Biochemistry, Biophysics, and Structural Biology Commons^™

Toxicity Studies Of 1'-S-1'-Acetoxychavicol Acetate In Rat Model, Ali Abdalla Yasir Osman

Student Works (2020-2029)

Natural compounds are the main source of therapeutic molecules for various diseases in this era, and most of the current medicines are derived from plants, microorganisms or animals. Nevertheless, the safety profile of these natural compounds has to be confirmed prior to their medicinal use. 1'-S-1'-acetoxychavicol acetate (ACA), a type of phenylpropanoid extracted from Alpinia conchigera Griff., is one of the natural compounds being investigated for its potential therapeutic purposes. ACA was previously reported to reduce tumour volume in athymic mice at the effective dose of 1.56 mg/kg body weight intraperitoneally and induce apoptotic death of tumour cells through the …

Protonic Capacitor: Elucidating The Biological Significance Of Mitochondrial Cristae Formation, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

For decades, it was not entirely clear why mitochondria develop cristae? The work employing the transmembrane-electrostatic proton localization theory reported here has now provided a clear answer to this fundamental question. Surprisingly, the transmembrane-electrostatically localized proton concentration at a curved mitochondrial crista tip can be significantly higher than that at the relatively flat membrane plane regions where the proton-pumping respiratory supercomplexes are situated. The biological significance for mitochondrial cristae has now, for the first time, been elucidated at a protonic bioenergetics level: 1) The formation of cristae creates more mitochondrial inner membrane surface area and thus more protonic capacitance for …

Short Tandem Repeats Diversity In Indian And Pakistani Population Living In United Arab Emirates, Ruksar Salim Damji

Biology Theses

Short Tandem Repeats (STRs), have become increasingly popular markers of choice due to its wide array of advantages in the sector of forensic investigation. It is necessary to expand genetic research into residing populations i.e., Indian and Pakistani, in the same geographic region such as in the United Arab Emirates (UAE). The objectives of this study were to: (1) assess the forensic efficiency parameters and population structure analysis of the autosomal STR loci for the most potent amplification kit (2) estimate the allele frequencies; and (3) determine the significance of increasing the number of STR loci used in forensic DNA …

Land Application Of Sewage Sludge: Physiological And Biochemical Response Of The Rio Grande Tomato, Nabil Charchar, Ali Elafri, Redwane Rais, Halassi Ismahen

Journal of Bioresource Management

Treated wastewater produces sewage sludge as a by-product that may have beneficial implications on agricultural practices. The effects of sludge amendments on growth, morphological and biochemical characteristics of the agro-industrial Tomato cultivar Rio Grande were observed. A pot culture experiment was carried out during 4 months (16 February 2019 to 18 June 2019), at an experimental green house in the locality of Salah Soufi, Guelma, north-eastern Algeria. There were significant differences between soil and sewage sludge samples. Total nitrogen (20.58 mg/kg) was more available in sewage sludge than in soil (N = 2.09 ± 0.3 mg/kg). In contrast, sludge …

Pooled Crispr Screens With Imaging On Microraft Arrays Reveals Stress Granule-Regulatory Factors, Emily C Wheeler, Anthony Q Vu, Jaclyn M Einstein, Matthew Disalvo, Noorsher Ahmed, Eric L Van Nostrand, Alexander A Shishkin, Wenhao Jin, Nancy L Allbritton, Gene W Yeo

Faculty, Staff and Students Publications

Genetic screens using pooled CRISPR-based approaches are scalable and inexpensive, but restricted to standard readouts, including survival, proliferation and sortable markers. However, many biologically relevant cell states involve cellular and subcellular changes that are only accessible by microscopic visualization, and are currently impossible to screen with pooled methods. Here we combine pooled CRISPR-Cas9 screening with microraft array technology and high-content imaging to screen image-based phenotypes (CRaft-ID; CRISPR-based microRaft followed by guide RNA identification). By isolating microrafts that contain genetic clones harboring individual guide RNAs (gRNA), we identify RNA-binding proteins (RBPs) that influence the formation of stress granules, the punctate protein-RNA …

Simultaneous Examination Of Cellular Pathways Using Multiplex Hextuple Luciferase Assaying, Alejandro Sarrion-Perdigones, Lyra Chang, Yezabel Gonzalez, Tatiana Gallego-Flores, Damian W Young, Koen J T Venken

Faculty, Staff and Students Publications

Multiplex experimentation that can assay multiple cellular signaling pathways in the same cells requires orthogonal genetically encoded reporters that report over large dynamic ranges. Luciferases are cost-effective, versatile candidates whose output signals can be sensitively detected in a multiplex fashion. Commonly used dual luciferase reporter assays detect one luciferase that is coupled to a single cellular pathway, and a second that is coupled to a control pathway for normalization purposes. We expanded this approach to multiplex hextuple luciferase assaying that can report on five cellular signaling pathways and one control, each of which is encoded by a unique luciferase. Light …

Rapid And Efficient Synthetic Assembly Of Multiplex Luciferase Reporter Plasmids For The Simultaneous Monitoring Of Up To Six Cellular Signaling Pathways, Alejandro Sarrion-Perdigones, Yezabel Gonzalez, Koen J T Venken

Faculty, Staff and Students Publications

High-throughput cell-based screening assays are valuable tools in the discovery of chemical probes and therapeutic agents. Such assays are designed to examine the effects of small compounds on targets, pathways, or phenotypes participating in normal and disease processes. While most cell-based assays measure single quantities, multiplexed assays seek to address these limitations by obtaining multiple simultaneous measurements. The signals from such measurements should be independently detectable and cover large dynamic ranges. Luciferases are good candidates for generation of such signals. They are genetically encoded, versatile, and cost-effective, and their output signals can be sensitively detected. We recently developed a multiplex …

Modeling Single Microtubules As A Colloidal System To Measure The Harmonic Interactions Between Tubulin Dimers In Bovine Brain Derived Versus Cancer Cell Derived Microtubules, Arooj Aslam

Dissertations

The local properties of tubulin dimers dictate the properties of the larger microtubule assembly. In order to elucidate this connection, tubulin-tubulin interactions are be modeled as harmonic interactions to map the stiffness matrix along the length of the microtubule. The strength of the interactions are measured by imaging and tracking the movement of segments along the microtubule over time, and then performing a fourier transform to extract the natural vibrational frequencies. Using this method the first ever reported experimental phonon spectrum of the microtubule is reported. This method can also be applied to other biological materials, and opens new doors …

Analysis And Exploration Of Novel Antibiotic-Producing Streptomyces Spp. In Spokane County, Washington, Kyle S. Kramer, Jenifer B. Walke Ph.D

2020 Symposium Posters

According to the Centers for Disease Control and Prevention, a US citizen is infected by an antibiotic-resistant pathogen every 11 seconds, and every 15 minutes, a patient dies as a result of these infections. Due to the increasing incidence of antibiotic-resistant pathogenic microbes, the study and exploration of novel antibiotics from novel environments are imperative as infectious diseases are the second leading cause of death in the United States. The purpose of this research is to investigate and analyze antibiotic-producing soil microbes in Spokane County, WA, with hopes of discovering novel antibiotic-producing microbes, specifically Streptomyces species, and explore some of …

Strong Temporal Variability In Methane Fluxes From Natural Gas Well Pad Soils, Seth N. Lyman, Huy N. Q. Tran, Marc L. Mansfield, Ric Bowers, Ann Smith

Bingham Research Center

We measured methane and carbon dioxide fluxes at natural gas well pad soils and undisturbed soils in the Rocky Mountain and Gulf Coast regions of the United States, including producing and gas storage wells. We collected both short-term (15 min) and multi-day (between 3 and 8), continuous measurements at 47 well pads and two undisturbed locations. Methane fluxes varied by more than an order of magnitude over periods as short as 30 min (e.g., 19–593 mg m⁻² h⁻¹ in one instance), and diurnal and seasonal variability was also significant (e.g., spring-to-fall change from 509 to 14174 mg m …

Mercury Biogeochemical Cycling: A Synthesis Of Recent Scientific Advances, Mae Sexauer Gustin, Michael S. Bank, Kevin Bishop, Katlin Bowman, Brian Branfireun, John Chételat, Chris S. Eckley, Chad R. Hammerschmidt, Carl Lamborg, Seth Lyman, Antonio Martínez-Cortizas, Jonas Sommar, Martin Tsz-Ki Tsui, Tong Zhang

Bingham Research Center

The focus of this paper is to briefly discuss the major advances in scientific thinking regarding: a) processes governing the fate and transport of mercury in the environment; b) advances in measurement methods; and c) how these advances in knowledge fit in within the context of the Minamata Convention on Mercury. Details regarding the information summarized here can be found in the papers associated with this Virtual Special Issue of STOTEN.

The Role Of Redox Chemistry Of Disulfide Bonds In Cysteine Residues Of Membrane Proteins By Cuprous And Cupric Ions In Cell Death Of E. Coli, Morgan R. Stewart

University Honors Theses

The antimicrobial properties of copper have been thoroughly researched, but is still unclear what the actual mechanism of cell death is. This study explores the theory that copper ions and other copper sources act as an antibiotic for E. coli by cleaving the disulfide bonds of membrane proteins through redox chemistry, disrupting the cell membrane and causing cell death. The focus of this study is Cu(I) and Cu(II) interactions with the thiol containing amino acid, cysteine, and how these interactions may be responsible for copper’s toxicity. Cuprous ions have been found to be more toxic to E.coli than cupric …

A Study On The Regulation Of Mitochondrial Biogenesis And Gluconeogenesis In S. Cerevisiae, Manika Bhondeley

LSU New Orleans Theses and Dissertations

Budding yeast has been used as a powerful model organism to study the network that communicate functions of nucleus, cytoplasm and mitochondria. Depending upon environmental cues, yeast cells regulate their metabolic programming, for example, presence of glucose repress utilization of alternate carbon source to produce energy. This phenomenon is called carbon catabolite repression, which is relieved when glucose is limiting, and alternate carbon source utilization is achieved by an increase in mitochondrial biogenesis (oxidative catabolism) and the upregulation of TCA cycle and gluconeogenesis. Most of genes involved in alternate carbon source utilization are encoded in the nucleus and undergo tight …

Influence Of Adjuvants On Pesticide Soil-Air Partition Coefficients: Laboratory Measurements And Predicted Effects On Volatilization, Supta Das, Kimberly J. Hageman

Chemistry and Biochemistry Faculty Publications

A solid-phase fugacity meter was used to measure the soil–air partition coefficients of three semivolatile pesticides (chlorpyrifos, pyrimethanil, and trifluralin) in the absence of additional adjuvants (K_{soil–air,AI}), as part of commercial formulations (K_{soil–air,formulation}), and as formulation mixtures with an additional spray adjuvant added (K_{soil–air,formulation+spray adjuvant}). Chlorpyrifos K_{soil–air,formulation} values were also measured over 15–30 °C, allowing for the change in internal energy of the phase transfer reaction (Δ_soil–airU) to be calculated and compared to the Δ_soil–airU for K_{soil–air,AI} from the literature. Measured K_soil–air values …

Mutagenesis Of The Btea Gene Encoding A Bordetella Virulence Protein, Xiaolei Mao

2020 Symposium Posters

Bordetella Type III Secretion System Effector A (BteA) is a virulence protein found in members of the genus Bordetella which include important pathogens of humans and other mammals. Bordetella pertussis is a causative agent of the whooping cough, a highly contagious respiratory disease that is especially dangerous, and sometimes deadly, for infants. The BteA protein appears to be an important factor in the ability of these pathogens to cause disease, as it leads to rapid killing of a wide range of mammalian cells. The aim of this project is to determine which regions of the DNA are important for mediating …

N3-Ligated Nickel(Ii) Diketonate Complexes: Synthesis, Characterization And Evaluation Of O2 Reactivity, Josiah G. D. Elsberg, Austin Peterson, Amy L. Fuller, Lisa M. Berreau

Chemistry and Biochemistry Faculty Publications

Interest in O₂-dependent aliphatic carbon–carbon (C–C) bond cleavage reactions of first row divalent metal diketonate complexes stems from the desire to further understand the reaction pathways of enzymes such as DKE1 and to extract information to develop applications in organic synthesis. A recent report of O₂-dependent aliphatic C–C bond cleavage at ambient temperature in Ni(II) diketonate complexes supported by a tridentate nitrogen donor ligand [(MBBP)Ni(PhC(O)CHC(O)Ph)]Cl (7-Cl; MBBP = 2,6-bis(1-methylbenzimidazol-2-yl)pyridine) in the presence of NEt₃ spurred our interest in further examining the chemistry of such complexes. A series of new TERPY-ligated Ni(II) diketonate complexes of the …

Age-Dependent Involvement Of Gut Mast Cells And Histamine In Post-Stroke Inflammation, Maria Pilar Blasco, Anjali Chauhan, Pedram Honarpisheh, Hilda Ahnstedt, John D'Aigle, Arunkumar Ganesan, Sriram Ayyaswamy, Frank Blixt, Susan Venable, Angela Major, David Durgan, Anthony Haag, Julia Kofler, Robert Bryan, Louise D Mccullough, Bhanu Priya Ganesh

Faculty, Staff and Students Publications

BACKGROUND: Risk of stroke-related morbidity and mortality increases significantly with age. Aging is associated with chronic, low-grade inflammation, which is thought to contribute to the poorer outcomes after stroke seen in the elderly. Histamine (HA) is a major molecular mediator of inflammation, and mast cells residing in the gut are a primary source of histamine.

METHODS: Stroke was induced in male C57BL/6 J mice at 3 months (young) and 20 months (aged) of age. Role of histamine after stroke was examined using young (Yg) and aged (Ag) mice; mice underwent MCAO surgery and were euthanized at 6 h, 24 h, …

Modulating Matrix Metalloproteases And Inflammation In Huntington’S Disease, Alejandro Lopez Ramirez

Natural Sciences and Mathematics | Biological Sciences Master's Theses

Huntington’s disease (HD) is a rare and incurable autosomal neurodegenerative disease affecting 1-10 in every 100,000 people in the world. There is no cure for HD and treatments available alleviate certain symptoms for short periods of time. Evidence suggests that neuropathology of HD begins with the proteolysis of the mutated Huntingtin (mHTT) protein. A variety of proteases, like the matrix metalloproteases, cleave mHTT creating proteinaceous fragments that are thought to be neurotoxic. As these fragments increase in the brain, the damage to neurons also increases, leading to chronic inflammation due to hyper reactive microglia and astrocytes attempting to minimize and …

Molecular Docking Study Of Itpa Protein Substrate Complex, Aulane Mpouli

2020 Symposium Posters

Inosine Triphosphatase (ITPA) is an enzymatic molecule that works to prevent the amassed of an intermediate in the formation of purine nucleotides, Inosine Triphosphate (ITP). DNA consists of purine nucleotides, and its metabolic pathway includes the formation of this intermediate. Overpopulation of ITP causes mutations of DNA leading to cancers, increased Inosine levels in DNA and other immunodeficiencies. In order to regulate the ITP concentration, ITPA binds ITP creating a substrate/enzyme complex. In this study, we used computational docking to explore bound conformation and energy of the binding of ITP to ITPA protein. The docking results reveal how ITPA and …

Tfeb Regulates Murine Liver Cell Fate During Development And Regeneration, Nunzia Pastore, Tuong Huynh, Niculin J Herz, Alessia Calcagni', Tiemo J Klisch, Lorenzo Brunetti, Kangho Ho Kim, Marco De Giorgi, Ayrea Hurley, Annamaria Carissimo, Margherita Mutarelli, Niya Aleksieva, Luca D'Orsi, William R Lagor, David D Moore, Carmine Settembre, Milton J Finegold, Stuart J Forbes, Andrea Ballabio

Faculty, Staff and Students Publications

It is well established that pluripotent stem cells in fetal and postnatal liver (LPCs) can differentiate into both hepatocytes and cholangiocytes. However, the signaling pathways implicated in the differentiation of LPCs are still incompletely understood. Transcription Factor EB (TFEB), a master regulator of lysosomal biogenesis and autophagy, is known to be involved in osteoblast and myeloid differentiation, but its role in lineage commitment in the liver has not been investigated. Here we show that during development and upon regeneration TFEB drives the differentiation status of murine LPCs into the progenitor/cholangiocyte lineage while inhibiting hepatocyte differentiation. Genetic interaction studies show that …