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https://www.readbyqxmd.com/read/28342734/integration-of-microbiome-and-epigenome-to-decipher-the-pathogenesis-of-autoimmune-diseases
#1
REVIEW
Beidi Chen, Luxi Sun, Xuan Zhang
The interaction between genetic predisposition and environmental factors are of great significance in the pathogenesis and development of autoimmune diseases (AIDs). The human mucosa is the most frequent site that interacts with the exterior environment, and commensal microbiota at the gut and other human mucosal cavities play a crucial role in the regulation of immune system. Growing evidence has shown that the compositional and functional changes of mucosal microbiota are closely related to AIDs. Gut dysbiosis not only influence the expression level of Toll-like receptors (TLRs) of antigen presenting cells, but also contribute to Th17/Treg imbalance...
March 22, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/28340709/an-overview-on-forensic-analysis-devoted-to-analytical-chemists
#2
REVIEW
L S Castillo-Peinado, M D Luque de Castro
The present article has as main aim to show analytical chemists interested in forensic analysis the world they will face if decision in favor of being a forensic analytical chemist is adopted. With this purpose, the most outstanding aspects of forensic analysis in dealing with sampling (involving both bodily and no bodily samples), sample preparation, and analytical equipment used in detection, identification and quantitation of key sample components are critically discussed. The role of the great omics in forensic analysis, and the growing role of the youngest of the great omics -metabolomics- are also discussed...
May 15, 2017: Talanta
https://www.readbyqxmd.com/read/28336923/integrative-analysis-of-multi-omics-data-reveals-distinct-impacts-of-ddb1-cul4-associated-factors-in-human-lung-adenocarcinomas
#3
Hong Yan, Lei Bi, Yunshan Wang, Xia Zhang, Zhibo Hou, Qian Wang, Antoine M Snijders, Jian-Hua Mao
Many DDB1-CUL4 associated factors (DCAFs) have been identified and serve as substrate receptors. Although the oncogenic role of CUL4A has been well established, specific DCAFs involved in cancer development remain largely unknown. Here we infer the potential impact of 19 well-defined DCAFs in human lung adenocarcinomas (LuADCs) using integrative omics analyses, and discover that mRNA levels of DTL, DCAF4, 12 and 13 are consistently elevated whereas VBRBP is reduced in LuADCs compared to normal lung tissues...
March 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28334930/rcas-an-rna-centric-annotation-system-for-transcriptome-wide-regions-of-interest
#4
Bora Uyar, Dilmurat Yusuf, Ricardo Wurmus, Nikolaus Rajewsky, Uwe Ohler, Altuna Akalin
In the field of RNA, the technologies for studying the transcriptome have created a tremendous potential for deciphering the puzzles of the RNA biology. Along with the excitement, the unprecedented volume of RNA related omics data is creating great challenges in bioinformatics analyses. Here, we present the RNA Centric Annotation System (RCAS), an R package, which is designed to ease the process of creating gene-centric annotations and analysis for the genomic regions of interest obtained from various RNA-based omics technologies...
February 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334215/systematic-inference-of-functional-phosphorylation-events-in-yeast-metabolism
#5
Yu Chen, Yonghong Wang, Jens Nielsen
Motivation: Protein phosphorylation is a post-translational modification that affects proteins by changing their structure and conformation in a rapid and reversible way, and it is an important mechanism for metabolic regulation in cells. Phosphoproteomics enables high-throughput identification of phosphorylation events on metabolic enzymes, but identifying functional phosphorylation events still requires more detailed biochemical characterization. Therefore, development of computational methods for investigating unknown functions of a large number of phosphorylation events identified by phosphoproteomics has received increased attention...
March 2, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28331849/a-review-of-recent-advancement-in-integrating-omics-data-with-literature-mining-towards-biomedical-discoveries
#6
REVIEW
Kalpana Raja, Matthew Patrick, Yilin Gao, Desmond Madu, Yuyang Yang, Lam C Tsoi
In the past decade, the volume of "omics" data generated by the different high-throughput technologies has expanded exponentially. The managing, storing, and analyzing of this big data have been a great challenge for the researchers, especially when moving towards the goal of generating testable data-driven hypotheses, which has been the promise of the high-throughput experimental techniques. Different bioinformatics approaches have been developed to streamline the downstream analyzes by providing independent information to interpret and provide biological inference...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28327601/bcip-a-gene-centered-platform-for-identifying-potential-regulatory-genes-in-breast-cancer
#7
Jiaqi Wu, Shuofeng Hu, Yaowen Chen, Zongcheng Li, Jian Zhang, Hanyu Yuan, Qiang Shi, Ningsheng Shao, Xiaomin Ying
Breast cancer is a disease with high heterogeneity. Many issues on tumorigenesis and progression are still elusive. It is critical to identify genes that play important roles in the progression of tumors, especially for tumors with poor prognosis such as basal-like breast cancer and tumors in very young women. To facilitate the identification of potential regulatory or driver genes, we present the Breast Cancer Integrative Platform (BCIP, http://omics.bmi.ac.cn/bcancer/). BCIP maintains multi-omics data selected with strict quality control and processed with uniform normalization methods, including gene expression profiles from 9,005 tumor and 376 normal tissue samples, copy number variation information from 3,035 tumor samples, microRNA-target interactions, co-expressed genes, KEGG pathways, and mammary tissue-specific gene functional networks...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28325553/metabolomics-through-the-lens-of-precision-cardiovascular-medicine
#8
REVIEW
Sin Man Lam, Yuan Wang, Bowen Li, Jie Du, Guanghou Shui
Metabolomics, which targets at the extensive characterization and quantitation of global metabolites from both endogenous and exogenous sources, has emerged as a novel technological avenue to advance the field of precision medicine principally driven by genomics-oriented approaches. In particular, metabolomics has revealed the cardinal roles that the environment exerts in driving the progression of major diseases threatening public health. Herein, the existent and potential applications of metabolomics in two key areas of precision cardiovascular medicine will be critically discussed: 1) the use of metabolomics in unveiling novel disease biomarkers and pathological pathways; 2) the contribution of metabolomics in cardiovascular drug development...
March 8, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28321398/unveiling-the-metabolic-changes-on-muscle-cell-metabolism-underlying-p-phenylenediamine-toxicity
#9
Igor Marín de Mas, Silvia Marín, Gisela Pachón, Juan C Rodríguez-Prados, Pedro Vizán, Josep J Centelles, Romà Tauler, Amaya Azqueta, Vitaly Selivanov, Adela López de Ceraín, Marta Cascante
Rhabdomyolysis is a disorder characterized by acute damage of the sarcolemma of the skeletal muscle leading to release of potentially toxic muscle cell components into the circulation, most notably creatine phosphokinase (CK) and myoglobulin, and is frequently accompanied by myoglobinuria. In the present work, we evaluated the toxicity of p-phenylenediamine (PPD), a main component of hair dyes which is reported to induce rhabdomyolysis. We studied the metabolic effect of this compound in vivo with Wistar rats and in vitro with C2C12 muscle cells...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28317029/listeriomics-an-interactive-web-platform-for-systems-biology-of-listeria
#10
Christophe Bécavin, Mikael Koutero, Nicolas Tchitchek, Franck Cerutti, Pierre Lechat, Nicolas Maillet, Claire Hoede, Hélène Chiapello, Christine Gaspin, Pascale Cossart
As for many model organisms, the amount of Listeria omics data produced has recently increased exponentially. There are now >80 published complete Listeria genomes, around 350 different transcriptomic data sets, and 25 proteomic data sets available. The analysis of these data sets through a systems biology approach and the generation of tools for biologists to browse these various data are a challenge for bioinformaticians. We have developed a web-based platform, named Listeriomics, that integrates different tools for omics data analyses, i...
March 2017: MSystems
https://www.readbyqxmd.com/read/28315793/highlighting-the-effects-of-coumarin-on-adult-plants-of-arabidopsis-thaliana-l-heynh-by-an-integrated-omic-approach
#11
Fabrizio Araniti, Monica Scognamiglio, Angela Chambery, Rosita Russo, Assunta Esposito, Brigida D'Abrosca, Antonio Fiorentino, Antonio Lupini, Francesco Sunseri, Maria Rosa Abenavoli
In this study, the effects of the allelochemical coumarin through a metabolomic, proteomic and morpho-physiological approach in Arabidopsis adult plants (25days old) were investigated. Metabolomic analysis evidenced an increment of amino acids and a high accumulation of soluble sugars, after 6days of coumarin treatment. This effect was accompanied by a strong decrease on plant fresh and dry weights, as well as on total protein content. On the contrary, coumarin did not affect leaf number but caused a reduction in leaf area...
March 1, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28300637/integrated-mass-spectrometry-imaging-and-omics-workflows-on-the-same-tissue-section-using-grid-aided-parafilm-assisted-microdissection
#12
Jusal Quanico, Julien Franck, Maxence Wisztorski, Michel Salzet, Isabelle Fournier
BACKGROUND: In spite of the number of applications describing the use of MALDI MSI, one of its major drawbacks is the limited capability of identifying multiple compound classes directly on the same tissue section. METHODS: We demonstrate the use of grid-aided, parafilm-assisted microdissection to perform MALDI MS imaging and shotgun proteomics and metabolomics in a combined workflow and using only a single tissue section. The grid is generated by microspotting acid dye 25 using a piezoelectric microspotter, and this grid was used as a guide to locate regions of interest and as an aid during manual microdissection...
March 11, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28291359/challenges-of-integrating-stochastic-dynamics-and-cryo-electron-tomograms-in-whole-cell-simulations
#13
Tyler M Earnest, Reika Watanabe, John E Stone, Julia Mahamid, Wolfgang Baumeister, Elizabeth Villa, Zaida Luthey-Schulten
Cryo-electron tomography (cryo-ET) has rapidly emerged as a powerful tool to investigate the internal, three-dimensional spatial organization of the cell. In parallel, the GPU-based technology to perform spatially resolved stochastic simulations of whole cells has arisen, allowing the simulation of complex biochemical networks over cell cycle timescales using data taken from -omics, single molecule experiments, and in vitro kinetics. By using real cell geometry derived from cryo-ET data, we have the opportunity to imbue these highly detailed structural data-frozen in time-with realistic biochemical dynamics and investigate how cell structure affects the behavior of the embedded chemical reaction network...
March 14, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28289683/multidimensional-integrative-genomics-approaches-to-dissecting-cardiovascular-disease
#14
REVIEW
Douglas Arneson, Le Shu, Brandon Tsai, Rio Barrere-Cain, Christine Sun, Xia Yang
Elucidating the mechanisms of complex diseases such as cardiovascular disease (CVD) remains a significant challenge due to multidimensional alterations at molecular, cellular, tissue, and organ levels. To better understand CVD and offer insights into the underlying mechanisms and potential therapeutic strategies, data from multiple omics types (genomics, epigenomics, transcriptomics, metabolomics, proteomics, microbiomics) from both humans and model organisms have become available. However, individual omics data types capture only a fraction of the molecular mechanisms...
2017: Frontiers in Cardiovascular Medicine
https://www.readbyqxmd.com/read/28289389/understanding-physiology-in-the-continuum-integration-of-information-from-multiple-omics-levels
#15
Kubra Kamisoglu, Alison Acevedo, Richard R Almon, Susette Coyle, Siobhan Corbett, Debra C Dubois, Tung T Nguyen, William J Jusko, Ioannis P Androulakis
In this paper, we discuss approaches for integrating biological information reflecting diverse physiologic levels. In particular, we explore statistical and model-based methods for integrating transcriptomic, proteomic and metabolomics data. Our case studies reflect responses to a systemic inflammatory stimulus and in response to an anti-inflammatory treatment. Our paper serves partly as a review of existing methods and partly as a means to demonstrate, using case studies related to human endotoxemia and response to methylprednisolone (MPL) treatment, how specific questions may require specific methods, thus emphasizing the non-uniqueness of the approaches...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28285833/integrative-proteomics-and-phosphoproteomics-profiling-reveals-dynamic-signaling-networks-and-bioenergetics-pathways-underlying-t-cell-activation
#16
Haiyan Tan, Kai Yang, Yuxin Li, Timothy I Shaw, Yanyan Wang, Daniel Bastardo Blanco, Xusheng Wang, Ji-Hoon Cho, Hong Wang, Sherri Rankin, Cliff Guy, Junmin Peng, Hongbo Chi
The molecular circuits by which antigens activate quiescent T cells remain poorly understood. We combined temporal profiling of the whole proteome and phosphoproteome via multiplexed isobaric labeling proteomics technology, computational pipelines for integrating multi-omics datasets, and functional perturbation to systemically reconstruct regulatory networks underlying T cell activation. T cell receptors activated the T cell proteome and phosphoproteome with discrete kinetics, marked by early dynamics of phosphorylation and delayed ribosome biogenesis and mitochondrial activation...
March 21, 2017: Immunity
https://www.readbyqxmd.com/read/28283424/modelling-plankton-ecosystems-in-the-meta-omics-era-are-we-ready
#17
REVIEW
Krzysztof Franciszek Stec, Luigi Caputi, Pier Luigi Buttigieg, Domenico D'Alelio, Federico Matias Ibarbalz, Matthew B Sullivan, Samuel Chaffron, Chris Bowler, Maurizio Ribera d'Alcalà, Daniele Iudicone
Recent progress in applying meta-omics approaches to the study of marine ecosystems potentially allows scientists to study the genetic and functional diversity of plankton at an unprecedented depth and with enhanced precision. However, while a range of persistent technical issues still need to be resolved, a much greater obstacle currently preventing a complete and integrated view of the marine ecosystem is the absence of a clear conceptual framework. Herein, we discuss the knowledge that has thus far been derived from conceptual and statistical modelling of marine plankton ecosystems, and illustrate the potential power of integrated meta-omics approaches in the field...
March 7, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28280501/high-throughput-and-computational-study-of-leaf-senescence-through-a-phenomic-approach
#18
Jae Il Lyu, Seung Hee Baek, Sukjoon Jung, Hyosub Chu, Hong Gil Nam, Jeongsik Kim, Pyung Ok Lim
Leaf senescence is influenced by its life history, comprising a series of developmental and physiological experiences. Exploration of the biological principles underlying leaf lifespan and senescence requires a schema to trace leaf phenotypes, based on the interaction of genetic and environmental factors. We developed a new approach and concept that will facilitate systemic biological understanding of leaf lifespan and senescence, utilizing the phenome high-throughput investigator (PHI) with a single-leaf-basis phenotyping platform...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28276747/proteogenomic-studies-on-cancer-drug-resistance-towards-biomarker-discovery-and-target-identification
#19
Shuyue Fu, Xiang Liu, Maochao Luo, Ke Xie, Edouard C Nice, Haiyuan Zhang, Canhua Huang
Chemoresistance is a major obstacle for current cancer treatment. Proteogenomics is a powerful multi-omics research field that uses customized protein sequence databases generated by genomic and transcriptomic information to identify novel genes (e.g. noncoding, mutation and fusion genes) from mass spectrometry-based proteomic data. By identifying aberrations that are differentially expressed between tumor and normal pairs, this approach can also be applied to validate protein variants in cancer, which may reveal the response to drug treatment...
March 6, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28273855/integration-of-traditional-and-metabolomics-biomarkers-identifies-prognostic-metabolites-for-predicting-responsiveness-to-nutritional-intervention-against-oxidative-stress-and-inflammation
#20
You Jin Kim, Iksoo Huh, Ji Yeon Kim, Saejong Park, Sung Ha Ryu, Kyu-Bong Kim, Suhkmann Kim, Taesung Park, Oran Kwon
Various statistical approaches can be applied to integrate traditional and omics biomarkers, allowing the discovery of prognostic markers to classify subjects into poor and good prognosis groups in terms of responses to nutritional interventions. Here, we performed a prototype study to identify metabolites that predict responses to an intervention against oxidative stress and inflammation, using a data set from a randomized controlled trial evaluating Korean black raspberry (KBR) in sedentary overweight/obese subjects...
March 4, 2017: Nutrients
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