Unveiling unique alternative splicing responses to low temperature in Zoysia japonica through ZjRTD1.0, a high-quality reference transcript dataset.

Inadequate reference databases in RNA-seq analysis can hinder data utilization and interpretation. In this study, we have successfully constructed a high-quality reference transcript dataset, ZjRTD1.0, for Zoysia japonica, a widely-used turfgrass with exceptional tolerance to various abiotic stress, including low temperatures and salinity. This dataset comprises 113,089 transcripts from 57,143 genes. BUSCO analysis demonstrates exceptional completeness (92.4%) in ZjRTD1.0, with reduced proportions of fragmented (3.3%) and missing (4.3%) orthologs compared to prior datasets. ZjRTD1.0 enables more precise analyses, including transcript quantification and alternative splicing assessments using public datasets, which identified a substantial number of differentially expressed transcripts (DETs) and differential alternative splicing (DAS) events, leading to several novel findings on Z. japonica's responses to abiotic stresses. First, spliceosome gene expression influenced alternative splicing significantly under abiotic stress, with a greater impact observed during low-temperature stress. Then, a significant positive correlation was found between the number of differentially expressed genes (DEGs) encoding protein kinases and the frequency of DAS events, suggesting the role of protein phosphorylation in regulating alternative splicing. Additionally, our results suggest possible involvement of serine/arginine-rich (SR) proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs) in generating inclusion/exclusion isoforms under low-temperature stress. Furthermore, our investigation revealed a significantly enhanced overlap between DEGs and differentially alternatively spliced genes (DASGs) in response to low-temperature stress, suggesting a unique co-regulatory mechanism governing transcription and splicing in the context of low-temperature response. In conclusion, we have proven that ZjRTD1.0 will serve as a reliable and useful resource for future transcriptomic analyses in Z. japonica.

Phenotypic dimorphism between honeybee queen and worker is regulated by complicated epigenetic modifications.

Phenotypic dimorphism between queens and workers is an important biological characteristic of honeybees that has been the subject of intensive research. The enormous differences in morphology, lifespan, physiology, and behavior between queens and workers are caused by a complicated set of factors. Epigenetic modifications are considered to play an important role in this process. In this study, we analyzed the differences in chromosome interactions and H3K27ac and H3K4me1 modifications between the queens and workers using high-throughput chromosome conformation capture (Hi-C) and Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) technologies. We found that the queens contain more chromosome interactions and more unique H3K27ac modifications than workers; in contrast, workers have more H3K4me1 modifications than queens. Moreover, we identified Map3k15 as a potential caste gene in queen-worker differentiation. Our results suggest that chromosomal conformation and H3K27ac and H3K4me1 modifications are involved in regulating queen-worker differentiation, which reveals that the queen-worker phenotypic dimorphism is regulated by multiple epigenetic modifications.

A Survey of Enhanced Cold Tolerance and Low-Temperature-Induced Anthocyanin Accumulation in a Novel Zoysia japonica Biotype.

Zoysia japonica is a warm-season turfgrass that is extensively used in landscaping, sports fields, and golf courses worldwide. Uncovering the low-temperature response mechanism of Z. japonica can help to accelerate the development of new cold-tolerant cultivars, which could be used to prolong the ornamental and usage duration of turf. A novel Z. japonica biotype, YueNong-9 (YN-9), was collected from northeastern China for this study. Phenotypic measurements, cold-tolerance investigation, and whole-transcriptome surveys were performed on YN-9 and LanYin-3 (LY-3), the most popular Z. japonica cultivar in Southern China. The results indicated the following: YN-9 has longer second and third leaves than LY-3; when exposed to the natural low temperature during winter in Guangzhou, YN-9 accumulated 4.74 times more anthocyanin than LY-3; after cold acclimation and freezing treatment, 83.25 ± 9.55% of YN-9 survived while all LY-3 leaves died, and the dark green color index (DGCI) value of YN-9 was 1.78 times that of LY-3; in YN-9, there was a unique up-regulation of Phenylalanine ammonia-lyase (PAL), Homeobox-leucine Zipper IV (HD-ZIP), and ATP-Binding Cassette transporter B8 (ABCB8) expressions, as well as a unique down-regulation of zinc-regulated transporters and iron-regulated transporter-like proteins (ZIPs) expression, which may promote anthocyanin biosynthesis, transport, and accumulation. In conclusion, YN-9 exhibited enhanced cold tolerance and is thus an excellent candidate for breeding cold-tolerant Z. japonica variety, and its unique low-temperature-induced anthocyanin accumulation and gene responses provide ideas and candidate genes for the study of low-temperature tolerance mechanisms and genetic engineering breeding.

Genome and Evolutionary Analysis of Nosema ceranae: A Microsporidian Parasite of Honey Bees.

Microsporidia comprise a phylum of single cell, intracellular parasites and represent the earliest diverging branch in the fungal kingdom. The microsporidian parasite Nosema ceranae primarily infects honey bee gut epithelial cells, leading to impaired memory, suppressed host immune responses and colony collapse under certain circumstances. As the genome of N. ceranae is challenging to assembly due to very high genetic diversity and repetitive region, the genome was re-sequenced using long reads. We present a robust 8.8 Mbp genome assembly of 2,280 protein coding genes, including a high number of genes involved in transporting nutrients and energy, as well as drug resistance when compared with sister species Nosema apis. We also describe the loss of the critical protein Dicer in approximately half of the microsporidian species, giving new insights into the availability of RNA interference pathway in this group. Our results provided new insights into the pathogenesis of N. ceranae and a blueprint for treatment strategies that target this parasite without harming honey bees. The unique infectious apparatus polar filament and transportation pathway members can help to identify treatments to control this parasite.

Thermal Effect and Mechanism Analysis of Flame-Retardant Modified Polymer Electrolyte for Lithium-Ion Battery.

In recent years, the prosperous electric vehicle industry has contributed to the rapid development of lithium-ion batteries. However, the increase in the energy density of lithium-ion batteries has also created more pressing safety concerns. The emergence of a new flame-retardant material with the additive ethoxy (pentafluoro) cyclotriphosphazene can ameliorate the performance of lithium-ion batteries while ensuring their safety. The present study proposes a new polymer composite flame-retardant electrolyte and adopts differential scanning calorimetry (DSC) and accelerating rate calorimetry to investigate its thermal effect. The study found that the heating rate is positively correlated with the onset temperature, peak temperature, and endset temperature of the endothermic peak. The flame-retardant modified polymer electrolyte for new lithium-ion batteries has better thermal stability than traditional lithium-ion battery electrolytes. Three non-isothermal methods (Kissinger; Kissinger-Akahira-Sunose; and Flynn-Wall-Ozawa) were also used to calculate the kinetic parameters based on the DSC experimental data. The apparent activation energy results of the three non-isothermal methods were averaged as 54.16 kJ/mol. The research results can provide valuable references for the selection and preparation of flame-retardant additives in lithium-ion batteries.

Ultrafast Flame-Induced Pyrolysis of Poly(dimethylsiloxane) Foam Materials toward Exceptional Superhydrophobic Surfaces and Reliable Mechanical Robustness.

Superhydrophobic surfaces are imperative in flexible polymer foams for diverse applications; however, traditional surface coatings on soft skeletons are often fragile and can hardly endure severe deformation, making them unstable and highly susceptible to cyclic loadings. Therefore, it remains a great challenge to balance their mutual exclusiveness of mechanical robustness and surface water repellency on flexible substrates. Herein, we describe how robust superhydrophobic surfaces on soft poly(dimethylsiloxane) (PDMS) foams can be achieved using an extremely simple, ultrafast, and environmentally friendly flame scanning strategy. The ultrafast flame treatment (1-3 s) of PDMS foams produces microwavy and nanosilica rough structures bonded on the soft skeletons, forming robust superhydrophobic surfaces (i.e., water contact angles (WCAs) > 155° and water sliding angles (WSAs) < 5°). The rough surface can be effectively tailored by simply altering the flame scanning speed (2.5-15.0 cm/s) to adjust the thermal pyrolysis of the PDMS molecules. The optimized surfaces display reliable mechanical robustness and excellent water repellency even after 100 cycles of compression of 60% strain, stretching of 100% strain, and bending of 90° and hostile environmental conditions (including acid/salt/alkali conditions, high/low temperatures, UV aging, and harsh cyclic abrasion). Moreover, such flame-induced superhydrophobic surfaces are easily peeled off from ice and can be healable even after severe abrasion cycles. Clearly, the flame scanning strategy provides a facile and versatile approach for fabricating mechanically robust and surface superhydrophobic PDMS foam materials for applications in complex conditions.

Thermal Stability Analysis of Lithium-Ion Battery Electrolytes Based on Lithium Bis(trifluoromethanesulfonyl)imide-Lithium Difluoro(oxalato)Borate Dual-Salt.

Lithium-ion batteries with conventional LiPF6 carbonate electrolytes are prone to failure at high temperature. In this work, the thermal stability of a dual-salt electrolyte of lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) and lithium difluoro(oxalato)borate (LiODFB) in carbonate solvents was analyzed by accelerated rate calorimetry (ARC) and differential scanning calorimetry (DSC). LiTFSI-LiODFB dual-salt carbonate electrolyte decomposed when the temperature exceeded 138.5 °C in the DSC test and decomposed at 271.0 °C in the ARC test. The former is the onset decomposition temperature of the solvents in the electrolyte, and the latter is the LiTFSI-LiODFB dual salts. Flynn-Wall-Ozawa, Starink, and autocatalytic models were applied to determine pyrolysis kinetic parameters. The average apparent activation energy of the dual-salt electrolyte was 53.25 kJ/mol. According to the various model fitting, the thermal decomposition process of the dual-salt electrolyte followed the autocatalytic model. The results showed that the LiTFSI-LiODFB dual-salt electrolyte is significantly better than the LiPF6 electrolyte in terms of thermal stability.

DGCR5 induces osteogenic differentiation by up-regulating Runx2 through miR-30d-5p.

BACKGROUND: Postmenopausal osteoporosis (PMOP) is a metabolic bone disease caused by unbalance between osteoblast bone formation and osteoclast bone resorption. In this study, the moderating effect of DGCR5 on osteogenic differentiation and its role in PMOP was assessed. METHODS: The expression levels of DGCR5, miR-30d-5p, and Runt-related transcription factor 2 (Runx2) mRNA and protein were determined by qRT-PCR and western blot, separately. The bone marrow human mesenchymal stem cells (hMSCs) were isolated from bone marrow of patients with PMOP or the healthy control. ALP activity and bone mineral density (BMD) were detected to reflect the osteogenic differentiation status. RIP and RNA pull-down assay were performed to explore the combination and interaction between DGCR5 and miR-30d-5p. RESULTS: Compared with the healthy control group (n = 20), DGCR5 was down-regulated in hMSCs from patients with PMOP (n = 20). Overexpression of DGCR5 induced osteogenic differentiation of hMSCs. DGCR5 up-regulated the expression of Runx2 through miR-30d-5p. DGCR5 up-regulated the expression of Runx2 through miR-30d-5p to induce osteogenic differentiation of hMSCs. CONCLUSION: DGCR5 negatively regulates miR-30d-5p, and it up-regulates Runx2 through miR-30d-5p, thereby inducing osteogenic differentiation of hMSCs, which may help to delay PMOP development.

Comparison of growth characteristics between skeletal muscle satellite cell lines from diploid and triploid olive flounder Paralichthys olivaceus.

OBJECTIVES: According to myosatellite cell lines (MSCs) established in vitro from diploid and triploid flounder, we compared the characters of growth and differentiation of their MSCs. The results would be useful for learning the muscle development mechanism in teleosts. MATERIALS AND METHODS: The skeletal muscle cells from the diploid and triploid olive flounder Paralichthys olivaceus were isolated and cultured in vitro, respectively, and the cells were characterized at the morphology and molecular level; meanwhile, the performance of these cells' proliferation and differentiation were analyzed. RESULTS: Two new skeletal muscle cell lines (POMSCS(2n) and POMSCS(3n)) from diploid and triploid flounder have been respectively subcultured for 67 times and 66 times. The cultured cells were mostly spindle-like mononuclear cells. They have normal flounder diploid karyotype (2n=48t) and triploid karyotype (3n=72t), respectively. Muscle satellite cell gene marker (pax7b) and myogenic cell protein marker (Desmin) were all expressed in cells of two cell lines. Both of the cells could differentiate into the large polynucleated muscle fibre cells, and immunofluorescence reactions of myosin heavy chain (MyHC) were positive. There were more cells of POMSCS(3n) to differentiate into the muscle fibre cells than that of POMSCS(2n). However, POMSCS(2n) cells proliferated more rapidly than those of POMSCS(3n) (P < 0.05). The significant fluorescent signals were observed in both POMSCS(2n) and POMSCS(3n) cells after transfected with pEGFP-N3 reporter plasmid. CONCLUSIONS: The two cell lines have been established and characterized as MSCs. We suppose that it might be the differentiation capacity, rather than the proliferation activity of MSCs to play a key role in the better growth of triploid ones than diploid. Both cell lines will become the ideal tools to learn the mechanism of fish MSCs proliferation, differentiation and regeneration during muscle development in the future.

Complete mitochondrial genome of copperband butterflyfish Chelmon rostratus (Teleostei, Perciformes, Chaetodontidae).

In this study, the complete mitochondrial (mt) genome of the copperband butterflyfish Chelmon rostratus from Beibu Bay, China, was determined. It is one of the most common coral reef fish in South China Sea. The total length of C. rostratus mitogenome is 16,538 bp, which consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a control region, with the genome organization and gene order being identical to other typical vertebrate mitogenomes. The overall nucleotide composition of the H-strand is 28.05% A, 28.94% T, 16.22% G and 26.79% C, with an A + T bias. This study will provide the first complete mitochondrial genome of Chelmon rostratus as useful information for the application of fish phylogenetic relationship analysis within the butterflyfish species.

[A case-control study on association between OAS1 polymorphism and susceptibility to spontaneous preterm birth and preterm premature rupture of membranes].

OBJECTIVE: To investigate the association between the genetic polymorphism of 2',5'-oligoadenylate synthetase 1 (OAS1) and susceptibility to spontaneous preterm birth (SPTB) and preterm premature rupture of membranes (PPROM). METHODS: The case-control study consisted of 599 preterm infants including 171 cases of PPROM, and 673 full-term infants without maternal histories of SPTB and PPROM as controls. The single nucleotide polymorphism (SNP) at OAS1 intron 5, rs10774671, was analyzed by polymerase chain reaction-restriction fragment length polymorphism. RESULTS: No significant differences were observed between the case and control groups in the frequencies of genotypes (AA, GA, and GG) and alleles (A and G) of OAS1 rs10774671. When the case group was divided into two subgroups with or without PPROM, no significant differences in the genotype and allele frequencies were found between each subgroup and the control group. When the case group was divided into three subgroups with different gestational ages at SPTB, no significant differences in the genotype and allele frequencies were detected between each subgroup and the control group. CONCLUSIONS: No association is identified between OAS1 SNP and susceptibility to SPTB and PPROM.

A MCP-1 promoter polymorphism at G-2518A is associated with spontaneous preterm birth.

Monocyte chemoattractant protein-1 (MCP-1) is an important chemokine involved in the pathogenesis of spontaneous preterm birth (SPTB). We examined whether the MCP-1 G-2518A polymorphism is associated with the risk of SPTB in a Chinese population. The MCP-1 G-2518A polymorphism was genotyped in 569 preterm singleton neonates and in 673 term neonates using polymerase chain reaction-restriction fragment length polymorphism analysis. The distribution of the MCP-1 G-2518A genotype and the allele frequencies between the SPTB patients and the controls were not significantly different in the overall sample. However, we found that the AA genotype was associated with significantly increased susceptibility to very SPTB (<32 weeks) [odds ratio (OR) 2.07; 95 % confidence interval (CI), 1.27-3.36; P = 0.005) and extremely SPTB (<28 weeks) (OR 2.74; 95 % CI, 1.10-6.72; P = 0.014) compared with -2518G-positive genotypes (GG + GA genotypes). When extremely preterm neonates and very preterm neonates were combined, the AA genotype was also significantly associated with increased susceptibility to SPTB (OR 2.23; 95 % CI, 1.40-3.54; P < 0.001). The MCP-1 G-2518A polymorphism was not associated with increased susceptibility to SPTB in patients with premature rupture of the membranes (PROM) or in those without PROM. Our findings suggest that the MCP-1 G-2518A polymorphism may plays a role in mediating the susceptibility to SPTB in the Chinese population. Knowledge of genetic factors contributing to the pathogenesis of SPTB may have implications for screening and treatment of this disorder.

The SEPS1 G-105A polymorphism is associated with risk of spontaneous preterm birth in a Chinese population.

Inflammation plays an important role in the etiology and pathophysiology of spontaneous preterm birth (SPTB), and selenoprotein S (SEPS1) is involved in regulating the inflammatory response. Recently the G-105A promoter polymorphism in SEPS1 was shown to increase pro-inflammatory cytokine expression. We examined whether this functional polymorphism was related to the risk of SPTB in a Chinese population. We also examined the impact of premature rupture of membranes (PROM) on susceptibility to SPTB. The SEPS1 G-105A polymorphism was genotyped in 569 preterm singleton neonates and 673 term neonates by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. χ (2) tests and logistic regression analyses were used to calculate the odds ratios (ORs) and 95% confidence intervals (95% CIs). We observed that, compared with the GG genotype, -105A positive genotypes (GA + AA genotypes) were associated with significantly increased susceptibility to SPTB (adjusted OR, 1.87; 95% CI, 1.36-2.57; P<0.001). The -105A positive genotypes were also significantly associated with increased susceptibility to SPTB, both in the patients with PROM (adjusted OR, 2.65; 95% CI, 1.73-4.03; P<0.001) and in those without PROM (adjusted OR, 1.56; 95% CI, 1.09-2.24; P = 0.015). The -105A positive genotypes were also significantly associated with increased susceptibility to SPTB between extremely preterm neonates and controls (adjusted OR, 4.46; 95% CI, 1.86-10.73; P = 0.002) and between moderately preterm neonates and controls (adjusted OR, 1.76; 95% CI, 1.25-2.47; P = 0.001). Our findings suggest that the SEPS1 G-105A polymorphism contributes to the risk of developing SPTB in a Chinese population.

[Anti-metastasis effect of thymoquinone on human pancreatic cancer].

Recent studies reported that thymoquinone (TQ), a component derived from the medicinal spice Nigella sativa (also called black cumin), exhibited inhibitory effects on cell proliferation of many cancer cell lines. This study was performed to investigate the anti-metastatic effect of thymoquinone on the pancreatic cancer in vitro and in vivo. The results showed that thymoquinone suppressed the migration and invasion of Panc-1 cells in a does-dependent manner. To investigate the possible mechanisms involved in these events, Western blotting analysis was performed, and found that thymoquinone significantly down-regulates NF-kappaB and MMP-9 in Panc-1 cells. In addition, metastatic model simulating human pancreatic cancer was established by orthotropic implantation of histologically intact pancreatic tumor tissue into the pancreatic wall of nude mice. And administration of thymoquinone significantly reduced tumor metastasis compared to untreated control. Furthermore, the expression of NF-kappaB and MMP-9 in tumor tissues was also suppressed after treatment with thymoquinone. Taken together, the results indicate that thymoquinone exerts anti-metastatic activity on pancreatic cancer both in vitro and in vivo, which may be related to down-regulation of NF-kappaB and its regulated molecules such as MMP-9 protein. Consequently, these results provide important insights into thymoquinone as an antimetastatic agent for the treatment of human pancreatic cancer.

CpG island methylator phenotype involving chromosome 3p confers an increased risk of non-small cell lung cancer.

PURPOSE: This study aims to explore the association of CpG island methylator phenotype (CIMP) involving tumor suppressor genes on short arm of chromosome 3 (3p) with increased risk of non-small cell lung cancer (NSCLC). METHODS AND MATERIALS: In this study, four NSCLC cell lines were cultured, and peripheral blood mononuclear cell (PBMC) specimens from 80 patients with NSCLC and 80 matched controls were collected for 3p-involved CIMP (3pCIMP) analysis. 3pCIMP was referred to as having at least three synchronously methylated genes of 3p per sample. Methylation-specific polymerase chain reaction was performed to examine the methylation status of each gene. DNA demethylation of NSCLC cell lines was achieved through the treatment with 5-aza-deoxycytidine. Logistic regression was used to assess odds ratios and 95% confidence intervals, which were adjusted for gender, age, and smoking status. RESULTS: Demethylation experiment showed that 3pCIMP status could play an important role in NSCLC cell proliferation. A total of 97.5% of PBMC specimens from NSCLC patients presented promoter methylation of any one of six genes (hOGG1, RAR-B, SEMA3B, RASSF1A, BLU, or FHIT) on 3p. Interestingly, 3pCIMP+ was found in 43.8% of NSCLC PBMC specimens and only in 6.3% of normal PBMC samples. The data suggest that 3pCIMP status is significantly associated with NSCLC and normal PBMC samples (p 0.001). More importantly, the results show that 3pCIMP positive carriers have a 12.8-fold increased risk of NSCLC (adjusted odds ratio, 12.8; 95% confidence interval, 4.38 -37.4, p 0.001) in Chinese population. CONCLUSIONS: This is the first evidence of an association between PBMC 3pCIMP and risk for NSCLC.

[Effects of high mobility group box-1 silencing upon the invasion and proliferation in human lung cancer cell L9981 by RNA inhibition].

OBJECTIVE: To investigate the effects of high mobility group box-1 (HMGB1) silencing upon the invasion and proliferation in human lung cancer cell L9981 by RNA inhibition. METHODS: L9981 cells were divided into 3 groups. Group 1 was transfected by HMGB1 small interfering RNA (HMGB1-siRNA group). Group 2 was transfected by negative sequence small interfering RNA (negative control group). Group 3 was blank group. The mRNA and protein of HMGB1 were determined by real-time PCR and Western blotting assay respectively. The proliferation ability was examined by cell viability assay. The growth status of cells was examined by MTT at 24, 48, 72 and 96 h post-transfection. Invasion ability was evaluated by Boyden chamber model. RESULTS: The relative expression of HMGB1 mRNA of HMGB1-siRNA group (1.0 +/- 0.0) was much lower than the negative control (12.8 +/- 1.3, P < 0.05) and blank groups (12.1 +/- 1.0, P < 0.05). HMGB1 protein expression was also significantly inhibited. Cell viability of HMGB1-siRNA group was much lower than other two groups. MTT indicated the growth of HMGB1-siRNA group was significantly inhibited than other two groups. Boyden chamber model indicated the number of penetrating membrane in HMGB1-siRNA group was less than other two groups. CONCLUSION: Down-regulating HMGB1 gene expression by HMGB1 siRNA can inhibit the invasion and proliferation of human lung cancer cell.

[The application of large-scale yeast two-hybrid to study protein--protein interaction].

The principle of yeast two-hybrid were summarized, the basis for large scale yeast two-hybrid screening of protein-protein interaction was given and the main application of yeast two-hybrid in large scale screening of protein-protein interaction was presented. The problems of large scale yeast two-hybrid screening of protein-protein interaction were also discussed. Because there were a lot of false positives and false negatives in the result of protein-protein interaction obtained by large-scale yeast two-hybrid screening, the employment of other methods to study protein-protein interaction in large scale in parallel was proposed if possible.