Mobile genetic elements: the agents of open source evolution

Horizontal genomics is a new field in prokaryotic biology that is focused on the analysis of DNA sequences in prokaryotic chromosomes that seem to have originated from other prokaryotes or eukaryotes. However, it is equally important to understand the agents that effect DNA movement: plasmids, bacteriophages and transposons. Although these agents occur in all prokaryotes, comprehensive genomics of the prokaryotic mobile gene pool or 'mobilome' lags behind other genomics initiatives owing to challenges that are distinct from cellular chromosomal analysis. Recent work shows promise of improved mobile genetic element (MGE) genomics and consequent opportunities to take advantage - and avoid the dangers - of these 'natural genetic engineers'. This review describes MGEs, their properties that are important in horizontal gene transfer, and current opportunities to advance MGE genomics.     

On the Epistemological Crisis in Genomics

There is an epistemological crisis in genomics. At issue is what constitutes scientific knowledge in genomic science, or systems biology in general. Does this crisis require a new perspective on knowledge heretofore absent from science or is it merely a matter of interpreting new scientific developments in an existing epistemological framework? This paper discusses the manner in which the experimental method, as developed and understood over recent centuries, leads naturally to a scientific epistemology grounded in an experimental-mathematical duality. It places genomics into this epistemological framework and examines the current situation in genomics. Meaning and the constitution of scientific knowledge are key concerns for genomics, and the nature of the epistemological crisis in genomics depends on how these are understood.     

Governing genomics in the 21st century: between risk and uncertainty

The paper reconstructs the governance of genomics by sketching the main features, modes of operation and tactics of the emerging genomics apparatus. Genomic governance in the 20th century is characterized by the simultaneous operation of a process of the stabilization of knowledge regimes, in particular via patenting. Furthermore, we observe a heterogenization and globalization of the actors and knowledge creating systems in genomics governance. A variety of different mechanisms and strategies of governance are mobilized simultaneously. The transition of governing via risk to governance by uncertainty is another important feature of contemporary genomics governance. The implications of these trends for the regulation of genomics are considerable and might lead to the emergence of new patterns and spaces of conflict and controversy. The governance of genomics in the 21st century could become a more complex challenge than currently anticipated by many policy makers and the scientific community.     

Governing genomics in the 21st century: between risk and uncertainty

Abstract

The paper reconstructs the governance of genomics by sketching the main features, modes of operation and tactics of the emerging genomics apparatus. Genomic governance in the 20th century is characterized by the simultaneous operation of a process of the stabilization of knowledge regimes, in particular via patenting. Furthermore, we observe a heterogenization and globalization of the actors and knowledge creating systems in genomics governance. A variety of different mechanisms and strategies of governance are mobilized simultaneously. The transition of governing via risk to governance by uncertainty is another important feature of contemporary genomics governance. The implications of these trends for the regulation of genomics are considerable and might lead to the emergence of new patterns and spaces of conflict and controversy. The governance of genomics in the 21st century could become a more complex challenge than currently anticipated by many policy makers and the scientific community.     

Understanding the industrial application potential of lactic acid bacteria through genomics

Lactic acid bacteria (LAB) are a heterogeneous group of bacteria contributing to various industrial applications, ranging from food and beverage fermentation, bulk and fine chemicals production to pharmaceuticals manufacturing. Genome sequencing is booming; hitherto, 25 genomes of LAB have been published and many more are in progress. Based on genomic content of LAB, this review highlights some findings related to applications revealed by genomics and functional genomics analyses. Finally, this review summarizes mathematical modeling strategies of LAB in the context of genomics, to further our understanding of industrial related features.     

植物功能基因组学的研究策略

植物基因组学是一门研究植物基因组内基因与遗传信息是如何有机结合并如何决定其功能的一门科学。随着植物基因组计划的顺利进行 ,植物基因组学的研究已从结构基因组学转向功能基因组学。近年来 ,多采用高通量 (highthroughput,HTP)序列分析技术、大规模实验技术及计算机统计分析技术研究植物基因组功能。概述了植物功能基因组学的最新进展。     

Reproductive biology in the era of genomics biology

Current and emerging technologies in reproductive biology, including assisted reproductive technologies and animal cloning, are discussed in the context of the impact of genomics era biology. The discussion focuses on the endocrinology associated with establishment and maintenance of pregnancy, fetal-placental development, lactation, and neonatal survival. Various aspects of uterine biology, including development during the neonatal period and function in adult females, are discussed with respect to reproductive efficiency. It is clear that combining strategies for use of conventional animal models for studying the reproductive system with new genomics technologies will provide exceptional opportunities in discovery research involving data integration and application of functional genomics to benefit animal agriculture and the biomedical community. New and emerging biotechnologies and comparative genomics approaches will greatly advance our understanding of genes that are critical to development of the reproductive system and to key events at each stage of the reproductive cycle of females and males.     

An essay on the necessity and feasibility of conservation genomics

The basic premise of conservation genetics is that small populations may be genetically threatened. The two steps leading to this premise are: (1) due to prominent influence of random genetic drift and inbreeding allelic and genotypic diversity in small populations is expected to be low, and (2) low allelic diversity and high homozygosity are expected to lead to immediate fitness decreases (inbreeding depression) and a compromised potential for evolutionary adaptation. Conservation genetic research has been strongly stimulated by the application of neutral molecular markers like microsatellites and AFLPs. In general these marker studies have provided evidence for step 1. It is less evident how these markers may provide evidence for step 2. In this essay we argue that, in order to get detailed insight in step 2, adopting a conservation genomic approach, in which conservation genetics will use approaches from ecological and evolutionary functional genomics (ecogenomics), is both necessary and feasible. Conservation genomics is necessary for studying functional genomic variation as function of drift and inbreeding, for studying the mechanisms that relate low genetic variation to low fitness, for integrating environmental and genetic approaches to conservation biology, and for developing modern, fast monitoring tools. The rapid technical and financial developments in genomics currently make conservation genomics feasible, and will improve feasibility in the very near future even further. We therefore argue that conservation genomics personifies part of the near future of conservation genetics.     

乳酸菌基因组学研究进展

乳酸菌广泛应用于食品发酵工业中,其中有些菌种是重要的益生菌。目前,对乳酸菌的研究已从最初的形态学研究进入到了分子水平的研究。乳酸菌全基因组测序研究已在全球展开。乳酸菌基因组研究有助于揭示乳酸菌的遗传和代谢机制,加速重要益生功能基因的挖掘,同时为乳酸菌的应用提供众多可能性。本文就乳酸菌基因组研究的概况、重要乳酸菌基因组、乳酸菌的功能基因组以及比较基因组进行了综述。     

Mediated speculations in the genomics futures markets

This article examines the interactions between the media and genomics, with particular reference to the case of deCODE Genetics in Iceland. It focuses on the role of "forward-looking statements" and other forms of speculation as they operate in the science of genomics, in the social relations that happen around genomics, and in the commercial genomics economy. The article discusses how these fundamentally anticipatory speech acts uttered or written by genomic corporate executives, journalists, or social scientists are simultaneously volatile, exceeding any formal practices of accounting or analysis, and demanding to be accounted for, analysed, or valued. The article discusses four speculative events or cases in the genomics economy: the March 2000 bursting out of the genomics bubble, prompted in part by remarks by President Clinton and Prime Minister Blair to the media concerning gene patenting; the new disclosure requirements of the US Securities and Exchange Commission (SEC) regarding "forward-looking statements" as they appear in genomics press releases; deCODE Genetics' registration statement with the SEC that discloses a settlement of a dispute over the ownership of a fragment of DNA; and the entanglement between the author's ethnographic fieldwork and the breaking news story of reported payoffs from deCODE to the Icelandic political parties.     

Use of genome information for the study of the pathogenesis of fungal infections and the development of diagnostic tools

One of the most exciting advances in Mycology is the application of genomic approaches. The advent of genomics, together with post-genomic studies, promises to revolutionize the studies on the pathogenesis of fungal infections. Approaches include comparative genomics to identify sequences that contribute to infection and disease and functional genomics and proteomics to analyze global patterns of gene and protein expression involved in fungal pathogenesis.     

遗传学与基因组学整合课程探讨

基因组学是遗传学的重要学科分支,具有全新研究思维和技术手段,已经形成一个系统而完整的体系。在本科课程中加强基因组学教学是遗传学学科发展的要求,有利于对学生进行科学思维训练、提高学生生物伦理学修养和学习兴趣。整合遗传学与基因组学课程符合学科发展规律和教学规律。目前国内已经基本具备相关教材,通过调整遗传学教学内容,合理选择教学方法,充分利用计算机辅助教学,在本科教学中整合遗传学与基因组学是可行的。     

Genomics,ICT and the formation of R&D networks

Research in genomics is an example of changes induced by information and communication technologies (ICT). The emergence of interconnected ICT support for scientific work and the handling of information have changed the challenges in genomics as well as other scientific fields. The promises are significant but a large degree of uncertainty remains. While the information space is opened up, R&D cooperation essential to reaping the benefits for companies is still difficult. Moreover, in order to benefit in full from the possibility to combine knowledge on a larger scale, knowledge repositories and places of knowledge creation need to be combined. This paper discusses the new strategies of information networking between companies that emerges in response to this challenge. It concludes with an outline of a research agenda for genomics and society.     

Genomics: Applications,Challenges, and Opportunities for the U.S. Environmental Protection Agency

Genomics information has great potential to enhance assessment of risks to human health and the environment. Although understanding genomic responses with respect to adverse ecological and human health outcomes is not, as yet, established, it is important to consider the likely future impacts of genomics technologies on risk assessment and decision-making. Four areas are identified as those likely to be influenced by the generation of genomics information within, and the submission of such information to, the U.S. Environmental Protection Agency (USEPA): risk assessment, prioritization of contaminants and contaminated sites, monitoring, and reporting provisions. For each of these risk assessment and regulatory applications, representative activities are presented to illustrate the application. Three major challenges for the USEPA associated with genomics are also identified in the areas of research, technical development, and capacity. The USEPA's initial activities to address these challenges are discussed. The Agency recognizes it must be prepared to use genomics information, and that many scientific, policy, ethical, and legal concerns will need to be addressed. The USEPA also recognizes it is essential to continue to collaborate with other federal agencies, academia, the regulated community, and other stakeholders in order to benefit from ongoing advances in genomics in the wider scientific and regulatory communities.     

Functional genomics in the study of yeast cell polarity: moving in the right direction

The budding yeast Saccharomyces cerevisiae has been used extensively for the study of cell polarity, owing to both its experimental tractability and the high conservation of cell polarity and other basic biological processes among eukaryotes. The budding yeast has also served as a pioneer model organism for virtually all genome-scale approaches, including functional genomics, which aims to define gene function and biological pathways systematically through the analysis of high-throughput experimental data. Here, we outline the contributions of functional genomics and high-throughput methodologies to the study of cell polarity in the budding yeast. We integrate data from published genetic screens that use a variety of functional genomics approaches to query different aspects of polarity. Our integrated dataset is enriched for polarity processes, as well as some processes that are not intrinsically linked to cell polarity, and may provide new areas for future study.