Biotechnological advancements in alfalfa improvement

Review of biotechnology research in alfalfa shows that molecular techniques are extensively being used for basic and applied research toward alfalfa improvement. Biotechnological approaches have been used in two major areas, genomics and transgenics. In genomics, molecular markers, structural and functional genomics allowed identification of genes of interest and their regulatory components. Alfalfa being obstinate to genetic and genomic analysis, comparative genomics is used for molecular and genetic dissection of various plant processes in alfalfa. Alternatively, transgenic approach involves incorporation of specific and useful genes into alfalfa to improve the traits of interest. Input traits to improve agronomic performance and output traits to improve forage quality, or to produce novel industrial/pharmaceutical proteins, are the focus of current transgenic research in alfalfa. However, transgenic approach is controversial requiring cautious experimental design to combat bioisafety concerns. Ideally, forage alfalfa needs to possess more fermentable carbohydrates, proteins with balanced amino acid profile that degrade slower in rumen, improved winter hardiness, better water use efficiency, pest resistance and no anti-quality factors. Concerted efforts are required to bring together maximum of these characteristic features into the alfalfa plant.     

Ethical and legal aspects of oncogenomics

The discovery of the genes and cellular pathways that play fundamental roles in several diseases, and the understanding of many diseases at a molecular level due to the advances in the field of genomics, have revolutionized the diagnosis, therapy and prevention of human diseases. Application of genetic testing in numerous medical fields, including pharmacogenomics and oncogenomics, raised numerous ethical questions and introduced legal instruments that are aimed at ensuring the appropriate protection of human research participants. For the effective development of human genomics and translation of novel, validated biomarkers into potentially useful clinical applications in personalized medicine, there is a need for clear ethical standards and principles in all phases of clinical research.     

Advances in cereal genomics and applications in crop breeding

Recent advances in cereal genomics have made it possible to analyse the architecture of cereal genomes and their expressed components, leading to an increase in our knowledge of the genes that are linked to key agronomically important traits. These studies have used molecular genetic mapping of quantitative trait loci (QTL) of several complex traits that are important in breeding. The identification and molecular cloning of genes underlying QTLs offers the possibility to examine the naturally occurring allelic variation for respective complex traits. Novel alleles, identified by functional genomics or haplotype analysis, can enrich the genetic basis of cultivated crops to improve productivity. Advances made in cereal genomics research in recent years thus offer the opportunities to enhance the prediction of phenotypes from genotypes for cereal breeding.     

Comparative genomics in the Brassicaceae: a family-wide perspective

Comparative genomics of Arabidopsis relatives has great potential to improve our understanding of molecular function and evolutionary processes. Recent studies of phylogenetic relationships within Brassicaceae and the publication of a new tribal classification scheme provide an important framework for comparative genomics research. Comparative linkage mapping and chromosome painting in the close relatives of Arabidopsis have inferred an ancestral karyotype of these species. In addition, comparative mapping to Brassica has identified genomic blocks that have been maintained since the divergence of the Arabidopsis and Brassica lineages. Several analyses of conserved non-coding regions have identified putative cis-regulatory sequences, and have highlighted the need for comparative sequencing at greater evolutionary distances. The development of new model species with novel physiological and ecological traits allows analysis of phenotypes that are not available in A. thaliana. Looking towards the future, we suggest a prioritized research agenda for comparative genomics in the Brassicaceae.     

分子标记在绿豆遗传连锁图谱构建和基因定位研究中的应用

绿豆(Vigna radiata(L.)Wilczek)作为一种医食两用作物,不仅是重要的食物资源,在改善土壤环境、提高农民收入等方面也发挥着重要作用。然而,相对于大宗作物而言,绿豆基础研究薄弱,基因组研究更是落后。近年来,分子标记技术迅速发展,在绿豆基因组学研究中发挥了重要的作用。国内外利用分子标记技术已构建了超过20张绿豆遗传连锁图谱。一些优良基因尤其是与抗性相关的基因被鉴定或精细定位,为绿豆分子标记辅助选择打下基础,加快了抗性新品种的培育进程。本研究通过对分子标记技术在绿豆遗传连锁图谱构建、重要功能基因的定位等方面的应用进行综述,以期为绿豆遗传育种研究及功能基因组学分析提供参考。     

蚯蚓基因组学的研究进展: 基于全基因组及线粒体基因组

蚯蚓被喻为土壤中的“生态系统工程师”, 具有高度的多样性且在全世界都有分布, 被用作土壤健康的指示生物。蚯蚓具有极强的环境适应能力, 在不断适应的过程中促进了自身基因组的进化。本文对近年来蚯蚓全基因组以及线粒体基因组的研究进展进行了综述。蚯蚓全基因组的测序、拼装和分析为研究蚯蚓生态学、污染物对蚯蚓致毒的分子机制、免疫防御的分子机制、蚯蚓再生的分子机制等奠定基础。而线粒体基因组多应用于蚯蚓分子系统发育方面的研究, 目前已有多种蚯蚓通过线粒体基因组测序完成了物种的鉴定。本文建议今后重点开展以下几方面的研究: (1)针对现有的4种蚯蚓全基因组测序结果, 进一步进行比较基因组学、进化基因组学和功能基因组学的研究。(2)完善不同种蚯蚓的基因文库和表达序列标签。(3)建立线粒体基因组、全基因组与蚯蚓物种多样性的关联分析。     

Educating health-care professionals about genetics and genomics

To biomedical researchers, this is the 'genome era'. Advances in genetics and genomics such as the sequence of the human genome, the human haplotype map, open access databases, cheaper genotyping and chemical genomics have already transformed basic and translational biomedical research. However, for most clinicians, the genome era has not yet arrived. For genomics to have an effect on clinical practice that is comparable to its impact on research will require advances in the genomic literacy of health-care providers. Here we describe the knowledge, skills and attitudes that genomic medicine will require, and approaches to integrate them into the health-care community.     

基于mRNA水平的差异表达基因筛选技术

随着分子生物学技术的深入发展,基因组研究重点已经由基因组测序转向基因功能鉴定,即由结构基因组学向功能基因组学转变。研究获得不同处理下基因的差异表达谱是功能基因组学的重要一环,目前已经有多种检测基因差异表达的技术可供选用。在减法杂交技术和PCR基础上发展起来的DDRT—PCR、cDNA—RDA、cDNA—AFLP和SSH技术因其实用性而得到广泛的应用,并取得了令人满意的结果。     

Cell biology, chemogenomics and chemoproteomics

The scientific techniques used in molecular biological research and drug discovery have changed dramatically over the past 10 years due to the influence of genomics, proteomics and bioinformatics. Furthermore, genomics and functional genomics are now merging into a new scientific approach called chemogenomics. Advancements in the study of molecular cell biology are dependent upon "omics" researchers realizing the importance of and using the experimental tools currently available to cell biologists. For example, novel microscopic techniques utilizing advanced computer imaging allow for the examination of live specimens in a fourth dimension, viz., time. Yet, molecular biologists have not taken full advantage of these and other traditional and novel cell biology techniques for the further advancement of genomic and proteomic-oriented research. The application of traditional and novel cellular biological techniques will enhance the science of genomics. The authors hypothesize that a stronger interdisciplinary approach must be taken between cell biology (and its closely related fields) and genomics, proteomics and bio-chemoinformatics. Since there is a lot of confusion regarding many of the "omics" definitions, this article also clarifies some of the basic terminology used in genomics, and related fields. It also reviews the current status and future potential of chemogenomics and its relationship to cell biology. The authors also discuss and expand upon the differences between chemogenomics and the relatively new term--chemoproteomics. We conclude that the advances in cell biology methods and approaches and their adoption by "omics" researchers will allow scientists to maximize our knowledge about life.     

Amplified genes as therapeutic targets in cancer

The most effective targeted cancer therapies have arisen from research into genetically altered oncogenes, including BCR-ABL, HER2, RAS and EGFR. Recent advances in cancer genetics have identified many regions of the genome that undergo amplification (increase in copy number) but, in most cases, the key oncogenic targets driving the growth and survival of cancer cells remain unknown. In this review, we discuss high-throughput technologies for the discovery of putative oncogenes, and clinical and functional validation of these genes as targets for therapy. New technologies in translational genomics facilitate the identification, validation and prioritization of candidate molecular targets for anti-cancer therapy.     

基于高通量测序的植物群体基因组学研究进展

作为群体遗传学一种新的表现形式,群体基因组学是将基因组概念和技术与群体遗传学理论体系相结合,通过覆盖全基因组范围内的多态位点的分布式样推测位点特异性效应和全基因组效应,从而提升人们对微进化的理解。近年来,随着第二代高通量测序技术的出现和改进,完成基因组测序的植物种类迅速增加,大规模的重测序也随之开展。与此同时,在一些尚未完成基因组测序的植物物种中,也开展了一些平行测序。这些重测序和平行测序极大地促进了群体基因组学的发展,加深了人们对相关植物种群在基因组水平上的遗传多样性、连锁不平衡水平、选择作用、群体历史及复杂性状的分子机理等群体基因组学方面的认识。本文简要介绍了群体基因组学的概念、研究方法等,重点综述了基于高通量测序的植物群体基因组学的研究动态,展望了植物群体基因组学的发展前景并讨论了存在的问题,以期为相关研究提供借鉴和参考。     

大麦基因组和分子育种研究进展

大麦(Hordeum vulgare L.)是世界上重要的谷类作物之一,其二倍体特性使其成为麦类作物基因组研究的重要材料。随着大量分子标记图谱、BACs文库、突变集合和DNA阵列技术的应用,大麦基因组测序工作已不断深入,越来越多的大麦基因组信息使综合分析大麦基因组结构和功能,了解基因表达网络同重要农艺性状之间的关系成为可能。就大麦基因组研究内容,如ESTs系统、物理图谱的构建、功能基因组学研究和大麦分子育种研究作简要综述,为进一步阐述大麦基因组结构和功能特性,提高大麦分子育种能力提供理论依据。     

Rice genome analysis to understand the rice plant as an assembly of genetic codes

Rice genome research is a recent topic in plant genomics. Because of its importance as the primary staple food for about half of the world's population, breeders, geneticists and molecular biologists in plant fields have strong interest in the resultant research. In this Minireview, results of rice genome research during the past 10 years and future prospects are presented. This revised version was published online in June 2006 with corrections to the Cover Date.     

On the birth of breast cancer

Breast carcinoma is one of the most common neoplasms in women and is a leading cause of cancer related deaths worldwide. In recent years improved diagnostic tools have made it possible to detect breast cancers at early, even pre-invasive stages leading to a significant decrease in breast cancer mortality rates over the past decades. The increased number of patients diagnosed with pre-invasive breast tumors opened up new avenues in research and new dilemmas in clinical practice, since our understanding of the pathophysiology of such lesions is just beginning to emerge. Part of the delay and difficulty with analyzing pre-invasive tumors including ductal carcinoma in situ has been due to the lack of appropriate techniques suitable for studies of small, frequently microscopic size tumors. Recently developed technologies such as DNA microarrays and SAGE (serial analysis of gene expression) have made it possible to obtain comprehensive gene expression profiles of breast carcinomas of all stages. The application of these genomics approaches in combination with the complete sequence of the human genome and extensive molecular epidemiological studies is likely to further our understanding of the molecular basis of mammary tumorigenesis and will identify targets for risk prediction, cancer prevention and treatment.     

Closing the Gap between Knowledge and Clinical Application: Challenges for Genomic Translation

Despite early predictions and rapid progress in research, the introduction of personal genomics into clinical practice has been slow. Several factors contribute to this translational gap between knowledge and clinical application. The evidence available to support genetic test use is often limited, and implementation of new testing programs can be challenging. In addition, the heterogeneity of genomic risk information points to the need for strategies to select and deliver the information most appropriate for particular clinical needs. Accomplishing these tasks also requires recognition that some expectations for personal genomics are unrealistic, notably expectations concerning the clinical utility of genomic risk assessment for common complex diseases. Efforts are needed to improve the body of evidence addressing clinical outcomes for genomics, apply implementation science to personal genomics, and develop realistic goals for genomic risk assessment. In addition, translational research should emphasize the broader benefits of genomic knowledge, including applications of genomic research that provide clinical benefit outside the context of personal genomic risk.     

基因组学方法在玉米种质资源研究中的应用

近年来,分子生物学和植物基因组学得到了飞速发展,包括分子标记技术在内的基因组学方法在玉米种质资源研究中得到了广泛应用。本将对玉米种质资源研究的主要领域如玉米的起源和进化、遗传多样性的形成机制及评估、基于多样性的新基因发掘等方面的最新进展进行评述,并提出我国在应用基因组学方法进行玉米种质资源研究的策略。     

Metabolic profiling, metabolomic and metabonomic procedures for NMR spectroscopy of urine, plasma, serum and tissue extracts

Metabolic profiling, metabolomic and metabonomic studies mainly involve the multicomponent analysis of biological fluids, tissue and cell extracts using NMR spectroscopy and/or mass spectrometry (MS). We summarize the main NMR spectroscopic applications in modern metabolic research, and provide detailed protocols for biofluid (urine, serum/plasma) and tissue sample collection and preparation, including the extraction of polar and lipophilic metabolites from tissues. 1H NMR spectroscopic techniques such as standard 1D spectroscopy, relaxation-edited, diffusion-edited and 2D J-resolved pulse sequences are widely used at the analysis stage to monitor different groups of metabolites and are described here. They are often followed by more detailed statistical analysis or additional 2D NMR analysis for biomarker discovery. The standard acquisition time per sample is 4-5 min for a simple 1D spectrum, and both preparation and analysis can be automated to allow application to high-throughput screening for clinical diagnostic and toxicological studies, as well as molecular phenotyping and functional genomics.