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Novel Regulators Of Human Gene Expression, Alexander Coley 2022 University of South Alabama

Novel Regulators Of Human Gene Expression, Alexander Coley

Theses and Dissertations

The human genome is rife with regulatory elements that control whether genes are expressed or silenced. While regulatory elements such as epigenomic modifications, transcription factors, promoters, and enhancers are well established, there still remain regulatory elements that are poorly characterized or even undiscovered. In recent years, noncoding RNAs derived from small nucleolar RNAs were identified and linked to gene regulation in a variety of human cancers. Adding to the growing understanding of these sdRNAs, we performed a computational analysis of castration-resistant prostate cancer patient data and identified 38 sdRNAs as significantly overexpressed in CRPC. Two of these, sdRNA-D19B and sdRNA-A24, …


Investigations Into Prg-2 And Its Involvement In Developing Gallus Gallus Retinal Neurons, Jeffrey Parham 2022 Winthrop University

Investigations Into Prg-2 And Its Involvement In Developing Gallus Gallus Retinal Neurons, Jeffrey Parham

Graduate Theses

I am interested in the development of the nervous system, especially since during development nerves grow and extend, but in adults, they do not regenerate if damaged. We are specifically interested in the molecules that guide nerves to the correct target during their development. Lysophosphatidic acid (LPA) is a bioactive molecule that has been shown to play a role in neural development. LPA, through repeated studies, has been shown to stop neurons from growing by causing a physical change in a neuron’s growth cone (a structure used for navigation and growth). Recently, a novel set of genes, called PRGs, have …


Functional Characterization Of The Newly Discovered Type V Crispr-Cas Protein Cas12a2, Dylan J. Keiser 2022 Utah State University

Functional Characterization Of The Newly Discovered Type V Crispr-Cas Protein Cas12a2, Dylan J. Keiser

All Graduate Theses and Dissertations

Similarly to people, bacteria are under the treat of infection by viruses. To circumvent these threats, bacteria evolve complex immune systems. Our understanding of some of these immune systems has led to many advancements in the field of Biotechnology including tools that made expressing proteins for study in a lab easier, tools that revolutionized the feasibility of gene editing, and tools that could change the way we think about viral diagnostics and cancer therapeutics. A certain type of immune system that bacteria use to fight virus is called a CRISPR system. Presented here is work to understand the function of …


Functional Analysis Of Legionella Pneumophila Effector Protein, Shreya Neupane 2022 Western Kentucky University

Functional Analysis Of Legionella Pneumophila Effector Protein, Shreya Neupane

Masters Theses & Specialist Projects

Legionella pneumophila is a gram-negative bacterium that causes Legionnaire’s disease (a severe form of pneumonia) in humans. L. pneumophila can cause infection by utilizing its Type IV secretion system, a protein secretion system that transports proteins from the bacterial cytosol into the infected macrophage. Effectors released from the Type Iv secretion system allow L. pneumophila to create a safe environment to survive, replicate and cause infection. One such effector, RavQ, inhibits cell proliferation of mammalian HEK 293T cells and localizes to the cell’s nucleus, leading us to hypothesize that RavQ interferes with cellular activity in the nucleus. To detect its …


Encapsulation Of Antimicrobial Peptides In Bicontinuous Microemulsions For Topical Delivery To Surgical Site Infections And Chronic Wounds, Madison A. Oehler 2022 University of Tennessee, Knoxville

Encapsulation Of Antimicrobial Peptides In Bicontinuous Microemulsions For Topical Delivery To Surgical Site Infections And Chronic Wounds, Madison A. Oehler

Masters Theses

Surgical site infections and chronic wounds, especially those caused by antibiotic-resistant microorganisms, result in hospitalization and fatalities each year. Methods to prevent these infections, such as cleaning and preparing medical tools, have had minimal success in preventing infections. Further, antibiotic treatments have become less successful in treating infections and wounds because of antibiotic-resistant bacteria. Antimicrobial peptides (AMP) are a possible treatment solution for wound infections. AMPs are oligopeptides that occur in nature or can be synthesized in vitro which possess a broad spectrum of antimicrobial activity against bacteria and other harmful microorganisms. AMPs operate by disrupting the packing arrangements of …


A Novel Transmembrane Ligand Inhibits T Cell Receptor Activation, Yujie Ye 2022 University of Tennessee, Knoxville

A Novel Transmembrane Ligand Inhibits T Cell Receptor Activation, Yujie Ye

Doctoral Dissertations

T lymphocytes (T cells) play essential roles in the adaptive immune system. Each mature T cell expresses one type of functional T cell receptor (TCR). The TCR recognizes antigens bound to the major histocompatibility complex (MHC) in antigen presenting cells. The resulting stimulation signal crosses the transmembrane domain of TCR and initiates downstream signaling cascades. The human immune system relies on TCRs to recognize a variety of pathogens. Normally, TCR can distinguish the self-antigens from pathogenic antigens. However, dysfunction or aberrant expression of TCRs causes different inflammatory and autoimmune diseases, which afflict millions of people annually (Chapter I). Current treatments …


A Pipeline To Generate Deep Learning Surrogates Of Genome-Scale Metabolic Models, Achilles Rasquinha 2022 University of Nebraska-Lincoln

A Pipeline To Generate Deep Learning Surrogates Of Genome-Scale Metabolic Models, Achilles Rasquinha

Computer Science and Engineering: Theses, Dissertations, and Student Research

Genome-Scale Metabolic Models (GEMMs) are powerful reconstructions of biological systems that help metabolic engineers understand and predict growth conditions subjected to various environmental factors around the cellular metabolism of an organism in observation, purely in silico. Applications of metabolic engineering range from perturbation analysis and drug-target discovery to predicting growth rates of biotechnologically important metabolites and reaction objectives within dierent single-cell and multi-cellular organism types. GEMMs use mathematical frameworks for quantitative estimations of flux distributions within metabolic networks. The reasons behind why an organism activates, stuns, or fluctuates between alternative pathways for growth and survival, however, remain relatively unknown. GEMMs …


Analyzing Interactions Of Calmodulin With Hiv-1 Matrix Protein, Andrea Sandoval, D. Mau, N. Karimi, K. Sakamaki, C. Owens, Jerry LaRue 2022 Chapman University

Analyzing Interactions Of Calmodulin With Hiv-1 Matrix Protein, Andrea Sandoval, D. Mau, N. Karimi, K. Sakamaki, C. Owens, Jerry Larue

Student Scholar Symposium Abstracts and Posters

Human immunodeficiency virus (HIV) attacks the immune system and if left untreated, could cause acquired immunodeficiency syndrome (AIDS). The HIV matrix protein (HIV-MA) is involved in replication and regulation of the HIV virus. Calmodulin (CaM), a calcium-binding protein found in all eukaryotes, has a potential role in the viral replication of HIV-MA which plays a key role in the replication of HIV. In order to investigate the interactions between calmodulin and the HIV-MA, a series of titrations with CaM are performed using circular dichroism. Circular dichroism (CD) uses circularly polarized light to observe the secondary structure of a molecule. The …


Chromatin Regulation By Rb-Interacting Proteins In Cellular Immune Functions, Seung June Kim 2022 The University of Western Ontario

Chromatin Regulation By Rb-Interacting Proteins In Cellular Immune Functions, Seung June Kim

Electronic Thesis and Dissertation Repository

The retinoblastoma protein (RB) is historically known for its function in cell cycle control. However, mice carrying targeted Rb1 mutations have revealed that RB serves various non-cell cycle control roles. Notably, RB acts as a scaffold that recruits chromatin regulatory proteins, condensin II and enhancer of zeste homolog 2 (EZH2). These complexes protect the genome integrity through maintaining proper chromosome condensation, long range contacts, and transcriptionally repressive histone modification. This thesis explores the mechanistic links that regulate such RB-condensin II complex or that are leveraged upon pharmacological inhibition of the RB-EZH2 complex. First, I identified potential phosphorylation sites in the …


Potential Use Of Proteolytic Bacteria Paenibacillus Dendritiformis (Bt7) Isolated From Batu Tannery Effluents For The Detergent Industry, Chandran Masi, Degafneh Tadesse, Abate Ayele 2022 Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University,

Potential Use Of Proteolytic Bacteria Paenibacillus Dendritiformis (Bt7) Isolated From Batu Tannery Effluents For The Detergent Industry, Chandran Masi, Degafneh Tadesse, Abate Ayele

Karbala International Journal of Modern Science

This research was aimed at identifying a bacterium that can produce alkaline proteases. As a result, bacteria that produce proteases were isolated from Batu tannery effluents, tested for protease synthesis on skim milk agar plates, and validated with a protease assay. Microscopic and molecular phylogenetic analyses identified Paenibacillus dendritiformis (BT7) as the bacterial isolate with the highest alkaline protease production. The isolate's maximum enzyme production was obtained by 2% inoculum size, 40°C temperature, 9.0 pH, and a 48-hour incubation time with production media components such as glucose, casein, MgCl2, and 2% NaCl. The maximal enzyme activity was 270 U/mL under …


College Of Natural Sciences Newsletter, September & October 2022, College of Natural Sciences 2022 South Dakota State University

College Of Natural Sciences Newsletter, September & October 2022, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 3, Issue 6

Page 1 Dean's Message
Page 2 Awards & Recognition
Page 3 Midwest Regional ACS Meeting
Page 4 North Central ASM Meeting
Page 5 Geography Department Travel
Page 6-7 Media Coverage of CNS
Page 7 REMAST Program at SDState receives national spotlight
Page 8 Celebrating the lives of those who touched the College
Page 9 Innovative Learning Spaces
Page 10 Open PRAIRIE Data
Page 11 2022 CNS Scholarship Brunch
Page 12-14 Fall 2022 Outreach Events


Occurrence Of Kanamycin-Resistant Bacteria Relative To Anthropogenic Pollution Along Richland Creek In Nashville, Tn​, Jolene Ho Mach, Annie Le, Brandon Torres Ramirez 2022 Belmont University

Occurrence Of Kanamycin-Resistant Bacteria Relative To Anthropogenic Pollution Along Richland Creek In Nashville, Tn​, Jolene Ho Mach, Annie Le, Brandon Torres Ramirez

Science University Research Symposium (SURS)

The overuse of antibiotics has caused an increase in antibiotic-resistant (AR) bacteria, which is a serious public health concern. Previous studies showed a significant correlation between anthropogenic pollution and AR bacteria. This project aims to identify AR bacteria in Richland Creek relative to local anthropogenic pollution. Water samples were collected at four locations along Richland Creek in Nashville, Tennessee. Bacteria resistant to the antibiotic kanamycin were isolated from the water samples, identified to genera using DNA barcoding, and compared among the sites. We expect to see a greater abundance and diversity of kanamycin-resistant bacteria closer to the end than near …


Conformational Dynamics And Aggregation Of Thermally Stressed Proteins Studied By Hydrogen/Deuterium Exchange Mass Spectrometry, Nastaran Nosrat Tajoddin 2022 The University of Western Ontario

Conformational Dynamics And Aggregation Of Thermally Stressed Proteins Studied By Hydrogen/Deuterium Exchange Mass Spectrometry, Nastaran Nosrat Tajoddin

Electronic Thesis and Dissertation Repository

Proteins perform various biological functions, e.g., as enzymes or transporters. In addition to naturally occurring proteins, the use of protein therapeutic drugs for treating cancer and other diseases is a rapidly growing area. A thorough biophysical characterization of proteins and protein therapeutics opens the door to a more comprehensive understanding of their role in health and disease. This dissertation aims to expand the capabilities of an existing technique (Hydrogen Deuterium Exchange Mass Spectrometry, HDX-MS), which is widely used for probing protein structure and dynamics. Conventionally, HDX-MS experiments are performed as a function of labelling time. Here we aim to establish …


Changes In Gene Expression From Long-Term Warming Revealed Using Metatranscriptome Mapping To Fac-Sorted Bacteria, Christopher A. Colvin 2022 University of Massachusetts Amherst

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 …


Characterization Of The Poly (Adp-Ribose) Polymerase Family In The Fusarium Oxysporum Species Complex, Daniel Norment 2022 University of Massachusetts Amherst

Characterization Of The Poly (Adp-Ribose) Polymerase Family In The Fusarium Oxysporum Species Complex, Daniel Norment

Masters Theses

Fusarium oxysporum is a filamentous fungus that is known to invade over a hundred different hosts and poses a major threat to the economy and food supply world-wide. Poly (Adenosine diphosphate-Ribose) Polymerase (PARP) is a family of regulatory proteins that affect change in the cell through transfer of ADP-Ribose moieties onto target molecules. The most well-studied PARP protein is the human PARP1, a PARylating nuclear protein that serves as our model PARP protein. F. oxysporum was found to contain a large expansion of PARP catalytic-domain-containing proteins compared to other filamentous fungi. We utilized in silico multiple sequence alignments and domain …


Chemosensory Receptors In Berghia Stephanieae: Bioinformatics And Localization, Kelsi L. Watkins 2022 University of Massachusetts Amherst

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 …


The Sos Response In Escherichia Coli K12: An Exploration Of Mutations In Lexa And Reca Using Fluorescence Microscopy, Steven Van Alstine 2022 University of Massachusetts Amherst

The Sos Response In Escherichia Coli K12: An Exploration Of Mutations In Lexa And Reca Using Fluorescence Microscopy, Steven Van Alstine

Doctoral Dissertations

Faithful replication of the genome is paramount for maintaining the fitness of an organism. Therefore, life has evolved inducible mechanisms to be able to repair damaged DNA and maintain evolutionary fitness. The SOS response is a highly conserved DNA damage inducible response that is tightly regulated. Multiple factors contribute to the ability of the cell to perform proper DNA repair and induction of the SOS response including the amount of RecA, mutations in RecA that affect competition for DNA, and other proteins that interact with the RecA filament. The complex relationship between RecA and LexA is the subject of this …


Chemical Biology Approaches For Tracking And Manipulation Of Macrophage Phenotypes, Javier A. Mas Rosario 2022 University of Massachusetts Amherst

Chemical Biology Approaches For Tracking And Manipulation Of Macrophage Phenotypes, Javier A. Mas Rosario

Doctoral Dissertations

Macrophages are white blood cells of the innate immune system that have the ability to change phenotypically depending on the stimuli present in their surroundings through a process commonly referred to as polarization. Macrophage phenotypes broadly range from pro-inflammatory, anti-tumor (M1) to immune-suppressing (M2). Of particular interest to this work, breast cancer progression and metastasis rely on the presence of M2-like tumor-associated macrophages (TAMs). While many studies have shown the involvement of macrophages in tumor progression and metastasis, there remains a need to further explore these interactions and the polarization process, including tracking of macrophage subtypes. Toward this end, I …


Principles Of Aaa+ Proteases, Samar Mahmoud 2022 University of Massachusetts Amherst

Principles Of Aaa+ Proteases, Samar Mahmoud

Doctoral Dissertations

ATPases associated with diverse cellular activities (AAA+) proteases in bacteria help maintain protein homeostasis by degrading misfolded and regulatory proteins. While a handful of protein targets for these proteases have been identified in Caulobacter crescentus and other organisms, more research is needed to elucidate mechanisms that govern substrate specificity. In the second chapter of this thesis, I will elaborate on how AAA+ substrate specificity is less rigid than previous work has suggested and how limiting ATP or mutations can alter substrate preferences of the ClpXP protease. In the third chapter, I will highlight our efforts to use a quantitative proteomics …


Rhamm As A Biomarker And Therapeutic Target In Triple-Negative Breast Cancer, Britney Messam 2022 The University of Western Ontario

Rhamm As A Biomarker And Therapeutic Target In Triple-Negative Breast Cancer, Britney Messam

Electronic Thesis and Dissertation Repository

Triple-negative breast cancer (TNBC) is a heterogeneous group of tumours characterized by early metastases and poor prognosis. Discovering novel biomarkers and therapeutic targets is necessary to improve TNBC patient outcomes as resistance to chemotherapy, the main therapeutic approach for TNBC, is common. In my study, RHAMM promoted proliferation of TNBC MDA-MB-231 tumour cells. RHAMM expression increased sensitivity to doxorubicin (p=0.0002) and strongly increased sensitivity to the FDA-approved MEK1/2 inhibitor trametinib (p≤0.0001). Doxorubicin and trametinib selectively killed RHAMM+/+ MDA-MB-231 tumour cells grown as co-cultures with RHAMM-/- MDA-MB-231 tumour cells. RHAMM-loss or trametinib decreased phosphorylated ERK1/2 protein levels and …


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