Week 1 at Ware Lab of Rutgers Newark

Day 1
On the Thursday 2 weeks ago, my first day began with Dr. Ware, my PI, introducing me to all the equipments in the laboratory, showing me pretty much where everything is around Rutgers, introducing me to other students, both graduate and undergraduate, and giving me the first assignment of the day. I also received my first project - I will sequence erythemis, a genus of dragonfly which many of its species have not been studied in the past, and are ambiguously placed in the phylogenetic tree. Aside from placing known species into the tree correctly, I will also determine if some samples are actually new species.

Crosslinker in action - a convenient device used to
sterilize equipment with x-ray

There are about 10 members in the lab, most of them on the first day were away either in vacation or field studies.My first assignment is to learn about some basic safety precautions, and how to extract DNA from sample insects. Dr. Ware told we to always sterilize every piece of equipment with a Crosslinker (see picture on the right) and wipe surface with ethanol. On the other hand, DNA extraction is a bit similar to plasmid transformation experiments during Biotechnology classes, except I have to first soak tissues into chemicals. On my first day, I used 2 legs, each from a dead cockroach, as an example. We preferably pick the legs of insects, since legs have the most amount of muscles to extract DNA from, and the least amount of exoskeleton to deal with.

After I soak the legs into 2 chemicals that lysed all the cells and left only DNA behind (see the picture on Day 6), I incubate it for further extraction (the rest of the procedures is pretty much the same as plasmid DNA extraction, with all those spin columns). After extractions, we run PCR with the extthermocycleracted DNA in a thermocycler. Again, this is really similar to what we did before, except there are different thermalcycle and primer you can choose to target a specific gene to amplify. Instead of Tacq, I used a different primer and chose a different thermocycle to amplify 16s gene, an rRNA gene.

Day2
This day I met one of the graduate students of the Lab- Melissa. She's working on a different project aside from mine, but she understands and can guide me through experiments.

Today I received my results from PCR, and run a gel electrophoresis with the amplified DNA. I also repeated the experiments yesterday with 6 dragonfly legs, marking the start of my project.

Day 3

Gene alignment - matching and aligning the genome of
differen species into a comparable form.
Usually you can shift a sequence by 1-4 cells to
fix a frameshift mutation, and the sequence will align
itself automatically, much like what I got above. But eventually,
 however, sequences will go haywire like the picture below,
and become difficult to fix.

Coming back from weekend, today my professor was away in the morning, and I was told to read some papers and articles. After lunch, I spent the rest of the day learning how to align gene sequences (see pictures on the left).

Day 4 and 5

On day 4 I met another graduate student - Will. He is a very outgoing person, and aside from lab works, I asked him about student live and culture around Rutgers. For my assignments today and tomorrow, I continued to align sequences, and run another PCR with different primer and thermocycle to target another gene to amplify, then I ran another gel electrophoresis.

Day 6

The piece of leg form collector,
soacked in chemicals, after
incubation.

Today, I received a leg of erythemis fro ma collector, and I performed DNA extraction, PCR and gel electrophoresis again, just this time I will try to preserve the leg as much as possible, returning it to the collector later on without deforming it. 

After today, my professor and most graduate students would go to Germany for a conference, so over the next week, I will attend a safety training course required to work in labs at Rutgers, and spent time reading articles and papers, and aligning sequences.