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https://www.readbyqxmd.com/read/28927698/biochemistry-of-mitochondrial-coenzyme-q-biosynthesis
#1
REVIEW
Jonathan A Stefely, David J Pagliarini
Coenzyme Q (CoQ, ubiquinone) is a redox-active lipid produced across all domains of life that functions in electron transport and oxidative phosphorylation and whose deficiency causes human diseases. Yet, CoQ biosynthesis has not been fully defined in any organism. Several proteins with unclear molecular functions facilitate CoQ biosynthesis through unknown means, and multiple steps in the pathway are catalyzed by currently unidentified enzymes. Here we highlight recent progress toward filling these knowledge gaps through both traditional biochemistry and cutting-edge 'omics' approaches...
September 16, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28926971/mini-review-the-contribution-of-intermediate-phenotypes-to-gxe-effects-on-disorders-of-body-composition-in-the-new-omics-era
#2
REVIEW
Edna J Nava-Gonzalez, Esther C Gallegos-Cabriales, Irene Leal-Berumen, Raul A Bastarrachea
Studies of gene-environment (GxE) interactions describe how genetic and environmental factors influence the risk of developing disease. Intermediate (molecular or clinical) phenotypes (IPs) are traits or metabolic biomarkers that mediate the effects of gene-environment influences on risk behaviors. Functional systems genomics discovery offers mechanistic insights into how DNA variations affect IPs in order to detect genetic causality for a given disease. Disorders of body composition include obesity (OB), Type 2 diabetes (T2D), and osteoporosis (OSTP)...
September 17, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28916559/omics-analyses-of-trichoderma-reesei-cbs999-97-and-qm6a-indicate-a-relevance-of-female-fertility-for-cazyme-and-transporter-levels
#3
Doris Tisch, Kyle R Pomraning, James R Collett, Michael Freitag, Scott E Baker, Chia-Ling Chen, Paul Wei-Che Hsu, Yu Chien Chuang, Andre Schuster, Christoph Dattenböck, Eva Stappler, Michael Sulyok, Stefan Böhmdorfer, Josua Oberlerchner, Ting-Fang Wang, Monika Schmoll
The filamentous fungus Trichoderma reesei is predominantly found in the tropics, but also in more temperate regions, such as Europe and is widely known as producer of high amounts of plant cell wall degrading enzymes. We sequenced the genome of the sexually competent isolate CBS999.97, which is phenotypically different from female sterile QM6a, but can cross sexually with QM6a. Transcriptome data for growth on cellulose showed that entire CAZyme families are consistently differentially regulated between these strains...
September 15, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28892251/genomes-of-rumen-bacteria-encode-atypical-pathways-for-fermenting-hexoses-to-short-chain-fatty-acids
#4
Timothy J Hackmann, David Kamanda Ngugi, Jeffrey L Firkins, Junyi Tao
Bacteria have been thought to follow only a few well-recognized biochemical pathways when fermenting glucose or other hexoses. These pathways have been chiseled in the stone of textbooks for decades, with most sources rendering them as they appear in the classic 1986 text by Gottschalk. Still, it is unclear how broadly these pathways apply, given that they were established and delineated biochemically with only a few model organisms. Here we show that well-recognized pathways often cannot explain fermentation products formed by bacteria...
September 11, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28890672/multivariate-strategy-for-the-sample-selection-and-integration-of-multi-batch-data-in-metabolomics
#5
Izabella Surowiec, Erik Johansson, Frida Torell, Helena Idborg, Iva Gunnarsson, Elisabet Svenungsson, Per-Johan Jakobsson, Johan Trygg
INTRODUCTION: Availability of large cohorts of samples with related metadata provides scientists with extensive material for studies. At the same time, recent development of modern high-throughput 'omics' technologies, including metabolomics, has resulted in the potential for analysis of large sample sizes. Representative subset selection becomes critical for selection of samples from bigger cohorts and their division into analytical batches. This especially holds true when relative quantification of compound levels is used...
2017: Metabolomics: Official Journal of the Metabolomic Society
https://www.readbyqxmd.com/read/28889270/uranium-and-the-central-nervous-system-what-should-we-learn-from-recent-new-tools-and-findings
#6
Céline Dinocourt
Increasing industrial and military use of uranium has led to environmental pollution, which may result in uranium reaching the brain and causing cerebral dysfunction. A recent literature review has discussed data published over the last 10 years on uranium and its effects on brain function (Dinocourt C, Legrand M, Dublineau I, et al., Toxicology 337:58-71, 2015). New models of uranium exposure during neonatal brain development and the emergence of new technologies (omics and epigenetics) are of value in identifying new specific targets of uranium...
2017: Advances in Neurobiology
https://www.readbyqxmd.com/read/28886166/assigning-ecological-roles-to-the-populations-belonging-to-a-phenanthrene-degrading-bacterial-consortium-using-omic-approaches
#7
Sabrina Festa, Bibiana Marina Coppotelli, Laura Madueño, Claudia Lorena Loviso, Marianela Macchi, Ricardo Martin Neme Tauil, María Pía Valacco, Irma Susana Morelli
The present study describes the behavior of a natural phenanthrene-degrading consortium (CON), a synthetic consortium (constructed with isolated strains from CON) and an isolated strain form CON (Sphingobium sp. AM) in phenanthrene cultures to understand the interactions among the microorganisms present in the natural consortium during phenanthrene degradation as a sole carbon and energy source in liquid cultures. In the contaminant degradation assay, the defined consortium not only achieved a major phenanthrene degradation percentage (> 95%) but also showed a more efficient elimination of the intermediate metabolite...
2017: PloS One
https://www.readbyqxmd.com/read/28885630/from-direct-to-indirect-lithium-targets-a-comprehensive-review-of-omics-data
#8
REVIEW
Magali Roux, Anthony Dosseto
Metal ions are critical to a wide range of biological processes. Among them, lithium (Li) has been recognised for its benefit as a treatment for bipolar disorder (BD). However, we are yet to grasp the extent of its role in biological processes, despite its molecular targets having been extensively studied. Here we review a wide range of transcriptomic, proteomic and metabolomic studies in order to obtain a full picture of Li effects at various levels. Multifarious patterns of Li-regulated genes, proteins and metabolites are identified...
September 8, 2017: Metallomics: Integrated Biometal Science
https://www.readbyqxmd.com/read/28885176/applications-of-bioinformatics-to-plant-biotechnology
#9
Diego F Gomez-Casati, María V Busi, Julieta Barchiesi, Diego A Peralta, Nicolás Hedin, Vijai Bhadauria
Bioinformatics encompasses many tools and techniques that today are essential for all areas of research in the biological sciences. New databases with a wealth of information about genomes, proteins, metabolites, and metabolic pathways appear almost daily. Particularly, for scientists who carry out research in plant biology, the amount of information has multiplied exponentially due to the large number of databases available for many individual plant species. In this sense, bioinformatics together with next generation sequencing and 'omics' approaches, can provide tools for plant breeding and the genetic engineering of plants...
September 8, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28870009/comprehensive-analysis-of-proteomic-differences-between-escherichia-coli-k-12-and-b-strains-using-multiplexed-isobaric-tandem-mass-tag-tmt-labeling
#10
Mee-Jung Han
The Escherichia coli K-12 and B strains are among the most frequently used bacterial hosts for scientific research and biotechnological applications. However, omics analyses have revealed that E. coli K-12 and B exhibit notably different genotypic and phenotypic attributes, even though they were derived from the same ancestor. In a previous study, we identified a limited number of proteins from the two strains using two-dimensional gel electrophoresis and tandem mass spectrometry (MS/MS). In this study, an in-depth analysis of the physiological behavior of the E...
September 5, 2017: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28869421/a-systemic-view-on-the-distribution-of-diet-derived-methanol-and-hepatic-acetone-in-mice
#11
Martin Kistler, Andreea Muntean, Vera Hoellriegl, Georg Matuschek, Ralf Zimmermann, Christoph Hoeschen, Martin Hrabe de Angelis, Jan Rozman
Volatile organic compounds (VOCs) from breath can successfully be used to diagnose disease-specific pathological alterations in metabolism. However, the exact origin and underlying biochemical pathways that could be mapped to VOC signatures are mainly unknown. There is a knowledge gap regarding the contribution of tissues, organs, the gut microbiome, and exogenous factors to the "sum signal" from breath samples. Animal models for human disease such as mutant mice provide the possibility to reproduce genetic predisposition to disease, thereby allowing the in-depth analysis of metabolic and biochemical functions...
September 4, 2017: Journal of Breath Research
https://www.readbyqxmd.com/read/28868294/integration-of-proteomics-and-metabolomics-in-exploring-genetic-and-rare-metabolic-diseases
#12
REVIEW
Michele Costanzo, Miriam Zacchia, Giuliana Bruno, Daniela Crisci, Marianna Caterino, Margherita Ruoppolo
BACKGROUND: Inherited metabolic disorders or inborn errors of metabolism are caused by deficiency of enzymatic activities in the catabolism of amino acids, carbohydrates, or lipids. These disorders include aminoacidopathies, urea cycle defects, organic acidemias, defects of oxidation of fatty acids, and lysosomal storage diseases. Inborn errors of metabolism constitute a significant proportion of genetic diseases, particularly in children; however, they are individually rare. Clinical phenotypes are very variable, some of them remain asymptomatic, others manifest metabolic decompensation in neonatal age, and others encompass mental retardation at later age...
July 2017: Kidney Diseases
https://www.readbyqxmd.com/read/28860003/sleep-restriction-induced-energy-methylation-and-lipogenesis-metabolic-switches-in-rat-liver
#13
Arjun Sengupta, Seth D Rhoades, Eun Ji Kim, Soumyashant Nayak, Gregory R Grant, Peter Meerlo, Aalim M Weljie
Sleep curtailment is ubiquitous in modern day society. Sleep debt is associated with maladaptive physiological changes that can lead to cardiometabolic and neuropsychiatric pathologies. Recent literature has shown the effects of sleep restriction (SR) on systemic metabolic profiles in biofluids, implying that tissue-specific metabolomes are impacted by SR. To test this hypothesis, we assessed hepatic metabolic profiles of rats after 5days of SR using UPLC-MS based metabolomics analysis and gene expression analysis...
August 28, 2017: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/28854898/omics-data-reveal-the-unusual-asexual-fruiting-nature-and-secondary-metabolic-potentials-of-the-medicinal-fungus-cordyceps-cicadae
#14
Yuzhen Lu, Feifei Luo, Kai Cen, Guohua Xiao, Ying Yin, Chunru Li, Zengzhi Li, Shuai Zhan, Huizhan Zhang, Chengshu Wang
BACKGROUND: Ascomycete Cordyceps species have been using as valued traditional Chinese medicines. Particularly, the fruiting bodies of Cordyceps cicadae (syn. Isaria cicadae) have long been utilized for the treatment of chronic kidney disease. However, the genetics and bioactive chemicals in this fungus have been largely unexplored. RESULTS: In this study, we performed comprehensive omics analyses of C. cicadae, and found that, in contrast to other Cordyceps fungi, C...
August 30, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28845460/integration-of-metabolomics-and-transcriptomics-reveals-a-complex-diet-of-mycobacterium-tuberculosis-during-early-macrophage-infection
#15
Michael Zimmermann, Maria Kogadeeva, Martin Gengenbacher, Gayle McEwen, Hans-Joachim Mollenkopf, Nicola Zamboni, Stefan Hugo Ernst Kaufmann, Uwe Sauer
Nutrient acquisition from the host environment is crucial for the survival of intracellular pathogens, but conceptual and technical challenges limit our knowledge of pathogen diets. To overcome some of these technical roadblocks, we exploited an experimentally accessible model for early infection of human macrophages by Mycobacterium tuberculosis, the etiological agent of tuberculosis, to study host-pathogen interactions with a multi-omics approach. We collected metabolomics and complete transcriptome RNA sequencing (dual RNA-seq) data of the infected macrophages, integrated them in a genome-wide reaction pair network, and identified metabolic subnetworks in host cells and M...
July 2017: MSystems
https://www.readbyqxmd.com/read/28843192/systems-and-synthetic-biology-for-the-biotechnological-application-of-cyanobacteria
#16
REVIEW
Martin Hagemann, Wolfgang R Hess
Cyanobacteria are the only prokaryotes that perform oxygenic photosynthesis. Their evolutionary relation to plastids in eukaryotic phototrophs and their increasing utilization as green cell factories initiated the use of systems biology approaches early on. For select model strains, extensive 'omics' data sets have been generated, and genome-wide models have been elucidated. Moreover, the results obtained may be used for the optimization of cyanobacterial metabolism, which can direct the biotechnological production of biofuels or chemical feedstock...
August 23, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28842640/cross-sectional-evaluation-of-the-gut-microbiome-metabolome-axis-in-an-italian-cohort-of-ibd-patients
#17
Maria Laura Santoru, Cristina Piras, Antonio Murgia, Vanessa Palmas, Tania Camboni, Sonia Liggi, Ivan Ibba, Maria Antonia Lai, Sandro Orrù, Anna Lisa Loizedda, Julian Leether Griffin, Paolo Usai, Pierluigi Caboni, Luigi Atzori, Aldo Manzin
Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the gastrointestinal tract of uncertain origin, which includes ulcerative colitis (UC) and Crohn's disease (CD). The composition of gut microbiota may change in IBD affected individuals, but whether dysbiosis is the cause or the consequence of inflammatory processes in the intestinal tissue is still unclear. Here, the composition of the microbiota and the metabolites in stool of 183 subjects (82 UC, 50 CD, and 51 healthy controls) were determined...
August 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28840392/advances-in-metabolome-information-retrieval-turning-chemistry-into-biology-part-i-analytical-chemistry-of-the-metabolome
#18
Abdellah Tebani, Carlos Afonso, Soumeya Bekri
Metabolites are small molecules produced by enzymatic reactions in a given organism. Metabolomics or metabolic phenotyping is a well-established omics aimed at comprehensively assessing metabolites in biological systems. These comprehensive analyses use analytical platforms, mainly nuclear magnetic resonance spectroscopy and mass spectrometry, along with associated separation methods to gather qualitative and quantitative data. Metabolomics holistically evaluates biological systems in an unbiased, data-driven approach that may ultimately support generation of hypotheses...
August 24, 2017: Journal of Inherited Metabolic Disease
https://www.readbyqxmd.com/read/28839183/trans-omics-approaches-used-to-characterise-fish-nutritional-biorhythms-in-leopard-coral-grouper-plectropomus-leopardus
#19
Miyuki Mekuchi, Kenji Sakata, Tomofumi Yamaguchi, Masahiko Koiso, Jun Kikuchi
Aquaculture is now a major supplier of fish, and has the potential to be a major source of protein in the future. Leopard coral groupers are traded in Asian markets as superior fish, and production via aquaculture has commenced. As feeding efficiency is of great concern in aquaculture, we sought to examine the metabolism of leopard coral groupers using trans-omics approaches. Metabolic mechanisms were comprehensively analysed using transcriptomic and metabolomic techniques. This study focused on the dynamics of muscular metabolites and gene expression...
August 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28830020/plant-secretory-structures-more-than-just-reaction-bags
#20
REVIEW
Alain Tissier
Plants have a remarkable capacity for the production of a wide range of metabolites. Much has been reported and reviewed on the diversity of these metabolites and how it is achieved, for example through the evolution of enzyme families. In comparison, relatively little is known on the extraordinary metabolic productivity of dedicated organs where many of these metabolites are synthesized and accumulate. Plant glandular trichomes are such specialized metabolite factories, for which recent omics analyses have shed new light on the adaptive metabolic strategies that support high metabolic fluxes...
August 19, 2017: Current Opinion in Biotechnology
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