PubMed

Mikrochim Acta. 2024 Aug 19;191(9):546. doi: 10.1007/s00604-024-06622-8.ABSTRACTTryptophan(Trp) is being explored as a potential biomarker for various diseases associated with decreased tryptophan levels; however, metabolomic methods are expensive and time-consuming and require extensive sample analysis, making them urgently needed for trace detection. To exploit the properties of Ti3C2 MXenes a rational porous methyl orange (MO)-delaminated Ti3C2 MXene was prepared via a facile mixing process for the electrocatalytic oxidation of Trp. The hollow-like 3D structure with a more open structure and the synergistic effect of MO and conductive Ti3C2 MXene enhanced its electrochemical catalytic capability toward Trp biosensing. More importantly, MO can stabilize Ti3C2 MXene nanosheets through noncovalent π-π interactions and hydrogen bonding. Compared with covalent attachment, these non-covalent interactions preserve the electronic conductivity of the Ti3C2 MXene nanosheets. Finally, the addition of MO-derived nitrogen (N) and sulfur (S) atoms to Ti3C2 MXene enhanced the electronegativity and improved its affinity for specific molecules, resulting in high-performance electrocatalytic activity. The proposed biosensor exhibited a wide linear response in concentration ranges of 0.01-0.3 µM and 0.5-120 µM, with a low detection limit of 15 nM for tryptophan detection, and high anti-interference ability in complex media of human urine and egg white matrices. The exceptional abilities of the MO/Ti3C2 nanocatalyst make it a promising electrode material for the detection of important biomolecules.PMID:39158725 | DOI:10.1007/s00604-024-06622-8

Food Funct. 2024 Aug 19. doi: 10.1039/d4fo00930d. Online ahead of print.ABSTRACTMonascus has the ability to produce secondary metabolites, such as monacolin K (MK), known for its physiological functions, including lipid-lowering effects. Widely utilized in industries such as health food and medicine, MK is a significant compound derived from Monascus. Quinoa, recognized by the Food and Agriculture Organization of the United Nations as "the only plant food that can meet human basic nutritional needs by itself", possesses dual advantages of high nutritional value and medicinal food homology. This study employed animal experiments to investigate the hypolipidemic activity of Monascus-fermented quinoa (MFQ) and explored the molecular mechanism underlying the lipid-lowering effect of MFQ on hyperlipidemic mice through transcriptomic and metabolomic analyses. The results demonstrated that high-dose MFQ intervention (1600 mg kg-1 d-1) effectively decreased weight gain in hyperlipidemic mice without significant changes in cardiac index, renal index, or spleen index. Moreover, hepatic steatosis in mice was significantly improved. Serum levels of total cholesterol, triglycerides, and low-density lipoprotein cholesterol were markedly reduced, demonstrating that the lipid-lowering effect of MFQ was comparable to the drug control lovastatin. Conversely, both low-dose MFQ (400 mg kg-1 d-1) and unfermented quinoa exhibited no significant lipid-lowering effect. Integrated analysis of the transcriptome and metabolome suggested that MFQ may regulate amino acid levels in hyperlipidemic mice by influencing metabolic pathways such as phenylalanine, tyrosine, and tryptophan metabolism. This regulation alleviates hyperlipidemia induced by a high-fat diet, resulting in a significant reduction in blood lipid levels in mice.PMID:39158509 | DOI:10.1039/d4fo00930d

Food Funct. 2024 Aug 19. doi: 10.1039/d4fo01723d. Online ahead of print.ABSTRACTInfant formulas are designed to provide sufficient energy and the necessary nutrients to support the growth and development of newborns. Currently, research on the functions of formula milk powder focuses on clinical research and cell experiments, and there were many cell experiments that investigated the effect of infant formulas on cellular growth. However, most of the cells used are tumor cell lines, which are unable to simulate the real digestion process of an infant. In this study, we innovatively proposed a method that integrates human small intestinal organoids (SIOs) with transcriptomics and metabolomics analysis. We induced directed differentiation of human embryonic stem cells into SIOs and simulated the intestinal environment of newborns with them. Then, three kinds of 1-stage infant formulas from the same brand were introduced to simulate the digestion, absorption, and metabolism of the infant intestine. The nutritional value of each formula milk powder was examined by multi-omics sequencing methods, including transcriptomics and metabolomics analysis. Results showed that there were significant alterations in gene expression and metabolites in the three groups of SIOs after absorbing different infant formulas. By analyzing transcriptome and metabolome data, combined with GO, KEGG, and GSEA analysis, we demonstrated the ability of SIOs to model the different aspects of the developing process of the intestine and discovered the correlation between formula components and their effects, including Lactobacillus lactis and lactoferrin. The study reveals the effect and mechanisms of formula milk powder on the growth and development of infant intestines and the formation of immune function. Furthermore, our method can help to construct a multi-level assessment model, detect the effects of nutrients, and evaluate the interactions between nutrients, which is helpful for future research and development of infant powders.PMID:39158038 | DOI:10.1039/d4fo01723d

Food Funct. 2024 Aug 19. doi: 10.1039/d4fo01522c. Online ahead of print.ABSTRACTAdvances in the understanding of bioavailability and metabolism of bioactive compounds have been achieved primarily through targeted or semi-targeted metabolomics approaches using the hypothesis of potential metabolized compounds. The recent development of untargeted metabolomics approaches can present great advantages in this field, such as in the discovery of new metabolized compounds or to study the metabolism of compounds from multiple matrices simultaneously. Thus, this study proposes the use of an untargeted metabolomics strategy based on HPLC-ESI-QTOF-MS for the study of bioavailability and metabolism of bioactive compounds from different vegetal sources. Specifically, this study has been applied to plasma samples collected in an acute human intervention study using three matrices (Hibiscus sabdariffa, Silybum marianum and Theobroma cacao). This approach allowed the selection of those significant variables associated with exogenous metabolites derived from the consumption of bioactive compounds for their subsequent identification. As a result, 14, 25 and 3 potential metabolites associated with supplement intake were significantly detected in the plasma samples from volunteers who ingested the H. sabdariffa (HS), S. marianum (SM) and T. cacao (TC) extracts. Furthermore, Tmax values have been computed for each detected compound. The results highlight the potential of untargeted metabolomics for rapid and comprehensive analysis when working with a wide range of exogenous metabolites from different plant sources in biological samples.PMID:39158031 | DOI:10.1039/d4fo01522c

J Proteome Res. 2024 Aug 19. doi: 10.1021/acs.jproteome.4c00340. Online ahead of print.ABSTRACTThe COVID-19 pandemic caused by the SARS-CoV-2 virus infected more than 775,686,716 humans and was responsible for the death of more than 7,054,093 individuals. COVID-19 has taught us that the development of vaccines, repurposing of drugs, and understanding the mechanism of a disease can be done within a short time. The COVID-19 proteomics and metabolomics has contributed to its diagnosis, understanding of its progression, host-virus interaction, disease mechanism, and also in the search of suitable anti-COVID therapeutics. Mass spectrometry based proteomics was used to find the potential biomarkers of different stages of COVID-19 including severe and nonsevere cases in the blood serum. Notably, protein-protein interaction techniques to understand host-virus interactions were also significantly useful. The single-cell proteomics studies were carried out to ascertain the changes in immune cell composition and its activation in mild COVID-19 patients versus severe COVID-19 patients using whole-blood and peripheral-blood mononuclear cells. Modern technologies were helpful to deal with the pandemic; however, there is still scope for further development. Further, attempts were made to understand the protein-protein, metabolite-metabolite, and protein-metabolite interactomes, derived from proteins and metabolite fingerprints of COVID-19 patients by reanalysis of COVID-19 public mass spectrometry based proteomics and metabolomics studies. Further, some of these interactions were supported by the literature as validations in the COVID-19 studies.PMID:39157976 | DOI:10.1021/acs.jproteome.4c00340

FASEB J. 2024 Aug 31;38(16):e70003. doi: 10.1096/fj.202401360R.ABSTRACTThe mechanism connecting gut microbiota to appetite regulation is not yet fully understood. This study identifies specific microbial community and metabolites that may influence appetite regulation. In the initial phase of the study, mice were administered a broad-spectrum antibiotic cocktail (ABX) for 10 days. The treatment significantly reduced gut microbes and disrupted the metabolism of arginine and tryptophan. Consequently, ABX-treated mice demonstrated a notable reduction in feed consumption. The hypothalamic expression levels of CART and POMC, two key anorexigenic factors, were significantly increased, while orexigenic factors, such as NPY and AGRP, were decreased. Notably, the levels of appetite-suppressing hormone cholecystokinin in the blood were significantly elevated. In the second phase, control mice were maintained, while the ABX-treated mice received saline, probiotics, and short-chain fatty acids (SCFAs) for an additional 10 days to restore their gut microbiota. The microbiota reconstructed by probiotic and SCFA treatments were quite similar, while microbiota of the naturally recovering mice demonstrated greater resemblance to that of the control mice. Notably, the abundance of Akkermansia and Bacteroides genera significantly increased in the reconstructed microbiota. Moreover, microbiota reconstruction corrected the disrupted arginine and tryptophan metabolism and the abnormal peripheral hormone levels caused by ABX treatment. Among the groups, SCFA-treated mice had the highest feed intake and NPY expression. Our findings indicate that gut microbes, especially Akkermansia, regulate arginine and tryptophan metabolism, thereby influencing appetite through the microbe-gut-brain axis.PMID:39157946 | DOI:10.1096/fj.202401360R

Food Funct. 2024 Aug 19. doi: 10.1039/d4fo02106a. Online ahead of print.ABSTRACTThe hepatoprotective effects of kiwifruit seed oil (KSO) were evaluated on acute liver injury (ALI) induced by carbon tetrachloride (CCl4) in vivo. Network pharmacology was used to predict active compounds and targets. Metabolomics and gut microbiota analyses were used to discover the activity mechanism of KSO. KSO improved the liver histological structure, significantly reduced serum proinflammatory cytokine levels, and increased liver antioxidant capacity. The metabolomics analysis showed that KSO may have hepatoprotective effects by controlling metabolites through its participation in signaling pathways like tryptophan metabolism, glycolysis/gluconeogenesis, galactose metabolism, and bile secretion. The gut microbiota analysis demonstrated that KSO improved the composition and quantity of the gut flora. Network pharmacological investigations demonstrated that KSO operated by altering Ptgs2, Nos2, Ppara, Pparg and Serpine1 mRNA levels. All evidence shows that KSO has a hepatoprotective effect, and the mechanism is connected to the regulation of metabolic disorders and intestinal flora.PMID:39157920 | DOI:10.1039/d4fo02106a

Allergy. 2024 Aug 19. doi: 10.1111/all.16275. Online ahead of print.ABSTRACTBACKGROUND: Noninvasive biomarkers for diagnosing and monitoring eosinophilic esophagitis (EoE) are currently lacking. This study evaluates 20 biomarkers in serum and saliva, aiming to assess their diagnostic potential in pediatric EoE patients and healthy individuals.METHODS: Blood and saliva from children undergoing upper endoscopy were analyzed for biomarkers, including absolute eosinophil count (AEC), eosinophil-derived neurotoxin (EDN), total and specific IgG4-antibodies (sIgG4), specific IgE-antibodies (sIgE) and 15-hydroxyeicosatetraenoic acid (15(S)-HETE). Some patients participated twice, forming a longitudinal cohort. The ability to use the biomarkers to predict the EoE diagnosis was evaluated.RESULTS: Analysis from 105 children divided into active EoE, remission, and healthy, revealed elevated levels of serum biomarkers (AEC, EDN, 15(S)-HETE, sIgG4, and sIgE) in active EoE compared to healthy individuals. A combination of biomarkers (AEC, EDN, sIgE to egg white and wheat) and symptoms showed an AUC of 0.92 in distinguishing between the three groups. We further showed that optimal cutoff values for these biomarkers could discriminate between active EoE and healthy with a sensitivity of 88% and a specificity of 100% in distinguishing EoE (active and in remission) from healthy. Longitudinally, levels of EDN, sIgG4 to Bos d 4, Bos d 5, Bos d 8, gliadin, and birch, and sIgE to milk decreased in patients progressing from active EoE to remission (p <.05).CONCLUSIONS: This study identified novel biomarkers associated with EoE and proposes a panel, together with symptoms, for effective discrimination between active EoE, EoE in remission, and healthy individuals. The findings may contribute to a less invasive diagnostic method and may be a potential surveillance tool for pediatric EoE patients.PMID:39157867 | DOI:10.1111/all.16275

J Chem Educ. 2024 Jul 16;101(8):3410-3417. doi: 10.1021/acs.jchemed.4c00270. eCollection 2024 Aug 13.ABSTRACTIsotopic labeling is an important tool in medicinal research, metabolomics, and for understanding reaction mechanisms. In this context, transition metal-catalyzed C-H activation has emerged as a key technology for deuterium incorporation via hydrogen isotope exchange. A detailed and easy-to-implement experimental procedure for a nondirected arene deuteration has been developed that exclusively uses commercial equipment and chemicals. The protocol is ideally suited for students and other prospective applicants who are not experts in catalysis. The degree of deuterium incorporation was analyzed via different means like mass spectrometry and 1H and 2H nuclear magnetic resonance (NMR). A hands-on understanding of quantitative NMR, as well as the influence of H/D exchange on experimental spectra, was conveyed by comparative NMR spin simulations. Students were measurably familiarized with the concepts of C-H activation, isotope effects, and basics in experimental catalysis.PMID:39157437 | PMC:PMC11327962 | DOI:10.1021/acs.jchemed.4c00270

J Reprod Infertil. 2024 Jan-Mar;25(1):3-11. doi: 10.18502/jri.v25i1.15193.ABSTRACTBACKGROUND: Testicular cancer (TC) is a relatively rare type of cancer in men. Early diagnosis of TC remains challenging. Metabolomics holds promise in offering valuable insights in this regard. In this study, a metabolic fingerprinting approach was employed to identify potential biomarkers in both serum and seminal plasma of TC patients.METHODS: A total of 9 patients with testicular cancer and 10 controls were included in the study. The metabolic fingerprinting approach was utilized as a rapid diagnostic tool to analyze the metabolome in serum and seminal plasma of TC patients in comparison to fertile men. Raman spectroscopy was applied for the analysis of metabolites in these biological samples.RESULTS: Principal component analysis (PCA) and functional group analysis showed that the differentiation between serum samples from healthy men and TC patients was not possible. However, when analyzing seminal plasma, a significant difference was found between the two groups (p<0.05). Functional group analysis of serum only showed an increase in tryptophan concentration ratio in TC patients as compared to healthy men (p=0.03). In contrast, in seminal plasma of TC patients, this increase was observed in all analyzed compounds, including phenylalanine, tyrosine, lipids, proteins, phenols (p<0.001).CONCLUSION: Our study highlights the potential of metabolic fingerprinting as a fast diagnostic tool for screening TC patients, with seminal plasma serving as a valuable biological sample. Furthermore, several potential biomarkers, particularly phenylalanine, were identified in seminal plasma. This research contributes to our understanding of TC pathogenesis and has the potential to pave the way for early detection and personalized treatment approaches.PMID:39157284 | PMC:PMC11330202 | DOI:10.18502/jri.v25i1.15193

ACS Omega. 2024 Jul 29;9(32):35182-35196. doi: 10.1021/acsomega.4c05688. eCollection 2024 Aug 13.ABSTRACTA realistic exposure to ionizing radiation (IR) from an improvised nuclear device will likely include individuals who are partially shielded from the initial blast delivered at a very high dose rate (VHDR). As different tissues have varying levels of radiosensitivity, e.g., hematopoietic vs gastrointestinal tissues, the effects of shielding on radiation biomarkers need to be addressed. Here, we explore how biofluid (urine and serum) metabolite signatures from male and female C57BL/6 mice exposed to VHDR (5-10 Gy/s) total body irradiation (TBI, 0, 4, and 8 Gy) compare to individuals exposed to partial body irradiation (PBI) (lower body irradiated [LBI] or upper body irradiated [UBI] at an 8 Gy dose) using a data-independent acquisition untargeted metabolomics approach. Although sex differences were observed in the spatial groupings of urine signatures from TBI and PBI mice, a metabolite signature (N6,N6,N6-trimethyllysine, carnitine, propionylcarnitine, hexosamine-valine-isoleucine, taurine, and creatine) previously developed from variable dose rate experiments was able to identify individuals with high sensitivity and specificity, irrespective of radiation shielding. A panel of serum metabolites composed from previous untargeted studies on nonhuman primates had excellent performance for separating irradiated cohorts; however, a multiomic approach to complement the metabolome could increase dose estimation confidence intervals. Overall, these results support the inclusion of small-molecule markers in biodosimetry assays without substantial interference from the upper or lower body shielding.PMID:39157112 | PMC:PMC11325421 | DOI:10.1021/acsomega.4c05688

Front Cell Dev Biol. 2024 Aug 2;12:1421566. doi: 10.3389/fcell.2024.1421566. eCollection 2024.ABSTRACTAmyotrophic lateral sclerosis (ALS) is a fatal disorder characterized by the selective degeneration of upper and lower motor neurons, leading to progressive muscle weakness and atrophy. The mean survival time is two to five years. Although the hunt for drugs has greatly advanced over the past decade, no cure is available for ALS yet. The role of intense physical activity in the etiology of ALS has been debated for several decades without reaching a clear conclusion. The benefits of organized physical activity on fitness and mental health have been widely described. Indeed, by acting on specific mechanisms, physical activity can influence the physiology of several chronic conditions. It was shown to improve skeletal muscle metabolism and regeneration, neurogenesis, mitochondrial biogenesis, and antioxidant defense. Interestingly, all these pathways are involved in ALS pathology. This review will provide a broad overview of the effect of different exercise protocols on the onset and progression of ALS, both in humans and in animal models. Furthermore, we will discuss challenges and opportunities to exploit physiological responses of imposed exercise training for therapeutic purposes.PMID:39156974 | PMC:PMC11327861 | DOI:10.3389/fcell.2024.1421566

World J Gastroenterol. 2024 Aug 7;30(29):3488-3510. doi: 10.3748/wjg.v30.i29.3488.ABSTRACTBACKGROUND: Hyperuricemia (HUA) is a public health concern that needs to be solved urgently. The lyophilized powder of Poecilobdella manillensis has been shown to significantly alleviate HUA; however, its underlying metabolic regulation remains unclear.AIM: To explore the underlying mechanisms of Poecilobdella manillensis in HUA based on modulation of the gut microbiota and host metabolism.METHODS: A mouse model of rapid HUA was established using a high-purine diet and potassium oxonate injections. The mice received oral drugs or saline. Additionally, 16S rRNA sequencing and ultra-high performance liquid chromatography with quadrupole time-of-flight mass spectrometry-based untargeted metabolomics were performed to identify changes in the microbiome and host metabolome, respectively. The levels of uric acid transporters and epithelial tight junction proteins in the renal and intestinal tissues were analyzed using an enzyme-linked immunosorbent assay.RESULTS: The protein extract of Poecilobdella manillensis lyophilized powder (49 mg/kg) showed an enhanced anti-trioxypurine ability than that of allopurinol (5 mg/kg) (P < 0.05). A total of nine bacterial genera were identified to be closely related to the anti-trioxypurine activity of Poecilobdella manillensis powder, which included the genera of Prevotella, Delftia, Dialister, Akkermansia, Lactococcus, Escherichia_Shigella, Enterococcus, and Bacteroides. Furthermore, 22 metabolites in the serum were found to be closely related to the anti-trioxypurine activity of Poecilobdella manillensis powder, which correlated to the Kyoto Encyclopedia of Genes and Genomes pathways of cysteine and methionine metabolism, sphingolipid metabolism, galactose metabolism, and phenylalanine, tyrosine, and tryptophan biosynthesis. Correlation analysis found that changes in the gut microbiota were significantly related to these metabolites.CONCLUSION: The proteins in Poecilobdella manillensis powder were effective for HUA. Mechanistically, they are associated with improvements in gut microbiota dysbiosis and the regulation of sphingolipid and galactose metabolism.PMID:39156502 | PMC:PMC11326090 | DOI:10.3748/wjg.v30.i29.3488

Kidney Int Rep. 2024 May 9;9(8):2559-2562. doi: 10.1016/j.ekir.2024.04.069. eCollection 2024 Aug.NO ABSTRACTPMID:39156147 | PMC:PMC11328555 | DOI:10.1016/j.ekir.2024.04.069

Anal Chem. 2024 Aug 19. doi: 10.1021/acs.analchem.4c01470. Online ahead of print.ABSTRACTThere is growing interest in limiting the use of fungicides and implementing innovative, environmentally friendly strategies, such as the use of beneficial bacteria-triggered immunity, to protect grapevines from natural pathogens. Therefore, we need rapid and innovative ways to translate the knowledge of the molecular mechanisms underlying the activation of grapevine defenses against pathogens to induced resistance. Here, we have implemented an in vivo minimally invasive approach to study the interaction between plants and beneficial bacteria based on metabolic signatures. Paraburkholderia phytofirmans strain PsJN and PsJN-grapevine were used as bacterial and plant-bacterium interaction models, respectively. Using an innovative tool, SpiderMass, based on water-assisted laser desorption ionization with an IR microsampling probe, we simultaneously detect metabolic and lipidomic species. A metabolomic spectrum was thus generated, which was used to build a library and identify the most variable and discriminative peaks between the two conditions. We then showed that caftaric acid (m/z 311.04), caftaric acid dimer (m/z 623.09), derived caftaric acid (m/z 653.15), and quercetin-O-glucuronide tended to accumulate in grapevine leaves after root bacterization with PsJN. In addition, together with these phenolic messengers, we identified lipid biomarkers such as palmitic acid, linoleic acid, and α-linoleic acid as important messengers of enhanced defense mechanisms in Chardonnay plantlets. Taken together, SpiderMass is the next-generation methodology for studying plant-microorganism metabolic interactions with the prospect of in vivo real-time analysis in viticulture.PMID:39155838 | DOI:10.1021/acs.analchem.4c01470

J Agric Food Chem. 2024 Aug 18. doi: 10.1021/acs.jafc.4c04756. Online ahead of print.ABSTRACTNitrogen (N) is a key factor for plant growth and affects anthocyanin synthesis. This study aimed to clarify the potential mechanisms of N levels (LN, 0 kg·ha-1; MN, 150 kg·ha-1; HN, 225 kg·ha-1) in anthocyanin synthesis and grain quality of colored grain wheat. HN increased the yield component traits and grain morphology traits in colored grain wheat while decreasing the processing and nutrient quality traits. Most quality traits were significantly negatively correlated with the yield composition and morphological traits. Anthocyanin was more accumulated under LN conditions, but other related yield and morphological traits of colored grain wheat declined. The anthocyanin content was the highest in blue wheat, followed by that in purple wheat. Cyanidin-3-O-(6-O-malonyl-β-d-glucoside) and cyanidin-3-O-rutinoside were the predominant anthocyanins in blue and purple wheat. The identified anthocyanin-related metabolites were associated with flavonoid biosynthesis, anthocyanin biosynthesis, and secondary metabolite biosynthesis. Therefore, the study provided information for optimizing nitrogen fertilizer management in producing high quality colored wheat and verified the close relationship between anthocyanin and low N condition.PMID:39155472 | DOI:10.1021/acs.jafc.4c04756

Methods Enzymol. 2024;702:317-352. doi: 10.1016/bs.mie.2024.07.001. Epub 2024 Jul 20.ABSTRACTMicroorganisms, plants, and animals alike have specialized acquisition pathways for obtaining metals, with microorganisms and plants biosynthesizing and secreting small molecule natural products called siderophores and metallophores with high affinities and specificities for iron or other non-iron metals, respectively. This chapter details a novel approach to discovering metal-binding molecules, including siderophores and metallophores, from complex samples ranging from microbial supernatants to biological tissue to environmental samples. This approach, called Native Metabolomics, is a mass spectrometry method in which pH adjustment and metal infusion post-liquid chromatography are interfaced with ion identity molecular networking (IIMN). This rule-based data analysis workflow that enables the identification of metal-binding species based on defined mass (m/z) offsets with the same chromatographic profiles and retention times. Ion identity molecular networking connects compounds that are structurally similar by their fragmentation pattern and species that are ion adducts of the same compound by chromatographic shape correlations. This approach has previously revealed new insights into metal binding metabolites, including that yersiniabactin can act as a biological zincophore (in addition to its known role as a siderophore), that the recently elucidated lepotchelin natural products are cyanobacterial metallophores, and that antioxidants in traditional medicine bind iron. Native metabolomics can be conducted on any liquid chromatography-mass spectrometry system to explore the binding of any metal or multiple metals simultaneously, underscoring the potential for this method to become an essential strategy for elucidating biological metal-binding molecules.PMID:39155117 | DOI:10.1016/bs.mie.2024.07.001

Methods Enzymol. 2024;702:215-227. doi: 10.1016/bs.mie.2024.06.005. Epub 2024 Jul 16.ABSTRACTThe sequencing of microbial genomes has far outpaced their functional annotation. Stable isotopic labeling can be used to link biosynthetic genes with their natural products; however, the availability of the required isotopically substituted precursors can limit the accessibility of this approach. Here, we describe a method for using inverse stable isotopic labeling (InverSIL) to link biosynthetic genes with their natural products. With InverSIL, a microbe is grown on an isotopically substituted medium to create a fully substituted culture, and subsequently, the incorporation of precursors of natural isotopic abundance can be tracked by mass spectrometry. This eliminates issues with isotopically substituted precursor availability. We demonstrate the utility of this approach by linking a luxI-type acyl-homoserine lactone synthase gene in a bacterium that grows on methanol with its quorum sensing signal products. In the future, InverSIL can also be used to link biosynthetic gene clusters hypothesized to produce siderophores with their natural products.PMID:39155113 | DOI:10.1016/bs.mie.2024.06.005

Phytochemistry. 2024 Aug 16:114249. doi: 10.1016/j.phytochem.2024.114249. Online ahead of print.ABSTRACTShort rotation coppices (SRCs) represent an important source of biomass. Since they are grown in various mixtures, SRCs represent an excellent opportunity for assessing the effects of local plant neighbourhoods on their performance. We used a common garden experiment consisting of plots that varied in genotype diversity of SRC willows to test for the effects of chemical traits of individual plants and chemical variation in the plots where they grew on insect herbivory. We also explored whether the composition of willows planted in a plot affected their chemistry. To do this, we performed untargeted metabolomics and quantified various chemical traits related to the total set of metabolites we detected, flavonoids, and salicinoids in four willow genotypes. We measured the leaf herbivory that the plants suffered. The genotypes differed in most chemical traits, yet we found only limited effects of individual traits on herbivory damage. Instead, herbivory damage was positively correlated with structural variation in salicinoids in a plot. When analysing the effects of plot chemical variation on herbivory damage separately for each genotype, we found both positive and negative correlations between the two, suggesting both associational resistance and susceptibility. Finally, we also observed a significant effect of the interaction between genotype and plot composition on structural variation in plant chemistry. Overall, our results suggest that high chemical variation in mixed willow SRCs does not necessarily lower the herbivory damage, possibly due to spillover effects of insect herbivores among genotypes. Our results also show that different genotypes respond differently to plot composition in terms of herbivory damage and chemical composition, which may affect their suitability for growing in mixed stands.PMID:39155032 | DOI:10.1016/j.phytochem.2024.114249

Sci Total Environ. 2024 Aug 16:175592. doi: 10.1016/j.scitotenv.2024.175592. Online ahead of print.ABSTRACTN-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine (6PPD), a widely used antioxidant in rubber products, and its corresponding ozone photolysis product N-(1,3-Dimethylbutyl)-N'-phenyl-p-phenylenediamine-quinone (6PPD-Q), have raised public concerns due to their environmental toxicity. However, there is an existing knowledge gap on the toxicity of 6PPD and 6PPD-Q to aquatic plants. A model aquatic plant, Chlorella vulgaris (C. vulgaris), was subjected to 6PPD and 6PPD-Q at concentrations of 50, 100, 200, and 400 μg/L to investigate their effects on plant growth, photosynthetic, antioxidant system, and metabolic behavior. The results showed that 6PPD-Q enhanced the photosynthetic efficiency of C. vulgaris, promoting growth of C. vulgaris at low concentrations (50, 100, and 200 μg/L) while inhibiting growth at high concentration (400 μg/L). 6PPD-Q induced more oxidative stress than 6PPD, disrupting cell permeability and mitochondrial membrane potential stability. C. vulgaris responded to contaminant-induced oxidative stress by altering antioxidant enzyme activities and active substance levels. Metabolomics further identified fatty acids as the most significantly altered metabolites following exposure to both contaminants. In conclusion, this study compares the toxicity of 6PPD and 6PPD-Q to C. vulgaris, with 6PPD-Q demonstrating higher toxicity. This study provides valuable insight into the risk assessment of tire wear particles (TWPs) derived chemicals in aquatic habitats and plants.PMID:39154997 | DOI:10.1016/j.scitotenv.2024.175592