LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Mass Spectrometry-Based Metabolic Fingerprinting Contributes to Unveil the Role of RSUME in Renal Cell Carcinoma Cell Metabolism'.
Answer: Clear cell renal cell carcinoma (ccRCC) is a heterogeneous disease with 50-80% patients exhibiting mutations in the von Hippel-Lindau (VHL) gene. RSUME (RWD domain (termed after three major RWD-containing proteins: RING finger-containing proteins, WD-repeat-containing proteins, and yeast DEAD (DEXD)-like helicases)-containing protein small ubiquitin-related modifier (SUMO) enhancer) acts as a negative regulator of VHL function in normoxia. A discovery-based metabolomics approach was developed by means of ultraperformance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (MS) for fingerprinting the endometabolome of a human ccRCC cell line 786-O and three other transformed cell systems (n = 102) with different expressions of RSUME and VHL. Cross-validated orthogonal projection to latent structures discriminant analysis models were built on positive, negative, and a combination of positive- and negative-ion mode MS data sets. Discriminant feature panels selected by an iterative multivariate classification allowed differentiating cells with different expressions of RSUME and VHL. Fifteen identified discriminant metabolites with level 1, including glutathione, butyrylcarnitine, and acetylcarnitine, contributed to understand the role of RSUME in ccRCC. Altered pathways associated with the RSUME expression were validated by biological and bioinformatics analyses. Combined results showed that in the absence of VHL, RSUME is involved in the downregulation of the antioxidant defense system, whereas in the presence of VHL, it acts in rerouting energy-related pathways, negatively modulating the lipid utilization, and positively modulating the fatty acid synthesis, which may promote deposition in droplets.
Question: Write a study description for the study titled 'The suberin transporter StABCG1 is required for barrier formation in potato leaves'.
Answer: Suberin is a hydrophobic biopolymer that acts as an internal and external diffusion and transpiration barrier in plants. It is involved in two phases of wound healing, i.e. initial closing layer formation and subsequent wound periderm development. Transcriptomic and metabolomic analyses of wounded potato leaf tissue revealed preferential induction of cell wall modifying processes during closing layer formation, accompanied by a highly active defense response. To address the importance of suberin in this process, we generated loss of function mutants by CRISPR-Cas9 editing the suberin transporter gene StABCG1. Both wound-induced StABCG1 transcript levels and suberin formation around wounded leaf tissue were reduced in CRISPR-lines. Moreover, wound-induced tissue damage was characterized by browning of wound-adjacent areas. Transcriptome analyses of these areas revealed up-regulation of genes encoding defense proteins and enzymes of the phenylpropanoid pathway. Levels of hydroxycinnamic acid amides, acting in defense and in cell wall reinforcement, were drastically enhanced in CRISPR compared to control plants. These results suggest that the reduction in suberin formation around wounded tissue leads to a loss of barrier function, resulting in tissue browning due to enhanced exposure to oxygen.Linked cross omic data sets:The related transciptome data was submitted to the NCBI SRA repository under accession PRJNA1132763.
Question: Write a study description for the study titled 'A database of high-resolution MS/MS spectra for lichen metabolites'.
Answer: While analytical techniques in natural products research massively shifted to liquid chromatography-mass spectrometry, lichen chemistry remains reliant on limited analytical methods, Thin Layer Chromatography being the gold standard. To meet the modern standards of metabolomics within lichenochemistry, we announce the publication of an open access MS/MS library with 250 metabolites, coined LDB for Lichen DataBase, providing a comprehensive coverage of lichen chemodiversity. These were donated by the Berlin Garden and Botanical Museum from the collection of Siegfried Huneck to be analyzed by LC-MS/MS. Spectra at individual collision energies were submitted to MetaboLights while merged spectra were uploaded to the GNPS platform (CCMSLIB00004751209 to CCMSLIB00004751517). Technical validation was achieved by dereplicating three lichen extracts using a Molecular Networking approach, revealing the detection of eleven unique molecules that would have been missed without LDB implementation to the GNPS. From a chemist's viewpoint, this database should help streamlining the isolation of formerly unreported metabolites. From a taxonomist perspective, the LDB offers a versatile tool for the chemical profiling of newly reported species.
Question: Write a study description for the study titled 'Lipid Data Analyzer: The LDA algorithm against the in silico library LipidBlast (LipidBlast benchmarking experiment)'.
Answer: Lipid Data Analyzer (LDA; http://genome.tugraz.at/lda2) provides automated and reliable annotation of lipid species and their molecular structures in high-throughput data from chromatography-coupled tandem mass spectrometry using embedded rule sets. Using various low- and high-resolution mass spectrometry instruments with several collision energies, the method's platform independence is proved. The software's reliability, flexibility, and ability to identify novel lipid molecular species may now render current state-of-the-art lipid libraries obsolete.  In a benchmark test of LDA versus LipidBlast, data from both the first control experiment and the biological experiment, both acquired on the Orbitrap Velos Pro in CID +50 and -50, was used. In addition, the biological experiment was benchmarked for the lower resolution QTRAP 4000 for +45 eV and -45 eV. For LipidBlast evaluation, the parameters recommended by NIST MSPepSearchGUI (http://peptide.nist.gov/software/ms_pep_search_gui/MSPepSearch.html) were used. The same m/z tolerances were applied in both LipidBlast and LDA. The specificity and sensitivity of LipidBlast depend on a so called matching factor, a value ranging from 0-999. Using the default setting of 450 for the matching factor, many lipid standards in Control experiment 1 were not detected. Consequently, the matching factor was lowered to 10, in which case LipidBlast detected almost all of the lipid standards in negative ion mode. Further reduction did not improve the sensitivity of LipidBlast. In positive ion mode, irrespective of the matching factor setting, LipidBlast was not able to identify as many lipid molecular species as was LDA. In this benchmark test, only lipid subclasses/adducts that both LDA and LipidBlast are able to detect were used. Correct assignment of lipid species and lipid molecular species identified in liver lipidomes was verified by manual inspection of the spectra, and by aligning them with the respective retention time data.Control experiment 1 assays for this study can be found in the MetaboLights study MTBLS394. Control experiment 2 assays for this study can be found in the MetaboLights study MTBLS391. Control experiment 3 assays for this study can be found in the MetaboLights study MTBLS398. Murine liver lipidome experiment assays for this study can be found in the MetaboLights study MTBLS396. HCD characterization and regioisomer detection assays for this study can be found in the MetaboLights study MTBLS462. Linked Studies: MTBLS391 MTBLS394 MTBLS396 MTBLS398 MTBLS462
Question: Write a study description for the study titled 'Quantitative 1H NMR metabolome profiling of Thai Jasmine rice (Oryza sativa) reveals primary metabolic response during brown planthopper infestation'.
Answer: Brown planthopper (BPH; Nilaparvata lugens) is a phloem feeding insect which is one of the most serious threats to rice crops in many countries throughout Asia. 1H NMR spectroscopy, combined with chemometrics, was used to analyze the polar metabolome from leaf extracts of Thai Jasmine rice (brown planthopper (BPH)-susceptible KD) and its BPH resistant isogenic lines (BPH-resistant IL7 and BPH-resistant+ IL308 varieties) with and without BPH infestation at various time points (days 1, 2, 3, 4 and 8). Physiological changes of the rice isogenic lines were different based on the quantitative trait loci of BPH resistance. Multivariate models were capable of distinguishing between the susceptible and the resistant rice varieties throughout the infestation. The concentration of 10 metabolites were significantly altered (p < 0.05) between the infested and the control groups of each examined rice variety. Metabolic pathway analysis suggested that BPH infestation could perturb transamination during the early stages of infestation (days 1–3) for all rice varieties. In addition, the IL7 and IL308 varieties responded earlier (day 3) than the KD variety (day 8) by perturbing amino acid metabolism, shikimate and gluconeogenesis pathways. By day 8 of the infestation, the KD cultivar responded by activating the amino acid-mediated-de novo pathway whereas the IL308 variety activated the purine and pyrimidine compound-mediated-salvage pathway for nucleotide biosynthesis. This study has identified, for the first time, several potential metabolic pathways for acclimatization and defense mechanisms against BPH infestation. These findings provide a valuable, first insight into BPH resistance mechanisms in Thai Jasmine rice.
Question: Write a study description for the study titled 'Activation of imprinted gene Pw1 promotes cardiac fibrosis after ischemic injury'.
Answer: Cardiac fibrosis, characterized by excessive extracellular matrix (ECM) deposition in the myocardium, is a critical target for heart disease treatments. Pw1 (paternally expressed gene 3) is an imprinted gene expressed from the paternally allele, and de novo purine biosynthesis (DNPB) is a crucial pathway for nucleotide synthesis. However, the roles of PW1 and DNPB in ECM production by cardiac fibroblasts during myocardial ischemia are not yet understood. To induce myocardial damage, we performed left anterior descending coronary artery ligation. We generated Pw1CreER-2A-eGFP and Pw12A-CreER knock-in mouse lines to evaluate the expression of the two Pw1 alleles in normal and injured hearts. Bisulfite sequencing was employed to analyze the DNA methylation of the Pw1 imprinting control region. We identified the phosphoribosylformylglycinamidine synthase (Pfas) gene, encoding the DNPB enzyme PFAS, as a direct target of PW1 using chromatin immunoprecipitation sequencing and real-time quantitative polymerase chain reaction. The role of DNPB in ECM production and cardiac fibrosis post-injury was examined in vitro using cultured cardiac fibroblasts and in vivo with Pfas-deficient mice. Our study demonstrates that myocardial infarction reduces DNA methylation at the imprinting control region of the maternally imprinted gene Pw1, triggering a switch from monoallelic imprinting to biallelic expression of Pw1 in cardiac fibroblasts. In activated cardiac fibroblasts, increased Pw1 expression promotes purine biosynthesis and induces ECM production by transcriptionally activating the DNPB factor Pfas. Notably, we identified that DNPB is essential for ECM production in activated fibroblasts and that loss of Pfas in fibroblasts limits cardiac fibrosis and improves heart function after heart injury. This study reveals that post-injury, the imprinting of Pw1 is disrupted, highlighting a novel role for the downstream DNPB pathway in cardiac fibrogenesis. Targeting DNPB presents a promising therapeutic strategy for improving cardiac repair following injury.
Question: Write a study description for the study titled 'Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative (Streptococcus pyogenes assays)'.
Answer: The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission is specifically for Streptococcus pyogenes.GC-MS and LC-MS Streptococcus pyogenes assays are reported in the current study MTBLS2324GC-MS and LC-MS Escherichia coli assays are reported in MTBLS2015GC-MS and LC-MS Staphylococcus aureus assays are reported in MTBLS1898GC-MS and LC-MS Klebsiella pneumoniae assays are reported in MTBLS2322GC-MS and LC-MS Streptococcus pneumoniae assays are reported in MTBLS2323
Question: Write a study description for the study titled 'Transcript, protein and metabolite temporal dynamics in the CAM plant Agave'.
Answer: Already a proven mechanism for drought sustainability, crassulacean acid metabolism (CAM) is a specialized type of photosynthesis that maximizes water-use efficiency (WUE) via an inverse (compared to C3 and C4 photosynthesis-performing species) day/night pattern of stomatal closure/opening to shift CO2 uptake to the nighttime, when evapotranspiration rates are low. A systems-level understanding spanning temporal molecular and metabolic controls is needed to define the cellular behavior that confers advantages in water-limited conditions. Here, we report high-resolution temporal behaviors of transcript, protein, and metabolite abundances across a CAM diel cycle and, where applicable, compare those observations to the well-established C3 model plant, Arabidopsis thaliana. A mechanistic finding that emerged is that CAM operates with a shifted altered redox poise relative to Arabidopsis thaliana. Moreover, we identify widespread rescheduled expression for genes associated with signal transduction mechanisms that are presented in guard cells to regulate stomatal opening/closing. Controlled production and degradation of transcript and proteins is a timing mechanism by which to regulate cellular function, yet knowledge of how this molecular timekeeping regulates CAM physiology is unknown. Here, we provide new insight into complex, post-transcriptional and -translational hierarchies that govern CAM in Agave. These data sets together provide a resource that could inform efforts to engineer traits of the more efficient CAM plant into economically valuable C3 crops.
Question: Write a study description for the study titled 'High metabolic variation for seaweeds in response to environmental changes: a case study of the brown algae Lobophora in coral reefs'.
Answer: In the marine environment, macroalgae face changing environmental conditions and some species are known for their high capacity to adapt to the new factors of their ecological niche. Some macroalgal metabolites play diverse ecological functions and belong to the adaptive traits of such species. Because algal metabolites are involved in many processes that shape marine biodiversity, understanding their sources of variation and regulation is therefore of utmost relevance. This work aims at exploring the possible sources of metabolic variations with time and space of four common algal species from the genus Lobophora (Dictyotales, Phaeophyceae) in the New Caledonian lagoon using a UHPLC-HRMS metabolomic fingerprinting approach. While inter-specific differences dominated, a high variability of the metabolome was noticed for each species when changing their natural habitats and types of substrates. Fatty acids derivatives and polyolefins were identified as chemomarkers of these changing conditions. The four seaweeds metabolome also displayed monthly variations over the 13-months survey and a significant correlation was made with sea surface temperature and salinity. This study highlights a relative plasticity for the metabolome of Lobophora species.
Question: Write a study description for the study titled 'Comparative metabolomics of Mycoplasma bovis and Mycoplasma gallisepticum reveals fundamental differences in active metabolic pathways and suggests novel gene annotations'.
Answer: Mycoplasmas are simple, but successful parasites that have the smallest genome of any free-living cell and are thought to have a highly streamlined cellular metabolism. Here we have undertaken a detailed metabolomic analysis of two species, Mycoplasma bovis and Mycoplasma gallisepticum, which cause economically important diseases in cattle and poultry, respectively. Untargeted GC/MS and LC/MS analyses of mycoplasma metabolite extracts revealed significant differences in the steady state levels of many metabolites in central carbon metabolism, while 13C stable isotope labelling studies revealed marked differences in carbon source utilization. These data were mapped onto in silico metabolic networks predicted from genome wide annotations. The analyses elucidated distinct differences, including a clear difference in glucose utilisation, with a marked decrease in glucose uptake and glycolysis in M. bovis compared to M. gallisepticum, which may reflect differing host nutrient availabilities. The 13C-labeling patterns also revealed several functional metabolic pathways that were previously unannotated in these species, allowing us to assign putative enzyme functions to the products of a number of genes of unknown function, especially in M. bovis. This study demonstrates the considerable potential of metabolomic analyses to assist in characterising significant differences in the metabolism of different bacterial species, and in improving genome annotation.
Question: Write a study description for the study titled 'Integrative Omics Analysis of Plant-Microbe Synergies in Petroleum Pollution Remediation'.
Answer: As the petrochemical industry continues to advance, the exacerbation of ecological imbalance and environmental degradation due to petroleum pollution is increasingly pronounced. The synergistic interaction between plants and microorganisms are pivotal in the degradation of petroleum hydrocarbons; however, the underlying degradation mechanisms are not yet fully understood. In this study, we employed a multi-omics approach, integrating transcriptomics, 16S rRNA gene sequencing and metabolomics, to analyze key differential genes, dominant microbial strains and root-secreted metabolites involved in petroleum hydrocarbon degradation in alfalfa. The results show that several stress-related genes are upregulated in alfalfa contaminated with petroleum hydrocarbon. Pseudomonas, Rhodococcus and Brevundimonas remain dominant species in the rhizosphere microbiome. Additionally, when applying pantothenic acid, malic acid and citric acid selected from metabolomics to the oil sediment used for growing alfalfa, the degradation rates significantly improved, with pantothenic acid application resulting in approximately a 10% higher degradation rate compared to other treatments. Our findings offer essential insights for optimizing phytoremediation strategies and improving the efficiency of soil decontamination
Question: Write a study description for the study titled 'Deciphering the Anti-Obesity Mechanisms of Pharmabiotic Probiotics through Advanced Multiomics Analysis'.
Answer: Probiotics with 'Pharmabiotic' properties are increasingly recognized as effective tools for combating obesity by altering gut microbiota and reducing body fat. However, the molecular mechanisms underlying their anti-obesity effects remain largely unexplored due to the absence of a universal methodology. Herein, we developed a multiomics-based strategy to elucidate how probiotics reduce lipid production in adipocytes. Our initial investigation assessed the impact of probiotics at defined adipocyte differentiation stages. Leveraging these insights, we performed comprehensive multiomics analyses at key intervals to identify the suppression mechanisms of lipid formation. Lactobacillus reuteri, specifically, targets early differentiation stages, inhibits branched-chain amino acid catabolism, and reduces lipid accumulation in adipocytes by suppressing Krüppel-like factor 5. Concurrently, enhanced hypoxia-inducible factor 1 expression impedes adipogenesis by downregulating lipin-1 expression. This study not only demonstrates the effectiveness of our approach in revealing complex host-microbe interactions but also significantly advances probiotic therapeutic development, offering promising avenues for obesity management.
Question: Write a study description for the study titled 'Proteolethargy is a pathogenic mechanism in chronic disease'.
Answer: The pathogenic mechanisms of many diseases are well understood at the molecular level, but there are prevalent diseases associated with pathogenic signaling, such as diabetes and chronic inflammatory disorders, where our understanding is more limited. Here we report that pathogenic signaling suppresses the mobility of a spectrum of proteins that play essential roles in cellular functions known to be dysregulated in these chronic diseases. This behavior was linked to cysteine residues in the affected proteins and signaling-related increases in excess reactive oxygen species. Diverse pathogenic stimuli, including hyperglycemia, dyslipidemia and inflammation, produce similar suppressed protein mobility phenotypes. We propose that suppressed protein mobility may account for various pathogenic features of diverse chronic diseases.
Question: Write a study description for the study titled 'A novel strategy for mining and identification of acylcarnitines using data-independent-acquisition (DIA) based retention time prediction modeling and pseudo-characteristic fragmentation ions matching'.
Answer: It is a challenging work to screen, identify, and quantify acylcarnitines in complex biological samples. A method, based on the retention time (RT) prediction and data-independent acquisition strategies, was proposed for the large-scale identification of acylcarnitines using liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS). Relative cumulative eluotropic strength was introduced as a novel descriptor in building a linear prediction model, which not only solves the problem that acylcarnitines with long carbon chains cannot be well predicted in traditional models but also proves its robustness and transferability across instruments in two data sets that were acquired in distinct chromatography conditions. The accessibility of both predictive RT and MS2 spectra of suspect features effectively reduced about 30% false-positive results, and consequently, 150 and 186 acylcarnitines were identified in the rat liver and human plasma (NIST SRM 1950), respectively. This method provides a new approach in large-scale analysis of acylcarnitine in lipidomic studies and can also be extended to the analysis of other lipids.