Effect of different aging treatments on the transport of nano-biochar in saturated porous media.

Widely used for soil amendment, carbon sequestration, and remediation of contaminated soils, biochars (BCs) inevitably produce a large number of nanoparticles with relatively high mobility. Geochemical aging alters chemical structure of these nanoparticles and thus affect their colloidal aggregation and transport behavior. In this study, the transport of ramie derived nano-BCs (after ball-milling) was investigated by different aging treatments (i.e., photo (PBC) and chemical aging (NBC)) as well as the managing BC under different physicochemical factors (i.e., flow rates, ionic strengths (IS), pH, and coexisting cations). Consequences of the column experiments indicated aging promoted the mobility of the nano-BCs. Compared to the nonaging BC, consequences of spectroscopic analysis demonstrated the aging BCs exhibited a number of tiny corrosion pores. Both of these aging treatments contribute to a more negative zeta potential and a higher dispersion stability of the nano-BCs, which is caused by the abundance of O-functional groups. Also the specific surface area and mesoporous volume of both aging BCs increased significantly, with the increase being more pronounced for NBC. The breakthrough curves (BTCs) obtained for the three nano-BCs were modelled by the advection-dispersion equation (ADE), which included first-order deposition and release terms. The ADE revealed high mobility of aging BCs, which meant their retention in saturated porous media was reduced. This work contributes to a comprehensive understanding of the transport of aging nano-BCs in the environment.

Dynamic Expression of Palmitoylation Regulators across Human Organ Development and Cancers Based on Bioinformatics.

Protein palmitoylation is a reversible modification process that links palmitate to cysteine residues via a reversible thioester bond. Palmitoylation exerts an important role in human organ development and tumor progression. However, a comprehensive landscape regarding the dynamic expression of palmitoylation regulators in human organ development remains unclear. In this study, we analyzed the dynamic expression of palmitoylation regulators in seven organ development and eight cancer types based on bioinformatics. We found that the expression levels of most palmitoylation regulators were altered after birth. In particular, ZDHHC7/20/21 exhibited converse expression patterns in multiple cancer types. Survival analysis showed that the poor prognosis in patients with kidney renal clear carcinoma (KIRC) is related to low expression of ZDHHC7/20/21, and a high expression of ZDHHC7/20/21 is related to worse survival in patients with liver hepatocellular carcinoma (LIHC). Furthermore, we found that the expression of ZDHHC7 is associated with infiltration levels of some types of immune cells in the tumor microenvironment (TME), and we explored the relationship between ZDHHC7 expression and immune checkpoint (ICP) genes across 33 cancer types. In addition, gene set enrichment analysis (GSEA) results indicated that ZDHHC7 might regulate different genes to mediate the same pathway in different organs. In summary, the comprehensive analysis of palmitoylation regulators reveals their functions in human organ development and cancer, which may provide new insights for developing new tumor markers.

Single-cell transcriptome analysis of Bisphenol A exposure reveals the key roles of the testicular microenvironment in male reproduction.

Testicular development during juvenile is crucial for subsequent male reproductive function. However, it remains poorly understood about the contribution of the testis microenvironment to human germ cell maturation. Therefore, we systematically analyzed scRNA-seq transcriptome and found the dramatic changes in cell-type composition in human testis during puberty. Then we constructed cell-cell communication networks between germ cells and somatic cells in the juvenile testis, which may be achieved via immune-related pathways. Our results showed that maturation-promoting factors are the switches of the Sertoli cells that drive sperm maturation. Furthermore, we found that Bisphenol A(BPA) enhanced the maturation and growth of germ cells through the Sertoli cell's secretory protein. Finally, our results indicate Bisphenol A would lead to the dysregulation of secreted protein expression in Sertoli cells during spermatogenesis, which in turn has direct cytotoxicity to Sertoli cells. Bisphenol A is one of the underlying causes of non-obstructive azoospermia (NOA). In summary, our results reveal the reproductive toxicity and molecular mechanism of Bisphenol A in Sertoli cells and male reproduction. Provide a reference for the toxicity of Bisphenol A to human reproduction.

ATD: a comprehensive bioinformatics resource for deciphering the association of autophagy and diseases.

Autophagy is the natural, regulated, destructive mechanism of the eukaryotes cell that disassembles unnecessary or dysfunctional components. In recent years, the association between autophagy and diseases has attracted more and more attention, but our understanding of the molecular mechanism about the association in the system perspective is limited and ambiguous. Hence, we developed the comprehensive bioinformatics resource Autophagy To Disease (ATD, http://auto2disease.nwsuaflmz.com) to archive autophagy-associated diseases. This resource provides bioinformatics annotation system about genes and chemicals about autophagy and human diseases by extracting results from previous studies with text mining technology. Based on the big data from ATD, we found that some classes of disease tend to be related with autophagy, including respiratory disease, cancer, urogenital disease and digestive system disease. We also found that some classes of autophagy-related diseases have a strong association among each other and constitute modules. Furthermore, we extracted the autophagy-disease-related genes (ADGs) from ATD and provided a novel algorithm Optimized Random Forest with Label model to predict potential ADGs. This bioinformatics annotation system about autophagy and human diseases may provide a basic resource for the further detection of the molecular mechanisms of autophagy pathway to disease.

Association of single nucleotide polymorphism rs3803662 with the risk of breast cancer.

Large scale association studies have identified the single nucleotide polymorphism rs3803662 associated with breast cancer risk. However, the sample size of most studies is too small. Here, we performed this meta-analysis to make the result more convincing. Relevant articles published up to 2016 were identified by searching the PubMed database. 13 studies, involving a total of 29405 participants, were included in the meta-analysis. Odds Ratios (ORs) with 95% confidence intervals (CIs) was calculated with random or fixed effects model. All data analyses were analyzed by Review Manger 5.3 software. In Caucasian subgroup: Dominant model (TT + CT vs CC): OR = 1.17 (1.06, 1.29), Recessive model (TT vs CT + CC): OR = 1.25 (1.13, 1.39) and Allele frequency (T vs C): OR = 1.15 (1.08, 1.22). The present meta-analysis suggests that rs3803662 polymorphism is significantly associated with breast cancer risk in Caucasian women, and we did not find the association in Asian women.

Association of single nucleotide polymorphism rs6983267 with the risk of prostate cancer.

Many studies have investigated the association between single nucleotide polymorphism (SNP) rs6983267 and the risk of prostate cancer. However, results of these studies are inconsistent. Therefore, we summarised available data and performed a meta-analysis to determine this association. Relevant articles were identified by searching the PubMed, Web of Science and Embase database. Odds ratios (ORs) with 95% confidence intervals (CIs) were calculated using random effects model. We used dominant model (GG + TG vs TT), recessive model (GG vs TG + TT) and additive model (GG +TT vs TG) to determine the association between the rs6983267 polymorphism and risk of prostate cancer. Summary, 9 studies involving 8726 participants were included in this meta-analysis. Overall, though no association was observed between the rs6983267 polymorphism and risk of prostate cancer, subgroup analysis according to ethnicity showed a significant association between the rs6983267 polymorphism and risk of prostate cancer among white European men [recessive model: GG vs TG + TT, OR=1.21, (95% CI: 1.03, 1.42), P=0.02]. Our results indicate that the GG genotype of the rs6983267 polymorphism will increase individual susceptibility to prostate cancer in white European men.

Anammox start-up in sequencing batch biofilm reactors using different inoculating sludge.

In this study, anammox bacteria were rapidly enriched in sequencing batch biofilm reactors (SBBRs) with different inoculations. The activated sludge taken from a sequencing batch reactor was used and inoculated to SBBR1, while SBBR2 was seeded with stored anaerobic sludge from an upflow anaerobic fixed bed (2-year stored at 5-15 °C). Nitrogen removal performance, anammox activity, biofilm characteristics and variation of the microbial community were evaluated. The maximum total nitrogen loading rate (NLR) of SBBR1 gradually reached to 1.62 kgN/(m³/day) with a removal efficiency higher than 88% and the NLR of SBBR2 reached to 1.43 kgN/(m³/day) with a removal efficiency of 86%. SBBR2 was more stable compared to SBBR1. These results, combined with molecular techniques such as scanning electron microscope, fluorescence in situ hybridization, and terminal restriction fragment length polymorphism, indicated that different genera of anammox bacteria became dominant. This research also demonstrates that SBBR is a promising bioreactor for starting up and enriching anammox bacteria.