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.     

Photomutagenicity of 16 polycyclic aromatic hydrocarbons from the US EPA priority pollutant list

The photomutagenicity of 16 polycyclic aromatic hydrocarbons (PAHs), all on the United States Environmental Protection Agency (US EPA) priority pollutant list, was studied. Concomitant exposing the Salmonella typhimurium bacteria strain TA102 to one of the PAHs and light (1.1 J/cm2 UVA+2.1 J/cm2 visible) without the activation enzyme S9, strong photomutagenic response is observed for anthracene, benz[a]anthracene, benzo[ghi]perylene, benzo[a]pyrene, indeno[1,2,3-cd]pyrene, and pyrene. Under the same conditions, acenaphthene, acenaphthylene, benzo[k]fluoranthene, chrysene, and fluorene are weakly photomutagenic. Benzo[b]fluoranthene, fluoranthene, naphthalene, phenanthrene, and dibenz[a,h]anthracene are not photomutagenic. These results indicate that PAHs can be activated by light and become mutagenic in Salmonella TA102 bacteria. At the same time, the mutagenicity for all the 16 PAHs was examined with the standard mutagenicity test with 10% S9 as the activation system. Benzo[b]fluoranthene, benzo[k]fluoranthene, chrysene, acenaphthylene, and fluorene are weakly mutagenic, while the rest of the PAHs are not. In general, the photomutagenicity of PAHs in TA102 does not correlate with their S9-activated mutagenicity in either TA102 or TA98/TA100 since they involve different activation mechanisms.     

EXAFS study on arsenic species and transformation in arsenic hyperaccumulator

Synchrotron radiation extended X-ray absorption fine structure (SR EXAFS) was employed to study the transformation of coordination environment and the redox speciation of arsenic in a newly discovered arsenic hyperaccumulator, Cretan brake (Pteris cretica L. var nervosa Thunb). It showed that the arsenic in the plant mainly coordinated with oxygen, except that some arsenic coordinated with S as As-GSH in root. The complexation of arsenic with GSH might not be the predominant detoxification mechanism in Cretan brake. Although some arsenic in root presented as As(V) in Na₂HAsO₄ treatments, most of arsenic in plant presented as As(III)-O in both treatments, indicating that As(V) tended to be reduced to As(III) after it was taken up into the root, and arsenic was kept as As(III) when it was transported to the above-ground tissues. The reduction of As(V) primarily proceeded in the root.     

内蒙古中东部草原大针茅的种群遗传分化

对内蒙古中东部草原区分布的 11个大针茅 (Stipa grandis P. Smirn)地理种群进行了 RAPD分析。从 10 0个随机引物中筛选出 18个有效引物 ,共扩增出 2 2 1条 DNA带 ,多态性 DNA带 12 1条 ,占 5 4 .75 % ,平均每个引物扩增的 DNA带数为 12 .2 8条 ;特异性 DNA带 2 5条 ,占 11.31%。基于 Jaccard遗传相似性系数对此 2 2 1条 DNA带进行 U PGMA聚类分析 ,将 11个种群分为 3类 ,白音锡勒牧场的 8个种群聚为一类 ,林西种群和克什克腾种群两个种群聚为一类 ,阿巴嘎种群单独成为第 3类。用Mantel检验作进一步分析表明 ,在相对较大的尺度上 ,大针茅的遗传分化与地理距离相关极显著 (g>g0 .0 0 5) ;而在相对较小的尺度上 (白音锡勒牧场 8个种群 ) ,相关不显著 (gg0 .0 5)。     

Attenuation of vaccinia Tian Tan strain by removal of viral TC7L-TK2L and TA35R genes

Vaccinia Tian Tan (VTT) was attenuated by deletion of the TC7L-TK2L and TA35R genes to generate MVTT3. The mutant was generated by replacing the open reading frames by a gene encoding enhanced green fluorescent protein (EGFP) flanked by loxP sites. Viruses expressing EGFP were then screened for and purified by serial plaque formation. In a second step the marker EGFP gene was removed by transfecting cells with a plasmid encoding cre recombinase and selecting for viruses that had lost the EGFP phenotype. The MVTT3 mutant was shown to be avirulent and immunogenic. These results support the conclusion that TC7L-TK2L and TA35R deletion mutants can be used as safe viral vectors or as platform for vaccines.     

鹿衔草化学成分的研究：羟基肾叶鹿蹄草甙的结构鉴定

从鹿衔草（Ｐｙｒｏｌａ ｃａｌｌｉａｎｔｈａ Ｈ．Ａｎｄｒｅｓ）分离得到两个化合物。经光谱分析,确定其中１个化合物为新化合物,命名为羟基肾叶鹿蹄草甙（１, ｈｙｄｒｏｘｙｌｒｅｎｉｆｏｌｉｎ）,另一化合物为儿茶素（３）。     

NaCl、Na_2SO_4和Na_2CO_3胁迫对小麦叶片自由基含量及质膜透性的比较研究

分别用浓度为２５ｍｍｏｌ／Ｌ、５０ｍｍｏｌ／Ｌ、１００ｍｍｏｌ／Ｌ和２００ｍｍｏｌ／Ｌ的ＮａＣｌ、Ｎａ２ＳＯ４和Ｎａ２ＣＯ３的营养液培养小麦４ｄ,较之不含盐的营养液,其自由基含量上升,产生速率增加,叶片质膜透性增加。不同盐的影响也不同,在低浓度时,ＮａＣｌ的影响大于Ｎａ２ＳＯ４,高浓度时,ＮａＣｌ影响小于Ｎａ２ＳＯ４,Ｎａ２ＣＯ３的影响最为显著。实验结果也表现出小麦叶片自由基含量和质膜透性呈现较好的相关性。因此可认为,盐胁迫促使自由基含量增加,自由基通过过氧化作用影响质膜透性,从而影响植物的生长。     

小鼠雌性生殖系统电穿孔与微泡增强超声波转EG即基因的研究（简报）

非病毒载体转基因法。如注射裸DNA或脂质体转染,不产生细胞毒性。但除了肌肉组织外其他组织的转导效率均不高。电脉冲可使细胞膜产生临时的微孔允许一些分子通过。因此应用此方法可将药物或基因转人动物组织。电穿孔常用于培养的细胞转基因,理论上,低强度、长脉冲。或高强度、短脉冲有利于电转导。选择适合的参数是电转导的关键。本实验比较了不同电压和脉冲时间对小鼠卵巢在体转入绿色荧光蛋白基因的效果．确定了最适的电转导参数。为卵巢疾病的药物、基因治疗和研究卵泡发育中的基因调控提供了实验手段。     

绿僵菌大孢变种的生物学特征及其对蛴螬的毒力研究

以报道较多的蛴螬病原真菌 布氏白僵菌、绿僵菌小孢变种作参照菌,系统研究了新分离鉴定的绿僵菌大孢变种的生物学特性,测定了其在偏低的自然气温下对蛴螬的致病能力.结果表明,绿僵菌大孢变种与参照菌的培养要求接近,最适宜的温度为25 ℃.3种供试的培养基中,PPDA为最适宜的培养基,其次为SDAY.在偏低的温度环境下绿僵菌大孢变种对蛴螬的毒杀能力强于布氏白僵菌,土壤和喷雾处理后累计僵虫率分别达88.23%和76.47%,有很好的田间应用前景.     

Molecular Cloning and Characterization of a Cytokinin Dehydrogenase Gene from Upland Cotton (Gossypium hirsutum L.)

Cytokinins are plant hormones that play crucial roles in plant growth and development. Cytokinin dehydrogenase (CKX), regarded as a main negative regulator in cytokinin metabolism in plants, irreversibly degrades cytokinins into adenine/adenosine moiety. A CKX homologous gene, designated GhCKX, was cloned from upland cotton (Gossypium hirsutum L.). Transgenic tobacco plants over-expressing GhCKX showed a typical cytokinin-deficient phenotype, while CKX-silenced tobacco plants exhibited cytokinin over-producing phenotype. Tissue specifically enhancing the expression of GhCKX in the ovule epidermis of transgenic cotton led to a significant decrease of trans-zeatin and trans-zeatin riboside contents in the ovule. The decline of cytokinins resulted in a significant decrease in fiber initials on a single ovule. Our results indicate that GhCKX encodes a functional CKX, and cytokinins may be required for the initiation of cotton fiber cells.