Collagen gene construction and evolution

Summary Collagen genes appear to have been assembled by the tandem repetition of homologous primary (9 base pair), secondary (54 base pair), and tertiary (702 base pair) modules. In vertebrate interstitial collagen genes many of the secondary modules are separated by introns, but in invertebrate collagen genes the non-coding sequences lie near the ends of supposed tertiary modules and are therefore about 702 (54×13) base pairs apart. The genes for vertebrate interstitial collagens (types I–III) seem to have been constructed by the tandem repetition of five tertiary modules, three of which were subsequently shortened by internal deletions. This shortening of the gene resulted in the non-integral relationship between the period of the fibrils and the length of the molecules of vertebrate collagens, and was therefore responsible for the mechanical properties of the completed product. Comparisons of the amino acid sequences of various collagens indicate that the main types of collagen evolved about 800–900 million years ago, a date that agrees well with the fossil record of primitive Metazoa.     

泉州市不同利用方式下土壤磷的吸附与解吸特性

分析了不同利用方式下泉州市土壤磷素吸附-解吸特征.结果表明:Langmuir等温方程式可以很好地表征土壤磷素的吸附特性;旱地和轮作地土壤对磷的吸附能力较强,而草地和林地土壤对磷的吸附能力较弱;磷的流失风险顺序为轮作地＞草地＞林地＞旱地;指导施磷量与吸附常数、最大缓冲量的大小顺序一致,为旱地＞轮作地＞林地＞草地;轮作地和草地的解吸率高于旱地和林地,土壤的缓冲能力顺序为旱地＞林地＞轮作地＞草地.主成分分析表明,平均解吸率、易解吸磷、磷吸附指数和磷零吸持平衡浓度4个指标最能反映土壤磷素流失潜力,可作为评价流失潜力的主要指标.     

Stem cells: Insights into the secretome

Stem cells have been considered as possible therapeutic vehicles for different health related problems such as cardiovascular and neurodegenerative diseases and cancer. Secreted molecules are key mediators in cell–cell interactions and influence the cross talk with the surrounding tissues. There is strong evidence supporting that crucial cellular functions such as proliferation, differentiation, communication and migration are strictly regulated from the cell secretome. The investigation of stem cell secretome is accumulating continuously increasing interest given the potential use of these cells in regenerative medicine. The scope of the review is to report the main findings from the investigation of stem cell secretome by the use of contemporary proteomics methods and discuss the current status of research in the field. This article is part of a Special Issue entitled: An Updated Secretome.     

Atypical Cohesin-Dockerin Complex Responsible for Cell Surface Attachment of Cellulosomal Components: BINDING FIDELITY,PROMISCUITY, AND STRUCTURAL BUTTRESSES*

The rumen bacterium Ruminococcus flavefaciens produces a highly organized multienzyme cellulosome complex that plays a key role in the degradation of plant cell wall polysaccharides, notably cellulose. The R. flavefaciens cellulosomal system is anchored to the bacterial cell wall through a relatively small ScaE scaffoldin subunit, which bears a single type IIIe cohesin responsible for the attachment of two major dockerin-containing scaffoldin proteins, ScaB and the cellulose-binding protein CttA. Although ScaB recruits the catalytic machinery onto the complex, CttA mediates attachment of the bacterial substrate via its two putative carbohydrate-binding modules. In an effort to understand the structural basis for assembly and cell surface attachment of the cellulosome in R. flavefaciens, we determined the crystal structure of the high affinity complex (K_d = 20.83 nm) between the cohesin module of ScaE (CohE) and its cognate X-dockerin (XDoc) modular dyad from CttA at 1.97-Å resolution. The structure reveals an atypical calcium-binding loop containing a 13-residue insert. The results further pinpoint two charged specificity-related residues on the surface of the cohesin module that are responsible for specific versus promiscuous cross-strain binding of the dockerin module. In addition, a combined functional role for the three enigmatic dockerin inserts was established whereby these extraneous segments serve as structural buttresses that reinforce the stalklike conformation of the X-module, thus segregating its tethered complement of cellulosomal components from the cell surface. The novel structure of the RfCohE-XDoc complex sheds light on divergent dockerin structure and function and provides insight into the specificity features of the type IIIe cohesin-dockerin interaction.     

Molecular characterization and transcriptional analysis of non-mammalian type Toll like receptor (TLR21) from rock bream (Oplegnathus fasciatus)

Toll-like receptors (TLRs) are a large family of pattern recognition receptors, which are involved in triggering host immune responses against various pathogens by detecting their evolutionarily conserved pathogen associated molecular patterns (PAMPs). TLR21 is a non-mammalian type TLR, which recognizes unmethylated CpG DNA, and is considered as a functional homolog of mammalian TLR9. In this study, we attempted to identify and characterize a novel TLR21 counterpart from rock bream (Oplegnathus fasciatus) designated as RbTLR21, at molecular level. The complete coding sequence of RbTLR21 was 2919 bp in length, which encodes a polypeptide of 973 amino acids with a predicted molecular mass of 112 kDa and a theoretical isoelectric point of 8.6. The structure of the deduced RbTLR21 protein is similar to that of the members of typical TLR family, and includes the ectodomain, which consists of 16 leucine rich repeats (LRRs), a transmembrane domain, and a cytoplasmic Toll/interleukin-1 receptor (TIR) domain. According to the pairwise sequence analysis data, RbTLR21 was homologous to that of the orange-spotted grouper (Epinephelus coioides) with 76.9% amino acid identity. Furthermore, our phylogenetic analysis revealed that RbTLR21 is closely related to E. coioides TLR21. The RbTLR21 was ubiquitously expressed in all the tissues tested, but the highest expression was found in spleen. Additionally, upon stimulation with Streptococcus iniae, rock bream iridovirus (RBIV), and Edwardsiella tarda, RbTLR21 mRNA was significantly up-regulated in spleen tissues. Collectively, our findings suggest that RbTLR21 is indeed an ortholog of the TLR21 family and may be important in mounting host immune responses against pathogenic infections.     

临床医学八年一贯制"代谢与能量"模块式教学的实践与思考

为了解决传统医学基础知识教育中存在的学习内容衔接矛盾、重叠、理论脱离实际、基础脱离临床、教师教法单一、学生学法被动等弊端,上海交通大学医学院于2009年对八年制临床医学专业进行了教学改革,以模块式教学代替传统教学模式。经过两年的教学实践,在取得可喜的优异成果的同时,探讨模块式教学目前存在的弊端,为深化模块式教学改革,进一步提高教学质量提供借鉴和参考。     

Interspecific networks in ground beetle (Coleoptera: Carabidae) assemblages

Although changes to interspecific relationships can significantly alter the composition of insect assemblages, they are often ignored when assessing impacts of environmental change. Long-term ground beetle data were used in this study to analyse ecological networks from three habitats at two sites in Scotland. A Bayesian Network inference algorithm was used to reveal interspecific relationships. The significance and strength of relationships between species (nodes) were estimated along with other network properties. Links were identified as positive relationships if co-occurrences of beetles correlated positively, and as negatives relationships if there was a negative correlation between the occurrences of the species. Most of the species had few links and only 10% of the nodes were connected with several links. Calathus fuscipes, a common carabid in the samples, was the most connected, with nine links to other species. More interspecific relationships were found to be positive than negative, with 48 and 23 links, respectively. The modular structure of the network was assessed and eight separate sub-networks were found. Habitat preferences of the species were clearly represented in the structure of the sets of those five sub-networks containing more than one species and were in line with the findings of the indicator species analysis. In our study, we showed that generated Bayesian networks can model interspecific relationships between carabid species. Due to the relative ease of the collection of field data and the high information content of the results, this method could be incorporated into everyday ecological analysis.     

The Myofibrillar Protein,Projectin, is Highly Conserved Across Insect Evolution Except for Its PEVK Domain

All striated muscles respond to stretch by a delayed increase in tension. This physiological response, known as stretch activation, is, however, predominantly found in vertebrate cardiac muscle and insect asynchronous flight muscles. Stretch activation relies on an elastic third filament system composed of giant proteins known as titin in vertebrates or kettin and projectin in insects. The projectin insect protein functions jointly as a “scaffold and ruler” system during myofibril assembly and as an elastic protein during stretch activation. An evolutionary analysis of the projectin molecule could potentially provide insight into how distinct protein regions may have evolved in response to different evolutionary constraints. We mined candidate genes in representative insect species from Hemiptera to Diptera, from published and novel genome sequence data, and carried out a detailed molecular and phylogenetic analysis. The general domain organization of projectin is highly conserved, as are the protein sequences of its two repeated regions—the immunoglobulin type C and fibronectin type III domains. The conservation in structure and sequence is consistent with the proposed function of projectin as a scaffold and ruler. In contrast, the amino acid sequences of the elastic PEVK domains are noticeably divergent, although their length and overall unusual amino acid makeup are conserved. These patterns suggest that the PEVK region working as an unstructured domain can still maintain its dynamic, and even its three-dimensional, properties, without the need for strict amino acid conservation. Phylogenetic analysis of the projectin proteins also supports a reclassification of the Hymenoptera in relation to Diptera and Coleoptera. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.