共查询到20条相似文献,搜索用时 15 毫秒
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A bioinformatics approach to investigating developmental pathways in the kidney and other tissues. 总被引:3,自引:0,他引:3
J B Bard 《The International journal of developmental biology》1999,43(5):397-403
Over the past few years, large amounts of data linking gene-expression (GE) patterns and other genetic data with the development of the mouse kidney have been published, and the next task will be to integrate these data with the molecular networks responsible for the emergence of the kidney phenotype. This paper discusses how a start to this task can be made by using the kidney database and its associated search tools, and shows how the data generated by such an approach can be used as a guide to future experimentation. Many of the events taking place as the kidney develops do, of course, also take place in other tissues and organisms and it will soon be possible to incorporate relevant information from these systems into analyses of kidney data as well as the new information from microarray technology. The key to success here will be the ability to access over the internet data from the textual and graphical databases for the mouse and other organisms now being established. In order to do this, informatic tools will be needed that will allow a user working with one database to query another. This paper also considers both the types of tools that will be necessary and the databases on which they will operate. 相似文献
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Culhane AC Thioulouse J Perrière G Higgins DG 《Bioinformatics (Oxford, England)》2005,21(11):2789-2790
SUMMARY: MADE4, microarray ade4, is a software package that facilitates multivariate analysis of microarray gene-expression data. MADE4 accepts a wide variety of gene-expression data formats. MADE4 takes advantage of the extensive multivariate statistical and graphical functions in the R package ade4, extending these for application to microarray data. In addition, MADE4 provides new graphical and visualization tools that aid in interpretation of multivariate analysis of microarray data. 相似文献
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《Fly》2013,7(6):313-315
Decapentaplegic (Dpp) is an essential morphogen in the TGF-β/BMP superfamily which patterns fields of cells during multiple stages of Drosophila development, including the ovary and embryo. We have found that type IV collagens bind to Dpp and play essential roles in the regulation of its signaling during these two developmental stages. This article primarily focuses on type IV collagens and embryonic Dpp signaling to discuss aspects of the type IV collagen mutant phenotype in the context of additional data from the field. In addition, the restriction of Dpp signaling in the the ovary by type IV collagens is described, as the differences between the embryonic and ovarian Dpp sources result in distinct effects of collagen IV proteins in the two systems. 相似文献
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The embryo phenotyping of genetic murine model is invaluable when investigating functions of genes underlying embryonic development and birth defect. Although traditional imaging technologies such as ultrasound are very useful for evaluating phenotype of murine embryos, the use of advanced techniques for phenotyping is desirable to obtain more information from genetic research. This letter tests the feasibility of optical coherence tomography (OCT) as a high‐throughput phenotyping tool for murine embryos. Three‐dimensional OCT imaging is performed for live and cleared mouse embryos in the late developmental stage (embryonic day 17.5). By using a dynamic focusing method and OCT angiography (OCTA) approach, our OCT imaging of the embryo exhibits rapid and clean visualization of organ structures deeper than 5 mm and complex microvasculature of perfused blood vessels in the murine embryonic body. This demonstration suggests that OCT imaging can be useful for comprehensively assessing embryo anatomy and angiography of genetically engineered mice. 相似文献
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Maratou K Forster T Costa Y Taggart M Speed RM Ireland J Teague P Roy D Cooke HJ 《Molecular reproduction and development》2004,67(1):26-54
Genetic understanding of male-factor infertility requires knowledge of gene expression patterns associated with normal germ cell differentiation. The mouse is one of the best models of mammalian fertility due to its well-characterized genetics and the existence of many infertile mutants both naturally occurring and experimentally induced. We used cDNA microarrays firstly to investigate normal gene expression in the wild-type (wt) testis and secondly to gain a better insight into the effect of the disruption of the Dazl gene on spermatogenesis. We constructed a cDNA microarray from a subtracted and normalized adult testis library and focused on six developmental time-points during the initial synchronous wave of spermatogenesis. The results suggest that in the wild-type testis, 89.5% of genes on our chip change expression dramatically during the time-course. To identify patterns in the gene-expression data, a k-means clustering algorithm and principal component analysis were used. In the Dazl knockout testes, the majority of genes remain at baseline levels of expression, because absence of Dazl has a severe effect on cell-types present in the testis. Although in the prepubescent Dazl-null mice the final point reached in germ cell development is the leptotene-zygotene stage, the microarray results suggest that lack of Dazl expression has a detectable effect on the mRNA complement of germ cells as early as day 5 when only type A spermatogonia are present. Mol. Reprod. Dev. 67: 26-54, 2004. 相似文献
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Kulesa PM 《Birth defects research. Part C, Embryo today : reviews》2004,72(3):260-266
The study of embryonic events using different animal model systems is crucial for gaining insights into human development and birth defects. Biological imaging plays a major role in this effort by providing a spatiotemporal framework to link complex cell movements with molecular data. However, depending on the age of the embryo and the location of a morphogenetic event, visualization often requires the design of novel culture and imaging techniques. One of the primary model systems for biological imaging is the avian embryo, due to its accessibility to manipulation, relatively two-dimensional morphogenesis early on, and viability when grown in culture. Significant work in avian embryo culture and cell labeling, together with advances in imaging technology, now make it possible to monitor many developmental events within the period from egg laying to hatching. Here, we present the latest in avian developmental imaging, focusing on cell labeling, embryo culture, and imaging technologies. 相似文献
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Particular attention has been paid to the pre-hatching period of embryonic development although blastocyst development is a poor indicator of embryo viability. Post-hatching embryonic development in vitro would allow for establishment of more accurate tools for evaluating developmental potential without the need for transfer to recipient animals. Such a system would require (1) definition of milestones of expected post-hatching embryonic development in vivo; and (2) development of adequate culture systems. We propose a stereomicroscopical staging system for post-hatching embryos defining the following stages: (1) Expanded hatched blastocyst stage where the embryo presents an inner cell mass (ICM) covered by trophoblast. (2) Pre-streak stage 1 where the embryonic disc is formed. (3) Pre-streak stage 2 where a crescent-shaped thickening of the caudal portion of the embryonic disk appears. (4) Primitive streak stage where the primitive streak has developed as an axis of cell ingression of cells for meso- and endoderm formation. (5) Neural groove stage where the neural groove is developing from the rostral pole of the embryo along with a proportional shortening of the primitive streak; and (6) Somite stage(s) where paraxial mesoderm gradually condensates to form somites. Post-hatching development of bovine embryos in vitro is compromised and although hatching occurs and elongation can be physically provoked by culture in agarose tunnels, the embryonic disk characterizing the pre-streak stage 1 is never established. Thus, particular focus should be placed on establishing culture conditions that support at least some of the above-mentioned critical phases of development that in vivo occur within the initial two (pig) to three (cattle) weeks. 相似文献
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Gilbert SF 《Ontogenez》2004,35(6):425-438
The production of phenotype is regulated by differential gene expression. However, the regulators of gene expression need not all reside within the embryo. Environmental factors, such as temperature, photoperiod, diet, population density, or the presence of predators, can produce specific phenotypes, presumably by altering gene-expression patterns. The field of ecological developmental biology seeks to look at development in the real world of predators, competitors, and changing seasons. Ecological concerns had played a major role in the formation of experimental embryology, and they are returning as the need for knowledge about the effects of environmental change on embryos and larvae becomes crucial. This essay reviews some of the areas of ecological developmental biology, concentrating on new studies of amphibia and Homo. 相似文献
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Chromatin organization within the three-dimensional (3D) nuclear space is important for proper gene expression and developmental programming. This organization is established during the dramatic reprogramming that occurs in early embryonic development. Thus, the early embryo is an ideal model for examining the formation and dynamics of 3D chromatin structure. Advances in high-resolution microscopy and single-nucleus genomic analyses have provided fundamental insights into the mechanisms driving genome organization in the early embryo. Here, we highlight recent findings describing the dynamics and driving mechanisms for establishing 3D chromatin organization and discuss the role such organization has on gene regulation in early embryonic development. 相似文献