Biochemistry, Biophysics, and Structural Biology Commons^™

Targeted-Ion Mass Spectrometry For The Identification Of Forensically Relevant Biological Fluids And Samples From Sexual Assault Evidence, Heather Erin Mckiernan

Electronic Theses and Dissertations

Forensic practitioners have long sought efficient and reliable means for identifying those samples that are best suited for successful genetic profiling. Traditional serological screening methodologies rely upon enzyme activity and antibody-based serological tests. These tests can be consumptive, laborious and costly while reliance on antibody-based serological testing can be prone to error. Positive results resulting from non-target biological fluids, the potential for cross- reactivity and non-specific binding events yield merely presumptive results. This has led forensic biologists to omit serological testing, at least in the case of sexual assault kit samples, in favor of Y-Screen assays. While these Y-Screen approaches …

Qualitative And Quantitative Fitness Consequences Of Advanced Maternal Age, Claudia Jean Hallagan

Electronic Theses and Dissertations

Parental age can affect offspring fitness across taxa and through various mechanisms. However, the effect(s) of advanced maternal age on offspring, particularly in insects, has not been comprehensively reviewed making it difficult to draw conclusions about the effects of advanced maternal age on offspring in insects. In my first chapter, I reviewed maternal age literature and found overall negative effects of advanced maternal age on offspring fitness. However, results vary depending on which fitness measures were used, the life stages at which offspring were measured, and the experimental design of the study. In my second chapter, I conducted an experiment …

Development Of A Hek293 Cell Line To Show Inhibition Of Tau Aggregation, Justin Ray Shady

Electronic Theses and Dissertations

Intracellular deposition of aggregated tau is the hallmark of several different tauopathies, the most widespread of these being Alzheimer's disease. Tau is a highly soluble, intrinsically disordered, microtubule associated protein. Tau's native function is to stabilize microtubule formation in the axons of neurons. Post translational modification such as hyperphosphorylation as well as several familial mutations allow tau to nucleate and form fibrils. These fibrils can recruit healthy monomers onto their ends in a fashion described as template-assisted growth. Tau has 6 isoforms that vary by the inclusion or exclusion of two N-terminal repeats and the inclusion or exclusion of the …

Data Collection Curated With An Application Ontology Describes The Methods And Results Upon Performing An Ex-Vivo Voltage-Clamp Assay On Outer Hair Cells Of The Mammalian Cochlea, Brenda Farrell, Jason Bengtson

Research Data

This data collection describes the electrical properties of outer hair cells isolated from the mammalian cochlea of the domestic guinea pig. This data was obtained by performing whole-cell patch clamp voltage clamp assay on cells and monitoring the electrical admittance during a DC voltage ramp. The membrane capacitance was then calculated at each membrane potential from this admittance, and the voltage-independent and voltage-dependent membrane capacitance was determined upon further analysis. In some case the DC conductance was also measured by interrogation of the cell with voltage-step function which was calculated from the change in the mean steady-state current with respect …

Mechanistic Insight Into Tau Fibril Cross-Seeding Barriers: Structural Order And Disorder, Hilary Ann Weismiller

Electronic Theses and Dissertations

Filamentous deposition of microtubule-associated protein tau is a hallmark for a number of neurodegenerative diseases collectively termed tauopathies. While tau fibrils are directly linked to the etiology and pathogenesis of these diseases, fibril morphology and their phenotypic presentation can be quite disparate. Alternative splicing of tau results in two main isoform groups, four-repeat (4R) tau and three-repeat (3R), identified by their number of microtubule binding repeats. Some diseases show deposition of both 4R and 3R isoforms, while others show preferential deposition of only one type. The conformational templated growth scheme and trans-synaptic spreading of fibrils is influenced by fibril conformation. …

Urban Aerobiological Risk Mapping Of Ornamental Trees Using A New Index Based On Lidar And Kriging: A Case Study Of Plane Trees, Raúl Pecero-Casimiro, Santiago Fernández-Rodríguez, Rafael Tormo-Molina, Alejandro Monroy-Colín, Inmaculada Silva-Palacios, Juan Pedro Cortés-Pérez, Ángela Gonzalo-Garijo, J. M. Maya-Manzano

Articles

Ornamental trees bring benefits for human health, including reducing urban pollution. However, some species, such as plane trees (Platanus sp.), produce allergenic pollen. Consequently, urban maps are a valuable tool for allergic patients and allergists, but they often fail to include variables that contribute to the “building downwash effect”, such as the width and shape of streets and the height of buildings. Other factors that directly influence pollen dispersion (slopes and other geographical features) also have not traditionally been discussed. The LiDAR (Laser Imaging Detection and Ranging) technique enables one to consider these variables with high accuracy. This work proposes …

Application And Comparison Of Active Learning Implementation Methods In Biochemistry Education, Dylan Thibaut

Honors Undergraduate Theses

Biochemistry has continued to be one of the most complex and important subjects in science education. The purpose of this research is to investigate active learning implementation methods in a Biochemistry I context to determine the most effective means of preparing current science undergraduates. Two Biochemistry I classes over two semesters were analyzed in this study, with class A using a variable active learning schedule and class B using a consistent active learning schedule. Four aspects were analyzed to determine active learning validity: perception of different active learning properties, standardized final exam grades, class grade, and teaching implementation. The consistent …

Progress Toward The Synthesis Of An Oxazolidinone Antibacterial Agent Incorporating A Bicyclo[1.1.1]Pentane (Bcp) Ring System, Evamarie Medendorp, Michael Barbachyn

Summer Research

The phenyloxazolidinones, exemplified by linezolid (1, marketed as Zyvox™), have emerged as useful antibacterial agents for treating a variety of infections caused by problematic Gram-positive bacteria. 1 Another clinical phenyloxazolidinone with somewhat improved potency and safety properties is PNU-288034 (2). 2 PNU288034 incorporates a 1,1-dioxothiomorpholine ring system and an additional fluorine atom.

Determining The Effectiveness Of Drugs Using Ec50 And Mic Assays, Sara Knapp, Rachael Baker, Amy Wilstermann

Summer Research

• Antibiotic resistance comes from bacterial mutations in the antibiotic binding site (which prevents antibiotic binding)
• These new antibiotics target both DNA Gyrase and DNA Topoisomerase IV (fluoroquinolones)
• This improves efficacy because if one binding site is mutated, the other is still available
• This makes it harder for bacteria to form resistance against the drug

Non-Hemolytic And Hemolytic Group B Streptococcus: Interactions With Cells In Vitro, Olivia S Harlow, Ethan Houskamp, Natalie Anumolu, Shannon Manning, Erica Boldenow

Summer Research

• Group B Streptococcus is a leading infectious cause of neonatal morbidity and mortality in the US1
• Ascending infection in the mother can cause adverse birth outcomes2,3
• GBS is defined as being beta-hemolytic, but about three percent of strains are non-hemolytic4
• Recent data suggests that non-hemolytic strains can also pose health risks to infants5
• Previously, we have seen that non-hemolytic strain GB37 displays hemolytic activity in liquid suspension
• We hypothesize that non-hemolytic strains cause inflammation, oxidative stress, and invasion/adhesion in cells similarly to hemolytic strains

Translation Of Partially Decayed Messenger Rnas In Yeast, Ana Luisa Franklin

Electronic Theses and Dissertations

Flaviviruses are positive-strand single-stranded RNA viruses that are known to form pseudo-knot RNA structures that halt the progression of 5’→3’ exonuclease Xrn1. We show that these viral Xrn1-resistant structures (xrRNAs) can be used to protect specific homologously-expressed messenger RNAs from 5’→3’ degradation. We investigated the effects of addition of xrRNAs, artificially-installed into the intergenic region of bicistronic mRNA reporters, in the observed levels of protein expression in yeast. The reporters also contain an internal ribosome entry site from the cricket paralysis virus (CrPV IRES) to allow for cap-independent translation of the decay-protected gene, LacZ, encoding the enzyme β-galactosidase. Through …

Investigation Of Transient Expression System In Nicotiana Bethamiana To Produce Novel Tales And The Development Of (Ds)Dna Detection With Quantum Dot-Labeled Proteins In Graphene Oxide Quenching Arrays, Colleen Jackson

Mahurin Honors College Capstone Experience/Thesis Projects

Our objective was to develop a faster method of quantitively detecting double stranded (ds)DNA of pathogenic bacteria such as the Shiga Toxin 2 gene present in E. coli O157. Transcription Activator-Like Effectors (TALEs) are a new class of DNA-binding proteins which selectively bind to dsDNA with the 12th and 13th amino acids of each repeat, called repeat variable diresidues (RVDs). Novel TALE proteins were designed to target the stx2 gene and were cloned into existing AvrBs3 TALE protein in the pMAL c2x vector system for bacterial BL-21 E. Coli expression. The protein’s DNA-binding region was then subcloned pEAQ vectors for …

Characterization Of Cytosolic Sulfotransferase Expression And Regulation In Human Liver And Intestine, Sarah Talal Dubaisi

Wayne State University Dissertations

SULTs are conjugation enzymes that can modify the activity of a myriad of foreign and endogenous molecules. SULT expression was detected in various human tissues, including liver, small intestine, and colon. There are 13 human SULT genes that are classified into 4 families, SULT1, SULT2, SULT4, and SULT6. In humans, SULT1 and SULT2 families include 11 genes that are further divided into 6 subfamilies. In addition to their role in xenobiotic detoxification and regulation of physiological processes, SULT enzymes were implicated in the bioactivation of procarcinogens. Previous studies detected the expression of most SULT1 and SULT2 enzymes during early development, …

Structure/Function Analysis Of Fega And Fhua In Bradyrhizobium Sp., Alexander James Herd

Senior Honors Projects, 2010-2019

Bradyrhizobium japonicum is a Gram-negative soil bacterium commonly known for its agriculturally significant mutualistic relationship with soybean. In this symbiosis, the bacteria and plant undergo complex molecular signaling characterized by sent and received signals resulting in the formation of infection threads and root nodules. This research aimed to compare two related bacterial outer membrane proteins, FegA and FhuA, associated with the molecular signaling between the bacteria and plant. Previous work has led to the hypothesis that the N-terminal domain (NTD) of FegA in B. japonicum is needed for a functional symbiosis to occur. Recombinant bacterial strains expressing altered FegA proteins …

Synthesis Of Trisubstituted Isoquinoline Alkaloids, Thao Tran, Zach Farrell, Kaitie C. Cartwight, Carolyn E. Anderson

Summer Research

Isoquinoline alkaloids encompasses a large and important group of naturally occurring substances that exhibit a diverse array of biological activity, including treating Yaws and worm infections,1 as well as showing activity as both topoisomerase inhibitors2 and as antibiotics against various quinoline-resistant gram-positive bacteria (Figure 1). 3 In this project, isoquinoline alkaloids, containing stereogenic centers on the backbone, are being pursued.

The Value Of Universally Available Raw Nmr Data For Transparency, Reproducibility, And Integrity In Natural Product Research., James B. Mcalpine, Shao-Nong Chen, Andrei Kutateladze, John B. Macmillan, Giovanni Appendino, Andersson Barison, Mehdi A. Beniddir, Maique W. Biavatti, Stefan Bluml, Asmaa Boufridi, Mark S. Butler, Robert J. Capon, Young H. Choi, David Coppage, Phillip Crews, Michael T. Crimmins, Marie Csete, Pradeep Dewapriya, Joseph M. Egan, Mary J. Garson, Grégory Genta-Jouve, William H Gerwick, Harald Gross, Mary Kay Harper, Precilia Hermanto, James M. Hook, Luke Hunter, Damien Jeannerat, Nai-Yun Ji, Tyler A. Johnson, David G. I. Kingston, Hiroyuki Koshino, Hsiau-Wei Lee, Guy Lewin, Jie Li, Roger G Linington, Miaomiao Liu, Kerry L Mcphail, Tadeusz F Molinski, Bradley S Moore, Joo-Won Nam, Ram P Neupane, Matthias Niemitz, Jean-Marc Nuzillard, Nicholas H Oberlies, Fernanda M M Ocampos, Guohui Pan, Ronald J Quinn, D Sai Reddy, Jean-Hugues Renault, José Rivera-Chávez, Wolfgang Robien, Carla M Saunders, Thomas J Schmidt, Christoph Seger, Ben Shen, Christoph Steinbeck, Hermann Stuppner, Sonja Sturm, Orazio Taglialatela-Scafati, Dean J Tantillo, Robert Verpoorte, Bin-Gui Wang, Craig M Williams, Philip G Williams, Julien Wist, Jian-Min Yue, Chen Zhang, Zhengren Xu, Charlotte Simmler, David C Lankin, Jonathan Bisson, Guido F Pauli

Natural Sciences and Mathematics | Faculty Scholarship

With contributions from the global natural product (NP) research community, and continuing the Raw Data Initiative, this review collects a comprehensive demonstration of the immense scientific value of disseminating raw nuclear magnetic resonance (NMR) data, independently of, and in parallel with, classical publishing outlets. A comprehensive compilation of historic to present-day cases as well as contemporary and future applications show that addressing the urgent need for a repository of publicly accessible raw NMR data has the potential to transform natural products (NPs) and associated fields of chemical and biomedical research. The call for advancing open sharing mechanisms for raw data …

Transcription Factor Binding Site Clusters Identify Target Genes With Similar Tissue-Wide Expression And Buffer Against Mutations., Peter Rogan, Ruipeng Lu

Biochemistry Publications

Background: The distribution and composition of cis-regulatory modules composed of transcription factor (TF) binding site (TFBS) clusters in promoters substantially determine gene expression patterns and TF targets. TF knockdown experiments have revealed that TF binding profiles and gene expression levels are correlated. We use TFBS features within accessible promoter intervals to predict genes with similar tissue-wide expression patterns and TF targets using Machine Learning (ML). Methods: Bray-Curtis Similarity was used to identify genes with correlated expression patterns across 53 tissues. TF targets from knockdown experiments were also analyzed by this approach to set up the ML framework. TFBSs were …

Progress Toward The Synthesis Of Regioisomeric Aminomethyl-Substituted Qpt-1 Bacterial Topoisomerase Inhibitors, Luke Burroughs, Tuba Jaherun, Yena Jin, Nathanael Kazmierczak, Michael Barbachyn

Summer Research

Bacterial resistance to antibiotics is a growing public health threat. Each year, ~2 million infections and 23,000 deaths are caused by antibiotic resistance in the US. 1 Agents targeting the essential bacterial type II topoisomerases DNA gyrase and topoisomerase IV, as exemplified by the fluoroquinolones (FQs), have been shown to be useful antibiotics. FQs such as ciprofloxacin, moxifloxacin, and levofloxacin, to name a few, are broadspectrum antibacterial agents that have been in clinical use since the 1980's. Unfortunately, heavy use of the FQs has inevitably led to the development of FQresistant pathogens. 2 A gyrase inhibitor lead compound called QPT-1 …

Preparation Of A Novel Trifluoroborate Reagent And Initial Investigations Into Its Use In Suzuki-Miyaura Cross-Coupling Reactions., Kangjin Lee, Michael Barbachyn

Summer Research

No abstract provided.

Synthesis Of Trisubstituted Indolizines From 2-Propargyloxypyridines, Colin T. Hartgerink, Jaimie E. Van De Burg, Carolyn E. Anderson

Summer Research

• Indolizines are a versatile heterocyclic core that occurs frequently in pharmaceutical leads for a variety of indications, including: anti-bacterial1 and anti-tumor agents,2 and targets for the treatment of Alzheimer’s disease,3 asthma,4 erectile dysfunction,5 and inflammation related to respiratory or cardiovascular disease.
• While evaluating the scope of a Au(I)-catalyzed rearrangement of 2- propargyloxypyridine 1, 7 substituted indolizine 4 was discovered as an unexpected by-product (Scheme 1). The structure of indolizine 4 was confirmed by NMR and Xray analysis. Investigations revealed that acetophenone, originally present as an impurity in the reaction, is a key reagent. The use of acetophenone as the solvent, …

Demonstration Of Single Ion Channel Activity In Lipid Bilayers With Temperature Control, Alex Van Kooten, Brian Seper, Loren Haarsma

Summer Research

Lipids are fat-soluble molecules that can naturally form bilayers when exposed to water. Lipid bilayers form the outer boundary of cells, providing a way for cells to isolate themselves from their environment. While bilayer membranes are generally impermeable to ions, proteins known as ion channels allow for ion transport across the membrane. Gramicidin A is one such molecule whose behavior has been studied. While some experimental and computational analysis of gramicidin A has been performed1,2,3, more work is needed to systematically study this ion channel’s behavior at high temperatures (above 50 °C) and in bilayers composed of different lipids. We …

Preliminary Design & Evaluation Of An Edna Assay For Wild Rice, Sage Riley, Kelli Laube, Drew Van Andel, William L. Miller

Summer Research

No abstract provided.

Role Of Dyslipidemia On Lipid Metabolism In Maintenance Hemodialysis Patients, Eno Latifi

Wayne State University Dissertations

Maintenance hemodialysis (MHD) patients experience various abnormalities such as systemic inflammation (SI), oxidative stress (OS), and dyslipidemia (D). Defined as an imbalance of plasma lipids, lipoproteins, and lipid metabolism enzymes, D has been associated with a rise in morbidity and mortality within ESRD patients due to cardiovascular disease (CVD). However, the contribution of each of these parameters to D is poorly understood; moreover, the impact of the following parameters on dyslipidemia in different ethnicities is unknown. Hence, the objective of this study was to characterize D in a multi-ethnic cohort of ESRD patients. We hypothesized that the degree of dyslipidemia …

Trna Aminoacylation: New Protein Players And New Reactions, Whitney Noel Wood

Wayne State University Dissertations

TRNA AMINOACYLATION: NEW PROTEIN PLAYERS AND NEW REACTIONS

by

WHITNEY N. WOOD

May 2019

Advisor: Dr. Tamara L. Hendrickson

Major: Chemistry (Biochemistry)

Degree: Doctor of Philosophy

Protein translation must usually occur with high accuracy for an organism to survive. However, Helicobacter pylori, Staphylococcus aureus, and many other microorganisms including important human pathogens, lack one or more aminoacyl-tRNA synthetase (aaRS), the enzymes that typically aminoacylate tRNAs for ribosomal translation. These organisms must use an indirect pathway to aminoacylate some tRNAs. Specifically, H. pylori lacks the genes that encode for asparaginyl- and glutaminyl-tRNA synthetases (AsnRS and GlnRS, respectively). Instead, H. pylori uses …

The Role Of The Cell-Surface Protease Tmprss13 In Colorectal Cancer, Fausto Alexander Varela

Wayne State University Dissertations

Colorectal cancer (CRC) is one of the most common and deadly cancers in both men and women in the United States. Extracellular proteolysis is often dysregulated in cancer including (CRC), resulting in degradation of extracellular matrix, as well as cleavage, processing, or shedding of cell adhesion molecules, growth factors, and cytokines. Several members of the type II transmembrane serine protease (TTSP) family have been shown to play critical roles in cancer progression; however, many family members have not yet been characterized in malignancy. We identified TMPRSS13 transcript to be upregulated in CRC compared to normal colon. This increase was confirmed …

Reintegrating Biology Through The Nexus Of Information And Energy, Kim L. Hoke, Sara L. Zimmer, Mary Jo Ondrechen, Amedee Des Georges, Adam B. Roddy, Nicole R. Buan, Craig E. Williamson

Department of Biochemistry: Faculty Publications

Recent rapid advances in biology have led to diversification and sub-specialization of many fields, as well as a corresponding explosion of new findings. Advances in tools ranging from genomic techniques and high-resolution imaging to automated ecosystem- and biosphere-level sensors, along with correspondingly advanced analytics, have led to critical new insights that are transforming our understanding of biological systems. One of the consequences of these rapid advances has been accelerated splintering of biology into sub-disciplines with highly focused questions, vocabulary, and techniques. This splintering creates barriers to synergy across fields of biology and hinders the insights that could be gained at …

Predicting The Structure And Selectivity Of Coiled-Coil Proteins, Mojtaba Jokar

Wayne State University Dissertations

A coiled-coil protein structure consists of two (in coiled-coil dimers) or more interacting α-helical strands that together form a left-handed supercoil structure. Many coiled-coil proteins are involved in significant biological functions such as the regulation of gene expression, known as transcription factors. Also coiled-coil structures entail unique mechanical properties critical to the function and integrity of various motor proteins, cytoskeletal filaments and extra-cellular matrix proteins. Engineering these transcription factors is also expected to create more efficient and practical solutions to treat neurodegenerative diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), amyotrophic lateral sclerosis (ALS) and prion …

Bog Flora In The Grand Rapids, Michigan, Area: A Comparative Study Across Sites And Over Time O 1901 To 2017, Devani Antuma Jolman, Jenna L. Van Donselaar, David P. Warners, Garrett E. Crow

Faculty and Professional Research

Michigan’s natural landscape includes a diverse assemblage of ecosystems, among the most distinctive of which are peatlands, and more specifically, those known colloquially as “bogs.” When botanist Emma J. Cole published the Grand Rapids Flora in 1901, she included a large number of bog species documented in the greater Grand Rapids area (16 townships in two counties, an area of 585 square miles). Cole’s Flora is still the most comprehensive catalog of vascular plants found in West Michigan. This study is part of an ongoing update of Cole’s work undertaken by the Calvin University Herbarium to relocate and inventory Emma …

Split Probe Detection Of The Influenza A Virus For Improved Diagnostics In A Point Of Care System, Tamar Yishay

Honors Undergraduate Theses

A group of Influenza viruses, RNA containing viruses of the Orthomyxoviridae family, consists of Influenza virus types A-D and has been known to cause the Flu, a respiratory illness associated with numerous detrimental symptoms that can lead to death. Influenza A virus (IAV) is constantly changing and is capable of causing pandemics. Currently used diagnostic methods include virus culturing, immunoassays including rapid influenza detection tests (RIDTs), and molecular assays including those based on RT-PCR. Most of the methods can be only performed in the certified diagnostic laboratories equipped with sophisticated instrumentation and/or special biosafety facilities. The results using these methods …

Urinalysis Screening Of Drugs In Adulterated Samples Via Direct Analysis In Real Time -- High Resolution/ Mass Spectrometry (Dart-Hr/Ms), Bianca E. Olivieri

Honors Undergraduate Theses

Current screening methods for drug analysis with urine samples includes examination of the sample with an immunoassay. These methods are used to determine the concentration of drug metabolites contained within the sample prior to further confirmatory testing. Drug testing plays a crucial role in maintaining safe workplace environments and safety of individuals. However, a positive result can lead to heavy consequences for the employee including suspension or removal from the workplace. Therefore, a majority of individuals add commonly known products into the sample to evade detection by developing a false negative result. Although specimen integrity examinations are performed to identify …