As many of you may have heard your Drosophila Board has hired a science writer, Ricki Lewis, a frequent contributor to The Scientist and many other publications, to provide descriptions of noteworthy advances in fly research reported at the ADRC. The links below offer two recent press releases of Drosophila news-worthiness from the 2012 ADRC.

In addition to these, we provide an example of Ricki’s less serious side in a guest blog entry for Scientific American magazine.

We hope you find these interesting and in the case of the blog entertaining. Please share the press release links to those who you think would be interested in knowing more about Drosophila’s contributions to translational research.

DROS1DiverseResearch.pdf

DROS2StemCells.pdf

Sci Am blog entry: The making of a mutant - a fruit-fly love story

Would you like to learn how to efficiently use FlyBase for your daily research needs? If so, please click over to the 2012 NAR Database Issue and read our article "FlyBase 101 - the basics of navigating FlyBase".

Peter McQuilton, Susan E. St. Pierre, Jim Thurmond, and the FlyBase Consortium
FlyBase 101 – the basics of navigating FlyBase.
Nucleic Acids Research (2011) 39:21; doi: 10.1093/nar/gkr1030

Since the 2007 publication of the 12 species genomes, the genomes of nine additional species have been sequenced, bringing the total to 21. The UCSD stock center has the strains of the newly sequenced species in addition to a number of other stocks of each of these. Please visit the DSSC website for more information:

https://stockcenter.ucsd.edu/info/welcome.php

FlyBase 2012 Release Schedule

The following are the tentative dates of FlyBase releases in 2012. There will be 6 releases this year.

• FB2012_01 - January 20^th
• FB2012_02 - March 2^nd
• FB2012_03 - May 4^th
• FB2012_04 - July 6^th
• FB2012_05 - September 7^th
• FB2012_06 - November 2^nd

Please feel free to Contact us with any questions or comments.

The following is a reproduction of an announcement by Developmental Dynamics:

Call for Papers for a Special Issue in DEVELOPMENTAL DYNAMICS on “Drosophila as a Model for Understanding Development and Disease”

We are pleased to announce a call for papers for a Special Issue of Developmental Dynamics celebrating the importance of research on Drosophila in development and disease. The issue will be guest-edited by Ken Irvine (irvinewaksman.rutgers.edu), Rutgers University, and Amit Singh (amit.singhnotes.udayton.edu ), University of Dayton.

Drosophila investigators are invited to submit papers to Developmental Dynamics for a special issue of the journal to be published in late 2011 or early 2012. Papers should be submitted no later than June 15, 2011, for consideration for the special issue. Research articles exploring mechanisms of development, Technique articles describing new techniques of broad impact, or Disease Connection articles describing novel models/preparations/approaches for understanding the developmental basis of disease are welcomed. Ideas for appropriate Reviews articles are also encouraged (contact the Reviews Editor, John F. Fallon: jffallonwisc.edu). All articles undergo thorough peer review to determine their merits for publication.

Developmental Dynamics is committed to publishing papers of central importance to the developmental biology community. All special issue articles are open access immediately upon publication, allowing your work to be disseminated widely throughout the scientific community. There are no page or color charges, and Developmental Dynamics is fully compliant with the open access policies of NIH, HHMI, and the Wellcome Trust.

Manuscripts should be submitted online at: http://mc.manuscriptcentral.com/dvdy-wiley

Author Guidelines can be found at:
http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1097-0177/homepage/ForAuthors.html

We look forward to receiving your submissions.

Best wishes,
Gary C. Schoenwolf, Ph.D.
Editor-in-Chief, Developmental Dynamics

We sadly announce that Dr. Victoria Finnerty, Professor of Biology at Emory University, has passed away at the age of 73. She remained a fully active faculty member until the end of last year. She was in Chicago with her son and his family during the last few months. After her graduate and postdoctoral studies with Art Chovnick at the University of Connecticut, Vickie came to Emory in 1976 where she maintained an active lab throughout her career. Her early seminal work focused on the use of high resolution recombinational analysis of the maroon-like gene to understand gene structure in Drosophila. Her interests then shifted to understanding the molecular function of the maroon-like gene in the production of a molybdenum-containing cofactor required for the activity of xanthine dehydrogenase (rosy) and other enzymes. Vickie was well-known as a gifted teacher and mentor, and during the last several years of her career she focused most of her efforts on undergraduate education in the Emory Biology Department. Her kindness, warmth, dedication and even-tempered manner will be greatly missed by her many friends in the Drosophila community. She was loved by all who knew her.

Respectfully,
Barry Yedvobnick, Janis O'Donnell & Bill Gelbart

FlyBase is pleased to note the publication on December 22, 2010 of an extremely important set of papers from the modENCODE project, including two integrative papers (one on Drosophila melanogaster and the other on Caenorhabditis elegans DNA elements) as well as a series of companion papers. The complete list of papers is available through the modENCODE website (http://blog.modencode.org/papers) and the major impact of the work is summarized in a press release from NHGRI (http://www.genome.gov/27542795).

On behalf of the Drosophila research community, we wish to acknowledge and thank NHGRI for its generous support of this major community resource project. FlyBase is in the process of working with the modENCODE project to incorporate the summary results of these studies into FlyBase. As data sets are incorporated, we will post notices describing the new data on FlyBase.

FlyBase 2011 Release Schedule

The following are the tentative dates of FlyBase releases in 2011. There will be 10 releases this year with no releases in August and December.

• FB2011_01 - January 21st
• FB2011_02 - February 18th
• FB2011_03 - March 18th March 21st
• FB2011_04 - April 22nd
• FB2011_05 - May 27th
• FB2011_06 - June 24th
• FB2011_07 - July 22nd
• FB2011_08 - September 2nd
• FB2011_09 - October 7th October 10th
• FB2011_10 - November 11th November 18th

Please feel free to Contact us with any questions or comments.

FlyBase has added support for Zotero to our reference reports and any search result that returns references.

To utilize this functionality you need to use Firefox and have Zotero installed. After you have satisfied those requirements you should see a Zotero icon in the Firefox location bar any time you view a FlyBase reference report or a search result. This icon indicates that you can import the current citation or list of citations into your Zotero database by clicking on it.

For more information about Zotero please see http://www.zotero.org/.

If you have a question or comment about FlyBase please feel free to Contact FlyBase.

Dear Drosophilist,

The Duplication Consortium, comprised of members of the Kaufman, Bellen and Hoskins labs, has used and is using the 83 kb P[acman] libraries (Nat Methods (2009) 6:431-434) to generate a set of duplications to cover the X chromosome. The initial set of these duplications are now available at the Bloomington Drosophila Stock Center and will soon appear on the GBrowse maps at FlyBase.

The specific coverage of each of these duplications can be viewed on the Pacman Resources website at http://pacmanfly.org/dups.php as well as on the BDSC web site http://fly.bio.indiana.edu/Browse/dp/DC-Dps.php. As more duplication lines are made they will be deposited at the BDSC and they will be added to these sites. Our goal is to provide, as far as is possible, complete coverage of the euchromatic X Chromosome. We hope those of you who may need them will find them useful. Any feedback about the stocks, will be appreciated.

Sincerely,

The Duplication Consortium

FlyBase 2010 Release Schedule

The following are the tentative dates of FlyBase releases in 2010. There will be 9 releases this year with no releases in July, August, and December.

• FB2010_01 - January 22nd
• FB2010_02 - February 19th
• FB2010_03 - March 19th
• FB2010_04 - April 23rd
• FB2010_05 - May 28th
• FB2010_06 - June 25th
• FB2010_07 - July 23rd- Canceled ¹
• FB2010_07 - September 3rd
• FB2010_08 - October 8th - Delayed until October 13th
• FB2010_09 - November 12th - Delayed until November 19th

Please feel free to Contact us with any questions or comments.

1. The July 23rd release has been canceled so that we can focus on a few new features and data types.

From this point forward FlyBase will be providing Apollo viewable annotation data in chado-xml format only. The latest version of Apollo has been modified to retrieve annotation data via the web in this format. Therefore, we recommend that you upgrade to the latest available version of Apollo

We will no longer provide annotation data in GAME-XML format and while Apollo is still able to load and view existing GAME-XML data the data files must be available on the local machine as web retrieval of GAME files is no longer supported.

Please be aware that when Apollo is retrieving annotation data from the web it is obtaining precomputed chunks of xml. While the pieces have been generated to not span any gene models retrieval by sequence range may not result in the exact sequence requested being loaded into Apollo.

Please use the contact FlyBase form to send questions and requests for help to FlyBase.

FlyBase offers direct "linkouts" from our gene report pages to other web-based Drosophila data services. The FlyBase Consortium wishes to thank the organizers and developers of these data sets for helping us provide a great deal of valuable information on Drosophila genes and genomes.

• BDGP in situ Gene Expression Database (http://toy.lbl.gov:8888/cgi-bin/ex/insitu.pl)
• Drosophila melanogaster Exon Database (http://proline.bic.nus.edu.sg/dedb/index.html)
• Drosophila RNAi Screening Center (http://www.flyrnai.org/)
• FLIGHT - Integrating Genomic and High-Throughput data (http://flight.licr.org/)
• Fly GRID Interaction Data (http://biodata.mshri.on.ca:80/fly_grid/servlet/SearchPage)
• FlyMine - integrated genomics and proteomics (http://www.flymine.org/)
• NCBI Gene Expression Omnibus (GEO) (http://www.ncbi.nlm.nih.gov/projects/geo/)
• Heidelberg Database for RNAi Phenotypes (http://www.dkfz-heidelberg.de/signaling/ernai/ernai.html)
• Hybrigenics Drosophila PIMRider (http://pim.hybrigenics.com/pimriderext/droso/index.html)
• Yale Developmental Gene Expression (http://genome.med.yale.edu/Lifecycle/)
• InParanoid computed orthology calls (http://inparanoid.cgb.ki.se/index.html)
• PANTHER ClassificationSystem (http://www.pantherdb.org/)

In addition to these links FlyBase also provide direct links to the Drosophila records in the major international nucleotide, protein and bibliographic databases.