Douglas G. Scofield, PhD

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Sedgwick Reserve, where I studied pollen and seed dispersal in Quercus agrifolia and Q. lobata.

 

Intron length distributions within the 5'UTR, coding sequence, and 3'UTR of Arabidopsis thaliana genes.

Intron length distribution in Arabidopsis

 

Flower of Delonix regia

photo of Delonix regia flower

 

Pollen from Delonix regia stained to estimate viability; viable grains are dark blue, nonviable grain is pale blue.

germinating pollen

 

Umeå Plant Science Centre

Comparative and population genomics

In my current position at Umeå Plant Science Centre, I'm part of the Norway spruce (Picea abies) and trembling aspen (Populus tremula) genome sequencing projects.

My first post-doctoral position was the study of gene and genome evolution with Michael Lynch at Indiana University. My research projects included the first thorough examination of the natural history and evolution of introns within untranslated regions of genes (UTRs), for which I received a NSF Postdoctoral Research Fellowship in Biological Informatics (DBI-0434671). The 5' and 3' UTRs which bracket the protein-coding sequence (CDS) are fundamental to the structure of every eukaryotic gene. However, the natural history and evolutionary dynamics of introns in UTRs have been largely unexplored. I work expand our knowledge of UTR introns through several interrelated goals: 

(1) summaries of basic natural history information for UTR introns; (2) development and testing of hypotheses concerning intron evolution within UTRs; (3) the estimation of UTR-specific rates of intron gain and loss in separate evolutionary lineages, and development of new analytic techniques to estimate lineage-specific rates of character evolution; (4) the determination of patterns and constraints on sequence evolution within UTR introns; and (5) the creation of a publicly-available database of UTR intron information. To address these research goals, I used a combination of bioinformatics techniques, theoretical modelling and extensive computer simulation.

Figure: Median intron size throughout the 5' UTR and CDS of four model organisms. I proposed an evolutionary model that explains the increased size of introns in the 5' UTR and the sharp drop in intron size at the 5' UTR-CDS boundary via differing strengths of selection against intron splice site shifts within the 5' UTR and CDS, arising from sequence constraints and the presence of potentially deleterious premature start codons (uAUGs) upstream of the true Start codon. Figure from Hong, Scofield and Lynch (2006). 23:2392-2404).

Catania, F., X. Gao and D. G. Scofield.  2009.  Endogenous mechanisms for the origins of spliceosomal introns.  Journal of Heredity 100:591-596.

Scofield, D. G. and M. Lynch.  2008.  Evolutionary diversification of the Sm family of RNA-associated proteins. Molecular Biology and Evolution 25:2255-2267.

Omilian A. R., D. G. Scofield and Lynch M.  2008.  Intron presence-absence polymorphisms in Daphnia. Molecular Biology and Evolution 25:2129-2139.

Scofield, D. G., X. Hong and M. Lynch.  2007.  Position of the final intron in full-length transcripts: Determined by NMD? Molecular Biology and Evolution 24:896-899.

Hong, X., D. G. Scofield and M. Lynch.  2006.  Intron size, abundance and distribution within untranslated regions of genes. Molecular Biology and Evolution 23:2392-2404.

Lynch, M., X. Hong and D. G. Scofield.  2006.  NMD and the evolution of eukaryotic gene structure. Pp. 197-211 in Nonsense-Mediated mRNA Decay, ed. L. E. Maquat. Landes Bioscience, Austin, Texas, USA.

Lynch, M., D. G. Scofield and X. Hong.  2005.  The evolution of transcription initiation sites. Molecular Biology and Evolution 22:1137-1146.