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Picture of me hiking in
the Flatirons above Boulder near the Royal Arch
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Welcome to the homepage of Jason Carnes!
I grew up in Hastings, Nebraska, a small town that instills good values such
as a passionate love for the best
college football team that ever was. I left home to attend Iowa State University, where I earned a
combined B.S./M.S. in Genetics. My
thesis work in Eric
Henderson's lab involved creating an artificial chromosome for the
ciliate Tetrahymena thermophila.
In 2002, I finished my Ph.D. in Molecular,
Cellular, and Developmental Biology at the University of Colorado at Boulder. My
thesis work in Leslie
Leinwand's lab focused on potential gene therapy strategies to ameliorate
pathologies caused by nonsense mutations. A brief synopsis of this work is
written below.
After working on a post-doctoral bioinformatics project with Rob Knight in Mike Yarus' Lab
in MCDB, I moved west to work at the Seattle
Biomedical Research Institute. My current research investigates the
phenomenon of RNA editing in Trypanosoma brucei, the causative agent
in African sleeping sickness.
contact me by
email at: jason.carnes_atsign_sbri.org
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Synopsis of my Doctoral Research
In the central dogma of molecular biology, DNA is transcribed into mRNA, and
mRNA is then translated into protein. Normally, a ribosome begins translating
an mRNA into protein at the start codon, and terminates when the ribosome
reaches the stop codon. However, nonsense mutations generate a premature stop
codon before the authentic stop codon, causing the ribosome to terminate
early and preventing translation of a full-length protein. The truncated
protein that results from a premature stop codon is frequently
non-functional, and the loss of function can lead to disease.
More than 200 known human diseases are caused by premature termination of
translation at nonsense mutations (Atkinson
& Martin 1994). In several human diseases caused by nonsense
mutations, small amounts of full-length protein could provide marked
improvement over the condition caused by its complete absence. In pathologies
such as hemophilia (Eyster,
Gill et al. 1978; Bray
and Luban 1987; Lofqvist,
Nilsson et al. 1997), cystic fibrosis (Dorin,
Farley et al. 1996), and muscular dystrophy (Phelps,
Hauser et al. 1995), only 1-5% of the normal amount of protein could
result in benefits. In contrast to a deletion mutation that actually
eliminates sequence information, a nonsense mutation only masks genetic
information that is still there, because release factors recognize the nonsense
mutation and prevent the remaining sequence from being translated by the
ribosome. Release factors are the proteins responsible for terminating
translation when the ribosome reaches an authentic stop codon. However, since
the release factors also recognize nonsense mutations, their activity leads
to truncated proteins from mutant mRNAs. If the activity of the release
factors could be decreased, then some ribosomes should translate past the
nonsense mutation (a process termed readthrough) and generate full-length
functional protein.
The purpose of doctoral research was to explore novel strategies to decrease
the activity of the release factors sufficiently to promote readthrough of
nonsense mutations. My thesis describes three RNA-based strategies for
reducing termination efficiency by decreasing the activity of the release
factors eRF1 and eRF3. In the first strategy, RNA Selex was used to isolate
RNA aptamers that specifically bind to the complex of eRF1 and eRF3
(eRF1•eRF3), and inhibit their activity. In the second strategy, antisense
oligonucleotides were used to target eRF1 mRNA for degradation, so that eRF1
protein concentration decreases. In the third strategy, small inhibitory RNAs
(siRNAs) were used to mediate RNA interference, in order to target eRF1 mRNA
for degradation. The results of the RNA Selex approach were published in the
journal RNA, and a .pdf file can be
downloaded here. The results of the antisense and siRNA approaches were
recently accepted by RNA, and a .pdf file
can be downloaded here.
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