Read by QxMD icon Read


Elena Kuzmin, Benjamin VanderSluis, Wen Wang, Guihong Tan, Raamesh Deshpande, Yiqun Chen, Matej Usaj, Attila Balint, Mojca Mattiazzi Usaj, Jolanda van Leeuwen, Elizabeth N Koch, Carles Pons, Andrius J Dagilis, Michael Pryszlak, Jason Zi Yang Wang, Julia Hanchard, Margot Riggi, Kaicong Xu, Hamed Heydari, Bryan-Joseph San Luis, Ermira Shuteriqi, Hongwei Zhu, Nydia Van Dyk, Sara Sharifpoor, Michael Costanzo, Robbie Loewith, Amy Caudy, Daniel Bolnick, Grant W Brown, Brenda J Andrews, Charles Boone, Chad L Myers
To systematically explore complex genetic interactions, we constructed ~200,000 yeast triple mutants and scored negative trigenic interactions. We selected double-mutant query genes across a broad spectrum of biological processes, spanning a range of quantitative features of the global digenic interaction network and tested for a genetic interaction with a third mutation. Trigenic interactions often occurred among functionally related genes, and essential genes were hubs on the trigenic network. Despite their functional enrichment, trigenic interactions tended to link genes in distant bioprocesses and displayed a weaker magnitude than digenic interactions...
April 20, 2018: Science
Lincoln B Sloas, Michael S Caudy, Faye S Taxman
With nearly 8.2% of Americans experiencing substance use disorders (SUDs), a need exists for effective SUD treatment and for strategies to assist treatment participants to complete treatment programs (Chandler, Fletcher, & Volkow, 2009). The purpose of the current research is to contribute to an emerging knowledge base about treatment readiness and its utility for predicting substance use treatment process performance measures. The study examines the relative salience of treatment readiness as a predictor of treatment engagement...
March 2017: Journal of Drug Education
Johanna B Folk, Jeffrey B Stuewig, Brandy L Blasko, Michael Caudy, Andres G Martinez, Stephanie Maass, Faye S Taxman, June P Tangney
Is the relationship between criminal thinking and recidivism the same for criminal justice-involved individuals from varying demographic backgrounds? Relying on two independent samples of offenders and two measures of criminal thinking, the current studies examined whether four demographic factors-gender, race, age, and education-moderated the relationship between criminal thinking and recidivism. Study 1 consisted of 226 drug-involved probationers enrolled in a randomized clinical trial. Study 2 consisted of 346 jail inmates from a longitudinal study...
February 1, 2017: International Journal of Offender Therapy and Comparative Criminology
Amy A Caudy, Michael Mülleder, Markus Ralser
Budding yeast has from the beginning been a major eukaryotic model for the study of metabolic network structure and function. This is attributable to both its genetic and biochemical capacities and its role as a workhorse in food production and biotechnology. New inventions in analytical technologies allow accurate, simultaneous detection and quantification of metabolites, and a series of recent findings have placed the metabolic network at center stage in the physiology of the cell. For example, metabolism might have facilitated the origin of life, and in modern organisms it not only provides nutrients to the cell but also serves as a buffer to changes in the cellular environment, a regulator of cellular processes, and a requirement for cell growth...
September 1, 2017: Cold Spring Harbor Protocols
Amy A Caudy
Fermentative growth on glucose is one of the most widely studied conditions of yeast growth in the laboratory. The production of ethanol from sugars is relevant to the wine, beer, and bread industries and to production of biofuels. Assaying the levels of glucose and ethanol in yeast growth medium allows the experimenter to determine the consumption of the carbon source glucose and the production of ethanol. This protocol describes enzyme-coupled assays for determination of glucose and ethanol concentrations in a sample of cell-free culture medium...
September 1, 2017: Cold Spring Harbor Protocols
Adam P Rosebrock, Amy A Caudy
Prior to mass spectrometric analysis, cellular small molecules must be extracted and separated from interfering components such as salts and culture medium. To ensure minimal perturbation of metabolism, yeast cells grown in liquid culture are rapidly harvested by filtration as described here. Simultaneous quenching of metabolism and extraction is afforded by immediate immersion in low-temperature organic solvent. Samples prepared using this method are suitable for a range of downstream liquid chromatography-mass spectrometry analyses and are stable in solvent for >1 yr at -80°C...
September 1, 2017: Cold Spring Harbor Protocols
Hongde Li, Geetanjali Chawla, Alexander J Hurlburt, Maria C Sterrett, Olga Zaslaver, James Cox, Jonathan A Karty, Adam P Rosebrock, Amy A Caudy, Jason M Tennessen
L-2-hydroxyglutarate (L-2HG) has emerged as a putative oncometabolite that is capable of inhibiting enzymes involved in metabolism, chromatin modification, and cell differentiation. However, despite the ability of L-2HG to interfere with a broad range of cellular processes, this molecule is often characterized as a metabolic waste product. Here, we demonstrate that Drosophila larvae use the metabolic conditions established by aerobic glycolysis to both synthesize and accumulate high concentrations of L-2HG during normal developmental growth...
February 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
Liana R Taylor, Michael Caudy, Brandy L Blasko, Faye S Taxman
BACKGROUND: Substance-involved females tend to have different clinical profiles than men (Adams, Leukefeld, & Peden, 2008 ); yet they do not appear to have worse treatment outcomes (Green, 2006 ; Hser, Huang, Teruya, & Anglin, 2003 ). As motivation for treatment is considered essential in the substance abuse treatment context (Cahill, Adinoff, Hosig, Muller, & Pulliam, 2003 ; Longshore & Teruya, 2006 ), it is possible that higher motivation among females could potentially counteract the negative effect of more risk factors...
March 21, 2017: Substance Use & Misuse
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...
January 25, 2017: Nucleic Acids Research
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
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
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
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
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
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
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
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
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
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
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
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"