Aspergillus Community News


 
circle Remember to submit A. nidulans knock out strains made with cassettes from FGSC (from Michelle Momany, January 2012)

The FGSC has sent out over 500 KO cassettes and gotten back 0 strains. Please submit your KO strains so that we can work toward a complete deletion collection. For more info see http://www.fgsc.net/Aspergillus/KO_Cassettes.htm
circle A. nidulans 70 mers free to a good home (from Michelle Momany, January 2012)

The NIAID Pathogen Functional Genomics Resource Center has closed. They are now looking for a home for the 70 mer A. nidulans oligos made for the ORF microarray. These oligos could be used for printing microarrays or any other application. There is no requirement to use the oligos for any community support nor do they come with any other strings attached. Below is a link to the PFGRC webpage that describes the microarray that was produced with the A. nidulans 70 mer collection. On this page are downloadable annotation files that contain all of the 70 mer gene target information and the 70 mer sequences.

http://pfgrc.jcvi.org/index.php/microarray/array_description/aspergillus_nidulans/version2.html

The 70 mers are stored in 96-well deep well blocks. There are 120 blocks that comprise the set which occupies 4 freezer racks (36 blocks per rack). All 70 mers are at a standardized concentration of 50uM (volume of oligo is variable throughout the plates). JCVI will provide with the 70 mers plate maps that define the identity and volume of each oligo in the collection.

If you are interested in giving these orphaned A. nidulans ORF oligos a home, please contact Bill Nierman () or Eric Snesrud ().
circle Knock-out cassettes for A. nidulans available at the FGSC (posted July 30, 2010)

The gene knock-out cassettes were produced at Dartmouth Medical School and have been shipped to the Fungal Genetics Stock Center (FGSC) as DNA suitable for transformation or amplification. More information about the resource is available on the FGSC web site, and a spreadsheet listing the cassettes and primers is available for download from the FGSC.
circle MochiView motif analysis and genome browser software (posted April 22, 2010)

An announcement from Oliver Homann:

Hello, I'd like to alert the community to the availability of a new platform-independent Java genome browser and motif analysis software called MochiView. Hopefully some of you may find it useful. The software was originally designed for visualization and analysis of C. albicans ChIP-Chip data, but has also been utilized for pure motif analysis as well as with ChIP-Seq/RNA-Seq data and with multiple additional genomes, including S. cerevisiae and humans. It takes ~10 minutes to download the software and install the necessary genome sequence and gene information (using the GFF files stored on SGD, CGD, or AspGD). A manuscript describing the software has just been published in BMC Biology. Visit the MochiView website to view: Contributions to the MochiView motif libraries would be appreciated! Contact us with suggestions, or to join the MochiView mailing list.
circle A. nidulans deletions (from Steve Osmani) (Posted June 4, 2009)

As you are aware, as part of the funding of the NIH PO1 grant of Dunlap et al. (Functional Analysis and Systems Biology of Filamentous Fungi), funds have been obtained to generate deletion constructs for all Aspergillus nidulans genes. The constructs are to be deposited at the FGSC from where labs can obtain them. The plan is to generate the constructs over an 18 month period and we wish to ask labs for the genes they are interested in deleting so that we can prioritize when the constructs would be made. Please send your request list for gene deletion constructs to aspergillus@plantbio.uga.edu.

We will need the Broad AN# found at:
http://www.broad.mit.edu/annotation/genome/aspergillus_group/MultiHome.html
So if you wanted to delete actin we would need: AN6542.3.

Please contact Steve Osmani (osmani.2@osu.edu) for further information or clarifications regarding this project.

Thanks,
Steve Osmani
circle The special issue of Aspergillus Genomics available online (Posted April 7, 2009)

A major effort from within the Aspergillus community has resulted in the publication of an exceptional supplement to the Elsevier journal Fungal Genetics and Biology. The supplement provides extensive studies based on the genome analysis of two Aspergillus species: Aspergillus niger and Aspergillus nidulans.
This supplement is now freely accessible online until June 15, 2009:

Thematic Issue: Aspergillus Genomics and Beyond
Edited by Jaap Visser, Jennifer Russo Wortman, Albert J.J. van Ooyen, Scott Baker, Jens Nielsen and Cees van den Hondel
Volume 46, Issue 1, Supplement 1, Pages S1-S190 (March 2009)

The publication was enabled by Eurofungbase, a coordination action program funded by the European Commission, and DSM.

circle Call for final input on deletion marker for Aspergillus nidulans knockouts (from Steve Osmani) (Posted April 7, 2009)

During the recent 6th Asperfest and 25th Fungal Genetics Conferences at Asilomar there was a lot of open discussion regarding the marker to use for the systematic deletion program funded by the NIH Program Project "Functional Analysis and Systems Biology of Filamentous Fungi" awarded to Jay Dunlap et al. As a follow up to these discussions I think its fair to say that there is not one perfect marker that will satisfy everyone. However there was consensus that the marker employed should allow operation of the heterokaryon rescue procedure meaning the marker has to be very tight. This effectively discounts drug resistance markers. After talking to most of the interested parties at the conferences a consensus was reached to use the pyrG marker.

In theory we can use the pyrG89 allele and complement using the A. fumigatus pyrG as is currently done in several labs including my own. However some have indicated (although we have not observed this) that the A. fumigatus pyrG may not fully complement pyrG89. One way to get around this would be to fully delete pyrG including removal of the promoter, the coding and 3' processing region to generate a new recipient strain. We can do this using 5-FOA selection generating a clean deletion with no marker involved. This would then allow use of the A. nidulans pyrG as the marker.

Another requested feature was that the marker should be reusable. In order to get around problems associated with repeated sequences (such as lox sites) and their affects on generation of the deletion constructs I would prefer not to incorporate any repeated sequence.

An alternative approach to remove pyrG from the deleted locus would be to make a linear replacement construct containing the targeting domains used for the deletion such that homologous recombination would remove the pyrG marker and return the deleted strain back to pyrG minus. 5-FOA selection can be used to select for the removal event (see for 5-FOA selection: Nielsen ML, Albertsen L, Lettier G, Nielsen JB, Mortensen UH (2006) Fungal Genetics and Biology 43,54 64).

If there are other issues that need to be considered please let me know at osmani.2@osu.edu NO LATER than April 13, 2009 as we would like to move forward with generating the deletion constructs.

Thanks,
Steve Osmani

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