Category Archives: Publications

Ahmed Moustafa’s Science Paper Online

MoustafaAAs mentioned previously, Ahmed Moustafa had his manuscript accepted by Science and it has recently been posted online.  This work provides insight into the evolution of diatoms (pics here and here) and provides unexpected analytical data from their genome, shedding light into a convoluted evolution. A perspective was also published in the same issue of Science providing some background and commentary on Ahmed’s paper.  Huge congrats to you Ahmed, nice job!

From Ahmed: Although the world’s oceans are currently dominated by phytoplankton such as diatoms and dinoflagellates that contain photosynthetic organelles (plastids) stolen from red algae, it was not always this way. Before the great end Permian extinction about 250 million years ago, the ocean was green, dominated by prasinophyte and other green algae. A clue to this major shift in the algal flora was provided by the recent comparative genome analysis by Moustafa et al. of two diatom species, Thalassiosira and Phaeodactylum. Using a phylogenomic pipeline designed and built in the Bhattacharya lab at the University of Iowa, the authors determined the origin of all 11,000 genes in each of these taxa. This work shows surprisingly that about 1,800 genes in each taxon are of green algal origin. This result provides strong evidence that diatoms and other marine phytoplankton that currently harbor a red algal derived plastid once contained a green algal endosymbiont that provided these “hidden” genes to their genome. This ancient cryptic endosymbiosis, rather than being an oddity, appears to have outfitted chromalveolates with genes from two taxonomically distantly related groups (green, followed by red algae), allowing them to complement their genetic potential. Many of the retained green genes provide key functions to chromalveolates such as enhanced photoprotection and a host of metabolite transporters to more effectively use dissolved nutrients in the environment, whereas many others likely have equally important but currently unknown functions. These data may therefore help to explain the rise to dominance of chromalveolates in the oceans. The work also reveals the genomic gymnastics that have occurred over millions of years in the marine environment resulting in highly chimeric nuclear genomes shaped by serial endosymbiosis.

5 Recent Iowa Genetics Publications

Click journal image for link.

Heather Brockway: Advanced access, May 2009.  Nucleic Acid Research.NAR

Lea Davis, Kacie Meyer, Danielle Rudd

Autism genome-wide copy number variation reveals ubiquitin and neuronal genes.  Nature, April 2009  nature
Ahmed Moustafa: Genomic Footprints of a Cryptic Plastid Endosymbiosis in Diatoms.  Science, June 2009.    science

Bill Lanier
Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas. Science, April 2009  science

Megan Ealy

A genome-wide analysis identifies genetic variants in the RELN gene associated with otosclerosis.  AJHG, March 2009  ajhg

Fedik Rahimov publishes in Nature Genetics

rahimovf1For those of us who have been following Fedik’s research knew that something good going.  In the November 2008 Nature Genetics issue, he published his work “Disruption of an AP-2alpha binding site in an IRF6 enhancer is associated with cleft lip” with Jeff Murray as senior author.”  Fedik is now a post-doc at Harvard

A photosynthetic animal…some background on Ahmed Moustafa’s PNAS paper

I asked Ahmed to provide a little background info on his recent PNAS paper when I found out how novel the research was (a photosynthetic animal).


From Ahmed: This work provides for the first time evidence for a horizontal gene transfer (HGT) of a nuclear gene (psbO; photosystem II manganese-stabilizing protein) from the stramenopile algal prey Vaucheria litorea to the nucleus of the predatory sea slug Elysia chlorotica. Elysia is renowned as a “solar-powered” sea slug, a marine species that is able to steal and harness the power of photosynthesis from an algal food source.

We are currently pursuing genome-wide analyses to determine the extent of HGTs that have taken place in this remarkable animal to plant transition. These data will help elucidate the key steps in the evolution of the genome and the transcriptome that enable the establishment of photosynthesis in a novel system. The sea slug also provides a potential source of photosynthetic cell lines for broader applications such as alternative energy and biofuel sources.

erik’s note: image from Ahmed’s paper (Rumpho et al., PNAS 2008): 
A.  E. chlorotica’s larval stage
B.  Slug stage, ingesting photsynthetic V. litorea 
C.  Young adult after feeding on V. litorea
D.  Adult sea slug (very very green)



erik’s update:  ahmed’s paper got the cover!

Update to Student Publications

pubmed1I hopped on PubMed today and found that many of us have been busy publishing recently.  Congrats to Ahmed Moustafa (PNAS), Aimee Buhr (AJHG), David Marion (Genetics), Shyam Ramachandran (J Leukoc Biol), Di Xu (Physiology and also in Am J Physiol Renal Physiol), Zen Abrera-Abeleda (Kidney Int as well as JMG) and Abe Sheffield (Mol Ther) all of whom recently published or I had not added to the webpage yet.  Keep up the good work. Go Iowa Genetics!  Here is the full list.

Cystic fibrosis pig model characterized in Science by Iowa Genetics faculty

As previously discussed during Student Seminar, Shyam Ramachandran elaborated on the development of the cystic fibrosis pig model that will allow better characterization of this disease in model organism.  Last week, Genetics faculty Mike Welsh and Paul McCray published in the journal Science (link to ScienceNow for background) characterizing the pig model noting many similarities with the human disease that have been difficult to recapitulate in an animal

 model.  Some genetics students were recognized in this publication as contributors to this important reserach, including Shyam, Erin Burnight and former Genetics student Jennifer Barlett.  This news has also been covered by the Press-Citizen and Daily Iowan as well as US News and science websites PhysOrg and ScienceDaily.  Congrats to all involved.