Biochemistry Commons^™

Liquid And Semisolid Lubricant Compositions , Methods Of Making , And Uses Thereof, Diana Berman, Kent Dean Chapman, Tervor Bradley Romsdahl, Edgar Benjamin Cahoon, Robert Earl Minto, Chunyu Zhang

Department of Biochemistry: Faculty Publications

Various liquid and semisolid lubricant compositions are provided, in particular lubricant compositions containing oil from the seeds of the Brassicaceae Orychophragmus violaceus, preferably those that have been esterified with one or more fatty acids such as palmitoleic acid, oleic acid, linoleic acid, lauric acid, palmitic acid, stearic acid, or a combination thereof. In various aspects, lubricant compositions are provided that include a petroleum or a synthetic base oil and about 40 % or less by weight of a liquid lubricant composition containing oil from the seeds of the Brassicaceae Orychophragmus violaceus preferably those that have been esterified with one …

Shift In Conformational Equilibrium Underlies The Oscillatory Phosphoryl Transfer Reaction In The Circadian Clock, Pyonghwa Kim, Neha Thati, Shreya Peshori, Hye-In Jang, Yongick Kim

Chemistry Faculty Research

Oscillatory phosphorylation/dephosphorylation can be commonly found in a biological system as a means of signal transduction though its pivotal presence in the workings of circadian clocks has drawn significant interest: for example in a significant portion of the physiology of Synechococcus elongatus PCC 7942. The biological oscillatory reaction in the cyanobacterial circadian clock can be visualized through its reconstitution in a test tube by mixing three proteins—KaiA, KaiB and KaiC—with adenosine triphosphate and magnesium ions. Surprisingly, the oscillatory phosphorylation/dephosphorylation of the hexameric KaiC takes place spontaneously and almost indefinitely in a test tube as long as ATP is present. This …

A Conserved Structural Role For The Walker-A Lysine In P-Loop Containing Kinases, Fatlum Hajredini, Ranajeet Ghose

Publications and Research

Bacterial tyrosine kinases (BY-kinases) and shikimate kinases (SKs) comprise two structurally divergent P-loop containing enzyme families that share similar catalytic site geometries, most notably with respect to their Walker-A, Walker-B, and DxD motifs. We had previously demonstrated that in BY-kinases, a specific interaction between the Walker-A and Walker-B motifs, driven by the conserved “catalytic” lysine housed on the former, leads to a conformation that is unable to efficiently coordinate Mg²⁺•ATP and is therefore incapable of chemistry. Here, using enhanced sampling molecular dynamics simulations, we demonstrate that structurally similar interactions between the Walker-A and Walker-B motifs, also mediated by …

Effects Of Exogenous Application Of Plant Growth Regulators (Snp And Ga3) On Phytoextraction By Switchgrass (Panicum Virgatum L.) Grown In Lead (Pb) Contaminated Soil, Adrianne Beavers, Marina Koether, Thomas C. Mcelroy, Sigurdur Greipsson

Faculty Articles

Soil lead (Pb) contamination is a major environmental and public health risk. Switch-grass (Panicum virgatum), a second-generation biofuel crop, is potentially useful for the long-term phytoremediation and phytoextraction of Pb contaminated soils. We evaluated the efficacy of a coor-dinated foliar application of plant growth regulators and soil fungicide and a chelator in order to optimize phytoextraction. Plants were grown in soil culture under controlled conditions. First, three exogenous nitric oxide (NO) donors were evaluated at multiple concentrations: (1) S-nitroso-N-acetylpenicillamine (SNAP); (2) sodium nitroprusside (SNP); and (3) S-nitrosoglutathione (GSNO). Second, the effect of SNP (0.5 µM) was examined further with the …

Analysis Of Single-Site Cysteine Mutation, I412c, In Human A Glycine Receptor States To Further Refine Structure And Allostery, Leah Engquist

Honors Program: Senior Projects (Public)

The glycine receptor (GlyR) is the major inhibitory receptor in the brain and spinal cord. A member of the pentameric ligand gated ion channel superfamily, crystal structures are available but there are still unresolved areas, specifically the C-terminal tail and TM3-TM4 intracellular loop. Further refinement can provide deeper understanding of the molecular mechanism and allow the creation of novel therapeutics to modulate its function. We propose to insert a single cysteine mutation, I412C, into a Cys null background (C41S/C290A/C345S) to study non- conducting states (resting, desensitized) or with F207G/A288G mutations to study the open state. Purified, reconstituted GlyR is crosslinked …

Mitochondrial Contact Site And Cristae Organizing System (Micos) Machinery Supports Heme Biosynthesis By Enabling Optimal Performance Of Ferrochelatase, Jonathan V. Dietz, Mathilda M. Willoughby, Robert B. Piel, Teresa A. Ross, Iryna Bohovych, Hannah G. Addis, Jennifer L. Fox, William N. Lanzilotta, Harry A. Dailey, James A. Wohlschlegel, Amit R. Reddi, Amy E. Medlock, Oleh Khalimonchuk

Department of Biochemistry: Faculty Publications

Heme is an essential cofactor required for a plethora of cellular processes in eukaryotes. In metazoans the heme biosynthetic pathway is typically partitioned between the cytosol and mitochondria, with the first and final steps taking place in the mitochondrion. The pathway has been extensively studied and its biosynthetic enzymes structurally characterized to varying extents. Nevertheless, understanding of the regulation of heme synthesis and factors that influence this process in metazoans remains incomplete. Therefore, we investigated the molecular organization as well as the physical and genetic interactions of the terminal pathway enzyme, ferrochelatase (Hem15), in the yeast Saccharomyces cerevisiae. Biochemical and …

Converging Technologies: Targeting The Hallmarks Of Cancer Using Ultrasound And Microbubbles, Janith Wanigasekara, Andressa Maria Aguiar De Carvalho, Patrick J. Cullen, Brijesh Tiwari, James F. Curtin

Articles

Various complex biological effects occur when ultrasonic compression waves travel through biological material. The myriad of biological outcomes instigated by ultrasound are evident when viewed through the lens of the hallmarks of cancer. Herein, we summarise the therapeutic potential of ultrasound, enhanced by microbubbles, for the treatment of cancer.

Fusion And Beyond: Satellite Cell Contributions To Loading-Induced Skeletal Muscle Adaptation, Kevin A. Murach, Christopher S. Fry, Esther E. Dupont-Versteegden, John J. Mccarthy, Charlotte A. Peterson

Health, Human Performance and Recreation Faculty Publications and Presentations

Satellite cells support adult skeletal muscle fiber adaptations to loading in numerous ways. The fusion of satellite cells, driven by cell-autonomous and/or extrinsic factors, contributes new myonuclei to muscle fibers, associates with load-induced hypertrophy, and may support focal membrane damage repair and long-term myonuclear transcriptional output. Recent studies have also revealed that satellite cells communicate within their niche to mediate muscle remodeling in response to resistance exercise, regulating the activity of numerous cell types through various mechanisms such as secretory signaling and cell-cell contact. Muscular adaptation to resistance and endurance activity can be initiated and sustained for a period of …

Hiv-1 Transcription Elongation By Tat-Mediated Recruitment Of P-Tefb, Elizabeth Griggs

Honors Program: Senior Projects (Public)

Over 38.0 million people live with the human immunodeficiency virus (HIV) as of 462019. HIV hijacks the host's cellular machinery to replicate its viral DNA and transcribe the corresponding RNA. HIV-1 transcription relies on both cellular and viral transcription factors for proper regulation. The viral transcriptional activator Tat is a primary regulator. Transcription activation and elongation is controlled through the interaction of Tat with Positive Transcription Elongation Factor b (P-TEFb), a cellular transcriptional activator. The focus of this paper is 1) an in-depth understanding of the interaction between P-TEFb and Tat in HIV transcription, and 2) a review of recent …

Covid-19 In Silico Drug With Zingiber Officinale Natural Product Compound Library Targeting The Mpro Protein, Renadya Maulani Wijaya, Muhammad Aldino Hafidzhah, Viol Dhea Kharisma, Arif Nur Muhammad Ansori, Arli Aditya Parikesit

Makara Journal of Science

Coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a worldwide pandemic. Ginger (Zingiber officinale) is a rhizome, which is commonly used for culinary and medicinal purposes. In Indonesia, ginger is taken as traditional medicine by processing it into a drink known as jamu. The present study aimed to assess and evaluate the bioactive compounds in ginger that can be used in drug design for treating COVID-19. The crystal structure of the SARS-CoV-2 main protease (M^pro) was generated from a protein sequence database, i.e., Protein Data Bank, …

Fe-Catalyzed Sulfide Oxidation In Hydrothermal Plumes Is A Source Of Reactive Oxygen Species To The Ocean, Timothy J. Shaw, George W. Luther Iii, Richard Rosas, Véronique E. Oldham, Nicole R. Coffey, John L. Ferry, Dewamunnage M. C. Dias, Mustafa Yücel, Aubin Thibault De Chanvalon

Faculty Publications

Historically, the production of reactive oxygen species (ROS) in the ocean has been attributed to photochemical and biochemical reactions. However, hydrothermal vents emit globally significant inventories of reduced Fe and S species that should react rapidly with oxygen in bottom water and serve as a heretofore unmeasured source of ROS. Here, we show that the Fe-catalyzed oxidation of reduced sulfur species in hydrothermal vent plumes in the deep oceans supported the abiotic formation of ROS at concentrations 20 to 100 times higher than the average for photoproduced ROS in surface waters. ROS (measured as hydrogen peroxide) were determined in hydrothermal …

Oxidation Alters The Architecture Of The Phenylalanyl-Trna Synthetase Editing Domain To Confer Hyperaccuracy, Pooja Srinivas, Rebecca E. Steiner, Ian J. Pavelich, Ricardo Guerrera-Ferreira, Puneet Juneja, Michael Ibba, Christine M. Dunham

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

High fidelity during protein synthesis is accomplished by aminoacyl-tRNA synthetases (aaRSs). These enzymes ligate an amino acid to a cognate tRNA and have proofreading and editing capabilities that ensure high fidelity. Phenylalanyl-tRNA synthetase (PheRS) preferentially ligates a phenylalanine to a tRNA^Phe over the chemically similar tyrosine, which differs from phenylalanine by a single hydroxyl group. In bacteria that undergo exposure to oxidative stress such as Salmonella enterica serovar Typhimurium, tyrosine isomer levels increase due to phenylalanine oxidation. Several residues are oxidized in PheRS and contribute to hyperactive editing, including against mischarged Tyr-tRNA^Phe, despite these oxidized residues not …

Small Studies, Big Decisions: The Role Of Pilot/Feasibility Studies In Incremental Science And Premature Scale-Up Of Behavioral Interventions, Michael William Beets, Lauren Von Klinggraeff, Robert G. Weaver, Bridget Ryan Armstrong, Sarah Burkart

Faculty Publications

Background: Careful consideration and planning are required to establish “sufficient” evidence to ensure an investment in a larger, more well-powered behavioral intervention trial is worthwhile. In the behavioral sciences, this process typically occurs where smaller-scale studies inform larger-scale trials. Believing that one can do the same things and expect the same outcomes in a larger-scale trial that were done in a smaller-scale preliminary study (i.e., pilot/feasibility) is wishful thinking, yet common practice. Starting small makes sense, but small studies come with big decisions that can influence the usefulness of the evidence designed to inform decisions about moving forward with a …

Targeting The Cdk6 Dependence Of Ph+ Acute Lymphoblastic Leukemia, Patrizia Porazzi, Marco De Dominici, Joseph Salvino, Bruno Calabretta

Department of Cancer Biology Faculty Papers

Ph+ ALL is a poor-prognosis leukemia subtype driven by the BCR-ABL1 oncogene, either the p190-or the p210-BCR/ABL isoform in a 70:30 ratio. Tyrosine Kinase inhibitors (TKIs) are the drugs of choice in the therapy of Ph+ ALL. In combination with standard chemotherapy, TKIs have markedly improved the outcome of Ph+ ALL, in particular if this treatment is followed by bone marrow transplantation. However, resistance to TKIs develops with high frequency, causing leukemia relapse that results in

Effects Of Copper Oxide (Cuo) And Zinc Oxide (Zno) Nano And Bulk Forms To Soil Fungal Community [Research Note], Jonathan Jaime Guerrero, Teresita Dalisay, Nolissa Organo, Ireneo Pangga

The Philippine Agricultural Scientist

The effects of copper oxide (CuO) and zinc oxide (ZnO) in bulk and nano forms on soil fungal community was determined. Lipa clay loam soil collected from the University of the Philippines Los Baños were placed in polypropylene bags and amended with 300 mg/L of CuO or ZnO in either forms. Colony-forming units (CFU) as well as average well color development (AWCD), functional richness and stress index were determined on day 1, 8 and 15 via indirect viable plate count method and community – level physiological profiling (CLPP). Fungal isolates from the same soil samples were likewise identified and tested …

Machine Learning And Solvation Theory For Drug Discovery, Lieyang Chen

Dissertations, Theses, and Capstone Projects

Drug discovery is a notoriously expensive and time-consuming process; hence, developing computational methods to facilitate the discovery process and lower the associated costs is a long-sought goal of computational chemists. Protein-ligand binding, which provides the physical and chemical basis for the mechanism of action of most drugs, occurs in an aqueous environment, and binding affinity is determined not only by atomic interactions between the protein and ligand but also by changes in their interactions with surrounding water molecules that occur upon binding. Thus, a quantitative understanding of the roles water molecules play in the protein-ligand binding process is an essential …

The Structural And Functional Role Of Photosensing In Rgs-Lov Proteins, Zaynab Jaber

Dissertations, Theses, and Capstone Projects

Light provides organisms with energy and spatiotemporal information. To survive and adapt, organisms have developed the ability to sense light to drive biochemical effects that underlie vision, entrainment of circadian rhythm, stress response, virulence, and many other important molecularly driven responses. Blue-light sensing Light-Oxygen-Voltage (LOV) domains are ubiquitous across multiple kingdoms of life and modulate various physiological events via diverse effector domains. Using a small molecule flavin chromophore, the LOV domain undergoes light-dependent structural changes leading to activation or repression of these catalytic and non-catalytic effectors. In silico analyses of high-throughput genomic sequencing data has led to the marked expansion …

The Role Of Estrogen Receptor Alpha In Regulating Messenger Rna 3’ End Processing And Controlling Gene Expression In Breast Cancer Cells, Sophia Varriano

Dissertations, Theses, and Capstone Projects

Estrogen signaling regulates various physiological processes within the female reproductive, cardiovascular, immune, and central nervous systems and is predominantly mediated by estrogen receptors (ER), ERα and ERβ. Transcriptional regulation by ERs has been widely studied, where activated ERs bind either directly to target genes through binding to estrogen response elements or indirectly through interacting with other proteins, resulting in changes in gene expression. However, the potential role of factors involved in the estrogen signaling pathway in posttranscriptional regulation has not been extensively documented. As 70-80% of breast cancers (BCs) are identified as ER(+), studying how these factors, particularly ERα, regulates …

Dual Control Of One Component Signaling: Mechanistic And Structural Insights Into El222 Active States, Uthama Phani R. Edupuganti

Dissertations, Theses, and Capstone Projects

Photoreceptors play a crucial role in signal transduction as specialized proteins which sense light as environmental stimuli and transduce the signal to control of downstream functions. Here we focus our attention on one class of these proteins, the Light-Oxygen-Voltage (LOV) domain, which is sensitive to blue light via an internally-bound flavin chromophore. Since their initial discovery in plant phototropins, many details of their photochemistry, chromophore interactions, and use with a diverse set of functional effectors have been described. However, several key details, especially a comprehensive understanding of signaling mechanism and its regulation, still remain elusive due in part to the …

Development Of High-Throughput Methods For Screening Venom Peptides, Tanya Napolitano

Dissertations, Theses, and Capstone Projects

Bioactive venom peptides are increasingly being explored as drug leads in pharmaceutical research because of their immense therapeutic potential, however there is a need to more efficiently screen and characterize these peptides to discover medicinal leads more quickly.1,2 The Holford lab has leveraged recent technological achievements in genomics, transcriptomics, and proteomics to produce a leap in the discovery of venom peptides from previously hard to characterize small and neglected venomous animals such as Terebridae, an understudied lineage of the Conoidea Superfamily.4, 5–7 With the rise of -omic technologies the floodgates have opened and venom researchers are awash with large datasets …

Three Lc-Ms Plant Metabolomics Studies Of Hop (Humulus) Species: Wild H. Neomexicanus, Drought Stress, And Agricultural Terroir, Taylan Morcol

Dissertations, Theses, and Capstone Projects

The hop plant (Humulus L., Cannabaceae) is a dioecious, perennial, twining vine with a long history of human use. Nowadays, hop plants are generally grown for their inflorescences (“cones”), which are used in brewing for their phytochemical metabolites. Many of these metabolites are involved in plant stress response and communication. Genetics and environment are two major factors that affect plant metabolism. In three separate metabolomics studies, this project examined the effects of both genetic and environmental factors on hop phytochemistry.

In the first study, 23 hop genotypes were grown in two different locations in the Pacific Northwest region of …

Molecular Dynamics Simulations Of Self-Assemblies In Nature And Nanotechnology, Phu Khanh Tang

Dissertations, Theses, and Capstone Projects

Nature usually divides complex systems into smaller building blocks specializing in a few tasks since one entity cannot achieve everything. Therefore, self-assembly is a robust tool exploited by Nature to build hierarchical systems that accomplish unique functions. The cell membrane distinguishes itself as an example of Nature’s self-assembly, defining and protecting the cell. By mimicking Nature’s designs using synthetically designed self-assemblies, researchers with advanced nanotechnological comprehension can manipulate these synthetic self-assemblies to improve many aspects of modern medicine and materials science. Understanding the competing underlying molecular interactions in self-assembly is always of interest to the academic scientific community and industry. …

Tools And Strategies For The Patterning Of Bioactive Molecules And Macromolecules, Daniel J. Valles

Dissertations, Theses, and Capstone Projects

Hypersurface Photolithography (HP) is a printing method for fabricating structures and patterns composed of soft materials bound to solid surfaces and with ~1 micrometer resolution in the x, y, and z dimensions. This platform leverages benign, low intensity light to perform photochemical surface reactions with spatial and temporal control of irradiation, and, as a result, is particularly useful for patterning delicate organic and biological material. In particular, surface- initiated controlled radical polymerizations can be leveraged to create arbitrary polymer and block- copolymer brush patterns. Chapter 1 will review the advances in instrumentation architectures from our group that have made these …

Oxydifficidin-Producing Bacillus Presents Novel Antimicrobial Activity Against Neisseria Gonorrhoeae Involving The Deda Protein, Jingbo Kan

Dissertations, Theses, and Capstone Projects

Bacterial human pathogens cause severe infectious diseases which are the second most common cause of death next to cancer and cardiovascular diseases in the world, especially in developing countries. Gonorrhea particularly, is the second most common sexually transmitted infection (STI) which is caused by the microorganism Neisseria gonorrhoeae (GC). Centers for Disease Control and Prevention (CDC) estimates that more than 1.6 million new gonorrhea cases emerged in USA in 2018 (“Detailed STD Facts - Gonorrhea” n.d.). Also, the WHO (World Health Organization) shows that gonorrhea is the most antibiotic resistant STI (“PAHO/WHO | Gonorrhea” n.d.), highlighting the shortage of efficient …

Don't Sell Them Short, There's More To Bacterial Natural Products Than Antibiotics, Alison Clare Domzalski

Dissertations, Theses, and Capstone Projects

Recent genomic studies of microbiomes have revealed an overwhelming number of biosynthetic genes of unknown function. Most of these “cryptic” biosynthetic genes are not expressed in laboratory monocultures of individual microbes. Thus, there remains tremendous untapped potential for natural products discovery. Here we employ mixed microbial culture (MMC) as a simple yet powerful approach to awaken cryptic biosynthetic gene clusters. Our preliminary studies demonstrated that arrays of metabolites could be induced in MMCs upon environmental cues, such as surface adhesion. Using this system, we have screened, identified, and isolated bioactive bacterial metabolites, which were characterized structurally and biologically. Of the …

Conserved Regions Mediate Interactions Between Canonical Nox Domains, Akua Acheampong

Symposium of Student Scholars

NAPDH oxidase (NOXes) are membrane-bound enzymes that generate reactive oxygen species (ROS) that play a role in immune response and signaling. Misregulation of NOXes is implicated in various human pathologies. NOXes contain a catalytic core comprised of a heme-containing transmembrane (TM) domain and a cytoplasmic dehydrogenase (DH) domain that binds FAD and NADPH. Several conserved regions at the interface of the TM and DH domains in eukaryotic NOXes have been suggested to mediate enzyme function and activity. In 2017, researchers successfully purified SpNox, a bona fide NOX homolog from Streptococcus pneumoniae and verified its NOX properties. SpNox’s robust activity in …

Nutritional Composition, Sensory Profile And Consumer Acceptability Of Wheat-Jackfruit Seed Composite Buns, Sarah S Ngwere, Richard J Mongi

Tanzania Journal of Science

Jackfruit seeds flour is very rich in nutrients and may be incorporated into wheat flour to develop nutrient dense baked products. Consumption of these products may improve the nutrition status of the people, hence fulfill sustainable development goal number two. In this study, nutritional composition, sensory profile, and consumer acceptability of wheat-jackfruit seeds composite buns (Mandazi) were investigated. Jackfruit seeds flour (JSF) was developed and incorporated into wheat flour (WF) at 10, 20, and 30% to produce composite flour used for bun preparation. Flours and buns were subjected to proximate, mineral, and sensory analyses with WF serving as a control …

Effects Of Osmotic Stress Induced By Polyethylene Glycol (Peg) 6000 And Mannitol On Seed Germination And Seedling Growth Of Durum Wheat, Ratiba Bousba, Rabah Bounar, Narimene Sedrati, Randa Lakhal, Chourouk Hamla, Malika Rached-Kanouni

Journal of Bioresource Management

Seed germination is generally the critical step in seed establishment and thus the determination of successful crop production. This study was focused at examination of the biochemical and germination parameters effected by low water potential which was generated by polyethylene glycol (PEG) 6000 and mannitol, related to drought stress and growth of Waha durum wheat genotype. Two tests were carried out in a growth chamber; the first comprises seed germination into Petri dishes in the presence of different concentrations of the two osmoticums (0, 5, 10, 15 and 20 % of PEG6000 and mannitol). The second test was carried out …

Insights Into Halophilic Microbial Adaptation: Analysis Of Integrons And Associated Genomic Structures And Characterization Of A Nitrilase In Hypersaline Environments, Sarah Sonbol

Theses and Dissertations

Hypersaline environments are extreme habitats that can be exploited as biotechnological resources. Here, we characterized a nitrilase (NitraS-ATII) isolated from Atlantis II Deep brine pool. It showed higher thermal stability and heavy metal tolerance compared to a closely related nitrilase.

We also studied integrons in halophiles and hypersaline environments. Integrons are genetic platforms in which an integron integrase (IntI) mediates the excision and integration of gene cassettes at specific recombination sites. In order to search for integrons in halophiles and hypersaline metagenomes, we used a PCR-based approach, in addition to different bioinformatics tools, mainly IntegronFinder.

We found that integrons and …

Down The Iron Path: Mitochondrial Iron Homeostasis And Beyond, Jonathan Dietz, Jennifer L. Fox, Oleh Khalimonchuk

Department of Biochemistry: Faculty Publications

Cellular iron homeostasis and mitochondrial iron homeostasis are interdependent. Mitochondria must import iron to form iron–sulfur clusters and heme, and to incorporate these cofactors along with iron ions into mitochondrial proteins that support essential functions, including cellular respiration. In turn, mitochondria supply the cell with heme and enable the biogenesis of cytosolic and nuclear proteins containing iron–sulfur clusters. Impairment in cellular or mitochondrial iron homeostasis is deleterious and can result in numerous human diseases. Due to its reactivity, iron is stored and trafficked through the body, intracellularly, and within mitochondria via carefully orchestrated processes. Here, we focus on describing the …