Organization of the Escherichia coli chromosome into macrodomains and its possible functional implications

Recent advances in fluorescent microscopy have revealed the non-random organization of chromosomes in bacterial cells. In Escherichia coli, segments included in two large regions show similar localization patterns allowing the definition of two macrodomains centered, respectively, on the centromere-like site migS (the Ori domain) and the replication terminus (the Ter domain). A genetic system measuring long distance DNA interactions confirmed the macrodomain organization of the chromosome and revealed the existence of two additional macrodomains flanking the Ter domain. Altogether, the E. coli chromosome appears to have an open ring-like conformation. Recent developments regarding various stages of chromosome biology such as replication, sister chromatid cohesion, segregation, and chromosome choreography, have considerably improved our understanding of the coordination of chromosome dynamics with the cell cycle. The possible involvement of macrodomains in these various processes is discussed.     

Why genetic investigation of psychiatric disorders is so difficult

Genetic investigations of psychiatric disease have historically relied on subjectively assessed disease diagnoses to define phenotypes. Recent developments in several areas have provided various new approaches to behavioral disorder phenotyping that promise to advance our understanding of the genetic and environmental etiologies of these traits. Such developments include re-evaluation of the boundaries between different psychiatric categories, implementation of quantitative neurobiological assessments that may serve as endophenotypes, generation of increasingly sophisticated animal behavioral models, and investigation of explicit environmental covariates. At the same time, movement toward large-scale, collaborative efforts is increasing the effectiveness of traditional genetic mapping approaches.     

Genome comparisons and analysis

As we enter the post-genomic era, with the accelerating availability of complete genome sequences, new theoretical approaches and new experimental techniques, our ability to dissect cellular processes at the molecular level continues to expand. Recent advances include the application of RNA interference methods to characterize loss-of-function phenotype genes in higher eukaryotes, comparative analysis of the human and mouse genome sequences, and methods for reconciling contradictory phylogenetic reconstructions. New developments feed into the increasingly rich content of databases such as the COG database. The next phase of research will be increasingly dominated by efforts to integrate the deluge of data into our understanding of biological systems.     

Maturation and degradation of RNA in bacteria

RNA decay plays an important role, not only in recycling nucleotides but also in determining the rapidity with which cells can react to changing growth conditions. The degradation process can be regulated, thus providing an often-underestimated means of controlling gene expression. Recent developments in the field of RNA maturation and decay in two key model organisms, Escherichia coli and Bacillus subtilis, include the resolution of the structures of many of the participants in these processes in E. coli and the identification of an enzyme in B. subtilis that appears to fit the bill as a major player in RNA decay in this organism.     

Pollen modelling, palaeoecology and archaeology: virtualisation and/or visualisation of the past?

Recent developments in pollen modelling and landscape reconstruction have the potential to have a profound impact on our understanding of landscape change related to human activity. Initial findings have already revealed the weaknesses of a number of key assumptions previously made about pollen–landscape relationships. Close interrelationships exist between landscape reconstruction based on pollen analysis and archaeology, and model-based developments raise a range of pertinent issues for both disciplines. These include the way in which past vegetation patterning is conceptualised (the patch vs. the matrix), the nature of the underlying physical environment in vegetation placement, the development of hypothesis-led approaches and the scale of landscapes under consideration. This paper discusses these issues, and also raises questions concerning the meaning of landscape. It may be erroneous to term pollen-based reconstructions as landscapes given the heavily charged meaning of the word as understood by companion and end user disciplines.     

Plant membrane transport.

Recent developments in plant membrane transport, particularly concerning the vacuolar and plasma membranes, have increased our understanding of molecular aspects of primary pumps, carrier systems and ion channels.     

When protons attack: microbial strategies of acid adaptation.

Inducible tolerance to acidic and alkaline environments is recognized as an important survival strategy for many prokaryotic and eukaryotic microorganisms. Recent developments in understanding this phenomenon include the identification of regulatory genes, specific tolerance mechanisms and genes associated with tolerance. In addition, there is significant evidence linking pH responses with virulence.     

Cyclin dependent kinase regulation

Cyclin-dependent kinases (CDKs) are key regulators of the cell cycle and their activities are consequently tightly regulated. Recent developments in the field of CDK regulation have included the discovery and characterization of CDK inhibitors. These developments have had an impact on our understanding of how other signalling pathways may be linked to the cell cycle machinery.     

Roles of fascin in cell adhesion and motility

Many cell interactions depend on the assembly of cell protrusions; these include cell attachment and migration in the extracellular matrix, cell-cell communication, and the ability of cells to sense their local environment. Cell protrusions are extensions of the plasma membrane that are supported internally by actin-based structures that impart mechanical stiffness. Fascin is a small, globular actin-bundling protein that has emerging roles in diverse forms of cell protrusions and in cytoplasmic actin bundles. The fascin-actin interaction is under complex regulation from the extracellular matrix, peptide factors and other actin-binding proteins. Recent developments advance our understanding of the multifaceted regulation of fascin and the roles of fascin-containing structures in cell adhesion, motility and invasion in the life of vertebrate organisms.     

Between a rock and a hard place?

Developing small-molecule inhibitors against protein-protein interaction targets is among the most difficult challenges in contemporary drug discovery. Recent developments in our understanding of this problem, and in the knowledge and tools available to address it, give cause for renewed hope, but substantial challenges remain.     

Genome analysis of Theileria parva

Recent technological developments in the field of genome analyses have advanced our knowledge of the structures of prokaryotic and eukoryotic genomes. Examples of these range from small bacterial genomes, such as Escherichia coli, to the more complex genomes of Caenorhabditis elegans, Drosophila, humans and mouse. Here, Subhash Morzona and John Young review developments in mapping the genome of on economically important protozoan parasite o f cattle, Theileria parva. This map provides a framework for more detailed analysis of the genome structure o f this organism. The methodologies developed in constructing the map also have application to the mapping of other protozoan genomes.     

Planar cell polarization: do the same mechanisms regulate Drosophila tissue polarity and vertebrate gastrulation?

Many types of cell show different aspects of polarization. Epithelial cells display a ubiquitous apical-basolateral polarity but often are also polarized in the plane of the epithelium - a feature referred to as 'planar cell polarity' (PCP). In Drosophila all adult epithelial cuticular structures are polarized within the plane, whereas in vertebrates examples of PCP include aspects of skin development, features of the inner ear epithelium, and the morphology and behavior of mesenchymal cells undergoing the morphogenetic movement called 'convergent extension'. Recent advances in the study of PCP establishment are beginning to unravel the molecular mechanisms that underlie this aspect of cell and tissue differentiation. Here I discuss new developments in our molecular understanding of PCP in Drosophila and compare them towhat is known about the regulation of convergent extension in vertebrates.     

包涵体蛋白体外复性的研究进展

外源基因在大肠杆菌中高水平表达时 ,通常会形成无活性的蛋白聚集体即包涵体。包涵体富含表达的重组蛋白 ,经分离、变性溶解后须再经过一个合适的复性过程实现变性蛋白的重折叠 ,才能够得到生物活性蛋白。近年来 ,发展了许多特异的策略和方法来从包涵体中复性重组蛋白。最近的进展包括固定化复性以及用一些低分子量的添加剂等来减少复性过程中蛋白质的聚集 ,提高活性蛋白的产率。     

The domestic dog: man's best friend in the genomic era

The domestic dog genome - shaped by domestication, adaptation to human-dominated environments and artificial selection - encodes tremendous phenotypic diversity. Recent developments have improved our understanding of the genetics underlying this diversity, unleashing the dog as an important model organism for complex-trait analysis.     

Tree diseases and landscape processes: the challenge of landscape pathology

Forest pathology inherently involves a landscape perspective, because tree pathogens propagate according to heterogeneous spatial patterns of flow and isolation. Landscape pathology is a field that is now emerging from the transdisciplinary cooperation of forest pathologists with landscape ecologists. Here, we review recent broad-scale assessments of tree disease risk, investigations of site and host preferences for several root rot pathogens, and regional historical analyses of pathogen outbreak in plantations. Crucial topics include fragmentation effects on pathogen spread and geophysical features that predispose forest patches to disease expression. Recent methodological developments facilitate the spatially explicit analysis of reciprocal coarse-scale relationships among hosts and pathogens. Landscape pathology studies fill a significant research gap in the context of our understanding of sustainable forest management, the introduction of exotic organisms and how climate change might affect the spread of disease.     

Rational engineering of Escherichia coli strains for plasmid biopharmaceutical manufacturing

Plasmid DNA (pDNA) has become very attractive as a biopharmaceutical, especially for gene therapy and DNA vaccination. Currently, there are a few products licensed for veterinary applications and numerous plasmids in clinical trials for use in humans. Recent work in both academia and industry demonstrates a need for technological and economical improvement in pDNA manufacturing. Significant progress has been achieved in plasmid design and downstream processing, but there is still a demand for improved production strains. This review focuses on engineering of Escherichia coli strains for plasmid DNA production, understanding the differences between the traditional use of pDNA for recombinant protein production and its role as a biopharmaceutical. We will present recent developments in engineering of E. coli strains, highlight essential genes for improvement of pDNA yield and quality, and analyze the impact of various process strategies on gene expression in pDNA production strains.     

蛋白质组技术在鼠胚胎早期发育研究中的应用

人类基因组大规模测序,揭示基因组精细结构的同时,还显示出基因数量的有限性和结构的相对稳定。随分析仪器和生物技术的飞速发展,创立了与基因组相对应的蛋白质组学,将精力集中于从生命功能的执行体---蛋白质水平研究基因的表达及功能。生殖技术的研究已取得了惊人的进展,但人们对生殖尤其是人类生殖的分子机制了解仍很贫乏。鼠胚胎发育过程蛋白质组的研究,为了解人类生殖健康和疾病发生的机制提供了有意义的资料 。     

Making mitochondrial mutants.

Mitochondrial DNA (mtDNA) encodes a mere 13 polypeptides, all with well-defined cellular functions in mitochondrial energy metabolism. It was first sequenced over two decades ago, yet our understanding of the wider physiological role of mtDNA is surprisingly sketchy. Partly, this reflects the fact that the mitochondrial gene products are essential for life; that is, most mtDNA mutations are expected to be lethal. The technical difficulty of engineering mtDNA mutations has been a major handicap in furthering our understanding of the mitochondrial genetic system. Recent developments now offer some possibilities for the genetic manipulation of mtDNA and for elucidating its contribution to human development, physiology and disease.     

Bioinformatics in the post-genome era

Recent years saw a dramatic increase in genomic and proteomic data in public archives. Now with the complete genome sequences of human and other species in hand, detailed analyses of the genome sequences will undoubtedly improve our understanding of biological systems and at the same time require sophisticated bioinformatic tools. Here we review what computational challenges are ahead and what are the new exciting developments in this exciting field.     

Microecology of the termite gut: structure and function on a microscale

Long considered simply as anoxic fermentors, termite guts are in fact axially and radially structured environments with physicochemically distinct microhabitats. Recent developments in termite gut microecology, which combined traditional and modern techniques, have focused on the spatial organization of important microbial populations and their in situ activities, and have significantly furthered our understanding of functional interactions within highly structured microenvironments.