Digital Commons Network^™

Beginner's Guide To Common Native Bees, Cody Zesiger, Elizabeth Cohen, Hannah Jarvis, Lori R. Spears, Ricardo Ramirez

All Current Publications

Utah is a superb place for beginning bee enthusiasts. Over 1,000 species of native bees exist in Utah (Cane, 2015). Southern Utah alone has approximately the same number of bee species as the entire eastern U.S. coast. There are many reasons for appreciating bees and encouraging their presence in the landscape. Specifically, bees are key to a sustainable environment as they are essential pollinators of food and fiber crops. Bees can also be appreciated for their striking diversity in color and size. This fact sheet highlights the different bee species that you may see in Utah.

Agricultural Research Service Weed Science Research: Past, Present, And Future, Stephen L. Young, James V. Anderson, Scott R. Baerson, Joanna Bajsa-Hirschel, Dana M. Blumenthal, Chad S. Boyd, Clyde D. Boyette, Eric B. Brennan, Charles L. Cantrell, Wun S. Chao, Joanne C. Chee-Sanford, Charlie D. Clements, F. Allen Dray, Stephen O. Duke, Kayla M. Eason, Reginald S. Fletcher, Michael R. Fulcher, Brenda J. Grewell, Erik P. Hamerlynck, Robert E. Hoagland, David P. Horvath, Eugene P. Law, Daniel E. Martin, Clint Mattox, Steven B. Mirsky, Patrick J. Moran, Rebecca C. Mueller, Vijay K. Nandula, Beth A. Newingham, Zhiqiang Pan, Lauren M. Porensky, Paul D. Pratt, Andrew J. Price, Brian G. Rector, Krishna N. Reddy, Roger L. Sheley, Lincoln Smith, Melissa C. Smith, Keirith A. Snyder, Matthew A. Tancos

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

The U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS) has been a leader in weed science research covering topics ranging from the development and use of integrated weed management (IWM) tactics to basic mechanistic studies, including biotic resistance of desirable plant communities and herbicide resistance. ARS weed scientists have worked in agricultural and natural ecosystems, including agronomic and horticultural crops, pastures, forests, wild lands, aquatic habitats, wetlands, and riparian areas. Through strong partnerships with academia, state agencies, private industry, and numerous federal programs, ARS weed scientists have made contributions to discoveries in the newest fields of robotics and genetics, as well …

When A Calorie Is Not Just A Calorie: Diet Quality And Timing As Mediators Of Metabolism And Healthy Aging, Maria M Mihaylova, Amandine Chaix, Mirela Delibegovic, Jon J Ramsey, Joseph Bass, Girish Melkani, Rajat Singh, Zheng Chen, William W Ja, Michele Shirasu-Hiza, Mary N Latimer, Julie A Mattison, Anna E Thalacker-Mercer, Vishwa Deep Dixit, Satchidananda Panda, Dudley W Lamming

Faculty, Staff and Student Publications

An epidemic of obesity has affected large portions of the world, increasing the risk of developing many different age-associated diseases, including cancer, cardiovascular disease, and diabetes. In contrast with the prevailing notion that "a calorie is just a calorie," there are clear differences, within and between individuals, in the metabolic response to different macronutrient sources. Recent findings challenge this oversimplification; calories from different macronutrient sources or consumed at different times of day have metabolic effects beyond their value as fuel. Here, we summarize discussions conducted at a recent NIH workshop that brought together experts in calorie restriction, macronutrient composition, and …

The Art Of A Slugslayer: An Exploration Of The Process Of Extracting Radulae From Lehmannia Valentiana For The Purpose Of Viewing In The Scanning Electron Microscope, Elizabeth Gannon

Mahurin Honors College Capstone Experience/Thesis Projects

A radula is an anatomical structure found exclusively in mollusks that acts as both tongue and teeth in feeding. Its structure has been studied for more than a century, yet published methods for identifying, dissecting, and cleaning radulae for microscopy are almost unintelligible to anyone not already familiar with molluscan anatomy. The purpose of this project was to identify the best method of garden slug radula isolation and present it in a manner that anyone could understand and successfully use.

After identifying the location of the radula in the slug, the easiest means of removal proved to be simply regurgitating …

In Vitro Evaluation Of Antibacterial And Anticoagulant Activities Of Harmala Alkaloids Roots, Amel Benbott, Sabah Boukeria, Hakima Beldi, Kanza Kadi, Abdelouahab Yahia

Journal of Bioresource Management

Peganum harmala L. is a wild herbal plant rich in active compounds, and is among the most used plants in local medicine. The purpose of this study is to contribute to the evaluation of some biological activities of alkaloids extract of P. harmala roots. Using the classical method of extraction of β-carboline alkaloids, the yield of alkaloids in the roots was estimated at 2.34 %. The thin layer chromatography (TLC) method identified the two components Harmine and Hrmaline in the total alkaloid extract of the roots. We evaluated the antibacterial activity of harmala alkaloids in roots against three referenced bacterial …

Assessment Of Antimicrobial Competence Of Epiphytes And Endophytes From Osmium Basilicum And Trigonella Foenum Graecum, Iram Asim, Atia Iqbal, Muhammad Ikrama Tanveer

Journal of Bioresource Management

Plant-associated bacteria are an unexplored group of microorganisms that has enormous potential. These bacteria are the source of finding new antimicrobial substances. The present study aimed to isolate and characterize the epiphytes and endophytes from Osmium basilicum and Trigonella foenum graecum plants and to determine their antimicrobial potential against pathogenic bacteria from Nishtar Hospital Multan, Pakistan. The sum of 18 stems and roots along leaf specimens were assembled as of the plant's Osmium basilicum plus Trigonella foenum graecum as of the distinct locales of the Multan city. Overall 73 bacterial strains were isolated and their colony morphology, gram staining, spore …

Symbiotic Ucyn-A Strains Co-Occurred With El Niño, Relaxed Upwelling, And Varied Eukaryotes Over 10 Years Off Southern California, Colette Fletcher-Hoppe, Yi-Chun Yeh, Yubin Raut, J. L. Weissman, Jed A. Fuhrman

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Biological nitrogen fixation, the conversion of N₂ gas into a bioavailable form, is vital to sustaining marine primary production. Studies have shifted beyond traditionally studied tropical diazotrophs. Candidatus Atelocyanobacterium thalassa (or UCYN-A) has emerged as a focal point due to its streamlined metabolism, intimate partnership with a haptophyte host, and broad distribution. Here, we explore the environmental parameters that govern UCYN-A’s presence at the San Pedro Ocean Time-series (SPOT), its host specificity, and statistically significant interactions with non-host eukaryotes from 2008-2018. 16S and 18S rRNA gene sequences were amplified by “universal primers” from monthly samples and resolved into Amplicon …

The City Blues Of An Iridescent Canary: Physiological, Behavioral, And Developmental Impacts Of Lead (Pb) On Songbirds Along An Urban-To-Rural Gradient, Michelle Ross

Master of Science in Integrative Biology Theses

Urbanization is rapidly changing the environment and creating new challenges in the lives of animals across the globe. Anthropogenic contaminants found commonly in old construction materials—including heavy metals like lead— persist within the environment for prolonged periods of time and present a widespread problem for all who live near contaminated areas. Despite the phase-out of lead usage, it continues to threaten the health of all organisms but especially those from urban areas where historical lead use was more common. Currently, the sub-lethal effects of lead on wildlife are not well understood, though lead is known to affect physiology and behavior …

A Guide To The Brain Initiative Cell Census Network Data Ecosystem, Michael Hawrylycz, Maryann E Martone, Giorgio A Ascoli, Jan G Bjaalie, Hong-Wei Dong, Satrajit S Ghosh, Jesse Gillis, Ronna Hertzano, David R Haynor, Patrick R Hof, Yongsoo Kim, Ed Lein, Yufeng Liu, Jeremy A Miller, Partha P Mitra, Eran Mukamel, Lydia Ng, David Osumi-Sutherland, Hanchuan Peng, Patrick L Ray, Raymond Sanchez, Aviv Regev, Alex Ropelewski, Richard H Scheuermann, Shawn Zheng Kai Tan, Carol L Thompson, Timothy Tickle, Hagen Tilgner, Merina Varghese, Brock Wester, Owen White, Hongkui Zeng, Brian Aevermann, David Allemang, Seth Ament, Thomas L Athey, Cody Baker, Katherine S Baker, Pamela M Baker, Anita Bandrowski, Samik Banerjee, Prajal Bishwakarma, Ambrose Carr, Min Chen, Roni Choudhury, Jonah Cool, Heather Creasy, Florence D'Orazi, Kylee Degatano, Benjamin Dichter, Song-Lin Ding, Tim Dolbeare, Joseph R Ecker, Rongxin Fang, Jean-Christophe Fillion-Robin, Timothy P Fliss, James Gee, Tom Gillespie, Nathan Gouwens, Guo-Qiang Zhang, Yaroslav O Halchenko, Nomi L Harris, Brian R Herb, Houri Hintiryan, Gregory Hood, Sam Horvath, Bingxing Huo, Dorota Jarecka, Shengdian Jiang, Farzaneh Khajouei, Elizabeth A Kiernan, Huseyin Kir, Lauren Kruse, Changkyu Lee, Boudewijn Lelieveldt, Yang Li, Hanqing Liu, Lijuan Liu, Anup Markuhar, James Mathews, Kaylee L Mathews, Chris Mezias, Michael I Miller, Tyler Mollenkopf, Shoaib Mufti, Christopher J Mungall, Joshua Orvis, Maja A Puchades, Lei Qu, Joseph P Receveur, Bing Ren, Nathan Sjoquist, Brian Staats, Daniel Tward, Cindy T J Van Velthoven, Quanxin Wang, Fangming Xie, Hua Xu, Zizhen Yao, Zhixi Yun, Yun Renee Zhang, W Jim Zheng, Brian Zingg

Faculty, Staff and Student Publications

Characterizing cellular diversity at different levels of biological organization and across data modalities is a prerequisite to understanding the function of cell types in the brain. Classification of neurons is also essential to manipulate cell types in controlled ways and to understand their variation and vulnerability in brain disorders. The BRAIN Initiative Cell Census Network (BICCN) is an integrated network of data-generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman …

Microcalorimeter As A Biologic Activity Monitor For The Study Of Brachiaria Brizantha Seed Germination Process, M. A. Barboza, P. L. O. Volpe, R. Usberti, J. F. G. Faigle, R. H. Aguiar

IGC Proceedings (1977-2023)

Calorimetry helps better understanding of biological processes (Calvet & Prat, 1963). Very sensitive thermal sensors and microcalorimeters allow real time investigation and monitoring heat production of seed germination but few experiments have been performed in this area (Sigstad & Prado, 1999). Moreover, experimental procedures correlating germination phenomena and chemical thermodynamics are exceptional (Barboza, 2002). One can detect calorimetrically the heat flow produced during seed germination and compare the results with data recorded using standard germination methodology (ISTA, 1985). Seed germination and the biomass increase respiration and determination of the energy involved aids understanding of the energetic cycle involved. This work …

Migratory Material: Epigenetics & Weaving At The Us-Mexico Border, Valerie Navarrete

Masters Theses

Discourse often sutures the body shut, disallowing representations of identity to outgrow sociopolitical interests. This issue may originate from borders, but also from the unnamable pathology that generational colonial trauma transmits to the mind, body, and environment. Without a direct form of translatability, this thesis proposes a new materialism that deviates from any object-oriented ontology. Untethered and intra-active, epigenetics and weaving represent objects that transform typical ways of knowing and seeing. Their sensitivity to the environment, in addition to their mobility across generations of time, broaden the spatiotemporal loci of the body and its embodiment. Proposing new materials that expand …

Non-Destructive Imaging Of Phytosulfokine Trafficking In Plants Using Fiber-Optic Fluorescence Microscopy, Bernard Abakah

Electronic Theses and Dissertations

Plants secrete peptide ligands and use receptor signaling to respond to stress and control development. Understanding these phenomena is key to improving plant health and productivity for food, fiber, and energy applications. Phytosulfokine (PSK), a sulfated peptide hormone, regulates plant cell division, growth, and stress tolerance via specific phytosulfokine receptors (PSKRs). This study uses fiber-optic fluorescence microscopy to elucidate trafficking of PSK in live plants. The microscope features two-color optics and an objective lens connected to a 1-m coherent imaging fiber mounted on either a conventional upright microscope body or 5-axis positioning system (X–Y–Z plus pitch and yaw). PSK and …

Mapping The Functional Interactions At The Tumor-Immune Checkpoint Interface, Behnaz Bozorgui, Elisabeth K Kong, Augustin Luna, Anil Korkut

Faculty, Staff and Student Publications

The interactions between tumor intrinsic processes and immune checkpoints can mediate immune evasion by cancer cells and responses to immunotherapy. It is, however, challenging to identify functional interactions due to the prohibitively complex molecular landscape of the tumor-immune interfaces. We address this challenge with a statistical analysis framework, immuno-oncology gene interaction maps (ImogiMap). ImogiMap quantifies and statistically validates tumor-immune checkpoint interactions based on their co-associations with immune-associated phenotypes. The outcome is a catalog of tumor-immune checkpoint interaction maps for diverse immune-associated phenotypes. Applications of ImogiMap recapitulate the interaction of SERPINB9 and immune checkpoints with interferon gamma (IFNγ) expression. Our analyses …

Research Progress Of Subcritical Extraction Technology In The Field Of Nutrient Component Extraction From Aquatic Products, Wang Wen-Jie, Chen Xiu-Biao, Chen Yun-Yun, Zhou Xu-Xia, Ding Yu-Ting

Food and Machinery

The fundamental extraction principle, production process, and instrument of the subcritical fluid (including water) technology in terms of the aquatic products materials were introduced in this review, and the academic progress of SFE technology in extracting and separating nutritional components from the aquatic products within the recent 10 years were summarized, in terms of proteins/peptides, lipids and polysaccharides from aquatic products. The advantages of different processing factors for the extraction of specific components were summarized, and the future development direction of SFE equipment and technology in the deep processing of aquatic products was prospected.

Examining The Different Soil Horizons Of White Oak Mountain, Tn And Their Effect On The Soil Microbial Community, Ji Won Moon, Timothy D. Trott

Research in Biology

Soil microorganisms participate in the diverse interaction within virtually all ecosystems, consequently affecting the associated human and animal population. Identifying how edaphic variables alter the functional and taxonomic diversity of the soil microbial community requires an examination of total microbial soil diversity and abundance. This research study examined the effect of soil depth and horizon on the soil microbial community composition of White Oak Mountain. The soil microbial community was characterized by 16S/18S/ITS rDNA amplicon sequencing of the DNA extract of six samples from the three major soil types identified: HcE, MoE, and uMvC. OTU clustering analysis and both alpha …

Detection Of A Diverse Endophyte Assemblage Within Fungal Communities Associated With The Arundo Leaf Miner, Lasioptera Donacis (Diptera: Cecidomyiidae), Marie-Claude Bon, John A. Goolsby, Guy Mercadier, Fatiha Guermache, Javid Kashef, Massimo Cristofaro, Ann T. Vacek, Alan Kirk

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

The larvae of Lasioptera donacis Coutin feed on fungal communities lining galleries within the mesophyll of leaf sheaths of Arundo donax in an aggregative manner. It has been stated that L. donacis could have established a fundamental symbiotic relationship with one fungus, although the fungal composition of these communities remains unsettled. Using a culture-dependent approach and ITS sequencing, the present work characterizes and compares the fungal communities associated with L. donacis in Eurasia with the endophytes of A. donax in Texas where L. donacis is absent. The 65 cultivable isolates obtained from L. donacis fungal communities were sorted into 15 …

Detection Of A Diverse Endophyte Assemblage Within Fungal Communities Associated With The Arundo Leaf Miner, Lasioptera Donacis (Diptera: Cecidomyiidae), Marie-Claude Bon, John A. Goolsby, Guy Mercadier, Fatiha Guermache, Javid Kashef, Massimo Cristofaro, Ann T. Vacek, Alan Kirk

School of Earth, Environmental, & Marine Sciences Faculty Publications

The larvae of Lasioptera donacis Coutin feed on fungal communities lining galleries within the mesophyll of leaf sheaths of Arundo donax in an aggregative manner. It has been stated that L. donacis could have established a fundamental symbiotic relationship with one fungus, although the fungal composition of these communities remains unsettled. Using a culture-dependent approach and ITS sequencing, the present work characterizes and compares the fungal communities associated with L. donacis in Eurasia with the endophytes of A. donax in Texas where L. donacis is absent. The 65 cultivable isolates obtained from L. donacis fungal communities were sorted into 15 …

A Distinct Pattern Of Growth And Rac1 Signaling In Melanoma Brain Metastasis Cells, Ioana Stejerean-Todoran, Phyllis A Gimotty, Andrea Watters, Patricia Brafford, Clemens Krepler, Tetiana Godok, Haiyin Li, Zuriñe Bonilla Del Rio, Anke Zieseniss, Dörthe M Katschinski, Sinem M Sertel, Silvio O Rizzoli, Bradley Garman, Katherine L Nathanson, Xiaowei Xu, Qing Chen, Jack H Oswald, Michal Lotem, Gordon B Mills, Michael A Davies, Michael P Schön, Ivan Bogeski, Meenhard Herlyn, Adina Vultur

Faculty, Staff and Student Publications

Background: Melanoma, the deadliest of skin cancers, has a high propensity to form brain metastases that are associated with a markedly worsened prognosis. In spite of recent therapeutic advances, melanoma brain lesions remain a clinical challenge, biomarkers predicting brain dissemination are not clear and differences with other metastatic sites are poorly understood.

Methods: We examined a genetically diverse panel of human-derived melanoma brain metastasis (MBM) and extracranial cell lines using targeted sequencing, a Reverse Phase Protein Array, protein expression analyses, and functional studies in vitro and in vivo.

Results: Brain-specific genetic alterations were not detected; however, MBM cells in vitro …

Role Of Microorganisms In Communication Between Soil And Plants, Domenico Prisa

Karbala International Journal of Modern Science

Microbial population in the rhizosphere establishes a number of important interactions with plants, whose study is crucial in perspective of sustainable agricultural production. Studies on various plant crops have revealed that, despite the complex microbial biodiversity of the soil, the bacterial microbiome is characterised by multiple functionalities. A better understanding of the molecular mechanisms, underlying the interactions between plants and the microbiome, could enable better development of plants, related to the beneficial action of microorganisms. Therefore, this review aims to describe the characteristics of the rhizosphere microbiome with the interactions that occur between soil and roots, as well as the …

The Microbiome And Its Impact On Allogeneic Hematopoietic Cell Transplantation, Florent Malard, Robert R Jenq

Faculty, Staff and Student Publications

Allogeneic hematopoietic cell transplantation (alloHCT) is a standard curative therapy for a variety of benign and malignant hematological diseases. Previously, patients who underwent alloHCT were at high risk for complications with potentially life-threatening toxicities, including a variety of opportunistic infections as well as acute and chronic manifestations of graft-versus-host disease (GVHD), where the transplanted immune system can produce inflammatory damage to the patient. With recent advances, including newer conditioning regimens, advances in viral and fungal infection prophylaxis, and novel GVHD prophylactic and treatment strategies, improvements in clinical outcomes have steadily improved. One modality with great potential that has yet to …

Adverse Pregnancy Outcomes And Long Term Risk Of Ischemic Heart Disease In Mothers: National Cohort And Co-Sibling Study, Casey Crump, Jan Sundquist, Mary Ann Mclaughlin, Siobhan M Dolan, Usha Govindarajulu, Weiva Sieh, Kristina Sundquist

Faculty, Staff and Student Publications

OBJECTIVE: To examine the associations between five major adverse pregnancy outcomes and long term risks of ischemic heart disease in mothers.

DESIGN: National cohort study.

SETTING: Sweden.

PARTICIPANTS: All 2 195 266 women with a first singleton delivery in Sweden during 1973-2015.

MAIN OUTCOME MEASURES: The main outcome measure was incidence of ischemic heart disease from delivery to 2018, identified from nationwide inpatient and outpatient diagnoses. Cox regression was used to calculate hazard ratios for ischemic heart disease associated with preterm delivery, small for gestational age, pre-eclampsia, other hypertensive disorders of pregnancy, and gestational diabetes, adjusting for other adverse pregnancy …

Retrospective Evaluation Of The Role Of Gemcitabine-Docetaxel In Well-Differentiated And Dedifferentiated Liposarcoma, Prapassorn Thirasastr, Heather Lin, Behrang Amini, Wei-Lien Wang, Jeffrey M Cloutier, Elise F Nassif, Emily Z Keung, Christina L Roland, Barry Feig, Dejka Araujo, Robert S Benjamin, Anthony P Conley, John A Livingston, Joseph Ludwig, Shreyaskumar Patel, Ravin Ratan, Vinod Ravi, Maria Alejandra Zarzour, Xiao Zhou, Neeta Somaiah

Faculty, Staff and Student Publications

OBJECTIVE: Well-differentiated (WDLPS) and dedifferentiated liposarcoma (DDLPS) account for the majority of liposarcomas. Although gemcitabine-docetaxel is used as second-line treatment in soft tissue sarcomas, its efficacy in WDLPS/DDLPS is not established. This study retrospectively analyzed the efficacy of gemcitabine regimens in WDLPS/DDLPS.

METHODS: All patients with WDLPS or DDLPS who received gemcitabine-based chemotherapy at our institution between September 2002 and January 2021 were included. Response was evaluated by an independent radiologist using RECIST 1.1. The Kaplan-Meier method was used to estimate distributions of survival outcomes and log-rank tests were used to compare survival outcomes between subgroups.

RESULTS: Sixty-five WDLPS/DDLPS patients …

Insight From Biology Program Learning Outcomes: Implications For Teaching, Learning, And Assessment, Noelle Clark, Jeremy L. Hsu

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Learning goals and objectives are a key part of instruction, informing curricular design, assessment, and learning. These goals and objectives are also applied at the programmatic level, with program learning outcomes (PLOs) providing insight into the skills that undergraduate biology programs intend for their students to master. PLOs are mandated by all major higher education accreditation agencies and play integral roles in programmatic assessment. Despite their importance, however, there have not been any prior attempts to characterize PLOs across undergraduate biology programs in the United States. Our study reveals that many programs may not be using PLOs to communicate learning …

Insights From The Management Of Offshore Energy Resources: Toward An Ecosystem-Services Based Management Approach For Deep-Ocean Industries, M. Emilia Bravo, Miriam I. Brandt, Jesse M. A. Van Der Grient, Thomas G. Dahlgren, Patricia Esquete, Sabine Gollner, Daniel O. B. Jones, Lisa A. Levin, Craig R. Mcclain, Bhavani E. Narayanaswamy, Tracey Sutton, Lissette Victorero, Erik E. Cordes

Marine & Environmental Sciences Faculty Articles

The deep ocean comprises complex ecosystems made up of numerous community and habitat types that provide multiple services that benefit humans. As the industrialization of the deep sea proceeds, a standardized and robust set of methods and metrics need to be developed to monitor the baseline conditions and any anthropogenic and climate change-related impacts on biodiversity, ecosystem function, and ecosystem services. Here, we review what we have learned from studies involving offshore-energy industries, including state-of-the-art technologies and strategies for obtaining reliable metrics of deep-sea biodiversity and ecosystem function. An approach that includes the detection and monitoring of ecosystem services, with …

Traditional Plants That Are Utilized To Treat Urinary Tract Infections: A Review, Rasha Hadi Saleh, Aseel Mohammad Omran, Rafah S. Almuttairi Alhilla

Maaen Journal for Medical Sciences

Among the most serious problems affecting public health is urinary tract infection (UTI). There are several parts of the urinary tract affected by this type of inflammation and affects women more frequently than men. As the antibacterial resistance problem is growing in urological medicine, there is a increasing and a continuing requirement to add antimicrobial medication which could be from medicinal herbs in regulatory UTIs. Since the beginning of civilization, medicinal plants have been an integral element of human society in the fight against diseases. For the aim of reducing costs, increasing the effectiveness of treatment and eliminating the side …

Developing Red Fluorescent Zn2+ Sensors And Characterizing Zn2+ Homeostasis In Mucolipidosis Type Iv Disease, Anna M. Dischler

Electronic Theses and Dissertations

Zinc (Zn²⁺) is a divalent, redox-inert metal that plays a vital role in many cellular processes either by acting as a catalytic cofactor or a labile signaling molecule in the cytoplasm. Cytosolic Zn²⁺ levels are tightly regulated to stay within a narrow window of concentrations, but fluctuations in Zn²⁺ signals have been detected in a variety of cells. We developed a genetically encoded, single red fluorescent protein (RFP) based Zn²⁺ sensor, RZnP1, that can be used alongside green-wavelength sensors for the simultaneous detection of different signaling molecules within the same cells or among different subcellular …

Insight Into Eleutherodactylus Coqui Resilience And Anuran Hypoxia Tolerance Utilizing Pincho, Randy Ortiz

Theses and Dissertations

The onset of high-throughput RNA-sequencing (RNA-seq) technology allowed research into transcriptomics to accelerate exponentially aided by the rapid advancement of bioinformatic pipelines. The Pincho workflow, my first research endeavor, is a transcriptomic workflow developed to create an avenue of high-quality reconstructions from RNA-seq data. High-quality reconstruction standards entail longer transcripts, more complete transcripts, and more raw data utilization. We have discovered an ideal trio of assemblers between transABySS, rnaSPAdes and TransLiG that would best reconstruct next-generation sequencing data according to these standards. We utilized Pincho to drive two distinct experiments: (1) exploring the genetic basis for the successful invasion of …

Mutational Analysis Of Mechanosensitive Ion Channels In The Carnivorous Venus Flytrap Plant, Carl Procko, Wen Mai Wong, Janki Patel, Seyed Ali Reza Mousavi, Tsegaye Dabi, Marc Duque, Lisa Baird, Sreekanth H. Chalasani, Joanne Chory

Biology: Faculty Scholarship

How the Venus flytrap (Dionaea muscipula) evolved the remarkable ability to sense, capture, and digest animal prey for nutrients has long puzzled the scientific community.1 Recent genome and transcriptome sequencing studies have provided clues to the genes thought to play a role in these tasks.2,3,4,5 However, proving a causal link between these and any aspect of the plant’s hunting behavior has been challenging due to the genetic intractability of this non-model organism. Here, we use CRISPR-Cas9 methods to generate targeted modifications in the Venus flytrap genome. The plant detects prey …

Bioorthogonal Tethering Of Drug Fragments To Engineered G Protein-Coupled Receptors, Jordan M. Mattheisen

Student Theses and Dissertations

G protein-coupled receptors (GPCRs) modulate diverse cellular signaling pathways and are important drug targets. Despite the availability of high-resolution structures for nearly 100 discrete GPCRs in complex with various ligands, discovering allosteric drugs that can modulate receptor signaling remains challenging. In principle, allosteric ligands have certain advantages because they bind to pockets on the receptor that do not directly impact the orthosteric site for agonist ligands, but still tune downstream signaling pathways. But identifying and validating allosteric ligands remains difficult partly due to the dynamic nature of GPCRs in native membranes. Of the more than 3700 distinct FDA-approved drugs, there …

Histomorphology Of The Distal Urogenital Ducts In The Male Northern Crawfish Frog, Rana Areolata Circulosa (Anura: Ranidae), S.E. Trauth, R.G. Neal

Journal of the Arkansas Academy of Science

We examined the microanatomy of the distal urogenital ducts in the male Northern Crawfish Frog (Rana areolata circulosa) from a small sample (n = 5) collected in February and March from central Arkansas over a 5-year period (2017–2022). Specifically, we sought information on the following structures: (1) the paired Wolffian (urogenital) ducts caudally from the kidneys to their merging with the urodeum of the cloaca, (2) the paired seminal vesicles (sperm storage structures), and (3) the paired Müllerian ducts and glands. This study provides new information on these urogenital ducts and promotes a clearer understanding of this anatomical region for …