Biology Commons^™

Insights Into The Role And Regulation Of The Mitochondrial Unfolded Protein Response During Pathogen Infection, Mohammed Adnan Qureshi

Biology Dissertations - Archive

Mitochondria are essential cellular organelles known for their role in energy production, apoptosis, aging, calcium signaling and others. Due to their essential nature, mitochondria are often under attack by numerous pathogens as a means to promote their infection. Consequently, mitochondrial function is often perturbed during infection, a phenomenon that must be mitigated in order for the host to survive. Cells employ various tactics to repair damaged mitochondria during stresses such as pathogenic infection. One way of countering mitochondrial stress is through the recovery mechanism known as the mitochondrial unfolded protein response (UPRmt). The UPRmt supports mitochondrial recovery by promoting mitochondrial …

Impacts Of Environmental And Anthropogenic Stressors On Amphibian Welfare, Diversity, And Distribution In The Upper Missouri River Basin, Kaitlyn Campbell

Dissertations and Theses

Climate change and anthropogenic stressors have contributed to rapid declines among various taxonomic groups; however, amphibian declines have been particularly intense and primarily stemmed from warming temperatures, habitat loss, exposure to contaminants, disease, and their subsequent interactions. Several climate mitigation strategies, like Bioenergy with Carbon Capture and Storage, have been proposed to alleviate the impact of rising temperatures; however, these proposals often fail to recognize and quantify the true impact on fauna, including changes in species distributions. To address this critical gap in knowledge, this research identified current amphibian distributions in the Upper Missouri River Basin and projected distribution changes …

Coevolutionary Methods Enable Robust Design Of Modular Repressors By Reestablishing Intra-Protein Interactions, Xian-Li Jiang, Rey P. Dimas, Clement T.Y. Chan, Faruck Morcos

Biology Faculty Publications and Presentations

enetic sensors with unique combinations of DNA recognition and allosteric response can be created by hybridizing DNA-binding modules (DBMs) and ligand-binding modules (LBMs) from distinct transcriptional repressors. This module swapping approach is limited by incompatibility between DBMs and LBMs from different proteins, due to the loss of critical module-module interactions after hybridization. We determine a design strategy for restoring key interactions between DBMs and LBMs by using a computational model informed by coevolutionary traits in the LacI family. This model predicts the influence of proposed mutations on protein structure and function, quantifying the feasibility of each mutation for rescuing hybrid …

Insight Into The Evolution Of Anuran Foot Flag Displays: A Comparative Study Of Color And Kinematics, Nigel K. Anderson, K. V. Gururaja, Lisa A. Mangiamele, Erin C. Netoskie, Sarah Smith, Matthew J. Fuxjager, Doris Preininger

Biological Sciences: Faculty Publications

Understanding how complex animal displays evolve is a major goal of evolutionary organismal biology. Here, we study this topic by comparing convergently evolved gestural displays in two unrelated species of frog (Bornean Rock Frog, Staurois parvus, and Kottigehara Dancing Frog, Micrixalus kottigeharensis). This behavior, known as a foot flag, is produced when a male ?waves' his hindlimb at another male during bouts of competition for access to mates. We assess patterns of variation in the color of frog feet and the kinematics of the display itself to help pinpoint similarities and differences of the visual signal elements. We find clear …

Large-Scale Genome Sampling Reveals Unique Immunity And Metabolic Adaptations In Bats, Diana D. Moreno Santillán, Tanya M. Lama, Yocelyn T. Gutierrez Guerrero, Alexis M. Brown, Paul Donat, Huabin Zhao, Stephen J. Rossiter, Laurel R. Yohe, Joshua H. Potter, Emma C. Teeling, Sonja C. Vernes, Kalina T.J. Davies, Eugene Myers, Graham M. Hughes, Zixia Huang, Federico Hoffmann, Angelique P. Corthals, David A. Ray, Liliana M. Dávalos

Biological Sciences: Faculty Publications

Comprising more than 1,400 species, bats possess adaptations unique among mammals including powered flight, unexpected longevity, and extraordinary immunity. Some of the molecular mechanisms underlying these unique adaptations includes DNA repair, metabolism and immunity. However, analyses have been limited to a few divergent lineages, reducing the scope of inferences on gene family evolution across the Order Chiroptera. We conducted an exhaustive comparative genomic study of 37 bat species, one generated in this study, encompassing a large number of lineages, with a particular emphasis on multi-gene family evolution across immune and metabolic genes. In agreement with previous analyses, we found lineage-specific …

V-Myb Avian Myel Oblast Viral Oncogene Homolog Like 1 (Mybl1) Knockdown And Its Role In A Triple Negative Breast Cancer, Nabras Mahmoud Abdulrahman

Theses (2016-Present)

Triple Negative Breast Cancer (TNBC) is defined as negative for three genes, estrogen receptor (ESR), progesterone receptor (PR) and Human epidermal growth factor receptor (HER2-neu) genes. Previous data show the V-Myb Avian Myel oblast Viral Oncogene Homolog Like 1 (MYBL1) gene is over-expressed in Triple negative breast cancer cell line (MDA-MB231). MYBL1 belongs to the MYB family of genes which are transcription factors and proto-oncogenes which are associated with cell cycle regulation, apoptosis, and differentiation, all of which are key events associated with cancers. It could be that MYBL1 contributes to these same processes in TNBC. Instead of studying MYBL1’s …

King Mackerel (Scomberomorus Cavalla), Aubrey L. Anthony, Erin Keeley, David Kerstetter

All Scans: Kerstetter Fisheries and Avian Ecology 3D Scan Series

Neurocranium from [length] cm total length (TL) King Mackerel (Scomberomorus Cavalla), collected from Bravo Market on 11/16/2021 by Aubrey Anthony

From Microbes To Management: Spatial And Temporal Variations In Available Vegetation Affect The Gut Microbiota In A Population Of Free-Ranging Generalist Herbivores, Olivia K. Rodríguez

Boise State University Theses and Dissertations

The effects of extrinsic environmental factors that shape ecological systems are not only seen at the macroscopic level, but additionally influence and govern the host-associated microbial communities of their mammalian hosts. These microbial communities are susceptible to the fluctuation of abiotic and biotic factors which affect their host organisms. The surge in the research of microbiota–communities of archaea, bacteria, fungi, and viruses residing in various environmental systems–has shown that these communities can profoundly influence animal health. As such, monitoring microbiota has allowed for a new approach to study animal health and physiology. This is of particular benefit in the conservation …

Exploration Of Dark Chemical Genomics Space Via Portal Learning: Applied To Targeting The Undruggable Genome And Covid-19 Anti-Infective Polypharmacology, Tian Cai, Li Xie, Muge Chen, Yang Liu, Di He, Shuo Zhang, Cameron Mura, Philip Boume, Lei Xie

Publications and Research

Advances in biomedicine are largely fueled by exploring uncharted territories of human biology. Machine learning can both enable and accelerate discovery, but faces a fundamental hurdle when applied to unseen data with distributions that differ from previously observed ones—a common dilemma in scientific inquiry. We have developed a new deep learning framework, called Portal Learning , to explore dark chemical and biological space. Three key, novel components of our approach include: (i) end-to-end, step-wise transfer learning, in recognition of biology’s sequence-structure-function paradigm, (ii) out-of-cluster meta-learning, and (iii) stress model selection. Portal Learning provides a practical solution to the out-of-distribution (OOD) …

The Role Of The Serine/Threonine Phosphatase Pstp In The Mycobacterial Cell Wall Regulation, Farah Shamma

Biology Dissertations - Archive

Mycobacterium tuberculosis (Mtb) is the causative agent of the deadly infection Tuberculosis (TB). The current standard antibiotic regimen for TB treatment combines fours drugs to be taken for at least six months. Mtb shows intrinsic phenotypic tolerance to antibiotics contributing to the long treatment regimen. In addition, Mtb cells can achieve a non-replicating state exhibiting antibiotic tolerance, reduced metabolism and altered cell wall staining. The changes in the cell wall and reduced permeability to antibiotics in stressed cells suggest that the regulation of the cell wall is a major contributor to antibiotic tolerance. The mycobacterial cell wall consists of covalently …

Herbivores Alleviate The Negative Effects Of Extreme Drought On Plant Community By Enhancing Dominant Species, Chong Xu, Yuguang Ke, Honghui Wu, Melinda D. Smith, Nathan P. Lemoine, Weiguo Zhang, Qiang Yu

Biological Sciences Faculty Research and Publications

Aims

Both extreme drought and insect herbivores can suppress plant growth in grassland communities. However, most studies have examined extreme drought and insects in isolation, and there is reason to believe that insects might alter the ability of grasslands to withstand drought. Unfortunately, few studies have tested the interactive effects of extreme drought and insect herbivores in grassland communities.

Methods

Here, we tested the drought–herbivore interactions using a manipulative experiment that factorially crossed extreme drought with the exclusion of insect herbivores in a temperate semiarid grassland in Inner Mongolia.

Important Findings

Our results demonstrated that both extreme drought and insect …

(R1412) Stability And Bifurcation Of A Cholera Epidemic Model With Saturated Recovery Rate, Huda Abdul-Satar, Raid K. Naji

Applications and Applied Mathematics: An International Journal (AAM)

In this paper, a Cholera epidemic model is proposed and studied analytically as well as numerically. It is assumed that the disease is transmitted by contact with Vibrio cholerae and infected person according to dose-response function. However, the saturated treatment function is used to describe the recovery process. Moreover, the vaccine against the disease is assumed to be utterly ineffective. The existence, uniqueness and boundedness of the solution of the proposed model are discussed. All possible equilibrium points and the basic reproduction number are determined. The local stability and persistence conditions are established. Lyapunov method and the second additive compound …

Characterization Of The Respiratory Syncytial Virus (Rsv) Attachment Protein Mucin Domains, Molly Kathleen Roe

Undergraduate Honors Thesis Collection

Respiratory Syncytial Virus (RSV) is currently a leading cause of acute lower respiratory infection (ALRI). Despite contributing to a significant mortality rate in young children and immunocompromised populations, it still lacks a vaccine. Live-attenuated vaccines are the preferred vaccination model for RSV, but achieving attenuation, immunogenicity, and stability can be difficult. Previous studies have indicated that deletion of the RSV G protein attenuates viral replication, but the role of the protein’s mucin domains has not been fully explored. We generate two new RSV strains here with varying G protein deletions: A2-line19F-G155 with deletion of the G-protein mucin domains, and A2- …

Patch Size Drives Colonization By Aquatic Insects, With Minor Priority Effects Of A Cohabitant, Reed C. Scott, Matthew R. Pintar, William J. Resetarits

Faculty and Student Publications

Patch size is one of the most important factors affecting the distribution and abundance of species, and recent research has shown that patch size is an important niche dimension affecting community structure in aquatic insects. Building on this result, we examined the impact of patch size in conjunction with presence of larval anurans on colonization by aquatic insects. Hyla chrysoscelis (Cope's gray treefrog) larvae are abundant and early colonists in fishless lentic habitats, and these larvae can fill multiple ecological roles. By establishing larvae in mesocosms prior to colonization, we were able to assess whether H. chrysoscelis larvae have priority …

Complete Vertebrate Mitogenomes Reveal Widespread Repeats And Gene Duplications, Giulio Formenti, Arang Rhie, Jennifer Balacco, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, Samara Brown, Marco Rosario Capodiferro, Farooq O. Al-Ajli, Roberto Ambrosini, Peter Houde, Sergey Koren, Karen Oliver, Michelle Smith, Jason Skelton, Emma Betteridge, Jale Dolucan, Craig Corton, Iliana Bista, James Torrance, Alan Tracey, Jonathan Wood, Marcela Uliano-Silva, Kerstin Howe, Shane Mccarthy, Sylke Winkler, Woori Kwak, Jonas Korlach, Arkarachai Fungtammasan, Et Al, Tanya M. Lama

Biological Sciences: Faculty Publications

Background: Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly. Results: As part of the Vertebrate Genomes Project (VGP) we develop mitoVGP, a fully automated pipeline for similarity-based identification of mitochondrial reads and de novo assembly of mitochondrial genomes that incorporates both long (> 10 kbp, PacBio or Nanopore) and short (100–300 bp, Illumina) reads. Our pipeline leads to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We observe that tissue type and library size selection have considerable impact on mitogenome …

The Brown Bear Gut Microbiome: A Novel Tool For Conservation & Management, Sarah M. Trujillo

All NMU Master's Theses

Gut microbiomes (GMBs), complex communities of microorganisms inhabiting the gastrointestinal tracts of their hosts, perform countless micro-ecosystem services such as facilitating energy uptake and modulating immune responses. While scientists increasingly recognize the role GMBs play in host health, the role of GMBs in wildlife ecology and conservation has yet to be realized fully. Here, I use brown bears (Ursus arctos) as an ecological model to investigate (1) how both extrinsic and intrinsic factors influence GMB community membership and structure; and (2) the correlation between GMB membership and brown bear health metrics. To achieve these aims, I subsampled archived …

Gather Round The Tree: Woody Aboveground Biomass Increases Animal Presence And Species Richness In A Tropical Forest-Savanna Ecotone, Merry Vanessa Marshall Davidson

Boise State University Theses and Dissertations

Boundaries between ecosystems are often biodiversity hotspots with relatively high vulnerability to global change. The boundary between tropical rainforest and savanna ecosystems in the Amazon presents an ecotone that is undergoing a shift in ecosystem structure, as a warming climate promotes the expansion of grassland. How animal communities in the Amazon will respond to changes in ecosystem structure is a crucial unanswered question with implications for the many ecosystem services that animals provide, from a food source for Indigenous people to seed dispersal for vulnerable tree populations. Recent modeling work has forecasted that faunal savannization will occur in the Amazon, …

Sex Differences In The Co-Expression Of Estrogen Receptor Alpha With Corticotropin Releasing Factor, Deborah Ariyibi

Biological Sciences

Women are far more likely to develop anxiety and depression than men. It is believed that the dysregulation of the HPA axis by the binding of corticotropin -releasing factor (CRF) to the corticotropin-releasing factor receptor 1 (CRFR1) contributes to the likelihood of these stress- related disorders. Estrogens acting through Estrogen receptor alpha (ERa) have been shown to increase anxiety production upon activating the HPA axis. In this current study, we explored whether CRF-expressing neurons in various regions of the brain express ERa. The levels of ERa were counted in the bed nucleus of the stria terminalis (BST), the medial preoptic …

Light Level Intensity Alters Anxiety, But Not Memory, During Open-Field And Novel Object Location Tasks In Male Rats, Angelina Tassone

Biological Sciences

Appropriate design and control of testing conditions during assessment of animal behavior is critical to maximize generalizability, replicability, and translational relevance. Some sensory stimuli are often controlled: for instance, during rodent behavioral testing, efforts are commonly made to reduce or eliminate olfactory and auditory distractions. However, less attention is paid to the ambient light level intensity (lux), which may vary even between rooms in the same facility. We sought to explore whether behavior is influenced by the standard illumination intensity in one of our behavioral testing rooms. To this end, we measured anxiety-like behaviors, exploration, and spatial memory performance in …

How Salivary Glands Recover From Fibrotic Injury, Gabriella Majka

Biological Sciences

Extracellular matrix deposition is required for repair after injury, but if left unresolved can result in fibrosis. Fibrosis is an excess deposition of extracellular matrix proteins following injury or aging that leads to eventual organ dysfunction. One surgical model that we have used to study mechanisms of fibrosis is the salivary gland ductal ligation model. During the process of ligation, a clip is placed on the main ducts of the submandibular (SMG) and sublingual gland (SLG) which leads from the salivary glands to the mouth. This causes the gland to atrophy, or waste away, resulting in decreased acinar cell differentiation …

Exploring The Role Of Stigmatic Exudate In The Water Lily (Nymphaceae) Pollination Mechanism Using N. Ampla (Salisb. Dc.), Luis Uribe

Theses and Dissertations

Water lilies are the only known plant group that uses hyperactive nectar glands to divest pollinators of their pollen. The nectar in Nymphaea ampla is thought to contain secondary metabolites that increase pollen deposition possibly by modifying pollinator behavior. This was explored utilizing visitation and fecundity data from the field coupled with survival and behavioral experiments in the laboratory. Replacing nectar with water reduced seed set in N. ampla which was attributed to reduced visitation in water-bearing flowers and not to effects on pollinator detention time. Exposure to nectar did not reduce survivability in Apis mellifera. Pollen and nectar foragers …

Characterization Of Soil Nematode Community As Influenced By Weedy Plants And Edaphic Properties, Orlando Garcia

Theses and Dissertations

Nematodes are one of the most critical species globally as they are part of most nutrient recycling. While nematodes play a vital role in nutrient cycling, little is known about them from an ecological standpoint. The majority of current research has focused on a singular component of the community, being those of herbivore/plant-parasitic nematodes. In this study, the community shifts of the nematode trophic groups were analyzed as influenced by native and invasive grasses species in the Lower Rio Grande Valley (LRGV) with the addition of edaphic soil properties.

In our study, the results indicate changes in the composition of …

Early Embryology In Collembola With An Emphasis On Wing Development, Samantha A. Gonzalez

Theses and Dissertations

The primary objective of this study was to further the understanding of the wing origin in insects. Currently there are several theories which are popular such as the tergum theory, the pleural plate theory, and the dual theory of wing origin. Studies for these theories have been done on crustaceans, the ancestors to modern day insects. By utilizing a pre insect hexapod, it may be possible to better understand the transition to insect wings. Members of the Collembola species Hypogastrurid are one of these pre-insect hexapods which may provide a clue into origins of wing development. During this study, the …

Prospecting For And Isolation Of Microalgae In South Texas, Mauricio Alejandro Peña

Theses and Dissertations

Microalgae is a very important microorganism that can be used for beneficial purposes for humans. One way to show the importance of algae in this planet is the contribution of Oxygen it provides to the atmosphere, which many organisms rely on (Medeiros et al., 2015). Carbon footprint has been one of the greatest causes for global warming and it is due to the use of fossils to create diesel. One of the ways to avoid contamination is to replace those fuels that are used on daily basis, such as for transportation. The microalgae are able to produce lipids that can …

Duet Phonology And Syntax Of The Red-Crowned Parrots In South Texas, Abigail Pozulp

Theses and Dissertations

Bird behavioral interaction systems show a preference for temporal precision. This preference is exemplified in the way many species avoid masking of vocal signals. Antiphonal duetting in songbirds suggest that overlapping notes are a sign of poor temporal coordination which can signify a weak pairbond, a possible cue for conspecifics seeking to usurp territories or mates. However, parrots (Psittacidae) are accomplished yet understudied duetters in nature. I recorded antiphonal duets produced by a wild population of red-crowned parrots (Amazona viridigenalis) in Brownsville, Texas. Temporal and acoustic variation of signals was assessed within and across a sample of mated …

Home Range Dynamics And Juvenile Dispersal Of Gray Hawks In The Lower Rio Grande Valley, Michael Stewart

Theses and Dissertations

Using GPS-GSM transmitters I determined when 14 juvenile Gray Hawks (Buteo plagiatus) in the Lower Rio Grande Valley of Texas fledged from their natal areas and how far they traveled once they dispersed. These transmitters also allowed me to calculate home range sizes for 22 adults. Additionally, with the GPS-GSM transmitters and 15 VHF transmitters, I discovered that adult Gray Hawks in the study area remained in their territories year-round. Home range sizes were calculated using the minimum convex polygon estimator, the estimation of kernel home-range, and the estimation of kernel Brownian bridge home-range. The same three methods allowed me …

Reintegrating Biology Through The Nexus Of Energy, Information, And Matter, Kim L. Hoke, Sara L. Zimmer, Adam B. Roddy, Mary Jo Ondrechen, Craig E. Williamson, Nicole R. Buan

Department of Biochemistry: Faculty Publications

Information, energy, and matter are fundamental properties of all levels of biological organization, and life emerges from the continuous flux of matter, energy, and information. This perspective piece defines and explains each of the three pillars of this nexus. We propose that a quantitative characterization of the complex interconversions between matter, energy, and information that compose this nexus will help us derive biological insights that connect phenomena across different levels of biological organization. We articulate examples from multiple biological scales that highlight how this nexus approach leads to a more complete understanding of the biological system. Metrics of energy, information, …

Spatial Distribution Of Conspecific Genotypes Within Chimeras Of The Branching Coral Stylophora Pistillata, Gabriele Guerrini, Dor Shefy, Jacob Douek, Nadav Shashar, Tamar L. Goulet, Baruch Rinkevich

Faculty and Student Publications

Chimerism is a coalescence of conspecific genotypes. Although common in nature, fundamental knowledge, such as the spatial distribution of the genotypes within chimeras, is lacking. Hence, we investigated the spatial distribution of conspecific genotypes within the brooding coral Stylophora pistillata, a common species throughout the Indo-Pacific and Red Sea. From eight gravid colonies, we collected planula larvae that settled in aggregates, forming 2–3 partner chimeras. Coral chimeras grew in situ for up to 25 months. Nine chimeras (8 kin, 1 non-related genotypes) were sectioned into 7–17 fragments (6–26 polyps/fragment), and genotyped using eight microsatellite loci. The discrimination power of each …

Rcb Initiates Arabidopsis Thermomorphogenesis By Stabilizing The Thermoregulator Pif4 In The Daytime, Yongjian Qiu, Elise K. Pasoreck, Chan Yul Yoo, Jiangman He, He Wang, Abhishesh Bajracharya, Meina Li, Haley D. Larsen, Stacey Cheung, Meng Chen

Faculty and Student Publications

Daytime warm temperature elicits thermomorphogenesis in Arabidopsis by stabilizing the central thermoregulator PHYTOCHROME INTERACTING transcription FACTOR 4 (PIF4), whose degradation is otherwise promoted by the photoreceptor and thermosensor phytochrome B. PIF4 stabilization in the light requires a transcriptional activator, HEMERA (HMR), and is abrogated when HMR’s transactivation activity is impaired in hmr-22. Here, we report the identification of a hmr-22 suppressor mutant, rcb-101, which surprisingly carries an A275V mutation in REGULATOR OF CHLOROPLAST BIOGENESIS (RCB). rcb-101/hmr-22 restores thermoresponsive PIF4 accumulation and reverts the defects of hmr-22 in chloroplast biogenesis and photomorphogenesis. Strikingly, similar to hmr, the null rcb-10 mutant impedes …

Climate And Seasonality Drive The Richness And Composition Of Tropical Fungal Endophytes At A Landscape Scale, Shuzo Oita, Alicia Ibáñez, François Lutzoni, Jolanta Miadlikowska, József Geml, Louise A. Lewis, Erik F. Y. Hom, Ignazio Carbone, Jana M. U’Ren, A. Elizabeth Arnold

Faculty and Student Publications

Understanding how species-rich communities persist is a foundational question in ecology. In tropical forests, tree diversity is structured by edaphic factors, climate, and biotic interactions, with seasonality playing an essential role at landscape scales: wetter and less seasonal forests typically harbor higher tree diversity than more seasonal forests. We posited that the abiotic factors shaping tree diversity extend to hyperdiverse symbionts in leaves—fungal endophytes—that influence plant health, function, and resilience to stress. Through surveys in forests across Panama that considered climate, seasonality, and covarying biotic factors, we demonstrate that endophyte richness varies negatively with temperature seasonality. Endophyte community structure and …