Hello again!
This week I still don't have much to do in the lab. The experiments I will be helping out with will happen in the summer, so besides getting training in the vivarium there won't be too much for me to do right now. I did get to empty the dishwasher today (I know, super exciting).
Later this week I will help the lab supervisor make a DNA ladder used for the gel electrophoresis. This is basically a bunch of known DNA fragments that have been cut by enzymes to specific lengths. As the gel runs, these fragments will spread out, and as they are made of known DNA, it is known how they should spread out, so we can see if the gel has run long enough. Previously the lab had bought these ladders premade, but they are trying to make their own now to cut costs. More on that later in the week!
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Because I am not doing much today, I took some pretty pictures of the lab. In order: my work space, pictures of mice, the cold room, the tiny centrifuge, the dry ice bin, two of the large freezers, and some pipettes.
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Hello to everyone who scrolled through all those pictures. Happy Friday!
On Wednesday I helped the lab manager make the DNA ladder. It failed because the DNA did not get digested (broken up) by the restriction enzymes. We think the problem is either that we didn't wait long enough for the DNA to be broken by the enzyme, or that we didn't use enough enzyme.
Today we are trying to wait for the DNA to be broken up for 4 hours, and then in another trial for 6 hours. If that doesn't work we will add twice as much enzyme per microgram of DNA. Hopefully we will get it working today and then we can make a full batch of DNA ladder on Monday. If it still doesn't work we will try waiting 16 hours for the DNA to be broken up by leaving it overnight on Monday night, and running it in a gel on Monday morning. We also found out that we might need to change the ratio of DNA to loading dye, so we will look into that too. It's the first time the lab has tried to make their own DNA ladder, so we have a lot to figure out.
Anyway, I will give an update on whether we got it working on Monday. Have a nice weekend!
Hi Serena! I am excited to see what you will do next week. I was wondering how the DNA ladder will contribute to your research. What role does it play? Thanks again!
ReplyDeleteThe DNA ladder is not directly related to my research. It will be used to check the genotype of the mice using gel electrophoresis.
DeleteHey Serena! In biology class, we just finished studying some biotechnology, including gel electrophoresis. I've only seen the one picture in the textbook, so it would be very interesting to see how yours turns out! What do they hope to find out from their gel electrophoresis? I'm sorry that you are not doing much in the lab currently, but I hope your summer is exciting. Good luck with your project!
ReplyDeletePlease keep updating us!
Please see my previous posts about the gels I have already run in the lab. They are using these to check the genotype of each of their mice.
DeleteReally cool! I was wondering what you will do next once the DNA is in the ladder?
ReplyDeleteA DNA ladder breaks up a sample of known DNA so we can see that the DNA is spreading out correctly in the gel. This will let us do genotyping on more mice.
DeleteHi Serena! I unfortunately have similar days of office work, so sometimes the week seems very slow. Will the gel electrophoresis be performed similarly to the ones we did in Biology on year with Mr. Nishan? And if so, what do you think might have been some of the errors in what we did that we had no bands showing?
ReplyDeleteWe're so close to finishing our project, so let's keep at it before the end.
Yes, it is the same as the lab we did in school. We might not have seen bands on our gels in school because we weren't looking at it under a UV light (the lab has a special box that shines UV light at the gel, and has a camera that takes a picture of the bands, while in school we were just looking at it under normal light). Additionally, if our gels sat around too long before being put in the electrophoresis tank, the DNA sample can disperse and get lost.
DeleteHey, Serena! Can't way to here about the DNA ladder, and I'm crossing my fingers that it worked!! Thanks for sharing those great pictures, too. Those pipettes look really fun to use. xD Are DNA ladders something new that's been "invented" (probably not the right word)? If they have been around for a while, shouldn't there be previous research to tell us the proper time to wait for the DNA to break down? Sorry if this question is confusing, maybe I just misread what's going on. You're doing a great job, and I'm really excited to read more!
ReplyDeleteYes, other people have made DNA ladders before, so there is lots of info on how long to wait, how much enzyme to use, etc. However, all of this varies depending on the type of enzyme you are using, which companies you buy it from, and what you are using it for. We need to find the right way to make it for our particular purposes.
DeleteGreat to hear that you will be able to continue the research this summer! For your presentation, what will you be focusing on for your experimental design?
ReplyDeleteMy main job while working in the lab was helping Derek image mouse brains for the sleep deprivation study he did as part of his Barrett thesis. I will be discussing the setup for that study, as well as mentioning previous tests the lab has conducted on their mice to insure they are effective models for schizophrenia.
DeleteHi Serena! I loved seeing the pictures from inside the lab! In regards to the DNA ladder, what role does it play in your research? Can't wait to hear more next week!
ReplyDeleteSophia Vaidya
The DNA ladder is used during genotyping. Genotyping is essential for the research in the lab to determine whether the mice are knockouts or wildtypes.
DeleteHi Serena! Great work. I was wondering what role the loading dye plays in the DNA ladder. Is it used to distinguish different parts of it? Thank you!
ReplyDeleteThe loading dye allows us to see how far the DNA in the gel is spreading, so we know when to stop the gel. It also has a glycerol component in it, which is basically a soap like chemical that weighs down the DNA and makes it sink into the wells on the gel.
DeleteHey Serena!
ReplyDeleteI'm sorry that the DNA ladder did notwork right away. How does each time interval affect the DNA, and why are you waiting precisely 4,6 and 16 hours? Also, could you clarify what the restriction enzymes are doing to the DNA. Have a great week!Looking forward to next week's post!
Julie Loison
The restriction enzymes cut the DNA at specific points, so it makes bands of the pieces of different lengths after the gel is run. We waited 1, 4, 6, and 16 hours because the instructions for the enzymes said it would take between 1 and 16 hours to work. We just picked intervals between that arbitrarily.
DeleteHey Serena, it sounds like fun to try making a DNA ladder. How did you begin the process of creating it? What materials did you begin with? Thanks!
ReplyDeleteWe added lambda DNA to a mixture with restriction enzyme and a buffer, diluted with water. Then we added that to the loading dye, which is made of glycerol, EDTA, Sodium dodecyl sulfate, and powered dye.
DeleteHey Serena? Thanks for sharing the pictures! What exactly is the loading dye that you mentioned? How does it work in relation to DNA?
ReplyDeleteThe loading dye allows us to see how far the DNA in the gel is spreading, so we know when to stop the gel. It also has a glycerol component in it, which is basically a soap like chemical that weighs down the DNA and makes it sink into the wells on the gel.
DeleteHey Serena, thank you for such an insightful post! How long did it take you to prepare the DNA ladder (since it was your first time making it) and was the process of creating it easy to understand or was it more of a trial and error process?
ReplyDeleteWe had instructions on how to make it, so it was not trial and error. The only issues we have had with it are associated with the enzymes not working correctly. Making the ladder took about an hour and a half.
DeleteHey Serena, thank you for all the photos, i have been in a couple labs before but each lab i have been to is different. i was wondering what specifically are the DNA ladders used for in your lab? keep up the good work!
ReplyDeleteDNA ladders are used during genotyping. It allows you to see that the restriction enzymes have cut the DNA correctly and the pieces separated correctly after the gel was run.
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