Biochemistry Commons^™

Development Of Ultrafast Broadband Electronic Sum Frequency Generation For Charge Dynamics At Surfaces And Interfaces, Gang-Hua Deng, Yuqin Qian, Yi Rao

Chemistry and Biochemistry Faculty Publications

Understandings of population and relaxation of charges at surfaces and interfaces are essential to improve charge collection efficiency for energy conversion, catalysis, and photosynthesis. Existing time-resolved surface and interface tools are limited to either under ultrahigh vacuum or in a narrow wavelength region with the loss of spectral information. There lacks an efficient time-resolved surface/interface-specific electronic spectroscopy under ambient conditions for the ultra fast surface/interface dynamics. Here we developed a novel technique for surface/interface-specific broadband electronic sum frequency generation (ESFG). The broadband ESFG was based on a stable two-stage BiB₃O₆ crystal-based optical parametric amplifier, which generates a …

Fabrication Of Miniaturized Paper-Based Microfluidic Devices (Micropads), E. Brandon Strong, Spencer A. Schultz, Andres Martinez, Nathaniel W. Martinez

Chemistry and Biochemistry

Microfluidic paper-based analytical devices (microPADs) are emerging as cost-effective and portable platforms for point-of-care assays. A fundamental limitation of microPAD fabrication is the imprecise nature of most methods for patterning paper. The present work demonstrates that paper patterned via wax printing can be miniaturized by treating it with periodate to produce higher-resolution, high-fidelity microPADs. The optimal miniaturization parameters were determined by immersing microPADs in various concentrations of aqueous sodium periodate (NaIO₄) for varying lengths of time. This treatment miniaturized microPADs by up to 80% in surface area, depending on the concentration of periodate and length of the reaction …

Radiation Dose Estimation By Completely Automated Interpretation Of The Dicentric Chromosome Assay, Peter Rogan, Yanxin Li, Ben Shirley, Ruth Wilkins, Farrah Norton, Joan Knoll

Biochemistry Publications

Accuracy of the automated dicentric chromosome (DC) assay relies on metaphase image selection. This study validates a software framework to find the best image selection models that mitigate inter-sample variability. Evaluation methods to determine model quality include the Poisson goodness-of-fit of DC distributions for each sample, residuals after calibration curve fitting and leave-one-out dose estimation errors. The process iteratively searches a pool of selection model candidates by modifying statistical and filter cut-offs to rank the best candidates according to their respective evaluation scores. Evaluation scores minimize the sum of squared errors relative to the actual radiation dose of the calibration …

A Bird's-Eye View Of The Multiple Biochemical Mechanisms That Propel Pathology Of Alzheimer's Disease: Recent Advances And Mechanistic Perspectives On How To Halt The Disease Progression Targeting Multiple Pathways., Caleb Vegh, Kyle Stokes, Dennis Ma, Darcy Wear, Jerome Cohen, Sidhartha D. Ray, Siyaram Pandey

Touro College of Pharmacy (New York) Publications and Research

Neurons consume the highest amount of oxygen, depend on oxidative metabolism for energy, and survive for the lifetime of an individual. Therefore, neurons are vulnerable to death caused by oxidative-stress, accumulation of damaged and dysfunctional proteins and organelles. There is an exponential increase in the number of patients diagnosed with neurodegenerative diseases such as Alzheimer’s (AD) as the number of elderly increases exponentially. Development of AD pathology is a complex phenomenon characterized by neuronal death, accumulation of extracellular amyloid-β plaques and neurofibrillary tangles, and most importantly loss of memory and cognition. These pathologies are most likely caused by mechanisms including …

Regulation Of Respiration And Apoptosis By Cytochrome C Threonine 58 Phosphorylation, Junmei Wan, Hasini A. Kalpage, Asmita Vaishnav, Jenney Liu, Icksoo Lee, Gargi Mahapatra, Alice A. Turner, Matthew P. Zurek, Qinqin Ji, Carlos T. Moraes, Maurice-Andre Recanati, Lawrence I. Grossman, Arthur R. Salomon, Brian Fp Edwards, Maik HüTtemann

Biochemistry and Molecular Biology Faculty Publications

Cytochrome c (cytc) is a multifunctional protein, acting as an electron carrier in the electron transport chain (ETC), where it shuttles electrons from bc1 complex to cytochrome c oxidase (COX), and as a trigger of type II apoptosis when released from the mitochondria. We previously showed that cytc is regulated in a highly tissue-specific manner: Cytc isolated from heart, liver, and kidney is phosphorylated on Y97, Y48, and T28, respectively. Here, we have analyzed the effect of a new Cytc phosphorylation site, threonine 58, which we mapped in rat kidney Cytc by mass spectrometry. We generated and overexpressed wild-type, phosphomimetic …

Identifying C-Mannosylatedproteins In Raw264.7 Cells Via In Vitro Hsc70 Co-Immunoprecipitation Strategies, Nicholas Ryan Kegley

Theses, Dissertations and Capstones

C-mannosylation is a specific type of glycosylation in which α-mannose is covalently bound to the C2 atom of a tryptophan via a carbon-carbon bond. Presently, it is known to occur on proteins that contain the W-x-x-W-x-x-W/C motif found within the Thrombospondin Type-1 Repeat (TSR), with ‘x’ denoting any amino acid. C-mannosylation has been implicated in a number of cellular functions, including protein secretion and type I cytokine receptor function. Previous research has shown that exogenous C-mannosylated peptides derived from TSR-containing proteins upregulate the production of the pro-inflammatory cytokine Tumor Necrosis Factor alpha (TNF-α) in RAW264.7 macrophage cells. This upregulation is …

Characterizing The Effects Of Environmental Stressors On The Photosynthetic Capacity Of Chlorella Vulgaris, Amanda Louise Smythers

Theses, Dissertations and Capstones

Chlorella vulgaris is a unicellular green algae grown throughout the world. Due to its multiple trophic modes as well as its ability to maintain high rates of growth under adverse conditions, it has been of global interest for use in ecological contamination studies, biofuel feedstock optimization, and studies of photosynthetic electron transfer. Using a wide-range of methods for physiological and photosynthetic characterization, the studies within seek to further extend the usefulness of C. vulgaris in a variety of environmentally important studies. Once the protocols were optimized specifically for this alga, they could be applied in both ecologically relevant and biodiesel …

Isolation And Identification Of Hsc70 Conjugates In Raw264.7 Murine Macrophage-Like Cells, Michael Arland Parsons

Theses, Dissertations and Capstones

IL12R- β2 is a Type I cytokine receptor and contains the WXXW (WSNWS) sequence that often predicates the post-translational addition of mannose to a tryptophan residue via a carbon-carbon bond. This study will stimulate expression of IL12R- β2 in RAW 264.7 Macrophage-Like Cells by shutting down the extracellular signal kinase (ERK) pathway and introducing inflammatory agents lipopolysaccharide and CpG DNA in order to collect a concentrated sample of IL12R- β2. These samples will be analyzed for the presence of C-mannosyltryptophan residue

Method Development For Structural Assessment Of Nanolipoprotein Particles With And Without Cross-Linked Lipids, Emma J. Mullen, Wei He, Sean Gilmore, Matthias Frank, Matthew Coleman, Megan Shelby

STAR Program Research Presentations

Membrane proteins make up approximately 30% of the cellular proteome and account for over 60% of pharmaceutical targets.1 Determining the structures of this class of proteins is critical to our understanding of disease states and will advance rational drug design. But membrane proteins have limited solubility, rarely form large crystals that diffract well, and often misfold outside of a bilayer, hindering crystallographic studies.1 Nanolipoprotein particles (NLPs) have arisen as a platform to readily solubilize membrane proteins while mimicking a native lipid environment. NLPs consist of a discoidal phospholipid bilayer encircled by an apolipoprotein belt. In an effort to optimize and …

Case 61: Inhibition Of Malarial Aspartate Protease, Dr. Kathleen Cornely

Chemistry & Biochemistry Case Studies

In this case study, students investigate the purification and kinetic properties of a malarial asparate protease.

Amelioration Of Alzheimer's Disease Pathology In 12-Month-Old Happ(Sweind) Transgenic Mice After Treatment With A Cysteine Rich Whey Supplement, Immunocal®, Srivalli Puttagunta

Electronic Theses and Dissertations

Deficits in Reelin expression and signaling play a pathogenic role in Alzheimer’s disease (AD). Thus, strategies aimed at correcting Reelin deficits may provide a novel therapeutic approach to treating AD. The cysteine-rich, whey protein supplement, Immunocal®, has recently been shown to rescue Reelin expression in a mouse model of Schizophrenia. Given that Reelin-expressing neurons of the entorhinal cortex region are a highly vulnerable population of cells that are lost early in AD, we examined the effects of Immunocal® in the hippocampal-entorhinal cortex formation in a mouse model of AD. Glutathione levels and Reelin expression in the hippocampal-entorhinal cortex formation (entorhinal …

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 …

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. …

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 …

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 …

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 …

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 …

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 …

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 …

Dna Methylation: Atherosclerosis Leading To Congenital Heart Diseases, Sher Khan, Rehana Rehman

Department of Biological & Biomedical Sciences

No abstract provided.

Identification Of Proteins Interacting With Zebrafish Miro Orthologs In The Yeast Two-Hybrid System, Yiran Tao

Honors Program Theses

The motility of mitochondria is required for providing energy and maintaining basic cellular functions in neurons. Mitochondrial Rho GTPase (Miro) is an essential component of the mitochondrial trafficking machinery, a protein complex that anchors mitochondria to the microtubule motor protein for long-distance transport. As a protein localizing to the mitochondrial outer membrane, Miro regulates the morphology and the motility of mitochondria. Upon mitochondrial depolarization, the PINK1/Parkin pathway is activated to arrest mitochondrial movement by targeting Miro for phosphorylation and ubiquitination in a calcium-sensitive manner. However, it remains unclear what effects the PINK1-dependent phosphorylation has on the structure and binding properties …