CPU-GPU hybrid accelerating the Zuker algorithm for RNA secondary structure prediction applications

Background

Different Cupriavidus metallidurans strains isolated from metal-contaminated and other anthropogenic environments were genotypically and phenotypically compared with C. metallidurans type strain CH34. The latter is well-studied for its resistance to a wide range of metals, which is carried for a substantial part by its two megaplasmids pMOL28 and pMOL30.

Results

Comparative genomic hybridization (CGH) indicated that the extensive arsenal of determinants involved in metal resistance was well conserved among the different C. metallidurans strains. Contrary, the mobile genetic elements identified in type strain CH34 were not present in all strains but clearly showed a pattern, although, not directly related to a particular biotope nor location (geographical). One group of strains carried almost all mobile genetic elements, while these were much less abundant in the second group. This occurrence was also reflected in their ability to degrade toluene and grow autotrophically on hydrogen gas and carbon dioxide, which are two traits linked to separate genomic islands of the Tn4371-family. In addition, the clear pattern of genomic islands distribution allowed to identify new putative genomic islands on chromosome 1 and 2 of C. metallidurans CH34.

Conclusions

Metal resistance determinants are shared by all C. metallidurans strains and their occurrence is apparently irrespective of the strain's isolation type and place. Cupriavidus metallidurans strains do display substantial differences in the diversity and size of their mobile gene pool, which may be extensive in some (including the type strain) while marginal in others.     

Multiple end joining mechanisms repair a chromosomal DNA break in fission yeast

Non-homologous end joining (NHEJ) is an important mechanism for repairing DNA double-strand breaks (DSBs). The fission yeast Schizosaccharomyces pombe has a conserved set of NHEJ factors including Ku, DNA ligase IV, Xlf1, and Pol4. Their roles in chromosomal DSB repair have not been directly characterized before. Here we used HO endonuclease to create a specific chromosomal DSB in fission yeast and examined the imprecise end joining events allowing cells to survive the continuous expression of HO. Our analysis showed that cell survival was significantly reduced in mutants defective for Ku, ligase IV, or Xlf1. Using Sanger sequencing and Illumina sequencing, we have characterized in depth the repair junction sequences in HO survivors. In wild type cells the majority of repair events were one-nucleotide insertions dependent on Ku, ligase IV, and Pol4. Our data suggest that fission yeast Pol4 is important for gap filling during NHEJ repair and can extend primers in the absence of terminal base pairing with the templates. In Ku and ligase IV mutants, the survivors mainly resulted from two types of alternative end joining events: one used microhomology flanking the HO site to delete sequences of hundreds to thousands of base pairs, the other rejoined the break using the HO-generated overhangs but also introduced one- or two-nucleotide base substitutions. The chromosomal repair assay we describe here should provide a useful tool for further exploration of the end joining repair mechanisms in fission yeast.     

Mammalian PIK3C3/VPS34: the key to autophagic processing in liver and heart

PIK3C3/Vps34 is the class III PtdIns3K that is evolutionarily conserved from yeast to mammals. Its central role in mammalian autophagy has been suggested through the use of pharmacological inhibitors and the study of its binding partners. However, the precise role of PIK3C3 in mammals is not clear. Using mouse strains that allow tissue-specific deletion of PIK3C3, we have described an essential role of PIK3C3 in regulating autophagy, and liver and heart function.     

Synthesis, cytotoxic activities and cell cycle arrest profiles of half-sandwich N-sulfonamide based dithio-o-carborane metal complexes

Two half-sandwich cobalt and rhodium complexes 2a and 2b with combination of carborane and N-Sulfonamide were synthesized and fully characterized by NMR spectroscopy, mass spectrometry, elemental analysis as well as X-ray crystallography. In an in vitro cytotoxicity assay toward the non-small cell lung cancer cell lines of A549 and NCI-H460, 2b showed the stronger activity than 2a, which was confirmed by the morphological test. Mechanistic studies for 2b showed that inhibition of NSCLC cell growth was mediated by G0/G1 cell cycle arrested without the significant apoptosis induction. Furthermore, 2b altered the mRNA levels of CCND1, CCNE1 and PCNA, which were known to control G0/G1 phase of the cell cycle. Our western blot analysis also showed that 2b-induced G0/G1 cell cycle arrest was mediated through the decreased expression of cyclin D1, cyclin E1 and PCNA.     

K5裂解酶在大肠杆菌中的表达、纯化及酶学性质分析

K5多糖裂解酶(Elma)能够裂解半合成肝素的底物-K5多糖,裂解产物是半合成法生产低分子量肝素的底物。利用PCR方法扩增elma,构建表达载体pET-28a-Elma,将构建好的质粒转化至大肠杆菌BL21中,以0.2 mmol/L的IPTG在16℃诱导5 h实现了高效表达,SDS-PAGE分析表明Elma表达量可达菌体总蛋白的30%以上。采用Ni2+-NTA亲和层析法和G-75分子筛层析纯化目的蛋白,其纯度大于95%。通过PAGE多糖电泳发现裂解前后的K5多糖分子量有明显的减小。根据Elma裂解产物产生双键从而在232 nm处有吸光度的变化来测Elma的酶活。其最适反应温度为37℃,反应的最适pH值为7.0。底物特异性分析发现Elma除K5多糖外对肝素和透明质酸也有降解作用。     

人胰高糖素样肽-1及其突变体在大肠杆菌BL21中的表达与生物活性研究

以人胰高糖素样肽-1（human glucagons-like peptide-1,GLP-1））为研究对象,以克隆载体pPblu2SKP/（GLP-1A2G）2基因为模板,利用PCR扩增获得GLP-1与其突变体GLP-1A2G的编码基因,并将其插入原核表达质粒pGEX-4T-1中,利用氯化钙法将其转入表达宿主大肠杆菌（Escherichia coli）BL21（DE3）中诱导表达,经IPTG诱导后,收集菌体。菌体经超声破碎后,裂解液用GST亲和层析纯化得到融合蛋白,经凝血酶酶解,用Superdex G-75凝胶层析,得到GLP-1及其突变体GLP-1A2G的样品,经SDS-PAGE电泳测定,样品纯度〉90%。小鼠糖耐量试验表明,相对于空白对照组而言,GLP-1及其突变体GLP-1A2G可以明显地控制血糖的水平,两者的生物活性并无明显差异。由于突变体GLP-1A2G较GLP-1可以更加有效的抵制DPPⅣ的降解,提示突变体GLP-1A2G较GLP-1在白蛋白融合或PEG修饰等方面具有更大的优势。     

RXLR-mediated entry of Phytophthora sojae effector Avr1b into soybean cells does not require pathogen-encoded machinery

Effector proteins secreted by oomycete and fungal pathogens have been inferred to enter host cells, where they interact with host resistance gene products. Using the effector protein Avr1b of Phytophthora sojae, an oomycete pathogen of soybean (Glycine max), we show that a pair of sequence motifs, RXLR and dEER, plus surrounding sequences, are both necessary and sufficient to deliver the protein into plant cells. Particle bombardment experiments demonstrate that these motifs function in the absence of the pathogen, indicating that no additional pathogen-encoded machinery is required for effector protein entry into host cells. Furthermore, fusion of the Avr1b RXLR-dEER domain to green fluorescent protein (GFP) allows GFP to enter soybean root cells autonomously. The conclusion that RXLR and dEER serve to transduce oomycete effectors into host cells indicates that the >370 RXLR-dEER-containing proteins encoded in the genome sequence of P. sojae are candidate effectors. We further show that the RXLR and dEER motifs can be replaced by the closely related erythrocyte targeting signals found in effector proteins of Plasmodium, the protozoan that causes malaria in humans. Mutational analysis of the RXLR motif shows that the required residues are very similar in the motifs of Plasmodium and Phytophthora. Thus, the machinery of the hosts (soybean and human) targeted by the effectors may be very ancient.     

Effects of vanadium-containing compounds on membrane lipids and on microdomains used in receptor-mediated signaling

There is increasing evidence for the involvement of plasma membrane microdomains in insulin receptor function. Moreover, disruption of these structures, which are typically enriched in sphingomyelin and cholesterol, results in insulin resistance. Treatment strategies for insulin resistance include the use of vanadium (V) compounds which have been shown in animal models to enhance insulin responsiveness. One possible mechanism for insulin-enhancing effects might involve direct effects of V compounds on membrane lipid organization. These changes in lipid organization promote the partitioning of insulin receptors and other receptors into membrane microdomains where receptors are optimally functional. To explore this possibility, we have used several strategies involving V complexes such as [VO(2)(dipic)](-) (pyridin-2,6-dicarboxylatodioxovanadium(V)), decavanadate (V(10)O(28)(6-), V(10)), BMOV (bis(maltolato)oxovanadium(IV)), and [VO(saltris)](2) (2-salicylideniminato-2-(hydroxymethyl)-1,3-dihydroxypropane-oxovanadium(V)). Our strategies include an evaluation of interactions between V-containing compounds and model lipid systems, an evaluation of the effects of V compounds on lipid fluidity in erythrocyte membranes, and studies of the effects of V-containing compounds on signaling events initiated by receptors known to use membrane microdomains as signaling platforms.