Friday: Morgan's end of rotation talk; experiment saga continues
11 a.m. Pause for lunch and update
Visited Salaita lab meeting. It was in a different room that was much warmer. I appreciated it being more, even if it was a bit excessive. This morning was freezing. Ian, the senior undergrad I talk to a lot whose project I worked on this summer, gave an interesting literature talk about one of Raine's papers, who isolated my ligating protein RtcB. Clearly, I need to read that paper and make sure I understand what's going on there a bit better.
Enjoyed Morgan's end-of-rotation talk. Got to ask a lot of my dumb questions that I'd been really wanting to ask. Got to eat some bagels and cream cheese - always a good thing. Afterward, the group took a new lab picture and I got to be in it! I wasn't sure if I should, but Yuan said definitely, and pulled me along, so I felt better about it.
Experiment Saga: Uncertain
Waiting on Lisa to get here. Asked Daniel my questions. He brought up the tube motion would be impossible to quantify / focus upon since they'd potentially be moving in and out of the z-plane, something Kevin and I already discussed yesterday. He was very dubious that the experiment should be attempted at all - something I kind of expected him to say - because, while I have papers showing that catalase bound to carbon nanotubes is still active, I do not have one showing that for peptide nanotubes, so he thinks I should do that first. He could be right. I don't see the harm in trying this though for the heck of it, since we have everything else necessary. Yue agreed with that view. Daniel and Kevin can't help, but I'm not worried about it. I think Anthony will be able to, after all. I'll probably try to Dr. Lynn in the afternoon if he's here - I may as well - maybe he'll have more ideas or say I'm insane and call off the whole thing. We'll see. At least, I can say I gave it my best shot, either way.
"Grandma's Cooking" Experiment
I performed what I like to call a "grandma's cooking" kind of experiment with Lisa. I talked with her and she said - ok, let's go ahead and do this! And we threw stuff together. Anthony was basically of the same mind - just have us come over and throw samples together. P.S. This is definitely not the way I like to do science, but I may as well have done it this way for this time. There wasn't much else that I could do. BUT. It's very embarrassing to me. Today has solidified in my mind just how much I want to really understand what I am doing, why I am doing it - I want to know all the details - the excitation of the dyes (which I found out); the best methods of adding dye to tubes (Anthony gave some cool pointers) and have thought through everything - how the instruments work, the tubes and their structures, go through more controls. *sigh* This experiment was not a "good experiment," in my opinion. It was wholly a quick and dirty one. But maybe, that's sometimes useful to do now and then. Daniel and Kevin also said that a 2-photon microscope wasn't the best tool for the job in this case, which I'd agree about much, but it's what Lisa uses and is familiar with, so we went for it anyway.
Results of the Grandma's Cooking Experiment - Something Interesting - Might Have Worked!
This microscope only images photos at fastest - once every 20 seconds. We first looked at the pY tubes. We'd sonicated them for an hour and it seemed as if they were definitely in fragments smaller than the normal - about 7 um long - perfect, I say. I added equal volume H2O2 at first (100 ul), and the first time, it took Anthony about a minute to figure out how to take the images and we might have missed the best window of opportunity, so we didn't see any motion, though Anthony said he saw motion early on, but that could be a result of all the liquid we added.
So, after that, we looked at the K tubes. I decided to add just 5 ul of a much more concentrated solution, very slowly, against the back wall of the well, to hopefully not disturb the solution much.
Somehow, Anthony managed to catch a single tube streaking across the surface, going straight, in one of the images and tube conglomerates moved into and out of the screen for about a minute after addition (5-6, 20 sec images). It was very exciting! It's very arguable that this motion was fake, but Anthony was focusing near the middle of a ~.5cm x ~.5cm well, near the bottom of it, to avoid seeing as much Brownian motion. The streaking tube we saw was only observed in one frame and disappeared thereafter. I am not convinced 5 drops carefully placed on the backwall would displace the middle of the solution near the bottom of the wells with 100 ul of solution in it enough to cause a tube to move that quickly. So, it's suggestive, but by no means conclusive.
Dr. Lynn still isn't here yet. I'll have to email him the good news. *headdesk* Oh my goodness. I'm still so embarrassed about this experiment though - it was so quick and dirty - I'm not sure one should call it an experiment as much as "playing around with peptides." And there were so many horrible things wrong with it that I'm not even going to outline it here. But - I'm very pleased anyway - I got to attempt an experiment on the last day of rotation. I can say I tried something. Lisa helped a lot. She did half and I did half, basically, and then Anthony imaged for us. I couldn't have done anything without her. Can't wait to tell Dr. Lynn! Setup a meeting with Dr. Scarborough on Monday at 11 a.m. Rolando says he'll ask me horribly difficult questions during my talk. I'm sure he will. Yes, yes, there's so much I don't know. I'm looking forward to digging into a system, and understanding it thoroughly - and looking up every possible detail - and expanding my understanding of inorganic and Pchem, which are pretty much nonexistent right now. I'm very grateful this was able to get done.
But really, actually, truly, any results we saw from this experiment would fall in the "questionable" column. So this was really the best result we could have had. I'm shocked we saw anything at all. It could have so easily not happened that way.
I'll go ahead and point out the biggest flaws of this experiment I'd like to see fixed: 1) we didn't do wash steps to get rid of excess catalase. Lisa was worried it might be difficult to centrifuge down the tubes each time. 2) We also didn't add the dye in the best way. Anthony said that its best to make a solution of the dye and other ingredients and then add the tubes, rather than adding the dye to the tubes. This is because adding dye to tubes means there will be a high local concentration of the dye in the spot it's added resulting in higher dye binding to those tubes and tube bundling. This makes a lot of sense. 3) We only incubated catalase with the tubes 1 hr. 4) We neglected to do the important control of imaging tubes and H2O2 without catalase. Finally, the K tubes have a positive inner and outer surface. Catalase could have been nonspecifically bound to either face. The addition of the H2O2 could have been handled better. We could use a better instrument for this setup - one that could capture movies. Yeah - that about covers the major points. I'm looking forward to seeing what Lisa does with this in future. I think it has a lot more potential once optimized.
Thursday: Outlining a potential experimental setup
Update (~7:43 pm): Just sent 2-page outline of potential experimental setup to Lisa, to be discussed tomorrow, after I talk to Daniel. Now ... I wait. We'll see what she thinks. Talked to her a little bit today about things.
Anthony was unfindable. But now I know where the physics labs are. They have the coolest commons room ever, with fantastically interesting old devices in it. Pictures of those coming soon. He did get back to me and say he'll show me the instrument tomorrow after a final. He didn't say when. Hence, Daniel is my backup plan.
Kevin says, it's possible I *might* be able to use the Salaita microscope Saturday. Feasibility of this, whether or not it's a good idea, potential difficulties and lots of questions, as yet to be discussed with Daniel. Must have lots of plans, just in case. It's possible I could do something Monday, after the final, but that's cutting things close and I'd rather have something attempted before then, whether it works or not. Pray it works out! Thanks.
Talked to Sarah Yang from Oxford today - she's in Dr. Dyer's biophysics class and ended up deciding not to do research this semester after all. She talked to me about it at the beginning of the semester. She's a junior, I believe. Good conversation. Saw Daniel (Heaven lab) this morning! He had his defense at 1 p.m.! I know he passed. He's a great guy.
Also, slowly (or not so slowly) eating all the cookies and soda in the Salaita lab student offices. Kornelia keeps telling me to eat it, so I do. You can blame her. Must have eaten at least 12 chocolate chip cookies today. Four - five at lunch and ate the rest that were left around 5:10 pm when I looked to see if Daniel was done w/ experiment yet (he wasn't). Cookies. So tasty.
Update (10:45 pm): Update: Got an email back from Lisa! She gave some good comments, said she'd done some of the experimental controls I suggested before, recommended using alexa633 instead of acridine orange, because she has some and has used it previously, gave some other tweaks, asked some questions, said she could make both Friday and Saturday times, and actually said it all sounded exciting and - let's do it! *grins* *slaps hands together* That's what I like to hear. ALL RIGHT! LET'S DO EEEETTT!! BOOYAH!! Silly comments in post.
Heard another grad student ask someone if Dr. Lynn was coming back tomorrow or not. *startled look* No, no, nooooOOOoOOoOo. *waves hands spastically* Stay away, Dr. Lynn, stay awaaaayy! You're not allowed to come back yet. I'm not done. And I don't want you to pounce upon me and scare the crap out of me until I am. Unlike Khalid, whom I miss terribly if he leaves, Dr. Lynn's leaving this week was a tremendous relief. I didn't have to look over my shoulder constantly and wonder how I was not meeting his expectations or what I was doing he disapproved of. He's nowhere near as scary as Bijoy, but still scary. I shouldn't be so uptight. But somehow, Khalid gives off this very comforting and accepting air, and Dr. Lynn does NOT. He just does not. Maybe we're on different wavelengths. ... Anyway ... no, Dr. Lynn, don't come back yet!! Not until I have at least done an experiment! THEN you can interrogate me. *holds door shut* *hides* *locks self in room with equipment and stuff* *peeks out from boxes at door*
Answered Prayers: I'm going to try to collect more of these soon this weekend or after finals, but I did notice and am very grateful for the fact that the Lord has provided opportunities for me to stay in touch with the Salaita lab, when I didn't think any would be available. I'm so grateful. I must be around the people I love or I get messed up / the shakes. This is why I cannot leave Georgia or go on trips without John. Salaita lab and Khalid are family to me now. Therefore, I have a constant large desire, like a magnetic pull, to be near them. Gratefully, I've gotten just enough minimal contact, plus extra, so that I'm no longer suffering. Definitely not enough to be satisfied though. I look forward to fixing that after I join, Lord willing, and talk to lab members and Khalid so much, they'll be thoroughly tired of me and I'll be thoroughly happy and finally satisfied. Just thinking about it makes me really happy.
Wednesday: Yoshie's defense and grading are done
Update: Congratulations to YOSHIE for a very cool, stellar and interesting defense!! She's the most professional, calm person I've ever seen give a talk so far. I hope to emulate you, O Yoshie of awesomeness. Also, thanks to her husband Nick for actually giving us coffee and cookies, who came to listen. We're not even defending and we get food?? Yeeeeuuussssssss. Sweetness.
Update: Final grades for my orgo lab class are FINALLY in!! Notebook quizzes took forever to grade. Online stuff went suitably much faster. For acknowledgements of great work on these last assignments, see here.
Update: Favorite new word of the day, "flocculation," according to Wikipedia means, "in the field of chemistry, is a process wherein colloids come out of suspension in the form of floc or flake; either spontaneously or due to the addition of a clarifying agent."
Tuesday: Not tired and depressed
Keon's funny pictures
Monday: Tired and encouraged
Update (4:39pm): Hmm. Yes. Clearly I've failed at using blocks of time for this effectively. Much improvement needed. Noted. Won't make deadline. But the stacks are decreasing. More online though. I'll go as long as possible. I'm glad mom suggested dropping me off today and having dad pick me up. Good thinking, after all. Proposal review assignments for biomol sent out this afternoon (due to late turn ins) and due by class tomorrow. I think I'll work on those late morning tomorrow sometime. Maybe by Tuesday evening, if grading is finished, I can do experiment stuff again! Final in bioorganic is next M I found out. That's good. Thought it was this Friday. Sadly the cume didn't make it. But, that chiral molecule paper is fascinating. Read a piece of it. It'll make good reading for later. Glad I have it.
Update (7:28pm): Made it home by 7ish! Going to sleep. Blog will be de-cluttered appropriately probably tomorrow.