LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Historical Biobanks in Breast Cancer Metabolomics - Challenges and Opportunities'.
Answer: BACKGROUND: Metabolomic characterization of tumours can potentially improve prediction of cancer prognosis and treatment response. Here, we describe efforts to validate previous metabolomic findings using a historical cohort of breast cancer patients and discuss challenges with using older biobanks collected with non-standardized sampling procedures.METHODS: In total, 100 primary breast cancer samples were analysed by high-resolution magic angle spinning magnetic resonance spectroscopy (HR MAS MRS) and subsequently examined by histology. Metabolomic profiles were related to the presence of cancer tissue, hormone receptor status, T-stage, N-stage and survival. RNA integrity number (RIN), and metabolomic profiles were compared with an ongoing breast cancer biobank.RESULTS: The 100 samples had a median RIN of 4.3, while the ongoing biobank had a significantly higher median RIN of 6.3 (p = 5.86 x 10^-7). A low RIN was associated with changes in choline-containing metabolites and creatine, and the samples in the older biobank showed metabolic differences previously associated with tissue degradation. The association between metabolomic profile and oestrogen receptor status was in accordance with previous findings, however, with a lower classification accuracy.CONCLUSIONS: Our findings highlight the importance of standardized biobanking procedures in breast cancer metabolomics studies.
Question: Write a study description for the study titled 'Automated, Parallel Mass Spectrometry Imaging and Structural Identification of Lipids'.
Answer: We report a method that enables automated data-dependent acquisition of lipid tandem mass spectrometry data in parallel with a high-resolution mass spectrometry imaging experiment. The method does not increase the total image acquisition time and is combined with automatic structural assignment. This lipidome-per-pixel approach automatically identified and validated 104 unique molecular lipids and their spatial locations from rat cerebellar tissue.
Question: Write a study description for the study titled 'The pyruvate kinase, a metabolic sensor powering glycolysis, drives the metabolic control of DNA replication'.
Answer: BACKGROUND: In all living organisms, DNA replication is exquisitely regulated in a wide range of growth conditions to achieve timely and accurate genome duplication prior to cell division. Failures in this regulation cause DNA damage with potentially disastrous consequences for cell viability and human health, including cancer. To cope with these threats, cells tightly control replication initiation using well-known mechanisms. They also couple DNA synthesis to nutrient richness and growth rate through a poorly understood process thought to involve central carbon metabolism. One such process may involve the cross-species conserved pyruvate kinase (PykA) which catalyzes the last reaction of glycolysis. Here we have investigated the role of PykA in regulating DNA replication in the model system Bacillus subtilis.RESULTS: On analysing mutants of the catalytic (Cat) and C-terminal (PEPut) domains of B. subtilis PykA we found replication phenotypes in conditions where PykA is dispensable for growth. These phenotypes are independent from the effect of mutations on PykA catalytic activity and are not associated with significant changes in the metabolome. PEPut operates as a nutrient-dependent inhibitor of initiation while Cat acts as a stimulator of replication fork speed. Disruption of either PEPut or Cat replication function dramatically impacted the cell cycle and replication timing even in cells fully proficient in known replication control functions. In vitro, PykA modulates activities of enzymes essential for replication initiation and elongation via functional interactions. Additional experiments showed that PEPut regulates PykA activity and that Cat and PEPut determinants important for PykA catalytic activity regulation are also important for PykA-driven replication functions.CONCLUSIONS: We infer from our findings that PykA typifies a new family of cross-species replication control regulators that drive the metabolic control of replication through a mechanism involving regulatory determinants of PykA catalytic activity. As disruption of PykA replication functions causes dramatic replication defects, we suggest that dysfunctions in this new family of universal replication regulators may pave the path to genetic instability and carcinogenesis.
Question: Write a study description for the study titled 'Untargeted metabolomics to understand the basis of phenotypic differences in amphotericin B-resistant Leishmania parasites'.
Answer: BACKGROUND: Protozoan Leishmania parasites are responsible for a range of clinical infections that represent a substantial challenge for global health. Amphotericin B (AmB) is increasingly used to treat Leishmania infection, so understanding the potential for resistance to this drug is an important priority. Previously we described four independently-derived AmB-resistant L. mexicana lines that exhibited resistance-associated genetic lesions resulting in altered sterol content. However, substantial phenotypic variation between these lines, including differences in virulence attributes, were not fully explained by these changes.METHODS: To identify alterations in cellular metabolism potentially related to phenotypic differences between wild-type and AmB-resistant lines, we extracted metabolites and performed untargeted metabolomics by liquid chromatography-mass spectrometry.RESULTS: We observed substantial differences in metabolite abundance between lines, arising in an apparently stochastic manner. Concerted remodeling of central carbon metabolism was not observed; however, in three lines, decreased abundance of several oligohexoses was observed. Given that the oligomannose mannogen is an important virulence factor in Leishmania, this could relate to loss of virulence in these lines. Increased abundance of the reduced forms of the oxidative stress-protective thiols trypanothione and glutathione was also observed in multiple lines.CONCLUSIONS: This dataset will provide a useful resource for understanding the molecular basis of drug resistance in Leishmania, and suggests a role for metabolic changes separate from the primary mechanism of drug resistance in determining the phenotypic profile of parasite lines subjected to experimental selection of resistance.
Question: Write a study description for the study titled 'Different regions of synaptic vesicle membrane regulate VAMP2 conformation for the SNARE assembly'.
Answer: Vesicle associated membrane protein 2 (VAMP2/synaptobrevin2), a core SNARE protein residing on synaptic vesicles (SVs), forms helix bundles with syntaxin-1 and SNAP25 for the SNARE assembly. Prior to the SNARE assembly, the structure of VAMP2 is unclear. Here, by using in-cell NMR spectroscopy, we describe the dynamic membrane association of VAMP2 SNARE motif in mammalian cells, and the structural change of VAMP2 upon the change of intracellular lipid environment. We analyze the lipid compositions of the SV membrane by mass-spectrometry-based lipidomic profiling, and further reveal that VAMP2 forms distinctive conformations in different membrane regions. In contrast to the non-raft region, the membrane region of cholesterol-rich lipid raft markedly weakens the membrane association of VAMP2 SNARE motif, which releases the SNARE motif and facilitates the SNARE assembly. Our work reveals the regulation of different membrane regions on VAMP2 structure and sheds light on the spatial regulation of SNARE assembly.
Question: Write a study description for the study titled 'Gut microbiota-derived butyric acid protected against secondary brain injury after SAH by inhibiting neuronal pyroptosis and regulating gut microbiota composition (Murine assays)'.
Answer: BACKGROUND: Subarachnoid hemorrhage (SAH) is a devastating cerebrovascular disease with a poor prognosis. Accumulating studies have reported that gut microbiota contributes to the pathophysiology of several central nervous system diseases. However, whether SAH can change gut microbiota composition and affected gut microbiota is involved in the development of secondary brain injury following SAH remains unclear.METHODS: A retrospective case-control study was performed in unruptured intracranial aneurysm (UIA, CTL) and ruptured intracranial aneurysm (SAH) patients. Patients' fecal and serum samples were collected and sequenced by metagenome and metabolome. The experimental SAH mice models were established, and their feces and serum were also analyzed by 16S rRNA and metabolic sequencing. Fecal microbiota from SAH patients and mice was transplanted to ABX mice to investigate the relationship between the gut microbiota and secondary brain injury following SAH.RESULTS: SAH seriously influenced gut microbiota composition and significantly increased the relative abundance of the genus Escherichia. SAH also considerably reduced the production of gut microbiota-derived butyric acid. Furthermore, SAH-induced gut microbiota dysbiosis aggravated brain injury and cognitive deficits in ABX mice by promoting inflammatory response. Sodium butyrate (NaB) administration protected against secondary brain injury following SAH by inhibiting pyroptosis-related neuroinflammation, which is mediated by NLRP1/Caspase-1/GSDMD and Caspase-3/GSDME signaling pathways. NaB drinking pretreatment also alleviated secondary brain injury following SAH by increasing the relative abundance of butyric acid-producing bacteria, such as Dubosiella and Faecalibaculum, and decreasing the Escherichia abundance.CONCLUSION: SAH contributed to gut microbiota dysbiosis and changed gut microbiota exacerbated secondary brain injury after SAH. Supplement with gut microbiota-derived butyric acid protected against brain injury following SAH by inhibiting NLRP1/Caspase-1/GSDMD and Caspase-3/GSDME-mediated neuronal pyroptosis.Linked studies:UPLC-MS/MS assays of murine samples are reported in this study.UPLC-MS/MS assays of human samples are reported in MTBLS9087.
Question: Write a study description for the study titled 'The genetic origin of evolidine, the first cyclopeptide discovered in plants, and related orbitides'.
Answer: Cyclic peptides are reported to have antibacterial, antifungal and other bioactivities. Orbitides are a class of cyclic peptide that are small, head-to-tail cyclized, composed of proteinogenic amino acids, and lack disulfide bonds; they are also known in several genera of the plant family Rutaceae. Melicope xanthoxyloides is the Australian rain forest tree of the Rutaceae family in which evolidine - the first plant cyclic peptide - was discovered. Evolidine (cyclo-SFLPVNL) has subsequently been all but forgotten in the academic literature, so to redress this we used tandem mass spectrometry and de novo transcriptomics to rediscover evolidine and decipher its biosynthetic origin from a short precursor just 48 residues in length. We also identify another six M. xanthoxyloides orbitides using the same techniques. These peptides have atypically diverse C-termini consisting of residues not recognized by either of the known proteases plants use to macrocyclize peptides, suggesting new cyclizing enzymes a wait discovery. We examined the structure of two of the novel orbitides by NMR, finding one had a definable structure, whereas the other did not. Mining RNA-seq and whole genome sequencingdata from other species of the Rutaceae familyrevealed a large and diverse family of peptides is encoded by similar sequences across the family and demonstrates how powerful de novo transcriptomics can be at accelerating the discovery of new peptide families.
Question: Write a study description for the study titled 'Pollutant depletion by gut bacterial communities'.
Answer: Per- and polyfluoroalkyl Substances (PFAS) – the so-called ‘forever chemicals’ – are a major cause of environmental and health concern due to their toxicity and long-term persistence. Yet, no efficient mechanisms for their removal have been identified. Here we report the potential of two communities of human gut bacteria to bioaccumulate or degrade common environmental pollutants.
Question: Write a study description for the study titled 'Integrated Physiological and Multi-Omics Analyses Reveal Nitrogen Fertilization Promotes Salix matsudana Growth and Soil Remediation'.
Answer:  Soil contamination with heavy metals, particularly lead (Pb) and cadmium (Cd), has become a growing environmental concern due to rapid industrialization. Salix matsudana, a woody energy plant with notable tolerance to heavy metals, exhibits considerable potential for use in phytoremediation. Although nitrogen (N) fertilization is known to promote the growth of S. matsudana, its dual role in enhancing plant development and improving soil conditions remains insufficiently understood. In this study, we systematically examined the effects of varying nitrogen fertilizer concentrations on the growth of S. matsudana, heavy metal uptake, and rhizosphere soil characteristics through integrated physiological and multi-omics approaches. Our findings revealed that high nitrogen levels significantly increased plant biomass and the accumulation of Pb and Cd compared to control conditions. Detailed physiological analyses demonstrated enhanced heavy metal absorption in roots under nitrogen fertilization. Microbial community analysis further indicated that nitrogen application altered rhizosphere microbial activity, particularly enriching bacterial taxa associated with metal mobilization. Metabolomic profiling corroborated improvements in soil quality, showing significant changes in organic acid metabolites involved in metal chelation. These results provide new insights into the mechanisms by which nitrogen fertilization synergistically enhances both the growth of S. matsudana and the efficiency of soil remediation, offering valuable guidance for optimizing phytoremediation strategies in heavy metal-contaminated environments.
Question: Write a study description for the study titled 'ArgR-dependent Bacterial Resistance to Host Lipid Droplets in Edwardsiella piscicida'.
Answer: Lipid droplets (LDs), as innate immune hubs, function in the front line of antimicrobial defense involved in the ongoing host-pathogen arms race. Particularly for intracellular bacterial pathogens, the endowed capacity to resist host LDs can effectively facilitate pathogen in vivo colonization and evasion from the host’s innate immune response. Here, to investigate the genetic mechanisms of intracellular bacteria response to host LDs, we utilized transposon insertion sequencing to dissect critical fitness determinants of Edwardsiella piscicida under the treatment of LDs isolated from its native host, turbot. Targeted metabolomics indicated that LD challenge resulted in the accumulation of intracellular arginine. The core arginine metabolism regulatory factor, ArgR, was found to play a pivotal role in combating LDs, emphasizing the importance of orchestrating intracellular arginine levels for bacterial LD adaptation. Specifically, ArgR enhanced the expressions of genes involved in arginine catabolism (speA/B and arcC) and diminished gene transcripts associated with arginine import (artP) and synthesis (argD/E/H). Furthermore, ArgR contributed to the pathogenesis of E. piscicida, promoting the proliferation in host cells and virulence in turbot. Collectively, our results shed light on the underlying mechanism of intracellular pathogens resisting LDs during bacterial infections and highlighting the crucial role of arginine in the host-pathogen interactions.
Question: Write a study description for the study titled 'Energy-stress-mediated AMPK activation inhibits ferroptosis'.
Answer: Energy stress depletes ATP and induces cell death. Here we identify an unexpected inhibitory role of energy stress on ferroptosis, a form of regulated cell death induced by iron-dependent lipid peroxidation. We found that ferroptotic cell death and lipid peroxidation can be inhibited by treatments that induce or mimic energy stress. Inactivation of AMP-activated protein kinase (AMPK), a sensor of cellular energy status, largely abolishes the protective effects of energy stress on ferroptosis in vitro and on ferroptosis-associated renal ischaemia-reperfusion injury in vivo. Cancer cells with high basal AMPK activation are resistant to ferroptosis and AMPK inactivation sensitizes these cells to ferroptosis. Functional and lipidomic analyses further link AMPK regulation of ferroptosis to AMPK-mediated phosphorylation of acetyl-CoA carboxylase and polyunsaturated fatty acid biosynthesis. Our study demonstrates that energy stress inhibits ferroptosis partly through AMPK and reveals an unexpected coupling between ferroptosis and AMPK-mediated energy-stress signalling.
Question: Write a study description for the study titled 'In plaque-mass spectrometry imaging of a bloom-forming alga during viral infection reveals a metabolic shift towards odd-chain fatty acid lipids (Imaging MS assays)'.
Answer: Tapping into the metabolic cross-talk between a host and its virus can reveal unique strategies employed during infection. Viral infection is a dynamic process that generates an evolving metabolic landscape. Gaining a continuous view into the infection process is highly challenging and is limited by current metabolomics approaches, which typically measure the average of the entire population at various stages of infection. Here, we took an innovative approach to study the metabolic basis of host-virus interactions between the bloom-forming alga Emiliania huxleyi and its specific virus. We combined a classical method in virology, the plaque assay, with advanced mass spectrometry imaging (MSI), an approach we termed ‘in plaque-MSI’. Taking advantage of the spatial characteristics of the plaque, we mapped the metabolic landscape induced during infection in a high spatiotemporal resolution, unfolding the infection process in a continuous manner. Further unsupervised spatially-aware clustering, combined with known lipid biomarkers, revealed a systematic metabolic shift during infection towards lipids containing the odd-chain fatty acid pentadecanoic acid (C15:0). Applying ‘in plaque-MSI’ might facilitate the discovery of bioactive compounds that mediate the chemical arms race of host-virus interactions in diverse model systems.  Imaging MS assays are reported in the current study MTBLS769.  GC- and LC-MS assays are reported in MTBLS767.
Question: Write a study description for the study titled 'Modulation of liver metabolism and gut microbiota by Alhagi-honey alleviated heat stress-induced liver damage'.
Answer: Alhagi-honey (AH) is a well-established traditional ethnic medicine with advantageous effects against diarrhea and headaches. We aim to explore the preventive effect of AH on liver damage induced by heat stress (HS) and its underlying mechanism. HS models were established by thermostat, and mice were treated at 39 °C for 10 h, lasting for 7 days. Hematoxylin-eosin (H&E) staining and Periodic Acid-Schiff (PAS) staining were used for histological observation, and transmission electron microscopy (TEM) was used for ultrastructure examination of hepatocytes. Gut microbiota (GM) composition and liver metabolites were respectively analyzed by 16S rRNA sequencing and non-targeted metabolome sequencing. AH pretreatment alleviated liver damage caused by heat stress in mice. The main manifestation was that AH alleviated serum aspartate transferase (AST) and aspartate transaminase (ALT). It was found that AH improved symptoms of hepatocyte damage. In addition, the relative abundance of f_Rikenellaceae, g_Incertae_Sedis and s_Staphylococcus_Orisratti, g_Lachnoclostridium, g_GCA-900066575 and s_Alistipes_inops were modified by AH and these bacterial genera showed association with 6 metabolites (2- (3,4-dihydroxyphenyl) acetamide, 3-hydroxy-3-methylpentanedioic acid, PC (17:0/17:1), Y-L-Glutamy-L-glutamic acid, L-Isoleucine, 5-Methyluridine, 8,8-dimethyl-2-phenyl-4H,8H-pyrano [2, 3-h] chromen-4-one). The Pearson analysis also showed a strong correlation between these microbes and 2 risk indicators (AST and ALT) of liver damage. AH alleviated HS-induced liver damage by regulating liver metabolism and maintaining normal GM. It demonstrated that AH held potential as a prophylactic drug for the prevention of HS-induced liver damage.
Question: Write a study description for the study titled 'Metabolomics analysis of the algU mutant strain under hyperosmotic stress.'.
Answer: Metabolomics analysis of the algU mutant strain under hyperosmotic stress.
Question: Write a study description for the study titled 'Gut fungal landscape in colorectal cancer and its cross-kingdom interplay with gut microbial ecology'.
Answer: Background: The gut microbiota is a key hallmark of tumor and plays a central role in colorectal cancer (CRC). However, the contribution of gut fungi, an important community of gut microbes, remains substantially understudied in CRC.Objective: To characterize the gut fungal landscape in CRC and elucidate its associations with bacterial communities, metabolites, and trace elements.Methods: We conducted metagenomic sequencing on fecal samples from three cohorts: healthy controls (n = 401), colorectal polyp patients (n = 162), and CRC patients (n = 253). The fungal genomic data from NCBI database (PRJNA833221) was served as the reference for annotating gut fungi. Metabolites and trace elements were quantified via liquid chromatography and inductively Coupled Plasma Mass Spectrometry (ICP-MS), respectively. Fungal diversity and compositional differences were analyzed across groups. A random forest model was trained to discriminate healthy controls from intestinal disease groups (polyps and CRC) based on microbial biomarkers, with an ablation study optimizing co-marker selection. Structural equation modeling (SEM) was employed to dissect interactions among fungi, bacteria, metabolites, and trace elements.Results: CRC patients exhibited increased fungal diversity at the genus level. Seven fungal genera displayed differential abundance across three groups: Rhizopus was specifically enriched in CRC, whereas Sporisorium, Cladosporium, Aureobasidium, Zygoascus, and Meyerozyma were enriched in polyps. Ablation study identified an optimal 31-microbial-marker panel (28 bacterial and 3 fungal species) that effectively distinguished intestinal disease groups (AUC = 0.89). SEM analysis identified three fungal markers—Penicillium citrinum, Penicillium sp. PG10607D, and Rhizopus stolonifera—that influence bacterial-metabolite-trace element networks through distinct correlations.Conclusion: This study plots the first gut fungal atlas for CRC and reveals complex cross-kingdom interactions involving fungi, bacteria, metabolites, and trace elements, providing new insights into CRC research.
Question: Write a study description for the study titled 'Gut microbiome drives individual memory variation in bumblebees'.
Answer: The potential of the gut microbiome as a driver of individual cognitive differences in natural populations of animals remains unexplored. Here, using metagenomic sequencing of individual bumblebee hindguts, we find a positive correlation between the abundance of Lactobacillus Firm-5 cluster and memory retention on a visual discrimination task. Supplementation with the Firm-5 species Lactobacillus apis (L. apis), but not other non-Firm-5 bacterial species, enhances bees’ memory. Untargeted metabolomics after L. apis supplementation show increased LPA (14:0) glycerophospholipid in the haemolymph. Oral administration of the LPA increases long-term memory significantly. Based on our findings and metagenomic/metabolomic analyses, we propose a molecular pathway for this gut-brain interaction. Our results provide insights into proximate and ultimate causes of cognitive differences in natural bumblebee populations.