Biology Commons^™

A Tale Of Two Regulators : Characterization Of The Novel Transcription Factor Abmr And The Small Non-Coding Rna Mcr11 In Mycobacterium Tuberculosis, Roxanne Candice Girardin

Legacy Theses & Dissertations (2009 - 2024)

Genes of unknown function make up nearly one third of Mtb’s genome (Cole,

Protein Aggregation As Hallmark Of Neurodegenerative Diseases, Viktoriia Stroilo

Legacy Theses & Dissertations (2009 - 2024)

Neurodegenerative diseases like Alzheimer’s, Parkinson’s, Huntington’s, Amyotrophic Lateral Sclerosis and Prion Diseases tend to have similar cellular and molecular mechanisms of protein aggregation and inclusion body formation. These processes suggest common mechanisms of pathogenesis. Similarities in structure, mechanism of formation and physiological effects of protein aggregates in neurodegenerative diseases may lead to development of common preventative or therapeutic strategies.

Inquiry-Based Laboratory Experiences Using Ecosystem Microcosms, Roger Sauterer

Research, Publications & Creative Work

Self-sustaining ecosystem microcosms, called ecosystem jars, can easily be collected from local ponds, streams, or lakes. Sealed and exposed to sunlight, these miniature ecosystems can sustain themselves for a decade or more. Unlike Winogradsky columns, ecosystem jars are optimized for protist, animal, and plant observations and experiments, and are not altered by addition of sulfur, carbon, or cellulose sources, more accurately representing natural ecosystems. Ecosystem jars can support a variety of inquiry-based experiments, including student-designed projects, from middle school to college levels. Students, with instructor assistance, formulate hypotheses, design experiments, observe and catalog organisms by microscopy, then record their data …

Cloning, Expression, And Activity Analysis Of Human Cathepsin C In The Yeast Pichia Pastoris, Cenk Dağlioğlu

Turkish Journal of Biology

The yeast Pichia pastorisexpression system was investigated for the production of human cathepsin C (CatC) recombinant protein. The full-length CatC cDNA, corresponding to amino acids 12-475, was synthesized from interleukin-2 (IL-2) stimulated human peripheral blood mononuclear cells and subcloned in the pGEM-T cloning vector. After confirming the DNA sequence of the insert, the gene was cloned into the pPICZ\alphaA expression vector under the control of the methanol-inducible alcohol oxidase (AOX1) promoter and transformed to P. pastoris X-33 cells. The expressed protein was secreted into the culture medium through the alpha-factor mating signal sequence of the expression vector. Analysis of the …

Optimization, Purification, And Characterization Of An Extracellular Antifungal Protein From Serratia Marcescens Dt3 Isolated From Soil In Vietnam, Tuyen Thi Do, Thao Thi Nguyen, Thanh Sy Le Nguyen, Hoang Thanh Le

Turkish Journal of Biology

Gram-negative Serratia marcescens is a potential biological control agent of fungal plant diseases in many tropical regions. Its antifungal activity is due to the production of prodigiosin, protease, chitinase, and other substances that act to weaken the fungal cell wall and cause lysis. In the following investigation, a novel extracellular protein with antifungal activity against Rhizoctonia solani and Fusarium oxysporum was optimally produced, purified, and characterized from a native Serratia marcescens DT3. Under optimal conditions (medium containing 1.25% peptone, 0.5% yeast extract; temperature of 28 °C; initial pH of 7; culture time of 28 h), the antifungal activity of the …

The Sca1+ Mesenchymal Stromal Subpopulation Promotesdendritic Cell Commitment In The Niche, Na Li, Dandan Yin, Huijie Zhang, Jinmei Xu, Fan Wen, Zheng Liu, Yaozhen Chen, Ning An, Jiajia Xin, Yazhou Wang, Wen Yin, Xingbin Hu

Turkish Journal of Biology

The hematopoietic microenvironment regulates self-renewal and differentiation of hematopoietic stem cells. Mesenchymal stromal cells (MSCs) contribute to the niche and participate in supporting dendritic cell (DC) commitment in vitro and in vivo. However, due to MSCs being heterogenic, it is necessary to understand the function of the MSC subpopulation in modulating the DC commitment. The current study showed that one of the bone-related Sca1+ MSCs enhanced bone marrow cell differentiation into DCs by direct cell-to-cell contact. Furthermore, the expression of STAT3 and STAT5 genes decreased in supernatant cells after Sca1+ MSCs were cocultured with bone marrow cells. In contrast, the …

Characterization And Pathogenicity Of Fusarium Proliferatum Andfusarium Verticillioides, Causal Agents Of Fusarium Ear Rot Of Corn, Nur Ain Izzati Mohd Zainudin, Farah Aqila Hamzah, Nor Azizah Kusai, Nur Syuhada Zambri, Suhaida Salleh

Turkish Journal of Biology

Fusarium ear rot is a significant disease of corn caused by several toxigenic Fusarium species including Fusarium proliferatum and Fusarium verticillioides. Forty-one Fusarium isolates were recovered from corn with Fusarium ear rot disease symptoms collected from Peninsular Malaysia. Isolates were classified into three described species known as F. proliferatum, F. verticillioides, and F. solani. Based on sexual compatibility test, four isolates from F. proliferatum (MATD-1) were crossed-fertile with tester isolate F. proliferatum D024853 (MATD-2), producing perithecia in the presence of ascospores. Meanwhile, the isolates from F. verticillioides (MATA-2) were crossed with tester isolate F. verticillioides A00149 (MATA-1), but were found …

Conditions Responsible For The Success Of Carnivorous Plants In Nutrient-Poor Wetlands, Matthew John Abbott

Electronic Theses and Dissertations

Despite the vast array of past research focused on carnivorous plants, few studies have investigated the ecological interactions between carnivorous and non-carnivorous plant species. I addressed the following three questions: (1) does niche complementarity promote coexistence between fire-adapted carnivorous and non-carnivorous species? (2) do carnivorous plants rely on both leaf traps and arbuscular mycorrhizal fungi to access different nutrients that are in high demand after fire in nutrient poor bogs? (3) why are carnivorous plants largely absent from nutrient-rich wetlands? I addressed the first question by examining the three-way interacting effects of fire, prey-derived nutrient availability, and root competition from …

The Impact Of Simulated Microgravity On The Growth Of The Model Legume Plant Medicago Truncatula, Gemma Elizabeth Lionheart

Electronic Theses and Dissertations

Simulated microgravity has been a useful tool to help understand plant development in altered gravity conditions. Thirty-one genotypes of the legume plant Medicago truncatula were grown in either simulated microgravity on a rotating clinostat, or a static, vertical environment. Twenty morphological features were measured and compared between these two gravity treatments. Within-species genotypic variation was a significant predictor of the phenotypic response to gravity treatment in 100% of the measured morphological and growth features. In addition, there was a genotype–environment interaction (G×E) for 45% of the response variables, including shoot relative growth rate (p < 0.0005), median number of roots (p ∼ 0.02), and root dry mass (p < 0.005). These findings are discussed in the context of improving future studies in plants space biology by controlling for genotypic differences, and by connecting traits to their underlying genetic causes by using genome-wide association (GWA) mapping. In the long-term, manipulation of genotype effects, in combination with M. truncatula’s symbiotic relationships with rhizobacteria and arbuscular mycorrhizal fungi, will be important for optimizing legumes for cultivation on long-term space missions.

The Reptile Gut Microbiome: Its Role In Host Evolution And Community Assembly, Timothy John Colston

Electronic Theses and Dissertations

I characterize the endogenous (gut) microbiome of Squamate reptiles, with a particular focus on the suborder Serpentes, and investigate the influence of the microbiome on host evolution and community assembly using samples I collected across three continents in the New and Old World. I developed novel methods for sampling the microbiomes of reptiles and summarized the current literature on non-mammalian gut microbiomes. In addition to establishing a standardized method of collecting and characterizing reptile microbiomes I made novel contributions to the future direction of the burgeoning field of host-associated microbiome research. Through persistent and rigorous fieldwork I amassed the largest …

Historical Refuges And Recolonization Routes In The Southern Appalachian Mountains, Inferred Through Phylogeographic Analysis Of The Spotted Wintergreen (Chimaphila Maculata), John Daniel Banusiewicz

Electronic Theses and Dissertations

Phylogeography has recently benefited from incorporation of coalescent modeling to test competing scenarios of population history of a species. Ecological niche modeling has also been useful in inferring areas of likely suitable habitat during past climate conditions. Several studies have examined the population history of biota in the Southern Appalachian Mountains and how they responded to climate change associated with the end of the Last Glacial Maximum (~18,000 years ago), though few studies have focused on understory plants. This study redressed that knowledge gap thorough examination of the phylogeographic history of the understory plant Chimaphila maculata, which is native to …

Bioelectrohydrogenesis And Inhibition Of Methanogenic Activity In Microbial Electrolysis Cells - A Review, Rengasamy Karthikeyan, Ka Yu Cheng, Ammaiyappan Selvam, Arpita Bose, Jonathan W.C. Wong

Biology Faculty Research

Microbial electrolysis cells (MECs) are a promising technology for biological hydrogen production. Compared to abiotic water electrolysis, a much lower electrical voltage (~0.2V) is required for hydrogen production in MECs. It is also an attractive waste treatment technology as a variety of biodegradable substances can be used as the process feedstock. Underpinning this technology is a recently discovered bioelectrochemical pathway known as "bioelectrohydrogenesis". However, little is known about the mechanism of this pathway, and numerous hurdles are yet to be addressed to maximize hydrogen yield and purity. Here, we review various aspects including reactor configurations, microorganisms, substrates, electrode materials, and …

Determination Of The Direct Protein-Protein Interactions In The Drosophila Sin3a Complex, Ian Moore

Wayne State University Theses

The proteins that comprise the Drosophila SIN3 220 and SIN3 187 complexes are currently known. Limited information with regard to interacting complex member proteins has been described. Much of these data are results of high-throughput investigations, and there have been no studies done to reconstitute all direct interactions within the complex. The unique C-terminal region of the SIN3 220 isoform was used to test for interactions with other complex proteins using the bacterial expression system. Additionally, the region of Caf1-55 necessary for interaction with SIN3 in vivo was identified using a truncation mutant. The results of this work identified novel …

Dna Metabarcoding Reveals Provisioning Of Pollution-Sensitive Aquatic Insects, Resource Partitioning, And Dietary Shifts Among Breeding Neotropical Migratory Songbirds In A Riparian Habitat, Brian K. Trevelline

Electronic Theses and Dissertations

Elucidating the diet of Neotropical migratory birds is essential to our understanding of their ecology and to their long-term conservation. Beyond broad taxonomic or morphological categories, however, the diet of Neotropical migrants is poorly documented. Using the molecular techniques of DNA barcoding and next-generation sequencing, we elucidated the diet of Neotropical migratory songbirds breeding in the riparian zones of headwater Appalachian streams. This approach resulted in a genus- or species-level description of diets that improved the current understanding of how songbirds utilize aquatic prey resources in riparian habitats. Furthermore, our approach revealed that breeding songbirds partition prey resources within a …

Primate Proteomic Composition Of Seminal Plasma And Prostate-Specific Transglutaminase Activity In Relation To Sexual Selection., Amanda M.C. Zielen

Electronic Theses and Dissertations

Humans (Homo sapiens), chimpanzees (Pan troglodytes), and gorillas (Gorilla gorilla) have diverse mating systems with varying levels of sperm competition. Several seminal plasma genes have been claimed to evolve under positive selection, while others are altered or lost. This study aims to identify biologically relevant differences among seminal plasma proteomes of primates in relation to mating systems and previous genomic studies. Seminal plasma from three individuals of each species were run in triplicate in shotgun liquid chromatography – tandem mass spectrometry (LC-MS/MS) and confirmed with Western blots. Over 7,000 peptides were identified across all …

Effects Of Estrogens On Astrocytes Exposed To Stressors, Bridget N. Smith

Theses and Dissertations

Hormone replacement therapy (HRT), used by many women to alleviate menopausal symptoms such as hot flashes and mood swings, is often a combination of horomones such as estrogens, progesterone, and conjugated equine estrogens (CEE), extracted from the urine of pregnant mares. Previous studies have found positive correlations between estradiol and cellular protection, but recent research has concluded CEE provide less protective mechanisms as compared to endogenous hormones. This research sought to compare the effects of estrogen treatments (single and combined estrogen) on viability when astrocytes were induced with stressors (epinephrine, cortisol, and low oxygen concentration). Cultured human astrocytes were treated …

Museum Collections: Natural History Training Bridges Time, Space, And Digital Platforms., Anna Monfils, Karen Powers, Christopher J. Marshall, James F. Smith, Chris Martine, L. Alan Prather

Faculty Journal Articles

Natural history collections offer a number of unique physical and virtual opportunities to create formal and informal progressive learning environments. Collections provide direct interaction with biodiversity as it changes through time and space. Collections-based experiences lead to an increased understanding and substantive interaction with the living world. Recent studies demonstrate how nature and outdoor experiences can improve learning. We discuss how collections, and the data associated with collections, are a critical component linking nature and scientific inquiry. Partnerships that develop around collections and collections-based science can foster innovative educational and research experiences that are enhanced by access to museum specimens. …

H+- And Na+- Elicited Rapid Changes Of The Microtubule Cytoskeleton In The Biflagellated Green Alga Chlamydomonas, Yi Liu, Mike Visetsouk, Michelle Mynlieff, Hongmin Qin, Karl F. Lechtreck, Pinfen Yang

Biological Sciences Faculty Research and Publications

Although microtubules are known for dynamic instability, the dynamicity is considered to be tightly controlled to support a variety of cellular processes. Yet diverse evidence suggests that this is not applicable to Chlamydomonas, a biflagellate fresh water green alga, but intense autofluorescence from photosynthesis pigments has hindered the investigation. By expressing a bright fluorescent reporter protein at the endogenous level, we demonstrate in real time discreet sweeping changes in algal microtubules elicited by rises of intracellular H⁺ and Na⁺. These results from this model organism with characteristics of animal and plant cells provide novel explanations regarding …

Infection Prevalence In A Novel Ixodes Scapularis Population In Northern Wisconsin, Mary Lynn Westwood

Browse all Theses and Dissertations

Ixodes scapularis (i.e. the blacklegged or deer tick) is an important vector of emerging human pathogens. Over the past few decades, the incidence of blacklegged tick-associated zoonotic diseases have increased in accordance with an expansion of the blacklegged tick geographic range. Data concerning the infection prevalence of blacklegged ticks in this region is highly variable and fragmentary. Using a novel population of these ticks, constituting part of the invasion front in Vilas County, Wisconsin, I examined infection prevalence and vector aspects of their ecology. During the summer of 2016, I collected 461 blacklegged ticks and screened them using a standard …

The Effect Of Nullomer-Derived Peptides 9r, 9s1r And 124r On The Nci-60 Panel And Normal Cell Lines, Abdelkrim Alileche, Greg Hampikian

Biology Faculty Publications and Presentations

Background: Nullomer peptides are the smallest sequences absent from databases of natural proteins. We first began compiling a list of absent 5-amino acid strings in 2006 (1). We report here the effects of Nullomer-derived peptides 9R, 9S1R and 124R on the NCI-60 panel, derived from human cancers of 9 organs (kidney, ovary, skin melanoma, lung, brain, lung, colon, prostate and the hematopoietic system), and four normal cell lines (endothelial HUVEC, skin fibroblasts BJ, colon epithelial FHC and normal prostate RWPE-1).

Methods: NCI-60 cancer cell panel and four normal cell lines were cultured in vitro in RPMI1640 supplemented with 10% Hyclone …

Insights Into The Ecology, Genetics And Distribution Of Lucanus Elaphus Fabricius (Coleoptera: Lucanidae), North America's Giant Stag Beetle, Michael D. Ulyshen, Louis G. Zachos, John O. Stireman Iii, Thomas N. Sheehan, Ryan C. Garrick

Biological Sciences Faculty Publications

1. Little is known about the biology or conservation status of Lucanus elaphus Fabricius in North America despite well-documented declines of a related species, Lucanus cervus (L.), in Europe. This study provides information critical to developing conservation plans for L. elaphus including the species’ larval substrate requirements, genetic data and range-wide estimates of habitat suitability. 2. In Mississippi floodplain forests, larval L. elaphus were recovered from a wide range of log sizes and rot types and were either found tunnelling within the wood or feeding beneath logs at the soil–wood interface. The species appears to require 1–2 years to complete …

Possible Mechanisms That Protect The Fetus From Maternal Rejection, Adina Ziemba-Goldfarb

The Science Journal of the Lander College of Arts and Sciences

There is no other foreign tissue transplant that has such a strongly parasitic relationship with its human host as the fetus. Although the fetus contains paternal genes, is completely tolerized by its maternal host in almost all pregnancies. This presents an immunological paradox and has generated a lot of attention from leading researchers in the reproductive and immunology fields. This paper reviews the leading explanations for this paradox; that it is attributed to a detailed mechanism of the maternal and fetal immune system in which tryptophan suppresses T-cells from attacking specific paternal cells, while maintaining a strong immune response against …

Full Issue: Volume 11, Number 1

The Science Journal of the Lander College of Arts and Sciences

No abstract provided.

Fit To Predict? Ecoinformatics For Predicting The Catchability Of A Pelagic Fish In Near Real-Time, Kylie L. Scales, Elliot L. Hazen, Sara M. Maxwell, Heidi Dewar, Suzanne Kohin, Michael G. Jacox, Christopher A. Edwards, Dana K. Briscoe, Larry B. Crowder, Rebecca L. Lewison, Steven J. Bograd

Biological Sciences Faculty Publications

The ocean is a dynamic environment inhabited by a diverse array of highly migratory species, many of which are under direct exploitation in targeted fisheries. The timescales of variability in the marine realm coupled with the extreme mobility of ocean-wandering species such as tuna and billfish complicates fisheries management. Developing ecoinformatics solutions that allow for near real-time prediction of the distributions of highly mobile marine species is an important step towards the maturation of dynamic ocean management and ecological forecasting. Using 25 years (1990-2014) of NOAA fisheries' observer data from the California drift gillnet fishery, we model relative probability of …

Experimental Evaluation Of Several Key Factors Affecting Root Biomass Estimation By 1500 Mhz Ground-Penetrating Radar, John C. Bain, Frank P. Day, John R. Butnor

Biological Sciences Faculty Publications

Accurate quantification of coarse roots without disturbance represents a gap in our understanding of belowground ecology. Ground penetrating radar (GPR) has shown significant promise for coarse root detection and measurement, however root orientation relative to scanning transect direction, the difficulty identifying dead root mass, and the effects of root shadowing are all key factors affecting biomass estimation that require additional research. Specifically, many aspects of GPR applicability for coarse root measurement have not been tested with a full range of antenna frequencies. We tested the effects of multiple scanning directions, root crossover, and root versus soil moisture content in a …

The Effects Of Treating Multispecies Biofilms With Bacteriophage, Alexandria Francis Cooper

Master's Theses

Biofilms can be found in any environment within proximity to water and are problematic in an assortment of industries. Numerous efforts have been employed to dislodge biofilms including bacteriophages (viruses that infect bacteria). Phage remediation is a promising solution for combatting biofilms that form on catheters in long term use patients. These biofilms often result in catheter-associated urinary tract infections (CAUTIs) and are the most common type of healthcare related infection reported. Additionally, they result in longer hospital stays and increased morbidity. To date, most of the research on the topic focuses on single species biofilms, despite their rarity in …

Survey Of Anuran Chytrid (Batrachochytrium Dendrobatidis) In Kansas And The Influence Of Anuran Life History In Occurrence, Ariel Snyder

Master's Theses or Doctor of Nursing Practice

Amphibians are one of the most threatened groups of organisms worldwide. Introduction of non-native predators and habitat destruction, degradation, and fragmentation can be attributed to many declines. However, declines in protected areas might be due to the emergence of novel diseases such as ranavirus and chytridiomycosis. Chytridiomycosis has been implicated in the decline of many species world-wide, including the decline of Boreal Toads and Yellow-Legged Frogs in North America. Chytridiomycosis is caused by the fungus Batrachochytrium dendrobatidis, or “chytrid”. Chytrid has been detected in Colorado, Nebraska, and Oklahoma, and was first reported in two counties in south-central Kansas in 2014. …

Survey Of A Neotropical Anuran Assemblage (Pacaya-Samiria Reserve, Peru), Eric Woebbe

Browse all Theses and Dissertations

The Pacaya-Samiria National Reserve of Peru is one of the largest protected areas of the Amazon rainforest, yet it has hosted only a few studies of frogs and toads (anurans). The primary goals of my study are: 1) To conduct an inventory of the local anuran species, 2) to quantify richness among habitats, 3) to compare differences in beta diversity across a river versus a continuous landscape, and 4) to compare difference in body size between nocturnal and diurnal individuals. After eight weeks of daytime and nighttime surveys during the dry season, a total of 601 individuals were identified across …

Responses Of The Ocellated Turkey (Meleagris Ocellata) To Human Disturbance, Thomas Hughes Martin

Electronic Theses and Dissertations

Habitat loss and habitat degradation are major drivers of the current biodiversity crisis. Nowhere else are these threats more severe than in the tropics. Because the tropics are estimated to contain as much as 60% of all the species on Earth, they are critically important for the conservation of biodiversity. To conserve species we need to understand both the factors that lead to extinction and how the taxa that persist are able to adapt to the rapid anthropogenic change of their environment. The Ocellated Turkey (Meleagris ocellata) is a Neotropical galliform bird of conservation concern because it faces a rapidly …

A Major Dna Double Strand Repair Pathway And Cancer-Associated Circulating Proteins Are Effecters Of Epigenetic Revision., Brittany Allen

Electronic Theses and Dissertations

DNA methylation is a vital epigenetic process that acts as a major control mechanism for gene expression. In addition to its essential role in many normal cellular processes, it is also implicated in a wide variety of disease states and processes including cancer. Along with genetic mutations, aberrant DNA methylation patterns, specifically the inappropriate DNA methylation or demethylation of CpG residues, may activate oncogenes or suppress tumor suppressor genes, respectively. These changes can generate or facilitate the progression of tumorigenesis and tend to accumulate throughout the development of cancer. Although they play such a major role in cancer and in …