Life Sciences Commons^™

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 …

Effect Of Biofertilizer In Organic And Conventional Systems On Growth, Yield And Baking Quality Of Hard Red Winter Wheat, Ammar Al-Zubade, Timothy D. Phillips, Mark A. Williams, Krista L. Jacobsen, David Van Sanford

Horticulture Faculty Publications

A two-year study (harvest years 2019 and 2020) was conducted to investigate the effect of a commercially available biofertilizer, in combination with variable nitrogen (N) rate, on bread baking quality and agronomic traits in hard winter wheat grown in conventional (CONV) and organic (ORG) farming systems in Kentucky, USA. The hard red winter wheat cultivar ‘Vision 45’ was used with three N rates (44, 89.6 and 134.5 kg/ha as Low, Med and High, respectively) and three biofertilizer spray regimes (no spray, one spray and two sprays). All traits measured were significantly affected by the agricultural production system (CONV or ORG) …

Finland, A Package Deal: Disciplinary Climate In Science Classes, Science Dispositions And Science Literacy, Larry J. Grabau, Jari Levonen, Kalle Juuti

Plant and Soil Sciences Faculty Publications

Finland’s educational prowess, though tempered by recent international assessments, has remained intact. This report focused on lessons that could be learned regarding secondary-level science education from the Program for International Student Assessment (PISA) 2015, science-focused assessment. That PISA iteration included not only science literacy but also students’ science dispositions (epistemology, enjoyment, interest, and self-efficacy) and the schools’ science climate measures (disciplinary climate and teaching support). Due to the hierarchical nature of the PISA data, multilevel models were employed in this Finnish study, involving 5582 students from 167 schools. Science dispositions (as outcome measures) were differently associated with teaching support and …

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 …

Cold Conditioned: Discovery Of Novel Alleles For Low-Temperature Tolerance In The Vavilov Barley Collection, Ahmad H. Sallam, Kevin P. Smith, Gongshe Hu, Jamie Sherman, Peter Stephen Baeziger, Jochum Wiersma, Carl Duley, Eric J. Stockinger, Mark E. Sorrells, Tamas Szinyei, Igor G. Loskutov, Olga N. Kovaleva, Jed Eberly, Brian J. Steffenson

Department of Agronomy and Horticulture: Faculty Publications

Climate changes leading to higher summer temperatures can adversely affect cool season crops like spring barley. In the Upper Midwest region of the United States, one option for escaping this stress factor is to plant winter or facultative type cultivars in the autumn and then harvest in early summer before the onset of high-temperature stress. However, the major challenge in breeding such cultivars is incorporating sufficient winter hardiness to survive the extremely low temperatures that commonly occur in this production region. To broaden the genetic base for winter hardiness in the University of Minnesota breeding program, 2,214 accessions from the …

Mixture Design Response Surface Methodology Analysis Of Seven Natural Bioactive Compounds To Treat Prostate Cancer, Ian Geddes Berlin

Theses and Dissertations

Natural bioactive compounds have drawn the interest of many researchers worldwide in their effort to find novel treatments, including prostate cancer (PC) treatment which is estimated to be 13.1% of all new cancer cases in the U.S. in 2021. Many of these bioactive compounds have been identified from treatments in traditional Chinese medicine (TCM), that often have multiple bioactive compounds present. However, in vitro studies frequently focus on the compounds in isolation, or in simple combinations of two compounds. We used mixture design response surface methodology (MDRSM) to assess changes in PC cell viability after 48 hours of treatment to …

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 …

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 …

On The Challenges And Rewards Of Analyzing Molecular Dynamics At The Terabyte And Millisecond Scale, Justin Roy Porter

Arts & Sciences Graduate Student Theses and Dissertations

Molecular Dynamics (MD) and Markov state models (MSMs) are powerful tools for estimating and concisely representing the conformational ensemble accessible to biological macromolecules, particularly proteins. Conformational ensembles are of special importance biological function, both in health and disease, because biology derives from molecules’ entire conformational distribution rather than any single structure. Consequently, MD is poised to become a powerful tool for personalized medicine and for the study of molecular sequence-function relationships generally. However, because of their hyperdimensionality and size, just generating MD datasets and Markov state models (MSMs) that represent biologically relevant molecules is a substantive technical challenge. Then, even …

Influence Of Aging And Cerebrovascular Disease On Neuroimaging Measures Of Alzheimer Disease, Lauren Nicole Koenig

Arts & Sciences Graduate Student Theses and Dissertations

The overall goal of this dissertation is to gain a better understanding of how Alzheimer disease relates to normal aging and cerebrovascular disease to impact neuroimaging measures in a clinically meaningful way. Both aging and cerebrovascular disease are known to influence measures of Alzheimer disease, making it difficult to separate what changes are attributable specifically to Alzheimer disease. We hypothesize that a better understanding of these relationships will allow future studies to appropriately take these factors into account. In Chapters 2 and 3 we attempt to separate out the influences of normal aging and Alzheimer disease on measures of atrophy. …

Deconvolving Genomic Regulatory Heterogeneity With Self-Reporting Transposons, Arnav Moudgil

Arts & Sciences Graduate Student Theses and Dissertations

A cell’s identity is a function of the genes expressed in that cell, which are in turn regulated by transcription factors. Over the last decade, single-cell RNA sequencing (RNA-seq) has emerged as a powerful class of techniques to characterize cellular diversity in heterogeneous tissues. These methods barcode transcripts by their cell-of-origin and assign them to specific genes. The resulting high-dimensional data are further processed to reveal clusters of cells sharing transcriptional states. Annotating these clusters, based on either known or discovered marker genes, offers a glimpse into the dynamic composition of an organ or biological process. While single-cell RNA-seq excels …

Defining The Epigenetic And Transcriptional Regulatory Mechanisms By Which Hrsv Ns1 Alters Host Transcriptional Response, Nina Rose Beri

Arts & Sciences Graduate Student Theses and Dissertations

No abstract provided.

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.

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 …

Genetic Diversity Of Huaya India (Melicoccus Oliviformis Kunth), A Neglected Neotropical Fruit Crop, Mónica I. Jiménez-Rojas, Rubén H. Andueza-Noh, Obed I. Noh-Ake, Daniel Potter, Matilde M. Ortiz-García, Renee S. Arias, Jaime Martínez-Castillo

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Currently, some species of Sapindaceae are important fruit crops worldwide. The Huaya India (Meliccocus oliviformis, Sapindaceae) is a neglected Neotropical fruit tree consumed locally in the Maya Lowlands of Mexico, where it exists in both wild and domesticated forms. Our objective was to evaluate the genetic diversity of the Huaya India in its possible domestication area and thus generate knowledge that serves as the basis for a commercial management. A total of 450 individuals collected from 15 natural vegetation sites and 15 Maya villages, were characterized using nine microsatellite loci and population genetics approaches were applied. STRUCTURE, Neighbor-Joining and PCoA …

Characterization Of Bacteriophage Targeting Bacillus Licheniformis In Milk Processes And Thermal Stability Of Bacteriophage During Htst Pasteurization, Jeremy Robert Arbon

Theses and Dissertations

An array of Bacillus licheniformis strains were isolated from a commercial powdered milk process. Bacteriophages exhibiting activity against B. licheniformis were isolated from cattle manure and effluent samples destined for a lagoon at a dairy farm. After sequencing, 8 of the 10 phages were found to be novel and genetically differentiated. Transmission electron scanning microscopy (TSEM) was performed. All bacteriophages were of the family Herelleviridae with contractile tail sheaths ranging from 80µm to 150µm and, surprisingly, survived a common fluid milk processing treatment used to inactivate vegetative cells. The survival of the phage after high temperature short time pasteurization of …

“Data Architecture For Pharmaceutical Product Development At Alkermes”, Peter Couture, Damon Warnock, Marcus O'Mahony

Level 3

This paper describes how Alkermes built a data architecture for efficient management of non-GXP and R&D data. Using a ‘Create’, ‘Store’, Describe’ ‘Access’ stepwise model, the ingredients to making the journey a success are described.

Driver Liability For Farm And Ranch Operations, Jessica Groskopf

Cornhusker Economics

One major concern of farming and/or ranching operations is the liability of semi-trucks and equipment when they are involved in a traffic accident.

Hyperlocal Air Quality Exposure Assessment To Support Health Studies, Pradeep Prathibha

McKelvey School of Engineering Graduate Student Theses & Dissertations

Hyperlocal air pollution exposure is driven by local emission sources, meteorology, and the built environment, with traffic-related emissions modulating primary and secondary pollutant concentrations against a variable background of similar contaminants from other sources. Recent studies show that intra-urban air quality has temporally persistent patterns that sharply vary 5-8 times within a city block; currently, regulatory ambient air quality monitoring (2-5 fixed-site monitors per 1000 km2 in U.S. census urban areas) cannot capture exposure at this spatial resolution. This dissertation aims to advance methods relying on fixed-site and mobile measurements using high-time resolution aerosol instruments as well as low-cost sensors …

Identification Of Candidate Microbial Biomarkers Of Disease And Design Of Engineered Microbial Therapeutics For The Gut Microbiome, Aura Lucia Ferreiro

McKelvey School of Engineering Graduate Student Theses & Dissertations

The human gut microbiome is a compositionally and functionally diverse community of microorganisms that profoundly influences the health of the host. Deep characterization of gut microbiomes via high-throughput sequencing has identified associations between the gut microbiome and disease states, and spurred development of engineered microbial therapeutics. Successful translation of these research efforts to the clinic will involve i) consideration of how engineered microbes behave and adapt in the gut, towards the implementation of biosafety mechanisms, and ii) identification and validation of microbial biomarkers of disease. This dissertation describes both investigative (Chapter 2) and engineering (Chapters 3 and 4) approaches to …

Defining The Role Of Elastic Fibers In Tendon Mechanics, Jeremy D. Eekhoff

McKelvey School of Engineering Graduate Student Theses & Dissertations

Tendons serve as a linking component of the musculoskeletal system by transferring forces between muscle and bone. As such, the structural proteins of the tendon extracellular matrix are of vital importance for the tissue to function properly and maintain its mechanical integrity. Collagen is the principal constituent of tendon and makes up its aligned hierarchical organization. Other structural proteins, such as elastin, are in comparison understudied and not well understood in relation to tendon function. Elastin, the main component of elastic fibers, has unique mechanical properties including high extensibility, fatigue resistance, and elasticity; these properties are important for elastin-rich tissues …

Quantifying Components Of Protein Translation And Metabolite Heterogeneity In Isogenic Microbial Populations, Alexander Schmitz

McKelvey School of Engineering Graduate Student Theses & Dissertations

Cell-to-cell variation in gene expression and metabolite levels have a significant impact on ensemble productivity of microbial bioproduction. New metabolic engineering tools and approaches are needed that consider cell cultures as an amalgam of uniquely behaving individuals to improve the slow commercialization of metabolically engineered systems. Stochastic cellular process including gene expression, metabolism, and growth lead to phenotypic variation between genetically identical cells. Understanding and the ability to control microbial phenotypic variation is key to improving microbial bioproduction metrics. During protein translation, codon usage strongly influences ensemble gene expression but the effect on the variation of gene expression was not …

A Study On The Hormonal Regulation And Novel Role Of Na+ Leak Channel, Non-Selective (Nalcn) In Human Myometrial Smooth Muscle Cells, Chinwendu Amazu

Arts & Sciences Graduate Student Theses and Dissertations

During pregnancy, the uterus transitions from a quiescent state to an excitable, highly contractile state to deliver the fetus. Two important contributors essential for this transition are progesterone (P4) and estrogen (E2), which promote quiescence or contraction, respectively, by acting on the myometrial smooth muscle cells (MSMCs). While these hormones regulate uterine contractions, it is unclear how they affect electrical activity of MSMCs, which underlies uterine contractile activity. Our lab recently identified Na+ leak channel, non-selective (NALCN) as a component of the leak current in human MSMCs and showed that mice lacking NALCN in the uterus have dysfunctional labor. In …

Regional Reprogramming And The Small Intestine: Analysis And Modeling Of Adaptive Regeneration Of The Epithelium, Sarah Elizabeth Waye

Arts & Sciences Graduate Student Theses and Dissertations

The small intestine in homeostasis is capable of regular regeneration, but in cases of massive injury like Short Bowel Syndrome, the innate human response often fails to fully compensate for the loss of nutrient absorptive surface area that accompanies bowel resection. Murine models display an active compensatory reaction deemed “adaptation” in which the surface area of the bowel is increased to accommodate nutrient absorptive needs. This observation has highlighted several gaps in knowledge regarding bowel adaptation. Firstly, what occurs on a molecular level in murine models during adaptation? Secondly, how can the findings in mice be applied to humans in …

Identification Of Multi-Tissue Protein Quantitative Trait Loci And Causal Inference Of Protein Effects In Neurological And Other Complex Human Diseases Via Mendelian Randomization, Chengran Yang

Arts & Sciences Graduate Student Theses and Dissertations

Alzheimer disease (AD) is the most common neurodegenerative disease, affecting 6.2 million people mostly aged 65 years or older in the United States as of early 2021. AD has been widely studied and characterized worldwide, but there is still no effective treatment or cure. Even the latest FDA-approved treatment, Aducanumab, cannot stop decline or improve cognition. To develop a truly effective treatments, researchers keep discovering genetic and molecular mechanisms underlying the disease. Protein biomarkers are keys to bridge the mechanisms to disease. Here, I first used a high-throughput proteomic dataset from three tissues (CSF, plasma, and brain) with array-based genotype …

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 …

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. …

Weedy Rice As A Model System For The Study Of Microevolutionary Interactions In Agricultural Contexts, Marshall Jon Wedger

Arts & Sciences Graduate Student Theses and Dissertations

Just under one-half of the global population relies on cultivated rice (Oryza sativa) astheir primary source of calories, making the optimization of rice agriculture immensely important. One of the primary constraints to rice agriculture is the de-domesticated (feral) form of rice known as ‘weedy rice’ that aggressively competes for space, soil nutrients, and light. Heavy infestation can reduce crop yields by as much as 80%. As a closely-related weedy descendant of cultivated rice, chemical control is difficult in rice fields, and physical weeding is labor intensive, time consuming, and largely ineffective due to early life-stage mimicry of the crop. Weedy …

Genetic Risk Factors For Neurodevelopmental Disorders: Insights From Hipsc-Cerebral Organoids, Michelle L. Wegscheid

Arts & Sciences Graduate Student Theses and Dissertations

Neurofibromatosis type 1 (NF1) is a common neurodevelopmental disorder (NDD) characterized by remarkable phenotypic variability, where affected children manifest a spectrum of central nervous system (CNS) abnormalities, including brain tumors, impairments in attention, behavior, learning disabilities, and an increased incidence of autism spectrum disorder (ASD). A significant barrier to the implementation of precision medicine strategies for children with NF1 is a lack of prognostic risk factors to guide clinical management. However, emerging population-based genotype-phenotype association studies have suggested that the germline NF1 gene mutation may represent one clinically actionable risk factor for NF1-associated neurodevelopmental abnormalities. As a critical step in …

Human Plcg2 Haploinsufficiency Results In A Novel Immunodeficiency, Joshua Brandon Alinger

Arts & Sciences Graduate Student Theses and Dissertations

NK cells are critical for the recognition and lysis of herpesvirus-infected cells. Patients with NK cell immunodeficiency may suffer from unusually severe and/or recurrent herpesvirus infections; however, the genetic cause is frequently unknown. PLCG2 encodes a signaling protein in NK cell and B cell receptor signaling, in which dominant-negative or gain-of-function mutations may cause cold urticaria, antibody deficiency, or autoinflammation. However, loss-of-function mutations and PLCG2 haploinsufficiency have never been reported in human disease. We examined 2 families with autosomal dominant NK cell immunodeficiency with dual high-dimensional techniques, mass cytometry and whole-exome sequencing, to identify the cause of disease. We identified …