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https://www.readbyqxmd.com/read/28335448/a-community-multi-omics-approach-towards-the-assessment-of-surface-water-quality-in-an-urban-river-system
#1
David J Beale, Avinash V Karpe, Warish Ahmed, Stephen Cook, Paul D Morrison, Christopher Staley, Michael J Sadowsky, Enzo A Palombo
A multi-omics approach was applied to an urban river system (the Brisbane River (BR), Queensland, Australia) in order to investigate surface water quality and characterize the bacterial population with respect to water contaminants. To do this, bacterial metagenomic amplicon-sequencing using Illumina next-generation sequencing (NGS) of the V5-V6 hypervariable regions of the 16S rRNA gene and untargeted community metabolomics using gas chromatography coupled with mass spectrometry (GC-MS) were utilized. The multi-omics data, in combination with fecal indicator bacteria (FIB) counts, trace metal concentrations (by inductively coupled plasma mass spectrometry (ICP-MS)) and in-situ water quality measurements collected from various locations along the BR were then used to assess the health of the river ecosystem...
March 14, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28334215/systematic-inference-of-functional-phosphorylation-events-in-yeast-metabolism
#2
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/28322544/graphene-oxide-quantum-dots-as-novel-nanozymes-for-alcohol-intoxication
#3
Anqi Sun, Li Mu, Xiangang Hu
Alcohol overconsumption as a worldwide issue results in alcoholic liver disease (ALD), such as steatosis, alcoholic hepatitis and cirrhosis. The treatment of ALD has been widely investigated but remains challenging. In this work, the protective effects of graphene oxide quantum dots (GOQDs) as novel nanozymes against alcohol overconsumption are discovered, and the specific mechanisms underlying these effects are elucidated via omics analysis. GOQDs dramatically alleviate the reduction of cell viability induced by ethanol and can act as nanozymes to accelerate ethanol metabolism and avoid the accumulation of toxic intermediates in cells...
March 21, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28321398/unveiling-the-metabolic-changes-on-muscle-cell-metabolism-underlying-p-phenylenediamine-toxicity
#4
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/28319856/systems-biology-solutions-for-biochemical-production-challenges
#5
REVIEW
Anne Sofie Lærke Hansen, Rebecca M Lennen, Nikolaus Sonnenschein, Markus J Herrgård
There is an urgent need to significantly accelerate the development of microbial cell factories to produce fuels and chemicals from renewable feedstocks in order to facilitate the transition to a biobased society. Methods commonly used within the field of systems biology including omics characterization, genome-scale metabolic modeling, and adaptive laboratory evolution can be readily deployed in metabolic engineering projects. However, high performance strains usually carry tens of genetic modifications and need to operate in challenging environmental conditions...
March 16, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28302330/precision-surgery-for-colorectal-liver-metastases-opportunities-and-challenges-of-omics-based-decision-making
#6
REVIEW
R P Jones, K W Brudvik, J M Franklin, G J Poston
Precision surgery involves improving patient selection to ensure that surgical intervention that is proven to benefit on a population level is the optimal treatment for each individual patient. For patients with colorectal liver metastases (CRLM), existing prognostic scoring systems rely on well-recognised histopathological features such as size and number of lesions. Advances in preoperative imaging algorithms mean that increasingly low volume disease can be detected, improving assessment of these factors...
March 6, 2017: European Journal of Surgical Oncology
https://www.readbyqxmd.com/read/28302035/translational-multimodality-neuroimaging
#7
Sushil K Sharma
Recently high-resolution, noninvasive, multimodality in-vivo molecular imaging with PET, SPECT, CT and MRI, employing fusion algorithms has revolutionized personalized medicine. However, specific radiopharmaceuticals (RPs) for the accurate diagnosis and effective treatment of progressive neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, drug addiction, and other cognitive impairments still remain in developmental phase. Currently, multimodality fusion neuroimaging is utilized for the determination of: pharmacokinetics and pre-clinical development of radiopharmaceuticals (RPs); in-vivo monitoring of stem cell transplantation therapy; nicotinic acetylcholine receptors (nAChRs) investigations; and regional cerebral blood flow and glucose metabolism in cognitively-impaired subjects employing noninvasive microPET and nano-SPECT imaging...
March 15, 2017: Current Drug Targets
https://www.readbyqxmd.com/read/28301739/systems-biology-of-metabolism
#8
Jens Nielsen
Metabolism is highly complex and involves thousands of different connected reactions; it is therefore necessary to use mathematical models for holistic studies. The use of mathematical models in biology is referred to as systems biology. In this review, the principles of systems biology are described, and two different types of mathematical models used for studying metabolism are discussed: kinetic models and genome-scale metabolic models. The use of different omics technologies, including transcriptomics, proteomics, metabolomics, and fluxomics, for studying metabolism is presented...
March 8, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28300637/integrated-mass-spectrometry-imaging-and-omics-workflows-on-the-same-tissue-section-using-grid-aided-parafilm-assisted-microdissection
#9
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/28296247/comprehensive-proteome-analysis-of-human-skeletal-muscle-in-cachexia-and-sarcopenia-a-pilot-study
#10
H Alexander Ebhardt, Simone Degen, Valentina Tadini, Alain Schilb, Neil Johns, Carolyn A Greig, Kenneth C H Fearon, Ruedi Aebersold, Carsten Jacobi
BACKGROUND: Cancer cachexia (cancer-induced muscle wasting) is found in a subgroup of cancer patients leaving the patients with a poor prognosis for survival due to a lower tolerance of the chemotherapeutic drug. The cause of the muscle wasting in these patients is not fully understood, and no predictive biomarker exists to identify these patients early on. Skeletal muscle loss is an inevitable consequence of advancing age. As cancer frequently occurs in old age, identifying and differentiating the molecular mechanisms mediating muscle wasting in cancer cachexia vs...
March 15, 2017: Journal of Cachexia, Sarcopenia and Muscle
https://www.readbyqxmd.com/read/28293020/untangling-the-relationship-between-diet-and-visceral-fat-mass-through-blood-metabolomics-and-gut-microbiome-profiling
#11
T Pallister, M A Jackson, T C Martin, C A Glastonbury, A Jennings, M Beaumont, R P Mohney, K S Small, A MacGregor, C J Steves, A Cassidy, T D Spector, C Menni, A M Valdes
BACKGROUND/OBJECTIVES: Higher visceral fat mass (VFM) is associated with an increased risk for developing cardio-metabolic diseases. The mechanisms by which an unhealthy diet pattern may influence VF development has yet to be examined through cutting-edge multi-omic methods. Therefore, our objective was to examine the dietary influences on VFM and identify gut microbiome and metabolite profiles that link food intakes to VFM. SUBJECTS/METHODS: In 2218 twins with VFM, food intake and metabolomics data available we identified food intakes most strongly associated with VFM in 50% of the sample, then constructed and tested the 'VFM diet score' in the remainder of the sample...
March 15, 2017: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/28289514/modern-trends-in-animal-venom-research-omics-and-nanomaterials
#12
EDITORIAL
Yuri N Utkin
Animal venom research is a specialized investigation field, in which a number of different methods are used and this array is constantly expanding. Thus, recently emerged omics and nanotechnologies have already been successfully applied to venom research. Animal venoms have been studied for quite a long time. The traditional reductionist approach has been to isolate individual toxins and then study their structure and function. Unfortunately, the characterization of the venom as a whole system and its multiple effects on an entire organism were not possible until recent times...
February 26, 2017: World Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28284392/diseases-of-the-synaptic-vesicle-a-potential-new-group-of-neurometabolic-disorders-affecting-neurotransmission
#13
E Cortès-Saladelafont, A Tristán-Noguero, R Artuch, X Altafaj, A Bayès, A García-Cazorla
The general concept of inborn error of metabolism is currently evolving into the interface between classical biochemistry and cellular biology. Basic neuroscience is providing increasing knowledge about the mechanisms of neurotransmission and novel related disorders are being described. There is a necessity of updating the classic concept of "inborn error of neurotransmitters (NT)" that considers mainly defects of synthesis and catabolism and transport of low weight NT molecules. Monogenic defects of the synaptic vesicle (SV), and especially those affecting the SV cycle are a potential new group of NT disorders since they end up in abnormal NT turnover and release...
November 2016: Seminars in Pediatric Neurology
https://www.readbyqxmd.com/read/28280501/high-throughput-and-computational-study-of-leaf-senescence-through-a-phenomic-approach
#14
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/28272908/metabolomics-assisted-biotechnological-interventions-for-developing-plant-based-functional-foods-and-nutraceuticals
#15
Arun Kumar, Kareem A Mosa, Liyao Ji, Udaykumar Kage, Dhananjay Dhokane, Shailesh Karre, Deepa Madalageri, Neemisha Pathania
Today, the dramatic changes in types of food consumed have led to an increased burden of chronic diseases. Therefore, the emphasis of food research is not only to ensure quality food that can supply adequate nutrients to prevent nutrition related diseases, but also to ensure overall physical and mental-health. This has led to the concept of functional foods and nutraceuticals (FFNs), which can be ideally produced and delivered through plants. Metabolomics can help in getting the most relevant functional information, and thus has been considered the greatest -OMICS technology to date...
March 8, 2017: Critical Reviews in Food Science and Nutrition
https://www.readbyqxmd.com/read/28272447/eggshell-membrane-powder-ameliorates-intestinal-inflammation-by-facilitating-the-restitution-of-epithelial-injury-and-alleviating-microbial-dysbiosis
#16
Huijuan Jia, Manaka Hanate, Wanping Aw, Hideomi Itoh, Kenji Saito, Shoko Kobayashi, Satoshi Hachimura, Shinji Fukuda, Masaru Tomita, Yukio Hasebe, Hisanori Kato
Gut microbiota is an essential factor in the shaping of intestinal immune system development and driving inflammation in inflammatory bowel disease (IBD). We report the effects and microbe-host interactions underlying an intervention using fine powder of eggshell membrane (ESM) against IBD. ESM attenuated lipopolysaccharide-induced inflammatory cytokine production and promoted the Caco-2 cell proliferation by up-regulating growth factors in vitro. In a murine model of dextran sodium sulphate-induced colitis, ESM significantly suppressed the disease activity index and colon shortening...
March 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28264562/heterologous-biosynthesis-of-spinosad-an-omics-guided-large-polyketide-synthase-gene-cluster-reconstitution-in-streptomyces
#17
Gao-Yi Tan, Kunhua Deng, Xinhua Liu, Hui Tao, Yingying Chang, Jia Chen, Kai Chen, Zhi Sheng, Zixin Deng, Tiangang Liu
With the advent of the genomics era, heterologous gene expression has been used extensively as a means of accessing natural products (NPs) from environmental DNA samples. However, the heterologous production of NPs often has very low efficiency or is unable to produce targeted NPs. Moreover, due to the complicated transcriptional and metabolic regulation of NP biosynthesis in native producers, especially in the cases of genome mining, it is also difficult to rationally and systematically engineer synthetic pathways to improved NPs biosynthetic efficiency...
March 13, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28263462/omics-for-understanding-the-gut-liver-microbiome-axis-and-precision-medicine
#18
Jag Khalsa, Linda C Duffy, Gabriela Riscuta, Pamela Starke-Reed, Van S Hubbard
Human metabolic disease opens a new view to understanding the contribution of the intestinal microbiome to drug metabolism and drug-induced toxicity in gut-liver function. The gut microbiome, a key determinant of intestinal inflammation, also plays a direct role in chronic inflammation and liver disease. Gut bacterial communities directly metabolize certain drugs, reducing their bioavailability and influencing individual variation in drug response. In addition, some microbiome-produced compounds may affect drug pharmacokinetics and pharmacodynamics via altered expression of metabolizing enzymes and drug transporters or genes coding for drug target proteins, drug response phenotypes, and disease states...
March 2017: Clinical Pharmacology in Drug Development
https://www.readbyqxmd.com/read/28263171/omics-markers-of-the-red-cell-storage-lesion-and-metabolic-linkage
#19
REVIEW
Angelo D'alessandro, Travis Nemkov, Julie Reisz, Monika Dzieciatkowska, Matthew J Wither, Kirk C Hansen
The introduction of omics technologies in the field of Transfusion Medicine has significantly advanced our understanding of the red cell storage lesion. While the clinical relevance of such a lesion is still a matter of debate, quantitative and redox proteomics approaches, as well quantitative metabolic flux analysis and metabolic tracing experiments promise to revolutionise our understanding of the role of blood processing strategies, inform the design and testing of novel additives or technologies (such as pathogen reduction), and evaluate the clinical relevance of donor and recipient biological variability with respect to red cell storability and transfusion outcomes...
March 2017: Blood Transfusion, Trasfusione del Sangue
https://www.readbyqxmd.com/read/28260722/high-resolution-magic-angle-spinning-1-h-nmr-spectroscopy-based-metabolic-profiling-of-hippocampal-tissue-in-rats-with-depression-like-symptoms
#20
Hayato Akimoto, Shinji Oshima, Kousuke Ohara, Akio Negishi, Hanako Hiroyama, Tadashi Nemoto, Daisuke Kobayashi
Depressive disorders cause large socioeconomic effects influencing not only the patients themselves but also their family and broader community as well. To better understand the physiologic factors underlying depression, in this study, we performed metabolomics analysis, an omics technique that comprehensively analyzes small molecule metabolites in biological samples. Specifically, we utilized high-resolution magic-angle spinning-(1)H NMR (HRMAS-(1)H NMR) spectroscopy to comprehensively analyze the changes in metabolites in the hippocampal tissue of rats exposed to chronic stress (CS) via multi-step principal component analysis (multi-step PCA)...
March 4, 2017: Biological & Pharmaceutical Bulletin
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