Fish, Embryos, Buffers, and... MATH
Welcome Back Fellow Fish Lovers,
We would like to begin this weeks post by announcing that our family has gotten a bit larger, because we got NEW FISH!!!!!! These fish are now the freshmen of lab, but no harm will come to them because we have a strict no hazing policy here in the Weicksel Lab. Safety is our top priority, as we want to keep our little guys and gals comfortable so that they will be ready to mate soon, and give us more embryos. You can never have to many embryos.
Yale:
Last Friday, the Weicksel Lab swam down to Yale to listen to research talks and gather zebrafish information. The first presentation was on stem cell growth and the supposed predetermined pathways of the cells. Although it does not pertain to our current research, it was still very interesting to see the progress Dr. Tianchi Xin and the Greco made in this field. The second presentation was on the optimization of CRISPR-Cas9 systems for Genome Editing in Zebrafish. Dr. Miguel A. Moreno-Mateos from Dr. Antonio J. Giraldez lab presented that their lab found a more efficient way of conducting CRISPR genome editing through temperature control. This presentation was especially interesting considering they used zebrafish in their own studies and their methods are possibly applicable to our own research using the CRISPR-Cas9 system for making genetically modified zebrafish for further studies.
Once the talks were over Dr. Weicksel took us on a tour of his old laboratory. We met his old research friends from Yale and even got the chance to see what a Research 1 (R1) university zebrafish setup looks like. They had hundreds of tanks in a controlled environment, similar to our own setup just way bigger. We finished our tour of Yale and swam over to one of Dr. Weicksel’s favorite food trucks outside the university for some lemon chicken. It was very delicious and we plan on visiting again sometime soon!
Weekly Updates:
This week is now the fourth week that the Weicksel Lab has been meeting.
On Monday, the team took a small field trip to Home Depot, in hopes that we could find something to improve our water flow to the fish. The four of us stood in the same aisle staring at the different types of piping, for what felt like forever. After feeling defeated by high prices, our lack of construction knowledge, and everything being the wrong size, we discovered Amazon had just what we needed (what doesn't Amazon have?).
When we got back to campus we prepared our gel extraction samples, from last week, for sequencing. We mixed the sample with a primer and a little water. Then they were labeled, packaged, and dropped off into the Fed-Ex bin. The team brainstormed ways to design and make figures for the poster.
Tuesday was filled with lots of poster preparation, fixing the abstract, writing a draft of the introduction and methods, and designing a figure for 3C: chromosome conformation capture. We found out our data from our first gel extraction wasn't all that pretty, which means we need to keep trying and do some troubleshooting.
Wednesday, was science day this week. We started our day by running a PCR and making buffers. The buffers are to help us obtain plasmids from bacteria. Plasmids are usually a circular strand of DNA that can replicate independently of the chromosome. This helps us save money because we can replicate certain enzymes we need from the plasmids. PCR stands for polymerase chain reaction, and we use it to amplify or copy lots of a certain segment of DNA. The PCR was run in a gel and then we cut it up to do another gel extraction, and off it went to GeneWiz from analysis. This time we hope our data turns out to be better. We finished the day by making glycerol stocks of the leftover bacteria we used earlier for the plasmids. This was very simple and all we had to do was take some bacteria, mix in glycerol, and put it in the freezer.
Thursday turned into buffer day, because those long awaited chemicals finally arrived. If you have taken chemistry you know that making buffers requires a lot of math, and math in the summer is not what college students love to do (surprising I know). We first had to dilute our chemicals, so math, and then take our dilutions and make buffers, so even more math. The buffers we made will allow us to begin our 3C: chromosome conformation capture library, which will hopefully help us identify many interactions between the hox genes and other genes. Before we left we set up fish to be mated in the morning, so that we can hopefully get lots and lots of embryos.
On Friday morning we put on a little Marvin Gaye, closed the curtain, and let the fish do their thing because we want their embryos. After we collected the embryos, we let them sit in the incubator before we could count them. Today's embryo count rang in at a whopping 1021. Then, we went over our sequencing results and discovered that our homemade tubes worked and our data turned out to be good. We finished the day by fixing the embryos with formaldehyde and glycine for 3C: chromosome conformation capture. We can't forget get that one of our fellow fish workers had their birthday today. Happy 20th Birthday Vasili! (hope that birthday donut was yummy!)
Thanks for swimming back to us this week. As always, if you have any questions or comments head over to the contact page. Keep those fins on the lookout for next weeks blog!
Swim By Again Soon,
The Weicksel Lab
