It is obvious to me that I am beyond stupidly blessed. There is no other explanation for the sheer miraculous number of coincidences that have occurred to get me where I am in my Lynn experiments. I would be completely lost without His help. What follows is a short summary of what's happened yesterday and today that's so amazing (and some other unrelated things). Keep in mind this was written in haste. Expect spelling mistakes until I can make time for editing (which could be a while).
Highlights of Tuesday
Discussion with Keon
After class, Keon and I talked, like I said. He said that he was really passionate about his research and was starting to find literature reading fun, and wanted to start compiling articles like I had described, by subject, publication date and length. He didn't want the final in the Conticello class because he's scared to death of his final in the Quantum Mechanics class, which he says, as a whole has so far murdered him. But, the Lord has taken care of both of us and everything we need. He says he's not stressed these days, despite the fact that he has almost 4x as much to do as he did when he was stressed in the beginning.
He was saying, "Jessica, you know, I really want to see Atlanta become the next Silicon Valley - the Silicon Valley of the South!" And I was like, "YES! That's exactly what I'm praying for." And I told him about feeling like we might be on the verge of another scientific breakthorough, like in Reformation times, where the Lord might start raising up a generation of scientists He can teaching things to - and Keon said - Yeah! I feel the exact same way!
He said when he was listening to Dr. Stubbe speak, he was thinking - OH MY! Will I have to study something 40 years to get good at it or accomplish anything? And he was despairing. But then suddenly he had the epiphany that the Lord can do in ONE DAY what it takes someone 40 years to do by themselves. So, he said, we can do 400x, to 4000x maybe even millions of times more with the Lord than what anyone else has done heretofore. I think that was the Lord, reminding him of that. As he was talking, I had my own ephiphany realizing how true that is and I was like ... [!] You know what? You're RIGHT! And we talked about that excitedly.
I really do think we might be on the verge of a revival of people knowing the Lord AND a revival of science at the same time. Wishful thinking? Maybe. It's hard to explain. I just FEEL it. Like .... almost like, there's this electric current or tsunami approaching that I can detect but cannot see (like animals detect disasters before they happen and run away, except this isn't a disaster, it's a blessing - of cataclysmic proportion!). It's impossible to explain. I guess we'll see! So, Keon and I got both really excited and were like YEAH YEAH! God is great! And we ended with a dance in the hallway. Ha.
We decided we'd each pray for each other to be Emory's best grad student ever. It's Biblical. Put others above yourselves - also hard to do - because, I'd wish to be the best. But thinking about it today, I was like - that's a really good thing to pray. I think, if the Lord gives me His mind, I can pray that more honestly and I look forward to His helping me with that. He already did some today.
What experiment am I working on setting up? A summary
It seems as if I've explained this Lynn experiment to a lot of people
I explained my project/proposal/question idea to Dr. Lynn on Tuesday. Today, I explained it to five more people. I've talked to a ridiculous number of people in 2 days somehow! I may as well explain it again, to this blog. Here goes.
What experiment am I trying to do in the Lynn lab? [...] I'm glad you asked.
Goal: Attaching catalase to the inner surface of peptide nanotube fragments (.5 - 1 um long) through electrostatic interactions. Add a 15% hydrogen peroxide solution to the tubes. The catalase will break down the hydrogen peroxide, resulting in motion of the tube (i.e. microjet).
Explanation of goal: What is a nanojet, or a microjet? People have figured out how to roll up metals into a micrometer-sized tube. The metal is capable of catalyzing the decomposition of hydrogen peroxide into water and oxygen. This reaction creates bubbles inside the tube, which flow through it toward whichever end is widest, resulting in fluid movement and a force when the bubble exits the tube, generating thrust. The catalase enzyme catalyzes the same decomposition reaction and should have the same effect.
Why is this useful? This is firstly useful because the metals used to do this are magnetic. I believe typically an alloy of Pt and Ni or Fe is used (I'll have to check again), allowing the directionality of the tubes to be guided by a magnet. Granted, as Ayusman Sen points out, this is not autonomous motion - meaning, you cannot direct the tubes individually in different directions - they all go in the same direction - but still cool.
Secondly, people have used these tubes to move 5 um polysterene beads. One paper described motion of ~58 polysterene beads at one time! The microjets are very fast - 275 um/s - and with all the beads, move at ~20 um/s - which still is not bad. This is in a 15% hydrogen peroxide solution.
How are the beads moved? The front of the tube is like a sucking vacuum due to the flow, so they stick to the front. No functionalization required. They also pushed around 10 nm thick and 50 um x 50 um metallic plates using this method, into different conformations. The cargo is released via a quick twist of the magnet, resulting in fast rotation of the tube, and the stuff on the front falling off. This group also picked up and toted cells this way - of course - the cells died in hydrogen peroxide - but it was still hilarious that they did it.
Kevin showed me a paper with an even more cool application - but that explanation will have to wait for a second.
What's so great about making motors like this out of peptide nanotubes? Why do it?
1) The metallic tubes are only possible to make on the micron scale. The nanometer scale has so far been impossible to construct. Peptide nanotubes offer readily tunable diameters at the nanometer scale.
2) One of the core problems with metallic motors is that the metal is toxic to biological systems. (Metal particles, I believe, can also dissolve in solution and eventually cause toxicity, though I'm not sure right now if that's the reason or part of it for their toxicity or if it's something else). They are also hydrophobic. People want to make motors out of a more biologically friendly material that could also be readily functionalized for bio applications (i.e. sticking things onto the surface through chemical modifications that would add additional functionality to the tubes). (Examples I've seen talked about with the metallic tubes: add lectins that would specifically bind to cancer cells and create a sensitive cancer cell detection assay - motors could swim around serum, bind to and sort cancer cells in it - AMAZING idea!!) Using peptide nanotubes addresses this problem, because peptides are already biological and readily functionalizable.
3) Aside: The other core problem is that the primary fuel used for these motors (hydrogen peroxide) is toxic to cells. I'm not addressing that. There are some interesting papers about using glucose as a fuel. Perhaps for catalase? I'd like to look more into that but I'm satisfied not to address it for now. I can't do everything in two weeks.
4) Aside 2: I just realized writing this note, for my tubes to work properly like I want, I'll also have to add Ni or Fe nanoparticles to the outer surface, so that they are directable. Well. I guess motion first would be nice. Yeah, so that can wait.
SO: I could type up here the preliminary experiment I'm planning so far and how I plan to go about it, but I'd rather go through the fun story of how all this got started, from scratch, late yesterday afternoon. It's funny to me how it all happened, because I had no idea what I was doing initially. And THEN, I'll tell you the preliminary experiment. Otherwise, it's spoiling it.
Story of this experiment getting put together miraculously
Keep in mind - this is only what has happened - SO FAR - in about 1.5 days.
Ready, set, go! Race to do experiment! Start: On Tuesday, I was feeling overwhelmed with the magnitude of attempting an experiment of this nature, that's new to me, in two weeks. I prayed the Lord would take over and show me what I needed to see (I prayed this constantly, throughout the day yesterday and today and with specifics, because it's so true - I have no idea what I'm doing.) I later found out from Kornelia, I actually only had 1.5 weeks. I told Dr. Lynn when my rotation was ending (next Friday) and he asked me to present next Wednesday. [!] *meltdown* *headdesk* I thought: Well. This is basically completely impossible. I know I can't do this. Lord, please help me do this anyway. If I can't do it... well, it's ok. I'll give it my best shot.
Step 1 - First thoughts: Initially, I planned to functionalize the peptide nanotube with Pt and Fe nanoparticles on the inner surface, but I had no idea how to functionalize them. I figured maybe streptavidin/biotin. Dr. Lynn had also told me that I should consider using TMV instead of peptide nanotubes, since I could purchase those and they'd be faster to obtain for the time scale I was looking at. (I misunderstood him slightly, but that's beside the point here.)
Step 2 - Asked Anil: So, I asked Anil if he knew anyone who'd done work functionalizing streptavidin / biotin on peptide nanotubes. Salaita lab does it all the time, but not with peptides. He said a former student had done it and directed me to his thesis. I put that in my drop box (still haven't examined it yet).
Step 3 - Googling: I googled TMV to see how big it was (would nanoparticles fit in it). On my first hit, I found this beautiful 2008 paper chapter of a larger work called, "Chapter 26: Synthesis and Characterization of Tobacco Mosaic Virus Templated Polymeric Nanomaterials," as well as other articles, but this was the most useful. It told me everything I needed to know. I decided at the time, TMV only has a 4 nm diameter, which I thought was too small to fit nanoparticles AND allow room for flow through it, upon H2O2 breakdown. So, I decided I HAD to use peptide nanotubes. (Actually, what Dr. Lynn meant was deposit metal in the TMV and bind the TMV to the inner surface of a peptide nanotube through streptavidin/biotin or something. But I didn't know that. He told me that Tuesday night after I told him what I'd done already and cleared this up.)
Step 4 - Talk to Kevin: After that, I felt as if I should talk to Kevin. He knows a lot about motors, so it made sense. But not peptides. But I guessed it was from the Lord, because it was a very instant almost calling, even while I was googling and doing and looking up the thesis that was essentially reverberating: GO TALK TO KEVIN, GO GO GO. So, I did.
I wasn't sure what he could tell me that was useful. But I plopped down in a chair by him and told him what I was trying to do. He said - Jessica! Can't you see - I'm WORKING SO HARD! (He was playing chess. Kevin loves chess.) Ha ha. I love joking with Kevin.
Kevin's idea and amazing papers: Anyway, he listened to my initial spiel and said - huh - you can do that same thing with catalase! In fact, that might work better. And proceeded to look up two AMAZING papers and sent them to me - one, a Joseph Wang paper (who is apparently voted one of the 100 most influential analytical chemists I found out later and he publishes a CRAP ton of nanomotor and nanotech work every single one of which looks to be a fascinating read) who made a micron tube from a polymer, plated the inner surface with gold, added catalase via thiol interactions, and showed that the tubes not only had motion, but functioned as wonderful sensor/assays to detect heavy metal ions in toxic water, since toxins inhibit catalase. This assay occurs in minutes rather than the 92 days it takes to kill fish in live fish toxicity assays (what is usually done). What a whopper of a paper combining awesome methodology and application ALL IN ONE!! WHOAAAAA!!! That's what I thought. I read it on the spot.
His other paper was one showing how one could use electrostatic interactions to functionalize things on a particle. Kevin said he thought I could functionalize the catalase to the peptides through charge, since it's negative.
Aside, Caveats: I still do not know how negative it is, or if that would work - but it's a start. That's what I'm going to look up more tomorrow. For the start of things, I was just trying to get a general outline of an experiment before diving into details. Since Kevin ALREADY uses and has catalase for his experiments, using catalase would mean 1) I don't have to learn how to make particles in the 2 weeks 2) I don't have to buy anything and wait for it to get here 3) it's biological, which is a plus. Catalase it is!
Step 5 - Read the paper and update Dr. Lynn: After I talked to Kevin, I read his paper. Then I went to the Salaita lab meeting (Weiwei and Daniel presented - very exciting!! And Yuan sat next to me, special, for the occasion. She usually sits in back. Kornelia fussed at her for changing chairs. She liked the back she said. Yuan said - no, no - I remember, I sat here one time, and when I did, it made me feel so good! Let's sit here! So Kornelia stole Kevin's usual seat. I found this whole exchange quite entertaining and hugged Yuan.) Just before the Salaita lab meeting, I briefed Dr. Lynn about what I'd figured out so far, and was planning on using catalase instead. He explained what he meant about the TMV and asked me - and how are you going to visualize these things? Is there a fluorophore on the catalase? *stops in tracks* Oh yeah. I have to see them moving. Hmm. No, there's not. I don't know but I'll get back to you about that - is pretty much what I said.
Thus ends the illustrious Tuesday.
Highlights of Wednesday
I agreed to take up the evaluations for Dr. Weinert's class to Ann. I had a purpose in this - I needed to see her anyway - I gave them to her - then simultaneously got back my Lynn cume and found out I got a full pass. [!] Seriously??? I didn't even read the papers it was based off of. I wasn't intending to take the cume either. It just happened, that it was about stuff I already knew, and Dr. Lynn had talked to me about the precise topics on the cume. Specifically, I got an 80 out of 100. Perfect score on the first two questions, half credit on the third and 3/4th credit on the last one, proposing an initial experiment on XNAs. It was a God thing. I tell you.
I also asked Ann questions about courses. I went to talk to Dr. Kindt. He was busy, but I came back later, and he was not busy. I asked him about taking Pchem. He gave me his advice. He also gave me a grimace, when I told him my background, that said, "Oh, you will die if you take it, you poor, poor soul." He also warned me against taking even biophysical without auditing something first. I felt myself bristling at this notion - and the illogical desire to take Pchem at any cost, whatever he thought, increased 100-fold. I knew that was illogical though and I should take Pchem for the right reasons - if it's really useful to me - and not just to prove to him that I could.
I talked to Khalid and summarized what Dr. Kindt said. He needed to sign my form because I also wanted to take virology, which is a biochemistry class and I need special permissions. He actually laughed at this and said he was sure I could take whatever course, whether or not it was in my field, and do well, but it WOULD consume a tremendous lot of time. That is exactly how I see it! YES. It would take a lot of time! But I could do it. If I wanted. When he said that, I felt so much better. *blinks as a measure of logic returns* *unruffles and deflates puffed up angry cat fur* Oh. Yes. I guess I don't really have to take Pchem. Maybe. Khalid is very nice. I appreciate his confidence. I feel like, he's a nice anchor. As long as I know one person thinks I'm capable, I feel less pressure to prove it to the world and can focus on more important, useful things.
I think he's right. He pretty much convinced me that biophysical - the one Dr. Dyer teaches - would be a good alternative. He let me borrow a book on the subject. I looked at it throughout lunch and walking around the rest of the day. It looks really like a great book. Maybe I'll read it over the summer. I was calculating how feasible this was later. However, it might be that I at some point HAVE to take Pchem anyway, no matter how useless it is to me - because - completely illogically - I just think I'll regret it if I don't. Everyone holds it up to almost divine status and I feel like - taking Pchem is like passing the bar in law - you're not a real chemist until you experience the pain all chem majors must feel.
AAAANNNNNDDDDD that's all I have time to write tonight sadly. I wrote too long already AHHHHHHHHHHHHHHHH!!! Pray I get enough sleep tonight and can do ... all this work - AHHHH!! Dr. Lynn keeps asking me to read his grant - and it's 39 pages - does he really want me to read them ALL, I wonder? *headdeskkkkkkk* And Weinert HW; proposal writing; experiment; TA grading; paper reading - I probably won't get to write unless the Lord makes another miracle time slot. Too bad too. Because really, today was WAY more amazing about stuff that happened than Tuesday. Or at least equally so. But - you'll just have to wait, I guess - oh mystery people of blog land. Darn. I hate unfinished stories. It makes me itch.
End of Wednesday: IN BRIEF
I left off on Tuesday not knowing how to visualize the peptides. I was very confused about this and worried. At first, I thought of nonspecifically adsorbing some of my FAM-labeled RNA to gold nanoparticles and adsorbing those to the outer surface of the peptide nanotubes. But I was pretty sure that wouldn't work and Kevin agreed. Then, suddenly, I remembered Congo Red. It's this small molecule that can bind peptide nanotubes and becomes more fluorescent upon binding that the Lynn lab uses all the time. The only problem was, I needed the mixed tubes Lisa had that were positive on the inside and negative on the outside, and Congo Red is negative.
During lab meeting, I sat down near Kathryn, and Anthony randomly started talking to me (the guy who presented about porphyrins in peptide nanotubes that one time). And he asked a lot of questions about my system and I told him about my problem. He said - oh - well - there's a positive dye you can use, [something] orange. I forgot the name *again*! *headdesk* And it does the same thing as Congo Red. He confirmed this, shouting over at Lisa.
After lab meeting, he and I talked a lot more about the system, because he said he found it completely fascinating, and might even be interested in doing similar experiments, since his catalysts should produce gas and maybe could even exhibit motion. He was always interested in motors. He said that since right now he was just waiting on stuff for his experiments and looking for jobs, he had a lot of time on his hands and would be more than happy to help me setup my experiments and get the details worked out - and just to let him know! He's in two different labs, kind of like Yue.
All of this just all fell out perfectly, despite the fact that on Wednesday, I felt numb with exhaustion like the walking dead (though not as bad as this week on Monday - HA!). I just kept talking to people and - somehow - ran into people who could help me.
I found out from Lisa tonight, that he's primarily in a lab in physics right now and could potentially get me setup on a microscrope to visualize motion. O.o Cool. That worked out amazingly well. Lisa had been thinking about this experiment as well and gave me her thoughts tonight. Who knows? Maybe this experiment attempt will happen after all! Pray it works out. I'll let you know what happens when I know more.
P.S. I found out from the Lynn website that Anthony might be a senior undergrad. If so, that would completely make sense why his presentation wasn't as polished as I anticipated, for a 5th year grad student. O.o :)