Exploring the evolutionary mechanism of hepatitis B and gastric cancer based on Mendelian randomization combined with bioinformatics analysis.

Chronic hepatitis B virus infection (HBV) infection appears to be associated with extrahepatic cancers. This study aims to evaluate the causality and evolutionary mechanism of chronic HBV infection and gastric cancer through Mendelian randomization (MR) analysis and bioinformatics analysis. We conducted 2-sample MR to investigate the causal relationship between chronic HBV infection and gastric cancer. We identified 5 independent genetic variants closely associated with exposure (chronic HBV infection) as instrumental variables in a sample of 1371 cases and 2938 controls of East Asian descent in Korea. The genome wide association study (GWAS) data for the outcome variable came from the Japanese Biobank. Bioinformatics analysis was used to explore the evolutionary mechanism of chronic HBV infection and gastric cancer. Differential expression analysis and weighted gene co-expression network analysis (WGCNA) were performed to identify key targets that are commonly associated with both diseases, and their biological functions were investigated. Multiple machine-learning models were employed to select hub genes. The MR analysis showed a positive causal relationship between chronic HBV infection and gastric cancer (IVW: OR = 1.165, 95% CI = 1.085-1.250, P < .001), and the result was robust in sensitivity analysis. According to the bioinformatics analysis, the 5 key targets were mainly enriched in Toll-like receptor signaling and PI3K-Akt signaling. Two hub genes, CXCL9 and COL6A2, were identified, and a high-performing predictive model was constructed. Chronic HBV infection is positively associated with gastric cancer, and the evolutionary mechanism may be related to Toll-like receptor signaling. Prospective studies are still needed to confirm these findings.

Untargeted metabolomics in Anectocillus roxburghii with habitat heterogeneity and the key abiotic factors affecting its active ingredients.

Introduction: Anoectochilus roxburghii is a rare, endangered herb with diverse pharmacological properties. Understanding the main metabolite types and characteristics of wild A. roxburghii is important for efficiently utilizing resources and examining quality according to origin. Methods: Samples were collected from the main production areas across five regions in Fujian Province, China. An untargeted metabolomics analysis was performed on the entire plants to explore their metabolic profiles. We utilized UPLC-MS/MS to specifically quantify eight targeted flavonoids in these samples. Subsequently, correlation analysis was conducted to investigate the relationships between the flavonoids content and both the biological characteristics and geographical features. Results: A comprehensive analysis identified a total of 3,170 differential metabolites, with terpenoids and flavonoids being the most prevalent classes. A region-specific metabolite analysis revealed that the Yongchun (YC) region showed the highest diversity of unique metabolites, including tangeretin and oleanolic acid. Conversely, the Youxi (YX) region was found to have the smallest number of unique metabolites, with only one distinct compound identified. Further investigation through KEGG pathway enrichment analysis highlighted a significant enrichment in pathways related to flavonoid biosynthesis. Further examination of the flavonoid category showed that flavonols were the most differentially abundant. We quantified eight specific flavonoids, finding that, on average, the YX region exhibited higher levels of these compounds. Correlation analysis highlighted a significant association between flavonoids and habitat, especially temperature and humidity. Discussion: Untargeted metabolomics via LC-MS was suitable for identifying region-specific metabolites and their influence via habitat heterogeneity. The results of this study serve as a new theoretical reference for unique markers exclusively present in a specific sample group.

Division of developmental phases of freshwater leech Whitmania pigra and key genes related to neurogenesis revealed by whole genome and transcriptome analysis.

The freshwater leech Whitmania pigra (W. pigra) Whitman (Annelida phylum) is a model organism for neurodevelopmental studies. However, molecular biology research on its embryonic development is still scarce. Here, we described a series of developmental stages of the W. pigra embryos and defined five broad stages of embryogenesis: cleavage stages, blastocyst stage, gastrula stage, organogenesis and refinement, juvenile. We obtained a total of 239.64 Gb transcriptome data of eight representative developmental phases of embryos (from blastocyst stage to maturity), which was then assembled into 21,482 unigenes according to our reference genome sequenced by single-molecule real-time (SMRT) long-read sequencing. We found 3114 genes differentially expressed during the eight phases with phase-specific expression pattern. Using a comprehensive transcriptome dataset, we demonstrated that 57, 49 and 77 DEGs were respectively related to morphogenesis, signal pathways and neurogenesis. 49 DEGs related to signal pathways included 30 wnt genes, 14 notch genes, and 5 hedgehog genes. In particular, we found a cluster consisting of 7 genes related to signal pathways as well as synapses, which were essential for regulating embryonic development. Eight genes cooperatively participated in regulating neurogenesis. Our results reveal the whole picture of W. pigra development mechanism from the perspective of transcriptome and provide new clues for organogenesis and neurodevelopmental studies of Annelida species.

Evolutionary differences in gene loss and pseudogenization among mycoheterotrophic orchids in the tribe Vanilleae (subfamily Vanilloideae).

Introduction: Galeola lindleyana is a mycoheterotrophic orchid belonging to the tribe Vanilleae within the subfamily Vanilloideae. Methods: In this study, the G. lindleyana plastome was assembled and annotated, and compared with other Vanilleae orchids, revealing the evolutionary variations between the photoautotrophic and mycoheterotrophic plastomes. Results: The G. lindleyana plastome was found to include 32 protein-coding genes, 16 tRNA genes and four ribosomal RNA genes, including 11 pseudogenes. Almost all of the genes encoding photosynthesis have been lost physically or functionally, with the exception of six genes encoding ATP synthase and psaJ in photosystem I. The length of the G. lindleyana plastome has decreased to 100,749 bp, while still retaining its typical quadripartite structure. Compared with the photoautotrophic Vanilloideae plastomes, the inverted repeat (IR) regions and the large single copy (LSC) region of the mycoheterotrophic orchid's plastome have contracted, while the small single copy (SSC) region has expanded significantly. Moreover, the difference in length between the two ndhB genes was found to be 682 bp, with one of them spanning the IRb/SSC boundary. The Vanilloideae plastomes were varied in their structural organization, gene arrangement, and gene content. Even the Cyrtosia septentrionalis plastome which was found to be closest in length to the G. lindleyana plastome, differed in terms of its gene arrangement and gene content. In the LSC region, the psbA, psbK, atpA and psaB retained in the G. lindleyana plastome were missing in the C. septentrionalis plastome, while, the matK, rps16, and atpF were incomplete in the C. septentrionalis plastome, yet still complete in that of the G. lindleyana. Lastly, compared with the G. lindleyana plastome, a 15 kb region located in the SSC area between ndhB-rrn16S was found to be inverted in the C. septentrionalis plastome. These changes in gene content, gene arrangment and gene structure shed light on the polyphyletic evolution of photoautotrophic orchid plastomes to mycoheterotrophic orchid plastomes. Discussion: Thus, this study's decoding of the mycoheterotrophic G. lindleyana plastome provides valuable resource data for future research and conservation of endangered orchids.

[Effects of growth-promoting strain Mycena sp. M23 on photosynthesis of Aronia melanocarpa]. / ä¿ƒç”Ÿå°è‡å±žèŒæ ªM23å¯¹é»‘æžœè ºè‚‹èŠ±æ¥¸å ‰åˆä½œç”¨çš„å½±å“.

The agronomic traits, chlorophyll content, physiological indices of Aronia melanocarpa were compared in five treatments, namely negative control (CK), positive control (PCK), low dose of microbial inoculant (T1, 50 g per seedling), moderate dose of microbial inoculant (T2, 100 g per seedling), high dose of microbial inoculant (T3, 200 g per seedling) in field. The diurnal variation of net photosynthetic rate was measured by Li-6400 portable photosynthesis system. The diurnal variation of net photosynthetic rate (Pn) of A. melanocarpa showed a pattern of bi-modal curve with photosynthetic "noon break" phenomenon, which occurred at 1:00 pm. At that time, stomatal conductance (gs) and transpiration rate (Tr) of A. melanocarpa showed a dramatic decline, while intercellular CO2 concentration (Ci) significantly rose. It was a photosynthetic "noon break" phenomenon caused by non-stomatal limitation. Application of inoculant to A. melanocarpa successfully avoided the photosynthetic "noon break" phenomenon. Compared with average value of CK and PCK, Pn, gs, Tr, water use efficiency (WUE) and light utilization efficiency (LUE) of inoculation groups increased by 113%, 91%, 50%, 48% and 117% at 1:00 pm. Daily mean of Pn, gs, Tr and LUE of inoculation group was 1.5, 1.9, 1.4 and 1.5 times as that of average value of CK and PCK. The inductive effect of high dose of microbial inoculant treatment was the best among inoculation treatments, with the seedling height 1.2 times as that of the moderate and low inoculant groups. All growth indices, photosynthetic parameters and resistant physiological indices of high dose group were superior to other groups. Our results suggested that fungi M23 could improve the adaptability of A. melanocarpa to environmental stresses and promote its growth by increasing photosynthesis, with the inductive effect of high dose being the best.

The Plant Growth-Promoting Fungus MF23 (Mycena sp.) Increases Production of Dendrobium officinale (Orchidaceae) by Affecting Nitrogen Uptake and NH 4 + Assimilation.

Dendrobium officinale Kimura et Migo is a traditional and scarce medicinal orchid in China. Mycorrhizal fungi could supply nitrogen (N) to orchids for seed germination and seedling recruitment. However, the N transport mechanism between orchids and the fungus is poorly understand. Early studies found that the fungus MF23 (Mycena sp.) could promote the growth of D. officinale. To better dissect the molecular interactions involved in N transport between D. officinale and MF23, transcriptome and metabolome analyses were conducted on conventional and mycorrhizal cultivations of D. officinale. Moreover, validation tests were carried out in the greenhouse to measure net fluxes of N O 3 - and N H 4 + of roots by a non-invasive micro-test technology (NMT), determine N assimilation enzyme activity by the ELISA, and analyze the expression level of differentially expressed genes (DEGs) of N transporters and DEGs involved in N metabolism by RT-qPCR. Combined transcriptome and metabolome analyses showed that MF23 may influence N metabolism in D. officinale. The expression of DoNAR2.1 (nitrate transporter-activating protein), DoAMT11 (ammonium transporter), DoATFs (amino acid transporters), DoOPTs (oligopeptide transporters), and DoGDHs (glutamate dehydrogenases) in symbiotic D. officinale was upregulated. NMT results showed a preference for N H 4 + in D. officinale and indicated that MF23 could promote the uptake of N O 3 - and N H 4 + , especially for N H 4 + . ELISA results showed that MF23 could increase the activity of glutamine synthetase (GS) and glutamate dehydrogenase. This study suggested that MF23 increases the production of D. officinale by affecting N uptake and N H 4 + assimilation capacity.

Use of transcriptomic profiling to identify candidate genes involved in Polyporus umbellatus sclerotial formation affected by oxalic acid.

Polyporus umbellatus is a precious medicinal fungus. Oxalic acid was observed to affect sclerotial formation and sclerotia possessed more medicinal compounds than mycelia. In this study, the transcriptome of P. umbellatus was analysed after the fungus was exposed to various concentrations of oxalic acid. The differentially expressed genes (DEGs) encoding a series of oxidases were upregulated, and reductases were downregulated, in the low-oxalic-acid (Low OA) group compared to the control (No OA) group, while the opposite phenomenon was observed in the high-oxalic-acid (High OA) group. The detection of reactive oxygen species (ROS) in P. umbellatus mycelia was performed visually, and Ca2+ and H2O2 fluxes were measured using non-invasive micro-test technology (NMT). The sclerotial biomass in the Low OA group increased by 66%, however, no sclerotia formed in the High OA group. The ROS fluorescence intensity increased significantly in the Low OA group but decreased considerably in the High OA group. Ca2+ and H2O2 influx significantly increased in the Low OA group, while H2O2 exhibited efflux in the High OA group. A higher level of oxidative stress formed in the Low OA group. Different concentrations of oxalic acid were determined to affect P. umbellatus sclerotial formation in different ways.

[Identification of water buffalo horn and its adulterants using COI barcode].

Bubali cornu (water buffalo horn) has been used as the substitute for Cornu rhinoceri asiatici (rhino horn) in clinical applications, and is the essential ingredient of Angong Niuhuang Wan. In recent years, there are a number of adulterants on the commercial herbal medicine markets. An efficient tool is required for species identification. In this study, 155 Bubali cornu samples have been taken from original animals and collected from commercial herbal medicine markets. 153 COI sequences have been successfully obtained from 155 samples through DNA extraction, PCR amplification, bidirectional sequencing and assembly. 93 COI sequences have been added to the DNA barcoding database of traditional Chinese animal medicine after validation using DNA barcoding GAP and tree-based methods. The species identification of the 62 commercial Bubali cornu medicines has been accomplished on the DNA barcoding system for identifying herbal medicine using the updated animal medicine database (www.tcmbarcode.cn). Except two samples failed to obtain COI sequences, 54.8% of the commercial Bubali cornu medicines were water buffalo horns and 29% were yak horns. Our results showed that yak horn was the major adulterant of Bubali cornu and the DNA barcoding method may accurately discriminate Bubali cornu and their adulterants. Therefore, we recommend that supervision on the herbal medicine markets should be strengthened with this new method to warren the effectiveness of herbal medicines.

[Molecular diversity of arbuscular mycorrhizal fungi in wild and cultured Gynostemma pentaphyllum roots in Xishuangbanna, Southwest China].

By using nested-PCR, DNA cloning, and sequencing techniques, this paper studied the diversity of the community structure of arbuscular mycorrhizal fungi (AMF) in wild and cultured Gynostemma pentaphyllum roots. A total of 551 clones containing 18S rDNA genes of AMF were obtained from the roots. After the analysis of the restriction fragment length polymorphism, 100 different RFLP types were obtained, which were further divided into 20 AMF phylotypes belonging to seven families. The comparison of the sequences of 20 AMF phylotypes with the GenBank database showed that there were 5 AMF phylotypes having high similarity to the sequences of reported AMF species Glomus viscosum, Claroideoglomus etunicatum, Racocetra tropicana, Acaulospora spinosa, and Acaulospora mellea, respectively. These sequences were then assessed for the similarities against the MaarjAM database, and 12 phylotypes showed high similarity to the corresponding molecular virtual taxa, of which, 7 phylotypes were not obtained by the morphological identification of soil asexual spores. Statistical analysis indicated that there were significant differences in the AMF community between wild and cultured G. pentaphyllum roots. The analysis of relative abundance data indicated that Glo-2, Amb-1, and Para-1 were the dominant phylotypes in wild G. pentaphyllum roots, while Glo-3, Glo-8, Glo-10, and Div-1 were the prevalent phylotypes in cultured ones. Claroideoglomeraceae and Ambisporaceae were only detected in wild G. pentaphyllum roots, and Diversisporaceae was only identified in cultured ones.