LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Metabolomic insights into the browning of the peel of bagging 'Rui Xue' apple fruit'.
Answer: BACKGROUND: Bagging is one of the most important techniques for the production of high-quality fruits. In the act of cultivation, we found a new kind of browning in peel of the apple fruit that occurs before harvest and worsens during the storage period. There are many studies on metabonomic analysis about the browning of storage fruits, but few studies on the mechanism of browning before harvest. This experiment was based on metabonomic studies to explore the effect of bagging on fruit peel browning.RESULTS: In this study, five-year-old trees of ‘Rui Xue’ were used as materials. Bagging fruits without browning (BFW) and bagging fruits with browning (BFB) were set as the experimental groups, non-bagging fruits (NBF) were set as control (CT). Our results show that 131 metabolites of BFW were significantly up-regulated and 217 metabolites were significantly down-regulated compared with NBF; 198 metabolites of BFB were significantly up-regulated and and 178 metabolites were significantly down-regulated compared with BFW (Variable important in projection (VIP) > 1 and p-value < 0.05). The synthesis and accumulation of flavonoids and lipids were significantly changed after bagging; compared with NBF, 11 flavonoids and 6 lipid molecules were significantly decreased in the BFW (top 50 metabolites). Compared with BFW, 11 flavonoids and 7 lipids were further decreased in BFB, but, 12 triterpenes were significantly accumulated in BFB. As the peel browning, galactose metabolism, ABC membrane transporter protein, flavonoid biosynthesis and linoleic acid metabolism pathways were significantly changed in BFW and BFB compared with NBF. Physiological indicators show that, compared with NBF, the MDA in peel of BFW and BFB significantly increased by 0.46 times and 2.94 times, respectively; and the cell membrane permeability of BFW and BFB were significantly increased by 15.7% and 28.2%, respectively. We analyzed the expression of related genes in the metabolic pathways of flavonoids, compared with NBF, the flavonoid synthesis genes MdLAR were significantly up-regulated by 2.55 and 9.37 times in BFW and BFB, and the MdANR genes were also significantly up-regulated by 2.33 and 2.69 times, respectively. In addition to this, the downstream flavonoids-related polymeric genes MdLAC7 and MdLAC14 were the most significantly expressed. Compared with NBF, MdLAC7 was significantly up-regulated by 0.43 and 13.88 times in BFW and BFB, and MdLAC14 was also significantly up-regulated by 7.13 and 3.17 times, respectively.CONCLUSIONS: Our findings demonstrated that the microenvironment of fruit was changed by bagging, the destruction of cell structure, the increase of lipid peroxidation of cell membrane, the decrease of flavonoids and the increase of triterpenoids were the main reasons for the browning of peel about bagging 'Rui Xue'.
Question: Write a study description for the study titled 'Transcriptomics and metabolomics analysis reveal the anti-oxidation and immune boosting effects of mulberry leaves in growing mutton sheep'.
Answer: INTRODUCTION: Currently, the anti-oxidation of active ingredients in mulberry leaves (MLs) and their forage utilization is receiving increasing attention. Here, we propose that MLs supplementation improves oxidative resistance and immunity. METHODS: We conducted a trial including 3 groups of growing mutton sheep, each receiving fermented mulberry leaves (FMLs) feeding, dried mulberry leaves (DMLs) feeding or normal control feeding without MLs. RESULTS: Transcriptomic and metabolomic analyses revealed that promoting anti-oxidation and enhancing disease resistance of MLs is attributed to improved tryptophan metabolic pathways and reduced peroxidation of polyunsaturated fatty acids (PUFAs). Furthermore, immunity was markedly increased after FMLs treatment by regulating glycolysis and mannose-6-phosphate pathways. Additionally, there was better average daily gain in the MLs treatment groups. CONCLUSION: These findings provide new insights for understanding the beneficial effects of MLs in animal husbandry and provide a theoretical support for extensive application of MLs in improving nutrition and health care values.
Question: Write a study description for the study titled 'The Poly (ADP-Ribose) Polymerase inhibitor Veliparib and Radiation Cause Significant Cell Line Dependent Metabolic Changes in Breast Cancer Cells'.
Answer: Breast tumors are characterized into different subtypes based on their surface marker expression, which affects their prognosis and treatment. For example, triple negative breast cancer cells (ER-/PR-/Her2-) show reduced susceptibility towards radiotherapy and chemotherapeutic agents. Poly (ADP-ribose) polymerase (PARP) inhibitors have shown promising results in clinical trials, both as single agents and in combination with other chemotherapeutics, in several subtypes of breast cancer patients. PARP1 is involved in DNA repair, apoptosis, and transcriptional regulation and an understanding of the effects of PARP inhibitors, specifically on metabolism, is currently lacking. Here, we have used NMR-based metabolomics to probe the cell line-specific effects of PARP inhibitor and radiation on metabolism in three distinct breast cancer cell lines. Our data reveal several cell line independent metabolic changes upon PARP inhibition, including an increase in taurine. Pathway enrichment and topology analysis identified that nitrogen metabolism, glycine, serine and threonine metabolism, aminoacyl-tRNA biosynthesis and taurine and hypotaurine metabolism were enriched after PARP inhibition in the three breast cancer cell lines. We observed that the majority of metabolic changes due to radiation as well as PARP inhibition were cell line dependent, highlighting the need to understand how these treatments affect cancer cell response via changes in metabolism. Finally, we observed that both PARP inhibition and radiation induced a similar metabolic response in the HCC1937 (BRCA mutant cell line), but not in MCF-7 and MDAMB231 cells, suggesting that radiation and PARP inhibition share similar interactions with metabolic pathways in BRCA mutant cells. Our study emphasizes the importance of differences in metabolic responses to cancer treatments in different subtypes of cancers.
Question: Write a study description for the study titled 'The ULK3 kinase is a key determinant of keratinocyte self-renewal and tumorigenesis targeting the arginine methylome'.
Answer: Epigenetic mechanisms oversee epidermal homeostasis and oncogenesis. The identification of kinases controlling these processes has direct therapeutic implications. We show that ULK3 is a nuclear kinase with elevated expression levels in squamous cell carcinomas (SCCs) arising in multiple body sites, including skin and Head/Neck. ULK3 loss by gene silencing or deletion reduces proliferation and clonogenicity of human keratinocytes and SCC-derived cells and affects transcription impinging on stem cell-related and metabolism programs. Mechanistically, ULK3 directly binds and regulates the activity of two histone arginine methyltransferases, PRMT1 and PRMT5 (PRMT1/5), with ULK3 loss compromising PRMT1/5 chromatin association to specific genes and overall methylation of histone H4, a shared target of these enzymes. These findings are of translational significance, as downmodulating ULK3 by RNA interference or locked antisense nucleic acids (LNAs) blunts the proliferation and tumorigenic potential of SCC cells and promotes differentiation in two orthotopic models of skin cancer.
Question: Write a study description for the study titled 'An Atlas of Ferroptosis-induced Secretomes promotes Macrophage priming'.
Answer: Cells undergoing regulated necrosis systemically communicate with the immune system via release of protein and non-protein secretomes. Ferroptosis is a recently described iron-dependent type of regulated necrosis driven by massive lipid peroxidation. While membrane rupture occurs during ferroptosis, a comprehensive appraisal of ferroptotic secretomes and their potential biological activity has been lacking. Here, we apply a multi-omics approach to provide an atlas of ferroptosis-induced secretomes and reveal a novel function in macrophage priming. While proteins with assigned DAMP and innate immune system function such as MIF, heat shock proteins (HSPs) and chaperonines were released from ferroptotic cells, this happened in the absence of bona fide inflammatory chemo- cytokines. Non-protein secretomes with assigned inflammatory function contained oxylipins as well as TCA- and methionine-cycle metabolites. Interestingly, incubation of bone marrow-derived macrophages (BMDMs) with ferroptotic supernatants induced transcriptional reprogramming consistent with priming. Indeed, exposure to ferroptotic enhanced LPS-induced cytokine production. These results define the spectrum of ferroptosis-induced secretomes and identify a biological activity in macrophage priming with important implications for the fine-tuning of inflammatory processes.
Question: Write a study description for the study titled 'GC-MS Based Plasma Metabolomics for Identification of Candidate Biomarkers for Hepatocellular Carcinoma in Egyptian Cohort'.
Answer: This study evaluates changes in metabolite levels in hepatocellular carcinoma (HCC) cases vs. patients with liver cirrhosis by analysis of human blood plasma using gas chromatography coupled with mass spectrometry (GC-MS). Untargeted metabolomic analysis of plasma samples from participants recruited in Egypt was performed using two GC-MS platforms: a GC coupled to single quadruple mass spectrometer (GC-qMS) and a GC coupled to a time-of-flight mass spectrometer (GC-TOFMS). Analytes that showed statistically significant changes in ion intensities were selected using ANOVA models. These analytes and other candidates selected from related studies were further evaluated by targeted analysis in plasma samples from the same participants as in the untargeted metabolomic analysis. The targeted analysis was performed using the GC-qMS in selected ion monitoring (SIM) mode. The method confirmed significant changes in the levels of glutamic acid, citric acid, lactic acid, valine, isoleucine, leucine, alpha tocopherol, cholesterol, and sorbose in HCC cases vs. patients with liver cirrhosis. Specifically, our findings indicate up-regulation of metabolites involved in branched-chain amino acid (BCAA) metabolism. Although BCAAs are increasingly used as a treatment for cancer cachexia, others have shown that BCAA supplementation caused significant enhancement of tumor growth via activation of mTOR/AKT pathway, which is consistent with our results that BCAAs are up-regulated in HCC.
Question: Write a study description for the study titled 'Discovery of urinary biomarkers to discriminate between exogenous and semi-endogenous thiouracil in cattle (Cow samples)'.
Answer: In the European Union, the use of thyreostats for animal fattening purposes has been banned because of their carcinogenic and teratogenic effects, whereby any residues in derived food products may hold a risk for human health. In this regard, potential abuse is monitored by targeted analysis of thyreostats with the application of a zero-tolerance policy. However, such a strategy is no longer adequate because of the semi-endogenous origin of some thyreostats, including thiouracil (TU). Additionally, the use of recommended TU concentration levels (10 or 30 µg/l) is also not fully conclusive. Therefore, this study aimed at defining urinary metabolite markers by which the true origin of detected TU could be ascertained. To this end, an in vivo study was carried out in which 11 calves were subjected to either a control treatment, a rapeseed-enriched diet (known to induce semi-endogenous formation) or a TU treatment. Urine samples (n = 165) were assessed through metabolic fingerprinting, employing ultra-high performance liquid-chromatography and Q-Exactive Orbitrap mass spectrometry. Urinary fingerprints were interpreted by multivariate data-analysis.  The targeted Calf samples assay for this study can be found in the MetaboLights study MTBLS554. Linked Studies: MTBLS554
Question: Write a study description for the study titled 'Gut Microbial and Metabolic Responses to Salmonella enterica Serovar Typhimurium and Candida albicans'.
Answer: The gut microbiota is increasingly recognized for playing a critical role in human health and disease, especially in conferring resistance to both virulent pathogens such as Salmonella, which infects 1.2 million people in the United States every year [1], and opportunistic pathogens like Candida, which causes an estimated 46,000 cases of invasive candidiasis each year in the United States [2]. The dynamics of pathogen-microbiome interactions and the metabolites involved in this process remain largely unknown. We use gnotobiotic mice infected with the virulent pathogen Salmonella enterica serovar Typhimurium or the opportunistic pathogen Candida albicans in combination with metagenomics and discovery metabolomics to identify changes in the community and metabolome during infection. To isolate the role of the microbiota in response to pathogens, we compared mice monocolonized with the pathogen, uninfected mice 'humanized' with a synthetic human microbiome, or infected humanized mice. We observe that changes in the community and in biosynthetic gene cluster potential occur within 3 days for the virulent Salmonella enterica serovar Typhimurium, but there are minimal changes with a poorly colonizing Candida albicans. In addition, the metabolome shifts depending on infection status, including changes in glutathione metabolites in response to Salmonella infection. The LC-MS metabolomic fingerprint of the cecum differed between mice monocolonized with either pathogen and humanized infected mice. Specifically, we identified an increase in glutathione disulfide, glutathione cysteine disulfide, inosine 5'-monophosphate, and hydroxybutyrylcarnitine in mice infected with Salmonella in contrast to uninfected mice and mice monocolonized with Salmonella. These metabolites potentially play a role in pathogen-induced oxidative stress. These results provide insight into how the microbiota community members interact with each other and with pathogens on a metabolic level.Ref:[1] Scallan E, Hoekstra RM, Angulo FJ, Tauxe RV, Widdowson MA, Roy SL, Jones JL, and Griffin PM. Foodborne Illness Acquired in the United States—Major Pathogens. Emerg Infect Dis 2011;17:7-15. doi.org/10.3201/eid1701.P11101[2] Centers for Disease Control and Prevention, Antibiotic Resistance Threats in the United States, 2013
Question: Write a study description for the study titled 'Absence of tmRNA increases the persistence to cefotaxime by upregulating the metabolites GlcNAc in Aeromonas veronii'.
Answer: Bacterial persisters refer to a small proportion of phenotypically heterogeneous variants with transient capability for survival when exposing to high concentrations of antibiotic, which constitute the major cause for recurrent infections both in human and aquatic infections. In pathogenic bacteria Aeromonas veronii, tmRNA (transfer-messenger RNA), the core factor of trans-translation system, was identified as a determinant regulator mediating the persistence to β-lactams. Compared with the wild type, the deletion of tmRNA exhibited unchanged growth rate, sustained susceptibility to cefotaxime, but did increase persister cell formation. Transcriptomic and metabolomic analyses revealed that, the absence of tmRNA not only upreglated the expressions of metabolic genes especially in the metabolic flux of peptidoglycan biosynthesis, but also significantly elevated the intercellular level of metabolite GlcNAc, thereby intensifying the contents of peptidoglycans in the cell wall. Eventually, exogenous GlcNAc stimulated significantly the bacterial growth and persistence to cefotaxime in a concentration dependent manner. Taken together, these results uncover a novel mechanism of persister formation mediated by tmRNA against the β-lactam challenges.
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 against Bacillus thuringiensis (Bt) infection. We find that MYb115-mediated protection depends on sphingolipids that are derived from an iterative type I polyketide synthase (PKS), PfSgaAB, thereby revealing a non-canonical pathway for the production of bacterial sphingolipids as secondary metabolites. Sphingolipid production is common in eukaryotes but was thought to be limited to a few bacterial phyla that encode the serine palmitoyltransferase (SPT) enzyme, which catalyzes the initial step in sphingolipid synthesis. We demonstrate that PfSgaB encodes a pyridoxal 5'-phosphate-dependent alpha-oxoamine synthase, which functions as SPT, and find homologous putative PKSs present across host-associated bacteria that are so far unknown sphingolipid producers. Moreover, 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 PKS and highlights the role of microbiota-derived sphingolipids in host protection against pathogens.
Question: Write a study description for the study titled 'Similar, but different: structurally related azelaic acid and hexanoic acid trigger differential metabolomic and transcriptomic responses in tobacco cells'.
Answer: BACKGROUND: Plants respond to various stress stimuli by activating an enhanced broad-spectrum defensive ability. The development of novel resistance inducers represents an attractive, alternative crop protection strategy. In this regard, hexanoic acid (Hxa, a chemical elicitor) and azelaic acid (Aza, a natural signaling compound) have been proposed as inducers of plant defense, by means of a priming mechanism. Here, we investigated both the mode of action and the complementarity of Aza and Hxa as priming agents in Nicotiana tabacum cells in support of enhanced defense.  RESULTS: Metabolomic analyses identified signatory biomarkers involved in the establishment of a pre-conditioned state following Aza and Hxa treatment. Both inducers affected the metabolomes in a similar manner and generated common biomarkers: caffeoylputrescine glycoside, cis-5-caffeoylquinic acid, feruloylglycoside, feruloyl-3-methoxytyramine glycoside and feruloyl-3-methoxytyramine conjugate. Subsequently, quantitative real time-PCR was used to investigate the expression of inducible defense response genes: phenylalanine ammonia lyase, hydroxycinnamoyl CoA quinate transferase and hydroxycinnamoyl transferase to monitor activation of the early phenylpropanoid pathway and chlorogenic acids metabolism, while ethylene response element-binding protein, small sar1 GTPase, heat shock protein 90, RAR1, SGT1, non-expressor of PR genes 1 and thioredoxin were analyzed to report on signal transduction events. Pathogenesis-related protein 1a and defensin were quantified to investigate the activation of defenses regulated by salicylic acid and jasmonic acid respectively. The qPCR results revealed differential expression kinetics and, in general (except for NPR1, Thionin and PR1a), the relative gene expression ratios observed in the Hxa-treated cells were significantly greater than the expression observed in the cells treated with Aza.  CONCLUSIONS: The results indicate that Aza and Hxa have a similar priming effect through activation of genes involved in the establishment of systemic acquired resistance, associated with enhanced synthesis of hydroxycinnamic acids and related conjugates.
Question: Write a study description for the study titled 'Gestational palmitic acid suppresses embryonic GATA-binding protein 4 signaling and causes congenital heart disease'.
Answer: Dysregulated maternal fatty acid metabolism increases the risk of congenital heart disease (CHD) in offspring with an unknown mechanism, and the effect of folic acid fortification in preventing CHD is controversial. Using gas chromatography coupled to either a flame ionization detector or mass spectrometer (GC-FID/MS) analysis, we find that the palmitic acid (PA) concentration increases significantly in serum samples of pregnant women bearing children with CHD. Feeding pregnant mice with PA increased CHD risk in offspring and cannot be rescued by folic acid supplementation. We further find that PA promotes methionyl-tRNA synthetase (MARS) expression and protein lysine homocysteinylation (K-Hcy) of GATA4 and results in GATA4 inhibition and abnormal heart development. Targeting K-Hcy modification by either genetic ablation of Mars or using N-acetyl-L-cysteine (NAC) decreases CHD onset in high-PA-diet-fed mice. In summary, our work links maternal malnutrition and MARS/K-Hcy with the onset of CHD and provides a potential strategy in preventing CHD by targeting K-Hcy other than folic acid supplementation.
Question: Write a study description for the study titled 'A noteworthy response process of Microcystis aeruginosa induced by exogenous reactive oxygen species in algae-laden water treatment'.
Answer: The effectiveness of reactive oxygen species (ROS) generated by advanced oxidation processes (AOPs) in inactivating harmful algae in drinking water varies considerably. Therefore, the physiological and biochemical reactions of algae need to be considered to clarify the underlying mechanisms. Herein, we studied the response mechanisms of Microcystis aeruginosa to exogenous ROS.
Question: Write a study description for the study titled 'The Immune Response to Leads to Dichroism and Blue Pigmentation in Spotted Lanternfly Forewings'.
Answer: Coloration in creatures is a historical and longstanding scientific research hotspot for the profound significance of color. Normally, the blue color in nature is surprisingly scarce and produced by the micro- and nano-structures in most blue animals. Here, we report a dichromatic mechanism that the forewings of the spotted lanternfly Lycorma delicatula turn from brown to blue pigmentation. The morphological data revealed that the multilayered procuticle of the wing base enhance reflectance intensity compared with the single-layered procuticle in the wing tip. The multi-omics analyses comprehensively illustrate that the mechanistic explanation of blue coloration involves host cell simulation and subsequent stress induced by pathogenic bacteria (a staphylococcal/streptococcal toxin), made in intracellular and humoral immune response via recognizing antigen interfered with a symbiotic virus (Alphavirus glycoprotein J) regulated by immune and neurological systems. In blue wings, five pigment types, namely, pterins, violacein, flavones, terpenoids and tetrapyrroles, metabolized into antibiotics or other medicinal substances resulting in dichroism. Our findings suggest that the underlying mechanisms of blue-brown dichroism in lanternflies involve innate and adaptive immunity, which deepens the understanding of the complex characteristics of biological coloration.