Microdissection of the gene expression codes driving nephrogenesis

The kidney represents an excellent model system for learning the principles of organogenesis. It is intermediate in complexity, and employs many commonly used developmental processes. As such, kidney development has been the subject of intensive study, using a variety of techniques, including in situ hybridization, organ culture and gene targeting, revealing many critical genes and pathways. Nevertheless, proper organogenesis requires precise patterns of cell type specific differential gene expression, involving very large numbers of genes. This review is focused on the use of global profiling technologies to create an atlas of gene expression codes driving development of different mammalian kidney compartments. Such an atlas allows one to select a gene of interest, and to determine its expression level in each element of the developing kidney, or to select a structure of interest, such as the renal vesicle, and to examine its complete gene expression state. Novel component specific molecular markers are identified, and the changing waves of gene expression that drive nephrogenesis are defined. As the tools continue to improve for the purification of specific cell types and expression profiling of even individual cells it is possible to predict an atlas of gene expression during kidney development that extends to single cell resolution.     

Microdissection of the gene expression codes driving nephrogenesis

The kidney represents an excellent model system for learning the principles of organogenesis. It is intermediate in complexity, and employs many commonly used developmental processes. As such, kidney development has been the subject of intensive study, using a variety of techniques, including in situ hybridization, organ culture and gene targeting, revealing many critical genes and pathways. Nevertheless, proper organogenesis requires precise patterns of cell type specific differential gene expression, involving very large numbers of genes. This review is focused on the use of global profiling technologies to create an atlas of gene expression codes driving development of different mammalian kidney compartments. Such an atlas allows one to select a gene of interest, and to determine its expression level in each element of the developing kidney, or to select a structure of interest, such as the renal vesicle, and to examine its complete gene expression state. Novel component specific molecular markers are identified, and the changing waves of gene expression that drive nephrogenesis are defined. As the tools continue to improve for the purification of specific cell types and expression profiling of even individual cells it is possible to predict an atlas of gene expression during kidney development that extends to single cell resolution.     

The molecular mechanisms of male reproductive organogenesis in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

Stamen is the male reproductive organ of rice (Oryza sativa L.), and the development is a considerably significant stage during the sexual reproduction. It is very important to reveal what is the molecular mechanisms which controlling the development of stamen, and will be helpful in producing hybrid seeds by manipulating the male sterility. This article reviews the progress on the molecular mechanisms of male reproductive organogenesis in rice, which would facilitate the further studies on male sterile genes in rice.     

The anatomy of organogenesis: Novel solutions to old problems

Understanding anatomical aspects of mammalian organ development, in both normal and mutant animals, is important for basic biology and also for regenerative medicine and tissue engineering. The size and complexity of developing organs, together with variations in their detailed anatomy, has made the obtaining of high-resolution time-courses of anatomical change difficult to obtain. The fact that organ development tends to use the same genes as early embryogenesis also makes genetic manipulation difficult, as so many mutant embryos die before organogenesis begins. These problems have seriously hampered the study of organogenesis. Here, we describe three significant advances that promise solutions: (1) the production of GFP-reporter mice that can be used for high-resolution live-imaging of small tissues as they grow, (2) RNA interference, which allows the manipulation of specific genes at any stage of organ development, and (3) optical projection tomography, which allows medium-resolution three-dimensional images of complete embryos to be obtained easily. We finish by looking ahead to the prospects of uniting these three technologies to allow accurate, high-throughput screening of mutants and automated comparison of biological data with computer predictions.     

The anatomy of organogenesis: novel solutions to old problems

Understanding anatomical aspects of mammalian organ development, in both normal and mutant animals, is important for basic biology and also for regenerative medicine and tissue engineering. The size and complexity of developing organs, together with variations in their detailed anatomy, has made the obtaining of high-resolution time-courses of anatomical change difficult to obtain. The fact that organ development tends to use the same genes as early embryogenesis also makes genetic manipulation difficult, as so many mutant embryos die before organogenesis begins. These problems have seriously hampered the study of organogenesis. Here, we describe three significant advances that promise solutions: (1) the production of GFP-reporter mice that can be used for high-resolution live-imaging of small tissues as they grow, (2) RNA interference, which allows the manipulation of specific genes at any stage of organ development, and (3) optical projection tomography, which allows medium-resolution three-dimensional images of complete embryos to be obtained easily. We finish by looking ahead to the prospects of uniting these three technologies to allow accurate, high-throughput screening of mutants and automated comparison of biological data with computer predictions.     

Downstream of homeotic genes: in the heart of Hox function

A functional organ is constituted of diverse cell types. Each one occupies a distinct position and is associated to specific morphological and physiological functions. The identification of the genetic programs controlling these elaborated and highly precise features of organogenesis is crucial to understand how a mature organ works under normal conditions, and how pathologies can develop. Recently, a number of studies have reported a critical role for Hox genes in one example of organogenesis: cardiogenesis in Drosophila. Beyond the interest in understanding the molecular basis of functional cardiogenesis, this system might provide a model for proposing new paradigms of how Hox genes achieve their action throughout development.     

药用植物基因工程的研究进展

从农杆菌诱导的转基因器官的培养,模式基因工程,目的基因的遗传转化等方面概述了药用植物基因工程研究及应用中的最新进展,并展望了今后发展的方向及前景。     

植物离体器官发生控制机理研究进展

植物离体器官发生不仅是获得大量无性繁殖植物和进行基因转化的重要途径, 而且亦是研究植物发育问题的主要实验系统之一。迄今为止, 包括营养器官和生殖器官在内的几乎所有的器官都可以在离体条件下得到再生, 为深入研究植物离体器官发生的分子机理奠定了基础。本文着重介绍了营养器官发生过程基因表达的调节及重要功能基因的作用, 并对器官特征决定基因在生殖器官发生过程中的作用进行了分析, 提出了揭示离体器官发生分子机理的主要途径。     

植物离体器官发生控制机理研究进展

植物离体器官发生不仅是获得大量无性繁殖植物和进行基因转化的重要途径,而且亦是研究植物发育问题的主要实验系统之一。迄今为止,包括营养器官和生殖器官在内的几乎所有的器官都可以在离体条件下得到再生,为深入研究植物离体器官发生的分子机理奠定了基础。本文着重介绍了营养器官发生过程基因表达的调节及重要功能基因的作用,并对器官特征决定基因在生殖器官发生过程中的作用进行了分析,提出了揭示离体器官发生分子机理的主要途径。     

Commercial potential of RNAi

The commercial potential of RNAi is assessed on the basis of successful translation of technology into applications in three areas: (1) drug discovery and research-currently the biggest segment; (2) potential therapeutic applications; and (3) the role of microRNA in molecular diagnostics. RNAi is an important method for analyzing gene function and identifying new drug targets that use dsRNA to knock down or silence specific genes. Sets of siRNAs focused on a specific gene class (siRNA libraries) have the capacity to greatly increase the pace of pathway analysis and functional genomics. RNAi plays an important role in drug discovery by facilitating target validation. The discovery of the role of microRNA (miRNAs) in various pathological processes opens up possible applications in molecular diagnostics, particularly that of cancer. The advantages of RNAi-based therapeutics over traditional pharmaceuticals include the capability for more specific therapies with small molecule siRNA. Drawbacks include the development of resistance in cancer and viral infections as well as the interferon effect. RNAi is closely related to gene therapy and the vectors developed for gene therapy are also being used for delivery of siRNAs. RNAi, along with other related technologies, will contribute to the development of personalised medicine. Although none of the RNAi-based drugs is in the market yet, some are in clinical trials. By the year 2010 the market for RNAi-based drugs is expected to be worth 3.5 billion dollars and is expected to expand to 10.5 billion dollars by the year 2015.     

基于基因本体论的模式生物分子功能分布异同

基因本体论是关于基因和蛋白质知识的标准词汇,也是今后实现各种与基因相关的数据统一、数据转换、数据挖掘的基础。本文通过分子功能基因本体论比较了不同模式生物基因产物分子功能分布的异同。结果发现:在动物类、植物类以及真菌类模式生物中,大部分已知功能基因的分布比例是基本一致的,存在一定的同源性;但在动物中结合类基因数量较多而在植物与真菌中反而催化类基因数量较多,信号传导相关基因在动物中的分布数量多间接证明了动物在进化上的高等性,而植物中特有的大分子传递相关编码基因,可能与植物的养分、水分在机体种的传输相关。     

Mutations affecting thymus organogenesis in Medaka, Oryzias latipes

The thymus is an organ for T lymphocyte maturation and is indispensable for the establishment of a highly developed immune system in vertebrates. In order to genetically dissect thymus organogenesis, we carried out a large-scale mutagenesis screening for Medaka mutations affecting recombination activating gene 1 (rag1) expression in the developing thymus. We identified 24 mutations, defining at least 13 genes, which led to a marked reduction of rag1 expression in the thymus. As thymus development depends on pharyngeal arches, we classified those mutations into three classes according to the defects in the pharyngeal arches. Class 1 mutants had no or slight morphological abnormalities in the pharyngeal arches, implying that the mutations may include defects in such thymus-specific events as lymphocyte development and thymic epithelial cell maturation. Class 2 mutants had abnormally shaped pharyngeal arches. Class 3 mutants showed severely attenuated pharyngeal arch development. In Class 2 and Class 3 mutants, the defects in thymus development may be due to abnormal pharyngeal arch development. Those mutations are expected to be useful for identifying the molecular mechanisms underlying thymus organogenesis.     

Analysis of WT1 gene expression during mouse nephrogenesis in organ culture

Summary The temporal and spatial expression patterns of the Wilms tumor gene, WT1, were studied during the organogenesis of the mouse kidneyin vitro. In situ hybridization and immunocytochemistry localized cellular expression of WT1 in whole kidney organ cultures to the induced metanephric mesenchyme and developing podocytes. Organ cultures were further characterized immunocytochemically with antibodies that specifically labeled the different tubular epithelial components and supporting mesenchyme of the developing nephrons. In organ cultures, the WT1 expression pattern could be visualized in induced metanephric mesenchyme and entire cell cohorts of differentiating podocytes. Expression of WT1 and cell specific markers were retained in short-term monolayer cultures of dissociated kidneys. The development of the metanephric kidneyin vitro involves a highly restricted temporal and spatial cellular expression pattern of WT1 which closely follows that observed in tissue sections from gestational kidney isolated during organogenesis in the mouse.     

Knockdown of chimeric glucocerebrosidase by green fluorescent protein-directed small interfering RNA

Gaucher disease, the most common type of lysosomal storage disorder, is characterized by an inherited deficiency of the membrane-associated hydrolase, glucocerebrosidase. Glucocerebrosidase catalyzes the hydrolysis of glucocerebroside to ceramide and glucose, a crucial step in the recycling of membrane sphingolipids. The exorbitant cost of the current treatment standard for Gaucher disease, enzyme replacement therapy, prevents many from receiving treatment. This limitation has led to a wide-spread search for more efficient and cost-effective methods of protein production and alternate therapies, resulting in a closer examination of glucocerebrosidase biosynthesis and current treatment techniques. The use of specific small interfering RNAs (siRNAs) to knock down target genes is an attractive option for studying such processes, though a glucocerebrosidase-specific siRNA has yet to be reported. We note, however, that green fluorescent protein (GFP)-directed siRNAs can not only provide a positive control to test siRNA delivery and system integrity, but also serve as a means to knock down a fusion partner without having to design siRNAs specific to the partner. After effectively co-transfecting COS-1 cells with enhanced GFP (EGFP)-tagged glucocerebrosidase constructs and GFP-directed siRNAs, we report successful knockdown of all EGFP-containing constructs at both the RNA and protein levels. This provides a method of examining enzyme biosynthesis and treatment options. Furthermore, this technique is applicable to other systems, since we have demonstrated the usefulness of GFP as a siRNA target in mammalian cells when fused to another gene of interest.     

Role of AUX1 in the control of organ identity during in vitro organogenesis and in mediating tissue specific auxin and cytokinin interaction in <Emphasis Type="Italic">Arabidopsis</Emphasis>

Classic plant tissue culture experiments have shown that exposure of cell culture to a high auxin to cytokinin ratio promotes root formation and a low auxin to cytokinin ratio leads to shoot regeneration. It has been widely accepted that auxin and cytokinin play an antagonistic role in the control of organ identities during organogenesis in vitro. Since the auxin level is highly elevated in the shoot meristem tissues, it is unclear how a low auxin to cytokinin ratio promotes the regeneration of shoots. To identify genes mediating the cytokinin and auxin interaction during organogenesis in vitro, three allelic mutants that display root instead of shoot regeneration in response to a low auxin to cytokinin ratio are identified using a forward genetic approach in Arabidopsis. Molecular characterization shows that the mutations disrupt the AUX1 gene, which has been reported to regulate auxin influx in plants. Meanwhile, we find that cytokinin substantially stimulates auxin accumulation and redistribution in calli and some specific tissues of Arabidopsis seedlings. In the aux1 mutants, the cytokinin regulated auxin accumulation and redistribution is substantially reduced in both calli and specific tissues of young seedlings. Our results suggest that auxin elevation and other changes stimulated by cytokinin, instead of low auxin or exogenous auxin directly applied, is essential for shoot regeneration. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.