Biochemistry, Biophysics, and Structural Biology Commons^™

Analysis Of Attitudinal Student Learning Benefits From A Course-Based Undergraduate Research Experience (Cure) Adapted For Online Format, Ambika Kapil, Luis C. Gonzalez Isoba, Niraj Pathak, Arthur Sikora, Santanu De

FDLA Journal

Course-based Undergraduate Research Experiences (CUREs) are an increasingly utilized model for exposing students to research. The lack of robust assessments is a major hurdle to wider adoption of CUREs. The Coronavirus Infectious Disease 2019 (COVID-19) pandemic necessitated a drastic shift of in-person courses to the online format. Using the Participant Perception Indicator (PPI) survey, we measured students’ self-reported changes in learning from such a biochemistry course at a large university in south Florida based on the Biochemistry Authentic Scientific Inquiry Lab (BASIL) model. By doing this, we were able to better understand the student-benefits of CUREs and how these benefits …

The Global Transcription Factor Fur Is Activated By Binding A [2fe-2s] Cluster To Maintain Iron Homeostasis In Escherichia Coli, Chelsey Rene Fontenot

LSU Doctoral Dissertations

Iron is an essential element for biological functions. Organisms have developed specific mechanisms to acquire, store, and export iron to manage intracellular iron homeostasis. These mechanisms are crucial not only for providing the cells with adequate iron for biological processes but also for ensuring that cells are not overloaded with excess iron, which is highly toxic. The Ferric uptake regulator (Fur) is a global transcription factor for maintaining intracellular iron homeostasis in bacteria. Previously, it was postulated that when the intracellular iron content is elevated, Fur binds ferrous iron to down-regulate the iron acquisition genes and up- regulate the iron …

The Application Of Microbial Source Tracking To Aid In Site Prioritization For Remediation In Lower Michigan, John J. Hart

Masters Theses

Non-point source fecal pollution is a threat to both the environment and public health. Climate change, aging infrastructure, and intensified agricultural practices are predicted to accentuate this issue. In Michigan, due to the high instance of aging infrastructure and intensified agriculture, non-point source fecal pollution has caused many waterbodies to exceed the state standards posing a risk to recreational activities and source water. Due to this threat, there is an increased effort to identify and remediate these sources. My study focused on improving the identification of non-point source fecal pollution through a combination of culture-based and molecular fecal indicator bacteria …

Characterizing Marr Homologs That Mediate Bacterial Fitness And Survival, George Chukwuemeka Nwokocha

LSU Doctoral Dissertations

Plant disease outbreaks are on the rise, threatening food security in many parts of the globe. To address these enormous challenges, new intervention strategies like bio-controls are being used as an important sustainable alternative to mitigate the negative effects of pathogens and increase the quality and productivity of agricultural crops. MarR family transcriptional regulators have been studied for their involvement in regulating bacterial virulence genes that help colonize plant hosts and therefore could serve as targets for biocontrol. The transcriptional regulator PecS, a member of the MarR family, is encoded by select bacterial pathogens and we show here that PecS …

The Effects Of Specialized Pro-Resolving Mediator Lipoxin A4 On Pseudomonas Aeruginosa Biofilms And Interactions With Monocytes, Julianne M. Thornton

Graduate School of Biomedical Sciences Theses and Dissertations

Pseudomonas aeruginosa (P. aeruginosa) is an opportunistic pathogen known as a major cause of hospital-acquired secondary infections, commonly causing chronic respiratory infections in immunocompromised individuals, especially those with cystic fibrosis, and often found in wound infections. P. aeruginosa uses the quorum sensing pathway to readily form protective biofilms, which reduce the efficacy of antibiotics and access by host immune cells to eradicate the pathogen. Specialized pro-resolving mediators (SPMs) are lipids endogenously produced by the host immune response to infection to aid in infection resolution. One SPM, Lipoxin A4 (LxA4), has been shown to be a robust quorum sensing inhibitor.

The …

Modeling The Tripartite Role Of Cyclin C In Cellular Stress Response Coordination, Steven J. Doyle

Graduate School of Biomedical Sciences Theses and Dissertations

For normal cellular function, exogenous signals must be interpreted and careful coordination must take place to ensure desired fates are achieved. Mitochondria are key regulatory nodes of cellular fate, undergoing fission/fusion cycles depending on the needs of the cell, and help mediate cell death fates. The CKM or Cdk8 kinase module, is composed of cyclin C (CC), Cdk8, Med12/12L, and Med13/13L. The CKM controls RNA polymerase II, acting as a regulator of stress-response and growth-control genes. Following stress, CC translocates to the mitochondria and interacts with both fission and iRCD apoptotic mediators. We hypothesize that CC represents a key mediator, …

Investigating The Antibacterial And Immunomodulatory Properties Of Lactobacillus Acidophilus Postbiotics, Rachael M. Wilson

Graduate School of Biomedical Sciences Theses and Dissertations

Probiotics are nonpathogenic microorganisms that have been extensively studied for their ability to prevent various infectious, gastrointestinal, and autoimmune diseases. The mechanisms underlying these probiotic effects have not been elucidated. However, we and other researchers have evidence suggesting that probiotic bacteria secrete metabolites that are antimicrobial and anti-inflammatory. As such, we developed a methodology to collect the secreted metabolites from a probiotic bacterium, Lactobacillus acidophilus, and tested this cell free filtrate (CFF) both in vitro and in vivo. Using this CFF, we have demonstrated that L. acidophilus secretes a molecule(s) that has specific bactericidal activity against the opportunistic pathogen, Pseudomonas …

Analysis Of Ssa4 Reporter Expression By Q-Pcr, Susveen Sharanshi, Rebecca Adams

[Archive] Belmont University Research Symposium (BURS)

The synthesis of genome-encoded proteins via mRNA translation is integral to cell survival. In eukaryotes, such as S. cerevisiae, the mRNA that is produced in the nucleus must be exported to the cytoplasm for translation to occur, and this process is highly regulated. Specifically, the export of mRNA occurs via travel through nuclear pore complexes (NPCs), which are selective doorways embedded in the nuclear envelope. During cellular stress, such as heat shock, the cell needs to regulate gene expression to permit survival, and mRNA export is one step at which this occurs. At these high temperatures, a cell’s proteins …

Med13 Degradation Defines A New Receptor-Mediated Autophagy Pathway Activated By Nutrient Deprivation, Sara E. Hanley

Graduate School of Biomedical Sciences Theses and Dissertations

Cells are exposed to an enormous amount of diverse extracellular cues but have a limited arsenal of weapons for protecting and maintaining homeostasis. To overcome these restrictions, nature has engineered proteins that have multiple functions. The pleiotropy of using one protein to carry out a variety of functions allows cells to rapidly execute tailored responses to a diverse set of signals. The Cdk8 kinase module (CKM) is a conserved detachable unit of the Mediator complex predominantly known for its role in transcriptional regulation. The CKM is composed of four proteins, the scaffolding proteins Med13 and Med12, as well as the …

Serving Justice Case By Case, Michael Becker

WRIT: Journal of First-Year Writing

Forensic Science is an integral part of serving justice in today's society, and majority of the world has little understanding of what forensics is. Read this article on forensic science and how it relates to writing in today's world.

Physics 422 Spring 2023 Syllabus, Ronald Koder

Open Educational Resources

Spring 2023 course syllabus for Physics 422, Biophysics, at the City College of New York

Investigation Of Cofactor Activities Of Endothelial Microparticle- Thrombomodulin With Liposomal Surrogate, Valentinas Gruzdys, Lin Wang, Dan Wang, Rachel Huang, Xue-Long Sun

Chemistry Faculty Publications

Thrombomodulin (TM) is a type I transmembrane glycoprotein mainly expressed on the endothelial cells, where it binds thrombin to form the thrombin-TM complex that can activate protein C and thrombin-activable fibrinolysis inhibitor (TAFI) and induce anticoagulant and anti-fibrinolytic reactions, respec-tively. Cell activation and injury often sheds microparticles that contain membrane TM, which circulate in biofluids like blood. However, the biological function of circulating microparticle-TM is still unknown even though it has been recognized as a biomarker of endothelial cell injury and damage. In comparison with cell membrane, different phospholipids are exposed on the microparticle surface due to cell membrane "flip-flop"upon …

Physics 422 Spring 2023 Syllabus - Medical Physics, Ronald Koder

Open Educational Resources

This is the Spring 2023 syllabus for Physics 315, Medical Physics, at CCNY

Will Populations Of Macroinvertebrate Functional Feeding Groups Survive Precipitation Changes?, Malika Gottfried, Laura Kim, Sophia Zuccala

Other Student Projects

Climate change is a pervasive issue that has the potential to have detrimental effects on many freshwater organisms and their habitats. Fluctuations in precipitation, changes in temperature, and other long-term shifts in weather patterns are just a few examples of the ways in which climate change is impacting the world around us (“What is Climate Change?” n.d.). The Mill River in Northampton, Massachusetts is an ideal location to measure some of these impacts on macroinvertebrates in various functional feeding groups. Macroinvertebrates are small organisms that lack an internal skeletal system, and their functional feeding groups refer to “the type of …

Characterization And Genomic Analysis Of Two Escherichia Coli O157:H7 Bacteriophages Isolated From Pigeons, Mohamad I. Alolama

Dissertations

Enterohemorrhagic Escherichia coli, also known as EHEC, is a subset of Shiga toxin-producing E. coli (STEC), and it has recently been identified as one of the principal foodborne pathogens. E. coli O157:H7 is the most important serotype of STEC for its role in causing foodborne illnesses. E. coli O157:H7 could cause various gastroenteritis symptoms such as diarrhea, hemolytic uremic syndrome, hemorrhagic colitis, and thrombotic thrombocytopenic purpura and may cause death. Elimination of E. coli O157:H7 during food processing and storage is a possible solution. Bacteriophages have a significant impact on bacterial populations in nature due to their ability to …

In Vitro Characterization Of Fluorogenic Chemical Tools To Study Human Carboxylesterases (Cess), Taylor Parish Spidle

Undergraduate Honors Theses

Human carboxylesterases (CESs) are enzymes that are responsible for the metabolism of many important pharmaceuticals. Although CESs are key players in the hydrolysis of many ester-containing drugs, they remain understudied. Our group hypothesizes that this is primarily because there are few methods capable of reporting activity in live cells. Here, I report a new series of fluorogenic chemical tools to study the CES activity of one of the two major CESs in humans, CES1, in live cells. MCP-Me, MCP-Et, and MCP-iPr utilize the same carbonate group of a previously developed chemical tool in our group, FCP-1, and work to mimic …

Ins And Outs Of Rocker Switch Mechanism In Major Facilitator Superfamily Of Transporters, Stephanie Sauve, Joseph Williamson, Adithya Polasa, Mahmoud Moradi

Chemistry & Biochemistry Faculty Publications and Presentations

The major facilitator superfamily (MFS) of transporters consists of three classes of membrane transporters: symporters, uniporters, and antiporters. Despite such diverse functions, MFS transporters are believed to undergo similar conformational changes within their distinct transport cycles, known as the rocker-switch mechanism. While the similarities between conformational changes are noteworthy, the differences are also important since they could potentially explain the distinct functions of symporters, uniporters, and antiporters of the MFS superfamily. We reviewed a variety of experimental and computational structural data on a select number of antiporters, symporters, and uniporters from the MFS family to compare the similarities and differences …

A Kinome-Wide Crispr Screen Identifies Ck1Α As A Target To Overcome Enzalutamide Resistance Of Prostate Cancer, Jinghui Liu, Yue Zhao, Daheng He, Katelyn M. Jones, Shan Tang, Derek B. Allison, Yanquan Zhang, Jing Chen, Qiongsi Zhang, Xinyi Wang, Chaohao Li, Chi Wang, Lang Li, Xiaoqi Liu

Markey Cancer Center Faculty Publications

Enzalutamide (ENZA), a second-generation androgen receptor antagonist, has significantly increased progression-free and overall survival of patients with metastatic prostate cancer (PCa). However, resistance remains a prominent obstacle in treatment. Utilizing a kinome-wide CRISPR-Cas9 knockout screen, we identified casein kinase 1a (CK1a) as a therapeutic target to overcome ENZA resistance. Depletion or pharmacologic inhibition of CK1a enhanced ENZA efficacy in ENZA-resistant cells and patient-derived xenografts. Mechanistically, CK1a phosphorylates the serine residue S1270 and modulates the protein abundance of ataxia telangiectasia mutated (ATM), a primary initiator of DNA double-strand break (DSB)-response signaling, which is compromised in ENZA-resistant cells and patients. Inhibition of …

Identification Of A Nacc1-Regulated Gene Signature Implicated In The Features Of Triple-Negative Breast Cancer, Chrispus Ngule, Hami Hemati, Xingcong Ren, Oluwafunminiyi Obaleye, Amos O. Akinyemi, Felix Oyelami, Xiaofang Xiong, Jianxun Song, Xia Liu, Jin-Ming Yang

Markey Cancer Center Faculty Publications

Triple-negative breast cancer (TNBC), characterized by a deficiency in estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor2 (HER2), is among the most lethal subtypes of breast cancer (BC). Nevertheless, the molecular determinants that contribute to its malignant phenotypes such as tumor heterogeneity and therapy resistance, remain elusive. In this study, we sought to identify the stemness-associated genes involved in TNBC progression. Using bioinformatics approaches, we found 55 up- and 9 downregulated genes in TNBC. Out of the 55 upregulated genes, a 5 gene-signature (CDK1, EZH2, CCNB1, CCNA2, and AURKA) involved in cell regeneration was positively correlated …

In Situ Microwave Fixation Provides An Instantaneous Snapshot Of The Brain Metabolome, Jelena A. Juras, Madison B. Webb, Lyndsay E. A. Young, Kia H. Markussen, Tara R. Hawkinson, Michael D. Buoncristiani, Kayli E. Bolton, Peyton T. Coburn, Meredith I. Williams, Lisa P. Y. Sun, William C. Sanders, Ronald C. Bruntz, Lindsey R. Conroy, Chi Wang, Matthew S. Gentry, Bret N. Smith, Ramon C. Sun

Markey Cancer Center Faculty Publications

Brain glucose metabolism is highly heterogeneous among brain regions and continues postmortem. In particular, we demonstrate exhaustion of glycogen and glucose and an increase in lactate production during conventional rapid brain resection and preservation by liquid nitrogen. In contrast, we show that these post- mortem changes are not observed with simultaneous animal sacrifice and in situ fixation with focused, high- power microwave. We further employ microwave fixation to define brain glucose metabolism in the mouse model of streptozotocin-induced type 1 diabetes. Using both total pool and isotope tracing analyses, we identified global glucose hypometabolism in multiple brain regions, evidenced by …