keyword
MENU ▼
Read by QxMD icon Read
search

Multiomics

keyword
https://www.readbyqxmd.com/read/29023486/the-sea-cucumber-genome-provides-insights-into-morphological-evolution-and-visceral-regeneration
#1
Xiaojun Zhang, Lina Sun, Jianbo Yuan, Yamin Sun, Yi Gao, Libin Zhang, Shihao Li, Hui Dai, Jean-François Hamel, Chengzhang Liu, Yang Yu, Shilin Liu, Wenchao Lin, Kaimin Guo, Songjun Jin, Peng Xu, Kenneth B Storey, Pin Huan, Tao Zhang, Yi Zhou, Jiquan Zhang, Chenggang Lin, Xiaoni Li, Lili Xing, Da Huo, Mingzhe Sun, Lei Wang, Annie Mercier, Fuhua Li, Hongsheng Yang, Jianhai Xiang
Apart from sharing common ancestry with chordates, sea cucumbers exhibit a unique morphology and exceptional regenerative capacity. Here we present the complete genome sequence of an economically important sea cucumber, A. japonicus, generated using Illumina and PacBio platforms, to achieve an assembly of approximately 805 Mb (contig N50 of 190 Kb and scaffold N50 of 486 Kb), with 30,350 protein-coding genes and high continuity. We used this resource to explore key genetic mechanisms behind the unique biological characters of sea cucumbers...
October 2017: PLoS Biology
https://www.readbyqxmd.com/read/28973931/systems-level-identification-of-pka-dependent-signaling-in-epithelial-cells
#2
Kiyoshi Isobe, Hyun Jun Jung, Chin-Rang Yang, J'Neka Claxton, Pablo Sandoval, Maurice B Burg, Viswanathan Raghuram, Mark A Knepper
G protein stimulatory α-subunit (Gαs)-coupled heptahelical receptors regulate cell processes largely through activation of protein kinase A (PKA). To identify signaling processes downstream of PKA, we deleted both PKA catalytic subunits using CRISPR-Cas9, followed by a "multiomic" analysis in mouse kidney epithelial cells expressing the Gαs-coupled V2 vasopressin receptor. RNA-seq (sequencing)-based transcriptomics and SILAC (stable isotope labeling of amino acids in cell culture)-based quantitative proteomics revealed a complete loss of expression of the water-channel gene Aqp2 in PKA knockout cells...
October 2, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28960106/multiomics-approach-to-asthma-navigating-the-network
#3
Merry-Lynn McDonald
No abstract text is available yet for this article.
October 2017: American Journal of Respiratory Cell and Molecular Biology
https://www.readbyqxmd.com/read/28937943/multiomics-analysis-of-tumor-microenvironment-reveals-gata2-and-mirna-124-3p-as-potential-novel-biomarkers-in-ovarian-cancer
#4
Esra Gov, Medi Kori, Kazim Yalcin Arga
Ovarian cancer is a common and, yet, one of the most deadly human cancers due to its insidious onset and the current lack of robust early diagnostic tests. Tumors are complex tissues comprised of not only malignant cells but also genetically stable stromal cells. Understanding the molecular mechanisms behind epithelial-stromal crosstalk in ovarian cancer is a great challenge in particular. In the present study, we performed comparative analyses of transcriptome data from laser microdissected epithelial, stromal, and ovarian tumor tissues, and identified common and tissue-specific reporter biomolecules-genes, receptors, membrane proteins, transcription factors (TFs), microRNAs (miRNAs), and metabolites-by integration of transcriptome data with genome-scale biomolecular networks...
September 22, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28867603/molecular-signatures-for-tumor-classification-an-analysis-of-tcga-data
#5
Yasin Mamatjan, Sameer Agnihotri, Anna Goldenberg, Peter Tonge, Sheila Mansouri, Gelareh Zadeh, Kenneth Aldape
Cancer classification in the clinic is primarily based on histological analysis in the proper clinical context, often supplemented by immunohistochemical and molecular studies. Recent genomic studies have shown the potential of integrated multiomics platforms for molecular classification. We performed unsupervised analyses of molecular platforms in TCGA data (n = 6216 samples) in comparison with tumor type. Our data showed that mRNA signatures and DNA methylation signatures mapped to histological diagnosis with high accuracy (95% and 88%, respectively) as individual platforms...
August 31, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28859259/mass-spectrometry-based-lipidomics
#6
Ting Hu, Jin-Lan Zhang
Lipids, which have core functions in energy storage, signalling and biofilm structures, play important roles in a variety of cellular processes because of the great diversity of their structural and physiochemical properties. Lipidomics is the large-scale profiling and quantification of biogenic lipid molecules, the comprehensive study of their pathways and the interpretation of their physiological significance based on analytical chemistry and statistical analysis. Lipidomics will not only provide insight into the physiological functions of lipid molecules but will also provide an approach to discovering important biomarkers for diagnosis or treatment of human diseases...
August 31, 2017: Journal of Separation Science
https://www.readbyqxmd.com/read/28768687/hit-ndrive-patient-specific-multidriver-gene-prioritization-for-precision-oncology
#7
Raunak Shrestha, Ermin Hodzic, Thomas Sauerwald, Phuong Dao, Kendric Wang, Jake Yeung, Shawn Anderson, Fabio Vandin, Gholamreza Haffari, Colin C Collins, S Cenk Sahinalp
Prioritizing molecular alterations that act as drivers of cancer remains a crucial bottleneck in therapeutic development. Here we introduce HIT'nDRIVE, a computational method that integrates genomic and transcriptomic data to identify a set of patient-specific, sequence-altered genes, with sufficient collective influence over dysregulated transcripts. HIT'nDRIVE aims to solve the "random walk facility location" (RWFL) problem in a gene (or protein) interaction network, which differs from the standard facility location problem by its use of an alternative distance measure: "multihitting time," the expected length of the shortest random walk from any one of the set of sequence-altered genes to an expression-altered target gene...
September 2017: Genome Research
https://www.readbyqxmd.com/read/28729681/multiomics-analysis-of-the-giant-triton-snail-salivary-gland-a-crown-of-thorns-starfish-predator
#8
U Bose, T Wang, M Zhao, C A Motti, M R Hall, S F Cummins
The giant triton snail (Charonia tritonis) is one of the few natural predators of the adult Crown-of-Thorns starfish (COTS), a corallivore that has been damaging to many reefs in the Indo-Pacific. Charonia species have large salivary glands (SGs) that are suspected to produce either a venom and/or sulphuric acid which can immobilize their prey and neutralize the intrinsic toxic properties of COTS. To date, there is little information on the types of toxins produced by tritons. In this paper, the predatory behaviour of the C...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28691013/identification-of-pharmacologically-tractable-protein-complexes-in-cancer-using-the-r-based-network-clustering-and-visualization-program-mcoder
#9
Sungjin Kwon, Hyosil Kim, Hyun Seok Kim
Current multiomics assay platforms facilitate systematic identification of functional entities that are mappable in a biological network, and computational methods that are better able to detect densely connected clusters of signals within a biological network are considered increasingly important. One of the most famous algorithms for detecting network subclusters is Molecular Complex Detection (MCODE). MCODE, however, is limited in simultaneous analyses of multiple, large-scale data sets, since it runs on the Cytoscape platform, which requires extensive computational resources and has limited coding flexibility...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28618237/effect-of-sweetened-dried-cranberry-consumption-on-urinary-proteome-and-fecal-microbiome-in-healthy-human-subjects
#10
Nell Bekiares, Christian G Krueger, Jennifer J Meudt, Dhanansayan Shanmuganayagam, Jess D Reed
The relationship among diet, human health, and disease is an area of growing interest in biomarker research. Previous studies suggest that the consumption of cranberries (Vaccinium macrocarpon) could beneficially influence urinary and digestive health. The present study sought to determine if daily consumption of sweetened dried cranberries (SDC) changes the urinary proteome and fecal microbiome, as determined in a prospective sample of 10 healthy individuals. Baseline urine and fecal samples were collected from the subjects in the fasted (8-12 h) state...
June 15, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28614633/differential-sensitivity-of-total-and-active-soil-microbial-communities-to-drought-and-forest-management
#11
Felipe Bastida, Irene F Torres, Manuela Andrés-Abellán, Petr Baldrian, Rubén López-Mondéjar, Tomáš Větrovský, Hans H Richnow, Robert Starke, Sara Ondoño, Carlos García, Francisco R López-Serrano, Nico Jehmlich
Climate change will affect semiarid ecosystems through severe droughts that increase the competition for resources in plant and microbial communities. In these habitats, adaptations to climate change may consist of thinning-that reduces competition for resources through a decrease in tree density and the promotion of plant survival. We deciphered the functional and phylogenetic responses of the microbial community to 60 years of drought induced by rainfall exclusion and how forest management affects its resistance to drought, in a semiarid forest ecosystem dominated by Pinus halepensis Mill...
June 14, 2017: Global Change Biology
https://www.readbyqxmd.com/read/28566324/multi-omics-analysis-identifies-atf4-as-a-key-regulator-of-the-mitochondrial-stress-response-in-mammals
#12
Pedro M Quirós, Miguel A Prado, Nicola Zamboni, Davide D'Amico, Robert W Williams, Daniel Finley, Steven P Gygi, Johan Auwerx
Mitochondrial stress activates a mitonuclear response to safeguard and repair mitochondrial function and to adapt cellular metabolism to stress. Using a multiomics approach in mammalian cells treated with four types of mitochondrial stressors, we identify activating transcription factor 4 (ATF4) as the main regulator of the stress response. Surprisingly, canonical mitochondrial unfolded protein response genes mediated by ATF5 are not activated. Instead, ATF4 activates the expression of cytoprotective genes, which reprogram cellular metabolism through activation of the integrated stress response (ISR)...
July 3, 2017: Journal of Cell Biology
https://www.readbyqxmd.com/read/28526980/a-multiomics-approach-to-study-the-microbiome-response-to-phytoplankton-blooms
#13
REVIEW
Liyan Song
Phytoplankton blooms are predictable features of marine and freshwater habitats. Despite a good knowledge base of the environmental factors controlling blooms, complex interactions between the bacterial and archaeal communities and phytoplankton bloom taxa are only now emerging. Here, the current research on bacterial community's structural and functional response to phytoplankton blooms is reviewed and discussed and further research is proposed. More attention should be paid on structure and function of autotrophic bacteria and archaea during phytoplankton blooms...
May 19, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28522454/multiomic-disease-signatures-converge-to-cytotoxic-cd8-t-cells-in-primary-sj%C3%A3-gren-s-syndrome
#14
Shinya Tasaki, Katsuya Suzuki, Ayumi Nishikawa, Yoshiaki Kassai, Maiko Takiguchi, Rina Kurisu, Yuumi Okuzono, Takahiro Miyazaki, Masaru Takeshita, Keiko Yoshimoto, Hidekata Yasuoka, Kunihiro Yamaoka, Kazuhiro Ikeura, Kazuyuki Tsunoda, Rimpei Morita, Akihiko Yoshimura, Hiroyoshi Toyoshiba, Tsutomu Takeuchi
OBJECTIVES: Multiomics study was conducted to elucidate the crucial molecular mechanisms of primary Sjögren's syndrome (SS) pathology. METHODS: We generated multiple data set from well-defined patients with SS, which includes whole-blood transcriptomes, serum proteomes and peripheral immunophenotyping. Based on our newly generated data, we performed an extensive bioinformatic investigation. RESULTS: Our integrative analysis identified SS gene signatures (SGS) dysregulated in widespread omics layers, including epigenomes, mRNAs and proteins...
August 2017: Annals of the Rheumatic Diseases
https://www.readbyqxmd.com/read/28511181/1-cmdb-a-curated-database-of-genomic-variations-of-the-one-carbon-metabolism-pathway
#15
Manoj K Bhat, Veerendra P Gadekar, Aditya Jain, Bobby Paul, Padmalatha S Rai, Kapaettu Satyamoorthy
BACKGROUND: The one-carbon metabolism pathway is vital in maintaining tissue homeostasis by driving the critical reactions of folate and methionine cycles. A myriad of genetic and epigenetic events mark the rate of reactions in a tissue-specific manner. Integration of these to predict and provide personalized health management requires robust computational tools that can process multiomics data. The DNA sequences that may determine the chain of biological events and the endpoint reactions within one-carbon metabolism genes remain to be comprehensively recorded...
2017: Public Health Genomics
https://www.readbyqxmd.com/read/28493232/anthracycline-induced-cardiotoxicity-biomarkers-and-omics-technology-in-the-era-of-patient-specific-care
#16
REVIEW
Shayan Moazeni, Martin Cadeiras, Eric H Yang, Mario C Deng, Kim-Lien Nguyen
Anthracyclines are highly effective against a variety of malignancies. However, their dose-dependent cardiotoxic effects can potentially limit their use. In the past decade, serum biomarkers have been used to diagnose, monitor, predict, and prognosticate disease. Biomarkers such as cardiac troponin and natriuretic peptides have some predictive value, but still lack reliability in this patient population. Novel biomarkers such as galectin-3, soluble ST-2 proteins, myeloperoxidase, and fibrocytes are being explored as potential biomarkers to reliably predict the onset of cardiotoxicity...
December 2017: Clinical and Translational Medicine
https://www.readbyqxmd.com/read/28435675/microbiome-effects-on-immunity-health-and-disease-in-the-lung
#17
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/multi-omics-of-tomato-glandular-trichomes-reveals-distinct-features-of-central-carbon-metabolism-supporting-high-productivity-of-specialized-metabolites
#18
Gerd U Balcke, Stefan Bennewitz, Nick Bergau, Benedikt Athmer, Anja Henning, Petra Majovsky, José M Jiménez-Gómez, Wolfgang Hoehenwarter, Alain 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 (13)C-labeling of type VI glandular trichomes and leaves from a cultivated (Solanum lycopersicum LA4024) and a wild (Solanum habrochaites LA1777) tomato accession...
May 2017: Plant Cell
https://www.readbyqxmd.com/read/28404159/a-microbiota-centric-view-of-diseases-of-the-upper-gastrointestinal-tract
#19
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
#20
REVIEW
Christine Desmedt, Gabriele Zoppoli, Christos Sotiriou, Roberto Salgado
Accounting for 10-15% 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 tumour 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 ILC case sets...
April 8, 2017: Seminars in Cancer Biology
keyword
keyword
66872
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"