LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Hfq Regulates Efflux Pump Expression and Purine Metabolic Pathway to Increase the Trimethoprim Resistance in Aeromonas veronii'.
Answer: Aeromonas veronii (A. veronii) is a zoonotic pathogen. It causes clinically a variety of diseases such as dysentery, bacteremia, and meningitis. And it also brings huge losses to aquaculture. A. veronii has been documented as a multiple antibiotic resistant bacterium. Hfq (host factor for RNA bacteriophage Qβ replication) plays vital regulation roles in a variety of cell programs. The deletion of hfq in A. veronii showed an increased sensitivity to the trimethoprim, accompanying by the down regulation of the efflux pump related genes acrA and acrB in transcriptomic data. Coherently, the complementation of acrA and acrB in ∆hfq recovered the trimethoprim resistance. Besides, the productions of adenosine and guanosine were revealed to augment in ∆hfq in metabonomic data. Both wild type and ∆hfq conferred more sensitive to trimethoprim after appending 1 mM adenosine or guanosine to M9 medium. These results demonstrated that Hfq mediated trimethoprim resistance by elevating efflux pump expression and degrading adenosine, and guanosine metabolites. Collectively, Hfq is a potential target to tackle trimethoprim resistance in A. veronii infection.
Question: Write a study description for the study titled 'Macrosteatosis Cause Graft Failure Via Proliferative Arrest in Rats after Liver Transplantation'.
Answer: We created a rat model with macrosteatosis (MaS) liver via methionine-cholinedeficient food (MCD) diet and transplanted the MaS liver into normal rats, then the rats without any MaS will be set as control. In the whole process of surgeries, we procured the liver tissue samples in different time points (before LT, 1 week after LT, and 4 months after LT). Then samples were prepared for further transcriptomic and metabolomic analysis.
Question: Write a study description for the study titled 'Study on Wax Secretion and Wax-secreting System of Mulberry Pest Paurocephala sauteri Enderlein (Hemiptera: Psyllidae).'.
Answer: Paurocephala sauteri Enderlein, one of the most important pests of mulberry trees in the tropical and subtropical regions, the nymphs and adults of this species penetrate the veins on the back of leaves and buds of mulberry trees, nymph and female adult can secrete wax, these wax accumulated on the mulberry leaves significantly effect photosynthesis of leaves and silkworm cultivation. Therefore, this study aimed to clearly understand the wax-secreting system and characteristics of wax secretion, and see if there is any possible strategy to control the species population from angle of the wax-secreting process. The main findings were as follow: scanning electron microscopy revealed that the nymphs and female adults secreted wax in the form of long tubes with spherical ends, male adults only secreted honeydew. Additionally, the wax-secreting system of the nymphs and female adults were different, the nymph owned a bending moon-shaped wax gland, the first instar nymph wax gland was consisted of one circle of rectangular and depressed cells, but second to fifth instar nymph wax gland was made of one circle of rectangular and depressed cells, and one circle of round depressed cells. There were a certain number of white pores inside of these depressed cells. Wax filaments produced by these pores converted the into dense, tight and hollow wax tube. Gas chromatography/mass spectrometry showed that the main constituents of P. sauteri wax were hydrocarbons. Wax tube as a water conservation pool during the P. sauteri developmental process, this physiological feature may as a key point for a potential strategy to control P. sauteri, even other secreting insects.
Question: Write a study description for the study titled 'Pseudomonas syringae infectivity correlates to altered transcript and metabolite levels of Arabidopsis Mediator mutants'.
Answer: Rapid metabolic responses to pathogens are essential for plant survival and depend on numerous transcription factors. Mediator is the major transcriptional co-regulator for integration and transmission of signals from transcriptional regulators to RNA polymerase II. Using four Arabidopsis Mediator mutants, med16, med18, med25 and cdk8, we studied how differences in regulation of their transcript and metabolite levels correlate to their responses to Pseudomonas syringae infection. We found that med16 and cdk8 were susceptible, while med25 showed increased resistance. Glucosinolates, phytoalexins and carbohydrates were reduced already before infection in med16 and cdk8, but increased in med25, which also display increased benzenoids levels. Early after infection, wild type plants showed reduced glucosinolate and nucleoside levels, but increases in amino acids, benzeniods, oxylipins and the phytoalexin Camalexin. The Mediator mutants showed altered levels of these metabolites and in regulation of genes encoding key enzymes for their metabolism. At later stage, mutants displayed defective levels of specific amino acids, carbohydrates, lipids and jasmonates which correlates to their infection response phenotypes. Our results reveal that MED16, MED25 and CDK8 are required for a proper, coordinated transcriptional response of genes which encode enzymes involved in important metabolic pathways for Arabidopsis responses to Pseudomonas syringae infection.
Question: Write a study description for the study titled 'A multi-omics approach reveals functions of Secretory Carrier-Associated Membrane Proteins in wood formation of Populus trees'.
Answer: Secretory Carrier-Associated Membrane Proteins (SCAMPs) are highly conserved proteins that are involved in membrane trafficking. An integrated approach was taken to elucidate function of SCAMPs in wood formation of Populus trees. The metabolomics analyses were performed in woody tissues of transgenic Populus trees carrying an RNAi construct for Populus tremula x tremuloides SCAMP3 (PttSCAMP3; Potri.019G104000). The secondary xylem of the transgenic trees displayed increases in the amounts of polysaccharide derived sugars as well as lignin oligomers, indicating increased deposition of both carbohydrate and lignin polymers in the secondary cell walls. Somewhat surprisingly, the transgenic lines showed significantly increased amounts of suberic acid in the secondary xylem tissues. Populus SCAMP proteins were shown to influence accumulation of secondary cell wall components including polysaccharides, polyphenolics, lipids and suberin in the woody tissues of Populus tree stems.
Question: Write a study description for the study titled 'Characterization of trotter horses urine metabolome by means of proton nuclear magnetic resonance spectroscopy'.
Answer: BACKGROUND: Metabolomics has been recognized as a powerful approach for disease screening. In order to highlight potential health issues in subjects, a key factor is the possibility to compare quantitatively the metabolome of their biofluids with reference values from healthy individuals. Such efforts towards the systematic characterization of the metabolome of biofluids in perfect health conditions, far from concluded for humans, have barely begun on horses.  OBJECTIVES: The present work attempts, for the first time, to give reference quantitative values for the molecules mostly represented in the urine metabolome of horses at rest and under light training, as observable by 1H-NMR.  METHODS: The metabolome of ten trotter horses, four male and six female, ranging from 3 to 8 years of age, has been observed by 1H-NMR spectroscopy before and after three training sessions.  RESULTS: We could characterize and quantify 54 molecules in trotter horse urine, originated from diet, protein digestion, energy generation or gut-microbial co-metabolism.  CONCLUSION: We were able to describe how gender, age and exercise affected their concentration, by means of a two steps protocol based on univariate and robust principal component analysis.
Question: Write a study description for the study titled 'Overexpression of tlr5 adrffects gut microbiota resistance to Salmonella infection'.
Answer: BACKGROUND: The gut microbiome and the host immune system interact synergistically to maintain intestinal health and defend against infections. Toll-like receptor 5 (TLR5), known for recognizing bacterial flagellin, plays a pivotal role in this regulatory network. Despite significant advances in understanding the gut microbiome and TLR5, the precise role of TLR5 in gut health and infection resistance remains unclear. This study aimed to elucidate the role of TLR5 in regulating gut microbiota and metabolites and their impact on resistance to Salmonella infection using a TLR5 intestinal-specific overexpression mouse model. METHODS: Fecal microbiota and metabolite transplantation experiments were conducted using feces from TLR5-overexpressing mice (TLR5+/+ group) and wild-type mice (WT group) into C57 mice, creating four experimental groups: Flora-TLR5-C57, Metabolite-TLR5-C57, Flora-WT-C57 and Metabolite-WT-C57. Mice were infected with Salmonella, and various parameters including survival time, fecal Salmonella load, and alterations in gut microbiota and metabolites were assessed. RESULTS: Despite notable shifts in gut microbiota composition and metabolite profiles induced by TLR5 overexpression, no significant differences in fecal Salmonella load or survival time were observed across the experimental groups. TLR5-overexpressing mice exhibited an enrichment of beneficial bacterial taxa and significant changes in metabolites; however, these alterations did not correlate with enhanced resistance to Salmonella infection. CONCLUSION: Our findings suggest that while TLR5 overexpression significantly modifies gut microbiota and metabolite profiles, these changes do not directly enhance resistance to Salmonella infection. The immune response to Salmonella is multifaceted and involves various components beyond the gut microbiota and metabolites. Further research is required to elucidate the detailed molecular pathways through which TLR5 influences infection outcomes and to explore potential combined therapeutic strategies for enhancing host defenses against enteric pathogens.
Question: Write a study description for the study titled 'Metabolomic homeostasis shifts after callus formation and shoot regeneration in tomato'.
Answer: Plants can regenerate from a variety of tissues on culturing in appropriate media. However, the metabolic shifts involved in callus formation and shoot regeneration are largely unknown. The metabolic profiles of callus generated from tomato (Solanum lycopersicum) cotyledons and that of shoot regenerated from callus were compared with the pct1-2 mutant that exhibits enhanced polar auxin transport and the shr mutant that exhibits elevated nitric oxide levels. The transformation from cotyledon to callus involved a major shift in metabolite profiles with denser metabolic networks in the callus. In contrast, the transformation from callus to shoot involved minor changes in the networks. The metabolic networks in pct1-2 and shr mutants were distinct from wild type and were rewired with shifts in endogenous hormones and metabolite interactions. The callus formation was accompanied by a reduction in the levels of metabolites involved in cell wall lignification and cellular immunity. On the contrary, the levels of monoamines were upregulated in the callus and regenerated shoot. The callus formation and shoot regeneration were accompanied by an increase in salicylic acid in wild type and mutants. The transformation to the callus and also to the shoot downregulated LST8 and upregulated TOR transcript levels indicating a putative linkage between metabolic shift and TOR signalling pathway. The network analysis indicates that shift in metabolite profiles during callus formation and shoot regeneration is governed by a complex interaction between metabolites and endogenous hormones.
Question: Write a study description for the study titled 'Rhythmic glucose metabolism regulates the redox circadian clockwork in human red blood cells (LC-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.LC-MS assay protocols and data are reported in the current study MTBLS1285.GC-MS assay protocols and data for this study are reported in MTBLS1286.
Question: Write a study description for the study titled 'Personalised therapeutic management of epileptic patients guided by pathway-driven breath metabolomics'.
Answer: BACKGROUND: Therapeutic management of epilepsy remains a challenge, since optimal systemic antiseizure medication (ASM) concentrations do not always correlate with improved clinical outcome and minimal side effects. We tested the feasibility of non-invasive real-time breath metabolomics as an extension of traditional therapeutic drug monitoring for patient-stratification by simultaneously monitoring drug-related and drug-modulated metabolites.METHODS: This proof-of-principle observational study involved 93 breath measurements of 54 paediatric patients monitored over a period of 2.5 years, along with an adults’ cohort of 37 patients measured in two different hospitals. Exhaled breath metabolome of epileptic patients was measured in real-time using secondary electrospray ionization-high resolution mass spectrometry (SESI-HRMS).RESULTS: We show that systemic ASM concentrations could be predicted by the breath test. Total and free valproic acid (VPA; an ASM) is predicted with concordance correlation coefficient (CCC) of 0.63 and 0.66, respectively. We also find i) high between- and within-subject heterogeneity in VPA metabolism; ii) several amino acid metabolic pathways are significantly enriched (p < 0.01) in patients suffering from side effects and iii) tyrosine metabolism is significantly enriched (p < 0.001), with downregulated pathway compounds in non-responders.CONCLUSIONS: These results show that real-time breath analysis of epileptic patients provides reliable estimations of systemic drug concentrations along with risk estimates for drug response and side effects.
Question: Write a study description for the study titled 'Regulatory Role of the VCL/ICAM-1 Pathway in Inflammatory Exudative Damage to the Gas-Blood Barrier in SARS-CoV-2 Infection: New Insights from the Omicron Paradigm'.
Answer: Infections by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), ranging from the initial Wildtype (WT) variant in Wuhan, China, to later variants including Omicron, have showcased a diverse spectrum of symptoms. This diversity underscores the need for ongoing exploration into the virus's elusive pathogenesis. This study employs multi-omics and collaborative validation methods to comprehensively understand SARS-CoV-2's pathology, offering insights that remain pertinent as the virus evolves. Through proteomic analysis, we have identified signaling pathways associated with damage to the vascular system. Importantly, the vinculin (VCL) pathway has been identified as a distinctive feature in Omicron infections, representing a key mechanism causing lung exudation. Metabolomic analysis uncovered disruptions in immune functions, cell membrane stability, and metabolic shifts. Integrated analysis highlighted the involvement of VCL in processes such as inflammation, cell adhesion, and extravasation. A validation cohort confirmed VCL and ICAM1 as Omicron-associated biomarkers. Our mouse model studies not only corroborated these findings but also indicated therapeutic potential of targeting VCL. In contrast to genomic studies highlighting host immunity and infection susceptibility in COVID-19, our research sheds light on the evolving physiological impacts induced by the Omicron variant via the VCL pathway. By our elucidation of key molecular mechanisms involved, provides a strategic direction for developing therapies to address emerging SARS-CoV-2 variants, emphasizing the need for continuous adaptation in combating viral challenges.
Question: Write a study description for the study titled 'A Novel Approach to Characterize the Lipidome of Marine Archaeon Nitrosopumilus maritimus by Ion Mobility Mass Spectrometry'.
Answer: Archaea are differentiated from the other two domains of life by their biomolecular characteristics. One such characteristic is the unique structure and composition of their lipids. Characterization of the whole set of lipids in a biological system (the lipidome) remains technologically challenging. This is because the lipidome is innately complex, and not all lipid species are extractable, separable or ionizable by a single analytical method. Furthermore, lipids are structurally and chemically diverse. Many lipids are isobaric or isomeric and often indistinguishable by the measurement of mass or even their fragmentation spectra. Here we developed a novel analytical protocol based on liquid chromatography ion mobility mass spectrometry to enhance the coverage of the lipidome and characterize the conformations of archaeal lipids by their collision cross-sections (CCSs). The measurements of ion mobility revealed the gas-phase ion chemistry of representative archaeal lipids and provided further insights into their attributions to the adaptability of archaea to environmental stresses. A comprehensive characterization of the lipidome of mesophilic marine thaumarchaeon, Nitrosopumilus maritimus (strain SCM1) revealed potentially an unreported phosphate- and sulfate-containing lipid candidate by negative ionization analysis. It was the first time that experimentally derived CCS values of archaeal lipids were reported. Discrimination of crenarchaeol and its proposed stereoisomer was, however, not achieved with the resolving power of the SYNAPT G2 ion mobility system, and a high-resolution ion mobility system may be required for future work. Structural and spectral libraries of archaeal lipids were constructed in non-vendor-specific formats and are being made available to the community to promote research of Archaea by lipidomics.
Question: Write a study description for the study titled 'Pb Stress and Ectomycorrhizas: Strong Protective Proteomic Responses in Poplar Roots Inoculated with Paxillus involutus Isolate and Characterized by Low Root Colonization Intensity'.
Answer: The commonly observed increased heavy metal tolerance of ectomycorrhized plants is usually linked with the protective role of the fungal hyphae covering colonized plant root tips. However, the molecular tolerance mechanisms in heavy metal stressed low-colonized ectormyocrrhizal plants characterized by an ectomycorrhiza-triggered increases in growth are unknown. Here, we examined Populus × canescens microcuttings inoculated with the Paxillus involutus isolate, which triggered an increase in poplar growth despite successful colonization of only 1.9% ± 0.8 of root tips. The analyzed plants, lacking a mantle-a protective fungal biofilter-were grown for 6 weeks in agar medium enriched with 0.75 mM Pb(NO3)2. In minimally colonized 'bare' roots, the proteome response to Pb was similar to that in noninoculated plants (e.g., higher abundances of PM- and V-type H+ ATPases and lower abundance of ribosomal proteins). However, the more intensive activation of molecular processes leading to Pb sequestration or redirection of the root metabolic flux into amino acid and Pb chelate (phenolics and citrate) biosynthesis coexisted with lower Pb uptake compared to that in controls. The molecular Pb response of inoculated roots was more intense and effective than that of noninoculated roots in poplars.
Question: Write a study description for the study titled 'A large-scale metabolomics study to harness chemical diversity and explore biochemical mechanisms in ryegrass (UPLC-MS C1 reverse phase NEG assay)'.
Answer: "Perennial ryegrass (Lolium perenne) is integral to temperate pastoral agriculture, which contributes most of the milk and meat production worldwide. Chemical profiles and diversity of ryegrass offer several opportunities to harness specific traits and elucidate underlying biological mechanisms for forage improvement. We conducted a large-scale metabolomics study of perennial ryegrass comprising 715 genotypes, representing 118 populations from 21 countries. Liquid/gas chromatography-mass spectrometry based targeted and non-targeted techniques were used to analyse fructan oligosaccharides, lipids, fatty acid methyl esters, polar and semi-polar compounds. Fructan diversity across all genotypes was evaluated, high- and low-sugar groups identified, and fructan accumulation mechanisms explored. Metabolites differentiating the two groups were characterised, modules and pathways they represent deduced, and finally, visualisation and interpretation provided in a biological context. We also demonstrate a workflow for large-scale metabolomics studies from raw data through to statistical and pathway analysis.  UPLC-MS C1 reverse phase NEG assay is reported in the current study MTBLS68. UPLC-MS HILIC POS assay is reported in MTBLS62. UPLC-MS HILIC NEG assay is reported in MTBLS63. UPLC-MS C18 reverse phase POS assay is reported in MTBLS64. UPLC-MS C18 reverse phase NEG assay is reported in MTBLS65. UPLC-MS C1 reverse phase POS and GC-MS FAME assays are reported in MTBLS66. HPLC-MS Hypercarb reverse phase NEG assay is reported in MTBLS529."
Question: Write a study description for the study titled 'Targeting the gut-lung axis by synbiotic feeding to infants in a randomized controlled trial'.
Answer: Synbiotics may modulate gut microbiota and prevent infections. In a randomized controlled trial (NCT01625273) infants weaned from breast milk were fed formula with prebiotics (fructo- and galactooligosaccharides) or the same prebiotic formula with Lactobacillus paracasei ssp. paracasei strain F19 (synbiotics) from 1 until 6 months of age. The objective was to examine synbiotic effects on gut microbiota maturation. Fecal samples collected at ages 1, 4, 6 and 12 months (324 samples for microbial and 197 samples for metabolic characterization) were analyzed. We demonstrate enrichment of Bifidobacterium and increases in antimicrobial metabolites derived from microbial fermentation of phenylalanine and pectins in the synbiotic group. The gut microbiota of infants with lower respiratory tract infections (LRTI) were depleted of Lactobacillales but enriched in Klebsiella species and associated antimicrobial resistance genes. These compositional and functional changes of the gut microbiota may be linked to the previously reported reduction of LRTI in the synbiotic group.