Biochemistry, Biophysics, and Structural Biology Commons^™

Installation Of Rain Gardens In The Alger Heights Community, Wesley Dykstra, Dena De Kryger, Mike Ryskamp, David P. Warners

Student Papers and Reports

No abstract provided.

Fatty Acid Recovery And Identification In Mars Analogue Soil Samples, Kimberly E. Lykens

STAR Program Research Presentations

A primary goal of NASA’s Mars 2020 mission is to gather and store samples of Mars soil that could possibly be returned to Earth in a future mission for investigations into past or present life. In years leading up to a potential sample return mission on Mars and potentially other worlds, samples taken from Chile’s Atacama Desert, the most arid, biologically limited desert in the world, are valuable in developing a capacity for biosignature detection, specifically when exploring fatty acid abundance. Eighteen samples were collected from two sites in the Atacama characterized by biological soil crusts (BSC). BSCs are areas …

How Many Particles Are Present In The Air? Bioaerosol Detection Using An Air Particle Counter, Angie Pamela Rivera, Parag Vaishampayan

STAR Program Research Presentations

Relative cleanliness in terms of particle abundance in spacecraft assembly facilities is determined by particle counts carried out in clean rooms during resting conditions. Particle counters assess total particles and particle size distribution, but do not distinguish inert particles from biological particles, which may include bacterial spores that are resistant to standard cleanroom sterilization procedures. Current cleanroom certifications do not fully assess the effects of human presence on spacecraft contamination since humans are known symbionts to enumerate microorganisms and assessments are performed at rest when there is no human presence. In this study, contamination risks and bioburden in spacecraft assembly …

Conformational Dynamics Of Dnaa Protein Of Bacillus Anthracis In The Initiation Of Dna Replication: A Fluorescence Resonance Energy Transfer Study, Meera J. Patel

Graduate School of Biomedical Sciences Theses and Dissertations

A precursor of the origin recognition complex proteins in eukaryotes, the DnaA protein, a single-subunit protein found in all prokaryotes, p1ays a significant role in the initiation of DNA replication. The DnaA protein in Gram-negative Escherichia coli (DnaA_EC) identifies, binds and activates specific DNA sequences at the origin of replication, oriC, initiating the duplication of the prokaryotic genome. Using DnaA_EC as a guide, we selected the full-length form of DnaA from Gram-positive Bacillus anthracis (DnaA_BA) as our model for studying. We have cloned, mutated, expressed and purified large quantities of DnaA_BA protein due to …

Producing Financially Literate Medical Graduates -- A National Need For A Brighter Pakistan, Rehana Rehman, Shah Jahan Katpar, Mehwish Hussain, Rakhshaan Khan

Department of Biological & Biomedical Sciences

Objective: To compare the awareness of financial wellness between male and female medical students.Methods: The cross-sectional questionnaire-based survey was conducted from February to December 2011 and comprised first year medical students belonging to different medical colleges of Karachi. Students from both genders, aged 19-24 years, belonging to all ethnic groups willing to participate were included. A close-ended questionnaire evaluated aspects of financial wellness, using four-point Likert's scale: never, sometimes, mostly, and always from 0 to 4. Besides, factor analysis was performed to investigate common financial wellness among the participants.Results: Of the total 800 students approached, complete responses were received from …

Evidence For The Persistence Of Food Web Structure After Amphibian Extirpation In A Neotropical Stream, Thomas R. Barnum, John M. Drake, Jose Checo Colón-Gaud, Amanda T. Rugenski, Therese C. Frauendorf, Scott Connelly, Susan S. Kilham, Matt R. Whiles, Karen R. Lips, Catherine M. Pringle

Biology: Faculty Publications

Species losses are predicted to simplify food web structure, and disease‐driven amphibian declines in Central America offer an opportunity to test this prediction. Assessment of insect community composition, combined with gut content analyses, was used to generate periphyton–insect food webs for a Panamanian stream, both pre‐ and post‐amphibian decline. We then used network analysis to assess the effects of amphibian declines on food web structure. Although 48% of consumer taxa, including many insect taxa, were lost between pre‐ and post‐amphibian decline sampling dates, connectance declined by less than 3%. We then quantified the resilience of food web structure by calculating …

Metal-Free Tandem Beckmann–Electrophilic Aromatic Substitution Cascade Affording Diaryl Imines, Ketones, Amines, And Quinazolines, Samuel Sarsah, Marlon R. Lutz Jr., Kailyn Chichi Bobb, Daniel Becker

Chemistry: Faculty Publications and Other Works

A cascade reaction sequence involving a Beckmann rearrangement on benzophenone oxime followed by an electrophilic aromatic substitution (EAS) on the intermediate nitrilium ion affords N-phenyl diaryl imines that may then be hydrolyzed to ketones, or reduced to the corresponding amines. Reaction with benzonitrile afforded 2,4-diphenylquinazoline through a Beckmann–Ritter–EAS cascade.

Analysis Of Novel Mta Nucleosidase Inhibitors As Anti-Parasitic Agents, Teslin Marie Botoy

Boise State University Theses and Dissertations

The parasitic protozoa Giardia intestinalis and Entamoeba histolytica are major health concerns and responsible for hundreds of millions of cases of intestinal disease per year. Strains of both parasites have been discovered that show resistance to metronidazole, the most prevalent treatment for these pathogens. Thus, there is a need to identify new drugs and drug targets to combat the growing threat of drug resistant parasites. The parasite enzyme methylthioadenosine nucleosidase (MTN) is one such potential target. Traditional drug development processes take almost a decade and hundreds of millions of dollars to complete. In an effort to shorten that timeline and …

A Less-Biased Analysis Of Metalloproteins Reveals Novel Zinc Coordination Geometries, Sen Yao, Robert M. Flight, Eric C. Rouchka, Hunter N. B. Moseley

Molecular and Cellular Biochemistry Faculty Publications

Zinc metalloproteins are involved in many biological processes and play crucial biochemical roles across all domains of life. Local structure around the zinc ion, especially the coordination geometry (CG), is dictated by the protein sequence and is often directly related to the function of the protein. Current methodologies in characterizing zinc metalloproteins' CG consider only previously reported CG models based mainly on nonbiological chemical context. Exceptions to these canonical CG models are either misclassified or discarded as "outliers." Thus, we developed a less-biased method that directly handles potential exceptions without pre-assuming any CG model. Our study shows that numerous exceptions …

Evaluation Of The Protein Recognition Properties Of Peptide Nucleic Acids, Crystal Cox Serrano

Master's Theses

The objective is to evaluate the ability of aminoacyl-tRNA synthetases (aaRS) to recognize the non-standard nucleic acid, PNA (peptide nucleic acid). PNA has immense potential in biomedical applications due to its increased thermostability and nuclease resistance over natural nucleic acids. PNA represents a superior alternative to natural nucleic acids in many biomedical applications due to its specificity, strong binding, and nuclease resistance. This study is the initial data set that indicates PNA are recognized by translation enzymes.

Pharmacodynamic Assays To Facilitate Preclinical And Clinical Development Of Pre-Mrna Splicing Modulatory Drug Candidates, Yihui Shi, Amanda S. Joyner, William Shadrick, Gustavo Palacios, Chandraiah Lagisetti, Philip M. Potter, Lidia C. Sambucetti, Stefan Stamm, Thomas R. Webb

Molecular and Cellular Biochemistry Faculty Publications

The spliceosome has recently emerged as a new target for cancer chemotherapy and novel antitumor spliceosome targeted agents are under development. Here, we describe two types of novel pharmacodynamic assays that facilitate drug discovery and development of this intriguing class of innovative therapeutics; the first assay is useful for preclinical optimization of small-molecule agents that target the SF3B1 spliceosomal protein in animals, the second assay is an ex vivo validated, gel-based assay for the measurement of drug exposure in human leukocytes. The first assay utilizes a highly specific bioluminescent splicing reporter, based on the skipping of exons 4-11 of a …

Gating Mechanisms Of The Canonical Trp Channel Isoform Trpc4, Dhananjay P. Thakur

Dissertations and Theses (Open Access)

Non-selective cation channels formed by Transient Receptor Potential Canonical (TRPC) proteins play important roles in regulatory and pathophysiological processes. These channels are known to be activated downstream from phospholipase C (PLC) signaling. However, the mechanism by which the PLC pathway activates TRPC4/C5 remains unclear. Uniquely, TRPC4 is maximally activated only when two separate G protein pathways, G_q/11 and G_i/o, are co-stimulated, making it a coincidence detector of G_q/11- and G_i/o -coupled receptor activation. Using HEK293 cells co-expressing mouse TRPC4β and selected G protein-coupled receptors, I observed that coincident stimulation of G_i/o proteins and …

Nmr-Based Structural Analysis Of Threonylcarbamoyl-Amp Synthase And Its Substrate Interactions, Kimberly A. Harris, Benjamin G. Bobay, Kathryn L. Sarachan, Alexis F. Sims, Yann Bilbille, Christopher Deutsch, Dirk Iwata-Reuyl, Paul F. Agris

Chemistry Faculty Publications and Presentations

The hypermodified nucleoside N(6)-threonylcarbamoyladenosine (t(6)A37) is present in many distinct tRNA species and has been found in organisms in all domains of life. This post-transcriptional modification enhances translation fidelity by stabilizing the anticodon/codon interaction in the ribosomal decoding site. The biosynthetic pathway of t(6)A37 is complex and not well understood. In bacteria, the following four proteins have been discovered to be both required and sufficient for t(6)A37 modification: TsaC, TsaD, TsaB, and TsaE. Of these, TsaC and TsaD are members of universally conserved protein families. Although TsaC has been shown to catalyze the formation of L-threonylcarbamoyl-AMP, a key intermediate in …

Coordinate Regulation Of The Wnt And Hippo Pathways By The Novel Ras Effector Nore1a., Marvin Lee Schmidt Jr.

Electronic Theses and Dissertations

Ras is the most frequently activated oncogene found in human cancer, but its mechanisms of action remain only partially understood. Ras activates multiple signaling pathways in order to promote transformation, but can also exhibit a potent ability to induce growth arrest and death. NORE1A (RASSF5) is a direct Ras effector that acts as a tumor suppressor promoting senescence and apoptosis. Its expression is frequently lost in human tumors and its mechanism of action remains unclear. Here I show that NORE1A forms a direct, Ras regulated, complex with β-TrCP, the substrate recognition component of the SCF-β-TrCP ubiquitin ligase complex. NORE1A also …

Paenibacillus Larvae Spore Germination And American Foulbrood Disease Development In Honey Bee Larvae, Israel Alvarado

UNLV Theses, Dissertations, Professional Papers, and Capstones

Honey bee (Apis mellifera) pollination plays an important role in meeting our agricultural needs, yet we are incapable of completely preventing a decline in bee health, partially due to bacterial diseases. American Foulbrood (AFB), a bacterial disease of honey bee larvae, is particularly troublesome because the infectious agent is the bacterial spore of Paenibacillus larvae. Bacterial spores are resistant to extreme temperatures, unaffected by antibiotics, withstand exposure to disinfectants, and can remain dormant for years until they can revert back to vegetative cells.

Our research investigated P. larvae spore germination at the functional and pathogen-host level. We have found that …

The Presence Of Clostridium Difficile On Environmental Surfaces In Healthcare Facilities Pre- And Post-Decontamination Of Patient Rooms, Theresa Trice

UNLV Theses, Dissertations, Professional Papers, and Capstones

Healthcare-associated infections (HAIs) are infections related to receiving medical care. HAIs are responsible for an excess of morbidity and mortality among hospitalized patients. Though most HAIs rates are on the decline, Clostridium difficile infection rates are at an all-time high, primarily due to the persistence of C. difficile spores in the environment. In the United States, Clostridium difficile-related mortality rates per million have increased from 5.7 in 1999 to 23.7 in 2004, with an estimated 26,642 deaths due to Clostridium difficile infections (CDIs). Clostridium difficile is transmitted via the fecal-oral route or aerosolized endospores, but it can also be transmitted …

Water Transport And The Functional Dynamics Of Aquaporins In Osmoregulatory Organs Of Fishes, Steffen S. Madsen, Morton B. Engelund, Christopher P. Cutler

Biology: Faculty Publications

Aquaporins play distinct roles for water transport in fishes as they do in mammals—both at the cellular, organ, and organismal levels. However, with over 32,000 known species of fishes inhabiting almost every aquatic environment, from tidal pools, small mountain streams, to the oceans and extreme salty desert lakes, the challenge to obtain consensus as well as specific knowledge about aquaporin physiology in these vertebrate clades is overwhelming. Because the integumental surfaces of these animals are in intimate contact with the surrounding milieu, passive water loss and uptake represent two of the major osmoregulatory challenges that need compensation. However, neither obligatory …

Structure And Composition Of Postsynaptic Densities, Madeline Farley

Dissertations and Theses (Open Access)

Communication between neurons within the brain occurs at chemical synapses and is fundamental for all brain functions. Modulation of the strength of communication is controlled by both presynaptic and postsynaptic mechanisms and is termed synaptic plasticity. One postsynaptic structure postulated to regulate synaptic strength is the postsynaptic density (PSD), a large electron dense protein complex located just below the synaptic membrane. The PSD, which is composed of signaling, scaffold and cytoskeletal proteins, supports and organizes neurotransmitter receptors within the synaptic membrane in addition to bridging signaling with the actin cytoskeletal network. The protein composition and structure of PSDs is known …

Investigating The Interaction Of Aurka And Ube2c In Colorectal Cancer Cells, Apurva M. Hegde

Dissertations and Theses (Open Access)

Colorectal cancer (CRC) is the third leading cause of cancer-related deaths in the US. Among the many genomic aberrations previously implicated in colorectal cancer, recurrent amplification of chromosome 20q is frequently associated with liver metastasis. Previous research in our lab identified a gene signature on chromosome 20q associated with colorectal cancer progression. In this study, one of the genes in the signature, the ubiquitin conjugating enzyme UBE2C, was identified through preliminary bioinformatics analysis as a candidate for further examination of its role in CRC progression. Co-expression analysis of UBE2C in tumor-normal datasets from the public database Oncomine revealed all the …

Prophylactic Cranial Irradiation Reduces The Incidence Of Brain Metastasis In A Mouse Model Of Metastatic Breast Cancer, Daniel L. Smith

Dissertations and Theses (Open Access)

Prophylactic cranial irradiation (PCI) is a preventative whole-brain irradiation technique used to reduce the incidence of brain metastasis and improve overall survival in select patients with small cell lung cancer and acute lymphoblastic leukemia. A population of breast cancer patients – stage IV, HER2+ or triple-negative – has emerged as having a high risk of developing brain metastases. Because only 10-20% of breast cancer patients diagnosed with brain metastases survive longer than one year, in this high-risk population the benefit of PCI – potential for reduced incidence of brain metastasis and improved overall survival – may outweigh the risks – …

Direct Regulation Of Apoptosis By Linear Ubiqutin Chain Assembly Complex (Lubac) And Feedback Regulation Of Lubac Function By Caspases, Donghyun Joo

Dissertations and Theses (Open Access)

Tumor Necrosis Factor-alpha (TNF-α) is a cytokine that plays a role in various cellular processes such as proliferation, differentiation (mainly through NF-κB signaling) and death (via apoptosis signaling). Recently, linear ubiquitination by LUBAC (linear ubiquitin chain assembly complex) was reported to have a regulatory function in TNF-α mediated NF-κB activation. Although LUBAC is suggested to control not only NF-kB signaling but also the apoptosis pathway, the precise mechanism of apoptosis regulation remains unknown. Moreover, NF-κB and apoptosis pathways have opposed but fundamental functions for various cellular processes. Although these two pathways actively interplay to balance the death and survival, the …

Histone H3 K4 Methylation Regulates The Spindle Assembly Checkpoint Through Direct Binding Of Multiple Checkpoint Components And Cdc20, Andria C. Schibler

Dissertations and Theses (Open Access)

Histone H3K4 methylation is conserved across species and is associated with active transcription. By using Saccharomyces cerevisiae, we found histone H3K4 methylation has a previously unknown role in regulating mitosis through the Spindle Assembly Checkpoint. The Spindle Assembly Checkpoint ensures duplicated chromosomes are segregated correctly and each daughter cell receives one full copy of the genome. Our data show SET1 mutants and histone H3K4 mutants display a resistance to the mitotic poison, benomyl. Moreover methylated histone H3 directly binds to Spindle Assembly Checkpoint proteins Bub3 and Mad2 as well as the activator of the Anaphase Promoting Complex (APC) protein …

Computational Modeling Of Rna-Small Molecule And Rna-Protein Interactions, Lu Chen

Dissertations and Theses (Open Access)

The past decade has witnessed an era of RNA biology; despite the considerable discoveries nowadays, challenges still remain when one aims to screen RNA-interacting small molecule or RNA-interacting protein. These challenges imply an immediate need for cost-efficient while predictive computational tools capable of generating insightful hypotheses to discover novel RNA-interacting small molecule or RNA-interacting protein. Thus, we implemented novel computational models in this dissertation to predict RNA-ligand interactions (Chapter 1) and RNA-protein interactions (Chapter 2).

Targeting RNA has not garnered comparable interest as protein, and is restricted by lack of computational tools for structure-based drug design. To test the potential …

Investigations Of Filarial Nematode Motility, Response To Drug Treatment, And Pathology, Charles Nutting

Dissertations

More than a billion people live at risk of chronic diseases caused by parasitic filarial nematodes. These diseases: lymphatic filariasis, onchocerciasis, and loaisis cause significant morbidity, degrading the health, quality of life, and economic productivity of those who suffer from them. Though treatable, there is no cure to rid those infected of adult parasites. The parasites can modulate the immune system and live for 10-15 years. Testing of compounds against filarial nematodes is complicated due to a lack of an objective platform on which to analyze in vitro treatments. There is no published, immunocompetent laboratory model for lymphatic filariasis. This …

Repsa Directed Assessment Of Native Cleavage Resistance Of Dna To Type Iis Restriction Endonucleases And Modification Of Repsa For High Temperature Application, Matthew Beyer

Master of Science in Chemical Sciences Theses

We have modified the combinatorial selection method Restriction Endonuclease Protection and Selection Assay (REPSA) to work in high temperature conditions for the discovery of new DNA-binding proteins in thermophiles (HT-REPSA). We utilized Thermus thermophilus (HB-8/ATCC 27634/DSM 579) as a test organism due to its amenable nature in a laboratory setting and current status as a model thermophilic organism. We used a TetR Family (TFR) transcription factor SbtR as the model protein for optimization of HT-REPSA protocols, as data had previously been obtained regarding SbtR physical characteristics and DNA-binding properties. REPSA was conducted until a cleavage resistant species arose after 7 …

The Mitochondrial Peptidase Pitrilysin Degrades Islet Amyloid Polypeptide In Beta-Cells, Hanjun Guan, K. Martin Chow, Eunsuk Song, Nirmal Verma, Florin Despa, Louis B. Hersh

Molecular and Cellular Biochemistry Faculty Publications

Amyloid formation and mitochondrial dysfunction are characteristics of type 2 diabetes. The major peptide constituent of the amyloid deposits in type 2 diabetes is islet amyloid polypeptide (IAPP). In this study, we found that pitrilysin, a zinc metallopeptidase of the inverzincin family, degrades monomeric, but not oligomeric, islet amyloid polypeptide in vitro. In insulinoma cells when pitrilysin expression was decreased to 5% of normal levels, there was a 60% increase in islet amyloid polypeptide-induced apoptosis. In contrast, overexpression of pitrilysin protects insulinoma cells from human islet amyloid polypeptide-induced apoptosis. Since pitrilysin is a mitochondrial protein, we used immunofluorescence staining …

Poly(N-Isopropylacrylamide) Hydrogels For Storage And Delivery Of Reagents To Paper-Based Analytical Devices, Haydn T. Mitchell, Spencer Schultz, Philip Costanzo, Andres W. Martinez

Chemistry and Biochemistry

The thermally responsive hydrogel N,N'-methylenebisacrylamide-cross-linked poly(N-isopropylacrylamide) (PNIPAM) was developed and evaluated as a reagent storage and delivery system for microfluidic paper-based analytical devices (microPADs). PNIPAM was shown to successfully deliver multiple solutions to microPADs in specific sequences or simultaneously in laminar-flow configuration and was found to be suitable for delivering four classes of reagents to the devices: Small molecules, enzymes, antibodies and DNA. PNIPAM was also able to successfully deliver a series of standard glucose solutions to microPADs equipped to perform a colorimetric glucose assay. The results of these tests were used to produce an external calibration …

An Extended Polyanion Activation Surface In Insulin Degrading Enzyme, Eun Suk Song, Mehmet Ozbil, Tingting Zhang, Michael Sheetz, David Lee, Danny Tran, Sheng Li, Rajeev Prabhakar, Louis B. Hersh, David W. Rodgers

Molecular and Cellular Biochemistry Faculty Publications

Insulin degrading enzyme (IDE) is believed to be the major enzyme that metabolizes insulin and has been implicated in the degradation of a number of other bioactive peptides, including amyloid beta peptide (Aβ), glucagon, amylin, and atrial natriuretic peptide. IDE is activated toward some substrates by both peptides and polyanions/anions, possibly representing an important control mechanism and a potential therapeutic target. A binding site for the polyanion ATP has previously been defined crystallographically, but mutagenesis studies suggest that other polyanion binding modes likely exist on the same extended surface that forms one wall of the substrate-binding chamber. Here we use …

Intra-Domain Cross-Talk Regulates Serine-Arginine Protein Kinase 1-Dependent Phosphorylation And Splicing Function Of Transformer 2Β1, Michael A. Jamros, Brandon E. Aubol, Malik M. Keshwani, Zhaiyi Zhang, Stefan Stamm, Joseph A. Adams

Molecular and Cellular Biochemistry Faculty Publications

Transformer 2β1 (Tra2β1) is a splicing effector protein composed of a core RNA recognition motif flanked by two arginine-serine-rich (RS) domains, RS1 and RS2. Although Tra2β1-dependent splicing is regulated by phosphorylation, very little is known about how protein kinases phosphorylate these two RS domains. We now show that the serine-arginine protein kinase-1 (SRPK1) is a regulator of Tra2β1 and promotes exon inclusion in the survival motor neuron gene 2 (SMN2). To understand how SRPK1 phosphorylates this splicing factor, we performed mass spectrometric and kinetic experiments. We found that SRPK1 specifically phosphorylates 21 serines in RS1, a process facilitated …

The Role Of The Pleckstrin Homology Domain-Containing Protein Ckip-1 In Activation Of P21-Activated Kinase 1 (Pak1), Yong-Bae Kim, Yong Jae Shin, Adhiraj Roy, Jeong-Ho Kim

Biochemistry and Molecular Medicine Faculty Publications

Upon growth factor stimulation, PAK1 is recruited to the plasma membrane and activated by a mechanism that requires its phosphorylation at S223 by the protein kinase CK2. However, the upstream signaling molecules that regulate this phosphorylation event are not clearly defined. Here, we demonstrate a major role of the CK2α-interacting protein CKIP-1 in activation of PAK1. CK2α, CKIP-1 and PAK1 are translocated to membrane ruffles in response to the epidermal growth factor (EGF), where CKIP-1 mediates the interaction between CK2α, and PAK1 in a PI3K-dependent manner. Consistently, we observe that PAK1 mediates phosphorylation and modulation of the activity of p41-Arc, …