Biology Commons^™

Mechanisms Of Substrate Recognition By The Cul3-Based E3 Ligase, Katia Graziella De Oliveira Rebola

Dissertations and Theses

Cul3-based E3 ligase is responsible for regulating a variety of cellular pathways, many of which are known to have profound effects on the proper function of multicellular organisms. Although progress over the past years has been truly impressive, our understanding of the mechanisms of E2 recruitment and selection by the BCR complex and all the roles that Cul3 plays on kidneys remains in its infancy. To explore these aspects, this dissertation aims to analyze the Cul3 complex using two different approaches: (1) We used the powerful tool of chimeric analysis to map the essential domain binding characteristics of Cul3 taking …

College Of Natural Sciences Newsletter, September 2021, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 2, Issue 9.

Page 1 Dean's Message
Page 2 Awards and Recognition
Page 3 Student Clubs in Natural Science
Page 4 Media Coverage of CNS
Page 5 Hobo Day Festivities
Page 6 Open PRAIRIE Data; Grants Awarded in CNS
Page 7 One Day for State Recap

The Structural And Functional Role Of Photosensing In Rgs-Lov Proteins, Zaynab Jaber

Dissertations, Theses, and Capstone Projects

Light provides organisms with energy and spatiotemporal information. To survive and adapt, organisms have developed the ability to sense light to drive biochemical effects that underlie vision, entrainment of circadian rhythm, stress response, virulence, and many other important molecularly driven responses. Blue-light sensing Light-Oxygen-Voltage (LOV) domains are ubiquitous across multiple kingdoms of life and modulate various physiological events via diverse effector domains. Using a small molecule flavin chromophore, the LOV domain undergoes light-dependent structural changes leading to activation or repression of these catalytic and non-catalytic effectors. In silico analyses of high-throughput genomic sequencing data has led to the marked expansion …

Complete Mitochondrial Genome Sequence Of The Gulf Coast Tick (Amblyomma Maculatum), Amanda E. Brenner, Rahul Raghavan

Biology Faculty Publications and Presentations

The complete circularized mitochondrial genome sequence of Amblyomma maculatum is 14,803 bp long. It encodes 13 protein coding genes, 2 rRNA genes, 22 tRNA genes, 2 tick box motifs, and 2 control regions. The gene arrangement and content are consistent with those of previously reported Metastriata tick mitochondrial genomes.

Three Lc-Ms Plant Metabolomics Studies Of Hop (Humulus) Species: Wild H. Neomexicanus, Drought Stress, And Agricultural Terroir, Taylan Morcol

Dissertations, Theses, and Capstone Projects

The hop plant (Humulus L., Cannabaceae) is a dioecious, perennial, twining vine with a long history of human use. Nowadays, hop plants are generally grown for their inflorescences (“cones”), which are used in brewing for their phytochemical metabolites. Many of these metabolites are involved in plant stress response and communication. Genetics and environment are two major factors that affect plant metabolism. In three separate metabolomics studies, this project examined the effects of both genetic and environmental factors on hop phytochemistry.

In the first study, 23 hop genotypes were grown in two different locations in the Pacific Northwest region of …

Understanding The Influence Of Zinc On Grain Cadmium Accumulation And Bioaccessibility In Rice, Michael A. Tavarez

Dissertations, Theses, and Capstone Projects

The effect of cadmium and zinc on mineral concentrations in three cultivars of rice

Interactions between the essential mineral zinc (Zn) and the toxic heavy metal cadmium (Cd) play an important role in regulating transport of both minerals to rice grains. Understanding these interactions is crucial for limiting cadmium and increasing zinc transfer to the food chain. Previous studies on the matter have had conflicting results suggesting synergistic and antagonistic relationships between the minerals. The goal of this work was to identify the effect of external cadmium and zinc on the uptake and translocation of both minerals from roots to …

Investigating Factors That Affect Hiv-1 Capsid Stability, Max Mao, Joshua Temple

The Yale Undergraduate Research Journal

TKH HIV caSVLd, a SURWHLQ VKHOO cRPSRVHd RI PRQRPHULc XQLWV RI CA, IRUPV a IXOOHUHQH cRQH WKaW SURWHcWV HIV¶V YLUaO JHQRPH aQd enzymes during infection. I am interested in elucidating the factors that influence stability of the capsid shell and capturing the structural interactions between HIV capsid, host restriction factors, and small molecules using biochemical and structural biology techniques. HIV capsid shell was broken down and purified into hexamer and pentamer units for in vitro study. Structural assays were performed using X-ray crystallography and biochemical analysis was performed using pelleting assays. By understanding capsid structure with factors that confer stability, …

Altering Sensory Learning By Chronic Inactivation Of Vip Interneurons, Christopher Alba, Hannah Selwyn, Katie Ferguson, Jessica Cardin

The Yale Undergraduate Research Journal

Vasoactive intestinal polypeptide-expressing interneurons (VIP-INs) play a key role in the regulation of cortical circuits and are implicated in perceptual function and psychiatric disease. However, their role in perceptual augmentation and learning remains understudied. We performed chronic, localized ablation of VIP-INs in the primary visual cortex of adult mice using caspase-induced apoptosis to better understand how VIP-INs contribute to visual perception and the ability to learn a visual detection task. We find that chronic VIP-IN ablation does not affect naïve performance on a full-screen visual contrast detection task. However, mice with suppressed levels of VIP-INs achieved their final expert state …

Examination Of Methylation Status And Occupancy Of Dna Methylation Modifying Proteins On Regulatory Regions Of The Dax-1 Gene, Caroline P. Riedstra

Master's Theses

Epigenetic modifications influence gene expression and thereby play a pivotal role in development and disease. Misregulation and mutations in the DAX-1 gene, or Dosage-Sensitive Sex Reversal, Adrenal Hypoplasia Congenita, Critical Region on the X chromosome, gene 1, have been implicated in Adrenal Hypoplasia Congenita (AHC) and Dosage Sensitive Sex Reversal (DSS). The orphan nuclear hormone receptor DAX-1 is expressed predominantly in tissues such as the testes, ovaries, breast, adrenal cortex, and lung. Critically, DAX-1 may serve as an indicator of aberrant growth in these tissues. Here we hypothesize that DAX-1 is epigenetically regulated, specifically in cancer cells, thereby reducing its …

College Of Natural Sciences Newsletter, August 2021, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 2, Issue 8.

Page 1 Dean's Message
Page 2 Awards and Recognition
Page 3 Student Summer Research
Page 4 Media Coverage of CNS
Page 5 Wintrode Student Success Center
Page 6-7 Welcome to our new Faculty & Staff!
Page 8 One Day for State: Thursday, Sept. 2nd
Page 7 Open PRAIRIE Data; Fall Faculty Retreat 2021

Investigation Of Techniques And Their Application For The Cryopreservation Of Algal Species, Jazmine Leija

Theses and Dissertations

An alternative source for petroleum-based crude oils are algae derived biofuels. Fossil fuels are harmful for the environment, expensive and becoming scarce. There has been an increase in research on environmentally sustainable energy, using lipids derived from microalgae, which can be converted into biofuel. The use of microalgae as a source for biofuels has a lot of benefits including decreasing greenhouse gas emissions, rapid fuel production, absorption of carbon dioxide, and production of a renewable source of energy.

Algae cryopreservation aids in the maintenance of the best algae strains selected for producing lipids for biofuels. Cryopreservation will help minimize genetic …

Unveiling Global Roles Of G-Quadruplexes And G4-22 In Human Genetics, Ruth Barros De Paula

Dissertations and Theses (Open Access)

G-quadruplexes are non-B DNA structures formed by four or more runs of repeated guanines that confer unique features to living organism’s genomes. These sequences are enriched in regulatory regions, such as promoters and 5’ UTRs, and have distinct regulatory roles in both health and disease states. Even though previous studies showed the impact of G4 in gene expression, none of them summarized the location-specific effect of G4. Also, there is no broad understanding about the most common G4 repeat in the human genome, named here as G4-22, and how it links to the evolution of mammals and their biology. In …

In The Search For Novel Treatments For Chagas' Disease Using Cutting-Edge Imaging Technology, Karsten Dieter Amezcua Winter

Open Access Theses & Dissertations

Chagas disease (ChD) is caused by Trypanosoma cruzi (T. cruzi), an intracellular protozoan parasite. ChD has a global mortality of 15,000 annual deaths, and approximately, 8-10 million people are infected. There is growing concern in the United States as autochthonous cases of ChD have been reported in the southern region. The two available treatments are only partially effective and highly toxic. N-aroyl derivatives and α, β-unsaturated ketones have been previously tested against Leishmania, a closely related parasite, demonstrating selective toxicity towards the microorganism. The objective of this study is to evaluate a drug library consisting of 21 α, β-unsaturated ketones …

Pacific Black Duck Ecology And Habitat Assessment In Aunu'u, American Samoa, And Their Relationship To Other Mallard-Like Ducks Of Oceania, Greater Indonesia, And The Philippines, Marissa Kaminski

Open Access Theses & Dissertations

Determining a species’ ecological needs, assessing the quality of their habitat, and determining genetic differentiation and connectivity among populations is essential to their conservation. My dissertation focuses on obtaining such a holistic view for a population of Pacific Black Ducks recently established on the Island of Aunu’u, American Samoa. Specifically, I present the first evaluation of the ecology and habitat of a recently established population of Pacific Black Ducks on the Island of Aunu’u, American Samoa, in Chapter 1, while I assess the genetic connectivity and relationship of this population to other Mallard-like ducks found in Greater Indonesia, Oceania, and …

Late Embryogenesis Abundant Proteins And Mitochondrial Membranes From An Animal Extremophile: Insights Into Severe Water Stress, John Marcus Anderson

LSU Doctoral Dissertations

This dissertation focuses on two major topics germane to mechanisms by which animals tolerate extreme water stress. First, the impact of transgenic expression of late embryogenesis abundant proteins (LEA) on water stress tolerance of the fruit fly Drosophila melanogaster was investigated. The overall aim was to extend current understanding of the protective properties of LEA proteins documented with isolated cells to a desiccation-sensitive organism during exposure to drying and hyperosmotic stress. Four lines of D. melanogaster were created that expressed transgenes encoding selected LEA proteins originally identified in embryos of the extremophile Artemia franciscana. After 80% tissue water loss, …

Screening Next-Generation Fluorine-19 Probe And Preparation Of Yeast-Derived G Proteins For Gpcr Conformation And Dynamics Study, Wenjie Zhao

USF Tampa Graduate Theses and Dissertations

GPCR regulates numerous diverse physiological processes relevant to diabetes, obesity, Alzheimer's diseases, and several central nervous system disorders and targets proteins in signaling pathways. It has created nearly 200 billion profits from its derivative drugs in 2018. There are near 400 structures of over 70 GPCRs have been resolved by X-ray crystallography, cryo-electron microscopy, and NMR spectroscopy. One of the current challenges that remain in the conformational transition and dynamics study using NMR spectroscopy is to obtain sufficient quantities of the G proteins and GPCRs. Pichia pastoris has shown its tremendous promise in expressing the GPCRs in a high yield, …

A Kinetic Model For Blood Biomarker Levels After Mild Traumatic Brain Injury, Sima Azizi, Daniel B. Hier, Blaine Allen, Tayo Obafemi-Ajayi, Gayla R. Olbricht, Matthew S. Thimgan, Donald C. Wunsch

Mathematics and Statistics Faculty Research & Creative Works

Traumatic brain injury (TBI) imposes a significant economic and social burden. The diagnosis and prognosis of mild TBI, also called concussion, is challenging. Concussions are common among contact sport athletes. After a blow to the head, it is often difficult to determine who has had a concussion, who should be withheld from play, if a concussed athlete is ready to return to the field, and which concussed athlete will develop a post-concussion syndrome. Biomarkers can be detected in the cerebrospinal fluid and blood after traumatic brain injury and their levels may have prognostic value. Despite significant investigation, questions remain as …

College Of Natural Sciences Newsletter, July 2021, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 2, Issue 7.

Page 1 Dean's Message
Page 2 Celebrating Three Years
Page 3 Summer School Travel
Page 4 Media Coverage of CNS
Page 5 Chemistry Teachers Visit
Page 5 Remembering Dr. Warren Hein
Page 6 Research Spotlights: Undergraduate Summer Experiences
Page 7 Open PRAIRIE Data; Grants Awarded in CNS

Ahr Expression On Rorc-Expressing Immune Cells Is Essential For I3c-Mediated Protection Against Colitis, Michal C. Williams

Senior Theses

Colitis is an inflammatory bowel disorder (IBD) whose etiology is attributed to modification in the luminal microbiota and dysregulation in the immune response. Indole is a signaling molecule which is naturally produced by gut luminal microbiota. Indole-3- carbinol (I3C) is a compound commonly found in vegetables and a ligand for the aryl hydrocarbon receptor (AhR). Previous studies have detected decreased expression and activation on the AhR receptor in colitis patients, thought to possibly alter gut microbiota metabolism, subsequently promoting colitis. 1 AhR, expressed in a variety of immune and epithelial cells, contributes to gut homeostasis by affecting vital mediators such …

Data Management Tools To Measure The Impact Of Core Facilities, Diane B. Smith, Tracy L. Yarnell, Barbara J. Jibben, Linda E. Liou, Carolyn J. Hovde, Julia Thom Oxford

Biology Faculty Publications and Presentations

The Biomolecular Research Center at Boise State University is a research core facility that supports the study of biomolecules with an emphasis on protein structure and function, molecular interactions, and imaging. The mission of the core is to facilitate access to instrumentation that might otherwise be unavailable because of the cost, training for new users, and scientific staff with specialized skills to support early-stage investigators, as well as more established senior investigators. Data collection and management of users and their research output is essential to understand the impact of the center on the research environment and research productivity. However, challenges …

Nanozymes—Hitting The Biosensing “Target”, Yingfen Wu, Diane Darland, Julia Zhao

Biology Faculty Publications

Nanozymes are a class of artificial enzymes that have dimensions in the nanometer range and can be composed of simple metal and metal oxide nanoparticles, metal nanoclusters, dots (both quantum and carbon), nanotubes, nanowires, or multiple metal-organic frameworks (MOFs). They exhibit excellent catalytic activities with low cost, high operational robustness, and a stable shelf-life. More importantly, they are amenable to modifications that can change their surface structures and increase the range of their applications. There are three main classes of nanozymes including the peroxidase-like, the oxidase-like, and the antioxidant nanozymes. Each of these classes catalyzes a specific group of reactions. …

Genetically Encoded Multivalent Liquid Glycan Array Displayed On M13 Bacteriophage, Amira Khalil, Mirat Sojitra, Jasmine Maghera, Emily Rodrigues, Eric J. Carpenter, Shaurya Seth, Daniel Ferrer Vinals, Todd L. Lowary

Pharmacy

The central dogma of biology does not allow for the study of glycans using DNA sequencing. We report a liquid glycan array (LiGA) platform comprising a library of DNA ‘barcoded’ M13 virions that display 30–1,500 copies of glycans per phage. A LiGA is synthesized by acylation of the phage pVIII protein with a dibenzocyclooctyne, followed by ligation of azido-modified glycans. Pulldown of the LiGA with lectins followed by deep sequencing of the barcodes in the bound phage decodes the optimal structure and density of the recognized glycans. The LiGA is target agnostic and can measure the glycan-binding profile of lectins, …

Somatic Inhibition By Microscopic Magnetic Stimulation, Hui Ye

Biology: Faculty Publications and Other Works

Electric currents can produce quick, reversible control of neural activity. Externally applied electric currents have been used in inhibiting certain ganglion cells in clinical practices. Via electromagnetic induction, a miniature-sized magnetic coil could provide focal stimulation to the ganglion neurons. Here we report that high-frequency stimulation with the miniature coil could reversibly block ganglion cell activity in marine mollusk Aplysia californica, regardless the firing frequency of the neurons, or concentration of potassium ions around the ganglion neurons. Presence of the ganglion sheath has minimal impact on the inhibitory effects of the coil. The inhibitory effect was local to the …

Evolution Of Targeted Therapy Resistance In Eml4-Alk Positive Non-Small Cell Lung Cancer, Robert Vander Velde

USF Tampa Graduate Theses and Dissertations

Targeted therapies have emerged as potent treatments that lead to the remission of many tumors. However, they rarely cure cancers in advanced, metastatic settings. This is due to the evolution of resistance, which in turn can be ascribed to the survival of small subpopulations of tolerant and/or resistant cells. Here we investigated the evolution of resistance to EML4-ALK inhibitors in non-small cell lung cancer (NSCLC) and demonstrated that resistance evolves gradually, from unique pre-treatment sub-populations, as multiple resistance mechanisms accumulate in a Darwinian fashion. Despite accumulating multiple changes, cells evolved, in parallel, toward similar inhibitor specific phenotypes. Evolving cells have …

Impacts Of Detritivore Diversity Loss On Instream Decomposition Are Greatest In The Tropics, Luz Boyero, Naiara López-Rojo, Alan M. Tonin, Javier Pérez, Francisco Correa-Araneda, Richard G. Pearson, Jaime Bosch, Ricardo J. Albariño, Sankarappan Anbalagan, Leon A. Barmuta, Ana Basaguren, Francis J. Burdon, Adriano Caliman, Marcos Callisto, Ian C. Campbell, Bradley J. Cardinale, J. Jesús Casas, Ana M. Chará-Serna, Eric Chauvet, Szymon Ciapała, Jose Checo Colón-Gaud, Aydeé Cornejo, Aaron M. Davis, Monika Degebrodt, Emerson S. Dias, María E. Díaz, Michael M. Douglas, Andrea C. Encalada, Ricardo Figueroa, Alexander S. Flecker, Tadeusz Fleituch, Erica A. García, Gabriela García, Pavel E. García, Mark O. Gessner, Jesús E. Gómez, Sergio Gómez, Jose F. Gonçalves Jr, Manuel A. S. Graça, Daniel C. Gwinn, Robert O. Hall Jr., Neusa Hamada, Cang Hui, Daichi Imazawa, Tomoya Iwata, Samuel K. Kariuki, Andrea Landeira-Dabarca, Kelsey A. Laymon, María Leal, Richard Marchant, Renato T. Martins, Frank O. Masese, Megan Maul, Brendan G. Mckie, Adriana O. Medeiros, Charles M. M’ Erimba, Jen A. Middleton, Silvia Monroy, Timo Muotka, Junjiro N. Negishi, Alonso Ramírez, John S. Richardson, José Rincón, Juan Rubio-Ríos, Gisele M. Dos Santos, Romain Sarremejane, Fran Sheldon, Augustine Sitati, Nathalie S. D. Tenkiano, Scott D. Tiegs, Janine R. Tolod, Michael Venarsky, Anne Watson, Catherine M. Yule

Biology: Faculty Publications

The relationship between detritivore diversity and decomposition can provide information on how biogeochemical cycles are affected by ongoing rates of extinction, but such evidence has come mostly from local studies and microcosm experiments. We conducted a globally distributed experiment (38 streams across 23 countries in 6 continents) using standardised methods to test the hypothesis that detritivore diversity enhances litter decomposition in streams, to establish the role of other characteristics of detritivore assemblages (abundance, biomass and body size), and to determine how patterns vary across realms, biomes and climates. We observed a positive relationship between diversity and decomposition, strongest in tropical …

Temperature Regulation Of Plant Hormone Signaling During Stress And Development, Christian Castroverde, Damaris Dina

Biology Faculty Publications

Global climate change has broad-ranging impacts on the natural environment and human civilization. Increasing average temperatures along with more frequent heat waves collectively have negative effects on cultivated crops in agricultural sectors and wild species in natural ecosystems. These aberrantly hot temperatures, together with cold stress, represent major abiotic stresses to plants. Molecular and physiological responses to high and low temperatures are intricately linked to the regulation of important plant hormones. In this review, we shall highlight our current understanding of how changing temperatures regulate plant hormone pathways during immunity, stress responses and development. This article will present an overview …

Rapid Warming Events In A Small Coastal Upwelling Embayment, Tatjana E. Ellis

Physics

Temperature variability in the nearshore coastal ocean influences various biological processes and can drive changes in biodiversity and habitat range. Despite recent progress, there are still significant gaps in the understanding of drivers of temperature variability in upwelling bays, particularly at higher frequencies. In this study, we analyzed a decade of nearshore temperature measurements both inside and outside a small coastal embayment located in central California [San Luis Obispo (SLO) bay], as well as temperature data from satellites, to characterize rapid warming events. We found that rapid warming events, defined using rates of temperature change across different thresholds, occurred more …

College Of Natural Sciences Newsletter, June 2021, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 2, Issue 6.

Page 1 Dean's Message
Page 2-6 Remembering the Life of Dr. Pengra and Celebrating His legacy for Entire Generations to Come.

An In Vitro Model Of Tumor Heterogeneity Resolves Genetic, Epigenetic, And Stochastic Sources Of Cell State Variability, Corey A. Hayford, Darren R. Tyson, C. Jack Robbins Iii, Peter L. Frick, Vito Quaranta, Leonard Harris

Biomedical Engineering Faculty Publications and Presentations

Tumor heterogeneity is a primary cause of treatment failure and acquired resistance in cancer patients. Even in cancers driven by a single mutated oncogene, variability in response to targeted therapies is well known. The existence of additional genomic alterations among tumor cells can only partially explain this variability. As such, nongenetic factors are increasingly seen as critical contributors to tumor relapse and acquired resistance in cancer. Here, we show that both genetic and nongenetic factors contribute to targeted drug response variability in an experimental model of tumor heterogeneity. We observe significant variability to epidermal growth factor receptor (EGFR) inhibition among …

Assessment Of The Quality And Quantity Of Organic Matter In The Rufiji Mangrove Surface Sediments Using Biochemical Composition, Daniel A Shilla

Tanzania Journal of Science

This study was carried out to investigate spatial changes in the quality and quantity of sedimentary organic matter in the Rufiji mangrove system, Tanzania. Sediment samples were collected from three sampling sites. Total organic matter in mangrove sediments ranged from 7.28 ± 2.02% to 10.58 ± 1.34%. Protein concentrations varied from 1,145.33 ± 20.33 μg/g to 2,747.50 ± 25.14 μg/g in the mangrove sediments. Total carbohydrates, lipids and biopolymeric carbon in mangrove sediments ranged between 1,110.50 ± 16.31 μg/g and 1,914.17 ± 27.79 μg/g, 1,436.50 ± 24.13 μg/g and 6,373.50 ± 25.79 μg/g, and 4,496 μg C/g and 10,231.50 μg …