An Atlas of Soybean Small RNAs Identifies Phased siRNAs from Hundreds of Coding Genes

Small RNAs are ubiquitous, versatile repressors and include (1) microRNAs (miRNAs), processed from mRNA forming stem-loops; and (2) small interfering RNAs (siRNAs), the latter derived in plants by a process typically requiring an RNA-dependent RNA polymerase. We constructed and analyzed an expression atlas of soybean (Glycine max) small RNAs, identifying over 500 loci generating 21-nucleotide phased siRNAs (phasiRNAs; from PHAS loci), of which 483 overlapped annotated protein-coding genes. Via the integration of miRNAs with parallel analysis of RNA end (PARE) data, 20 miRNA triggers of 127 PHAS loci were detected. The primary class of PHAS loci (208 or 41% of the total) corresponded to NB-LRR genes; some of these small RNAs preferentially accumulate in nodules. Among the PHAS loci, novel representatives of TAS3 and noncanonical phasing patterns were also observed. A noncoding PHAS locus, triggered by miR4392, accumulated preferentially in anthers; the phasiRNAs are predicted to target transposable elements, with their peak abundance during soybean reproductive development. Thus, phasiRNAs show tremendous diversity in dicots. We identified novel miRNAs and assessed the veracity of soybean miRNAs registered in miRBase, substantially improving the soybean miRNA annotation, facilitating an improvement of miRBase annotations and identifying at high stringency novel miRNAs and their targets.     

MiR-124 retards bladder cancer growth by directly targeting CDK4

MicroRNAs （miRNAs） are a class of non-coding small RNAs that act as negative regulators of gene expression by binding to the 31-untranslated region （3＇UTR） of target mRNAs. In order to investigate the physiological role of miR-124 in bladder cancer, target genes of miR-124 were predicted by the TargetScan software, and cyclin-depend- ent kinase （CDK4）, which has been implicated as a regula- tor of cell cycle, was chosen for further study. MiR-124 could significantly repress CDK4 expression by targeting its binding site in the 31UTR of CDK4 in vitro. In both bladder cancer cell lines and tissues, the expression of miR- 124 was significantly down-regulated, while CDK4 expres- sion was up-regulated. Ectopic expression of miR-124 in transplanted HTl197 cells resulted in the retardation of tumor growth in mouse tumor xenografts. And the expres- sion of miR-124 and CDK4 showed an obvious inverse cor- relation in these xenograft tissues, which was also observed in human bladder cancer tissue samples. Taken together, our results strongly suggest that miR-124 can arrest cell cycle and restrain the growth of bladder cancer by targeting CDK4 directly.     

Shared and distinct functions of two Gti1/Pac2 family proteins in growth,morphogenesis and pathogenicity of Magnaporthe oryzae

Gti1/Pac2 are conserved family proteins that regulate morphogenic transition in yeasts such as Schizosaccharomyces pombe and Candida albicans, and they also control toxin production and pathogenicity in filamentous fungus Fusarium graminearum. To test the functions of Gti1/Pac2 paralogues MoGti1 and MoPac2 in the rice blast fungus Magnaporthe oryzae, we generated respective ΔMogti1 and ΔMopac2 mutant strains. We found that MoGti1 and MoPac2 exhibit shared and distinct roles in hyphal growth, conidiation, sexual reproduction, stress responses, surface hydrophobility, invasive hyphal growth and pathogenicity. Consistent with the putative conserved function of MoGti1, we showed that MoGti1‐GFP is localized to the nucleus, whereas MoPac2‐GFP is mainly found in the cytoplasm. In addition, we provided evidence that the nuclear localization of MoGti1 could be subject to regulation by MoPmk1 mitogen‐activated protein kinase. Moreover, we found that the reduced pathogenicity in the ΔMopac2 mutant corresponds with an increased expression of plant defence genes, including PR1a, AOS2, LOX1, PAD4, and CHT1. Taken together, our studies provide a comprehensive analysis of two similar but distinct Gti1/Pac2 family proteins in M. oryzae, which underlines the important yet conserved functions of these family proteins in plant pathogenic fungi.     

An ionic liquid as reaction media for radiation-induced grafting of thermosensitive poly (N-isopropylacrylamide) onto microcrystalline cellulose

This paper reports a homogeneous modification of microcrystalline cellulose (MCC) in ionic liquids via radiation-induced grafting. Thermosensitive poly (N-isopropylacrylamide) (PNIPAAm) was successfully grafted onto MCC in 1-butyl-3-methylimidazolium chloride ([Bmim]Cl) ionic liquid using γ-ray irradiation technique at room temperature. The grafting yield (GY) increased with dose up to 40 kGy, while decreased slightly with dose rate from 22 to 102 Gy/min. The results of TGA indicated that cellulose grafted PNIPAAm (cellulose-g-PNIPAAm) had higher thermal stability than that of ungrafted regenerated cellulose (reg-cellulose). The crystalline structure of original MCC was largely destroyed during the dissolution process according to the XRD profiles, and grafting PNIPAAm onto cellulose further decreased the intensity of crystallinity. SEM showed that reg-cellulose and cellulose-g-PNIPAAm films displayed dense and homogeneous morphology. Moreover, the resulting cellulose-g-PNIPAAm exhibited obvious thermal sensitivity with a lower critical solution temperature around 35 °C, which was observed from the swelling behavior in water at different temperatures.     

Functional analysis of the plasmid pM4 replicon from Lactobacillus plantarum M4: Determination of the minimal replicon and functionality identification of the putative sso

In order to determine the minimal replicon and the single strand origin (sso) of the plasmid pM4, different fragments of pM4 were amplified by polymerase chain reaction (PCR) and cloned into pBEm, a replication probe vector for Lactobacillus. The deletion analysis results showed that the minimal replicon of pM4 could be determined within a 1280 bp fragment consisting of double strand origin (dso) and rep gene encoding replication protein. Based on plasmid segregation stability assay and its ability to convert single-stranded DNA (ssDNA) to double-stranded DNA (dsDNA) by Southern hybridization, an sso of replication was located at nucleotides −118–92 in the plasmid pM4, about 300 bp upstream of dso. In addition, the host range assay indicated that plasmid pM4 could replicate in L. casei 05–21, L. rhamnosus AS 1.2466^T and L. plantarum 05–19 of all the tested Lactobacillus strains. Analysis of the pM4 replicon will allow its use in constructing a food-grade vector for application in food industry.     

Inhalation of environmental stressors & chronic inflammation: autoimmunity and neurodegeneration

Human life expectancy and welfare has decreased because of the increase in environmental stressors in the air. An environmental stressor is a natural or human-made component present in our environment that upon reaching an organic system produces a coordinated response. This response usually involves a modification of the metabolism and physiology of the system. Inhaled environmental stressors damage the airways and lung parenchyma, producing irritation, recruitment of inflammatory cells, and oxidative modification of biomolecules. Oxidatively modified biomolecules, their degradation products, and adducts with other biomolecules can reach the systemic circulation, and when found in higher concentrations than normal they are considered to be biomarkers of systemic oxidative stress and inflammation. We classify them as metabolic stressors because they are not inert compounds; indeed, they amplify the inflammatory response by inducing inflammation in the lung and other organs. Thus the lung is not only the target for environmental stressors, but it is also the source of a number of metabolic stressors that can induce and worsen pre-existing chronic inflammation. Metabolic stressors produced in the lung have a number of effects in tissues other than the lung, such as the brain, and they can also abrogate the mechanisms of immunotolerance. In this review, we discuss recent published evidence that suggests that inflammation in the lung is an important connection between air pollution and chronic inflammatory diseases such as autoimmunity and neurodegeneration, and we highlight the critical role of metabolic stressors produced in the lung. The understanding of this relationship between inhaled environmental pollutants and systemic inflammation will help us to: (1) understand the molecular mechanism of environment-associated diseases, and (2) find new biomarkers that will help us prevent the exposure of susceptible individuals and/or design novel therapies.     

番茄Lehsp23.8启动子的热诱导表达调控序列鉴定

番茄线粒体小分子热激蛋白(Lehsp23.8)启动子是典型的热诱导启动子。为了研究热激条件下该启动子的调控序列,本研究将不同长度的Lehsp23.8启动子序列与gus基因融合,构建5′缺失植物表达载体。然后用农杆菌介导法转化烟草,PCR及Southern blotting结果表明融合基因已经整合到烟草基因组中。GUS组织化学染色结果表明:不同长度Lehsp23.8启动子转基因植株热激处理后,在幼苗根、茎、叶以及花和果实中均表现出GUS活性,只是染色强弱有差异。叶片中GUS荧光活性测定结果表明:在热激处理条件下,565bp的Lehsp23.8启动子介导的GUS表达最强;而255bp的Lehsp23.8启动子介导的GUS表达最弱。说明Lehsp23.8启动子中255bp的序列即能满足该启动子的热激表达,-565bp～-255bp之间存在明显的增强子元件,而-871bp～-565bp之间的片段具有一定的抑制作用。     

Rapid decolourization of azo dyes by a new isolated higher manganese peroxidase producer: Phanerochaete sp. HSD

In the present paper, a strain of higher MnP producer, Phanerochaete sp. HSD, was screened and the important medium components influencing MnP production were optimized using fractional factorial design and central composite experimental design; statistical analysis suggested diammonium tartrate and Mn²⁺ were the important factors and under the optimum conditions, MnP activity reached 2613 ± 22 U/l, accorded with the predicted value from response surface analysis. The feasibility of using this fungus to decolourize azo dyes was examined too. Results indicated that crude enzyme solution of it could decolourize three azo dyes efficiently and speedily: for 120 and 350 mg/l of Congo red, 95% decolourization rate was observed at the 5th and 8th hour; for 200, 350 and 600 mg/l methyl orange, 95% decolourization rate was obtained at the 5th, 6th and 9th hour; furthermore, the decolourization rates of 150 and 300 mg/l of Eriochrome black T were up to 97.1% and 91.4% at the 7th and 13th hour, respectively. In addition, MnP played a crucial role in the decolourization process.