Life Sciences Commons^™

An Antiviral Response Unleashed: Deciphering The Relationship Between Shiftless And Rna Granules During Kshv Infection, David C. Hatfield

Masters Theses

Herpesviruses persist as a parasitic actor among many species. These viral agents can rapidly seize control over host cells by influencing global gene expression. Through a process known as host shutoff, herpesviruses cause a widespread degradation event of host transcripts within the cytoplasm. Specifically, Kaposi Sarcoma associated herpesvirus (KSHV) encodes for an endoribonuclease, termed SOX, that orchestrates this manipulation of gene expression. We and others have discovered certain transcripts that escape this fate; we suggest that this is an active escape, where transcripts have 3’ UTR elements that disallow SOX cleavage. One of the escapees that has been found is …

The Impacts Of Tilled-In Biodegradable Plastic Mulch On Soil Microbial Communities, Corissa L. Martin

Masters Theses

Plastics mulch films are used in agriculture to help increase crop production by regulating soil water retention and soil temperature while also preventing weed growth. Despite these benefits, plastic mulches have led to higher levels of microplastic pollution as weathering occurs. In response to this issue, biodegradable plastic mulches (BDMs) have been introduced to help reduce plastic pollution as they are designed to be tilled into soil after each growing season to continue degradation. Degradation of these mulch films is dependent on climate and, in some areas, complete degradation can take years. Since some biodegradable plastic mulches are made of …

The Discovery Of A Novel Bacteria From A Large Co-Assembly Of Metagenomes, Matthew Finkelberg

Masters Theses

In the summer of 2022, a co-assembly of metagenome was created using the microbes found at Barres Woods in Harvard Forest. 14 samples were taken, and sample was split into the organic and mineral layer, which totals 28 Bulk MAGs. Within this Co-assembly, 4 different genomes were found which were designated with the phylum of FCPU426. Three of which were considered medium quality and one being assigned high quality. The novel phyla first appeared in NCBI and GTDB databases in June 2018. The name FCPU426 dates to 2010 and was named based on the 16s amplicon sequencing.

The novel phylum …

Climate Change, Giant Viruses And Their Putative Hosts, Sarah K. Tucker

Masters Theses

Viruses hold our attention for the horrific impact they have on human health and welfare. However, viruses are a critical part of our ecosystem and facilitate the cycling of carbon and other important nutrients. The cycle of virus infection, followed by host resistance and the subsequent evolution of new strains enables adaptation to changing hosts and the environment. Giant viruses, some with particle sizes large enough to be visible in light microscopes and their bewildering array of accessory genes, have captivated scientists and the general public since their discovery two decades ago. Giant viruses are part of the Nucleocytoviricota (NCV) …

Enhanced Killing Of Mycobacterium Abscessus By Nanosponge Delivery Of Antimycobacterials, Casey Albano

Masters Theses

The increasing prevalence of bacterial infections has made it necessary to find novel methods of combatting the resistance of bacteria to conventional antibiotics. Mycobacterium abscessus is an increasingly prevalent pathogen that is intrinsically drug resistant, therefore difficult to treat. The use of phytochemicals as a source of alternate antibiotics has been explored, however, the poor solubility of phytochemicals in water makes it difficult to effectively deliver them to bacterial biofilms. In this study, I investigated the efficacy of nanosponge-emulsified phytochemicals in killing M. abscessus biofilms. The nanosponge technology was used to improve the solubility and stability of the phytochemicals, allowing …

Pregnancy Influences On The Rumen Environment Of Angus Heifers Differing In Feed Efficiency, Miranda Gabrielle Martin

Masters Theses

With an expected increase in population by 2050, the demand for more animal protein will increase. To improve the sustainability of US cattle production, producers and researchers have historically focused on improving the feed efficiency of steers, producing a more marketable beef product. However, without a successful pregnancy, there would be no marketable animal to feed. The objective of this study was to examine the physiological changes that occur during pregnancy and their impact on the rumen microbial communities and the correlation to feed efficiency status in Angus heifers. Utilizing 17 cannulated Angus heifers, feed efficiency data was previously collected …

Molecular Biodiversity Of Foraminifera, Rabindra Thakur

Masters Theses

Foraminifera are a diverse clade of mostly shell-building single-celled organisms. Estimation of foraminiferal diversity is critical for understanding past and present climatic conditions, as they are highly sensitive to environmental perturbations. Biodiversity estimates of foraminifera began with the counting of test (i.e., shell) microfossils composed of calcium carbonate, as they are well preserved in sediment samples. However, this view has changed with molecular biodiversity estimates, which suggest that early-diverging single-chamber (i.e., "monothalamid") species that lack preservation ability are more diverse than anticipated. Although biodiversity estimates of foraminifera at the molecular level have changed our perceptions, they possess various challenges, especially …

The Application Of Microbial Source Tracking To Aid In Site Prioritization For Remediation In Lower Michigan, John J. Hart

Masters Theses

Non-point source fecal pollution is a threat to both the environment and public health. Climate change, aging infrastructure, and intensified agricultural practices are predicted to accentuate this issue. In Michigan, due to the high instance of aging infrastructure and intensified agriculture, non-point source fecal pollution has caused many waterbodies to exceed the state standards posing a risk to recreational activities and source water. Due to this threat, there is an increased effort to identify and remediate these sources. My study focused on improving the identification of non-point source fecal pollution through a combination of culture-based and molecular fecal indicator bacteria …

Application Of Nitrate To An Anaerobic Subsurface Bioremediation, Cassie Marie Roberts

Masters Theses

"The highly contaminated subsurface matrix of the Baird and McGuire Superfund site is currently threatening the health and safety of the surrounding environment of Holbrook, MA. Contaminants of significant concern due to high concentration are inorganic arsenite and petroleum hydrocarbons, such as naphthalene. Parsons Corporation and the Massachusetts Department of Environmental Protection have implemented a bioremediation pilot to attempt to degrade the hydrocarbons and arsenic with the application of nitrate. The nitrate would act as an electron acceptor for biodegradation of the hydrocarbon contaminants, produce nitrite that would oxidize reduced iron, and iron oxides would sequester arsenic. Preliminary data showed …

Comparison Of The Humoral Immune Response Following Both Bacterial Challenge And Rnai Of Major Factors On Proliferation Of Bartonella Quintana In The Human Louse, Jake Zina

Masters Theses

Human body lice, Pediculus humanus humanus, and head lice, Pediculus humanus capitis, have been hematophagous ectoparasites of humans for thousands of years. Despite being ecotypes, only body lice are known to transmit bacterial diseases to humans, and it appears that lower humoral and cellular immune responses allow body lice to possess a higher vector competence. We previously observed that the transcription level of the defensin 1 gene was up-regulated only in head lice following oral challenge of Bartonella quintana, a causative agent of trench fever, and also that body lice excreted more viable B. quintana in their …

Neutrophil Subtype Differentiation In Campylobacter Jejuni Infection And Its Impact On T Cells And Colonic Epithelial Cells, Carolina Dolislager

Masters Theses

The discovery of neutrophil subtypes has expanded what is known about neutrophil functions, yet there is still much to learn about the role of these subtypes during bacterial infection. We investigated whether Campylobacter jejuniinduced differentiation of human neutrophils into the hypersegmented, CD16^hi/CD62L^lo[CD16hi/CD62Llo] subtype. In addition, we investigated whether C. jejuni-dependent differentiation of this neutrophil subtype induced cancer promoting activities ofhuman T cells and colonocytes, whichwere observed in other studies of hypersegmented, CD16^hi/CD62L^lo[CD16hi/CD62Llo] neutrophils. We found that C. jejunicauses a significant shift in human neutrophil populations to the hypersegmented, CD16 …

Ecological Controls On Successional Patterns In Bloom-Forming Cyanobacteria, Kyla L. Hooker

Masters Theses

Harmful algal blooms are widespread in lake ecosystems but the ecological factors underlying their formation and maintenance are poorly understood. We revisit classical ecological theories which characterize and evaluate contrasting bottom-up and top-down influences on the selection of phytoplankton groups, such as Microcystis aeruginosa. We begin with a data compilation and analysis of environmental data from Lake Erie. This data analysis of nutrient concentrations, pigment concentrations, and zooplankton biomasses helps us understand and interpret what is happening in the environment throughout the year. Thus, allowing us to build a mathematical model to test our hypothesis. Our mathematical model asses …

Screening For Binding Partners And Protein-Protein Interactions Of A Fungal Transcription Factor- Xdr1, Nishadi Punsara Gallala Gamage

Masters Theses

Clarireedia spp. (formerly Sclerotinia homoeocarpaF.T. Bennett) is the causal agent dollar spot, the most economically important turfgrass disease impacting golf courses in North America. The most effective strategy for dollar spot control is repeated application of multiple classes of fungicides. However, reliance on chemical application has led to resistance to four classes of fungicides as well as multidrug resistance (MDR). Fungi are known to detoxify xenobiotics, like fungicides, through transcriptional regulation of three detoxification phases: modification, conjugation and secretion. Little is known, however, of the protein-protein interactions that facilitate these pathways. Following next-generation RNA sequencing of Clarireedia spp., a …

Metabolic Modeling Of Cystic Fibrosis Airway Microbiota From Patient Samples, Arsh Vyas

Masters Theses

Cystic Fibrosis (CF) is a genetic disorder, found with higher prevalence in the Caucasian population, affecting > 30,000 individuals in the United States and > 70,000 worldwide. Due to the astoundingly high rate of mortality among CF patients being attributed to respiratory failure brought on by chronic bacterial infections and subsequent airway inflammation, there has been a lot of focus on systematically analyzing CF lung airway communities. While it is observed traditionally that Pseudomonas aeruginosa is the most threatening and persistent CF colonizer due to high antibiotic resistance, recent studies have elicited the roles of other pathogens and it has been widely …

The Role Of Low-Molecular Weight Fungal Metabolites In Eutypa Dieback Grapevine Trunk Disease, Dana Sebestyen

Masters Theses

Eutypa dieback, one of several grapevine trunk diseases (GTDs), is of serious concern to the grape industry globally. This disease is caused by the fungus Eutypa lata but it is often seen in consortia growth with Phaeoacremonium minimum and Phaeomoniella chlamydospora. It is vital to understand the mechanisms for how this disease functions to develop control measures to combat it. Brown rot fungi are able to use a complex of low molecular weight (LMW) metabolites to induce a Fenton reaction to deconstruct woody tissue. These metabolites are part of a chelator mediated Fenton (CMF) chemistry that produces reactive oxygen …

Structure-Function Studies Of The Trypanosome Mitochondrial Replication Protein Polib, Raveen Armstrong

Masters Theses

Trypanosoma brucei and related protists are distinguished from all other eukaryotes by an unusual mitochondrial genome known as kinetoplast DNA (kDNA) that is a catenated network composed of minicircles and maxicircles. Replication of this single nucleoid involves a release, replicate, and reattach mechanism for the thousands of catenated minicircles and requires at least three DNA polymerase (POLIB, POLIC and POLID) with similarity to E. coli DNA polymerase I. Like other proofreading replicative DNA polymerases, POLIB has both an annotated polymerase domain and an exonuclease domain. Predictive modelling of POLIB indicates that it has the canonical right hand …

Factors Influencing Primate Hair Microbiome Diversity, Catherine Kitrinos

Masters Theses

Primate hair is both a substrate upon which essential social interactions occur and an important host-pathogen interface. As commensal microbes provide important immune functions for their hosts, understanding the microbial diversity in primate hair could provide insight into primate immunity and disease transmission. While studies of human hair and skin microbiomes show differences in microbial communities across body regions, little is known about the nonhuman primate hair microbiome. In this study, we collected hair samples (n=159) from 8 body regions across 12 nonhuman primate species housed at 3 US institutions to examine 1) the diversity and composition of the primate …

Investigating The Mechanisms And Specificity Of Bacterial Virulence In An Entomopathogenic Symbiosis, Elizabeth Ransone

Masters Theses

Microbial symbionts contribute to the health of their host in both positive and negative ways. In the Steinernema nematode symbiosis, Xenorhabdus symbionts traditionally mediate insect virulence by producing toxins and other virulence proteins against the insect prey that they both need for sustenance. In this work, I took a bidirectional approach to the question: what is the larger role of Xenorhabdus in virulence against insect prey? 1) I investigated a novel protein family, typified by the Xenorhabdus bovienii polymorphic protein (Xbpp) with strain-level protein diversity. I found that Xbpp contributes to X. bovienii virulence in a Manduca sexta tobacco hornworm …

Effects Of Traditional And Microbially-Focused Restoration Techniques On Soil Communities In Tallgrass Prairies, Zachary J. Whitacre

Masters Theses

Tallgrass prairies have virtually disappeared in many parts of their former range due to the conversion of this ecosystem to farmland. In more recent years there have been efforts to restore these prairies on reclaimed agricultural land. However, these restored prairies do not resemble their remnant counterparts in many ways, such as in soil microbial community composition and metrics related to carbon storage. In Chapter 1, I show that bacterial communities in a restored prairie and an adjacent remnant prairie in southwest Michigan differ in their immediate and longer-term responses to prescribed fire, a commonly used prairie restoration and maintenance …

Investigating Microbial Genes Involved In Plant Colonization And The Effects On Plant Microbiome Assembly, David Grant

Masters Theses

The use of chemical fertilizers and pesticides has had negative impacts on ecological systems and alternatives will be needed to both enhance agricultural production and remediate waste that has accumulated via fertilizer use. A promising alternative to tackle both problems utilizes beneficial organisms in microbial communities associated with plants, which are known as bioinoculants. However, the benefits of bioinoculants are inconsistent in field application and require more research in order to harness them in ways to make them a suitable replacement for chemical fertilizers. Here, I investigate characteristics required to enhance bioinoculant efficiency, including mechanisms required to increase microbial colonization …

The Shape Of U: Mapping Out Protective Elements In Mrna Escapees, Jacob Miles

Masters Theses

A crucial step of the viral life cycle of Kaposi’s Sarcoma Herpesvirus (KSHV) lytic infection is the triggering of a massive RNA decay event termed “Host Shutoff”. Host Shutoff is driven by the viral endonuclease SOX which leads to the destruction of over 70% of the total transcriptome. This process cripples cellular gene expression and allows for viral reprograming of the cell for the purpose of viral replication. Co-evolution has led to the host developing a multitude of antiviral defenses aimed at preserving certain cellular RNAs linked to antiviral responses. One such defense are RNA secondary structures located within the …

Phytophthora Capsici In Tennessee: Fungicide Resistance, Population Genetics And Cultural Control, Timothy Brent Siegenthaler

Masters Theses

Phytophthora capsici, a plant pathogenic oomycete, is the causal agent of the vegetable disease Phytophthora blight of pepper and cucurbits. Since the identification of P. capsici in 1922, a significant amount of research has been conducted to understand its biology and disease management. Despite this, little research had been conducted on this species in the state of Tennessee. Three studies were done from 2018 to 2020, focusing on fungicide resistance, population genetics, and testing management strategies in the field. In 2018 and 2019 a total of 248 isolate of P. capsici were collected from five counties in Tennessee. These isolates …

Carbon Metabolism In Cave Subaerial Biofilms, Victoria E. Frazier

Masters Theses

Subaerial biofilms (SABs) grow at the interface between the atmosphere and rock surfaces in terrestrial and subterranean environments around the world. Multi-colored SABs colonizing relatively dry and nutrient-limited cave surfaces are known to contain microbes putatively involved in chemolithoautotrophic processes using inorganic carbon like carbon dioxide (CO₂) or methane (CH₄). However, the importance of CO₂ and CH₄ to SAB biomass production has not been quantified, the environmental conditions influencing biomass production and diversity have not been thoroughly evaluated, and stable carbon and nitrogen isotope compositions have yet to be determined from epigenic cave SABs. …

Dietary Oligosaccharides Modulate Bifidobacterial Production Of The Neurotransmitter Gamma-Aminobutyric Acid, Michelle Rozycki

Masters Theses

Bifidobacteria are the predominant members of the infant gut, colonize adults to a lesser extent, and are recognized as beneficial microbes. Various bifidobacterial species produce ��-aminobutryic acid (GABA), the chief inhibitory neurotransmitter in the mammalian central nervous system. It is postulated that in order to produce GABA, the bifidobacterial genome must contain the gadB and gadC genes which encode a glutamate decarboxylase and a glutamate/GABA antiporter, respectively. Once exported by GadC, GABA is absorbed and transported systemically throughout the host. We hypothesize that specific dietary oligosaccharides will modulate bifidobacterial production of GABA due to varying intracellular concentrations of glutamate. To …

Lmea, A Conserved Cell-Envelope Protein In Mycobacteria, Is Important For Antibiotic Resistance And Cell Envelope Permeability, Sarah Hassan Osman

Masters Theses

The cell envelope of mycobacteria is critical for the survival and virulence of pathogenic species during infection, and its biosynthesis has been a proven drug target. Therefore, finding new targets in the biosynthetic pathway of cell envelope components is of great interest. Mycobacterium smegmatis is a model organism for the study of the devastating pathogen Mycobacterium tuberculosis. Previously, lipomannan elongation factor A (LmeA) has been identified as a cell envelope protein that is critical for the control of mannan chain length of lipomannan (LM) and lipoarabinomannan (LAM), lipoglycan components of the cell envelope. The deletion mutant, ∆lmeA, accumulates abnormal LM/LAM …

Utilization Of Emulsion Chemistries For Delivery And Antiviral Application Of Carvacrol, Hao-Yuan Hsu

Masters Theses

Human norovirus (HuNoVs) are the most common enteric pathogen around the world that cause ~50% of foodborne illness of disease outbreaks annually. HuNoVs are the member of the Caliciviridae family, which consist of small (38 nm), unenveloped, single stranded RNA (ssRNA) viruses. Norovirus are divided into 5 genogroup (GI, GII, GIII, GIV, GV, GVI and GVII). The GI, GII, and GIV cause human illness, in addition, GII.4 genotype cause the most human disease. Due to HuNoVs are difficult cultured in vitro, the cultivable HuNoVs surrogates have been widely studied. Recently, some studies have been conducted with HuNoVs surrogates, for …

Evaluation Of The Symbiotic Relation Between Endophyte And Poplar Trees Exposed To Landfill Leachate, Catalina Vega Hurtado

Masters Theses

“The contamination of soil and groundwater from leachate leakage from landfill has turned, nowadays, into a global public issue. One of the main concerns about this pollutant is the potential threat to human and ecosystem health. The current research studied endophyte bacteria in association with poplar trees (Populus sp.), as a method of bioremediation of landfill leachates. The objective of the project was to identify treatment strategies that may improve plant performance (survival rates, plant fitness, and degradation efficacy) with the purpose of being implemented in phytoremediation plots, aimed to intercept and treat landfill leachate, before the contamination of watershed. …

Studies On The Interaction And Organization Of Bacterial Proteins On Membranes, Mariana Brena

Masters Theses

Bacteria have developed various means of secreting proteins that can enter the host cell membrane. In this work I focus on two systems: cholesterol-dependent cytolysins and Type III Secretion.

Cholesterol is a molecule that is critical for physiological processes and cell membrane function. Not only can improper regulation lead to disease, but also the role cholesterol plays in cell function indicates it is an important molecule to understand. In response to this need, probes have been developed that detect cholesterol molecules in membranes. However, it has been recently shown that there is a need for probes that only respond to …

Xylan Metabolism By Caulobacter Crescentus, Viet Bui

Masters Theses

Bacteria present unique opportunities to explore the molecular mechanisms of nutrient acquisition processes at single cell level under various experimental conditions. Caulobacter crescentus is a gram-negative oligotrophic environmental bacterium with adaptive physiological responses, such as slow growth or complete arrest of cell cycle, presence of sessile and motile progenies with the sessile cells growing stalk to enhance nutrient uptake for growth in low-nutrient conditions. Details of plant polysaccharide-derived carbon compound, such as cellobiose, maltose, and xylose utilization by C. crescentus can be found but molecular details or mechanisms of polysaccharide utilization, such as xylan, has not been reported. Database analyses …

Detection Of Beta-Lactamase Variants In Municipal Wastewater And Fresh Water, Sunil Pandey

Masters Theses

The occurrence and spread of antibiotic-resistant genes (ARGs) are pressing public health problems worldwide. A key factor contributing to the spread of ARGs is lateral gene transfer. Wastewater treatment plants (WWTPs) are measured hot spots of microbial diversity and resistance because they receive polluted wastewater from diverse sources and contain a variety of different environments with dense bacterial loads. Due to the overuse of antibiotics the genetic capacities of microbes have profited. This helps every source of resistance gene and every means of horizontal gene transmission to develop the multiple mechanism of resistance to each antibiotic used clinically, agriculturally, or …