Reports & Publications

  1. YphC and YsxC GTPases assist the maturation of the central protuberance, GTPase associated region and functional core of the 50S ribosomal subunit. – 2016
    Ni Xiaodan ,Davis Joseph H ,Jain Nikhil ,Razi Aida et al. – Nucleic acids research. PubMed: PMID:27484475
    YphC and YsxC are GTPases in Bacillus subtilis that facilitate the assembly of the 50S ribosomal subunit, however their roles in this process are still uncharacterized. To explore their function, we used strains in which the only copy of the yphC or ysxC genes were …
  2. Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium. – 2015
    Freschi Luca ,Jeukens Julie ,Kukavica-Ibrulj Irena ,Boyle Brian et al. – Frontiers in microbiology. PubMed: PMID:26483767
    The International Pseudomonas aeruginosa Consortium is sequencing over 1000 genomes and building an analysis pipeline for the study of Pseudomonas genome evolution, antibiotic resistance and virulence genes. Metadata, including genomic and phenotypic data for each isolate of the collection, are available through the International Pseudomonas Consortium …
  3. Bioinformatics of antimicrobial resistance in the age of molecular epidemiology. – 2015
    McArthur Andrew G ,Wright Gerard D – Current opinion in microbiology. PubMed: PMID:26241506
    Antimicrobial resistance is a global health challenge and has an evolutionary trajectory ranging from proto-resistance in the environment to untreatable clinical pathogens. Resistance is not static, as pathogenic strains can move among patient populations and individual resistance genes can move among pathogens. Effective treatment of …
  4. IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis. – 2015
    Dhillon Bhavjinder K ,Laird Matthew R ,Shay Julie A ,Winsor Geoffrey L et al. – Nucleic acids research. PubMed: PMID:25916842
    IslandViewer (http://pathogenomics.sfu.ca/islandviewer) is a widely used web-based resource for the prediction and analysis of genomic islands (GIs) in bacterial and archaeal genomes. GIs are clusters of genes of probable horizontal origin, and are of high interest since they disproportionately encode genes …
  5. The transcriptional response to oxidative stress during vertebrate development: effects of tert-butylhydroquinone and 2,3,7,8-tetrachlorodibenzo-p-dioxin. – 2014
    Hahn Mark E ,McArthur Andrew G ,Karchner Sibel I ,Franks Diana G et al. – PloS one. PubMed: PMID:25402455
    Oxidative stress is an important mechanism of chemical toxicity, contributing to teratogenesis and to cardiovascular and neurodegenerative diseases. Developing animals may be especially sensitive to chemicals causing oxidative stress. The developmental expression and inducibility of anti-oxidant defenses through activation of NF-E2-related factor 2 (NRF2) affect …
  6. Inhibition of endogenous MTF-1 signaling in zebrafish embryos identifies novel roles for MTF-1 in development. – 2014
    O’Shields Britton ,McArthur Andrew G ,Holowiecki Andrew ,Kamper Martin ,Tapley Jeffrey ,Jenny Matthew J – Biochimica et biophysica acta. PubMed: PMID:24751692
    The metal responsive element-binding transcription factor-1 (MTF-1) responds to changes in cellular zinc levels caused by zinc exposure or disruption of endogenous zinc homeostasis by heavy metals or oxygen-related stress. Here we report the functional characterization of a complete zebrafish MTF-1 in comparison with the …
  7. The comprehensive antibiotic resistance database. – 2013
    McArthur Andrew G ,Waglechner Nicholas ,Nizam Fazmin ,Yan Austin et al. – Antimicrobial agents and chemotherapy. PubMed: PMID:23650175
    The field of antibiotic drug discovery and the monitoring of new antibiotic resistance elements have yet to fully exploit the power of the genome revolution. Despite the fact that the first genomes sequenced of free living organisms were those of bacteria, there have been few …
  8. A small molecule discrimination map of the antibiotic resistance kinome. – 2011
    Shakya Tushar ,Stogios Peter J ,Waglechner Nicholas ,Evdokimova Elena et al. – Chemistry & biology. PubMed: PMID:22195561
    Kinase-mediated resistance to antibiotics is a significant clinical challenge. These enzymes share a common protein fold characteristic of Ser/Thr/Tyr protein kinases. We screened 14 antibiotic resistance kinases against 80 chemically diverse protein kinase inhibitors to map resistance kinase chemical space. The screens identified molecules with …
  9. Identification and developmental expression of the full complement of Cytochrome P450 genes in Zebrafish. – 2010
    Goldstone Jared V ,McArthur Andrew G ,Kubota Akira ,Zanette Juliano ,Parente Thiago ,Jönsson Maria E ,Nelson David R ,Stegeman John J – BMC genomics. PubMed: PMID:21087487
    Increasing use of zebrafish in drug discovery and mechanistic toxicology demands knowledge of cytochrome P450 (CYP) gene regulation and function. CYP enzymes catalyze oxidative transformation leading to activation or inactivation of many endogenous and exogenous chemicals, with consequences for normal physiology and disease processes. Many …
  10. Non-neutral evolution and reciprocal monophyly of two expressed Mhc class II B genes in Leach’s storm-petrel. – 2015
    Dearborn Donald C ,Gager Andrea B ,Gilmour Morgan E ,McArthur Andrew G ,Hinerfeld Douglas A ,Mauck Robert A – Immunogenetics. PubMed: PMID:25416539
    The major histocompatibility complex (Mhc) is subject to pathogen-mediated balancing selection and can link natural selection with mate choice. We characterized two Mhc class II B loci in Leach’s storm-petrel, Oceanodroma leucorhoa, focusing on exon 2 which encodes the portion of the protein that binds pathogen …

Full Pubmed list for Andrew McArthur

  1. Total Synthesis and Activity of the Metallo-β-lactamase Inhibitor Aspergillomarasmine A. – 2016
    Koteva Kalinka ,King Andrew M ,Capretta Alfredo ,Wright Gerard D – Angewandte Chemie (International ed. in English). PubMed: PMID:26709849
    Resistance to β-lactam antibiotics is mediated primarily by enzymes that hydrolytically inactivate the drugs by one of two mechanisms: serine nucleophilic attack or metal-dependent activation of a water molecule. Serine β-lactamases are countered in the clinic by several codrugs that inhibit these enzymes, thereby rescuing …
  2. (125)I-Tetrazines and Inverse-Electron-Demand Diels-Alder Chemistry: A Convenient Radioiodination Strategy for Biomolecule Labeling, Screening, and Biodistribution Studies. – 2016
    Albu Silvia A ,Al-Karmi Salma A ,Vito Alyssa ,Dzandzi James P K et al. – Bioconjugate chemistry. PubMed: PMID:26699913
    A convenient method to prepare radioiodinated tetrazines was developed, such that a bioorthogonal inverse electron demand Diels-Alder reaction can be used to label biomolecules with iodine-125 for in vitro screening and in vivo biodistribution studies. The tetrazine was prepared by employing a high-yielding oxidative halo …
  3. Fluorous Analogue of Chloramine-T: Preparation, X-ray Structure Determination, and Use as an Oxidant for Radioiodination and s-Tetrazine Synthesis. – 2015
    Dzandzi James P K ,Beckford Vera Denis R ,Genady Afaf R ,Albu Silvia A ,Eltringham-Smith Louise J ,Capretta Alfredo ,Sheffield William P ,Valliant John F – The Journal of organic chemistry. PubMed: PMID:26030355
    A fluorous oxidant that can be used to introduce radioiodine into small molecules and proteins and generate iodinated tetrazines for bioorthogonal chemistry has been developed. The oxidant was prepared in 87% overall yield by combining a fluorous amine with tosyl chloride, followed by chlorination using aqueous …
  4. Structure-guided optimization of protein kinase inhibitors reverses aminoglycoside antibiotic resistance. – 2013
    Stogios Peter J ,Spanogiannopoulos Peter ,Evdokimova Elena ,Egorova Olga et al. – The Biochemical journal. PubMed: PMID:23758273
    Activity of the aminoglycoside phosphotransferase APH(3′)-Ia leads to resistance to aminoglycoside antibiotics in pathogenic Gram-negative bacteria, and contributes to the clinical obsolescence of this class of antibiotics. One strategy to rescue compromised antibiotics such as aminoglycosides is targeting the enzymes that confer resistance …
  5. HDAC inhibition suppresses primary immune responses, enhances secondary immune responses, and abrogates autoimmunity during tumor immunotherapy. – 2013
    Bridle Byram W ,Chen Lan ,Lemay Chantal G ,Diallo Jean-Simon et al. – Molecular therapy : the journal of the American Society of Gene Therapy. PubMed: PMID:23295947
    Histone deacetylase inhibitors (HDACi) can modulate innate antiviral responses and render tumors more susceptible to oncolytic viruses (OVs); however, their effects on adaptive immunity in this context are largely unknown. Our present study reveals an unexpected property of the HDACi MS-275 that enhances viral vector-induced …
  6. Chemical perturbation of secondary metabolism demonstrates important links to primary metabolism. – 2012
    Craney Arryn ,Ozimok Cory ,Pimentel-Elardo Sheila Marie ,Capretta Alfredo ,Nodwell Justin R – Chemistry & biology. PubMed: PMID:22921069
    Bacterially produced secondary metabolites are used as antibiotics, anticancer drugs, and for many other medicinal applications. The mechanisms that limit the production of these molecules in the laboratory are not well understood, and this has impeded the discovery of many important compounds. We have identified …
  7. Synthesis of substituted isoquinolines via Pd-catalyzed cross-coupling approaches. – 2011
    Todorovic Nick ,Awuah Emelia ,Albu Silvia ,Ozimok Cory ,Capretta Alfredo – Organic letters. PubMed: PMID:22066469
    Palladium complexes incorporating ligands based on a 1,3,5,7-tetramethyl-2,4,8-trioxa-6-phosphaadamantanyl scaffold were used to catalyze the arylation of ethyl cyanoacetate, malononitrile, and various ketones. The products from these reactions can be elaborated to substituted β-arylethylamines and used in microwave-assisted Pictet-Spengler reactions. The protocol developed is …
  8. Development of methods for the synthesis of libraries of substituted maleimides and α,β-unsaturated-γ-butyrolactams. – 2011
    Awuah Emelia ,Capretta Alfredo – The Journal of organic chemistry. PubMed: PMID:21438546
    Synthetic methods for the preparation of maleimide and α,β-unsaturated-γ-butyrolactam compound collections are described. These routes take advantage of Pd cross-coupling and conjugate addition/elimination reactions to permit the facile production of bisaryl-maleimides, anilinoaryl-maleimides, and bisanilino-maleimides while allowing control over the synthesis of symmetrical or …
  9. Strategies and synthetic methods directed toward the preparation of libraries of substituted isoquinolines. – 2010
    Awuah Emelia ,Capretta Alfredo – The Journal of organic chemistry. PubMed: PMID:20704434
    Strategies for the production of substituted isoquinoline libraries were developed and explored. Routes involving microwave-assisted variants of the Bischler-Napieralski or Pictet-Spengler reaction allowed for cyclization of substituted beta-arylethylamine derivatives. The dihydroisoquinolines and tetrahydroisoquinolines thus generated could then be oxidized to their corresponding isoquinoline analogues. An …
  10. Chemical genomics in Escherichia coli identifies an inhibitor of bacterial lipoprotein targeting. – 2009
    Pathania Ranjana ,Zlitni Soumaya ,Barker Courtney ,Das Rahul et al. – Nature chemical biology. PubMed: PMID:19783991
    One of the most significant hurdles to developing new chemical probes of biological systems and new drugs to treat disease is that of understanding the mechanism of action of small molecules discovered with cell-based small-molecule screening. Here we have assembled an ordered, high-expression clone set …

Full Pubmed list for Alfredo Capretta

  1. Population-level effects of suppressing fever. – 2014
    Earn David J D ,Andrews Paul W ,Bolker Benjamin M – Proceedings. Biological sciences / The Royal Society. PubMed: PMID:24452021
    Fever is commonly attenuated with antipyretic medication as a means to treat unpleasant symptoms of infectious diseases. We highlight a potentially important negative effect of fever suppression that becomes evident at the population level: reducing fever may increase transmission of associated infections. A higher transmission …
  2. Second-pandemic strain of Vibrio cholerae from the Philadelphia cholera outbreak of 1849. – 2014
    Devault Alison M ,Golding G Brian ,Waglechner Nicholas ,Enk Jacob M et al. – The New England journal of medicine. PubMed: PMID:24401020
    In the 19th century, there were several major cholera pandemics in the Indian subcontinent, Europe, and North America. The causes of these outbreaks and the genomic strain identities remain a mystery. We used targeted high-throughput sequencing to reconstruct the Vibrio cholerae genome from the preserved …
  3. Effects of school closure on incidence of pandemic influenza in Alberta, Canada. – 2012
    Earn David J D ,He Daihai ,Loeb Mark B ,Fonseca Kevin ,Lee Bonita E ,Dushoff Jonathan – Annals of internal medicine. PubMed: PMID:22312137
    Control of pandemic influenza by social-distancing measures, such as school closures, is a controversial aspect of pandemic planning. However, investigations of the extent to which these measures actually affect the progression of a pandemic have been limited.
  4. A draft genome of Yersinia pestis from victims of the Black Death. – 2011
    Bos Kirsten I ,Schuenemann Verena J ,Golding G Brian ,Burbano Hernán A et al. – Nature. PubMed: PMID:21993626
    Technological advances in DNA recovery and sequencing have drastically expanded the scope of genetic analyses of ancient specimens to the extent that full genomic investigations are now feasible and are quickly becoming standard. This trend has important implications for infectious disease research because genomic data …
  5. Herald waves of cholera in nineteenth century London. – 2011
    Tien Joseph H ,Poinar Hendrik N ,Fisman David N ,Earn David J D – Journal of the Royal Society, Interface / the Royal Society. PubMed: PMID:21123253
    Deaths from cholera in London, UK, were recorded weekly from 1824 to 1901. Three features of the time series stand out: (i) cholera deaths were strongly seasonal, with peak mortality almost always in the summer, (ii) the only non-summer outbreaks occurred in the spring of 1832, the autumn …
  6. Effect of influenza vaccination of children on infection rates in Hutterite communities: a randomized trial. – 2010
    Loeb Mark ,Russell Margaret L ,Moss Lorraine ,Fonseca Kevin et al. – JAMA. PubMed: PMID:20215608
    Children and adolescents appear to play an important role in the transmission of influenza. Selectively vaccinating youngsters against influenza may interrupt virus transmission and protect those not immunized.
  7. Vaccinating to protect a vulnerable subpopulation. – 2007
    Dushoff Jonathan ,Plotkin Joshua B ,Viboud Cecile ,Simonsen Lone ,Miller Mark ,Loeb Mark ,Earn David J D – PLoS medicine. PubMed: PMID:17518515
    Epidemic influenza causes serious mortality and morbidity in temperate countries each winter. Research suggests that schoolchildren are critical in the spread of influenza virus, while the elderly and the very young are most vulnerable to the disease. Under these conditions, it is unclear how best …
  8. Dynamical resonance can account for seasonality of influenza epidemics. – 2004
    Dushoff Jonathan ,Plotkin Joshua B ,Levin Simon A ,Earn David J D – Proceedings of the National Academy of Sciences of the United States of America. PubMed: PMID:15557003
    Influenza incidence exhibits strong seasonal fluctuations in temperate regions throughout the world, concentrating the mortality and morbidity burden of the disease into a few months each year. The cause of influenza’s seasonality has remained elusive. Here we show that the large oscillations in incidence may …
  9. Vaccination and the theory of games. – 2004
    Bauch Chris T ,Earn David J D – Proceedings of the National Academy of Sciences of the United States of America. PubMed: PMID:15329411
    Voluntary vaccination policies for childhood diseases present parents with a subtle challenge: if a sufficient proportion of the population is already immune, either naturally or by vaccination, then even the slightest risk associated with vaccination will outweigh the risk from infection. As a result, individual …
  10. A simple model for complex dynamical transitions in epidemics. – 2000
    Earn D J ,Rohani P ,Bolker B M ,Grenfell B T – Science (New York, N.Y.). PubMed: PMID:10650003
    Dramatic changes in patterns of epidemics have been observed throughout this century. For childhood infectious diseases such as measles, the major transitions are between regular cycles and irregular, possibly chaotic epidemics, and from regionally synchronized oscillations to complex, spatially incoherent epidemics. A simple model can …

Full Pubmed list for David Earn

  1. Antibacterial drug discovery in the resistance era. – 2016
    Brown Eric D ,Wright Gerard D – Nature. PubMed: PMID:26791724
    The looming antibiotic-resistance crisis has penetrated the consciousness of clinicians, researchers, policymakers, politicians and the public at large. The evolution and widespread distribution of antibiotic-resistance elements in bacterial pathogens has made diseases that were once easily treatable deadly again. Unfortunately, accompanying the rise in global …
  2. Antagonism screen for inhibitors of bacterial cell wall biogenesis uncovers an inhibitor of undecaprenyl diphosphate synthase. – 2015
    Farha Maya A ,Czarny Tomasz L ,Myers Cullen L ,Worrall Liam J et al. – Proceedings of the National Academy of Sciences of the United States of America. PubMed: PMID:26283394
    Drug combinations are valuable tools for studying biological systems. Although much attention has been given to synergistic interactions in revealing connections between cellular processes, antagonistic interactions can also have tremendous value in elucidating genetic networks and mechanisms of drug action. Here, we exploit the power …
  3. Discovery of a small molecule that inhibits bacterial ribosome biogenesis. – 2014
    Stokes Jonathan M ,Davis Joseph H ,Mangat Chand S ,Williamson James R ,Brown Eric D – eLife. PubMed: PMID:25233066
    While small molecule inhibitors of the bacterial ribosome have been instrumental in understanding protein translation, no such probes exist to study ribosome biogenesis. We screened a diverse chemical collection that included previously approved drugs for compounds that induced cold sensitive growth inhibition in the model …
  4. Metabolic suppression identifies new antibacterial inhibitors under nutrient limitation. – 2013
    Zlitni Soumaya ,Ferruccio Lauren F ,Brown Eric D – Nature chemical biology. PubMed: PMID:24121552
    Characterizing new drugs and chemical probes of biological systems is hindered by difficulties in identifying the mechanism of action (MOA) of biologically active molecules. Here we present a metabolite suppression approach to explore the MOA of antibacterial compounds under nutrient restriction. We assembled an array …
  5. Inhibition of WTA synthesis blocks the cooperative action of PBPs and sensitizes MRSA to β-lactams. – 2013
    Farha Maya A ,Leung Alexander ,Sewell Edward W ,D’Elia Michael A et al. – ACS chemical biology. PubMed: PMID:23062620
    Rising drug resistance is limiting treatment options for infections by methicillin-resistant Staphylococcus aureus (MRSA). Herein we provide new evidence that wall teichoic acid (WTA) biogenesis is a remarkable antibacterial target with the capacity to destabilize the cooperative action of penicillin-binding proteins (PBPs) that underlie β-lactam …
  6. Combinations of antibiotics and nonantibiotic drugs enhance antimicrobial efficacy. – 2011
    Ejim Linda ,Farha Maya A ,Falconer Shannon B ,Wildenhain Jan ,Coombes Brian K ,Tyers Mike ,Brown Eric D ,Wright Gerard D – Nature chemical biology. PubMed: PMID:21516114
    Combinations of antibiotics are commonly used in medicine to broaden antimicrobial spectrum and generate synergistic effects. Alternatively, combination of nonantibiotic drugs with antibiotics offers an opportunity to sample a previously untapped expanse of bioactive chemical space. We screened a collection of drugs to identify compounds …
  7. Chemical genomics in Escherichia coli identifies an inhibitor of bacterial lipoprotein targeting. – 2009
    Pathania Ranjana ,Zlitni Soumaya ,Barker Courtney ,Das Rahul et al. – Nature chemical biology. PubMed: PMID:19783991
    One of the most significant hurdles to developing new chemical probes of biological systems and new drugs to treat disease is that of understanding the mechanism of action of small molecules discovered with cell-based small-molecule screening. Here we have assembled an ordered, high-expression clone set …
  8. Lesions in teichoic acid biosynthesis in Staphylococcus aureus lead to a lethal gain of function in the otherwise dispensable pathway. – 2006
    D’Elia Michael A ,Pereira Mark P ,Chung Yu Seon ,Zhao Wenjun et al. – Journal of bacteriology. PubMed: PMID:16740924
    An extensive study of teichoic acid biosynthesis in the model organism Bacillus subtilis has established teichoic acid polymers as essential components of the gram-positive cell wall. However, similar studies pertaining to therapeutically relevant organisms, such as Staphylococcus aureus, are scarce. In this study we have …
  9. Multicopy suppressors for novel antibacterial compounds reveal targets and drug efflux susceptibility. – 2004
    Li Xiaoming ,Zolli-Juran Michela ,Cechetto Jonathan D ,Daigle Denis M ,Wright Gerard D ,Brown Eric D – Chemistry & biology. PubMed: PMID:15489169
    Gene dosage has frequently been exploited to select for genetic interactions between a particular mutant and clones from a random genomic library at high copy. We report here the first use of multicopy suppression as a forward genetic method to determine cellular targets and potential …

Full Pubmed list for Eric Brown

  1. YphC and YsxC GTPases assist the maturation of the central protuberance, GTPase associated region and functional core of the 50S ribosomal subunit. – 2016
    Ni Xiaodan ,Davis Joseph H ,Jain Nikhil ,Razi Aida et al. – Nucleic acids research. PubMed: PMID:27484475
    YphC and YsxC are GTPases in Bacillus subtilis that facilitate the assembly of the 50S ribosomal subunit, however their roles in this process are still uncharacterized. To explore their function, we used strains in which the only copy of the yphC or ysxC genes were …
  2. Binding properties of YjeQ (RsgA), RbfA, RimM and Era to assembly intermediates of the 30S subunit. – 2016
    Thurlow Brett ,Davis Joseph H ,Leong Vivian ,F Moraes Trevor ,Williamson James R ,Ortega Joaquin – Nucleic acids research. PubMed: PMID:27382067
    Our understanding regarding the function of YjeQ (also called RsgA), RbfA, RimM and Era in ribosome biogenesis has been derived in part from the study of immature 30S particles that accumulate in null strains lacking one of these factors. However, their mechanistic details are still …
  3. Porphyrin-phospholipid liposomes permeabilized by near-infrared light. – 2014
    Carter Kevin A ,Shao Shuai ,Hoopes Matthew I ,Luo Dandan et al. – Nature communications. PubMed: PMID:24699423
    The delivery of therapeutic compounds to target tissues is a central challenge in treating disease. Externally controlled drug release systems hold potential to selectively enhance localized delivery. Here we describe liposomes doped with porphyrin-phospholipid that are permeabilized directly by near-infrared light. Molecular dynamics simulations identified …
  4. Functional domains of the 50S subunit mature late in the assembly process. – 2014
    Jomaa Ahmad ,Jain Nikhil ,Davis Joseph H ,Williamson James R ,Britton Robert A ,Ortega Joaquin – Nucleic acids research. PubMed: PMID:24335279
    Despite the identification of many factors that facilitate ribosome assembly, the molecular mechanisms by which they drive ribosome biogenesis are poorly understood. Here, we analyze the late stages of assembly of the 50S subunit using Bacillus subtilis cells depleted of RbgA, a highly conserved GTPase. …
  5. Pch2 is a hexameric ring ATPase that remodels the chromosome axis protein Hop1. – 2014
    Chen Cheng ,Jomaa Ahmad ,Ortega Joaquin ,Alani Eric E – Proceedings of the National Academy of Sciences of the United States of America. PubMed: PMID:24367111
    In budding yeast the pachytene checkpoint 2 (Pch2) protein regulates meiotic chromosome axis structure by maintaining the domain-like organization of the synaptonemal complex proteins homolog pairing 1 (Hop1) and molecular zipper 1 (Zip1). Pch2 has also been shown to modulate meiotic double-strand break repair outcomes to favor recombination …
  6. The C-terminal helix in the YjeQ zinc-finger domain catalyzes the release of RbfA during 30S ribosome subunit assembly. – 2015
    Jeganathan Ajitha ,Razi Aida ,Thurlow Brett ,Ortega Joaquin – RNA (New York, N.Y.). PubMed: PMID:25904134
    YjeQ (also called RsgA) and RbfA proteins in Escherichia coli bind to immature 30S ribosome subunits at late stages of assembly to assist folding of the decoding center. A key step for the subunit to enter the pool of actively translating ribosomes is the release …
  7. Structural determinants stabilizing the axial channel of ClpP for substrate translocation. – 2013
    Alexopoulos John ,Ahsan Bilal ,Homchaudhuri Lopamudra ,Husain Nabiha ,Cheng Yi-Qiang ,Ortega Joaquin – Molecular microbiology. PubMed: PMID:23927726
    Acyldepsipeptides (ADEPs) antibiotics bind to Escherichia coli ClpP mimicking the interactions that the IGL/F loops in ClpA or ClpX ATPases establish with the hydrophobic pockets surrounding the axial pore of the tetradecamer that the protease forms. ADEP binding induces opening of the gates blocking …
  8. Escherichia coli rimM and yjeQ null strains accumulate immature 30S subunits of similar structure and protein complement. – 2013
    Leong Vivian ,Kent Meredith ,Jomaa Ahmad ,Ortega Joaquin – RNA (New York, N.Y.). PubMed: PMID:23611982
    Assembly of the Escherichia coli 30S ribosomal subunits proceeds through multiple parallel pathways. The protein factors RimM, YjeQ, RbfA, and Era work in conjunction to assist at the late stages of the maturation process of the small subunit. However, it is unclear how the functional …
  9. Understanding ribosome assembly: the structure of in vivo assembled immature 30S subunits revealed by cryo-electron microscopy. – 2011
    Jomaa Ahmad ,Stewart Geordie ,Martín-Benito Jaime ,Zielke Ryszard ,Campbell Tracey L ,Maddock Janine R ,Brown Eric D ,Ortega Joaquin – RNA (New York, N.Y.). PubMed: PMID:21303937
    Four decades after early in vitro assembly studies demonstrated that ribosome assembly is a controlled process, our understanding of ribosome assembly is still incomplete. Just as structure determination has been so important to understanding ribosome function, so too will it be critical to sorting out …
  10. Acyldepsipeptide antibiotics induce the formation of a structured axial channel in ClpP: A model for the ClpX/ClpA-bound state of ClpP. – 2010
    Li Dominic Him Shun ,Chung Yu Seon ,Gloyd Melanie ,Joseph Ebenezer et al. – Chemistry & biology. PubMed: PMID:20851345
    In ClpXP and ClpAP complexes, ClpA and ClpX use the energy of ATP hydrolysis to unfold proteins and translocate them into the self-compartmentalized ClpP protease. ClpP requires the ATPases to degrade folded or unfolded substrates, but binding of acyldepsipeptide antibiotics (ADEPs) to ClpP bypasses this …

Full Pubmed list for Joaquin Ortega

  1. Nucleotide second messenger-mediated regulation of a muralytic enzyme in Streptomyces. – 2015
    St-Onge Renée J ,Haiser Henry J ,Yousef Mary R ,Sherwood Emma ,Tschowri Natalia ,Al-Bassam Mahmoud ,Elliot Marie A – Molecular microbiology. PubMed: PMID:25682701
    Peptidoglycan degradative enzymes have important roles at many stages during the bacterial life cycle, and it is critical that these enzymes be stringently regulated to avoid compromising the integrity of the cell wall. How this regulation is exerted is of considerable interest: promoter-based control and …
  2. Development, antibiotic production, and ribosome assembly in Streptomyces venezuelae are impacted by RNase J and RNase III deletion. – 2014
    Jones Stephanie E ,Leong Vivian ,Ortega Joaquin ,Elliot Marie A – Journal of bacteriology. PubMed: PMID:25266378
    RNA metabolism is a critical but frequently overlooked control element affecting virtually every cellular process in bacteria. RNA processing and degradation is mediated by a suite of ribonucleases having distinct cleavage and substrate specificity. Here, we probe the role of two ribonucleases (RNase III and …
  3. Comparative analysis of non-coding RNAs in the antibiotic-producing Streptomyces bacteria. – 2013
    Moody Matthew J ,Young Rachel A ,Jones Stephanie E ,Elliot Marie A – BMC genomics. PubMed: PMID:23947565
    Non-coding RNAs (ncRNAs) are key regulatory elements that control a wide range of cellular processes in all bacteria in which they have been studied. Taking advantage of recent technological innovations, we set out to fully explore the ncRNA potential of the multicellular, antibiotic-producing Streptomyces bacteria.
  4. A novel nucleoid-associated protein specific to the actinobacteria. – 2013
    Swiercz Julia P ,Nanji Tamiza ,Gloyd Melanie ,Guarné Alba ,Elliot Marie A – Nucleic acids research. PubMed: PMID:23427309
    Effective chromosome organization is central to the functioning of any cell. In bacteria, this organization is achieved through the concerted activity of multiple nucleoid-associated proteins. These proteins are not, however, universally conserved, and different groups of bacteria have distinct subsets that contribute to chromosome architecture. …
  5. Crp is a global regulator of antibiotic production in streptomyces. – 2012
    Gao Chan ,Hindra ,Mulder David ,Yin Charles ,Elliot Marie A – mBio. PubMed: PMID:23232715
    Cyclic AMP receptor protein (Crp) is a transcription regulator controlling diverse cellular processes in many bacteria. In Streptomyces coelicolor, it is well established that Crp plays a critical role in spore germination and colony development. Here, we demonstrate that Crp is a key regulator of …
  6. Aerial development in Streptomyces coelicolor requires sortase activity. – 2012
    Duong Andrew ,Capstick David S ,Di Berardo Christina ,Findlay Kim C ,Hesketh Andrew ,Hong Hee-Jeon ,Elliot Marie A – Molecular microbiology. PubMed: PMID:22296345
    Streptomyces coelicolor is a multicellular bacterium whose life cycle encompasses three differentiated states: vegetative hyphae, aerial hyphae and spores. Among the factors required for aerial development are the ‘chaplins’, a family of eight secreted proteins that coat the surface of aerial hyphae. Three chaplins (the …
  7. Dual amyloid domains promote differential functioning of the chaplin proteins during Streptomyces aerial morphogenesis. – 2011
    Capstick David S ,Jomaa Ahmad ,Hanke Chistopher ,Ortega Joaquin ,Elliot Marie A – Proceedings of the National Academy of Sciences of the United States of America. PubMed: PMID:21628577
    The chaplin proteins are functional amyloids found in the filamentous Streptomyces bacteria. These secreted proteins are required for the aerial development of Streptomyces coelicolor, and contribute to an intricate rodlet ultrastructure that decorates the surfaces of aerial hyphae and spores. S. coelicolor encodes eight chaplin …
  8. Cell wall hydrolases affect germination, vegetative growth, and sporulation in Streptomyces coelicolor. – 2009
    Haiser Henry J ,Yousef Mary R ,Elliot Marie A – Journal of bacteriology. PubMed: PMID:19717604
    Peptidoglycan is a major cell wall constituent of gram-positive bacteria. It is a dynamic macromolecule that is actively remodeled to enable cell growth and differentiation through a tightly choreographed interplay of hydrolytic and biosynthetic enzyme activities. The filamentous bacterium Streptomyces coelicolor has a complex life …
  9. Small non-coding RNAs in Streptomyces coelicolor. – 2008
    Swiercz Julia P ,Hindra ,Bobek Jan ,Bobek Jan ,Haiser Henry J ,Di Berardo Christina ,Tjaden Brian ,Elliot Marie A – Nucleic acids research. PubMed: PMID:19008244
    In bacteria, small RNAs (sRNAs) make important regulatory contributions to an ever increasing number of cellular processes. To expand the repertoire of known sRNAs, we sought to identify novel sRNAs in the differentiating, multicellular bacterium Streptomyces coelicolor. We describe a combined bioinformatic and experimental approach …
  10. Developmentally regulated cleavage of tRNAs in the bacterium Streptomyces coelicolor. – 2008
    Haiser Henry J ,Karginov Fedor V ,Hannon Gregory J ,Elliot Marie A – Nucleic acids research. PubMed: PMID:18084030
    The ability to sense and respond to environmental and physiological signals is critical for the survival of the soil-dwelling Gram-positive bacterium Streptomyces coelicolor. Nutrient deprivation triggers the onset of a complex morphological differentiation process that involves the raising of aerial hyphae and formation of spore …

Full Pubmed list for Marie Elliot

  1. PhoPQ regulates acidic glycerophospholipid content of the Salmonella Typhimurium outer membrane. – 2014
    Dalebroux Zachary D ,Matamouros Susana ,Whittington Dale ,Bishop Russell E ,Miller Samuel I – Proceedings of the National Academy of Sciences of the United States of America. PubMed: PMID:24449881
    Gram-negative bacteria have two lipid membranes separated by a periplasmic space containing peptidoglycan. The surface bilayer, or outer membrane (OM), provides a barrier to toxic molecules, including host cationic antimicrobial peptides (CAMPs). The OM comprises an outer leaflet of lipid A, the bioactive component of …
  2. A divergent Pseudomonas aeruginosa palmitoyltransferase essential for cystic fibrosis-specific lipid A. – 2013
    Thaipisuttikul Iyarit ,Hittle Lauren E ,Chandra Ramesh ,Zangari Daniel et al. – Molecular microbiology. PubMed: PMID:24283944
    Strains of Pseudomonas aeruginosa (PA) isolated from the airways of cystic fibrosis patients constitutively add palmitate to lipid A, the membrane anchor of lipopolysaccharide. The PhoPQ regulated enzyme PagP is responsible for the transfer of palmitate from outer membrane phospholipids to lipid A. This enzyme …
  3. Inscribing the perimeter of the PagP hydrocarbon ruler by site-specific chemical alkylation. – 2010
    Khan M Adil ,Moktar Joel ,Mott Patrick J ,Vu Mary ,McKie Aaron H ,Pinter Thomas ,Hof Fraser ,Bishop Russell E – Biochemistry. PubMed: PMID:20853818
    The Escherichia coli outer membrane phospholipid:lipid A palmitoyltransferase PagP selects palmitate chains using its β-barrel-interior hydrocarbon ruler and interrogates phospholipid donors by gating them laterally through an aperture known as the crenel. Lipid A palmitoylation provides antimicrobial peptide resistance and modulates inflammation signaled through …
  4. PagP crystallized from SDS/cosolvent reveals the route for phospholipid access to the hydrocarbon ruler. – 2010
    Cuesta-Seijo Jose Antonio ,Neale Chris ,Khan M Adil ,Moktar Joel ,Tran Christopher D ,Bishop Russell E ,Pomès Régis ,Privé Gilbert G – Structure (London, England : 1993). PubMed: PMID:20826347
    Enzymatic reactions involving bilayer lipids occur in an environment with strict physical and topological constraints. The integral membrane enzyme PagP transfers a palmitoyl group from a phospholipid to lipid A in order to assist Escherichia coli in evading host immune defenses during infection. PagP measures …
  5. A thiolate anion buried within the hydrocarbon ruler perturbs PagP lipid acyl chain selection. – 2010
    Khan M Adil ,Moktar Joel ,Mott Patrick J ,Bishop Russell E – Biochemistry. PubMed: PMID:20175558
    The Escherichia coli outer membrane phospholipid:lipid A palmitoyltransferase PagP exhibits remarkable selectivity because its binding pocket for lipid acyl chains excludes those differing in length from palmitate by a solitary methylene unit. This narrow detergent-binding hydrophobic pocket buried within the eight-strand antiparallel beta-barrel is …
  6. Molecular mechanism for lateral lipid diffusion between the outer membrane external leaflet and a beta-barrel hydrocarbon ruler. – 2009
    Khan M Adil ,Bishop Russell E – Biochemistry. PubMed: PMID:19769329
    Membrane-intrinsic enzymes are embedded in lipids, yet how such enzymes interrogate lipid substrates remains a largely unexplored fundamental question. The outer membrane phospholipid:lipid A palmitoyltransferase PagP combats host immune defenses during infection and selects a palmitate chain using its beta-barrel interior hydrocarbon ruler. Both …
  7. PagP activation in the outer membrane triggers R3 core oligosaccharide truncation in the cytoplasm of Escherichia coli O157:H7. – 2008
    Smith Abigail E ,Kim Sang-Hyun ,Liu Feng ,Jia Wenyi ,Vinogradov Evgeny ,Gyles Carlton L ,Bishop Russell E – The Journal of biological chemistry. PubMed: PMID:18070877
    The Escherichia coli outer membrane phospholipid:lipid A palmitoyltransferase PagP is normally a latent enzyme, but it can be directly activated in outer membranes by lipid redistribution associated with a breach in the permeability barrier. We now demonstrate that a lipid A myristate deficiency in …
  8. Gauging a hydrocarbon ruler by an intrinsic exciton probe. – 2007
    Khan M Adil ,Neale Chris ,Michaux Catherine ,Pomès Régis ,Privé Gilbert G ,Woody Robert W ,Bishop Russell E – Biochemistry. PubMed: PMID:17375935
    The structural basis of lipid acyl-chain selection by membrane-intrinsic enzymes is poorly understood because most integral membrane enzymes of lipid metabolism have proven refractory to structure determination; however, robust enzymes from the outer membranes of gram-negative bacteria are now providing a first glimpse at the …
  9. Lipid trafficking controls endotoxin acylation in outer membranes of Escherichia coli. – 2004
    Jia Wenyi ,El Zoeiby Ahmed ,Petruzziello Tania N ,Jayabalasingham Bamini ,Seyedirashti Seyedreza ,Bishop Russell E – The Journal of biological chemistry. PubMed: PMID:15319435
    The biogenesis of biological membranes hinges on the coordinated trafficking of membrane lipids between distinct cellular compartments. The bacterial outer membrane enzyme PagP confers resistance to host immune defenses by transferring a palmitate chain from a phospholipid to the lipid A (endotoxin) component of lipopolysaccharide. …
  10. A hydrocarbon ruler measures palmitate in the enzymatic acylation of endotoxin. – 2004
    Ahn Victoria E ,Lo Eileen I ,Engel Christian K ,Chen Lu ,Hwang Peter M ,Kay Lewis E ,Bishop Russell E ,Privé Gilbert G – The EMBO journal. PubMed: PMID:15272304
    The ability of enzymes to distinguish between fatty acyl groups can involve molecular measuring devices termed hydrocarbon rulers, but the molecular basis for acyl-chain recognition in any membrane-bound enzyme remains to be defined. PagP is an outer membrane acyltransferase that helps pathogenic bacteria to evade …

Full Pubmed list for Russell Bishop

  1. Evaluation of excipients for enhanced thermal stabilization of a human type 5 adenoviral vector through spray drying. – 2016
    LeClair Daniel A ,Cranston Emily D ,Xing Zhou ,Thompson Michael R – International journal of pharmaceutics. PubMed: PMID:27130366
    We have produced a thermally stable recombinant human type 5 adenoviral vector (AdHu5) through spray drying with three excipient formulations (l-leucine, lactose/trehalose and mannitol/dextran). Spray drying leads to immobilization of the viral vector which is believed to prevent viral protein unfolding, aggregation and inactivation. …
  2. Role of B Cells in Mucosal Vaccine-Induced Protective CD8+ T Cell Immunity against Pulmonary Tuberculosis. – 2015
    Khera Amandeep K ,Afkhami Sam ,Lai Rocky ,Jeyanathan Mangalakumari et al. – Journal of immunology (Baltimore, Md. : 1950). PubMed: PMID:26268652
    Emerging evidence suggests a role of B cells in host defense against primary pulmonary tuberculosis (TB). However, the role of B cells in TB vaccine-induced protective T cell immunity still remains unknown. Using a viral-vectored model TB vaccine and a number of experimental approaches, we …
  3. Novel chimpanzee adenovirus-vectored respiratory mucosal tuberculosis vaccine: overcoming local anti-human adenovirus immunity for potent TB protection. – 2015
    Jeyanathan M ,Thanthrige-Don N ,Afkhami S ,Lai R et al. – Mucosal immunology. PubMed: PMID:25872483
    Pulmonary tuberculosis (TB) remains to be a major global health problem despite many decades of parenteral use of Bacillus Calmette-Guérin (BCG) vaccine. Developing safe and effective respiratory mucosal TB vaccines represents a unique challenge. Over the past decade or so, the human serotype 5 adenovirus (…
  4. New approaches to TB vaccination. – 2014
    Xing Zhou ,Jeyanathan Mangalakumari ,Smaill Fiona – Chest. PubMed: PMID:25180725
    Pulmonary TB remains a leading global health issue, but the current Bacille Calmette-Guérin (BCG) vaccine fails to control it effectively. Much effort has gone into developing safe and effective boost vaccine candidates for use after the BCG prime vaccination. To date, almost all the …
  5. Targeted prostaglandin E2 inhibition enhances antiviral immunity through induction of type I interferon and apoptosis in macrophages. – 2014
    Coulombe François ,Jaworska Joanna ,Verway Mark ,Tzelepis Fanny et al. – Immunity. PubMed: PMID:24726877
    Aspirin gained tremendous popularity during the 1918 Spanish Influenza virus pandemic, 50 years prior to the demonstration of their inhibitory action on prostaglandins. Here, we show that during influenza A virus (IAV) infection, prostaglandin E2 (PGE2) was upregulated, which led to the inhibition of type I interferon (…
  6. Pulmonary M. tuberculosis infection delays Th1 immunity via immunoadaptor DAP12-regulated IRAK-M and IL-10 expression in antigen-presenting cells. – 2014
    Jeyanathan M ,McCormick S ,Lai R ,Afkhami S et al. – Mucosal immunology. PubMed: PMID:24172845
    Interaction of mycobacteria with the host leads to retarded expression of T helper cell type 1 (Th1) immunity in the lung. However, the immune mechanisms remain poorly understood. Using in vivo and in vitro models of Mycobacterium tuberculosis (M. tb) infection, we find the immunoadaptor DAP12 (…
  7. A human type 5 adenovirus-based tuberculosis vaccine induces robust T cell responses in humans despite preexisting anti-adenovirus immunity. – 2013
    Smaill Fiona ,Jeyanathan Mangalakumari ,Smieja Marek ,Medina Maria Fe et al. – Science translational medicine. PubMed: PMID:24089406
    There is an urgent need to develop new tuberculosis (TB) vaccines to safely and effectively boost Bacille Calmette-Guérin (BCG)-triggered T cell immunity in humans. AdHu5Ag85A is a recombinant human type 5 adenovirus (AdHu5)-based TB vaccine with demonstrated efficacy in a number …
  8. Marked improvement of severe lung immunopathology by influenza-associated pneumococcal superinfection requires the control of both bacterial replication and host immune responses. – 2013
    Damjanovic Daniela ,Lai Rocky ,Jeyanathan Mangalakumari ,Hogaboam Cory M ,Xing Zhou – The American journal of pathology. PubMed: PMID:23831294
    Bacterial superinfection and associated lung immunopathology are major contributors to hospitalizations and mortality after influenza. However, the underlying mechanisms and effective intervention strategies remain poorly defined. By using a model of influenza and pneumococcal superinfection, we found that dual-infected animals experienced rapid weight loss and …
  9. Global gene transcriptome analysis in vaccinated cattle revealed a dominant role of IL-22 for protection against bovine tuberculosis. – 2013
    Bhuju Sabin ,Aranday-Cortes Elihu ,Villarreal-Ramos Bernardo ,Xing Zhou ,Singh Mahavir ,Vordermeier H Martin – PLoS pathogens. PubMed: PMID:23300440
    Bovine tuberculosis (bTB) is a chronic disease of cattle caused by Mycobacterium bovis, a member of the Mycobacterium tuberculosis complex group of bacteria. Vaccination of cattle might offer a long-term solution for controlling the disease and priority has been given to the development of a …
  10. Mechanisms of delayed anti-tuberculosis protection in the lung of parenteral BCG-vaccinated hosts: a critical role of airway luminal T cells. – 2012
    Horvath C N ,Shaler C R ,Jeyanathan M ,Zganiacz A ,Xing Z – Mucosal immunology. PubMed: PMID:22453678
    The immune mechanisms underlying unsatisfactory pulmonary mucosal protection by parenteral Bacillus Calmette-Guérin (BCG) immunization remain poorly understood. We found that parenteral BCG immunization failed to elicit airway luminal T cells (ALT) whereas it induced significant T cells in the lung interstitium. After Mycobacterium tuberculosis (…

Full Pubmed list for Zhou Xing