LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Integrated multi-omics analysis of adverse cardiac remodeling and metabolic inflexibility upon ErbB2 and ERRα deficiency'.
Answer: Functional oncogenic links between ErbB2 and ERRα in HER2+ breast cancer patients support a therapeutic benefit of co-targeted therapies. However, ErbB2 and ERRα also play key roles in heart physiology, and this approach could pose a potential liability to cardiovascular health. Herein, using integrated phosphoproteomic, transcriptomic and metabolic profiling, we uncovered molecular mechanisms associated with the adverse remodeling of cardiac functions in mice with combined attenuation of ErbB2 and ERRα activity. Genetic disruption of both effectors results in profound effects on cardiomyocyte architecture, inflammatory response and metabolism, the latter leading to a decrease in fatty acyl-carnitine species further increasing the reliance on glucose as a metabolic fuel, a hallmark of failing hearts. Furthermore, integrated omics signatures of ERRα loss-of-function and doxorubicin treatment exhibit common features of chemotherapeutic cardiotoxicity. These findings thus reveal potential cardiovascular risks in discrete combination therapies in the treatment of breast and other cancers.
Question: Write a study description for the study titled 'α-ketoglutarate maintains AMPK translation for energy sensing in human cancer cells_lipid'.
Answer: The energy sensor AMPK promotes tumor cell survival under stress, but how to prevent AMPK activation to blunt tumor progression remains unclear. Here we show that the metabolite α-ketoglutarate (α-KG) controls AMPK translation through a TET-YBX1 axis, which can be exploited to sensitize human cancer cells to energy stress. α-KG-deficient cells fail to activate AMPK under glucose starvation, which elicits cytosolic NADPH depletion and cell death . Mechanistically, α-KG insufficiency inhibits TET-dependent transcription of YBX1, an RNA-binding protein required for human-specific AMPK translation. Similarly, α-KG competitors including succinate and itaconate inhibit the YBX1-AMPK axis and sensitize cancer cells to glucose starvation. Finally, co-targeting oncogenic YBX1 and GLUT1 creates a synthetic lethality and therapeutically blunts tumor growth in vivo. Together, our findings link α-KG to energy sensing through AMPK translation, and propose that targeting α-KG-YBX1-dependent AMPK translation can sensitize human cancer cells to energy stress for treatment.
Question: Write a study description for the study titled 'A multi-omics dataset of C57 BL/6J mice regulated function by feed with ε-polylysine'.
Answer: The proteomic and metabolomic differences in mice fed ε-polylysine were detected by high-throughput sequencing and screening. The effects of ε-polylysine on the proteome and metabolomics of C57 BL/6J mice were studied. DIA proteome sequencing and liquid chromatography-mass spectrometry (LC-MS) were used to compare ε-polylysine-modified mouse proteome and metabolome. In this study, we analyzed the regulatory effects of ε-polysine on glycerophospholipid metabolism, glutathione metabolism and ABC transporters pathways. The sequencing data and LC-MS/MS raw data of samples are stored in MetaboLights and ProteomeXchange databases for efficient reuse and to explore the differences in metabolism and protein expression among mice fed with different levels of ε-polylysine, aiming to screen for critical proteins and differential metabolites in valuable regulatory pathways. Mice in each group (n=20) were fed the same diet (AIN-76A) supplemented with 0 (group A), 300 (group B), 600 (group C), and 1,200 (group D) mg/kg ε-polylysine, respectively.Liver metabolomics is reported in the current study MTBLS4273.Plasma metabolomics is reported in MTBLS4270.
Question: Write a study description for the study titled 'Anti-anemia drug FG4592 retards the AKI to CKD transition by improving vascular regeneration and anti-oxidative capability (day 10)'.
Answer: Acute kidney injury (AKI) is a known risk factor for the development of chronic kidney disease (CKD), with no satisfactory strategy to prevent the progression of AKI to CKD. Damage to the renal vascular system and subsequent hypoxia are common contributors to both AKI and CKD. Hypoxia inducible factor (HIF) is reported to protect the kidney from acute ischemic damage and a novel HIF stabilizer, FG4592 (Roxadustat), has become available in the clinic as an anti-anemia drug. However, the role of FG4592 in the AKI-to-CKD transition remains elusive. In the present study, we investigated the role of FG4592 in the AKI-to-CKD transition induced by unilateral kidney ischemia-reperfusion (UIR). The results showed that FG4592, given to mice 3 days after UIR, markedly alleviated kidney fibrosis and enhanced renal vascular regeneration, possibly via activating the HIF-1α/vascular endothelial growth factor A (VEGFA)/VEGF receptor 1 (VEGFR1) signaling pathway and driving the expression of the endogenous antioxidant superoxide dismutase 2 (SOD2). In accordance with the improved renal vascular regeneration and redox balance, the metabolic disorders of the UIR mice kidneys were also attenuated by treatment with FG4592. However, the inflammatory response in the UIR kidneys was not affected significantly by FG-4592. Importantly, in the kidneys of CKD patients, we also observed enhanced HIF-1α expression which was positively correlated with the renal levels of VEGFA and SOD2. Together, these findings demonstrated the therapeutic effect of the anti-anemia drug FG-4592 in preventing the AKI-to-CKD transition related to ischemia and the redox imbalance.Linked study:UPLC-MS assay of mice kidney tissues sacrificed at day 21 after UIR is reported in MTBLS3003
Question: Write a study description for the study titled 'Probiotics alleviated heat stress-induced spermatogenesis dysfunction by remodeling gut microbiota and producing arginine and pantothenic acid'.
Answer: BACKGROUND: Large-scale farms struggle to effectively address summer heat stress (HS) in dairy goats, which impairs spermatogenesis and reduces reproductive performance by compromising gut and reproductive organ health in male animals. Although Clostridium butyricum (CB) and Enterococcus faecium (EF) have been used to alleviate gut dysbiosis, their protective effects and mechanisms against HS-induced spermatogenic dysfunction in dairy goats remain unclear. This study aims to evaluate the efficacy of CB and EF in mitigating HS-induced spermatogenic disorders in male dairy goats and elucidate the underlying mechanisms.RESULTS: HS leads to a significant decline in sperm quality. CB and EF ameliorate HS-induced sperm quality deterioration by reducing pro-inflammatory factors and oxidative stress levels in blood, while modulating the disrupted reproductive hormone levels caused by heat stress. 16S rRNA-based microbiota analysis revealed that CB and EF treatment shifted the gut microbiota of HS-treated male dairy goats toward a composition resembling that of the NC. To investigate whether the protective effects of these probiotics on sperm quality are mediated through gut microbiota modulation, we transplanted fecal microbiota from HS-treated dairy goats (with or without probiotic intervention) into antibiotic-induced microbiome-depleted (AIMD) mice, followed by heat stress exposure. We observed severe testicular damage and spermatogenic impairment in mice receiving HS group microbiota, whereas these pathological manifestations were significantly alleviated in mice receiving microbiota from probiotic-treated HS goats, indicating that CB and EF mitigate HS-induced spermatogenic damage in a microbiota-dependent manner. Furthermore, non-targeted metabolomics sequencing identified significant reductions in arginine (Arg) and pantothenic acid (PaA) levels in both HS-treated goats and HS microbiota-transplanted mice, metabolites that showed correlation with sperm quality parameters. Subsequent studies demonstrated that supplementation with Arg and PaA effectively attenuated the elevation of pro-inflammatory factors and oxidative stress in mouse blood, restored intercellular junctions, and ultimately ameliorated spermatogenic disorders.CONCLUSION: This study demonstrates that CB and EF alleviate HS-induced sperm quality decline in dairy goats by modulating the gut microbiota to increase blood levels of Arg and PaA. These findings highlight novel therapeutic avenues for preventing HS-induced spermatogenic disorders in dairy goats and provide fresh insights into the application of probiotics to mitigate heat stress-associated impairments in sperm production.
Question: Write a study description for the study titled 'Changes and correlations of intestinal flora and liver metabolite profiles in mice with gallstones'.
Answer: There is increased appreciation for the roles of the gut-liver axis in liver and gall diseases. Specific gut microbes are associated with susceptibility to gallstone diseases,while the relationship between intestinal flora and liver metabolism in the formation of gallstones remains unclear. C57BL/6J male mice received a dietary intervention for 8 weeks, with a lithogenic diet given to the test group and a normal diet to the control group. An integrated 16S rRNA gene sequencing and LC/MS-based nontargeted metabolomics approach was performed to explore the impact of the lithogenic diet on the intestinal flora and liver metabolic phenotype, and Spearman correlation analysis established a network between the gut and liver.
Question: Write a study description for the study titled 'Resolving coral photoacclimation dynamics through coupled photophysiological and metabolomic profiling'.
Answer: Corals continuously adjust to short term variation in light availability on shallow reefs. Long-term light alterations can also occur due to natural and anthropogenic stressors, as well as management interventions such as coral transplantation. Although short term photophysiological responses are relatively well-understood in corals, little information is available regarding photoacclimation dynamics over weeks of altered light availability. We coupled photophysiology and metabolomic profiling to explore changes that accompany longer-term photoacclimation in a key Great Barrier Reef coral species (Acropora muricata). High (HL) and low light (LL) acclimated corals were collected from the reef and reciprocally exposed to high and low light ex situ. Rapid light curves using Pulse Amplitude Modulation (PAM) fluorometry revealed photophysiological acclimation of LL to HL and HL to LL shifted corals within 21 days. A subset of colonies sampled at 7 and 21 days for untargeted LC-MS and GC-MS metabolomic profiling revealed metabolic reorganization before acclimation was detected using PAM fluorometry. Metabolomic shifts were more pronounced for LL to HL treated corals than their HL to LL counterparts. Compounds driving metabolomic separation between HL-exposed and LL control colonies included amino acids, organic acids, fatty acids and sterols. Reduced glycerol and campesterol suggest decreased translocation of photosynthetic products from symbiont to host in LL to HL shifted corals, with concurrent increases in fatty acid abundance indicating reliance on stored lipids for energy. We discuss how these data provide novel insight into environmental regulation of metabolism and implications for management strategies that drive rapid changes in light availability.
Question: Write a study description for the study titled 'Functional Characterization of the Lin28/let-7 Circuit During Forelimb Regeneration in Ambystoma mexicanum and Its Influence on Metabolic Reprogramming'.
Answer: The axolotl (Ambystoma mexicanum) is a caudate amphibian, which has an extraordinary ability to restore a wide variety of damaged structures by a process denominated epimorphosis. While the origin and potentiality of progenitor cells that take part during epimorphic regeneration are known to some extent, the metabolic changes experienced and their associated implications, remain unexplored. However, a circuit with a potential role as a modulator of cellular metabolism along regeneration is that formed by Lin28/let-7. In this study, we report two Lin28 paralogs and eight mature let-7 microRNAs encoded in the axolotl genome. Particularly, in the proliferative blastema stage amxLin28B is more abundant in the nuclei of blastemal cells, while the microRNAs amx-let-7c and amx-let-7a are most downregulated. Functional inhibition of Lin28 factors increase the levels of most mature let-7 microRNAs, consistent with an increment of intermediary metabolites of the Krebs cycle, and phenotypic alterations in the outgrowth of the blastema. In summary, we describe the primary components of the Lin28/let-7 circuit and their function during axolotl regeneration, acting upstream of metabolic reprogramming events.
Question: Write a study description for the study titled 'Saline pasture improve meat quality in Qinghai Tibetan sheep through changes in the rumen microbiota'.
Answer: Introduction: This study aimed to investigate the effects of natural forage from different regions (saline-alkali and non-saline-alkali areas) on the rumen microbiota, muscle metabolites, and meat quality of Tibetan sheep. Methods: Targeted and non-targeted metabolomics were used to comprehensively analyze both pasture and meat quality, metabolites. Additionally, 16S rDNA sequencing was employed to analyze the rumen microbial community structure of Tibetan sheep.Results: The results showed that the natural saline-alkali forage (HG group) had higher protein content, lower fiber content, higher relative feed value, and better quality. Metabolomic analysis revealed significant accumulation of flavonoids and upregulation of amino acid metabolism in the HG group. Additionally, the natural saline-alkali forage significantly increased amino acid deposition in Tibetan sheep muscle, markedly enhanced the redness value (a*), and significantly reduced the yellowness value (b*). Furthermore, the natural saline-alkali forage altered the rumen fermentation patterns in Tibetan sheep, leading to a significant increase in the abundance of F082 and WCHB1-41, while significantly reducing the abundance of Prevotellaceae_UCG-003. Correlation analysis revealed that these microbial taxa were significantly influenced by the natural saline-alkali forage,while also showing significant associations with muscle quality parameters (a*, b*) and metabolites (cysteine, C18:1n9, etc.).Discussion: Overall, the natural saline-alkali forage demonstrated superior quality and metabolite content compared to natural non-saline-alkali forage. Furthermore, this saline-alkali forage significantly influenced the abundance of specific rumen microbiota in Tibetan sheep, consequently regulating
Question: Write a study description for the study titled 'A general non-self response as part of plant immunity'.
Answer: Plants, like other multicellular lifeforms, are colonized by microorganisms. How plants respond to their microbiota is currently not well understood. We used a phylogenetically diverse set of 39 endogenous bacterial strains from Arabidopsis thaliana leaves to assess host transcriptional and metabolic adaptations to bacterial encounters. We identified a molecular response, which we termed the general non-self response (GNSR) that involves the expression of a core set of 24 genes. The GNSR genes are not only consistently induced by the presence of most strains, they also comprise the most differentially regulated genes across treatments and are predictive of a hierarchical transcriptional reprogramming beyond the GNSR. Using a complementary untargeted metabolomics approach we link the GNSR to the tryptophan-derived secondary metabolism, highlighting the importance of small molecules in plant-microbe interactions. We demonstrate that several of the GNSR genes are required for resistance against the bacterial pathogen Pseudomonas syringae. Our results suggest that the GNSR constitutes a defence adaptation strategy that is consistently elicited by diverse strains from various phyla, contributes to host protection and involves secondary metabolism.
Question: Write a study description for the study titled 'Integrated metabolomics and transcriptomics analysis elucidate the candidate genes for polyphyllin biosynthesis in Paris'.
Answer: Polyphyllins are the key components in Paris, with varying levels and compositions among different species. This study investigated polyphyllin compositions of 206 Paris samples from 16 different producing areas. 9 Paris polyphylla var. yunnanensis, 3 Paris fargesii and 3 Paris forrestii were selected based on polyphyllin levels and composition for metabolome and transcriptome analysis. A total of 1243 metabolites and 1007 SCMs were identified among these samples, along with 92.11 Gb of full-length transcriptome data. Through a comprehensive analysis of the metabolome and transcriptome, a total of six 2,3-oxidized squalene cyclases (OSCs), 120 cytochrome P450s (CYPs) and 138 UDP-glycosyltransferases (UGTs) were annotated. Phylogenetic tree analysis narrowed down the candidate genes for OSC, CYP and UGT to 6, 12 and 26, respectively. By integrating metabolic and genetic differences, a total of 17 candidate genes including 2 OSCs, 4 CYPs and 11 UGTs, were identified. This study provides potential candidate genes involved in polyphyllins synthesis in Paris, aiming to facilitate the biosynthesis of different polyphyllins.
Question: Write a study description for the study titled 'LION-web validation lipidomics experiments (FA-incorporation, membrane fluidty)'.
Answer: A major challenge for lipidomic analyses is the handling of the large amounts of data and the translation of results to interpret the involvement of lipids in biological systems. We built a new lipid ontology (LION) that associates over 50,000 lipid species to biophysical, chemical and cell biological features. By making use of enrichment algorithms, we used LION to develop a web-based interface (LION/web) that allows identification of lipid-associated terms in lipidomes. LION/web was validated by analyzing a lipidomic dataset derived from well-characterized sub-cellular fractions of RAW 264.7 macrophages. Comparison of isolated plasma membranes with the microsomal fraction showed a significant enrichment of relevant LION-terms including plasma membrane, headgroup with negative charge, glycerophosphoserines, above average bilayer thickness and below average lateral diffusion. A second validation was performed by analyzing the membrane fluidity of CHO cells incubated with arachidonic acid. An increase in membrane fluidity was observed both experimentally by using pyrene decanoic acid and by using LION/web, showing significant enrichment of terms associated with high membrane fluidity (above average, very high and high lateral diffusion and below average transition temperature). The results demonstrate the functionality of LION/web, which is freely accessible in a platform-independent way.
Question: Write a study description for the study titled 'Discovery of A-type procyanidin dimers in yellow raspberries by untargeted metabolomics and correlation based data analysis'.
Answer: Introduction:Raspberries are becoming increasingly popular due to their reported health beneficial properties. Despite the presence of only trace amounts of anthocyanins yellow varieties seems to show similar or better effects in comparison to conventional raspberries.Objectives:The aim of this work is to characterize the metabolic differences between red and yellow berries, focussing on the compounds showing a higher concentration in yellow varieties.Methods:The metabolomic profile of 13 red and 12 yellow raspberries (of different varieties, locations and collection dates) was determined by UPLC-TOF-MS and a novel correlation based approach was implemented to extract the pseudospectra of the most relevant biomarkers from high energy LC-MS runs.Results:Among the metabolites showing higher concentration in yellow raspberries it was possible to identify a series of compounds showing a pseudospectrum similar to that of A-type procyanidin polymers. The annotation of this group of compounds was confirmed by specific MS/MS experiments and performing standard injections.Conclusion:In berries lacking anthocyanins the polyphenol metabolism might be shifted to the formation of a novel class of A-type procyanidin polymers.
Question: Write a study description for the study titled 'Multiple acyl-coA dehydrogenase deficiency kills Mycobacterium tuberculosis in vitro and during infection'.
Answer: The human pathogen Mycobacterium tuberculosis (Mtb) devotes a significant fraction of its genome to fatty acid metabolism. Although Mtb depends on host fatty acids as a carbon source, fatty acid b-oxidation is mediated by genetically redundant enzymes, which has hampered the development of antitubercular drugs targeting this metabolic pathway. Here, we identify rv0338c, referred to as etfDMtb, to encode a membrane dehydrogenase essential for fatty acid b-oxidation in Mtb. An etfD deletion mutant (DetfD) was incapable of growing on fatty acids in vitro, with long-chain fatty acids being bactericidal, and failed to grow and survive in mice. The DetfD metabolome revealed a block in b-oxidation at the step catalyzed by acyl-CoA dehydrogenases (ACADs). In many organisms, including humans, ACADs are functionally dependent on an electron transfer flavoprotein (ETF) and cognate dehydrogenase. Immunoprecipitation identified EtfD in complex with FixA (EtfBMtb). FixA (EtfBMtb) and FixB (EtfAMtb) are homologous to the human ETF subunits. Our results demonstrate that EtfBAMtb constitutes Mtb’s ETF, while EtfDMtb, although not homologous to human EtfD, functions as the dehydrogenase. These findings identify Mtb’s fatty acid b-oxidation as a novel potential target for TB drug development.
Question: Write a study description for the study titled 'Determination and comparison of SCFAs in serum and colon content samples: Alzheimer's disease rat as a case study (Method validation)'.
Answer: SCFAs are the main microbial fermentation products from dietary fibers in colon and play a key role in keeping healthy in the whole-body. However, differences of SCFAs concentration in the serum and colon samples collected from rats had attracted few attentions. Here, we optimized the extract and analysis methods for quantification of ten SCFAs in both serum and colon content samples. Methanol and acetonitrile were chosen for extraction of SCFAs from serum and colon content samples, respectively. Biological samples collected from Alzheimer's disease rats treated by extract of Schisandra chinensis (Turcz.) Baill (SC-extract) were taken as research objects. The results showed that, the relative peak intensities of SCFAs in colon content from all groups were quite similar, and the trend was identical in serum samples. Compared with the values in human, the ratio of ten SCFAs in rat's colon was similar, while the percent of acetate in rat's serum was significantly higher. For therapy of AD, SC-extract decreased the concentration of butyrate, 3-Methyvalerate and caproate in serum samples towards the trend of normal rats. The present study may help to understand the transport of SCFAs across colonic epithelium in healthy and diseased organisms.Method validation is reported in the current study MTBLS2146SCFA serum and colon content determination is reported in study MTBLS2088