LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Computational mass spectrometry accelerates C=C position-resolved untargeted lipidomics using oxygen attachment dissociation'.
Answer: Mass spectrometry-based untargeted lipidomics has revealed the lipidome atlas of living organisms at the molecular species level. Despite the double bond (C=C) position being a crucial factor for enzyme preference, cellular membrane milieu, and biological activity, the C=C defined structures have not yet been characterized. Here, we present a novel approach for C=C position-resolved untargeted lipidomics using a combination of oxygen attachment dissociation and computational mass spectrometry to increase the rate of annotation. We validated the accuracy of our platform as per the authentic standards of 21 lipid subclasses and the biogenic standards of 51 molecules containing polyunsaturated fatty acids (PUFAs) from the cultured cells fed with various fatty acid-enriched media. By analyzing human and mice-derived biological samples, we characterized 675 unique lipid structures with the C=C position-resolved level encompassing 22 lipid subclasses defined by LIPID MAPS. Our platform also illuminated the unique profiles of tissue-specific lipids containing n-3 and/or n-6 very long-chain PUFAs (carbon M 28 and double bonds a 4) in the eye, testis, and brain of the mouse.
Question: Write a study description for the study titled 'Mono-Locus and Pyramided Resistant Grapevine Cultivars Reveal Early Putative Biomarkers Upon Artificial Inoculation With Plasmopara viticola'.
Answer: One of the most economically important grapevine diseases is Downy mildew (DM) caused by the oomycete Plasmopara viticola. A strategy to reduce the use of fungicides to compensate for the high susceptibility of V. vinifera is the selection of grapevine varieties showing pathogen-specific resistance. We applied a metabolomics approach to evaluate the metabolic modulation in mono-locus resistant genotypes carrying one locus associated with P. viticola resistance (Rpv) (BC4- Rpv1, Bianca- Rpv3-1, F12P160- Rpv12, Solaris- Rpv10), as well as in pyramided resistant genotypes carrying more than one Rpv (F12P60- Rpv3-1; Rpv12 and F12P127- Rpv3-1, Rpv3-3; Rpv10) taking as a reference the susceptible genotype Pinot Noir. In order to understand if different sources of resistance are associated with different degrees of resistance and, implicitly, with different responses to the pathogen, we considered the most important classes of plant metabolite primary compounds, lipids, phenols and volatile organic compounds at 0, 12, 48, and 96 h post-artificial inoculation (hpi). We identified 264 modulated compounds; among these, 22 metabolites were found accumulated in significant quantities in the resistant cultivars compared to Pinot Noir. In mono-locus genotypes, the highest modulation of the metabolites was noticed at 48 and 96 hpi, except for Solaris, that showed a behavior similar to the pyramided genotypes in which the changes started to occur as early as 12 hpi. Bianca, Solaris and F12P60 showed the highest number of interesting compounds accumulated after the artificial infection and with a putative effect against the pathogen. In contrast, Pinot Noir showed a less effective defense response in containing DM growth.
Question: Write a study description for the study titled 'A Combined Proteomic and Metabolomic Strategy for Allergens Characterization in Natural and Fermented Brassica napus Bee Pollen'.
Answer: Bee pollen is consumed for its nutritional and pharmacological benefits, but it also contains hazardous allergens which has not been identified. Here, we identified 2 potential allergens, glutaredoxin and oleosin-B2, in Brassica napus (B. napus) bee pollen using mass spectrometry-based proteomics analyses, and used bioinformatics to predict their antigenic epitopes. Comparison of fermented (by Saccharomyces cerevisiae) and unfermented bee pollen samples indicated that glutaredoxin and oleosin-B2 contents were significantly decreased following fermentation, while the contents of their major constituent oligopeptides and amino acids were significantly increased based on metabolomics analyses. Immunoblot analysis indicated that the IgE-binding affinity with extracted bee pollen proteins was also significantly decreased after fermentation, suggesting a reduction in the allergenicity of fermented bee pollen. Furthermore, fermentation apparently promoted the biosynthesis of L-valine, L-isoleucine, L-tryptophan and L-phenylalanine, as well as their precursors or intermediates. Thus, fermentation could potentially alleviate allergenicity, while also positively affecting nutritional properties of B. napus bee pollen. Our findings might provide a scientific foundation for improving the safety of bee pollen products to facilitate its wider application.
Question: Write a study description for the study titled 'Risk assessment with gut microbiome and metabolite markers in NAFLD development'.
Answer: A growing body of evidence suggests interplay between the gut microbiota and the pathogenesis of nonalcoholic fatty liver disease (NAFLD). However, the role of the gut microbiome in early detection of NAFLD is unclear. Prospective studies are necessary for identifying reliable, microbiome markers for early NAFLD. We evaluated 2487 individuals in a community-based cohort who were followed up 4.6 years after initial clinical examination and biospecimen sampling. Metagenomic and metabolomic characterizations using stool and serum samples taken at baseline were performed for 90 participants who progressed to NAFLD and 90 controls who remained NAFLD free at the follow-up visit. Cases and controls were matched for gender, age, body mass index (BMI) at baseline and follow-up, and 4-year BMI change. Machine learning models integrating baseline microbial signatures (14 features) correctly classified participants (auROCs of 0.72 to 0.80) based on their NAFLD status and liver fat accumulation at the 4-year follow up, outperforming other prognostic clinical models (auROCs of 0.58 to 0.60). We confirmed the biological relevance of the microbiome features by testing their diagnostic ability in four external NAFLD case-control cohorts examined by biopsy or magnetic resonance spectroscopy, from Asia, Europe, and the United States. Our findings raise the possibility of using gut microbiota for early clinical warning of NAFLD development.
Question: Write a study description for the study titled 'Longitudinal metabolomics and lipidomics analyses reveal markers of envenoming by Bothrops asper and Daboia russelii in an experimental murine model'.
Answer: Longitudinal metabolomics and lipidomics analysis was carried out in the blood plasma of mice injected intramuscularly with venoms of the viperid species Bothrops asper and Daboia russelii. Blood samples were collected 1, 3, 6 and 24 h after venom injection, and a control group of non-envenomed mice was included. Significant perturbations in metabolomics and lipidomics were observed at 1, 3 and 6 h, while values returned close to those of control mice by 24 h, hence reflecting a transient pattern of metabolic disturbance. Both venoms induced significant changes in amino acids, as well as in several purines and pyrimidines, and in some metabolites of the tricarboxylic acid cycle. KEGG analysis identified metabolic pathways that showed the highest changes, i.e., aminoacyl tRNA synthesis and amino acid biosynthesis and metabolism pathways. Regarding lipid metabolism, there was an increase of triglycerides and some acyl carnitines, concomitantly with a drop in the levels of some phospholipids. In addition, envenomed mice had higher levels of cortisol, heme and some oxidative stress markers. The overall pattern of metabolic changes in envenomed mice bears similarities with the patterns described in several traumatic injuries, thus underscoring a metabolic response/adaptation to the injurious action of the venoms.
Question: Write a study description for the study titled 'Infection-Induced Peroxisome Biogenesis Is a Metabolic Strategy for Herpesvirus Replication'.
Answer: Peroxisomes are primarily metabolic organelles with important functions in lipid metabolism, such as fatty acid oxidation and ether phospholipid synthesis (e.g. plasmalogens). Certain viruses, such as human cytomegalovirus (HCMV), hijack organelle functions to facilitate their replication and spread. However, the role of peroxisomes in herpesvirus replication remains elusive. Following a discovery that peroxisome proteins are upregulated upon HCMV infection, we quantified the production of plasmalogens, lipids that require peroxisome functions. In agreement with the increase in peroxisome protein abundance, plasmalogen production was increased by HCMV infection.
Question: Write a study description for the study titled 'Unraveling the metabolic response of Brassica oleracea exposed to Xanthomonas campestris pv. campestris'.
Answer: BACKGROUND: Brassica crops together with cereals represent the basis of world supplies. Due to their importance, the production losses caused by Xanthomonas campestris pv. campestris (Xcc) infection represent a high economic impact. Understanding molecular and biochemical mechanisms of plants is essential to develop resistant crops with durable protection against diseases. In this regard, metabolomics has emerged as a valuable technology to provide an overview of the biological status of a plant exposed to a disease. This study investigated the dynamic changes in the metabolic profile of Brassica oleracea plants during an Xcc infection from leaves collected at five different days post infection using a mass spectrometry approach. RESULTS: Results showed that Xcc infection causes dynamic changes in the metabolome of B. oleracea. Moreover, induction/repression pattern of the metabolites implicated in the response follows a complex dynamics during infection progression, indicating a complex temporal response. Specific metabolic pathways such as alkaloids, coumarins or sphingolipids are postulated as promising key role candidates in the infection response.CONCLUSION: This work tries to decipher the changes produced on Brassica crops metabolome under Xcc infection and represents a step forward in the understanding of B. oleracea–Xcc interaction.
Question: Write a study description for the study titled 'The impact of nutritional supplementation on sweat metabolomic content'.
Answer: Sweat is emerging as a prominent biosource for real-time human performance monitoring applications. Although promising, sources of variability must be identified to truly utilize sweat for biomarker applications. In this proof-of-concept study, a targeted metabolomics method was applied to sweat collected from the forearms of participants in a 12-week exercise program who ingested either low or high nutritional supplementation twice daily. The data establish the use of dried powder mass as a method for metabolomic data normalization from sweat samples. Additionally, the results support the hypothesis that ingestion of regular nutritional supplementation semi-quantitatively impact the sweat metabolome. For example, a receiver operating characteristic (ROC) curve of relative normalized metabolite quantities show an area under the curve of 0.82 suggesting the sweat metabolome can moderately predict if an individual is taking nutritional supplementation. Finally, a significant correlation between physical performance and the sweat metabolome are established. For instance, the data illustrate that by utilizing multiple linear regression modeling approaches, sweat metabolite quantities can predict VO2 max (p = 0.0346), peak lower body Windage (p = 0.0112), and abdominal circumference (p = 0.0425). The results illustrate the need to account for dietary nutrition in biomarker discovery applications involving sweat as a biosource.
Question: Write a study description for the study titled 'Effects of Radiofrequency Field from 5G Communications on fecal microbiome and metabolome profiles in mice'.
Answer: With the rapid development of 5G networks, the influence of the radiofrequency field (RF) generated from 5G communication equipment on human health are gathering increasing attention. This study aimed at assessing the effects of long-term exposure to 4.9 GHz (one of the working frequency of 5G communication) RF field on fecal microbiome and metabolome profiles in 9-week-old male C57BL/6 mice. The animals were divided into sham group (n = 8) and radiofrequency group (RF group; n = 8), then whole body exposed or sham exposed to RF field for one hour per day during 3 weeks (21 days) at whole body Specific Absorption Rate (SAR) of 6.3 W/kg. After RF exposure, the mice fecal samples were collected to detect gut microorganisms and metabolites by 16S rRNA gene sequencing method and LC-MS method, respectively. The results showed that intestinal microbial compositions were altered in RF group, as evidenced by reduced microbial diversity and changed microbial community distribution. Metabolomics profiling identified 258 significantly differentially abundant metabolites in RF group, 57 of which can be classified to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Besides, functional correlation analysis showed that changes in gut microbiota genera were significantly correlated with changes in fecal metabolites. In summary, the results suggested that altered gut microbiota and metabolic profile are associated with 4.9 GHz radiofrequency exposure.
Question: Write a study description for the study titled 'The impact of slyA on cell metabolism of Salmonella Typhimurium: a joint study of transcriptomics and metabolomics'.
Answer: Salmonella Typhimurium (S. typhimurium), a gram-negative foodborne pathogen, is the leading cause of Salmonella food poisoning in humans. slyA has been demonstrated to be a critical transcriptional regulator in S. typhimurium, enabling the pathogen to survive in host cells by modulating the expression of hundreds of genes.In this study, we used gas chromatography coupled with tandem mass spectrometry (GC-MS/MS) to investigate the potential effect of slyA on the cell metabolism of S. typhimurium. The metabolite profiling data were linked to the transcriptomic data to elucidate the possible roles of slyA in the metabolism of Salmonella. The metabolome data indicated that several glycolysis- and lipid metabolism-associated pathways, including the turnover of glycerolipid, pyruvate, butanoate and glycerophospholipid, were affected in the absence of slyA. In addition, the mRNA levels of several genes associated with glycolysis and lipid turnover were downregulated when slyA was deleted, including pagP, fadL, mgtB, iacp and yciA. Collectively, this evidence suggests that SlyA might impact glycolysis and lipid turnover in Salmonella at the transcriptional level.Linked Data:The transcriptomic data haa been deposited in the NCBI SRS database, access number PRJNA656165.
Question: Write a study description for the study titled 'Nontargeted Metabolomic Analysis of Four Different Parts of Platycodon grandiflorum Grown in Northeast China'.
Answer: Platycodonis radix is extensively used for treating cough, excessive phlegm, sore throat, bronchitis and asthma in the clinic. Meanwhile, the stems, leaves and seeds of Platycodon grandiflorum (PG) have some pharmaceutical activities such as anti-inflammation and anti-oxidation effects, etc. These effects must be caused by the different metabolites in various parts of herb. In order to profile the different parts of PG, the ultra-high performance liquid chromatography combined with quadrupole time-of- flight mass spectrometry (UPLC-QTOF-MSE) coupled with UNIFI platform and multivariate statistical analyses was used in this study. Consequently, for the constituent screening, 73, 42, 35, 44 compounds were characterized from the root, stem, leaf and seed, respectively. The stem, leaf and seed contain more flavonoids but few saponins that can be easily discriminated in the root. For the metabolomic analysis, 15, 5, 7, 11 robust biomarkers enabling the differentiation among root, stem, leaf and seed, were discovered. These biomarkers can be used for rapid identification of four different parts of PG grown in northeast China.
Question: Write a study description for the study titled 'Impacts of the Callipyge mutation on ovine plasma metabolites'.
Answer: The ovine Callipyge mutation causes postnatal muscle hypertrophy localized to the pelvic limbs and torso, as well as body leanness. The mechanism underpinning enhanced muscle mass is unclear, as is the systemic impact of the mutation. To investigate potential systemic effects of the mutation, 1H NMR spectra of plasma taken from lambs at 8 and 12 weeks of age were measured. Multivariate statistical analysis of plasma metabolite profiles demonstrated effects of development and genotype but not gender. Plasma from Callipyge lambs at 12 weeks of age, but not 8 weeks, was characterized by a metabolic profile consistent with contributions from the affected hypertrophic fast twitch glycolytic muscle fibres. We conclude that there is an indirect systemic effect of the Callipyge mutation in skeletal muscle in the form of changes of blood metabolites, which may contribute to secondary phenotypes such as body leanness.
Question: Write a study description for the study titled 'Integration of metabolomics and transcriptome reveals toxicity variations of Alternaria'.
Answer: Alternaria, a widespread fungal genus, infects a wide range of crops and produces various toxins, such as Tentoxin (TEN), Tenuazonic acid (TeA), Alternariol (AOH) during infection, leading to a major concern about safety of these crops. Although the toxin-producing ability varies among different Alternaria species, the underlying mechanisms are still unclear. In this study, several Alternaria toxins were frequently detected in Tibetan barley (Hordeum vulgare var. coeleste Linnaeus) and wheat (Triticum aestivum Linn) in Tibet, especially TEN and TeA, which were detected in half of the crops. 153 barley and wheat samples collected from 5 different regions in Tibet were used for toxin detection/quantification, isolation and identification of the corresponding toxin producing fungi. According to levels of toxins produced in vivo, different isolates of Alternaria alternaria recovered from the above collected sampled were divided into three groups designated as high toxin-producing strains (HT), medium toxin-producing strains (LT) and no toxin-producing strains (NT). Metabolomics and transcriptomics were employed to investigate the potential mechanism of variations in toxin production among different isolates. Metabolomics analysis revealed high levels of amino acids and secondary metabolites in HT. Various precursors of TeA/TEN were also highly accumulated in HT, especially isoleucine ( which was one of essential gradients of TEN biosynthesis, which may account for high toxin production in HT strains in metabolome. Further transcriptome analysis revealed that the expression levels of genes relevant to precursors of TEN/TeA were higher in HT, especially CC77DRAFT_360136, CC77DRAFT_546209, CC77DRAFT_1033655 and CC77DRAFT_1090532, showing the molecular basis for toxin-producing variations among three strains. Importantly, our topological regulation network results identified the candidate genes that regulated these four genes involved in toxin-producing, and these genes may be essential for variations in toxin producing ability of these Alternaria strains. Overall, this comprehensive analysis expects to provide a better understanding to decipher the mechanism of toxicity based on molecular and metabolic levels.
Question: Write a study description for the study titled 'Dietary hispidulin ameliorated chemically-Induced colitis by inhibiting epithelial cell ferroptosis via the ACAT2-GPX4 axis and remodeling the gut microbiota'.
Answer: Hispidulin, a dietary flavonoid occurring naturally in brown algae, has attracted considerable interest owing to its functions in modulating inflammatory responses and neutralizing reactive oxygen species. This study examined the consequences of hispidulin in a model of chemically induced acute colitis. RNA sequencing (RNA_seq), 16s rRNA_seq, and non-targeted metabolome were conducted to determine the mechanisms underlying hispidulin-induced effects on colitis. The findings revealed that hispidulin exhibited significant therapeutic benefits against colitis. In addition, treatment with hispidulin led to a decrease in pro-inflammatory cytokine levels as well as serum FITC-dextran concentrations. RNA_seq analysis demonstrated a notable increase in colonic ACAT2 expression in mice with colitis following hispidulin treatment. Furthermore, hispidulin administration resulted in the upregulation of GPX4, a reduction in ROS levels, and inhibition of epithelial ferroptosis in mice with colitis. Both genetic inhibition of ACAT2 in vitro and AAV-mediated knockdown of ACAT2 in vivo substantially negated the effects of hispidulin on GPX4/GSH levels, ROS levels, and lipid hydroperoxide accumulation in both NCM460 cells and epithelial cells derived from DSS exposed murine models. 16s rRNA_seq results showed that hispidulin increased abundance of Lactobacillus, NK4A136_group, Oscillibacter, Peptococcus, Adlercreutzia and decreased abundance of Turicimonas in colitic mice. Non-targeted metabolome results showed that hispidulin facilitated the metabolism of galactose and promoted unsaturated fatty acid biosynthesis in colitic mice. In summary, hispidulin reduced the advancement of acute colitis in mice by lessening ACAT2-mediated ferroptosis in epithelial cells, as well as altering composition of gut microbiota.
Question: Write a study description for the study titled 'Effects of soil and genotype mediated root exudates on the quality of Salvia miltiorrhiza'.
Answer: This study used in-situ soil from five different cultivation areas (Beijing, Henan, Sichuan, Shandong, Shaanxi) to plant 4 different varieties of Salvia miltiorrhiza. At the same time, Beijing soil was separately selected for bacterial agent pot experiments. These root exudates were collected at different growth stages of Salvia miltiorrhiza for metabolomics detection and analysis. The effects of different soil types and genotypes mediated root exudates on Salvia miltiorrhiza quality were observed, as well as the effects of different microbial agents mediated root exudates on the active ingredients of Salvia miltiorrhiza.
Question: Write a study description for the study titled 'The measurement of spatial distribution of grape metabolites in berry tissues using LC-MS'.
Answer: The study aims to describe the differential spatial distrubution of secondary metabolites in different grape species,. The aims is to describe the characteristics that differentiate wild grapes from good quality vinifera grapes, understand the limits and advantages from both classes.