Genome Comparison In Silico in Neisseria Suggests Integration of Filamentous Bacteriophages by their Own Transposase

We have identified filamentous prophages, Nf (Neisserial filamentousphages), during an in silico genome comparison in Neisseria.Comparison of three genomes of Neisseria meningitidis and oneof Neisseria gonorrhoeae revealed four subtypes of Nf. Elevenintact copies are located at different loci in the four genomes.Each intact copy of Nf is flanked by duplication of 5'-CT and,at its right end, carries a transposase homologue (pivNM/irg)of RNaseH/Retroviral integrase superfamily. The phylogeny ofthese putative transposases and that of phage-related proteinson Nfs are congruent. Following circularization of Nfs, a promoter-likesequence forms. The sequence at the junction of these predictedcircular forms (5'-atCTtatat) was found in a related plasmid(pMU1) at a corresponding locus. Several structural variantsof Nfs—partially inverted, internally deleted and truncated—werealso identified. The partial inversion seems to be a productof site-specific recombination between two 5'-CTtat sequencesthat are in inverse orientation, one at its end and the otherupstream of pivNM/irg. Formation of internally deleted variantsprobably proceeded through replicative transposition that alsoinvolved two 5'-CTtat sequences. We concluded that the PivNM/Irgtransposase on Nfs integrated their circular forms into thechromosomal 5'-CT-containing sequences and probably mediatedthe above rearrangements.     

茂原链霉菌谷氨酰胺转胺酶序列分析及三维结构建模

利用DNASTAR、VectorNTI9、SignalP等生物信息学平台对茂原链霉菌(Streptomyces mobaraensis)谷氨酰胺转胺酶(TGase)进行了序列分析和三维结构建模。结果表明:茂原链霉菌TGase同已报道其他微生物来源的TGase有较高的同源性,无信号肽,存在一个跨膜结构区,二级结构是由多个α螺旋、转角和少量β折叠构成。同时在一二级结构分析的基础上,利用同源建模的方法完成了三维结构的建模。     

A scenario-based approach to modeling development: a prototype model of C. elegans vulval fate specification

Studies of developmental biology are often facilitated by diagram “models” that summarize the current understanding of underlying mechanisms. The increasing complexity of our understanding of development necessitates computational models that can extend these representations to include their dynamic behavior. Here we present a prototype model of Caenorhabditis elegans vulval precursor cell fate specification that represents many processes crucial for this developmental event but that are hard to integrate using other modeling methodologies. We demonstrate the integrative capabilities of our methodology by comprehensively incorporating the contents of three seminal papers, showing that this methodology can lead to comprehensive models of developmental biology. The prototype computational model was built and is run using a language (Live Sequence Charts) and tool (the Play-Engine) that facilitate the same conceptual processes biologists use to construct and probe diagram-type models. We demonstrate that this modeling approach permits rigorous tests of mutual consistency between experimental data and mechanistic hypotheses and can identify specific conflicting results, providing a useful approach to probe developmental systems.     

Relevance of the N-terminal NLS-like sequence of the prion protein for membrane perturbation effects

We investigated the nuclear localization-like sequence KKRPKP, corresponding to the residues 23-28 in the mouse prion protein (mPrP), for its membrane perturbation activity, by comparing effects of two mPrP-derived peptides, corresponding to residues 1-28 (mPrPp(1-28)) and 23-50 (mPrPp(23-50)), respectively. In erythrocytes, mPrPp(1-28) induced ∼ 60% haemoglobin leakage after 30 min, whereas mPrPp(23-50) had negligible effects. In calcein-entrapping, large unilamellar vesicles (LUVs), similar results were obtained. Cytotoxicity estimated by lactate dehydrogenase leakage from HeLa cells, was found to be ∼ 12% for 50 μM mPrPp(1-28), and ∼ 1% for 50 μM mPrPp(23-50). Circular dichroism spectra showed structure induction of mPrPp(1-28) in the presence of POPC:POPG (4:1) and POPC LUVs, while mPrPp(23-50) remained a random coil. Membrane translocation studies on live HeLa cells showed mPrPp(1-28) co-localizing with dextran, suggesting fluid-phase endocytosis, whereas mPrPp(23-50) hardly translocated at all. We conclude that the KKRPKP-sequence is not sufficient to cause membrane perturbation or translocation but needs a hydrophobic counterpart.     

中美医学院病原生物学教学比较和借鉴

从课程设置、教学方法、教材建设和教学手段等方面对中国和美国高校病原生物学教学进行了比较和探讨。     

The genome of <Emphasis Type="Italic">Streptomyces rimosus</Emphasis> subsp. <Emphasis Type="Italic">rimosus</Emphasis> shows a novel structure compared to other <Emphasis Type="Italic">Streptomyces</Emphasis> using DNA/DNA microarray analysis

DNA/DNA genome microarray analysis together with genome sequencing suggests that the genome of members of the genus Streptomyces would seem to have a common structure including a linear genomic structure, a core of common syntenous Actinomycete genes, the presence of species specific terminal regions and two intermediate group of syntenous genes that seem to be genus specific. We analyzed Streptomyces species using DNA/DNA microarray comparative genome analysis. Only Streptomyces rimosus failed to give a congruent genome pattern for the genes found in Streptomyces coelicolor. We expanded the analysis to include a number of strains related to the type strain of S. rimosus and obtained a similar divergence from the main body of Streptomyces species. These strains showed very close identity to the original strain with no gene deletion or duplication detected. The 16S rRNA sequences of these S. rimosus strains were confirmed as very similar to the S. rimosus sequences available from the Ribosomal Database Project. When the SSU ribosomal RNA phylogeny of S. rimosus is analyzed, the species is positioned at the edge of the Streptomyces clade. We conclude that S. rimosus represents a distinct evolutionary lineage making the species a worthy possibility for genome sequencing.     

嗜水气单胞菌气溶素基因的克隆与序列分析

以嗜水气单胞菌BZ和NK分离株的DNA为模板, 采用PCR技术, 扩增气溶素基因(aerA)的DNA片段, 将其克隆到pMD18-T载体上。通过序列测定, 分析结果表明：所克隆的1393 bp片段为aerA部分序列, 编码产生464个氨基酸。BZ与NK之间aerA核苷酸同源性为97.6%, 氨基酸同源性为98.3%, 与其它分离物核苷酸同源性为71.6%~97.5%, 氨基酸同源性为68.0%~98.9%。利用邻接法构建了aerA分子树状图, 树状图分析表明：气单胞菌属各分离物聚为三支, 其中嗜水气单胞菌各菌株之间关系密切, 被聚类为同一支。     

Enhanced fitness due to higher fecundity,increased defence against a specialist and tolerance towards a generalist herbivore in an invasive annual plant

Aims The superior performance of many non-indigenous species in a new range can be attributed to different factors such as pre-adaptation to environmental conditions in new areas or to factors inherent to displacement mechanisms such as loss of co-evolved pathogens and herbivores that increase the speed of evolutionary change towards a shift in allocation from defence to growth and reproduction. To assess the importance of the different mechanisms governing the success of Conyza canadensis, a globally successful invader, we simultaneously tested several recent hypotheses potentially explaining the factors leading to biological invasion.Methods We tested (i) whether plants from the non-native range showed a higher fitness than plants from the native North American range, (ii) whether they differed in resistance against an invasive generalist herbivore, the slug Arion lusitanicus and against a recently established specialist aphid herbivore, Uroleucon erigeronense and (iii) experimentally assessed whether C. canadensis releases allelopathic chemicals that have harmful effects on competing species in the non-native range. We compared populations along a similar latitudinal gradient both in the native North American and invasive European range and analysed patterns of adaptive clinal variation in biomass production.Important findings The invasion success of C. canadensis in Europe cannot be attributed to a single trait, but to a combination of factors. Invasive plants benefited from increased growth and above all, increased reproduction (a key trait in an annual plant) and were less attacked by a co-migrated specialist enemy. The observed loss of defence against generalist slugs did not translate into a decreased fitness as invasive C. canadensis plants showed a high re-growth potential. In contrast to earlier in vitro studies, we detected no allelopathic effects on the competing flora in the non-native range. The latitudinal cline in vegetative biomass production in the non-native range observed in our common garden study indicates a high adaptive potential. However, only further genetic studies will provide conclusive evidence whether the differentiation in the non-native range is caused by pre-adaptation and sorting-out processes of putatively repeatedly introduced populations of this composite, long-distance disperser with highly volatile seeds or evolved de novo as a rapid response to new selection pressures in the non-native range.     

Characterization of midgut trypsin-like enzymes and three trypsinogen cDNAs from the lesser grain borer, Rhyzopertha dominica (Coleoptera: Bostrichidae)

Protein digestion in the lesser grain borer, Rhyzopertha dominica (F.) (Coleoptera: Bostrichidae), results from the action of a complex of serine proteinases present in the midgut. In this study we partially characterized trypsin-like enzyme activity against N-alpha-benzoyl-L-arginine p-nitroanilide (BApNA) in midgut preparations and cloned and sequenced three cDNAs for trypsinogen-like proteins. BApNAase activity in R. dominica midgut was significantly reduced by serine proteinase inhibitors and specific inhibitors of trypsin, whereas BApNAase activity was not sensitive to specific inhibitors of chymotrypsin or aspartic proteinases. However, trans-epoxysuccinyl-L-leucylamido-(4-guanidino) butane (E-64) inhibited BApNAase activity by about 30%. BApNAase was most active in a broad pH range from about pH 7 to 9.5. The gut of R. dominica is a tubular tract approximately 2.5 mm in length. BApNAase activity was primarily located in the midgut region with about 1.5-fold more BApNAase activity in the anterior region compared to that in the posterior region. Proteinases with apparent molecular masses of 23-24 kDa that were visualized on casein zymograms following electrophoresis were inhibited by TLCK. Three cDNAs for trypsinogen-like proteins were cloned and sequenced from mRNA of R. dominica midgut. The full cDNA sequences consisted of open reading frames encoding 249, 293, and 255 amino acid residues for RdoT1, RdoT2, and RdoT3, respectively. cDNAs RdoT1, RdoT2, and RdoT3 shared 77-81% sequence identity. The three encoded trypsinogens shared 54-62% identity in their amino acid sequences and had 16-18 residues of signal peptides and 12-15 residues of activation peptides. The three predicted mature trypsin-like enzymes had molecular masses of 23.1, 28, and 23.8 kDa for RdoT1, RdoT2, and RdoT3, respectively. Typical features of these trypsin-like enzymes included the conserved N-terminal residues IVGG62-65, the catalytic amino acid triad of serine proteinase active sites (His109, Asp156, Ser257), three pairs of conserved cysteine residues for disulfide bridges, and the three residues (Asp251, Gly274, Gly284) that determine specificity in trypsin-like enzymes. In addition, RdoT2 has both a PEST-like sequence at the C-terminus and a free Cys158 near the active site, suggesting instability of this enzyme and/or sensitivity to thiol reagents. The sequences have been deposited in GenBank database (accession numbers AF130840 for RdoT1, AF130841 for RdoT2, and AF130842 for RdoT3).     

Attitudes toward forest diversity and forest ecosystem services—a cross-cultural comparison between China and Switzerland

Aims Despite the current interest in services provided by ecosystems and the role of biodiversity, the relationship among human attitudes, biodiversity and ecosystem services has hardly been investigated. Moreover, few studies have examined attitudes toward nature in cross-cultural comparisons. This study investigates the attitudes of Chinese and Swiss people, both environmental experts and laypersons, toward forest biodiversity and ecosystem services.Methods Overall, 640 people in China and Switzerland were interviewed with the help of a standardized questionnaire. In each country, the study population was equally divided into an urban (80 city dwellers and 80 environmental science students) and a rural (80 forest visitors and 80 farmers) study group. The 15-minute interviews took place in the cities of Beijing and Zurich and in the rural forested areas of Dujiangyan, Sichuan Province and Lake Sempach, canton Lucerne. Attitudes toward forest biodiversity were investigated with the help of color photographs that depicted both monocultures and species-rich forests typical for China and Switzerland. Attitudes toward ecosystem services were investigated with the help of 13 statements on provisioning, regulating, cultural and supporting services of forests.Important findings On average, Chinese participants showed no strong preferences for biodiversity, whereas the Swiss clearly preferred species-rich forests over monocultures. However, Chinese environmental science students did prefer species-rich forests and attributed to them a higher conservation value because of their higher biodiversity. Although there were no strong preferences for Chinese versus Swiss forests, all participants correctly answered that Chinese forests are more species rich in terms of plants and animals and thus found them less boring and more interesting, but also less managed, than Swiss forests. All participants highly valued the ecosystem services provided by forests; especially the regulating and supporting ones. Environmental science students and farmers placed more importance on the provisioning services, whereas city dwellers and forest visitors emphasized more on the regulating services. The disjuncture between the high ecological quality of species-rich forests and their low attractiveness to Chinese study participants points to a potential conflict between conservation policies and the public's preferences. A better communication of ecosystem services provided by forest biodiversity to the public might change these preferences in favor of ecological quality, as already observed among Chinese environmental science students.