LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Novel Potential Diagnostic Serum Biomarkers of Metabolomics in Osteoarticular Tuberculosis Patients: A Preliminary Study'.
Answer: Osteoarticular tuberculosis is one of the extrapulmonary tuberculosis, which is mainly caused by direct infection of Mycobacterium tuberculosis or secondary infection of tuberculosis in other parts. Due to the low specificity of the current detection method, it is leading to a high misdiagnosis rate and subsequently affecting the follow-up treatment and prognosis. Metabolomics is mainly used to study the changes of the body's metabolites in different states, so it can be served as an important means in the discovery of disease-related metabolic biomarkers and the corresponding mechanism research. Liquid chromatography tandem mass spectrometry (LC-MS/MS) was used to detect and analyze metabolites in the serum with osteoarticular tuberculosis patients, disease controls and healthy controls to find novel metabolic biomarkers that could be used in the diagnosis of osteoarticular tuberculosis. Our results showed that 68 differential metabolites (p＜0.05, Fold Change＞1.0) were obtained in osteoarticular tuberculosis serum after statistical analysis. Then, through the evaluation of diagnostic efficacy, PC(o-16:1(9Z)/18:0), PC(20:4(8Z,11Z,14Z,17Z)/18:0), PC(18:0/22:5(4Z,7Z,10Z,13Z,16Z)), SM(d18:1/20:0), and SM(d18:1/18:1(11Z)) were found as potential biomarkers with high diagnostic efficacy. Using bioinformatics analysis, we further found that these metabolites share many lipids metabolic signaling pathways, such as choline metabolism, sphingolipid signaling, retrograde endocannabinoid signaling, sphingolipid and glycerophospholipid, these results suggest that lipid metabolism plays an important role in the pathological process of tuberculosis. This study can provide certain reference value for the study of metabolic biomarkers of osteoarticular tuberculosis and the mechanism of lipid metabolism in osteoarticular tuberculosis and even other tuberculosis diseases.
Question: Write a study description for the study titled 'Dynamic change of IDO1 activity predicts survival in patients with unresectable stage III NSCLC and chemoradiotherapy'.
Answer: OBJECTIVES: High activity of Indoleamine 2,3-dioxygenase1 (IDO1) in lung cancer patients converts tryptophan (Trp), which is the essential amino acid for T cell metabolism, to kynurenine (Kyn) and consequently suppresses anti-tumor immune responses. We aimed to track the dynamics of IDO1 activity in stage III non-small cell lung cancer (NSCLC) patients who received first-line radiotherapy (RT) and explore its association with survival outcomes.MATERIALS AND METHODS: Systemic IDO1 activity was calculated by Kyn:Trp ratio. Plasma levels of Kyn and Trp in 113 thoracic RT-received stage III NSCLC patients were measured by high-performance liquid chromatography before the initiation of RT. Dynamic change of IDO1 activity was followed in 24 patients by measuring Kyn:Trp ratio before, during and after RT administration.RESULTS: In 24 patients with dynamic tracking of plasma IDO1 activity, there was no significant alterations observed among the 3 time points (Friedman test, p=0.13). The changing pattern of Kyn:Trp ratio was divided into 4 groups: decreased consistently during RT, first increased then decreased, increased consistently, first decreased then increased. Patients whose Kyn:Trp ratio kept decreasing or first increased then decreased were defined as good-change group. The good-change status was identified as an independent positive factor for overall survival (OS) and progression-free survival (PFS) (p=0.04; p=0.01) in multivariate analysis among evaluated parameters. Patients with good change showed significantly superior local control than bad-change group (p=0.01, HR=0.22). In 113 stage III NSCLC patients with pre-radiation Kyn:Trp ratio, a trend that high baseline IDO1 activity was associated with short OS was observed (p=0.079).CONCLUSION: Favorable change of IDO1 activity during RT was associated with superior OS, PFS and local control. IDO1 activity is a promising biomarker for prognosis in stage III NSCLC patients.
Question: Write a study description for the study titled 'Marine metabolomics: measurement of metabolites in seawater by gas chromatography mass spectrometry (The effect of salt and water on metabolite detection)'.
Answer: One of the major bottlenecks in describing marine ecosystems is characterizing the metabolome of seawater, as salt prevents metabolite analysis. We present SeaMet, a method that can detect hundreds of metabolites in less than one ml of seawater and quantifies them down to nano-molar levels using gas chromatography-mass spectrometry. Our method provides a major advance in marine metabolomics by enabling the unbiased analysis of primary metabolites across saltwater habitats.  The effect of salt and water on metabolite detection is reported in the current study MTBLS839. Method development is reported in MTBLS826. Cell culture sampling is reported MTBLS843. Environmental sampling is reported MTBLS844. Method quantification is reported in MTBLS848. Solid phase extraction is reported in MTBLS849.  Linked Studies: MTBLS826 MTBLS843 MTBLS844 MTBLS848 MTBLS849
Question: Write a study description for the study titled 'Two UGT84A Family Glycosyltransferases Regulate Phenol, Flavonoid, and Tannin Metabolism in Juglans regia (English Walnut)'.
Answer: We showed previously that gallic acid is produced in walnut from 3-dehydroshikimate by a shikimate dehydrogenase (JrSkDH). This study focuses on the next step in the hydrolysable tannin pathway, the formation of 1-O-galloyl-β-D-glucose from the phenolic gallic acid and UDP glucose by a glycosyltransferase. JrGGT1 (UGT84A73) and JrGGT2 (UGT84A74) are predicted to be two such glycosyltransferases, which we expressed in tobacco plants. GC-MS analysis of the transgenic tobacco revealed moderate, yet significant alterations in plant secondary metabolism, such as depleted phenolic acids, including gallic acid. We postulate that these effects are due to JrGGT1 and JrGGT2 activity, as JrGGT orthologs glycosylate these phenolic compounds in vitro. Moreover, JrGGT expression in tobacco caused upregulation of shikimic acid pathway metabolites and differing responses in phenylpropanoids, such as phenolic acids and flavonoids. In transcriptome analysis of walnut pellicle tissues, both JrGGTs showed substantial and significant expression correlations with the gallic acid-producing JrSkDHs and were highly coexpressed with the genetic circuits constituting the shikimic acid and phenylpropanoid biosynthetic pathways. Verification of JrGGT gene expression by transcriptome analysis of 20 walnut tissues revealed striking similarities with that of the pellicle data, with the greatest expression in roots, wood, buds, and leaves of Juglans regia cv. Chandler: tissues that typically accumulate hydrolysable tannins. Like the transgenic tobacco, pellicle metabolomic analyses revealed that many phenylpropanoids correlated negatively with JrGGT expression, while shikimic acid pathway metabolites correlated positively with JrGGT expression. This research supports the hypothesis that JrGGT1 and JrGGT2 play non-trivial roles in metabolism of phenolic acids, flavonoids, and ostensibly, tannins.
Question: Write a study description for the study titled 'Firefly genomes illuminate parallel origins of bioluminescence in beetles'.
Answer: Fireflies and their luminous courtships have inspired centuries of scientific study. Today firefly luciferase is widely used in biotechnology, but the evolutionary origin of bioluminescence within beetles remains unclear. To shed light on this long-standing question, we sequenced the genomes of two firefly species that diverged over 100 million-years-ago: the North American Photinus pyralis and Japanese Aquatica lateralis. To compare bioluminescent origins, we also sequenced the genome of a related click beetle, the Caribbean Ignelater luminosus, with bioluminescent biochemistry near-identical to fireflies, but anatomically unique light organs, suggesting the intriguing hypothesis of parallel gains of bioluminescence. Our analyses support independent gains of bioluminescence in fireflies and click beetles, and provide new insights into the genes, chemical defenses, and symbionts that evolved alongside their luminous lifestyle.
Question: Write a study description for the study titled 'Large-Scale Plasma Analysis Revealed New Mechanisms and Molecules Associated with the Host Response to SARS-CoV-2'.
Answer: The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread to nearly every continent, registering over 1,250,000 deaths worldwide. The effects of SARS-CoV-2 on host targets remains largely limited, hampering our understanding of Coronavirus Disease 2019 (COVID-19) pathogenesis and the development of therapeutic strategies. The present study used a comprehensive untargeted metabolomic and lipidomic approach to capture the host response to SARS-CoV-2 infection. We found that several circulating lipids acted as potential biomarkers, such as phosphatidylcholine 14:0_22:6 (area under the curve (AUC) = 0.96), phosphatidylcholine 16:1_22:6 (AUC = 0.97), and phosphatidylethanolamine 18:1_20:4 (AUC = 0.94). Furthermore, triglycerides and free fatty acids, especially arachidonic acid (AUC = 0.99) and oleic acid (AUC = 0.98), were well correlated to the severity of the disease. An untargeted analysis of non-critical COVID-19 patients identified a strong alteration of lipids and a perturbation of phenylalanine, tyrosine and tryptophan biosynthesis, phenylalanine metabolism, aminoacyl-tRNA degradation, arachidonic acid metabolism, and the tricarboxylic acid (TCA) cycle. The severity of the disease was characterized by the activation of gluconeogenesis and the metabolism of porphyrins, which play a crucial role in the progress of the infection. In addition, our study provided further evidence for considering phospholipase A2 (PLA2) activity as a potential key factor in the pathogenesis of COVID-19 and a possible therapeutic target. To date, the present study provides the largest untargeted metabolomics and lipidomics analysis of plasma from COVID-19 patients and control groups, identifying new mechanisms associated with the host response to COVID-19, potential plasma biomarkers, and therapeutic targets.
Question: Write a study description for the study titled 'Determination of metabolite differences between loquat nectar and honey by UPLC-MS/MS'.
Answer: Honey is a widely consumed natural agricultural product due to its unique flavour, taste and its nutritional content. Honey bees form honey by collecting nectar from different flowers and then metabolising it to form honey which is stored in the hive. Currently attention is always focussed on the material composition of monofloral honeys from different plant sources. There is a lack of understanding of the differences in the transformation and composition of metabolites between plant nectar and the honey that is processed by bees after nectar feeding. In this study, loquat nectar and mature loquat honey were used for the detection of metabolites in both by Ultra Performance Liquid Chromatography-Tandem mass spectrometry (UPLC-MS/MS). The results showed that there was a significant difference in the relative content of non-volatile metabolites between the two. We detected a total of 914 non-volatile metabolites, of which 834 were detected in loquat nectar and 759 in loquat honey.
Question: Write a study description for the study titled 'Celery (Apium graveolens L.) Juice Fermented with Lactiplantibacillus plantarum NCU116 Mitigates Type 2 Diabetes in Mice: Mechanistic Insights from Gut Microbiota and Metabolomics'.
Answer: This study aimed to investigate the metabolic effects of fermented celery juice (FCJ) and non-fermented celery juice (NFCJ) in a mouse model of type 2 diabetes. Fresh celery juice was fermented with Lactiplantibacillus plantarum NCU116 under controlled conditions. Male C57BL/6J mice were divided into normal, diabetic, and intervention groups receiving NFCJ or FCJ for 4 weeks. Colonic contents were collected and subjected to non-targeted metabolomics using ultra-high-performance liquid chromatography coupled with tandem mass spectrometry (UHPLC–MS/MS). This dataset contains the raw LC–MS data of colonic metabolites, providing a resource for understanding the metabolic impact of fermented and non-fermented celery juice in diabetic mice.
Question: Write a study description for the study titled 'Metabolomics guides rational development of a simplified cell culture medium for drug screening against Trypanosoma brucei'.
Answer: In vitro culture methods underpin many experimental approaches to biology and drug discovery. The modification of established cell culture methods to be more biologically relevant, or to optimise growth, is traditionally a laborious task. Emerging metabolomics technology enables rapid evaluation of intra- and extra-cellular metabolites, and can be applied to the rational development of cell culture medium. In this study, untargeted semi-quantitative, and targeted quantitative, metabolomic analyses of fresh and spent media revealed the major nutritional requirements for growth of bloodstream-form Trypanosoma brucei. The standard culture medium (HMI11) contained unnecessarily high concentrations of 32 nutrients that were subsequently removed to more closely resemble concentrations normally found in blood. Our new minimal medium (CMM) supports in vitro growth equivalent to HMI11, and causes no significant perturbation of metabolite levels for 94% of the detected metabolome (< 3-fold change; a = 0.05). Importantly, improved sensitivity was observed for drug activity studies in whole cell phenotypic screens, and in metabolomics mode of action assays. 400-fold decreases in IC50 were observed for pentamidine and methotrexate, suggesting inhibition of activity by nutrients present in HMI11. CMM is suitable for routine cell culture and offers important advantages for metabolomics studies and drug activity screening.
Question: Write a study description for the study titled 'Machine Learning-Based Retention Time Prediction of Trimethylsilyl Derivatives of Metabolites'.
Answer: In gas chromatography-mass spectrometry-based untargeted metabolomics, metabolites are identified by comparing mass spectra and chromatographic retention time with reference databases or standard materials. In that sense, machine learning has been used to predict the retention time of metabolites lacking reference data. However, the retention time prediction of trimethylsilyl derivatives of metabolites, typically analyzed in untargeted metabolomics using gas chromatography, has been poorly explored. Here, we provide a rationalized framework for machine learning-based retention time prediction of trimethylsilyl derivatives of metabolites in gas chromatography. We compared different machine learning paradigms, in addition to exploring the influence of the computational molecular structure representation to train the prediction models: fingerprint class and fingerprint calculation software. Our study challenged predicted retention time when using chemical ionization and electron impact ionization sources in simulated and real cases, demonstrating a good correct identity ranking capability by machine learning, despite observing a limited false identity filtering power in cases where a spectrum or a monoisotopic mass match to multiple candidates. Specifically, machine learning prediction yielded median absolute and relative retention index (relative retention time) errors of 37.1 retention index units and 2%, respectively. In addition, fingerprint class and fingerprint calculation software, as well as the molecular structural similarity between the training and test or real case sets, showed to be critical modulators of the prediction performance. Finally, we leveraged the structural similarity between the training and test or real case set to determine the probability that the prediction error is below a specific threshold. Overall, our study demonstrates that predicted retention time can provide insights into the true structure of unknown metabolites by ranking from the most to the least plausible molecular identity, and sets the guidelines to assess the confidence in metabolite identification using predicted retention time data.
Question: Write a study description for the study titled 'Dual metal electrolysis in theta capillary for lipid analysis'.
Answer: Increasing studies associating glycerophospholipids with various pathological conditions highlight the need for their thorough characterization. However, the intricate composition of the lipidome due to the presence of lipid isomers poses significant challenges to structural lipidomics. This study uses the anodic corrosion of two metals in a single theta nESI emitter as a tool to simultaneously characterize lipids at multiple isomer levels. Anodic corrosion of cobalt and copper in the positive ion mode generates the metal-adducted lipid complexes, [M+Co]2+ and [M+Cu]+, respectively. Optimization of parameters such as the distances of the electrodes from the nESI tip allowed the achievement of the formation of one metal-adducted lipid product at a time. Collision-induced dissociation (CID) of [M+Co]2+ results in preferential loss of the fatty acyl (FA) chain at the sn-2 position, thus generating singly charged sn-specific fragment ions. Whereas, multistage fragmentation of [M+Cu]+ via CID generated a C=C bond position-specific characteristic ion pattern induced by the π-Cu+ interaction. The feasibility of the method was tested on PC lipid extract from egg yolk to identify lipids on multiple isomer levels. Thus, the application of dual metal anodic corrosion allows lipid isomer identification with reduced sample preparation time, no signal suppression by counter anions, low sample consumption and no need for an extra apparatus.
Question: Write a study description for the study titled 'Ovothiol A is the Main Antioxidant in Fish Lens'.
Answer: Tissue protection from oxidative stress by antioxidants is of vital importance for cellular metabolism. The lens mostly consists of fiber cells lacking nuclei and organelles, having minimal metabolic activity; therefore, the defense of the lens tissue from the oxidative stress strongly relies on metabolites. Protein-free extracts from lenses and gills of freshwater fish, Sander lucioperca and Rutilus rutilus lacustris, were subjected to analysis using high-field 1H NMR spectroscopy and HPLC with optical and high-resolution mass spectrometric detection. It was found that the eye lenses of freshwater fish contain high concentrations of ovothiol A (OSH), i.e., one of the most powerful antioxidants exciting in nature. OSH was identified and quantified in millimolar concentrations. The concentration of OSH in the lens and gills depends on the fish genus and on the season. A possible mechanism of the reactive oxygen species deactivation in fish lenses is discussed. This work is the first to report on the presence of OSH in vertebrates. The presence of ovothiol in the fish tissue implies that it may be a significantly more common antioxidant in freshwater and marine animals than was previously thought.
Question: Write a study description for the study titled 'The response of Chlamydomonas reinhardtii to nitrogen deprivation: a systems biology analysis'.
Answer: Drastic alteration in macronutrients causes large changes in gene expression in the photosynthetic unicellular alga Chlamydomonas reinhardtii. Preliminary data suggested that cells follow a biphasic response to this change hinging on the initiation of lipid accumulation, and we hypothesized that drastic repatterning of metabolism also followed this biphasic modality. To test this hypothesis, transcriptomic, proteomic, and metabolite changes that occur under nitrogen (N) deprivation were analyzed. Eight sampling times were selected covering the progressive slowing of growth and induction of oil synthesis between 4 and 6 h after N deprivation. Results of the combined, systems-level investigation indicated that C. reinhardtii cells sense and respond on a large scale within 30 min to a switch to N-deprived conditions turning on a largely gluconeogenic metabolic state, which then transitions to a glycolytic stage between 4 and 6 h after N depletion. This nitrogen-sensing system is transduced to carbon- and nitrogen-responsive pathways, leading to down-regulation of carbon assimilation and chlorophyll biosynthesis, and an increase in nitrogen metabolism and lipid biosynthesis. For example, the expression of nearly all the enzymes for assimilating nitrogen from ammonium, nitrate, nitrite, urea, formamide/acetamide, purines, pyrimidines, polyamines, amino acids and proteins increased significantly. Although arginine biosynthesis enzymes were also rapidly up-regulated, arginine pool size changes and isotopic labeling results indicated no increased flux through this pathway.Data availability:The proteomics data have been deposited into the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD002377.
Question: Write a study description for the study titled 'Fruit setting rewires central metabolism via gibberellin cascades'.
Answer: Fruit set is the process whereby ovaries develop into fruits after pollination and fertilization. The process is induced by the phytohormone gibberellin (GA) in tomatoes, as determined by the constitutive GA response mutant procera However, the role of GA on the metabolic behavior in fruit-setting ovaries remains largely unknown. This study explored the biochemical mechanisms of fruit set using a network analysis of integrated transcriptome, proteome, metabolome, and enzyme activity data. Our results revealed that fruit set involves the activation of central carbon metabolism, with increased hexoses, hexose phosphates, and downstream metabolites, including intermediates and derivatives of glycolysis, the tricarboxylic acid cycle, and associated organic and amino acids. The network analysis also identified the transcriptional hub gene SlHB15A, that coordinated metabolic activation. Furthermore, a kinetic model of sucrose metabolism predicted that the sucrose cycle had high activity levels in unpollinated ovaries, whereas it was shut down when sugars rapidly accumulated in vacuoles in fruit-setting ovaries, in a time-dependent manner via tonoplastic sugar carriers. Moreover, fruit set at least partly required the activity of fructokinase, which may pull fructose out of the vacuole, and this could feed the downstream pathways. Collectively, our results indicate that GA cascades enhance sink capacities, by up-regulating central metabolic enzyme capacities at both transcriptional and posttranscriptional levels. This leads to increased sucrose uptake and carbon fluxes for the production of the constituents of biomass and energy that are essential for rapid ovary growth during the initiation of fruit set.