Biology Commons^™

Employing High Probability Gene Choice Elements To Understand Singular Odorant Receptor Expression, Raena Mina

Dissertations, Theses, and Capstone Projects

The ability to detect odorous chemicals in the environment is the oldest of the senses necessary for survival, from escaping danger, finding mates, to locating food. It is said that humans can identify and discriminate up to a trillion different odor mixtures. For chemoreception to have such a high discriminatory power, would require a diverse population of cells dedicated for odor detection. These detector cells are the olfactory sensory neurons (OSNs), which express odorant receptors (ORs) that bind to chemical odors in the environment. In order to increase specificity and sensitivity, an essential property in olfaction is for each OSN …

Structure And Evolution Of Lizard Immunity Genes, Trent Santonastaso

LSU New Orleans Theses and Dissertations

One of the most important gene families to play a role in adaptive immunity is the major histocompatibility complex (MHC). MHC class II loci are considered to be the most variable loci in the vertebrate genome, and studies have shown that this variability can be maintained through complex co-evolutionary dynamics between host and parasite. Despite the rich body of research into the MHC, there is comparatively little understanding of its genomic architecture in reptiles. Similarly, loci associated with innate immunity have received little attention in reptiles compared to other vertebrates. In the first chapter, we investigated the structure and organization …

Identifying Positive Selection In Multiple Subspecies Of Xylella Fastidiosa, Daniel Doroteo Flores

Theses and Dissertations

For this study, we will be looking to identify positive selection in eight genomes of the bacterial plant pathogen Xylella fastidiosa. A previous study used a branching method that identified 2 genes with positive selection along with a site-specific method identifying 34 genes showing positive selection. This current study focused specifically on the site-specific method, resulting in 28 genes (of 1,039 tested) showing positive selection. Of the 28 genes showing positive selection, 12 of them come from the pathogenicity, virulence and cellular structural categories. The remaining genes are found in the biosynthesis, metabolism, macro metabolism, and cellular process categories. …

Model-Based Analysis Of Chromatin Interactions From Dcas9-Based Capture-3c-Seq., Yong Chen, Yunfei Wang, Xin Liu, Jian Xu, Michael Q Zhang

College of Science & Mathematics Departmental Research

Deciphering long-range chromatin interactions is critical for understanding temporal and tissue-specific gene expression regulated by cis- and trans-acting factors. By combining the chromosome conformation capture (3C) and biotinylated dCas9 system, we previously established a method CAPTURE-3C-seq to unbiasedly identify high-resolution and locus-specific long-range DNA interactions. Here we present the statistical model and a flexible pipeline, C3S, for analysing CAPTURE-3C-seq or similar experimental data from raw sequencing reads to significantly interacting chromatin loci. C3S provides all steps for data processing, quality control and result illustration. It can automatically define the bin size based on the binding peak of the dCas9-targeted regions. …

Arabidopsis Heat Shock Granules Exhibit Dynamic Cellular Behavior And Can Form In Response To Protein Misfolding In The Absence Of Elevated Temperatures, Rosalie Lawrence , '12, Nicholas J. Kaplinsky

Biology Faculty Works

No abstract provided.

Wild Mice With Different Social Network Sizes Vary In Brain Gene Expression, Patricia C. Lopes, Barbara König

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Background

Appropriate social interactions influence animal fitness by impacting several processes, such as mating, territory defense, and offspring care. Many studies shedding light on the neurobiological underpinnings of social behavior have focused on nonapeptides (vasopressin, oxytocin, and homologues) and on sexual or parent-offspring interactions. Furthermore, animals have been studied under artificial laboratory conditions, where the consequences of behavioral responses may not be as critical as when expressed under natural environments, therefore obscuring certain physiological responses. We used automated recording of social interactions of wild house mice outside of the breeding season to detect individuals at both tails of a distribution …

Characterization Of The Overexpression Of The Native H+-Pumping Pyrophosphatase In The Microalga Picochlorum Soloecismus, Kimberly T. Wright

Biology ETDs

Microalgae are of interest for the creation of sustainable and cost competitive alternatives to petroleum-based fuels and chemicals. However, cultivation, extraction and processing of algal biomass requires improved yields to achieve economic feasibility. The advancement of microalgal biotechnology and various genetic engineering techniques allow the improvement of microalgae biomass for this purpose. Here, the characterization of the overexpression of the native vacuolar H+ pumping pyrophosphate (AVP1) in Picochlorum soloecismus was examined. AVP1 overexpression causes biomass increase in relevant plant crops. When overexpressed in this microalga it increases carbon storage in the form of starch in a closed laboratory photobioreactor. However, …

Inactivation Of Hippo And Cjun-N-Terminal Kinase (Jnk) Signaling Mitigate Fus Mediated Neurodegeneration In-Vivo, Ankita Sarkar, Abijeet Singh Mehta, Prajakta Deshpande, Madhuri Kango-Singh, Udai Bhan Pandey, Amit Singh

Biology Faculty Publications

Amyotrophic Lateral Sclerosis (ALS), a late-onset neurodegenerative disorder characterized by the loss of motor neurons in the central nervous system, has no known cure to-date. Disease causing mutations in human Fused in Sarcoma (FUS) leads to aggressive and juvenile onset of ALS. FUS is a well-conserved protein across different species, which plays a crucial role in regulating different aspects of RNA metabolism. Targeted misexpression of FUS in Drosophila model recapitulates several interesting phenotypes relevant to ALS including cytoplasmic mislocalization, defects at the neuromuscular junction and motor dysfunction. We screened for the genetic modifiers of human FUS-mediated neurodegenerative phenotype using molecularly …

Elucidating The Role Of Apl-1, The C. Elegans Ortholog Of The Human Amyloid Precursor Protein, Adanna G. Alexander

Dissertations, Theses, and Capstone Projects

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder, impacting approximately 6 million Americans. AD is the leading cause of dementia amongst the aged population. Post mortem analysis of the brains of AD patients shows high quantities of extracellular Aβ peptide deposits, which are derived from cleavage of the amyloid precursor protein (APP). Mutations in APP and proteins responsible for APP cleavage, PSENs, greatly increase the incidence of developing AD at an early age. Despite its strong correlation to the progression of AD, the role of APP remains unclear.

Here we investigate the role of the Caenorhabditis elegans ortholog, APL-1. We …

Molecular Roles Of Small Inner Membrane Proteins In Escherichia Coli Cell Envelope Integrity, Aaron Mychack

Dissertations, Theses, and Capstone Projects

The biological membrane is an essential, defining feature of all cells. Biological membranes comprise phospholipid bilayers as well as a complement of proteins which are unique to a given organism. These proteins play a central role in dictating the biochemical state of the cell’s internal cytoplasm by controlling selective passage of solutes in and out of the cell, transducing signals in response to extracellular stimuli, and controlling the biogenesis of the bilayer itself which is critical towards barrier function. For most bacteria, the periphery of the cell is multi-layered, including both a biological membrane as well as a peptidoglycan cell …

Elucidating The Role Of The High Aliphatic Glucosinolate ( Hag ) Genes In Pennycress ( Thlaspi Arvense L. ) Glucosinolate Production, Dalton Williams

Theses and Dissertations

Pennycress (Thlaspi arvense L.) is a Brassica species being developed into an oilseed-producing winter cash cover crop. Similar to its relatives, rapeseed (Brassica napus L.) and camelina (Camelina sativa L.), pennycress seeds produce high levels of oil and protein (~34% oil and ~19% protein dry weight). For pennycress to be economically viable and environmentally sustainable as a crop, both the oil and seed meal must be utilized. Pennycress like other Brassicaceae, produces high levels of glucosinolates in the seed coat. Glucosinolates taste bitter and can be metabolized by the enzyme, myrosinase, into toxic isothiocyanates, nitriles, and epithionitriles. Seed meal containing …

Genome Skimming And Microsatellite Analysis Reveal Contrasting Patterns Of Genetic Diversity In A Rare Sandhill Endemic (Erysimum Teretifolium, Brassicaceae), José Carlos Del Valle, Julie A. Herman, Justen B. Whittall

Biology

Barriers between islands often inhibit gene flow creating patterns of isolation by distance. In island species, the majority of genetic diversity should be distributed among isolated populations. However, a self-incompatible mating system leads to higher genetic variation within populations and very little between-population subdivision. We examine these two contrasting predictions in Erysimum teretifolium, a rare self-incompatible plant endemic to island-like sandhill habitats in Santa Cruz County, California. We used genome skimming and nuclear microsatellites to assess the distribution of genetic diversity within and among eight of the 13 remaining populations. Phylogenetic analyses of the chloroplast genomes revealed a deep …

Effects Of Aurora Kinase C Expression On Retina Pigmented Epithelial Cell Migration, Proliferation, And Anchorage Independent Growth, Justin Bejar

Seton Hall University Dissertations and Theses (ETDs)

Cancer is a common and deadly disease in the United States with 1,806,590 new cancer cases in 2019 and 606,520 cancer deaths projected in 2020. These deaths are primarily due to the uncontrolled cell proliferation and migratory nature of the disease. Many cancer cells express genes normally restricted to meiotic cells. For example, Aurora Kinase C (AURKC) is known to regulate chromosome segregation in meiotic cells yet it is expressed in many different types of cancer, such as breast, prostate, colorectal, liver, cervical, thyroid, and testicular cancers. As a means to study the function of AURKC, an …

Determining The Genetic Control Of Neural Tube Malformation Through Genetic Interactions With Idgf3, Elli N. Fox

Honors Projects

Genetic mutations disrupting human neural tube formation can lead to birth defects such as spina bifida and anencephaly. Defects can result in lack of neural tube closure in either the caudal (spina bifida) or cranial (anencephaly) regions. Little is known about the genes that cause these malformations. Researchers have been using the model organism Drosophila melanogaster in an attempt to determine genes responsible for neural tube malformations. Recently, an ortholog of human chitin-like protein, imaginal disc growth factor 3 (Idgf3), has been identified as important in the proper formation of Drosophila egg dorsal appendages. However, the molecular mechanism responsible for …

Generation And Characterization Of A Rack1 Knockout Cell Line, Roy Missall

Seton Hall University Dissertations and Theses (ETDs)

The µ-opioid receptor (MOR) is an important regulator of nociception, bearing the largest role in analgesia of all opioid receptors. This function has made MOR an effective drug-target for the clinical treatment of pain. However, opioid drugs such as morphine and fentanyl are highly addictive, and prolonged abuse can be fatal due to respiratory depression. A key determinant in the cellular and systemic responses to opioids is MOR. At the transcriptional level, MOR is positively regulated by the transcription factors, including poly-C binding protein 1 (PCBP1). Using the two-hybrid screening, PCBP1 was found to interact with receptor for activated C …

Population Genetics Of A Recent Range Expansion By The Southern Pine Beetle, Dendroctonus Frontalis, Into The Northeastern United States, Megan Stubbs

Honors Theses

Population genetics as a field of study aims to determine the genetic variation among individuals in a population, and differences among populations. Certain population genetic analyses can provide such information and be used to better understand the biological aspects to a species’ expansion beyond its native range. The southern pine beetle (SPB), Dendroctonus frontalis, has become an invasive pest to pine forests in northeastern United States with its recent range expansion. Nine microsatellite loci were first developed and then used in analyses. To determine what the genetic variation is among individuals in SPB populations across its entire range, including …

A Genomic Analysis Of Bobcat Populations In North America With A Comparison To The Canada Lynx: An Assessment Of Local Adaptation To Unique Ecoregions And Phylogeography, Jennifer C. Broderick

Electronic Theses and Dissertations

Bobcats (Lynx rufus) are an ecologically and genetically diverse species with a large contiguous range throughout North America. The species not only has a wide array of phenotypic variation compared to other mammals, but shows marked adaptability across ecozones with differing ecological influences. It is these various selective pressures in distinctive parts of the continent that have likely led to localized adaptations within the bobcat metapopulations. The species is also marked by its ability to maintain connectivity and populations in anthropogenically developed areas, an advantage it has over other felids, including its close relative the Canada lynx ( …

Investigating The Redox Sensitivity Of Mitf Splice Variants, Rachel Berryman

Senior Theses

Within pigment-producing cells known as melanocytes, the transcription factor MITF is intimately involved in regulating genes associated with cell cycle maintenance and melanocyte differentiation. Research, however, has provided conflicting results on the relationship between the expression levels of MITF and melanocyte cell fate. To complicate matters, two splice variants of MITF exist, differing by only 18 base pairs. These variants have been observed at variable levels of expression in melanocyte and melanoma cells, raising the question as to their functional purpose. Building upon previous research by the Leachman/Cassidy lab that identified the redox sensitivity of MITF while additionally establishing a …

Genetic Analysis Of Flower Color Differences Between A Hummingbird-Pollinated And A Self-Pollinated Monkeyflower (Mimulus) Species, Caitlin Foster

University Scholar Projects

Flower color plays an important role in pollinator discrimination and speciation. Understanding the genetic contributions to flower color differences between two closely related species, Mimulus cardinalis and Mimulus parishii, can improve understanding of how they developed different pollination syndromes and diverged from a recent common ancestor. M. cardinalis is hummingbird-pollinated and has large, bright red flowers while M. parishii is self-pollinated and has small, pale pink flowers. An F2 hybrid population between these two species was created to establish a platform for analysis of the genetic architecture controlling the differences in anthocyanin pigmentation. Statistical analysis of anthocyanin concentration distribution …

Assessing The Influence Of Riparian Invasion By The Shrub Lonicera Maackii On Terrestrial Subsidies To Headwater Streams, Erin C. Rowekamp, Julia I. Chapman, Ryan Mcewan

Biology Faculty Publications

Invasion of Amur honeysuckle (Lonicera maackii) into riparian areas of headwater streams creates strong potential for alterations of terrestrial subsidies that may drive bottom-up effects on aquatic biota. In this study, we analyzed effects of L. maackii on terrestrial subsidies in stream sites that represented a gradient of invasion intensity in temperate deciduous forests of southwestern Ohio (USA). Leaf litter biomass, terrestrial and aquatic fine woody debris (0.5–9.9 cm diameter) volume and count, and terrestrial and aquatic coarse woody debris (>9.9 cm diameter) volume were analyzed. Based on previous research, we hypothesized that sites with a higher …

Differences In Learning And Gene Expression In Brains Of Male And Female Bicyclus Anynana, Gabrielle Agcaoili

Biological Sciences Undergraduate Honors Theses

One way to understand the variation in the behavior of animals is by looking at the genes involved. We were particularly interested in behavioral differences between the sexes. How might these differences be manifested in the brain? This study worked to answer this question by using male and female butterflies of the species Bicyclus anynana, examining what is going on in the brains of males and females as they learned from a social exposure. We focused in on how sex plays a role in behavior and learning; it has been seen that males and females respond to the same social …

Understanding Cytochrome C Maturation In Anaerobic Archaea, Blake Wojciechowski

Biological Sciences Undergraduate Honors Theses

Methanoperedens nitroreducens (MPEBLZ), an archaeal methanotroph and close relative of Methanosarcina acetivorans, contain numerous cytochrome c proteins. However, difficulty in using these organisms as a model for cytochrome cresearch has created a pressure to express cytochrome c proteins in an organism that is much easier to work with. A punitive cytochrome c protein (MPEBLZ_04274) from M. nitroreducens was attempted to be cloned into a model methanogen M. acetivorans as well as Escherichia coli. Cytochrome c proteins are important for many metabolic processes within anaerobic archaea. In order for a mature cytochrome c to be formed heme must …

Efficient Conditional Inactivation Of Rdh10 Reveals Important Role Of Retinoic Acid During Lung Branching Morphogenesis., Nhut Quang Huy Tran

Electronic Theses and Dissertations

Birth defects are complicated pathological processes. Many birth defects can be traced back to disrupted regulation of molecular signaling pathways during embryogenesis. One of the most important gene regulatory factors during embryo development is retinoic acid (RA). However, studying the specific roles of RA in each organ during embryogenesis in vivo is challenging. The Sandell laboratory has a conditional mutant mouse model that can potentially be used for studying the role of RA during embryogenesis by inducing stage-specific RA deficiency. This model allows retinol dehydrogenase 10 (Rdh10), a gene required for RA production, to be inactivated at a …

Construction Of A Target-Specific Crispr-Cas9 Vector For The Purpose Of Introducing Mutations Into The Fum1 Gene Of Fusarium Verticillioides, Jennifer Petsche

Honors Program Theses

In molecular biology, CRISPR-Cas9 is a useful gene editing tool that takes advantage of a powerful cleaving enzyme and DNA sequences found in prokaryotes. In this study, a target-specific CRISPR-Cas9 vector containing an RNA-guided Cas9 nuclease specific for the FUM1 gene was constructed for the purpose of introducing mutations into the FUM1 gene of Fusarium verticillioides. Plasmids pFC332 and pFC334 were isolated. A guide RNA sequence was designed and amplified using Polymerase Chain Reaction (PCR) with pFC334 as the template. Sticky ends were created through restriction enzyme digestion of pFC332. These pieces were combined using Uracil-Specific Excision Reagent (USER) …

Investigation Of The Individual Soybean Root Nodule Microbiome, Parris Mica Mayhood

Graduate Theses/Dissertations

Soybean is a valuable crop that establishes a symbiotic association with nitrogen-fixing microorganisms. Previous research suggests members of the genus Bradyrhizobium are the major nitrogen-fixing inhabitants of soybean root nodules. However, results from recent studies identified the presence of other bacteria, so called non-rhizobial endophytes (NREs), inside root nodules. All previous research has pooled nodules of different plants for bacterial community analysis, but this study investigated the presence and relative abundance of rhizobia and NREs within multiple root nodules of a single plant. Three sites were selected on Kendrick Farm in Springfield, MO, where three plants and rhizosphere soil were …

Barcoding Adelpha Immatures To Understand Host Breadth, Connor P. Soderstrom, Elizabeth Song, Rylie Towne

Pacific Undergraduate Research and Creativity Conference (PURCC)

No abstract provided.

A Basic Ddradseq Two‐Enzyme Protocol Performs Well With Herbarium And Silica‐Dried Tissues Across Four Genera, Ingrid E. Jordon-Thaden, James B. Beck, Catherine A. Rushworth, Michael D. Windham, Nicolas Diaz, Jason T. Cantley, Christopher T. Martine, Carl J. Rothfels

Faculty Journal Articles

Premise

The ability to sequence genome‐scale data from herbarium specimens would allow for the economical development of data sets with broad taxonomic and geographic sampling that would otherwise not be possible. Here, we evaluate the utility of a basic double‐digest restriction site–associated DNA sequencing (ddRADseq) protocol using DNAs from four genera extracted from both silica‐dried and herbarium tissue.

Methods

DNAs from Draba, Boechera, Solidago, and Ilex were processed with a ddRADseq protocol. The effects of DNA degradation, taxon, and specimen age were assessed.

Results

Although taxon, preservation method, and specimen age affected data recovery, large phylogenetically informative …

Genetic Variance In Flocculin Protein Family, Sarah Dooley, Dale Beach

Virtual 2020 Spring Student Showcase for Research and Creative Inquiry

Yeast fermentation produces a number of commercially important products, most typically represented by alcoholic beverages. In craft breweries that do not use expensive filtration systems, selecting a yeast variety for fermentation can determine the clarity of the product from hazy Belgian pilsner to a crisp, clear American lager. Flocculation refers to a stress response behavior in yeast to group together (flocculate) in conditions like low sugar or high alcohol content as experienced at the end of fermentation. Higher levels of flocculation increase the clarity. The process of flocculation is genetically controlled through a series of complicated interactions and depends on …

158— Optimization And Development Of The Luria-Delbrück Experiment For Geneseo Genetics Labs, Abigail Scheffler

GREAT Day Posters

The classic genetics experiment by Salvador Luria and Max Delbruck showed that mutations are present prior to selection rather than arising in response to selective pressures. In this experiment, we used Escherichia coli as our model organism and the antibiotics streptomycin and rifampicin to show students in a laboratory setting how this hypothesis can be applied. Specifically, we optimized antibiotic concentrations and the amount of bacterial cells to use in order for the activity to run smoothly and consistently in a student laboratory. We found that the ideal conditions are 1000 cells/ml and 25 micrograms/ml of streptomycin. These concentrations showed …

Biol 250: Curly Hair Trait: Homozygous Or Heterozygous, Kaysi Bing

Virtual 2020 Spring Student Showcase for Research and Creative Inquiry

Research Aim: To connect the SNP rs17646946 AG genotype and curly hair

Hypothesis: People expressing a GG genotype at the SNP rs17646946 are most likely to have the curly hair trait