PubMed

Curr Pharm Biotechnol. 2024 Oct 9. doi: 10.2174/0113892010322778240927073617. Online ahead of print.ABSTRACTBACKGROUND: This study is the first report on the sequence of the transcriptome of Drimia indica, a non-model plant with medicinal properties found in a forest tribal belt, using the Illumina NovaSeq platform. The primary objectives of this study were to elucidate the gene expression profiles in different tissues, identify key regulatory genes and pathways involved in secondary metabolite biosynthesis, and explore the plant's potential pharmacological properties.METHODS: The study generated 670087 unigenes from both leaves and roots and identified putative homologs of annotated sequences against UniProt/Swiss-Prot and KEGG databases. The functional annotation of the identified unigenes revealed the secondary metabolite biosynthetic process as the most prominent pathway, with gene enrichment analysis predominantly accounting for secondary metabolite pathways, such as terpenoid, steroid, flavonoid, alkaloid, selenocompound, and cortisol synthesis. The study also identified regulatory genes NAC, Bhlh, WRKY, and C2H2 on the transcriptome dataset.RESULTS: The functionally annotated unigenes suggested phytocompounds in Drimia indica to have multi-potent properties, such as anti-cancer, anti-inflammatory, and anti-diabetic activities, which has been further validated by GC-MS-based metabolite profiling. Notably, we have identified two novel molecules, di-azo progesterone and 4H-pyran-4-one 2,3-dihydro-3,5-dihydroxy- 6-methyl, with potential BCL2 inhibitory anticancer properties, supported by stable binding interactions observed in molecular docking and dynamics simulations. Additionally, an abundance of mono-nucleotide SSR markers has been identified, useful for genetic diversity studies.CONCLUSION: This study provides a foundational understanding of the molecular mechanisms in Drimia indica, highlighting its potential as a source for novel therapeutic agents and contributing valuable insights for future pharmacological and agricultural applications. However, further in vivo studies are warranted to confirm these findings and validate their pharmacological efficacy and therapeutic potential. The SSR markers identified also offer valuable tools for molecular genetics, plant breeding, and sustainable drug development.PMID:39410890 | DOI:10.2174/0113892010322778240927073617

Gut Microbes. 2024 Jan-Dec;16(1):2412381. doi: 10.1080/19490976.2024.2412381. Epub 2024 Oct 16.ABSTRACTHigh-fat diet (HFD) has been linked to female infertility. However, the specific age at which HFD impacts ovarian function and the underlying mechanisms remain poorly understood. Here, we administered a HFD to female mice at various developmental stages: pre-puberty (4 weeks old), post-puberty (6 weeks old), young adult (9 weeks old), and middle age (32 weeks old). Our observations indicated that ovarian function was most significantly compromised when HFD was initiated at post-puberty. Consequently, post-puberty mice were chosen for further investigation. Through transplantation of fecal bacteria from the HFD mice to the mice on a normal diet, we confirmed that gut microbiota dysbiosis contributed to HFD-induced deteriorated fertility and disrupted estradiol synthesis. Utilizing untargeted and targeted metabolomics analyses, we identified L-saccharopine as a key metabolite, which was enriched in the feces, serum, and ovaries of HFD and HFD-FMT mice. Subsequent in vitro and in vivo experiments demonstrated that L-saccharopine disrupted mitochondrial homeostasis by impeding AMPKα/MFF-mediated mitochondrial fission. This disruption ultimately hindered estradiol synthesis and compromised oocyte quality. AICAR, an activator of AMPKα, ameliorated L-saccharopine induced mitochondrial damage in granulosa cells and oocytes, thereby enhancing E2 synthesis and improving oocyte quality. Collectively, our findings indicate that the accumulation of L-saccharopine may play a pivotal role in mediating HFD-induced ovarian dysfunction. This highlights the potential therapeutic benefits of targeting the gut microbiota-metabolite-ovary axis to address HFD-induced ovarian dysfunction.PMID:39410876 | DOI:10.1080/19490976.2024.2412381

Diagnostics (Basel). 2024 Oct 4;14(19):2214. doi: 10.3390/diagnostics14192214.ABSTRACTBackground/Objectives: Nasal and nasopharyngeal swabs are commonly used for detecting respiratory viruses, including influenza, which significantly alters host cell metabolites. This study aimed to develop a machine learning model to identify biomarkers that differentiate between influenza-positive and -negative cases using clinical metabolomics data. Method: A publicly available dataset of 236 nasopharyngeal samples screened via liquid chromatography-quadrupole time-of-flight (LC/Q-TOF) mass spectrometry was used. Among these, 118 samples tested positive for influenza (40 A H1N1, 39 A H3N2, 39 Influenza B), while 118 were negative controls. A stacking-based model was proposed using the top 20 selected features. Thirteen machine learning models were initially trained, and the top three were combined using predicted probabilities to form a stacking classifier. Results: The ExtraTrees stacking model outperformed other models, achieving 97.08% accuracy. External validation on a prospective cohort of 96 symptomatic individuals (48 positive and 48 negatives for influenza) showed 100% accuracy. SHAP values were used to enhance model explainability. Metabolites such as Pyroglutamic Acid (retention time: 0.81 min, m/z: 84.0447) and its in-source fragment ion (retention time: 0.81 min, m/z: 130.0507) showed minimal impact on influenza-positive cases. On the other hand, metabolites with a retention time of 10.34 min and m/z 106.0865, and a retention time of 8.65 min and m/z 211.1376, demonstrated significant positive contributions. Conclusions: This study highlights the effectiveness of integrating metabolomics data with machine learning for accurate influenza diagnosis. The stacking-based model, combined with SHAP analysis, provided robust performance and insights into key metabolites influencing predictions.PMID:39410618 | DOI:10.3390/diagnostics14192214

Foods. 2024 Oct 9;13(19):3208. doi: 10.3390/foods13193208.ABSTRACTSoil mulching is a useful agronomic practice that promotes early fruit maturation and affects fruit quality. However, the regulatory mechanism of fruit metabolites under soil-mulching treatments remains unknown. In this study, variations in the gene sets and metabolites of grape berries after mulching (rice straw + felt + plastic film) using transcriptome and metagenomic sequencing were investigated. The results of the cluster analysis and orthogonal projection to latent structures discriminant analysis of the metabolites showed a difference between the mulching and control groups, as did the principal component analysis results for the transcriptome. In total, 36 differentially expressed metabolites were identified, of which 10 (resveratrol, ampelopsin F, piceid, 3,4'-dihydroxy-5-methoxystilbene, ε-viniferin, trans resveratrol, epsilon-viniferin, 3'-hydroxypterostilbene, 1-methyl-resveratrol, and pterostil-bene) were stilbenes. Their content increased after mulching, indicating that stilbene synthase activity increased after mulching. The weighted gene co-expression network analysis revealed that the turquoise and blue modules were positively and negatively related to stilbene compounds. The network analysis identified two seed genes (VIT_09s0054g00610, VIT_13s0156g00260) and two transcription factors (VIT_13s0156g00260, VIT_02s0025g04590). Overall, soil mulching promoted the accumulation of stilbene compounds in grapes, and the results provided key genetic information for further studies.PMID:39410242 | DOI:10.3390/foods13193208

Foods. 2024 Oct 4;13(19):3163. doi: 10.3390/foods13193163.ABSTRACTMomordica charantia L. saponins (MCS) may promote wound-healing properties but the underlying mechanisms are unclear. This study aimed to examine the effects and mechanisms of MCS on diabetic wounds. The results have shown that higher MCS intake lowered fasting blood glucose levels, serum lipids, and lipopolysaccharides in diabetic mice. MCS-treated diabetic mice exhibited faster wound healing than the diabetic control groups. After three days, the diabetic control groups exhibited a wound area reduction of only 19.3%, while a 39.75% reduction was observed following high-dose MCS treatment. Five potential biomarkers were screened in the metabolomics study. The results revealed that MCS mainly regulated glycerophospholipid metabolism, fructose and mannose metabolism, steroid hormone biosynthesis, pyrimidine metabolism, and the Krebs cycle, thus affecting wound healing. Overall, MCS could not only exert a hypoglycemic effect but also promote diabetic wound healing, making it a potential treatment option for diabetes-related wounds.PMID:39410199 | DOI:10.3390/foods13193163

Foods. 2024 Sep 29;13(19):3114. doi: 10.3390/foods13193114.ABSTRACTJiuqu (starter) makes an important contribution to the formation of the flavor characteristics of Hongqu rice wine (HQW). Gutian Qu (GTQ) and Wuyi Qu (WYQ) are two kinds of Jiuqu commonly used in HQW brewing, but the comparison of the two kinds of HQW is still insufficient at present. The objective of this study was to compare the dynamic changes of amino acids (AAs), higher alcohols (HAs), bioamines (BAs), volatile flavor compounds (VFCs), and microbial communities in HQW fermentation, with GTQ and WYQ as starter. This study used an automatic amino acid analyzer, GC, HPLC, and GC-MS to detect AAs, HAs, Bas, and VFCs during fermentation; metagenomic sequencing technology was used to elucidate the microbial community and its functional characteristics. The results showed that the contents of AAs and HAs in HQW brewed with WYQ (WYW) were significantly higher than those in HQW brewed with GTQ (GTW). On the contrary, the majority of BAs in GTW were significantly higher than those in WYW. The composition of VFCs in WYW and GTW were obviously different, as most of the VFCs were notably enriched in WYW, while ethyl caproate, isoamyl acetate, ethyl heptanoate, ethyl nonanoate, 1-decanol, citronellol, phenethyl acetate, and hexanoic acid were more abundant in GTW. Burkholderia gladioli, Pantoea dispersa, Weissella cibaria, Monascus purpureus, and Saccharomyces cerevisiae were the predominant microbial populations in GTW brewing at the species level, while Sphingomonas sp., Kosakonia cowanii, Enterobacter asburiae, Leuconostoc lactis, Aspergillus niger, and Saccharomyces cerevisiae were the dominant microbial species in WYW brewing. The abundance of functional genes involved in BAs biosynthesis were much higher in GTW brewing, while the abundance of functional genes related to the metabolism of characteristic VFCs were much higher in WYW brewing. Collectively, these findings provided evidence for elucidating the effects of Jiuqu and microbial communities on HQW flavor quality, and laid a solid foundation for the improvement of HQW flavor quality.PMID:39410149 | DOI:10.3390/foods13193114

Foods. 2024 Sep 28;13(19):3102. doi: 10.3390/foods13193102.ABSTRACTA maternal diet rich in dietary fiber, such as β-glucan, plays a crucial role in the offspring's acquisition of gut microbiota and the subsequent shaping of its microbiome profile and metabolome. This in turn has been shown to aid in neurodevelopmental processes, including early microglial maturation and immunomodulation via metabolites like short chain fatty acids (SCFAs). This study aimed to investigate the effects of oat β-glucan supplementation, solubilized by citric acid hydrolysis, from gestation to adulthood. Female C57BL/6J mice were orally supplemented with soluble oat β-glucan (ObG) or carboxymethyl cellulose (CMC) via drinking water at 200 mg/kg body weight during breeding while the control group received 50 mg/kg body weight of carboxymethyl cellulose. ObG supplementation increased butyrate production in the guts of both dams and 4-week-old pups, attributing to alterations in the gut microbiota profile. One-week-old pups from the ObG group showed increased neurodevelopmental markers similar to four-week-old pups that also exhibited alterations in serum markers of metabolism and anti-inflammatory cytokines. Notably, at 8 weeks, ObG-supplemented pups exhibited the highest levels of spatial memory and cognition compared to the control and CMC groups. These findings suggest a potential enhancement of neonatal neurodevelopment via shaping of early-life gut microbiome profile, and the subsequent increased later-life cognitive function.PMID:39410136 | DOI:10.3390/foods13193102

Foods. 2024 Sep 27;13(19):3092. doi: 10.3390/foods13193092.ABSTRACTWampee (Clausena lansium (Lour.) Skeels) has natural bioactive components with diverse health benefits, but its detailed metabolism and tissue distribution are not fully understood. Here, widely targeted metabolomics analysis methods were employed to analyze the wampee fruit (peel, pulp, and seed) of 17 different varieties. A total of 1286 metabolites were annotated, including lipids, flavonoids, polyphenols, carbazole alkaloids, coumarins, and organic acids, among others. The quantitative analysis and matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) analysis indicated remarkable variations in metabolite categories and content in the peel, pulp, and seed of wampee fruit. Additionally, the difference analysis found that the metabolic components of peel contributed dominantly to the differences among varieties, and 7 potential biomarkers were identified. In this study, a comprehensive metabolome landscape of wampee fruit was established, which provided important information for the isolation and identification of functional components, food industry application, and nutritional improvement breeding.PMID:39410126 | DOI:10.3390/foods13193092

Foods. 2024 Sep 27;13(19):3089. doi: 10.3390/foods13193089.ABSTRACTCyclocarya paliurus tea, also known as "sweet tea", an herbal tea with Cyclocarya paliurus leaves as raw material, is famous for its unique nutritional benefits and flavor. However, due to the unique "bittersweet" of Cyclocarya paliurus tea, it is still unable to fully satisfy consumers' high-quality taste experience and satisfaction. Therefore, this study aimed to explore metabolites in Cyclocarya paliurus leaves during their growth period, particularly composition and variation of sweet and bitter taste compounds, by combining multi-platform metabolomics analysis with an electronic tongue system and molecular docking simulation technology. The results indicated that there were significant differences in the contents of total phenols, flavonoids, polysaccharides, and saponins in C. paliurus leaves in different growing months. A total of 575 secondary metabolites were identified as potential active metabolites related to sweet/bitter taste using nontargeted metabolomics based on UHPLC-MS/MS analysis. Moreover, molecular docking technology was utilized to study interactions between the candidate metabolites and the sweet receptors T1R2/T1R3 and the bitter receptors T2R4/T2R14. Six key compounds with high sweetness and low bitterness were successfully identified by using computational simulation analysis, including cis-anethole, gluconic acid, beta-D-Sedoheptulose, asparagine, proline, and citrulline, which may serve as candidates for taste modification in Cyclocarya paliurus leaves. These findings provide a new perspective for understanding the sweet and bitter taste characteristics that contribute to the distinctive sensory quality of Cyclocarya paliurus leaves.PMID:39410123 | DOI:10.3390/foods13193089

Foods. 2024 Sep 27;13(19):3079. doi: 10.3390/foods13193079.ABSTRACTInfluenza and other respiratory infections cause annual epidemics worldwide, with high incidence and mortality rates reported among immunocompromised infants and elderly individuals. Probiotics can modulate the immune system through their bacterial compositions and metabolites, affecting influenza infections and effectively responding to viral mutations. Therefore, we evaluated the anti-influenza effects of mixed probiotics administered orally before and after influenza infection. The results showed that the mixed probiotics consisting of Lacticaseibacillus rhamnosus CCFM1279, Limosilactobacillus reuteri CCFM1145, and Lacticaseibacillus casei CCFM1127 inhibited viral replication and reduced lung inflammatory damage against influenza. In addition, the mixed-probiotics treatment activated the systemic immune response of the host. The gut microbiota analysis revealed a notable increase in the abundance of Alistipes and Rikenella following mixed-probiotic supplementation. The metabolomic analysis indicated a significant increase in adenosine levels, which was positively correlated with the abundance of Parvibacter. These findings highlight the effectiveness of mixed probiotics in fighting influenza viruses and suggest that certain gut microbiota and their metabolites may play a significant role in influencing the outcomes of influenza infections.PMID:39410114 | DOI:10.3390/foods13193079

Cancers (Basel). 2024 Oct 1;16(19):3366. doi: 10.3390/cancers16193366.ABSTRACTObjectives: This study aimed to examine the relationship between health-related quality of life (HRQoL) and sociodemographic and clinical variables in survivors of head and neck cancer (HNC) treated with radiotherapy, with or without surgery. Materials and Methods: HRQoL was measured using the functional assessment of cancer therapy-head and neck (FACT-H&N) in a cross-sectional survey involving 150 patients. Of these, 60 had nasopharyngeal cancer (NPC), treated exclusively with radiotherapy, while 90 had oral cavity squamous cell cancer (OSCC), undergoing radical surgery followed by adjuvant radiotherapy. Key variables included cancer type, age, gender, partnership status, education, and employment, with additional clinical variables assessed in patients with OSCC. Statistical analyses included multiple regression, ANOVA, and t-tests to explore relationships between variables and HRQoL. Results: Cancer type, surgical treatment, and employment status emerged as significant independent predictors of HRQoL in HNC patients. Patients with NPC reported better HRQoL on three FACT-H&N subscales-social/family well-being, functional well-being, and additional concerns-compared to patients with OSCC. Unemployed individuals exhibited lower HRQoL on four subscales. In patients with OSCC, partnership status and segmental mandibulectomy were found to predict HRQoL independently. Conclusions: This study concludes that cancer type, surgical intervention, and employment status notably influence HRQoL among HNC patients undergoing radiotherapy. In addition, partnership status is a key factor affecting HRQoL in patients with OSCC.PMID:39409986 | DOI:10.3390/cancers16193366

Cancers (Basel). 2024 Sep 30;16(19):3352. doi: 10.3390/cancers16193352.ABSTRACTBackground/Objectives: Cancer-associated cachexia in head and neck squamous cell carcinoma (HNSCC) is challenging to diagnose due to its complex pathophysiology. This study aimed to identify metabolic biomarkers linked to cachexia and survival in HNSCC patients using [18F]FDG-PET/CT imaging and machine learning (ML) techniques. Methods: We retrospectively analyzed 253 HNSCC patients from Vienna General Hospital and the MD Anderson Cancer Center. Automated organ segmentation was employed to quantify metabolic and volumetric data from [18F]FDG-PET/CT scans across 29 tissues and organs. Patients were categorized into low weight loss (LoWL; grades 0-2) and high weight loss (HiWL; grades 3-4) groups, according to the weight loss grading system (WLGS). Machine learning models, combined with Cox regression, were used to identify survival predictors. Shapley additive explanation (SHAP) analysis was conducted to determine the significance of individual features. Results: The HiWL group exhibited increased glucose metabolism in skeletal muscle and adipose tissue (p = 0.01), while the LoWL group showed higher lung metabolism. The one-year survival rate was 84.1% in the LoWL group compared to 69.2% in the HiWL group (p < 0.01). Pancreatic volume emerged as a key biomarker associated with cachexia, with the ML model achieving an AUC of 0.79 (95% CI: 0.77-0.80) and an accuracy of 0.82 (95% CI: 0.81-0.83). Multivariate Cox regression confirmed pancreatic volume as an independent prognostic factor (HR: 0.66, 95% CI: 0.46-0.95; p < 0.05). Conclusions: The integration of metabolic and volumetric data provided a strong predictive model, highlighting pancreatic volume as a key imaging biomarker in the metabolic assessment of cachexia in HNSCC. This finding enhances our understanding and may improve prognostic evaluations and therapeutic strategies.PMID:39409971 | DOI:10.3390/cancers16193352

Animals (Basel). 2024 Oct 9;14(19):2912. doi: 10.3390/ani14192912.ABSTRACTMolecular differences exist between birds with high residual water intake (HRWI) compared to those with low residual water intake (LRWI). Residual water intake (RWI) is defined as the difference between the water intake of a bird and the expected water intake corrected for metabolic body weight, feed intake, and body weight gain. Tissue metabolomic analysis revealed significantly increased kidney glucose, fructose, and arabitol in the LRWI group compared to the HRWI group. mRNA expression analysis of apical sodium glucose cotransporters SGLT1, SGLT4, SGLT5, and SGLT6 showed decreased expression of SGLTs 1, 5, and 6 in LRWI birds (p < 0.05), whereas SGLT4 expression was increased compared with HRWI birds (p < 0.01). An analysis of basal glucose transporters GLUT1, GLUT2, GLUT5, and GLUT9 showed significantly increased GLUT2 expression in LRWI birds compared with HRWI birds (p < 0.01). We postulate that SGLT4 is the main apical transporter in chicken kidneys and that its increased expression reduces these birds' need for water, resulting in less drinking. This is balanced by the increased expression of the basal transporter GLUT2, indicating better glucose retention, which may partly explain the physiological mechanism behind why these birds drink less water. Innately driven broiler water intake could therefore be influenced by the expression of kidney solute transporters.PMID:39409861 | DOI:10.3390/ani14192912

Animals (Basel). 2024 Oct 8;14(19):2893. doi: 10.3390/ani14192893.ABSTRACTThe objective of this study was to investigate the regulatory effects of a high-fiber content feed on the productive performance, meat quality, and fat acid composition. A total of 18 120-day-old Yushan pigs with similar initial body weight were randomly allotted into high-concentrate diet (high energy, HE) and high-fiber diet (low energy, LE) treatments for the determination of regulatory effects on productive performance, meat quality, and fatty acid content. Further, blood metabolomic, gut microbiota, and liver energy-related gene expression measurements were used to investigate the underlying mechanisms. Results showed that the LE treatment significantly increased ADFI while decreasing carcass weight, fat percentage, and IMF. Metabolomic results showed that the high-fiber treatment significantly down-regulated metabolites that participated in lipid metabolism such as cyclic ADP-ribose and hippuric acid, while up-regulated metabolites were mainly enriched in nitrogen metabolism such as DL-arginine and propionylcarnitine (p < 0.05). Microbial results showed relative abundances of Lactobacillus and Bifidobacterium are significantly proliferated in the high-fiber feeding treatments (p < 0.05). Transcriptomic results showed that genes mainly enriched into the lipid metabolism are significantly up-regulated under the high-fiber dietary treatment (p < 0.05). Conclusion: higher dietary fiber significantly reduced dietary energy provision, effectively decreased the backfat and abdominal fat content of Yushan pigs through proliferating intestinal fiber-degradable bacteria, and up-regulating the hepatic lipolysis-related gene expression.PMID:39409842 | DOI:10.3390/ani14192893

Animals (Basel). 2024 Oct 5;14(19):2873. doi: 10.3390/ani14192873.ABSTRACTCordyceps militaris extract (CME) contains many bioactive compounds, mainly cordycepin (CPN). This study aimed to investigate the possible mechanisms underlying the amelioration of LPS-induced acute liver injury in piglets by CME or CPN supplementation using multi-omics analysis. Twenty-four weaned piglets were randomly distributed into 4 groups (n = 6): the control and LPS groups were fed basal diets; the CPN + LPS (CPN-LPS) and CME + LPS (CME-LPS) groups were fed the basal diets supplemented with CME or CPN. The results showed that CPN or CME supplementation significantly decreased the C-reactive protein level (p < 0.05) and improved liver tissue pathology to prevent acute liver injury after LPS treatment. Compared with LPS, the transcriptomic analysis indicated that CPN supplementation significantly downregulated cell adhesion molecules, while CME supplementation significantly downregulated inflammatory mediator regulation of TRP channels, complement and coagulation cascades and cytokine-cytokine receptor interaction. The metabolomic results showed that CPN or CME supplementation significantly reduced disease biomarker of bicyclo-prostaglandin E2, and increased levels of deoxyinosine and 3-hydroxyanthranilic acid (p < 0.05). The combined transcriptome and metabolome helped identify two metabolites PC 34:2 and PC 36:0, which may be associated with the restoration of liver cell morphology. In conclusion, CPN and CME could attenuate LPS-induced acute liver injury by regulating immune-related genes and metabolites. This study elucidates the potential protective mechanism of CPN or CME supplementation against acute liver injury.PMID:39409822 | DOI:10.3390/ani14192873

Plants (Basel). 2024 Sep 30;13(19):2741. doi: 10.3390/plants13192741.ABSTRACTThe by-products of green coffee processing are rich in compounds that can be recycled for their possible use in the production of beverages, fertilizers and weed control in production areas. The objective of this work was to identify the organic and inorganic bioactive compounds of green coffee and the coffee by-products related to the production of origin, such as dried cascara (skin-pulp), parchment and silverskin (unroasted), in order to investigate the role their biomolecules may have in reuse through practices and local knowledge, not yet valued. The metabolomic profile by HPLC-ESI-HRMS of the aqueous extract of the dried cascara highlighted 93 non-volatile molecules, the highest number reported for dried cascara. They belong to groups of organic acids (12), alkaloids (5), sugars (5), fatty acids (2), diglycerides (1), amino acids (18), phospholipids (7), vitamins (5), phenolic acids (11), flavonoids (8), chlorogenic acids (17), flavones (1) and terpenes (1). For the first time, we report the use of direct analysis in real-time mass spectrometry (DART-MS) for the identification of metabolites in aqueous extracts of dried cascara, parchment, silverskin and green coffee. The DART analysis mainly showed the presence of caffeine and chlorogenic acids in all the extracts; additionally, sugar adducts and antioxidant compounds such as polyphenols were detected. The mineral content (K, Ca, P, S, Mg and Cl) by EDS spectrometry in the by-products and green coffee showed a relatively high content of K in the dried cascara and green coffee, while Ca was detected in double quantity in the silverskin. These metabolomic and mineral profile data allow enhancement of the link between the quality of green coffee and its by-products and the traditional local practices in the crop-growing area. This consolidates the community's experience in reusing by-products, thereby minimizing the impact on the environment and generating additional income for coffee growers' work, in accordance with the principles of circular economy and bioeconomy.PMID:39409611 | DOI:10.3390/plants13192741

Plants (Basel). 2024 Sep 29;13(19):2732. doi: 10.3390/plants13192732.ABSTRACTAlbizia odoratissima is a deciduous tree species belonging to the family Leguminosae. It is widely distributed in the southern subtropical and tropical areas of China and has important ecological and economic value. The growth and metabolic processes of A. odoratissima are affected by drought stress, but the molecular mechanisms remain unknown. Therefore, this study investigated the physicochemical properties, gene expression, and metabolites of A. odoratissima seedlings under drought stress. The results show that, in leaves of A. odoratissima seedlings, drought stress reduced the moisture content, chlorophyll content, photosynthetic efficiency, superoxide dismutase (SOD) activity, and gibberellin (GA) and indoleacetic acid (IAA) contents while increasing the catalase (CAT) and peroxidase (POD) activities and malondialdehyde (MDA), proline, soluble sugar, and soluble protein contents. Within the CK5 (Day 5 of control group) vs. T5 (Day 5 of drought treatment), CK10 vs. T10, CK15 vs. T15, and CK20 vs. T20 groups (CK: control group; T: drought treatment), a total of 676 differentially expressed genes (DEGs) were upregulated and 518 DEGs were downregulated, and a total of 228 and 143 differential accumulation metabolites (DAMs) were identified in the CK10 vs. T10 and CK20 vs. T20 groups. These were mainly involved in the amino acid and alkaloid metabolism pathways in the leaves of the A. odoratissima seedlings. In the amino acid and alkaloid biosynthesis pathways, the relative expression levels of the AoproA (Aod04G002740, ORTHODONTIC APPLIANCE), AoOAT (Aod07G015970, ORNITHINE-OXO-ACID TRANSAMINASE), and AoAOC3 (Aod12G005010/08G003360/05G023920/08G003000/08G003010, AMINE OXIDASE COPPER CONTAINING 3) genes increased, which concurrently promoted the accumulation of arginine, proline, piperine, cadaverine, and lysine. Furthermore, some key transcription factors in the response to drought were identified in the leaves using the weighted gene co-expression network analyses (WGCNA) method. These findings reveal that A. odoratissima seedlings respond to drought stress by improving the capacities of the antioxidant system and secondary metabolism.PMID:39409602 | DOI:10.3390/plants13192732

Plants (Basel). 2024 Sep 28;13(19):2714. doi: 10.3390/plants13192714.ABSTRACTSoybean improvement has entered a new era with the advent of multi-omics strategies and bioinformatics innovations, enabling more precise and efficient breeding practices. This comprehensive review examines the application of multi-omics approaches in soybean-encompassing genomics, transcriptomics, proteomics, metabolomics, epigenomics, and phenomics. We first explore pre-breeding and genomic selection as tools that have laid the groundwork for advanced trait improvement. Subsequently, we dig into the specific contributions of each -omics field, highlighting how bioinformatics tools and resources have facilitated the generation and integration of multifaceted data. The review emphasizes the power of integrating multi-omics datasets to elucidate complex traits and drive the development of superior soybean cultivars. Emerging trends, including novel computational techniques and high-throughput technologies, are discussed in the context of their potential to revolutionize soybean breeding. Finally, we address the challenges associated with multi-omics integration and propose future directions to overcome these hurdles, aiming to accelerate the pace of soybean improvement. This review serves as a crucial resource for researchers and breeders seeking to leverage multi-omics strategies for enhanced soybean productivity and resilience.PMID:39409584 | DOI:10.3390/plants13192714

Plants (Basel). 2024 Sep 26;13(19):2698. doi: 10.3390/plants13192698.ABSTRACTRhodiola linearifolia Boriss., a perennial alpine plant from the Crassulaceae family, is renowned for its unique medicinal properties. However, existing research on this species is limited, particularly regarding the impact of altitude on its physiological and medicinal compounds. The current study employed morphophysiological and anatomical methods to explore the adaptive mechanisms of R. linearifolia across different altitudinal gradients, while also examining photosynthetic pigments and metabolomic changes. Our results indicate that despite the simultaneous effects of various mountain abiotic factors, significant correlations can be identified between altitude and trait variation. An optimal growth altitude of 2687 m above sea level was identified, which is pivotal for sustainable ecosystem management and potential species introduction strategies. It is noted that increasing altitude stress enhances the synthesis of secondary antioxidant metabolites in R. linearifolia, enhancing its pharmaceutical potential.PMID:39409568 | DOI:10.3390/plants13192698

Plants (Basel). 2024 Sep 26;13(19):2693. doi: 10.3390/plants13192693.ABSTRACTSinopodophyllum hexandrum (Royle) Ying, an endangered perennial medicinal herb, exhibits morpho-physiological dormancy in its seeds, requiring cold stratification for germination. However, the precise molecular mechanisms underlying this transition from dormancy to germination remain unclear. This study integrates transcriptome and plant hormone-targeted metabolomics techniques to unravel these intricate molecular regulatory mechanisms during cold stratification in S. hexandrum seeds. Significant alterations in the physicochemical properties (starch, soluble sugars, soluble proteins) and enzyme activities (PK, SDH, G-6-PDH) within the seeds occur during stratification. To characterize and monitor the formation and transformation of plant hormones throughout this process, extracts from S. hexandrum seeds at five stratification stages of 0 days (S0), 30 days (S1), 60 days (S2), 90 days (S3), and 120 days (S4) were analyzed using UPLC-MS/MS, revealing a total of 37 differential metabolites belonging to seven major classes of plant hormones. To investigate the biosynthetic and conversion processes of plant hormones related to seed dormancy and germination, the transcriptome of S. hexandrum seeds was monitored via RNA-seq, revealing 65,372 differentially expressed genes associated with plant hormone synthesis and signaling. Notably, cytokinins (CKs) and gibberellins (GAs) exhibited synergistic effects, while abscisic acid (ABA) displayed antagonistic effects. Furthermore, key hub genes were identified through integrated network analysis. In this rigorous scientific study, we systematically elucidate the intricate dynamic molecular regulatory mechanisms that govern the transition from dormancy to germination in S. hexandrum seeds during stratification. By meticulously examining these mechanisms, we establish a solid foundation of knowledge that serves as a scientific basis for facilitating large-scale breeding programs and advancing the artificial cultivation of this highly valued medicinal plant.PMID:39409563 | DOI:10.3390/plants13192693