Beyond the genome

It is the year 2025. In a leading teaching hospital, in London, New York, Paris, or Tokyo, a little girl is born. Her parents have elected to try an innovative new service that is being offered there--at a price--to all parents of newborns: whole genome analysis....     

MBGD: microbial genome database for comparative analysis

MBGD is a workbench system for comparative analysis of completely sequenced microbial genomes. The central function of MBGD is to create an orthologous gene classification table using precomputed all-against-all similarity relationships among genes in multiple genomes. In MBGD, an automated classification algorithm has been implemented so that users can create their own classification table by specifying a set of organisms and parameters. This feature is especially useful when the user's interest is focused on some taxonomically related organisms. The created classification table is stored into the database and can be explored combining with the data of individual genomes as well as similarity relationships among genomes. Using these data, users can carry out comparative analyses from various points of view, such as phylogenetic pattern analysis, gene order comparison and detailed gene structure comparison. MBGD is accessible at http://mbgd.genome.ad.jp/.     

Community-wide analysis of microbial genome sequence signatures

Background  

Analyses of DNA sequences from cultivated microorganisms have revealed genome-wide, taxa-specific nucleotide compositional characteristics, referred to as genome signatures. These signatures have far-reaching implications for understanding genome evolution and potential application in classification of metagenomic sequence fragments. However, little is known regarding the distribution of genome signatures in natural microbial communities or the extent to which environmental factors shape them.     

Beyond the genome: Reconstituting the new genetics

The mapping and sequencing of the human genome has been the 'Holy Grail' of the new genetics, and its publication marks a turning point in the development of modern biotechnology. However, the question remains: what has been the impact of this discovery on how biotechnology develops in science, and in society at large? Using concepts developed in the social studies of science and technology, the paper begins by rehearsing the historical development of the Human Genome Project (HGP), and suggests that its translation into genomics has been achieved through a process of 'black-boxing' to ensure stabilization. It continues by exploring the extent to which the move to genomics is part of a paradigm shift in biotechnology resulting from the conceptual and organizational changes that have occurred following the completion of HGP. The discussion then focuses on whether genomics can be seen as part of the development of socially robust knowledge in late modernity. The paper suggests that there is strong evidence that a transformation is indeed taking place. It concludes by sketching a social scientific agenda for investigating the reconstitution of the new genetics in a post-genomic era using a 'situated' analytic approach based on an understanding of techno-scientific change as both emergent and contingent.     

Statistical bioinformatic methods in microbial genome analysis

It is probable that, increasingly, genome investigations are going to be based on statistical formalization. This review summarizes the state of art and potentiality of using statistics in microbial genome analysis. First, I focus on recent advances in functional genomics, such as finding genes and operons, identifying gene conversion events, detecting DNA replication origins and analysing regulatory sites. Then I describe how to use phylogenetic methods in genome analysis and methods for genome-wide scanning for positively selected amino acids. I conclude with speculations on the future course of genome statistical modeling.     

Beyond the sequence: cellular organization of genome function

Genomes are more than linear sequences. In vivo they exist as elaborate physical structures, and their functional properties are strongly determined by their cellular organization. I discuss here the functional relevance of spatial and temporal genome organization at three hierarchical levels: the organization of nuclear processes, the higher-order organization of the chromatin fiber, and the spatial arrangement of genomes within the cell nucleus. Recent insights into the cell biology of genomes have overturned long-held dogmas and have led to new models for many essential cellular processes, including gene expression and genome stability.     

The world of archaea: genome analysis,evolution and thermostable enzymes

Pyrococcus sp. KOD1 is a newly isolated hyperthermophilic archaeon from a solfatara at a wharf on Kodakara Island, Kagoshima, Japan. A physical map of the KOD1 chromosome was constructed using pulsed-field gel electrophoresis of restriction fragments generated by AscI, PacI and PmeI. The order of the AscI fragments was deduced from Southern hybridization using the AscI, PmeI and PacI fragments as a probe. The derived physical map indicates that KOD1 possesses a circular-form genome and its size was estimated to be 2036 kb. Several cloned genes were hybridized to restriction fragments to locate their positions on the physical map. Some genes involved in the central dogma were located on the restricted segment of the genome. Novel characteristics of KOD1 enzymes are also introduced in this article.     

Beyond biogeographic patterns: processes shaping the microbial landscape

Recently, microbiologists have established the existence of biogeographic patterns among a wide range of microorganisms. The focus of the field is now shifting to identifying the mechanisms that shape these patterns. Here, we propose that four processes - selection, drift, dispersal and mutation - create and maintain microbial biogeographic patterns on inseparable ecological and evolutionary scales. We consider how the interplay of these processes affects one biogeographic pattern, the distance-decay relationship, and review evidence from the published literature for the processes driving this pattern in microorganisms. Given the limitations of inferring processes from biogeographic patterns, we suggest that studies should focus on directly testing the underlying processes.     

Exploring the diversity of the microbial world

Yale's Microbial Diversity Institute (MDI) comprises scientists who seek to understand the largely unknown microbial world. In the first MDI symposium at Yale's West Campus in October 2010, four speakers discussed their research in diverse fields within the microbial sciences. The highlights of the symposium are presented here along with an outlook on the future of the MDI.     

Synergistic interactions in the microbial world

After several decades of microbiological research has focused on pure cultures, synergistic effects between different types of microorganisms find increasing interest. Interspecies interactions between prokaryotic cells have been studied into depth mainly with respect to syntrophic cooperations involved in methanogenic degradation of electron-rich substrates such as fatty acids, alcohols, and aromatics. Partners involved in these processes have to run their metabolism at minimal energy increments, with only fractions of an ATP unit synthesized per substrate molecule metabolized, and their cooperation is intensified by close proximity of the partner cells. New examples of such syntrophic activities are anaerobic methane oxidation by presumably methanogenic and sulfate-reducing prokaryotes, and microbially mediated pyrite formation. Syntrophic relationships have also been discovered to be involved in the anaerobic metabolization of amino acids and sugars where energetical restrictions do not necessarily force the partner organisms into strict interdependencies. The most highly developed cooperative systems among prokaryotic cells appear to be the structurally organized phototrophic consortia of the Chlorochromatium and Pelochromatium type in which phototrophic and chemotrophic bacteria not only exchange metabolites but also interact at the level of growth coordination and tactic behaviour. This revised version was published online in August 2006 with corrections to the Cover Date.     

Horizontal gene transfer among microbial genomes: new insights from complete genome analysis

The determination and analysis of complete genome sequences has led to the suggestion that horizontal gene transfer may be much more extensive than previously appreciated. Many of these studies, however, rely on evidence that could be generated by forces other than gene transfer including selection, variable evolutionary rates, and biased sampling.     

微生物基因组研究进展

本综述了微生物全基因组测序的基本方法,数据收集和组装,序列缺口的填充、全基因组序列注释。同时对微生物基因组的研究现状和重大意义也作了简单概述。     

Beyond host-pathogen interactions: microbial defense strategy in the host environment

Many extracellular pathogenic bacteria colonize human or animal bodies through evasion of the host immune system, a process called host-pathogen interaction. What happens when other intruders try to invade the same host and try to establish themselves in the same niche is largely unknown. In one well-studied case, Pseudomonas aeruginosa is known to secrete the protein azurin as a weapon against such invaders as cancers, parasites and viruses. The production of such weapons by pathogenic bacteria could provide important insights into how a pathogen responds in the post-colonization state to impede other intruders for its own survival. Moreover, these molecules might find use in the pharmaceutical industry as next-generation therapeutics.