Analysis of allopolyploidy-induced rapid genetic and epigenetic changes and their relationship in wheat.

We used the conventional and methylation-sensitive randomly amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) analyses to assess genome-wide changes and explore the relationships between genetic and epigenetic variations among individuals of a newly synthesized allohexaploid wheat line whose genomic constitution is identical to that of the natural common wheat, compared with its parent plants and a natural counterpart named Chinese Spring. We found rapid, extensive, and predominantly consistent non-Mendelian changes in the form of genetic and DNA methylation variations in the allohexaploid individuals. Specifically, at least 30-40% of the epigenetic component was truly independent of genetic changes, which answered a critical question, i.e. its autonomy in relation to the genetic context. Striking correlations were detected between genetic and epigenetic changes. Interestingly, as previously reported, the paternally donated nuclear genomes showed more genetic changes than the maternally donated ones; the loss of paternal bands was significantly correlated with the hypomethylation of CG or CHG sequences, suggesting an unknown link between genetic instability and hypomethylation. Sequence analysis indicated that most variations occurred in the cellular genes and sequences related to transposable elements. Based on these findings, the possible mechanisms and effects of the genomic changes in allopolyploid speciation and evolution were discussed.

Glyphosate biodegradation and potential soil bioremediation by Bacillus subtilis strain Bs-15.

Glyphosate and glyphosate-containing herbicides have an adverse effect on mammals, humans, and soil microbial ecosystems. Therefore, it is important to develop methods for enhancing glyphosate degradation in soil through bioremediation. We investigated the potential of glyphosate degradation and bioremediation in soil by Bacillus subtilis Bs-15. Bs-15 grew well at high concentrations of glyphosate; the maximum concentration tolerated by Bs-15 reached 40,000 mg/L. The optimal conditions for bacterial growth and glyphosate degradation were less than 10,000 mg/L glyphosate, with a temperature of 35°C and a pH of 8.0. Optimal fermentation occurred at 180 rpm for 60 h with an inoculum ratio of 4%. Bs-15 degraded 17.65% (12 h) to 66.97% (96 h) of glyphosate in sterile soil and 19.01% (12 h) to 71.57% (96 h) in unsterilized soil. Using a BIOLOG ECO plate test, we observed no significant difference in average well color development values between the soil inoculated with Bs-15 and the control soil before 72 h, although there was a significant difference (P < 0.01) after 72 h. In the presence of Bs-15, the 5 functional diversity indices (Shannon index, Shannon uniformity, Simpson index, McIntosh index, and McIntosh uniformity) were greater (P < 0.01) compared with the control soil. These results indicate that Bs-15 could be used to alleviate contamination from glyphosate-containing herbicides, increasing the microbial functional diversity in glyphosate-contaminated soils and thus enhancing the bioremediation of glyphosate-contaminated soils.

Exploring laccase genes from plant pathogen genomes: a bioinformatic approach.

To date, research on laccases has mostly been focused on plant and fungal laccases and their current use in biotechnological applications. In contrast, little is known about laccases from plant pathogens, although recent rapid progress in whole genome sequencing of an increasing number of organisms has facilitated their identification and ascertainment of their origins. In this study, a comparative analysis was performed to elucidate the distribution of laccases among bacteria, fungi, and oomycetes, and, through comparison of their amino acids, to determine the relationships between them. We retrieved the laccase genes for the 20 publicly available plant pathogen genomes. From these, 125 laccase genes were identified in total, including seven in bacterial genomes, 101 in fungal genomes, and 17 in oomycete genomes. Most of the predicted protein models of these genes shared typical fungal laccase characteristics, possessing four conserved domains with one cysteine and ten histidine residues at these domains. Phylogenetic analysis illustrated that laccases from bacteria and oomycetes were grouped into two distinct clades, whereas fungal laccases clustered in three main clades. These results provide the theoretical groundwork regarding the role of laccases in plant pathogens and might be used to guide future research into these enzymes.

Expression of claudin-1 and its relationship with lymphatic microvessel generation in hypopharyngeal squamous cell carcinoma.

We investigated the relationship between claudin-1 and micro-lymphatic vessel density (MLVD) by detecting claudin-1 and protein D2-40 expression in cancer tissue specimens obtained from 97 patients with hypopharyngeal squamous cell carcinoma (HSCC). We also explored the correlation between the expression of these proteins and clinical tumor stage, pathological grading, and clinical prognosis in the patients. Moreover, we studied the mechanism of lymph node metastasis in HSCC, thereby providing information for treating HSCC and inhibiting lymph node metastasis. We detected levels of claudin-1 and protein D2-40 expression in cancer tissue from 97 patients with HSCC and para-tumor tissue from 90 patients by immunohistochemistry; we analyzed the correlation between markers and clinicopathological features by using the Pearson chi-square test and conducted survival analysis by the log-rank test. Claudin-1 expression was high in HSCC and was related to tumor differentiation and lymph node metastasis; Kaplan-Meier analysis showed that claudin-1 expression was related to patient survival rate (P = 0.012). There was a significant relationship between MLVD in the tissues adjacent to the carcinoma and the indices of histopathological grade, clinical stage, and lymph node metastasis. There was also a positive correlation between claudin-1 expression and MLVD. High expression of claudin-1 might induce the generation of tumor lymphatic vessels, which increases metastasis in the lymph node. Because claudin-1 is related to patient survival rate, it may be useful as a monitoring index for postoperative HSCC and might be a new target for treating the disease.

Analysis of the expression of HMGB-1, CXCL16, miRNA-30a, and TGF-ß1 in primary nephritic syndrome patients and its significance.

We investigated the expression levels of high-mobility group box protein 1 (HMGB-1), CXC chemokine ligand 16 (CXCL16), microRNA (miRNA)-30a and transforming growth factor ß1 (TGF-ß1) in primary nephritic syndrome (PNS) patients and the clinical significance of this expression. A total of 56 patients with PNS were included in the PNS group, while 50 healthy subjects formed the normal control group. Serum levels of HMGB-1, CXCL16, miRNA-30a, and urinary TGF-ß1 concentrations were quantified along with other biochemical indices, including serum albumin, triglyceride (TG), total cholesterol (TC), low-density lipoprotein (LDL), high-density lipoprotein, and urinary proteins. The correlation between levels of HMGB-1, CXCL16, miRNA-30a, and TGF-ß1 and biochemical indexes was further analyzed. PNS group patients had significantly higher levels of HMGB-1, CXCL16, miRNA- 30a, and TGF-ß1 compared to the control group (P < 0.05). PNS patients also had higher 24-h urinary protein, TG, TC, and LDL levels but lower serum albumin compared to subjects in the control group (P < 0.05). Serum HMGB-1, CXCL16, miRNA-30a, and urinary TGF-ß1 levels were all negatively correlated with serum albumin levels, but were positively correlated with TG, TC, LDL, and 24-h urinary protein (P < 0.05 in all cases). Additionally, a positive correlation existed among serum HMGB-1, CXCL16, miRNA-30a, and urinary TGF-ß1 levels (P < 0.01). HMGB-1, CXCL16, miRNA-30a, and urinary TGF-ß1 were highly expressed in PNS patients and may play important roles in the pathogenesis and development of PNS.