LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'The putative ceramide-conjugation protein Cwh43 regulates G0 quiescence, nutrient metabolism and lipid homeostasis in fission yeast (Lipidome assay)'.
Answer: Cellular nutrient states control whether cells proliferate, or whether they enter or exit quiescence. Here, we report characterizations of fission yeast temperature-sensitive (ts) mutants of the evolutionarily conserved transmembrane protein, Cwh43, and explore its relevance to utilization of glucose, nitrogen-source, and lipids. GFP-tagged Cwh43 localizes at ER associated with the nuclear envelope and the plasma membrane, as in budding yeast. We found that cwh43 mutants failed to divide in low glucose and lost viability during quiescence under nitrogen starvation. In cwh43 mutant, comprehensive metabolome analysis demonstrated dramatic changes in marker metabolites that altered under low glucose and/or nitrogen starvation, although cwh43 apparently consumed glucose in the culture media. Furthermore, we found that cwh43 mutant had elevated levels of triacylglycerols (TGs) and coenzyme A, and that it accumulated lipid droplets. Notably, TG biosynthesis was required to maintain cell division in cwh43 mutant. Thus, Cwh43 affects utilization of glucose and nitrogen-sources, as well as storage lipid metabolism. These results may fit to a notion developed in budding yeast that Cwh43 conjugates ceramide to GPI (glycosylphosphatidylinositol)-anchored proteins and maintains integrity of membrane organization.  Lipidome assay data is reported in the current study MTBLS578.  Metabolome assay data associated to this study is reported in MTBLS577.  Linked Studies: MTBLS577
Question: Write a study description for the study titled 'Mapping immune variation and var gene switching in naive hosts infected with Plasmodium falciparum'.
Answer: Falciparum malaria is clinically heterogeneous and the relative contribution of parasite and host in shaping disease severity remains unclear. We explored the interaction between inflammation and parasite variant surface antigen (VSA) expression, asking whether this relationship underpins the variation observed in controlled human malaria infection (CHMI). We uncovered marked heterogeneity in the host response to blood challenge; some volunteers remained quiescent, others triggered interferon-stimulated inflammation and some showed transcriptional evidence of myeloid cell suppression. Significantly, only inflammatory volunteers experienced hallmark symptoms of malaria. When we tracked temporal changes in parasite VSA expression to ask whether variants associated with severe disease rapidly expand in naive hosts, we found no transcriptional evidence to support this hypothesis. These data indicate that parasite variants that dominate severe malaria do not have an intrinsic growth or survival advantage; instead, they presumably rely upon infection-induced changes in their within-host environment for selection.
Question: Write a study description for the study titled 'DIATAGeR: Triacylglycerol Annotation of Data-Independent Acquisition based Lipidomics'.
Answer: Triacylglycerols (TGs) are the most abundant lipids in the human body and the primary source of energy storage. Altered TGs are implicated in metabolic syndrome and detailed structural information may provide novel insights into diseases pathology. TGs are comprised of three fatty acyls with various lengths and double bond composition, complicating structural annotation. DIA-based lipidomics enables a continuous and unbiased acquisition of all TGs, creating the potential for more comprehensive TG analysis. However, DIA generates multiplexed tandem mass spectra (MS2) that pose challenges to identifying TGs. Here, we present DIATAGeR, an R package aimed to automate and improve TG identification to the molecular species level in DIA-based lipidomics. With DIATAGeR, TGs are identified using a TG-centric approach, where each TG in the reference database is considered as an analysis target, searched in DIA spectra, and scored using a logistic regression machine learning algorithm. Additionally, DIATAGeR uses an FDR correction calculated by a target-decoy approach to improve the confidence of TG identification and limit false positives due to interference from unrelated ions. The performance of DIATAGeR was validated in a lipidomic study of liver and plasma samples from mice with metabolic dysfunction-associated steatohepatitis (MASH) and healthy controls. All 9 TG standards were annotated at an FDR < 0.1 in both datasets. When benchmarked against MS-DIAL, TGs identified by DIATAGeR contained 16% and 12% more even-carbon fatty acyls in liver and plasma datasets, respectively. DIATAGeR is a valuable tool for streamlining complex TG annotation in DIA-lipidomics data and freely available at https://github.com/Velenosi-Lab/DIATAGeR.
Question: Write a study description for the study titled 'Quantitative LC-MS study of compounds found predictive of COVID-19 severity and outcome'.
Answer: INTRODUCTION: Since the beginning of the SARS-CoV-2 pandemic in December 2019 multiple metabolomics studies have proposed predictive biomarkers of infection severity and outcome. Whilst some trends have emerged, the findings remain intangible and uninformative when it comes to new patients.OBJECTIVES: In this study, we accurately quantitate a subset of compounds in patient serum that were found predictive of severity and outcome.METHODS: A targeted LC-MS method was used in 46 control and 95 acute COVID-19 patient samples to quantitate the selected metabolites. These compounds included tryptophan and its degradation products kynurenine and kynurenic acid (reflective of immune response), butyrylcarnitine and its isomer (reflective of energy metabolism) and finally 3’,4’-didehydro-3’-deoxycytidine, a deoxycytidine analogue, (reflective of host viral defence response). We subsequently examine changes in those markers by disease severity and outcome relative to those of control patients’ levels.RESULTS & CONCLUSION: Finally, we demonstrate the added value of the kynurenic acid / tryptophan ratio for severity and outcome prediction and highlight the viral detection potential of ddhC.
Question: Write a study description for the study titled '"Fuel for the Damage Induced"""": Untargeted Metabolomics in Elite Rugby Union Match Play"'.
Answer: The metabolic perturbations caused by competitive rugby are not well characterized. Our aim is to utilize untargeted metabolomics to develop appropriate interventions, based on the metabolic fluctuations that occur in response to this collision-based team sport. Seven members of an English Premiership rugby squad consented to provide blood, urine, and saliva samples daily, over a competitive week including gameday (GD), with physical demands and dietary intake also recorded. Sample collection, processing and statistical analysis were performed in accordance with best practice set out by the metabolomics standards initiative employing 700 MHz NMR spectroscopy. Univariate and multivariate statistical analysis were employed to reveal the acute energy needs of this high intensity sport are met via glycolysis, the TCA cycle and gluconeogenesis. The recovery period after cessation of match play and prior to training recommencing sees a re-entry to gluconeogenesis, coupled with markers of oxidative stress, structural protein degradation, and reduced fatty acid metabolism. This novel insight leads us to propose that effective recovery from muscle damaging collisions is dependent upon the availability of glucose. An adjustment in the periodisation of carbohydrate to increase GD+1 provision may prevent the oxidation of amino acids which may also be crucial to allay markers of structural tissue degradation. Should we expand the 'Fuel for the work required' paradigm in collision-based team sports to include 'Fuel for the damage induced'?
Question: Write a study description for the study titled 'Post-mortem changes in metabolomic profiles of human serum, aqueous humor and vitreous humor'.
Answer: INTRODUCTION: Application of metabolomic methods to forensic studies may expand the limits of the post-mortem interval (PMI) estimation, and improve the accuracy of the estimation. To this end, it is important to determine which tissue is the most suitable for analysis, and which compounds are the most promising candidates for PMI estimation.OBJECTIVES: This work is aimed at the comparison of human serum, aqueous humor (AH), and vitreous humor (VH) as per- spective tissues for metabolomic-based PMI estimation, at the determination of most promising PMI biomarkers, and at the development of method of PMI estimation based on the measurement of concentrations of PMI biomarkers.METHODS: Quantitative metabolomic pro ling of samples of the human serum, AH, and VH taken at di erent PMIs has been performed with the use of NMR spectroscopy.RESULTS: It is found that the metabolomic changes in anatomically isolated ocular uids are slower and smoother than that in blood. A good positive time correlation (Pearson coe cient r > 0.5) was observed for several metabolites, including hypox- anthine, choline, creatine, betaine, glutamate, and glycine. A model for PMI estimation based on concentrations of several metabolites in AH and VH is proposed.CONCLUSIONS: The obtained results demonstrate that the metabolomic analysis of AH and VH is more suitable for the PMI estimation than that of serum. The compounds with good positive time correlation can be considered as potential PMI biomarkers.
Question: Write a study description for the study titled 'Brown-fat-mediated tumour suppression by cold-altered global metabolism'.
Answer: Glucose uptake is essential for cancer glycolysis and is involved in non-shivering thermogenesis of adipose tissues. Most cancers use glycolysis to harness energy for their infinite growth, invasion and metastasis. Activation of thermogenic metabolism in brown adipose tissue (BAT) by cold and drugs instigates blood glucose uptake in adipocytes. However, the functional effects of the global metabolic changes associated with BAT activation on tumour growth are unclear. Here we show that exposure of tumour-bearing mice to cold conditions markedly inhibits the growth of various types of solid tumours, including clinically untreatable cancers such as pancreatic cancers. Mechanistically, cold-induced BAT activation substantially decreases blood glucose and impedes the glycolysis-based metabolism in cancer cells. The removal of BAT and feeding on a high-glucose diet under cold exposure restore tumour growth, and genetic deletion of Ucp1-the key mediator for BAT-thermogenesis-ablates the cold-triggered anticancer effect. In a pilot human study, mild cold exposure activates a substantial amount of BAT in both healthy humans and a patient with cancer with mitigated glucose uptake in the tumour tissue. These findings provide a previously undescribed concept and paradigm for cancer therapy that uses a simple and effective approach. We anticipate that cold exposure and activation of BAT through any other approach, such as drugs and devices either alone or in combination with other anticancer therapeutics, will provide a general approach for the effective treatment of various cancers.
Question: Write a study description for the study titled 'Distinct metabolic profiling is correlated with bisexual flowers formation resulting from exogenous ethephon induction in melon (Cucumis melo L.)'.
Answer: Melon (Cucumis melo L.) is an agronomically important vegetable. Most cultivars of melon are andromonoecious and bisexual flowers only emerged from the leaf axil of lateral branches. However, the regulatory mechanism contributing to the occurrence of bisexual flowers were still obscure. In this study, ethephon was applied in two common cultivars of melon. In control without ethephon treatment, no bisexual flower was made in the main stem. However, 6.56 ± 1.42 and 6.63 ± 0.55 bisexual flowers were respectively induced in main stem of ‘Yangjiaocui-QX’ and ‘Lvbao’ after ethephon treatment, and induced bisexual flowers distributed in 12–20 nodes of main stem. During the formation of bisexual flowers, 41 metabolites were significantly up-regulated and 98 metabolites were significantly down-regulated. According to the KEGG enrichment analysis of 139 different metabolites, a total of 30 pathways were mapped and KEGG terms of “Phenylalanine, tyrosine and tryptophan biosynthesis”, “Phenylalanine metabolism” and “Flavone and flavonol biosynthesis” were significantly enriched. In three significantly enriched KEGG terms, shikimic acid, L-tryptophan, L-phenylalanine and kaempferol were significantly up-regulated while L-tyrosine, 4-hydroxycinnami acid and luteolin were significantly down-regulated in ET compared to CK. Different metabolites were also classified depend on major class features and 14 classes were acquired. The results of metabonomics and endogenous hormone identification indicated that ethylene could enhance the concentration of salicylic acid, methyl jasmonate, ABA and IAA. This study provided an important theoretical foundation for inducing bisexual flowers in main stem and breeding new varieties of melon in future.
Question: Write a study description for the study titled 'Postprandial Metabolism is Impaired in Overweight Normoglycemic Young Adults without Family History of Diabetes'.
Answer: While the risk factors for Type 2 diabetes (T2DM) are known, early predictive markers of transition from normal to a prediabetes state are unidentified. We studied the basal metabolism and metabolic response to a mixed-meal challenge in 110 healthy subjects in the age group of 18 to 40 years (Male:Female = 1:1); grouped into first degree relatives of patients with T2DM (n = 30), those with a body mass index >23 kg/m2 but <30 kg/m2 (n = 30), those with prediabetes (n = 20) and normal controls (n = 30). We performed an untargeted metabolomics analysis of plasma and related that with clinical and biochemical parameters, markers of inflammation, and insulin sensitivity. Similar to prediabetes subjects, overweight subjects had insulin resistance and significantly elevated levels of C-peptide, adiponectin and glucagon and lower level of ghrelin. Metabolites such as MG(22:2(13Z, 16Z)/0:0/0:0) and LysoPC (15:0) were reduced in overweight and prediabetes subjects. Insulin sensitivity was significantly lower in men. Fasting levels of uric acid, xanthine, and glycochenodeoxycholic-3-glucuronide were elevated in men. However, both lysophospholipids and antioxidant defense metabolites were higher in women. Impaired postprandial metabolism and insulin sensitivity in overweight normoglycemic young adults indicates a risk of developing hyperglycemia. Our results also indicate a higher risk of diabetes in young men.
Question: Write a study description for the study titled 'Grazer-induced transcriptomic and metabolomic response of the chain-forming diatom Skeletonema marinoi'.
Answer: Diatoms and copepods are main actors in marine food webs. The prey-predator interactions between them affect bloom dynamics, shape marine ecosystems and impact the energy transfer to higher trophic levels. Recently it has been demonstrated that the presence of grazers may affect the diatom prey beyond the direct effect of grazing. Here, we investigated the response of the chain-forming centric diatom Skeletonema marinoi to grazer cues, including changes in morphology, gene expression and metabolic profile. S. marinoi cells were incubated with Calanus finmarchicus or with Centropages typicus and in both cases responded by reducing the chain length, whereas changes in gene expression indicated an activation of stress response, changes in the lipid and nitrogen metabolism, in cell cycle regulation and in frustule formation. Transcripts linked to G protein-coupled receptors and to nitric oxide synthesis were differentially expressed suggesting involvement of these signalling transduction pathways in the response. Downregulation of a lipoxygenase in the transcriptomic data and of its products in the metabolomic data also indicate an involvement of oxylipins. Our data contribute to a better understanding of the gene function in diatoms, providing information on the nature of genes implicated in the interaction with grazers, a crucial process in marine ecosystems.
Question: Write a study description for the study titled 'Circulating sepsis-related metabolite sphinganine could protect against intestinal damage during sepsis'.
Answer: INTRODUCTION: Sepsis is intricately linked to intestinal damage and barrier dysfunction. At present times, there is a growing interest in a metabolite-based therapy for multiple diseases.METHODS: Serum samples from septic patients and healthy individuals were collected and their metabonomics profiling assessed using Ultra-Performance Liquid Chromatography-Time of Flight Mass Spectrometry (UPLC-TOFMS). The eXtreme Gradient Boosting algorithms (XGBOOST) method was used to screen essential metabolites associated with sepsis, and five machine learning models, including Logistic Regression, XGBoost, GaussianNB(GNB), upport vector machines(SVM) and RandomForest were constructed to distinguish sepsis including a training set (75%) and validation set(25%). The area under the receiver-operating characteristic curve (AUROC) and Brier scores were used to compare the prediction performances of different models. Pearson analysis was used to analysis the relationship between the metabolites and the severity of sepsis. Both cellular and animal models were used to HYPERLINK 'javascript:;' assess the function of the metabolites.RESULTS: The occurrence of sepsis involve metabolite dysregulation. The metabolites mannose-6-phosphate and sphinganine as the optimal sepsis-related variables screened by XGBOOST algorithm. The XGBoost model (AUROC=0.956) has the most stable performance to establish diagnostic model among the five machine learning methods. The SHapley Additive exPlanations (SHAP) package was used to interpret the XGBOOST model. Pearson analysis reinforced the expression of Sphinganine, Mannose 6-phosphate were positively associated with the APACHE-II, PCT, WBC, CRP and IL-6. We also demonstrated that sphinganine strongly diminished the LDH content in LPS-treated Caco-2 cells. In addition, using both in vitro and in vivo examination, we revealed that sphinganine strongly protects against sepsis-induced intestinal barrier injury.DISCUSSION: These findings highlighted the potential diagnostic value of the ML, and also provided new insight into enhanced therapy and/or preventative measures against sepsis.
Question: Write a study description for the study titled 'Age-, sex- and proximal-distal-resolved multi-omics identifies regulators of intestinal aging in non-human primates.'.
Answer: The incidence of intestinal diseases increases with age, but the regulators of gut aging and the molecules linking gut aging and diseases remain largely unknown. By profiling the transcriptome, proteome, phosphoproteome and metabolome of 104 Macaca fascicularis large intestinal tissues, we unveiled asynchronous aging within the proximal and distal colon. The levels of many gene products, phosphosites and metabolites changed with age in a location- and sex-dependent manner, and many of these changes occurred at distinct rates or even in opposite directions at different locations. Assessment of 60 age-related molecules (genes, phosphosites, metabolites) across C. elegans, mice, and cell lines identified 32 crucial regulators of gut atrophy and barrier integrity. Notably, we found that tryptophan metabolism via the kynurenine and serotonin (5-HT) pathways was more active in the proximal and distal colon, respectively. In a mouse colitis model, reducing 5-HT production with a Tph1 inhibitor alleviated distal but not proximal colitis, while adding 5-HT aggravated distal symptoms, indicating that distal colitis is more sensitive to 5-HT fluctuations. Moreover, we identified 24 proteins, particularly HPX, that potentially link gut aging to colorectal cancer (CRC). High levels of HPX in CRC predicted poor prognosis in patients older than 50 yr but not in younger patients, suggesting that an age-linked HPX increase in the gut may contribute to CRC progression. Collectively, this work reveals the heterogeneity of large intestinal aging in non-human primates and offers promising targets for preventing gut aging and diseases.
Question: Write a study description for the study titled 'Mechanistic insights revealed by lipid profiling in monogenic insulin resistance syndromes (Mouse data)'.
Answer: Evidence from several recent metabolomic studies suggests that increased concentrations of triacylglycerols (TAGs) with shorter (14-16 carbon atoms), saturated fatty acids are associated with insulin resistance and the risk of type 2 diabetes. Although causality cannot be inferred from association studies, patients in whom the primary cause of insulin resistance can be genetically defined, offer unique opportunities to address this challenge. Therefore, we compared metabolite profiles in patients with congenital lipodystrophy or loss-of-function insulin resistance (INSR) mutations with healthy controls. The absence of significant differences in TAG species in the INSR group suggest that changes previously observed in epidemiological studies are not purely a consequence of insulin resistance. The presence of TAGs with lower carbon numbers and high saturation in patients with lipodystrophy suggests that these metabolite changes may be associated with primary adipose tissue dysfunction. The observed pattern of TAG species is indicative of increased de novo lipogenesis (DNL). To test this we investigated the distribution of these TAGs in lipoprotein fractions using size exclusion chromatography prior to mass spectrometry. This associated these TAGs with VLDL particles, and hence release of TAGs into the blood from the liver. To test further the hepatic origin of these TAGs we induced DNL in the mouse, comparing ob/ob and wild type mice on a chow or high fat diet, confirming that DNL induced an increase in relatively shorter, more saturated fatty acids. Overall, these studies highlight DNL in the pathogenesis of metabolic dyslipidaemia in states where energy intake exceeds the capacity of adipose tissue.  The protocols and data for mice samples are reported in current study MTBLS327. The protocols and data for human samples are reported in study MTBLS162.
Question: Write a study description for the study titled 'Apoplastic metabolomics reveals sugars as mesophyll messengers regulating guard cell ion transport under red light'.
Answer: Here we sought to identify mesophyll messenger(s) that promote stomatal opening under red light. We first established a method to isolate leaf apoplastic fluids from Arabidopsis thaliana and Vicia faba and ascertained that the apoplastic fluid enhances red light-induced stomatal opening. We then applied multiple targeted and non-targeted metabolomics approaches, detecting 464 metabolites as components of the plant apoplastic metabolome – a rich resource for future studies. We identified several small and organic molecules as red light-stimulated apoplastic metabolites in both species and tested the impacts of these candidate mesophyll messengers on stomatal responses. We found that low concentrations of sugars, including sucrose, strongly enhanced stomatal opening under red light. The sucrose enhancement effect was diminished in the H+ ATPase null mutant, aha1-6, and phosphopeptide immunohistochemical assays demonstrated sugar upregulation of H+ ATPase phosphorylation in wild-type, which is correlated with increased ATPase activity. Our whole cell patch clamp assays revealed inhibition of anion efflux through slow anion channels by low (1-3 mM) sucrose concentrations. These regulatory impacts on ion transporters are explanatory of the observed enhancement of stomatal opening. This comprehensive study thus answers the decades-long question concerning the presence, identity, and mechanistic impact of the mesophyll messenger.