LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Semi‐polar root exudates in natural grassland communities'.
Answer: In the rhizosphere, plants are exposed to a multitude of different biotic and abiotic factors, to which they respond by exuding a wide range of secondary root metabolites. So far, it has been unknown to which degree root exudate composition is species-specific and is affected by land use, the local impact and local neighborhood under field conditions. In this study, root exudates of 10 common grassland species were analyzed, each five of forbs and grasses, in the German Biodiversity Exploratories using a combined phytometer and untargeted liquid chromatography-mass spectrometry (LC-MS) approach. Redundancy analysis and hierarchical clustering revealed a large set of semi-polar metabolites common to all species in addition to species-specific metabolites. Chemical richness and exudate composition revealed that forbs, such as Plantago lanceolata and Galium species, exuded more species-specific metabolites than grasses. Grasses instead were primarily affected by environmental conditions. In both forbs and grasses, plant functional traits had only a minor impact on plant root exudation patterns. Overall, our results demonstrate the feasibility of obtaining and untargeted profiling of semi-polar metabolites under field condition and allow a deeper view in the exudation of plants in a natural grassland community.
Question: Write a study description for the study titled 'Exercise Activates Interferon Immune Response of the Liver via Gpld1 to Enhance Antiviral Innate Immunity'.
Answer: Healthy behavioral patterns could modulate organ functions to enhance the body’s immunity. However, whether exercise regulates antiviral innate immunity remains elusive. Here, we found that exercise promotes type-I IFN (IFN-I) production in the liver and enhances IFN-I immune activity of the body. Despite the possibility that many exercise-induced factors could regulate IFN-I production, we identified Gpld1 as a crucial molecule and the liver as the major organ to promote IFN-I production after exercise. Exercise largely loses the efficiency to induce IFN-I in Gpld1-/- mice. Further studies demonstrated that exercise-produced 3-hydroxybutanoic acid (3-HB) critically induces Gpld1 expression in the liver. Gpld1 blocks the PP2A-IRF3 interaction and therefore enhances IRF3 activation and IFN-I production, and improves the body’s antiviral ability. This study reveals that the exercise behavior improves antiviral innate immunity by linking the liver metabolism to systemic IFN-I activity, and uncovers an unknown function of liver cells in innate immunity.
Question: Write a study description for the study titled 'A female gametocyte-specific ABC transporter plays a role in lipid metabolism in the malaria parasite'.
Answer: ATP-binding cassette (ABC) transporters serve a variety of physiological functions as well as play key roles in drug resistance. The genome of the human malaria parasite, Plasmodium falciparum, encodes multiple members of this family, one of which, gABCG2, is transcribed predominantly in the gametocyte stage. Here we use gene deletion and tagging to investigate the expression, localization and function of gABCG2. The protein is found in a single dot-like lipid-rich structure within female, but not male, gametocytes. gABCG2-knockout cell lines produce more gametocytes of both sexes. By contrast, cholesteryl esters, diacylglycerols and triacylglycerols are significantly reduced in gABCG2-knockout gametocyte stages. We propose a role for gABCG2 in the regulation of gametocyte numbers and in the accumulation of neutral lipids, which are likely important for parasite development in the insect stages of the parasite life cycle.
Question: Write a study description for the study titled 'Parabacteroides distasonis Improving osteoporosis progression through glycerophospholipid metabolism_blood'.
Answer: Backround&Aim: Dysbiosis of gut microbiota is closely related to the pathogenesis of osteoporosis (OP). This study aimed to identify probiotic candidates and gut-derived metabolites capable of ameliorating osteoporosis via modulation of bone metabolism. Methods: Ovariectomized (OVX) rats were used to model PMOP. Multi-omics analyses, including 16S rDNA sequencing, metagenomics, and untargeted metabolomics, were conducted to characterize gut microbiota(GM) and metabolic alterations following icariin (ICA) administration. Probiotic candidates enriched by ICA treatment were screened based on microbial and metabolic profiles. The effects of P. distasonis (LPD) were evaluated via oral gavage and fecal microbiota transplantation (FMT) in pseudo-germ-free OVX rats. Fecal samples from PMOP patients were analyzed using qPCR to assess LPD abundance. In vitro assays were performed to examine the osteogenic and anti-resorptive activities of glycerophospholipid metabolites derived from LPD.Results: ICA administration improved bone microarchitecture and mechanical strength in OVX rats, restored intestinal barrier integrity, and altered GM composition. Multi-omics analysis identified Parabacteroides distasonis as a key bacterium enriched by ICA. Oral gavage of LPD and FMT from ICA-treated donors ameliorated bone loss in pseudo-germ-free OVX rats. Quantitative PCR of fecal samples confirmed reduced LPD abundance in PMOP patients. Metabolomic profiling revealed that ICA and LPD elevated circulating levels of phosphatidylcholine (PC), lysophosphatidylethanolamine (Lyso PE), and lysophosphatidylcholine (Lyso PC), which were positively correlated with bone formation markers. In vitro, these metabolites enhanced osteoblast differentiation and suppressed osteoclastogenesis.Conclusions: ICA exerts anti-osteoporotic effects via GM modulation, in part through enrichment of LPD and its glycerophospholipid metabolites. These findings highlight LPD as a promising probiotic candidate and support the therapeutic potential of targeting the gut-bone axis in PMOP.
Question: Write a study description for the study titled 'Exogenous L-Alanine promotes phagocytosis multidrug-resistant bacterial pathogens (L-Alanine-treated macrophage metabolomics)'.
Answer: Multidrug-resistant bacteria present a major threat to public health. Therefore, new drugs or approaches are urgently needed to manage and mitigate this threat. Here, we screen the molecular candidates that allow the survival of mice upon Vibrio parahaemolyticus infection by integrated proteomic and metabolomics analysis, where L-Alanine metabolism and phagocytosis are highly correlated. The role of L-Alanine on boosting mouse survival is further confirmed with in vivo bacterial challenge studies on bacteria including V. parahaemolyticus, Escherichia coli, Pseudomonas aeruginosa and Klebsiella pneumoniae. Functional studies demonstrate that exogenous L-Alanine promotes phagocytosis to these different species of multidrug-resistant pathogens. The underlying mechanism involves two events that are L-Alanine-dependently increased TLR4 expression and L-Alanine-enhanced TLR4 signaling via increasing the biosynthesis and secretion of fatty acids such as palmitate. Palmitate enhances the binding of LPS to TLR4 and thereby promotes TLR4 dimmer formation and endocytosis for the subsequent activation of PI3K/Akt and NF-κB pathways and phagocytosis of bacteria. These results suggest that modulation of metabolic environment is a plausible approach for combating infection with multidrug-resistant bacteria.L-Alanine-treated macrophage metabolomics is reported in the current study MTBLS7986.V. parahaemolyticus-infected spleen metabolomics is reported in MTBLS7996.
Question: Write a study description for the study titled 'Paternal microbiome perturbations impact offspring fitness'.
Answer: The gut microbiota operates at the interface of host-environment interactions to influence human homeostasis and metabolic networks. Environmental factors that unbalance gut microbial ecosystems can therefore elicit physiological and disease-associated responses across somatic tissues. However, the systemic impact of the gut microbiome on the germline - and consequently on the F1 offspring it gives rise to - is unexplored. Here we show that the gut microbiota act as a key interface between paternal preconception environment and intergenerational health in mice. Perturbations to the gut microbiota of prospective fathers increase the probability of their offspring presenting with low birth weight, severe growth restriction and premature mortality. Transmission of disease risk occurs via the germline and is provoked by pervasive gut microbiome perturbations, including non-absorbable antibiotics or osmotic laxatives, but is rescued by restoring the paternal microbiota before conception. This effect is linked with a dynamic response to induced dysbiosis in the male reproductive system, including impaired leptin signalling, altered testicular metabolite profiles and remapped small RNA payloads in sperm. As a result, dysbiotic fathers trigger an elevated risk of in utero placental insufficiency, revealing a placental origin of mammalian intergenerational effects. Our study defines a regulatory ‘gut-germline axis’ in males, which is sensitive to environmental exposures and programs offspring fitness through impacting placental function.
Question: Write a study description for the study titled 'A new perspective on semen quality of aged male: The characteristics of metabolomics and proteomics'.
Answer: BACKGROUND: Semen quality is negatively correlated with male age and is mainly quantified by a routine semen analysis, which is descriptive and inconclusive. Sperm proteins or semen metabolites are used as the intermediate or end-products, reflecting changes in semen quality, and hold much promise as a new biomarker to predict fertility in advanced-aged males.OBJECTIVES: In this study, we sought to assess whether the semen metabolome and proteome of aged males can affect semen quality and serve as biomarkers for predicting semen quality.MATERIALS AND METHODS: We retrospectively analyzed 12825 males that underwent semen routine analysis to understand the age-dependent changes in sperm quality. To identify the difference between aged and young adults, metabolomics (n=60) analyses of semen and proteomics (n=12) analyses of sperm were conducted. Finally, integrated machine learning of metabolomics was conducted to screen biomarkers to identify aging semen.RESULTS: We discovered that male age was positively correlated with sperm concentration as well as DNA fragmentation index(DFI), and negatively with progressive motile sperm count, total sperm count, sperm volume and progressive sperm motility. The differential metabolites were significantly enriched in various metabolic pathways, and four of these differential metabolites (Pipamperone, 2,2-Bis(hydroxymethyl)-2,2',2''-nitrilotriethanol, Arg-Pro and Triethyl phosphate) were utilized to establish a biomarker panel to identify aging semen. Proteomic analysis showed that differential proteins were significantly enriched in protein digestion and absorption and some energy-related pathways. An integrated analysis of the metabolome and proteome identified differential energy metabolism and oxidative stress-related proteins, which could explain the decreased motility and the increased DFI of aging sperm.DISCUSSION AND CONCLUSION: We provide compelling evidence that the changes in semen metabolome and sperm proteome are related to the decline of semen quality in aged males. Moreover, a biomarker panel based on four metabolites was established to identify aging semen.
Question: Write a study description for the study titled 'Rhythmic glucose metabolism regulates the redox circadian clockwork in human red blood cells (GC-MS)'.
Answer: Circadian clocks coordinate mammalian behaviour and physiology enabling organisms to anticipate 24-hour cycles. Transcription-translation feedback loops are thought to drive these clocks in most of mammalian cells. However, red blood cells (RBCs), which do not contain a nucleus, and cannot perform transcription or translation, nonetheless exhibit circadian redox rhythms. Here we show human RBCs display circadian regulation of glucose metabolism, which is required to sustain daily redox oscillations. We found daily rhythms of metabolite levels and flux through glycolysis and the pentose phosphate pathway (PPP). We show that inhibition of critical enzymes in either pathway abolished 24-hour rhythms in metabolic flux and redox oscillations, and determined that metabolic oscillations are necessary for redox rhythmicity. Furthermore, metabolic flux rhythms also occur in nucleated cells, and persist when the core transcriptional circadian clockwork is absent in Bmal1 knockouts. Thus, we propose that rhythmic glucose metabolism is an integral process in circadian rhythms.GC-MS assay protocols and data are reported in the current study MTBLS1286.LC-MS assay protocols and data for this study are reported in MTBLS1285.
Question: Write a study description for the study titled 'Quantitative metabolomic analysis of the human cornea and aqueous humor'.
Answer: INTRODUCTION: Cornea is the outermost part of the eye supplied mostly by aqueous humor (AH). Therefore, the comparison of the metabolomic compositions of AH and cornea may help to determine which compounds are produced inside the cornea, and which penetrate into cornea from AH for intra-corneal consumption. Keratoconus (KC) is the most common form of the cornea dystrophy, and the analysis of KC corneas can unravel the metabolomic changes occurring in AH and cornea of KC patients.  OBJECTIVES: The work is aimed at the determination of concentrations of a wide range of metabolites in the human cornea and AH, the comparison of the metabolomic profiles of cornea and AH, and the comparison of the metabolomic compositions of samples taken from KC patients and normal donors (post-mortem).  METHODS: The quantitative metabolomic profiling was carried out with the use of two independent methods—high-frequency 1H NMR spectroscopy and HPLC with high-resolution ESI-MS detection.  RESULTS: The concentrations of 71 most abundant metabolites in cornea and AH from keratoconus patients and from human cadavers have been measured. It is found that the concentrations of purines and organic acids in cornea are significantly higher than in AH. The KC corneas are characterized by the enhanced levels of acetate and citrate, and also by low values of GSH/GSSG ratios.  CONCLUSION: A significant difference in the metabolomic compositions of the human AH and cornea has been revealed. The concentrations of glucose and some amino acids in cornea are significantly lower than in AH, indicating their fast consumption inside the cornea. The high levels of organic acids, purines and GSH in cornea should be attributed to their production in the cornea. The enhanced levels of acetate and citrate as well as the low values of GSH/GSSG ratios in KC corneas are the indicators of the oxidative stress.
Question: Write a study description for the study titled 'A fungal endophyte alters poplar leaf chemistry, deters insect feeding and shapes insect community assembly'.
Answer: The endophytic fungi of certain grasses and herbaceous plants provide anti-herbivore defense compounds, thus living in mutualistic interaction with their hosts. Still, there is little information on such cooperation for tree-associated endophytes. We investigate the influence of the endophytic fungus Cladosporium cladosporioides on the chemical defenses of black poplar Populus nigra trees and the consequences on feeding preference, fitness of herbivorous insects, and insect community assembly. Strikingly, endophyte colonization increases both constitutive- and induced poplar defenses. Generalist Lymantria dispar larvae prefer and perform better on uninfected poplars due to the higher concentrations of salicinoids and fungal alkaloid stachydrine in endophyte-infected leaves. Under field conditions, the endophytic fungus shapes insect community assembly in young black poplar trees. Our results show that endophytic fungi can play a significant role in defending trees against herbivorous insects and structuring insect communities.
Question: Write a study description for the study titled 'Serum protein N-glycosylation changes in multiple myeloma'.
Answer: BACKGROUND: Multiple myeloma is characterized by clonal proliferation of malignant plasma cells in the bone marrow that produce monoclonal immunoglobulins. N-glycosylation changes of these monoclonal immunoglobulins have been reported in multiple myeloma, but previous studies only detected limited serum N-glycan features.METHODS: Here, a more detailed study of the human serum N-glycome of 91 multiple myeloma patients and 51 controls was performed. We additionally analyzed sequential samples from patients (n = 7) which were obtained at different time points during disease development as well as 16 paired blood serum and bone marrow plasma samples. N-glycans were enzymatically released and measured by mass spectrometry after linkage specific derivatization of sialic acids.RESULTS: A decrease in both α2,3- and α2,6-sialylation, galactosylation and an increase in fucosylation within complex-type N-glycans were found in multiple myeloma patients compared to controls, as well as a decrease in difucosylation of diantennary glycans. The observed glycosylation changes were present in all ISS stages, including the 'low-risk' ISS I. In individual patients, difucosylation of diantennary glycans decreased with development of the disease. Protein N-glycosylation features from blood and bone marrow showed strong correlation. Moreover, associations of monoclonal immunoglobulin (M-protein) and albumin levels with glycan traits were discovered in multiple myeloma patients.CONCLUSIONS & GENERAL SIGNIFICANCE: In conclusion, serum protein N-glycosylation analysis could successfully distinguish multiple myeloma from healthy controls. Further studies are needed to assess the potential roles of glycan trait changes and the associations of glycans with clinical parameters in multiple myeloma early detection and prognosis.
Question: Write a study description for the study titled 'Candidatus Alkanophaga archaea from Guaymas Basin hydrothermal vent sediment oxidize petroleum alkanes'.
Answer: Methanogenic and methanotrophic archaea produce and consume the greenhouse gas methane, respectively, using the reversible enzyme methyl-coenzyme M reductase (Mcr). Recently, Mcr variants that can activate multi-carbon alkanes have been recovered from archaeal cultures. These enzymes, called alkyl-coenzyme M reductase (Acrs), are widespread in the environment but remain poorly understood. Here, we produced anoxic cultures degrading mid-chain petroleum n-alkanes from pentane (C5) to tetradecane (C14) at 70°C using oil-rich Guaymas Basin sediments. In these cultures, archaea of the genus Candidatus Alkanophaga activate the alkanes with Acrs and completely oxidize the alkyl groups to CO2. Ca. Alkanophaga form a deep-branching sister clade to the methanotrophs ANME-1 and are closely related to the short-chain alkane oxidizers Ca. Syntrophoarchaeum. Incapable of sulfate reduction, Ca. Alkanophaga shuttle electrons from alkane oxidation to the sulfate-reducing Ca. Thermodesulfobacterium syntrophicum. These syntrophic consortia are potential key players in petroleum degradation in heated oil reservoirs.
Question: Write a study description for the study titled 'Untangling the wine metabolome by combining untargeted SMPE-GCxGC-TOF-MS and sensory analysis to profile Sauvignon blanc co-fermented with seven different yeasts'.
Answer: Saccharomyces cerevisiae (SC) is the main driver of alcoholic fermentation however for aroma and flavour formation in wine non-Saccharomyces species can have a powerful effect. This study aimed to compare untargeted volatile compound profiles from SPME-GCxGC-TOF-MS and sensory analysis data of Sauvignon blanc wine inoculated with six different non-Saccharomyces yeasts followed by SC. Torulaspora delbrueckii (TD), Lachancea thermotolerans (LT), Pichia kluyveri (PK) and Metschnikowia pulcherrima (MP) where commercial starter strains, while Candida zemplinina (CZ) and Kazachstania aerobia (KA), were isolated from wine grape environments. Each fermentation produced a distinct profile both sensorially and chemically. SC and CZ were the most distinct in both of these cases. SC had guava, grapefruit, banana, and pineapple aromas while CZ was driven by fermented apple, dried peach/apricot, and stewed fruit as well as sour flavor. Chemically over 300 unique features were identified as significantly different across the fermentations. SC had the highest number of esters in the highest relative concentration but all the yeasts had distinct ester profiles. CZ displayed the highest number of terpenes in high concentration but also produced a large amount of acetic acid. KA was high in ethyl acetate. TD had fewer esters but three distinctly higher thiol compounds. LT showed a relatively high number of increased acetate esters and certain terpenes. PK had some off odor compounds while the MP had high levels of different methyl butyl-, methyl propyl-, and phenethyl esters. Overall, this study gives a more detailed profile of these yeasts than anything previously reported.
Question: Write a study description for the study titled 'The effect of pvdA in the cadmium absorption by Pseudomonas umsongensis CR14 through metabolic analysis'.
Answer: In this study, the effects of the Cd-resistant and pyoverdine-producing strain Pseudomonas umsongensis CR14 on Cd stabilization and the mechanisms were investigated. Compared with the control, CR14 markedly reduced the Cd concentration in a Cd-containing solution. The genes pvdA, 4498, 4499, and pchF, which are associated with pyoverdine production, were identified in CR14. The mutants of genes concerning the production of pyoverdine were constructed. Among these mutants, the CR14ΔpvdA mutant showed a greater impact on Cd stabilization. The mutant CR14ΔpvdA brought a lower Cd concentration in the solution, with higher levels of cell surface-adsorbed and intracellular accumulated Cd, content of lipopolysaccharide (LPS), expression of the LPS producing genes lptD and lpxL, and cell surface particles. Additionally, CR14ΔpvdA demonstrated increased interactions between the hydroxyl, carboxyl, amino, or ether groups and Cd. These results suggest that the CR14ΔpvdA mutant immobilized Cd by increasing LPS production and cell surface particle numbers, upregulating the expression of LPS-producing genes, and increasing cell surface adsorption and intracellular accumulation in Cd-polluted solutions.
Question: Write a study description for the study titled 'Phyllosphere microbes mediate variety-specific accumulation of di-n-butyl phthalate in choysum (Brassica parachinensis)'.
Answer: Plant-microbe interactions in the phyllosphere have been demonstrated to facilitate plant growth and enhance resistance to diverse stresses; nevertheless, their role in the bioaccumulation of contaminants by plants is rarely considered. Here, by comparing differences in the phyllosphere morphology, bacterial community assembly and metabolites between two choysum (Brassica parachinensis) varieties differing in di-n-butyl phthalate (DBP) accumulation, we revealed the pivotal roles of key phyllosphere exudate (fumarate) and recruited specific microbes in determining the variety-specific DBP accumulation in choysum. The low-DBP accumulation variety (LAV) enhanced the recruitment of phyllosphere microbes capable of degrading DBP by increasing fumarate secretion, relative to the high-DBP accumulation variety (HAV), thereby facilitating the colonization of DBP-degrading bacteria via the induction of biofilm formation and ultimately resulting in lower DBP accumulation in leaves. These findings offer novel insights into the LAV formation from the phyllosphere microbial perspective and highlight the role of phyllosphere microbes in mediating pollutant accumulation within crops, which is instrumental in minimizing pollutant accumulation through regulating the phyllosphere microbial community.