Paenibacillus brassicae sp. nov., isolated from cabbage rhizosphere in Beijing, China

A novel Gram-positive, rod-shaped, motile, spore-forming, nitrogen-fixing bacterium, designated strain 112^T, was isolated from cabbage rhizosphere in Beijing, China. The strain was found to grow at 10–40 °C and pH 4–11, with an optimum of 30 °C and pH 7.0, respectively. Phylogenetic analysis based on a fragment of the full-length 16S rRNA gene sequence revealed that strain 112^T is a member of the genus Paenibacillus. High levels of 16S rRNA gene similarities were found between strain 112^T, Paenibacillus sabinae DSM 17841^T (97.82 %) and Paenibacillus forsythiae DSM 17842^T (97.22 %). However, the DNA–DNA hybridization values between strain 112^T and the type strains of these two species were 10.36 and 6.28 %, respectively. The predominant menaquinone was found to be menaquinone 7 (MK-7). The major fatty acids were determined to be anteiso-C_15:0 and C_16:0. The major polar lipids were found to be diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and unknown aminophospholipids. The cell wall peptidoglycan was found to contain meso-diaminopimelic acid. The DNA G+C content was determined to be 55.4 mol%. On the basis of its phenotypic characteristics, 16S rRNA gene sequence analysis and the value of DNA–DNA hybridization, strain 112^T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus brassicae sp. nov. is proposed. The type strain is 112^T (= ACCC 01125^T = DSM 24983^T).     

The mechanical stability of ubiquitin is linkage dependent

Ubiquitin chains are formed through the action of a set of enzymes that covalently link ubiquitin either through peptide bonds or through isopeptide bonds between their C terminus and any of four lysine residues. These naturally occurring polyproteins allow one to study the mechanical stability of a protein, when force is applied through different linkages. Here we used single-molecule force spectroscopy techniques to examine the mechanical stability of N-C-linked and Lys48-C-linked ubiquitin chains. We combined these experiments with steered molecular dynamics (SMD) simulations and found that the mechanical stability and unfolding pathway of ubiquitin strongly depend on the linkage through which the mechanical force is applied to the protein. Hence, a protein that is otherwise very stable may be easily unfolded by a relatively weak mechanical force applied through the right linkage. This may be a widespread mechanism in biological systems.     

低温处理对侧耳属栽培菌株菌丝体酯酶同工酶谱的影响

应用垂直板聚丙烯酰胺凝胶电泳对不同低温、不同缓化方式处理后的侧耳属(Pleurotus)不同栽培种12个菌株进行酯酶(EST)同工酶谱分析。结果表明:不同菌株对低温的耐受能力不同,缓化方式对于酯酶基因表达的影响不同,但低温并没有使其酯酶酶活力完全丧失。     

云南省6个松墨天牛种群形态差异分析

对云南省松墨天牛Monochamus alternatus Hope 6个地理种群159个个体体长、前胸背板纵长、前胸背板横宽值及前胸背板斑纹进行了差异系数计算、聚类分析及判别分析.各松墨天牛种群间的差异系数均小于1.28;聚类分析表明,畹町种群形态与其他5个种群差异较大;基于4个形态特征建立的判别函数可以将畹町种群与云南其他种群区别开来.畹町种群与其他松墨天牛种群的形态差异可能由于其遗传差异造成.     

Towards precise classification of cancers based on robust gene functional expression profiles

Background

Despite the continuous production of genome sequence for a number of organisms, reliable, comprehensive, and cost effective gene prediction remains problematic. This is particularly true for genomes for which there is not a large collection of known gene sequences, such as the recently published chicken genome. We used the chicken sequence to test comparative and homology-based gene-finding methods followed by experimental validation as an effective genome annotation method.

Results

We performed experimental evaluation by RT-PCR of three different computational gene finders, Ensembl, SGP2 and TWINSCAN, applied to the chicken genome. A Venn diagram was computed and each component of it was evaluated. The results showed that de novo comparative methods can identify up to about 700 chicken genes with no previous evidence of expression, and can correctly extend about 40% of homology-based predictions at the 5' end.

Conclusions

De novo comparative gene prediction followed by experimental verification is effective at enhancing the annotation of the newly sequenced genomes provided by standard homology-based methods.     

IPBES的建立、前景及应对策略

生物多样性和生态系统服务政府间科学-政策平台(IPBES)是一个类似于气候变化专门委员会(IPCC)的独立的政府间机构,其目标是建立科学界和决策者之间的沟通平台,推动全球生物多样性和生态系统服务的保护.从2008年11月到2010年6月,联合国环境规划署(UNEP)主持召开了三次政府间谈判会议.在最后一次会议上各国同意建立IPBES,并形成了一份《釜山成果》文件,确定其基本职能主要是开展评估,还确定IPBES的决策机构是全体会议,向联合国所有会员国和区域经济一体化组织开放,政府间组织和其他利益相关方可作为观察员.IPBES的建立将会在国际社会产生深刻的影响,但其未来走向也有一定的不确定性:一是如何保持科学独立性的问题,二是评估尺度可能会影响其成功,三是能否促进发展中国家的广泛参与.为使我国能在IPBES中发挥重要作用,建议今后应加强对IPBES运作模式的研究,加强评估工具和方法的开发以及加强生物多样性的监测.     

邮票中的蘑菇属种类及其分布

截至2010年,通过对全世界范围蘑菇邮票的收集和统计得知,世界上76个国家和地区共发行了蘑菇属24个种计126枚邮票,从中大致了解世界范围上蘑菇属真菌的资源分布和栽培状况。     

Sarcocystis cruzi: comparative studies confirm natural infections of buffaloes

Controversy exists concerning whether cattle and water buffalo sustain infections with cysts of distinct arrays of species in the genus Sarcocystis. In particular, morphologically similar parasites have been alternately ascribed to Sarcocystis cruzi or to Sarcocystis levinei, depending on their occurrence in cattle or water buffalo. We used light and transmission electron microscopy, genetic analysis, and experimental infections of definitive canine hosts to determine whether consistent differences could be identified from parasites derived from several natural infections of each host, examining several tissue types (esophagus, skeletal muscles, and heart). Cysts derived from cattle and water buffalo shared similar structure; variation among 18S rRNA sequences did not segregate consistently according to intermediate host type; parasites derived from cattle and water buffalo induced similar outcomes in the canine definitive host. One cattle specimen harbored unusually large (macroscopic) sarcocysts which nonetheless conformed to previously reported ultrastructural and genetic features of S. cruzi. Finding no consistent basis to differentiate between them, we conclude that the parasites infecting each host and tissue type correspond to S. cruzi. In our sample, no phylogenetically distinct taxon was sampled which might correspond to a distinct taxon previously described as S. levinei. Either that taxon was missed by our sampling effort, or it may represent a junior synonym to S. cruzi, which would then cycle between dogs and a broader range of intermediate bovine hosts than was previously considered.     

细柱五加茎中6种化合物体外对人肺癌细胞株A549的生长抑制作用

目的:观察细柱五加茎中6个化合物对人肺癌细胞株A549的抑制作用.方法:从细柱五加茎中提取得到16-α-羟-19-贝壳杉烷酸、16αH,17 - isovaleryloxy - ent - kauran - 19 - oic acid、贝壳杉烷酸苷A、紫丁香苷、松柏苷、刺五加苷D等6个化合物,采用MTT法测定其对人肺癌细胞株A549的生长抑制.结果:发现化合物16-α-羟-19 -贝壳杉烷酸、16αH,17 - isovaleryloxy - ent - kauran - 19 - oic acid、贝壳杉烷酸苷A、紫丁香苷、松柏苷对人肺癌A549细胞均具有不同程度的抑制作用,与空白对照相比具有显著性差异(P＜0.05).刺五加苷D对人肺癌A549细胞的增殖抑制率与其浓度成负相关,随着浓度的增加细胞生长抑制率不断降低.结论:6个化合物呈现不同的体外抗肿瘤作用,为细柱五加茎中的抗肿瘤活性成分.     

NELIN, a new F-actin associated protein, stimulates HeLa cell migration and adhesion

A new gene (GenBank Accession No. AF114264) was cloned from umbilical vein wall tissue by using RT-PCR. The gene shares high similarity to the gene encoding F-actin binding protein nexilin, so named as NELIN. A clone of 2737bp contains open reading frame of 1344bp extending from 412 to 1755. NELIN was expressed primarily in the heart and skeletal muscle among eight tested normal tissues. Immunofluorescence and immunoprecipitation demonstrated that NELIN product was associated with F-actin. Stable transfection of NELIN into HeLa cells increased the cell migration by 2.17-fold and the adhesion by 1.67-fold, respectively, compared to cells with the empty vector (P<0.05). The results support that NELIN product is an F-actin associated protein and mediates cell motility.