Monday, April 27, 2015, 5'-end labeling my RNA with new reagents
Lots going on this week: Kornelia had her third year report and passed! YAY! Christian Wallen in the Scarborough lab has his third year report - many reports are happening.
Since I last wrote, I was able to incorporate aminoallyl-UTP into my RNA. I attempted to label it with Cy3b and was partially successful. However, I also saw some degradation and the reaction was not optimized. I think that I've determined the degradation is probably from contaminated DMSO - I used the lab's stock - which is used a lot by everyone for DNA work. I bought my own, and today, tried part 1 of the experiment to label my RNA 5' ends with 5-iodoacetamidofluorescein. Wish me luck!
I will get to an actual update sometime soon. Partly, I have been scarce lately due to a lot going on and to adding gaming with John back in as a hobby, rather than only blogging. I was feeling restless for something relaxing to do, and this has really helped. Unfortunately, however, it has also made writing more scarce. Class has ended, so that helps a lot. I hope to write more and not just technically. Things will happen slowly - I'm still working out what I want my summer schedule to be. I may schedule a day for writing. However, it is late, so I can't do much today.
Since I last wrote, I was able to incorporate aminoallyl-UTP into my RNA. I attempted to label it with Cy3b and was partially successful. However, I also saw some degradation and the reaction was not optimized. I think that I've determined the degradation is probably from contaminated DMSO - I used the lab's stock - which is used a lot by everyone for DNA work. I bought my own, and today, tried part 1 of the experiment to label my RNA 5' ends with 5-iodoacetamidofluorescein. Wish me luck!
I will get to an actual update sometime soon. Partly, I have been scarce lately due to a lot going on and to adding gaming with John back in as a hobby, rather than only blogging. I was feeling restless for something relaxing to do, and this has really helped. Unfortunately, however, it has also made writing more scarce. Class has ended, so that helps a lot. I hope to write more and not just technically. Things will happen slowly - I'm still working out what I want my summer schedule to be. I may schedule a day for writing. However, it is late, so I can't do much today.
Thursday, April 9, 2015, My modified UTP came ALREADY!
TODAY! My aminoallyl-UTP came!! YESSSSS. I was SO excited. I wanted to do an experiment with it right then, but I knew I didn't have time. But TOMORROW MORNING IT WILL HAPPEN IMMEDIATELY. Transcribing my RNA with the modified UTP. WOOHOO!!!
Photo Notes: Also, in the morning, I found this giant slug on the pavement. It was so cool. I love giant slugs. I put him in the bushes of course. There were pretty flowers on the way to class, so I took a picture of those too. Maybe you like them better than the slug? I don't know. It's a toss up to me.
Sam had a test today, but still came into lab after it, and helped me pour a gel. I was so grateful. Thanks to him, I could actually get things done at a reasonable hour. AND THERE WAS NO REACTION IN THE NEGATIVE CONTROL TODAY!! That's a super good thing, just sayin'. I have no idea why there's been autoligation / reaction without enzyme earlier, but there has been and it's annoying as heck.
I also spend a portion of the day pouring over notes on NHS ester dye coupling reactions and talking to Yun about them. I think I'm going to try Cy3b first, because that's what we have available in the dye box.
In class, I ate my lunch and a quarter of a huge chocolate rabbit. The professor talked about adenoviruses. I was exhausted all day - I think it was the heat. But I finally got Claritin so my eyes aren't *as* itchy. Pollen count of 6,125 today! Ok bye, got to sleep!
Photo Notes: Also, in the morning, I found this giant slug on the pavement. It was so cool. I love giant slugs. I put him in the bushes of course. There were pretty flowers on the way to class, so I took a picture of those too. Maybe you like them better than the slug? I don't know. It's a toss up to me.
Sam had a test today, but still came into lab after it, and helped me pour a gel. I was so grateful. Thanks to him, I could actually get things done at a reasonable hour. AND THERE WAS NO REACTION IN THE NEGATIVE CONTROL TODAY!! That's a super good thing, just sayin'. I have no idea why there's been autoligation / reaction without enzyme earlier, but there has been and it's annoying as heck.
I also spend a portion of the day pouring over notes on NHS ester dye coupling reactions and talking to Yun about them. I think I'm going to try Cy3b first, because that's what we have available in the dye box.
In class, I ate my lunch and a quarter of a huge chocolate rabbit. The professor talked about adenoviruses. I was exhausted all day - I think it was the heat. But I finally got Claritin so my eyes aren't *as* itchy. Pollen count of 6,125 today! Ok bye, got to sleep!
Wednesday, April 8, 2015, Figuring out RNA labeling
Today, I read about a way of labeling my RNA - by using modified nucleotides in the transcription reaction. I thought about this idea almost a year ago, but didn't want to do it, because I feared it would mess with DNAzyme binding to the target, but since I've now tried everything else and it didn't work very well, it suddenly seems like a more interesting option.
And I'm so encouraged! I think it'll work! I found exactly what I needed: aminoallyl-UTP, that goes right with the transcription kit I'm currently using. I'm so pleased! I ordered it and new supplies! I can't WAIT til it comes in and I can try it out!
Meanwhile, I finished labeling the 5'end of some transcribed RNA that Sam made with a FAM. I'll have to see if it worked and the RNA didn't degrade tomorrow. It seems as if the RNA pellet was the correct dyed color at least, which is a good sign. I also autoclaved pipet tips, checked the calibration of Kevin's pipets that I always use (they were great) and am currently baking some glassware and spatulas in the oven overnight so they will be RNase free.
For lunch, I ate with Brandon Greene, Amanda (Heaven lab) and Zed (Lian lab), taking Dr. Wang out to lunch. Kira asked if we'd host him and we agreed. He was giving a private seminar to faculty only. I felt kind of privileged to be asked to host him with the rest, though honestly, someone in the Hill lab should have subbed in. He works on batteries and nanomaterials related to those things. I tried 4 cheese ravioli at Amanda's suggestion at Saba for the first time. It was, thankfully, quite good! I needed something good. Before lunch, I drank peppermint tea and immediately got an awful headache for some reason. I decided maybe my body was revolting against a non-caffeinated drink.
LOTS TO DO!
And I'm so encouraged! I think it'll work! I found exactly what I needed: aminoallyl-UTP, that goes right with the transcription kit I'm currently using. I'm so pleased! I ordered it and new supplies! I can't WAIT til it comes in and I can try it out!
Meanwhile, I finished labeling the 5'end of some transcribed RNA that Sam made with a FAM. I'll have to see if it worked and the RNA didn't degrade tomorrow. It seems as if the RNA pellet was the correct dyed color at least, which is a good sign. I also autoclaved pipet tips, checked the calibration of Kevin's pipets that I always use (they were great) and am currently baking some glassware and spatulas in the oven overnight so they will be RNase free.
For lunch, I ate with Brandon Greene, Amanda (Heaven lab) and Zed (Lian lab), taking Dr. Wang out to lunch. Kira asked if we'd host him and we agreed. He was giving a private seminar to faculty only. I felt kind of privileged to be asked to host him with the rest, though honestly, someone in the Hill lab should have subbed in. He works on batteries and nanomaterials related to those things. I tried 4 cheese ravioli at Amanda's suggestion at Saba for the first time. It was, thankfully, quite good! I needed something good. Before lunch, I drank peppermint tea and immediately got an awful headache for some reason. I decided maybe my body was revolting against a non-caffeinated drink.
LOTS TO DO!
Other news, in real life
I've gotten interested in books again. That's a good sign, I think. This past week since Monday has been my first week of feeling free and relatively unstressed since the beginning of the year and it's been great. I'm listening to A Wise Man's Fear on my drives home lately. I'm on chapter 6 I think. I also heard that our friend Matt downloaded SWTOR and that made me ecstatic! I hope he enjoys the game and decides to play. I healed Ravagers with my friends Six, Vivek and other TSV folks on Tuesday night. I was slightly grumpy today because I was tired from staying up too late. But I got over it. I'm hoping to help my parents plant more tomatoes in their garden soon. There's a kind Khalid told me about that I want to try planting. I can't wait to read more science articles. I read lots of manuals today which made me happy. Only two weeks of class left! Life is good!
Tuesday, April 7, 2015, My parent's 30th anniversary and experiment bust
Tuesday was my parent's 30th anniversary!
Class was LONG. That's one thing I remember. And the professor talked so fast it hurt to listen. I wanted to absorb what he was saying, but I couldn't at that speed. He was talking about Epstein-Barr virus (mono) which I've had, so I was really interested. It's actually kind of a fascinating virus and indirectly related to the enzyme I'm studying right NOW - which amused me greatly.
The experiment was kind of a bust. I forgot to do something to it - but if I had - it would have taken too long almost to be worth doing - so I don't know what I should think about that. But oh well - it was useful-ish.
Class was LONG. That's one thing I remember. And the professor talked so fast it hurt to listen. I wanted to absorb what he was saying, but I couldn't at that speed. He was talking about Epstein-Barr virus (mono) which I've had, so I was really interested. It's actually kind of a fascinating virus and indirectly related to the enzyme I'm studying right NOW - which amused me greatly.
The experiment was kind of a bust. I forgot to do something to it - but if I had - it would have taken too long almost to be worth doing - so I don't know what I should think about that. But oh well - it was useful-ish.
Monday, April 6, 2015, Ms. Harmon's students come to visit!
I was feeling blah Monday but that all changed when Ms. Harmon's students came to visit! They had been planning to come for a while. I almost forgot til I checked my email. It was a blast! They were so excited about everything, and I loved showing them what I could. They shadowed me for the whole day - watched my gel experiment, and even stayed late to see the imaging! I explained by project and gave them a lab tour. While the gel was running, we got a cookie at Ali's Cookie store in Emory Village. I had always wanted to go there. While it stained, they played with the ferrofluids! All of us got free ice-cream from Emory grad student appreciation week booth, and they loved seeing the gel imaging. They got to throw away an old gel of mine for fun, visit the Weinert -80C freezer and see the NMR and X-ray crystallography center with me. I was SO happy they had such a great time - it made me SO happy. I love excited students.