Biology Commons^™

Elucidating The Priming Mechanism Of Clpxp Protease By Single-Domain Response Regulator Cpdr In Caulobacter Crescentus, Kimberly E. Barker

Masters Theses

In Caulobacter crescentus, progression through the cell cycle is regulated by the AAA+ protease ClpXP, and there are several classes of cell-cycle substrates that require adaptors in order to be degraded. CpdR, a single domain-response regulator, binds the N-terminal domain of ClpXP and primes the protease for degradation of downstream factors (Lau et al., 2015). The ability of CpdR to bind ClpX is regulated by its phosphorylation state. In the unphosphorylated state, CpdR binds ClpXP and guides its localization to the cell pole during the swarmer to stalked transition, where CpdR is mediates degradation of substrates such as PdeA. …

Comparison Of The Humoral Immune Response Following Both Bacterial Challenge And Rnai Of Major Factors On Proliferation Of Bartonella Quintana In The Human Louse, Jake Zina

Masters Theses

Human body lice, Pediculus humanus humanus, and head lice, Pediculus humanus capitis, have been hematophagous ectoparasites of humans for thousands of years. Despite being ecotypes, only body lice are known to transmit bacterial diseases to humans, and it appears that lower humoral and cellular immune responses allow body lice to possess a higher vector competence. We previously observed that the transcription level of the defensin 1 gene was up-regulated only in head lice following oral challenge of Bartonella quintana, a causative agent of trench fever, and also that body lice excreted more viable B. quintana in their …

Changes In Gene Expression From Long-Term Warming Revealed Using Metatranscriptome Mapping To Fac-Sorted Bacteria, Christopher A. Colvin

Masters Theses

Soil microbiomes play pivotal roles to the health of the environment by maintaining metabolic cycles. One question is how will climate change affect soil bacteria over time and what could the repercussions be. To answer these questions, the Harvard Forest Long-Term Warming Experiment was established to mimic predicted climate change by warming plots of land 5℃ above ambient conditions. In 2017, 14 soil core samples were collected from Barre Woods warming experiment to mark 15 years since the establishment of the soil warming in that location. These samples underwent traditional metatranscriptomics to generate an mRNA library as well as a …

Chemosensory Receptors In Berghia Stephanieae: Bioinformatics And Localization, Kelsi L. Watkins

Masters Theses

Chemosensation is achieved through the binding of chemical signals to chemoreceptor proteins embedded in the membranes of sensory neurons. The molecular identity of these receptors, as well as the downstream processing of chemosensory signals, has been well studied in arthropods and vertebrates. However, very little is known about molluscan chemosensation. The identity of chemoreceptor proteins in the nudibranch mollusc Berghia stephanieae are unknown. Data from other protostome and molluscan studies suggest Berghia may use ionotropic receptors for some forms of chemoreception. This study used a bioinformatics approach to identify potential chemosensory ionotropic receptors in the transcriptome of Berghia. A …

Screening For Binding Partners And Protein-Protein Interactions Of A Fungal Transcription Factor- Xdr1, Nishadi Punsara Gallala Gamage

Masters Theses

Clarireedia spp. (formerly Sclerotinia homoeocarpaF.T. Bennett) is the causal agent dollar spot, the most economically important turfgrass disease impacting golf courses in North America. The most effective strategy for dollar spot control is repeated application of multiple classes of fungicides. However, reliance on chemical application has led to resistance to four classes of fungicides as well as multidrug resistance (MDR). Fungi are known to detoxify xenobiotics, like fungicides, through transcriptional regulation of three detoxification phases: modification, conjugation and secretion. Little is known, however, of the protein-protein interactions that facilitate these pathways. Following next-generation RNA sequencing of Clarireedia spp., a …

A Tipping Point In The Ecuadorian Amazon Rainforest: Current And Future Land-Use And Climate Change Trends, Alula Shields

Masters Theses

Many regions of the Amazon are experiencing drastic changes as deforestation and climate change drive the world’s largest continuous rainforest towards a ‘tipping point’. These disturbances are changing natural cycles that once past a critical threshold, will mark an unstoppable transition to an altered ecosystem. Losing areas of the Amazon rainforest will have implications for the global climate, global carbon budget, and global hydrological regimes. Scholars have projected these tipping points for areas of the eastern Amazon rainforest, but much less scholarship focuses on the headwaters of the Western Amazon, an area of great cultural and biological importance. Ecuador is …

The Time Course And Neuroanatomy Of Rhinophore Regeneration In The Nudibranch Berghia Stephanieae, Ani Maroyan

Masters Theses

Within five weeks, the nudibranch, Berghia stephanieae (Gastropoda, Mollusca) can regenerate a severed rhinophore, the main olfactory appendage, such that it is indistinguishable from a non-lesioned rhinophore. The rhinophore is a 2 mm long stalk with lateral sides covered in ridges and the distal third covered in fluorescent pigmentation. Its internal morphology is dominated by longitudinal musculature, overlaid by a complex neuronal plexus, which contains neurons that express various neuroactive substances including serotonin and small cardioactive peptide (SCP). Two large nerves originate in the rhinophore ganglion at the base of the rhinophore and run the length of the rhinophore. To …

Development Of A New Behavioral Assay For Juvenile Berghia Stephanieae, Kelly E. Fischer

Masters Theses

Developing robust behavioral assays to study olfactory-driven behaviors allows for greater insight into the neural mechanisms behind them. Oftentimes, olfactory behavioral assays require a two-choice design, consistent variables, and controlled stimulus application. This can be challenging when working with marine dwelling organisms such as nudibranchs. Extensive work shows the importance of olfaction in both pre-metamorphic larval development and adult stage nudibranchs (Gastropoda, Mollusca). However, there is little research investigating how olfaction plays a role in rapidly developing, post-metamorphic juvenile nudibranchs such as Berghia stephanieae. To study olfactory-associated behaviors in juvenile Berghia, a novel behavioral microfluidic chip was designed which …

Factors Influencing Primate Hair Microbiome Diversity, Catherine Kitrinos

Masters Theses

Primate hair is both a substrate upon which essential social interactions occur and an important host-pathogen interface. As commensal microbes provide important immune functions for their hosts, understanding the microbial diversity in primate hair could provide insight into primate immunity and disease transmission. While studies of human hair and skin microbiomes show differences in microbial communities across body regions, little is known about the nonhuman primate hair microbiome. In this study, we collected hair samples (n=159) from 8 body regions across 12 nonhuman primate species housed at 3 US institutions to examine 1) the diversity and composition of the primate …

Improving Growth And Survival Of Cultured Yellow Lampmussel (Lampsilis Cariosa) For Restoring Populations, Virginia Martell

Masters Theses

In North America 72% of freshwater mussel species are endangered, threatened, or of special concern due to factors such as habitat loss and degradation, biological invasion, and land use change. Propagation of freshwater mussels has been considered a necessary conservation strategy for population restoration where threats have been mitigated but small population sizes limit population viability. Yellow lampmussel is a species of freshwater mussel that is endangered, threatened, or imperiled throughout its range; therefore, I evaluated laboratory techniques (probiotic supplements and secondary rearing designs) to improve culture of yellow lampmussel for population restoration. Several aquaculture facilities commonly use probiotics; thus, …

Characterizing The Interaction Between Non-Pathogenic Fusarium Oxysporum And Arabidopsis Thaliana To Determine Beneficial Effects Conferred To The Model Plant Host, Kathryn Isabelle Vescio

Masters Theses

Fusarium oxysporum (Fo) is a soil-borne fungal pathogen that causes vascular wilt disease on a broad range of plants, including agricultural crops and the model plant Arabidopsis thaliana. There are non-pathogenic members of the Fo species complex that confer defense benefits against other pathogens to the host plant, however alteration to the host’s physiology through interaction with one of these strains, Fo47, have not been described. In this study, we aimed to establish the Fo47-A. thaliana interaction and determine if Fo47 reduces disease severity of a pathogenic Fo isolate, Fo5176. Additionally, we sought to use bioinformatics to mine …

Visual Attention In Jumping Spiders, Margaret Bruce

Masters Theses

The different ways that animals extract and analyze visual information from their environment is of interest to sensory ecologists. Jumping spiders, well-known for visually guided mating and hunting behavior, are an interesting model for the study of visual attention because they quickly and efficiently integrate information from eight eyes with a small brain. Stimuli in front of the spider are examined by two functionally and morphologically distinct pairs of forward-facing eyes. The principal eyes discern fine details and have small retinas and thus a small visual field. However, their position at the back of moveable tubes within the cephalothorax expands …

Plants, Parasites, And Pollinators: The Effects Of Medicinal Pollens On A Common Gut Parasite In Bumble Bees, George Locascio

Masters Theses

Declines in several pollinator species are due to a variety of factors, including pathogens. Incorporating pollinator-friendly plant species into wild and agricultural habitats could reduce the stress of pathogens if food sources act medicinally against pathogens. Previous research demonstrated one domesticated sunflower cultivar (Helianthus annuus) can dramatically reduce a gut pathogen (Crithidia bombi) of the common eastern bumble bee, Bombus impatiens. To ascertain the breadth of this medicinal trait, we tested whether pollen from several H. annuus cultivars and four relatives could also reduce C. bombi infections in B. impatiens. We also investigated whether …

Microenvironment Regulates Fusion Of Breast Cancer Cells, Peiran Zhu

Masters Theses

Fusion of cancer cells has been observed in tumors for more than a century and is thought to contribute to tumor development and drug resistance. The low frequency of cell fusion events and the instability of fused cells have hindered our ability to understand the molecular mechanisms that govern cell fusion. We have developed a patterned gel system that can isolate cell fusion events and we demonstrate that several breast cancer cell lines can fuse into multinucleated giant cells in vitro, and the initiation and longevity of fused cells can be regulated solely by biophysical factors. Dynamically tuning the adhesive …

Transposable Elements In Fusarium Oxysporum & Growth Inhibition Of Fusarium Oxysporum Using Pepper Extracts, Taylor Aguiar

Masters Theses

The following contains two projects focused on the fungal pathogen, Fusarium oxysporum. The first project was purely computational in the examination of transposable elements (TEs), which are mobile sequences with the ability to multiply and move in their host genome. In F. oxysporum, TEs such as miniature impala elements are associated with the secreted in xylem gene that are related to its virulence over its host. The F. oxysporum species complex can be utilized as a model system for the examination of TE content and TE expression during the infection cycle. To find whether TEs play a role …

Characterization Of Calcium Homeostasis Parameters In Trpv3 And Cav3.2 Double Null Mice, Aujan Mehregan

Masters Theses

In mammals, calcium influx is required for oocyte maturation and egg activation, as it supports the persistent calcium oscillations induced by fertilization. These oscillations are required for the initiation of embryo development. The molecular identities of the plasma membrane calcium-permeant channels that underlie calcium influx are not established. Among these channels, Transient Receptor Potential Vanilloid, member 3 (TRPV3) allows divalent cations, namely strontium (Sr²⁺) and calcium (Ca²⁺) with high permeability, into cells, and its expression pattern seems to predict an essential role in the initiation of development. Another channel that was identified to be expressed in …

Uncovering Tasselsheath3. A Genomic And Phenotypic Analysis Of A Maize Floral Mutant., Thompson Zhang

Masters Theses

In the modern era, maize has become the most successful crop grown in the United States. According to the USDA over 90 million acres of land are planted to corn and 96.2% of the U.S feed grain production is made up of the cereal. Part of the success of maize is due to its floral architecture, and its pollination technique in which the flower opens, exposing stamens containing pollen into the air. A unique organ called the lodicule functions as a release mechanism, forcing the flower to open. Lodicules from grasses and eudicot petals are homologous, yet there is little …

Factors Influencing Impact Of Biological Control Agents Of The Emerald Ash Borer, Theresa Murphy

Masters Theses

Agrilus planipennis, the emerald ash borer (EAB), is a destructive invasive forest pest decimating North American ash trees. Population-wide management of EAB focuses on biological control, with the introduction of four parasitic wasps; one egg parasitoid, Oobius agrili and three larval parasitoids- Spathius galinae, Spathius agrili and Tetrastichus planipennisi. This thesis examines some of the factors influencing the establishment of these larval biocontrol agents. Chapter 1 examines the relationship between woodpeckers and the parasitoids S. agrili and T. planipennisi. Both woodpeckers and these parasitoids attack the larval stage of EAB, which means their impacts overlap and …

An Adult Zebrafish Brain Atlas To Investigate Shh Mediated Cell-Cell Signaling In Neurogenic Zones, Alyssa P. Lutservitz

Masters Theses

Adult neurogenesis occurs in proliferative zones of the brain that contain neural progenitor cell populations capable of differentiating into specific cell types. However, we remain limited in our understanding of the signals that regulate neural progenitor cell proliferation and differentiation in adults. Recently zebrafish (Danio rerio) have emerged as an excellent model for studying the molecular mechanisms behind adult neurogenesis, because sixteen proliferative zones remain active in the adult brains. Thousands of fluorescent transgenic reporter lines have been generated in zebrafish that reveal gene expression patterns of cell-cell signaling systems, some of which may regulate neurogenesis in these …

The Role Of Micrornas In Regulating The Translatability And Stability Of Target Messenger Rnas During The Atrophy And Programmed Cell Death Of The Intersegmental Muscles Of The Tobacco Hawkmoth Manduca Sexta., Elizabeth Chan

Masters Theses

A variety of diseases lead to the atrophy and/or death of skeletal muscle. To better understand the molecular mechanisms that mediate these processes, I have taken advantage of the intersegmental muscles (ISMs) of the tobacco hawkmoth Manduca sexta, which undergo sequential programs of atrophy and programmed cell death at the end of metamorphosis. ISM death is mediated by changes in gene expression and numerous cell-death associated transcripts have been identified. MicroRNAs (miRs) are small (~22 nucleotide) non-coding RNAs that bind to sequences in messenger RNAs (mRNAs) and either cause translational arrest or mRNA degradation. To test the hypothesis that …

Curcumin And Its Oxidative Degradation Products: Their Comparative Effects On Inflammation, Julia Zhu

Masters Theses

The anti-inflammatory agent curcumin degrades rapidly, leading to speculations that curcumin’s reported effects stem from its degradation products. Curcumin can degrade via hydrolysis, and more recently it was discovered that curcumin can degrade via oxidation at physiological pH. Additionally, bicyclopentadione is the major degradation product from this oxidation reaction. Evidence from the literature suggests that curcumin degrades primarily through oxidation. However, the biology of the oxidation products is not well characterized, and there is debate on whether oxidation intermediates or curcumin itself is more biologically active. To further elucidate the biology of the oxidation products, their effects on inflammation were …

Evaluating A Novel Photochemical Tool For Labeling And Tracking Live, Endogenous Calcium-Permeable Ampars, Rosamund Elizabeth Combs-Bachmann

Masters Theses

The purpose of this research is to advance development of a photochemical tool designed to probe the role of ionotropic glutamate receptor signaling in neurodegenerative processes, and to delve more deeply into the biological processes underlying the role of these receptors in signaling and memory formation. This ligand-targeted nanoprobe was designed and developed in our lab to label endogenous calcium-permeable AMPARs (CP-AMPARs) in live cells with minimal disruption to native receptor activity. Nanoprobe is designed to use naphthyl acetyl spermine (NASPM) as a photocleavable ligand to target and covalently label native CP-AMPARs with a non-perturbing, fluorescent marker that then allows …

Promoting Extracellular Matrix Crosslinking In Synthetic Hydrogels, Marcos M. Manganare

Masters Theses

The extracellular matrix (ECM) provides mechanical and biochemical support to tissues and cells. It is crucial for cell attachment, differentiation, and migration, as well as for ailment-associated processes such as angiogenesis, metastases and cancer development. An approach to study these phenomena is through emulation of the ECM by synthetic gels constructed of natural polymers, such as collagen and fibronectin, or simple but tunable materials such as poly(ethylene glycol) (PEG) crosslinked with short peptide sequences susceptible to digestion by metalloproteases and cell-binding domains. Our lab uses PEG gels to study cell behavior in three dimensions (3D). Although this system fosters cell …

The Effects Of Ovarian Hormones And Exercise On Gene Markers Of Cardiac Dysfunction, Anisha S. Patel

Masters Theses

Heart disease is the leading cause of death in women in the United States. Premenopausal women appear to have better cardiac function and lower risk of heart disease compared to male postmenopausal female counterparts. Ovarian hormone loss influences blood pressure homeostasis and causes systemic inflammation, which may result in chronic stress on the heart. Two key physiological changes in cardiac dysfunction are reemergence of the fetal gene pattern and myocardial remodeling. Physical activity has been linked to improved cardiac function. The purpose of this study was to investigate the effects of ovariectomy on early markers of cardiac dysfunction and fibrosis …

Rnai Mediated Silencing Of Cell Wall Invertase Inhibitors To Increase Sucrose Allocation To Sink Tissues In Transgenic Camelina Sativa Engineered With A Carbon Concentrating Mechanism, Joshua Zuber

Masters Theses

Plant invertases are a class of proteins that have enzymatic function in cleaving sucrose to fructose and glucose. Cell wall invertase, located on the exterior of the cell wall of plant cells, plays a key role in the unloading of sucrose from the apoplast to the sink tissues. Cell wall invertase interacts with an inhibitor, cell wall invertase inhibitor, post-transcriptionally to regulate its activity. The inhibitor is constitutively expressed in pollen development, early developing seeds, and senescing leaves: indicative of sucrose allocation being a limiting factor at these stages of development. We introduced algal bicarbonate transporters LCIA/CCP1 to Camelina sativa …

Thermocycle-Regulated Wall Regulator Interacting Bhlh Encodes A Protein That Interacts With Secondary-Cell-Wall-Associated Transcription Factors, Ian P. Whitney

Masters Theses

Lignocellulosic biomass is one of the most abundant raw materials on earth that can be utilized to created carbon-neutral biofuels as a replacement for conventional fossil fuels. In order to create ideal energy crops, the regulation and deposition of cell wall polysaccharides must first be fully understood. Improved understanding of cell wall regulation will enable selection of traits that can optimize biofuel feedstocks. Herein, I utilize the grass model system Brachypodium distachyon in order to understand the transcriptional regulation of secondary cell wall deposition. Gene expression profiling was used to elucidate transcription factors that regulate secondary cell wall biosynthesis. Through …

Efficient Irrigation For Recreational Turfgrass In New England: Evapotranspiration And Crop Coefficients, James W. Poro

Masters Theses

As water demand increases it will become more imperative for golf course superintendents, landscape managers, and other industry professionals to improve water use efficiency in the management of recreational turfgrass. Scheduling irrigation according to actual turfgrass evapotranspiration rates (ET_T) is an integral component of efficient irrigation practices. Impracticality of field derived ET_T for industry use, however, directs the need of weather station derived reference (predicted) evapotranspiration (ET₀). To accurately predict (estimate) ET_T of turf and other crops, scientifically derived landscape (crop) coefficients (K_c values) are used in conjunction with mathematical models that incorporate …

Spatio-Temporal Factors Affecting Human-Black Bear Interactions In Great Smoky Mountains National Park, Nathan Buckhout

Masters Theses

Wildlife managers use models to aid in predicting high risk areas for human and black bear (Ursus americanus) interactions (HBI). These tools help managers implement management strategies to minimize HBI. Over 3,000 incidents of HBI were compiled from management reports at Great Smoky Mountains National Park (GSMNP) during 1998-2011, a park with 9-10.2 million visitors per year and a black bear population of about 1,600 bears.

We used data from bear management reports along with annual visitor use, mast and bear abundance data to develop a series of generalized linear models to assess the spatial and temporal factors …

The Role Of The Novel Lupus Antigen, Acheron, In Moderating Life And Death Decisions, Ankur Sheel

Masters Theses

Programmed cell death (PCD) is a major regulatory mechanism employed during development and homeostasis. The term PCD was coined to describe the death of the intersegmental muscles (ISMs) of moths at the end of metamorphosis. The timing of ISM death in the Tobacco Hawkmoth, Manduca sexta, is regulated by a fall in the titer of the steroid molting hormone 20-hydroxyecdysone (20E) late on day 17of pupal-adult development. This triggers the release of the peptide hormone, Eclosion Hormone (EH), which mediates its effects via the secondary messenger cGMP. It has been previously demonstrated that ISM death requires de novo gene expression. …

Rapid Method Of Processing Sperm For Nucleic Acid Extraction In Clinical Research, Matthew K. De Gannes

Masters Theses

Background: Sperm contain highly compact nuclei, inhibiting DNA extraction using traditional techniques. Current methods extracting sperm DNA involve lengthy lysis and no means of stabilizing DNA, hindering clinical research.

Objective: We sought to optimize an efficient method of extracting high quality human sperm DNA.

Methods: Sperm from three volunteers were isolated using PureCeption. We tested 1) proteinase K with DNA/RNA Shield, 2) DTT and TCEP as reducing agents, 3) QIAshredder homogenization, and 4) stability of sperm DNA fresh (baseline) or after 4 weeks of storage at 4^OC in DNA/RNA Shield using modified Quick-gDNA MiniPrep. DNA was PCR amplified …