LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Alcohol-Induced Bone Loss: Driven by Dysregulated Spatial Distribution of Gut Microbiota and PGD2-IL17 Pathway-Mediated Osteoclast Activation'.
Answer: Purpose: Alcohol-induced damage to bone microstructure leads to alcoholic osteopenia (AOP). While prior studies have demonstrated alcohol's negative impact on bone density, the mechanisms by which alcohol induces osteoporosis through immune pathways, gut microbiota dysbiosis, and metabolic alterations remain insufficiently characterized. Given that alcohol is primarily absorbed in the upper gastrointestinal tract, the research aims to elucidate the role of spatial distribution disorders in gut microbiota and metabolites in the pathogenesis of alcohol-induced osteoporosis and to evaluate the potential of microbiota supplementation and targeted immunosuppressants as therapeutic strategies for related bone diseases. Methods: Eight-week-old male C57BL/6 mice were used to establish an osteoporosis model via the force-feeding method. Bone loss was validated using micro-computed tomography (micro-CT). Segmented intestinal samples and fecal samples were analyzed by 16S rRNA sequencing and metabolomics. Mechanistic studies were conducted by supplementing R. intestinalis, prostaglandin D2 (PGD2), and its specific immune inhibitor, Ramatroban. Analytical methods included tartrate-resistant acid phosphatase (TRAP) staining, flow cytometry, and enzyme-linked immunosorbent assay (ELISA). For statistical analysis, paired t-tests were used for comparisons between two groups, while one-way analysis of variance (ANOVA) followed by Tukey's post hoc test was employed for multiple group comparisons.Results: Alcohol disrupts the spatial complexity of intestinal segments and fecal microbiota in mice, causing metabolic dysregulation and ultimately leading to elevated PGD2 levels. This, in turn, triggers Th17/Treg immune imbalance and osteoclast activation, resulting in bone loss. Supplementation with the probiotic R. intestinalis or inhibition of PGD2 can significantly improve bone density and alleviate inflammation.Conclusion: Due to the complex spatial distribution of gut microbiota, fecal or colonic microbiota alone cannot fully represent the entire gut environment. The microbiota and metabolites in the lower gastrointestinal tract are better indicators of the host's systemic metabolic status, while the sensitive changes in microbial diversity in the upper gastrointestinal tract also play a significant role in disease progression. This study demonstrates that alcohol-induced elevation of prostaglandin D2 (PGD2) is a key pathogenic factor in alcohol-induced osteoporosis (AOP). PGD2 accelerates bone loss by promoting osteoclast formation through the activation of Th17 cells. Furthermore, this study highlights the importance of investigating the spatial distribution of gut microbiota and metabolites, providing potential targets and novel strategies for the precise treatment of AOP and other diseases associated with external stimuli.
Question: Write a study description for the study titled 'Metabolomics Analysis Identifies Glutamic acid and Cystine imbalances in COVID-19 Patients Without Comorbid Conditions. Implications on Redox Homeostasis and COVID-19 Pathophysiology'.
Answer: It is well known that the presence of comorbidities and age-related health issues may hide biochemical and metabolic features triggered by SARS-CoV-2 infection and other diseases associated to hypoxia, as they are by themselves chronic inflammatory conditions that may potentially disturb metabolic homeostasis and thereby negatively impact on COVID-19 progression. To unveil the metabolic abnormalities inherent to hypoxemia caused by COVID-19, we here applied gas chromatography coupled to mass spectrometry to analyze the main metabolic changes exhibited by a population of male patients less than 50 years of age with mild/moderate and severe COVID-19 without pre-existing comorbidities known to predispose to life-threatening complications from this infection. Several differences in serum levels of particular metabolites between normal controls and patients with COVID-19 as well as between mild/moderate and severe COVID-19 were identified. These included increased glutamic acid and reduced glutamine, cystine, threonic acid and proline levels. In particular, using the entire metabolomic fingerprint obtained, we observed that glutamine/glutamate metabolism was associated with disease severity as patients in the severe COVID-19 group presented the lowest and higher serum levels of these amino acids, respectively. These data highlight the hypoxia-derived metabolic alterations provoked by SARS-CoV-2 infection in the absence of pre-existing co-morbidities as well as the value of amino acid metabolism in determining reactive oxygen species recycling pathways, which when impaired may lead to increased oxidation of proteins and cell damage. They also provide insights on new supportive therapies for COVID-19 and other disorders that involve altered redox homeostasis and lower oxygen levels that may lead to better outcomes of disease severity.
Question: Write a study description for the study titled 'Metabolic phenotyping of ex-vivo breast samples by DESI mass spectrometry imaging'.
Answer: This study involves the analysis of surgically resected samples from patients undergoing breast surgery. The samples published here have been used as part of the publication by [1], and all experimental details can be found within. Desorption electrospray ionisation mass spectrometry imaging (DESI MSI) was used to provide spatially resolved metabolic profiles across the various tissue samples, which in combination with histological assessment allows characterisation of changes across distinct tissue types. In being able to characterise the metabolic differences between tissue types, it becomes possible to predict future unknown samples using a data-driven histological approach to enhance current disease prognoses.  Ref: [1] Guenther S, Muirhead LJ, Speller AV, Golf O, Strittmatter N, Ramakrishnan R, Goldin RD, Jones E, Veselkov K, Nicholson J, Darzi A, Takats Z. Spatially resolved metabolic phenotyping of breast cancer by desorption electrospray ionization mass spectrometry. Cancer Res. 2015 May 1;75(9):1828-37. doi:10.1158/0008-5472.CAN-14-2258. PMID:25691458
Question: Write a study description for the study titled 'Metabolomics Identifies Metabolic Markers of Maturation in Human Pluripotent Stem Cell-Derived Cardiomyocytes'.
Answer: Cardiovascular disease is a leading cause of death worldwide. Human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) hold immense clinical potential and recent studies have enabled generation of virtually pure hPSC-CMs with high efficiency in chemically defined and xeno-free conditions. Despite these advances, hPSC-CMs exhibit an immature phenotype and are arrhythmogenic in vivo, necessitating development of methods to mature these cells. hPSC-CMs undergo significant metabolic alterations during differentiation and maturation. A detailed analysis of the metabolic changes accompanying maturation of hPSC-CMs may prove useful in identifying new strategies to expedite the maturation process and also provide biomarkers for testing or validating hPSC-CM maturation. In this study we identified global metabolic changes which take place during long-term culture and maturation of hPSC-CMs derived from three different hPSC lines. We have identified several metabolic pathways, including phospholipid metabolism and pantothenate and Coenzyme A metabolism, which showed significant enrichment upon maturation in addition to fatty acid oxidation and metabolism. We also identified an increase in glycerophosphocholine and reduction in phosphocholine as potential metabolic biomarkers of maturation. These biomarkers were also affected in a similar manner during murine heart development in vivo. These results support that hPSC-CM maturation is associated with extensive metabolic rewiring and understanding the role of these metabolic changes in maturation process has the potential to develop novel approaches to monitor and expedite hPSC-CM maturation.
Question: Write a study description for the study titled 'Enhanced photosynthetic CO2 fixation in mutualistic Chlorella sp. and Mesorhizobium loti co-cultures'.
Answer: It was further confirmed the stimulatory effect of M. loti-derived eCA on microalgae, highlighting key carbon metabolic pathways, including the Calvin cycle, TCA cycle and antioxidant defense response.
Question: Write a study description for the study titled 'Lipid mediators of inflammation in BALF 6-19 days after infection with influenza'.
Answer: In this study broncho-alveolar lavage fluid (BALF) from mice infected with influenza A virus, PR8 (280 PFU) was analyzed for lipidomic host response in comparison with the mock infected animals. Time Points: 6, 9, 11, 13 and 19 days post infection, done in 8-10 replicates.)
Question: Write a study description for the study titled 'Metabolomics uncovers the dual effects of high-pressure and ultra-shear processing in juice'.
Answer: This study investigated the chemical changes in a blended fruit and vegetable juice induced by innovative food processing technologies - high-pressure processing (HPP; 400 MPa, 40oC) and ultra-shear technology (UST; 400 MPa, 40 and 72 °C) - in comparison to conventional thermal treatments at 40 and 72 °C. Using an untargeted metabolomics approach, we explored the relationships between process parameters and compositional outcomes to evaluate implications for food quality. The results revealed clear compositional separation between untreated and treated samples, with pressure-based technologies further distinguishable from conventional thermal ones. Anthocyanins and other phenolics, such as proanthocyanidins, epicatechin, and phloridzin, degraded across all treatments. Concurrently, degradation products like 3,4-dihydroxybenzoic acid increased in abundance, suggesting thermal-like degradation pathways. Conversely, several compounds, including hydroxycinnamic acids, ellagic acid, and proline, showed increased levels in treated samples, likely due to cell disruption and release mechanisms. Among the technologies evaluated, heat induced the most pronounced compositional changes, while pressure and ultra-shear stress had more moderate effects. Overall, results suggest that compound release may outweigh degradation, emphasizing the value of untargeted metabolomics in capturing both loss and liberation of bioactive compounds during processing. These findings contribute to a deeper understanding of how emerging processing technologies affect food composition and quality.
Question: Write a study description for the study titled 'Analysis of sex-specific lipid metabolism of Plasmodium falciparum points to the importance of sphingomyelin for gametocytogenesis'.
Answer: Male and female Plasmodium falciparum gametocytes are the parasite lifecycle stage responsible for transmission of malaria from the human host to the mosquito vector. Not only are gametocytes able to survive in radically different host environments, but they are also precursors for male and female gametes that reproduce sexually soon after ingestion by the mosquito. Here, we investigate the sex-specific lipid metabolism of gametocytes within their host red blood cell. Comparison of the male and female lipidome identifies cholesteryl esters and dihydrosphingomyelin enrichment in female gametocytes. Chemical inhibition of each of these lipid types in mature gametocytes suggests dihydrosphingomyelin synthesis but not cholesteryl ester synthesis is important for gametocyte viability. Genetic disruption of each of the two sphingomyelin synthase genes points towards sphingomyelin synthesis contributing to gametocytogenesis. This study shows that gametocytes are distinct from asexual stages, and that the lipid composition is also vastly different between male and female gametocytes, reflecting the different cellular roles these stages play. Taken together, our results highlight the sex-specific nature of gametocyte lipid metabolism, which has the potential to be targeted to block malaria transmission. This article has an associated First Person interview with the first author of the paper.
Question: Write a study description for the study titled 'Identification of Conserved and Diverse Metabolic Shifts during Rice Grain Development (LC-MS neg assay)'.
Answer: Seed development dedicates to reserve synthesis and accumulation and uncovering its genetic and biochemical mechanisms has been a major research focus. Although proteomic and transcriptomic analyses revealed dynamic changes of genes and enzymes involved, the information regarding concomitant metabolic changes is missing. Here we investigated the dynamic metabolic changes along the rice grain development of two japonica and two indica cultivars using non-targeted metabolomics approach, in which we successfully identified 214 metabolites. Statistical analyses revealed both cultivar and developmental stage dependent metabolic changes in rice grains. Generally, the stage specific metabolic kinetics corresponded well to the physiological status of the developing grains, and metabolic changes in developing rice grain are similar to those of dicot Arabidopsis and tomato at reserve accumulation stage but are different from those of dicots at seed desiccation stage. The remarkable difference in metabolite abundances between japonica and indica rice grain was observed at the reserve accumulation stage. Metabolite-metabolite correlation analysis uncovered potential new pathways for several metabolites. Taken together, this study uncovered both conserved and diverse development associated metabolic kinetics of rice grains, which facilitates further study to explore fundamental questions regarding the evolution of seed metabolic capabilities as well as their potential applications in crop improvement.LC-MS pos assay is reported in MTBLS286.LC-MS neg assay is reported in MTBLS287.GC-MS assay is reported in MTBLS288.
Question: Write a study description for the study titled 'Transcriptome and metabolite profiling reveals that prolonged drought modulates the phenylpropanoid and terpenoid pathway in white grapes (Vitis vinifera L.) (Carotenoids; UPLC-DAD assay)'.
Answer: BACKGROUND: Secondary metabolism contributes to the adaptation of a plant to its environment. In wine grapes, fruit secondary metabolism largely determines wine quality. Climate change is predicted to exacerbate drought events in several viticultural areas, potentially affecting the wine quality. In red grapes, water deficit modulates flavonoid accumulation, leading to major quantitative and compositional changes in the profile of the anthocyanin pigments; in white grapes, the effect of water deficit on secondary metabolism is still largely unknown.RESULTS: In this study we investigated the impact of water deficit on the secondary metabolism of white grapes using a large scale metabolite and transcript profiling approach in a season characterized by prolonged drought. Irrigated grapevines were compared to non-irrigated grapevines that suffered from water deficit from early stages of berry development to harvest. A large effect of water deficit on fruit secondary metabolism was observed. Increased concentrations of phenylpropanoids, monoterpenes, and tocopherols were detected, while carotenoid and flavonoid accumulations were differentially modulated by water deficit according to the berry developmental stage. The RNA-sequencing analysis carried out on berries collected at three developmental stages-before, at the onset, and at late ripening-indicated that water deficit affected the expression of 4,889 genes. The Gene Ontology category secondary metabolic process was overrepresented within up-regulated genes at all the stages of fruit development considered, and within down-regulated genes before ripening. 18 phenylpropanoid, 16 flavonoid, 9 carotenoid, and 16 terpenoid structural genes were modulated by water deficit, indicating the transcriptional regulation of these metabolic pathways in fruit exposed to water deficit. An integrated network and promoter analyses identified a transcriptional regulatory module that encompasses terpenoid genes, transcription factors, and enriched drought-responsive elements in the promoter regions of those genes as part of the grapes response to drought.CONCLUSION: Our study reveals that grapevine berries respond to drought by modulating several secondary metabolic pathways, and particularly, by stimulating the production of phenylpropanoids, the carotenoid zeaxanthin, and of volatile organic compounds such as monoterpenes, with potential effects on grape and wine antioxidant potential, composition, and sensory features.UPLC-DAD assay of Carotenoids is reported in the current study MTBLS889.SPME-GC-MS assay of Volatile organic compounds is reported in MTBLS892.UPLC-MS/MS assay of Phenolics is reported in MTBLS897.
Question: Write a study description for the study titled '1H NMR chemometric models for classification of Czech wine type and variety'.
Answer: A set of 917 wines of Czech origin registered in a national competition were analysed using nuclear magnetic resonance spectroscopy (NMR) with the aim to build and evaluate multivariate statistical models and machine learning methods for the classification of type (5 types), variety (13 varieties) and location (4 locations) based on 1H NMR spectra. The predictive models afforded more than 93% of correctness for classification of dry and medium dry, medium, sweet white wines and dry red wines. The trained Random Forest (RF) method is able to classify Pinot noir with 96% of correctness, Blaufränkisch 96%, Riesling 92%, Cabernet Sauvignon 77%, Chardonnay 76%, Gewürtztraminer 60%, Hibernal 60%, Grüner Veltliner 52%, Pinot gris 48%, Sauvignon Blanc 45%, Pálava 40%. Pinot blanc and Chardonnay are varieties, which are often misplaced and were discriminated with 71% of correctness. Chemometrics represents prospective tool to predict important features in wine, potentially important in quality assessment and fraud detection.
Question: Write a study description for the study titled 'Adipocyte-specific Zeb1 confers breast cancer progression by triggering the tumor-associated adipose microenvironment remodeling'.
Answer: Upon penetrating the basement membrane, breast cancer cells directly interact with their surrounding adipose tissue, which forms a unique tumor-associated adipose microenvironment (TAME). However, the underlying mechanism involved in the regulation of lipid metabolic remodeling in the TAME remains elusive. Herein, we identified a Zeb1-orchestrated bidirectional communication between breast cancer cells and their adjacent cancer-associated adipocytes (CAAs). At the molecular level, breast cancer cells, through the secretion of adrenomedullin (AM), induce downregulation of Zeb1 expression to activate the Atgl/Hsl/Scd-depedent lipolysis in CAAs, which subsequently results in the release of palmitoleic acid (POA) into the TAME. In turn, accumulated POA triggers the malignant growth and metastasis of breast cancer cells and their production of AM via an ARA-PDG2-mediated membrane phospholipid replacement mechanism. Importantly, disruption of Zeb1-dependent lipolytic activity and/or membrane phospholipid remodeling within the TAME, severely diminishes the aggressiveness of breast cancer in vitro and in vivo.
Question: Write a study description for the study titled 'Overexpression of vesicle-associated membrane protein PttVAP27-17 as a tool to improve biomass production and the overall saccharification yields in Populus trees'.
Answer: BackgroundBioconversion of wood into bioproducts and biofuels is hindered by the recalcitrance of woody raw material to bioprocesses such as enzymatic saccharification. Targeted modification of the chemical composition of the feedstock can improve saccharification but this gain is often abrogated by concomitant reduction in tree growth.ResultsIn this study, we report on transgenic hybrid aspen (Populus tremula × tremuloides) lines that showed potential to increase biomass production both in the greenhouse and after 5 years of growth in the field. The transgenic lines carried an overexpression construct for Populus tremula × tremuloides vesicle-associated membrane protein (VAMP)-associated protein PttVAP27-17 that was selected from a gene-mining program for novel regulators of wood formation. Analytical-scale enzymatic saccharification without any pretreatment revealed for all greenhouse-grown transgenic lines, compared to the wild type, a 20-44% increase in the glucose yield per dry weight after enzymatic saccharification, even though it was statistically significant only for one line. The glucose yield after enzymatic saccharification with a prior hydrothermal pretreatment step with sulfuric acid was not increased in the greenhouse-grown transgenic trees on a dry-weight basis, but increased by 26-50% when calculated on a whole biomass basis in comparison to the wild-type control. Tendencies to increased glucose yields by up to 24% were present on a whole tree biomass basis after acidic pretreatment and enzymatic saccharification also in the transgenic trees grown for 5 years on the field when compared to the wild-type control.ConclusionsThe results demonstrate the usefulness of gene-mining programs to identify novel genes with the potential to improve biofuel production in tree biotechnology programs. Furthermore, multi-omic analyses, including transcriptomic, proteomic and metabolomic analyses, performed here provide a toolbox for future studies on the function of VAP27 proteins in plants.
Question: Write a study description for the study titled 'Molecular evidence of shipping noise impact on the blue mussel, a key species for the sustainability of coastal marine environments'.
Answer: Anthropogenic oceanic noise due to shipping has increased up to 32-fold over the last five decades, putting marine organisms at risk. While the impact of noise on marine mammals is well documented, its effect on molluscs, which hold immense economic and ecological importance, remain largely unknown. To investigate the consequences of noise on mollusc metabolism during crucial early life stages, mussel larvae were exposed to shipping noise in a laboratory setting until the post-larval stage and their metabolome analysed. Multivariate analyses of the metabolomes showed that shipping noise induces stress-related inflammation with increased energy demands, higher protein turnover and disrupted nervous system activity. Consequently, noise promoted a delayed metamorphosis in suboptimal habitats with greater metabolic costs, which may impact ecosystem and aquaculture sustainability as competent mussel larvae struggle to select suitable development habitats. Without action to limit underwater noise, such impacts could disrupt population structures and marine biodiversity.