In silico tools for signal transduction research

Signal transduction is a fundamental process that takes place in all living organisms and understanding how this event occurs at the cellular level is of vital importance to virtually all fields of biomedicine. There are several major steps involved in deciphering the signalling pathways: (a) Which molecules are involved in signalling? (b) Who talks to whom?, ie making sense of the molecular interactions in a context-dependent way. (c) Where are the signalling events taking place?, eg when a resting cell becomes activated. The challenge lies in reconstructing signalling modules and networks evoked in a particular response to a single input as well as correlating the signalling response to different cellular inputs. There is also the need for interpretation of cross-talk between signalling modules in response to single and multiple inputs. To follow up these questions there are many good databases that provide an information system on regulatory networks. This review aims to find some of the bioinformatics tools and websites available to conduct signal transduction research and to discuss the representation of databases available for the processes of signalling. The databases considered here can provide a well-structured overview on the subject and a basis for advanced bioinformatics analysis to interpret the function of genomic sequences or to analyse signalling networks within a cell. However, the knowledge of most signalling pathways is incomplete and for this reason the existing databases will provide insight, but very rarely a more complete picture.     

CpG基元的免疫学进展及基因治疗策略

CpG诱发免疫反应的能力对免疫预防是一大优点 ,但在基因治疗中 ,质粒中所含的CpG基元能够阻止基因转移或导致巨大副作用 (炎症和毒性 )。本文简单综述了CpG基元的免疫学活性、主要作用和信号转导通路 ,并且针对它在基因治疗中存在的问题及可能的解决办法进行探讨。     

Valvulogenesis: the moving target

Valvulogenesis is an extremely complex process by which a fragile gelatinous matrix is populated and remodelled during embryonic development into thin fibrous leaflets capable of maintaining unidirectional flow over a lifetime. This process occurs during exposure to constantly changing haemodynamic forces, with a success rate of approximately 99%. Defective valvulogenesis results in impaired cardiac function and lifelong complications. This review integrates what is known about the roles of genetics and mechanics in the development of valves and how changes in either result in impaired morphogenesis. It is hoped that appropriate developmental cues and phenotypic endpoints could help engineers and clinicians in their efforts to regenerate living valve alternatives.     

植物光反应突变体

光信号转导途径是植物发育调控机制的中心组成部分。目前在植物光信号受体及下游转导组分突变体筛选方面已经取得许多重要结果。本文综述了这些突变体和光信号转导途径组成及调控机制研究方面的进展。     

Structural and evolutionary division of phosphotyrosine binding (PTB) domains

Proteins encoding phosphotyrosine binding (PTB) domains function as adaptors or scaffolds to organize the signaling complexes involved in wide-ranging physiological processes including neural development, immunity, tissue homeostasis and cell growth. There are more than 200 proteins in eukaryotes and nearly 60 human proteins having PTB domains. Six PTB domain encoded proteins have been found to have mutations that contribute to inherited human diseases including familial stroke, hypercholesteremia, coronary artery disease, Alzheimer's disease and diabetes, demonstrating the importance of PTB scaffold proteins in organizing critical signaling complexes. PTB domains bind both peptides and headgroups of phosphatidylinositides, utilizing two distinct binding motifs to mediate spatial organization and localization within cells. The structure of PTB domains confers specificity for binding peptides having a NPXY motif with differing requirements for phosphorylation of the tyrosine within this recognition sequence. In this review, we use structural, evolutionary and functional analysis to divide PTB domains into three groups represented by phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like and phosphotyrosine-independent Dab-like PTBs, with the Dab-like PTB domains representing nearly 75% of proteins encoding PTB domains. In addition, we further define the binding characteristics of the cognate ligands for each group of PTB domains. The signaling complexes organized by PTB domain encoded proteins are largely unknown and represents an important challenge in systems biology for the future.     

Switching roles: the functional plasticity of adult tissue stem cells

Adult organisms have to adapt to survive, and the same is true for their tissues. Rates and types of cell production must be rapidly and reversibly adjusted to meet tissue demands in response to both local and systemic challenges. Recent work reveals how stem cell (SC) populations meet these requirements by switching between functional states tuned to homoeostasis or regeneration. This plasticity extends to differentiating cells, which are capable of reverting to SCs after injury. The concept of the niche, the micro‐environment that sustains and regulates stem cells, is broadening, with a new appreciation of the role of physical factors and hormonal signals. Here, we review different functions of SCs, the cellular mechanisms that underlie them and the signals that bias the fate of SCs as they switch between roles.     

Receptor phenotype underlies differential response of hepatocytes and nonparenchymal cells to heparin-binding fibroblast growth factor type 1 (aFGF) and type 2 (bFGF)

Summary Heparin-binding fibroblast growth factors (HBGF) have been implicated in the regeneration of both parenchymal and nonparenchymal cells of the liver. The response to and phenotype of hepatocyte receptors for HBGF-1 (acidic fibroblast growth factor) and HBGF-2 (basic fibroblast growth factor) were compared to keratinocytes, fibroblasts, and endothelial cells. HBGF-1 stimulated DNA synthesis in hepatocytes, keratinocytes, fibroblasts, and endothelial cells whereas activity of HBGF-2 was limited to fibroblasts and endothelial cells. HBGF-2 antagonized the mitogenic activity of HBGF-1 for hepatocytes and keratinocytes. Hepatocytes and keratinocytes exhibited both high- and low-affinity, nonmatrix receptor sites for HBGF-1, but only low-affinity sites for HBGF-2. The mesenchymal cells displayed only high-affinity sites for both HBGF-1 and HBGF-2. Northern blot and immunochemical analysis revealed that the expression of HBGF receptor genesbek andflg are partitioned between normal hepatocytes and nonparenchymal cells, respectively. Expression of epithelial cell-specific, mesenchymal cell-derived HBGF-7 (keratinocyte growth factor) mRNA in regenerating liver tissue was undetectable relative to HBGF-1. The results support a multifunctional role of HBGF-1 acting through different receptor phenotypes in hepatocyte and nonparenchymal cells during liver regeneration.