Digital Commons Network^™

The Temporal Dynamics Of The Tracheal Microbiome In Tracheostomised Patients With And Without Lower Respiratory Infections., Marcos Pérez-Losada, Robert J Graham, Madeline Coquillette, Amenah Jafarey, Eduardo Castro-Nallar, Manuel Aira, Robert J Freishtat, Jonathan M Mansbach

Computational Biology Institute

Background: Airway microbiota dynamics during lower respiratory infection (LRI) are still poorly understood due, in part, to insufficient longitudinal studies and lack of uncontaminated lower airways samples. Furthermore, the similarity between upper and lower airway microbiomes is still under debate. Here we compare the diversity and temporal dynamics of microbiotas directly sampled from the trachea via tracheostomy in patients with (YLRI) and without (NLRI) lower respiratory infections. Methods: We prospectively collected 127 tracheal aspirates across four consecutive meteorological seasons (quarters) from 40 patients, of whom 20 developed LRIs and 20 remained healthy. All aspirates were collected when patients had no …

Assessment Of Disease Lesion Removal As A Method To Control Chronic Montipora White Syndrome, Silvia Beurmann, Christina M. Runyon, Patrick Videau, Sean M. Callahan, Greta S. Aeby

Research & Publications

Coral colonies in Ka–ne‘ohe Bay, Hawai‘i (USA), are afflicted with the tissue loss disease chronic Montipora white syndrome (cMWS). Here we show that removal of chronic disease lesions is a potential method to slow the progression of cMWS in M. capitata. Over the 24 wk observation period, treatment colonies lost almost half the amount of tissue that was lost by control colonies. The percentage of tissue loss at each sampling interval (mean ± SEM; treatment: 1.17 ± 0.47%, control: 2.25 ± 0.63%) and the rate of tissue loss per day (treatment: 0.13 ± 0.04%, control: 0.27 ± 0.08%) were both …

Identification And Characterization Of Fungal Isolates From Land-Applied Sewage Sludge, Vaille Swenson, Hope L. Juntunen, R Honour, R C. Hale, Michael Gaylor, Patrick Videau

Research & Publications

Approximately eight million dry tons of sewage sludge is generated in the U.S. each year, with more than half of that now land-applied as the primary method of disposal. Despite the proliferation of this practice, little is known about the microbial constituents of these noxious materials. To address this knowledge gap, we isolated and characterized fungi present in archived samples of land-disposed sewage sludge collected from the Snoqualmie National Forest (Washington State). Sludge samples were resuspended in sterile water and 15 fungal isolates were selected and purified on sabouraud dextrose agar plates supplemented with 50 mg/L of chloramphenicol. Fungal morphology …

Hepatocyte-Specific Deletion Of Tristetraprolin Family Of Rna Binding Proteins Result In The Development Of Hepatocellular Carcinomas, Sonika Patial

Hepatobiliary Cancers: Pathobiology and Translational Advances

No abstract provided.

Identifying The Relevance Of C-Reactive Protein Conformers And The Advancement Of A Membrane Curvature Binding Assay, Carrie Leine Moon

Electronic Theses and Dissertations

Lipid membranes play a vital role in cell signaling processes. Membrane shape and lipid content affect interactions between cellular membranes and proteins. This research focuses on characterizing those interactions and their impact by using various biochemical and biophysical assays. These assays were applied to C-reactive protein (CRP), an immune system protein that interacts with lipid membranes and has at least two forms with different properties. Native, pentameric CRP (pCRP) is found in blood serum and is commonly used as a marker for inflammation. The modified form of CRP (mCRP) binds to the protein C1q, which activates the complement immune response. …

Mechanistic Insights Into The Radical S-Adenosyl L-Methionine Enzyme Mftc, Bulat Khaliullin

Electronic Theses and Dissertations

Mycofactocin is a putative peptide-derived redox cofactor in Mycobacterium family. Its putative biosynthetic pathway is encoded by the operon mftABCDEF. The initial step of this pathway is a posttranslational modification of a peptide precursor MftA, which is catalyzed by MftC enzyme. This modification only occurs in the presence of chaperone MftB. Here, we demonstrate that MftC is a radical S-adenosyl L-methionine (SAM) enzyme and we examine its catalytic mechanism. We show that the modification of MftA requires two equivalents of SAM and is implemented in two steps: (i) the decarboxylation of a C-terminal tyrosine, resulting in formation of an …

Paper-Based Diagnostic Devices, Spencer A. Schultz, Isabelle C. Noxon, Tyler A. Sisley, Andres W. Martinez

Chemistry and Biochemistry

This chapter will provide an overview of existing diagnostic devices made primarily out of paper and then focus on paper-based microfluidic devices, the next generation of paper-based diagnostic devices that promises to extend the use of paper as a material for fabricating diagnostic devices well into the future.

Chapter Contents:

• 2.1 Introduction
• 2.2 Current paper-based diagnostic devices
• 2.2.1 Dipstick devices
• 2.2.2 Lateral-flow devices
• 2.2.2.1 Vertical-flow devices
• 2.2.3 Paper-based arrays
• 2.3 Paper-based microfluidic devices
• 2.3.1 Fabrication of paper-based microfluidic devices
• 2.3.2 Applications of paper-based microfluidic devices
• 2.4 Conclusions
• References

Alignment Of Mitotic Chromosomes In Human Cells Involves Sr-Like Splicing Factors Btf And Trap150, Sapna Varia, Divya Cheedu, Michael P. Markey, Keshia Torres-Shafer, Vishnu P. Battini, Athanasios Bubulya, Paula A. Bubulya

Biochemistry and Molecular Biology Faculty Publications

Serine-arginine-rich (SR) or SR-like splicing factors interact with exon junction complex proteins during pre-mRNA processing to promote mRNA packaging into mature messenger ribonucleoproteins (mRNPs) and to dictate mRNA stability, nuclear export, and translation. The SR protein family is complex, and while many classical SR proteins have well-defined mRNA processing functions, those of other SR-like proteins is unclear. Here, we show that depletion of the homologous non-classical serine-arginine-rich (SR) splicing factors Bcl2-associated transcription factor (Btf or BCLAF) and thyroid hormone receptor-associated protein of 150 kDa (TRAP150) causes mitotic defects. We hypothesized that the depletion of these SR-like factors affects mitosis indirectly …

Pseudoalteromonas Piratica Sp. Nov., A Budding, Prosthecate Bacterium From Diseased Montipora Capitata, And Emended Description Of The Genus Pseudoalteromonas, Silvia Beurmann, Blake Ushijima, Christina M. Svoboda, Patrick Videau, Ashley M. Smith, Stuart P. Donachie, Greta S. Aeby, Sean M. Callahan

Research & Publications

A Gram-stain-negative, motile, rod-shaped bacterium designated OCN003T was cultivated from mucus taken from a diseased colony of the coral Montipora capitata in Kāne‘ohe Bay, O‘ahu, Hawai‘i. Colonies of OCN003T were pale yellow, 1–3 mm in diameter, convex, smooth and entire. The strain was heterotrophic, strictly aerobic and strictly halophilic. Cells of OCN003T produced buds on peritrichous prosthecae. Growth occurred within the pH range of 5.5 to 10, and the temperature range of 14 to 39 °C. Major fatty acids were 16 : 1!7c, 16 : 0, 18 : 1!7c, 17 : 1!8c, 12 : 0 3-OH and 17 : 0. …

Neuronal Gq Structures In Neurodegeneration, Damian S. Mcaninch

Electronic Theses and Dissertations

This study investigates protein nucleic acid interactions between various proteins and G quadruplex (GQ) forming messenger RNAs (mRNAs) in human neurological disorders. GQ structures are formed in DNA/RNA, when four guanine residues form planar tetrads stabilized by Hoogsteen base pairing, that stack forming a GQ structure stabilized by potassium ions. These GQ structures are targeted by the arginine-glycine-glycine (RGG) repeat domain containing RNA-binding domain.

Three RGG domain containing RNA-binding proteins, all of which have been implicated in neurological disorders, and their interactions with GQ forming mRNAs, were investigated in this study: fused in sarcoma (FUS), fragile X mental retardation protein …

Dense Core Vesicle Heterogeneity In Anterior Pituitary Cells, Kelly Sinak

Electronic Theses and Dissertations

Peptides, which are packaged in dense core vesicles, are an integral part of the function of the endocrine and neurological systems. The dense core vesicles function as an efficient form of peptide storage prior to regulated exocytosis. Two different dense core specific transmembrane proteins traffic different when comparted to retained prolactin cores, offering evidence of heterogeneity of vesicles within a single cell. By comparing synaptotagmin 1 and 7 distribution in male rat and lactating female lactotrophs, a distinct pattern emerges. Cells that retain prolactin cores after exocytosis correspond with those that contain synaptotagmin 1. This finding is a reversal for …

Code For "Noise-Enhanced Coding In Phasic Neuron Spike Trains", Cheng Ly, Brent D. Doiron

Statistical Sciences and Operations Research Data

This zip file contains Matlab scripts and ode (XPP) files to calculate the statistics of the models in "Noise-Enhanced Coding in Phasic Neuron Spike Trains". This article is published in PLoS ONE.

Development Of Cellular Assays To Monitor Enzymatic And Biological Activity Of Cd73: A Key Modulator Of Anti-Tumor Immune Response, Alexandra Fanuka

Graduate School of Biomedical Sciences Theses and Dissertations

Ecto-5’-nucleotidase, known as CD73, is an extracellular enzyme that converts adenosine monophosphate (AMP) to adenosine and has recently been identified as a potential drug target for cancer immunotherapy. Its immunosuppressive effects, mediated by the activity of adenosine, are associated with higher rates of tumor invasion and metastasis, as well as poorer prognoses overall in many cancer types. CD73 is often co-expressed with ectonucleoside triphosphate diphosphohydrolase-1 (CD39), which catalyzes the conversion of adenosine triphosphate (ATP) to adenosine diphosphate (ADP), and ADP to AMP on the surface of tumor cells. Dual expression further propagates immunosuppressive effects of adenosine in the tumor microenvironment. …

Genetic Polymorphisms In Caveolin-1 Associate With Breast Cancer Risk In Chinese Han Population, M Wang, T Tian, X Ma, W Zhu, Y Guo, Z Duan, J Fan, S Lin, K Liu, Y Zheng, Q Sheng, Z J. Dai, H Peng

Biochemistry and Molecular Medicine Faculty Publications

Caveolin-1(CAV-1) was demonstrated to be a tumor suppressor gene and be implicated in the development of breast cancer (BC). Numerous potentially functional polymorphisms in CAV-1 have been identified, but their effects on BC were not clear. This case-control study aims to evaluate the relationship between CAV-1 polymorphisms and BC risk. 560 BC patients and 583 healthy controls were enrolled in the present study, all from Chinese Han population. We detected 3 single nucleotide polymorphisms (rs3807987, rs1997623, and rs7804372) in CAV-1 using the Sequenom MassARRAY method. The association between CAV-1genotypes and BC risk was assessed in six genetic …

Probing For Binding Regions Of The Ftsz Protein Surface Through Site-Directed Insertions: Discovery Of Fully Functional Ftsz-Fluorescent Proteins, Desmond A. Moore, Zakiya N. Whatley, Chandra P. Joshi, Masaki Osawa, Harold P. Erickson

Biology Faculty Publications

FtsZ, a bacterial tubulin homologue, is a cytoskeletal protein that assembles into protofilaments that are one subunit thick. These protofilaments assemble further to form a “Z ring” at the center of prokaryotic cells. The Z ring generates a constriction force on the inner membrane and also serves as a scaffold to recruit cell wall remodeling proteins for complete cell division in vivo. One model of the Z ring proposes that protofilaments associate via lateral bonds to form ribbons; however, lateral bonds are still only hypothetical. To explore potential lateral bonding sites, we probed the surface of Escherichia coli FtsZ …

Airborne Measurements Of Western U.S. Wildfire Emissions: Comparison With Prescribed Burning And Air Quality Implications, Xiaoxi Liu, L. Gregory Huey, Robert J. Yokelson, Vanessa Selimovic, Isobel J. Simpson, Markus Müller, Jose L. Jimenez, Pedro Campuzano-Jost, Andreas J. Beyersdorf, Donald R. Blake, Zachary Butterfield, Yonghoon Choi, John D. Crounse, Douglas A. Day, Glenn S. Diskin, Manvendra K. Dubey, Edward Fortner, Thomas F. Hanisco, Weiwei Hu, Laura E. King, Lawrence Kleinman, Simone Meinardi, Tomas Mikoviny, Timothy B. Onasch, Brett B. Palm, Jeff Peischl, Ilana B. Pollack, Thomas B. Ryerson, Glen W. Sachse, Arthur J. Sedlacek, John E. Shilling, Stephen Springston, Jason M. St. Clair

Chemistry and Biochemistry Faculty Publications

Wildfires emit significant amounts of pollutants that degrade air quality. Plumes from three wildfires in the western U.S. were measured from aircraft during the Studies of Emissions and Atmospheric Composition, Clouds and Climate Coupling by Regional Surveys (SEAC4RS) and the Biomass Burning Observation Project (BBOP), both in summer 2013. This study reports an extensive set of emission factors (EFs) for over 80 gases and 5 components of submicron particulate matter (PM1) from these temperate wildfires. These include rarely, or never before, measured oxygenated volatile organic compounds and multifunctional organic nitrates. The observed EFs are compared with previous measurements of temperate …

A Dual-Chamber Method For Quantifying The Effects Of Atmospheric Perturbations On Secondary Organic Aerosol Formation From Biomass Burning Emissions, Daniel S. Tkacik, Ellis S. Robinson, Adam Ahern, Rawad Saleh, Chelsea Stockwell, Patrick Veres, Isobel J. Simpson, Simone Meinardi, Donald R. Blake, Robert J. Yokelson, Albert A. Presto, Ryan C. Sullivan, Neil M. Donahue, Allen L. Robinson

Chemistry and Biochemistry Faculty Publications

Biomass burning (BB) is a major source of atmospheric pollutants. Field and laboratory studies indicate that secondary organic aerosol (SOA) formation from BB emissions is highly variable. We investigated sources of this variability using a novel dual-smog-chamber method that directly compares the SOA formation from the same BB emissions under two different atmospheric conditions. During each experiment, we filled two identical Teflon smog chambers simultaneously with BB emissions from the same fire. We then perturbed the smoke with UV lights, UV lights plus nitrous acid (HONO), or dark ozone in one or both chambers. These perturbations caused SOA formation in …

In Situ Measurements Of Water Uptake By Black Carbon-Containing Aerosol In Wildfire Plumes, Anne E. Perring, Joshua P. Schwarz, Milos Z. Markovic, David W. Fahey, Jose L. Jimenez, Pedro Campuzano-Jost, Brett D. Palm, Armin Wisthaler, Tomas Mikoviny, Glenn Diskin, Glen Sachse, Luke Ziemba, Bruce Anderson, Taylor Shingler, Ewan Crosbie, Armin Sorooshian, Robert Yokelson, Ru Shan Gao

Chemistry and Biochemistry Faculty Publications

Water uptake by black carbon (BC)-containing aerosol was quantified in North American wildfire plumes of varying age (1 to ~40 h old) sampled during the SEAC4RS mission (2013). A Humidified Dual SP2 (HD-SP2) is used to optically size BC-containing particles under dry and humid conditions from which we extract the hygroscopicity parameter, κ, of materials internally mixed with BC. Instrumental variability and the uncertainty of the technique are briefly discussed. An ensemble average κ of 0.04 is found for the set of plumes sampled, consistent with previous estimates of bulk aerosol hygroscopicity from biomass burning sources. The temporal evolution of …

Development Of Tools For Phosphosite-Specific Kinase Identification And Discovery Of Phosphatase Substrates, Pavithra Maheshani Dedigama Arachchige

Wayne State University Dissertations

Phosphorylation is a ubiquitous post translational modification implicated in many diseases, such as cancer. The phosphorylation status of cellular proteins is regulated by the activity of kinases and phosphatases. The biological significance of many phosphorylation events remain unknown because the methods to determine which kinase or phosphatase is responsible for phosphorylation are limited. Previously, we established kinase-catalyzed labeling where kinases accept γ-modified ATP analogs, such as ATP-arylazide and ATP-biotin, to label phosphoproteins. To study substrates of kinases and phosphatases, here we developed two new methods using kinase-catalyzed labeling. As one application, we developed K-CLASP (Kinase-catalyzed CrossLinking And Streptavdin Purification) to …

Design, Synthesis And Biological Evaluation Of Histone Deacetylase (Hdac) Inhibitors: Saha (Vorinostat) Analogs And Biaryl Indolyl Benzamide Inhibitors Display Isoform Selectivity, Ahmed Negmeldin

Wayne State University Dissertations

HDAC proteins have emerged as interesting targets for anti-cancer drugs due to their involvement in cancers, as well as several other diseases. Several HDAC inhibitors have been approved by the FDA as anti-cancer drugs, including SAHA (suberoylanilide hydroxamic acid, Vorinostat). Unfortunately, SAHA inhibits most HDAC isoforms, which limit its use as a pharmacological tool and may lead to side effects in the clinic. In this work we were interested in developing isoform selective HDAC inhibitors, which may decrease or eliminate the side effects associated with non-selective inhibitors treatment. In addition, isoform selective HDAC inhibitors can be used as biological tools …

Development Of Chemical Tools To Investigate Protein S-Glutathionylation In Response To Metabolic Alteration, Kusal Theekshana Gayan Samarasinghe

Wayne State University Dissertations

Oxidative stress is a common characteristic of age-related diseases such as vascular diseases, diabetes and cancer. Many diseases are known to be regulated by glutathionylation. Glutathionylation is referred to as the formation of disulfide bond between a protein cysteine and a glutathione. To understand the molecular mechanisms behind the disease initiation and progression, identification of such glutathionylated proteins is important. Even though existing methods have been widely used, several limitations of these methods hinder the identification of such proteins in disease conditions. Therefore, we developed a versatile chemical method that generates clickable glutathione inside the cells. In this method, we …

Ligand Binding Studies Of A Peptide Targeting Helix 69 Of 23s Rrna In Bacterial Ribosomes, Hyosuk Seo

Wayne State University Dissertations

In the development of finding a peptide targeting H69 of 23S rRNA in bacterial ribosomes, phage display was employed at pH 5.5, a buffer condition previously reported of H69 preferring a closed conformation. After sequencing, several peptides were chosen through sequence alignment, followed by preparation using solid-phase peptide synthesis. The peptides were characterized using MALDI-TOF and purified with HPLC. A truncated peptide TARHIY was selected from FID assay. Through binding studies using ESI-MS, SPR, BLItz, and NMR, the binding properties of the peptide to H69 were determined, such as binding affinity, stoichiometry, and interaction site. The peptide exhibited moderate binding …

The Development Of Chemical Methods To Discover Kinase Substrates And Map Cell Signaling With Gamma-Modified Atp Analog-Dependent Kinase-Catalyzed Phosphorylation, Dissanayaka Mudiyanselage Maheeka Madhubashini Embogama

Wayne State University Dissertations

Kinase-catalyzed phosphorylation plays an important role in cell physiology by regulating a myriad of cellular functions. Thus aberrant kinase activity is implicated in various diseases. Methods are needed to discover kinase substrates and map signaling pathways to explore biology and to help drug discovery. A few techniques are currently available to discover kinase substrate and map cell signaling. However, to augment kinase substrate discovery approaches, it is essential to develop alternative techniques. Pflum has recently discovered cosubstrate promiscuity of protein kinases with gamma-modified ATP analogs. Here, kinase-catalyzed biotinylation with ATP-biotin was used to develop novel tools to discover kinase substrates …

Ptpro Represses Erbb2-Driven Breast Oncogenesis By Dephosphorylation And Endosomal Internalization Of Erbb2., H Dong, L Ma, J Gan, W Lin, Rakesh Kumar, +9 Additional Authors

Biochemistry and Molecular Medicine Faculty Publications

The plasma membrane-associated tyrosine phosphatase PTPRO is frequently transcriptionally repressed in cancers and signifies poor prognosis of breast cancer patients. In this study, deletion of Ptpro inMMTV-Erbb2 transgenic mice dramatically shortened the mammary tumor latency and accelerated tumor growth due to loss of Ptpro within the breast cancer cells but not in surrounding tissue as confirmed by hetero-transplantation studies. Both in vitro and in vivo data demonstrated that the phosphatase activity was required for the inactivation of ERBB2 and its downstream signaling. PTPRO regulated the phosphorylation status of ERBB2 at Y1248. Co-immunoprecipitation and proximity ligation assay (Duolink) indicated that …

Biomuta And Bioxpress: Mutation And Expression Knowledgebases For Cancer Biomarker Discovery, Hayley Dingerdissen, John Torcivia-Rodriguez, Yu Hu, Ting-Chia Chang, Raja Mazumder, Robel Kashay

Biochemistry and Molecular Medicine Faculty Publications

Single-nucleotide variation and gene expression of disease samples represent important resources for biomarker discovery. Many databases have been built to host and make available such data to the community, but these databases are frequently limited in scope and/or content. BioMuta, a database of cancer-associated single-nucleotide variations, and BioXpress, a database of cancer-associated differentially expressed genes and microRNAs, differ from other disease-associated variation and expression databases primarily through the aggregation of data across many studies into a single source with a unified representation and annotation of functional attributes. Early versions of these resources were initiated by pilot funding for specific research …

Nanoparticle Targeting To The Central Nervous System, Emily Baker

Williams Honors College, Honors Research Projects

Drug delivery to the central nervous system is complicated by the blood-brain barrier, a vascular structure that prevents free diffusion of molecules into brain tissue. In this study, we examined the in vitro properties of a nanoparticle-based drug delivery system. We used several nanoparticle formulations, both LTP based and PLGA based, to test the cellular uptake and toxicity in microglial cells. Using immunofluorescence imaging, we show that LTP nanoparticles are taken up by microglia. We confirmed that our nanoparticle formulations are non-toxic by two cell viability assays. These results suggest that nanoparticle formulations may be a biocompatible method of delivering …

Dream Of A Conducive Learning Environment: One Dreem For All Medical Students!, Rehana Rehman, Kulsoom Ghias, Syeda Sadia Fatima, Mehwish Hussain, Faiza Alam

Department of Biological & Biomedical Sciences

Objective: To compare students' response assessed by Dundee Ready Educational Environment Measure on the basis of the year of study, gender and pre-medical educational background.Methods: This cross-sectional study was carried out at the Aga Khan University Medical College, Karachi, Pakistan, from June 2014 to March 2015, and comprised medical students. The average scores of Dundee Ready Educational Environment Measure scales and subscales were compared between gender and educational background. Responses were also compared on the basis of year of study.Results: Of the 416 participants, 184 (44%) were males and 232 (56%) were females. There were 100 (24%) students in the …

A New Model For Phd Elective Course, H R. Ahmad, Satwat Hashmi, M H. Mahmood

Department of Biological & Biomedical Sciences

No abstract provided.

Investigating Medicinally Important Portein-Protein And Protein-Ligand Interactions : A Computational Approach, Cooper Ashley Taylor

Honors Theses

Molecular dynamics (MD) simulations and computational chemistry allow for an atomistic understanding of protein-protein and protein-ligand binding motifs. Through the use of MD, medicinally relevant complexes can be examined in detail unattainable by experimental methods. Within this work, systems pertinent to both Alzheimer’s Disease and HIV-1 are probed and thoroughly sampled to help elucidate potential therapeutic pathways. We used molecular dynamics and free energy estimations to gauge the affinity for the binary and ternary complexes of KLC1, APP and JIP1, three proteins all believed to be involved in the propagation of Alzheimer’s Disease. Two areas of thought exist suggesting that …

Myeloperoxidase-Mediated Protein Lysine Oxidation Generates 2- Aminoadipic Acid And Lysine Nitrile In Vivo, Hongqiao Lin, Bruce S. Levison, Jennifer A. Buffa, Ying Huang, Xiaoming Fu, Zeneng Wang, Valentin Gogonea, Joseph A. Didonato, Stanley L. Hazen

Chemistry Faculty Publications

Recent studies reveal 2-aminoadipic acid (2-AAA) is both elevated in subjects at risk for diabetes and mechanistically linked to glucose homeostasis. Prior studies also suggest enrichment of protein-bound 2-AAA as an oxidative post-translational modification of lysyl residues in tissues associated with degenerative diseases of aging. While in vitro studies suggest redox active transition metals or myeloperoxidase (MPO) generated hypochlorous acid (HOCl) may produce protein-bound 2-AAA, the mechanism(s) responsible for generation of 2- AAA during inflammatory diseases are unknown. In initial studies we observed that traditional acid- or basecatalyzed protein hydrolysis methods previously employed to measure tissue 2-AAA can artificially generate …