Digital Commons Network^™

A Bioinformatics Analysis Of Microbial Diversity And Its Correlation With Human Lifestyle, Diet, And Health Variables, Alivia Ankrum, Kate Cooper

Theses/Capstones/Creative Projects

The abundant impact of microbiota on human physiology suggests a need for exploration into their impact on human health and disease. The American Gut Project (AGP) was established to aggregate microbiome sequencing data as well as health, diet, and lifestyle metadata. This study proposes to identify taxonomic species and build a phylogenetic tree representation from the AGP participant sample collection as well as find their respective alpha and beta diversity of all metadata variables based on patient questionnaire data. Additionally, this study will involve a chimeric sequence extraction from the 16S rRNA sequences of the AGP. The expected results are …

Effects Of Ahcc On The Interaction Between T And B Lymphocytes, Sajina Poudel

Theses (2016-Present)

AHCC is a beta-glucan derived from the shiitake mushroom. It is used as an immune supplement and is known to boost the immune system. The mechanisms involved are increased lymphocyte proliferation and reduction of inflammation. The effects have been well studied in T cells. However, factors produced by T cells that affect B cells have not been studied. In this study, we explored the gene products stimulated by the AHCC exposure in T lymphocytes which play a role in B cell function. Data from a prior gene array experiment were used to delineate the effects of AHCC on the interaction …

An Overview Of The Extracurricular Polysaccaride Production Of Probiotic Lactic Acid Bacteria, Olujimi Babajide Olowokere

Theses (2016-Present)

The study focuses on a comprehensive review of lactic acid bacteria and their production of extracellular polysaccharide substrates (EPS). Two important factors are addressed in the work; and these are 1) identification of LAB stains found in the commercially sold daily milk, 2) significant factors impacting polysaccharide production. Motivation behind these focus points is to allow further inquiries and studies on exploring these strains of bacteria for human wellness promotion. With microbial EPS production being a recent interest of study among healthcare and food industries sectors, new species of bacteria are extensively exploited for further investigation to improve human health, …

College Of Natural Sciences Newsletter, July & August 2022, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 3, Issue 5

Page 1 Dean's Message
Page 2 Awards & Recognition
Page 3 Resources for Student Success
Page 4 Welcome to New Faculty & Staff
Page 5 Summer Activities in CNS
Page 9 Celebrating the lives of those who touched the College
Page 10 Media Coverage of CNS
Page 12 Open PRAIRIE Data
Page 13 Snaps from he start of the semester
Page 14 Science as Art Competition

Examination Of Changes In Gene Family Size In Carnivorous Plants Through Genomic Analysis, Moonia Ammari

Theses, Dissertations and Culminating Projects

The traits associated with carnivory in plants have independently evolved within several orders of Angiosperm. Despite this lack of a common origin, carnivorous plants show many remarkably similar adaptations, suggesting that common evolutionary pressures may have shaped these species. Here, we hypothesize that one common trait carnivorous plants share is the number of genes associated with specific biological functions, such as nutrient transport. To test this hypothesis, we first identified genes and gene families in the model plant species Arabidopsis thaliana that are associated with previously characterized biological functions that may be important for plant carnivory. We then compared the …

Non-Photic Mechanisms Of Entrainment In Bmal1 Deficient Conditions, Jamie Tran

Dissertations and Theses (Open Access)

Maintaining our internal circadian (i.e. 24 -hour) clock is imperative to our daily biological and mental well-being. Large epidemiological studies have shown that disruptions of our circadian rhythms can lead to poor mental health, metabolic diseases, and various types of cancer. Various external cues that have become a part of the modern times such as electricity, shift -work, rapid travel across various time zones, easier access to nutritionally unbalanced food items, and various rigid social demands have deleterious effects on our internal clock, and generally reduce robustness of the circadian clock. The two following projects aim to examine two fundamental …

Natural History And Development Of Melittobia Acasta On Megachile Rotunda , Alan R. Anderson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Alfalfa is one of the most economically important crops in North America. To produce alfalfa seed, a pollinator must release plant reproductive organs by applying pressure to keel petals. The alfalfa leafcutting bee, Megachile rotundata, is the primary commercial pollinator of alfalfa. U.S. bee managers struggle to maintain populations due to many mortality factors. One cause is attack from parasitoid wasps such as Melittobia acasta. Females can lay hundreds of eggs and have multiple generations, which can decimate bee stocks. Chapter Two investigates the life cycle and base temperature that allows development of M. acasta on bee hosts. …

Maternal Effects And Management Of Alfalfa Leafcutting Bees, Makenna May Johnson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Most bees are solitary and important contributors to pollination of a variety of crops. Solitary bees do not live in colonies. Instead, females work individually to construct nests and provision nutrients for each offspring. However, solitary bees can be difficult to manage, especially on a large scale like honey bees, because of differences in how species provision for their offspring and construct nests. Variations in the timing of offspring development to adulthood even within species makes commercial management difficult. Variations in reproductive strategy, like how many offspring to make, how much provision to give each, and when to make them …

Orthotrichum Lyellii As An Active Moss Biomonitor: Examining The Interplay Between Ambient Pm10, Bulk Deposition And Heavy Metals In An Urban Environment, Scott Bradley Kiel

Dissertations and Theses

The importance of monitoring and preventing pollution in the environment is a globally recognized issue. Of the criteria pollutants outlined by the United States Environmental Protection Agency, particulate matter is among these least understood in relation to toxicity and most wide-spread. Many governments have employed continuous air quality monitoring networks to track ambient levels of particulate matter, but are often too widespread to capture the heterogeneity of the urban environment, especially for heavy metal deposition. In Portland, OR, the epiphytic moss Orthotrichum lyellii was successfully used as a low-cost passive biomonitor to increase the spatial resolution of pollution around the …

Mtorc1 And Mtorc2 Complexes Regulate The Untargeted Metabolomics And Amino Acid Metabolites Profile Through Mitochondrial Bioenergetic Functions In Pancreatic Beta Cells, Ghada A. Soliman, Rinat Abzalimov, Ye He

Advanced Science Research Center

Background: Pancreatic beta cells regulate bioenergetics efficiency and secret insulin in response to glucose and nutrient availability. The mechanistic Target of Rapamycin (mTOR) network orchestrates pancreatic progenitor cell growth and metabolism by nucleating two complexes, mTORC1 and mTORC2. Objective: To determine the impact of mTORC1/mTORC2 inhibition on amino acid metabolism in mouse pancreatic beta cells (Beta-TC-6 cells, ATCC-CRL-11506) using high-resolution metabolomics (HRM) and live-mitochondrial functions. Methods: Pancreatic beta TC-6 cells were incubated for 24 h with either: RapaLink-1 (RL); Torin-2 (T); rapamycin (R); metformin (M); a combination of RapaLink-1 and metformin (RLM); Torin-2 and metformin (TM); compared to the control. …

Biological Flora Of Coastal Wetlands: Sporobolus Cynosuroides (L.) P.M. Peterson & Saarela, Richard Stalter, Robert I. Lonard

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

Sporobolus cynosuroides (L.) P.M. Peterson & Saarela¼Spartina cynosuroides (L.) Roth is a temperate zone rhizomatous grass that often is a dominant species in coastal brackish marshes on the Gulf coast and Atlantic coasts of the United States where salinity ranges from 0 to 10 psu. Sporobolus cynosuroides (L.) P.M. Peterson & Saarela ¼ Spartina cynosuroides (L.) Roth is usually absent where salinity values are .12 psu. Sporobolus cynosuroides occurs in coastal habitats characterized by infrequent tidal flooding and moderate nutrient levels. Also known as big cordgrass, it may account for net productivity in high marshes that rivals productivity of Sporobolus …

Interspecific Differences In The Flow Regimes And Drag Of North Pacific Skate Egg Cases, Kayla C. Hall, Jaida N. Elcock, Gerald R. Hoff, Duane E. Stevenson, Adam P. Summers, Cassandra M. Donatelli

Engineering Faculty Articles and Research

Skates are a diverse group of dorso-ventrally compressed cartilaginous fishes found primarily in high-latitude seas. These slow-growing oviparous fishes deposit their fertilized eggs into cases, which then rest on the seafloor. Developing skates remain in their cases for 1-4 years after they are deposited, meaning the abiotic characteristics of the deposition sites, such as current and substrate type, must interact with the capsule in a way to promote long residency. Egg cases are morphologically variable and can be identified to species. Both the gross morphology and the microstructures of the egg case interact with substrate to determine how well a …

Near-Infrared Spectroscopy Aids Ecological Restoration By Classifying Variation Of Taxonomy And Phenology Of A Native Shrub, Brecken C. Robb, Peter J. Olsoy, T. Trevor Caughlin, Stephanie J. Galla, Marcella R. Fremgen-Tarantino, Jordan D. Nobler, Jennifer S. Forbey

Biology Faculty Publications and Presentations

Plant communities are composed of complex phenotypes that not only differ among taxonomic groups and habitats but also change over time within a species. Restoration projects (e.g. translocations and reseeding) can introduce new functional variation in plants, which further diversifies phenotypes and complicates our ability to identify locally adaptive phenotypes for future restoration. Near-infrared spectroscopy (NIRS) offers one approach to detect the chemical phenotypes that differentiate plant species, populations, and phenological states of individual plants over time. We use sagebrush (Artemisia spp.) as a case study to test the accuracy by which NIRS can classify variation within taxonomy and …

Worldwide Consequences Of Covid-19 On Research In Stem, Michelle Hoang, Santanu De

Biology Faculty Articles

A global public health emergency like the Coronavirus Infectious Disease 2019 (COVID-19) pandemic requires accurate and timely data collection in the research community. High-impact research in science, technology, engineering, and mathematics (STEM) has been prioritized in the fight against COVID-19. The present study analyzed the consequences of COVID-19 on STEM research and the collaboration between research institutions and industries worldwide. It was noted that COVID19 had caused significant delays in non-COVID-19-related research projects and the onset of several remote studies. Most importantly, researchers in the STEM fields directed their attention and expertise to help mitigate virus transmission, treat patients, and …

What Are Mycorrhizal Traits?, V. Bala Chaudhary, E. Penelope Holland, Suw Charman-Anderson, Aidee Guzman, Lukas Bell-Dereske, Tanya E. Cheeke, Adriana Corrales, Jessica Duchicela, Cameron Egan, Pushpa G. Soti

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

Highlights

• Applying trait-based approaches to ecological research on mycorrhizal symbioses broadens ecological inferences, but there is no single unified framework to unite disparate language, terminology, and methods across the many multidisciplinary scientists studying mycorrhizas.
• We propose an inclusive framework for trait-based mycorrhizal ecology aimed to stimulate scientists around the world to collect and use more mycorrhizal trait data, particularly in understudied areas. This would widen our understanding regarding the ecological role of mycorrhizal symbioses at individual, species, community, and ecosystem scales.
• Analyzing how mycorrhizal symbioses fit within existing trait definitions highlights significant theoretical and empirical knowledge gaps, novel questions, and …

Plant Growth-Promoting Activity Of Bacteria Isolated From Asian Rice (Oryza Sativa L.) Depends On Rice Genotype, Nasim Maghboli Balasjin, James Maki, Michael Schläppi, Christopher Marshall

Biological Sciences Faculty Research and Publications

Asian rice is one of the most important crops because it is a staple food for almost half of the world’s population. To have production of rice keep pace with a growing world population, it is anticipated that the use of fertilizers will also need to increase, which may cause environmental damage through runoff impacts. An alternative strategy to increase crop yield is the use of plant growth-promoting bacteria. Thousands of microbial species can exist in association with plant roots and shoots, and some are critical to the plant’s survival. We isolated 140 bacteria from two distantly related rice accessions …

Scientist's Warning On Climate Change And Insects, Jeffrey A. Harvey, Kévin Tougeron, Rieta Gols, Robin Heinen, Mariana Abarca, Et Al

Biological Sciences: Faculty Publications

Climate warming is considered to be among the most serious of anthropogenic stresses to the environment, because it not only has direct effects on biodiversity, but it also exacerbates the harmful effects of other human-mediate threats. The associated consequences are potentially severe, particularly in terms of threats to species preservation, as well as in the preservation of an array of ecosystem services provided by biodiversity. Among the most affected groups of animals are insects—central components of many ecosystems—for which climate change has pervasive effects from individuals to communities. In this contribution to the scientists’ warning series, we summarize the effect …

Methyltransferase Mystery: Epigenetic Mechanisms Induced By Food Limitation In Daphnia Pule, Trenton C. Agrelius

Theses and Dissertations

Daphnia are ecologically important organisms that have been well studied in the context of evolution, ecology, ecotoxicity, and genomics. Daphnia have strong maternal effects in which the environment experienced by the mother can alter offspring disease resistance, life history traits, and morphology, as well as gene expression and methylation for multiple generations. Coupled with their ability to reduce genetic differences via parthenogenesis, Daphnia are an ideal system for epigenetic studies involving the transmission of maternal effects. Using two clones of Daphnia pulex, we investigated the plasticity of life history and DNA methyltransferase (Dnmt) gene expression with respect to food …

Activating Connexin43 Gap Junctions Primes Adipose Tissue For Therapeutic Intervention, Yi Zhu, Na Li, Mingyang Huang, Xi Chen, Yu A An, Jianping Li, Shangang Zhao, Jan-Bernd Funcke, Jianhong Cao, Zhenyan He, Qingzhang Zhu, Zhuzhen Zhang, Zhao V Wang, Lin Xu, Kevin W Williams, Chien Li, Kevin Grove, Philipp E Scherer

Faculty, Staff and Students Publications

Adipose tissue is a promising target for treating obesity and metabolic diseases. However, pharmacological agents usually fail to effectively engage adipocytes due to their extraordinarily large size and insufficient vascularization, especially in obese subjects. We have previously shown that during cold exposure, connexin43 (Cx43) gap junctions are induced and activated to connect neighboring adipocytes to share limited sympathetic neuronal input amongst multiple cells. We reason the same mechanism may be leveraged to improve the efficacy of various pharmacological agents that target adipose tissue. Using an adipose tissue-specific Cx43 overexpression mouse model, we demonstrate effectiveness in connecting adipocytes to augment metabolic …

Comparing Brood Care Behaviors Across Five Fertility Castes In The Invasive Fire Ant,Solenopsis Invicta,And The Expression Of Inotocin, Alexis Masnjak

USF Tampa Graduate Theses and Dissertations

The fire ant, Solenopsis invicta, is one of the most successful of the invasive eusocial invertebrates. The fire ant’s prolific reproductive capacity and its division of labor among five fertility castes are key factors to its successful invasion and global colonization across all continents except Antarctica. Although the rate of self-care and brood care by sterile S. invicta workers is well known, little is known about the rate of self-care and brood care by the other four fertility castes. In this study, I quantified the frequency and duration of behaviors by alate males, alate queens, newly mated queens, older mature …

Crispr/Cas13 Effectors Have Differing Extents Of Off-Target Effects That Limit Their Utility In Eukaryotic Cells, Yuxi Ai, Dongming Liang, Jeremy E Wilusz

Faculty, Staff and Students Publications

CRISPR/Cas13 effectors have garnered increasing attention as easily customizable tools for detecting and depleting RNAs of interest. Near perfect complementarity between a target RNA and the Cas13-associated guide RNA is required for activation of Cas13 ribonuclease activity. Nonetheless, the specificity of Cas13 effectors in eukaryotic cells has been debated as the Cas13 nuclease domains can be exposed on the enzyme surface, providing the potential for promiscuous cleavage of nearby RNAs (so-called collateral damage). Here, using co-transfection assays in Drosophila and human cells, we found that the off-target effects of RxCas13d, a commonly used Cas13 effector, can be as strong as …

Why Are There So Many Mosquitoes?, Alan L. Gillen, Savannah Childs, Megan Goin, Karly Mckinney

Faculty Publications and Presentations

Mosquitoes have been challenging man and animals alike since the fall.Mosquitoes number in the trillions worldwide. Not only is the mosquito a nuisance with the constant buzz around your ear, they also are the primary vector of many dangerous diseases including the West Nile Virus (WNV). WNV has become a more prominent mosquito-transmitted disease in the United States and more specifically in Colorado, Texas, and other states in the Midwest. While commonly found in the genus Culex, WNV and other diseases can be found in differentgenera of mosquito, including Aedes and Anopheles. While these two are not themost common regarding …

The Roleo F Selectionin Maintaining Mhc Variationi N Mammals: Heterozygotaed Vantage,R Area Llelea Dvantagea Nd Mate Choice, Carol Titterton Ms

Student Scholarship

The major histocompatibility complex (MHC) is the most polymorphic gene

region in jawed vertebrates. Its gene products play a critical role in determining

individual and population fitness by presenting foreign antigens to immune system

cells, thereby initiating immune response to pathogen and parasite infections and

cancer. I surveyed the literature to investigate how selection maintains such

important adaptive diversity in mammalian populations and how MHC diversity

affects individual and population fitness. Balancing selection in the form of either

heterozygote advantage or rare allele advantage has long been proposed as the key

mechanism for maintaining the extreme diversity in MHC gene …

Long Chain Fatty Acids And Virulence Repression In Intestinal Bacterial Pathogens, Mary K. Mitchell, Melissa Ellermann

Faculty Publications

When bacterial pathogens enter the gut, they encounter a complex milieu of signaling molecules and metabolites produced by host and microbial cells or derived from external sources such as the diet. This metabolomic landscape varies throughout the gut, thus establishing a biogeographical gradient of signals that may be sensed by pathogens and resident bacteria alike. Enteric bacterial pathogens have evolved elaborate mechanisms to appropriately regulate their virulence programs, which involves sensing and responding to many of these gut metabolites to facilitate successful gut colonization. Long chain fatty acids (LCFAs) represent major constituents of the gut metabolome that can impact bacterial …

Climate And Intraspecific Geographic Variation Of Nests And Eggs In The Eastern Kingbird Tyrannus Tyrannus, Samantha Marie Gillette

Dissertations and Theses

The reproductive success of birds is ultimately driven by the traits of nests, eggs, and incubation behavior and the interactions among them. Avian reproduction varies on large geographic scales, most prominently between tropic- vs. temperate-breeding species, but also on finer scales, such as along latitudinal and elevational geographic gradients. However, despite the importance of eggs and nests, how their traits vary geographically in response to differences in regional climate remains understudied.

We studied Eastern Kingbirds (Tyrannus tyrannus), which have been previously demonstrated to alter incubation length in response to local climate conditions. Our study sites, Kansas (KS), New …

Maternal Responses In The Face Of Infection Risk, Patricia C. Lopes, Brenna M. G. Gormally, Aubrey Emmi, Delilah Schuerman, Chathuni Liyanage, Ursula K. Beattie, L. Michael Romero

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

When animals are sick, their physiology and behavior change in ways that can impact their offspring. Research is emerging showing that infection risk alone can also modify the physiology and behavior of healthy animals. If physiological responses to environments with high infection risk take place during reproduction, it is possible that they lead to maternal effects. Understanding whether and how high infection risk triggers maternal effects is important to elucidate how the impacts of infectious agents extend beyond infected individuals and how, in this way, they are even stronger evolutionary forces than already considered. Here, to evaluate the effects of …

Parasitism Of Corn Earworm, Helicoverpa Zea (Boddie) (Lepidoptera: Noctuidae), By Tachinid Flies In Cultivated Hemp, Armando Falcon-Brindis, John O. Stireman Iii, Zenaida J. Viloria, Raul T. Villanueva

Biological Sciences Faculty Publications

In a survey on hemp grown in western Kentucky we found an average of 27.8 CEW larvae per plant. We recorded 45% parasitism of CEW in these fields by two species of tachinid flies, Winthemia rufopicta and Lespesia aletiae. Most parasitized larvae were third to sixth instars at the time of collection. We found up to 22 tachinid eggs per host larva, 89% of which typically bore between 1 and 5 eggs on the thorax. 45.9% of CEW bearing eggs died. The number of tachinid eggs per host was unrelated to host body mass, but both the number of tachinid …

College Of Natural Sciences Newsletter, May & June 2022, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 3, Issue 4

Page 1 Dean's Message
Page 2 Awards and Recognition
Page 3-4 The path to a Doctorate Degree
Page 4 American Indian Student Center Native Graduate Honoring Ceremony
Page 5 Celebrating the lives of those who touched the College
Page 6 Media coverage of CNS
Page 7 Open PRAIRIE
Page 8-10 CNS Graduation Festivities
Page 11-14 Spring 2022 Dean's List
Page 16 Richard and Janice Vetter Endowed Professorship in Biotechnology.position

The Use Of Actinobacteria To Improve The Efficacy Of Phytoremediation Of Heavy Metal-Polluted Soils In The United Arab Emirates, Fatima Abdulmoneim Hussain

Theses

In an effort to gain the advantages provided by actinobacterial enzyme (1- aminocyclopropane-1-carboxylic acid) (ACC) deaminase (ACCD) in the phytoremediation of heavy metals from the environment, the ability of native actinobacteria with ACC deaminase activity to promote the growth of Bermuda grass (Cynodon dactylon L.) in soils contaminated with nickel nitrate was evaluated under greenhouse conditions. This enzyme hydrolyzes (ACC), the immediate biosynthetic precursors of the hormone ethylene (ET) in plant tissues to ammonia and α keto-butyrate. The main objectives of this study were: (1) Isolating beneficial native heavy metal-tolerant actinobacteria from the United Arab Emirates (UAE) contaminated soil capable …

The Life Cycle Of Polyploid Giant Cancer Cells And Dormancy In Cancer: Opportunities For Novel Therapeutic Interventions, Jinsong Liu, Na Niu, Xiaoran Li, Xudong Zhang, Anil K Sood

Faculty, Staff and Student Publications

Recent data suggest that most genotoxic agents in cancer therapy can lead to shock of genome and increase in cell size, which leads whole genome duplication or multiplication, formation of polyploid giant cancer cells, activation of an early embryonic program, and dedifferentiation of somatic cells. This process is achieved via the giant cell life cycle, a recently proposed mechanism for malignant transformation of somatic cells. Increase in both cell size and ploidy allows cells to completely or partially restructures the genome and develop into a blastocyst-like structure, similar to that observed in blastomere-stage embryogenesis. Although blastocyst-like structures with reprogrammed genome …