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https://www.readbyqxmd.com/read/28819152/dissecting-the-genomic-activity-of-a-transcriptional-regulator-by-the-integrative-analysis-of-omics-data
#1
Giulio Ferrero, Valentina Miano, Marco Beccuti, Gianfranco Balbo, Michele De Bortoli, Francesca Cordero
In the study of genomic regulation, strategies to integrate the data produced by Next Generation Sequencing (NGS)-based technologies in a meaningful ensemble are eagerly awaited and must continuously evolve. Here, we describe an integrative strategy for the analysis of data generated by chromatin immunoprecipitation followed by NGS which combines algorithms for data overlap, normalization and epigenetic state analysis. The performance of our strategy is illustrated by presenting the analysis of data relative to the transcriptional regulator Estrogen Receptor alpha (ERα) in MCF-7 breast cancer cells and of Glucocorticoid Receptor (GR) in A549 lung cancer cells...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28819133/combined-transcriptome-and-metabolome-analyses-of-metformin-effects-reveal-novel-links-between-metabolic-networks-in-steroidogenic-systems
#2
Sameer S Udhane, Balazs Legeza, Nesa Marti, Damian Hertig, Gaëlle Diserens, Jean-Marc Nuoffer, Peter Vermathen, Christa E Flück
Metformin is an antidiabetic drug, which inhibits mitochondrial respiratory-chain-complex I and thereby seems to affect the cellular metabolism in many ways. It is also used for the treatment of the polycystic ovary syndrome (PCOS), the most common endocrine disorder in women. In addition, metformin possesses antineoplastic properties. Although metformin promotes insulin-sensitivity and ameliorates reproductive abnormalities in PCOS, its exact mechanisms of action remain elusive. Therefore, we studied the transcriptome and the metabolome of metformin in human adrenal H295R cells...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28817585/selecting-targets-for-the-diagnosis-of-schistosoma-mansoni-infection-an-integrative-approach-using-multi-omic-and-immunoinformatics-data
#3
Gardenia B F Carvalho, Daniela M Resende, Liliane M V Siqueira, Marcelo D Lopes, Débora O Lopes, Paulo Marcos Z Coelho, Andréa Teixeira-Carvalho, Jeronimo C Ruiz, Cristina T Fonseca
In order to effectively control and monitor schistosomiasis, new diagnostic methods are essential. Taking advantage of computational approaches provided by immunoinformatics and considering the availability of Schistosoma mansoni predicted proteome information, candidate antigens of schistosomiasis were selected and used in immunodiagnosis tests based on Enzime-linked Immunosorbent Assay (ELISA). The computational selection strategy was based on signal peptide prediction; low similarity to human proteins; B- and T-cell epitope prediction; location and expression in different parasite life stages within definitive host...
2017: PloS One
https://www.readbyqxmd.com/read/28816643/pharmacometabolomics-informs-quantitative-radiomics-for-glioblastoma-diagnostic-innovation
#4
Theodora Katsila, Minos-Timotheos Matsoukas, George P Patrinos, Dimitrios Kardamakis
Applications of omics systems biology technologies have enormous promise for radiology and diagnostics in surgical fields. In this context, the emerging fields of radiomics (a systems scale approach to radiology using a host of technologies, including omics) and pharmacometabolomics (use of metabolomics for patient and disease stratification and guiding precision medicine) offer much synergy for diagnostic innovation in surgery, particularly in neurosurgery. This synthesis of omics fields and applications is timely because diagnostic accuracy in central nervous system tumors still challenges decision-making...
August 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28814280/assisted-clustering-of-gene-expression-data-using-ancut
#5
Sebastian J Teran Hidalgo, Mengyun Wu, Shuangge Ma
BACKGROUND: In biomedical research, gene expression profiling studies have been extensively conducted. The analysis of gene expression data has led to a deeper understanding of human genetics as well as practically useful models. Clustering analysis has been a critical component of gene expression data analysis and can reveal the (previously unknown) interconnections among genes. With the high dimensionality of gene expression data, many of the existing clustering methods and results are not as satisfactory...
August 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28812256/the-potential-for-emerging-microbiome-mediated-therapeutics-in-asthma
#6
REVIEW
Ayse Bilge Ozturk, Benjamin Arthur Turturice, David L Perkins, Patricia W Finn
PURPOSE OF REVIEW: In terms of immune regulating functions, analysis of the microbiome has led the development of therapeutic strategies that may be applicable to asthma management. This review summarizes the current literature on the gut and lung microbiota in asthma pathogenesis with a focus on the roles of innate molecules and new microbiome-mediated therapeutics. RECENT FINDINGS: Recent clinical and basic studies to date have identified several possible therapeutics that can target innate immunity and the microbiota in asthma...
August 10, 2017: Current Allergy and Asthma Reports
https://www.readbyqxmd.com/read/28811702/precision-medicine-in-need-of-guidance-and-surveillance
#7
EDITORIAL
Jian-Zhen Lin, Jun-Yu Long, An-Qiang Wang, Ying Zheng, Hai-Tao Zhao
Precision medicine, currently a hotspot in mainstream medicine, has been strongly promoted in recent years. With rapid technological development, such as next-generation sequencing, and fierce competition in molecular targeted drug exploitation, precision medicine represents an advance in science and technology; it also fulfills needs in public health care. The clinical translation and application of precision medicine - especially in the prevention and treatment of tumors - is far from satisfactory; however, the aims of precision medicine deserve approval...
July 28, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28810121/comparative-proteomic-and-transcriptomic-analysis-of-follistatin-induced-skeletal-muscle-hypertrophy
#8
Caroline Barbé, Fabrice Bray, Marine Gueugneau, Stéphanie Devassine, Pascale Lause, Caroline Tokarski, Christian Rolando, Jean-Paul Thissen
Skeletal muscle, the most abundant body's tissue, plays vital roles in locomotion and metabolism. Myostatin is a negative regulator of skeletal muscle mass. In addition to increase muscle mass, Myostatin inhibition impacts on muscle contractility and energy metabolism. To decipher the mechanisms of action of the Myostatin inhibitors, we used proteomic and transcriptomic approaches to investigate the changes induced in skeletal muscles of transgenic mice overexpressing Follistatin, a physiological Myostatin inhibitor...
August 15, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28808785/conserved-dna-methylation-combined-with-differential-frontal-cortex-and-cerebellar-expression-distinguishes-c9orf72-associated-and-sporadic-als-and-implicates-serpina1-in-disease
#9
Mark T W Ebbert, Christian A Ross, Luc J Pregent, Rebecca J Lank, Cheng Zhang, Rebecca B Katzman, Karen Jansen-West, Yuping Song, Edroaldo Lummertz da Rocha, Carla Palmucci, Pamela Desaro, Amelia E Robertson, Ana M Caputo, Dennis W Dickson, Kevin B Boylan, Rosa Rademakers, Tamas Ordog, Hu Li, Veronique V Belzil
We previously found C9orf72-associated (c9ALS) and sporadic amyotrophic lateral sclerosis (sALS) brain transcriptomes comprise thousands of defects, among which, some are likely key contributors to ALS pathogenesis. We have now generated complementary methylome data and combine these two data sets to perform a comprehensive "multi-omic" analysis to clarify the molecular mechanisms initiating RNA misregulation in ALS. We found that c9ALS and sALS patients have generally distinct but overlapping methylome profiles, and that the c9ALS- and sALS-affected genes and pathways have similar biological functions, indicating conserved pathobiology in disease...
August 14, 2017: Acta Neuropathologica
https://www.readbyqxmd.com/read/28804556/anti-tumor-efficacy-evaluation-of-a-novel-monoclonal-antibody-targeting-neutral-amino-acid-transporter-asct2-using-patient-derived-xenograft-mouse-models-of-gastric-cancer
#10
Noriyuki Kasai, Aya Sasakawa, Kenta Hosomi, Tze Wei Poh, Bernadette Lynn Chua, Wei Peng Yong, Jimmy So, Shing Leng Chan, Richie Soong, Koji Kono, Toshihiko Ishii, Kazuya Yamano
ASC amino acid transporter 2 (ASCT2), also known as solute linked carrier family 1 member A5 (SLC1A5) is a Na+-dependent glutamine/neutral amino acid transporter. ASCT2 acts as a high-affinity transporter of L-glutamine (Gln) and has been reported to be up-regulated in a variety of cancerous tissues including stomach, liver, and kidney. In this study, we evaluated anti-tumor efficacy of a novel anti-ASCT2 humanized monoclonal antibody, KM8094, which has a neutralizing activity against glutamine uptake, as a therapeutic antibody against gastric cancer and explored clinical predictive biomarker candidates by utilizing patient-derived xenograft (PDX) mouse models...
2017: American Journal of Translational Research
https://www.readbyqxmd.com/read/28803495/molecular-signature-of-complex-regional-pain-syndrome-crps-and-its-analysis
#11
Simone König, Tanja Schlereth, Frank Birklein
Complex Regional Pain Syndrome (CRPS) is a rare, but often disabling pain disease. Biomarkers are lacking, but several inflammatory substances have been associated with the pathophysiology. This review outlines the current knowledge with respect to target biomolecules and the analytical tools available to measure them. Areas covered: Targets include cytokines, neuropeptides and resolvins; analysis strategies are thus needed for different classes of substances such as proteins, peptides, lipids and small molecules...
August 14, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28798504/molecular-aspects-of-wound-healing-and-the-rise-of-venous-leg-ulceration-omics-approaches-to-enhance-knowledge-and-aid-diagnostic-discovery
#12
REVIEW
Daniel A Broszczak, Elizabeth R Sydes, Daniel Wallace, Tony J Parker
Chronic wounds, in particular venous leg ulcers (VLU), represent a substantial burden for economies, healthcare systems and societies worldwide. This burden is exacerbated by the recalcitrant nature of these wounds, despite best practice, evidence-based care, which substantially reduces the quality of life of patients. Furthermore, co-morbidities such as diabetes and cardiovascular disease within ageing populations further contribute to the increasing prevalence in developed countries. This review provides an overview of the literature concerning the cellular and molecular mechanisms of wound healing and aspects where this process fails, resulting in a chronic wound...
February 2017: Clinical Biochemist. Reviews
https://www.readbyqxmd.com/read/28798503/working-up-a-good-sweat-the-challenges-of-standardising-sweat-collection-for-metabolomics-analysis
#13
REVIEW
Joy N Hussain, Nitin Mantri, Marc M Cohen
INTRODUCTION: Human sweat is a complex biofluid of interest to diverse scientific fields. Metabolomics analysis of sweat promises to improve screening, diagnosis and self-monitoring of numerous conditions through new applications and greater personalisation of medical interventions. Before these applications can be fully developed, existing methods for the collection, handling, processing and storage of human sweat need to be revised. This review presents a cross-disciplinary overview of the origins, composition, physical characteristics and functional roles of human sweat, and explores the factors involved in standardising sweat collection for metabolomics analysis...
February 2017: Clinical Biochemist. Reviews
https://www.readbyqxmd.com/read/28795660/systems-and-synthetic-biology-perspective-of-the-versatile-plant-pathogenic-and-polysaccharide-producing-bacterium-xanthomonas-campestris
#14
Sarah Schatschneider, Jessica Schneider, Jochen Blom, Fabien Létisse, Karsten Niehaus, Alexander Goesmann, Frank-Jörg Vorhölter
Bacteria of the genus Xanthomonas are a major group of plant pathogens. They are hazardous to important crops and closely related to human pathogens. Being collectively a major focus of molecular phytopathology, an increasing number of diverse and intricate mechanisms are emerging by which they communicate, interfere with host signalling and keep competition at bay. Interestingly, they are also biotechnologically relevant polysaccharide producers. Systems biotechnology techniques have revealed their central metabolism and a growing number of remarkable features...
August 10, 2017: Microbiology
https://www.readbyqxmd.com/read/28793788/improvements-in-algal-lipid-production-a-systems-biology-and-gene-editing-approach
#15
Avik Banerjee, Chiranjib Banerjee, Sangeeta Negi, Jo-Shu Chang, Pratyoosh Shukla
BACKGROUND: In the wake of rising energy demands, microalgae have emerged as potential sources of sustainable and renewable carbon-neutral fuels, such as bio-hydrogen and bio-oil. PURPOSE: For rational metabolic engineering, the elucidation of metabolic pathways in fine detail and their manipulation according to requirements is the key to exploiting the use of microalgae. Emergence of site-specific nucleases have revolutionized applied research leading to biotechnological gains...
August 9, 2017: Critical Reviews in Biotechnology
https://www.readbyqxmd.com/read/28783155/histocat-analysis-of-cell-phenotypes-and-interactions-in-multiplex-image-cytometry-data
#16
Denis Schapiro, Hartland W Jackson, Swetha Raghuraman, Jana R Fischer, Vito R T Zanotelli, Daniel Schulz, Charlotte Giesen, Raúl Catena, Zsuzsanna Varga, Bernd Bodenmiller
Single-cell, spatially resolved omics analysis of tissues is poised to transform biomedical research and clinical practice. We have developed an open-source, computational histology topography cytometry analysis toolbox (histoCAT) to enable interactive, quantitative, and comprehensive exploration of individual cell phenotypes, cell-cell interactions, microenvironments, and morphological structures within intact tissues. We highlight the unique abilities of histoCAT through analysis of highly multiplexed mass cytometry images of human breast cancer tissues...
August 7, 2017: Nature Methods
https://www.readbyqxmd.com/read/28781759/new-frontiers-in-metabolomics-from-measurement-to-insight
#17
REVIEW
Eli Riekeberg, Robert Powers
Metabolomics is the newest addition to the "omics" disciplines and has shown rapid growth in its application to human health research because of fundamental advancements in measurement and analysis techniques. Metabolomics has unique and proven advantages in systems biology and biomarker discovery. The next generation of analysis techniques promises even richer and more complete analysis capabilities that will enable earlier clinical diagnosis, drug refinement, and personalized medicine. A review of current advancements in methodologies and statistical analysis that are enhancing and improving the performance of metabolomics is presented along with highlights of some recent successful applications...
2017: F1000Research
https://www.readbyqxmd.com/read/28780062/metabolic-disruption-of-zebrafish-danio-rerio-embryos-by-bisphenol-a-an-integrated-metabolomic-and-transcriptomic-approach
#18
Elena Ortiz-Villanueva, Laia Navarro-Martín, Joaquim Jaumot, Fernando Benavente, Victoria Sanz-Nebot, Benjamín Piña, Romà Tauler
Although bisphenol A (BPA) is commonly recognized as an endocrine disruptor, the metabolic consequences of its exposure are still poorly understood. In this study, we present a non-targeted LC-MS based metabolomic analysis in combination with a full-genome, high-throughput RNA sequencing (RNA-Seq) to reveal the metabolic effects and the subjacent regulatory pathways of exposing zebrafish embryos to BPA during the first 120 hours post-fertilization. We applied multivariate data analysis methods to extract biochemical information from the LC-MS and RNA-Seq complex datasets and to perform testable predictions of the phenotypic adverse effects...
August 3, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28769804/metabolomics-and-integrative-omics-for-the-development-of-thai-traditional-medicine
#19
REVIEW
Sakda Khoomrung, Kwanjeera Wanichthanarak, Intawat Nookaew, Onusa Thamsermsang, Patcharamon Seubnooch, Tawee Laohapand, Pravit Akarasereenont
In recent years, interest in studies of traditional medicine in Asian and African countries has gradually increased due to its potential to complement modern medicine. In this review, we provide an overview of Thai traditional medicine (TTM) current development, and ongoing research activities of TTM related to metabolomics. This review will also focus on three important elements of systems biology analysis of TTM including analytical techniques, statistical approaches and bioinformatics tools for handling and analyzing untargeted metabolomics data...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28768216/a-multi-omics-based-ecological-analysis-of-coastal-marine-sediments-from-gladstone-in-australia-s-central-queensland-and-heron-island-a-nearby-fringing-platform-reef
#20
D J Beale, J Crosswell, A V Karpe, W Ahmed, M Williams, P D Morrison, S Metcalfe, C Staley, M J Sadowsky, E A Palombo, A D L Steven
The impact of anthropogenic factors arising from point and non-point pollution sources at a multi commodity marine port and its surrounding ecosystems were studied using sediment samples collected from a number of onshore (Gladstone Harbour and Facing Island) and offshore (Heron Island and Fitzroy Reefs) sites in Australia's Central Queensland. Sediment samples were analyzed for trace metals, organic carbon, polycyclic aromatic hydrocarbons (PAH), emerging chemicals of concern (ECC) and sterols. Similarly, the biological and biochemical interaction between the reef and its environment was analyzed by the multi-omic tools of next-generation sequencing characterization of the bacterial community and microbial community metabolic profiling...
July 30, 2017: Science of the Total Environment
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