PubMed

iScience. 2024 Jun 28;27(8):110414. doi: 10.1016/j.isci.2024.110414. eCollection 2024 Aug 16.ABSTRACTCell functions are based on the integrity of actin filaments. The actin cytoskeleton is typically the target but also the source of signals. Arabidopsis PRL1 (Pleiotropic Regulatory Locus 1), regulates multiple cellular processes and physiological responses. However, the precise mechanisms underlying PRL1`s multiple functions are unclear. Here, we show that PRL1 maintains actin integrity and concomitant cellular homeostasis. The cortical actin cytoskeleton was de-polymerized in the prl1 mutant, causing the developmental root defect. Actin depolymerization, rather than reactive oxygen species (ROS) imbalance, constituted the fundamental cause of retarded root growth in prl1. ANAC085 upregulation by, and cooperation with, actin depolymerization triggered stele cell death in prl1 roots. Differential gene expression and alternative splicing defects resulting from actin depolymerization occurred independently in prl1. Our work establishes the cause-effect relationships between actin depolymerization and downstream stress-related signals, revealing a novel function of PRL1 and enhancing the understanding of PRL`s functional mechanisms.PMID:39108734 | PMC:PMC11301084 | DOI:10.1016/j.isci.2024.110414

Iran J Pharm Res. 2024 Apr 20;23(1):e143494. doi: 10.5812/ijpr-143494. eCollection 2024 Jan-Dec.ABSTRACTBACKGROUND: Cancer remains the leading cause of death globally, with breast cancer being the foremost cause among women and lung cancer ranking second for both women and men.OBJECTIVES: This study aimed to identify the metabolomic content of Coleus amboinicus leaves and evaluate their anticancer activities against breast and lung cancer cells, thereby providing insights into potential alternative treatments for these cancers and initiating research on active isolates from C. amboinicus leaves.METHODS: The research methodology involved maceration using ethanol, followed by multistage partitioning with solvents n-hexane, chloroform, and ethyl acetate. Phytochemical screening was performed using standard reagents to detect the presence of alkaloids, phenolics, polyphenols, flavonoids, steroids/triterpenoids, and saponins. Metabolomic profiling was conducted using LC/HRMS, and the anticancer activities against lung cancer cells (A549) and breast cancer cells (MCF-7) were assessed using the MTT assay.RESULTS: The results showed that the C. amboinicus extract contains various secondary metabolite groups such as alkaloids, phenolics and polyphenols, flavonoids, steroids, triterpenoids, and saponins.CONCLUSIONS: The diverse metabolomic profile of the C. amboinicus leaf extract demonstrated potential activity against cancer, as evidenced by in vitro tests on lung (A549) and breast (MCF-7) cancer cells. C. amboinicus leaf extract shows promise as an active ingredient in the prevention and alternative natural treatment of lung and breast cancer. Further research and testing, both in vivo and clinically, are warranted.PMID:39108647 | PMC:PMC11302430 | DOI:10.5812/ijpr-143494

Food Chem X. 2024 Jul 13;23:101653. doi: 10.1016/j.fochx.2024.101653. eCollection 2024 Oct 30.ABSTRACTThe luxS/AI-2 quorum sensing (QS) system of Streptococcus thermophilus regulates strain acid tolerance, yet its impact on milk fermentation remains unclear. This study aimed to elucidate the mechanism of luxS and pfs gene overexpression in the luxS/AI-2 system of S. thermophilus ABT-T on fermented milk quality using metabolomics. Results showed that pfs gene overexpression had a greater impact on milk quality than the wild-type strain or luxS gene overexpression strain. Overexpression of the pfs gene significantly enhanced AI-2 secretion, reducing fermented milk pH, increasing acidity, improving fermented milk protein hydrolysis, and altering texture and water-holding capacity. Nineteen volatile flavor compounds were identified, with decreased ketone compounds due to the pfs gene overexpression. KEGG analysis suggested significant alterations in amino acid metabolism pathways due to the pfs gene overexpression. This study provides insights into the role of QS in fermented foods.PMID:39108626 | PMC:PMC11300903 | DOI:10.1016/j.fochx.2024.101653

Hortic Res. 2024 Jun 27;11(8):uhae176. doi: 10.1093/hr/uhae176. eCollection 2024 Aug.ABSTRACTSynaptotagmin A (SYTA), renowned for its indispensable role in mammalian vesicle trafficking, has recently captured attention in plant biology owing to its potential regulatory functions. This study meticulously delves into the involvement of Solanum lycopersicum SlSYTA in plant immunity, focusing on its response to an array of pathogens affecting tomatoes. Our comprehensive inquiry uncovers that SlSYTA overexpression heightens susceptibility to tobacco mosaic virus (TMV), Phytophthora capsici, Botrytis cinerea, and Pseudomonas syringae pv. tomato DC3000, whereas RNA interference (RNAi) plants show a robust and encompassing resistance to these pathogens. Remarkably, our findings shed light on SlSYTA's negative regulation of pivotal aspects of pattern-triggered immunity (PTI) defense, notably hindering the reactive oxygen species (ROS) burst, impeding stomatal closure, and curtailing callose deposition. Through meticulous scrutiny via transcriptome and metabolome analyses, our studies reveal SlSYTA's profound impact on diverse plant defense pathways, specifically influencing phenylpropanoid metabolism, hormone signaling, and oxidative phosphorylation, primarily via NADPH synthesis modulation in the pentose phosphate pathway, and ultimately interplay within ROS signaling. Collectively, our research presents groundbreaking insights into the intricate molecular mechanisms governing plant immunity, emphasizing the significant role of SlSYTA in orchestrating plant responses to biotic stress.PMID:39108586 | PMC:PMC11301315 | DOI:10.1093/hr/uhae176

Hortic Res. 2024 Jun 27;11(8):uhae177. doi: 10.1093/hr/uhae177. eCollection 2024 Aug.ABSTRACTCitrus reticulata 'Chachi' (CRC) has long been recognized for its nutritional benefits, health-promoting properties, and pharmacological potential. Despite its importance, the bioactive components of CRC and their biosynthetic pathways have remained largely unexplored. In this study, we introduce a gap-free genome assembly for CRC, which has a size of 312.97 Mb and a contig N50 size of 32.18 Mb. We identified key structural genes, transcription factors, and metabolites crucial to flavonoid biosynthesis through genomic, transcriptomic, and metabolomic analyses. Our analyses reveal that 409 flavonoid metabolites, accounting for 83.30% of the total identified, are highly concentrated in the early stage of fruit development. This concentration decreases as the fruit develops, with a notable decline in compounds such as hesperetin, naringin, and most polymethoxyflavones observed in later fruit development stages. Additionally, we have examined the expression of 21 structural genes within the flavonoid biosynthetic pathway, and found a significant reduction in the expression levels of key genes including 4CL, CHS, CHI, FLS, F3H, and 4'OMT during fruit development, aligning with the trend of flavonoid metabolite accumulation. In conclusion, this study offers deep insights into the genomic evolution, biosynthesis processes, and the nutritional and medicinal properties of CRC, which lay a solid foundation for further gene function studies and germplasm improvement in citrus.PMID:39108584 | PMC:PMC11301317 | DOI:10.1093/hr/uhae177

Hortic Res. 2024 Jun 21;11(8):uhae167. doi: 10.1093/hr/uhae167. eCollection 2024 Aug.ABSTRACTThe formation of high-quality Chinese medicinal materials is a micro-evolutionary process of multiple genes involving quantitative inheritance under environmental stress. Atractylodes lancea is a traditionally used medicinal plant in China that is broadly distributed and possesses a considerable amount of essential oils. However, to date, limited research has been conducted to characterize the genetics and metabolites of A. lancea shaped by natural variation. Hence, we assembled a high-quality genome of A. lancea, featuring a contig N50 of 1.18 Mb. We further integrated population resequencing of A. lancea and conducted analyses to characterize its genetic diversity, population evolution, and rewiring of volatile metabolites. The natural variation effect exerted significant pressure on A. lancea from different geographic locations, resulting in genetic differentiation among three groups. Correlation analysis of metabolites in A. lancea revealed significant natural variations of terpenoids, heterocyclic compounds, ketones, and esters. We also found that 427 metabolites displayed noteworthy divergence due to directional selection. Additionally, our genome-wide association studies on the metabolome for medicinal quality traits identified several candidate genes, such as AlZFP706 and AlAAHY1, exhibiting significant correlations with atractylodin and hinesol levels, respectively. Overall, this study provides an intricate genomic resource for A. lancea, thereby expanding our understanding of the effect of natural variation on metabolites and facilitating the genetic improvement of its medicinal properties.PMID:39108583 | PMC:PMC11300843 | DOI:10.1093/hr/uhae167

Hortic Res. 2024 Jun 21;11(8):uhae168. doi: 10.1093/hr/uhae168. eCollection 2024 Aug.ABSTRACTOlive is a valuable oil-bearing tree with fruits containing high levels of fatty acids. Oil production is a multifaceted process involving intricate interactions between fatty acid biosynthesis and other metabolic pathways that are affected by genetics and the developmental stages of the fruit. However, a comprehensive understanding of the underlying regulatory mechanisms is still lacking. Here, we generated a gap-free telomere-to-telomere assembly for Olea europaea cv. 'Leccino', representing an olive genome with the highest contiguity and completeness to date. The combination of time-course metabolomics and transcriptomics datasets revealed a negative correlation between fatty acid and flavonoid biosynthesis in the initial phase of olive fruit development, which was subject to an opposing regulatory mechanism mediated by the hub transcription factor MYC2. Multifaceted molecular assays demonstrated that MYC2 is a repressor of fatty acid biosynthesis by downregulating the expression of BCCP2 (biotin carboxylase carrier protein 2), while it acts as an activator of FLS (flavonol synthase), leading to an increase in flavonoid synthesis. Furthermore, the expression of MYC2 is regulated by fluctuations of methyl jasmonate content during olive fruit development. Our study completes a high-quality gapless genome of an olive cultivar, and provides new insight into the regulatory mechanisms underlying the biosynthesis of fatty acids and flavonoids in its fruit.PMID:39108575 | PMC:PMC11300844 | DOI:10.1093/hr/uhae168

medRxiv [Preprint]. 2024 Jul 24:2024.07.23.24310540. doi: 10.1101/2024.07.23.24310540.ABSTRACTBACKGROUND: Women with type 2 diabetes (T2D) have a 50% excess risk of coronary heart disease (CHD) than men with T2D. We compared circulating metabolites and their associations with CHD in men and women across glycemic status.METHODS: We used metabolomic data (lipoproteins, fatty acids, amino acids, glycolysis, ketones, inflammation, and fluid balance) for 87,326 CHD-free UK Biobank participants. We used linear regressions to examine the association of sex and metabolites (log) in newly diagnosed T2D (diagnosis<2 yrs from baseline), prediabetes (A1c 5.7-6.5%), and euglycemia, accounting for age, race, Deprivation Index, income, smoking, alcohol drinking, obesity, physical activity, medications for hypertension, hyperlipidemia, and diabetes. We used Cox models to evaluate the association of metabolites and CHD risk by sex, adjusting the same covariates and menopausal status (women). All analyses were FDR-adjusted.FINDINGS: We included 1250 individuals with new T2D, 12,706 with prediabetes, and 83,315 with euglycemia. In adjusted linear regressions, women showed a progressive increase in atherogenic lipid and lipoprotein markers and inflammatory marker, glycoprotein acetyls, compared to men as their glycemic status advanced. However, women had lower levels of albumin during this transition. Menopausal status did not alter these sex differences. In a 10-year follow-up, an SD higher total TG, TG in VLDL, LDL, and HDL, saturated fatty acids (SFA) were positively associated with a higher risk of CHD in women with T2D but not in men (p-interactions 0.03-0.15).INTERPRETATION: With advancing glycemic status, women exhibited higher levels of atherogenic lipids and lipoproteins, as well as inflammatory markers, but lower circulating albumin. Women with T2D appear to be at a higher risk of CHD associated with TG, VLDL-TG, LDL-TG, and HDL-TG, and SFA than men with T2D.PMID:39108525 | PMC:PMC11302618 | DOI:10.1101/2024.07.23.24310540

medRxiv [Preprint]. 2024 Jul 27:2024.07.27.24310936. doi: 10.1101/2024.07.27.24310936.ABSTRACTBACKGROUND: Maternal obesity is a health concern that may predispose newborns to a high risk of medical problems later in life. To understand the transgenerational effect of maternal obesity, we conducted a multi-omics study, using DNA methylation and gene expression in the CD34+/CD38-/Lin-umbilical cord blood hematopoietic stem cells (uHSCs) and metabolomics of the cord blood, all from a multi-ethnic cohort (n=72) from Kapiolani Medical Center for Women and Children in Honolulu, Hawaii (collected between 2016 and 2018).RESULTS: Differential methylation (DM) analysis unveiled a global hypermethylation pattern in the maternal pre-pregnancy obese group (BH adjusted p<0.05), after adjusting for major clinical confounders. Comprehensive functional analysis showed hypermethylation in promoters of genes involved in cell cycle, protein synthesis, immune signaling, and lipid metabolism. Utilizing Shannon entropy on uHSCs methylation, we discerned notably higher quiescence of uHSCs impacted by maternal obesity. Additionally, the integration of multi-omics data-including methylation, gene expression, and metabolomics-provided further evidence of dysfunctions in adipogenesis, erythropoietin production, cell differentiation, and DNA repair, aligning with the findings at the epigenetic level.CONCLUSIONS: This study reveals the significant correlation between pre-pregnancy maternal obesity and multi-omics level molecular changes in the uHSCs of offspring, particularly in DNA methylation.PMID:39108521 | PMC:PMC11302719 | DOI:10.1101/2024.07.27.24310936

medRxiv [Preprint]. 2024 Jul 25:2024.07.24.24310961. doi: 10.1101/2024.07.24.24310961.ABSTRACTBACKGROUND: Two general phenotypes of heart failure (HF) are recognized: HF with reduced ejection fraction (HFrEF) and with preserved EF (HFpEF). To develop HF disease phenotype-specific approaches to define and guide treatment, distinguishing biomarkers are needed. The goal of this study was to utilize quantitative metabolomics on a large, diverse population to replicate and extend existing knowledge of the plasma metabolic signatures in human HF.METHODS: Quantitative, targeted LC/MS plasma metabolomics was conducted on 787 samples collected by the Penn Medicine BioBank from subjects with HFrEF (n=219), HFpEF (n=357), and matched non-failing Controls (n=211). A total of 90 metabolites were analyzed, comprising 28 amino acids, 8 organic acids, and 54 acylcarnitines. 733 of these samples were also processed via an OLINK protein panel for proteomic profiling.RESULTS: Consistent with previous studies, unsaturated forms of medium/long chain acylcarnitines were elevated in the HFrEF group to a greater extent than the HFpEF group compared to Controls. A number of amino acid derivatives, including 1- and 3-methylhistidine, homocitrulline, and symmetric (SDMA) and asymmetric (ADMA) dimethylarginine were elevated in HF, with ADMA elevated uniquely in HFpEF. Plasma branched-chain amino acids (BCAA) were not different across the groups; however, short-chain acylcarnitine species indicative of BCAA catabolism were significantly elevated in both HF groups. The ketone body 3-hydroxybutyrate (3-HBA) and its metabolite C4-OH carnitine were uniquely elevated in the HFrEF group. Linear regression models demonstrated a significant correlation between plasma 3-HBA and NT-proBNP in both forms of HF, stronger in HFrEF.CONCLUSIONS: These results identify plasma signatures that are shared as well as potentially distinguish between HFrEF and HFpEF. Metabolite markers for ketogenic metabolic re-programming in extra-cardiac tissues were identified as unique signatures in the HFrEF group, possibly related to the lipolytic action of increased levels of BNP. Future studies will be necessary to further validate these metabolites as HF biosignatures that may guide phenotype-specific therapeutics and provide insight into the systemic metabolic responses to HFpEF and HFrEF.CLINICAL PERSPECTIVE: What Is New?: "Real world" targeted metabolomic profiling on wide range of metabolites in a diverse population of patients with HFrEF and HFpEF.Levels of 3-hydroxybutyrate and its metabolite C4OH-carnitine were uniquely increased in the HFrEF group and correlated with levels of plasma NT-proBNP in both the heart failure groups, indicating the possibility of a heart-adipose-liver axis.Asymmetric dimethylarginine, a known inhibitor of nitric oxide synthase, was uniquely upregulated in HFpEF suggesting that there may also be an underlying component of vascular dysregulation contributing to HFpEF pathophysiology.What Are the Clinical Implications?: The plasma metabolomic changes seen in the heart failure cohorts support the existing theory of metabolic reprogramming, providing further rationale for the pursuit of therapeutic targets for the treatment of heart failure.Quantitative metabolomic profiling shows promise for guiding therapeutic decisions in HFrEF and HFpEF.Modulation of natriuretic peptides may enhance the delivery of ketone and fatty acids to the "fuel starved" failing heart.PMID:39108509 | PMC:PMC11302718 | DOI:10.1101/2024.07.24.24310961

Res Sq [Preprint]. 2024 Jul 22:rs.3.rs-3617016. doi: 10.21203/rs.3.rs-3617016/v1.ABSTRACTInitially focused on the European population, multiple genome-wide association studies (GWAS) of complex diseases, such as type-2 diabetes (T2D), have now extended to other populations. However, to date, few ancestry-matched omics datasets have been generated or further integrated with the disease GWAS to nominate the key genes and/or molecular traits underlying the disease risk loci. In this study, we generated and integrated plasma proteomics and metabolomics with array-based genotype datasets of European (EUR) and African (AFR) ancestries to identify ancestry-specific muti-omics quantitative trait loci (QTLs). We further applied these QTLs to ancestry-stratified T2D risk to pinpoint key proteins and metabolites underlying the disease-associated genetic loci. We nominated five proteins and four metabolites in the European group and one protein and one metabolite in the African group to be part of the molecular pathways of T2D risk in an ancestry-stratified manner. Our study demonstrates the integration of genetic and omic studies of different ancestries can be used to identify distinct effector molecular traits underlying the same disease across diverse populations. Specifically, in the AFR proteomic findings on T2D, we prioritized the protein QSOX2; while in the AFR metabolomic findings, we pinpointed the metabolite GlcNAc sulfate conjugate of C21H34O2 steroid. Neither of these findings overlapped with the corresponding EUR results.PMID:39108494 | PMC:PMC11302687 | DOI:10.21203/rs.3.rs-3617016/v1

Res Sq [Preprint]. 2024 Jul 25:rs.3.rs-4559624. doi: 10.21203/rs.3.rs-4559624/v1.ABSTRACTGut microbial metabolites have been theorized to play a causative role in the pathophysiology of autism spectrum disorder (ASD). This hypothesis is based on results from mechanistic preclinical studies and several correlational studies showing differences in gut microbial composition between ASD subjects and neurotypical (NT) controls. However, alterations in how the human brain interacts with the gut microbiome in ASD have not been examined. In this cross-sectional, case-control observational study, fecal metabolomics, task-based functional magnetic resonance imaging (fMRI), and behavioral assessments were obtained from 43 ASD and 41 NT children aged 8-17. The fMRI tasks were based on socio-emotional and sensory paradigms that commonly show strong evoked brain differences in ASD participants. General linear models and mediational modeling were applied to examine the links between tryptophan metabolism and evoked brain activity and behavior. Results indicated that fecal levels of specific tryptophan-related metabolites were associated with: 1) brain activity atypicalities in regions previously implicated in ASD (i.e., insula and cingulate); and 2) ASD severity and symptomatology (i.e., ADOS scores, disgust propensity, and sensory sensitivities). Importantly, activity in the mid-insula and mid-cingulate significantly mediated relationships between the microbial tryptophan metabolites, indolelactate and tryptophan betaine, and ASD severity and disgust sensitivity. To our knowledge, this is the first study to elucidate how interactions between gut metabolites and brain activity may impact autism symptomatology, particularly in functional brain pathways associated with vagal and interoceptive/emotion processing.PMID:39108481 | PMC:PMC11302680 | DOI:10.21203/rs.3.rs-4559624/v1

Physiol Plant. 2024 Jul-Aug;176(4):e14452. doi: 10.1111/ppl.14452.ABSTRACTSalinity is considered one of the abiotic stresses that have the greatest impact on soybean production worldwide. Lanthanum (La) is a rare earth element that can reduce adverse conditions on plant growth and productivity. However, the regulatory mechanism of La-mediated plant response to salt stress has been poorly studied, particularly in soybeans. Therefore, our study investigated the mechanisms of La-mediated salt stress alleviation from the perspectives of the antioxidant system, subcellular structure, and metabolomics responses. The results indicated that salt stress altered plant morphology and biomass, resulting in an increase in peroxidation, inhibition of photosynthesis, and damage to leaf structure. Exogenous La application effectively promoted the activity of superoxide dismutase (SOD) and peroxidase (POD), as well as the soluble protein content, while decreasing the Na+ content and Na+/K+ ratio in roots and leaves, and reducing oxidative damage. Moreover, transmission electron microscopy (TEM) demonstrated that La prevented the disintegration of chloroplasts. Fourier-transform infrared spectroscopy (FTIR) analysis further confirmed that La addition mitigated the decline in protein, carbohydrates, and pectin levels in the leaves. Lanthanum decreased the leaf flavonoid content and synthesis by inhibiting the content of key substances in the phenylalanine metabolism pathway during NaCl exposure. Collectively, our research indicates that La reduces cell damage by regulating the antioxidant system and secondary metabolite synthesis, which are important mechanisms for the adaptive response of soybean leaves, thereby improving the salt tolerance of soybeans.PMID:39108068 | DOI:10.1111/ppl.14452

Mol Nutr Food Res. 2024 Aug 6:e2400246. doi: 10.1002/mnfr.202400246. Online ahead of print.ABSTRACTSCOPE: Dietary constituents modulate development of obesity and type 2 diabetes. The metabolic impact from different food sources in western diets (WD) on obesity development is not fully elucidated. This study aims to identify dietary sources that differentially affect obesity development and the metabolic processes involved.METHODS AND RESULTS: Mice were fed isocaloric WDs with protein and fat from different food groups, including egg and dairy, terrestrial meat, game meat, marine, vegetarian, and a mixture of all. This study evaluates development of obesity, glucose tolerance, insulin sensitivity, and plasma and cecal metabolome. WD based on marine or vegetarian food sources protects male mice from obesity development and insulin resistance, whereas meat-based diets promote obesity. The intake of different food sources induces marked differences in the lipid-related plasma metabolome, particularly impacting phosphatidylcholines. Fifty-nine lipid-related plasma metabolites are positively associated with adiposity and a distinct cecal metabolome is found in mice fed a marine diet.CONCLUSION: This study demonstrates differences in obesity development between the food groups. Diet specific metabolomic signatures in plasma and cecum associated with adiposity, where a marine based diet modulates the level of plasma and cecal phosphatidylcholines in addition to preventing obesity development.PMID:39107912 | DOI:10.1002/mnfr.202400246

BMC Plant Biol. 2024 Aug 6;24(1):753. doi: 10.1186/s12870-024-05408-7.ABSTRACTBACKGROUND: When subject to stress conditions such as nutrient limitation microalgae accumulate triacylglycerol (TAG). Fatty acid, a substrate for TAG synthesis is derived from de novo synthesis or by membrane remodeling. The model industrial alga Chlorellasorokiniana accumulates TAG and other storage compounds under nitrogen (N)-limited growth. Molecular mechanisms underlying these processes are still to be elucidated.RESULT: Previously we used transcriptomics to explore the regulation of TAG synthesis in C. sorokiniana. Surprisingly, our analysis showed that the expression of several key genes encoding enzymes involved in plastidic fatty acid synthesis are significantly repressed. Metabolic labeling with radiolabeled acetate showed that de novo fatty acid synthesis is indeed downregulated under N-limitation. Likewise, inhibition of the Target of Rapamycin kinase (TOR), a key regulator of metabolism and growth, decreased fatty acid synthesis. We compared the changes in proteins and phosphoprotein abundance using a proteomics and phosphoproteomics approach in C. sorokiniana cells under N-limitation or TOR inhibition and found extensive overlap between the N-limited and TOR-inhibited conditions. We also identified changes in the phosphorylation status of TOR complex proteins, TOR-kinase, and RAPTOR, under N-limitation. This indicates that TOR signaling is altered in a nitrogen-dependent manner. We find that TOR-mediated metabolic remodeling of fatty acid synthesis under N-limitation is conserved in the chlorophyte algae Chlorella sorokiniana and Chlamydomonas reinhardtii.CONCLUSION: Our results indicate that under N-limitation there is significant metabolic remodeling, including fatty acid synthesis, mediated by TOR signaling. This process is conserved across chlorophyte algae. Using proteomic and phosphoproteomic analysis, we show that N-limitation affects TOR signaling and this in-turn affects the metabolic status of the cells. This study presents a link between N-limitation, TOR signaling and fatty acid synthesis in green-lineage.PMID:39107711 | DOI:10.1186/s12870-024-05408-7

BMC Genomics. 2024 Aug 6;25(1):763. doi: 10.1186/s12864-024-10666-8.ABSTRACTEdible fungi cultivation serves as an efficient biological approach to transforming agroforestry byproducts, particularly Korshinsk peashrub (KP) branches into valuable mushroom (Lentinus edodes) products. Despite the widespread use of KP, the molecular mechanisms underlying its regulation of mushroom development remain largely unknown. In this study, we conducted a combined analysis of transcriptome and metabolism of mushroom fruiting bodies cultivated on KP substrates compared to those on apple wood sawdust (AWS) substrate. Our aim was to identify key metabolic pathways and genes that respond to the effects of KP substrates on mushrooms. The results revealed that KP induced at least a 1.5-fold increase in protein and fat content relative to AWS, with 15% increase in polysaccharide and total sugar content in mushroom fruiting bodies. There are 1196 differentially expressed genes (DEGs) between mushrooms treated with KP relative to AWS. Bioinformatic analysis show significant enrichments in amino acid metabolic process, oxidase activity, malic enzyme activity and carbon metabolism among the 698 up-regulated DEGs induced by KP against AWS. Additionally, pathways associated with organic acid transport and methane metabolism were significantly enriched among the 498 down-regulated DEGs. Metabolomic analysis identified 439 differentially abundant metabolites (DAMs) in mushrooms treated with KP compared to AWS. Consistent with the transcriptome data, KEGG analysis on metabolomic dataset suggested significant enrichments in carbon metabolism, alanine, aspartate and glutamate metabolism among the up-regulated DAMs by KP. In particular, some DAMs were enhanced by 1.5-fold, including D-glutamine, L-glutamate, glucose and pyruvate in mushroom samples treated with KP relative to AWS. Targeted metabolomic analysis confirmed the contents of DAMs related to glutamate metabolism and energy metabolism. In conclusion, our findings suggest that reprogrammed carbon metabolism and oxidoreductase pathways act critical roles in the enhanced response of mushroom to KP substrates.PMID:39107700 | DOI:10.1186/s12864-024-10666-8

Sci Rep. 2024 Aug 7;14(1):18278. doi: 10.1038/s41598-024-69373-9.ABSTRACTTo decipher the molecular bases governing seed germination, this study presents the pivotal role of the cap-binding complex (CBC), comprising CBP20 and CBP80, in modulating the inhibitory effects of abscisic acid (ABA) in barley. Using both single and double barley mutants in genes encoding the CBC, we revealed that the double mutant hvcbp20.ab/hvcbp80.b displays ABA insensitivity, in stark contrast to the hypersensitivity observed in single mutants during germination. Our comprehensive transcriptome and metabolome analysis not only identified significant alterations in gene expression and splicing patterns but also underscored the regulatory nexus among CBC, ABA, and brassinosteroid (BR) signaling pathways.PMID:39107424 | DOI:10.1038/s41598-024-69373-9

Am J Hum Genet. 2024 Jul 31:S0002-9297(24)00251-9. doi: 10.1016/j.ajhg.2024.07.007. Online ahead of print.ABSTRACTMendelian randomization (MR) utilizes genome-wide association study (GWAS) summary data to infer causal relationships between exposures and outcomes, offering a valuable tool for identifying disease risk factors. Multivariable MR (MVMR) estimates the direct effects of multiple exposures on an outcome. This study tackles the issue of highly correlated exposures commonly observed in metabolomic data, a situation where existing MVMR methods often face reduced statistical power due to multicollinearity. We propose a robust extension of the MVMR framework that leverages constrained maximum likelihood (cML) and employs a Bayesian approach for identifying independent clusters of exposure signals. Applying our method to the UK Biobank metabolomic data for the largest Alzheimer disease (AD) cohort through a two-sample MR approach, we identified two independent signal clusters for AD: glutamine and lipids, with posterior inclusion probabilities (PIPs) of 95.0% and 81.5%, respectively. Our findings corroborate the hypothesized roles of glutamate and lipids in AD, providing quantitative support for their potential involvement.PMID:39106865 | DOI:10.1016/j.ajhg.2024.07.007

Curr Biol. 2024 Aug 5;34(15):R712-R714. doi: 10.1016/j.cub.2024.07.004.ABSTRACTInterview with Shuang Wu, who studies plant organ formation and tissue patterning at Fujian Agriculture and Forestry University in Fuzhou.PMID:39106823 | DOI:10.1016/j.cub.2024.07.004

Poult Sci. 2024 Jul 17;103(10):104112. doi: 10.1016/j.psj.2024.104112. Online ahead of print.ABSTRACTThis investigation sought to reveal the effects of heat stress on the meat quality of geese. Wuzong geese were subjected to heat stress at 35°C for 25 d or 4 h to examine different heat stress time on meat quality. Short-time heat stress reduced muscle drip loss and meat color L* value while increasing pH value and meat color a* and b* values. Long-time heat stress decreased body weight and increased leg muscle pH value and meat color b* value. Amino acid profile of geese breast muscle revealed that both LHS and SHS can induce L-Cystine but reduced L-Cystathionine, which were positive correlated with cooking loss and meat color lightness, respectively. Lipidome analysis indicated that heat stress would alter the synthesis of unsaturated fatty acids, and the difference between LHS and SHS on lipids mainly focused on Hex1Cer and TG. Non-target metabolome analysis indicated effects of heat stress on Glycerolipid metabolism, Arachidonic acid metabolism, and Pyrimidine metabolism. Proteome analysis showed that heat stress mainly affects cellular respiration metabolism and immune response. These findings highlight the diverse effects of heat stress on meat quality, amino acid composition, lipidome, metabolome, and proteome in geese.PMID:39106699 | DOI:10.1016/j.psj.2024.104112