LC‐MS Data Processing with MAVEN: A Metabolomic Analysis and Visualization Engine

Clasquin, Michelle; Melamud, Eugene; Rabinowitz, Joshua D.

doi:10.1002/0471250953.bi1411s37

Cited by 436 publications

(380 citation statements)

References 28 publications

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“…Metabolites identities were determined in silico via exact mass and retention time matching using MAVEN that also calculated area counts for each compound Clasquin et al, 2012). For proteomic measurements, samples were analyzed by 2-dimensional liquid chromatography-mass spectrometry on an LTQOrbitrap-Velos (Thermo Fisher) following protein extraction and digestion, as described previously .…”

Section: Bioinformatic Analysismentioning

confidence: 99%

Nutrients drive transcriptional changes that maintain metabolic homeostasis but alter genome architecture in Microcystis

Steffen¹,

Dearth²,

Dill³

et al. 2014

The ISME Journal

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The cyanobacterium Microcystis aeruginosa is a globally distributed bloom-forming organism that degrades freshwater systems around the world. Factors that drive its dispersion, diversification and success remain, however, poorly understood. To develop insight into cellular-level responses to nutrient drivers of eutrophication, RNA sequencing was coupled to a comprehensive metabolomics survey of M. aeruginosa sp. NIES 843 grown in various nutrient-reduced conditions. Transcriptomes were generated for cultures grown in nutrient-replete (with nitrate as the nitrogen (N) source), nitrogen-reduced (with nitrate, urea or ammonium acting as the N sources) and phosphate-reduced conditions. Extensive expression differences (up to 696 genes for urea-grown cells) relative to the control treatment were observed, demonstrating that the chemical variant of nitrogen available to cells affected transcriptional activity. Of particular note, a high number of transposase genes (up to 81) were significantly and reproducibly up-regulated relative to the control when grown on urea. Conversely, phosphorus (P) reduction resulted in a significant cessation in transcription of transposase genes, indicating that variation in nutrient chemistry may influence transcription of transposases and may impact the highly mosaic genomic architecture of M. aeruginosa. Corresponding metabolomes showed comparably few differences between treatments, suggesting broad changes to gene transcription are required to maintain metabolic homeostasis under nutrient reduction. The combined observations provide novel and extensive insight into the complex cellular interactions that take place in this important bloom-forming organism during variable nutrient conditions and highlight a potential unknown molecular mechanism that may drive Microcystis blooms and evolution.

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Section: Bioinformatic Analysismentioning

confidence: 99%

Nutrients drive transcriptional changes that maintain metabolic homeostasis but alter genome architecture in Microcystis

Steffen¹,

Dearth²,

Dill³

et al. 2014

The ISME Journal

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“…Data analysis and metabolite identification were performed using the Metabolomic Analysis and Visualization Engine (MAVEN) software program (52). Metabolites were excluded from analysis if they failed to give a signal greater than 1,000 counts in any sample analyzed.…”

Section: Methodsmentioning

confidence: 99%

Plasmodium falciparum responds to amino acid starvation by entering into a hibernatory state

Babbitt

Altenhofen

Cobbold

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

151

242

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The human malaria parasite Plasmodium falciparum is auxotrophic for most amino acids. Its amino acid needs are met largely through the degradation of host erythrocyte hemoglobin; however the parasite must acquire isoleucine exogenously, because this amino acid is not present in adult human hemoglobin. We report that when isoleucine is withdrawn from the culture medium of intraerythrocytic P. falciparum, the parasite slows its metabolism and progresses through its developmental cycle at a reduced rate. Isoleucine-starved parasites remain viable for 72 h and resume rapid growth upon resupplementation. Protein degradation during starvation is important for maintenance of this hibernatory state. Microarray analysis of starved parasites revealed a 60% decrease in the rate of progression through the normal transcriptional program but no other apparent stress response. Plasmodium parasites do not possess a TOR nutrient-sensing pathway and have only a rudimentary amino acid starvation-sensing eukaryotic initiation factor 2α (eIF2α) stress response. Isoleucine deprivation results in GCN2-mediated phosphorylation of eIF2α, but kinase-knockout clones still are able to hibernate and recover, indicating that this pathway does not directly promote survival during isoleucine starvation. We conclude that P. falciparum, in the absence of canonical eukaryotic nutrient stress-response pathways, can cope with an inconsistent bloodstream amino acid supply by hibernating and waiting for more nutrient to be provided.protease | artemesinin | autophagy

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“…Raw data and MRM parameters are deposited in www.ebi.ac.uk/metabolights (MTBLS225). Data analysis, including peak integration was performed using MAVEN (Clasquin et al, 2012). One-way ANOVA was performed in SAS 9.3.…”

Section: Targeted Urinary Metabolomicsmentioning

confidence: 99%

Dose-Dependent Metabolic Reprogramming and Differential Gene Expression in TCDD-Elicited Hepatic Fibrosis

Nault¹,

Fader²,

Ammendolia³

et al. 2016

Toxicol. Sci.

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We have previously shown that in response to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)-elicited NAFLD progression, central carbon, glutaminolysis, and serine/folate metabolism are reprogrammed to support NADPH production and ROS defenses. To further investigate underlying dose-dependent responses associated with TCDD-induced fibrosis, female C57BL/6 mice were gavaged with TCDD every 4 days (d) for 28 d or 92 d. RNA-Seq, ChIP-Seq (2 h), and 28 d metabolomic (urine, serum, and hepatic extract) analyses were conducted with complementary serum marker assessments at 92 d. Additional vehicle and 30 mg/kg treatment groups were allowed to recover for 36 d following the 92-d treatment regimen to examine recovery from TCDD-elicited fibrosis. Histopathology revealed dose-dependent increases in hepatic fat accumulation, inflammation, and periportal collagen deposition at 92 days, with increased fibrotic severity in the recovery group. Serum proinflammatory and profibrotic interleukins-1b, -2, -4, -6, and -10, as well as TNF-a and IFN-c, exhibited dose-dependent induction. An increase in glucose tolerance was observed with a concomitant 3.0-fold decrease in hepatic glycogen linked to increased ascorbic acid biosynthesis and proline metabolism, consistent with increased fibrosis. RNASeq identified differential expression of numerous matrisome genes including an 8.8-fold increase in Tgfb2 indicating myofibroblast activation. Further analysis suggests reprogramming of glycogen, ascorbic acid, and amino acid metabolism in support of collagen deposition and the use of proline as a substrate for ATP production via the proline cycle. In summary, we demonstrate that glycogen, ascorbic acid, and amino acid metabolism are also reorganized to support remodeling of the extracellular matrix, progressing to hepatic fibrosis in response to chronic injury from TCDD.

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LC‐MS Data Processing with MAVEN: A Metabolomic Analysis and Visualization Engine

Cited by 436 publications

References 28 publications

Nutrients drive transcriptional changes that maintain metabolic homeostasis but alter genome architecture in Microcystis

Nutrients drive transcriptional changes that maintain metabolic homeostasis but alter genome architecture in Microcystis

Plasmodium falciparum responds to amino acid starvation by entering into a hibernatory state

Dose-Dependent Metabolic Reprogramming and Differential Gene Expression in TCDD-Elicited Hepatic Fibrosis

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