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--- 4dn:phase1:perspective_paper_final_draft [2019/01/24 16:40]
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-====== Perspective paper (final draft) ======
-**The final draft for the 4DN perspective is now available. **
-[[https://docs.google.com/a/eng.ucsd.edu/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDo2NjdkNTJkZmI0ZWFmYTVk|Final version, 01/16/2017]]. Available for comment between 01/17/2017 and 01/23/2017. To comment, please send email to corresponding author at: <job.dekker@umassmed.edu>.
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-**Previous versions: **
-. Main text.  [[https://docs.google.com/document/d/1E7VDSicZXclgkzwOV5AgLF-8ALiIchR94zF71uyxrpI/edit|The 4D Nucleome Project]], September 19, 2016. Please contact Job Dekker for editing rights.
-[[https://docs.google.com/document/d/1N8ZgdQen2VFO30vyk4fHlpKko18bZIaYfQdbtordhnU/edit|Box 1: Genomic technologies currently in use or in development in the 4DN network]], 9/19/2016
-[[https://docs.google.com/document/d/1FLQtRX66UPHhQHIg4oS67hw7n-2uSagoqMlqNSPRGXM/edit|Box 2: Labels, Microscopy, and Applications]],  9/19/2016
-[[https://sites.google.com/a/4dnucleome.org/4d-nucleome-wiki/concept-paper/4D-Nucleome-Article-fig-revised2017.jpg?attredirects=0|Final figure (v7), January 9, 2017]]
-**Previous versions:**
-[[https://docs.google.com/document/d/1OdLfkTa5LPX9e32_iKVJUav5Us3KxAchgYd0v8ESpVk/edit|The 4D Nucleome Project]]. August 26, 2016
-[[https://docs.google.com/document/d/1ls322GWyEHkCvVWjN7UX8VPgzf3QZRVgiyeTDOB89gk/edit|Box 1: Genomic technologies currently in use or in development in the 4DN network. ]]August 26, 2016
-[[https://docs.google.com/document/d/1LxZrq_lmqzDyvQLk6yHgrv0iOV-KKi02gVdKXMQa2fs/edit|The 4D Nucleome Project, May 16, 2016]]
-[[https://docs.google.com/a/eng.ucsd.edu/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnw0ZG5kYXdpa2l8Z3g6MjhhOGZmZGMwYzQwNmVlNA|The 4D Nucleome Project perspective paper, August 13, 2016]]
-[[https://sites.google.com/a/4dnucleome.org/4d-nucleome-wiki/concept-paper/4D-Nucleome-sketchrevised4.jpg?attredirects=0|Draft figure, Sept 15, 2016]].
-[[https://sites.google.com/a/4dnucleome.org/4d-nucleome-wiki/concept-paper/4DN-concept-article-figdraft3.jpg?attredirects=0|Draft figure, August 13, 2016]]
-[[https://sites.google.com/a/4dnucleome.org/4d-nucleome-wiki/concept-paper/4D-Nucleome-fig-new4.jpg?attredirects=0|Draft figure, Nov 24, 2016]]
-[[https://sites.google.com/a/4dnucleome.org/4d-nucleome-wiki/concept-paper/4D-Nucleome-fig-FinalRevised.jpg?attredirects=0|Draft figure, Nov 25, 2016]]
-[[https://sites.google.com/a/4dnucleome.org/4d-nucleome-wiki/concept-paper/4D-Nucleome-fig-Circle.jpg?attredirects=0|Draft figure (v6), December 2, 2016]]
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-Previous suggestions (prior to September, 2016):
-Bing suggested to put the organizational structure of the funded groups into another figure for the perspective paper. Here are [[https://docs.google.com/a/eng.ucsd.edu/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnw0ZG5kYXdpa2l8Z3g6MTI1NTk4ODgxN2EwODQ2Yg|reference figures on the organizational structure]] provided by Olivier Blondel.
-Reference materials provided by Andrew Belmont; uploaded by Sheng Zhong with Andy's permission on 8/29/2016:
-"STEDandSIM_CHOK.tiff" shows a composite of SIM DAPI staining (blue) and STED speckle (SON) staining (green).  It only shows two compartments therefore but it at least gives an idea of DNA and the relative size of the ICGs (speckles) nuclear bodies.  There are large DAPI-free holes that are likely nucleoli and possibly we could paint something in as a mixed illustration / image.
-The powerpoint slide I attached shows on the left a very nice energy loss TEM image which shows the Phosphorus distribution and therefore RNA and DNA in a quadrant of a nucleus.  You can nicely see chromatin and ICGs (speckles) and at the very top left corner a piece of a nucleolus, most of which is cropped.  I got this from Michael Hendzel and I'm pretty sure he would be glad to contribute a full image of a nucleus in this imaging mode.  What's nice is a single image would show chromatin, ICGs, nucleoli of the whole nucleus.  Unfortunately, I can't find the original images that Michael sent me years ago that I would have been able to show you.
-Finally, check out Fig2_ann_small, panels B and D.  Panel B is an EM image I took years ago showing chromatin, nucleolus, and ICGs (speckles) all at once.  It is from a detergent extracted nucleus though but shows the chromatin nicely.  In contrast, Panel D is another energy loss mode TEM picture that Michael Hendzel gave me.  It is from an intact cell and in this case shows chromatin and nucleolus.
-Some of these do not represent a final image to use in the figure, but provide ideas for what might work.  If you like Michael Hendzel's type images, i could contact him for an image with an entire nuclear cross-section. I can also provide higher resolution versions of the Fig. 2 images or point you to a published paper with something similar. "
-Older versions: [[https://sites.google.com/a/4dnucleome.org/4d-nucleome-wiki/concept-paper/4Dnucleome-articlefigdraft2.jpg?attredirects=0&attachauth=ANoY7cqO31sr0H8hMV8ogy1AgmdS3wCzsfDVqFQzT2mTlj8JDdih9FStTaA5e4TGMZdWVNvC3K-8zs5Pp6Xku4zllvWknMVBtvlaryZfyfcB1X4N3OIqIxZCYP6icwPsZMMcDlf01GyXBOjtTixhqV03uYzoLo3yjyazz6kiGS707lwNB7xnhfXGfeRNzUowlX94IAO6WpEiDS5Hx8YSNY7wvc6UAAV8a6ks1kx8nMA-T3vnBMiaUL_XUQ7ZmLO2doonFUqG8YFA|Draft figure]], July 22, 2016.
-Editorial notes (Victor Leshyk): I intend to continue refining the many crude areas in this draft, but attached is my quick attempt at a comprehensive figure draft that might work for tomorrow's group discussion, based on Job's recent sketch of the 4D Nucleome approach.  Although I think the comparison between "messy specimen" at left and "virtual omniscience" at right seems clear, my rendering of a 3D browser at bottom right is still very messy and imprecise: as shown, the colored segments are meant to represent the entire color-coded linear genome mirrored in the colored domains on the virtual model, but I realize that the plotted overlapping interactions may seem much too heavy-handed at that scale, so I could re-draw this area to simply show one chromosome's detail....also, the hairlike colored "strands" that are shown pointing down from the virtual model are meant as vectors that show multilayered data being Integrated into the browser's many plotted connections, but this seems overly sloppy to me still.  Finally, the appearance of the virtual 4D model is meant to look artificial and lurid in colors, but with a bit more time to draw on the image, I can render the nuclear features more as 3d shapes, with proper highlighting and shadows, to suggest more of a sophisticated approach to modeling the geometry.
-Editorial notes (Job Dekker): The figure needs to show -multiple- 3D models to indicate the ensemble of structures occurring in the population.

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