerevisiae has revealed that this transmembrane sensor endows yeast cells with resistance to oxidative stress through a signaling mechanism called the cell wall integrity pathway (CWI). We observed upregulation of multiple heat shock proteins (HSPs), proteins associated with the formation of stress granules, and the phosphatase subunit of trehalose 6-phosphate synthase which suggests that mtl1Δ strains undergo intrinsic activation of a non-lethal heat stress response. Furthermore, quantitative global proteomic analysis conducted on TMT-labeled proteins combined with metabolome analysis revealed that mtl1Δ strains exhibit decreased levels of metabolites of carboxylic acid metabolism, decreased …

Evaluating The Role Of The Stringent Response Mechanism In Clostridioides Difficile Survival And Pathogenesis, Astha Pokhrel

Chemistry & Biochemistry Theses & Dissertations

The human pathogen Clostridioides difficile is increasingly tolerant of multiple antibiotics and causes infections with a high rate of recurrence, creating an urgent need for new preventive and therapeutic strategies. The stringent response, a universal bacterial response to extracellular stresses, governs antibiotic survival and pathogenesis in diverse organisms but has not previously been characterized in C. difficile. This dissertation explores the ability of C. difficile to mount the stringent response. The bacteria encode a full-length, canonical bifunctional Rel/Spo Homolog or RSH enzyme. C. difficile RSH is incapable of utilizing GTP as a substrate but readily synthesizes putative 5’-pGpp-3’ alarmones. …

Mitochondrial Transfer From Mesenchymal Stem Cells Improves Neuronal Metabolism After Oxidant Injury In Vitro: The Role Of Miro1, Nancy Tseng, Scott C Lambie, Christopher Q Huynh, Bridget Sanford, Manisha Patel, Paco S Herson, D Ryan Ormond

Faculty, Staff and Students Publications

Stroke-induced cerebral ischemia is a major cause of death and disability. The disruption of blood flow results in neuronal and glial cell death leading to brain injury. Reperfusion restores oxygen to the affected tissue, but can also cause damage through an enhanced oxidative stress and inflammatory response. This study examines mitochondrial transfer from MSC to neurons and the role it plays in neuronal preservation after oxidant injury. We observed the transfer of mitochondria from MSC to mouse neurons in vitro following hydrogen peroxide exposure. The observed transfer was dependent on cell-to-cell contact and led to increased neuronal survival and improved …

Insights Into Viral Genome Function Through Comparative Structural Analysis, Lydia Phillips

UNO Student Research and Creative Activity Fair

Enteroviruses are single stranded RNA viruses which have caused many public health concerns, particularly in children. These viruses are responsible for polio, hand, foot, and mouth disease, many polio-like neurological diseases, and the common cold. The enterovirus called Coxsackievirus B3 (CVB3), a close relative to poliovirus, has been shown responsible for severe human disease, including pancreatitis, myocarditis, and type 1 diabetes. A unique advantage of studying CVB3 is the existence of a naturally occurring strain (CVB3/GA) which displays no known pathogenicity. Earlier comparative genomic studies have shown that the primary difference between avirulent CVB3/GA and the virulent strains of CVB3 …

A Comparison Of Intertidal Metazoan Biodiversity Between Previously Oiled Sheared And Intact Marsh Margins And Between Multiple Salinity Zones In The Coastal Marshes Of Louisiana, Patrick M. Rayle

LSU Master's Theses

Marshes in Louisiana are under threat from numerous natural and anthropogenic sources. A consequence of these threats are sheared marsh margins, which result from the impact of storm surge on previously oiled, weakened marsh. These conditions occurred in Louisiana marshes after Hurricane Isaac in 2012 followed the Deepwater Horizon oil spill in 2010, particularly in the shorelines surrounding Bay Jimmy. The second and third chapters of this thesis focus on the differences in biodiversity between the sheared and intact marsh margins in impacted sites in Bay Jimmy. Metabarcoding methods were used to determine community composition of the sediment within marsh …

College Of Natural Sciences Newsletter, March 2021, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 2. Issue 3

Contents:

Page 1 Dean's Message
Page 2-3 Awards and Recognition
Page 4 Student Club Spotlight: MICROBIOLOGY CLUB
Page 5 Research Spotlight: Dr. Chakravarty
Page 6 Open PRAIRIE Data; Grants Awarded in CNS; Research Collquia
Page 7 A Busy Month in Review; Media Coverage of the College

Rasagiline Effects On Glucose Metabolism, Cognition, And Tau In Alzheimer’S Dementia, Dawn C. Matthews, Aaron Ritter, Ronald G. Thomas, Randolph D. Andrews, Ana S. Lukic, Carolyn Revta, Jefferson W. Kinney, Babak Tousi, James B. Leverenz, Howard Fillit, Kate Zhong, Howard H. Feldman, Jeffrey Cummings

Integrated Health Sciences Faculty Research

Background: A Phase II proof of concept (POC) randomized clinical trial was conducted to evaluate the effects of rasagiline, a monoamine oxidase B (MAO-B) inhibitor approved for Parkinson disease, in mild to moderate Alzheimer's disease (AD). The primary objective was to determine if 1 mg of rasagiline daily for 24 weeks is associated with improved regional brain metabolism (fluorodeoxyglucose–positron emission tomography [FDG-PET]) compared to placebo. Secondary objectives included measurement of effects on tau PET and evaluation of directional consistency of clinical end points. Methods: This was a double-blind, parallel group, placebo-controlled, community-based, three-site trial of 50 participants randomized 1:1 to …

The C. Neoformans Cell Wall: A Scaffold For Virulence, Christine Chrissian

Dissertations, Theses, and Capstone Projects

Cryptococcus neoformans is a globally distributed opportunistic fungal pathogen and the causative agent of life threatening cryptococcal meningoencephalitis in immunocompromised individuals, resulting in ~180,000 deaths each year worldwide. A primary virulence-associated trait of this organism is the production of melanin. Melanins are a class of diverse pigments produced via the oxidation and polymerization of aromatic ring compounds that have a characteristically complex, heterogenous, and amorphous structure. They are synthesized by representatives of all biological kingdoms and share a multitude of remarkable properties such as the ability to absorb ultraviolet (UV) light and protect against ionizing radiation. Melanin production in fungi …

Transcriptional Coupling And Repair Of 8-Oxog Activate A Reca-Dependent Checkpoint That Controls The Onset Of Sporulation In Bacillus Subtilis, Valeria P. Suárez, Lissett E. Martínez, Hilda C. Leyva-Sánchez, Luz I. Valenzuela-García, Reyna Lara-Martínez, Luis F. Jiménez-García, Norma Ramírez-Ramírez, Armando Obregon-Herrera, Mayra Cuéllar-Cruz, Eduardo A. Robleto, Mario Pedraza-Reyes

Life Sciences Faculty Research

© 2021, The Author(s). During sporulation Bacillus subtilis Mfd couples transcription to nucleotide excision repair (NER) to eliminate DNA distorting lesions. Here, we report a significant decline in sporulation following Mfd disruption, which was manifested in the absence of external DNA-damage suggesting that spontaneous lesions activate the function of Mfd for an efficient sporogenesis. Accordingly, a dramatic decline in sporulation efficiency took place in a B. subtilis strain lacking Mfd and the repair/prevention guanine oxidized (GO) system (hereafter, the ∆GO system), composed by YtkD, MutM and MutY. Furthermore, the simultaneous absence of Mfd and the GO system, (i) sensitized sporulating …

Inhibition Of Biofilm Formation By The Synergistic Action Of Egcg-S And Antibiotics, Shrameeta Shinde, Lee Lee, Tinchun Chu

Department of Biology Faculty Scholarship and Creative Works

Biofilm, a stress-induced physiological state, is an established means of antimicrobial tolerance. A perpetual increase in multidrug resistant (MDR) infections associated with high mortality and morbidity have been observed in healthcare settings. Multiple studies have indicated that the use of natural products can prevent bacterial growth. Recent studies in the field have identified that epigallocatechin gallate (EGCG), a green tea polyphenol, could disrupt bacterial biofilms. A modified lipid-soluble EGCG, epigallocatechin-3-gallate-stearate (EGCG-S), has enhanced the beneficial properties of green tea. This study focuses on utilizing EGCG-S as a novel synergistic agent with antibiotics to prevent or control biofilm. Different formulations of …

Single-Cell Fluidic Force Microscopy Reveals Stress- Dependent Molecular Interactions In Yeast Mating, Marion Mathelié-Guinlet, Felipe Viela, JéRôMe Dehullu, Sviatlana Filimonava, Jason M. Rauceo, Peter N. Lipke, Yves F. DufrêNe

Publications and Research

Sexual agglutinins of the budding yeast Saccharomyces cerevisiae are proteins mediating cell aggregation during mating. Complementary agglutinins expressed by cells of opposite mating types “a” and “α” bind together to promote agglutination and facilitate fusion of haploid cells. By means of an innovative single-cell manipulation assay combining fluidic force microscopy with force spectroscopy, we unravel the strength of single specific bonds between a- and α-agglutinins (~100 pN) which require pheromone induction. Prolonged cell–cell contact strongly increases adhesion between mating cells, likely resulting from an increased expression of agglutinins. In addition, we highlight the critical role of disulfide bonds of the …

Optimized Microbial Recombinant Production Of Hiv-1 Anti-Envelope Antibody Fragments With Applications To Single Particle Tracking Of Virus Assembly, Merissa Michelle Bruns

Electronic Theses and Dissertations

In my findings, I have established a set series of protocols to recombinantly produce, purify and apply various fluorescent probes in vitro for the fluorescent labeling and study of the human immunodeficiency virus type 1 (HIV-1) envelope (Env) protein during HIV viral assembly. There remains insufficient knowledge about the molecular dynamics and interactions of HIV-1 Env protein with its counterpart, Gag, on the inner host cell surface during assembly of a mature virus particle. There also remains an insufficient amount of data for the understanding and clarification of the mechanism of action of a known host cell HIV-1 restriction factor, …

Green Team - Ecological Restoration Of Plaster Creek, Jia Luchs, Caleb Mathai, Rachel Warners, David Warners, Deanna Geelhoed

Student Papers and Reports

Plaster Creek, though its watershed is home to many potential stewards in Grand Rapids, is the most polluted creek in West Michigan. The Green Team, a branch of Plaster Creek Stewards, is a group of students that work during the summer with a focus on research, education, and working directly to restore Plaster Creek. The team works toward this goal through urban green infrastructure, utilizing native plants to manage stormwater. Two Calvin students, Caleb Mathai and Jia Luchs, one high school intern, Ben Zwart, and twelve high school students living in the Plaster Creek watershed were hired by PCS this …

The Inhibition Of Growth Of S. Cerevisiae, U. Maydis, And M. Lychinidis-Dioicae By Apiaecea Plant Extracts, Jackson M Hoffman, Jared Scott, David Schultz Phd

Undergraduate Arts and Research Showcase

The Apiaceae family of plants contains over 3,500 species, many of which are used as food crops: vegetables (carrot, parsnip, celery, etc.), herbs (cilantro, fennel, dill, etc.), and spices (cumin, anise, caraway, etc.). Many spices have been shown to exhibit antimicrobial properties against both bacteria and fungi. We set out to determine if the Apiaceae spice extracts currently used in our lab for anticancer studies exhibit any antimicrobial properties. Ethanolic extracts were made from several Apiaceae seeds: Apium graveolens (celery), Cuminum cyminum (cumin), Anethum graveolens(dill), Foeniculum vulgare (fennel), Coriandrum satvium (coriander), Pimpinella ansium (anise), Trachyspermum ammi (ajwain), Carum carvi …

Tracking The Subcellular Localization Of Surface Proteins In Staphylococcus Aureus By Immunofluorescence Microscopy, Salvatore J. Scaffidi, Mac A. Shebes, Wenqi Yu

Molecular Biosciences Faculty Publications

Surface proteins of Staphylococcus aureus and other Gram-positive bacteria play essential roles in bacterial colonization and host-microbe interactions. Surface protein precursors containing a YSIRK/GXXS signal peptide are translocated across the septal membrane at mid-cell, anchored to the cell wall peptidoglycan at the cross-wall compartment, and presented on the new hemispheres of the daughter cells following cell division. After several generations of cell division, these surface proteins will eventually cover the entire cell surface. To understand how these proteins travel from the bacterial cytoplasm to the cell surface, we describe a series of immunofluorescence microscopy protocols designed to detect the stepwise …

Dcaf14 Promotes Stalled Fork Stability To Maintain Genome Integrity, Arik Townsend, Gabriella Lora, Justin Engel, Neysha Tirado-Class, Huzefa Dungrawala

Molecular Biosciences Faculty Publications

No abstract provided.

Global Coordination Between Gene Expression Processes In C. Crescentus, James Raymond Aretakis

Wayne State University Dissertations

Gene expression is an essential process of all organisms which occurs in two steps, mRNA transcription, and translation and which is shut off by mRNA decay. For a bacterium to grow and divide, these steps need to be tuned to optimize the synthesis rates of thousands of proteins from their genes. Genome-wide experiments were used to determine the absolute transcription rates, mRNA degradation rates, and translation rates on a gene by gene basis in the model bacterium Caulobacter crescentus. This not only provides a system biology view of the organism’s gene expression resource allocation, but also provides a chance to …

Host Factors Affecting Group Ii Intron Retrotransposition, Justin Michael Waldern

Legacy Theses & Dissertations (2009 - 2024)

Group II introns are self-splicing mobile elements that are thought to be the evolutionary ancestors of eukaryotic retrotransposons, the spliceosome, and spliceosomal introns. Yet, little is known about how group II introns have coevolved within their native hosts or about the corresponding host biology.Using the Ll.LtrB intron in its native host, Lactococcus lactis, I first sought to identify host factors that influence retrotransposition. Since retrotransposition can be costly to the host organism, group II introns must achieve a delicate balance between self-proliferation and host preservation. By utilizing the native host organism, my goal was to unearth retrotransposition-related mechanisms that have …

Retrotransposon-Mediated Transduction Of An Environmental Cue To Regulate Centrosome Fate, Shawn Patrick Murphy

Legacy Theses & Dissertations (2009 - 2024)

In 1969, the enrichment of mobile element repeat sequences led Britton and Davidson to propose the hypothesis that gene expression in higher eukaryotes is regulated through the exaptation of mobile elements. In this work, I have explored the hypothesis that mobile elements can also be harnessed by the host to regulate asymmetric cell division, thereby determining cell fate. Retrotransposons are ubiquitous eukaryotic mobile elements that transpose through an RNA intermediate. They are often active in cell types that divide asymmetrically to yield daughter cells with different fates, such as embryonic stem cells, germline stem cells, neuronal stem cells and the …

The Phosphodiesterase, Rv0805, Is An Unheralded Component Of Tb Complex Mycobacterial Physiology In And Beyond Camp Homeostasis, James R. Mcdowell

Legacy Theses & Dissertations (2009 - 2024)

Phosphodiesterases (PDEs) are integral components of 3’,5’-cyclic adenosine monophosphate (cAMP) signaling pathways by degrading cAMP to modulate the concentration, duration, and localization of the cAMP signal which maintains the specificity of cAMP pathways. The human pathogen, Mycobacterium tuberculosis (Mtb) has a unique cAMP network architecture with at least 15 adenylyl cyclases (ACs) that generate cAMP, but only one characterized PDE, Rv0805, which is found exclusively in pathogenic mycobacteria. Rv0805 can influence Mtb cAMP levels but the absence of Rv0805 orthologs in non-pathogenic mycobacteria and apparent separation of Rv0805 from cAMP directed roles led to numerous questions surrounding PDE function in …

College Of Natural Sciences 2021 Year-End Publication, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Page 2 Welcome, Table of Contents
Page 3 Our Departments: Highlights From 2021
Page 4 Overview of the College
Page 5 Overview of Bold & Blue
Pages 6, 7 Announcing the First Endowed Professorship in the College of Natural Sciences
Page 8 Spooky Science, Astronomy Outreach, SDSU Chemistry Research Features on Journal Cover
Page 9 Students Win Business Plan Competition With Aims to Improve Shelf Life of Produce, Summer Researchers
Page 10 NIH Grant Helps Unravel Rare Inflammatory Genetic Disorders, International Excellence in South Dakota
Page 11 The Next Frontier of Science Education: Virtual Reality, SDSU Researchers Uncover how Cancer …

Entry And Replication Of Negative-Strand Rna Viruses, Kerri Boggs

Theses and Dissertations--Molecular and Cellular Biochemistry

Hendra virus (HeV) and human metapneumovirus (HMPV) are negative-sense, singled-stranded RNA viruses. The paramyxovirus HeV is classified as a biosafety level 4 pathogen due to its high fatality rate and the lack of a human vaccine or antiviral treatment. HMPV is a widespread pneumovirus that causes respiratory tract infections which are particularly dangerous for young children, immunocompromised individuals, and the elderly. Like HeV, no vaccines or therapies are available to combat HMPV infections. These viruses fuse their lipid envelopes with a cell to initiate infection. Blocking cell entry is a promising approach for antiviral development, and many vaccines are designed …

Substrate Trafficking Within The Type Vii Secretion Systems Of Pathogenic Mycobacteria, Zachary A. Williamson

Theses and Dissertations--Molecular and Cellular Biochemistry

Tuberculosis (TB), primarily caused by infection of Mycobacterium tuberculosis (Mtb) in the lungs, is the deadliest infectious bacterial disease killing 1.5 million people annually. A major determinant of virulence is active secretion through three specialized type VII secretion (ESX) systems; ESX-1, ESX-3, and ESX-5. A large group of substrates exported by the ESX systems is the PE (Proline-Glutamine) and PPE (Proline-Proline-Glutamate) families of proteins, which are highly expanded in the pathogenic species of Mycobacteria and encompass over 7% of Mtb’s genome coding capacity. PE and PPE proteins interact together to form PE-PPE heterodimers, and are secreted through …

Covid19 Disease Map, A Computational Knowledge Repository Of Virus–Host Interaction Mechanisms, Marek Ostaszewski, Tomáš Helikar, Bhanwar Lal Puniya, A Host Of Co-Authors, Covid-19 Disease Map Community

Department of Biochemistry: Faculty Publications

We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, …

Molecular And Genetic Studies On A Sipd/Ipad-Related Virulence Spike Protein From Immune-Suppressive Particles Of A Drosophila Parasitoid, Carlo Miguel A. Sevilla

Dissertations and Theses

Parasitoid wasps are effective biological control agents that have evolved intricate host immune suppression strategies to overcome host immune defenses. The most important anti-parasite defense mechanism is encapsulation, where the host’s blood cells surround the wasp egg. In the Drosophila/Leptopilina host-parasitoid system, extracellular vesicles (EVs) are oviposited along with the wasp egg. The EVs possess spikes and contain hundreds of proteins, some of which enable wasp eggs to escape encapsulation by changing the morphology and function of hemocytes, or killing them. Previous studies have identified an abundant surface/spike protein (SSp40) from Leptopilina heterotoma EVs. While p40, a predicted …

Initial And Advanced Stages Of Microbiota Establishment Within The Tsetse Fly, Miguel Eduardo Medina Munoz

Graduate Theses, Dissertations, and Problem Reports (ETD)

Symbiosis is a long-term physical association between two or more species, although little is known regarding its evolutionary origins, particularly at the genetic level. Tsetse flies are the vector of African trypanosomes, causative agents of Human and Animal African Trypanosomiases. Tsetse provide an ideal model for studying initial and advanced stages of symbiosis. Tsetse have a simple digestive tract microbiota primarily consisting of two bacteria; the ancient mutualist Wigglesworthia glossinidia and the recently acquired Sodalis glossinidius. This work presents a chronological study in evolutionary terms of the history of a microbial-insect association. First, I present concepts on symbiosis and …

Stomatal Conductance And Reed Canary Grass Suppression Of Native Michigan Trees, David E. Martinez Vasquez, Martin L. Vanderschoot, David Warners

Faculty and Professional Research

Reed canary grass (Phalaris arundinacea), a prominent invasive understory species, threatens native Michigan biodiversity statewide. A notable affected area includes a stretch of agricultural land along Schooley Drain in Caledonia, MI, located in the headwaters of the Plaster Creek watershed. Our study pursues the following questions: “Do native trees provide enough shade to reduce the growth of Reed canary grass?” and “Which native trees best transpire water from a floodplain?”: To answer these questions, we initiated a long-term evaluation of seven different species of native Michigan trees to investigate which species best inhibits the growth of reed canary grass and …

Plaster Creek Floodplain And Adjacent Ravines Near Stanaback Park: Botanical Inventory Highlights And Management Considerations, David Warners, Garrett Crow, Haley Weesies

Faculty and Professional Research

In the summer of 2021, the research team visited this area of ravines and floodplain a total of twenty-one times to conduct our field research. During the visits, they carefully walked throughout different sections of the study site, identifying each vascular plant species they saw growing there and observing how the flora developed throughout the season. In addition to keeping detailed field notes, they documented permanent records of the findings of our inventory by collecting voucher specimens that have been deposited in the Calvin University Herbarium. Additionally, they sent duplicate specimens to the Michigan State University Herbarium and/or University of …

Botanical Inventory Highlights And Management Considerations For Covenant Park, David Warners, Garrett Crow, Haley Weesies

Faculty and Professional Research

In the spring and summer of 2021, Calvin University students and faculty conducted a botanical inventory and assessment of the natural areas in Covenant Park, located at 3724 Shaffer Avenue SE, Kentwood, MI 49512. Given that the property was recently acquired by the City of Kentwood Parks & Recreation, the purpose of this inventory is to inform Kentwood Parks and Recreation staff about the site’s floristic quality, diversity, and ecological significance. The specific objectives of this study are to 1) provide a comprehensive inventory of the species of plants occurring on the property, 2) identify particular areas that would benefit …