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https://www.readbyqxmd.com/read/28435675/microbiome-effects-on-immunity-health-and-disease-in-the-lung
#1
REVIEW
Shakti D Shukla, Kurtis F Budden, Rachael Neal, Philip M Hansbro
Chronic respiratory diseases, including asthma, chronic obstructive pulmonary disease (COPD) and cystic fibrosis (CF), are among the leading causes of mortality and morbidity worldwide. In the past decade, the interest in the role of microbiome in maintaining lung health and in respiratory diseases has grown exponentially. The advent of sophisticated multiomics techniques has enabled the identification and characterisation of microbiota and their roles in respiratory health and disease. Furthermore, associations between the microbiome of the lung and gut, as well as the immune cells and mediators that may link these two mucosal sites, appear to be important in the pathogenesis of lung conditions...
March 2017: Clinical & Translational Immunology
https://www.readbyqxmd.com/read/28408661/multiomics-of-tomato-glandular-trichomes-reveals-distinct-features-of-central-carbon-metabolism-supporting-high-productivity-of-specialized-metabolites
#2
Gerd Balcke, Stefan Bennewitz, Nick Bergau, Benedikt Athmer, Anja Henning, Petra Majovsky, José M Jiménez-Gómez, Wolfgang Hoehenwarter, Alain F Tissier
Glandular trichomes are metabolic cell factories with the capacity to produce large quantities of secondary metabolites. Little is known about the connection between central carbon metabolism and metabolic productivity for secondary metabolites in glandular trichomes. To address this gap in our knowledge, we performed comparative metabolomics, transcriptomics, proteomics and 13C-labeling of type VI glandular trichomes and leaves from a cultivated (Solanum lycopersicum LA4024) and a wild (Solanum habrochaites LA1777) tomato accession...
April 13, 2017: Plant Cell
https://www.readbyqxmd.com/read/28404159/a-microbiota-centric-view-of-diseases-of-the-upper-gastrointestinal-tract
#3
REVIEW
Gerardo Nardone, Debora Compare, Alba Rocco
The distinctive anatomy and physiology of the upper gastrointestinal tract and the difficulty of obtaining samples led to the theory that it was bacteria free. However, multiomics studies are indicating otherwise. Although influenced by both oral and gastric bacteria, the resident microbial ecosystem in the oesophagus is dominated by Streptococcus. A shift from Gram-positive to Gram-negative bacteria occurs in oesophagitis and Barrett's oesophagus, and this shift might be involved in the pathogenesis of oesophageal adenocarcinoma...
April 2017: Lancet. Gastroenterology & Hepatology
https://www.readbyqxmd.com/read/28400203/transcriptomic-and-genomic-features-of-invasive-lobular-breast-cancer
#4
REVIEW
Christine Desmedt, Gabriele Zoppoli, Christos Sotiriou, Roberto Salgado
Accounting for 10% to 15% of all breast neoplasms, invasive lobular breast cancer (ILC) is the second most common histological subtype of breast cancer after invasive ductal breast cancer (IDC). Understanding ILC biology, which differs from IDC in terms of clinical presentation, treatment response, relapse timing and patterns, is essential in order to adopt novel, disease-specific management strategies. While the contribution of the histological subtypes to tumor biology has been poorly investigated and acknowledged in the past, recently several major, independent efforts have led to the assembly and molecular characterization of well-annotated ILBCILC case sets...
April 8, 2017: Seminars in Cancer Biology
https://www.readbyqxmd.com/read/28385856/updated-reference-genome-sequence-and-annotation-of-mycobacterium-bovis-af2122-97
#5
Kerri M Malone, Damien Farrell, Tod P Stuber, Olga T Schubert, Ruedi Aebersold, Suelee Robbe-Austerman, Stephen V Gordon
We report here an update to the reference genome sequence of the bovine tuberculosis bacillus Mycobacterium bovis AF2122/97, generated using an integrative multiomics approach. The update includes 42 new coding sequences (CDSs), 14 modified annotations, 26 single-nucleotide polymorphism (SNP) corrections, and disclosure that the RD900 locus, previously described as absent from the genome, is in fact present.
April 6, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28275586/colistin-resistance-in-acinetobacter-baumannii-mdr-zj06-revealed-by-a-multiomics-approach
#6
Xiaoting Hua, Lilin Liu, Youhong Fang, Qiucheng Shi, Xi Li, Qiong Chen, Keren Shi, Yan Jiang, Hua Zhou, Yunsong Yu
Acinetobacter baumannii has emerged as an important opportunistic pathogen due to its ability to acquire resistance to most currently available antibiotics. Colistin is often considered as the last line of therapy for infections caused by multidrug-resistant A. baumannii (MDRAB). However, colistin-resistant A. baumannii strain has recently been reported. To explore how multiple drug-resistant A. baumannii responded to colistin resistance, we compared the genomic, transcriptional and proteomic profile of A. baumannii MDR-ZJ06 to the induced colistin-resistant strain ZJ06-200P5-1...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28206814/biomarkers-in-tumor-microenvironment-upregulation-of-fibroblast-activation-protein-%C3%AE-correlates-with-gastric-cancer-progression-and-poor-prognosis
#7
Mengmou Hu, Chengjia Qian, Ziwei Hu, Bojian Fei, Haibo Zhou
Gastric cancer is the third leading cause of cancer-related mortality worldwide. Recent evidence points to importance of cross talk between cancer cells and the surrounding stroma on gastric cancer progression. Tumor microenvironment biomarkers thus represent a new opportunity for diagnostics innovation. Reactive stromal fibroblasts selectively express the fibroblast activation protein alpha (FAP-α), a homodimeric integral membrane gelatinase that belongs to the serine protease family. We report here that FAP-α expression is significantly elevated in gastric cancer samples by more than fivefold (p < 0...
January 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28165029/quantitative-global-proteome-and-lysine-succinylome-analyses-provide-insights-into-metabolic-regulation-and-lymph-node-metastasis-in-gastric-cancer
#8
Yongxi Song, Jun Wang, Zhongyi Cheng, Peng Gao, Jingxu Sun, Xiaowan Chen, Chen Chen, Yunlong Wang, Zhenning Wang
With the rapid development of high-throughput quantitative proteomic and transcriptomic approaches, the molecular mechanisms of cancers have been comprehensively explored. However, cancer is a multi-dimensional disease with sophisticated regulations, and few studies focus on the crosstalk among multiomics. In order to explore the molecular mechanisms of gastric cancer (GC), particularly in the process of lymph node metastasis (LNM), we investigated dynamic profiling changes as well as crosstalk between long non-coding RNAs (lncRNAs), the proteome, and the lysine succinylome...
February 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28152499/contributions-of-polyunsaturated-fatty-acids-pufa-on-cerebral-neurobiology-an-integrated-omics-approach-with-epigenomic-focus
#9
Nabarun Chakraborty, Seid Muhie, Raina Kumar, Aarti Gautam, Seshamalini Srinivasan, Bintu Sowe, George Dimitrov, Stacy-Ann Miller, Marti Jett, Rasha Hammamieh
The epigenetic landscape is vulnerable to diets. Here, we investigated the influence of different polyunsaturated fatty acids (PUFA) dietary supplements on rodents' nervous system development and functions and potential consequences to neurodegenerative disorders. Our previous nutrigenomics study showed significant impact of high n-3 PUFA-enriched diet (ERD) on synaptogenesis and various neuromodulators. The present study introduced a second equicaloric diet with n-6 PUFA balanced by n-3 PUFA (BLD). The typical lab diet with high n-6 PUFA was the baseline...
January 5, 2017: Journal of Nutritional Biochemistry
https://www.readbyqxmd.com/read/28126735/integrated-analysis-of-multiomic-data-reveals-the-role-of-the-antioxidant-network-in-the-quality-of-sea-buckthorn-berry
#10
Caiyun He, Guoyun Zhang, Jianguo Zhang, Yanfei Zeng, Juanjuan Liu
Berries of sea buckthorn, known as the "king of vitamin C," are abundant in antioxidants, have attractive colors, and are an excellent material with which to study the relationships between berry color, antioxidants, and berry quality. No study has yet determined the molecular basis of the relationship between sea buckhorn berries and their color and antioxidant levels. By using RNA-seq, liquid chromatography-MS/MS, and liquid chromatography/GC-MS technology and selecting red (darkest colored) and yellow (lightest colored) sea buckthorn berries at different development stages, this study showed that the red and yellow berry resulted from a higher ratio of lycopene to β-carotene and of β-carotene to lycopene content, respectively...
January 26, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28118095/multiomics-approach-to-novel-therapeutic-targets-for-cancer-and-aging-related-diseases-role-of-sld7-in-yeast-aging-network
#11
Irem E Dayan, Kazim Yalcin Arga, Kutlu O Ulgen
Genome instability has long been implicated as a salient causal factor in aging and age-related diseases such as cancer and neurodegeneration. However, the molecular mechanisms associated with genome instability remain unclear. Recent studies suggest growth signaling in the organism Saccharomyces cerevisiae and in higher eukaryotes might affect oxidative stress and aging/age-related diseases by activating DNA replication stress that causes DNA damage. In this broader integrative biology and clinical context, MDM two binding protein (MTBP) is a binding protein that has a role in activation of the tumor suppressor protein p53...
February 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28104774/microrna-biomarkers-and-platelet-reactivity-the-clot-thickens
#12
REVIEW
Nicholas Sunderland, Philipp Skroblin, Temo Barwari, Rachael P Huntley, Ruifang Lu, Abhishek Joshi, Ruth C Lovering, Manuel Mayr
Over the last few years, several groups have evaluated the potential of microRNAs (miRNAs) as biomarkers for cardiometabolic disease. In this review, we discuss the emerging literature on the role of miRNAs and other small noncoding RNAs in platelets and in the circulation, and the potential use of miRNAs as biomarkers for platelet activation. Platelets are a major source of miRNAs, YRNAs, and circular RNAs. By harnessing multiomics approaches, we may gain valuable insights into their potential function. Because not all miRNAs are detectable in the circulation, we also created a gene ontology annotation for circulating miRNAs using the gene ontology term extracellular space as part of blood plasma...
January 20, 2017: Circulation Research
https://www.readbyqxmd.com/read/28092275/mechanistic-insights-from-combining-genomics-with-metabolomics
#13
Fotios Drenos
PURPOSE OF REVIEW: Metabolomics directly measure substrates and products of biological processes and pathways. Based on instrumentation and throughput advances, the use of metabolomics has only recently become feasible at the population level. This has led to an intense interest in using the new information in combination with genomics, and other omics technologies, to give biological context to the rapidly accumulating associations between genes and diseases or their risk factors. RECENT FINDINGS: The use of metabolomics-genomic associations for the metabolic characterization of genes of interest has confirmed known pathways and permitted the identification of new ones...
January 13, 2017: Current Opinion in Lipidology
https://www.readbyqxmd.com/read/28089370/single-cell-multiomics-multiple-measurements-from-single-cells
#14
REVIEW
Iain C Macaulay, Chris P Ponting, Thierry Voet
Single-cell sequencing provides information that is not confounded by genotypic or phenotypic heterogeneity of bulk samples. Sequencing of one molecular type (RNA, methylated DNA or open chromatin) in a single cell, furthermore, provides insights into the cell's phenotype and links to its genotype. Nevertheless, only by taking measurements of these phenotypes and genotypes from the same single cells can such inferences be made unambiguously. In this review, we survey the first experimental approaches that assay, in parallel, multiple molecular types from the same single cell, before considering the challenges and opportunities afforded by these and future technologies...
February 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28067231/multiomics-reveal-non-alcoholic-fatty-liver-disease-in-rats-following-chronic-exposure-to-an-ultra-low-dose-of-roundup-herbicide
#15
Robin Mesnage, George Renney, Gilles-Eric Séralini, Malcolm Ward, Michael N Antoniou
The impairment of liver function by low environmentally relevant doses of glyphosate-based herbicides (GBH) is still a debatable and unresolved matter. Previously we have shown that rats administered for 2 years with 0.1 ppb (50 ng/L glyphosate equivalent dilution; 4 ng/kg body weight/day daily intake) of a Roundup GBH formulation showed signs of enhanced liver injury as indicated by anatomorphological, blood/urine biochemical changes and transcriptome profiling. Here we present a multiomic study combining metabolome and proteome liver analyses to obtain further insight into the Roundup-induced pathology...
January 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/27801551/sample-preparation-method-considerations-for-integrated-transcriptomic-and-proteomic-analysis-of-tumors
#16
Anupama Rajan Bhat, Manoj Kumar Gupta, Priya Krithivasan, Kunal Dhas, Jayalakshmi Nair, Ram Bhupal Reddy, Holalugunda Vittalamurthy Sudheendra, Sandip Chavan, Harsha Vardhan, Sujatha Darsi, Lavanya Balakrishnan, Shanmukh Katragadda, Vikram Kekatpure, Amritha Suresh, Pramila Tata, Binay Panda, Moni A Kuriakose, Ravi Sirdeshmukh
Sample processing protocols that enable compatible recovery of differentially expressed transcripts and proteins are necessary for integration of the multiomics data applied in the analysis of tumors. In this pilot study, we compared two different isolation methods for extracting RNA and protein from laryngopharyngeal tumor tissues and the corresponding adjacent normal sections. In Method 1, RNA and protein were isolated from a single tissue section sequentially and in Method 2, the extraction was carried out using two different sections and two independent and parallel protocols for RNA and protein...
November 1, 2016: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/27726639/genetics-of-sickle-cell-associated-cardiovascular-disease-an-expert-review-with-lessons-learned-in-africa
#17
Amy Geard, Gift D Pule, David Chelo, Valentina Josiane Ngo Bitoungui, Ambroise Wonkam
Sickle cell disease (SCD) vastly impacts the African continent and is associated with cardiovascular diseases. Stroke, kidney disease, and pulmonary hypertension are considered as proxies of severity in SCD with several genomic loci implicated in their heritability. The present expert review examined the current data on epidemiology and genetic risk factors of stroke, pulmonary hypertension, and kidney disease associated with SCD, as indexed in PubMed(®) and Google Scholar(®). Studies collectively show that stroke and kidney disease each affect ∼10% of SCD patients, with pulmonary hypertension displaying a higher prevalence of 30% among adults with SCD...
October 2016: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/27689071/embracing-integrative-multiomics-approaches
#18
REVIEW
Daniel M Rotroff, Alison A Motsinger-Reif
As "-omics" data technology advances and becomes more readily accessible to address complex biological questions, increasing amount of cross "-omics" dataset is inspiring the use and development of integrative bioinformatics analysis. In the current review, we discuss multiple options for integrating data across "-omes" for a range of study designs. We discuss established methods for such analysis and point the reader to in-depth discussions for the various topics. Additionally, we discuss challenges and new directions in the area...
2016: International Journal of Genomics
https://www.readbyqxmd.com/read/27559923/sygnaling-a-red-light-for-glioblastoma
#19
Aaron N Brooks, William F Mueller, Lars M Steinmetz
A new multiomic network inference pipeline, SYGNAL, integrates patient data with mechanistically accurate transcriptional regulatory networks to predict drug combinations with synergistic anti-proliferative effects on glioblastoma multiforme.
August 2016: Cell Systems
https://www.readbyqxmd.com/read/27492622/in-vitro-acute-and-developmental-neurotoxicity-screening-an-overview-of-cellular-platforms-and-high-throughput-technical-possibilities
#20
REVIEW
Béla Z Schmidt, Martin Lehmann, Simon Gutbier, Erastus Nembo, Sabrina Noel, Lena Smirnova, Anna Forsby, Jürgen Hescheler, Hasan X Avci, Thomas Hartung, Marcel Leist, Julianna Kobolák, András Dinnyés
Neurotoxicity and developmental neurotoxicity are important issues of chemical hazard assessment. Since the interpretation of animal data and their extrapolation to man is challenging, and the amount of substances with information gaps exceeds present animal testing capacities, there is a big demand for in vitro tests to provide initial information and to prioritize for further evaluation. During the last decade, many in vitro tests emerged. These are based on animal cells, human tumour cell lines, primary cells, immortalized cell lines, embryonic stem cells, or induced pluripotent stem cells...
January 2017: Archives of Toxicology
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