LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Metabolic plasticity confers increased resilience to climate variability in temperate compared to tropical lizards'.
Answer: Patterns in functional diversity of organisms at large spatial scales can provide insight into possible responses to future climate change, but it remains a challenge to link large-scale patterns at the organismal level to their underlying physiological mechanisms. The climate variability hypothesis predicts that temperate ectotherms will be less vulnerable to climate warming than tropical ectotherms, due to their superior acclimatization capacity. However, metabolic acclimatization occurs over multiple levels of the biological hierarchy, from the enzyme and cellular level, through organ systems, to whole-organism metabolic rate. Previous studies have focused on one or a few biological hierarchy levels, leaving us without a general understanding of how metabolic acclimatization might differ between tropical and temperate species. Here, we investigate thermal acclimatization of 3 species of Takydromus lizards distributed along a broad latitudinal gradient in China, by studying metabolic modifications at the level of the whole organism, organ, mitochondria, metabolome and proteome. As predicted by the climate variability hypothesis, the 2 temperate species T. septentrionalis and T. wolteri had an enhanced acclimation response at the whole organism level compared to the tropical species T. sexlineatus, as measured by respiratory gas exchange rates. However, the mechanisms by which whole organism performance was modified was strikingly different in the 2 temperate species: widespread T. septentrionalis modified organ sizes, while the narrowly distributed T. wolteri relied on mitochondrial, proteomic and metabolomic regulation. We suggest that these 2 mechanisms of thermal acclimatization may represent general strategies used by ectotherms, with distinct ecological costs and benefits. Lacking either of these mechanisms of thermal acclimatization capacity, the tropical species is likely to have increased vulnerability to climate change.
Question: Write a study description for the study titled 'Metabolite profiling of Arabidopsis mutants of enzymes of lower glycolysis'.
Answer: We have previously shown that in Arabidopsis the three enzymes of lower glycolysis phosphoglycerate mutase (PGAM), enolase and pyruvate kinase form a complex which play an important role in co-sub-cellar localization the mitochondria to the chloroplast. Given that their metabolites of these mutants, the complementation of pgam mutant and overexpression of PGAM are still unclear, here, we present the gas chromatography mass spectrometry-based metabolomics data and plant growth phenotypes of them. Compared with wild type, both sugar and amino acid are significantly changed at mutants of phosphoglycerate mutase, enolase, pyruvate kinase. Overexpression the PGAM could decrease the content of 3PGA, sugar and several amino acids and increase the content of alanine and pyruvate. In addition, pgam mutant could not be fully complemented by nuclear sub-localized, the side-directed-mutated and the E.coli PGAM at plant phenotype and metabolites profiling, especially the content of 3PGA, serine and intermediates of TCA cycle. These data suggested that the low glycolysis complex play an important role at both mitochondria-chloroplast co-subcellar localization and the metabolites exchange.
Question: Write a study description for the study titled 'Kynurenic acid underlies sex-specific immune responses to COVID-19'.
Answer: Sex-related differences in Coronavirus Disease (COVID-19) severity and mortality exist, with the male sex being a potential risk factor1. It was recently shown that patients with mild to moderate SARS-CoV-2 infection have elevated levels of inflammatory cytokines and chemokines, and sex-differences in these immune responses. In this study, we used an untargeted metabolomics workflow with multivariable logistic regression to identify metabolites that were associated with COVID-19 disease. Serum samples were analyzed from COVID-19 patients (n=22 women and n=17 men), and healthcare worker (HCW) controls that had no evidence of COVID-19 disease (n=10 women and n=10 men). We further investigated the sex differences in the associations between metabolites and immune markers, and found that the relevance of kynurenic acid, KYAT and AhR activation in COVID-19 could be of utmost importance.
Question: Write a study description for the study titled 'Comparative analysis of proteomic and metabolomic profiles of different species of Paris'.
Answer: An extract prepared from species of Paris is the most widely consumed herbal product in China. The genus Paris includes a variety of genotypes with different medicinal component contents but only two are defined as official sources. Closely related species have different medicinal properties because of differential expression of proteins and metabolites. To better understand the molecular basis of these differences, we examined proteomic and metabolomic changes in rhizomes of P. polyphylla var. chinensis, P. polyphylla var. yunnanensis, and P. fargesii var. fargesii using a technique known as sequential window acquisition of all theoretical mass spectra as well as gas chromatography-time-of-flight mass spectrometry. In total, 419 proteins showed significant abundance changes, and 33 metabolites could be used to discriminate Paris species. A complex analysis of proteomic and metabolomic data revealed a higher efficiency of sucrose utilization and an elevated protein abundance in the sugar metabolic pathway of P. polyphylla var. chinensis. The pyruvate content and efficiency of acetyl-CoA-utilization in saponin biosynthesis were also higher in P. polyphylla var. chinensis than in the other two species. The results expand our understanding of the proteome and metabolome of Paris and offer new insights into the species-specific traits of these herbaceous plants.SIGNIFICANCE: The traditional Chinese medicine Paris is the most widely consumed herbal product for the treatment of joint pain, rheumatoid arthritis and antineoplastic. All Paris species have roughly the same morphological characteristics; however, different members have different medicinal compound contents. Efficient exploitation of genetic diversity is a key factor in the development of rare medicinal plants with improved agronomic traits and malleability to challenging environmental conditions. Nevertheless, only a partial understanding of physiological and molecular mechanisms of different plants of Paris can be achieved without proteomics. To better understand the molecular basis of these differences and facilitate the use of other Paris species, we examine proteomic metabolomic changes in rhizomes of Paris using the technique known as SWATH-MS and GC/TOF-MS. Our research has provided information that can be used in other studies to compare metabolic traits in different Paris species. Our findings can also serve as a theoretical basis for the selection and cultivation of other Paris species with a higher medicinal value.
Question: Write a study description for the study titled 'Multi-omics reveals that alkaline mineral water improves the respiratory health and growth performance of transported calves'.
Answer: BACKGROUND: Long-distance transportation, a frequent practice in the cattle industry, stresses calves and results in morbidity, mortality and growth suppression, leading to welfare concerns and economic losses. Alkaline mineral water (AMW) is an electrolyte additive containing multiple mineral elements and shows stress-mitigating effects on humans and bovines.RESULTS: Here, we monitored the respiratory health status and growth performance of 60 Simmental calves subjected to 30 hours of road transportation using a clinical scoring system. Within the three days of commingling before the transportation and 30 days after the transportation, calves in the AMW group (n = 30) were supplied with AMW, while calves in the Control group (n = 29) were not. On three specific days, namely the day before transportation (day -3), the 30th day (day 30) and the 60th day (day 60) after transportation, sets of venous blood, serum and nasopharyngeal swab samples were collected from ten calves for routine blood testing, serology detection, whole blood transcriptomic sequencing, serum untargeted metabolic sequencing and 16S rDNA sequencing. The field data showed that calves in the AMW group displayed lower rectal temperatures (38.967 vs 39.022 °C; p < 0.001), respiratory scores (0.079 vs 0.144; p < 0.001), appetite scores (0.024 vs 0.055; p < 0.001), ocular and ear scores (0.185 vs 0.338; p < 0.001), nasal discharge scores (0.143 vs 0.241; p < 0.001) and higher body weight gains (30.87 vs 7.552 kg; p < 0.001). The outcomes of laboratory and high throughput sequencing data revealed that the calves in the AMW group demonstrated higher cellular and humoral immunities, antioxidant capacities, intestinal absorption and lipogenesis abilities, and lower inflammatory levels on days -3 and 60. The nasopharynx 16S rDNA microbiome results revealed the different composition and structure of the nasopharyngeal microflora in the two groups of calves on day 30. Joint analysis of multi-omics revealed that on days -3 and 30, bile secretion was a shared pathway enriched by differentially expressed genes and metabolites, and there were strong correlations between the differentially expressed metabolites and the main genera in the nasopharynx.CONCLUSIONS: These results suggest that AMW supplementation enhances peripheral immunity, nutrition absorption and metabolic processes, subsequently affecting the nasopharyngeal microbiota and improving the respiratory health and growth performance of transported calves. This investigation provided a practical approach to mitigate transportation stress and explored its underlying mechanisms, which are beneficial for the development of the livestock industry.
Question: Write a study description for the study titled 'Serum metabolomic profiles for distinguishing lung cancer from pulmonary tuberculosis: identification of rapid and noninvasive biomarker'.
Answer: BACKGROUND: Pulmonary tuberculosis (TB) and lung cancer (LC) have similar clinical symptoms and atypical imaging findings which are easily misdiagnosed. There is an urgent need for a noninvasive, rapid and accurate biomarker for distinguishing LC from TB.METHODS: A total of 694 subjects were enrolled and divided into discovery set (n=122), validation set (n=214) and another validation set (n=358). Metabolites were identified by multivariate and univariate analyses. The random forest (RF) algorithm and receiver operating characteristic curve analysis were used to evaluate the diagnostic efficacy of the biomarkers.RESULTS: Seven metabolites were identified and validated. The mean decrease accuracy of phenylalanylphenylalanine ranked first in RF analysis. The area under the curve of phenylalanylphenylalanine was 0.8885 (95% CI 0.8444-0.9326), the sensitivity was 71.43%, and the specificity was 92.13%. Compared with that in NC subjects, the level of phenylalanylphenylalanine was elevated in LC patients (fold change = 2.92, p value < 0.01) and reduced in TB patients (fold change = 0.80, p value < 0.05).CONCLUSIONS: The metabolomic profile of LC and TB was described and a key biomarker, phenylalanylphenylalanine, was identified. We produced a rapid and noninvasive method to supplement existing clinical diagnostic examinations for distinguishing LC from TB.
Question: Write a study description for the study titled 'Metabolism Disorder Promotes Isoproterenol-induced Myocardial Injury in Mice with High Temperature and High Humidity and High-Fat Diet'.
Answer: Isoproterenol (ISO) provides a simple and non-invasive method for inducing myocardial injury with lower mortality and higher reproducibility. Phlegm-damp syndrome, as known as “Tanshi” in Chinese, is one of Traditional Chinese Medicine (TCM) syndrome differentiation, which plays an important role in the development of cardiovascular diseases. However, the underlying mechanism remains unknown. In our present study, a myocardial injury mouse model was introduced by ISO administration combined with high temperature and high humidity and high fat diet to simulate phlegm-damp syndrome. Nontargeted metabolomics with LC-MS/MS was adopted to reveal serum metabolism profile for elucidating the possible molecular mechanism.
Question: Write a study description for the study titled 'Transcriptomic and lipidomic profiling of subcutaneous and visceral adipose tissues in 15 vertebrates'.
Answer: The storage of lipids as energy in adipose tissue (AT) has been conserved over the course of evolution. However, substantial differences in ATs physiological activities were reported between species. Hence, establishing the mechanisms shaping evolutionarily divergence in ATs transcriptomes could provide a deeper understanding of AT regulation and its roles in obesity-related diseases. While previous studies performed anatomical, physiological and morphological comparisons between ATs across different species, little is currently understood at the molecular phenotypic levels. Here, we characterized transcriptional and lipidomic profiles of available subcutaneous and visceral ATs samples across 15 vertebrate species, spanning more than 300 million years of evolution, including placental mammals, birds and reptiles. We provide detailed descriptions of the datasets produced in this study and report gene expression and lipid profiles across samples. These resources should provide researchers could insights into the molecular and evolutionary mechanisms underlying functional differences between ATs in vertebrate species.
Question: Write a study description for the study titled 'Seipin Governs Caveolin-1 Trafficking Through Modulating Sphingolipid-Glycerolipid Balance'.
Answer: Dysregulation of Caveolin-1 (CAV1), a key component of caveolae, leads to pleiotropic disorders; yet, the mechanisms controlling its trafficking remain unclear. Here, we show that the lipid droplet (LD) biogenesis factor seipin controls CAV1 localization. Seipin deficiency in mice and HeLa cells resulted in the accumulation of saturated lipids and ceramides, disrupting the membrane order of the trans-Golgi network (TGN). This impaired CAV1 trafficking to the plasma membrane, reduced caveolae formation, and redirected CAV1 to LDs - an effect also observed in seipin-deficient patient fibroblasts. We reproduced this phenotype in wild-type cells by supplementing them with palmitate or ceramide, or by inhibiting stearoyl-CoA desaturase 1, which suggests that accumulating saturated lipids are the root cause. Inhibiting fatty acid synthase in seipin knockout cells rescued CAV1 localization. Our findings indicate that seipin modulates lipid partitioning between glycerolipids and sphingolipids, which is critical for maintaining TGN function in CAV1 sorting and trafficking.
Question: Write a study description for the study titled 'Polyketide synthase-derived sphingolipids determine microbiota-mediated protection against pathogens in C. elegans'.
Answer: Protection against pathogens is a major function of the gut microbiota. Although bacterial natural products have emerged as crucial components of host-microbiota interactions, their exact role in microbiota-mediated protection is largely unexplored. We addressed this knowledge gap with the nematode Caenorhabditis elegans and its microbiota isolate Pseudomonas fluorescens MYb115 that is known to protect Bacillus thuringiensis (Bt) infection. We find that MYb115-mediated protection depends on sphingolipids that are encoded by the iterative type I polyketide synthase (PKS) biosynthetic gene cluster, thereby describing a noncanonical pathway of bacterial sphingolipid production. We provide evidence that MYb115-derived sphingolipids affect C. elegans tolerance to Bt infection by altering host sphingolipid metabolism. This work establishes sphingolipids as structural outputs of bacterial PKSs and highlights the role of microbiota-derived sphingolipids in host protection against pathogens.
Question: Write a study description for the study titled 'IDH1 Mutations Induce Organelle Defects Via Dysregulated Phospholipids (CSHNeg)'.
Answer: Infiltrating gliomas are devastating and incurable tumors. Amongst all gliomas, those harboring an isocitrate dehydrogenase 1 mutation (IDHmut), acquire a different tumor biology and clinical manifestation than those that are IDHWT. Understanding the unique metabolic profile reprogrammed by IDH1 mutation has the potential to identify new molecular targets for glioma therapy. Herein, we discovered monounsaturated (MUFA) to polyunsaturated (PUFA) lipid imbalances in organelles, generated by IDH mutation in cells and patient tissue, that were responsible for Golgi and ER dilation. We demonstrated a direct link between the IDH mutation and these organelle morphology via D-2HG-induced stearyl-CoA desaturase (SCD) overexpression, the rate limiting enzyme in MUFA biosynthesis. Inhibition of IDH mutation or SCD silencing restored ER and Golgi morphology, while D-2HG and oleic acid induced morphological defects in these organelles. Moreover, addition of oleic acid, which tilted the balance towards elevated levels of MUFA, produced IDH1mut-specific cellular apoptosis. Collectively, these results suggest that IDH1mut-induced SCD overexpression can rearrange the biodistribution of lipids in the organelles of glioma, providing a new insight on the link between lipids metabolism and organelle morphology in these cells, with potential and unique therapeutic implications.Linked studies;MTBLS1967 FA_HILICZMTBLS1974 LCMS(CSHPos)
Question: Write a study description for the study titled 'MaHPIC Experiment 23: Metabolomics from Macaca mulatta infected with Plasmodium cynomolgi B strain to produce and integrate clinical, hematological, parasitological, and omics measures of acute primary infection and relapses'.
Answer: MaHPIC Experimental Description: Malaria-naive male rhesus macaques (Macaca mulatta), approximately four years of age, were inoculated intravenously with salivary gland sporozoites produced and isolated at the Centers for Disease Control and Prevention from multiple Anopheles species (An. dirus, An. gambiae, and An. stephensi) and then profiled for clinical, hematological, parasitological, immunological, functional genomic, lipidomic, proteomic, and metabolomic measurements. The experiment was designed for about 100 days, with pre- and post-100 day periods to prepare subjects and administer curative treatments respectively. During the 100-day period subjects experienced periods of patent and sub- patent infection. The anti-malarial drug artemether was subcuratively administered to subjects after the initial peak of infection, if subjects were not able to self-resolve. Blood-stage curative artemether was administered to all subjects following peak infection, and following a period of relapse infection. All peaks were clinically determined for each subject. The anti-malarial drugs primaquine and chloroquine were administered to all subjects at the end of the study for curative treatment of the liver and blood-stage infections, respectively. Capillary blood samples were collected daily for the measurement of CBCs, reticulocytes, and parasitemias. Capillary blood samples were collected every other day to obtain plasma for metabolomic analysis. Venous blood and bone marrow samples were collected at seven time points for functional genomic, proteomic, lipidomic, and immunological analyses. Within the MaHPIC, this project is known as 'Experiment 23'. This is an iteration of Experiment 04 with the same parasite-host combination and sampling and treatment adjustments made, and this is the first in a series of experiments that includes subsequent homologous (Experiment 24, P. cynomolgi B strain) and heterologous (Experiment 25, P. cynomolgi strain ceylonensis) challenges of individuals from the Experiment 23 cohort. One subject was not included in subsequent experiments due to persistent behavioral issues that prevented sample collection. This dataset was produced by Dean Jones at Emory University. To access other publicly available results from E23 and other MaHPIC Experiments, including clinical results (specifics on drugs administered, diet, and veterinary interventions), and other omics, visit http://plasmodb.org/plasmo/mahpic.jsp. This page will be updated as datasets are released to the public. The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC).Linked Studies: Malaria Host-Pathogen Interaction Center (MaHPIC)
Question: Write a study description for the study titled 'Metabolomic signature of mouse cerebral cortex following Toxoplasma gondii infection'.
Answer: BACKGROUND: The protozoan parasite Toxoplasma gondii infects and alters the neurotransmission in cerebral cortex and other brain regions, leading to neurobehavioral and neuropathologic changes in humans and animals. However, the molecules that contribute to these changes remain largely unknown.METHODS: We have investigated the impact of T. gondii infection on the overall metabolism of mouse cerebral cortex. Mass-spectrometry-based metabolomics and multivariate statistical analysis were employed to discover metabolomic signatures that discriminate between cerebral cortex of T. gondii-infected and uninfected control mice.RESULTS: Our results identified 73, 67 and 276 differentially abundant metabolites, which were involved in 25, 37 and 64 pathways at 7, 14 and 21 days post-infection (dpi), respectively. Metabolites in the unsaturated fatty acid biosynthesis pathway were upregulated as the infection progressed, indicating that T. gondii induces the biosynthesis of unsaturated fatty acids to promote its own growth and survival. Some of the downregulated metabolites were related to pathways, such as steroid hormone biosynthesis and arachidonic acid metabolism. Nine metabolites were identified as T. gondii responsive metabolites, namely galactosylsphingosine, arachidonic acid, LysoSM(d18:1), L-palmitoylcarnitine, calcitetrol, 27-Deoxy-5b-cyprinol, L-homophenylalanine, oleic acid and ceramide (d18:1/16:0).CONCLUSIONS: Our data provide novel insight into the dysregulation of the metabolism of the mouse cerebral cortex during T. gondii infection and have important implications for studies of T. gondii pathogenesis.
Question: Write a study description for the study titled 'Fat Deposition in the Muscle of Female and Male Yak and the Correlation of Yak Meat Quality with Fat'.
Answer: Background:  The study of fat deposition in yaks of different gender plays a positive role in improving the meat quality and breeding of yaks. In this work, the characteristic of fat deposition in male and female yaks, and the regulations of gender difference to fat deposition in yaks were explored. Result:  Compared with male yaks, the female yaks possessed higher or more body fat rate (BFR) of visceral except liver, fat content in muscle and liver and subcutaneous fat ( p Conclusion:  The fat and cholesterol synthesis increased in liver of female yaks, and the fat transport in blood of female yaks increased too. In subcutaneous fat of female yaks, the high levels of myo-inositol activated the calcium signaling, following the increase of secretion in fat cell. Then, the high levels of LEP and 13(S)-HODE strengthened PPAR signal, and the fat synthesis, cholesterol synthesis, fatty acid biosynthesis of the linoleic and linolenic acid being the precursor increased, whereas lipolysis and fatty acid oxidation decreased by the regulation of downstream genes in PPAR signal. Meanwhile, SREBF1 also played an important part in the regulation of fat metabolism in yaks of different gender.