Sunday, April 25, 2010

Gymnosporangium

I was driving along today and saw a particularly striking example of Gymnosporangium juniperi-virginianae (cedar-apple rust) in action!  I saw at least three trees in the area with this amazing bright orange fungus, but one of them was completely covered!  Here are a few photos that I took:

A side view of one of the fungal fruiting bodies progressing through the stages of maturity.

A particularly juicy fruiting body as seen from below.

A small portion of the tree covered in the fungus.


[Photos by Brendan Hodkinson.]


Wednesday, April 21, 2010

Lichen Photomorphs in Costa Rica

Last year I traveled to Costa Rica in search of lichens. One of the most exciting lichenological phenomena that I observed was the presence of 'photomorphs' in the lichen-forming fungal genus Sticta. Photomorphs (a.k.a., photosymbiodemes) are created when the same fungus associates with two entirely different photobionts (most noticeable when one photobiont is a green alga and the other is a cyanobacterium). I observed this in several species of Sticta while in Costa Rica. This photo shows one example, where the bright green lobes are associated with a green alga and the darker brown lobes are associated with a cyanobacterium:
Some other nice photos from my trip include a moth disguising itself as a lichen...
...and a rainbow over some lichen-covered fence posts by the side of the highway near Cerro de la Muerte.
Costa Rica is beautiful; I look forward to returning some day!

- Brendan


[Travel and research expenses for the field component of this trip were covered by a handful of small grants: Christiane and Christopher Tyson OTS Research Fellowship, Lewis and Clark Fund for Exploration and Field Research Grant, Sally Hughes-Schrader Travel Grant, & Explorers Club Diversa Award.]

Sunday, April 11, 2010

Lichens in the Community

Haven't you always wanted to go to a festival and find an exhibit all about lichens?!  This weekend I was lucky enough to have an opportunity to participate in the 10th Annual WOODSmont Children's Festival sponsored by Duke University's Wilderness Outdoor Opportunities for Durham Students ('WOODS').  I set up a table with a full exhibit including 'touch and feel' lichens, a microscope (so that children could see the lichens up close), a collage of amazing photos of lichens from around the world (thanks to Robert L├╝cking for compiling these), and 'pet lichens' for children to take home. Here is a photo of the exhibit itself:

This picture shows an action shot of some local children becoming aware of the lichens in their neighborhood:

It was a great day, and I look forward to more opportunities for this type of outreach!

-Brendan

[Many thanks to the National Science Foundation for funding my research and associated outreach through a recent Doctoral Dissertation Improvement Grant: DEB-1011504.]

Tuesday, April 6, 2010

Submitting to GenBank

Anyone who does much in the way of DNA sequencing/analysis eventually has to deal with depositing sequences in GenBank.  For a sequence or two, it is relatively simple to use the online 'BankIt' submission system.  However, for larger batches it becomes necessary to take advantage of the batch functions available with the 'Sequin' program.  To get to the point of being able to submit large batches each containing multiple 'features', there is quite a steep learning curve (especially if you are trying to teach yourself).  Unfortunately, the web-pages on the NCBI website do not seem quite sufficient to make submission a simple process.  While submitting sequences for a number of recent papers (e.g., Hodkinson & Lutzoni 2009, Hodkinson & Lendemer 2010, Lendemer & Hodkinson 2009, 2010), I wrote myself a tutorial on how to submit RNA-encoding sequences (rRNA, introns, transcribed spacers, etc.) to GenBank.  Most of this will apply to all sequence types, but getting the information for protein-coding sequences correct might still be an issue requiring some extra assistance.  In the 16-step outline below, the most difficult and problematic aspect (i.e., annotating multiple sequence features) is emphasized and greater detail is given in this area.

GenBank Submission Using SEQUIN:
1)  Make a FASTA+GAP file with bracketed modifiers for all basic info that varies between sequences (e.g., organism, isolate, specimen-voucher, etc.; for basic formatting see http://www.ncbi.nlm.nih.gov/Sequin/QuickGuide/sequin.htm#AlignmentFormats; for appropriate modifiers see http://www.ncbi.nlm.nih.gov/Sequin/QuickGuide/sequin.htm#DefinitionLine).
2) Run SEQUIN and type in the authorship, contact, and citation information that applies to all sequences.
3) Import file into SEQUIN as a 'Phylogenetic Study' set in 'FASTA+GAP' format.
4) Click 'Edit' 'Alignment Assistant...'.
5) Click 'Features' 'Apply To Alignment >' 'RNA'.
6) For the feature that you wish to annotate, be sure to check the box saying if the 5' or 3' end is partial, if either one is.
7) Type in the alignment coordinates of the particular feature that you are annotating.
8) In the 'RNA Type' box, pick the type of feature (e.g., 'misc_RNA' for ITS1 and ITS2, or 'rRNA' for 18S, 5.8S, or 28S).
9) In the field next to 'RNA Name', put in the specific type of RNA (18S ribosomal RNA, internal transcribed spacer 1, etc.).
10) Click 'Accept.'
11) Repeat steps 5-10 for each section of RNA in the sequence set.
12) In the 'Alignment Assistant' window, go to the 'File' menu and click 'Close'.
13) To check/edit your work: next to 'Target Sequence' choose 'ALL SEQUENCES' and next to 'Format' choose 'Graphic' (double-click on any particular feature annotation to see details and/or make changes; if a particular annotation is entirely erronious, highlight the annotation and go to 'Edit' then 'Clear').
14) Click 'Done' on the main viewing window.
15) When it asks 'Are you ready to save the record?' click 'Yes'.
16) Save the file to the hard drive and email it to 'gb-sub@ncbi.nlm.nih.gov'.

I have been told that this protocol is helpful in getting Sequin to 'work'.  I hope that posting it here will help even more people!

- Brendan


[If you found this post to be a useful guide, and employed the information found here as part of the GenBank submission process, please cite this work as follows:

Hodkinson, B. P. 2010. Submitting to GenBank. Squamules Unlimited, Durham, NC. http://squamules.blogspot.com/2010/04/submitting-to-genbank.html

Many thanks!]



Works Cited:

Hodkinson, B. P., and F. Lutzoni. 2009. A microbiotic survey of lichen-associated bacteria reveals a new lineage from the Rhizobiales. Symbiosis 49: 163-180.
Download publication (PDF file)
Download alignment (NEXUS file)

Hodkinson, B. P., and J. C. Lendemer. In press. Molecular analyses reveal semi-cryptic species in Xanthoparmelia tasmanica. Bibliotheca Lichenologica.
Download draft (PDF file)
Download alignment (NEXUS file)

Lendemer, J. C., and B. P. Hodkinson. 2009. The Wisdom of Fools: new molecular and morphological insights into the North American apodetiate species of Cladonia. Opuscula Philolichenum 7: 79-100.
Download publication (PDF file)
Download alignment (NEXUS file)

Lendemer, J. C., and B. P. Hodkinson. 2010. A new perspective on Punctelia subrudecta in North America: previously-rejected morphological characters corroborate molecular phylogenetic evidence and provide insight into an old problem. The Lichenologist 42(4): 405-421.
Download publication (PDF file)
Download alignment (NEXUS file)