Genomes and Genes
metabolic networks and pathways
Summary: Complex sets of enzymatic reactions connected to each other via their product and substrate metabolites.
- Grasso F, Coppola M, Carbone F, Baldoni L, Alagna F, Perrotta G, et al. The transcriptional response to the olive fruit fly (Bactrocera oleae) reveals extended differences between tolerant and susceptible olive (Olea europaea L.) varieties. PLoS ONE. 2017;12:e0183050 pubmed publisher..oleae. ..
- Theorell A, Leweke S, Wiechert W, Nöh K. To be certain about the uncertainty: Bayesian statistics for 13 C metabolic flux analysis. Biotechnol Bioeng. 2017;114:2668-2684 pubmed publisher..In addition, the widely applied chi-square test, as a means of testing whether the model reproduces the data, is examined closer. ..
- Li L, Jiang H, Qiu Y, Ching W, Vassiliadis V. Discovery of metabolite biomarkers: flux analysis and reaction-reaction network approach. BMC Syst Biol. 2013;7 Suppl 2:S13 pubmed publisher..Two efficient and effective computational methods are proposed for the identification of biomarkers in this article. Furthermore, the biomarkers found by our proposed methods are shown to be significant determinants for diabetes. ..
- Fukushige T, Smith H, Miwa J, Krause M, Hanover J. A Genetic Analysis of the Caenorhabditis elegans Detoxification Response. Genetics. 2017;206:939-952 pubmed publisher..Epistatic relationships among the xrep mutants and their interacting partners allow us to propose an ordered genetic pathway by which endogenous and exogenous stressors induce the phase II detoxification response. ..
- Guo X, Yu C, Luo L, Wan H, Zhen N, Xu T, et al. Transcriptome of the floral transition in Rosa chinensis 'Old Blush'. BMC Genomics. 2017;18:199 pubmed publisher..The DEGs are candidates for functional analyses of genes affecting the floral transition in the rose, which is a precious resource that reveals the molecular mechanism of mediating floral transition in other perennial plants. ..
- Gonzalez Muniesa P, Martinez Gonzalez M, Hu F, Despres J, Matsuzawa Y, Loos R, et al. Obesity. Nat Rev Dis Primers. 2017;3:17034 pubmed publisher..Finally, understanding the epigenetic and genetic factors as well as metabolic pathways that take advantage of 'omics' technologies could play a very relevant part in combating obesity within a precision approach. ..
- Blighe K, Chawes B, Kelly R, Mirzakhani H, McGeachie M, Litonjua A, et al. Vitamin D prenatal programming of childhood metabolomics profiles at age 3 y. Am J Clin Nutr. 2017;106:1092-1099 pubmed publisher..This trial was registered at clinicaltrials.gov as NCT00920621. ..
- Shen H, Campanello G, Flicker D, Grabarek Z, Hu J, Luo C, et al. The Human Knockout Gene CLYBL Connects Itaconate to Vitamin B12. Cell. 2017;171:771-782.e11 pubmed publisher..Our work de-orphans the function of human CLYBL and reveals that a consequence of exposure to the immunomodulatory metabolite itaconate is B12 inactivation. ..
- Castex J, Willmann D, Kanouni T, Arrigoni L, Li Y, Friedrich M, et al. Inactivation of Lsd1 triggers senescence in trophoblast stem cells by induction of Sirt4. Cell Death Dis. 2017;8:e2631 pubmed publisher..In conclusion, by repression of Sirt4, Lsd1 directs the epigenetic control of TSC immortality via maintenance of metabolic flexibility. ..
- Asif M, Lakhwani D, Pathak S, Gupta P, Bag S, Nath P, et al. Transcriptome analysis of ripe and unripe fruit tissue of banana identifies major metabolic networks involved in fruit ripening process. BMC Plant Biol. 2014;14:316 pubmed publisher..The datasets developed in this study will help in developing strategies to manipulate banana fruit ripening and reduce post harvest losses. ..
- Lee J, Li Z, Miller E. Vibrio Phage KVP40 Encodes a Functional NAD+ Salvage Pathway. J Bacteriol. 2017;199: pubmed publisher..The pathway is conserved in other large, dsDNA phages in which the two genes, nadV and natV, share an evolutionary history in their respective phage-host group. ..
- Yang Z, Zhang Y, Jiang Y, Zhu F, Zeng L, Wang Y, et al. Transcriptional responses in the hepatopancreas of Eriocheir sinensis exposed to deltamethrin. PLoS ONE. 2017;12:e0184581 pubmed publisher..sinensis for the first time and will help in understanding the toxicity and molecular metabolic mechanisms of deltamethrin in E. sinensis. ..
- Tsokos G, Rose N. Immune cell signaling in autoimmune diseases. Clin Immunol. 2017;181:1-8 pubmed publisher..This document should provide the reader with a quick update on these topics and help instigate novel studies. ..
- Mobasheri A, Rayman M, Gualillo O, Sellam J, van der Kraan P, Fearon U. The role of metabolism in the pathogenesis of osteoarthritis. Nat Rev Rheumatol. 2017;13:302-311 pubmed publisher..We also highlight areas for future research, such as the potential to target metabolic pathways and mediators therapeutically. ..
- Figueiredo A, Kouril T, Esser D, Haferkamp P, Wieloch P, Schomburg D, et al. Systems biology of the modified branched Entner-Doudoroff pathway in Sulfolobus solfataricus. PLoS ONE. 2017;12:e0180331 pubmed publisher..These new results reveal how enzyme kinetics and metabolomics synergizes with mathematical modelling to unveil new systemic properties of the ED pathway in S.solfataricus in terms of its adaptation and robustness. ..
- Oromi N, Jove M, Pascual Pons M, Royo J, Rocaspana R, Aparicio E, et al. Differential metabolic profiles associated to movement behaviour of stream-resident brown trout (Salmo trutta). PLoS ONE. 2017;12:e0181697 pubmed publisher..This study reveals the contribution of the metabolomic analyses to better understand the behaviour of organisms. ..
- Flynn J, Ross D, Hunt K, Bond D, Gralnick J. Enabling unbalanced fermentations by using engineered electrode-interfaced bacteria. MBio. 2010;1: pubmed publisher..coli. Linking microbial biocatalysis to current production can eliminate redox constraints by shifting other unbalanced reactions to yield pure products and serve as a new platform for next-generation bioproduction strategies. ..
- Chen V, Paisley J, Lu X. Revealing common disease mechanisms shared by tumors of different tissues of origin through semantic representation of genomic alterations and topic modeling. BMC Genomics. 2017;18:105 pubmed publisher..The results indicate that applying topic modeling to semantic representations of tumors identifies patterns in the combinations of altered functional pathways in cancer. ..
- Mulas F, Li A, Sherr D, Monti S. Network-based analysis of transcriptional profiles from chemical perturbations experiments. BMC Bioinformatics. 2017;18:130 pubmed publisher..Additionally, the method has broad applicability beyond the uses here described and could be used as an alternative or as a complement to standard approaches of differential gene expression analysis. ..
- Wan X, Liu Y, Zhao Y, Sun X, Fan D, Guo L. Orexin A affects HepG2 human hepatocellular carcinoma cells glucose metabolism via HIF-1?-dependent and -independent mechanism. PLoS ONE. 2017;12:e0184213 pubmed publisher..These findings provide new insight into the regulation of glucose metabolism by orexin A in hepatocellular carcinoma cells. ..
- Labhsetwar P, Melo M, Cole J, Luthey Schulten Z. Population FBA predicts metabolic phenotypes in yeast. PLoS Comput Biol. 2017;13:e1005728 pubmed publisher..We find that a core set of 51 constraints are essential but that additional constraints are still necessary to recover the observed growth rate distribution in SD medium. ..
- Linossier M, Amirova L, Thomas M, Normand M, Bareille M, Gauquelin Koch G, et al. Effects of short-term dry immersion on bone remodeling markers, insulin and adipokines. PLoS ONE. 2017;12:e0182970 pubmed publisher..This finding confirms the role of bone as an endocrine organ in humans. Furthermore, visfatin for which a great responsiveness was observed could represent an early and sensitive marker of unloading in humans. ..
- Chan S, Simons M, Maranas C. SteadyCom: Predicting microbial abundances while ensuring community stability. PLoS Comput Biol. 2017;13:e1005539 pubmed publisher..SteadyCom provides an important step towards the cross-cutting task of predicting the composition of a microbial community in a given environment. ..
- Kotera M, Tabei Y, Yamanishi Y, Moriya Y, Tokimatsu T, Kanehisa M, et al. KCF-S: KEGG Chemical Function and Substructure for improved interpretability and prediction in chemical bioinformatics. BMC Syst Biol. 2013;7 Suppl 6:S2 pubmed publisher..KCF and KCF-S can be automatically converted from Molfile format, enabling to deal with molecules from any data sources. ..
- Gao B, Chi L, Mahbub R, Bian X, Tu P, Ru H, et al. Multi-Omics Reveals that Lead Exposure Disturbs Gut Microbiome Development, Key Metabolites, and Metabolic Pathways. Chem Res Toxicol. 2017;30:996-1005 pubmed publisher..Taken together, these results demonstrated that lead exposure not only altered the gut microbiome community structures/diversity but also greatly affected metabolic functions, leading to gut microbiome toxicity. ..
- Tivendale N, Ross J, Cohen J. The shifting paradigms of auxin biosynthesis. Trends Plant Sci. 2014;19:44-51 pubmed..Indeed, it appears that in certain organs of some species, other pathways can operate. Here we review the key advances that have led to our current understanding of auxin biosynthesis and its many pro-posed pathways. ..
- Dong X, Fu J, Yin X, Qu C, Yang C, He H, et al. Induction of Apoptosis in HepaRG Cell Line by Aloe-Emodin through Generation of Reactive Oxygen Species and the Mitochondrial Pathway. Cell Physiol Biochem. 2017;42:685-696 pubmed publisher..These findings underscore the need for risk assessment of human exposure to aloe-emodin. ..
- Thao N, Kitani S, Nitta H, Tomioka T, Nihira T. Discovering potential Streptomyces hormone producers by using disruptants of essential biosynthetic genes as indicator strains. J Antibiot (Tokyo). 2017;70:1004-1008 pubmed publisher..Our finding that 24% of actinomycetes (12 of 51 strains) showed avenolide activity revealed for the first time that the butenolide-type Streptomyces hormone is also common in actinomycetes. ..
- Uppal K, Salinas J, Monteiro W, Val F, Cordy R, Liu K, et al. Plasma metabolomics reveals membrane lipids, aspartate/asparagine and nucleotide metabolism pathway differences associated with chloroquine resistance in Plasmodium vivax malaria. PLoS ONE. 2017;12:e0182819 pubmed publisher..Metabolomics phenotyping of P. vivax samples from patients with well-defined clinical CQ-resistance is promising for the development of new tools to understand the biological process and to identify potential biomarkers of PvCR. ..
- Beaudet J, Tulman E, Pflaum K, Liao X, Kutish G, Szczepanek S, et al. Transcriptional Profiling of the Chicken Tracheal Response to Virulent Mycoplasma gallisepticum Strain Rlow. Infect Immun. 2017;85: pubmed publisher..Early perturbations in tissue-wide gene expression, as observed here, may underpin a profound immune dysregulation, setting the stage for disease manifestations characteristic of M. gallisepticum infection. ..
- Jaakkola M, Elo L. Empirical comparison of structure-based pathway methods. Brief Bioinform. 2016;17:336-45 pubmed publisher..In the more challenging diabetes studies, almost all the tested methods detected as significant only few pathways if any. ..
- González Domenech C, Belda E, Patiño Navarrete R, Moya A, Peretó J, Latorre A. Metabolic stasis in an ancient symbiosis: genome-scale metabolic networks from two Blattabacterium cuenoti strains, primary endosymbionts of cockroaches. BMC Microbiol. 2012;12 Suppl 1:S5 pubmed publisher..FBA performed on the reconstructed networks from the two bacteria helps to refine the functional analysis of the genomes enabling us to postulate how slightly different host metabolic contexts drove their parallel evolution. ..
- Wang C, Zhu J. HPLC-MS/MS targeted metabolic profiling reveals distinct metabolic profiles from Staphylococcus aureus small-colony variants. J Chromatogr B Analyt Technol Biomed Life Sci. 2017;1060:340-346 pubmed publisher..aureus SCV formation, and to assist the potential future development of targeted treatment for S. aureus SCV infections. ..
- Castillo J, Jelinek D, Wei H, Gannon N, Vaughan R, Horwood L, et al. The Niemann-Pick C1 gene interacts with a high-fat diet to promote weight gain through differential regulation of central energy metabolism pathways. Am J Physiol Endocrinol Metab. 2017;313:E183-E194 pubmed publisher..In conclusion, these studies demonstrate that the Npc1 gene interacts with a HFD to promote weight gain through differential regulation of central energy metabolism pathways. ..
- Quinn R, Lim Y, Maughan H, Conrad D, Rohwer F, Whiteson K. Biogeochemical forces shape the composition and physiology of polymicrobial communities in the cystic fibrosis lung. MBio. 2014;5:e00956-13 pubmed publisher..Novel therapies that are designed to disrupt understudied survival strategies of the CF microbial community may succeed against otherwise untreatable or antibiotic-resistant microbes. ..
- Pande S, Kost C. Bacterial Unculturability and the Formation of Intercellular Metabolic Networks. Trends Microbiol. 2017;25:349-361 pubmed publisher..Thus, bacteria likely function as networks of interacting cells that reciprocally exchange nutrients and biochemical functions rather than as physiologically autonomous units. ..
- Vital M, Howe A, Tiedje J. Revealing the bacterial butyrate synthesis pathways by analyzing (meta)genomic data. MBio. 2014;5:e00889 pubmed publisher..This study will help in understanding the role of butyrate producers in health and disease and may assist the development of treatments for functional dysbiosis. ..
- Cossart P, Helenius A. Endocytosis of viruses and bacteria. Cold Spring Harb Perspect Biol. 2014;6: pubmed publisher..In this review, we discuss the endocytic entry processes used by viruses and bacteria and compare the strategies used by these dissimilar classes of pathogens. ..
- Chien C, Chow C, Wu N, Chiang Hsieh Y, Hou P, Chang W. EXPath: a database of comparative expression analysis inferring metabolic pathways for plants. BMC Genomics. 2015;16 Suppl 2:S6 pubmed publisher..itps.ncku.edu.tw, is a database resource that collects and utilizes gene expression profiles derived from microarray platforms under various conditions to infer metabolic pathways for plants. ..
- Silberberg Y, Kupiec M, Sharan R. GLADIATOR: a global approach for elucidating disease modules. Genome Med. 2017;9:48 pubmed publisher..The source code for GLADIATOR can be downloaded from http://www.cs.tau.ac.il/~roded/GLADIATOR.zip . ..
- Okahashi N, Matsuda F, Yoshikawa K, Shirai T, Matsumoto Y, Wada M, et al. Metabolic engineering of isopropyl alcohol-producing Escherichia coli strains with 13 C-metabolic flux analysis. Biotechnol Bioeng. 2017;114:2782-2793 pubmed publisher..coli may be achieved by fine-tuning the cofactor ratio and concentrations, as well as optimizing the metabolic pathways and culture conditions. ..
- Dasgupta D, Ghosh D, Bandhu S, Adhikari D. Lignocellulosic sugar management for xylitol and ethanol fermentation with multiple cell recycling by Kluyveromyces marxianus IIPE453. Microbiol Res. 2017;200:64-72 pubmed publisher..2kg sugarcane bagasse yielded 193.4g yeast cell, and with multiple times cell recycling generated 125.56g xylitol and 289.2g ethanol (366mL). ..