LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Maternal steroids during pregnancy and their associations with ambient air pollution and temperature during preconception and early gestational periods'.
Answer: Hormones play critical roles in facilitating pregnancy progression and the onset of parturition. Several classes of environmental contaminants, including fine particulate matter (PM2.5) and ambient temperature, have been shown to alter hormone biosynthesis or activity. However, epidemiologic research has not considered PM2.5 in relation to a broader range of steroid hormones, particularly in pregnant women. Using metabolomics data collected within 20-40 weeks of gestation in an ethnically diverse pregnancy cohort study, we identified 42 steroid hormones that we grouped into five classes (pregnenolone, androgens, estrogens, progestin, and corticosteroids) based on their biosynthesis type. We found that exposure to PM2.5 during the pre-conception and early prenatal periods was associated with higher maternal androgen concentrations in late pregnancy. We also detected a positive association between early pregnancy PM2.5 exposure and maternal pregnenolone levels and a marginal positive association between early pregnancy PM2.5 exposure and progestin levels. When considering each hormone metabolite individually, we found positive associations between early pregnancy PM2.5 exposure and five steroids, two of which survived multiple comparison testing: 11beta-hydroxyandrosterone glucuronide (a pregnenolone steroid) and adrosteroneglucuronide (a progestin steroid). None of the steroid classes were statistically significant associated with ambient temperature. In sex-stratified analyses, we did not detect any sex differences in our associations. This is the first study showing that exposure to fine particulate matter during the pre-conception and early prenatal periods can lead to altered steroid adaptation during the state of pregnancy, which has been shown to have potential consequences on maternal and child health.
Question: Write a study description for the study titled 'Identification of amniotic fluid metabolomic and placental transcriptomic changes associated with abnormal development of cloned pig fetuses'.
Answer: Piglets cloned by somatic cell nuclear transfer (SCNT) show a high incidence of malformations and a high death rate during the perinatal period. To investigate the underlying mechanisms for abnormal development of cloned pig fetuses, we compared body weight, amniotic fluid (AF) metabolome, and placental transcriptome between SCNT- and artificial insemination (AI)-derived pig fetuses. Results showed that the body weight of SCNT pig fetuses was significantly lower than that of AI pig fetuses. The identified differential metabolites between the two groups of AF were mainly involved in bile acids and steroid hormones. The levels of all detected bile acids in SCNT AF were significantly higher than those in AI AF. The increase in the AF bile acid levels in SCNT fetuses was linked with the downregulation of placental bile acid transporter expression and the abnormal development of placental folds (PFs), both of which negatively affected the transfer of bile acids from AF across the placenta into the mother's circulation. Alteration in the AF steroid hormone levels in cloned fetuses was associated with decreased expression of enzymes responsible for steroid hormone biosynthesis in the placenta. In conclusion, cloned pig fetuses undergo abnormal intrauterine development associated with alteration of bile acid and steroid hormone levels in AF, which may be due to the poor development of PFs and the erroneous expression of bile acid transporters and enzymes responsible for steroid hormone biosynthesis in the placentas.
Question: Write a study description for the study titled 'Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative (Staphylococcus aureus 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 Staphylococcus aureus.GC-MS and LC-MS Staphylococcus aureus assays are reported in the current study MTBLS1898GC-MS and LC-MS Escherichia coli assays are reported in MTBLS2015GC-MS and LC-MS Klebsiella pneumoniae assays are reported in MTBLS2322GC-MS and LC-MS Streptococcus pneumoniae assays are reported in MTBLS2323GC-MS and LC-MS Streptococcus pyogenes assays are reported in MTBLS2324
Question: Write a study description for the study titled 'LC–MS-Based Metabolomics Discriminates Premium from Standard Chilean cv. Cabernet Sauvignon Wines from Different Valleys'.
Answer: Cabernet Sauvignon grapes in Chile, mainly grown between the 30 °S and 36 °S, account for more than 30% of Chilean wine production, and yield wines with different characteristics which influence their quality. The aim of this study was to apply an LC-MS based metabolomic protocol to investigate the quality differentiation in a sample set of monovarietal wines from eight valleys covering 679 km of the north-south extension. All samples were produced using a standardized red winemaking process and classified according to a company categorization in two major groups: premium and standard, and each group in two subcategories. The results pointed out that N-containing metabolites (mainly small peptides) are promising biomarkers for quality differentiation. Moreover, the premium wines were characterized by higher amounts of anthocyanins and other glycosylated and acetylated flavonoids, as well as phenolic acids; standard quality wines, on the other hand, presented stilbenoids and sulfonated catabolites of tryptophan and flavanols.
Question: Write a study description for the study titled 'Biosynthesis of Isonitrile Lipopeptides by Conserved Non-ribosomal Peptide Synthetase Gene Clusters in Actinobacteria'.
Answer: A putative lipopeptide biosynthetic gene cluster is conserved in many species of Actinobacteria, including Mycobacterium tuberculosis and Mycobacterium marinum, but the specific function of the encoding proteins has been elusive. Using both in vivo heterologous reconstitution and in vitro biochemical analyses, we have revealed that the five encoding biosynthetic enzymes are capable of synthesizing a new family of isonitrile lipopeptides (INLPs) through a thio-template mechanism. The biosynthesis features the generation of isonitrile from a single precursor Gly promoted by a thioesterase and a non-heme iron(II)-dependent oxidase homologue, and the acylation of both amino groups of Lys by the same isonitrile acyl chain facilitated by a single condensation domain of a non-ribosomal peptide synthetase (NRPS). In addition, the deletion of INLP biosynthetic genes in M. marinum has decreased the intracellular metal concentration, suggesting the role of this biosynthetic gene cluster in metal transport.
Question: Write a study description for the study titled 'Microbiome and Metabolome Integrated Analysis: Exploring Potential Diagnostic Approaches for Parkinson’s Disease Using Tongue Coating Samples'.
Answer: Parkinson's disease (PD) is a prevalent neurodegenerative disorder with complex pathogenesis and limited treatment options. The current reliance on clinical evaluation for diagnosis, due to the absence of reliable non-invasive methods, presents significant challenges. Traditional diagnostic approaches, including cerebrospinal fluid (CSF) or blood sampling, are invasive, pose risks of infection, are costly, and often require complex procedures. Tongue coating sampling offers a non-invasive, cost-effective and repeatable alternative, showing promise for early detection and monitoring of PD. This study explores the feasibility of using tongue coating samples as a diagnostic tool for PD through microbiome analysis, with metabolomics data providing additional context and validation via machine learning models.
Question: Write a study description for the study titled 'PRDM15 is a master regulator of metabolism essential to sustain B-cell lymphomagenesis'.
Answer: PRDM family members are sequence-specific transcriptional regulators involved in cell identity and fate determination and are often dysregulated in cancer. The PRDM15 gene is of particular interest, given its relatively low expression in adult tissues and its overexpression in follicular lymphomas (FL). Despite its well characterized role in stem cell biology and during early development, the role of PRDM15 in cancer remains obscure. Herein, we demonstrate that while PRDM15 is largely dispensable for mouse adult somatic cell homeostasis in vivo, it plays an essential role in B cell lymphomagenesis. Mechanistically, PRDM15 regulates a transcriptional program pertinent to the activity of the PI3K/AKT/mTOR pathway and glycolysis in B cell lymphomas. Abrogation of PRDM15 induces a metabolic crisis and selective death of lymphoma cells. Collectively, our data demonstrate that PRDM15 fuels the metabolic requirement of B cell lymphomas and validate it as an attractive and previously unrecognized target in oncology.
Question: Write a study description for the study titled 'Dysregulation of lipid metabolism and pathological inflammation in patients with COVID-19'.
Answer: In recent months, Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread throughout the world. COVID-19 patients show mild, moderate or severe symptoms with the latter ones requiring access to specialized intensive care. SARS-CoV-2 infections, pathogenesis and progression have not been clearly elucidated yet, thus forcing the development of many complementary approaches to identify candidate cellular pathways involved in disease progression. Host lipids play a critical role in the virus life, being the double-membrane vesicles a key factor in coronavirus replication. Moreover, lipid biogenesis pathways affect receptor-mediated virus entry at the endosomal cell surface and modulate virus propagation. In this study, targeted lipidomic analysis coupled with proinflammatory cytokines and alarmins measurement were carried out in serum of COVID-19 patients characterized by different severity degree. Serum IL-26, a cytokine involved in IL-17 pathway, TSLP and adiponectin were measured and correlated to lipid COVID-19 patient profiles. These results could be important for the classification of the COVID-19 disease and the identification of therapeutic targets.
Question: Write a study description for the study titled 'Exogenous L-Alanine promotes phagocytosis multidrug-resistant bacterial pathogens (V. parahaemolyticus-infected spleen metabolomics)'.
Answer: Multidrug-resistant bacteria present a major threat to public health. Therefore, new drugs or approaches are urgently needed to manage and mitigate this threat. Here, we screen the molecular candidates that allow the survival of mice upon Vibrio parahaemolyticus infection by integrated proteomic and metabolomics analysis, where L-Alanine metabolism and phagocytosis are highly correlated. The role of L-Alanine on boosting mouse survival is further confirmed with in vivo bacterial challenge studies on bacteria including V. parahaemolyticus, Escherichia coli, Pseudomonas aeruginosa and Klebsiella pneumoniae. Functional studies demonstrate that exogenous L-Alanine promotes phagocytosis to these different species of multidrug-resistant pathogens. The underlying mechanism involves two events that are L-Alanine-dependently increased TLR4 expression and L-Alanine-enhanced TLR4 signaling via increasing the biosynthesis and secretion of fatty acids such as palmitate. Palmitate enhances the binding of LPS to TLR4 and thereby promotes TLR4 dimmer formation and endocytosis for the subsequent activation of PI3K/Akt and NF-κB pathways and phagocytosis of bacteria. These results suggest that modulation of metabolic environment is a plausible approach for combating infection with multidrug-resistant bacteria.V. parahaemolyticus-infected spleen metabolomics is reported in the current study MTBLS7996.L-Alanine-treated macrophage metabolomics is reported in MTBLS7986.
Question: Write a study description for the study titled 'Unexpected similarities between the Schizosaccharomyces and human blood metabolomes, and novel human metabolites (Blood plasma and RBC fractions)'.
Answer: Metabolomics, a new branch of chemical biology, provides compositional and quantitative information about the state of organism or cell at the levels of metabolite constituents. We here report non-targeted metabolome of human blood that is made up of plasma and red blood cells (RBCs), using liquid-chromatography and mass spectrometry (LC-MS). Previously, metabolome of a microbe, the fission yeast Schizosaccharomyces pombe, was reported. Two sets of metabolome results are highly similar in their compositions: among 133 compounds identified in human blood, 101 (75%) are also present in S. pombe, and among 57 compounds enriched in RBC, 45 (78%) are also present in S. pombe. Most abundant metabolites are ATP, glutathione and glutamine. Many of other relatively abundant metabolites identified are also implicated in energy, anti-oxidant and amino acid metabolism. We show fourteen newly-identified blood compounds; citramalate, GDP-glucose, trimethyl-histidine, trimethyl-phenylalanine, trimethyl-tryptophan, trimethyl-tyrosine, UDP-acetyl-glucosamine, UDP-glucuronate, dimethyl-lysine, glutamate methyl ester, N-acetyl-(iso)leucine, N-acetyl-glutamate, N2-acetyl-lysine, and N6-acetyl-lysine (the first eight are enriched in RBC). Ten of them are also detected in S. pombe, and ten of them are methylated or acetylated, amino acids. Trimethylated or acetylated free amino acids are also abundant in white blood cell. Their physiologic role may be investigated in the future by yeast genetics.  Blood was separated by low speed (120 x g) centrifugation for 15 min. Resulting supernatant (plasma fraction) and pellet (RBC fraction) were collected (each 0.2 ml). Blood was donated four times within 24 hours bysingle person, samples were processed separetely. By measuring metabolites we could determine their distribution between plasma and RBC fractions.
Question: Write a study description for the study titled 'Rare and common genetic determinants of metabolic individuality and their effects on human health (EPIC-Norfolk study assays)'.
Answer: Garrod’s concept of “chemical individuality” has contributed to comprehension of the molecular origins of human diseases. Untargeted high-throughput metabolomic technologies provide an in-depth snapshot of human metabolism at scale. We studied the genetic architecture of the human plasma metabolome using 913 metabolites assayed in 19,994 individuals and identified 2,599 variant-metabolite associations (P<1.25x10^-11) within 330 genomic regions, with rare variants (MAF≤1%) explaining 9.4% of associations. Jointly modelling metabolites in each region, we identified 423 regional, co-regulated, variant-metabolite clusters called GIMs (Genetically Influenced Metabotypes). We assigned causal genes for 62.4% of GIMs, providing new insights into fundamental metabolite physiology and their clinical relevance, including metabolite guided discovery of potential adverse drug effects (DPYD, SRD5A2). We show strong enrichment of Inborn Errors of Metabolism (IEM)-causing genes, with examples of metabolite associations and clinical phenotypes of non-pathogenic variant carriers matching characteristics of IEMs. Systematic, phenotypic follow-up of metabolite-specific genetic scores revealed multiple potential aetiological relationships.EPIC-Norfolk study assays are reported in the current study MTBLS833INTERVAL study assays are reported in MTBLS834
Question: Write a study description for the study titled 'Metabolon template'.
Answer: Insert information here such as publication abstract
Question: Write a study description for the study titled 'The Kalanchoe genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism'.
Answer: Crassulacean acid metabolism (CAM) is a water-use efficient adaptation of photosynthesis that has evolved independently many times in diverse lineages of flowering plants. We hypothesize that convergent evolution of protein sequence and temporal gene expression underpins the independent emergences of CAM from C3 photosynthesis. To test this hypothesis, we generated a de novo genome assembly and genome-wide transcript expression data for Kalanchoe fedtschenkoi, an obligate CAM species within the core eudicots with a relatively small genome (~260 Mb). Our comparative analyses identified signatures of convergence in protein sequence and re-scheduling of diel transcript expression of genes involved in nocturnal CO2 fixation, stomatal movement, heat tolerance, circadian clock and carbohydrate metabolism in K. fedtschenkoi and other CAM species in comparison with non-CAM species. These findings provide new insights into molecular convergence and building blocks of CAM and will facilitate CAM-into-C3 photosynthesis engineering to enhance water-use efficiency in crops.
Question: Write a study description for the study titled 'Metabolomics analyses of cancer tissue from patients with colorectal cancer.'.
Answer: The alteration of metabolism is essential for the initiation and progression of numerous types of cancer, including colorectal cancer (CRC). Metabolomics has been used to study CRC. At present, the reprogramming of the metabolism in CRC remains to be fully elucidated. In the present study, comprehensive untargeted metabolomics analysis was performed on the paired CRC tissues and adjacent normal tissues from patients with CRC (n=35) using ultra‑high‑performance liquid chromatography‑mass spectrometry. Subsequently, bioinformatic analysis was performed on the differentially expressed metabolites. The changes in these differential metabolites were compared among groups of patients based on sex, anatomical tumor location, grade of tumor differentiation and stage of disease. A total of 927 metabolites were detected in the tissue samples, and 24 metabolites in the CRC tissue were significantly different compared with the adjacent normal tissue. The present study revealed that the levels of three amino acid metabolites were increased in the CRC tissue, specifically, N‑α‑acetyl‑ε‑(2‑propenal)‑Lys, cyclo(Glu‑Glu) and cyclo(Phe‑Glu). The metabolites with decreased levels in the CRC tissue included quinaldic acid (also referred to as quinoline‑2‑carboxilic acid), 17α‑ and 17β‑estradiol, which are associated with tumor suppression activities, as well as other metabolites such as, anhydro‑β‑glucose, Asp‑Arg, lysophosphatidylcholine, lysophosphatidylethanolamine (lysoPE), lysophosphatidylinositol, carnitine, 5'‑deoxy‑5'‑(methylthio) adenosine, 2'‑deoxyinosine‑5'‑monophosphate and thiamine monophosphate. There was no difference in the levels of the differential metabolites between male and female patients. The differentiation of CRC also showed no impact on the levels of the differential metabolites. The levels of lysoPE were increased in the right side of the colon compared with the left side of the colon and rectum. Analysis of the different tumor stages indicated that 2‑aminobenzenesulfonic acid, P‑sulfanilic acid and quinoline‑4‑carboxylic acid were decreased in stage I CRC tissue compared with stage II, III and IV CRC tissue. The levels of N‑α‑acetyl‑ε‑(2‑propenal)‑Lys, methylcysteine and 5'‑deoxy‑5'‑(methylthio) adenosine varied at different stages of tumorigenesis. These differential metabolites were implicated in multiple metabolism pathways, including carbohydrate, amino acid, lipid, nucleotide and hormone. In conclusion, the present study demonstrated that CRC tumors had altered metabolites compared with normal tissue. The data from the metabolic profile of CRC tissues in the present study provided supportive evidence to understand tumorigenesis.
Question: Write a study description for the study titled 'Seagrass excretes sugars to their rhizosphere making them the sweet spots in the sea (Plant tissues; GC-MS assay)'.
Answer: Seagrasses are one of the most efficient natural sinks of carbon dioxide (CO2) on Earth. Despite covering less than 0.1% of coastal regions, they have the capacity to bury up to 10% of marine organic matter and can bury the same amount of carbon 35 times faster than tropical rainforests. On land, the soil’s ability to sequestrate carbon is intimately linked to microbial metabolism. Despite the growing attention to the link between plant production, microbial communities, and the carbon cycle in terrestrial ecosystems, these processes remain enigmatic in the sea. Here, we show that seagrasses excrete organic sugars, namely in the form of sucrose, into their rhizospheres. Surprisingly, the microbial communities living underneath meadows do not fully use this sugar stock in their metabolism. Instead, sucrose piles up in the sediments to mM concentrations underneath multiple types of seagrass meadows. Sediment incubation experiments show that microbial communities living underneath a meadow use sucrose at low metabolic rates. Our metagenomic analyses revealed that the distinct community of microorganisms occurring underneath meadows is limited in their ability to degrade simple sugars, which allows these compounds to persist in the environment over relatively long periods of time. Our findings reveal how seagrasses form blue carbon stocks despite the relatively small area they occupy. Unfortunately, anthropogenic disturbances are threatening the long-term persistence of seagrass meadows. Given that these sediments contain a large stock of sugars that heterotopic bacteria can degrade, it is even more important to protect these ecosystems from degradation.GC-MS assay of Plant tissues is reported in the current study MTBLS1579GC-MS assay of Seawater sediment is reported in MTBLS1570GC-MS assay of Sediment porewater is reported in MTBLS1610MALDI-MSI assay of Plant roots is reported in the MTBLS1746
Question: Write a study description for the study titled 'Comparison of Two Different Astragali Radix by 1H NMR based Metabolomic Approach'.
Answer: Astragali Radix (AR) is a commonly used herbal drug in Traditional Chinese Medicine, and widely used for the treatment of diabetes, cardiovascular diseases, nephropathy and neuropathy. The main source of AR is the dried root of Astragalus membranaceus var. mongholicus (Bge.) Hsiao in China, and both cultivated and wild ARs are used in the clinic. Systematic comparison of cultivated AR and wild AR should be performed to ensure the efficacy and safety in clinic. In this study, the chemical compositions of two different ARs, collected in Shanxi (wild) and Gansu (cultivated) Provinces, were compared by NMR based metabolic fingerprint coupled with multivariate analysis. Then SX-AR and GS-AR induced metabolic changes of endogenous metabolites in mice were also compared. The results showed that SX-AR and GS-AR differed significantly not only in the primary metabolites, but also the secondary metabolites. However, alterations of endogenous metabolites in serum, lung, liver and spleen were relatively small between them. This study provided a novel and valuable method for consistency and diversity evaluation of herbal drugs, and further studies should be conducted on the difference of polysaccharide as well as biological effect between the two kinds of ARs.