LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Glycerol 3-phosphate phosphatase/PGPH-2 counters metabolic stress and promotes healthy aging via a glycogen sensing-AMPK-HLH-30-autophagy axis in C. elegans'.
Answer: Metabolic stress caused by excess nutrients accelerates aging. We recently demonstrated that the newly discovered enzyme glycerol-3-phosphate phosphatase (G3PP; gene Pgp), which operates an evolutionarily conserved glycerol shunt that hydrolyzes glucose-derived glycerol-3-phosphate to glycerol, counters metabolic stress and promotes healthy aging in C. elegans. However, the mechanism whereby G3PP activation extends healthspan and lifespan, particularly under glucotoxicity, remained unknown. Here, we show that the overexpression of the C. elegans G3PP homolog, PGPH-2, decreases fat levels and mimics, in part, the beneficial effects of calorie restriction, particularly in glucotoxicity conditions, without reducing food intake. PGPH-2 overexpression depletes glycogen stores activating AMP-activate protein kinase, which leads to the HLH-30 nuclear translocation and activation of autophagy, promoting healthy aging. Transcriptomics reveal an HLH-30-dependent longevity and catabolic gene expression signature with PGPH-2 overexpression. Thus, G3PP overexpression activates three key longevity factors, AMPK, the TFEB homolog HLH-30, and autophagy, and may be an attractive target for age-related metabolic disorders linked to excess nutrients.
Question: Write a study description for the study titled 'Metabolomic profiling reveals the effects of early-life lactoferrin intervention on protein synthesis, energy production and antioxidative capacity in the liver of suckling piglets'.
Answer: The objective of this study was to reveal the effects of early life lactoferrin intervention on the liver metabolism in the suckling piglets. Sixty newborn piglets with an average initial body weight (BW) of 1.51 ± 0.05 kg were assigned to the control (CON) group and the lactoferrin (LF) group. Piglets in the LF group were orally administered LF solution (0.5 g/kg BW per day) from 1 to 7 days of age, and the piglets in the CON group were orally administrated with the same dose of physiological saline. Plasma, jejunum and liver samples were collected on day 8 and 21. The LF piglets had a decreased level of plasma urea nitrogen on day 8 and an increased level of plasma albumin on day 21. Pathway analysis of metabolomic profiles showed that LF treatment affected amino acid metabolism in the liver of piglets. Additionally, LF treatment upregulated the gene expression of proteolytic enzyme and amino acid transporters (APA, aminopeptidases A; APN, aminopeptidases N; EAAC 1, excitatory amino acid carrier 1; Pept 1, peptide transporter 1) in the jejunum, and enhanced phosphorylation levels of mTOR and p70S6K in the liver. Moreover, LF treatment upregulated the expression of β oxidation related gene (CPT 1, carnitine palmitoyl transferase-1) and affected tricarboxylic acid (TCA) cycle in the liver on day 21. Furthermore, LF piglets had a lower level of MDA and a higher level of GSH and GSH-px in the liver mitochondria. Overall, the early life LF intervention affected protein synthesis, energy production and antioxidative capacity in the liver of neonatal piglets.
Question: Write a study description for the study titled 'Regulatory actors and alternative routes for Arabidopsis seed germination are revealed using a pathway‐based analysis of transcriptomic datasets'.
Answer: Regulation of seed germination by dormancy relies on a complex network of transcriptional and post‐transcriptional modifications during seed imbibition that controls seed adaptive responses to environmental cues. High‐throughput technologies have brought significant progress in the understanding of this phenomenon and have led to identify major regulators of seed germination, mostly by studying the behaviour of highly differentially expressed genes. However, the actual models of transcriptome analysis cannot catch additive effects of small variations of gene expression in individual signalling or metabolic pathways, which are also likely to control germination. Therefore, the comprehension of the molecular mechanism regulating germination is still incomplete and to gain knowledge about this process we have developed a pathway‐based analysis of transcriptomic Arabidopsis datasets, to identify regulatory actors of seed germination. The method allowed quantifying the level of deregulation of a wide range of pathways in dormant versus non‐dormant seeds. Clustering pathway deregulation scores of germinating and dormant seed samples permitted the identification of mechanisms involved in seed germination such as RNA transport or vitamin B6 metabolism, for example. Using this method, which was validated by metabolomics analysis, we also demonstrated that Col and Cvi seeds follow different metabolic routes for completing germination, demonstrating the genetic plasticity of this process. We finally provided an extensive basis of analysed transcriptomic datasets that will allow further identification of mechanisms controlling seed germination.
Question: Write a study description for the study titled 'Functional metabolomics as a tool to analyze Mediator function and structure in plants'.
Answer: Mediator is a multiprotein transcriptional co-regulator complex composed of four modules; Head, Middle, Tail, and Kinase. It conveys signals from promoter-bound transcriptional regulators to RNA polymerase II and thus plays an essential role in eukaryotic gene regulation. We describe subunit localization and activities of Mediator in Arabidopsis through metabolome and transcriptome analyses from a set of Mediator mutants. Functional metabolomic analysis based on the metabolite profiles of Mediator mutants using multivariate statistical analysis and heat-map visualization shows that different subunit mutants display distinct metabolite profiles, which cluster according to the reported localization of the corresponding subunits in yeast. Based on these results, we suggest localization of previously unassigned plant Mediator subunits to specific modules. We also describe novel roles for individual subunits in development, and demonstrate changes in gene expression patterns and specific metabolite levels in med18 and med25, which can explain their phenotypes. We find that med18 displays levels of phytoalexins normally found in wild type plants only after exposure to pathogens. Our results indicate that different Mediator subunits are involved in specific signaling pathways that control developmental processes and tolerance to pathogen infections.
Question: Write a study description for the study titled 'Metabolomics to elucidate the effects of novel sustainable feed additives in the feed of farmed salmon (HoloFood Trial C - blue mussel ensilage-dose response)'.
Answer: Testing the effect of blue mussel ensilage as a novel cost-efficient protein feed source for Atlantic salmon feed. Fermentation of novel raw materials for fish feed is a new practice with little prior experience of direct relevance to aquaculture and fish farming. In Trial C, alternative processing of the raw blue mussel meat was tested where the protein was ensilaged before use instead of processed into a dry meal. By using this preservation process, a significant part of small peptides and free amino acids is generated. This trial aimed to examine whether the provision of better protein utilisation and a different microbiome in the gut of the fish can lead to a satisfactory utilisation of this ensilaged protein source by salmon. Earlier published results have shown that ensilaged fish protein provides better protein utilization and growth in Atlantic salmon. It is our assumption that the nutrient value of this product, therefore, is different compared to the more traditional protein meal tested in Trial B. It may also influence the microbiota in the gut differently based on the same arguments. The results from trial C will be very important as this ensilage-based treatment has not yet been used at a routine level, so any new information on its effect on fish health and growth will be highly useful to the aquaculture industry at large.HoloFood Trial C - blue mussel ensilage-dose response is reported in the current study MTBLS4384.HoloFood Trial A - seaweed-dose response is reported in MTBLS4381.HoloFood Trial B - blue mussel-dose response is reported in MTBLS4382.HoloFood Trial D - fermented seaweed open water-dose response is reported in MTBLS6733.HoloFood Trial 1/2/3 is reported in MTBLS6988.Linked cross omic data sets:Nucleic acid data associated with this study are available in the European Nucleotide Archive (ENA): accession number PRJEB43192.Metagenomic data associated with this study are available from MGnify under the Super Study 'holofood'.
Question: Write a study description for the study titled 'Omics analysis in truffle (Tuber magnatum Pico): comparison of samples from different regions of Italy and from different seasons'.
Answer: Truffles are among the most expensive foods available in the market, usually used as flavoring additives for their distinctive aroma. The most valuable species is Tuber magnatum Pico, better known as 'Alba white truffle', in which bis(methylthio)methane is the key aroma compound. Given the high economical value of genuine white truffles, analytical approaches are required to be able to discriminate between natural or synthetic truffle aroma. With the proteomic approach based on 2-DE followed by mass spectrometry, we were able to identify proteins specifically linked to sample origin. We further associated the proteomic results to an RNA-seq profiling, which confirmed the possibility to differentiate samples according to their source and provided a basis for the detailed analysis of genes involved in a specific metabolism, that of sulfur compounds. Finally, geographical specificities could be associated to the set of volatile compounds produced by the fruiting bodies, as quantitatively and qualitatively determined through PTR-MS and GC-MS. In particular, a PLS-DA model built from the latter data was able to return high confidence predictions of sample source.
Question: Write a study description for the study titled 'The role of FYCO1-dependent autophagy in lens fiber cell differentiation.'.
Answer: FYCO1 (FYVE and coiled-coil domain containing 1) is an adaptor protein, expressed ubiquitously and required for microtubule-dependent, plus-end-directed transport of macroautophagic/autophagic vesicles. We have previously shown that loss-of-function mutations in FYCO1 cause cataracts with no other ocular and/or extra-ocular phenotype. Here, we show fyco1 homozygous knockout (fyco1-/-) mice recapitulate the cataract phenotype consistent with a critical role of FYCO1 and autophagy in lens morphogenesis. Transcriptome coupled with proteome and metabolome profiling identified many autophagy-associated genes, proteins, and lipids respectively perturbed in fyco1-/- mice lenses. Flow cytometry of FYCO1 (c.2206C>T) knock-in (KI) human lens epithelial cells revealed a decrease in autophagic flux and autophagic vesicles resulting from the loss of FYCO1. Transmission electron microscopy showed cellular organelles accumulated in FYCO1 (c.2206C>T) KI lens-like organoid structures and in fyco1-/- mice lenses. In summary, our data confirm the loss of FYCO1 function results in a diminished autophagic flux, impaired organelle removal, and cataractogenesis.
Question: Write a study description for the study titled 'Clostridium butyricum MIYAIRI 588-induced protectin D1 has an anti-inflammatory effect on antibiotic-induced intestinal disorder'.
Answer: Metabolites are thought as the end products in cellular regulatory processes and their levels show the strongest relationships with the phenotype. Previously, we showed that the administration of Clostridium butyricum MIYAIRI 588 (CBM 588) upregulated protectin D1, an anti-inflammatory lipid metabolite, in colon tissue under antibiotic therapy. However, how CBM 588 induces protectin D1 expression and whether the metabolite has anti-inflammatory effects on antibiotic-induced inflammation are unclear. Therefore, here, we evaluated the effect of CBM 588 on lipid metabolism and protectin D1 in gut protection from antibiotic-induced intestinal disorders. In the CBM 588 treatment group, expression levels of genes encoding lipid receptors related to the conversion of DHA to protectin D1, such as polyunsaturated fatty acid (PUFA) receptors, G-protein coupled receptor 120 (GPR120), and 15-lipoxygenase (LOX), were increased in colon tissue. CD4+ cells producing interleukin (IL)-4, the main component of T helper type 2 (Th2) cells that can activate 15-LOX, also increased in CBM 588-treated groups even after clindamycin co-administration. In addition, similar to CBM 588, exogenously administered protectin D1 reduced inflammatory cytokines, while IL-10 and TGF-β1, works as anti-inflammatory cytokines, were increased. Our data revealed that CBM 588 activated 15-LOX to enhance protectin D1 production by increasing IL-4-producing CD4+ cell population in the intestinal tract. Additionally, CBM 588-induced protectin D1 clearly upregulated IL-10-producing CD4+ cells to control antibiotic-induced gut inflammation. We provide new insights into CBM 588-mediated lipid metabolism induction for the treatment of gut inflammatory diseases.
Question: Write a study description for the study titled 'Gut Commensal Bacteria-Derived Methionine is Required for Host Reproduction by Modulating RNA m6A Methylation of the Insulin Receptor_targeted metabolites'.
Answer: Gut commensal bacteria promote host reproduction by modulating metabolism and nutrition, but the molecular mechanisms by which microbes regulate reproduction remain unclear. Here, we show that gut commensal bacteria promote host reproduction by providing amino-acid methionine, which controls the RNA m6A modification level of insulin receptor (InR) in the ovary of the invasive insect Bactrocera dorsalis. Antibiotic-treated B. dorsalis showed reduced RNA m6A methylation levels and methionine content, resulting in arrested ovarian development and decreased fecundity. Gut commensal bacteria Enterobacter hormaechei-derived metabolite methionine restored the decreased RNA m6A level and the reproductive defects. Notably, knockdown of METTL3 and METTL14, two genes encoding the RNA m6A methyltransferases, reduced InR mRNA and protein levels, and impaired ovarian development of in B. dorsalis. Our findings further expand the functional landscape of m6A modification to include nutrient-dependent control of ovarian development and highlight the essential role of epigenetic regulation in microbe-host interactions.
Question: Write a study description for the study titled 'Highly sensitive feature detection for high resolution LC/MS'.
Answer: BACKGROUND: Liquid chromatography coupled to mass spectrometry (LC/MS) is an important analytical technology for e.g. metabolomics experiments. Determining the boundaries, centres and intensities of the two-dimensional signals in the LC/MS raw data is called feature detection. For the subsequent analysis of complex samples such as plant extracts, which may contain hundreds of compounds, corresponding to thousands of features -- a reliable feature detection is mandatory.RESULTS: We developed a new feature detection algorithm centWave for high-resolution LC/MS data sets, which collects regions of interest (partial mass traces) in the raw-data, and applies continuous wavelet transformation and optionally Gauss-fitting in the chromatographic domain. We evaluated our feature detection algorithm on dilution series and mixtures of seed and leaf extracts, and estimated recall, precision and F-score of seed and leaf specific features in two experiments of different complexity.CONCLUSION: The new feature detection algorithm meets the requirements of current metabolomics experiments. centWave can detect close-by and partially overlapping features and has the highest overall recall and precision values compared to the other algorithms, matchedFilter (the original algorithm of XCMS) and the centroidPicker from MZmine. The centWave algorithm was integrated into the Bioconductor R-package XCMS and is available from (http://www.bioconductor.org/).
Question: Write a study description for the study titled 'Sex-specific effects of CD248 on metabolism and the adipose tissue lipidome'.
Answer: Cd248 has recently been associated with adipose tissue physiology, demonstrated by reduced weight gain in high fat diet-fed mice with genetic deletion of Cd248 relative to controls. Here we set out to determine the metabolic consequences of loss of Cd248. Strikingly, we find these to be sex specific; By subjecting Cd248-/- and Cd248+/+ mice to a high fat diet and indirect calorimetry study, we identified that only male Cd248-/- mice show reduced weight gain compared to littermate control wildtype mice. In addition, male (but not female) mice showed a lower respiratory exchange ratio on both chow and high fat diets, indicating a predisposition to metabolise lipid. Lipidomic studies on specific fat depots found reduced triglyceride and diglyceride deposition in male Cd248-/- mice, and this was supported by reduced expression of lipogenic and adipogenic genes. Finally, metabolomic analysis of isolated, differentiated preadipocytes found alterations in metabolic pathways associated with lipid deposition in cells isolated from male, but not female, Cd248-/- mice. Overall, our results highlight the importance of sex controls in animal studies and point to a role for Cd248 in sex- and depot-specific regulation of lipid metabolism.
Question: Write a study description for the study titled 'Bacterial Pathogens Hijack the Innate Immune Response by Activation of the Reverse Transsulfuration Pathway'.
Answer: The reverse transsulfuration pathway is the major route for the metabolism of sulfur-containing amino acids. The role of this metabolic pathway in macrophage response and function is unknown. We show that the enzyme cystathionine γ-lyase (CTH) is induced in macrophages infected with pathogenic bacteria through signaling involving phosphatidylinositol 3-kinase (PI3K)/MTOR and the transcription factor SP1. This results in the synthesis of cystathionine, which facilitates the survival of pathogens within myeloid cells. Our data demonstrate that the expression of CTH leads to defective macrophage activation by (i) dysregulation of polyamine metabolism by depletion of S-adenosylmethionine, resulting in immunosuppressive putrescine accumulation and inhibition of spermidine and spermine synthesis, and (ii) increased histone H3K9, H3K27, and H3K36 di/trimethylation, which is associated with gene expression silencing. Thus, CTH is a pivotal enzyme of the innate immune response that disrupts host defense. The induction of the reverse transsulfuration pathway by bacterial pathogens can be considered an unrecognized mechanism for immune escape.IMPORTANCE: Macrophages are professional immune cells that ingest and kill microbes. In this study, we show that different pathogenic bacteria induce the expression of cystathionine γ-lyase (CTH) in macrophages. This enzyme is involved in a metabolic pathway called the reverse transsulfuration pathway, which leads to the production of numerous metabolites, including cystathionine. Phagocytized bacteria use cystathionine to better survive in macrophages. In addition, the induction of CTH results in dysregulation of the metabolism of polyamines, which in turn dampens the proinflammatory response of macrophages. In conclusion, pathogenic bacteria can evade the host immune response by inducing CTH in macrophages.
Question: Write a study description for the study titled 'MetaboKit: a comprehensive data extraction tool for untargeted metabolomics (Mouse liver assays)'.
Answer: We have developed MetaboKit, a comprehensive software package for compound identification and relative quantification in mass spectrometry-based untargeted metabolomics analysis. In data dependent acquisition (DDA) analysis, MetaboKit constructs a customized spectral library with compound identities from reference spectral libraries, adducts, dimers, in-source fragments (ISF), MS/MS fragmentation spectra, and more importantly the retention time information unique to the chromatography system used in the experiment. Using the customized library, the software performs targeted peak integration for precursor ions in DDA analysis and for precursor and product ions in data independent acquisition (DIA) analysis. With its stringent identification algorithm requiring matches by both MS and MS/MS data, MetaboKit provides identification results with significantly greater specificity than the competing software packages without loss in sensitivity. The proposed MS/MS-based screening of ISFs also reduces the chance of unverifiable identification of ISFs considerably. MetaboKit's quantification module produced peak area values highly correlated with known concentrations in a DIA analysis of the metabolite standards at both MS1 and MS2 levels. Moreover, the analysis of Cdk1Liv-/- mouse livers showed that MetaboKit can identify a wide range of lipid species and their ISFs, and quantitatively reconstitute the well-characterized fatty liver phenotype in these mice. In DIA data, the MS1-level and MS2-level peak area data produced similar fold change estimates in the differential abundance analysis, and the MS2-level peak area data allowed for quantitative comparisons in compounds whose precursor ion chromatogram was too noisy for peak integration.Mouse liver assays are reported in the current study MTBLS1266.Standard mixture assay is reported in MTBLS1311.
Question: Write a study description for the study titled 'Metabolomic Characterization of Knock-Out Mutants in Arabidopsis - Development of a Metabolite Profiling Database for Knock-Out Mutants in Arabidopsis (MeKO)'.
Answer: Despite recent intensive research efforts in functional genomics, the functions of only a limited number of Arabidopsis (Arabidopsis thaliana) genes have been determined experimentally. Thus, improving gene annotation remains a major challenge in plant science. Because metabolite profiling can characterize the metabolomic phenotype of a genetic perturbation of plant metabolism, it provides clues to the function of genes of interest. In this regard, we chose 50 Arabidopsis mutants including a set of characterized and uncharacterized mutants, which resemble wild-type plants. We performed metabolite profiling of the plants using gas chromatography-mass spectrometry (GC-MS). To make the dataset available as an efficient public functional genomics tool for hypothesis generation, we developed the MeKO database, which allows evaluation of whether a mutation affects metabolism during normal growth. This database contains images of mutants, statistical data analyses, and data on differential metabolite accumulation. Non-processed data, including chromatograms, mass spectra, and experimental meta-data, follow the guidelines of the Metabolomics Standards Initiative (MSI) and are freely downloadable. Proof-of-concept analysis suggests that the MeKO database is highly useful for gene annotation and for generation of hypotheses for genes of interest. MeKO is publicly available at http://prime.psc.riken.jp/meko/.