The Complete Genome Sequence Resource of Rhizospheric Soil-Derived Bacillus velezensis Yao, with Biocontrol Potential Against Fusarium solani-Induced Pepper Root Rot.

The pepper rhizospheric soil-derived Bacillus velezensis Yao from the Shangqiu region of the Henan province in China possesses antagonistic activity against Fusarium solani, which causes pepper root rot. In this report, we introduced the entire genomic sequence of B. velezensis Yao, which is 3,951,864 bp long, with 46.61% G+C content, and 4,097 genes. Using antiSMASH analysis, we predicted 12 gene clusters that encode for secondary antimicrobial metabolites and multiple genes that regulate plant bacterial interactions. The B. velezensis Yao genome data may be a valuable resource as this strain may serve as an effective biocontrol agent against pepper root rot.

Transcriptional response of wolfberry to infestation with the endophytic Fusarium nematophilum strain NQ8GII4.

Fusarium nematophilum NQ8GII4 is an endophytic fungus isolated from the root of healthy wolfberry (Lycium barbarum). Previous studies have reported that NQ8GII4 could dwell in wolfberry roots and enhance the defense responses in wolfberry against root rot, which is caused by F. oxysporum. To further elucidate the molecular mechanism of wolfberry disease resistance induced by NQ8GII4, in the present study, we adopted RNA sequencing analysis to profile the transcriptome of wolfberry response to NQ8GII4 infestation over a time course of 3 and 7 days post-inoculation (dpi). Gene ontology (GO) enrichment analysis revealed that DEGs were enriched related to biological regulation, response to stimulus, signaling, detoxification, immune system process, transporter activity, electron carrier activity, transcription factor activity, nucleic acid binding transcription factor, and antioxidant activity. Through Kyoto encyclopedia of genes and genomes (KEGG) analysis, it was found that many of these DEGs were enriched in pathways related to plant-pathogen interactions, hormone signal transduction, and phenylpropanoid biosynthesis pathway in wolfberry. This suggests that innate immunity, phytohormone signaling, and numerous phenylpropanoid compounds, which comprise a complex defense network in wolfberry. Chloroplast 50S ribosomal proteins (50S RP) were consistently located at the core position of the response in wolfberry following infestation with NQ8GII4 analyzed by protein-protein interaction (PPI) network. This study elucidated the molecular mechanism underlying the interaction between NQ8GII4 and wolfberry, clarified the wolfberry immune response network to endophytic fungi infestation, identified candidate resistance genes in wolfberry, and provided a fundamental date for subsequent work.

Typical Aroma of Merlot Dry Red Wine from Eastern Foothill of Helan Mountain in Ningxia, China.

Aroma is an important aspect of wine quality and consumer appreciation. The volatile organic compounds (VOCs) and olfactory profiles of Merlot dry red wines from the Eastern Foothill of Helan Mountain (EFHM) were analyzed using gas chromatography-mass spectrometry and quantitative descriptive analysis. The results showed that Merlot wines from EFHM were characterized by intense flavors of drupe and tropical fruits compared with the Gansu region. Nineteen VOCs were defined as essential compounds contributing to the aroma characteristics of the Merlot wines through gas chromatography-olfactometry/mass spectrometry and odor activity value analysis. Predominantly, geranyl isovalerate, which contributed to the herbal odors of the Merlot wines, was detected in the grape wine of EFHM for the first time. The addition experiment revealed that geranyl isovalerate influenced the aroma quality of wine by increasing herbal odors and enhancing the olfactory intensities of tropical fruits. These results are helpful for further understanding the aroma of Merlot wines from EFHM and improving the quality of wine aromas.

4-octyl Itaconate inhibits lipopolysaccharide (LPS)-induced osteoarthritis via activating Nrf2 signalling pathway.

Small molecule drug intervention for chondrocytes is a valuable method for the treatment of osteoarthritis (OA). The 4-octyl itaconate (OI) is a cellular derivative of itaconate with sound cell permeability and transformation rate. We attempted to confirm the protective role of OI in chondrocytes and its regulatory mechanism. We used lipopolysaccharide (LPS) to induce chondrocyte inflammation injury. After the OI treatment, the secretion and mRNA expression of Il-6, Il-10, Mcp-1 and Tnf-α were detected by ELISA and qPCR. The protective effect of OI on articular cartilage was further verified in surgical destabilization of the medial meniscus model of OA. Cell death and apoptosis were evaluated based on CCK8, LDH, Typan blue staining, Annexin V and TUNEL analyses. The small interfering RNAs were used to knockout the Nrf2 gene of chondrocytes to verify the OI-mediated Nrf2 signalling pathway. The results revealed that OI protects cells from LPS-induced inflammatory injury and attenuates cell death and apoptosis induced by LPS. Similar protective effects were also observed on articular cartilage in mice. The OI activated Nrf2 signalling pathway and promoted the stable expression and translocation of Nrf2 into the nucleus. When the Nrf2 signalling pathway was blocked, the protective effect of OI was significantly counteracted in chondrocytes and a mouse arthritis model. Both itaconate and its derivative (i.e., OI) showed important medical effects in the treatment of OA.

First Report of Powdery Mildew Caused by Podosphaera xanthii on Glandularia tenera in China.

Glandularia tenera (syn. Verbena tenera) is an herbaceous perennial ornamental plant used in gardens as an edging plant with beautiful white, red, or purple flowers. In autumn 2020 and 2021, severe powdery mildew infection was observed on G. tenera cultivar Xianghe in Renming Botanical garden in Shangqiu, Henan province, China (34.4568° N, 115.6640° E). Approximately 80% of leaves on each plant were symptomatic, and about 90% of the plants were infected. Powdery mildew colonies appeared as white spots on the adaxial surface of the leaves and stems of the plants in the initial infection stage. Later, mycelial growth was amphigenous, thick, forming irregular white patches, and effused to cover the whole leaf surface. Finally, leaves turned yellow and senescence occurred. Samples of symptomatic leaves were stained with trypan blue and examined under a Leica DM2500 microscope. Microscopic observations showed that conidia on infected leaves were hyaline and ellipsoid to oval with fibrosin bodies, measured 25 to 37 × 14 to 23 µm with a length/width ratio of 1.4 to 2.0. Conidiophores were unbranched, straight, 80 to 210× 10 to 14 µm in size, and produced two to five immature conidia in chains. Foot cells of conidiophores were cylindrical with slight constrictions at basal septa, and followed by one to three short cells. Fungal hyphae were septate, branched, and flexuous to straight and 4 to 7µm wide with indistinct to slightly nipple-shaped appressoria. Chasmothecia were not observed. These morphological characteristics were identical with the previous description of Podosphaera xanthii (Castagne) U. Braun & Shishkoff (Braun and Cook 2012). To confirm the identification, the sequence of ITS1-5.8s-ITS2 region of rDNA for the isolate SQVT was amplified from conidia collected from infected leaves with universal primers ITS1 and ITS4, sequenced and analyzed using the BLASTn search of GenBank. Amplicon was 565 bp (OM293967) and showed 99.82% similarity with sequence of P. xanthii from Eclipta prostrate (MT260063) in China (Xu et al. 2020), from Youngia denticulate (AB040351) in Japan (Hirata et al. 2000), and 99.65% with sequence of P. xanthii from V. brasiliensis in Korea (Cho et al. 2014). The domains D1 and D2 of the 28S rDNA for the isolate SQVTPX-1 was amplified with primer NL1/NL4. Amplicon was 613 bp (ON259308) and showed 100% similarity with sequence of P. xanthii from V. brasiliensis (AB936277) (Meeboon and Takamatsu, 2015). Pathogenicity tests were conducted by gently pressing the infected leaves onto leaves of five healthy G. tenera cultivar Xianghe plants. Five non-inoculated plants served as controls. Plants were maintained in a greenhouse at 25 ± 2°C. Eight days after inoculation, symptoms similar to those observed under natural conditions developed on the inoculated leaves of G. tenera plants, whereas the control plants remained symptomless. The fungus on inoculated leaves was morphologically identical to that first observed in the field. P. xanthii is a cosmopolitan powdery mildew fungus, parasitic on numerous plant species, especially Cucurbitaceae and Compositae plants. The pathogen has been reported infecting V. bonariensis (Hong et al. 2021), V. × hybrida in China (Zhuang 2005), and V. brasiliensis in Korea (Cho et al. 2014). Interestingly, G. tenera plants infected by P. xanthii were adjacent with V. × hybrida plants infected by P. xanthii in Renming Botanical garden. Incidence of P. xanthii on G. tenera add information on pathogen's host range and help us develop comprehensive survey and effective management of the disease. To our knowledge, this is the first report of P. xanthii on G. tenera in China (Farr and Rossman 2021). Braun, U., and Cook, R. T. A. 2012. Taxonomic Manual of the Erysiphales (Powdery Mildews). CBS Biodiversity Series No. 11. CBS, Utrecht, the Netherlands. Cho, S. E., et al. 2014. Plant Dis. 98: 1159. Farr, D. F., and Rossman, A. Y. 2021. Fungal Databases, Syst. Mycol. Microbiol. Lab., ARS, USDA. Hong, Q. Q., et al. 2021. Plant Dis. 105: 3297. Hirata, T., et al. 2000. Can. J. Bot. 78: 1521-1530. Meeboon, J. and Takamatsu, S. 2015. Mycoscience . 56: 243-251. Xu, D. D., et al. 2020. Plant Dis. 104: 3263. Zhuang, W. Y. 2005. Fungi of northwestern China. Mycotaxon, Ltd., Ithaca, NY.

Naringin attenuates cisplatin- and aminoglycoside-induced hair cell injury in the zebrafish lateral line via multiple pathways.

Exposure to ototoxic drugs is a significant cause of hearing loss that affects about 30 thousand children with potentially serious physical, social and psychological dysfunctions every year. Cisplatin (CP) and aminoglycosides are effective antineoplastic or bactericidal drugs, and their application has a high probability of ototoxicity which results from the death of hair cells (HCs). Here, we describe the therapeutic effect of the flavonoid compound naringin (Nar) against ototoxic effects of cisplatin and aminoglycosides include gentamicin (GM) and neomycin (Neo) in zebrafish HCs. Animals incubated with Nar (100-400 µmol/L) were protected against the pernicious effects of CP (150-250 µmol/L), GM (50-150 µmol/L) and Neo (50-150 µmol/L). We also provide evidence for the potential mechanism of Nar against ototoxicity, including antioxidation, anti-apoptosis, promoting proliferation and hair cell regeneration. We found that mRNA levels of the apoptotic- and pyroptosis-related genes are regulated by Nar both in vivo and in vitro. Finally, by proving that Nar does not affect the anti-tumour efficacy of CP and antibacterial activity of aminoglycosides in vitro, we highlight its value in clinical application. In conclusion, these results unravel a novel therapeutic role for Nar as an otoprotective drug against the adverse effects of CP and aminoglycosides.

Lamivudine improves cognitive decline in SAMP8 mice: Integrating in vivo pharmacological evaluation and network pharmacology.

The reverse transcriptase inhibitors such as lamivudine (3TC) play important roles in anti-ageing, but their effects on neurodegenerative diseases caused by ageing are not clear, especially on the functions of the nervous system such as cognition. In this study, we administered 3TC to senescence-accelerated mouse prone 8 (SAMP8) mice by gastric perfusion (100 mg/kg) for 4 weeks. Our results showed that 3TC significantly improved the ageing status of SAMP8 mice, especially the decline of cognitive ability evaluated by the Morris water maze test. To further investigate the molecular mechanisms of improving the ageing status of SAMP8 mice by 3TC, the qPCR and tissue staining methods were used to study the brain tissues (i.e., hippocampus and cortex) of mice, while the network pharmacology analysis was applied to investigate the potential targets of 3TC. The results showed that the mRNA levels of genes related to long interspersed element-1, type 1 interferon response, the senescence-associated secretion phenotype and the Alzheimer's disease in the hippocampus and cortex of SAMP8 mice were increased due to senescence, but this trend was reversed partially by 3TC. Results of histological studies showed that 3TC reduced the death of hippocampal neurons, while the results of network pharmacology analysis indicated that 3TC may exert its influence through multiple pathways, including the oestrogen signalling and the PI3K/Akt and neuroactive ligand-receptor interaction signalling pathways, which we have verified through in vitro experiments. These findings provide evidence for the therapeutic potential of 3TC in the treatment of neurodegenerative diseases.

Effect of lipophilicity on drug distribution and elimination: Influence of obesity.

AIMS: For a given passively-distributed lipophilic drug, the extent of in vivo distribution (pharmacokinetic volume of distribution, Vd ) in obese individuals increases in relation to the degree of obesity. The present study had the objective of evaluating drug distribution in relation to in vitro lipophilicity, and the relative increase in Vd associated with obesity across a series of drugs. METHODS: Cohorts of normal-weight control and obese subjects received single doses of drugs ranging from hydrophilic (acetaminophen, salicylate) to lipophilic (imipramine, verapamil). Lipid solubility was measured by the log-transformed values of the high-pressure liquid chromatographic (HPLC) retention index (Log10 (HPLC)), and the octanol-water partition coefficient (LogP). RESULTS: Among normal-weight controls, Vd normalized for protein binding was highly correlated with Log10 (HPLC) (R2 = .65) and with LogP (R2 = .78). Vd of all drugs was increased in the obese cohort, but the relative increase (compared to controls) for individual drugs was disproportionately greater as lipid solubility increased. Since clearance was unrelated to lipophilicity, the increased Vd produced a parallel disproportionate increase in elimination half-life in the obese cohort that was associated with Log10 (HPLC) (R2 = .62). CONCLUSION: Lipophilicity is a principal correlate of in vivo Vd , as well as the increased Vd of drugs in obese patients. The consequent prolongation of half-life in obesity has clinical safety implications in terms of delayed drug accumulation and washout during and after chronic dosage. The magnitude and importance of this effect for a given drug depends on the degree of obesity, as well as the lipid-solubility of the specific drug.

Comparison of the transcriptomic responses of two Chrysanthemum morifolium cultivars to low light.

BACKGROUND: Low light is a primary regulator of chrysanthemum growth. Our aim was to analyse the different transcriptomic responses of two Chrysanthemum morifolium cultivars to low light. METHODS AND RESULTS: We conducted a transcriptomic analysis of leaf samples from the 'Nannonggongfen' and 'Nannongxuefeng' chrysanthemum cultivars following a 5-day exposure to optimal light (70%, control [CK]) or low-light (20%, LL) conditions. Gene Ontology (GO) classification of upregulated genes revealed these genes to be associated with 11 cellular components, 9 molecular functions, and 15 biological processes, with the majority being localized to the chloroplast, highlighting the role of chloroplast proteins as regulators of shading tolerance. Downregulated genes were associated with 11 cellular components, 8 molecular functions, and 16 biological processes. Heat map analyses suggested that basic helix-loop-helix domain genes and elongation factors were markedly downregulated in 'Nannongxuefeng' leaves, consistent with the maintenance of normal stem length, whereas no comparable changes were observed in 'Nanonggongfen' leaves. Subsequent qPCR analyses revealed that phytochrome-interacting factors and dormancy-associated genes were significantly upregulated under LL conditions relative to CK conditions, while succinate dehydrogenase 1, elongated hypocotyls 5, and auxin-responsive gene of were significantly downregulated under LL conditions. CONCLUSIONS: These findings suggest that LL plants were significantly lower than those of the CK plants. Low-light tolerant chrysanthemum cultivars may maintain reduced indole-3-acetic acid (IAA) and elongation factor expression as a means of preventing the onset of shade-avoidance symptoms.

First Report of Powdery Mildew Caused by Podosphaera fusca on Helianthus tuberosus in China.

Helianthus tuberosus L. (Jerusalem artichoke) is an herbaceous perennial plant in the Asteraceae that is native to North America but introduced to China in the 17th century. The tubers of H. tuberosus are used as a vegetable, for the pharmaceutical production of inulin and as a source of ethanol biofuel, several B vitamins and minerals。From June to September 2009, severe powdery mildew infection was observed on H. tuberosus in a vegetable garden at Shangqiu Normal University, Shangqiu, China. Approximately 60% of leaves on individual plants were symptomatic, and almost 70% of the plants were infected. Initially, discrete powdery mildew colonies appeared on the upper surface of the leaves and on stems of the plants. Later, mycelial growth was amphigenous, thick, forming irregular white patches, covering the whole leaf surface. Eventually, leaves turned yellow, withered, and abscissed. Microscopic observations showed that conidia on infected leaves were ellipsoid-ovoid to barrel-shaped, with distinct fibrosin bodies visible in their cytoplasm, measuring 28 to 38 × 15 to 22 µm (n = 40). Conidiophores were unbranched, straight, 80 to 210 × 8 to 14 µm (n = 40) in size, and produced two to six immature conidia in chains with intercellular diaphragms. Foot cells of conidiophores were cylindrical and 45 to 65 µm × 8 to 14 µm (n = 40), with slight constrictions at basal septa, and followed by one to three short cells. Fungal hyphae were septate, branched, and flexuous to straight and 5 to 8 µm wide with indistinct to slightly nipple-shaped appressoria. These structures are typical of the genus Podosphaera, although chasmothecia were not observed. The sequence of ITS1-5.8s-ITS2 region of rDNA were amplified from conidia collected from infected leaves with universal primers ITS1F and ITS4 (White et al. 1990), sequenced and analyzed using the BLASTn search of GenBank. Amplicons were 603 bp (GQ927254) and exhibited 99.83% sequence identity with sequence of P. fusca from Cucurbita pepo (KJ698669) in Italy (Pirondi et al. 2015). The fungal species was identified as P. fusca (synonym P. xanthii ) by morphological characteristics and molecular analysis (Braun and Takamatsu 2000; Braun and Cook 2012). Pathogenicity tests were conducted by gently pressing the infected leaves onto leaves of six healthy H. tuberosus plants while six noninoculated plants served as controls. Plants were maintained in a greenhouse at 25 ± 2°C. Eight days after inoculation, symptoms similar to those observed under natural conditions developed on the inoculated leaves of H. tuberosus plants, whereas the control plants remained symptomless. The fungus on inoculated leaves was morphologically identical to that first observed in the field. P. fusca parasitizes a large number of asteraceous species including Euryops pectinatus (Saenz et al. 2000), Coreopsis lanceolata (Garibaldi et al. 2007), Cosmos caudatus (Siddiqui et al. 2011), Herba eupatorii (Ding et al. 2013) and etc. Powdery mildew caused by P. fusca has been reported on H. tuberosus in Russia (Farr and Rossman 2019). Golovinomyces ambrosiae was previously recorded on H. tuberosus in China (Huang et al. 2017; Radisek et al. 2018). This is the first report to our knowledge of powdery mildew P. fusca on H. tuberosus in China. It could cause significant yield losses and become a threat to production of H. tuberosus .

DSab-origin: a novel IGHD sensitive VDJ mapping method and its application on antibody response after influenza vaccination.

BACKGROUND: Functional antibody genes are often assembled by VDJ recombination and then diversified by somatic hypermutation. Identifying the combination of sourcing germline genes is critical to understand the process of antibody maturation, which may facilitate the diagnostics and rapid generation of human monoclonal antibodies in therapeutics. Despite of successful efforts in V and J fragment assignment, method in D segment tracing remains weak for immunoglobulin heavy diversity (IGHD). RESULTS: In this paper, we presented a D-sensitive mapping method called DSab-origin with accuracies around 90% in human monoclonal antibody data and average 95.8% in mouse data. Besides, DSab-origin achieved the best performance in holistic prediction of VDJ segments assignment comparing with other methods commonly used in simulation data. After that, an application example was explored on the antibody response based on a time-series antibody sequencing data after influenza vaccination. The result indicated that, despite the personal response among different donors, IGHV3-7 and IGHD4-17 were likely to be dominated gene segments in these three donors. CONCLUSIONS: This work filled in a computational gap in D segment assignment for VDJ germline gene identification in antibody research. And it offered an application example of DSab-origin for studying the antibody maturation process after influenza vaccination.

SEPPA 2.0--more refined server to predict spatial epitope considering species of immune host and subcellular localization of protein antigen.

Spatial Epitope Prediction server for Protein Antigens (SEPPA) has received lots of feedback since being published in 2009. In this improved version, relative ASA preference of unit patch and consolidated amino acid index were added as further classification parameters in addition to unit-triangle propensity and clustering coefficient which were previously reported. Then logistic regression model was adopted instead of the previous simple additive one. Most importantly, subcellular localization of protein antigen and species of immune host were fully taken account to improve prediction. The result shows that AUC of 0.745 (5-fold cross-validation) is almost the baseline performance with no differentiation like all the other tools. Specifying subcellular localization of protein antigen and species of immune host will generally push the AUC up. Secretory protein immunized to mouse can push AUC to 0.823. In this version, the false positive rate has been largely decreased as well. As the first method which has considered the subcellular localization of protein antigen and species of immune host, SEPPA 2.0 shows obvious advantages over the other popular servers like SEPPA, PEPITO, DiscoTope-2, B-pred, Bpredictor and Epitopia in supporting more specific biological needs. SEPPA 2.0 can be accessed at http://badd.tongji.edu.cn/seppa/. Batch query is also supported.

Systematic toxicity mechanism analysis of proton pump inhibitors: an in silico study.

Proton pump inhibitors (PPIs) are extensively used for the treatment of gastric acid-related disorders. PPIs appear to be well tolerated and almost have no short-term side effects. However, the clinical adverse reactions of long-term PPI usage are increasingly reported in recent years. So far, there is no study that elucidates the side effect mechanisms of PPIs comprehensively and systematically. In this study, a well-defined small molecule perturbed microarray data set of 344 compounds and 1695 samples was analyzed. With this high-throughput data set, a new index (Identity, I) was designed to identify PPI-specific differentially expressed genes. Results indicated that (1) up-regulated genes, such as RETSAT, CYP1A1, CYP1A2, and UGT, enhanced vitamin A's metabolism processes in the cellular retinol metabolism pathway; and that (2) down-regulated genes, such as C1QA, C1QC, C4BPA, C4BPB, CFI, and SERPING1, enriched in the complement and coagulation cascades pathway. In addition, strong association was observed between these PPI-specific differentially expressed genes and the reported side effects of PPIs by the gene-disease association network analysis. One potential toxicity mechanism of PPIs as suggested from this systematic PPI-specific gene expression analysis is that PPIs are enriched in acidic organelles where they are activated and inhibit V-ATPases and acid hydrolases, and consequently block the pathways of antigen presentation, the synthesis and secretion of cytokines, and complement component proteins and coagulation factors. The strategies developed in this work could be extended to studies on other drugs.

Pharmacokinetic Variability of Oral Cannabidiol and Its Major Metabolites after Short-Term High-Dose Exposure in Healthy Subjects.

Introduction: Cannabidiol (CBD) is a widely utilized nonpsychoactive cannabinoid available as a prescriptive drug treatment and over-the-counter supplement. In humans, CBD is metabolized and forms the major active metabolite 7-hydroxy-cannabidiol (7-OH-CBD), which is further metabolized to 7-carboxy-cannabidiol (7-COOH-CBD). In the current study, plasma concentrations of CBD, 7-OH-CBD, and 7-COOH-CBD were measured, and the potential influences of sex, race, and body mass index (BMI) on the pharmacokinetic variability were assessed. Methods: Blood samples from a previously conducted CBD drug interaction study in healthy volunteers (n = 12) were utilized. The subjects received orally administered CBD (Epiodiolex®), 750 mg twice daily for 3 days and a single dose on the 4th day. Nine plasma samples were collected, and plasma concentrations of CBD, 7-OH-CBD, and 7-COOH-CBD were analyzed by LC-MS/MS. Peak plasma concentration (Cmax), time to Cmax (Tmax), area under the curve (AUC), and metabolite-to-parent drug exposure ratios (MPR) were calculated. Statistical analysis was performed to determine the correlations of Cmax, AUC, and MPR of CBD, 7-OH-CBD, and 7-COOH-CBD in different sex, race, BMI, and body weight. Results: For CBD, the mean Cmax was 389.17 ± 153.23 ng/mL, and the mean AUC was 1,542.19 ± 488.04 ng/mL*h. For 7-OH-CBD, the mean Cmax was 81.35 ± 36.64 ng/mL, the mean AUC was 364.70 ± 105.59 ng/mL*h, and the mean MPR was 0.25 ± 0.07. For 7-COOH-CBD, the mean Cmax was 1,717.33 ± 769.22 ng/mL, the mean AUC was 9,888.42 ± 3,961.47 ng/mL*h, and the mean MPR was 7.11 ± 3.48. For 7-COOH-CBD, a 2.25-fold higher Cmax was observed in female subjects (p = 0.0155) and a 1.97-fold higher AUC for female subjects (p = 0.0285) with the normalization of body weight. A significant linearity (p = 0.0135) of 7-OH-CBD AUC with body weight in females was observed. No significant differences were identified in Cmax, AUC, and PMR with race and BMI. Conclusion: Observed differences in sex were in agreement with previously reported findings. A larger population pharmacokinetics study is warranted to validate the observed higher Cmax and AUC in females and significant linearity with body weight in females from the current study.

Community ecological succession of endophytic fungi associates with medicinal compound accumulation in Sophora alopecuroides.

Endophytic fungi of medicinal plants are symbiotic with the host and play an important role in determining metabolites. To understand the relationship between the accumulation of Sophora alopecuroides' medicinal bioactive compounds and the ecological succession of endophytic fungi, here we collected samples from S. alopecuroides at four developmental stages (adult, flowering, podding, and mature) and different organs (roots, stems, leaves, and seeds) at the mature stage. We then used high-performance liquid chromatography-mass spectrometry and high-throughput sequencing on the internal transcribed spacer region to identify the medicinal compounds and endophytic fungal communities in each sample. The endophytic fungal community characteristics and accumulation of medicinally bioactive compounds of S. alopecuroides varied with the host's developmental stages and organs, with the highest total alkaloids content of 111.9 mg/g at the mature stage. Membership analysis and network connection analysis showed a total of 15 core endophytic fungi in different developmental stages and 16 core endophytic fungi in different organs at the mature stage. The unclassified Ascomycota, Aspergillus, and Alternaria were significantly and positively correlated with the medicinal compounds of S. alopecuroides at the mature stage (r > 0.6 or r < -0.6; P < 0.05). In this study, we identified key endophytic fungal resources that affect the content of medicinally bioactive compounds in S. alopecuroides. This discovery could lay the foundation for enhancing the yield of medicinally bioactive compounds in S. alopecuroides and the development and application of functional endophytic fungi.IMPORTANCESophora alopecuroides is a traditional Chinese herbal medicine. The major medicinal chemicals are considered to be quinolizidine alkaloids. Quinolizidine alkaloids have been widely used for the treatment of tumors, dysentery, and enteritis. Previous studies have found that endophytic fungi in S. alopecuroides can promote the accumulation of host quinolizidine alkaloids. However, the relationship between the accumulation of S. alopecuroides' medicinal bioactive compounds and the ecological succession of endophytic fungi remains unclear. In this study, we screened the key endophytic fungal resources affecting the content of medicinally bioactive compounds and laid the foundation for subsequent research on the mechanism by which endophytic fungi promote the accumulation of medicinally bioactive compounds in S. alopecuroides.

Extracellular vesicles in plant-microbe interactions: Recent advances and future directions.

Extracellular vesicles (EVs) are membrane-enclosed nanoparticles that have a crucial role in mediating intercellular communication in mammals by facilitating the transport of proteins and small RNAs. However, the study of plant EVs has been limited for a long time due to insufficient isolation and detection methods. Recent research has shown that both plants and plant pathogens can release EVs, which contain various bioactive molecules like proteins, metabolites, lipids, and small RNAs. These EVs play essential roles in plant-microbe interactions by transferring these bioactive molecules across different kingdoms. Additionally, it has been discovered that EVs may contribute to symbiotic communication between plants and pathogens. This review provides a comprehensive summary of the pivotal roles played by EVs in mediating interactions between plants and microbes, including pathogenic fungi, bacteria, viruses, and symbiotic pathogens. We highlight the potential of EVs in transferring immune signals between plant cells and facilitating the exchange of active substances between different species.

Machine learning-based prediction model for distant metastasis of breast cancer.

BACKGROUND: Breast cancer is the most prevalent malignancy in women. Advanced breast cancer can develop distant metastases, posing a severe threat to the life of patients. Because the clinical warning signs of distant metastasis are manifested in the late stage of the disease, there is a need for better methods of predicting metastasis. METHODS: First, we screened breast cancer distant metastasis target genes by performing difference analysis and weighted gene co-expression network analysis (WGCNA) on the selected datasets, and performed analyses such as GO enrichment analysis on these target genes. Secondly, we screened breast cancer distant metastasis target genes by LASSO regression analysis and performed correlation analysis and other analyses on these biomarkers. Finally, we constructed several breast cancer distant metastasis prediction models based on Logistic Regression (LR) model, Random Forest (RF) model, Support Vector Machine (SVM) model, Gradient Boosting Decision Tree (GBDT) model and eXtreme Gradient Boosting (XGBoost) model, and selected the optimal model from them. RESULTS: Several 21-gene breast cancer distant metastasis prediction models were constructed, with the best performance of the model constructed based on the random forest model. This model accurately predicted the emergence of distant metastases from breast cancer, with an accuracy of 93.6 %, an F1-score of 88.9 % and an AUC value of 91.3 % on the validation set. CONCLUSION: Our findings have the potential to be translated into a point-of-care prognostic analysis to reduce breast cancer mortality.

Variations in the oral microbiome and metabolome of methamphetamine users.

Drug addiction can seriously damage human physical and mental health, while detoxification is a long and difficult process. Although studies have reported changes in the oral microbiome of methamphetamine (METH) users, the role that the microbiome plays in the process of drug addiction is still unknown. This study aims to explore the function of the microbiome based on analysis of the variations in the oral microbiome and metabolome of METH users. We performed the 16S rRNA sequencing analysis based on the oral saliva samples collected from 278 METH users and 105 healthy controls (CTL). In addition, the untargeted metabolomic profiling was conducted based on 220 samples. Compared to the CTL group, alpha diversity was reduced in the group of METH users and the relative abundances of Peptostreptococcus and Gemella were significantly increased, while the relative abundances of Campylobacter and Aggregatibacter were significantly decreased. Variations were also detected in oral metabolic pathways, including enhanced tryptophan metabolism, lysine biosynthesis, purine metabolism, and steroid biosynthesis. Conversely, the metabolic pathways of porphyrin metabolism, glutathione metabolism, and pentose phosphate were significantly reduced. It was speculated that four key microbial taxa, i.e., Peptostreptococcus, Gemella, Campylobacter, and Aggregatibacter, could be involved in the toxicity and addiction mechanisms of METH by affecting the above metabolic pathways. It was found that with the increase of drug use years, the content of tryptamine associated with neuropsychiatric disorders was gradually increased. Our study provides novel insights into exploring the toxic damage and addiction mechanisms underlying the METH addiction.IMPORTANCEIt was found that with the increase of drug use years, the content of tryptamine associated with neuropsychiatric disorders gradually increased. The prediction models based on oral microbiome and metabolome could effectively predict the methamphetamine (METH) smoking. Our study provides novel insights into the exploration of the molecular mechanisms regulating the toxic damage and addiction of METH as well as new ideas for early prevention and treatment strategies of METH addiction.

An Edge-cloud-aided Private High-order Fuzzy C-means Clustering Algorithm in Smart Healthcare.

Smart healthcare has emerged to provide healthcare services using data analysis techniques. Especially, clustering is playing an indispensable role in analyzing healthcare records. However, large multi-modal healthcare data imposes great challenges on clustering. Specifically, it is hard for traditional approaches to obtain desirable results for healthcare data clustering since they are not able to work for multi-modal data. This paper presents a new high-order multi-modal learning approach using multimodal deep learning and the Tucker decomposition (F- HoFCM). Furthermore, we propose an edge-cloud-aided private scheme to facilitate the clustering efficiency for its embedding in edge resources. Specifically, the computationally intensive tasks, such as parameter updating with high-order back propagation algorithm and clustering through high-order fuzzy c-means, are processed in a centralized location with cloud computing. The other tasks such as multi-modal data fusion and Tucker decomposition are performed at the edge resources. Since the feature fusion and Tucker decomposition are nonlinear operations, the cloud cannot obtain the raw data, thus protecting the privacy. Experimental results state that the presented approach produces significantly more accurate results than the existing high-order fuzzy c-means (HOFCM) on multi-modal healthcare datasets and furthermore the clustering efficiency are significantly improved by the developed edge-cloud-aided private healthcare system.

Chrysanthemum morifolium ß-carotene hydroxylase overexpression promotes Arabidopsis thaliana tolerance to high light stress.

The ß-carotene hydroxylase gene (BCH) regulates zeaxanthin production in response to high light levels ro protect Chrysanthemum morifolium plants against light-induced damage. In this study, the Chrysanthemum morifolium CmBCH1 and CmBCH2 genes were cloned and their functional importance was assessed by overexpressing them in Arabidopsis thaliana. These transgenic plants were evaluated for gene-related changes in phenotypic characteristics, photosynthetic activity, fluorescence properties, carotenoid biosynthesis, aboveground/belowground biomass, pigment content, and the expression of light-regulated genes under conditions of high light stress relative to wild-type (WT) plants. When exposed to high light stress, WT A. thaliana leaves turned yellow and the overall biomass was reduced compared to that of the transgenic plants. WT plants exposed to high light stress also exhibited significant reductions in the net photosynthetic rate, stomatal conductance, Fv/Fm, qP, and ETR, whereas these changes were not observed in the transgenic CmBCH1 and CmBCH2 plants. Lutein and zaxanthin levels were significantly increased in the transgenic CmBCH1 and CmBCH2 lines, with progressive induction with prolonged light exposure, whereas no significant changes were observed in light-exposed WT plants. The transgenic plants also expressed higher levels of most carotenoid biosynthesis pathway genes, including phytoene synthase (AtPSY), phytoene desaturase (AtPDS), lycopene-ß-cyclase (AtLYCB), and ζ-carotene desaturase (AtZDS). The elongated hypocotyl 5 (HY5) and succinate dehydrogenase (SDH) genes were significantly induced following exposure to high light conditions for 12h, whereas phytochrome-interacting factor 7 (PIF7) was significantly downregulated in these plants.