Shewanella oneidensis MR-1-Induced Fe(III) Reduction Facilitates Roxarsone Transformation

Although microbial activity and associated iron (oxy)hydroxides are known in general to affect the environmental dynamics of 4-hydroxy-3-nitrobenzenearsonic acid (roxarsone), the mechanistic understanding of the underlying biophysico-chemical processes remains unclear due to limited experimental information. We studied how Shewanella oneidensis MR-1 –a widely distributed metal-reducing bacterium, in the presence of dissolved Fe(III), affects roxarsone transformations and biogeochemical cycling in a model aqueous system. The results showed that the MR-1 strain was able to anaerobically use roxarsone as a terminal electron acceptor and to convert it to a single product, 3-amino-4-hydroxybenzene arsonic acid (AHBAA). The presence of Fe(III) stimulated roxarsone transformation via MR-1-induced Fe(III) reduction, whereby the resulting Fe(II) acted as an efficient reductant for roxarsone transformation. In addition, the subsequent secondary Fe(III)/Fe(II) mineralization created conditions for adsorption of organoarsenic compounds to the yielded precipitates and thereby led to arsenic immobilization. The study provided direct evidence of Shewanella oneidensis MR-1-induced direct and Fe(II)-associated roxarsone transformation. Quantitative estimations revealed a candidate mechanism for the early-stage environmental dynamics of roxarsone in nature, which is essential for understanding the environmental dynamics of roxarsone and successful risk assessment.     

A bedr way of genomic interval processing

Background

Next-generation sequencing is making it critical to robustly and rapidly handle genomic ranges within standard pipelines. Standard use-cases include annotating sequence ranges with gene or other genomic annotation, merging multiple experiments together and subsequently quantifying and visualizing the overlap. The most widely-used tools for these tasks work at the command-line (e.g. BEDTools) and the small number of available R packages are either slow or have distinct semantics and features from command-line interfaces.

Results

To provide a robust R-based interface to standard command-line tools for genomic coordinate manipulation, we created bedr. This open-source R package can use either BEDTools or BEDOPS as a back-end and performs data-manipulation extremely quickly, creating R data structures that can be readily interfaced with existing computational pipelines. It includes data-visualization capabilities and a number of data-access functions that interface with standard databases like UCSC and COSMIC.

Conclusions

bedr package provides an open source solution to enable genomic interval data manipulation and restructuring in R programming language which is commonly used in bioinformatics, and therefore would be useful to bioinformaticians and genomic researchers.

     

种子物理休眠研究进展

种子物理休眠是由种皮不透水层引起的一种休眠类型,是植物在长期系统发育进程中获得的一种适应环境变化的特性。该文简述了种子物理休眠的定义与概念;从不透水层、种皮的特殊水孔器结构以及胚的形态特异性等方面,综述了物理休眠种子的形态特征、物理休眠与综合休眠的解除方法以及物理休眠的可能解除机制;利用Angiosperm Phylogeny Group Ⅲ(APG Ⅲ)系统分析了种子物理休眠的植物在系统发育中的位置;最后提出了今后种子物理休眠有待研究的主要问题。     

Heterologous expression of oxytetracycline biosynthetic gene cluster in Streptomyces venezuelae WVR2006 to improve production level and to alter fermentation process

Applied Microbiology and Biotechnology - Heterologous expression is an important strategy to activate biosynthetic gene clusters of secondary metabolites. Here, it is employed to activate and...     

Cellulosic Butanol (ABE) Biofuel Production from Sweet Sorghum Bagasse (SSB): Impact of Hot Water Pretreatment and Solid Loadings on Fermentation Employing <Emphasis Type="Italic">Clostridium beijerinckii</Emphasis> P260

A novel butanol fermentation process was developed in which sweet sorghum bagasse (SSB) was pretreated using liquid hot water (LHW) pretreatment technique followed by enzymatic hydrolysis and butanol (acetone butanol ethanol (ABE)) fermentation. A pretreatment temperature of 200 °C resulted in the generation of a hydrolyzate that inhibited butanol fermentation. When SSB pretreatment temperature was decreased to 190 °C (0-min holding time), the hydrolyzate was successfully fermented without inhibition and an ABE productivity of 0.51 g L^?1 h^?1 was achieved which is comparable to the 0.49 g L^?1 h^?1 observed in the control fermentation where glucose was used as a feedstock. These results are based on the use of 86 g L^?1 SSB solid loadings in the pretreatment reactors. We were also able to increase SSB solid loadings from 120 to 200 g L^?1 in the pretreatment step (190 °C) followed by hydrolysis and butanol fermentation. As pretreatment solid loadings increased, ABE yield remained in the range of 0.38–0.46. In these studies, a maximum ABE concentration of 16.88 g L^?1 was achieved. Using the LHW pretreatment technique, 88.40–96.00 % of polymeric sugars (cellulose + hemicellulose) were released in the SSB hydrolyzate. The LHW pretreatment technique does not require chemical additions and is environmentally friendly, and the hydrolyzate can be used successfully for butanol fermentation.     

Abrupt Decline in Tuberculosis among Foreign-Born Persons in the United States

While the number of reported tuberculosis (TB) cases in the United States has declined over the past two decades, TB morbidity among foreign-born persons has remained persistently elevated. A recent unexpected decline in reported TB cases among foreign-born persons beginning in 2007 provided an opportunity to examine contributing factors and inform future TB control strategies. We investigated the relative influence of three factors on the decline: 1) changes in the size of the foreign-born population through immigration and emigration, 2) changes in distribution of country of origin among foreign-born persons, and 3) changes in the TB case rates among foreign-born subpopulations. Using data from the U.S. National Tuberculosis Surveillance System and the American Community Survey, we examined TB case counts, TB case rates, and population estimates, stratified by years since U.S. entry and country of origin. Regression modeling was used to assess statistically significant changes in trend. Among foreign-born recent entrants (<3 years since U.S. entry), we found a 39.5% decline (-1,013 cases) beginning in 2007 (P<0.05 compared to 2000–2007) and ending in 2011 (P<0.05 compared to 2011–2014). Among recent entrants from Mexico, 80.7% of the decline was attributable to a decrease in population, while the declines among recent entrants from the Philippines, India, Vietnam, and China were almost exclusively (95.5%–100%) the result of decreases in TB case rates. Among foreign-born non-recent entrants (≥3 years since U.S. entry), we found an 8.9% decline (-443 cases) that resulted entirely (100%) from a decrease in the TB case rate. Both recent and non-recent entrants contributed to the decline in TB cases; factors contributing to the decline among recent entrants varied by country of origin. Strategies that impact both recent and non-recent entrants (e.g., investment in overseas TB control) as well as those that focus on non-recent entrants (e.g., expanded targeted testing of high-risk subgroups among non-recent entrants) will be necessary to achieve further declines in TB morbidity among foreign-born persons.     

Knockdown of RPL34 inhibits the proliferation and migration of glioma cells through the inactivation of JAK/STAT3 signaling pathway

Ribosomal protein L34 (RPL34), belonging to the L34E family of ribosomal proteins, was reported to be dysregulated in several types of cancers and plays important roles in tumor progression. However, the expression and roles of RPL34 in human glioma remain largely unknown. Thus, the objective of this study was to investigate the expression and role of RPL34 in glioma. We report here that RPL34 is highly expressed in human glioma tissues and cell lines. Knockdown of RPL34 markedly inhibited the proliferation, migration, and invasion, as well as prevented the epithelial-mesenchymal transition phenotype in glioma cells. Further, mechanistic analysis showed that knockdown of RPL34 significantly downregulated the levels of p-JAK and p-STAT3 in glioma cells. Taken together, our findings indicated that knockdown of RPL34 inhibits the proliferation and migration of glioma cells through the inactivation of JAK/STAT3 signaling pathway. Thus, RPL34 may serve as a potential therapeutic target for the treatment of glioma.