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 NFP locus of Medicago truncatula controls an early step of Nod factor signal transduction upstream of a rapid calcium flux and root hair deformation

Establishment of the Rhizobium-legume symbiosis depends on a molecular dialogue, in which rhizobial nodulation (Nod) factors act as symbiotic signals, playing a key role in the control of specificity of infection and nodule formation. Using nodulation-defective (Nod-) mutants of Medicago truncatula to study the mechanisms controlling Nod factor perception and signalling, we have previously identified five genes that control components of a Nod factor-activated signal transduction pathway. Characterisation of a new M. truncatula Nod- mutant led to the identification of the Nod Factor Perception (NFP) locus. The nfp mutant has a novel phenotype among Nod- mutants of M. truncatula, as it does not respond to Nod factors by any of the responses tested. The nfp mutant thus shows no rapid calcium flux, the earliest detectable Nod factor response of wild-type plants, and no root hair deformation. The nfp mutant is also deficient in Nod factor-induced calcium spiking and early nodulin gene expression. While certain genes controlling Nod factor signal transduction also control the establishment of an arbuscular mycorrhizal symbiosis, the nfp mutant shows a wild-type mycorrhizal phenotype. These data indicate that the NFP locus controls an early step of Nod factor signal transduction, upstream of previously identified genes and specific to nodulation.     

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.     

花鲈微卫星标记分离及其多态性分析

该文利用FIASCO法(fast isolation by AFLP of sequences containing repeats)和GenBank数据库搜索法开发花鲈微卫星标记,并对筛选的标记进行多态性检测.两种方法共获得54条能够设计引物的序列,扩增结果显示15对引物具有多态性,多态性微卫星位点的等位基因数为2～10个.15个多态性位点中,4个位点偏离了Hardy-Weinberg平衡;各位点间没有连锁不平衡现象;仅位点SP52可能存在无效等位基因;除SP17和SP468外,其余引物的P1C值均在0.5以上,可用于花鲈群体遗传分析等研究.     

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。