I wrote this post over Friday and Saturday night – an update on the last few days of the week, with a lot of random philosophizing thrown in between. Alas, it’s a freakishly long post of unnecessary girth. Still, it's not the longest I've ever written by far. I discuss what happened during the week and some future events - Weinert proposal writing, RNA seminar, a few funny stories, and our St. Louis trip next week.
Thursday: working on Weinert proposal for bioorganic class
I woke up later than I should have in the morning, but I was too tired to worry about it. I worked on sifting through the protein corona articles and writing notes. My background needed a lot of work. I had written it in a five or six hour period one day.
The paper my proposal is based around
Basically, my Weinert proposal was based on a 2013 Nature Biotechnology paper describing transferrin functionalized nanoparticles that lose their targeting in the presence of serum.
Translation: transferrin is an iron binding protein that can be used to target cancer cells, since cancer cells tend to overexpress the receptor for it on their surfaces. The nanoparticles have transferrin bound to their surface. When they are exposed to human serum, the proteins in the serum apparently stick to them, forming the expected “protein corona” which blocks the transferrin binding pockets and they can no longer bind the transferrin receptors on cells, rendering them invisible to the cells. They lose their specificity.
PEG is usually used to shield nanoparticles from the protein corona but it does not completely avoid it. Apparently, zwitterions do a better job. Oddly enough, I’ve been able to find very few papers on them but what I have been able to find suggests as much, as well as Rotello’s papers, who came to speak about nanoparticles. He says a lot of interesting things.
What I wanted to try doing – a somewhat sketchy idea
I was wondering if you could functionalize these transferrin particles also with PEG-linker-zwitterion ends that would extend past the transferrins – to see if the zwitterions could shield the transferrins from the protein corona and result in restoring their cell targeting.
I kind of doubt this would work. I’m not sure one could get enough zwitterions functionalized in conjunction with the transferrins to form an effective screen. I’m also not sure if they did form a screen, if they wouldn’t also block targeting in their own right from cells. I don’t consider it a ‘real’ proposal – it’s kind of cheating – it’s really just an extension of a paper. However, it was the best idea I had on short notice. And I noticed, reading other people’s when we swapped, that other students have done similar things.
I didn’t spend very much time on this proposal – it’s somewhat embarrassing. Morgan said she spent an incredibly amount of time on hers – but she did use hers for the NSF proposal. This one I did not. Like I said, I wrote the first draft in a ~7 hr period. I wrote the second draft in about the same time. I’m not sure where all my time has gone, but it tends to evaporate. I spent most of my time on the NSF proposal, doing experiments and studying bioorganic notes. Biomolecular has been pretty neglected so far, which I’m attempting shortly to fix.
Lately, I’ve also been trying to make sure that I talk to people in the Lynn lab and do my best to work hard on refining my ideas. I want to make sure I work hard for Dr. Lynn, so that he knows I’m doing my best, and am not neglecting him or being lazy. I wouldn’t want him to feel like I would work hard for Khalid, but not for him – that would be disrespectful. However, so far I don’t feel I’ve been really effective at ANYTHING I’ve tried to do. I feel largely diffuse and impotent at everything.
Interesting RNA seminar
I took a break around 3:30 pm or so, and went to a seminar about the visualizing of single molecules of mRNA in situ – a seminar Khalid told us about. I like RNA and it sounded really cool. I thought it would give me a break from thinking about the proposal. I didn’t know where the Winship Cancer Institute was but I eventually figured it out, Googling the address and putting it in my phone. I can’t believe I actually found it in time. I didn’t think I would.
Khalid was there and it was good to see him – for some reason I didn’t expect him to be. I don’t know why not. He told me about it! Ha. Listening to him talk was fun. I was surprised more people weren’t there. It was a fantastically interesting seminar. The speaker had labeled single mRNA’s fluorescently and taken a five minute video of them – you could see them moving around – it was the most cool thing I’ve seen in a WHILE! That was my favorite part. It’s like you could visualize information ITSELF moving. Watching it, I felt like one could philosophize about this for hours. He was describing his labeling method. I wish I could have understood it all better, but I thought he said a lot of really useful information and took notes on it. I wrote down his papers to look up later.
Khalid asked interesting questions – which is almost always the case. I love listening to his questions. I listened to them all, vibrating with pride and thinking, Ha, that’s my future boss, the smartest person in the room. I don’t measure intelligence always by what people know but how passionate they are about attacking what they don’t know and their ability to chase after and acquire necessary information – everyone is ignorant in large amounts – what it is just differs person to person. And Khalid seems amazingly good at this. He always knows all the interesting things going on – speakers and such. I’d like to do better at that. No one else asked questions openly. Maybe, the other people already knew everything they wanted to know, being biochemists – I assume they were biochemists or biologists – but I’ve found that this is almost never the case and if you are actively thinking, you can almost always think of questions because there’s always more to know.
I wish I asked more questions at seminars. Just sometimes, I can’t always form them coherently fast enough. I’m trying to improve. I always pray that the Lord would teach me Himself what the speaker is saying, help me focus, point stuff out to me, and give me good questions to ask. Listening isn’t always easy for me. Reading comes much more naturally.
I wonder what Khalid talked to the speaker about afterward. I’ll have to ask. I kind of wanted to stay but I had to get back as quickly as possible and keep working on my proposal.
Philosophizing – February can’t come fast enough
In spite of my insistence on not counting the days or weeks, I can’t help noticing how much time has NOT passed so far. I’d like it to hurry up – the understatement of the century. Patience is NOT necessarily one of my virtues. Perhaps that’s another thing the Lord is teaching me.
After I join the Salaita lab, I can drop all pretense at my overwhelming partiality to it and Khalid, and not feel like I’m slighting other professors. It’s no secret, but regardless, I feel as if I’m ‘required’ to be more ‘impartial’ and rather feel as if I’m walking on egg shells. Even so, I claim Khalid and treat him as if he were already my adviser. I’m happy that he keeps me in the loop about lab things, and I feel as if he treats me as if I were already his student. Being adviserless and rotating around in labs – I kind of feel like an orphan, while it’s going on – I have no home – it keeps changing. But fortunately, I do have a very nice one with loving people waiting for me. It’s such a comfort.
Khalid has a magnetic effect on me. I feel like I’m a piece of iron, to his magnetism. If he is in a room, I notice at once, regardless if I react or not, and immediately feel a strong pull in his direction. It’s like the rule for “Menoth’s Gaze” for the Avatar of Menoth in Warmachine: While the Avatar is casting “gaze,” other “…models that begin their activation within 8” of this model and in its line of sight can advance only toward [the Avatar].”
What I’d always prefer to do: *notices Khalid* [!] *zoom* *roots self beside him* *sighs contentedly* Even if I don’t obey it, the pull is always there. I feel like I’m a plant soaking up and turning toward the light that spills from him in all directions. If he’s talking, I can’t help but hear, though I may or may not be actually listening. It depends. Khalid always talks about interesting things. It doesn’t matter – I’d act the same way, whether I wanted to listen or not. This is the case for all people I love overwhelmingly. I just like being near them. And will follow them around. Perhaps unfortunately, Khalid has gained a shadow, though he may or may not know this yet. Hopefully, he won’t be annoyed. I don’t intend to be obtrusive about it. But if he notices and is annoyed, I’ll retreat and give him space. Some people don’t like to have shadows.
This was also my mode of operation around Ms. Harmon. Often times, I’d study in her outer office, just because being near her was comforting. Around her I felt safe, loved and protected. This is also how Khalid makes me feel. And for Ms. Harmon it's still true - she feels like my mom. And I’d always follow her around whenever possible. John is my biggest attachment of course. To him, Ms. Harmon and Khalid, I feel like there are invisible cords attaching me and anything that happens to them, good or bad, happens to me.
During rotations, I can’t follow Khalid or shadow him so visibly for now, or I’d be really conspicuous, and risk offending other professors. But after I join, all bets are off… FINALLY. I’m probably still really obvious. I’m just not a very sneaky person.
I hope that Khalid will still enjoy talking with me after I join. It’s my favorite activity. I'm not actually an incredibly social person - there's only a few people I enjoy talking to this much. My preferred activities at Emory, in order of favorites:
1. Talking to Khalid – doesn’t matter about what (Ding, ding ding! Score 10. Favorite activity. I hate it when I have to leave off talking – though one has to be realistic – work actually has to get done. Good conversations make me feel warm and happy.)
2. Doing experiments (Score 9. I love doing experiments and thinking about them.)
3. Reading papers (Score 8. I also love reading papers.)
4. Talking to people in other labs about their projects or asking them questions (Score 6-8. Median enjoyment.)
5. Going to seminars (Score 4-8, depending on the topic).
Dr. Lynn’s cume: something I didn’t expect
I got back at 5:30 p.m. from the RNA seminar and was working on my proposal, when Rolando walked in and wished me luck on the cume. I said oh, I wasn’t taking it, but he said I should. I thought about it. I said well, I’d go look at it, after all, I guess. It was Dr. Lynn’s cume – over two papers and nucleic acids – it sounded like a good one to do but I just was so worried about the proposal … I’m glad I went. I should have read those papers – dang it!
I looked at the cume. It was four questions. […] I’ve never read a cume that looked so completely easy and answerable! I felt like this was the first one I’d seen that I actually had a chance on! I hadn’t intended to take it, but I couldn’t resist. It was mostly philosophizing about DNA and protein and XNAs – stuff I’d already read about anyway – and I can philosophize all day. Man, if I had read the papers, I probably could have gotten a full pass. I was seriously disappointed I hadn’t been more in tune to my surroundings this week to do so. As it was, I had heard of some of the topics from conversations with Dr. Lynn, so I could guess at what the papers might have said, and gave answering the questions my best shot. There were copies of the papers available for us to read I found out later, but I didn’t realize at the time that we were allowed to look at them, so I didn’t.
The last question was – if you had any resources to do an experiment to synthesize any XNAs you wanted – what kind of XNA would you make and what would be the first experiment you would do and why? Be bold. That’s kind of what it was, I think. That was a very fun question to think about. A world of possibilities opened before me. What WOULD I do? […] Hmm. Hmm. I don’t think I know quite enough about XNAs to really suggest super cool experiments. As it was, I talked about synthesizing 20mer XNAs with a S backbone and comparing it to regular DNA with a P backbone or other XNA with an N backbone, and how that would affect the XNA structure and any catalytic activity (if it was in a DNAzyme, for example). I’d be genuinely interested in that question. I bet someone has already looked at that though and I just haven’t read it. I know Fish has a project kind of related to that, in the Lynn lab.
I would be really surprised if I got any of those questions anywhere near right … but I don’t know. Maybe I’ll get a half pass … if I do, I will laugh hysterically, because I was so not expecting one. This cume was very strangely easy. Gokul was suspicious too. Dr. Lynn did say that it was easy before he left us to work on it. Gokul thought he was being sarcastic but I really don’t think so. I guess I’ll just really have to take all the cumes no matter what on the off chance that one might be possible to pass, even if I risk failing something else the next day.
Finishing the proposal
I managed to finish the proposal staying up only until one, thank goodness. I got four hours of sleep.
Friday: very tired, unexpected points, and sliding off the deep end in the evening
Friday morning, I was completely exhausted. Class was interesting, more or less. Afterward, I went to see Ann and ask her about registration, because I was really confused about when it was happening. She gave me the Davies cume back. Oh. My. Word. That was a surprise – completely made my day! It was the first cume I’d taken and I only tried to answer the first question for about two hours – they were all impossible looking – and based off of three volumes of the journal Organic Chemistry Letters. The first question looked like a Diels Alder variety of reaction, so I just attempted to apply “organic chemistry logic” to it, but I never thought I’d actually guess part of the mechanism correctly! There were all these check marks and 8 out of 10 marked for it. I’ve never been happier about a failed test in my life.
Dr. Lynn asked how the cume was and my stupid response
I ran into Dr. Lynn and he asked how the cume was. […] *headdesk* I think my answer was basically the following:
“Well, I wasn’t planning on taking it, but then when I looked at it, the questions looked so answerable! So, I gave it my best shot. It was a fun cume! As cume’s go.”
*sigh* I have a knack for saying exactly what I think, especially when I’m tired, in a way that makes me sound like a complete idiot. That was a pretty ridiculous response. Hopefully, Dr. Lynn won’t know which one is mine by my handwriting. Khalid probably would and/or would have recognized me from what I said, but hopefully Dr. Lynn won’t have that advantage.
Working on the Weinert HW due next Monday
I ate lunch at Rise and Dine and afterward Morgan, Hyunmin, Gokul and I tried to work on the Weinert homework around noon. Gokul had stayed up all night and Morgan and Hyunmin weren’t that much better off. I probably had the most sleep of everyone, but I almost felt as if I’d stayed up all night anyway. So, we weren’t that effective. However, I did manage to find the paper that I suspect Dr. Weinert based the homework off of.
After we looked at the homework, I was so tired and I decided that I would go home early. While I was at my laptop about to pack up my stuff, Eric Zhang came up behind me and scared the crap out of me. He’s come in one other time and gave me a surprise mystery hug. I knew it had to be him. No one else would do that. This time, I slapped him and told him he was evil. He said he was about to take a biology test. He got a 97% on the first one, and this time, he wanted to get a 100%, to prove to those biologists who was boss – chemistry! And I was YEAH! You show them! Beast it. I know he will. He’s like that.
Going home and everything falling apart
I left at 2 p.m. but I’m not sure I should have. I was torn. But I thought I could take a nap, then get up, feel better and get work done. I think, looking back on it, I should have just stayed in lab. The world kind of fell apart when I went home. It was weird.
James was home and talked to me when I got home. I took a nap. It was very, very nice – from about 4 p.m. to 6:40 p.m., but honestly, I think I could have slept through the whole night without noticing much. Maybe I should have. But I wanted to try to work.
Mom, dad and James were out shopping for a suit for James, since his friend Andrew is getting married and he’s in the wedding. I was immediately lonely. I went to Which Which and ate there for dinner. I was just so terribly lonely and missing John. He went to Brian’s house for his RP. I’ve never been attacked with such intense loneliness in an incredibly long time. I think this week I got kicked out of balance. I feel like I haven’t seen John hardly at all in two weeks and it sucks. When I get home, I just work furiously and he lays knocked out on the bed, more or less. I tried to call him but he didn’t answer.
After I got home, I went upstairs and John called me back. Listening to him talk just made me ache worse and I burst into tears, shaking. He was going to be there until 11 p.m. It was then 8:15 p.m. and sitting there alone for nearly three hours just seemed unbearable torture to me, so I immediately left and went to Brian’s house and sat next to John, clinging to him until I felt better. Then I wrote part of this note. I listened to their RP until it ended at midnight. I wasn’t able to work. I just had to be next to John. I was craving his presence.
I decided I’d spend a great majority of the weekend with him – lately when he goes to Tower Games on Saturday, I haven’t been going, because it’s hard to study up there. But at this point, nothing matters to me but getting back into balance and spending more time with him. I just NEED him. I feel like I’m going to have to demolish anything that gets in the way of that, until I can make sure I see more of him. I can’t take it anymore. I also need to spend more time with the Lord.
Saturday: resting; and what we're doing next week
At least, I can say, taking the antibiotics has helped me get better so much faster. I feel at about 90%. All this resting has helped a lot as well. I feel lazy taking naps – but they’re so good – I can’t really feel guilty about it.
Unfortunately, it seems both John and my mom have caught the evil cold. However, they CLAIM it might not have been my fault – apparently – people at my mom’s work and John’s work have also been spreading this thing. John said he heard on the radio that at one elementary school, so many students were sick there were not enough left to keep the school open and they had to cancel it.
Later this week: trip to St. Louis for Warmachine Weekend
John and some of our ATL Warmachine cohert are traveling to St. Louis together for one of the biggest Warmachine tournaments in the country. John really wanted to go last year, but couldn’t get the time off in time – we thought about it too late. I’m going, because I can’t be away from him. I think, at this point, it will KILL ME. I have to go. Fortunately, I got it arranged with Dr. Weinert so I present after the trip. I warned Dr. Conticello as well. It’s terribly inconvenient. But, I’d really rather be in the habit of being inconvenienced for John’s sake. He’s worth a lot more to me than that. And, I think it’ll be fun. If I want to, I could participate in the “young bloods” tournaments – geared toward beginners – no time limits on turns – etc. That might be fun. There will also be a lot of board gaming going on.
I already told John I’m expecting to spend time with him up there with JUST US, away from the passel of guys. I like the Warmachine crew. But I’m also possessive of my John. Maybe we can do some sight-seeing. I’d like to see the Arch. We’ve never been to St. Louis. Maybe we can go to a mysterious restaurant somewhere for dinner. We’ve discussed these options. I think we’ll have a good time. Maybe this is just what we both need right now. The last month or two have been incredibly tiring, intense and we haven’t seen much of each other. I don’t know how much work I can get done though I’ll try. Working in a strange place isn’t easy for me. But, for John’s sake, and because I need to recharge with him anyway, I pretty much don’t care about that.
We leave Thursday at noon in a fifteen passenger van with 10 other ATL Warmachiners – Brian (2nd place team winner in the world tournament! I’ll never get over saying that.), Steven, Walter, Matt, David Kelly (also some of the best players in the country), Max and Jessie… I think that’s everyone. At the tournament, there’ll be a last chance qualifier for the 16th spot in the Invitational – a tournament you can only play in by winning select qualifier tournaments around the country – it’s kind of like the championship. Brian and David Kelly have spots in it. Steven has a good shot at the last chance qualifier. Last year, he was 9th of 96 players.
I think that’s about all the news so far. I’ll be posting pictures and stories of the trip next week as I’m able. May you all be blessed with the Lord’s peace!