Digitizing the Chicken: Filling in the Chicken Genome

Many Clemson students are training to be
future scientists, but some are actively assisting the scientific
community already. There are dozens upon dozens of papers where
chicken genes have been described, but it’s an immense task to find
all of the relevant information in one place.
A Creative Inquiry team led by Dr. Susan Chapman from the
biological sciences department reviews literature and extracts
information to add to the Gallus Expression in Situ Hybridization
Analysis database (GEISHA), an international resource for
chicken genes visualized in embryos. Chicken embryos are very
similar to mammalian embryos, but they are more easily obtained.
Therefore, visualizing gene expression in chicken embryos helps
scientists better understand gene expression in our own species.
Genetics and molecular biology have grown exponentially in the
last decade. Technology makes sequencing an entire genome fast
and relatively inexpensive. In fact, experts estimate that anyone will
be able to transcribe their own genome for $1,000 soon. However,
being able to sequence genes quickly presents a problem: how can
all this data be sorted and made accessible to scientists and the
general public? Bioinformatics databases fill this need. For example,
the University of California-San Diego maintains a Human
Genome browser where a scientist can specify a particular area on a
chromosome and find relevant information at that specific location,
like diseases linked to that area or how many different species share
that same sequence.
The GEISHA database is specifically for genes expressed in the
first six days of chick development. A GEISHA entry is annotated
with information about the gene from the National Center for
Biotechnology Information’s databases and specific images. These
images show where the gene is physically expressed through dyes
with tags for specific anatomy parts. Some genes are expressed only
at certain stages in development, and sometimes at very specific
locations, so it’s useful to have this information available in one
place.
Students at the University of Arizona, Brigham Young University
in Utah, and Clemson University, under the direction of Dr.
Chapman and Dr. Diana Darnell at Arizona, become curators
for the GEISHA website. Curators select a gene that hasn’t been
processed for the database yet and are given the name of the paper
where it is referenced. They must then read through the paper to
find the accession number of the gene and take screenshots of
appropriate figures to upload to the website. The accession number
is used in other web databases to find more information to link,
such as the exact DNA sequence of the gene. About 25 Clemson
University students have participated, and although the other
schools have a larger number of students involved, the Clemson
branch has submitted a substantially higher number of entries. This
could be because at Clemson, the GEISHA project is the focus
of a Creative Inquiry whereas at BYU it is part of a biology lab or
course as an optional project.
According to Dr. Chapman, technology has really made science
accessible to undergraduates, giving them the ability to make real
world contributions. In the Spring 2012 semester, a facebook
group was added for students and the professors to troubleshoot
issues and Dr. Chapman thinks that video tutorials could be added.
Eventually, the GEISHA curation system could be opened to high
school students, increasing community involvement in real science
through crowdsourcing.
This Creative Inquiry worked for three semesters from Spring
2011 through Spring 2012. Dr. Chapman enjoys projects like these
because they allow students to participate in real science as an undergraduate. “I don’t think people come into biology for a degree. I
think they come in because it’s fun,” Dr. Chapman says. n
GEISHA is accessible to the general public at
http://geisha.arizona.edu