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https://www.readbyqxmd.com/read/28812256/the-potential-for-emerging-microbiome-mediated-therapeutics-in-asthma
#1
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
#2
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/28811553/cascaded-multi-view-canonical-correlation-camcco-for-early-diagnosis-of-alzheimer-s-disease-via-fusion-of-clinical-imaging-and-omic-features
#3
Asha Singanamalli, Haibo Wang, Anant Madabhushi
The introduction of mild cognitive impairment (MCI) as a diagnostic category adds to the challenges of diagnosing Alzheimer's Disease (AD). No single marker has been proven to accurately categorize patients into their respective diagnostic groups. Thus, previous studies have attempted to develop fused predictors of AD and MCI. These studies have two main limitations. Most do not simultaneously consider all diagnostic categories and provide suboptimal fused representations using the same set of modalities for prediction of all classes...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28810121/comparative-proteomic-and-transcriptomic-analysis-of-follistatin-induced-skeletal-muscle-hypertrophy
#4
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/28809429/dissection-of-the-module-network-implementation-lemontree-enhancements-towards-applications-in-metagenomics-and-translation-in-autoimmune-maladies
#5
Youtao Lu, Xiaoyuan Zhou, Christine Nardini
Under the current deluge of omics, module networks distinctively emerge as methods capable of not only identifying inherently coherent groups (modules), thus reducing dimensionality, but also hypothesizing cause-effect relationships between modules and their regulators. Module networks were first designed in the transcriptomic era and further exploited in the multi-omic context to assess (for example) miRNA regulation of gene expression. Despite a number of available implementations, expansion of module networks to other omics is constrained by a limited characterization of the solutions' (modules plus regulators) accuracy and stability - an immediate need for the better characterization of molecular biology complexity in silico...
August 15, 2017: Molecular BioSystems
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
#6
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/28806595/advances-in-stem-cell-proteomics
#7
REVIEW
Nade Abazova, Jeroen Krijgsveld
Stem cells are at the basis of organismal development, characterized by their potential to differentiate towards specific lineages upon receiving proper signals. To understand the molecular principles underlying gain and loss of pluripotency, proteomics plays an increasingly important role owing to technical developments in mass spectrometry and implementation of innovative biochemical approaches. Here we review how quantitative proteomics has been used to investigate protein expression, localization, interaction and modification in stem cells both in vitro and in vivo, thereby complementing other omics approaches to study fundamental properties of stem cell plasticity...
August 11, 2017: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/28806583/plant-genome-scale-reconstruction-from-single-cell-to-multi-tissue-modelling-and-omics-analyses
#8
REVIEW
Cristiana Gomes de Oliveira Dal'Molin, Lars Keld Nielsen
In this review, we present the latest developments in plant systems biology with particular emphasis on plant genome-scale reconstructions and multi-omics analyses. Understanding multicellular metabolism is far from trivial and 'omics' data are difficult to interpret in the absence of a systems framework. 'Omics' data appropriately integrated with genome-scale reconstructions and modelling facilitates our understanding of how individual components interact and influence overall cell, tissue or organisms function...
August 11, 2017: Current Opinion in Biotechnology
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
#9
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/28804491/phylloremediation-of-air-pollutants-exploiting-the-potential-of-plant-leaves-and-leaf-associated-microbes
#10
REVIEW
Xiangying Wei, Shiheng Lyu, Ying Yu, Zonghua Wang, Hong Liu, Dongming Pan, Jianjun Chen
Air pollution is air contaminated by anthropogenic or naturally occurring substances in high concentrations for a prolonged time, resulting in adverse effects on human comfort and health as well as on ecosystems. Major air pollutants include particulate matters (PMs), ground-level ozone (O3), sulfur dioxide (SO2), nitrogen dioxides (NO2), and volatile organic compounds (VOCs). During the last three decades, air has become increasingly polluted in countries like China and India due to rapid economic growth accompanied by increased energy consumption...
2017: Frontiers in Plant Science
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/28798368/global-temporal-dynamic-landscape-of-pathogen-mediated-subversion-of-arabidopsis-innate-immunity
#14
Bharat Mishra, Yali Sun, Hadia Ahmed, Xiaoyu Liu, M Shahid Mukhtar
The universal nature of networks' structural and physical properties across diverse systems offers a better prospect to elucidate the interplay between a system and its environment. In the last decade, several large-scale transcriptome and interactome studies were conducted to understand the complex and dynamic nature of interactions between Arabidopsis and its bacterial pathogen, Pseudomonas syringae pv. tomato DC3000. We took advantage of these publicly available datasets and performed "-omics"-based integrative, and network topology analyses to decipher the transcriptional and protein-protein interaction activities of effector targets...
August 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28797473/biomarker-research-to-improve-clinical-outcomes-of-peritoneal-dialysis-consensus-of-the-european-training-and-research-in-peritoneal-dialysis-eutripd-network
#15
REVIEW
Christoph Aufricht, Robert Beelen, Matthias Eberl, Michel Fischbach, Donald Fraser, Achim Jörres, Klaus Kratochwill, Manuel LópezCabrera, Peter Rutherford, Claus-Peter Schmitt, Nicholas Topley, Janusz Witowski
Peritoneal dialysis (PD) therapy substantially requires biomarkers as tools to identify patients who are at the highest risk for PD-related complications and to guide personalized interventions that may improve clinical outcome in the individual patient. In this consensus article, members of the European Training and Research in Peritoneal Dialysis Network (EuTRiPD) review the current status of biomarker research in PD and suggest a selection of biomarkers that can be relevant to the care of PD patients and that are directly accessible in PD effluents...
August 8, 2017: Kidney International
https://www.readbyqxmd.com/read/28797229/odg-omics-database-generator-a-tool-for-generating-querying-and-analyzing-multi-omics-comparative-databases-to-facilitate-biological-understanding
#16
Joseph Guhlin, Kevin A T Silverstein, Peng Zhou, Peter Tiffin, Nevin D Young
BACKGROUND: Rapid generation of omics data in recent years have resulted in vast amounts of disconnected datasets without systemic integration and knowledge building, while individual groups have made customized, annotated datasets available on the web with few ways to link them to in-lab datasets. With so many research groups generating their own data, the ability to relate it to the larger genomic and comparative genomic context is becoming increasingly crucial to make full use of the data...
August 10, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28795660/systems-and-synthetic-biology-perspective-of-the-versatile-plant-pathogenic-and-polysaccharide-producing-bacterium-xanthomonas-campestris
#17
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/28795278/frozen-tissue-preparation-for-high-resolution-multiplex-histological-analyses-of-human-brain-specimens
#18
Fangjie Shao, Wenhong Jiang, Qingqing Gao, Baizhou Li, Chongran Sun, Qiyuan Wang, Qin Chen, Bing Sun, Hong Shen, Keqing Zhu, Jianmin Zhang, Chong Liu
The availability of a comprehensive tissue library is essential for elucidating the function and pathology of human brains. Considering the irreplaceable status of the formalin-fixation-paraffin-embedding (FFPE) preparation in routine pathology and the advantage of ultra-low temperature to preserve nucleic acids and proteins for multi-omics studies, these methods have become major modalities for the construction of brain tissue libraries. Nevertheless, the use of FFPE and snap-frozen samples is limited in high-resolution histological analyses because the preparation destroys tissue integrity and/or many important cellular markers...
August 9, 2017: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/28794807/prognostic-and-predictive-biomarkers-in-prostate-cancer-latest-evidence-and-clinical-implications
#19
REVIEW
Naoki Terada, Shusuke Akamatsu, Takashi Kobayashi, Takahiro Inoue, Osamu Ogawa, Emmanuel S Antonarakis
Advances in our understanding of the mechanisms driving castration-resistant prostate cancer have promoted the development of several new drugs including androgen receptor-directed therapy and chemotherapy. Concomitant docetaxel treatment at the beginning of hormonal therapy for metastatic prostate cancer has resulted in longer overall survival than with hormonal therapy alone. Elucidating an appropriate treatment sequence using these therapies is important for maximizing clinical benefit in castration-sensitive and castration-resistant prostate cancer patients...
August 2017: Therapeutic Advances in Medical Oncology
https://www.readbyqxmd.com/read/28793788/improvements-in-algal-lipid-production-a-systems-biology-and-gene-editing-approach
#20
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
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