Developmental biology meets with reproductive engineering; interdisciplinary science area as a breakthrough.

It has been postulated many times that different scientific topics and strategies often encounter each other, which create cutting edge research field resulting in further significant progresses of science. This was also a lesson bestowed by Prof. Raymond Wegmann where he created innovative research field for biology, molecular biology and biochemistry-biophysics. Progresses of developmental biology were boosted by molecular biology and reproductive engineering where ES cells and embryonic manipulation are necessary. There are no questions about the utility of their technologies. Reviews on their contributions with respect to the condition of genome manipulation are addressed.     

The use of evolutionary biology concepts for genome annotation

The past decade has seen the completion of numerous whole-genome sequencing projects, began with bacterial genomes and continued with eukaryotic species from different phyla: fungi, plants and animals. Besides, more biological information are produced and are shared thanks to information exchange systems, and more biological concepts, as well as more bioinformatics tools, are available. In this article, we will describe how the evolutionary biology concepts, as well as computer science, are useful for a better understanding of biology in general and genome annotation in particular. The genome annotation process consists of taking the raw DNA produced, for example, by the genome sequencing projects, adding the layers of analysis and interpretation necessary to extract its biological significance and placing it in the context of our understanding of biological processes. Genome annotation is a multistep process falling into two broad categories: structural and functional annotation.     

Mass spectrometry in the biology of RNA and its modifications

Many powerful analytical techniques for investigation of nucleic acids exist in the average modern molecular biology lab. The current review will focus on questions in RNA biology that have been answered by the use of mass spectrometry, which means that new biological information is the purpose and outcome of most of the studies we refer to. The review begins with a brief account of the subject "MS in the biology of RNA" and an overview of the prevalent RNA modifications identified to date. Fundamental considerations about mass spectrometric analysis of RNA are presented with the aim of detailing the analytical possibilities and challenges relating to the unique chemical nature of nucleic acids. The main biological topics covered are RNA modifications and the enzymes that perform the modifications. Modifications of RNA are essential in biology, and it is a field where mass spectrometry clearly adds knowledge of biological importance compared to traditional methods used in nucleic acid research. The biological applications are divided into analyses exclusively performed at the building block (mainly nucleoside) level and investigations involving mass spectrometry at the oligonucleotide level. We conclude the review discussing aspects of RNA identification and quantifications, which are upcoming fields for MS in RNA research. This article is part of a Special Section entitled: Understanding genome regulation and genetic diversity by mass spectrometry.     

基因组结构信息在动物系统发育研究中的应用

随着人类基因组和一些模式生物、重要经济生物以及大量微生物基因组测序的完成,生物学整体研究业已进入基因组时代.最近5～10年以来,利用基因组结构信息进行系统发育推断的研究形成了分类学和进化生物学中的前沿领域之一.相对于核苷酸或氨基酸序列中的突变而言,基因组的结构变化--内含子的插入/缺失、反转录子的整合、签名序列、基因重复以及基因排序等--是更大空间(或者时间空间)尺度上的相对稀缺的系统发育信息,一般用于科和科以上阶元间的亲缘关系研究.基因组全序列的获得和其中各基因位置的确定有利于将基因组中不同层次的系统发育信息综合起来,利用全面分子证据(total molecular evidence;包括基因组信息,DNA、RNA、蛋白质的序列信息,RNA和蛋白质的高级结构等)进行分子系统学研究.     

Plant molecular biology in China: Opportunities and challenges

In the 21st century, mankind has witnessed great advances in life sciences, including completion of theArabidopsis thaliana genome sequence and major advances with the rice genome. But, along with global economic development, urbanization, and depletion of natural resources, many serious problems are emerging (for example, environment, food, population, energy), which reinforce the need for sustainable development in many countries and in many institutions and prompt progress in life sciences globally. Plants offer the globe its only renewable resource of food, building material, and energy. Plants have highly sophisticated, concerted, short- and long-term adaptive mechanisms to the environment. Plants have great importance in global sustainable economic development. Plant molecular biology is a most essential and powerful tool in this process. Globally, plant molecular biology research is progressing rapidly, from use of model plants to cereal crops and from cellular processes to evolutionary mechanisms. Results of these studies have value in ecosystem regulation and environmental phytoremediation. China is a large agricultural country with one-fifth of the world's population. The gap for the level of plant molecular biology research in China is large, compared with that in other developed nations. However, some Chinese laboratories (notably those of academicians Jiayang Li, Zhihong Xu, Zhensheng Li, Mengmin Hong, Qifa Zhang and professors Yonbiao Xue, Shouyi Chen, and Zhen Zhu) have kept pace with international developments in plant molecular biology. How to fully utilize plant biodiversity in China requires future advances in plant molecular biology. This minireview discusses opportunities and challenges in plant molecular biology in China, analyzes the current status of international plant molecular biology, and provides suggestions to accelerate and advance international efforts. These authors contributed to this paper equally. Editorial note: This paper, with minor editing, is as it was presented by the authors at the Genetics Advancing Meeting of the Chinese Society of Genetics, Xiamen University, China, 13–17 May 2004.     

A gentle introduction to SNP analysis: resources and tools

Bioinformatics is the use of informatics tools and techniques in the study of molecular biology, genetic, or clinical data. The field of bioinformatics has expanded tremendously to cope with the large expansion of information generated by the mouse and human genome projects, as newer generations of computers that are much more powerful have emerged in the commercial market. It is now possible to employ the computing hardware and software at hand to generate novel methodologies in order to link data across the different databanks generated by these international projects and derive clinical and biological relevance from all of the information gathered. The ultimate goal would be to develop a computer program that can provide information correlating genes, their single nucleotide polymorphisms (SNPs), and the possible structural and functional effects on the encoded proteins with relation to known information on complex diseases with great ease and speed. Here, the recent developments of available software methods to analyze SNPs in relation to complex diseases are reviewed with emphasis on the type of predictions on protein structure and functions that can be made. The need for further development of comprehensive bioinformatics tools that can cope with information generated by the genomics communities is emphasized.     

竹子分子生物学研究进展(英文)

对2003年以来的竹子分子生物学研究进展进行了综述,包括现代分子手段在竹子分类学研究中的开发与应用,鞭芽发育、快速生长、开花、抗逆等相关的重要功能基因研究,基因组测序和转录组测序,遗传转化体系的建立等。这些为今后竹子生物学的研究提供了依据。     

Genomes and genome projects of protozoan parasites

Protozoan parasites are causing some of the most devastating diseases world-wide. It has now been recognised that a major effort is needed to be able to control or eliminate these diseases. Genome projects for the most important protozoan parasites have been initiated in the hope that the read-out of these projects will help to understand the biology of the parasites and identify new targets for urgently needed drugs. Here, I will review the current status of protozoan parasite genome projects, present findings obtained as a result of the availability of genomic data and discuss the potential impact of genome information on disease control.     

Genome evolution and biodiversity in teleost fish

Teleost fish, which roughly make up half of the extant vertebrate species, exhibit an amazing level of biodiversity affecting their morphology, ecology and behaviour as well as many other aspects of their biology. This huge variability makes fish extremely attractive for the study of many biological questions, particularly of those related to evolution. New insights gained from different teleost species and sequencing projects have recently revealed several peculiar features of fish genomes that might have played a role in fish evolution and speciation. There is now substantial evidence that a round of tetraploidization/rediploidization has taken place during the early evolution of the ray-finned fish lineage, and that hundreds of duplicate pairs generated by this event have been maintained over hundreds of millions of years of evolution. Differential loss or subfunction partitioning of such gene duplicates might have been involved in the generation of fish variability. In contrast to mammalian genomes, teleost genomes also contain multiple families of active transposable elements, which might have played a role in speciation by affecting hybrid sterility and viability. Finally, the amazing diversity of sex determination systems and the plasticity of sex chromosomes observed in teleost might have been involved in both pre- and postmating reproductive isolation. Comparison of data generated by current and future genome projects as well as complementary studies in other species will allow one to approach the molecular and evolutionary mechanisms underlying genome diversity in fish, and will certainly significantly contribute to our understanding of gene evolution and function in humans and other vertebrates.     

昆虫基因组及数据库研究进展

基因组序列为昆虫分子生物学研究提供丰富的数据资源,推动系统生物学在古老的昆虫学中蓬勃发展。昆虫基因组学研究已经成为当前的研究热点,目前在NCBI登录注册的昆虫基因组测序计划有494项,其中已提交原始测序数据的昆虫有225种,完成基因组拼接的有215种,具有基因注释的有65种,公开发表的昆虫基因组有43篇。本文综述了测序技术发展的历史及其对昆虫基因组研究的推动作用、昆虫基因组的组装和注释及其存在的问题、昆虫基因组测序进展、昆虫基因组数据库的发展及基因数据挖掘利用的基本思路和对策,以及昆虫基因大数据在害虫防治和资源昆虫利用中的应用前景。     

MACROALGAL CANDIDATES FOR GENOMICS

Waaland, J. R.¹ & Stiller, J. W.^{2 1}Department of Botany, University of Washington, Seattle, WA 98195 USA; ²Department of Biology, East Carolina University, Greenville, NC 27858 USA Macroalgae are important components of aquatic ecosystems. Some are harvested or cultivated for economic uses while others are of interest for their phylogenetic or systematic positions. Although most genes known from macroalgae have been isolated for comparative evolutionary analysis, some have been the subject of more detailed molecular investigations. We examine the current state of knowledge for several macroalgae as candidates for genomic study. Selection criteria for target taxa include features such as a well known sexual life history, availability of established laboratory cultures, mutant strains, basic genetic studies, fossil records, and ecological and economic importance. Among the algae to be considered are: Porphyra, Gracilaria, Ectocarpus, Macrocystis, Laminaria, Fucus, Ulva, Chara and Nitella. A strong case can be made for each of these taxa; however, we will emphasize Porphyra yezoensis because of its importance as a food source, its well-characterized and easily manipulated reproductive biology, its relatively small genome size, and recent technical advances in genetic manipulation that should lead to fruitful exploitation of genomic information as it becomes available. Further, the genome of a red alga is an attractive target for comparison with those of other multicellular eukaryotes that have been the object of sequencing projects thus far.     

ASTRO-FOLD: a combinatorial and global optimization framework for Ab initio prediction of three-dimensional structures of proteins from the amino acid sequence

The field of computational biology has been revolutionized by recent advances in genomics. The completion of a number of genome projects, including that of the human genome, has paved the way toward a variety of challenges and opportunities in bioinformatics and biological systems engineering. One of the first challenges has been the determination of the structures of proteins encoded by the individual genes. This problem, which represents the progression from sequence to structure (genomics to structural genomics), has been widely known as the structure-prediction-in-protein-folding problem. We present the development and application of ASTRO-FOLD, a novel and complete approach for the ab initio prediction of protein structures given only the amino acid sequences of the proteins. The approach exhibits many novel components and the merits of its application are examined for a suite of protein systems, including a number of targets from several critical-assessment-of-structure-prediction experiments.     

A passion for the science of the human genome

The complete sequencing of the human genome introduced a new knowledge base for decoding information structured in DNA sequence variation. My research is predicated on the supposition that the genome is the most sophisticated knowledge system known, as evidenced by the exquisite information it encodes on biochemical pathways and molecular processes underlying the biology of health and disease. Also, as a living legacy of human origins, migrations, adaptations, and identity, the genome communicates through the complexity of sequence variation expressed in population diversity. As a biomedical research scientist and academician, a question I am often asked is: “How is it that a black woman like you went to the University of Michigan for a PhD in Human Genetics?” As the ASCB 2012 E. E. Just Lecturer, I am honored and privileged to respond to this question in this essay on the science of the human genome and my career perspectives.

“Knowledge is power, but wisdom is supreme.”

     

Monitoring genome-wide expression in plants

When completed this year, the Arabidopsis genome will represent the first plant genome to be fully sequenced. This sequence information, together with the large collection of expressed sequence tags, has established the basics for new approaches to studying gene expression patterns in plants on a global scale. We can now look at biology from the perspective of the whole genome. This revolution in the study of how all genes in an organism respond to certain stimuli has encouraged us to think in new dimensions. Expression profiles can be determined over a range of experimental conditions and organized into patterns that are diagnostic for the biological state of the cell. The field of genome-wide expression in plants has yet to produce its fruit; however, the current application of microarrays in yeast and human research foreshadows the diverse applications this technology could have in plant biology and agriculture.     

Gene regulatory network inference: Data integration in dynamic models—A review

Systems biology aims to develop mathematical models of biological systems by integrating experimental and theoretical techniques. During the last decade, many systems biological approaches that base on genome-wide data have been developed to unravel the complexity of gene regulation. This review deals with the reconstruction of gene regulatory networks (GRNs) from experimental data through computational methods. Standard GRN inference methods primarily use gene expression data derived from microarrays. However, the incorporation of additional information from heterogeneous data sources, e.g. genome sequence and protein–DNA interaction data, clearly supports the network inference process. This review focuses on promising modelling approaches that use such diverse types of molecular biological information. In particular, approaches are discussed that enable the modelling of the dynamics of gene regulatory systems. The review provides an overview of common modelling schemes and learning algorithms and outlines current challenges in GRN modelling.     

The expanding footprint of CRISPR/Cas9 in the plant sciences

CRISPR/Cas9 has evolved and transformed the field of biology at an unprecedented pace. From the initial purpose of introducing a site specific mutation within a genome of choice, this technology has morphed into enabling a wide array of molecular applications, including site-specific transgene insertion and multiplexing for the simultaneous induction of multiple cleavage events. Efficiency, specificity, and flexibility are key attributes that have solidified CRISPR/Cas9 as the genome-editing tool of choice by scientists from all areas of biology. Within the field of plant biology, several CRISPR/Cas9 technologies, developed in other biological systems, have been successfully implemented to probe plant gene function and to modify specific crop traits. It is anticipated that this trend will persist and lead to the development of new applications and modifications of the CRISPR technology, adding to an ever-expanding collection of genome-editing tools. We envision that these tools will bestow plant researchers with new utilities to alter genome complexity, engineer site-specific integration events, control gene expression, generate transgene-free edited crops, and prevent or cure plant viral disease. The successful implementation of such utilities will represent a new frontier in plant biotechnology.     

The yeast genome: on the road to the Golden Age

Having the complete genome sequence of Saccharomyces cerevisiae makes us aware of the ultimate goal of yeast molecular biology: the 'solution' of the cell, that is, an understanding of the function of all approximately 6000 proteins (and a few RNAs) and how they interact with each other and the environment. The recent development of 'genomic' approaches for studying gene function makes this goal seem reachable in the foreseeable future. When this is accomplished, we will have entered a Golden Age, when we will have the information necessary for designing truly incisive experiments to reveal biological function.