Global Genomic Regulatory Code for the gastrula stage sea urchin embryo
原肠胚阶段海胆胚胎的全球基因组监管代码
基本信息
- 批准号:8055256
- 负责人:
- 金额:$ 3.56万
- 依托单位:
- 依托单位国家:美国
- 项目类别:
- 财政年份:2009
- 资助国家:美国
- 起止时间:2009-06-01 至 2014-05-31
- 项目状态:已结题
- 来源:
- 关键词:AddendumAreaBiologicalBiological ProcessBooksCellsCodeDNA SequenceDataDevelopmentDevelopmental BiologyDevelopmental GeneEctodermEmbryoEndodermEndomesodermEtiologyEvolutionGastrocoeleGastrulaGene ExpressionGenesGenomeGenomicsGrantHandHindgutInstructionKnowledgeLengthLiteratureMesoderm CellMethodologyMethodsMidgutOralOrganismPaperPathway AnalysisPatternPerformancePhasePlant RootsPlayPrimitive foregut structurePrintingProceduresProcessProgress ReportsProteinsPublished CommentPublishingRegulator GenesResearchSamplingSea UrchinsSignal TransductionSpecific qualifier valueStagingStructureSystemTechnologyTimeUpdateValidationWorkbasec newcell typefollow-upgastrulationimprovednetwork modelsnew technologynotch proteinoperationoral ectodermprogramstheoriestranscription factor
项目摘要
I am gratified at the level of enthusiasm expressed by reviewers of this Component, which is consequently little altered from the original in this submission. Everything can be improved however, and some additional clarifications have been added in places where Reviewers commented that the approaches were insufficiently described, or particular problems that might be encountered were raised. Specifically these addenda are: (1) I have dealt more explicitly with the problem of controlling perturbations of genes when and
where desired, particularly for the not infrequent case that a regulatory gene is required at an earlier phase of development (# vi under procedural discussion of S.A.I). (2) I have clarified conceptual procedures for the global network project (additional discussion in # 1 of S.A.4).
A reviewer commented that the methodology to be utilized in examining vertebrate GRNs as they emerge for significant homologies with sea urchin GRNs was "vague." I would like to note that virtually the only systematic trans-clade GRN homology studies (in the strict sense) in the literature have come from our works, and this matter is discussed critically and at length in Chapter 5 of my recent book "The Regulatory Genome:
Gene Networks in Development and Evolution" (2006).
S.A. 7 is now focused exclusively on providing GRN explanations for the dynamic changes in spatial expression of the key genes that are the subject of S.A.I of the McClay Component. This objective is motivated strongly by the very recent work of Smith and Davidson (In press, 2008b; Appendix; summarized in Progress Report), which has expanded even further the potency of GRNs as an explanation for development:
here we show how the genomic code directly controls a dynamic, spatially changing pattern of Wnt8 and Notch signaling. This work shows the way to be followed in additional problems of causality in understanding dynamic patterning.
A reviewer commented that there may be less integration between the Bronner-Fraser Component and the Davidson Component in re S.A.S, which is explicitly directed toward that interaction. I would like to note in this connection the recent track record: the published works of Marianne Bronner-Fraser display extensive evidence of the close influence our GRN theory and practice has had on her research orientation:
she is using BioTapestry; she is organizing perturbation analyses in her system directly analogous to ours; she is using many of our methods; she is carrying out cis-regulatory studies of key genes just as do we; etc. The current plans will accentuate and intensify these interactions, but the point is that they are already scientifically real and important.
Figure 2. has been updated as the GRN has grown particularly in the endoderm area since the original Application was submitted; and Fig.9, the provisional ectoderm GRN, likewise.
Finally, since the original application, we have data showing the brilliant performance of the NanoString nCounter, a small sample of which is now illustrated in Section 3c2. Also in the way of progress, 7 papers acknowledging this Grant have appeared in print or are newly in Press in the months since the original Application was submitted. Many of these were discussed in that Application, as they were then In Press,
including the paper on the new technology for blocking gene expression under c/s-regulatory control (Smith et al, 2008a). There is in addition a paper describing NanoString technology and its initial validation (Geiss et al, 2008). However, the paper of Smith et al (2008b) on programming of dynamically changing spatial patterns mentioned above is of particular importance and is included here as an Appendix, together with a brief review
on GRN circuitry (Davidson and Levine, 2008).
我对审稿人对这一组成部分所表达的热情程度感到满意,因此,这一组成部分在提交的文件中几乎没有改变。但是,一切都可以改进,并且在评论者评论方法描述不够充分的地方添加了一些额外的澄清,或者提出了可能遇到的特定问题。具体来说,这些补充是:(1)我已经更明确地处理了控制基因扰动的问题
项目成果
期刊论文数量(0)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
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ERIC H DAVIDSON其他文献
ERIC H DAVIDSON的其他文献
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{{ truncateString('ERIC H DAVIDSON', 18)}}的其他基金
Depth and Breadth of Explanatory Power in Developmental GRNs
发展 GRN 解释力的深度和广度
- 批准号:
8752112 - 财政年份:2014
- 资助金额:
$ 3.56万 - 项目类别:
GLOBAL GENE REGULATORY NETWORKS FOR SPECIFIC CELL TYPES OF THE SEA URCHIN EMBRYO
海胆胚胎特定细胞类型的全球基因调控网络
- 批准号:
8288724 - 财政年份:2010
- 资助金额:
$ 3.56万 - 项目类别:
GLOBAL GENE REGULATORY NETWORKS FOR SPECIFIC CELL TYPES OF THE SEA URCHIN EMBRYO
海胆胚胎特定细胞类型的全球基因调控网络
- 批准号:
8022781 - 财政年份:2010
- 资助金额:
$ 3.56万 - 项目类别:
Global Genomic Regulatory Code for the gastrula stage sea urchin embryo
原肠胚阶段海胆胚胎的全球基因组监管代码
- 批准号:
8092699 - 财政年份:2010
- 资助金额:
$ 3.56万 - 项目类别:
Specialized Research Support Core (SRC CORE)
专业研究支持核心(SRC CORE)
- 批准号:
8092702 - 财政年份:2010
- 资助金额:
$ 3.56万 - 项目类别:
GLOBAL GENE REGULATORY NETWORKS FOR SPECIFIC CELL TYPES OF THE SEA URCHIN EMBRYO
海胆胚胎特定细胞类型的全球基因调控网络
- 批准号:
8463580 - 财政年份:2010
- 资助金额:
$ 3.56万 - 项目类别:
GLOBAL GENE REGULATORY NETWORKS FOR SPECIFIC CELL TYPES OF THE SEA URCHIN EMBRYO
海胆胚胎特定细胞类型的全球基因调控网络
- 批准号:
8149931 - 财政年份:2010
- 资助金额:
$ 3.56万 - 项目类别:
Scientific and Administrative Coordination Core (SAC CORE)
科学和行政协调核心(SAC CORE)
- 批准号:
8092703 - 财政年份:2010
- 资助金额:
$ 3.56万 - 项目类别:
Egg to Embryo: Gene Regulatory Circuitry in Development
卵子到胚胎:发育中的基因调控回路
- 批准号:
8049418 - 财政年份:2010
- 资助金额:
$ 3.56万 - 项目类别:
Egg to Embryo: Gene Regulatory Circuitry in Development
卵子到胚胎:发育中的基因调控回路
- 批准号:
7881821 - 财政年份:2009
- 资助金额:
$ 3.56万 - 项目类别:
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