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https://www.readbyqxmd.com/read/27903914/proteomic-analysis-of-the-human-keops-complex-identifies-c14orf142-as-a-core-subunit-homologous-to-yeast-gon7
#1
Leo C K Wan, Pierre Maisonneuve, Rachel K Szilard, Jean-Philippe Lambert, Timothy F Ng, Noah Manczyk, Hao Huang, Rob Laister, Amy A Caudy, Anne-Claude Gingras, Daniel Durocher, Frank Sicheri
The KEOPS/EKC complex is a tRNA modification complex involved in the biosynthesis of N(6)-threonylcarbamoyladenosine (t(6)A), a universally conserved tRNA modification found on ANN-codon recognizing tRNAs. In archaea and eukaryotes, KEOPS is composed of OSGEP/Kae1, PRPK/Bud32, TPRKB/Cgi121 and LAGE3/Pcc1. In fungi, KEOPS contains an additional subunit, Gon7, whose orthologs outside of fungi, if existent, remain unidentified. In addition to displaying defective t(6)A biosynthesis, Saccharomyces cerevisiae strains harboring KEOPS mutations are compromised for telomere homeostasis, growth and transcriptional co-activation...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27897198/mitochondrial-control-through-nutritionally-regulated-global-histone-h3-lysine-4-demethylation
#2
Maria Soloveychik, Mengshu Xu, Olga Zaslaver, Kwanyin Lee, Ashrut Narula, River Jiang, Adam P Rosebrock, Amy A Caudy, Marc D Meneghini
Histone demethylation by Jumonji-family proteins is coupled with the decarboxylation of α-ketoglutarate (αKG) to yield succinate, prompting hypotheses that their activities are responsive to levels of these metabolites in the cell. Consistent with this paradigm we show here that the Saccharomyces cerevisiae Jumonji demethylase Jhd2 opposes the accumulation of H3K4me3 in fermenting cells only when they are nutritionally manipulated to contain an elevated αKG/succinate ratio. We also find that Jhd2 opposes H3K4me3 in respiratory cells that do not exhibit such an elevated αKG/succinate ratio...
November 29, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27708008/a-global-genetic-interaction-network-maps-a-wiring-diagram-of-cellular-function
#3
Michael Costanzo, Benjamin VanderSluis, Elizabeth N Koch, Anastasia Baryshnikova, Carles Pons, Guihong Tan, Wen Wang, Matej Usaj, Julia Hanchard, Susan D Lee, Vicent Pelechano, Erin B Styles, Maximilian Billmann, Jolanda van Leeuwen, Nydia van Dyk, Zhen-Yuan Lin, Elena Kuzmin, Justin Nelson, Jeff S Piotrowski, Tharan Srikumar, Sondra Bahr, Yiqun Chen, Raamesh Deshpande, Christoph F Kurat, Sheena C Li, Zhijian Li, Mojca Mattiazzi Usaj, Hiroki Okada, Natasha Pascoe, Bryan-Joseph San Luis, Sara Sharifpoor, Emira Shuteriqi, Scott W Simpkins, Jamie Snider, Harsha Garadi Suresh, Yizhao Tan, Hongwei Zhu, Noel Malod-Dognin, Vuk Janjic, Natasa Przulj, Olga G Troyanskaya, Igor Stagljar, Tian Xia, Yoshikazu Ohya, Anne-Claude Gingras, Brian Raught, Michael Boutros, Lars M Steinmetz, Claire L Moore, Adam P Rosebrock, Amy A Caudy, Chad L Myers, Brenda Andrews, Charles Boone
We generated a global genetic interaction network for Saccharomyces cerevisiae, constructing more than 23 million double mutants, identifying about 550,000 negative and about 350,000 positive genetic interactions. This comprehensive network maps genetic interactions for essential gene pairs, highlighting essential genes as densely connected hubs. Genetic interaction profiles enabled assembly of a hierarchical model of cell function, including modules corresponding to protein complexes and pathways, biological processes, and cellular compartments...
September 23, 2016: Science
https://www.readbyqxmd.com/read/26065001/heterogeneity-of-polyneuropathy-associated-with-anti-mag-antibodies
#4
Laurent Magy, Raphaël Kaboré, Stéphane Mathis, Prisca Lebeau, Karima Ghorab, Christiane Caudie, Jean-Michel Vallat
Polyneuropathy associated with IgM monoclonal gammopathy and anti-myelin associated glycoprotein (MAG) antibodies is an immune-mediated demyelinating neuropathy. The pathophysiology of this condition is likely to involve anti-MAG antibody deposition on myelin sheaths of the peripheral nerves and it is supposed to be distinct from chronic inflammatory demyelinating neuropathy (CIDP), another immune-mediated demyelinating peripheral neuropathy. In this series, we have retrospectively reviewed clinical and laboratory findings from 60 patients with polyneuropathy, IgM gammopathy, and anti-MAG antibodies...
2015: Journal of Immunology Research
https://www.readbyqxmd.com/read/25598559/does-substance-misuse-moderate-the-relationship-between-criminal-thinking-and-recidivism
#5
Michael S Caudy, Johanna B Folk, Jeffrey B Stuewig, Alese Wooditch, Andres Martinez, Stephanie Maass, June P Tangney, Faye S Taxman
PURPOSE: Some differential intervention frameworks contend that substance use is less robustly related to recidivism outcomes than other criminogenic needs such as criminal thinking. The current study tested the hypothesis that substance use disorder severity moderates the relationship between criminal thinking and recidivism. METHODS: The study utilized two independent criminal justice samples. Study 1 included 226 drug-involved probationers. Study 2 included 337 jail inmates with varying levels of substance use disorder severity...
January 2015: Journal of Criminal Justice
https://www.readbyqxmd.com/read/25534794/challenges-of-analyzing-different-classes-of-metabolites-by-a-single-analytical-method
#6
REVIEW
Fatemeh S Mirnaghi, Amy A Caudy
Complex biological samples include thousands of metabolites that range widely in both physiochemical properties and concentration. Simultaneously analyzing metabolites with different properties using a single analytical method is very challenging. The analytical process for metabolites comprises multiple steps including sampling, quenching, sample preparation, separation and detection. Each step can have a significant effect on the reliability and precision of ultimate analytic results. The aim of review is a discussion of considerations and challenges for the simultaneous analysis of metabolites using LC- and GC-MS systems...
2014: Bioanalysis
https://www.readbyqxmd.com/read/25201272/targeted-metabolomics-in-cultured-cells-and-tissues-by-mass-spectrometry-method-development-and-validation
#7
Anas M Abdel Rahman, Judy Pawling, Michael Ryczko, Amy A Caudy, James W Dennis
Metabolomics is the identification and quantitation of small bio-molecules (metabolites) in biological samples under various environmental and genetic conditions. Mass spectrometry provides the unique opportunity for targeted identification and quantification of known metabolites by selective reaction monitoring (SRM). However, reproducibility of this approach depends on careful consideration of sample preparation, chemical classes, and stability of metabolites to be evaluated. Herein, we introduce and validate a targeted metabolite profiling workflow for cultured cells and tissues by liquid chromatography-triple quadrupole tandem mass spectrometry...
October 3, 2014: Analytica Chimica Acta
https://www.readbyqxmd.com/read/24823668/heritability-and-genetic-basis-of-protein-level-variation-in-an-outbred-population
#8
Leopold Parts, Yi-Chun Liu, Manu M Tekkedil, Lars M Steinmetz, Amy A Caudy, Andrew G Fraser, Charles Boone, Brenda J Andrews, Adam P Rosebrock
The genetic basis of heritable traits has been studied for decades. Although recent mapping efforts have elucidated genetic determinants of transcript levels, mapping of protein abundance has lagged. Here, we analyze levels of 4084 GFP-tagged yeast proteins in the progeny of a cross between a laboratory and a wild strain using flow cytometry and high-content microscopy. The genotype of trans variants contributed little to protein level variation between individual cells but explained >50% of the variance in the population's average protein abundance for half of the GFP fusions tested...
August 2014: Genome Research
https://www.readbyqxmd.com/read/24721214/broad-metabolic-sensitivity-profiling-of-a-prototrophic-yeast-deletion-collection
#9
Benjamin VanderSluis, David C Hess, Colin Pesyna, Elias W Krumholz, Tahin Syed, Balázs Szappanos, Corey Nislow, Balázs Papp, Olga G Troyanskaya, Chad L Myers, Amy A Caudy
BACKGROUND: Genome-wide sensitivity screens in yeast have been immensely popular following the construction of a collection of deletion mutants of non-essential genes. However, the auxotrophic markers in this collection preclude experiments on minimal growth medium, one of the most informative metabolic environments. Here we present quantitative growth analysis for mutants in all 4,772 non-essential genes from our prototrophic deletion collection across a large set of metabolic conditions...
April 10, 2014: Genome Biology
https://www.readbyqxmd.com/read/24687277/uniform-nomenclature-for-the-mitochondrial-contact-site-and-cristae-organizing-system
#10
Nikolaus Pfanner, Martin van der Laan, Paolo Amati, Roderick A Capaldi, Amy A Caudy, Agnieszka Chacinska, Manjula Darshi, Markus Deckers, Suzanne Hoppins, Tateo Icho, Stefan Jakobs, Jianguo Ji, Vera Kozjak-Pavlovic, Chris Meisinger, Paul R Odgren, Sang Ki Park, Peter Rehling, Andreas S Reichert, M Saeed Sheikh, Susan S Taylor, Nobuo Tsuchida, Alexander M van der Bliek, Ida J van der Klei, Jonathan S Weissman, Benedikt Westermann, Jiping Zha, Walter Neupert, Jodi Nunnari
The mitochondrial inner membrane contains a large protein complex that functions in inner membrane organization and formation of membrane contact sites. The complex was variably named the mitochondrial contact site complex, mitochondrial inner membrane organizing system, mitochondrial organizing structure, or Mitofilin/Fcj1 complex. To facilitate future studies, we propose to unify the nomenclature and term the complex "mitochondrial contact site and cristae organizing system" and its subunits Mic10 to Mic60...
March 31, 2014: Journal of Cell Biology
https://www.readbyqxmd.com/read/24590948/case-studies-from-three-states-breaking-down-silos-between-health-care-and-criminal-justice
#11
Matthew J Bechelli, Michael Caudy, Tracie M Gardner, Alice Huber, David Mancuso, Paul Samuels, Tanya Shah, Homer D Venters
The jail-involved population-people with a history of arrest in the previous year-has high rates of illness, which leads to high costs for society. A significant percentage of jail-involved people are estimated to become newly eligible for coverage through the Affordable Care Act's expansion of Medicaid, including coverage of substance abuse treatment and mental health care. In this article we explore the need to break down the current policy silos between health care and criminal justice, to benefit both sectors and reduce unnecessary costs resulting from lack of coordination...
March 2014: Health Affairs
https://www.readbyqxmd.com/read/24529378/interspecies-systems-biology-uncovers-metabolites-affecting-c-elegans-gene-expression-and-life-history-traits
#12
Emma Watson, Lesley T MacNeil, Ashlyn D Ritter, L Safak Yilmaz, Adam P Rosebrock, Amy A Caudy, Albertha J M Walhout
Diet greatly influences gene expression and physiology. In mammals, elucidating the effects and mechanisms of individual nutrients is challenging due to the complexity of both the animal and its diet. Here, we used an interspecies systems biology approach with Caenorhabditis elegans and two of its bacterial diets, Escherichia coli and Comamonas aquatica, to identify metabolites that affect the animal's gene expression and physiology. We identify vitamin B12 as the major dilutable metabolite provided by Comamonas aq...
February 13, 2014: Cell
https://www.readbyqxmd.com/read/24409662/comparison-of-commercial-tests-for-detecting-multiple-anti-ganglioside-autoantibodies-in-patients-with-well-characterized-immune-mediated-peripheral-neuropathies
#13
COMPARATIVE STUDY
Christiane Caudie, Arnaud Quittard Pinon, Françoise Bouhour, Christophe Vial, Lorna Garnier, Nicole Fabien
BACKGROUND: To assess the performance of commercial anti-ganglioside antibody assays, we determined anti-ganglioside antibody IgG and IgM isotype profiles of patients with acute and chronic well-characterized immune-mediated peripheral neuropathies by one immunodot assays (Zentec/Ingen: Dotzen Ganglio Profile Ab, Euroimmun/BioAdvance: Euroline ganglioprofile), two line-immuno assay (GA Generic Assays/Labodia: Anti-Gangli osid Dot, Euroimmun/BioAdvance: Euroline ganglioprofile), and one enzyme-linked immunosorbent assay (ELISA) (Bühlmann: GanglioCombi)...
2013: Clinical Laboratory
https://www.readbyqxmd.com/read/24243840/the-reactome-pathway-knowledgebase
#14
David Croft, Antonio Fabregat Mundo, Robin Haw, Marija Milacic, Joel Weiser, Guanming Wu, Michael Caudy, Phani Garapati, Marc Gillespie, Maulik R Kamdar, Bijay Jassal, Steven Jupe, Lisa Matthews, Bruce May, Stanislav Palatnik, Karen Rothfels, Veronica Shamovsky, Heeyeon Song, Mark Williams, Ewan Birney, Henning Hermjakob, Lincoln Stein, Peter D'Eustachio
Reactome (http://www.reactome.org) is a manually curated open-source open-data resource of human pathways and reactions. The current version 46 describes 7088 human proteins (34% of the predicted human proteome), participating in 6744 reactions based on data extracted from 15 107 research publications with PubMed links. The Reactome Web site and analysis tool set have been completely redesigned to increase speed, flexibility and user friendliness. The data model has been extended to support annotation of disease processes due to infectious agents and to mutation...
January 2014: Nucleic Acids Research
https://www.readbyqxmd.com/read/24210219/biochemical-and-structural-studies-of-conserved-maf-proteins-revealed-nucleotide-pyrophosphatases-with-a-preference-for-modified-nucleotides
#15
Anatoli Tchigvintsev, Dmitri Tchigvintsev, Robert Flick, Ana Popovic, Aiping Dong, Xiaohui Xu, Greg Brown, Wenyun Lu, Hong Wu, Hong Cui, Ludmila Dombrowski, Jeong Chan Joo, Natalia Beloglazova, Jinrong Min, Alexei Savchenko, Amy A Caudy, Joshua D Rabinowitz, Alexey G Murzin, Alexander F Yakunin
Maf (for multicopy associated filamentation) proteins represent a large family of conserved proteins implicated in cell division arrest but whose biochemical activity remains unknown. Here, we show that the prokaryotic and eukaryotic Maf proteins exhibit nucleotide pyrophosphatase activity against 5-methyl-UTP, pseudo-UTP, 5-methyl-CTP, and 7-methyl-GTP, which represent the most abundant modified bases in all organisms, as well as against canonical nucleotides dTTP, UTP, and CTP. Overexpression of the Maf protein YhdE in E...
November 21, 2013: Chemistry & Biology
https://www.readbyqxmd.com/read/24194787/a-statistical-method-for-synthesizing-meta-analyses
#16
Liansheng Larry Tang, Michael Caudy, Faye Taxman
Multiple meta-analyses may use similar search criteria and focus on the same topic of interest, but they may yield different or sometimes discordant results. The lack of statistical methods for synthesizing these findings makes it challenging to properly interpret the results from multiple meta-analyses, especially when their results are conflicting. In this paper, we first introduce a method to synthesize the meta-analytic results when multiple meta-analyses use the same type of summary effect estimates. When meta-analyses use different types of effect sizes, the meta-analysis results cannot be directly combined...
2013: Computational and Mathematical Methods in Medicine
https://www.readbyqxmd.com/read/24167267/yeast-metabolic-and-signaling-genes-are-required-for-heat-shock-survival-and-have-little-overlap-with-the-heat-induced-genes
#17
Patrick A Gibney, Charles Lu, Amy A Caudy, David C Hess, David Botstein
Genome-wide gene-expression studies have shown that hundreds of yeast genes are induced or repressed transiently by changes in temperature; many are annotated to stress response on this basis. To obtain a genome-scale assessment of which genes are functionally important for innate and/or acquired thermotolerance, we combined the use of a barcoded pool of ~4,800 nonessential, prototrophic Saccharomyces cerevisiae deletion strains with Illumina-based deep-sequencing technology. As reported in other recent studies that have used deletion mutants to study stress responses, we observed that gene deletions resulting in the highest thermosensitivity generally are not the same as those transcriptionally induced in response to heat stress...
November 12, 2013: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/23953166/short-term-trajectories-of-substance-use-in-a-sample-of-drug-involved-probationers
#18
Michael S Caudy, Liansheng Tang, Alese Wooditch, Faye S Taxman
The current study estimates trajectories of illegal substance use in a sample of 251 drug-involved probationers to identify risk profiles that predict group membership and explores the impact of treatment participation across these trajectories. Trajectory analyses reveal five patterns of drug use during probation supervision. Age and the use of hard drugs are identified as the strongest predictors of involvement in illicit drug use while on probation. The effect of participation in substance use treatment varies across treatment settings and trajectory groups...
February 2014: Journal of Substance Abuse Treatment
https://www.readbyqxmd.com/read/23852385/a-new-system-for-comparative-functional-genomics-of-saccharomyces-yeasts
#19
Amy A Caudy, Yuanfang Guan, Yue Jia, Christina Hansen, Chris DeSevo, Alicia P Hayes, Joy Agee, Juan R Alvarez-Dominguez, Hugo Arellano, Daniel Barrett, Cynthia Bauerle, Namita Bisaria, Patrick H Bradley, J Scott Breunig, Erin Bush, David Cappel, Emily Capra, Walter Chen, John Clore, Peter A Combs, Christopher Doucette, Olukunle Demuren, Peter Fellowes, Sam Freeman, Evgeni Frenkel, Daniel Gadala-Maria, Richa Gawande, David Glass, Samuel Grossberg, Anita Gupta, Latanya Hammonds-Odie, Aaron Hoisos, Jenny Hsi, Yu-Han Huang Hsu, Sachi Inukai, Konrad J Karczewski, Xiaobo Ke, Mina Kojima, Samuel Leachman, Danny Lieber, Anna Liebowitz, Julia Liu, Yufei Liu, Trevor Martin, Jose Mena, Rosa Mendoza, Cameron Myhrvold, Christian Millian, Sarah Pfau, Sandeep Raj, Matt Rich, Joe Rokicki, William Rounds, Michael Salazar, Matthew Salesi, Rajani Sharma, Sanford Silverman, Cara Singer, Sandhya Sinha, Max Staller, Philip Stern, Hanlin Tang, Sharon Weeks, Maxwell Weidmann, Ashley Wolf, Carmen Young, Jie Yuan, Christopher Crutchfield, Megan McClean, Coleen T Murphy, Manuel Llinás, David Botstein, Olga G Troyanskaya, Maitreya J Dunham
Whole-genome sequencing, particularly in fungi, has progressed at a tremendous rate. More difficult, however, is experimental testing of the inferences about gene function that can be drawn from comparative sequence analysis alone. We present a genome-wide functional characterization of a sequenced but experimentally understudied budding yeast, Saccharomyces bayanus var. uvarum (henceforth referred to as S. bayanus), allowing us to map changes over the 20 million years that separate this organism from S. cerevisiae...
September 2013: Genetics
https://www.readbyqxmd.com/read/23754847/the-psychometric-properties-of-the-simple-screening-instrument-for-substance-abuse
#20
Roger A Boothroyd, Roger H Peters, Mary I Armstrong, Sarah Rynearson-Moody, Michael Caudy
The Simple Screening Instrument for Substance Abuse (SSI-SA) is gaining widespread use as a self-report measure of substance abuse; yet, little information exists regarding the instrument's psychometric properties. This study examined the SSI's psychometric properties within a population of 6,664 adult Medicaid enrollees in Florida, who responded to a survey conducted as part of a statewide evaluation of Medicaid services. The SSI-SA had excellent internal consistency (.85). Evidence of the SSI's validity was strong; SSI-SA scores distinguished among individuals with and without substance abuse needs and were significantly correlated with a measure of functioning in daily living...
December 2015: Evaluation & the Health Professions
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