Advantage Of Precision Metagenomics For Urinary Tract Infection Diagnostics,
2023
Advanta Genetics
Advantage Of Precision Metagenomics For Urinary Tract Infection Diagnostics, Sadia Almas, Rob E. Carpenter, Chase Rowan, Vaibhav Tamrakar, Rahul Sharma
Human Resource Development Faculty Publications and Presentations
Background: Urinary tract infections (UTIs) remain a diagnostic challenge and often promote antibiotic overuse. Despite urine culture being the gold standard for UTI diagnosis, some uropathogens may lead to false-negative or inconclusive results. Although PCR testing is fast and highly sensitive, its diagnostic yield is limited to targeted microorganisms. Metagenomic next-generation sequencing (mNGS) is a hypothesis-free approach with potential of deciphering the urobiome. However, clinically relevant information is often buried in the enormous amount of sequencing data.
Methods: Precision metagenomics (PM) is a hybridization capture-based method with potential of enhanced discovery power and better diagnostic yield without diluting clinically relevant …
Targeting Brd4 In The Treatment Of Pleural Fibrosis,
2023
University of Texas at Tyler
Targeting Brd4 In The Treatment Of Pleural Fibrosis, Joy Adewumi
Biotechnology Theses
Pleural fibrosis (PF) is a respiratory disorder that refers to the thickening and scarring of the pleura. Currently, there is a lack of pharmaceutic treatment options for PF. Pleural mesothelial to mesenchymal transition (MesoMT) is a critical process that contributes to the development of PF. Bromodomain-containing protein 4 (BRD4), a transcriptional and epigenetic regulator, has recently been implicated in a wide range of lung injuries. However, whether BRD4 is involved in regulating MesoMT and the development of PF remains unclear and was explored in this study. Primary human pleural mesothelial cells (HPMCs) were used to test the role of BRD4 …
Studies On The Leukocyte-Associated Ig-Like Inhibitory Receptor-1 Signaling Pathway In T Lymphocytes,
2023
University of Tennessee Health Science Center
Studies On The Leukocyte-Associated Ig-Like Inhibitory Receptor-1 Signaling Pathway In T Lymphocytes, Chidi Zacheaus
Theses and Dissertations (ETD)
Inflammation is a natural process in which the immune system concertedly responds to pathogens and abnormal cell growth to protect the host. For an efficient/effective immune response that circumvents tissue atrophy, a delicate balance between stimulatory and inhibitory mechanisms is essential for the proper functioning of the immune system. Immuno-receptor Tyrosine-based Inhibitory Motif (ITIM)-bearing receptors in immune cells, including T lymphocytes, play a major role in preventing autoimmune responses. Leukocyte-associated Ig-like Inhibitory Receptor 1 (LAIR-1) is one of ITIM-bearing receptors. The mechanism by which LAIR-1 attenuates T-cell response has yet to be completely understood. In this study, I investigated a …
Functional Impact Of Ethyl-Β-D-Glucuronide On Mycobacterium Tuberculosis Stimulated Lung Macrophages,
2023
University of Texas at Tyler
Functional Impact Of Ethyl-Β-D-Glucuronide On Mycobacterium Tuberculosis Stimulated Lung Macrophages, Charles Inaku
Biotechnology Theses
Chronic alcohol abuse has been shown to alter immune defense mechanisms in humans and mice which makes the host susceptible to infections, including Mycobacterium tuberculosis (Mtb) infection. However, limited information is available on the mechanisms involved in alcohol-mediated host immune system dysfunction.
In this study, we determined the effects of ethyl-β-d-glucuronide (EtG), an alcohol-derived metabolite, on immune response of mice lung macrophages. We measured cytokine and chemokine production by gamma-irradiated mtb (γ-mtb) stimulated mice lung macrophages in the presence or absence of EtG. We also determined the effect of EtG on the metabolic state of γ-mtb stimulated mice lung macrophages. …
Starvation Sensing By Mycobacterial Rela/Spot Homologue Through Constitutive Surveillance Of Translation,
2023
Thomas Jefferson University
Starvation Sensing By Mycobacterial Rela/Spot Homologue Through Constitutive Surveillance Of Translation, Yunlong Li, Soneya Majumdar, Ryan Treen, Manjuli R. Sharma, Jamie Corro, Howard B. Gamper, Swati R. Manjari, Jerome Prusa, Nilesh K. Banavali, Christina L. Stallings, Ya-Ming Hou, Rajendra K. Agrawal, Anil K. Ojha
Department of Biochemistry and Molecular Biology Faculty Papers
The stringent response, which leads to persistence of nutrient-starved mycobacteria, is induced by activation of the RelA/SpoT homolog (Rsh) upon entry of a deacylated-tRNA in a translating ribosome. However, the mechanism by which Rsh identifies such ribosomes in vivo remains unclear. Here, we show that conditions inducing ribosome hibernation result in loss of intracellular Rsh in a Clp protease-dependent manner. This loss is also observed in nonstarved cells using mutations in Rsh that block its interaction with the ribosome, indicating that Rsh association with the ribosome is important for Rsh stability. The cryo-EM structure of the Rsh-bound 70S ribosome in …
Changes In Nascent Chromatin Structure Regulate Activation Of The Pro-Fibrotic Transcriptome And Myofibroblast Emergence In Organ Fibrosis,
2023
Thomas Jefferson University
Changes In Nascent Chromatin Structure Regulate Activation Of The Pro-Fibrotic Transcriptome And Myofibroblast Emergence In Organ Fibrosis, Morgan D. Basta, Svetlana Petruk, Ross Summer, Joel Rosenbloom, Peter J. Wermuth, Edward J. Macarak, Alex V. Levin, Alexander Mazo, Janice L. Walker
Department of Biochemistry and Molecular Biology Faculty Papers
Cell reprogramming to a myofibroblast responsible for the pathological accumulation of extracellular matrix is fundamental to the onset of fibrosis. Here, we explored how condensed chromatin structure marked by H3K72me3 becomes modified to allow for activation of repressed genes to drive emergence of myofibroblasts. In the early stages of myofibroblast precursor cell differentiation, we discovered that H3K27me3 demethylase enzymes UTX/KDM6B creates a delay in the accumulation of H3K27me3 on nascent DNA revealing a period of decondensed chromatin structure. This period of decondensed nascent chromatin structure allows for binding of pro-fibrotic transcription factor, Myocardin-related transcription factor A (MRTF-A) to nascent DNA. …
The Involvement Of Ubiquitin In Med13 Cyclin C Degradation Following Cellular Stress,
2023
Rowan University
The Involvement Of Ubiquitin In Med13 Cyclin C Degradation Following Cellular Stress, Ayesha Gurnani, Brittany Friedson, Katrina Cooper
Stratford Campus Research Day
The Cdk8 Kinase Module is a dissociable regulator of cellular stress response genes, with degradation of its components Med13 and cyclin C eventually determining cell fate decisions such as engaging cell survival or cell death mechanisms. We aimed to explore the roles of ubiquitin in degradation of the Cdk8 Kinase Module following nitrogen starvation, with respect to the potential involvement of deubiquitinating enzyme Doa4, lysine linkage at position K63, and E2 ubiquitin conjugating enzymes Ubc4 and Ubc5. We utilized Western blot analysis to observe nitrogen starvation-induced degradation of Med13-HA in wild-type, doa4 mutant, and K63R yeast strains; degradation of cyclin …
Identifying Co-Factors That Drive Tra-1 Activator Function,
2023
Rowan University
Identifying Co-Factors That Drive Tra-1 Activator Function, Jibran Imtiaz, Youngquan Shen, Ronald Ellis
Stratford Campus Research Day
Gli proteins are involved in cell fate determination, proliferation, and patterning in many species and are major effectors of Hedgehog (Hh) signaling. There are three Gli proteins in humans, and mutations or errors in their regulation lead to a variety of developmental disorders or cancer. However, the mechanisms by which they interact with co-factors are poorly understood. We are analyzing co-factors of Gli proteins using TRA-1 in Caenorhabditis nematodes. The TRA-1 zinc fingers are structurally like those of other Gli proteins, and TRA-1 can be cleaved like other Gli proteins to form a repressor. However, its function has changed during …
Acute Kidney Injury In The Elderly,
2023
University of Connecticut
Acute Kidney Injury In The Elderly, Zachary Palanza
Honors Scholar Theses
Acute kidney injury (AKI) is a significant clinical concern in the elderly, marked by heightened incidence rates, increased morbidity and mortality, and impaired kidney repair mechanisms. AKI often has severe consequences, including extended hospital stays, heightened rates of chronic kidney disease, and elevated healthcare costs. The vulnerability of elderly individuals to AKI is amplified by age-related structural and functional changes in the kidneys, reduced physiological reserve, and increased exposure to nephrotoxic agents. The impaired kidney repair mechanisms observed in the elderly pose further complexities in AKI management. With age, the regenerative capacity of the kidneys diminishes, resulting in incomplete recovery …
Immunomodulatory Effects Of Resolvin D2 In A Model Of Infection,
2023
Rowan University
Immunomodulatory Effects Of Resolvin D2 In A Model Of Infection, Prem Yugandhar Kadiyam Sundarasivarao
Graduate School of Biomedical Sciences Theses and Dissertations
Dysregulated hyperinflammatory host immune response to underlying bacterial infections is a characteristic of sepsis. In sepsis, bacteria often trigger abnormal hyperinflammatory responses which can cause multiple organ failure and if sustained can lead to an immunosuppressive phase where the host is susceptible to secondary infections caused by opportunistic bacteria like Pseudomonas aeruginosa (P. aeruginosa). In our studies, we used a 2-hit model of cecal ligation and puncture (CLP) followed by P. aeruginosa secondary lung infection to investigate cellular and molecular mechanisms in the beneficial action of resolvin D2 (RvD2). Resolvins of the D-series are a group of fatty acids known …
In Vivo Multi-Modal Imaging Approaches For Cancer, Stem And Immune Cells,
2023
Western University
In Vivo Multi-Modal Imaging Approaches For Cancer, Stem And Immune Cells, Nourhan Shalaby
Electronic Thesis and Dissertation Repository
Introduction: Molecular imaging allows for non-invasive longitudinal visualization of cellular functions in vivo. This area of research has provided better understanding of fundamental molecular and biochemical processes, enabled optimization of pre-clinical and clinical assessments for new treatments, and allowed for more accurate and early detection of many pathologies. Extensive research for novel imaging techniques and emerging technologies have rapidly advanced the field. However, an ideal single imaging modality or approach does not exist. Alternatively, multi-modal imaging approaches are commonly applied to overcome limitations of individual technologies. In this thesis, we design, develop, validate, and image various cell types using …
Candidate Variants In Dna Replication And Repair Genes In Early-Onset Renal Cell Carcinoma Patients Referred For Germline Testing,
2023
Thomas Jefferson University
Candidate Variants In Dna Replication And Repair Genes In Early-Onset Renal Cell Carcinoma Patients Referred For Germline Testing, Elena V. Demidova, Ilya G. Serebriiskii, Ramilia Vlasenkova, Simon Kelow, Mark D. Andrake, Tiffiney R. Hartman, Tatiana Kent, James Virtucio, Gail L. Rosen, Richard T. Pomerantz, Roland L. Dunbrack, Erica A. Golemis, Michael J. Hall, David Y.T. Chen, Mary B. Daly, Sanjeevani Arora
Department of Biochemistry and Molecular Biology Faculty Papers
Background: Early-onset renal cell carcinoma (eoRCC) is typically associated with pathogenic germline variants (PGVs) in RCC familial syndrome genes. However, most eoRCC patients lack PGVs in familial RCC genes and their genetic risk remains undefined.
Methods: Here, we analyzed biospecimens from 22 eoRCC patients that were seen at our institution for genetic counseling and tested negative for PGVs in RCC familial syndrome genes.
Results: Analysis of whole-exome sequencing (WES) data found enrichment of candidate pathogenic germline variants in DNA repair and replication genes, including multiple DNA polymerases. Induction of DNA damage in peripheral blood monocytes (PBMCs) significantly elevated numbers of …
Meta-Narrative Review Of Possible Impacts Of Genetic Screening On Treatment Of Breast Cancer,
2023
The University of Texas MD Anderson Cancer Center
Meta-Narrative Review Of Possible Impacts Of Genetic Screening On Treatment Of Breast Cancer, Toqa Al Alawi, Sheza Khan, Ivey Knebel, Steven Luong, Vilma Sanchez, Kamilah Walker-Charles
Research Methods Poster Session 2023
Objective: To examine the impacts of genetic screening on the treatment of breast cancer, in relation to differences, outcomes and decisions in treatment plans or surgery in patients that performed genetic screening versus those that did not.
Background: Genetic screening technology has become commercially available, yet standard preventative care for breast cancer has no genetic screening involved. Genetic screening in breast cancer treatment is performed, but its usage is not standardized.
Methods: Findings were synthesized using the meta-narrative review style to examine articles retrieved from searches of digital databases PubMed and the M.D. Anderson Scholarly Library.
Discussion: Articles were selected …
Mechanisms Of Chromosomal Instability (Cin) Tolerance In Aggressive Tumors: Surviving The Genomic Chaos,
2023
Thomas Jefferson University
Mechanisms Of Chromosomal Instability (Cin) Tolerance In Aggressive Tumors: Surviving The Genomic Chaos, Brittiny Dhital, Veronica Rodriguez-Bravo
Student Papers, Posters & Projects
Chromosomal instability (CIN) is a pervasive feature of human cancers involved in tumor initiation and progression and which is found elevated in metastatic stages. CIN can provide survival and adaptation advantages to human cancers. However, too much of a good thing may come at a high cost for tumor cells as excessive degree of CIN-induced chromosomal aberrations can be detrimental for cancer cell survival and proliferation. Thus, aggressive tumors adapt to cope with ongoing CIN and most likely develop unique susceptibilities that can be their Achilles' heel. Determining the differences between the tumor-promoting and tumor-suppressing effects of CIN at the …
The Revolutionary Genome Editor: Crispr-Cas9 Systems,
2023
Liberty University
The Revolutionary Genome Editor: Crispr-Cas9 Systems, Grace Spade
Senior Honors Theses
Genetic engineering is the modification of an organism's genetic material to alter its traits through adding, deleting, or changing specific genes. CRISPR-Cas9 systems are groundbreaking tools for genetic engineering, in short utilizing a molecule called RNA to guide a protein called Cas9 to a specific location in DNA to add, delete, or replace genes. The history of how the CRISPR-Cas9 systems came into existence, how it was adapted from a natural defense system in bacteria, and its mechanism of action in both are explained. Its applications, both present and future, competing genetic modifiers, advantages and disadvantages, and the ethical dilemmas …
In Vitro Gametogenesis: A Research Timeline And Implications For The Future Of Assisted Reproductive Technology,
2023
Liberty University
In Vitro Gametogenesis: A Research Timeline And Implications For The Future Of Assisted Reproductive Technology, Nicole Buckley
Senior Honors Theses
The novel reproductive technology, In Vitro Gametogenesis (IVG), includes the process of obtaining mature viable germ cells from pluripotent stem cells. To do so, embryonic stem cells and induced pluripotent stem cells are specified to primordial germ cells and differentiated to form gametes that undergo further maturation, which subsequently may undergo in vitro fertilization to form an embryo. With this capability, IVG holds the power to provide a novel treatment option for human infertility. As of now, research has been conducted on mice successfully, and with limited success in humans. Future research will likely focus on discovering the species-specific differences …
Regeneration Of Neurons In Human Brain Tissue; A Revolutionary Concept With Therapeutic Potential,
2023
Grand Valley State University
Regeneration Of Neurons In Human Brain Tissue; A Revolutionary Concept With Therapeutic Potential, Mackenzie R. Dunn
Other Undergraduate Research
There is current research to suggest that endogenous neuronal regeneration, exogenous neuronal stem cell transplantation and glial cell reprogramming could be prospective therapeutic treatments for neurodegeneration and traumatic injury. With these conditions, there is significant brain atrophy, loss of neurons and loss of synaptic connections which can have devastating effects on executive functioning, cognition, learning and memory. This review will examine these modern approaches to adult neurogenesis, and assess the viable mechanisms and future outlook of these three therapies for neurological regenerative medicine.
Protocol To Identify The Core Gene Supported By An Essential Gene In E. Coli Bacteria Using A Genome-Wide Suppressor Screen,
2023
Thomas Jefferson University
Protocol To Identify The Core Gene Supported By An Essential Gene In E. Coli Bacteria Using A Genome-Wide Suppressor Screen, Isao Masuda, Ya-Ming Hou
Department of Biochemistry and Molecular Biology Faculty Papers
We describe here a genome-wide screening approach to identify the most critical core reaction among a network of many that are supported by an essential gene to establish cell viability. We describe steps for maintenance plasmid construction, knockout cell construction, and phenotype validation. We then detail isolation of suppressors, whole-genome sequencing analysis, and reconstruction of CRISPR mutants. We focus on E. coli trmD, which encodes an essential methyl transferase that synthesizes m1G37 on the 3'-side of the tRNA anticodon. For complete details on the use and execution of this protocol, please refer to Masuda et al. (2022).
Developing A Bacterial Panel For The Evaluation Of Novel Anti-Infective Compounds,
2023
University of Nebraska at Omaha
Developing A Bacterial Panel For The Evaluation Of Novel Anti-Infective Compounds, Clare Euteneuer
UNO Student Research and Creative Activity Fair
Antibiotic resistance is one of the leading causes of concern for the world health community. Drugs used to stop various infections for years are now becoming easier for bacteria to resist due to mutations and plasmids conferring resistance. To combat this problem, new drug can help alleviate this concern. We developed an assay that allows us to screen novel drug-like compounds against bacteria in an effort to identify promising new anti-infective compounds. Our assay was designed using known drugs against a panel of gram positive and negative bacilli and cocci including S. epidermidis, P. mirabilis, N. mucosa, and E. …
Acute Acat1/Soat1 Blockade Increases Mam Cholesterol And Strengthens Er-Mitochondria Connectivity.,
2023
Thomas Jefferson University
Acute Acat1/Soat1 Blockade Increases Mam Cholesterol And Strengthens Er-Mitochondria Connectivity., Taylor C Harned, Radu V Stan, Ze Cao, Rajarshi Chakrabarti, Henry N Higgs, Catherine C Y Chang, Ta Yuan Chang
Department of Pathology, Anatomy, and Cell Biology Faculty Papers
Cholesterol is a key component of all mammalian cell membranes. Disruptions in cholesterol metabolism have been observed in the context of various diseases, including neurodegenerative disorders such as Alzheimer's disease (AD). The genetic and pharmacological blockade of acyl-CoA:cholesterol acyltransferase 1/sterol O-acyltransferase 1 (ACAT1/SOAT1), a cholesterol storage enzyme found on the endoplasmic reticulum (ER) and enriched at the mitochondria-associated ER membrane (MAM), has been shown to reduce amyloid pathology and rescue cognitive deficits in mouse models of AD. Additionally, blocking ACAT1/SOAT1 activity stimulates autophagy and lysosomal biogenesis; however, the exact molecular connection between the ACAT1/SOAT1 blockade and these observed benefits remain …
