Biochemistry Commons^™

Metalloproteases Of The Inner Mitochondrial Membrane, Roman M. Levytskyy, Iryna Bohovych, Oleh Khalimonchuk

Department of Biochemistry: Faculty Publications

The inner mitochondrial membrane (IM) is among most protein-rich cellular compartments. The metastable IM sub-proteome where the concentration of proteins is approaching oversaturation creates a challenging protein folding environment with high probability for protein malfunction or aggregation. Failure to maintain protein homeostasis in such a setting can impair functional integrity of the mitochondria and drive clinical manifestations. The IM is equipped with a series of highly conserved, proteolytic complexes dedicated to the maintenance of normal protein homeostasis within this mitochondrial sub-compartment. Particularly important is a group of membrane-anchored metallopeptidases commonly known as m-AAA and i-AAA proteases, and the ATP-independent Oma1 …

The Role Of Interactions Of Long Non-Coding Rnas And Heterogeneous Nuclear Ribonucleoproteins In Regulating Cellular Functions, Xinghui Sun, Mohamed Sham Shihabudeen Haider Ali, Matthew Moran

Department of Biochemistry: Faculty Publications

Long non-coding RNAs (lncRNAs) are emerging as critical regulators of various biological processes and human diseases. The mechanisms of action involve their interactions with proteins, RNA and genomic DNA. Most lncRNAs display strong nuclear localization. Heterogeneous nuclear ribonucleoproteins (hnRNPs) are a large family of RNA-binding proteins that are important for multiple aspects of nucleic acid metabolism. hnRNPs are also predominantly expressed in the nucleus. This review discusses the interactions of lncRNAs and hnRNPs in regulating gene expression at transcriptional and post-transcriptional levels or by changing genomic structure, highlighting their involvements in glucose and lipid metabolism, immune response, DNA damage response, …

Accurate Cytogenetic Biodosimetry Through Automated Dicentric Chromosome Curation And Metaphase Cell Selection, Jin Liu, Yanxin Li, Ruth Wilkins, Canadian Nuclear Laboratories, Joan H. Knoll, Peter Rogan

Biochemistry Publications

Accurate digital image analysis of abnormal microscopic structures relies on high quality images and on minimizing the rates of false positive (FP) and negative objects in images. Cytogenetic biodosimetry detects dicentric chromosomes (DCs) that arise from exposure to ionizing radiation, and determines radiation dose received based on DC frequency. Improvements in automated DC recognition increase the accuracy of dose estimates by reclassifying FP DCs as monocentric chromosomes or chromosome fragments. We also present image segmentation methods to rank high quality digital metaphase images and eliminate suboptimal metaphase cells. A set of chromosome morphology segmentation methods selectively filtered out FP DCs …

Carbonyl Reduction By Ymfi Completes The Modification Of Ef-P In Bacillus Subtilis To Prevent Accumulation Of An Inhibitory Modification State, Katherine R. Hummels, Anne Witzky, Andrei Rajkovic, Rodney Tollerson Ii, Lisa A. Jones, Michael Ibba, Daniel B. Kearns

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Translation elongation factor P (EF‐P) in Bacillus subtilis is required for a form of surface migration called swarming motility. Furthermore, B. subtilis EF‐P is post‐translationally modified with a 5‐aminopentanol group but the pathway necessary for the synthesis and ligation of the modification is unknown. Here we determine that the protein YmfI catalyzes the reduction of EF‐P‐5 aminopentanone to EF‐P‐5 aminopentanol. In the absence of YmfI, accumulation of 5‐aminopentanonated EF‐P is inhibitory to swarming motility. Suppressor mutations that enhanced swarming in the absence of YmfI were found at two positions on EF‐P, including one that changed the conserved modification site (Lys …

Characterization Of Reagent Pencils For Deposition Of Reagents Onto Paper-Based Microfluidic Devices, Cheyenne H. Liu, Isabelle C. Noxon, Leah E. Cuellar, Amanda L. Thraen, Chad Immoos, Andres W. Martinez, Philip J. Costanzo

Chemistry and Biochemistry

Reagent pencils allow for solvent-free deposition of reagents onto paper-based microfluidic devices. The pencils are portable, easy to use, extend the shelf-life of reagents, and offer a platform for customizing diagnostic devices at the point of care. In this work, reagent pencils were characterized by measuring the wear resistance of pencil cores made from polyethylene glycols (PEGs) with different molecular weights and incorporating various concentrations of three different reagents using a standard pin abrasion test, as well as by measuring the efficiency of reagent delivery from the pencils to the test zones of paper-based microfluidic devices using absorption spectroscopy and …

Plant Performance In Curb Cut Rain Gardens, Max Deyoung, Gregory Manni, David P. Warners

Student Papers and Reports

No abstract provided.

Determination Of Amino Acids Involved In Specificity And Activity Of Chladub2, Trent S. Arbough, John M. Hausman, Chittaranjan Das

The Summer Undergraduate Research Fellowship (SURF) Symposium

Chlamydia trachomatis is a pathogen which infects humans as a sexually transmitted disease or through ocular infection, causing ocular trachoma. Ocular trachoma is the leading cause of non-congenital blindness in developing countries. The bacteria employs the deubiquitinating enzyme ChlaDUB2 to remove ubiquitin from its inclusion membrane in order to avoid lysosomal degradation. Key amino acids involved in ubiquitin recognition and cleavage were mutated in order to probe substrate specificity and catalytic activity of ChlaDUB2. Mutants were used in fluorometry assays in order to determine how the mutations affect the ability of ChlaDUB2 to release the amino methyl coumarin (AMC) group …

Determining The Role Of Epigenetic Factors In Antifungal Drug Resistance, Abigail R. Gress, Scott D. Briggs, Nina Serratore

The Summer Undergraduate Research Fellowship (SURF) Symposium

Epigenetic factors are proteins that regulate gene expression by altering transcriptional machinery access to nucleosomes, DNA wrapped around histone proteins. Two classes of epigenetic factors are ATP-dependent chromatin remodelers and histone modifiers such as histone methyltransferases (HMTs), proteins that add methyl groups to histone tails. This study focuses on AIF4 (Antifungal-Induced Factor 4), a possible HMT induced upon neutral lipid depletion that we hypothesize is regulating antifungal drug resistance genes. Overexpression of AIF4 results in hypersensitivity to antifungal drugs. Studying epigenetic factors in the yeast Saccharomyces cerevisiae, including AIF4, can lead to better understanding of cell adaptation to their environments …

Tumor Formation In Response To Loss Of Chromatin Remodeler Chd5 In Zebrafish, Taylor R. Sabato, Erin L. Sorlien, Dr. Joseph P. Ogas

The Summer Undergraduate Research Fellowship (SURF) Symposium

Chromodomain helicase DNA binding protein 5 (CHD5) has been identified as a tumor suppressor in humans. Deletion or mutation of CHD5 has been observed in numerous cancers, including neuroblastoma and melanoma. We hypothesize that chd5 is also a tumor suppressor in zebrafish, a powerful model system to study tumorigenesis. Many genes involved in tumorigenesis are conserved in zebrafish, and they develop fully penetrant tumor phenotypes. We have created chd5 knock-out zebrafish using CRISPR/Cas9 and are monitoring them for tumor development. In addition to the chd5 knock-outs, we are undertaking a double-mutant approach by coupling loss …

Performing A Genetic Screen To Identify Factors That Promote Lncrna-Dependent Gene Repression, Chrishan Fernando, Cecilia Yiu, Sara Cloutier, Siwen Wang, Elizabeth Tran

The Summer Undergraduate Research Fellowship (SURF) Symposium

Long non-coding RNAs (lncRNAs) were once thought not to have useful functions in organisms but rather to be products of aberrant transcription. However, roles are being found for lncRNAs in beneficial processes such as controlling gene expression. In some of these cases, lncRNAs form R-loops in vivo. R-loops are nucleic acid structures consisting of hybridized strands of single-stranded DNA (ssDNA) and single-stranded RNA (ssRNA) as well as the displaced strand of ssDNA. Formation of these R-loops is important for gene regulation by the lncRNAs. However, factors that promote formation of lncRNA R-loops are not known. The gene PHO84 is being …

Another Route For Amino Acid Production?: Reverse Genetic Probing For A Functional Cytosolic Shikimate Pathway In Plants, Gabrielle C. Buck, Joseph Lynch, Natalia Dudareva

The Summer Undergraduate Research Fellowship (SURF) Symposium

The shikimate pathway is a metabolic pathway that produces the three aromatic amino acids—phenylalanine, tryptophan, and tyrosine—which are essential to human diets and necessary for many plant functions. Consequently, the shikimate pathway is commonly targeted for antibiotic and herbicide strategies as well as genetic engineering in several fields. This pathway is known to be localized in the plastids, or double membrane-bound organelles, of plant cells; however, there is enzymatic evidence of another shikimate pathway in the cell fluid, or cytosol. To determine whether a complete cytosolic shikimate pathway exists, we used a modified gene for the first enzyme of the …

Fret Biosensors: Engineering Fluorescent Proteins As Biological Tools For Studying Parkinson’S Disease, Nathan J. Leroy, Jacob R. Norley, Saranya Radhakrishnan, Mathew Tantama

The Summer Undergraduate Research Fellowship (SURF) Symposium

Parkinson’s Disease (PD) is a common neurodegenerative disease with over 200,000 new cases each year. In general, the cause of the disease is unknown, but oxidative stress inside of neurons has been associated with the disease’s pathology for some time. Currently, techniques to study the onset of PD inside of neurons are limited. This makes treatments and causes difficult to discover. One solution to this has been fluorescent protein biosensors. In short, these proteins can be engineered to glow when a certain state is achieved inside a cell. The present research discusses the engineering of a genetically-encoded fluorescent protein (FP) …

Fluorescent Protein Biosensor For Use In Parkinson's Research, Piper R. Miller, Keelan Trull, Mathew Tantama

The Summer Undergraduate Research Fellowship (SURF) Symposium

Purinergic signaling is a type of extracellular communication that occurs between cells, mediated by adenosine triphosphate (ATP), adenosine diphosphate (ADP), and adenosine. In Parkinson’s Disease, purinergic signaling is disrupted, which contributes to neurodegeneration. In order to monitor this change in cell-to-cell signaling, there is a need for the development of a fluorescent protein (FP) biosensor to study the changes in the concentration of the signaling molecule ATP and its decomposition bioproduct ADP. This summer a genetically encoded ADP sensor that measures changes in ADP concentration was developed. This sensor utilizes Forster Resonance Energy Transfer (FRET) which is a sensing technique …

Unraveling The Interactions Of The Physiological Reductant Flavodoxin With The Different Conformations Of The Fe Protein In The Nitrogenase Cycle, Natasha Pence, Monika Tokmina-Lukaszewska, Zhi-Yong Yang, Rhesa N. Ledbetter, Lance C. Seefeldt, Brian Bothner, John W. Peters

Chemistry and Biochemistry Faculty Publications

Nitrogenase reduces dinitrogen (N2) to ammonia in biological nitrogen fixation. The nitrogenase Fe protein cycle involves a transient association between the reduced, MgATP-bound Fe protein and the MoFe protein and includes electron transfer, ATP hydrolysis, release of Pi, and dissociation of the oxidized, MgADP-bound Fe protein from the MoFe protein. The cycle is completed by reduction of oxidized Fe protein and nucleotide exchange. Recently, a kinetic study of the nitrogenase Fe protein cycle involving the physiological reductant flavodoxin reported a major revision of the rate-limiting step from MoFe protein and Fe protein dissociation to release of Pi. Because the Fe …

A Bipyridine-Ligated Zinc(Ii) Complex With Bridging Flavonolate Ligation: Synthesis, Characterization, And Visible-Light-Induced Co Release Reactivity, Shayne Sorenson, Marina Popova, Atta M. Arif, Lisa M. Berreau

Chemistry and Biochemistry Faculty Publications

Metal-flavonolate compounds are of significant current interest as synthetic models for quercetinase enzymes and as bioactive compounds of importance to human health. Zinc-3-hydroxyflavonolate compounds, including those of quercetin, kampferol, and morin, generally exhibit bidentate coordination to a single ZnII center. The bipyridine-ligated zinc-flavonolate compound reported herein, namely bis(μ-4-oxo-2-phenyl-4H-chromen-3-olato)-κ3O3:O3,O4;κ3O3,O4:O3-bis[(2,2′-bipyridine-κ2N,N′)zinc(II)] bis(perchlorate), {[Zn2(C15H9O3)2(C10H8N2)2](ClO4)2}n, (1), provides an unusual example of bridging 3-hydroxyflavonolate ligation in a dinuclear metal complex. The symmetry-related ZnII centers of (1) exhibit a distorted octahedral geometry, with weak coordination of a perchlorate anion trans to the bridging deprotonated O atom of the flavonolate ligand. Variable-concentration conductivity measurements provide evidence that, when …

Stormwater Capture Via Green Infrastructure In The Plaster Creek Watershed, Skyler Fish, Ben Johnson, Deanna Geelhoed, David P. Warners

Student Papers and Reports

No abstract provided.

Green Team-Urban Ecological Restoration, Aracely Eikenberry, Stephanie Praamsma, Gail Heffner, David P. Warners

Student Papers and Reports

No abstract provided.

Elongation Factor P Interactions With The Ribosome Are Independent Of Pausing, Rodney Tollerson Ii, Anne Witzky, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Bacterial elongation factor P (EF-P) plays a pivotal role in the translation of polyproline motifs. To stimulate peptide bond formation, EF-P must enter the ribosome via an empty E-site. Using fluorescence-based single-molecule tracking, Mohapatra et al. (S. Mohapatra, H. Choi, X. Ge, S. Sanyal, and J. C. Weisshaar, mBio 8:e00300-17, 2017, https://doi.org/10.1128/mBio.00300-17 ) monitored the cellular distribution of EF-P and quantified the frequency of association between EF-P and the ribosome under various conditions. Findings from the study showed that EF-P has a localization pattern that is strikingly similar to that of ribosomes. Intriguingly, EF-P was seen to bind ribosomes more …

Crispr/Cas9 In Leishmania Genome Editing : Towards A Proof Of Concept, Zein Kasbo

Theses, Dissertations and Culminating Projects

Leishmaniasis is a parasitic Neglected Tropical Disease (NTD) that affects mostly poor countries of the third word due to their limited access to clean water and health care. The disease is transmitted through the bite of a sand fly of the genus Phlebotomus in the Old World, and of the genus Lutzomyia in the New World. Historically, NTDs have not been given adequate attention or research funding and finding curative treatments has been slow. However, the fact that the insect vector and the parasite can live and thrive in any ecological system in the world, and under the current circumstances …

Immunological Strategies To Study Grp170 In Caenorhabditis Elegans, Raven P. Baxter-Christian

Biology Theses

Characterization of the ER protein folding chaperone GRP170 of Caenorhabditis elegans could be greatly facilitated by an antibody which recognized the chaperone. Antibodies have not been raised against nematode GRP170. Groups have prepared polyclonal antibodies against vertebrate forms of GRP170. My thesis goal was to investigate whether anti-vertebrate GRP170 antibodies can recognize the nematode homologue on a standard Western Blot assay. Sequences of antigens that groups used to generate anti-vertebrate GRP170 antibodies were analyzed. Peptides used by Ruan et al. (2013), which correspond to regions of human GRP170, shared greatest sequence similarity with nematode GRP170. I investigated whether the Ruan …

Membrane Surface Engineering For Biochemical Applications, Anh T. Vu

Graduate Theses and Dissertations

Synthetic membranes have been frequently used for many fields, such as, the food and beverage, biopharmaceutical, and biofuel industries. In the beer industry, microfiltration frequently suffers from fouling due to the interaction between different species. It is shown that polyphenols can form cross-links with protein molecules, forming insoluble aggregates. However, by adding an optimal amount of polysaccharides these aggregates can be disrupted thus reducing fouling by the aggregates. Confocal laser scanning microscopy (CLSM) is a powerful technique to locate the foulants inside the wet membrane in order to understand more about the behavior of fouling in microfiltration.

Membrane surface modification …

Characterizing Reactive Glutamines In Fibrinogen And Elucidating Factor Xiii Substrate Specificity., Kelly Njine Mouapi

Electronic Theses and Dissertations

Fibrinogen is the most abundant protein involved in blood coagulation and has been associated with many pathological implications in cardiovascular disease. At the final stages of blood clot formation, the transglutaminase Factor XIIIa introduces γ-glutamyl-ε-lysinyl covalent bonds between reactive glutamines and lysines in fibrin, which results in a tighter clot network that is resistant to fibrinolysis. Factor XIIIa crosslinks specific reactive glutamines on fibrinogen, selecting more reactive glutamines in the αC region of fibrinogen than any other chain. Although crosslinking pairs in the αC region have been identified, little is known about the extent of crosslinking and the role played …

Mechanism Investigation Of Pseudouridine Synthases Trub And Rlua With Rna Containing 5-Fluorouridine And 4-Thiouridine., Uyen T. Duong

Electronic Theses and Dissertations

Pseudouridine synthases (Ψ synthases) are the enzymes that catalyze the isomerization of uridine (U) to pseudouridine (Ψ), which is the most prevalent post-transcriptional modification of RNA. The Ψ synthases fall into six different families that share no significant global sequence similarity; however, they all involve a conserved aspartic acid residue which is absolutely essential for activity. Tyrosine is a conserved residue in the active site in five of the six families of Ψ synthases (phenylalanine in the TruD family) and was hypothesized as the general base for the isomerization reaction. To confirm the function of Tyr-96, Y96F RluA was assayed …

Application Of Open-Access Databases To Determine Functional Connectivity Between Resveratrol-Binding Protein Qr2 And Colorectal Carcinoma, Barbara B. Doonan, Evelien Schaafsma, John T. Pinto, Joseph M. Wu, Tze-Chen Hsieh

NYMC Faculty Publications

Colorectal cancer (CRC) is a major cause of cancer-associated deaths worldwide. Recently, oral administration of resveratrol (trans-3,5,4'-trihydroxystilbene) has been reported to significantly reduce tumor proliferation in colorectal cancer patients, however, with little specific information on functional connections. The pathogenesis and development of colorectal cancer is a multistep process that can be categorized using three phenotypic pathways, respectively, chromosome instability (CIN), microsatellite instability (MSI), and CpG island methylator (CIMP). Targets of resveratrol, including a high-affinity binding protein, quinone reductase 2 (QR2), have been identified with little information on disease association. We hypothesize that the relationship between resveratrol and different CRC etiologies …

A Novel Method For Synthesis Of Hydroxytyrosol, Emmanuel Onobun

Electronic Theses and Dissertations

Hydroxytyrosol, 3,4-dihydroxyphenolethanol, a naturally occurring polyphenol most common in olive tree (Olea europaea), is one of the most effective member of the polyphenols family, because of its remarkable antioxidant activity, its ability to inhibit oxidation of low density lipids (LDL), and its protection against DNA oxidative damage. Hydroxytyrosol, which is widely used in cosmetics and food supplements industries, can be purchased as an olive oil extract that contains low concentration of hydroxytyrosol besides other polyphenols. The price and low natural abundance of hydroxytyrosol make alternative synthetic sources very attractive. In this research, a novel method for the synthesis of pure …

Identification And Metabolite Profiling Of Chemical Activators Of Lipid Accumulation In Green Algae, Nishikant Wase, Boqiang Tu, James Allen, Paul N. Black, Concetta Dirusso

Department of Biochemistry: Faculty Publications

Microalgae are proposed as feedstock organisms useful for producing biofuels and coproducts. However, several limitations must be overcome before algae-based production is economically feasible. Among these is the ability to induce lipid accumulation and storage without affecting biomass yield. To overcome this barrier, a chemical genetics approach was employed in which 43,783 compounds were screened against Chlamydomonas reinhardtii, and 243 compounds were identified that increase triacylglyceride (TAG) accumulation without terminating growth. Identified compounds were classified by structural similarity, and 15 were selected for secondary analyses addressing impacts on growth fitness, photosynthetic pigments, and total cellular protein and starch concentrations. TAG …

Determination Of Coenzyme A And Acetyl-Coenzyme A In Biological Samples Using Hplc With Uv Detection, Yevgeniya Shurubor, M D'Aurelio, J Clark-Matott, E Isakova, Y Deryabina, M Beal, Arthur Cooper, Boris Krasnikov

NYMC Faculty Publications

Coenzyme A (CoA) and acetyl-coenzyme A (acetyl-CoA) play essential roles in cell energy metabolism. Dysregulation of the biosynthesis and functioning of both compounds may contribute to various pathological conditions. We describe here a simple and sensitive HPLC-UV based method for simultaneous determination of CoA and acetyl-CoA in a variety of biological samples, including cells in culture, mouse cortex, and rat plasma, liver, kidney, and brain tissues. The limits of detection for CoA and acetyl-CoA are >10-fold lower than those obtained by previously described HPLC procedures, with coefficients of variation

Functionalization Of Indium-Based Quantum Dots For Use As A Non-Viral Gene Therapy Vector, Nicholas A. Mundt

Graduate Theses/Dissertations

This work aims to develop functionalized, water-soluble indium-based quantum dots (QDs) as a non-viral gene therapy vector. The QDs were solubilized in water by exchanging native hydrophobic surface ligands with 11-mercaptoundecanioc acid (MUA); an amphiphilic ligand providing terminal carboxylate groups that impart water solubility to the QDs. The aqueous QDs were then functionalized with a terminal tertiary amine to impart a positive surface charge, allowing negatively-charged DNA to complex with the nanoparticles. The QDs were characterized via electrophoresis to determine their ability to bind DNA. Results show that further work is needed to optimize DNA binding. In addition, this work …

Investigating The Role Of Prmt1 And Arginine Methylation Of Hsp70 In Human Pancreatic Cancer, Liang Wang

Dissertations and Theses (Open Access)

Protein arginine methyltransferase 1 (PRMT1) is the major arginine methyltransferase, which catalyzes the addition of one or two methyl groups to the arginine residues of its substrate proteins. The best-known substrate for PRMT1 is histone, while more and more non-histone proteins are now found to be methylated by PRMT1. Dysregulation of PRMT1 is reported in several human cancer types. However, its biological roles in human pancreatic cancer initiation and development are still unclear. In the first part of this study, I found that the expression level of PRMT1 was elevated in both human and mouse pancreatic cancer tissues in immunohistochemistry …

Membranes For Food And Bioproduct Processing, Alexandru Marius Avram

Graduate Theses and Dissertations

Modified membranes for process intensification in biomass hydrolysis

Production of biofuels and chemicals from lignocellulosic biomass is one of the leading candidates for replacement of petroleum based fuels and chemicals. However, conversion of lignocellulosic biomass into fuels and chemicals is not cost effective compared to the production of fuels and chemicals from crude oil reserves. Some novel and economically feasible approaches involve the use of ionic liquids as solvents or co-solvents, since these show improved solvation capability of cellulose over simple aqueous systems. Membranes offer unique opportunities for process intensification which involves fractionation of the resulting biomass hydrolysate leading to …