Life Sciences Commons^™

Sub-Stage Climatic Shifts During Mis 11 Refined From Diatom Assemblage Reconstruction In The Valles Caldera, New Mexico, Savannah Cutler

Earth and Planetary Sciences ETDs

Diatom assemblage reconstruction from the Valles Caldera sediment core (VC-3) was utilized to infer climatic and aquatic changes during a 50-thousand-year [ka] period in the Mid-Pleistocene (435-385 ka). This 50 ka interval spans most of Marine Isotope Stage 11 (MIS 11) – one of the most prominent interglacials of the past 500 ka – and is widely considered an analog for the Holocene and future climate regimes. Nearly all records from MIS 11 are either marine or ice-core based, making VC-3 unique among lacustrine sediment records as it captures insolation variations and climatic changes during the mid-Pleistocene. Analysis of the …

Analysis And Computation Of Constrained Sparse Coding On Emerging Non-Von Neumann Devices, Kyle Henke

Mathematics & Statistics ETDs

This dissertation seeks to understand how different formulations of the neurally inspired Locally Competitive Algorithm (LCA) represent and solve optimization problems. By studying these networks mathematically through the lens of dynamical and gradient systems, the goal is to discern how neural computations converge and link this knowledge to theoretical neuroscience and artificial intelligence (AI). Both classical computers and advanced emerging hardware are employed in this study. The contributions of this work include:

1. Theoretical Work: A comprehensive convergence analysis for networks using both generic Rectified Linear Unit (ReLU) and Rectified Sigmoid activation functions. Exploration of techniques to address the binary …

Impact Of Renal Cell Carcinoma Molecular Subtypes On Immunotherapy And Targeted Therapy Outcomes, Renée Maria Saliby, Chris Labaki, Tejas R Jammihal, Wanling Xie, Maxine Sun, Eddy Saad, Soki Kashima, Katherine Sadak, Talal El Zarif, Deepak Poduval, Robert J Motzer, Thomas Powles, Brian I Rini, Laurence Albiges, Sumanta K Pal, Bradley A Mcgregor, Rana R Mckay, Sabina Signoretti, Eliezer M Van Allen, Sachet A Shukla, Toni K Choueiri, David A Braun

Faculty, Staff and Student Publications

Saliby et al. show that a machine learning approach can accurately classify clear cell renal cell carcinoma (RCC) into distinct molecular subtypes using transcriptomic data. When applied to tumors biospecimens from the JAVELIN Renal 101 (JR101) trial, a benefit is observed with immune checkpoint inhibitor (ICI)-based therapy across all molecular subtypes.

Mammographic Density Mediates The Protective Effect Of Early-Life Body Size On Breast Cancer Risk, Marina Vabistsevits, George Davey Smith, Tom G Richardson, Rebecca C Richmond, Weiva Sieh, Laurel A Habel, Bethan Lloyd-Lewis, Eleanor Sanderson

Faculty, Staff and Student Publications

The unexplained protective effect of childhood adiposity on breast cancer risk may be mediated via mammographic density (MD). Here, we investigate a complex relationship between adiposity in childhood and adulthood, puberty onset, MD phenotypes (dense area (DA), non-dense area (NDA), percent density (PD)), and their effects on breast cancer. We use Mendelian randomization (MR) and multivariable MR to estimate the total and direct effects of adiposity and age at menarche on MD phenotypes. Childhood adiposity has a decreasing effect on DA, while adulthood adiposity increases NDA. Later menarche increases DA/PD, but when accounting for childhood adiposity, this effect is attenuated. …

The Crosstalk Between Macrophages And Cancer Cells Potentiates Pancreatic Cancer Cachexia, Mingyang Liu, Yu Ren, Zhijun Zhou, Jingxuan Yang, Xiuhui Shi, Alex X Arreola, Kar-Ming Fung, Chao Xu, Ryan D Nipp, Michael S Bronze, Lei Zheng, Yi-Ping Li, Courtney W Houchen, Yuqing Zhang, Min Li

Faculty, Staff and Student Publications

With limited treatment options, cachexia remains a major challenge for patients with cancer. Characterizing the interplay between tumor cells and the immune microenvironment may help identify potential therapeutic targets for cancer cachexia. Herein, we investigate the critical role of macrophages in potentiating pancreatic cancer induced muscle wasting via promoting TWEAK (TNF-like weak inducer of apoptosis) secretion from the tumor. Specifically, depletion of macrophages reverses muscle degradation induced by tumor cells. Macrophages induce non-autonomous secretion of TWEAK through CCL5/TRAF6/NF-κB pathway. TWEAK promotes muscle atrophy by activating MuRF1 initiated muscle remodeling. Notably, tumor cells recruit and reprogram macrophages via the CCL2/CCR2 axis …

Towards Dignity: Understanding The Relationship Between Food Banks & The Right To Food In The United States, Marguerite Leek

Theses - ALL

In the United States, there is no legal right to food. The right to food is more than food security, it encompasses dignity, access, choice, financial security, and more. Rather than addressing food insecurity through a human rights-based approach, the US relies on a complex system of emergency food providers, including food banks. Food banks most often take a charity approach to providing individuals with food, failing to meaningfully recognize or address the structural causes of hunger and poverty. In recent years there have been increased efforts made by civil society to move conversation and state level policy in the …

Knockout Of Highly Conserved Seminal Fluid Protein Ablates Male Fertility In Drosophila Melanogaster, Dominic Hockenbury

Theses - ALL

ABSTRACT In Drosophila, seminal fluid proteins (SFPs) are key components of the male ejaculate and are essential determiners of reproductive fitness. SFPs are required for inducing a range of post-mating physiological responses in females. To date nearly 300 SFPs have been identified, however the vast majority of these remain uncharacterized and their role in reproduction and/or postcopulatory sexual selection is not clear. SFPs are functionally diverse and contain proteins from a variety of biochemical processes, most notably proteases and protease inhibitors that are thought to be critically important in biochemical interactions with female proteins. Another class of proteins that is …

Does Increased Productivity Ensure Food Security And Food Sovereignty? Case Study: Productivity, Food Security, And Gender Participation Within The Framework Of The “Sustenta” Project In Nampula Province, Mozambique., Arcenia Notilija Vilanculo

Theses - ALL

When food security and sovereignty are viewed from a gendered lens, critical questions arise concerning inclusive participation in food systems. While policymaking is pivotal in ensuring gender parity in these systems, the lack of stakeholder engagement and buy-in during the policy design process hinders governmental efforts to create and implement policies that effectively ensure food and nutritional security for all. This research examines agricultural productivity, food security, land tenure, and stakeholder engagement in the context of SUSTENTA project in Nampula. The methodology adopts a qualitative approach, incorporating data from semi-structured interviews, featuring predefined questions and topics and a thorough literature …

Intraguild Competition Is More Severe In Obligate Mutualisms Than In Facultative Mutualisms, Thomas Johnson

Theses - ALL

Mutualism, or the beneficial interaction of species, is an important and widespread interaction type in nature. Mutualist species exchange goods or services that benefit the species involved. These benefits can include protection from predators, parasites, and disease, dispersal of individuals, offspring, or gametes, and provisioning of various nutrients. Well-known mutualisms include the pollination of flowering plants by insects, birds, and other animals and the interaction between clownfish and sea anemones. Many mutualistic associations are less visible than these examples, as organisms often form beneficial relationships with microorganisms, like the many beneficial bacteria that live in the human gut, or the …

Standard Rodent Diets Differentially Impact Alcohol Consumption, Preference, And Gut Microbiome Diversity, Aline Zaparte, Evan Dore, Selby White, Franciely Paliarin, Cameron Gabriel, Katherine Copenhaver, Samhita Basavanhalli, Emily Garcia, Rishith Vaddavalli, Meng Luo, Christopher M. Taylor, David Allen Welsh, Rajani Maiya

School of Graduate Studies Faculty Publications

Alcohol use disorder (AUD) is a complex and widespread disease with limited pharmacotherapies. Preclinical animal models of AUD use a variety of voluntary alcohol consumption procedures to recapitulate different phases of AUD, including binge alcohol consumption and dependence. However, voluntary alcohol consumption in mice is widely variable, making it difficult to reproduce results across labs. Accumulating evidence indicates that different brands of commercially available rodent chow can profoundly influence alcohol intake. In this study, we investigated the effects of three commercially available and widely used rodent diet formulations on alcohol consumption and preference in C57BL/6 J mice using the 24 …

Investigating Vocal Development In Humpback Whales: Caller Identification, Acoustic And Movement Behavior, And Comparisons Across Age, Julia Marie Zeh

Dissertations - ALL

Studying variation in individual behavior can elucidate drivers related to factors like age, social context, and the environment. Differences in behavior with age are a product of survival needs and developmental differences as animals physiologically mature and modify their behaviors in response to experience. Learning is of particular interest across taxa because it is fundamental to the development of complex behaviors, from problem-solving to social hierarchies to animal songs and human language. Humpback whales (Megaptera noveaeangliae) exhibit a variety of complex and culturally transmitted behaviors across their range, including a diverse acoustic repertoire. Despite decades of research on adult behavior, …

The Impact Of School-Based Education Program On Body Image In Middle School Students, Elizabeth Hendon

Honors Theses

Body dissatisfaction is an emerging public health concern and carries significant health-related consequences. These implications encompass mental health challenges, eating disorders, unhealthy weight management practices, adverse effects on self-esteem, and potential physical health consequences. Because adolescence is a critical period for healthy body image development due to age-related transitions occurring at this time, it is essential to implement an education program to promote positive body image. Educational programs focused on protective factors designed to enhance self-compassion can potentially improve body image, eating attitudes, and body satisfaction. School-based body image education programs aim to provide adolescents with the knowledge, skills, and …

Transcriptional And Environmental Regulation Of A Putative Xylan Biosynthesis Gene, Ptrparvus2 In Poplar, Dan Wang

Dissertations - ALL

Secondary cell wall (SCW) biosynthesis plays a crucial role in plant development and biomass production, with implications for various industries, including biofuels and forestry. Understanding the regulatory mechanisms governing SCW formation is essential for manipulating plant cell wall composition and properties to improve biomass yield and quality. In this study, we investigated the regulatory mechanisms controlling SCW biosynthesis in poplar, focusing on the transcriptional regulation of PtrPARVUS2, a putative gene involved in SCW formation. The regulatory mechanisms governing SCW biosynthesis in poplar were investigated, with a focus on the transcriptional regulation of PtrPARVUS2. Bioinformatic analysis of the PtrPARVUS2 promoter revealed …

Characterization Of Zmsnrk1 Genes And Their Response To Aphid Feeding, Drought And Cold Stress, M. Aydin Akbudak, Kubra Yildiz, Durmus Cetin, Utka Yukselbaba, Vibha Srivastava

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

The SnRK1 complex in plants regulates metabolism in response to environmental stresses and glucose depletion, for stress adaptation and energy homeostasis. Through phosphorylation of various targets, SnRK1 orchestrates intricate regulatory mechanisms involved in autophagy, nutrient remobilization, and TOR activity inhibition, showcasing its pivotal role in coordinating plant metabolism and stress responses. The present study aimed to identify members of the SnRK1 gene family in the maize genome and characterize them using bioinformatics and expression analyses under aphid feeding, drought, and cold stress. The focus of the study was to conduct a comprehensive analysis towards determining gene diversity of ZmSnRK1 genes, …

Agroecology And Soil Stewardship: Values And Techniques Of Smallholder Farmers In Bernalillo County, Stephanie Olivas

Geography ETDs

Agrarian movements around the world use agroecology to build sovereignty and steward dynamic ecosystems. Research has shown that agroecological farmers steward more resilient crops, more resilient soil biomes, and greater biodiversity than conventional agriculture. GIS and remote sensing offer many tools to detect the impacts of these farmers on the environment, but it is less clear how such technologies fit into agroecological goals. This study asks: what values, experiences and knowledge do smallholder producers in Bernalillo County embody in their soil stewardship practices? Also, what experience or knowledge do smallholder producers in Bernalillo County have about remote sensing, and would …

Acute Effects Of Virtual Reality Gameplay On The Visual System: An Observational Study, Aaron Loe, Gavin Rataj, Leah Jackson

Science Symposium

PURPOSE: Virtual reality (VR) has an increasing breadth of utilization, from at home entertainment to a tool used in professional athletic and clinical settings. A review of literature shows altered visual performance (VP) post-VR gameplay in children and adult athletes, particularly in acuity, accommodation and convergence, but has been limited to the immediate effects on vision. This study aims to repeat similar test measures, expanding on aspects of VP, pre- and post-VR gameplay in a healthy, collegiate-aged population, while exploring the feasibility of repeated testing to observe any ocular changes that may occur over time once gameplay has ceased. METHODS: …

A Flavorful Adventure: Interning At Old Dutch Foods, Ashton Olson, Jonathan Ibisch, Jeff Port

Science Symposium

This is an internship in which I worked at Old Dutch Foods for a summer working as a lab technician. I performed many daily tasks as well as larger projects for just my boss as a form of "research" and data analytics. I learned many things about lab etiquette and analysis, professionalism, as well as workplace communication.

Synthesis Of Disubstituted Β-Hydroxy Acids For The Enzymatic Synthesis Of Chiral Β-Lactones, Laura Charlotte Underwood, James Christenson

Science Symposium

Beta-lactone synthetases are a class of enzymes which produce chiral beta-lactones, four-membered cyclic esters, from racemic beta-hydroxy acid substrates. Chiral beta-lactones are used as chemical synthons and as bioactive compounds, such as the FDA-approved drug, Orlistat. However, substrate specificity of stand-alone beta-lactone synthetases are poorly understood, and their use in chemoenzymatic synthesis of chiral bioactive compounds remains unexplored. This research focused on the organic synthesis of beta-hydroxy acids to probe the substrate specificity of this class of enzymes and to generate potentially bioactive compounds against essential tuberculosis enzymes. The beta-hydroxy acid 2-[(5-chlorofuran-2-yl)(hydroxy) methyl]hexanoic acid was synthesized from lithiated hexanoate and …

Closing The Gap: Methodological Consideration In Predicting Suitable Habitat For Ouachita Fanshell (Cyprogenia Sp Cf Aberti) With Documentation Of Mussel Communities In Small Tributaries In The Ouachita River Watershed, Seth Drake

ATU Theses and Dissertations 2021 - Present

Freshwater mussels are one of the most imperiled taxonomic groups in the world, consequently, much effort is being expended to document the distribution of many mussel species. One tool that can aid in characterizing mussel distributions are species distribution models (SDM). I conducted two studies pertaining to freshwater mussel distributions: (1) utilize Maximum Entropy (MAXENT) modeling to predict potential areas of suitable habitat for the threatened Ouachita Fanshell (Cyprogenia sp cf aberti), and (2) survey small tributaries of the Ouachita River watershed to fill a portion of the information gap surrounding mussel communities in under-surveyed streams. Through changing …

Precipitation Seasonality Amplifies As Earth Warms, Xiaoyu Wang, Ming Luo, Fengfei Song, Sijia Wu, Yongqin David Chen, Wei Zhang

Plants, Soils, and Climate Faculty Publications

Precipitation exhibits a pronounced seasonal cycle, of which the phase and amplitude are closely associated with water resource management. While previous studies suggested an emerged delaying phase in the past decades, whether the amplified amplitude has emerged is controversial. Using multiple observational data sets and climate simulations, here we show that the amplification of precipitation annual cycle has emerged in most global land areas since the 1980s, especially in the tropics. These amplifications are mainly driven by anthropogenic emissions, and will be further intensified by 17.6% in the future (2081–2100) under high emission scenario (Shared Socioeconomic Pathways, SSP585), and limited …

Ecotoxicity Evaluation Using The Avoidance Response Of The Oribatid Mite Oppia Nitens (Acari: Oribatida) In Bioplastics, Microplastics, And Contaminated Superfund Field Sites, Philips Akinwole, Nina Shaffer '25, Catarina Zabot Pansini '26, Kaija Carr '25, Kenneth L. Brown, Olugbenga J. Owojori

Biology Faculty publications

Bioplastics are considered sustainable alternatives to conventional microplastics which are recognized as a threat to terrestrial ecosystems. However, little is known about the potential ecotoxicological effects of bioplastics on soil fauna and ecosystems. The present study assessed the toxicity of microplastics [Polystyrene (PS), Polyethylene (PE)] and bioplastics [Polyvinyl alcohol (PVA), Sodium polyacrylate (NaPa) on a key soil fauna Oppia nitens, a soil oribatid mite, and investigated the ecological relevance of O. nitens avoidance response as a valuable tool for the risk assessment of contaminated soils such as the Superfund sites. Findings showed that the mites’ net response indicated avoidance …

The Tissue-Specific Role Of Smn-1 In C. Elegans, Lindsey Philips

Biological Sciences Theses and Dissertations

Spinal muscular atrophy (SMA) is an autosomal recessive disease that results from mutations in the Survival Motor Neuron (SMN-1) gene. Although SMN is a ubiquitously expressed protein that acts as an RNA-binding protein (RBP), SMA is characterized by the selective degeneration of motor neurons of the lower spinal cord. Despite a clear understanding of the genetic causes underlying SMA, the mechanisms associated with low SMN levels to disease pathogenesis remains unclear. Here, we investigate the role SMN-1 has in different tissues to begin understanding possible mechanisms. This project has three aims that has guided our experiments. The first aim is …

Unveiling The Nexus Of Cellular Quality Control: Exploring The Interplay Between Ribosome-Associated Protein Quality Control And Mitochondrial Quality Control Pathways, Foozhan Tahmasebinia

Biological Sciences Theses and Dissertations

In eukaryotic cells, the intricate interplay between cellular quality control mechanisms is crucial for maintaining homeostasis and safeguarding the integrity of vital processes, spanning from macromolecule synthesis to the renewal of entire cellular organelles.

Disruption of these networks can lead to severe diseases such as metabolic disorders, underscoring the interconnected nature and feedback control mechanisms inherent in biological systems, including cellular quality control systems. This interconnectedness extends to the intricate communication between organelles, enabling coordinated functioning and adaptation to changing cellular conditions, particularly in response to stressors.

While the exact mechanisms governing these communications within cellular quality control systems remain …

Screen For Beneficial Genetic And Chemical Modifiers In Drosophila Models Of Als And Traumatic Brain Injury, Will Bonderer

Biological Sciences Theses and Dissertations

The underlying molecular processes of aberrant protein expression in neurodegeneration are intricate and multifaceted, with ribosome-associated quality control (RQC) emerging as a promising avenue of exploration. Ribosome-associated quality control is integral to cellular function. Its evolutionarily conserved pathway encompasses a network of mechanisms designed to ensure the fidelity of protein synthesis, folding, and degradation within the cells of all eukaryotes. The ribosome, central to protein synthesis, plays a pivotal role in this quality control network, and its malfunction can lead to the accumulation of misfolded or aberrant proteins. In the context of neurodegenerative disorders, this dysfunction can have dire consequences. …

The Lipid-Heart Hypothesis And The Keys Equation Defined The Dietary Guidelines But Ignored The Impact Of Trans-Fat And High Linoleic Acid Consumption, Mary T. Newport, Fabian M. Dayrit

Chemistry Faculty Publications

In response to a perceived epidemic of coronary heart disease, Ancel Keys introduced the lipid-heart hypothesis in 1953 which asserted that high intakes of total fat, saturated fat, and cholesterol lead to atherosclerosis and that consuming less fat and cholesterol, and replacing saturated fat with polyunsaturated fat, would reduce serum cholesterol and consequently the risk of heart disease. Keys proposed an equation that would predict the concentration of serum cholesterol (ΔChol.) from the consumption of saturated fat (ΔS), polyunsaturated fat (ΔP), and cholesterol (ΔZ): ΔChol. = 1.2(2ΔS - ΔP) + 1.5ΔZ. However, the Keys equation conflated natural saturated fat and …

Biogeographic Patterns In Phyllosphere Bacterial Communities On Southern Magnolia Trees In A Small Town, Elizabeth M. Eckard, Venkat K. Kota, Kurre T. Luber

Honors Theses

The phyllosphere, consisting of aerial plant surfaces colonized by microorganisms, remains a relatively understudied ecosystem in terms of bacterial biogeography, particularly at intermediate spatial scales. This study characterized the bacterial community on the leaves of 89 Magnolia grandiflora trees throughout a small town, encompassing an area of approximately 60 km². Sequencing of the 16S ribosomal RNA gene revealed the dominant bacterial phyla to be Alphaproteobacteria, Bacteroidetes, and Acidobacteria, consistent with other studies of the phyllosphere. Unlike other studies over smaller spatial scales, there was no significant relationship between phyllosphere community similarity and distance between trees (i.e., trees further …

Effects Of Vdac 1 And 2 N-Terminal Peptides On Bax Conformation Assessed By Blue Native Gel Electrophoresis, Allison G. Dupree

Honors Theses

Members of the Bcl-2 family are responsible for regulating the intrinsic pathway of apoptosis through Bcl-2 homology 3 (BH3) domain interactions of pro- and anti-apoptotic members. Apoptosis occurs when BH3-only pro-death members overwhelm the pro-survival ones, leading to oligomerization of the multi-BH domain pro-death protein Bax to signal death by releasing cytochrome c from mitochondria into the cytoplasm. This process is essential for proper embryonic tissue development as well as maintenance of mature tissues. While BH3-only proteins such as Bim and Bid bind to and activate Bax through their BH3 domains, other regulators of this mitochondrial permeabilizer may exist. Two …

And Food Justice For All: Advancing Access To Just And Sustainable Food Systems, Makenna Grace Landry

Graduate Student Portfolios, Professional Papers, and Capstone Projects

A collection of work exploring food justice and food access programming in Western Montana, as well as a critique of the Bayer-Monsanto merger.

Variability In Large Mammal Activity Patterns When Visiting Water In New Mexico, Juan E. Camacho

Biology ETDs

Studying activity patterns of animals can provide vital information about how different species react to environmental changes, yet camera trap studies typically neglect the temporal aspect of the data. Using a 10-year camera trap dataset on Sevilleta National Wildlife Refuge, NM, we explored daily activity patterns when visiting water of five large mammal species. The species of study were mule deer, pronghorn, elk, oryx, and coyote. All species showed significant variability in activity patterns from site to site across the refuge. Within a site, differences in activity across years and seasons were less pronounced. Mule deer and coyote showed very …

Paleoecology Of The Late Cretaceous Western Interior Seaway And Gulf Coastal Plain, Ceara Kathleen Quinn Purcell

Earth and Planetary Sciences ETDs

This dissertation presents research into the paleobiogeography and paleoecology of the Western Interior Seaway (WIS) and Gulf Coastal Plain (GCP) during the Late Cretaceous. The dataset utilized here includes an extensive record of marine invertebrates from over 200 years of fossil collecting and sedimentary data collated from over 45 different literature sources, representing approximately 17 million years of deposition. The high-resolution of this dataset, and its extensive geographic distribution and temporal duration, make it ideal for exploring various ecological questions. Using these data, I have attempted to reconstruct paleobiogeographic provinces as published in prior works, explore functional diversity patterns, and …