基于转录终点序列特征预测大肠杆菌sRNA

细菌sRNA是一类长度在40～500nt的调控RNA,在细菌与环境相互作用中发挥重要功能,因此,细菌sRNA识别研究具有重要意义。然而,与蛋白编码基因具有易于识别的特征不同,目前细菌sRNA识别仍是一件比较困难的事。此方法介绍了一个基于已知细菌sRNA转录终点的碱基频率矩阵来识别sRNA的预测策略,并在大肠杆菌K-12 MG1655中进行了sRNA的预测。结果表明,该模型在独立测试集中具有较高的特异性和阳性检出率,因此,这一方法将为实验发现细菌sRNA提供较好的生物信息学支持。     

Identification and analysis of the gene cluster involved in biosynthesis of paenibactin, a catecholate siderophore produced by Paenibacillus elgii B69

Bacteria belonging to the genus Paenibacillus are recognized as rich sources of bioactive natural products. To date, there are few characterized siderophores from this genus. Here, through genome analysis, we identified a non-ribosomal peptide biosynthetic gene cluster (pae) responsible for siderophore assembly in Paenibacillus elgii B69. The 12.8 kb gene cluster comprises six open reading frames encoding proteins similar to the components of the bacillibactin biosynthetic machinery and bacillibactin esterase. To examine the product of the pae gene cluster, we cultured P. elgii B69 in iron-deficient medium for siderophore expression. A novel siderophore structurally similar to bacillibactin, designated paenibactin, was purified and characterized. Its structure was determined as a cyclic trimeric lactone of 2,3-dihydroxybenzoyl-alanine-threonine. The involvement of the pae gene cluster in paenibactin biosynthesis was confirmed by the biochemical assay of adenylation domain specificity. Furthermore, we demonstrated that the pae gene cluster evolves from an ancestral bacillibactin biosynthetic gene cluster via sequence and phylogenetic analyses. The structural difference between paenibactin and bacillibactin may stem from a mutation-induced change in the adenylation domain specificity. Based on these findings and published models for bacillibactin, we proposed models for paenibactin biosynthesis, ferric-paenibactin uptake and paenibactin-bounded iron release.     

Optimum induction of recombinant thymidine phosphorylase and its application

Recombinant E. coli pDEOA was constructed and lactose can be used instead of IPTG to induce the expression of thymidine phosphorylase by pDEOA. The use of lactose at concentrations higher than 0.5 mmol/L had an induction effect similar to that of IPTG but resulted in a longer initial induction time and better cell growth. The thymidine phosphorylase induced by lactose was very stable at 50°C. Intact pDEOA cells induced by lactose can be used as a source of thymidine phosphorylase. Under standard reaction conditions, several deoxynucleosides were effectively produced from thymidine.     

IFN-α/β and autophagy: tug-of-war between HCV and the host

Hepatitis C virus (HCV) infects approximately 130 million people worldwide. The clinical sequelae of this chronic disease include cirrhosis, functional failure and carcinoma of the liver. HCV induces autophagy, a fundamental cellular process for maintaining homeostasis and mediating innate immune response, and also inhibits autophagic protein degradation and suppresses antiviral immunity. In addition to this ploy, the HCV serine protease composed of the viral non-structural proteins 3/4A (NS3/4A) can enzymatically digest two cellular proteins, mitochondria-associated anti-viral signaling protein (MAVS) and Toll/interleukin-1 receptor domain containing adaptor inducing IFN-β (TRIF). Since these two proteins are the adaptor molecules in the retinoic acid-inducible gene I (RIG-I) and TLR3 pathways, respectively, their cleavage has been suggested as a pivotal mechanism by which HCV blunts the IFN-α/β signaling and antiviral responses. Thus far, how HCV perturbs autophagy and copes with IFN-α/β in the liver remains unclear.     

IL-1 polymorphisms in children with peptic symptoms in South China

Background: Polymorphisms of IL‐1 gene cluster are reported to be associated with histological changes and IL‐1β expression in the gastric mucosa in adults, especially in Helicobacter pylori–infected subjects. As H. pylori infecting adults and children own different virulence genotypes, the aim of this study was to investigate whether IL‐1 polymorphisms are risk factors in young children in South China. Materials and Methods: A total of 128 children with peptic symptoms were enrolled in this study. Polymorphisms of IL‐1B‐511 and IL‐1B‐31 were identified by dual fluorescence PCR. Variable number of tandem repeat region in IL‐1RN was detected by conventional PCR and IL‐1β mRNA expression by real‐time PCR ddCT assay. Results: IL‐1B‐31T and IL‐1B‐511C were completely linked in this study. Significant differences of IL‐1B‐511/‐31 genotypes were observed among different clinical outcomes (p = .001). The IL‐1B‐511TT/‐31CC was mostly found in the moderate gastritis and the above (severe gastritis or gastric ulcer) groups, with percentage of 60.7%. While no association was observed between IL‐1RN genotypes and the gastric mucosal histological changes (p = .128). Also no relationships were found between IL‐1 polymorphisms and H. pylori infection or gastric mucosal IL‐1β mRNA expression level. Conclusion: Children with IL‐1B‐511TT/‐31CC may have a risk to develop relatively severe gastric mucosal histological changes in South China.     

Continuous preparation of (S)-3-hydroxy-3-phenylpropionate by asymmetric reduction of 3-oxo-3-phenylpropionic acid ethyl ester with <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis> CGMCC No.2266 in a membrane reactor

In this study, (S)-3-hydroxy-3-phenylpropionate was prepared continuously by coupling microbial transformation and membrane separation. The effect of several factors on membrane flux, reactor capacity, and reaction conversion were investigated. A kinetic model of the continuous reduction process was also developed. The appropriate molecular weight cut-off of the ultrafiltration membrane was 30 kDa. The reactor capacity reached a maximum of 0.136/h at a biomass concentration and membrane flux of 86 g/L (dry weight/reaction volume) and 20 mL/h, respectively. The (S)-3-hydroxy-3-phenylpropionate yield was 3.68 mmol/L/day after continuous reduction over seven days. The enantiometric excess of (S)-3-hydroxy-3-phenylpropionate reached above 99.5%. The kinetic constants of continuous reduction were as follows: r _m = 3.00 × 10⁻³ mol/L/h, k _cat = 3.49 × 10⁻⁴ mol/L/h, k ₁ = 3.09 × 10⁻² mol/L, and k ₂ = 5.00 × 10⁻⁷ mol/L. The kinetic model was in good agreement with the experimental data obtained during continuous reduction. Compared with batch reduction, continuous reduction can significantly improve the catalytic efficiency of microbial cells and increase the reactor capacity.     

Applicability of the fluorescein diacetate assay for metabolic activity measurement of Microcystis aeruginosa (Chroococcales,Cyanobacteria)

The fluorescein diacetate (FDA) assay has been widely used to measure metabolic activity in phytoplankton. It was found that FDA fluorescence values did not decrease in some stressed cells, demonstrating that the applicability of the method needs to be assessed further in the context of growth‐influencing conditions. In the present study, changes of FDA fluorescence values were studied in bloom‐forming cyanobacterial Microcystis aeruginosa Kütz cells under stress conditions such as nitrogen (N) or phosphorus (P) deficiency, or darkness and low temperature (10°C), respectively. The results demonstrated that esterase activity decreased immediately in dark‐stressed cells, which correlated with the decline of biomass and photosynthetic activity. Under the other three stress conditions, however, especially at low temperature, the cells lost photosynthetic activity but had the highest esterase activity, which was five times higher than the control group. These findings contrast with the assay criteria that the expression of a stain should reflect the change of photosynthetic activity and that stressed cells should have a lower staining intensity than the control cells. According to these results, the esterase activity response was dependent on environmental factors. Furthermore, higher fluorescence intensity did not mean higher metabolic activity, but a discrepant value indicated a severe stress.     

Mixed Magnetism for Refrigeration and Energy Conversion

The efficient coupling between lattice degrees of freedom and spin degrees of freedom in magnetic materials can be used for refrigeration and energy conversion. This coupling is enhanced in materials exhibiting the giant magnetocaloric effect. First principle electronic structure calculations on hexagonal MnFe(P, Si) reveal a new form of magnetism: the coexistence of strong and weak magnetism in alternate atomic layers. The weak magnetism of Fe layers (disappearance of local magnetic moments at the Curie temperature) is responsible for a strong coupling with the crystal lattice while the strong magnetism in adjacent Mn‐layers ensures Curie temperatures high enough to enable operation at and above room temperature. Varying the composition on these magnetic sublattices gives a handle to tune the working temperature and to achieve a strong reduction of the undesired thermal hysteresis. In this way we design novel materials based on abundantly available elements with properties matched to the requirements of an efficient refrigeration or energy‐conversion cycle.