Biochemistry Commons^™

Data-Driven Computational Approach To Study Bio-Molecular Interactions, Misagh Naderi

LSU Doctoral Dissertations

Proteins commonly convey their functions in coordination with other proteins, small molecules and/or other biological assemblies such as sugars, lipids, DNA or RNA. Understanding the nature of these interactions is therefore central to improving our knowledge of biological systems. This body of work is a consolidation of three different computational approaches to study bio-molecular interactions: large-scale protein-ligand modeling, fragment-based cheminformatics, and computational analysis of interactions in single proteins.

The first issue that is addressed in this study is the scarcity of atomic crystal structures of protein-drug complexes. In general, a drug molecule’s affinity for multiple protein targets may causes unsolicited …

Elemental Analysis Of Beer Manufactured In Virginia Satellite Breweries, Jennifer Wiliams

Student Scholar Showcase

Financial incentives from the state and wider distribution potential have lured many west coast brewers to open satellite breweries in Virginia. Quality control is crucial for any brewery and especially important in satellite breweries that need to imitate the standard set by the parent brewery. Zinc, magnesium, iron, sodium manganese, and calcium are trace elements found in wort and are essential for enzymes that catalyze fermentation reactions. These elements protect against cell stress, play a crucial role in flocculation, and can affect the flavoring and coloration of beer. Barley, water, and hops are the sources of these elements in beer. …

Cloning, Purification, And Preliminary Dna-Binding And Unfolding Results For The Dna Polymerase I From The Psychrophile Psychromonas Ingrahamii, John Tod Baker

LSU Master's Theses

Psychromonas ingrahamii is a psychrophilic bacterium that lives in Arctic polar sea ice and grows at a temperature range of -12 to 10º C. This bacterium resides within veins inside the ice where the salinity is high, resulting in a freezing point depression and liquid water. The large fragment of DNA polymerase I from Psychromonas ingrahamii, called Klenpin, has been cloned, expressed, and purified in our laboratory. Although enzyme kinetic studies have been performed on a few psychrophilic enzymes, the thermodynamics of ligand binding and of protein stability have not been well studied for this class of extremophilic proteins. …

Anti-Fungal Compounds From Native Prairie Plants, Sarah Mcmichael, Kirk Manfredi

Research in the Capitol

Plant compounds can be found in many consumer products such as nutritional supplements (nutraceuticals), soaps, shampoos, and other personal care products. They are not yet used in these products as preservatives. This area of research focusses on identifying compounds from native prairie plants that can be used as preservatives in personal care products. An objective of this research is to isolate compounds that can be used to replace synthetic parabens. Synthetic parabens have been found to be harmful to humans and the environment. Our isolate would be a natural preservative and eliminate the harmful synthetic. This research presentation will discuss …

Ef-P Post-Translational Modification Has Variable Impact On Polyproline Translation In Bacillus Subtilis, Anne Witzky, Katherine R. Hummels, Rodney Tollerson Ii, Andrei Rajkovic, Lisa A. Jones, Daniel B. Kearns, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Elongation factor P (EF-P) is a ubiquitous translation factor that facilitates translation of polyproline motifs. In order to perform this function, EF-P generally requires posttranslational modification (PTM) on a conserved residue. Although the position of the modification is highly conserved, the structure can vary widely between organisms. In Bacillus subtilis, EF-P is modified at Lys³² with a 5-aminopentanol moiety. Here, we use a forward genetic screen to identify genes involved in 5-aminopentanolylation. Tandem mass spectrometry analysis of the PTM mutant strains indicated that ynbB, gsaB, and ymfI are required for modification and that yaaO, yfkA, and …

Evaluation Of Controlled-Release Nitrogen And Potassium Fertilizer In Louisiana Sugarcane Production, Samuel Kwakye

LSU Master's Theses

Sugarcane (Saccharum spp) production is an integral part of Louisiana's economy. Proper fertilizer management, particularly nitrogen (N) and potassium (K), optimizes sugarcane production. An experiment was established in 2015 at the LSU AgCenter Sugar Research Station in St. Gabriel, Louisiana to: (1) assess the effect of N and K fertilizer sources on sugarcane yield and quality parameters, and (2) monitor the changes in inorganic N and K levels in the soil at different sugarcane growth stages. The experiment was arranged in a randomized complete block design on a Sharkey clay soil and complete randomized design on a Commerce …

Breaking Conventions: Ohrr, A Transcriptional Regulator From Burkholderia Thailandensis, Anuja Rajiv Pande

LSU Doctoral Dissertations

Organic peroxides (OPs) are highly toxic oxidants. They directly react with cellular macromolecules rendering them inactive. Soil bacteria live in an oxidative environment rich in OPs from plant exudates and other xenobiotic compounds. Bacteria also face a burst of organic peroxides (lipid peroxides) in the macrophages during host invasion. Prokaryotes sense oxidative changes in environment and modulate their gene expression as an adaptive response for survival. MarR (multiple antibiotic resistance regulators) proteins enable bacteria to respond to such stress. Resistance to organic oxidants has been hypothesized to help bacteria survive in presence of disinfectants. This increases nosocomial infection rate.

Bacteria …

Vesicles Mimicking Normal And Cancer Cell Membranes Exhibit Differential Responses To The Cell-Penetrating Peptide Pep-1, Bashiyar Almarwani, Esther Nzuzi Phambu, Christopher Alexander, Ha Aimee T. Nguyen, Nsoki Phambu, Anderson Sunda-Meya

Chemistry Faculty Research

The cell-penetrating peptide (CPP) Pep-1 presents a great potential in drug delivery due to its intrinsic property to cross plasma membrane. However, its mechanism of entry into the cell remains unresolved. In this study, we compare the selectivity of Pep-1 towards vesicles mimicking normal and cancer cell membranes. The interaction was performed in a wide range of peptide-to-lipid molar ratios using infrared (IR), fluorescence, scanning electron microscopy (SEM), thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC) techniques. At low peptide concentration, fluorescence experiments show that lipid-phosphatidylserine (PS) seems to enable Pep-1 translocation into cancer cell membrane as evidenced by the …

Changes In Carbon, Nutrient, And Trace Metal Concentrations During The Transition From Freshwater To Marine Environments - A Case Study In Southwest Louisiana, Songjie He

LSU Doctoral Dissertations

Rivers carry terrestrial nutrients and other materials to estuaries, affecting biogeochemical cycles and ecosystems in coastal margins. This dissertation research incorporated five studies to investigate the dynamics of carbon, nutrients, and trace metals in four major coastal rivers in southwest Louisiana – the Sabine, Calcasieu, Mermentau, and Vermilion Rivers. The overarching goal of this research was to broaden the knowledge and understanding of biogeochemical processes in freshwater – saltwater mixing zones. These studies employed decade-long monitoring records of water chemistry, utilized monthly field measurements conducted over a two-year period, and used analysis of over 200 water samples for carbon, nitrogen, …

Biomimetic Studies Of Oxidation Reactions By Metalloporphyrins Through Ligand Effect And Kinetic Studies Of Photo-Generated Porphyrin-Iron(Iv)- Oxocompound Ii Models, Dharmesh J. Patel

Masters Theses & Specialist Projects

High-valent iron(IV)-oxo porphyrins are the central oxidizing species in hemecontaining enzymes and synthetic oxidation catalysts. Many transition metal complexes have been extensively studied as models of the ubiquitous cytochrome P450 enzymes to probe the sophisticated oxygen atom transfer (OAT) mechanism as well as to invent enzyme-like oxidation catalysts. In this work, two metalloporphyrin complexes have been successfully synthesized, and spectroscopically characterized. A new photochemical entry to porphyrin-iron(IV)-oxo derivatives, commonly referred to as compound II models, was also investigated in two porphyrin ligands that differ in electronic and steric environments. As determined by their distinct UV-vis spectra and kinetic behaviors, iron(IV)-oxo …

Untargeted Bioassay Strategy For Medicinal Plants: In Vitro Antidiabetic Activity And 13c Nmr Profiling Of Extracts From Vitex Negundo L, Fabian M. Dayrit, Myrnille Joy B. Zabala, Lolita G. Lagurin

Chemistry Faculty Publications

Bioassay-guided fractionation is the principal method for the identification of active constituents in medicinal plants. By design, this method aims to identify the most active compound in a complex mixture with the objective of discovering novel drug candidates. Described here is a complementary method for the identification of known bioactive compounds in medicinal plants which is untargeted and which takes advantage of the large NMR database of known natural products and availability of statistical software. This untargeted bioassay strategy is demonstrated as a proof of principle in the determination of the antidiabetic compounds in Vitex negundo L. Crude methanol and …

Magnetic Properties Of Acenes And Their O-Quinone Derivatives: Computer Simulation, A. A. Starikova, A. G. Starikov, R. M. Minyaev, Alexander I. Boldyrev, V. I. Minkin

Chemistry and Biochemistry Faculty Publications

Quantum chemical study (DFT UB3LYP/6-311++G(d,p)) of the structure and properties of acenes functionalized with two o-benzoquinone groups and their complexes with sodium cations has been performed. An increase in the number of fused rings has been shown to result in the stabilization of biradicaloid state of acenes and the switching of the character of exchange interactions between redox-active moieties from antiferromagnetic to ferromagnetic. The obtained results allow one to consider o-quinone acene derivatives as a basis for designing magnetoactive compounds.

Detection Of Amyloid Beta (Aβ) Oligomeric Composition Using Matrix-Assisted Laser Desorption Ionization Mass Spectrometry (Maldi Ms)., Jasmine S-H Wang, Shawn N Whitehead, Ken K-C Yeung

Chemistry Publications

The use of MALDI MS as a fast and direct method to detect the Aβ oligomers of different masses is examined in this paper. Experimental results suggest that Aβ oligomers are ionized and detected as singly charged ions, and thus, the resulting mass spectrum directly reports the oligomer size distribution. Validation experiments were performed to verify the MS data against artifacts. Mass spectra collected from modified Aβ peptides with different propensities for aggregation were compared. Generally, the relative intensities of multimers were higher from samples where oligomerization was expected to be more favorable, and vice versa. MALDI MS was also …

Intraperitoneal Nanotherapy For Metastatic Ovarian Cancer Based On Sirna-Mediated Suppression Of Dj-1 Protein Combined With A Low Dose Of Cisplatin, Canan Schumann, Stephanie Chan, Jess A. Miller, Yuliya Bortnyak, Katherine Carey, Alex Fedchyk, Leon Wong, Tetiana Korzun, Abraham S. Moses, Anna Lorenz, Delany Shea, Olena Taratula, Oleh Khalimonchuk, Oleh Taratula

Department of Biochemistry: Faculty Publications

Herein, we report an efficient combinatorial therapy for metastatic ovarian cancer based on siRNA-mediated suppression of DJ-1 protein combined with a low dose of cisplatin. DJ-1 protein modulates, either directly or indirectly, different oncogenic pathways that support and promote survival, growth, and invasion of ovarian cancer cells. To evaluate the potential of this novel therapy, we have engineered a cancer-targeted nanoplatform and validated that DJ-1 siRNA delivered by this nanoplatform after intraperitoneal injection efficiently downregulates the DJ-1 protein in metastatic ovarian cancer tumors and ascites. In vivo experiments revealed that DJ-1 siRNA monotherapy outperformed cisplatin alone by inhibiting tumor growth …

Inpatient Satisfaction At Different Public Sector Hospitals Of A Metropolitan City In Pakistan: A Comparative Cross-Sectional Study, Mehwish Hussain, Rehana Rehman, Zia Ikramuddin, Nava Asad, Ayesha Farooq

Department of Biological & Biomedical Sciences

Objective: To observe inpatient satisfaction at different public sector hospitals of Karachi, Pakistan.
Methods: A cross sectional study was carried out during 2010-2012 in four major public sector hospitals of Karachi. A total of 710 patients completed the study. Responses were gathered in a self-structured questionnaire that comprised of four dimensions of satisfaction with doctor, staff, administration and treatment. Average Score of each dimension was taken and compared using one way analysis of variance.
Result: Satisfaction with doctors, staff and administration of provincial and federal hospitals were comparatively similar (P > 0.05). However, satisfaction with treatment significantly differed in all four …

Cross Talk Between Serum Kisspeptin-Leptin During Assisted Reproduction Techniques, Rehana Rehman, Zehra Jamil, Aqsa Khalid, Syeda Sadia Fatima

Department of Biological & Biomedical Sciences

Background & Objective: Leptin facilitates onset of puberty by impact on hypothalamic Kisspeptin, gonadotropin releasing hormone, follicle stimulating and luteinizing hormone. The link of peripheral Leptin-Kisspeptin in regulating the ovarian and endometrial tissue in relation to adiposity is unknown. Therefore, we wanted to identify Kisspeptin-Leptin association with body mass index (BMI) and success of assisted reproductive treatments (ART) in infertile females.
Methods: A cross sectional study was carried from August 2014 till May 2016 after receiving ethical approval at Australian Concept Infertility Medical Centre, and Aga Khan University. The study group comprised of females with an age range …

Role Of The Snf2 Homolog, Irc20, In Yeast Genome Maintenance, Deena Mohamed Galal Eldin Ahmed

Theses

In eukaryotes, DNA is wrapped around histone proteins forming a highly compact structure, the chromatin. All DNA-based processes must occur within the complex organization of the chromatin, and this requires modulation of its structure when needed. This is accomplished by covalent histone modifications that alter histone-DNA contacts, as well as through the actions of ATP-dependent chromatin remodelers. These multi-subunit complexes play major roles in transcription regulation, replication and repairing DNA damage. This thesis aims to characterize a poorly studied member of the SWI/SNF family of ATPases/helicases, Irc20, from Saccharomyces cerevisiae. Previously, Irc20 has been shown to be involved in …

Advancing Professional Development Strategies For Chemistry And Biochemistry Undergraduates, Christian A. Brown

Senior Theses

In the Department of Chemistry and Biochemistry at the University of South Carolina (the Department), most curriculum-driven professional development is reserved for third- and fourth-year students. Classroom learning occurs at all levels, but the context comes late. Early exposure to career options and hands-on training is imperative for undergraduates to obtain maximum experiential learning. The purpose of this project is to advance the current professional development strategies of the Department, specifically targeting second- and third-year students. The study surveyed students' current involvement in professional development activities. The data on extracurricular experience and post-graduation interest was used to design a workshop …

Influenza D Virus M2 Protein Exhibits Ion Channel Activity In Xenopus Laevis Oocytes, Evan Daniel Kesinger

School of Biological Sciences: Dissertations, Theses, and Student Research

The Influenza virus M2 ion channel has good potential as a target for antiviral drugs, as the channel is necessary for viral replication. M2 of Influenza A and B viruses has beenstudied extensively, and is understood to function as a proton channel. Antiviral drugs like amantadine and rimantadine have been used to block the function of Influenza A virus M2. Influenza C virus M2 has also been researched and is understood to act as a chloride ion channel. However, the M2 channel of Influenza D virus (DM2) has been studied very little, and the activity and mechanism of the channel …

Prediction Of Lncrna-Disease Associations Based On Inductive Matrix Completion, Chengqian Lu, Mengyun Yang, Feng Luo, Fang-Xiang Wu, Min Li, Yi Pan, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Motivation: Accumulating evidences indicate that long non-coding RNAs (lncRNAs) play pivotal roles in various biological processes. Mutations and dysregulations of lncRNAs are implicated in miscellaneous human diseases. Predicting lncRNA–disease associations is beneficial to disease diagnosis as well as treatment. Although many computational methods have been developed, precisely identifying lncRNA–disease associations, especially for novel lncRNAs, remains challenging.

Results: In this study, we propose a method (named SIMCLDA) for predicting potential lncRNA– disease associations based on inductive matrix completion. We compute Gaussian interaction profile kernel of lncRNAs from known lncRNA–disease interactions and functional similarity of diseases based on disease–gene and gene–gene onotology …