Can you briefly describe your experience at JGI? What were your responsibilities as an
intern? Did you enjoy your experience?
“My experience with JGI has been fascinating. At JGI, I joined a team of student
researchers that essentially analyzed public bacterial genomes. Using genome editing and
viewing software developed by the Sanger Institute, a genomic research center in the UK,
our team inspected each genome to assess the quality of published genomes. By double
checking error reports produced by JGI staff we examined the annotations of several dozen
finished sequences. The experience here complemented what I learned in LS187 very much.
Similar to the sequencing done at UGRI, interns from other programs participated in the
sequencing of new microbial genomes; however, I got a glimpse into what happens after the
sequencing has been completed.”
“At the end of my internship, I actually got sent to an international microbial genomic
conference at the University of Wisconsin, Madison. During poster sessions, I described
the group's contribution to JGI during the summer. I also got a chance to present a
poster on UGRI and surprisingly many top-notch researchers took more interest in the
undergraduate endeavor in sequencing Ammonifex degensii than my work at JGI. Being in
the midst of top researchers in the field was a bit overwhelming; nonetheless, the
speakers were extremely interesting. Before this conference, I hadn't realized the impact
of microbial genomics on issues such as environmental remediation, energy production, and
medical applications. The opportunity to listen to these speakers ultimately rose from
working my way up from participating in LS187 and UGRI to interning at JGI.”
“I suppose the Microbial Genomics staff at JGI liked my work during the summer because
next thing I knew, my supervisors offered me a position after graduation. Now, my primary
job is similar to what I did during the summer, the only difference is that I actually
get to analyze genomes sequenced here at JGI before they get published to public
databases. Since I've gotten pretty good at this task, they've also allowed me to start
analyzing metabolic pathways found across all organisms in order to maintain their
in-house database system.”
Looking back on the techniques and knowledge you learned in LS187, were there any skills
learned in the class that you were able to utilize at JGI?
“LS187 provided the foundational knowledge I needed to fully comprehend my work
at JGI. Unlike any other class that I've taken at UCLA, UGRI and LS187 gave me hands-on
experience of DNA sequencing that must take place in order for genomic analysis to begin.
Albeit, there are more automated processes for producing much higher quantities of
sequences at these research facilities; however, using the 64-lane electrophoresis Li-Cor
was more than enough to grasp the fundamentals of DNA sequencing. While most of my work
at JGI is computational, if one wanted to continue in actual sequencing procedures,
LS187's introduction to sequencing is like a learner's permit to what sequencers do at
JGI do everyday. In spite of all the robotics and automated processes used in this high
tech facility, the concepts, the reactions and substrates are all pretty much the same.
Another key aspect of LS187's curriculum that I found helpful at JGI was being part of a
team. Learning to operate efficiently both as an independent scientist and as well as a
team member showed me the importance of staying on task and communicating with
co-researchers. At JGI, communication was essential to avoid time-consuming errors and
prevent unnecessary work. Above all, it was nice to be able to brag about having actual
hands-on experience in DNA sequencing to other students who did not have such an
opportunity at their schools.”
Is there anything you would add to LS187 to help better prepare students for research or
to work in the industry?
“I think the LS187 curriculum is very efficient in producing results while introducing the
students to most aspects of sequencing a microbial genome. Of course, as the students
approach completion of sequencing, there will need to be additional tasks such as
utilizing what we learned of BLAST, COG, and KEGG databases into actually annotating
Ammonifex degensii's genome. By incorporating assembly procedures, students will
realize the difficulties and ambiguities that arise when compiling coherent genomic
sequences. My last change would be to find a laboratory dedicated to this class so that
more students can participate in this eye-opening program.”