Biochemistry Commons^™

Data On Spectrum-Based Fluorescence Resonance Energy Transfer Measurement Of E. Coli Multidrug Transporter Acrb, Yuguang Cai, Thomas E. Wilkop, Yinan Wei

Chemistry Faculty Publications

This paper presented the dataset of correction parameters used in the determination of the energy transfer efficiencies from the spectrum-based fluorescence resonance energy transfer (FRET) measurement in a trimeric membrane protein AcrB. The cyan fluorescent protein (CFP) and yellow fluorescent protein (YPet) were used as the donor and acceptor, respectively. Two AcrB fusion proteins were constructed, AcrB-CFP and AcrB-YPet. The proteins were co-expressed in Escherichia coli cells, and energy transfer efficiency were determined in live cells. To obtain reliable energy transfer data, a complete set of correction parameters need to be first determined to accommodate for factors such as background …

Role Of P300 Zz Domain In Chromatin Association And Histone Acetylation, Yongming Xue

Dissertations and Theses (Open Access)

Transcription is strictly regulated by numerous factors including transcription coactivators. The p300 protein and its close paralogue CREB-binding protein (CREBBP, aka CBP) are well-known transcriptional coactivators that have intrinsic lysine acetyltransferase activity. The functions of p300/CBP largely rely on their capabilities to bind to chromatin and to acetylate the histone substrates. However, the molecular mechanisms underlying the regulation of these processes are not fully understood.

Through combination of various biochemical, biophysical and molecular approaches, we show that the ZZ-type zinc finger (ZZ) domain of p300 functions as a histone reader that specifically binds the N-terminal tail of histone H3. Crystal …

A Role For Epac1 And Epac2 In Nociceptor Hyperexcitability And Chronic Pain After Spinal Cord Injury, Samantha Berkey

Dissertations and Theses (Open Access)

Chronic pain is a major complaint of those living with spinal cord injury (SCI), affecting 65-80% of the SCI population, but the treatment options remain limited or non-existent. The cAMP sensor EPAC has previously been shown to play a key role in chronic inflammatory and neuropathic pain, though the contribution from each of its two main isoforms, EPAC1 and EPAC2, is unclear. Here I test the hypothesis that both EPAC1 and EPAC2 play a key role in the maintenance of persistent nociceptor hyperexcitability and chronic pain after SCI.

Using both a T9 SCI mouse model and a T10 SCI rat …

Sip-428, A Sir2 Deacetylase Enzyme And Its Role In Biotic Stress Signaling Pathway, Bal Krishna Chand Thakuri

Electronic Theses and Dissertations

SABP2 (Salicylic Acid Binding Protein 2) plays a vital role in the salicylic acid signaling pathway of plants both regarding basal resistance and systemic acquired resistance against pathogen infection. SIP-428 (SABP2 Interacting Protein-428) is a Silent information regulator 2 (SIR2) like deacetylase enzyme that physically interacts with SABP2 in a yeast two-hybrid interaction and confirmed independently by a GST pull-down assay. We demonstrated that SIP- 428 is an NAD+ dependent SIR2 deacetylase enzyme. Transgenic tobacco plants silenced in SIP- 428 expression via RNAi showed enhanced basal resistance to microbial pathogens. Moreover, these SIP-428-silenced lines also exhibited a robust induction of …

Temperature And Polyunsaturated Fatty Acid’S Effect On Daphnia Magna Reproduction, Mark Albright

Electronic Theses and Dissertations

Organisms adapt to their environments by adjusting their biochemistry and physiology; such adaptation is limited by resource availability and physiological constraints. The freshwater crustacean Daphnia magna inhabits a wide range of environments and must survive and reproduce within a range of temperatures. One limit to low-temperature adaptation is thought to be the availability of unsaturated fatty acids necessary to maintain proper fluidity of cellular membranes. D. magna maintained at 10 ºC on a diet poor in unsaturated fatty acids have been observed to produce clutches that fail to develop. However, this has not been observed on a diet rich in …

Ca2+ - Induced Structural Change Of Multi-Domain Collagen Binding Segments Of Collagenases Colg And Colh From Hathewaya Histolytica, Christopher Eric Ruth

Graduate Theses and Dissertations

Hathewaya histolytica, previously renamed as Clostridium histolyticum, secretes at least two collagenases, ColH and ColG, that allow for degradation of extracellular matrices of animal tissue. Hathewaya histolytica virulence factors are proposed to undergo domain rearrangement upon secretion from the bacteria to the host. In order to accomplish this, collagenases seek the least ordered regions in collagen to efficiently disassemble the fibril. Two types of domains, Polycystic Kidney Disease-like (PKD) and Collagen Binding Domain (CBD), direct the collagenases ability to disassemble the fibril. Calcium dependent structural change have been reported to increase in thermal stability and in tighter collagen binding for …

Investigation Of The Molecular Mechanisms Of The Shigella Type Iii Secretion System Tip Complex, Abram R. Bernard

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Shigella are bacteria that are responsible for millions of infections and hundreds of thousands of deaths every year. The emergence of antibiotic resistant Shigella adds to the potentially devastating effect that these bacteria can have on human health. Shigella flexneri utilize specialized molecular machinery called the Type III secretion system to infect humans and cause disease. Research of this machinery promises to provide the knowledge, tools, and direction for the development of new avenues to combat shigellosis. This dissertation presents studies of two Shigella proteins, invasion plasmid antigens C and D (IpaC and IpaD). These proteins are part of a …

A Gcn5-Related N-Acetyltransferase (Gnat) Capable Of Acetylating Polymyxin B And Colistin Antibiotics In Vitro, Mateusz P. Czub, Brian Zhang, M. Paul Chiarelli, Karolina A. Majorek, Layton Joe, Pryemyslaw J. Prebski, Alina Revilla, Weiming Wu, Daniel P. Becker, Wladek Minor, Misty L. Kuhn

Chemistry: Faculty Publications and Other Works

Deeper exploration of uncharacterized Gcn5-related N-acetyltransferases has the potential to expand our knowledge of the types of molecules that can be acylated by this important superfamily of enzymes and may offer new opportunities for biotechnological applications. While determining native or biologically relevant in vivo functions of uncharacterized proteins is ideal, their alternative or promiscuous in vitro capabilities provide insight into key active site interactions. Additionally, this knowledge can be exploited to selectively modify complex molecules and reduce byproducts when synthetic routes become challenging. During our exploration of uncharacterized Gcn5-related N-acetyltransferases from Pseudomonas aeruginosa, we identified such an …

Metformin, Oxidative Stress, And Infertility: A Way Forward, Rehana Rehman, Syed Hani Abidi, Faiza Alam

Department of Biological & Biomedical Sciences

No abstract provided.

Molecular Fossils From Phytoplankton Reveal Secular Pco2 Trend Over The Phanerozoic, Caitlyn R. Witkowski, Johan W. H. Weijers, Brian S. Blais, Stefan Schouten, Jaap S. Sinninghe Damsté

Science and Technology Department Faculty Journal Articles

Past changes in the atmospheric concentration of carbon dioxide (PCO2) have had a major impact on earth system dynamics; yet, reconstructing secular trends of past PCO2 remains a prevalent challenge in paleoclimate studies. The current long-term PCO2reconstructions rely largely on the compilation of many different proxies, often with discrepancies among proxies, particularly for periods older than 100 million years (Ma). Here, we reconstructed Phanerozoic PCO2 from a single proxy: the stable carbon isotopic fractionation associated with photosynthesis (Ɛp) that increases as PCO2 increases. This concept has been widely applied to alkenones, but here, we …

Decreasing Phosphatidylcholine On The Surface Of The Lipid Droplet Correlates With Altered Protein Binding And Steatosis, Laura Listenberger, Elizabeth Townsend, Cassandra Rickertsen, Anastasia Hains, Elizabeth Brown, Emily G. Inwards, Angela K. Stoeckman

Chemistry Faculty Publications

Alcoholic fatty liver disease (AFLD) is characterized by an abnormal accumulation of lipid droplets (LDs) in the liver. Here, we explore the composition of hepatic LDs in a rat model of AFLD. Five to seven weeks of alcohol consumption led to significant increases in hepatic triglyceride mass, along with increases in LD number and size. Additionally, hepatic LDs from rats with early alcoholic liver injury show a decreased ratio of surface phosphatidylcholine (PC) to phosphatidylethanolamine (PE). This occurred in parallel with an increase in the LD association of perilipin 2, a prominent LD protein. To determine if changes to the …

A Crispr Platform For Rapid And Inducible Genome Editing In Human Non-Small Cell Lung Cancer Cells, Lloyd Bartley

Posters-at-the-Capitol

Non-small cell lung cancer (NSCLC) accounts for about 85% of lung cancer, which is the leading cause of cancer death in the world. High mortality rate associated with NSCLC is partially attributed to the limited understanding of NSCLC as well as ineffective therapeutic treatments. The initiation and progression of NSCLC involves genetic changes leading to alterations in the control of tissue development and homeostatic maintenance. Better knowledge about these genetic abnormalities is imperative for developing new chemotherapeutic drugs for NSCLC. Recent research demonstrates that the expression of paraoxonase 2 (PON2), a lactonase/arylesterase with anti-oxidant properties, are markedly enhanced in cancer …

Fatty Acid Amides And Their Biosynthetic Enzymes Found In Insect Model Systems, Ryan L. Anderson

USF Tampa Graduate Theses and Dissertations

A fatty acid amide is precisely as the name suggests: A fatty acid (CHn-COOH), in which the hydroxyl group of the carboxylic acid is displaced by an amine functional group from a biogenic amine (R-NH2), ultimately forming an amide bond. Furthermore, these fatty acid amides can be composed of a variety of different acyl chain lengths donated by the fatty acid and a myriad of different biogenic amines. Thus, these molecules can be subdivided in a number of different ways including the separation of short chain (acetyl to heptanoyl) and long chain (palmitoyl to arachidonoyl) and also based off the …

Investigating The Roles Of Fucosylation And Calcium Signaling In Melanoma Invasion, Tyler S. Keeley

USF Tampa Graduate Theses and Dissertations

Melanoma is the deadliest form of skin cancer. Prognosis for early stage melanoma patients is excellent, and surgery is often curative for these patients. However, once patients have presented with invasive disease, the average 5-year survival rate drops significantly from over 90% to between 10 and 15%. Several therapies have been developed to target a commonly mutated oncogene BRAF, or its downstream effectors. Unfortunately, while these treatments show robust initial response, most patients relapse within a year. Moreover, therapy-resistant tumors are often more invasive and metastatic. Therefore, it is important to investigate the molecular mechanisms underlying melanoma invasion and metastasis, …

Crystallographic And Computational Characterization Of Methyl Tetrel Bonding In S-Adenosylmethionine-Dependent Methyltransferases, Raymond C. Trievel, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Tetrel bonds represent a category of non-bonding interaction wherein an electronegative atom donates a lone pair of electrons into the sigma antibonding orbital of an atom in the carbon group of the periodic table. Prior computational studies have implicated tetrel bonding in the stabilization of a preliminary state that precedes the transition state in S_N2 reactions, including methyl transfer. Notably, the angles between the tetrel bond donor and acceptor atoms coincide with the prerequisite geometry for the S_N2 reaction. Prompted by these findings, we surveyed crystal structures of methyltransferases in the Protein Data Bank and discovered …

Predicting Response To Platin Chemotherapy Agents With Biochemically-Inspired Machine Learning, Peter Rogan, Eliseos J. Mucaki, Dan Lizotte

Biochemistry Publications

Selection of effective genes that accurately predict chemotherapy response could improve cancer outcomes. We compare optimized gene signatures for cisplatin, carboplatin, and oxaliplatin response in the same cell lines, and respectively validate each with cancer patient data. Supervised support vector machine learning was used to derive gene sets whose expression was related to cell line GI₅₀ values by backwards feature selection with cross-validation. Specific genes and functional pathways distinguishing sensitive from resistant cell lines are identified by contrasting signatures obtained at extreme vs. median GI₅₀ thresholds. Ensembles of gene signatures at different thresholds are combined to reduce dependence …

Urban Re-Greening: A Case Study In Multi-Trophic Biodiversity And Ecosystem Functioning In A Post-Industrial Landscape, Frank Gallagher, Nina M. Goodey, Diane Hagmann, Jay Prakash Singh, Claus Holzapfel, Megan Litwhiler, Jennifer Adams Krumins

Department of Chemistry and Biochemistry Faculty Scholarship and Creative Works

The biodiversity of urban and post-industrial ecosystems is a highly relevant and growing new frontier in ecological research. Even so, the functionality of these ecosystems may not always be successfully predicted based on prior biodiversity and ecosystem functioning theory. Indeed, evidence suggests that the general biological impoverishment within the urban context envisioned thirty years ago was overstated. Many of the world’s urban centers support some degree of biodiversity that is indigenous, as well as a complex array of non-native species, resulting in highly functional, and often, novel communities. For over two decades, a multi-disciplinary team has examined the sub-lethal impact …

Synthesis And Biological Evaluation Of Phaeosphaeride A Derivatives As Antitumor Agents, Victoria Abzianidze, Petr Beltyukov, Sofya Zakharenkova, Natalia Moiseeva, Jennifer Mejia, Alvin Holder, Yuri Trishin, Alexander Berestetskiy, Victor Kuznetsov

Chemistry & Biochemistry Faculty Publications

New derivatives of phaeosphaeride A (PPA) were synthesized and characterized. Anti-tumor activity studies were carried out on the HCT-116, PC3, MCF-7, A549, К562, NCI-Н929, Jurkat, THP-1, RPMI8228 tumor cell lines, and on the HEF cell line. All of the compounds synthesized were found to have better efficacy than PPA towards the tumor cell lines mentioned. Compound 6 was potent against six cancer cell lines, HCT-116, PC-3, K562, NCI-H929, Jurkat, and RPMI8226, showing a 47, 13.5, 16, 4, 1.5, and 7-fold increase in anticancer activity comparative to those of etoposide, respectively. Compound 1 possessed selectivity toward the NCI-H929 cell line (IC …

Combining Mass Spectrometry And Nmr Improves Metabolite Detection And Annotation, Fatema Bhinderwala, Nishikant Wase, Concetta Dirusso, Robert Powers

Department of Biochemistry: Faculty Publications

Despite inherent complementarity, nuclear magnetic resonance spectroscopy (NMR) and mass spectrometry (MS) are routinely separately employed to characterize metabolomics samples. More troubling is the erroneous view that metabolomics is better served by exclusively utilizing MS. Instead, we demonstrate the importance of combining NMR and MS for metabolomics by using small chemical compound-treatments of Chlamydomonas reinhardtii as an illustrative example. A total of 102 metabolites were detected (82 by GC-MS, 20 by NMR and 22 by both techniques). Out of these 47 metabolites of interest were identified, where 14 metabolites were uniquely identified by NMR and 16 metabolites were uniquely identified …

Nrh:Quinone Oxidoreductase 2 (Nqo2) And Glutaminase (Gls) Both Play A Role In Large Extracellular Vesicles (Lev) Formation In Preclinical Lncap-C4-2b Prostate Cancer Model Of Progressive Metastasis, Thambi Dorai, Ankeeta Shah, Faith Summers, Rajamma Mathew, Jing Huang, Tze-Chen Hsieh, Joseph M. Wu

NYMC Faculty Publications

In the course of studies aimed at the role of oxidative stress in the development of metastatic potential in the LNCaP-C4-2B prostate cancer progression model system, we found a relative decrease in the level of expression of the cytoplasmic nicotinamide riboside: quinone oxidoreductase (NQO2) and an increase in the oxidative stress in C4-2B cells compared to that in LNCaP or its derivatives C4 and C4-2. It was also found that C4-2B cells specifically shed large extracellular vesicles (LEVs) suggesting that these LEVs and their cargo could participate in the establishment of the osseous metastases. The level of expression of caveolin-1 …