Peptide signaling in Hydra

Peptides play a number of crucial roles as signaling molecules in metazoans. In order to elaborate a more complete picture of the roles played by peptides in a single organism, we launched the "Hydra Peptide Project". For this project, we used Hydra magnipapillata, a species belonging to Cnidaria, one of the most basal metazoan phyla, and using a peptidomic approach, we systematically identified a number of peptide signaling molecules, their encoding genes and their functions. In this article, we report the peptides isolated from Hydra and other cnidarians, as well as their synthesis, processing and release from the cells to the target. Possible peptide signaling pathways are overviewed and finally we discuss the evolution of the peptide signaling system.     

Cellular roles of DNA polymerase zeta and Rev1 protein

The majority of both spontaneous and DNA damage-induced mutations in eukaryotes result from replication processes in which DNA polymerase zeta (Polzeta) and Rev1 protein (Rev1p) play major roles. Understanding these roles is likely to provide information relevant to the origin of genetic diseases, such as cancer, and may provide new insights for their prevention. DNA Polzeta also appears to be involved in the somatic hypermutability that occurs during development of the immune response. The results from a variety of genetic and enzymological investigations have started to delineate the cellular roles of these enzymes, but a number of important issues have not yet been resolved and much remains to be learned. Questions concerning the possible existence of other subunits to these enzymes, of their possible association with one another or with other proteins, of the nature of their enzymatic activities and of the relative roles played by these and other DNA polymerases in the bypass of different kinds of DNA damage, require further investigation. Finally, very little is known about the way these enzymes are regulated and brought into play when needed.     

The Aurora kinase family in cell division and cancer

The Aurora protein kinase family (consisting of Aurora-A, -B and -C) is an important group of enzymes that controls several aspects of cell division in mammalian cells. Dysfunction of these kinases has been associated with a failure to maintain a stable chromosome content, a state that can contribute to tumourigenesis. Additionally, Aurora-A is frequently found amplified in a variety of tumour types and displays oncogenic activity. On the other hand, therapeutic inhibition of these kinases has shown great promise as potential anti-cancer treatment, most likely because of their essential roles during cell division. This review will focus on our present understanding of the different roles played by these kinases, their regulation throughout cell division, their deregulation in human cancers and on the progress that is made in targeting these important regulators in the treatment of cancer.     

Native and invasive hosts play different roles in host–parasite networks

Parasites are often key players in biological invasions since they can mediate the impact of host invasions or can themselves become invasive species. However, the nature and extent of parasite-mediated invasions are often difficult to delineate. Here, we used individual-based, weighted bipartite networks to study the roles (degrees of interactions of individuals in a modular network according to their within- and among-module connections) played by native and invasive host individuals to their parasite communities. We studied two phylogenetically and ecologically close fish species, Mugil cephalus s.l. and Planiliza haematocheilus (Teleostei: Mugilidae). Planiliza haematocheilus is native to the Sea of Japan and invasive in the Sea of Azov whereas, M. cephalus s.l. is native to both seas. Based on the common evolutionary history that drives native host–parasite networks, we hypothesised that 1) native networks have higher modularity than invaded ones; and 2) invasive hosts in the invaded area play a peripheral role to structure parasite communities. We analysed the whole parasite community and subsets based on transmission strategy and host specificity of the parasite species to establish whether modularity and host roles are related to these features in the native and invaded areas. All networks were found to be modular. However, modularity tended to be higher in networks of the native area rather than those of the invaded area. Host individuals of both fish species played similar roles in the native area, whereas invasive hosts played a peripheral role in the networks of the invaded area. We propose that long-term monitoring of the roles of invasive hosts in parasite communities can be a useful proxy for estimating the maturity of the establishment of the invasive hosts in an ecosystem.     

Microbial biofilms in nature: unlocking their potential for agricultural applications

Soil environments are dynamic and the plant rhizosphere harbours a phenomenal diversity of micro-organisms which exchange signals and beneficial nutrients. Bipartite beneficial or symbiotic interactions with host roots, such as mycorrhizae and various bacteria, are relatively well characterized. In addition, a tripartite interaction also exists between plant roots, arbuscular mycorrhizal fungi (AMF) and associated bacteria. Bacterial biofilms exist as a sheet of bacterial cells in association with AMF structures, embedded within a self-produced exopolysaccharide matrix. Such biofilms may play important functional roles within these tripartite interactions. However, the details about such interactions in the rhizosphere and their relevant functional relationships have not been elucidated. This review explores the current understanding of naturally occurring microbial biofilms, and their interaction with biotic surfaces, especially AMF. The possible roles played by bacterial biofilms and the potential for their application for a more productive and sustainable agriculture is discussed in this review.     

Probing membrane protein–lipid interactions

Structure determination of membrane proteins has highlighted the many roles played by lipids in influencing overall protein architecture. It is now widely accepted that lipids surrounding membrane proteins play crucial roles by modulating their conformational, structural, and functional properties. Capturing often transient lipid interactions and defining their chemical identity, however, remains challenging. Recent advances in mass spectrometry have resolved questions concerning lipid interactions by providing the molecular composition of intact complexes in association with lipids. Together with other biophysical tools, a picture is emerging of the dynamic nature of lipid-mediated interactions and their effects on conformation, interactions, and signaling.     

现代生物化学与分子生物学研究技术在植物微生物生态学中的应用

植物微生物生态学是研究植物微生态系统的一门学科,以植物组织细胞内微生物的组成、功能、演替,以及微生物之间和微生物与宿主之间的相互作用关系为研究对象。现代生物化学与分子生物学技术在植物微生物生态学研究领域的作用日益明显。介绍了上述技术及其在植物微生物生态学研究领域的应用进展,并对其在该领域的利用和发展进行了展望。     

TGF beta inhibitors. New and unexpected requirements in vertebrate development

Analysis of embryonic induction has pointed to the importance of the antagonistic roles played by secreted inducing factors and their soluble inhibitory binding proteins. These interactions have been particularly well characterized in patterning the primary axes of insects and vertebrates. New results implicate similar antagonistic relationships in numerous later events of embryogenesis.     

alphavbeta3 integrin and angiogenesis: a moody integrin in a changing environment

In the adult, angiogenesis, the formation of new blood vessels from pre-existing vasculature contributes to the pathogenesis of many disorders including cancer. The role of adhesion molecules, especially integrins, in pathological angiogenesis has long been the subject of investigation, mostly because of their potential as anti-angiogenic targets. Recent studies have highlighted the complexities connected with understanding the roles of one particular integrin, alphavbeta3, in neovascularization. This integrin is notoriously promiscuous and its precise functions in angiogenesis are unclear. Here, I have firstly summarized some of the salient features of the roles played by alphavbeta3 during angiogenesis; secondly attempted to address the apparently conflicting issues surrounding this topic; and finally raised some questions that appear to be unanswered.     

Proteoglycans: key partners in bone cell biology

The diversity of bone proteoglycan (PG) structure and localisation (pericellular, extracellular in the organic bone matrix) reflects a broad spectrum of biological functions within a unique tissue. PGs play important roles in organizing the bone extracellular matrix, taking part in the structuring of the tissue itself as active regulators of collagen fibrillogenesis. PGs also display selective patterns of reactivity with several constituents including cytokines and growth factors, such as transforming growth factor-beta or osteoprotegerin thereby modulating their bio-availability and biological activity in the bone tissue. In this review, the complex PG composition in bone will be addressed together with the specific role played by PGs (or their GAGs chains) in bone biology, as regulatory molecules for bone resorption and their involvement in bone tumor development. These roles have been determined after modulation of PG expression or mutations in their corresponding genes, which revealed specific roles for these compounds in bone pathologies (e.g. perlecan or glypican-3 mutations observed respectively in chondrodysplasia or dysmorphic syndrome). Finally, the potential therapeutic interest of PGs is discussed based on recent data, more particularly on bone tumor-associated osteolysis as these molecules are involved both in bone resorption and tumor development.     

Draft genome sequences for Clostridium thermocellum wild-type strain YS and derived cellulose adhesion-defective mutant strain AD2

Clostridium thermocellum wild-type strain YS is an anaerobic, thermophilic, cellulolytic bacterium capable of directly converting cellulosic substrates into ethanol. Strain YS and a derived cellulose adhesion-defective mutant strain, AD2, played pivotal roles in describing the original cellulosome concept. We present their draft genome sequences.     

Phenotypic switching in Candida glabrata accompanied by changes in expression of genes with deduced functions in copper detoxification and stress

Most strains of Candida glabrata switch spontaneously between a number of phenotypes distinguishable by graded brown coloration on agar containing 1 mM CuSO4, a phenomenon referred to as "core switching." C. glabrata also switches spontaneously and reversibly from core phenotypes to an irregular wrinkle (IWr) phenotype, a phenomenon referred to as "irregular wrinkle switching." To identify genes differentially expressed in the core phenotypes white (Wh) and dark brown (DB), a cDNA subtraction strategy was employed. Twenty-three genes were identified as up-regulated in DB, four in Wh, and six in IWr. Up-regulation was verified in two unrelated strains, one a and one alpha strain. The functions of these genes were deduced from the functions of their Saccharomyces cerevisiae orthologs. The majority of genes up-regulated in DB (78%) played deduced roles in copper assimilation, sulfur assimilation, and stress responses. These genes were differentially up-regulated in DB even though the conditions of growth for Wh and DB, including CuSO4 concentration, were identical. Hence, the regulation of these genes, normally regulated by environmental cues, has been usurped by switching, presumably as an adaptation to the challenging host environment. These results are consistent with the suggestion that switching provides colonizing populations with a minority of cells expressing a phenotype that allows them to enrich in response to an environmental challenge, a form of rapid adaptation. However, DB is the most commonly expressed phenotype at sites of host colonization, in the apparent absence of elevated copper levels. Hence, up-regulation of these genes by switching suggests that in some cases they may play roles in colonization and virulence not immediately obvious from the roles played by their orthologs in S. cerevisiae.     

绿叶挥发物产生特征及其生态生理作用研究进展

该文系统综述了植物绿叶挥发物(green leaf volatiles, GLVs)的形成特征、对植物的生态生理作用及调控机制等方面的最新研究进展。GLVs是指植物经十八碳烷酸途径过氧化物酶分支途径产生的含6个碳原子的醛、醇及其酯。除叶片外, 植物的根、茎、果实、种子等部位均可以合成该类化合物, 合成调控存在转录和转录后水平的调控。在特定植物中, GLVs合成及其组分还受到植物生长发育阶段和生长季节等外源环境的影响。昆虫啃食、微生物感染以及有益真菌的定植等生物逆境与缺氮等物理逆境均具有诱导GLVs合成的作用。除了参与植物特有气味形成外, GLVs在植物直接和间接防御应答中发挥着重要的作用。GLVs不仅具有抑制微生物和多种昆虫繁殖的作用, 还具有诱导多种防御化合物合成、预置(prime)有关信号途径的作用。基于GLVs在植物界的广泛存在性和在防御应答中的多层次作用, 该文作者提出了GLVs在道地药材品质形成中的潜在作用及开展相关研究的必要性和紧迫性。     

Dream narratives of Muslims' martyrdom: Constant and changing roles past and present.

Dreams of martyrdom experienced by alleged Muslim martyrs, their families, and friends are considered highly significant within Muslim societies. They are frequently understood as God-given veridical dreams that can show the true status of the martyr and predict the future. The author examined the narratives of these dreams in both early Islamic and contemporary sources and explored the roles that they have played, whether ongoing and constant or changing in response to new conditions. (PsycINFO Database Record (c) 2011 APA, all rights reserved)     

What are antibiotics? Archaic functions for modern activities

Secondary metabolites are proposed to have played important roles in the evolution of the reactions of living forms on earth, in effecting and modulating reactions during biochemical evolution by chemical and structural interaction with 'receptor' sites in primitive macromolecular templates. For example, in the evolution of the translation system, as the polymerizing reactions became more complex and proteins became involved, the low molecular-weight effectors were functionally replaced by polypeptides, but retained their ability to interact with receptor sites in nucleic acids and proteins. Many of these low molecular-weight effectors now play a different role, that of antagonists, by interacting with the original receptor sites in macromolecular structures; this explains their contemporary activity as antibiotics.     

Role of Amino Acids in Plant Responses to Stresses

Plants subjected to stress show accumulation of proline and other amino acids. The role played by accumulated amino acids in plants varies from acting as osmolyte, regulation of ion transport, modulating stomatal opening, and detoxification of heavy metals. Amino acids also affect synthesis and activity of some enzymes, gene expression, and redox-homeostasis. These roles played by amino acids have been critically examined and reviewed.     

Repetitive sequences and epigenetic modification: inseparable partners play important roles in the evolution of plant sex chromosomes

Planta - The present review discusses the roles of repetitive sequences played in plant sex chromosome evolution, and highlights epigenetic modification as potential mechanism of repetitive...