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Molecular Typing And Virulence Analysis Of Multidrug Resistant Klebsiella Pneumoniae Clinical Isolates Recovered From Egyptian Hospitals, Reham Wasfi, Walid F. Elkhatib, Hossam M. Ashour

Molecular Biosciences Faculty Publications

Klebsiella pneumonia infection rates have increased dramatically. Molecular typing and virulence analysis are powerful tools that can shed light on Klebsiella pneumonia infections. Whereas 77.7% (28/36) of clinical isolates indicated multidrug resistant (MDR) patterns, 50% (18/36) indicated carpabenem resistance. Gene prevalence for the AcrAB efflux pump (82.14%) was more than that of the mdtK efflux pump (32.14%) in the MDR isolates. FimH-1 and mrkD genes were prevalent in wound and blood isolates. FimH-1 gene was prevalent in sputum while mrkD gene was prevalent in urine. Serum resistance associated with outer membrane protein coding gene (traT) was found in all blood …

Integrated Strategy Improves The Prediction Accuracy Of Mirna In Large Dataset., Bin Xue, David Lipps, Sree Devineni

Molecular Biosciences Faculty Publications

MiRNAs are short non-coding RNAs of about 22 nucleotides, which play critical roles in gene expression regulation. The biogenesis of miRNAs is largely determined by the sequence and structural features of their parental RNA molecules. Based on these features, multiple computational tools have been developed to predict if RNA transcripts contain miRNAs or not. Although being very successful, these predictors started to face multiple challenges in recent years. Many predictors were optimized using datasets of hundreds of miRNA samples. The sizes of these datasets are much smaller than the number of known miRNAs. Consequently, the prediction accuracy of these predictors …

A Novel Rrm3 Function In Restricting Dna Replication Via An Orc5-Binding Domain Is Genetically Separable From Rrm3 Function As An Atpase/Helicase In Facilitating Fork Progression, Salahuddin Syed, Claus Desler, Lene J Rasmussen, Kristina H Schmidt

Molecular Biosciences Faculty Publications

In response to replication stress cells activate the intra-S checkpoint, induce DNA repair pathways, increase nucleotide levels, and inhibit origin firing. Here, we report that Rrm3 associates with a subset of replication origins and controls DNA synthesis during replication stress. The N-terminal domain required for control of DNA synthesis maps to residues 186-212 that are also critical for binding Orc5 of the origin recognition complex. Deletion of this domain is lethal to cells lacking the replication checkpoint mediator Mrc1 and leads to mutations upon exposure to the replication stressor hydroxyurea. This novel Rrm3 function is independent of its established role …

The Heat Shock Transcription Factor Hsf1 Induces Ovarian Cancer Epithelial-Mesenchymal Transition In A 3d Spheroid Growth Model., Chase D Powell, Trillitye R Paullin, Candice Aoisa, Christopher J Menzie, Ashley Ubaldini, Sandy D. Westerheid

Molecular Biosciences Faculty Publications

Ovarian cancer is the most lethal gynecological cancer, with over 200,000 women diagnosed each year and over half of those cases leading to death. The proteotoxic stress-responsive transcription factor HSF1 is frequently overexpressed in a variety of cancers and is vital to cellular proliferation and invasion in some cancers. Upon analysis of various patient data sets, we find that HSF1 is frequently overexpressed in ovarian tumor samples. In order to determine the role of HSF1 in ovarian cancer, inducible HSF1 knockdown cell lines were created. Knockdown of HSF1 in SKOV3 and HEY ovarian cancer cell lines attenuates the epithelial-to-mesenchymal transition …

Quantitative Proteomic Profiling Reveals Hepatic Lipogenesis And Liver X Receptor Activation In The Pander Transgenic Model., Mark G. Athanason, Whitney A. Ratliff, Dale Chaput, Catherine B. Marelia, Melanie N. Kuehl, Stanley M. Stevens Jr., Brant R. Burkhardt

Molecular Biosciences Faculty Publications

PANcreatic-DERived factor (PANDER) is a member of a superfamily of FAM3 proteins modulating glycemic levels by metabolic regulation of the liver and pancreas. The precise PANDER-induced hepatic signaling mechanism is still being elucidated and has been very complex due to the pleiotropic nature of this novel hormone. Our PANDER transgenic (PANTG) mouse displays a selective hepatic insulin resistant (SHIR) phenotype whereby insulin signaling is blunted yet lipogenesis is increased, a phenomena observed in type 2 diabetes. To examine the complex PANDER-induced mechanism of SHIR, we utilized quantitative mass spectrometry-based proteomic analysis using Stable Isotope Labeling by Amino Acids in Cell …

The Skp1 Homologs Skr-1/2 Are Required For The Caenorhabditis Elegans Skn-1 Antioxidant/Detoxification Response Independently Of P38 Mapk., Cheng-Wei Wu, Andrew Deonarine, Aaron Przybysz, Kevin Strange, Keith P. Chloe

Molecular Biosciences Faculty Publications

SKN-1/Nrf are the primary antioxidant/detoxification response transcription factors in animals and they promote health and longevity in many contexts. SKN-1/Nrf are activated by a remarkably broad-range of natural and synthetic compounds and physiological conditions. Defining the signaling mechanisms that regulate SKN-1/Nrf activation provides insights into how cells coordinate responses to stress. Nrf2 in mammals is regulated in part by the redox sensor repressor protein named Keap1. In C. elegans, the p38 MAPK cascade in the intestine activates SKN-1 during oxidative stress by promoting its nuclear accumulation. Interestingly, we find variation in the kinetics of p38 MAPK activation and tissues with …

Intrinsic Disorder In Transmembrane Proteins: Roles In Signaling And Topology Prediction, Jérôme Bürgi, Bin Xue, Vladimir N Uversky, F Gisou Van Der Goot

Molecular Biosciences Faculty Publications

Intrinsically disordered regions (IDRs) are peculiar stretches of amino acids that lack stable conformations in solution. Intrinsic Disorder containing Proteins (IDP) are defined by the presence of at least one large IDR and have been linked to multiple cellular processes including cell signaling, DNA binding and cancer. Here we used computational analyses and publicly available databases to deepen insight into the prevalence and function of IDRs specifically in transmembrane proteins, which are somewhat neglected in most studies. We found that 50% of transmembrane proteins have at least one IDR of 30 amino acids or more. Interestingly, these domains preferentially localize …

Neddylation Promotes Stress Granule Assembly, Aravinth Kumar Jayabalan, Anthony Sanchez, Ra Young Park, Sang Pil Yoon, Gum-Yong Kang, Je-Hyun Baek, Paul Anderson, Younghoon Kee, Takbum Ohn

Molecular Biosciences Faculty Publications

Stress granules (SGs) harbour translationally stalled messenger ibonucleoproteins and play important roles in regulating gene expression and cell fate. Here we show that neddylation promotes SG assembly in response to arsenite-induced oxidative stress. Inhibition or depletion of key components of the neddylation machinery concomitantly inhibits stress-induced polysome disassembly and SG assembly. Affinity purification and subsequent mass-spectrometric analysis of Nedd8-conjugated proteins from translationally stalled ribosomal fractions identified ribosomal proteins, translation factors and RNA-binding proteins (RBPs), including SRSF3, a previously known SG regulator. We show that SRSF3 is selectively neddylated at Lys85 in response to arsenite. A non-neddylatable SRSF3 (K85R) mutant do …

Staphylococcus Aureus Coordinates Leukocidin Expression And Pathogenesis By Sensing Metabolic Fluxes Via Rpirc, Divya Balasubramanian, Elizabeth A Ohneck, Jessica Chapman, Andy Weiss, Min Kyung Kim, Tamara Reyes-Robles, Judy Zhong, Lindsey N. Shaw, Desmond S. Lun, Beatrix Ueberheide, Bo Shopsin, Victor J Torres

Molecular Biosciences Faculty Publications

Staphylococcus aureus is a formidable human pathogen that uses secreted cytolytic factors to injure immune cells and promote infection of its host. Of these proteins, the bicomponent family of pore-forming leukocidins play critical roles in S. aureus pathogenesis. The regulatory mechanisms governing the expression of these toxins are incompletely defined. In this work, we performed a screen to identify transcriptional regulators involved in leukocidin expression in S. aureus strain USA300. We discovered that a metabolic sensor-regulator, RpiRc, is a potent and selective repressor of two leukocidins, LukED and LukSF-PV. Whole-genome transcriptomics, S. aureus exoprotein proteomics, and metabolomic analyses revealed that …

The Exceptionally High Reactivity Of Cys 621 Is Critical For Electrophilic Activation Of The Sensory Nerve Ion Channel Trpa1, Parmvir K. Bahia, Thomas A. Parks, Katherine R. Stanford, David A. Mitchell, Sameer Varma, Stanley M. Stevens Jr., Thomas E. Taylor-Clark

Molecular Biosciences Faculty Publications

Activation of the sensory nerve ion channel TRPA1 by electrophiles is the key mechanism that initiates nociceptive signaling, and leads to defensive reflexes and avoidance behaviors, during oxidative stress in mammals. TRPA1 is rapidly activated by subtoxic levels of electrophiles, but it is unclear how TRPA1 outcompetes cellular antioxidants that protect cytosolic proteins from electrophiles. Here, using physiologically relevant exposures, we demonstrate that electrophiles react with cysteine residues on mammalian TRPA1 at rates that exceed the reactivity of typical cysteines by 6,000-fold and that also exceed the reactivity of antioxidant enzymes. We show that TRPA1 possesses a complex reactive cysteine …

Characterization Of A Silac Method For Proteomic Analysis Of Primary Rat Microglia, Ping Zhang, Ashley E. Culver-Cochran, Stanley M. Stevens Jr., Bin Liu

Molecular Biosciences Faculty Publications

Microglia play important and dynamic roles in mediating a variety of physiological and pathological processes during the development, normal function and degeneration of the central nervous system. Application of SILAC-based proteomic analysis would greatly facilitate the identification of cellular pathways regulating the multifaceted phenotypes of microglia. We and others have successfully SILAC-labeled immortalized murine microglial cell lines in previous studies. In this study, we report the development and evaluation of a SILAC-labeled primary rat microglia model. Although the isotope labeling scheme for primary microglia is drastically different from that of immortalized cell lines, our de novo and uninterrupted primary culture …

Structural And Activity Characterization Of Human Phpt1 After Oxidative Modification, Daniel R. Martin, Priyanka Dutta, Shikha Mahajan, Sameer Varma, Stanley M. Stevens Jr.

Molecular Biosciences Faculty Publications

Phosphohistidine phosphatase 1 (PHPT1), the only known phosphohistidine phosphatase in mammals, regulates phosphohistidine levels of several proteins including those involved in signaling, lipid metabolism, and potassium ion transport. While the high-resolution structure of human PHPT1 (hPHPT1) is available and residues important for substrate binding and catalytic activity have been reported, little is known about post-translational modifications that modulate hPHPT1 activity. Here we characterize the structural and functional impact of hPHPT1 oxidation upon exposure to a reactive oxygen species, hydrogen peroxide (H2O2). Specifically, liquid chromatography-tandem mass spectrometry was used to quantify site-specific oxidation of redox-sensitive residues of hPHPT1. Results from this …

Role Of Deubiquitinating Enzymes In Dna Repair, Younghoon Kee, Tony T. Huang

Molecular Biosciences Faculty Publications

Both proteolytic and nonproteolytic functions of ubiquitination are essential regulatory mechanisms for promoting DNA repair and the DNA damage response in mammalian cells. Deubiquitinating enzymes (DUBs) have emerged as key players in the maintenance of genome stability. In this minireview, we discuss the recent findings on human DUBs that participate in genome maintenance, with a focus on the role of DUBs in the modulation of DNA repair and DNA damage signaling.

Genome-Wide Annotation, Identification, And Global Transcriptomic Analysis Of Regulatory Or Small Rna Gene Expression In Staphylococcus Aureus, Ronan K. Carroll, Andy Weiss, William H. Broach, Richard E Wiemels, Austin B. Mogen, Kelly C. Rice, Lindsey N. Shaw

Molecular Biosciences Faculty Publications

In Staphylococcus aureus, hundreds of small regulatory or small RNAs (sRNAs) have been identified, yet this class of molecule remains poorly understood and severely understudied. sRNA genes are typically absent from genome annotation files, and as a consequence, their existence is often overlooked, particularly in global transcriptomic studies. To facilitate improved detection and analysis of sRNAs in S. aureus, we generated updated GenBank files for three commonly used S. aureus strains (MRSA252, NCTC 8325, and USA300), in which we added annotations for >260 previously identified sRNAs. These files, the first to include genome-wide annotation of sRNAs in S. aureus, were …

The Two-Component System Cpxra Negatively Regulates The Locus Of Enterocyte Effacement Of Enterohemorrhagic Escherichia Coli Involving Σ32 And Lon Protease, Miguel A. De La Cruz, Jason K. Morgan, Miguel A. Ares, Jorge A. Yáñez-Santos, James T. Riordan, Jorge A. Girón

Molecular Biosciences Faculty Publications

Enterohemorrhagic Escherichia coli (EHEC) is a significant cause of serious human gastrointestinal disease worldwide. EHEC strains contain a pathogenicity island called the locus of enterocyte effacement (LEE), which encodes virulence factors responsible for damaging the gut mucosa. The Cpx envelope stress response of E. coli is controlled by a two-component system (TCS) consisting of a sensor histidine kinase (CpxA) and a cytoplasmic response regulator (CpxR). In this study, we investigated the role of CpxRA in the expression of LEE-encoded virulence factors of EHEC. We found that a mutation in cpxA significantly affected adherence of EHEC to human epithelial cells. Analysis …

Global Regulator Of Virulence A (Grva) Coordinates Expression Of Discrete Pathogenic Mechanisms In Enterohemorrhagic Escherichia Coli Through Interactions With Gadw-Gade, Jason K. Morgan, Ronan K. Carroll, Carly M. Harro, Khoury W Vendura, Lindsey N. Shaw, James T. Riordan

Molecular Biosciences Faculty Publications

UNLABELLED: Global regulator of virulence A (GrvA) is a ToxR-family transcriptional regulator that activates locus of enterocyte effacement (LEE)-dependent adherence in enterohemorrhagic Escherichia coli (EHEC). LEE activation by GrvA requires the Rcs phosphorelay response regulator RcsB and is sensitive to physiologically relevant concentrations of bicarbonate, a known stimulant of virulence systems in intestinal pathogens. This study determines the genomic scale of GrvA-dependent regulation and uncovers details of the molecular mechanism underlying GrvA-dependent regulation of pathogenic mechanisms in EHEC. In a grvA-null background of EHEC strain TW14359, RNA sequencing analysis revealed the altered expression of over 700 genes, including the downregulation …

Identification Of Novel Cyclic Lipopeptides From A Positional Scanning Combinatorial Library With Enhanced Antibacterial And Antibiofilm Activities, Nina Bionda, Renee M. Fleeman, César De La Fuente-Núñez, Maria C. Rodriguez, Fany Reffuveille, Lindsey N. Shaw, Irena Pastar, Stephen C Davis, Robert E W Hancock, Predrag Cudic

Molecular Biosciences Faculty Publications

Treating bacterial infections can be difficult due to innate or acquired resistance mechanisms, and the formation of biofilms. Cyclic lipopeptides derived from fusaricidin/LI-F natural products represent particularly attractive candidates for the development of new antibacterial and antibiofilm agents, with the potential to meet the challenge of bacterial resistance to antibiotics. A positional-scanning combinatorial approach was used to identify the amino acid residues responsible for driving antibacterial activity, and increase the potency of these cyclic lipopeptides. Screening against the antibiotic resistant ESKAPE pathogens revealed the importance of hydrophobic as well as positively charged amino acid residues for activity of this class …

Measurement Of Elastic Modulus Of Collagen Type I Single Fiber, Pavel Dutov, Olga Antipova, Sameer Varma, Joseph P R O Orgel, Jay D Schieber

Molecular Biosciences Faculty Publications

Collagen fibers are the main components of the extra cellular matrix and the primary contributors to the mechanical properties of tissues. Here we report a novel approach to measure the longitudinal component of the elastic moduli of biological fibers under conditions close to those found in vivo and apply it to type I collagen from rat tail tendon. This approach combines optical tweezers, atomic force microscopy, and exploits Euler-Bernoulli elasticity theory for data analysis. This approach also avoids drying for measurements or visualization, since samples are freshly extracted. Importantly, strains are kept below 0.5%, which appear consistent with the linear …

Mir494 Reduces Renal Cancer Cell Survival Coinciding With Increased Lipid Droplets And Mitochondrial Changes, Punashi Dutta, Edward Haller, Arielle Sharp, Meera Nanjundan

Molecular Biosciences Faculty Publications

Background: miRNAs can regulate cellular survival in various cancer cell types. Recent evidence implicates the formation of lipid droplets as a hallmark event during apoptotic cell death response. It is presently unknown whether MIR494, located at 14q32 which is deleted in renal cancers, reduces cell survival in renal cancer cells and if this process is accompanied by changes in the number of lipid droplets.

Methods: 769-P renal carcinoma cells were utilized for this study. Control or MIR494 mimic was expressed in these cells following which cell viability (via crystal violet) and apoptotic cell numbers (via Annexin V/PI staining) were …

Direct Analysis In Real Time (Dart) Of An Organothiophosphate At Ultrahigh Resolution By Fourier Transform Ion Cyclotron Resonance Mass Spectrometry And Tandem Mass Spectrometry, Laszlo Prokai, Stanley M. Stevens Jr.

Molecular Biosciences Faculty Publications

Direct analysis in real time (DART) is a recently developed ambient ionization technique for mass spectrometry to enable rapid and sensitive analyses with little or no sample preparation. After swab-based field sampling, the organothiophosphate malathion was analyzed using DART-Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS) and tandem mass spectrometry (MS/MS). Mass resolution was documented to be over 800,000 in full-scan MS mode and over 1,000,000 for an MS/MS product ion produced by collision-induced dissociation of the protonated analyte. Mass measurement accuracy below 1 ppm was obtained for all DART-generated ions that belonged to the test compound in the …

Effect Of Hydroxychloroquine And Characterization Of Autophagy In A Mouse Model Of Endometriosis, A. Ruiz, S. Rockfield, N. Taran, E. Haller, Robert Engelman, I Flores, P Panina-Bordignon, Meera Nanjundan

Molecular Biosciences Faculty Publications

In endometriosis, the increased survival potential of shed endometrial cells (which normally undergo anoikis) is suggested to promote lesion development. One mechanism that may alter anoikis is autophagy. Using an autophagic flux inhibitor hydroxychloroquine (HCQ), we identified that it reduces the in vitro survival capacity of human endometriotic and endometrial T-HESC cells. We also identified that HCQ could decrease lesion numbers and disrupt lesion histopathology, as well as increase the levels of peritoneal macrophages and the IP-10 (10 kDa interferon-γ-induced protein) chemokine in a mouse model of endometriosis. We noted that RNA levels of a subset of autophagic …

Using Student Writing And Lexical Analysis To Reveal Student Thinking About The Role Of Stop Codons In The Central Dogma, Luanna B Prevost, Michelle K. Smith, Jennifer K. Knight

Molecular Biosciences Faculty Publications

Previous work has shown that students have persistent difficulties in understanding how central dogma processes can be affected by a stop codon mutation. To explore these difficulties, we modified two multiple-choice questions from the Genetics Concept Assessment into three open-ended questions that asked students to write about how a stop codon mutation potentially impacts replication, transcription, and translation. We then used computer-assisted lexical analysis combined with human scoring to categorize student responses. The lexical analysis models showed high agreement with human scoring, demonstrating that this approach can be successfully used to analyze large numbers of student written responses. The results …

Self-Regulation Of Functional Pathways By Motifs Inside The Disordered Tails Of Beta-Catenin, Bi Zhao, Bin Xue

Molecular Biosciences Faculty Publications

Background: Beta-catenin has two major functions: coordinating cell-cell adhesion by interacting with cadherin in cadherin junction formation pathway; and regulating gene expression through Wnt signaling pathway. Accomplishing these two functions requires synergistic action of various sequential regions of the same beta-Catenin molecule, including the N-terminal tail, the middle armadillo domain, and the C-terminal tail. Although the middle armadillo domain is the major functional unit of beta-Catenin, the involvement of tails in the regulation of interacti on between beta-Catenin and its partners has been well observed. Nonetheless, the regulatory processes of both tails are still elusive. In addition, it is interesting …

Towards The Complete Small Rnome Of Acinetobacter Baumannii, Andy Weiss, William H. Broach, Mackenzie C. Lee, Lindsey N. Shaw

Molecular Biosciences Faculty Publications

In recent years, the Gram-negative bacterium Acinetobacter baumannii has garnered considerable attention for its unprecedented capacity to rapidly develop resistance to antibacterial therapeutics. This is coupled with the seemingly epidemic emergence of new hyper-virulent strains. Although strain-specific differences for A. baumannii isolates have been well described, these studies have primarily focused on proteinaceous factors. At present, only limited publications have investigated the presence and role of small regulatory RNA (sRNA) transcripts. Herein, we perform such an analysis, describing the RNA-seq-based identification of 78 A. baumannii sRNAs in the AB5075 background. Together with six previously identified elements, we include each of …

Peptidoglycan Recycling In Gram-Positive Bacteria Is Crucial For Survival In Stationary Phase, Marina Borisova, Rosmarie Gaupp, Amanda Duckworth, Alexander Schneider, Désirée Dalügge, Maraike Mühleck, Denise Deubel, Sandra Unsleber, Wenqi Yu, Günther Muth, Markus Bischoff, Friedrich Götz, Christoph Mayer

Molecular Biosciences Faculty Publications

Peptidoglycan recycling is a metabolic process by which Gram-negative bacteria reutilize up to half of their cell wall within one generation during vegetative growth. Whether peptidoglycan recycling also occurs in Gram-positive bacteria has so far remained unclear. We show here that three Gram-positive model organisms, Staphylococcus aureus, Bacillus subtilis, and Streptomyces coelicolor, all recycle the sugar N-acetylmuramic acid (MurNAc) of their peptidoglycan during growth in rich medium. They possess MurNAc-6-phosphate (MurNAc-6P) etherase (MurQ in E. coli) enzymes, which are responsible for the intracellular conversion of MurNAc-6P to N-acetylglucosamine-6-phosphate and d-lactate. By applying mass spectrometry, we observed accumulation of MurNAc-6P in …

Antibodies Against A Secreted Product Of Staphylococcus Aureus Trigger Phagocytic Killing, Lena Thomer, Carla Emolo, Vilasack Thammavongsa, Hwan Keun Kim, Molly E. Mcadow, Wenqi Yu, Matthew Kieffer, Olaf Schneewind, Dominique Missiakas

Molecular Biosciences Faculty Publications

Host immunity against bacteria typically involves antibodies that recognize the microbial surface and promote phagocytic killing. Methicillin-resistant Staphylococcus aureus (MRSA) is a frequent cause of lethal bloodstream infection; however, vaccines and antibody therapeutics targeting staphylococcal surface molecules have thus far failed to achieve clinical efficacy. S. aureus secretes coagulase (Coa), which activates host prothrombin and generates fibrin fibrils that protect the pathogen against phagocytosis by immune cells. Because of negative selection, the coding sequence for the prothrombin-binding D1-D2 domain is highly variable and does not elicit cross-protective immune responses. The R domain, tandem repeats of a 27-residue peptide that bind …

Mir146a-Mediated Targeting Of Fancm During Inflammation Compromises Genome Integrity, Devakumar Sundaravinayagam, Hye R. Kim, Ting T. Wu, Hyun H. Kim, Hyun-Seo Lee, Semo Jun, Jeong-Heon Cha, Younghoon Kee, Ho J. You, Jung-Hee Lee

Molecular Biosciences Faculty Publications

Inflammation is a potent inducer of tumorigenesis. Increased DNA damage or loss of genome integrity is thought to be one of the mechanisms linking inflammation and cancer development. It has been suggested that NF-κB-induced microRNA-146 (miR146a) may be a mediator of the inflammatory response. Based on our initial observation that miR146a overexpression strongly increases DNA damage, we investigated its potential role as a modulator of DNA repair. Here, we demonstrate that FANCM, a component in the Fanconi Anemia pathway, is a novel target of miR146a. miR146a suppressed FANCM expression by directly binding to the 3’ untranslated region of the gene. …

Potential Role Of Pctaire-2, Pctaire-3 And P-Histone H4 In Amyloid Precursor Protein-Dependent Alzheimer Pathology, Dale Chaput, Lisa Kirouac, Stanley M. Stevens Jr., Jaya Padmanabhan

Molecular Biosciences Faculty Publications

Amyloid Precursor Protein (APP) is regulated in a mitosis-specific manner and plays a role in proliferative signaling in cells. Though APP-derived Aβ generation has a well-established role in neurodegeneration, the mechanistic role of APP in this process is not fully understood. Here, we performed an unbiased, comprehensive analysis of the phosphoproteome signature in APP-null neuroblastoma cells (B103) compared to those expressing APP-695 isoform (B103-695) to determine if APP expression affects protein phosphorylation. Stable isotope labeling by amino acids in cell culture (SILAC) followed by mass spectrometry-based phosphoproteomic analysis with PolyMAC identified a total of 2,478 phosphopeptides in the B103 and …

Transcriptomic Analysis Of Staphylococcal Srnas: Insights Into Species-Specific Adaption And The Evolution Of Pathogenesis, William H. Broach, Andy Weiss, Lindsey N. Shaw

Molecular Biosciences Faculty Publications

Next-generation sequencing technologies have dramatically increased the rate at which new genomes are sequenced. Accordingly, automated annotation programs have become adept at identifying and annotating protein coding regions, as well as common and conserved RNAs. Additionally, RNAseq techniques have advanced our ability to identify and annotate regulatory RNAs (sRNAs), which remain significantly understudied. Recently, our group catalogued and annotated all previously known and newly identified sRNAs in several Staphylococcus aureus strains. These complete annotation files now serve as tools to compare the sRNA content of S. aureus with other bacterial strains to investigate the conservation of their sRNomes. Accordingly, in …