Integrated metabolomic and transcriptomic strategies to reveal alkali-resistance mechanisms in wild soybean during post-germination growth stage.

MAIN CONCLUSION: The keys to alkali-stress resistance of barren-tolerant wild soybean lay in enhanced reutilization of reserves in cotyledons as well as improved antioxidant protection and organic acid accumulation in young roots. Soil alkalization of farmlands is increasingly serious, adversely restricting crop growth and endangering food security. Here, based on integrated analysis of transcriptomics and metabolomics, we systematically investigated changes in cotyledon weight and young root growth in response to alkali stress in two ecotypes of wild soybean after germination to reveal alkali-resistance mechanisms in barren-tolerant wild soybean. Compared with barren-tolerant wild soybean, the dry weight of common wild soybean cotyledons under alkali stress decreased slowly and the length of young roots shortened. In barren-tolerant wild soybean, nitrogen-transport amino acids asparagine and glutamate decreased in cotyledons but increased in young roots, and nitrogen-compound transporter genes and genes involved in asparagine metabolism were significantly up-regulated in both cotyledons and young roots. Moreover, isocitric, succinic, and L-malic acids involved in the glyoxylate cycle significantly accumulated and the malate synthetase gene was up-regulated in barren-tolerant wild soybean cotyledons. In barren-tolerant wild soybean young roots, glutamate and glycine related to glutathione metabolism increased significantly and the glutathione reductase gene was up-regulated. Pyruvic acid and citric acid involved in pyruvate-citrate metabolism increased distinctly and genes encoding pyruvate decarboxylase and citrate synthetase were up-regulated. Integrated analysis showed that the keys to alkali-stress resistance of barren-tolerant wild soybean lay in enhanced protein decomposition, amino acid transport, and lipolysis in cotyledons as well as improved antioxidant protection and organic acid accumulation in young roots. This study provides new ideas for the exploitation and utilization of wild soybean resources.

Wild soybean salt tolerance metabolic model: Assessment of storage protein mobilization in cotyledons and C/N balance in the hypocotyl/root axis.

Salt stress has become one of the main factors limiting crop yield in recent years. The post-germinative growth is most sensitive to salt stress in soybean. In this study, cultivated and wild soybeans were used for an integrated metabonomics and transcriptomics analysis to determine whether wild soybean can resist salt stress by maintaining the mobilization of stored substances in cotyledons and the balance of carbon and nitrogen in the hypocotyl/root axis (HRA). Compared with wild soybean, the growth of cultivated soybean was significantly inhibited during the post-germinative growth period under salt stress. Integrating analysis found that the breakdown products of proteins, such as glutamate, glutamic acid, aspartic acid, and asparagine, increased significantly in wild soybean cotyledons. Asparagine synthase and fumarate hydratase genes and genes encoding HSP20 family proteins were specifically upregulated. In wild soybean HRA, levels of glutamic acid, aspartic acid, asparagine, citric acid, and succinic acid increased significantly, and the glutamate decarboxylase gene and the gene encoding carbonic anhydrase in nitrogen metabolism were significantly upregulated. The metabolic model indicated that wild soybean enhanced the decomposition of stored proteins and the transport of amino acids to the HRA in cotyledons and the GABA shunt to maintain carbon and nitrogen balance in the HRA to resist salt stress. This study provided a theoretical basis for cultivating salt-tolerant soybean varieties and opened opportunities for the development of sustainable agricultural practices.

Deep Learning Denoising of Low-Dose Computed Tomography Chest Images: A Quantitative and Qualitative Image Analysis.

PURPOSE: To assess deep learning denoised (DLD) computed tomography (CT) chest images at various low doses by both quantitative and qualitative perceptual image analysis. METHODS: Simulated noise was inserted into sinogram data from 32 chest CTs acquired at 100 mAs, generating anatomically registered images at 40, 20, 10, and 5 mAs. A DLD model was developed, with 23 scans selected for training, 5 for validation, and 4 for test.Quantitative analysis of perceptual image quality was assessed with Structural SIMilarity Index (SSIM) and Fréchet Inception Distance (FID). Four thoracic radiologists graded overall diagnostic image quality, image artifact, visibility of small structures, and lesion conspicuity. Noise-simulated and denoised image series were evaluated in comparison with one another, and in comparison with standard 100 mAs acquisition at the 4 mAs levels. Statistical tests were conducted at the 2-sided 5% significance level, with multiple comparison correction. RESULTS: At the same mAs levels, SSIM and FID between noise-simulated and reconstructed DLD images indicated that images were closer to a perfect match with increasing mAs (closer to 1 for SSIM, and 0 for FID).In comparing noise-simulated and DLD images to standard-dose 100-mAs images, DLD improved SSIM and FID. Deep learning denoising improved SSIM of 40-, 20-, 10-, and 5-mAs simulations in comparison with standard-dose 100-mAs images, with change in SSIM from 0.91 to 0.94, 0.87 to 0.93, 0.67 to 0.87, and 0.54 to 0.84, respectively. Deep learning denoising improved FID of 40-, 20-, 10-, and 5-mAs simulations in comparison with standard-dose 100-mAs images, with change in FID from 20 to 13, 46 to 21, 104 to 41, and 148 to 69, respectively.Qualitative image analysis showed no significant difference in lesion conspicuity between DLD images at any mAs in comparison with 100-mAs images. Deep learning denoising images at 10 and 5 mAs were rated lower for overall diagnostic image quality ( P < 0.001), and at 5 mAs lower for overall image artifact and visibility of small structures ( P = 0.002), in comparison with 100 mAs. CONCLUSIONS: Deep learning denoising resulted in quantitative improvements in image quality. Qualitative assessment demonstrated DLD images at or less than 10 mAs to be rated inferior to standard-dose images.

Remodeling and protecting the membrane system to resist phosphorus deficiency in wild soybean (Glycine soja) seedling leaves.

MAIN CONCLUSION: The poor-soil-tolerant wild soybean resist phosphorus deficiency by remodeling membrane lipids to reuse phosphorus. The plants synthesize phenolic acids and flavonoids to remove reactive oxygen species and protect membrane stability. Poor soil largely limits plant yields, and the development and utilization of high-quality wild plant resources is an effective approach to resolving this problem. Two ecotypes of wild soybean were used as experimental materials in this experiment. We integrated metabolomics and transcriptomics to determine whether wild soybean (Glycine soja) could resist phosphorus deficiency by remodeling and protecting its membrane system. Under phosphorus-deficient conditions, the plant height and aboveground fresh and dry weight of poor-soil-tolerant wild soybean seedlings were less inhibited than those in common wild soybean. In poor-soil-tolerant wild soybean seedling leaves, the glycerol-3-phosphate content decreased significantly, while caffeic acid, ferulic acid, shikimic acid, phenylalanine, tyrosine, and tryptophan increased significantly. ß-Glucosidase and chalcone synthase genes and those that encode SQD2, a crucial enzyme in thiolipid biosynthesis, were specifically up-regulated, whereas the glucosyltransferase UGT74B1 gene was down-regulated. The poor-soil-tolerant wild soybean enhanced glycerolipid metabolism to decompose phospholipids and release phosphorus for reuse to improve resistance to phosphorus deficiency. The plants synthesized thiolipids to replace phospholipids and maintain membrane structure integrity and inhibited glucosinolate biosynthesis to promote phenylpropanoid biosynthesis, leading to the production of phenolic acids and flavonoids that removed reactive oxygen species and protected membrane system stability. The experiments evaluated and provided insight into the innovative utilization of wild soybean germplasm resources.

Galacto-Oligosaccharides and the Elderly Gut: Implications for Immune Restoration and Health.

The increasing prevalence of noncommunicable diseases in the aging population has been correlated with a decline in innate and adaptive immune responses; hence, it is imperative to identify approaches to improve immune function, prevent related disorders, and reduce or treat age-associated health complications. Prebiotic supplementation is a promising approach to modulate the gut microbiome and immune system, offering a potential strategy to maintain the integrity of immune function in older individuals. This review summarizes the current research on prebiotic galacto-oligosaccharide (GOS) immunomodulatory mechanisms mediated by bacterial-derived metabolites, including short-chain fatty acids and secondary bile acids, to maintain immune homeostasis. The potential applications of GOS as immunotherapy for age-related disease prevention in older individuals are also highlighted. This aligns with the global shift toward proactive healthcare and emphasizes the significance of early intervention in directing an individual's health trajectory.

Comparative differences in maintaining membrane fluidity and remodeling cell wall between Glycine soja and Glycine max leaves under drought.

Water shortage is one of the most important environmental factors limiting crop yield. In this study, we used wild soybean (Glycine soja Sieb. et Zucc.) and soybean (Glycinemax (L.) Merr.) seedlings as experimental materials, simulated drought stress using soil gravimetry, measured growth and physiological parameters, and analyzed differentially expressed genes and metabolites in the leaves of seedling by integrated transcriptomics and metabolomics techniques. The results indicate that under water deficit, Glycine soja maintained stable photosynthate by accumulating Mg2+, Fe3+, Mn2+, Zn2+ and B3+, and improved water absorption by increasing root growth. Notably, Glycine soja enhanced linoleic acid metabolism and plasma membrane intrinsic protein (PIP1) gene expression to maintain membrane fluidity, and increased pentose, glucuronate and galactose metabolism and thaumatin protein genes expression to remodel the cell wall, thereby increasing water-absorption to better tolerate to drought stress. In addition, it was found that secondary phenolic metabolism, such as phenylpropane biosynthesis, flavonoid biosynthesis and ascobate and aldarate metabolism were weakened, resulting in the collapse of the antioxidant system, which was the main reason for the sensitivity of Glycine max to drought stress. These results provide new insights into plant adaptation to water deficit and offer a theoretical basis for breeding soybean varieties with drought tolerance.

Network analysis of depression and anxiety symptoms and their associations with mobile phone addiction among Chinese medical students during the late stage of the COVID-19 pandemic.

Network analysis provides a novel approach to discovering associations between mental disorders at the symptom level. This study aimed to examine the characteristics of the network of depression and anxiety symptoms and their associations with mobile phone addiction (MPA) among Chinese medical students during the late stage of the COVID-19 pandemic. A total of 553 medical students were included. Depression and anxiety symptoms and MPA were measured by the nine-item Patient Health Questionnaire (PHQ-9), the seven-item Generalized Anxiety Disorder Scale (GAD-7), and the Mobile Phone Addiction Index (MPAI), respectively. Central and bridge symptoms were identified with centrality indices and bridge centrality indices. Network stability was examined using the case-dropping procedure. "Uncontrollable worry", "restlessness" and "nervousness" were the central symptoms in the depression and anxiety network. "Restlessness" and "motor" were the most central bridge symptoms linking depression and anxiety. "Concentration", "anhedonia" and "sleep" were most strongly associated with MPA. "Uncontrollable worry", "restlessness", "nervousness," and "motor" may be the symptoms for interventions to target in medical students with comorbid depression and anxiety. From a network perspective, depressive symptoms may be more important than anxiety symptoms in medical students with MPA.

Anatomical factors associated with the development of anterior tibial spine fractures based on MRI measurements.

BACKGROUND: Numerous studies have investigated anatomic factors for anterior cruciate ligament (ACL) injuries, such as posterior tibial slope (PTS) and notch width index (NWI). However, anterior tibial spine fracture (ATSF) as a specific pattern of ACL injury, a bony avulsion of the ACL from its insertion on the intercondylar spine of the tibia, has rarely been explored for its anatomical risk factors. Identifying anatomic parameters of the knee associated with ATSF is important for understanding injury mechanisms and prevention. METHODS: Patients who underwent surgery for ATSF between January 2010 and December 2021 were retrospectively reviewed, and 38 patients were included in the study group. Thirty-eight patients who suffered from isolated meniscal tear without other pathologic findings were matched in a 1:1 fashion by age, sex and BMI to the study group. The lateral posterior tibial slope (LPTS), medial posterior tibial slope (MPTS), medial tibial depth, lateral tibial height, lateral femoral condyle ratio (LFCR) and NWI were measured and compared between the ATSF and control groups. Binary logistic regressions identified independent predictors of ATSF. Receiver operator characteristic (ROC) curves were performed to compare the diagnostic performance and determine the cutoff values of associated parameters. RESULTS: The LPTS, LFCR and MPTS were significantly larger in the knees in the ATSF group than in the control group (P = 0.001, P = 0.012 and P = 0.005, respectively). The NWI was significantly smaller in the knees in the ATSF group than in the control group (P = 0.005). According to the results of logistic regression analysis, the LPTS, LFCR and NWI were independently associated with ATSF. The LPTS was the strongest predictor variable, and the ROC analysis revealed 63.2% sensitivity and 76.3% specificity (area under the curve, 0.731; 95% CI 0.619-0.844) for values above 6.9. CONCLUSION: The LPTS, LFCR and NWI were found to be associated with the ATSF; in particular, LPTS could provide the most accurate predictive performance. The findings of this study may aid clinicians in identifying people at risk for ATSF and taking individualized preventive measures. However, further investigation regarding the pattern and biomechanical mechanisms of this injury is required.

Comparative study of leaf nutrient reabsorption by two different ecotypes of wild soybean under low-nitrogen stress.

Wild soybean (Glycine soja), the ancestor of cultivated soybean, has evolved into many ecotypes with different adaptations to adversity under the action of divergent evolution. Barren-tolerant wild soybean has developed adaptation to most nutrient-stress environments, especially with respect to low nitrogen (LN) conditions. This study describes the differences in physiological and metabolomic changes between common wild soybean (GS1) and barren-tolerant wild soybean(GS2) under LN stress. Compared with plants grown under the unstressed control (CK) conditions, the young leaves of barren-tolerant wild soybean under LN conditions maintained relatively stable chlorophyll, concentration and rates of photosynthesis and transpiration, as well as increased carotenoid content, whereas the net photosynthetic rate (PN) of GS1 decreased significantly 0.64-fold (p < 0.05) in the young leaves of GS1. The ratio of internal to atmospheric CO2 concentrations increased significantly 0.07-fold (p < 0.05), 0.09-fold (p < 0.05) in the young leaves of GS1 and GS2, respectively, and increased significantly 0.05-fold (p < 0.05) and 0.07-fold (p < 0.05) in the old leaves of GS1 and GS2, respectively, relative to the CK. The concentration of chlorophylls a and b decreased significantly 0.45-fold (p < 0.05), 0.13-fold (p > 0.05) in the young leaves of GS1 and GS2, respectively, and decreased significantly 0.74-fold (p < 0.01) and 0.60-fold (p < 0.01) in the old leaves of GS1 and GS2, respectively. Under LN stress, nitrate concentration in the young leaves of GS1 and GS2 decreased significantly 0.69- and 0.50-fold (p < 0.01), respectively, relative to CK, and decreased significantly 2.10-fold and 1.77-fold (p < 0.01) in the old leaves of GS1 and GS2, respectively. Barren-tolerant wild soybean increased the concentration of beneficial ion pairs. Under LN stress, Zn2+ significantly increased by 1.06- and 1.35-fold (p < 0.01) in the young and old leaves of GS2 (p < 0.01), but there was no significant change in GS1. The metabolism of amino acids and organic acids was high in GS2 young and old leaves, and the metabolites related to the TCA cycle were significantly increased. The 4-aminobutyric acid (GABA) concertation decreased significantly 0.70-fold (p < 0.05) in the young leaves of GS1 but increased 0.21-fold (p < 0.05) significantly in GS2. The relative concentration of proline increased significantly 1.21-fold (p < 0.01) and 2.85-fold (p < 0.01) in the young and old leaves of GS2. Under LN stress, GS2 could maintain photosynthesis rate and enhance the reabsorption of nitrate and magnesium in young leaves, compared to GS1. More importantly, GS2 exhibited increased amino acid and TCA cycle metabolism in young and old leaves. Adequate reabsorption of mineral and organic nutrients is an important strategy for barren-tolerant wild soybeans to survive under LN stress. Our research provides a new perspective on the exploitation and utilization of wild soybean resources.

Integration of the transcriptome and metabolome reveals the mechanism of resistance to low phosphorus in wild soybean seedling leaves.

Plant growth, development, yield and quality are limited by barren soil. Soil phosphorus deficiency is one of the common factors causing soil barrenness. Plants have evolved morphological, physiological and molecular adaptations to resist to phosphorus deficiency. Wild soybean, a wild relative of cultivated soybean, has an obvious genetic relationship with cultivated soybean and has many beneficial characteristics such as strong low phosphorus resistance. Therefore, in this study, the integration analysis of transcriptome and metabolome of wild and cultivated soybean seedlings leaves were applied under phosphorus deficiency to reveal the mechanism of resistance to low phosphorus stress in wild soybean leaves, especially the key role of membrane phospholipid reuse and protection. Under phosphorus deficiency, wild soybean resisted low phosphorus stress by enhancing phosphorus reuse and strengthening membrane protection mechanisms, that is, by enhancing phospholipid metabolism, degrading membrane phospholipids, releasing phosphorus, increasing phosphorus reuse, and enhancing galactolipid biosynthesis. This, in turn, produced digalactosyl diacylglycerol to replace missing phospholipids for membrane maintenance and enhanced glutathione metabolism to protect the membrane system from damage. At the same time, phosphorus deficiency increased the levels of the intermediate metabolites glycine and ornithine, while significantly regulating the expression of transcription factors WRKY75 and MYB86. The enhancement of these metabolic pathways and the significant regulation of gene expression play an important role in improving the low phosphorus tolerance of wild soybean. This study will provide a useful theoretical basis for breeding soybean with low phosphorus tolerance.

Green synthesis of silver nanoparticles using sodium alginate and tannic acid: characterization and anti-S. aureus activity.

Multi-drug resistance and biofilm formation are a growing problem in the treatment of Staphylococcus aureus contamination. Advances in nanotechnology allow the synthesis of metal nanoparticles that can be assembled into complex architectures for controlling bacterial growth. This study aims to investigate the ultrasonic-assisted green synthesis of silver nanoparticles (AgNPs) by tannic acid (TA) and sodium alginate (Na-Alg) as the reducing and stabilizing agents, respectively, and evaluation of their antibacterial and antibiofilm activities. The UV-Vis spectroscopy and transmission electron microscopy (TEM), energy dispersive spectroscopy (EDS), zetasizer, FT-IR spectroscopy, and X-ray diffraction (XRD) studies showed that the optimum produces were spherical, stable, and monodispersed AgNPs with an average size of particle sizes of 18.52 ± 0.07 nm. The antibacterial and antibiofilm activities of the AgNPs loaded TA/Na-Alg constructs against S. aureus ATCC 6538 were investigated. The minimum inhibitory concentration (MIC) of the AgNPs was 31.25 µg/mL. After exposure to the AgNPs, planktonic S. aureus showed irreversible cell membrane damage, decreased cell viability, and changes in cellular morphology. In addition, the AgNps significantly inhibited S. aureus biofilm formation at 1/32 MIC. The biofilm elimination rate was 58.87% after exposure to MIC AgNPs. The results suggested that the development of AgNPs loaded TA/Na-Alg constructs with biomedical potentialities obtained through a simple, green, and cost-effective approach, may be suitable for the formulation of a new strategy for combating S. aureus.

Response of microbial community assembly and succession pattern to abiotic factors during the second round of light-flavor Baijiu fermentation.

The regulation of microbial communities is an important strategy for fermentation management. Dynamic microbiota during the Baijiu fermentation is shaped by a variety of abiotic factors. Therefore, this study aims to investigate the effects of the microbiota of the fermentation starter Daqu on the microbial assembly and the interaction of microbiota succession and abiotic factors during the second round (Ercha) of light-flavor Baijiu fermentation. The results revealed that Streptomyces, Bacillus, Lactobacillus, and Staphylococcus were the dominant bacterial genera in the initial fermentation, while Lactobacillus was dominant during the middle and later stages. Pichia and Saccharomycopsis were the dominant fungal genera during the whole fermentation process. A total of 54 volatile compounds were identified during the fermentation, among which 15 compounds, mainly including ethyl acetate, diethyl azelate, ethyl 2-hydroxyisocaproate, 3-furaldehyde, and ethylidene diacetate, were identified as important flavor metabolites. The SourceTracker software revealed that Daqu contributed 52.3 % of the bacterial community and 38.6 % of the fungal community to the fermentation. Ethanol, moisture, and pH were the major factors regulating the succession of dominant bacteria and fungi during the fermentation. The microbial succession and co-occurrence pattern driven by abiotic factors played a crucial role in shaping flavor profiles. These results provide guidance for controlling the fermentation process by optimizing operational parameters or bioaugmentation with specific microbes.

Understanding the Interactions between Staphylococcus aureus and the Raw-Meat-Processing Environment Isolate Klebsiella oxytoca in Dual-Species Biofilms via Discovering an Altered Metabolic Profile.

In a raw-meat-processing environment, members of the Enterobacteriaceae family can coexist with Staphylococcus aureus to form dual-species biofilms, leading to a higher risk of food contamination. However, very little is known about the effect of inter-species interactions on dual-species biofilm formation. The aim of this study was to investigate the interactions between S. aureus and raw-meat-processing environment isolates of Klebsiella oxytoca in dual-species biofilms, by employing an untargeted metabolomics tool. Crystal violet staining assay showed that the biomass of the dual-species biofilm significantly increased and reached its maximum after incubation for 21 h, compared with that of single species grown alone. The number of K. oxytoca in the dual-species biofilm was significantly higher than that of S. aureus. Field emission scanning electron microscopy (FESEM) revealed that both species were evenly distributed, and were tightly wrapped by extracellular polymeric substances in the dual-species biofilms. Ultra-high-pressure liquid chromatography equipped with a quadrupole-time-of-flight mass spectrometer (UHPLC-Q-TOF MS) analysis exhibited a total of 8184 positive ions, and 6294 negative ions were obtained from all test samples. Multivariate data analysis further described altered metabolic profiling between mono- and dual-species biofilms. Further, 18 and 21 different metabolites in the dual-species biofilm were screened as biomarkers by comparing the mono-species biofilms of S. aureus and K. oxytoca, respectively. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways that were exclusively upregulated in the dual-species biofilm included ABC transporters, amino acid metabolism, and the two-component signal transduction system. Our results contribute to a better understanding of the interactive behavior of inter-species biofilm communities, by discovering altered metabolic profiling.

Deciphering the Shifts in Microbial Community Diversity From Material Pretreatment to Saccharification Process of Fuyu-Flavor Baijiu.

The microbiota of the pretreatment phase is crucial to the assembly of the microbial community in the saccharification of fuyu-flavor baijiu. This study investigates the shifts in microbial community diversity from the pretreatment of raw materials to the end of saccharification. High-throughput sequencing reveals that Lactobacillus, Weissella, and Bacillus in the bacterial community and Rhizopus, Candida, Pichia, and Aspergillus in the fungal community are predominant during raw material pretreatment and saccharification processes. Also, 11 bacterial genera, including Bacillus, Lactobacillus, Leuconostoc, Weissella, Lactococcus, and Acetobacter, and eight yeast genera, including Candida, Pichia, Saccharomyces, and Wickerhamomyces, were isolated from the initial saccharification stage by culture-dependent approaches. Sourcetracker analysis indicates that the cooling grains and rice husks were the main contributors to the bacterial community composition of the saccharification process, and Qu was the main contributor to the shaping of the fungal community structure during the saccharification process. Abundance variation of the predictive functional profiles of microbial communities encoding for key enzymes involved in pyruvate metabolism, starch and sucrose metabolism, and glycolysis/gluconeogenesis during the pretreatment and saccharification phases were inferred by PICRUSt2 analysis. The results of this study will be utilized to produce consistently high-quality fuyu-flavor baijiu via better controlling the shaping of microbial community structures during the pretreatment and fermentation processes.