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Integrated visualization of a multi-omics study of starvation in mouse intestine

Martijn P. van Iersel, Milka Sokolović, Kaatje Lenaerts, Martina Kutmon, Freek G. Bouwman, Wouter H. Lamers, Edwin C.M. Mariman, Chris T. Evelo
2014 Journal of Integrative Bioinformatics  
Visualization of the integrated dataset on pathways led to new observations on gene-regulation in the response of the gut to starvation.  ...  We aimed to improve methods for integrating and visualizing different types of omics data.  ...  of Limburg (tUL).  ... 
doi:10.1515/jib-2014-235 fatcat:3luyg6mmzncchmgmdcaquwvu54

Integrated visualization of a multi-omics study of starvation in mouse intestine

Martijn P van Iersel, Milka Sokolović, Kaatje Lenaerts, Martina Kutmon, Freek G Bouwman, Wouter H Lamers, Edwin C M Mariman, Chris T Evelo
2014 Journal of Integrative Bioinformatics  
Visualization of the integrated dataset on pathways led to new observations on gene-regulation in the response of the gut to starvation.  ...  We aimed to improve methods for integrating and visualizing different types of omics data.  ...  of Limburg (tUL).  ... 
doi:10.2390/biecoll-jib-2014-235 pmid:24675236 fatcat:cvakxhzyenb2nhtz7yjgjvrmku

A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Intestinal Infection

Brooke L. Deatherage Kaiser, Jie Li, James A. Sanford, Young-Mo Kim, Scott R. Kronewitter, Marcus B. Jones, Christine T. Peterson, Scott N. Peterson, Bryan C. Frank, Samuel O. Purvine, Joseph N. Brown, Thomas O. Metz (+4 others)
2013 PLoS ONE  
We used a multi-omics "systems" approach, incorporating proteomics, metabolomics, glycomics, and metagenomics, to explore the molecular interplay between the murine host, the pathogen Salmonella enterica  ...  Typhimurium may take advantage of increased fucose moieties to metabolize fucose while growing in the gut.  ...  Christine Peterson is a pre-doctoral student in the Immunology & Microbiology Program of the Institute for Biomedical Sciences at the George Washington University and this publication partially contributes  ... 
doi:10.1371/journal.pone.0067155 pmid:23840608 pmcid:PMC3694140 fatcat:vq5rxo4ribfe3hppblm6vbws3m

Multi-compartment metabolomics and metagenomics reveal major hepatic and intestinal disturbances in cancer cachectic mice

Sarah A Pötgens, Morgane M Thibaut, Nicolas Joudiou, Martina Sboarina, Audrey M Neyrinck, Patrice D Cani, Sandrine P Claus, Nathalie M Delzenne, Laure B Bindels
2021 Journal of Cachexia, Sarcopenia and Muscle  
Our work also reveals a reduction of different beneficial intestinal bacterial activities in cancer cachexia.  ...  of a Cori cycle in this model.  ...  All authors of this manuscript comply with the guidelines of ethical authorship and publishing in the Journal of Cachexia, Sarcopenia and Muscle. 99 Conflict of interest Online supplementary material  ... 
doi:10.1002/jcsm.12684 pmid:33599103 fatcat:3fic5lb5ijbzrbdu3tah2bcu7e

Spectral tracing of deuterium for imaging glucose metabolism

Luyuan Zhang, Lingyan Shi, Yihui Shen, Yupeng Miao, Mian Wei, Naixin Qian, Yinong Liu, Wei Min
2019 Nature Biomedical Engineering  
We also show that STRIDE can be used to image glucose metabolism in many mouse tissues, including tumours, brain, intestine and liver, at a detection limit of 10 mM of carbon-deuterium bonds.  ...  STRIDE can also use spectral differences derived from different glucose isotopologues to visualize temporally separated glucose populations using a pulse-chase protocol.  ...  W.M. acknowledges support from a National Institutes of Health Director's New Innovator Award (1DP2EB016573), NIH R01 (grant EB020892), the Alfred P.  ... 
doi:10.1038/s41551-019-0393-4 pmid:31036888 pmcid:PMC6599680 fatcat:rh2hasnfkndr5bjuvtjvz4k644

Argininosuccinate synthase 1 is an intrinsic Akt repressor transactivated by p53

Takafumi Miyamoto, Paulisally Hau Yi Lo, Naomi Saichi, Koji Ueda, Makoto Hirata, Chizu Tanikawa, Koichi Matsuda
2017 Science Advances  
The transcription factor p53 is at the core of a built-in tumor suppression system that responds to varying degrees of stress input and is deregulated in most human cancers.  ...  Our findings uncover a new function of p53 in the regulation of Akt signaling and reveal how p53, ASS1, and Akt are interrelated to each other.  ...  Schematics of the integrated multi-OMICS approach. fig. S2 . Examination of genotoxic stress-induced ASS1 mRNA expression. fig. S3 . ASS1 gene expression in a p53-dependent manner. fig. S4 .  ... 
doi:10.1126/sciadv.1603204 pmid:28560349 pmcid:PMC5438217 fatcat:leg5oslju5amnmxdzwqrfphk4i

Neural signaling modulates metabolism of gastric cancer

Hanne-Line Rabben, Gøran Troseth Andersen, Magnus Kringstad Olsen, Anders Øverby, Aleksandr Ianevski, Denis Kainov, Timothy Cragin Wang, Steinar Lundgren, Jon Erik Grønbech, Duan Chen, Chun-Mei Zhao
2021 iScience  
Here, we identify a metabolic signature of human and mouse model of gastric cancer and show that vagotomy in the mouse model reverses the metabolic reprogramming, reflected by metabolic switch from glutaminolysis  ...  These findings point to the importance of neural signaling in modulating the tumor metabolism and provide a rational basis for clinical translation of the potential strategy for gastric cancer.  ...  Table S5 , Signaling pathways involved in mouse gastric cancer (GC), related to Figure 5A : Multi-omics integrative analysis in IPA revealed 41 signaling pathways that appeared exclusively in Mouse GC  ... 
doi:10.1016/j.isci.2021.102091 pmid:33598644 pmcid:PMC7869004 fatcat:tcm6raq4rrbzdiramfsbxkbpdy

Cardiovascular Metabolomics

Robert W. McGarrah, Scott B. Crown, Guo-Fang Zhang, Svati H. Shah, Christopher B. Newgard
2018 Circulation Research  
Pooled metabolite samples are commonly used in nontargeted metabolomics and are prepared by mixing a small, but equal amount of sample from a fraction of the studies samples, e.g. for a study of 1000 samples  ...  Metabolomics, one of the newer "omics" technologies, has emerged as a powerful tool for defining changes in both global and cardiac-specific metabolism that occur across a spectrum of cardiovascular disease  ...  Acknowledgments Sources of Funding  ... 
doi:10.1161/circresaha.117.311002 pmid:29700070 pmcid:PMC6029726 fatcat:6zeg3njphbegrcibsli2onwxfq

Fecal Microbiota Transplantation Beneficially Regulates Intestinal Mucosal Autophagy and Alleviates Gut Barrier Injury

Saisai Cheng, Xin Ma, Shijie Geng, Xuemei Jiang, Yuan Li, Luansha Hu, Jianrong Li, Yizhen Wang, Xinyan Han
2018 mSystems  
In addition, intestinal morphology was improved, a result that coincided with the decrease of intestinal permeability and the enhancement of mucins and mucosal expression of tight junction proteins in  ...  A total of 289 differentially expressed proteins were annotated with 4,068 gene ontology (GO) function entries in the intestinal mucosa, and the levels of autophagy-related proteins in the forkhead box  ...  The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.  ... 
doi:10.1128/msystems.00137-18 pmid:30320222 pmcid:PMC6178585 fatcat:nt4dahkjd5fehchhf7cquwwwmm

ATF3 Sustains IL-22-Induced STAT3 Phosphorylation to Maintain Mucosal Immunity Through Inhibiting Phosphatases

Doaa Glal, Janaki N Sudhakar, Hsueh-Han Lu, Ming-Che Liu, Hung-Yu Chiang, Yen-Chun Liu, Ching-Feng Cheng, Jr-Wen Shui
2018 Frontiers in Immunology  
In gut epithelium, IL-22 transmits signals through STAT3 phosphorylation (pSTAT3) which provides intestinal immunity.  ...  Collectively, our results suggest that via IL-22-pSTAT3 signaling in the epithelium and IL-6-pSTAT3 signaling in Th17 cells, ATF3 mediates a cross-regulation in the barrier to maintain mucosal homeostasis  ...  Tsonwin Hai (The Ohio State University) for ATF3 flox/flox mice in our study.  ... 
doi:10.3389/fimmu.2018.02522 pmid:30455690 pmcid:PMC6230592 fatcat:3qoz6gpu55b7jprtt4dql2xtmu

Tumor microenvironment evaluation promotes precise checkpoint immunotherapy of advanced gastric cancer

Dongqiang Zeng, Jiani Wu, Huiyan Luo, Yong Li, Jian Xiao, Jianjun Peng, Zilan Ye, Rui Zhou, Yunfang Yu, Gaofeng Wang, Na Huang, Jianhua Wu (+11 others)
2021 Journal for ImmunoTherapy of Cancer  
Exploration of TME in multi-omics gastric cancer data may provide the impetus for precision immunotherapy.  ...  study highlighted the promising predictive value of TMEscore for patients with mGC.  ...  of TCGA-STAD and ACRG cohorts.  ... 
doi:10.1136/jitc-2021-002467 pmid:34376552 pmcid:PMC8356190 fatcat:vmv6xqw2kvb4zcyhq27v56gaoa

Open Frontiers in Neural Cell Type Investigations; Lessons From Caenorhabditis elegans and Beyond, Toward a Multimodal Integration

Georgia Rapti
2022 Frontiers in Neuroscience  
A closer look in mapped neural circuits and understudied terrains offers insights for the best implementation of these approaches.  ...  It proposes unified platforms to allow integrated annotation of large-scale datasets, gene-function studies, published or unpublished findings and community feedback.  ...  I thank Scott Emmons, David Hall, Stephen Larson, and Mei Zhen for permitting use of images from open-source websites.  ... 
doi:10.3389/fnins.2021.787753 pmid:35321480 pmcid:PMC8934944 fatcat:ynbsuctaqjbnxph2nul25ijnt4

Contribution of Extracellular Matrix and Signal Mechanotransduction to Epithelial Cell Damage in Inflammatory Bowel Disease Patients: A Proteomic Study

Manuela Moriggi, Luca Pastorelli, Enrica Torretta, Gian Eugenio Tontini, Daniele Capitanio, Stefano Ferrero Bogetto, Maurizio Vecchi, Cecilia Gelfi
2017 Proteomics  
., Changes in muscle cell metabolism and mechanotransduction are associated with myopathic phenotype in a mouse model of collagen VI deficiency.  ...  Thus, it appears that studies focusing on intestinal epithelium are warranted.  ... 
doi:10.1002/pmic.201700164 pmid:29027377 fatcat:ckjl4nsfsbcejjrn5j4s4cazmu

Dynamic Regulation of the 26S Proteasome: From Synthesis to Degradation

Richard S. Marshall, Richard D. Vierstra
2019 Frontiers in Molecular Biosciences  
Subsequent proteasomal digestion is essential and influences a myriad of cellular processes in species as diverse as plants, fungi and humans.  ...  Most of this turnover is catalyzed by the 26S proteasome, an intricate, multi-subunit proteolytic machine.  ...  ACKNOWLEDGMENTS The authors thank past and present members of the Vierstra lab for many stimulating discussions on the topics covered in this manuscript.  ... 
doi:10.3389/fmolb.2019.00040 pmid:31231659 pmcid:PMC6568242 fatcat:dytujaen2zbbzj25zntawqc5sm

Metabolic phenotyping of malnutrition during the first 1000 days of life

Jordi Mayneris-Perxachs, Jonathan R. Swann
2018 European Journal of Nutrition  
Metabolic phenotyping (metabolomics/metabonomics) simultaneously measures a diverse range of low molecular weight metabolites in a sample providing a comprehensive assessment of the individual's biochemical  ...  There are a growing number of studies applying such approaches to characterize the metabolic derangements induced by various forms of early-life malnutrition.  ...  representation of metabolic data by showing the abundances and significances of measured metabolites in networks allowing the integration of different omics datasets [9] .  ... 
doi:10.1007/s00394-018-1679-0 pmid:29644395 fatcat:pnq5yhnpzncd3norudzp3cfrf4
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