New perspective: Symbiotic pattern and assembly mechanism of Cantharellus cibarius-associated bacteria.

Cantharellus cibarius, an ectomycorrhizal fungus belonging to the Basidiomycetes, has significant medicinal and edible value, economic importance, and ecological benefits. However, C. cibarius remains incapable of artificial cultivation, which is thought to be due to the presence of bacteria. Therefore, much research has focused on the relationship between C. cibarius and bacteria, but rare bacteria are frequently overlooked, and symbiotic pattern and assembly mechanism of the bacterial community associated with C. cibarius remain unknown. In this study, the assembly mechanism and driving factors of both abundant and rare bacterial communities of C. cibarius were revealed by the null model. The symbiotic pattern of the bacterial community was examined using a co-occurrence network. Metabolic functions and phenotypes of the abundant and rare bacteria were compared using METAGENassist2, and the impacts of abiotic variables on the diversity of abundant and rare bacteria were examined using partial least squares path modeling. In the fruiting body and mycosphere of C. cibarius, there was a higher proportion of specialist bacteria compared with generalist bacteria. Dispersal limitation dominated the assembly of abundant and rare bacterial communities in the fruiting body and mycosphere. However, pH, 1-octen-3-ol, and total phosphorus of the fruiting body were the main driving factors of bacterial community assembly in the fruiting body, while available nitrogen and total phosphorus of the soil affected the assembly process of the bacterial community in the mycosphere. Furthermore, bacterial co-occurrence patterns in the mycosphere may be more complex compared with those in the fruiting body. Unlike the specific potential functions of abundant bacteria, rare bacteria may provide supplementary or unique metabolic pathways (such as sulfite oxidizer and sulfur reducer) to enhance the ecological function of C. cibarius. Notably, while volatile organic compounds can reduce mycosphere bacterial diversity, they can increase fruiting body bacterial diversity. Findings from this study further, our understanding of C. cibarius-associated microbial ecology.

Comparative Transcriptome Analysis Reveals bmo-miR-6497-3p Regulate Circadian Clock Genes during the Embryonic Diapause Induction Process in Bivoltine Silkworm.

Diapause is one of the survival strategies of insects for confronting adverse environmental conditions. Bombyx mori displays typical embryonic diapause, and offspring diapause depends on the incubation environment of the maternal embryo in the bivoltine strains of the silkworm. However, the molecular mechanisms of the diapause induction process are still poorly understood. In this study, we compared the differentially expressed miRNAs (DEmiRs) in bivoltine silkworm embryos incubated at diapause- (25 °C) and non-diapause (15 °C)-inducing temperatures during the blastokinesis (BK) and head pigmentation (HP) phases using transcriptome sequencing. There were 411 known miRNAs and 71 novel miRNAs identified during the two phases. Among those miRNAs, there were 108 and 74 DEmiRs in the BK and HP groups, respectively. By the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the predicted target genes of the DEmiRs, we found that aside from metabolism, the targets were also enriched in phototransduction-fly and insect hormone biosynthesis in the BK group and the HP group, respectively. Dual luciferase reporter assay illustrated that bmo-miR-6497-3p directly regulated Bmcycle and subsequently regulated the expression of circadian genes. These results imply that microRNAs, as vitally important regulators, respond to different temperatures and participate in the diapause induction process across species.

Tn5 Transposase Applied in Genomics Research.

The development of high-throughput sequencing (next-generation sequencing technology (NGS)) and the continuous increase in experimental throughput require the upstream sample processing steps of NGS to be as simple as possible to improve the efficiency of the entire NGS process. The transposition system has fast "cut and paste" and "copy and paste" functions, and has been innovatively applied to the NGS field. For example, the Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-Seq) uses high-throughput sequencing to detect chromatin regions accessible by Tn5 transposase. Linear Amplification via Transposon Insertion (LIANTI) uses Tn5 transposase for linear amplification, haploid typing, and structural variation detection. Not only is it efficient and simple, it effectively shortens the time for NGS sample library construction, realizes large-scale and rapid sequencing, improves sequencing resolution, and can be flexibly modified for more technological innovation.

Pharmacokinetics of Polyethylene Glycol-Modified Canine Uricase Following Single and Multiple Intravenous Injections in Cynomolgus Monkeys.

BACKGROUND AND OBJECTIVE: Polyethylene glycol-modified canine uricase (PEG-UHC) prepared with a lower-molecular-weight (5 kDa) PEG is used to treat gout. This study investigated the comparative pharmacokinetics of single and multiple doses of PEG-UHC administered intravenously and a single dose of uricase (UHC) administered intravenously in cynomolgus monkeys. METHODS: A noncompartmental model was used to fit the plasma drug concentration-time curve and calculate the pharmacokinetic parameters of PEG-UHC, which were compared with those obtained for UHC at the equivalent dose (2 mg/kg). To study the pharmacokinetics after multiple dose administration, cynomolgus monkeys were administered five intravenous injections of PEG-UHC (0.5 mg/kg), with one injection performed every 15 days. RESULTS: The area under the curve (AUC) and the maximum plasma concentration (Cmax) of PEG-UHC were positively correlated with dose, whereas plasma half-life (t1/2) and clearance (CL) did not change significantly with increasing dose, suggesting that these pharmacokinetic characteristics are linear. Intravenous PEG-UHC exhibited an average t1/2 that was 125.79 times longer and an AUC0-t that was 64.45 times larger than the corresponding values for UHC at the same dose (2 mg/kg), while the CL of PEG-UHC was 1/72.73 times the CL of intravenous UHC. The plasma drug concentration reached a steady state after five injections, and the t1/2 values following the first and last drug administration did not differ significantly. CONCLUSION: Our data show that PEG-UHC is markedly superior to UHC in terms of duration of action, and that the pharmacokinetics of PEG-UHC in cynomolgus monkeys are linear. Sequential administration of PEG-UHC did not accelerate drug clearance. Our findings provide the basis for future clinical studies of PEG-UHC.

Species and sex differences in the blood clearance and immunogenicity of PEGylated uricase: A comparative 26-week toxicity study in rats and monkeys.

Low response rates and high immunogenicity were observed after repeated injections of pegloticase (Krystexxa) into gout patients during clinical trials. However, related research had not been reported in preclinical animal experiments, which has limited the development of this drug. In this study, the toxicity of mPEG-UHC was studied in rats and monkeys over a 26-week period of repeated intravenous dosing. There were no obvious toxic reactions in the tested animals, with the exception of mPEG-UHC blood clearance and immunogenicity. After repeated injections of mPEG-UHC, rapid loss of uricolytic activity (RLA) was not detected in rats, whereas RLA was observed in 44.4% of drug-treated monkeys. In these monkeys, RLA was observed in 11.1% of males and 77.8% of females, and such incidences increased with higher dosing. High titres of anti-uricase IgG antibodies were associated with RLA but did not result in any toxicity. Remission and recurrence of RLA occurred in one female monkey in the high-dose group because of suppressed and altered immune responses in this animal. The predicted incidence of RLA after repeated injections of mPEG-UHC in gout patients may be lower than that of pegloticase. In this study, the no-observed-adverse-effect levels (NOAELs) of mPEG-UHC in rats and monkeys were 32.0 mg/kg and 20.0 mg/kg, respectively. Therefore, the results showed that rats and monkeys could tolerate long-term and high-dose administrations of mPEG-UHC, and mPEG-UHC blood clearance and immunogenicity showed obvious species and sex differences. These findings will provide valuable information to direct the clinical use of mPEG-UHC.

Ara-c induces cell cycle G1/S arrest by inducing upregulation of the INK4 family gene or directly inhibiting the formation of the cell cycle-dependent complex CDK4/cyclin D1.

Cytosine arabinoside (Ara-c) is a pyrimidine anti-metabolite that is capable of interfering with cellular proliferation by inhibiting DNA synthesis. Each inhibitor of cyclin-dependent kinase 4 (INK4) family member has the ability to bind to cyclin-dependent kinase 4 (CDK4) and inhibit the formation of the cell cycle-dependent CDK4/cyclin D1 complex, subsequently leading to cell cycle arrest in the G1/S phase. In this study, the expression of INK4 family genes in kidney cancer and the impact of these genes on patient prognosis were examined. Additionally, the effects of INK4 family genes and Ara-c on cell proliferation and tumor formation and development were examined. Finally, a potential association between Ara-c-induced cell cycle arrest and INK4-associated gene expression was evaluated. An upregulation of INK4 family genes was found to be positively correlated with the prognosis of patients with kidney cancer. Both the INK4 family genes and Ara-c were shown to induce cell cycle arrest and inhibit tumor formation and development. Moreover, Ara-c-induced cell cycle arrest was found to be associated with an Ara-c-induced upregulation of INK4 family gene expression, which ultimately inhibited the formation of the CDK4/cyclin D1 complex. These findings suggested that an upregulation of INK4 family genes has a positive effect on kidney cancer prognosis and can inhibit the formation and development of tumors. Moreover, Ara-c was shown to promote the upregulation of INK4 family genes, at the same time, Ara-c could directly regulate the cell cycle-dependent genes CDK4 and cyclin D1 (CCND1), independent of the INK4 family genes.

Effects of P27/Bmdacapo, in the CIP/KIP family, on cell proliferation, growth and development in the silkworm (Bombyx mori).

We investigated changes in expression of the CIP/KIP family-related genes and the cycle-dependent factors Pcna, Cdk4 and Cdk2 during the growth and development of mice, Drosophila and silkworms. When the organism was in a period of rapid development, the related genes of the CIP/KIP family had low expression level and the cell cycle-dependent genes were highly expressed. In mammals, the CIP/KIP family includes three genes, p21, p27/Dacapo and p57. However, only one gene, P27/Dacapo, exists in the CIP/KIP family in silkworm and the orthologous gene in the silkworm is named Bmdacapo. Down-regulation of Bmdacapo in silkworm embryos caused overdevelopment of the embryos and indicated that Bmdacapo can inhibit silkworm growth and development. Up-regulation of Bmdacapo in silkworm cells inhibited cell proliferation, whereas down-regulation of Bmdacapo promoted cell proliferation. In order to explore the mechanism of Bmdacapo regulated silkworm development and cell proliferation, the effect of Bmdacapo on cell cycle changes was examined. The results demonstrate that Bmdacapo was able to induce G1/S phase arrest in the cell cycle. In silkworm cells, Bmdacapo inhibits the expression of Pcna, CDK4 and CDK2, which affects the cell cycle and ultimately inhibits cell proliferation. This regulatory mechanism is particularly different from mammals.

HP-CagA+ Regulates the Expression of CDK4/CyclinD1 via reg3 to Change Cell Cycle and Promote Cell Proliferation.

Previous studies have shown that regeneration gene 3 (reg3) is significantly expressed in gastric mucosa tissues with Helicobacter pylori (HP) cytotoxin-associated gene A (CagA)-positive (HP-CagA+). CagA-positive HP increases the risk of gastric cancer. The purpose of this study was to investigate the correlation between reg3 and HP-CagA+ and explore the effects of reg3 on the proliferation of gastric cancer cells and the development of tissues and organs. We analyzed the expression of reg3 in human tissues and organs. The results showed that reg3 expression in gastric tissues was significantly higher than that in other tissues and organs. In addition, reg3 influenced the prognosis of gastric, lung, and ovarian cancers. Immunohistochemical analysis indicated that the expression of reg3 and CagA in cancerous tissues was higher than that in adjacent tissues. HP-CagA+ infection of gastric cancer cells promotes reg3 expression, suggesting that reg3 may be a target gene of CagA in gastric cancer, which together affects the formation and development of gastric cancer. reg3 and CagA promote cell proliferation, and then affect the development of mouse tissues and organs by regulating G1/S phase transition of the cell cycle via the formation of the cell cycle-dependent complex CDK4/CyclinD1. This is the first study that shows the influence of CagA on the cell cycle and induction of cell proliferation by promoting reg3 expression.

Genome-Wide Identification and Characterization of Tyrosine Kinases in the Silkworm, Bombyx mori.

The tyrosine kinases (TKs) are important parts of metazoan signaling pathways and play significant roles in cell growth, development, apoptosis and disease. Genome-wide characterization of TKs has been conducted in many metazoans, however, systematic information about this family in Lepidoptera is still lacking. We retrieved 33 TK-encoding genes in silkworm and classified them into 25 subfamilies by sequence analysis, without members in AXL, FRK, PDGFR, STYK1 and TIE subfamilies. Although domain sequences in each subfamily are conserved, TKs in vertebrates tend to be remarkably conserved and stable. Our results of phylogenetic analysis supported the previous conclusion for the second major expansion of TK family. Gene-Ontology (GO) analysis revealed that a higher proportion of BmTKs played roles in binding, catalysis, signal transduction, metabolism, biological regulation and response to stimulus, compared to all silkworm genes annotated in GO. Moreover, the expression profile analysis of BmTKs among multiple tissues and developmental stages demonstrated that many genes exhibited stage-specific and/or sex-related expression during embryogenesis, molting and metamorphosis, and that 8 BmTKs presented tissue-specific high expression. Our study provides systematic description of silkworm tyrosine kinases, and may also provide further insights into metazoan TKs and assist future studies addressing their functions.