Microbiology Commons^™

Monitoring Lake Sinclair, Margaret Blackledge

Graduate Research Showcase

Algae, a polyphyletic group of aquatic primary producers, play a great part in earth’s biosphere. They produce half of the world’s oxygen and are major contributors to aquatic biodiversity. When conditions are favorable to a species, algae will bloom. Some algal species will produce algal toxins during a bloom as a potential mechanism to concentrate carbon. Due to the integral part they play in aquatic food webs, nutrient cycling and the potential for harmful algal blooms, algal communities are monitored to determine the health and safety of aquatic environments. Lake Sinclair in middle Georgia is a good model where in …

Choices On Sampling, Sequencing, And Analyzing Dna Influence The Estimation Of Community Composition Of Plant Fungal Symbionts, Jonathan A. Cale, Natalie Scott, Gregory J. Pec, Simon M. Landhäusser, Justine Karst

Publications: Biology

Plant root symbionts, namely mycorrhizal fungi, can be characterized using a variety of methods, but most of these rely on DNA. While Sanger sequencing still fulfills particular research objectives, next‐generation sequencing currently dominates the f ield, thus understanding how the two methods differ is important for identifying both opportunities and limitations to characterizing fungal communities. In addition to testing sequencing methods, we also examined how roots and soils may yield different fungal communities and how disturbance may affect those differences. We sequenced DNA from ectomycorrhizal fungi colonizing roots of Pinus banksiana and found that operational taxonomic unit richness was higher, …

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 …

Characterization Of Clostridium Cochlearium As A Potential Probiotic For Obesity Management, Paba Edirisuriya

Wayne State University Dissertations

ABSTRACTCHARACTERIZATION OF CLOSTRIDIUM COCHLEARIUM AS A POTENTIAL PROBIOTIC FOR OBESITY MANAGEMENT

ByPABA EDIRISURIYA MAY 2021 Advisor: Dr. Kequan Zhou Major: Nutrition and food science Degree: Doctor of Philosophy Emerging evidence indicates that manipulation of gut microflora is a potential therapeutic approach for managing obesity. Probiotic effects on host weight reduction have repeatedly been revealed through previous studies. Clostridium cochlearium is a butyrate-producing, spore-forming bacteria that have been reported to present in the mammalian gut. Our simulated Invitro digestion model revealed that C. cochlearium could survive in the unfavorable conditions of the human gastrointestinal tract, including low pH (pH2), high bile …

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, …

Characterization Of Microbial Populations In Landfill Leachate, Umut M. Bicim, Hanna Fulford, Lori A. Hoagland, Alejandro R. Sanchez, Amisha D. Shah, Inez Hua

Discovery Undergraduate Interdisciplinary Research Internship

In the United States, municipal solid waste (MSW) landfills remain a potential mining source of recoverable materials, including but not limited to critical, precious, and rare earth metals found in electronic waste. This is possible due to collectible leachate that filters through MSW landfills, carrying metals, nutrients of value, and microbes—some of which may hold key metal bioleaching properties—within. The purpose of this study is to begin analyzing leachate from MSW landfills in the American Midwest to understand the composition of microbial communities within these landfills. Landfill leachate samples sourced in northern Indiana, representing the landfill process during unique times …

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.

Antimicrobial Activity Of Silver(I) Cyanoximates Against Streptococcus Mutans Ua159 Planktonic Growth And Biofilm Formation, Sarah Hameer

Honors Program Theses

Streptococcus mutans is identified as the causative agent of human dental caries, with biofilm formation serving as its most important virulence factor. Biofilms are typically more challenging to treat than planktonic or free-floating bacteria, adding to the already challenging issue of antibiotic resistance. This has led to an increased need for the discovery of alternative antibacterial compounds other than antibiotics. Among these compounds, silver(I) cyanoximates have been demonstrated to have antibacterial activity against a variety of microorganisms, specifically those that colonize in-dwelling medical devices. To assess the antibacterial properties of two silver(I) cyanoximate compounds, silver(I) nitrosodicyanomethanide (Ag(ACO)) and silver(I)α-oximido-(2-benzoyl)acetonitrile (Ag(BCO)), …

The Influence Of Infant Formula On The Growth Of Commensal And Pathogenic Streptococcus Species In The Infant Oral Cavity, Geneva Waynick

Undergraduate Honors Theses

The oral microbiome is a complex community of microorganisms that can both reflect and greatly influence the health of the human host. A number of diseases are associated with dysbiotic oral microflora in infants and children, including dental (e.g. dental caries, gingivitis, and periodontal disease), and gastrointestinal diseases (e.g. pediatric appendicitis, celiac disease, and pediatric inflammatory bowel disease). A variety of factors can influence the composition of the oral microbial community in infants, including gestation length, mode of delivery, feeding method, and diet. This study focuses on the effects of diet on the growth of a commensal bacterium (Streptococcus …

Review: Formation And Metabolic Function Of Coral Rubble Biofilms In The Reef Ecosystem, Andres Sanchez-Quinto, Luisa I. Falcon

Gulf and Caribbean Research

When coral dies, their calcareous skeletons constitute coral rubble in conjunction with the cementing activity of coralline algae and bacteria, creating a secondary reef structure which takes from years to decades to form. Healthy coral reefs differ from coral—rubble dominated reefs in microbial taxonomic composition and metabolic functional roles. The metabolisms of healthy reefs are dominated by autotrophic pathways, where carbon and nitrogen fixation dominate, while the metabolism of rubble—dominated reefs predominate in degradation of organic matter. Nitrogen fixation is 3 orders of magnitude lower in rubble—dominated reefs than in healthy reefs. Coral—rubble harbors a vast diversity of microbes that …

Identification Of Loci Influencing Teosinte Crossing Barrier 1 (Tcb1) Efficacy In Maize By Quantitative Trait Loci (Qtl) Mapping And Genome-Wide Association Study (Gwas), Namrata Maharjan

Electronic Theses and Dissertations

Pollen cross-contamination has been a major problem for maize breeders. Various mechanical methods applied to avoid the contaminations are ineffective. The genetic factors related to maize fertilization can be used to develop an effective method to prevent pollen contamination. Pollen rejection ability controlled by Teosinte crossing barrier 1 (Tcb1) is such a genetic system. Silks possessing dominant Tcb1-s reject pollen possessing the recessive allele (tcb1). Successful fertilization occurs when Tcb1-s pollen falls upon tcb1 silks. The efficacy of dominant Tcb1-s was, however, reduced when repeatedly backcross with maize inbred lines, which suggests that there are modifiers to Tcb1-s. To find …

A Biocontrol Pesticide Derived From Mycovirus-Infected Sclerotinia Sclerotiorum Can Induce Plant Resistance, Connor Pedersen

Electronic Theses and Dissertations

Soybean leaf-associated gemycircularvirus-1 (SlaGemV-1) is a novel mycovirus discovered through the metagenomic sequencing of soybean leaves which is capable of inducing hypovirulence in the highly pathogenic fungus Sclerotinia sclerotiorum. RNASeq analysis techniques were used to determine the transcriptional changes caused by the infection of virus in S. sclerotiorum, as well as the transcriptional changes in Glycine max caused by the colonization of hypovirulent, SlaGemV-1-infected S. sclerotiorum. RNASeq results indicate that viral infection leading to hypovirulence may attenuate expression of genes relating to cell wall synthesis, microtubule formation, and metabolism of steroids and natural antibiotics. Cytochrome P450-related genes, kinesin domain genes, …

Exploration Of Host Health Benefits By A Defined Consortium Of Butyrate-Producing Human Gut Bacteria In Gnotobiotic Mouse Model, Linto Antony

Electronic Theses and Dissertations

Aberrant gut microbiota composition is found to be associated with several human diseases such as inflammatory bowel diseases (IBD). Reduction in butyrate producing bacteria is one of the characteristic features of such dysbiotic bacterial community in the gut. Modulation of gut microbiota to bring the dysbiotic state back to normal healthy state is a promising therapeutic strategy to cure several diseases like recurrent Clostridium difficile infection (rCDI) and IBD where traditional therapies using pharmacological substances fails to make a difference. Restoration of butyrate producers is found to be an effective method of such gut microbiota modulation. The potential to produce …

Electrical Sensing In Non-Excitable Cells To Promote Galvanotaxis And Tissue Survival, Anyesha Sarkar

Electronic Theses and Dissertations

Weak DC fields have been shown to induce polarity, cell migration and cell proliferation in 2D cultures in vitro. To understand the mechanism by which non-excitable cells sense such weak EFs, we have investigated the mechanism of cathode-directed water flow (electro-osmosis) in the boundary layer of cells by reducing it with neutral, viscous polymers. Our results indicate that low molecular weight polymers decrease cathodal migration and promote anodal migration in a concentration dependent manner. High molecular weight polymers do not affect directionality and can be explained using porosity and hydraulic permeability between the polymers. These results provide the first evidence …

Improving Nutritional Properties And Extractability Of Pea Proteins For Human Consumption Via Fungal Bioprocessing, Camille Massmann

Electronic Theses and Dissertations

Yellow peas are a rich source of protein and phytochemicals. Peas are compatible with many diets restricted by sensitivities, allergies, or personal choice. As a result, peas are gaining popularity in food markets, despite the challenges they present. The biggest challenges for pea proteins in food markets are high content of fiber, starch, and saponins. These components cause processing challenges and create undesirable textures and bitter flavors. Pea proteins are typically extracted with alkaline extraction or air classification methods which result in 80% and 50% protein products respectively. With low protein purity, these products are not competitive with other, more …

Study On The Human Gut Bacteria Under Different Ecological Conditions: Antibiotic Perturbation And Dietary Quercetin, Shruti Shashidharan Menon

Electronic Theses and Dissertations

The human intestine encompasses a vast community of microorganisms known as the gut microbiota that play a crucial role in maintaining health. Common perturbations such as changes in the normal diet, antibiotic treatment, and changes in environmental conditions can alter the gut microbiome. This can create dysbiosis in the gut leading to disease conditions. Therefore, it becomes important to determine the forces that influence the gut microbial ecology. In the first study, we focus on antibiotic perturbations on microbial succession and resilience in a synthetic consortium consisting of the most prevalent gut bacteria in humans. In addition, we investigated the …

Characterization Of The Rumen Bacterial Communities Of Bison Heifers Fed A Grass-Based Diet Vs A Grain-Based Free-Choice Diet, Anlly Miley Fresno Rueda

Electronic Theses and Dissertations

A century ago, the North American grasslands and prairie ecosystems were dominated by bison. At least 30 million bison roamed the Great Plains when the first explorers arrived. By 1900, there were little over a thousand bison remained in the United States and Canada. Recovery efforts has been made since the 20th century to reestablish the herds and increase the bison population. Today, over 500,000 bison are distributed across North America, with more than 90% of the existing bison population under commercial production. Modern conservation strategies are made via the collaborative efforts of conservationist, producers, and researchers, resulting in increased …

Assaying Bacillus Amyloliquefaciens Isolates 1ba And 1d3 For Biosurfactant Production And Utilization Of Petroleum Hydrocarbons And Phenolic Acids, Pavan Kulkarni

Electronic Theses and Dissertations

Several Bacillus amyloliquefaciens isolates obtained from wheat residue have been studied as biological agents to control wheat diseases. Notable traits of isolates 1BA and 1D3 include growth with high salt (10% NaCl), at temperatures up to 50°C and over a wide pH range. BIOLOG Gen III plates were used to study and further characterize Bacillus amyloliquefaciens 1BA and 1D3. Both isolates showed tolerance to high salt concentration supporting previous studies. They also grew in the presence of lithium chloride, potassium tellurite, and sodium bromate. Both isolates grew at pH 5, with almost identical carbon source utilization fingerprints. However, D-serine, quinic …

Investigating The Development Of Fecal Bacterial Communities In Growing Dairy Calves, Emily Fowler

Electronic Theses and Dissertations

The gut development of young calves is crucial for the producer and the calf's future. Many factors can affect the development of a young calf's gastrointestinal system, and there has been little research into the fecal microbiome development of calves from 0 to 12 weeks of age. To gain further insight into this process, development of the fecal microbiome in 12 dairy calves was investigated. Fecal bacterial composition was determined at four time points (weeks 0, 4, 8 and 12) using the 16S rRNA gene through PCR-amplification of the V1-V3 regions from fecal microbial genomic DNA, followed by Illumina MiSeq …

Impact Of Arbuscular Mycorrhizal Fungi On Conyza Canadensis Drought Responses And Possible Mechanisms, Kian G.M. Speck, Ylva Lekberg, Anna Sala

Undergraduate Theses, Professional Papers, and Capstone Artifacts

• Arbuscular mycorrhizal fungi (AMF) are important plant mutualists that can facilitate plant responses to various environmental stressors, such as drought. A plant that may benefit from AMF-induced drought tolerance is Conyza canadensis due to its ability to thrive in dry conditions and its high colonization rate. However, no studies have researched C. canadensis in this context and the exact mechanisms of AMF-induced drought tolerance are still unknown.
• To better understand if and how AMF facilitate drought response in C. canadensis, we conducted a greenhouse experiment comparing the response of mycorrhizal and non-mycorrhizal plants to three watering levels. We measured …

Passive Immunization Against Invasive Salmonella Enterica, Angelene Richards

Legacy Theses & Dissertations (2009 - 2024)

The Gram-negative bacterium, Salmonella enterica is a prominent etiologic agent of both diarrheal disease and enteric fever that encompasses over 2500 serovars, including S. Typhimurium (STm) and S. Typhi (STy). S. enterica is transmitted through contaminated food and water and, following ingestion, invades the gastrointestinal (GI) mucosa. The bacterium uses flagellar-based motility to target microfold (M) cells overlying gut-associated lymphoid tissues known as Peyer’s patches in the small intestine. Entry into Peyer’s patch tissues is a pivotal step in the infection process, as the bacterium can then disseminate systemically in the host. Given the rise in antibiotic resistance amongst S. …

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 …

The Role Of Conserved Poly(A) Sequences In The 3'Utr Of Zika Virus Gene Expression, Kristen Kaytes

Legacy Theses & Dissertations (2009 - 2024)

Following its discovery in 1947, Zika virus garnered little attention in the global stage until 2015, when a rapidly spreading epidemic brought the virus, and its devastating clinical manifestations to light. Zika virus pathologies include Congenital Zika Syndrome, a known causative of microcephaly, as well as spontaneous miscarriages and the development of Guillain Barré syndrome. Despite recent advances in research, the molecular biology of Zika virus is largely unknown.

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 …

Rna Modifications As A Novel Mediator Of Viral Infection, Rachel Netzband

Legacy Theses & Dissertations (2009 - 2024)

Viral epitranscriptomics is a novel field of RNA biology. Chemical groups are appended to RNA nucleotides under different conditions in cells, and I examine these changes using a mass spectrometry-based approach. Various changes are found to occur in post-transcriptional modifications (PTMs) during viral infection. The field primarily studies a small number of PTMS, such as m6A, while I explore a variety of novel modifications and their impact on viral infection. Hepatitis C virus (HCV) infection induces a variety of modification changes, including the novel presence of dimethylcytosine (m5Cm/m44C). One Writer enzyme for this modification is determined to likely be METTL15, …

Describing The Gut Microbiome Of Amblema Plicata, Lauren Lawson

Electronic Theses and Dissertations

Freshwater mussels are important for nutrient cycling and ecosystem health, as they filter feed on their surrounding water column. This form of feeding makes these bivalves especially sensitive to conditions in their environment. Gut microbial communities (microbiomes) have been recognized as important to both host organism and ecosystem health; however, how microbiomes are organized and influenced is still unclear. In this study, the gut microbiomes of 58 individuals of the freshwater mussel Amblema plicata were compared across two river basins, five rivers, and nine sites in the southeastern USA. Planctomycetes, Firmicutes, and Cyanobacteria were the most common phyla within all …