SCALiR: a web application for automating absolute quantification of mass spectrometry-based metabolomics data DOI Creative Commons
Stephanie L. Bishop,

Luis F. Ponce-Alvarez,

Sören Wacker

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Aug. 16, 2023

ABSTRACT Metabolomics is an important approach for studying complex biological systems. Quantitative liquid chromatography-mass spectrometry (LC-MS)-based metabolomics becoming a mainstream strategy but presents several technical challenges that limit its widespread use. Computing metabolite concentrations using standard curves generated from mixtures of known labor-intensive process which often performed manually. Currently, there are few options open-source software tools can automatically calculate concentrations. Herein, we introduce SCALiR (Standard Curve Application determining Linear Ranges), new web-based tool specifically built this task, allows users to transform LC-MS signal data into absolute quantitative ( https://www.lewisresearchgroup.org/software ). The algorithm used in finds the equation line best fit each curve and uses compound their signal. Using mix containing 77 metabolites, found excellent correlation between calculated by expected (R 2 = 0.99) reproducibly mid-range standards across ten analytical batches (average coefficient variation 0.091). offers advantages, including it (1) vendor agnostic; (2) requires only 10 seconds analysis time compute >75 compounds; (3) facilitates automation workflows; (4) performs deterministic evaluation quantification limits. provides community with simple rapid enables rigorous reproducible studies.

Language: Английский

To metabolomics and beyond: a technological portfolio to investigate cancer metabolism DOI Creative Commons
Federica Danzi,

Raffaella Pacchiana,

Andrea Mafficini

et al.

Signal Transduction and Targeted Therapy, Journal Year: 2023, Volume and Issue: 8(1)

Published: March 22, 2023

Abstract Tumour cells have exquisite flexibility in reprogramming their metabolism order to support tumour initiation, progression, metastasis and resistance therapies. These reprogrammed activities include a complete rewiring of the bioenergetic, biosynthetic redox status sustain increased energetic demand cells. Over last decades, cancer field has seen an explosion new biochemical technologies giving more tools than ever before navigate this complexity. Within cell or tissue, metabolites constitute direct signature molecular phenotype thus profiling concrete clinical applications oncology. Metabolomics fluxomics, are key technological approaches that mainly revolutionized enabling researchers both qualitative mechanistic model cancer. Furthermore, upgrade from bulk single-cell analysis provided unprecedented opportunity investigate biology at cellular resolution allowing depth quantitative complex heterogenous diseases. More recently, advent functional genomic screening allowed identification pathways, processes, biomarkers novel therapeutic targets concert with other allow patient stratification treatment regimens. This review is intended be guide for metabolism, highlighting current emerging technologies, emphasizing advantages, disadvantages potential leading development innovative anti-cancer

Language: Английский

Citations

114
Deep Learning-based Multi-Brain Capsule network for Next-Gen Clinical Emotion Recognition using EEG Signals DOI Creative Commons
Ravinder Dahiya,

G Mamatha,

Shila Jawale

et al.

Neuroscience Informatics, Journal Year: 2025, Volume and Issue: 5(2), P. 100203 - 100203

Published: April 28, 2025

Language: Английский

Citations

0
Microbial Metabolomics: A Futuristic Approach in Biotechnology DOI

Babita Thakur,

Sukhminderjit Kaur, Hippolyte Tene Mouafo

et al.

Published: Jan. 1, 2025

Language: Английский

Citations

0
Reduced Sulfur Diet Reshapes the Microbiome and Metabolome in Mild–Moderate Ulcerative Colitis DOI Open Access
Jiayu Ye, Maitreyi Raman, Lorian Taylor

et al.

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(10), P. 4596 - 4596

Published: May 11, 2025

This pilot study investigated the effects of a reduced sulfur (RS) diet on gut microbiome composition and fecal metabolome in individuals with remitted or active ulcerative colitis (UC). Thirteen participants maintained their habitual (control), while nine followed an RS for eight weeks (Wk8). Stool plasma samples were collected at baseline Wk8. The intake decreased group (−28 g/1000 kcal) versus control (−1.7 kcal; p < 0.001). exhibited significant decrease lipopolysaccharide-binding protein (−5280 ng/mL), these levels increased (620 ng/mL; 0.05). analysis showed alpha diversity Wk8 (p 0.01), suggesting microbial shift intake. metabolic alterations indicated enhanced nitrogen disposal (increased uric acid, methyluric N-acetyl-L-glutamate) higher energy demand (elevated ubiquinol glucose-pyruvate). beneficial microbes Collinsella stercoris, Asaccharobacter celatus, Alistipes finegoldii, decreasing pathobionts Eggerthella lenta Romboutsia ilealis. Methyluric acid correlated positively C. stercoris (β = 0.70) negatively E. −0.77) utilized this metabolite influenced composition. In conclusion, promoted diversity, adaptations, inflammation, highlighting its potential as novel strategy UC management.

Language: Английский

Citations

0
SCALiR: A Web Application for Automating Absolute Quantification of Mass Spectrometry-Based Metabolomics Data DOI
Luis F. Ponce, Stephanie L. Bishop, Sören Wacker

et al.

Analytical Chemistry, Journal Year: 2024, Volume and Issue: 96(17), P. 6566 - 6574

Published: April 20, 2024

Quantitative liquid chromatography-mass spectrometry (LC-MS)-based metabolomics is becoming an important approach for studying complex biological systems but presents several technical challenges that limit its widespread use. Computing metabolite concentrations using standard curves generated from mixtures of known a labor-intensive process often performed manually. Currently, there are few options open-source software tools can automatically calculate concentrations. Herein, we introduce SCALiR (standard curve application determining linear ranges), new web-based tool specifically built this task, which allows users to transform LC-MS signals into absolute quantitative data (https://www.lewisresearchgroup.org/software). uses algorithm finds the equation line best fit each and compound signal. Using mix containing 77 metabolites, show close correlation between calculated by expected (

Language: Английский

Citations

3
Effect of Operational Parameters on the Cultivation of the Gut Microbiome in Continuous Bioreactors Inoculated with Feces: A Systematic Review DOI Creative Commons
David Felipe García Mendez, Janeth Sanabria, Julien Wist

et al.

Journal of Agricultural and Food Chemistry, Journal Year: 2023, Volume and Issue: 71(16), P. 6213 - 6225

Published: April 18, 2023

Since the early 1980s, multiple researchers have contributed to development of

Language: Английский

Citations

8
Butyrate reduces adherent-invasive E. coli -evoked disruption of epithelial mitochondrial morphology and barrier function: involvement of free fatty acid receptor 3 DOI Creative Commons
Samira Hamed, A Mohan,

Saranya Navaneetha Krishnan

et al.

Gut Microbes, Journal Year: 2023, Volume and Issue: 15(2)

Published: Dec. 11, 2023

Gut bacteria provide benefits to the host and have been implicated in inflammatory bowel disease (IBD), where adherent-invasive E. coli (AIEC) pathobionts (e.g., strain LF82) are associated with Crohn's disease. coli-LF82 causes fragmentation of epithelial mitochondrial network, leading increased permeability. We hypothesized that butyrate would limit disruption caused by coli-LF82. Human colonic organoids T84 cell line infected (MOI = 100, 4 h) showed a significant increase network fission was reduced (10 mM) co-treatment. Butyrate loss membrane potential expression PGC-1α mRNA, master regulator biogenesis. Metabolomics revealed significantly altered central carbon metabolism diminished glucose uptake succinate secretion. Correlating preservation form/function, transcytosis across T84-cell monolayers. The use G-protein inhibitor, pertussis toxin, GPCR signaling as critical effect butyrate, free fatty acid receptor three (FFAR3, GPR41) agonist, AR420626, reproduced butyrate's terms ameliorating barrier function reducing observed T84-cells organoids. These data indicate helps maintain form/function when challenged this occurs, at least part, via FFAR3. Thus, butyrate-producing IBD context contribute functions could evoke and/or exaggerate low-grade inflammation.

Language: Английский

Citations

8
Weighted Gene Co-Expression Network Analysis Identifies a Functional Guild and Metabolite Cluster Mediating the Relationship between Mucosal Inflammation and Adherence to the Mediterranean Diet in Ulcerative Colitis DOI Open Access

Jaclyn Strauss,

Natasha Haskey, Hena R. Ramay

et al.

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(8), P. 7323 - 7323

Published: April 15, 2023

Diet influences the pathogenesis and clinical course of inflammatory bowel disease (IBD). The Mediterranean diet (MD) is linked to reductions in biomarkers alterations microbial taxa metabolites associated with health. We aimed identify features gut microbiome that mediate relationship between MD fecal calprotectin (FCP) ulcerative colitis (UC). Weighted gene co-expression network analysis (WGCNA) was used modules co-abundant correlated FCP. considered were taxa, serum metabolites, dietary components, short-chain fatty acid bile profiles participants experienced an increase (n = 13) or decrease FCP 16) over eight weeks. WGCNA revealed ten containing sixteen key acted as mediators Three (Faecalibacterium prausnitzii, Dorea longicatena, Roseburia inulinivorans) a cluster four (benzyl alcohol, 3-hydroxyphenylacetate, 3-4-hydroxyphenylacetate phenylacetate) demonstrated strong mediating effect (ACME: -1.23, p 0.004). This study identified novel association diet, inflammation microbiome, providing new insights into underlying mechanisms how may influence IBD. See clinicaltrials.gov (NCT04474561).

Language: Английский

Citations

7
Pharmacomicrobiomics and type 2 diabetes mellitus: A novel perspective towards possible treatment DOI Creative Commons
Liyang Jia, Shiqiong Huang,

Boyu Sun

et al.

Frontiers in Endocrinology, Journal Year: 2023, Volume and Issue: 14

Published: March 23, 2023

Type 2 diabetes mellitus (T2DM), a major driver of mortality worldwide, is more likely to develop other cardiometabolic risk factors, ultimately leading diabetes-related mortality. Although set measures including lifestyle intervention and antidiabetic drugs have been proposed manage T2DM, problems associated with potential side-effects drug resistance are still unresolved. Pharmacomicrobiomics an emerging field that investigates the interactions between gut microbiome response variability or toxicity. In recent years, increasing evidence supports microbiome, as second genome, can serve attractive target for improving efficacy safety by manipulating its composition. this review, we outline different composition in T2DM highlight how these microbiomes actually play vital role development. Furthermore, also investigate current state-of-the-art knowledge on pharmacomicrobiomics microbiome's modulating drugs, well provide innovative personalized treatments, approaches predicting treatment improve reduce

Language: Английский

Citations

6
Distinct global metabolomic profiles of the model organismCaenorhabditis elegansduring interactions withStaphylococcus aureusandSalmonella entericaSerovar Typhi DOI

Balasubramanian C. Muthubharathi,

V. Ravichandiran, Krishnaswamy Balamurugan

et al.

Molecular Omics, Journal Year: 2023, Volume and Issue: 19(7), P. 574 - 584

Published: Jan. 1, 2023

Specific metabolic regulations during the interaction of candidate distinct bacterial pathogens.

Language: Английский

Citations

1