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Quantitative Characterization Of Microbial Ecologies In Dysbiosis And Infection, Eric Keen

Arts & Sciences Graduate Student Theses and Dissertations

In 1973, Theodosius Dobzhansky famously wrote that nothing in biology makes sense except in the light of evolution. Today, nearly 50 years later, little in microbiology – or in biology, for that matter – makes sense except in the light of genomics. Microbial genomics populates the field with innumerable testable hypotheses for evaluation in vitro and in vivo, allows us to monitor microbial populations in real time and at a massive scale, and underpins our approach to entire domains of microbiology, including microbial evolution. In this Thesis, I present three studies from my graduate research united by their common theme …

Causal Function And Bias Correlation Of The Orbitofrontal Cortex In Economic Choices, Shi Weikang

Arts & Sciences Graduate Student Theses and Dissertations

Economic choices entail two mental processes, value calculation and value comparison (Niehans, 1990). Studies in the last twenty years have shown that neurons in the orbitofrontal cortex (OFC) could support both processes. Namely, in the studies in which monkeys chose between two juice options with various amounts, three functional cell groups had been found in the OFC: offer value cells encode the value of individual juices, chosen juice cells encode the choice in a binary way and chosen value cells encode the value of the chosen juice (Padoa-Schioppa and Assad, 2006). These results suggest a decision circuit within OFC with …

Regulatory Effects Of The E. Coli Recbcd Nuclease Domain On Dna Unwinding Kinetics, Nicole Fazio

Arts & Sciences Graduate Student Theses and Dissertations

I have examined the effects of deleting the nuclease domain of the E. coli helicase RecBCD on the rates of ATP-independent DNA melting, single stranded (ss) DNA translocation, and double stranded (ds) DNA unwinding by RecBCD. The canonical role of the nuclease domain is DNA degradation, but the removal of this domain showed unexpected effects on other RecBCD activities including DNA binding, melting, and unwinding. This thesis presents a mechanistic study of DNA unwinding by RecBCD and a RecBCD variant with the nuclease domain deleted (RecBΔnucCD). I examined the rates of ssDNA translocation and dsDNA unwinding by RecBCD and RecBΔnucCD …

Slo2.1 Channels: A New Molecular Mechanism To Regulate Uterine Excitability, Juan Jose Ferreira

Arts & Sciences Graduate Student Theses and Dissertations

At the end of pregnancy, the uterus transitions from a non-contractile state to a highly contractile state. Two processes primarily drive this transition. First, from the 28th week of pregnancy until labor, the resting membrane potential of uterine (myometrial) smooth muscle cells (MSMCs) gradually becomes more positive (depolarizes) (Parkington et al. 1999). Second, at the end of pregnancy, MSMCs express more oxytocin receptors and become more sensitive to oxytocin (Kimura et al. 1996). However, the detailed mechanisms by which these processes occur have not been determined. My central hypothesis was that the Na+-activated K+ channel SLO2.1 plays a key role …

Surveillance And Dynamics Of Bacteria And Resistance Genes In Humans And Hospitals, Alaric Wences D'Souza

Arts & Sciences Graduate Student Theses and Dissertations

Bacteria live in, on, and around us. These bacteria affect human health through beneficial commensal interactions that promote normal development and through harmful infections or perturbations leading to disease. Understanding the prevalence, spread, and resilience of these bacteria in humans and human environments is critical to clinical medicine and epidemiology. I investigated environmental and human resident bacteria to understand dynamics in bacterial communities and how these dynamics may impact human health.Hospitals are one critical location of human-bacterial interactions. Bacteria can contaminate hospital surfaces from patients or environmental sources and subsequently transmit from surfaces to vulnerable patients. I analyzed bacteria from …

The Role Of Neuronal Atp-Sensitive Potassium Channels In Learning And Memory, Shaul Vladimir Yahil

Arts & Sciences Graduate Student Theses and Dissertations

ATP-sensitive potassium (KATP) channels link cellular metabolism and membrane excitability in many tissues, including brain and pancreas. Gain-of-function (GOF) mutations to KATP channels cause neonatal diabetes, with some patients exhibiting developmental delay, epilepsy, and neonatal diabetes (DEND) syndrome. Diabetic symptoms have been attributed to loss of membrane excitability and insulin secretion in pancreatic β-cells, though the origin of neurological deficits and the effects of neuronal KATP-GOF mutations more generally remain elusive. In this dissertation, I will present evidence that mice expressing KATP-GOF mutations pan-neuronally (nKATP-GOF) demonstrated sensorimotor and cognitive deficits, whereas hippocampus-specific hKATP-GOF mice exhibited predominantly learning and memory deficits. …

Detecting Apple Crop Pest Insects From Eptesicus Fuscus (Big Brown Bat) Feces Using Metabarcoding In Southern Michigan Apple Orchards, Randi Lesagonicz

Masters Projects

Michigan is ranked third in the U.S. for apple production. Michigan State University identified 78 pest insect species that cause damage to Michigan’s crop. Orchards using conventional and integrated pest management (IPM) spend thousands of dollars on pest control substances, which are hazardous to the environment and human health, and do not prevent 100% of crop damage and losses. The public’s increasing desire for “cleaner” foods has led to studies on how to incorporate more naturally occurring pest biocontrol agents. Bats have been recognized as pest insect biocontrol agents in numerous U.S. agroecosystems like corn, cotton, and pecans; however, little …

Greta Thunberg: A Small But Mighty Voice For The Environment, Madilyn Mortelliti

Faculty Curated Undergraduate Works

Abstract

This research paper discusses Greta Thunberg and the impact she has as a climate change activist. Thunberg faces many challenges as a young woman, but overcomes these difficulties while encouraging others to follow in her footsteps. She presents herself as a positive role model for younger generations. Thunberg has many accomplishments as an extremely young woman that leads to her global iconicity. She makes her power known in front of the highest ranked men in the world which forces legislation to make a change. Thunberg motivates others to make a difference before all hope is lost.

Investigating Antimicrobial Properties Of Snake Venoms Against B. Cereus, B. Subtilis, E. Coli, And P. Vulgaris, Savannah Elaine Berger

Honors Program Theses and Research Projects

The increasing incidence of antibiotic resistant bacterial infections has provoked the attention of health officials and scientists as a major threat to global public health. Antibiotic resistance is the product of overprescription by doctors, ineffective or shortened dosing by the patient, and more. When a bacterial infection is ineffectively treated as such, persistent pathogenic cells are given the opportunity to proliferate and spread their resistance to other cells. With bacteria utilizing such tools to fight and ultimately resist our current treatment methods, investigation towards the next novel mechanism of inhibition is essential. Venom is of particular interest to many scientists …

The Effects Of Molecular Chaperone Modulation On Protein Folding, Prion Formation, And Prion Propagation In Saccharomyces Cerevisiae, Leeran Blythe Dublin Ryan

Arts & Sciences Graduate Student Theses and Dissertations

Proper and efficient protein folding is vital for cell survival. Many factors affect protein folding fidelity and prion formation, including molecular chaperone availability and activity. Research has shown that modulating chaperone availability and function can affect protein misfolding and aggregation, as well as de novo prion formation and propagation. However, the factors involved and underlying mechanisms influencing prion formation and protein folding are largely unknown. The following work aims to elucidate these areas. The Nascent Polypeptide-Associated Complex (NAC) is the first point of chaperone contact for nascent polypeptides. Previous work has shown that disruption of the NAC leads to improved …

On Arousal And The Internal Regulation Of Brain Function: Theory And Evidence Across Modalities And Species, Ryan Raut

Arts & Sciences Graduate Student Theses and Dissertations

The brain is an organ. It is subject to the same physiological regulatory processes that engage the rest of the body’s organs, sculpted over hundreds of millions of years to sustain life so effectively. The central message of this thesis is that the holistic functioning of the brain, rather than operating at some level above or independent from these systemic regulatory processes, is deeply related to them. In short, as our limited attention spans might suggest: brain function is internally regulated. I propose that this internal regulation is a primary function of intrinsic brain activity. Chapter 2 provides a theoretical …

Virology: Mutagenizing The Proteolytic Cleavage Site In The Major Capsid Protein In Ssv1, Thejanee Liyanaarachchi

University Honors Theses

SSV1, spindle-shaped virus 1, is an archaeal virus with a unique shape that belongs to the family of fuselloviruses and infects hyperthermophilic archaea that thrive at 80°C and pH 3. SSV1 has two capsid proteins, VP1 and VP3, that presumably produce the lemon-shaped virion structure characteristic of fuselloviruses. The VP1 amino acid sequence is highly conserved among SSVs. Here, we investigate the importance of the proteolytic cleavage site in position E66 in VP1 by changing its glutamic acid to the other 19 amino acids. We have developed a new protocol for creating SSV1 mutants through HiFi Assembly (NEB) to increase …

Active Targeting Of Estrogen Receptor (Er)-Positive Breast Cancer Cells Using Nanotechnology, Molly White

Theses and Dissertations

The American Cancer Society has predicted an estimated 281,550 new invasive breast cancer cases for 2021. Chemotherapy is one of the main options available to treat this disease, but it can result in drug resistance and harmful side effects, as traditional methods do not directly target the cancer cells. To address this issue, nano formulations have been widely researched for targeted delivery of anticancer drugs. The primary objective of this project was to develop a novel nanodrug, rapamycin-loaded gold nanorods functionalized with polyethylene glycol and epithelial cell adhesion molecule (EpCAM), to selectively target breast cancer cells. The work involved characterizing …

Sex- And Age - Specific Migratory Strategies Of Blue Whales In The Northeast Pacific, Christina Blevins

Biology ETDs

Sequential subsampling of blue whale baleen plates can yield information of individual migratory plasticity of this endangered species in the northeast Pacific Ocean. We measured δ13C and δ15N isotope values along baleen from thirteen whales of different age and sex. Results showed sex/age-specific migratory strategies. Adult females exhibited relatively stable cyclical movements between temperate and subtropical regions. Adult males exhibited two strategies, most remained within temperate latitudes, whereas two migrated to subtropical latitudes. Movement patterns in juveniles were erratic. These patterns are potentially driven by energetic requirements of females, intraspecific competitions among adult males, and inexperience in locating prey in …

Water Color: Inspiring Conservation Of Freshwater Ecosystems By Painting With Algae, Kate Lochridge

Honors Projects

“Water Color: Inspiring Conservation of Freshwater Systems by Painting With Algae” is a project that focuses on raising awareness of harmful algal blooms in Lake Erie through the creation of algae-based paint. Its goal is to provide a multidisciplinary outlet for understanding complex interactions between the causes, effects, and solutions of Harmful Algal Blooms (HABs). The novel part of this project is the creation of watercolor paint from algae cells. This paint was used to create algae-based artwork that facilitates an aesthetic interaction with the science of HABs when other informative materials- such as journal articles- can be confusing and …

Processing Binding Data Using An Open-Source Workflow, Errol L G Samuel, Secondra L Holmes, Damian W Young

Faculty, Staff and Students Publications

The thermal shift assay (TSA)—also known as differential scanning fluorimetry (DSF), thermofluor, and Tm shift—is one of the most popular biophysical screening techniques used in fragment-based ligand discovery (FBLD) to detect protein–ligand interactions. By comparing the thermal stability of a target protein in the presence and absence of a ligand, potential binders can be identified. The technique is easy to set up, has low protein consumption, and can be run on most real-time polymerase chain reaction (PCR) instruments. While data analysis is straightforward in principle, it becomes cumbersome and time-consuming when the screens involve multiple 96- or 384-well plates. There …

An Insider's Guide To Cell Biology, Katie Ludwig

Honors Projects

An Insider's Guide to Cell Biology is a comic book that follows Alanine the amoeba who tells the reader all about how the cell works.

People That Score High On Psychopathic Traits Are Less Likely To Yawn Contagiously, Andrew Gallup, Mariska E. Kret, Omar T. Eldakar, Julia Folz, Jorg J. M. Massen

Biology Faculty Articles

Considerable variation exists in the contagiousness of yawning, and numerous studies have been conducted to investigate the proximate mechanisms involved in this response. Yet, findings within the psychological literature are mixed, with many studies conducted on relatively small and homogeneous samples. Here, we aimed to replicate and extend upon research suggesting a negative relationship between psychopathic traits and yawn contagion in community samples. In the largest study of contagious yawning to date (N = 458), which included both university students and community members from across 50 nationalities, participants completed an online study in which they self-reported on their yawn contagion …

An Investigation Of Chronic Pain As A Much-Neglected Symptom Of Hypermobile Ehlers-Danlos Syndrome, Sydney Collins

Honors Theses

Ehlers Danlos Syndrome is a group of heritable loose connective tissue disorders with 13 distinguished subtypes. The hypermobile type of Ehlers Danlos Syndrome (hEDS) is the most common subtype and is caused by a genetic mutation that leads to defective collagen fibrils. This leads to joint instability and hypermobility, skin elasticity, widespread pain, fatigue, and generalized tissue fragility. Chronic pain is reported to be a symptom in as high as 92% of the hEDS population (Voermans et al., 2010); despite this prevalence, there is a significant lack of research, awareness, and treatment standardization regarding pain in hEDS. This literature review …

The Art Of Amphibian Conservation: Linking In-Situ And Ex-Situ Populations Of Endangered Species Through Genome Banking, Isabella Joann Burger

Theses and Dissertations

Limited breeding success in captive breeding programs has necessitated the development of assisted reproductive technologies (ART) to preserve and increase genetic variation and population numbers of both captive and wild amphibian groups. ART has been shown to be successful in numerous anuran species, and current studies focus on the application of ART in ex-situ populations. The focus of this project is to show that linking in-situ and ex-situ amphibian populations through sperm cryopreservation, genome banking, and in-vitro fertilization is possible, with the goal of increasing gene diversity throughout groups in order to produce self-sustaining, wild populations in the future. Specific …

Synthetic Hagfish Slime Mimetics: Mechanical Characterization, Hayden Johns, Spencer Walker

Fall Student Research Symposium 2021

Hagfish are ancient animals that eject a slime when attacked by predators. The slime that the hagfish emit is almost entirely composed of water but protein strands within the slime cause the slime to have incredible strength. However, these protein strands will be formed synthetically for the purposes of our experiment. To defend against foes, the Navy launches plastic ropes into the propellers of enemy warships in order to decrease the thrust of the motors. In a push to find a more biodegradable solution, the utilization of hagfish slime has shown great promise in stopping propellers.While we know that the …

Effect Of Basal Diet And Black Raspberry Supplementation On Gene Biomarkers Of "Leaky Gut" In Mouse Model Of Colitis-Associated Colorectal Cancer, Eliza Stewart

Fall Student Research Symposium 2021

Colorectal cancer is currently the third leading cause of cancer death in the world. The risk of developing colorectal cancer increases significantly in individuals who suffer from colitis, which is inflammation of the colon lining, seen in Irritable Bowel Disease. The term “leaky gut” is often used to describe increased intestinal permeability and is closely related to colitis. Leaky gut is associated with dysbiosis of the gut microbiota, which can occur through diet. This dysbiosis leads to pro-longed inflammation and affects genes that encode for proteins involved in the tight junctions between cells. Compromised intestinal integrity allows for translocation of …

The Scoop On Composting: A Comprehensive Literature Review On Composting With A Focus On Grand Valley State University, Alexandria Snabes

Honors Projects

This comprehensive review discusses the main microbial processes, methods, efficiency strategies, benefits, and drawbacks related to composting. Specifically, anaerobic, aerobic, and intermediate, or cold composting, decomposition processes are defined and assessed. This leads into a discussion of some common methods of composting, both large- and small-scale, which utilize these microbial processes to result in differing advantages and disadvantages. The efficiency of these methods can be increased using strategies that monitor oxygen levels, moisture levels, temperate levels, and overall size. Some benefits of composting discussed include diverting waste from landfills, improving soil nutrition and quality long-term, and increasing plant growth and …

Aquaporin Expression And Cholesterol Content In Eel Swimbladder Tissue, Victoria Drechsel, Gabriel Schneebauer, Birgit Fiechtner, Christopher P. Cutler, Bernd Pelster

Biology: Faculty Publications

Leakiness of the swimbladder wall of teleost fishes must be prevented to avoid diffusional loss of gases out of the swimbladder. Guanine incrustation as well as high concentrations of cholesterol in swimbladder membranes in midwater and deep-sea fish has been connected to a reduced gas permeability of the swimbladder wall. On the contrary, the swimbladder is filled by diffusion of gases, mainly oxygen and CO2, from the blood and the gas gland cells into the swimbladder lumen. In swimbladder tissue of the zebrafish and the Japanese eel, aquaporin mRNA has been detected, and the aquaporin protein has been considered important …

Surface Architecture Of The Mouth Cavity Of Pagellus Affinis (Boulenger, 1888), Kamal Ahmed Baaoom, Manal Haj Obbed

Hadhramout University Journal of Natural & Applied Sciences

The topological characteristics of the mouth cavity of the carnivorous fish Pagellus affinis was studied by using a light microscope. The results revealed that all the teeth of P. affinis are pointed and canine-like, papilliform teeth present on the premaxillae and the anterior regions of the dentaries are associated with seizing, grasping and holding of prey. The morphology and distribution of different taste buds of P. affinis were predominantly localized at the anterior and tongue regions of the mouth cavity. Two types of taste buds are elevated from the epithelium at different levels, which may be useful for ensuring full …

Field Study To Identify The Composition Of Plant Vegetation In Wadi Al- Ain - Hadramout – Yemen, Murad Mohammed Kanji, Mohammed Saeed Bn Qadim, Alawiya Abdullah Al Awad, Abdulkarim Saber Ali

Hadhramout University Journal of Natural & Applied Sciences

This study was conducted during the period of April 2016 - December 2017 to determine the plant vegetation of Wadi Al-Ain. The results of the field survey identified a total of 86 plant species 37 families and 77 genera, including 58 wild plant species grown naturally. The total number of cultivated plants was 26 plant species, but only two plant species are grown as both wild and cultivated species. The number of plant species that appeared as an ecological form of shrubs reached 34 plant species, while the number of plant species that appeared ecologically in the form of herbs …

The Effect Of Flaveria Trinervia Plant Extract On Germination And Growth Of Onion Seeds (Allium Cepa L), Mahrous Abdullah Bahoirth, Yaser Saeed Bahurmuz

Hadhramout University Journal of Natural & Applied Sciences

This part of the study applied in the laboratory experiment to know the effect of water extracts of the vegetation and rootlet of the Flaveria trinervia in the four levels (0,10,20,30%) on germination and growth onion seeds. These crop was added 10 seeds in a petri dish, and 5 mL of the extract was added, with four replicates per treatment. After two weeks, the measurements were taken on the studied traits (germination ratio, speed, length of the plumule, the rootlet, the soft and dry weight of the plumule and the rootlet). The results showed that the effect of the rootlet …

A Survey Of Weeds Present In Al- Qatten Diroctorate Farms Hadhramout Governorate, Yaser Saeed Bahurmuz, Ahmed Subait Bamosa, Abdulgader Ali Hassan

Hadhramout University Journal of Natural & Applied Sciences

An exclusive study of weeds present in Alqatten Directorate farms, was carried out this study aimed to identify types and number of weeds in the farms. The study area included (20) Farms in five different regions. 39 plant species belonging to 20 plant Family have been identified. Grassy famil was the most present with 7 species. the most wide spread grass was, Cynodon dactylon and Setaria verticillata; as they were found in all studied farms. While Withania somnifera and Rhazya stricta, were less prevalent, as they were present in two farms only.The study reveals that there is defference in the …

Limited Range-Filling Among Endemic Forest Herbs Of Eastern North America And Its Implications For Conservation With Climate Change, Stephanie K. Erlandson, Jesse Bellemare, David A. Moeller

Biological Sciences: Faculty Publications

Biodiversity hotspots host a high diversity of narrowly distributed endemic species, which are increasingly threatened by climate change. In eastern North America, the highest concentration of plant diversity and endemism occurs in the Southern Appalachian Mountains (SAM). It has been hypothesized that this region served as a refugium during Pleistocene glacial cycles and that postglacial migration northward was dispersal limited. We tested this hypothesis using species distribution models for eight forest herb species. We also quantified the extent to which the geography of suitable habitat shifted away from the current range with climate change. We developed species distribution models for …

Annotated Checklist Of The Bryophytes Observed At The Gordon Natural Area West Chester University, Pa) 2007-2021. Version Ii, Nur Ritter, Noah Long

Gordon Natural Area Baseline Plant Survey Documents

Summary: Data Number of Taxa: 38 Species, in 31 Genera, 24 Families, and 13 Orders.

Description: The bryophytes are an informal group that is composed of three divisions of non-vascular plants: the liverworts, hornworts, and mosses. Of these, the mosses are the most familiar to most people, but the three groups are similar in appearance, and differ only in their reproductive structures. All bryophytes lack specialized tissues for transporting resources (i.e., vascular tissue); hence, they are characteristically small in stature. Additionally, bryophytes do not produce flowers or seeds; rather, reproduction is through spores. Bryophytes have received relatively little investigation at …