Life Sciences Commons^™

Cooperation And Conflict In The Social Amoeba Dictyostelium Discoideum And Its Paraburkholderia Endosymbionts, James Medina

Arts & Sciences Graduate Student Theses and Dissertations

A big question in biology is how organisms compete in an environment of competitors for scarce resources. Part of the answer lies in distinguishing friend from foe and in forging cooperative bonds in the face of cheaters. The social amoeba – bacteria system I have studied here is an excellent place to explore these tensions. The first part of my thesis research involves a review of cooperation and conflict in the social amoeba Dictyostelium discoideum and a study of the limits on obligate social cheating in this species. The second part focuses on the benefits of associating with D. discoideum …

Inferring Adaptation In Social Microbes From Experimental Evolution Under Relaxed Selection, Tyler John Larsen

Arts & Sciences Graduate Student Theses and Dissertations

Microbes exist against a backdrop of other organisms, and the interactions between microbes have major consequences on their traits, their evolution, and their impact on the world. Microbial interactions and the adaptations that enable them are extremely diverse – they can unlock abilities beyond the reach of individual cells or lead to a population’s destruction, they can be temporary or permanent, they can be between genetically identical cells or different species entirely. The first chapter of this dissertation reviews microbial interactions and the related concept of the evolution of conflict and cooperation.To be certain a trait is an adaptation at …

The Enemy Within: An Investigation Of The Intracellular Bacteria In Urinary Tract Infections, Jennie Elizabeth Hazen

Arts & Sciences Graduate Student Theses and Dissertations

Urinary tract infections (UTIs) are common diseases that are associated with significant morbidities. Multiple studies have indicated that multiple species of uropathogenesis bacteria invade and persist within bladder epithelial cells as a necessary step of uropathogenesis. Interestingly, many of these species are not canonically associated with intracellular infections. Although the first study describing bacteria within the urothelium was published two decades ago, this critical step of uropathogenesis remains relatively understudied.I established a murine model of community-acquired A. baumannii UTI, a previously unstudied manifestation of the disease. While immunocompetent mice resolved their infections quickly, immunocompromised mice displayed high bacterial burdens throughout …

A Universal Mechanism Of G Protein Inhibition, Tyson Daniel Todd

Arts & Sciences Graduate Student Theses and Dissertations

G protein coupled receptors transduce a truly staggering number of diverse extracellular signals including chemical messengers, physical force, and even photons into specific cellular responses through their coupling to heterotrimeric G proteins. G proteins amplify the originating signal through their binding to downstream effectors, activating a complex network of overlapping responses that allow the cell to respond perfectly to that specific stimulus. It is critical to the cell that this process is carried out faithfully in order to respond to the myriad environmental cues and avoid injury, exhaustion, and death for the individual cell or the development of pathology if …

Genetic And Transcriptomic Aspects Of Major Depressive Disorder: In Vivo Functional Assays Of Risk-Associated Variation, Candidate Disease Cell Types, And Their Pharmacologic And Sex Interactions, Bernard Mulvey

Arts & Sciences Graduate Student Theses and Dissertations

Major depressive disorder (MDD) is a debilitating illness that affects hundreds of millions globally, with substantial personal, medical, economic, and societal consequences. While depression occurs more commonly in females, the biology of the brain and sex underlying this skewed prevalence remains unclarified. This body of work explores two aspects of how biological sex may influence the brain at the level of gene expression: through intrinsic sex differences and through sex-mediated effects of depression risk genetics.The monoamine hypothesis of depression suggests that modulatory neurotransmitters including serotonin and norepinephrine constitute a key axis in development of MDD. Large-scale studies of MDD treatment …

Mechanisms For High Light Tolerance In A Fast-Growing Cyanobacterium, Patricia Walker

Arts & Sciences Graduate Student Theses and Dissertations

Through oxygenic photosynthesis, cyanobacteria, algae, and plants convert light into chemical energy. However, highly energetic light often damages the photosynthetic apparatus, which can lead to the decline of photosynthetic activity (photoinhibition), and prolonged photoinhibition can lead to cell death. Cyanobacteria enact various protective mechanisms to mitigate photodamage, many of which have been conserved in plants. Repair of PSII reaction centers, decreased light absorption, quenching of excess absorbed energy, and biosynthesis of antioxidants all work to mitigate damage during high light. Due to the adjustments to photosynthesis, acclimation to high light requires remodeling of cellular metabolism and physiology. Therefore, phototrophs have …

Roles Of Behavioral Novelty And Organismal Energetics In The Evolution Of Extreme Encephalization, Erika Laurie Schumacher

Arts & Sciences Graduate Student Theses and Dissertations

Brains and their component brain regions vary widely in size and structure across vertebrates. However, extreme increases in total brain size relative to body size (extreme encephalization) and increases in specific major brain region sizes independent of other brain regions (mosaic brain evolution) are relatively rare. There are several hypotheses as to why, but the energetic cost of increased brain tissue and the regional interconnectedness in both brain development and function likely constrain how brains are able to change in response to selection. In this dissertation, I sought to address both how behavioral novelty relates to evolutionary changes in brain …

Dysregulation Of Gene Expression In Non-Photosensitive Trichothiodystrophy, Brittany Townley

Arts & Sciences Graduate Student Theses and Dissertations

The pre-mRNA life cycle requires intron processing; yet, how intron processing defects influence splicing and gene expression is unclear. Here, we find TTDN1, which is frequently mutated in non-photosensitive trichothiodystrophy (NP-TTD), functionally links intron lariat processing to the spliceosome. The conserved TTDN1 C-terminal region directly binds lariat debranching enzyme DBR1, while its N-terminal intrinsically disordered region (IDR) binds the intron binding complex (IBC). The IDR forms condensates in vitro and is needed for IBC interaction. TTDN1 loss causes significant intron lariat accumulation, as well as splicing and gene expression defects, mirroring phenotypes observed in NP-TTD patient cells. Ttdn1∆/∆ mice recapitulate …

Mechanisms Regulating Photoreceptor Subtype Specification And Chromophore Utilization In Zebrafish, Leo Volkov

Arts & Sciences Graduate Student Theses and Dissertations

The first step in vision is the detection of light by a photoreceptor cell. The spectral sensitivity of a photoreceptor, in turn, is determined by the composition of its visual pigment, which consists of an opsin protein and a covalently bound chromophore derived from either vitamin A1 or vitamin A2. In the course of evolution, opsin gene duplication and functional divergence led to the emergence of four distinctive cone opsins, maximally sensitive to ultraviolet (UV), blue, green, or red light, as well as the rod opsin. Subsequently, the expression of these functionally distinct opsins was segregated into distinct cell types …

Understanding Gene Regulation With High-Throughput Genome-Integrated Reporter Assays, Clarice Hong

Arts & Sciences Graduate Student Theses and Dissertations

Proper spatiotemporal gene expression depends on specific interactions between cis-regulatory sequences (CRSs) and chromatin modifications at a genomic location. However, we do not yet understand the rules that determine how CRSs work together to influence gene expression. The goal of this thesis is to systematically assay and quantify how different genomic environments interact with CRSs to control gene expression output using a variety of genome-integrated massively parallel reporter assays (MPRAs). First, we tested the hypothesis that core promoters confer specificity by only responding to compatible enhancers and chromatin in specific genomic environments. We measured the activities of hundreds of core …

Pavement Ants (Tetramorium Immigrans Santschi), Ryan S. Davis, Lori R. Spears, Austin Taylor

All Current Publications

This fact sheet describes pavement ants. It covers identification, biology and habits, and management.

Invasive Fruit Pest Guide For Utah: Insect & Disease Identification, Monitoring & Management, Claudia Nischwitz, Diane G. Alston, Lori R. Spears, Clint Burfitt

All Current Publications

This invasive fruit pest guide covers insects and diseases affecting fruit in Utah and reviews monitoring and management.

Japanese Beetle (Popillia Japonica Newman), Lori R. Spears, Diane G. Alston, Joey Caputo, Erin Hodgson, Cory Stanley, Kristopher Watson

All Current Publications

This fact sheet describes Japanese beetles and reviews damage symptoms, life cycle, monitoring, and management.

Invasive Pests Of Landscape Trees In Utah, Lori R. Spears, Ann Mull, Anna Fabiszak, Marion Murray, Ryan Davis, Diane G. Alston, Ricardo Ramirez

All Current Publications

This guide provides an overview of the Utah First Detector Program and how to submit samples. The guide reviews the diseases and insects that affect landscape trees in Utah.

Invasive Species Handbook: A Resource For Educators - Grades 3-8, Natalie D'Souza, Marion Murray, Lori R. Spears

All Current Publications

This handbook includes six chapters that discuss invasive species and their environmental, economic, and health impacts. It also reviews pathways of invasive species spread and prevention, monitoring, and control. The handbook is a resource for educators teaching children in grades 3 through 8. Learning objectives, activities, and vocabulary are also included.

3d Imaging Analysis On An Organoid-Based Platform Guides Personalized Treatment In Pancreatic Ductal Adenocarcinoma, Ya'an Kang, Jenying Deng, Jianhua Ling, Xinqun Li, Yi-Ju Chiang, Huamin Wang, Paul J Chiao, Mark W Hurd, Manoop S Bhutani, Jeffrey H Lee, Brian R Weston, Anirban Maitra, Naruhiko Ikoma, Ching-Wei D Tzeng, Jeffrey E Lee, Ronald A Depinho, Robert A Wolff, Shubham Pant, Florencia Mcallister, Matthew Hg Katz, Jason B Fleming, Michael P Kim

Faculty, Staff and Student Publications

BACKGROUNDPancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignancies, with unpredictable responses to chemotherapy. Approaches to assay patient tumors before treatment and identify effective treatment regimens based on tumor sensitivities are lacking. We developed an organoid-based platform (OBP) to visually quantify patient-derived organoid (PDO) responses to drug treatments and associated tumor-stroma modulation for personalized PDAC therapy.METHODSWe retrospectively quantified apoptotic responses and tumor-stroma cell proportions in PDOs via 3D immunofluorescence imaging through annexin A5, α-smooth muscle actin (α-SMA), and cytokeratin 19 (CK-19) levels. Simultaneously, an ex vivo organoid drug sensitivity assay (ODSA) was used to measure responses to standard-of-care …

The Challenges And Opportunities Of Scrna-Seq In Covid-19 Research And Clinical Translation, Wendao Liu, Xiaohua Ye, Zhiqiang An, Zhongming Zhao

Faculty, Staff and Student Publications

The application of single-cell RNA sequencing in COVID-19 research has greatly improved our understanding of COVID-19 pathogenesis and immunological characteristics. In this commentary, we discuss the current challenges, limitations, and perspectives in harnessing the power of single-cell RNA sequencing to accelerate both basic research and therapeutic development for COVID-19 and other emerging infectious diseases.

Frequency And Burden Of Neurological Manifestations Upon Hospital Presentation In Covid-19 Patients: Findings From A Large Brazilian Cohort, Milena Soriano Marcolino, Fernando Anschau, Luciane Kopittke, Magda Carvalho Pires, Izabela Guimarães Barbosa, Lucas Emanuel Ferreira Ramos, André Soares De Moura Costa, Matheus Carvalho Alves Nogueira, Helena Duani, Karina Paula Medeiros Prado Martins, Leila Beltrami Moreira, Carla Thais Cândida Alves Da Silva, Neimy Ramos De Oliveira, Patricia Klarmann Ziegelmann, Milton Henriques Guimarães-Júnior, Mauro Oscar Soares De Souza Lima, Rubia Laura Oliveira Aguiar, Luanna Silva Monteiro Menezes, Talita Fischer Oliveira, Maíra Dias Souza, Bárbara Lopes Farace, Christiane Corrêa Rodrigues Cimini, Amanda De Oliveira Maurílio, Silvana Mangeon Mereilles Guimarães, Silvia Ferreira Araújo, Guilherme Fagundes Nascimento, Daniel Vitório Silveira, Karen Brasil Ruschel, Thainara Conceição De Oliveira, Alexandre Vargas Schwarzbold, Luiz Antônio Nasi, Maiara Anschau Floriani, Veridiana Baldon Dos Santos, Carolina Marques Ramos, Joice Coutinho De Alvarenga, Ana Luiza Bahia Alves Scotton, Euler Roberto Fernandes Manenti, Gabriela Petry Crestani, Joanna D'Arc Lyra Batista, Daniela Ponce, Juliana Machado-Rugolo, Adriana Falangola Benjamin Bezerra, Petrônio José De Lima Martelli, Heloisa Reniers Vianna, Luís César De Castro, Cássia Regina Gotler Medeiros, Giovanna Grunewald Vietta, Elayne Crestani Pereira, José Miguel Chatkin, Mariana Frizzo De Godoy, Polianna Delfino-Pereira, Antonio Lucio Teixeira

Faculty, Staff and Student Publications

BACKGROUND: Scientific data regarding the prevalence of COVID-19 neurological manifestations and prognosis in Latin America countries is still lacking. Therefore, the study aims to understand neurological manifestations of SARS-CoV 2 infection and outcomes in the Brazilian population.

METHODS: This study is part of the Brazilian COVID-19 Registry, a multicentric cohort, including data from 37 hospitals. For the present analysis, patients were grouped according to the presence of reported symptoms (i.e., headache; anosmia and ageusia; syncope and dizziness) vs. clinically-diagnosed neurological manifestations (clinically-defined neurological syndrome: neurological signs or diagnoses captured by clinical evaluation) and matched with patients without neurological manifestations by …

Outcomes In Patients With Poor-Risk Cytogenetics With Or Without Tp53 Mutations Treated With Venetoclax And Azacitidine, Daniel A Pollyea, Keith W Pratz, Andrew H Wei, Vinod Pullarkat, Brian A Jonas, Sunil Babu, Monique Dail, Yan Sun, Jalaja Potluri, Brenda Chyla, Courtney D Dinardo

Faculty, Staff and Student Publications

PURPOSE: To evaluate efficacy and safety of venetoclax + azacitidine in treatment-naïve patients with acute myeloid leukemia harboring poor-risk cytogenetics and TP53mut or TP53wt.

PATIENTS AND METHODS: We analyzed data from a phase III study (NCT02993523) comparing venetoclax (400 mg orally days 1-28) + azacitidine (75 mg/m2 days 1-7) or placebo + azacitidine, and from a phase Ib study (NCT02203773) of venetoclax + azacitidine. Patients were ineligible for intensive therapy. TP53 status was analyzed centrally; cytogenetic studies were performed locally.

RESULTS: Patients (n = 127) with poor-risk cytogenetics receiving venetoclax + azacitidine (TP53wt = 50; TP53mut = 54) were compared …

The Turkey Tail Mushroom And Its Many Look-Alikes, August Camp, Tara Bal

Open Access Books

A field guide to small polypores of the north woods, especially focused on macroscopic identification of the genus Trametes, and polypores found in northeastern North America that resemble the popular turkey tail mushroom, Trametes versicolor.

Comprehensive Molecular And Morphological Resolution Of Blubber Stratification In A Deep-Diving, Fasting-Adapted Seal, J. I.. Khudyakov, K. N. Allen, D. E. Crocker, N. S. Trost, A. H. Roberts, L. Pirard, C. Debier, E. R. Piotrowski, J. P. Vázquez-Medina

Pacific Faculty Work

Blubber is a modified subcutaneous adipose tissue in marine mammals that provides energy storage, thermoregulation, hydrodynamic locomotion, and buoyancy. Blubber displays vertical stratification by lipid content, fatty acid composition, and vascularization, leading to the assumption that deeper blubber layers are metabolically active, while superficial layers are mainly structural and thermoregulatory. However, few studies have examined functional stratification of marine mammal blubber directly, especially in pinnipeds. We characterized morphological and transcriptional differences across blubber layers in the northern elephant seal, a deep-diving and fasting-adapted phocid. We collected blubber from seals early in their fasting period and divided blubber cores into three …

Effect Of Climate History On The Genetic Structure Of An Antarctic Soil Nematode, Abigail C. Jackson

Theses and Dissertations

Historical climate disturbances such as glacial cycling and fluctuating stream, lake, and sea levels strongly influence the distribution and evolutionary trajectories of Antarctic terrestrial species. Antarctic invertebrates, with limited long-range mobility, including the ubiquitous sentinel nematode species Scottnema lindsayae, are especially sensitive to climate disturbances. We tested hypotheses associated with the historical geographic and population genetic structure of this species as it occurs across the McMurdo Dry Valleys (MDVs) of Antarctica. In order to reconstruct the influence of climate disturbance and ecological conditions on this species, partial mitochondrial COI gene sequences were sequenced and analyzed from individual S. lindsayae collected …

Probiotic Bc30 Improves Amino Acid Absorption From Plant Protein Concentrate In Older Women, Kylie E. Walden, Anthony M. Hagele, Logan S. Orr, Kristen N. Gross, Joesi M. Krieger, Ralf Jäger, Chad M. Kerksick

Faculty Scholarship

Weizmannia coagulans GBI-30, 6086 (BC30) has previously been shown to increase protein digestion in an in vitro model of the stomach and small intestine and amino acid appearance in healthy men and women after ingestion of milk protein concentrate. The impact of ingesting BC30 with other protein sources or in other demographics is largely unknown. The purpose of this study was to examine the impact of adding BC30 to a 20-g dose of a blend of rice and pea protein on postprandial changes in blood amino acids concentrations in healthy, older women. Healthy, older females (n = 30, 58.5 …

Rural Movers Studies ... People Are Moving For Community Attributes And Jobs, Marilyn R. Schlake

Cornhusker Economics

University of Minnesota researchers conducted a Rural Movers Study to determine the motivations of people who moved within one to five years to rural Minnesota communities. Their findings are not unlike earlier research conducted at the University of Nebraska in 2008. The Rural Movers Study showed that 31 % of respondents moved due to a job or job offer. However, this was not one of the primary reasons individuals moved. For those individuals who did not move for employment, 76% wanted to find a good environment for raising their children, 67% moved to be closer to relatives, 64% looked for …

Core Microbiome To Fingerprint Dust Emission Sources Across The Western United States Of America, Detiare Lisa Leifi

Theses and Dissertations

Over the past century, dust emissions have increased in frequency and intensity due to anthropogenic influences and extended droughts. Dust transports microbes, nutrients, heavy metals and other materials that may then change the biogeochemistry of the receiving environments. The purpose of this study was to find whether unique bacterial communities may provide distinct fingerprints of dust sources in the Western USA. We collaborated with the National Wind Erosion Research Network (NWERN) to identify bacterial core communities (core) of dust from ten NWERN sites, and compared communities to location, soil, and regional characteristics. In order of importance, precipitation levels (F = …

Growth Productivity As A Determinant Of The Inoculum Effect For Bactericidal Antibiotics, Gabriela Diaz-Tang, Estefania Marin Meneses, Kavish Patel, Sophia Mirkin, Laura Garcia-Dieguez, Camryn Pajon, Ivana Barraza, Vijay Patel, Helana Ghali, Angelica P. Tracey, Christopher Blanar, Allison J. Lopatkin, Robert P. Smith

Biology Faculty Articles

Understanding the mechanisms by which populations of bacteria resist antibiotics has implications in evolution, microbial ecology, and public health. The inoculum effect (IE), where antibiotic efficacy declines as the density of a bacterial population increases, has been observed for multiple bacterial species and antibiotics. Several mechanisms to account for IE have been proposed, but most lack experimental evidence or cannot explain IE for multiple antibiotics. We show that growth productivity, the combined effect of growth and metabolism, can account for IE for multiple bactericidal antibiotics and bacterial species. Guided by flux balance analysis and whole-genome modeling, we show that the …

The Effect Of Gut Microbiota On Overwintering Success In Mule Deer, Emma Wilcox

Theses and Dissertations

Mule deer are an important rangeland grazer, large prey species, and game animal for the state of Utah, so herd size is monitored and managed actively. A significant cause of population decline is poor overwintering survival, including from the lack of available forage during winter months. Mule deer energy storage is correlated with greater overwintering success, so physical estimates of energy storage including body condition score (BCS), rump fat (RF), and loin thickness (LT), can be used to track and predict a herd's health. Current methods of collecting deer information are costly, time consuming, and cause physical stress to deer, …

Investigating Biometrics Of Perimyotis Subflavus In Traditional And Nontraditional Hibernacula In The Southeastern United States As It Relates To Susceptibility To White-Nose Syndrome., Makayla Ferrari

Master of Science in Integrative Biology Theses

Perimyotis subflavus, or tricolored bat, populations have declined significantly since the emergence of white-nose syndrome (WNS) and has been proposed for listing as “endangered” under the United States Endangered Species Act. Traditionally, bats use caves as hibernacula, but as anthropogenic impacts have increased so has the use of manmade structures like culverts and bridges for roosting by several bat species. The internal environment of these anthropogenic structures is influenced by external temperature and humidity differently than caves and may influence P. subflavus winter activity, and thus susceptibility to WNS. One of the most significant differences in P. subflavus roosting behavior …

Detection Of Stroke With Retinal Microvascular Density And Self-Supervised Learning Using Oct-A And Fundus Imaging, Sergio Salazar-Marioni, Amanda Jagolino, Charles Green, Mozhdeh Bahrainian, Roomasa Channa, Sunil A Sheth, Luca Giancardo

Faculty, Staff and Student Publications

Acute cerebral stroke is a leading cause of disability and death, which could be reduced with a prompt diagnosis during patient transportation to the hospital. A portable retina imaging system could enable this by measuring vascular information and blood perfusion in the retina and, due to the homology between retinal and cerebral vessels, infer if a cerebral stroke is underway. However, the feasibility of this strategy, the imaging features, and retina imaging modalities to do this are not clear. In this work, we show initial evidence of the feasibility of this approach by training machine learning models using feature engineering …

Potential Risks Inherent In Robotic Process Automation, Colin L. Robinson, David Y. Chan

Journal of Vincentian Social Action

Robotic process automation (RPA) uses automation technologies to perform tasks typically performed by humans. Although such technology has been instrumental in expediting business operations and lowering costs, it has also created several risks that warrant scrutiny. When discussing the drawbacks of automation, many will point to the number of jobs lost to the influx of automation. However, there are technology risks that organizations must consider such as fraud and cybersecurity. Fraudsters may utilize RPA to commit more novel and subtle technological and cyber security fraud. Organizations may implement internal control measures to prevent or mitigate such schemes, segregation of duties, …