LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'MaHPIC Experiment 30: Quantitative Metabolomics from the pilot experiment for Macaca mulatta infected with Plasmodium knowlesi Malayan strain sporozoites to produce and integrate clinical, hematological, parasitological, omics, telemetric and histopathological measures of acute primary infection'.
Answer: Telemetry devices (DSI, model L11) with blood pressure sensors and electrocardiogram (ECG) leads were surgically implanted in two malaria-naive male rhesus macaques (Macaca mulatta), approximately three years of age. After a resting period of two weeks, physiological data that include activity, temperature, ECG, and blood pressure were continuously collected. Two weeks after activation of the telemetry implant, the macaques were inoculated intravenously with cryopreserved P. knowlesi Malayan strain salivary gland sporozoites, obtained from Anopheles dirus infected with parasites from the Pk1A+ clone. The P. knowlesi sporozoites were produced, isolated and cryopreserved at the Centers for Disease Control and Prevention. After inoculation, the macaques were profiled for clinical, hematological, parasitological, immunological, functional genomic, lipidomic, proteomic, metabolomic, telemetric and histopathological measurements. The experiment was designed for pathology studies, with terminal necropsies on days 11 (RKy15) or 19 (Red16). The anti-malarial drug artemether was subcuratively administered selectively to one subject (REd16) during the primary parasitemia to suppress clinical complications. Capillary blood samples were collected daily for the measurement of complete blood counts, reticulocytes, and parasitemias. Capillary blood samples were collected every other day to obtain plasma for metabolomic analysis. Venous blood and bone marrow samples were collected at five timepoints for functional genomic, proteomic, lipidomic, and immunological analyses. Physiological data were continuously captured via telemetry. Within the MaHPIC, this project is known as 'Experiment 30'. This dataset was produced by Dr. Regina Cordy and Manoj Khadka at Emory University. To access other publicly available results from 'E30' and other MaHPIC Experiments, including clinical results (specifics on drugs administered, diet, and veterinary interventions), and other omics, visit http://plasmodb.org/plasmo/mahpic.jsp. This page will be updated as datasets are released to the public. The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC) and the MRMC Office of Research Protection Animal Care and Use Review Office (ACURO). Linked Studies: Malaria Host-Pathogen Interaction Center (MaHPIC)
Question: Write a study description for the study titled 'Chlorophyll biosynthesis under the control of arginine metabolism.'.
Answer: In natural environments, photosynthetic organisms adjust their metabolism to cope with the fluctuating availability of combined nitrogen sources, a growth-limiting factor. For acclimation, the dynamic degradation/synthesis of tetrapyrrolic pigments, as well as of the amino acid arginine, is pivotal; however, there has been no evidence that these processes could be functionally coupled. Using co-immunopurification and spectral shift assays, we found that in the cyanobacterium Synechocystis sp. PCC 6803, the arginine metabolism-related ArgD and CphB enzymes form protein complexes with Gun4, an essential protein for chlorophyll biosynthesis. Gun4 binds ArgD with high affinity, and the Gun4-ArgD complex accumulates in cells supplemented with ornithine, a key intermediate of the arginine pathway. Elevated ornithine levels restricted de novo synthesis of tetrapyrroles, which arrested the recovery from nitrogen deficiency. Our data reveal a direct crosstalk between tetrapyrrole biosynthesis and arginine metabolism that highlights the importance of balancing photosynthetic pigment synthesis with nitrogen homeostasis.
Question: Write a study description for the study titled 'A Combined LC-MS Metabolomics- and 16S rRNA Sequencing Platform to Assess Interactions between Herbal Medicinal Products and Human Gut Bacteria in Vitro: a Pilot Study on Willow Bark Extract'.
Answer: Herbal preparations are complex mixtures of natural products, many of which are able to reach the distal gut. There, they influence the microbial communities, and can be metabolized into bioactive metabolites. The aim of this study was to establish an interdisciplinary platform to unravel interactions of herbal medicine and intestinal microbiota, using a combined LC-MS metabolomics and 16S rRNA microbiome sequencing approach. Willow bark extract (WBE), a herbal medicinal product with well-established anti-inflammatory activity, was incubated with human fecal suspension under anoxic conditions. Samples were drawn after 0.5, 4 and 24 h of incubation.Microbiome analyses revealed that incubation with WBE had a marked effect on microbial community composition and functions. In particular, the proportion of Bacterioides sp., generally regarded as beneficial for the gut ecosystem, was clearly enhanced in WBE-treated samples. LC-MS analysis showed that WBE constituents were readily metabolized by fecal bacteria. Numerous microbial metabolites could be annotated, allowing the construction of putative microbial degradation pathways for the main groups of WBE constituents.We suggest that studies of this type help to increase the knowledge on bioactive principles of herbal medicine, since gut microbial metabolites have certainly been underestimated as a source of bioactive compounds in the past.
Question: Write a study description for the study titled 'Biological Characteristics of SARS-CoV-2 Resistant Populations: A Cohort Comparison Study through Integrated Gut Microbiota Sequencing, Metabolomics and Proteomics'.
Answer: Objective: Most research reports on COVID-19 infections have focused on the correlation between the severity of the disease symptoms and immune deficits, while the mechanisms affecting the susceptibility to SARS-CoV-2 remain largely unknown. The study aimed to comprehensively analyze the differences in immunity, gut microbiota, metabolism, and proteomics between the SARS-CoV-2 resistant population and susceptible population. Methods and Results: In this cohort comparison study, participants were rigorously selected based on inclusion and exclusion criteria in a continuous enrollment manner through continuous enrollment using combined questionnaires and clinical data, ultimately including 25 SARS-CoV-2 resistant volunteers versus 16 SARS-CoV-2 infected patients.The clinical information of the participants was recorded in detail, and fecal and blood samples were collected in a standardized manner for subsequent multi omics analysis, including gut microbiota sequencing, metabolomics, and proteomics. This study has preliminarily elucidated the characteristics of the gut microbiota, serum metabolites, and serum proteins in the SARS-CoV-2 resistant population. It exhibits a unique metabolic signature characterized by elevated levels of serum phosphatidylinositol and the abundance of Prevotella, which may serve as a potential predictive biomarker for resistance to SARS-CoV-2. Conclusion: Given the crucial role of phosphatidylinositol in cell membrane architecture and viral infectivity, this study provides a promising entry point for further research into the pathogenesis and prevention strategies of COVID-19.
Question: Write a study description for the study titled 'Comparative metabolomic analysis of exudates of microcystin-producing and microcystin-free Microcystis aeruginosa strains'.
Answer: Cyanobacterial harmful algal blooms (cHABs) dominated by Microcystis aeruginosa threaten the ecological integrity and beneficial uses of lakes globally. In addition to producing hepatotoxic microcystins (MC), M. aeruginosa exudates (MaE) contain various compounds with demonstrated toxicity to aquatic biota. Previously, we found that the ecotoxicity of MaE differed between MC-producing and MC-free strains at exponential (E-phase) and stationary (S-phase) growth phases. However, the components in these exudates and their specific harmful effects were unclear. In this study, we performed untargeted metabolomics based on liquid chromatography-mass spectrometry to reveal the constituents in MaE of a MC-producing and a MC-free strain at both E-phase and S-phase. A total of 409 metabolites were identified and quantified based on their relative abundance. These compounds included lipids, organoheterocyclic compounds, organic acid, benzenoids and organic oxygen compounds. Multivariate analysis revealed that strains and growth phases significantly influenced the metabolite profile. The MC-producing strain had greater total metabolites abundance than the MC-free strain at S-phase, whereas the MC-free strain released higher concentrations of benzenoids, lipids, organic oxygen, organic nitrogen and organoheterocyclic compounds than the MC-producing strain at E-phase. Total metabolites had higher abundance in S-phase than in E- phase in both strains. Analysis of differential metabolites (DMs) and pathways suggest that lipids metabolism and biosynthesis of secondary metabolites were more tightly coupled to growth phases than to strains. Abundance of some toxic lipids and benzenoids DMs were significantly higher in the MC-free strain than the MC-producing one. This study builds on the understanding of MaE chemicals and their biotoxicity, and adds to evidence that non-MC-producing strains of cyanobacteria may also pose a threat to ecosystem health.
Question: Write a study description for the study titled 'GREM1 Deficiency induced Bone Marrow Adipose Niche promotes B-cell Acute Lymphoblastic Leukemia Disease Progression'.
Answer: Relapse and disease progression are the primary causes of treatment failure and subsequent mortality in children B-cell acute lymphocytic leukemia (B-ALL). At diagnosis and during treatment, the bone marrow adipose microenvironment is commonly observed in pediatric leukemia. However, the relationship between the bone marrow adipose microenvironment and disease progression is still not well understood.
Question: Write a study description for the study titled 'Therapeutic Effect of Buyang Huanwu Decoction on the Gut Microbiota and Hippocampal Metabolism in a Rat Model of Cerebral Ischemia'.
Answer: Buyang Huanwu decoction (BHD) is a well-known Chinese herbal prescription. It has been widely used in the clinical treatment of cerebral ischemia (CI) in China. However, the mechanism underlying the treatment of CI with BHD remains to be elucidated. In this study, we combined microbiomic and metabolomic strategies to explore the therapeutic effects of BHD on middle cerebral artery occlusion (MCAO) in rats. Our results showed that BHD could effectively improve neurological severity scores and alleviate neuronal damage in rats with MCAO. BHD could also reduce the level of peripheral proinflammatory cytokines and inhibit neuroinflammation. 16S rRNA sequencing showed that BHD could increase the relative abundances of the genera Lactobacillus, Faecalibacterium, Ruminococcaceae_UCG-002, etc., while decreasing the relative abundances of the genera Escherichia-Shigella, Klebsiella, Streptococcus, Coprococcus_2, Enterococcus, etc. Untargeted metabolomic analysis of hippocampal samples showed that 17 significantly differentially abundant metabolites and 9 enriched metabolic pathways were linked with BHD treatment. We also found that the regulatory effects of BHD on metabolites were correlated with the differentially abundant microbial taxa. The predicted function of the gut microbiota and the metabolic pathway enrichment results showed that purine metabolism, glutamatergic synapses, arginine and proline metabolism, and alanine, aspartic acid and glutamate metabolism were involved in the effects of BHD. These pathways may be related to pathological processes such as excitotoxicity, neuroinflammation, and energy metabolism disorder in CI. In summary, these findings suggest that regulation of hippocampal metabolism and of the composition and function of the gut microbiota may be important mechanisms underlying the effect of BHD in the treatment of CI.
Question: Write a study description for the study titled 'BCAA insufficiency leads to premature ovarian insufficiency via ceramide-induced elevation of ROS (targeted metabolomics)'.
Answer: Premature ovarian insufficiency (POI) is a disease featured by early menopause before 40 years of age, accompanied by an elevation of follicle-stimulating hormone. Though POI affects many aspects of women's health, its major causes remain unknown. Many clinical studies have shown that POI patients are generally underweight, indicating a potential correlation between POI and metabolic disorders. To understand the pathogenesis of POI, we performed metabolomics analysis on serum and identified branch-chain amino acid (BCAA) insufficiency-related metabolic disorders in two independent cohorts from two clinics. A low BCAA diet phenotypically reproduced the metabolic, endocrine, ovarian and reproductive changes of POI in young C57BL/6J mice. A mechanism study revealed that the BCAA insufficiency-induced POI is associated with abnormal activation of the ceramide-reactive oxygen species (ROS) axis and consequent impairment of ovarian granulosa cell function. Significantly, the dietary supplement of BCAA prevented the development of ROS-induced POI in female mice. The results of this pathogenic study will lead to the development of specific therapies for POI.Targeted metabolomics is reported in the current study MTBLS6267.Untargeted lipidomics is reported in MTBLS6249.
Question: Write a study description for the study titled 'Cyclooxygenase-2, Asymmetric Dimethylarginine, and the Cardiovascular Hazard From Nonsteroidal Anti-Inflammatory Drugs (Murine kidney and plasma UPLC-MS/MS assay)'.
Answer: "BACKGROUND: Large-scale, placebo-controlled trials established that nonsteroidal anti-inflammatory drugs confer a cardiovascular hazard: this has been attributed to depression of cardioprotective products of cyclooxygenase (COX)-2, especially prostacyclin. An alternative mechanism by which nonsteroidal anti-inflammatory drugs might constrain cardioprotection is by enhancing the formation of methylarginines in the kidney that would limit the action of nitric oxide throughout the vasculature.METHODS: Targeted and untargeted metabolomics were used to investigate the effect of COX-2 deletion or inhibition in mice and in osteoarthritis patients exposed to nonsteroidal anti-inflammatory drugs on the l-arginine/nitric oxide pathway.RESULTS: Analysis of the plasma and renal metabolome was performed in postnatal tamoxifen-inducible Cox-2 knockout mice, which exhibit normal renal function and blood pressure. This revealed no changes in arginine and methylarginines compared with their wild-type controls. Moreover, the expression of genes in the l-arginine/nitric oxide pathway was not altered in the renal medulla or cortex of tamoxifen inducible Cox-2 knockout mice. Therapeutic concentrations of the selective COX-2 inhibitors, rofecoxib, celecoxib, and parecoxib, none of which altered basal blood pressure or renal function as reflected by plasma creatinine, failed to elevate plasma arginine and methylarginines in mice. Finally, plasma arginine or methylarginines were not altered in osteoarthritis patients with confirmed exposure to nonsteroidal anti-inflammatory drugs that inhibit COX-1 and COX-2. By contrast, plasma asymmetrical dimethylarginine was increased in mice infused with angiotensin II sufficient to elevate blood pressure and impair renal function. Four weeks later, blood pressure, plasma creatinine, and asymmetrical dimethylarginine were restored to normal levels. The increase in asymmetrical dimethylarginine in response to infusion with angiotensin II in celecoxib-treated mice was also related to transient impairment of renal function.CONCLUSIONS: Plasma methylarginines are not altered by COX-2 deletion or inhibition but rather are elevated coincident with renal compromise.Murine kidney and plasma UPLC-MS/MS assay protocols and data are reported in the current study MTBLS680.Murine and human plasma quantitative L-arginine and methylarginines UPLC-MS/MS assay protocols and data are reported in MTBLS685."
Question: Write a study description for the study titled 'Investigation of Brazilian grape juice metabolomic profile changes caused by methyl jasmonate pre-harvest treatment'.
Answer: Grape juice is a major source of potential health-promoting bioactive polyphenols, especially for children and those who do not consume wine. Since the subtropical climate may negatively affect the concentrations of grape polyphenols, especially anthocyanins, elicitors such as methyl jasmonate (MeJa) could be used to promote polyphenol biosynthesis. This work aimed at investigating the impact of MeJa treatment on grape juice produced via a traditional low-cost process from two Vitis labrusca cultivars and in two Brazilian regions. The untargeted LC-MS analytical protocol demonstrated that Isabel Precoce juices strongly benefited from MeJa treatment, especially regarding their anthocyanic profile, regardless of the cultivation region. Known MeJa markers in wine and V. vinifera grapes (flavanols, flavonols and stilbenes) in this experiment had mixed behaviours depending on the region/variety/cultivation. Moreover, it was found that all the detected hydroxycinnamates were influenced by the treatment, especially the concentration of their glucosides, which was increased. Glutathione, 2-S-glutathionyl caftaric acid and indole lactic acid glucoside were identified for the first time as MeJa treatment biomarkers in grape products, indicating a possible positive effect on juice antioxidant properties.
Question: Write a study description for the study titled 'Integration of metabolomics, genomics and immune phenotypes reveals the causal roles of metabolites in disease'.
Answer: BACKGROUND: Recent studies highlight the role of metabolites in immune diseases, but it remains unknown how much of this effect is driven by genetic and non-genetic host factors.RESULT: We systematically investigate circulating metabolites in a cohort of 500 healthy subjects (500FG) in whom immune function and activity are deeply measured and whose genetics are profiled. Our data reveal that several major metabolic pathways, including the alanine/ glutamate pathway and the arachidonic acid pathway, have a strong impact on cytokine production in response to ex vivo stimulation. We also examine genetic regulation of metabolites associated with immune phenotypes through genome-wide association analysis and identify 29 significant loci, including eight novel independent loci. Of these, one locus (rs174584-FADS2) associated with arachidonic acid metabolism is causally associated with Crohn’s disease, suggesting it is a potential therapeutic target.CONCLUSION: This study provides a comprehensive map of the integration between the blood metabolome and immune phenotypes, reveals novel genetic factors that regulate blood metabolite concentrations, and proposes an integrative approach for identifying new disease treatment targets.
Question: Write a study description for the study titled 'Biochemical Profiling of the Brain and Blood Metabolome in a Mouse Model of Prodromal Parkinson’s Disease Reveals Distinct Metabolic Profiles (MS assays)'.
Answer: Parkinson’s disease is the second most common neurodegenerative disease. In the vast majority of cases the origin is not genetic and the cause is not well understood, although progressive accumulation of α-synuclein aggregates appears central to the pathogenesis. Currently, treatments that slow disease progression are lacking, and there are no robust biomarkers that can facilitate the development of such treatments or act as aids in early diagnosis. Therefore, we have defined metabolomic changes in the brain and serum in an animal model of prodromal Parkinson’s disease. We biochemically profiled the brain tissue and serum in a mouse model with progressive synucleinopathy propagation in the brain triggered by unilateral injection of preformed α-synuclein fibrils in the olfactory bulb. In total, we accurately identified and quantified 71 metabolites in the brain and 182 in serum using 1H NMR and targeted mass spectrometry, respectively. Using multivariate analysis, we accurately identified which metabolites explain the most variation between cases and controls. Using pathway enrichment analysis, we highlight significantly perturbed biochemical pathways in the brain and correlate these with the progression of the disease. Furthermore, we identified the top six discriminatory metabolites and were able to develop a model capable of identifying animals with the pathology from healthy controls with high accuracy (AUC (95% CI) = 0.861 (0.755–0.968)). Our study highlights the utility of metabolomics in identifying elements of Parkinson’s disease pathogenesis and for the development of early diagnostic biomarkers of the disease.  MS assays are reported in the current study MTBLS674  NMR assay is reported in MTBLS640.  Linked Studies: MTBLS640
Question: Write a study description for the study titled 'Untargeted metabolomics sheds light on the secondary metabolism of fungi triggered by choline-based ionic liquids'.
Answer: Fungal secondary metabolites constitute a rich source of yet undiscovered bioactive compounds. Their production is often silent under standard laboratory conditions, but the production of some compounds can be triggered simply by altering the cultivation conditions. The usage of an organic salt - ionic liquid – as growth medium supplement can greatly impact the biosynthesis of secondary metabolites, leading to higher diversity of compounds accumulating extracellularly. This study examines if such supplements, specifically cholinium-based ionic liquids, can support the discovery of bioactive secondary metabolites across three model species: Neurospora crassa, Aspergillus nidulans and Aspergillus fumigatus. Enriched organic extracts obtained from medium supernatant revealed high diversity in metabolites. The supplementation led apparently to increased levels of either 1-aminocyclopropane-1-carboxylate or α-aminoisobutyric acid. The extracts where bioactive against two major foodborne bacterial strains: Staphylococcus aureus and Escherichia coli. In particular, those retrieved from N. crassa cultures showed greater bactericidal potential compared to control extracts derived from non-supplemented cultures. An untargeted mass spectrometry analysis using the Global Natural Product Social Molecular Networking tool enabled to capture the chemical diversity driven by the ionic liquid stimuli. Diverse macrolides, among other compounds, were putatively associated with A. fumigatus; whereas an unexpected richness of cyclic (depsi)peptides with N. crassa. Further studies are required to understand if the identified peptides are the major players of the bioactivity of N. crassa extracts, and to decode their biosynthesis pathways as well.