69 An anatomical atlas is an essential reference for any experimental organism in which form and ... more 69 An anatomical atlas is an essential reference for any experimental organism in which form and function are of interest. After a dozen years of explosive growth as a model organism, the zebrafish is finally getting its own atlas. In 1995, Kimmel and colleagues published the famous zebrafish embryonic staging series (http://zfin.org/zf_info/zfbook/stages/ index.html) that adorns the wall of many a zebrafish laboratory.1 Wolfgang Driever then volunteered his labís plastic sections of 24, 48, 72, and 120 hour old embryos (http://zfin.org/ zf_info/anatomy.html) as a starting point for an atlas of histological anatomy. In 1999, community-wide interest in a comprehensive life-span atlas was articulated in a Zebrafish Anatomic Dictionary meeting at the NIH (http:// zfin.org/zf_info/anatomy/dict/mtg2.html). The plan emerging from this meeting was to create web-based atlas resources. The web-based atlas resources for the zebrafish community were to include the gorgeous whole mount in situ images of the Thisse and Dawid labs, a 3D embryonic atlas by the Verbeek lab (http://bio-imaging.liacs.nl/), and a life-span atlas by the Cheng and Moorman labs. These resources would ultimately be integrated with mutant, morphant, and disease data through ZFIN. NIH (NCRR) funding for the life-span virtual atlas of the zebrafish began in July 2004. This atlas will be based on serial tissue sections stained with hematoxylin and eosin. Each section will then be digitized into virtual slides using high power microscope objectives (Cheng lab). Serverbased software and image files will then be used to turn any computer with a high-speed internet connection into a virtual microscope. The virtual slides will also be used to generate 3D reconstructions (Moorman lab). Standardization of data collection and formats, and integrations with other databases are being planned. Anatomical terms are currently being chosen to facilitate accurate cross-referencing across phylogeny. The zebrafish atlas comprises a foundation for cross-phylogenetic, life-span integrations of anatomy with gene expression and functional data, which we are calling Systems Morphogenetics. A FASEB symposium dedicated to this topic will take place in April 2005. Progress on the atlas project can be found at ZFatlas. psu.edu. We have been developing a number of related, collaborative projects with engineers, computer scientists, and other zebrafish labs. Questions about joining the atlas effort, as well as details regarding histology and virtual slides, may be sent to [email protected]. Questions about details of 3D reconstruction and anatomy should be sent to Stephen.Moorman@ umdnj.edu. All inquiries pertaining to the atlas should be copied to the zebrafish atlas coordinator (Christina Wentz, [email protected], through July 2006).
Historical confusion in thinking about skin color and race derives from the state of science at t... more Historical confusion in thinking about skin color and race derives from the state of science at the time human classifications were proposed, and from our incomplete understanding of the genetics of human pigmentation and human ancestry. The pervasiveness of racism reflects the universal human desire for kinship, in settings of competition for resources, where it is common to devalue and
Anatomical atlases in standard coordinates are necessary for the interpretation and integration o... more Anatomical atlases in standard coordinates are necessary for the interpretation and integration of research findings in a common spatial context. However, the two mostused mouse brain atlases, the Franklin and Paxinos (FP) and the common coordinate framework (CCF) from the Allen Institute for Brain Science, have accumulated inconsistencies in anatomical delineations and nomenclature, creating confusion among neuroscientists. To overcome these issues, we adopted the FP labels into the CCF to merge two labels in the single atlas framework. We used cell type specific transgenic mice and an MRI atlas to adjust and further segment our labels. Moreover, new segmentations were added to the dorsal striatum using cortico-striatal connectivity data. Lastly, we have digitized our anatomical labels based on the Allen ontology, created a web-interface for visualization, and provided tools for comprehensive comparisons between the Allen and FP labels. Our open-source labels signify a key step towards a unified mouse brain atlas.
Model organism (MO) research provides a basic understanding of biology and disease due to the evo... more Model organism (MO) research provides a basic understanding of biology and disease due to the evolutionary conservation of the molecular and cellular language of life. MOs have been used to identify and understand the function of orthologous genes, proteins, cells and tissues involved in biological processes, to develop and evaluate techniques and methods, and to perform whole-organismbased chemical screens to test drug efficacy and toxicity. However, a growing richness of datasets and the rising power of computation raise an important question: How do we maximize the value of MOs? In-depth discussions in over 50 virtual presentations organized by the National Institutes of Health across more than 10 weeks yielded important suggestions for improving the rigor, validation, reproducibility and translatability of MO research. The effort clarified challenges and opportunities for developing and integrating tools and resources. Maintenance of critical existing infrastructure and the implementation of suggested improvements will play important roles in maintaining productivity and facilitating the validation of animal models of human biology and disease.
Chi sites, consisting of the nucleotide octamer 5' G-C-T-G-G-T-G-G 3', stimulate coliphage)~ reco... more Chi sites, consisting of the nucleotide octamer 5' G-C-T-G-G-T-G-G 3', stimulate coliphage)~ recombination mediated by the Escherichia coli RecBC recombination pathway. In a sensitive genetic assay using phage ~ crosses, three of four Chi-like sequences tested, namely
69 An anatomical atlas is an essential reference for any experimental organism in which form and ... more 69 An anatomical atlas is an essential reference for any experimental organism in which form and function are of interest. After a dozen years of explosive growth as a model organism, the zebrafish is finally getting its own atlas. In 1995, Kimmel and colleagues published the famous zebrafish embryonic staging series (http://zfin.org/zf_info/zfbook/stages/ index.html) that adorns the wall of many a zebrafish laboratory.1 Wolfgang Driever then volunteered his labís plastic sections of 24, 48, 72, and 120 hour old embryos (http://zfin.org/ zf_info/anatomy.html) as a starting point for an atlas of histological anatomy. In 1999, community-wide interest in a comprehensive life-span atlas was articulated in a Zebrafish Anatomic Dictionary meeting at the NIH (http:// zfin.org/zf_info/anatomy/dict/mtg2.html). The plan emerging from this meeting was to create web-based atlas resources. The web-based atlas resources for the zebrafish community were to include the gorgeous whole mount in situ images of the Thisse and Dawid labs, a 3D embryonic atlas by the Verbeek lab (http://bio-imaging.liacs.nl/), and a life-span atlas by the Cheng and Moorman labs. These resources would ultimately be integrated with mutant, morphant, and disease data through ZFIN. NIH (NCRR) funding for the life-span virtual atlas of the zebrafish began in July 2004. This atlas will be based on serial tissue sections stained with hematoxylin and eosin. Each section will then be digitized into virtual slides using high power microscope objectives (Cheng lab). Serverbased software and image files will then be used to turn any computer with a high-speed internet connection into a virtual microscope. The virtual slides will also be used to generate 3D reconstructions (Moorman lab). Standardization of data collection and formats, and integrations with other databases are being planned. Anatomical terms are currently being chosen to facilitate accurate cross-referencing across phylogeny. The zebrafish atlas comprises a foundation for cross-phylogenetic, life-span integrations of anatomy with gene expression and functional data, which we are calling Systems Morphogenetics. A FASEB symposium dedicated to this topic will take place in April 2005. Progress on the atlas project can be found at ZFatlas. psu.edu. We have been developing a number of related, collaborative projects with engineers, computer scientists, and other zebrafish labs. Questions about joining the atlas effort, as well as details regarding histology and virtual slides, may be sent to [email protected]. Questions about details of 3D reconstruction and anatomy should be sent to Stephen.Moorman@ umdnj.edu. All inquiries pertaining to the atlas should be copied to the zebrafish atlas coordinator (Christina Wentz, [email protected], through July 2006).
Historical confusion in thinking about skin color and race derives from the state of science at t... more Historical confusion in thinking about skin color and race derives from the state of science at the time human classifications were proposed, and from our incomplete understanding of the genetics of human pigmentation and human ancestry. The pervasiveness of racism reflects the universal human desire for kinship, in settings of competition for resources, where it is common to devalue and
Anatomical atlases in standard coordinates are necessary for the interpretation and integration o... more Anatomical atlases in standard coordinates are necessary for the interpretation and integration of research findings in a common spatial context. However, the two mostused mouse brain atlases, the Franklin and Paxinos (FP) and the common coordinate framework (CCF) from the Allen Institute for Brain Science, have accumulated inconsistencies in anatomical delineations and nomenclature, creating confusion among neuroscientists. To overcome these issues, we adopted the FP labels into the CCF to merge two labels in the single atlas framework. We used cell type specific transgenic mice and an MRI atlas to adjust and further segment our labels. Moreover, new segmentations were added to the dorsal striatum using cortico-striatal connectivity data. Lastly, we have digitized our anatomical labels based on the Allen ontology, created a web-interface for visualization, and provided tools for comprehensive comparisons between the Allen and FP labels. Our open-source labels signify a key step towards a unified mouse brain atlas.
Model organism (MO) research provides a basic understanding of biology and disease due to the evo... more Model organism (MO) research provides a basic understanding of biology and disease due to the evolutionary conservation of the molecular and cellular language of life. MOs have been used to identify and understand the function of orthologous genes, proteins, cells and tissues involved in biological processes, to develop and evaluate techniques and methods, and to perform whole-organismbased chemical screens to test drug efficacy and toxicity. However, a growing richness of datasets and the rising power of computation raise an important question: How do we maximize the value of MOs? In-depth discussions in over 50 virtual presentations organized by the National Institutes of Health across more than 10 weeks yielded important suggestions for improving the rigor, validation, reproducibility and translatability of MO research. The effort clarified challenges and opportunities for developing and integrating tools and resources. Maintenance of critical existing infrastructure and the implementation of suggested improvements will play important roles in maintaining productivity and facilitating the validation of animal models of human biology and disease.
Chi sites, consisting of the nucleotide octamer 5' G-C-T-G-G-T-G-G 3', stimulate coliphage)~ reco... more Chi sites, consisting of the nucleotide octamer 5' G-C-T-G-G-T-G-G 3', stimulate coliphage)~ recombination mediated by the Escherichia coli RecBC recombination pathway. In a sensitive genetic assay using phage ~ crosses, three of four Chi-like sequences tested, namely
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