tanarill: (Science!)
I’m making a note here: HUGE SUCCESS.
It’s hard to overstate my satisfaction.
Aperture Science
We do what we must
because we can.
For the good of all of us.
Except the ones who are dead.
But there’s no sense crying over every mistake.
You just keep on trying till you run out of cake.
And the Science gets done.
And you make a neat gun.
For the people who are still alive.

Ok. So the problem is: codons. A codon is the three-nucleotide-long section of DNA that a ribosome reads as "this specific amino acid." There are sixty-four codons; three of them mean "stop making protein." The other sixty-one code for amino acids. There are twenty amino acids, so obviously each amino acid has more than one codon. Basically everything on the planet reads codons the same way; it doesn't matter if you are en E. coli or a Homo sapiens, AGG codes for the amino acid arginine.

However, and this is a real kicker, different species use the codons with different frequencies. We humans like using AGG when we need an arginine; E. coli use AGG less than one half of one percent of time. They would rather use any other arginine codon, basically. And this is problematic, because if you ask an E. coli to make a human protein, but the gene that you are using contains too many codons that E. coli hates, it will simply refuse to make said protein.

We were unable to get the bacteria to make our protein. We ordered a "codon-fixed" gene, which produces all of amino acids, and in the right order, but using codons that E. coli prefers. It finally came last week. After magically getting that gene into the bacteria, we have finally gotten them to make our protein. Pics to follow.

Headache

Oct. 9th, 2013 04:13 pm
tanarill: (Science!)
Today was shit. Mostly it was that I could not get to sleep last night, so I was running around on probably not more than six hours of sleep. I have learned that if I take the two sleeping pills as recommended, they will work as advertised. I was hesitant because I didn't want to be groggy in the morning, but I'm groggy anyway from not sleeping. In the future, I will RTFM.

Seminar: This is yesterday's seminar, from a German researcher named Otto. He works with a protein called "Mx," which is a protein that most lab mice don't have. The ones who do have it are much more immune to influenza, by which I mean when you deliberately inject the flu into mice, the ones without Mx die in a week and the ones with Mx just shrug it off.

Humans have two Mx-like proteins, called MxA and MxB. Otto works on MxA, and did a lot of experiments in petri dishes and the by making transgenic mice (mice which have human MxA instead of their normal Mx) and testing their immunities. What he has found is that MxA is really very active against viruses that attack other species. Or, in other words, only viruses that have evolved to be "invisible" to MxA can attack humans. He proved this by showing that both the 1918 pandemic strain of flu and the 2009 pandemic H1N1 strain of flu had the same mutations, those apparently being the mutations a flu virus has to make to become MxA-invisible. Then they were able to cross the species gap from pigs/birds to humans, and cause a pandemic.

This might seem like a failure, but actually it is very good. A virus generation is a few hours long. In the ninety-one years between 1918 and 2009, viruses had time for 265,720 generations, and they only successfully made the species jump . . . twice. So it seems that Mx, and proteins like it, form a very high barrier for viruses to become human-infectious. It protects us from getting sick constantly because of bets like cats and dogs and cockatrices. Once viruses are human-infectious, Mx is kind of useless.

Also, teaching friend Max to be learn chemistry. I learned this in my senior year of high school, during AP chem, so it has been six years. Still, I seem to have retained it fairly well. I've got him setting the problems up correctly, at least, so hopefully he'll be able to do it well on the test. It is good to be able to help.
tanarill: (Default)
It is October 6. There are twenty-five imaginary candles on my imaginary cake. In real life, the landlady made birthday brownies (yay!) and we're going our for either Indian food or sushi later.

My friend Brett lent me his Tahoe. Tahoes, as it turns out, are massive beasts of trucks; you drive around in one and find yourself thinking "aw look at the cute little Rav4s." But they are also fully and easily capable of accommodating thirty cubic feet of dresser with room to spare. So I drove down to Ventura, retrieved said dresser, drove back up to Goleta, unloaded said dresser with help from my roommate and her friends and our landlady, and then returned the Tahoe. Thank you Brett, as I have now retrieved all of the furniture I plan to keep. Also, I have drawers to put things in. Mission accomplished.

Now I am doing laundry, which I do every Sunday because clean clothes. Later, I will sleep. It is a good day. :D
tanarill: (Science!)
So Dr. P, whose student I am, had to run off to Chicago for a Sudden Family Emergency. I am no expert, but when a person is running a 109F fever, that's emergency levels of not-good and it is reasonable for relatives to suddenly fly off. As a result, I am teaching Dr. P's class tomorrow. I hope that, after TAing this class twice, I am reasonably good at it.

Okay, so I am trying to order an oligonucleotide from Integrated DNA Technologies. This is routine, and there are some labs who do this on a daily basis. So I go to make the order, annnnd . . . the website goes down halfway through. I mean, as in, I cannot open the website home page from Google. I even tried on another computer. Then I called to let them know, and it took me more than a couple of minutes to get the tech person to understand that it was a complete 'website not available' on my end. But they were very helpful once they did understand the problem.

Now for some good news: I won an award! The award I won was for asking the good questions in Seminar, which apparently people think I do. :U To me it always feels like the logical extension of whatever the persons were talking about. I guess people like them, though. Kudos to me!

Today's Seminar was about a guy who is working on targeted drug delivery. This is a big field right now, because it is kind of the holy grail of cancer research to be able to say to a poison, "You see those cells? Go kill them. Ignore all other cells" instead of the carpet-bombing and hoping-to-hit-the-cancer that we do now. But chemicals are stupid, so you end up having to say things like, "You see those cells with the receptor for folates? We're going to stick a folate on your butt, that's your guidance system, go hit cells with folate receptors." Which is good, in the sense that very few cells that aren't cancer express folate receptors*.

In patients whose cancers display folate censors, this is useful not only for getting drugs into cancer cells, but even for just figuring out where the tumors are. You just replace the drug part of the molecule with a fluorescent dye or even a radiolabelled tag (if you want to see it by MRI) and then you can say, 'this person's ovarian cancer has metastasized here, here, and here,' before operating to cut out aaaaaaaall the tumors. Then you follow that up by hitting them with the drug-armed version. It extends life expectancy by fourteen months, which for ovarian cancer is quite good. Of course, you have to have folate-receptor type cancer, but we're working on hitting other types of receptors too.

End result: less poison and less cancer.

Science!

*Except fetuses. Fortunately, fetuses don't share blood supplies with mom, so there's no way for the drug to even get to the fetus.

$$$

Oct. 1st, 2013 10:01 pm
tanarill: (Default)
I have a second 37.5% TAship, for a total of 50%! I will get to pay my bills this term with no borrowing! I am okay.

This is the last flashback, but only to the last day of the symposium, which was only last Wednesday. On that day, I only went to a few talks, because only they looked interesting. The one that I remember, so it must have been best, was on how to use graphite that you dug out of the ground to make nano-computers. They are really bad at it, only in 8-bit right now, but they are flexible. In the future, it might be possible to roll up your computer, or crumple it and then reshape it . . .

It is October! My Bday is soon! I miss the smell of bonfires and leaf-mold, which doesn't happen here in California. I want my autumn, damn it!
tanarill: (Default)
Watch as I fall off the internet again.

Labmate S seems to have come to his senses, in that he is asking to send off plasmid in test tubes this Thursday. This would not have been possible had I not already done my magic, so logic-win for me. Still, MW and Panda make the point that I need assertiveness training. This proves to be a problem, since assertiveness training this term conflicts with my TAship. $$$ > training, because I need one of them to live.

In the meantime, it is no longer holiday. This is a good thing, as we'd had too many holidays. But they, and almost the entire first month of the Jewish year, is done. Now nothing until Khannukah, which is only really eve a thing because Christian advertisers wanted to show how not-anti-semitic they were. They just failed to do the research, so I don't think the message came out quite as they intended.

[flashback]
Tuesday was the day of flying home. First we stopped at Zieman's bakery to pick up the cake I had ordered . . . only there was no cake. Someone flubbed the order. They sold me some day-old but I was still so pissed.

Then I went to the airport, got on a plane, got to LAX, got off the plane, and called people to tell them I had arrived safely. While I was doing this, there was a call . . . to tell me my cake was ready. I chewed that moron out. Not like I won't make the attempt to buy one more such cake the next time I am in Detroit, but it is so frustrating. I told you to have it ready at 9:00 AM for a reason, and the reason was I was leaving the state.

Then I slept on the bus ride home, and did laundry, and went to sleep. That's the end of my wedding adventure.
[/flashback]

Now I am wrestling with my prof's computer, which ought to be plug-and-play but isn't. Grr. I will get this worked out before the term is done though. I will.
tanarill: (Science!)
But actually a thing happened and I am really upset about it.

So lab mate S ordered a kit with some stuff, including a plasmid. A plasmid is a ring of DNA that bacteria make and humans exploit shamelessly, although I will not quite get into how. When we were talking about ordering it, I said that the first thing I was going to do when it arrived was put the plasmid into some DH5-alpha cells, because that particular kind of cell is good at making plasmids. End result: LOTS of plasmid. The kit does not come with much, but we have the technology . . .

Anyway, so the kit came today, and that is what I did. I called lab mate and told him that I had done this. His response? "I appreciate that you are eager to get started, but please let me know next time before you start on something that I ordered. You have no idea what I had planned to do with the materials or my concerns on how they are handled. Next time speak with me beforehand so we can make sure we’re in agreement."

Uh, I did. Maybe not today, but we did talk. Last week. You didn't object when I told you my plans, you said, "Okay, that's great," which I took to mean you approved of the plans. Okay, so I will admit maybe I should have called you. Maybe you should check your email so you see when these packages come in, or, you know, show up to lab more than once a week. Also, I took one microliter. They sent us one hundred microliters, it's not like you are going to be hurting for material. Also also, this is not only your project. You don't get to order me around, we are supposed to be partners; we agreed that I'd do the lab monkey stuff you hate, and you'd do the data analysis stuff I hate. This is my half of the work, I do it the sane way.

So. Frustrate.

Will relate more regarding both symposia and vacations to Michigan during Hell month when I am not so heart-sick.
tanarill: (Science!)
Okay there's another one! I didn't know about it until today but I am attending the interesting presentations. They include: beta-barrel folding and insertion into the membrane, (restriction of) water as a means to do even more cool things, nanogels, and self-assembly of viral capsids.

Also, I went to the Chabad port-a-Sukkah for lunch today, both to eat and to finally perform the shaking of the lulav. Mission accomplished.

[flashback]
So Monday was originally the day I planned to be with the Boy, but that plan got nixed because my parents decided, without telling me, that we were going to spend Monday cleaning the house in our old neighborhood. Because bad renters not performing maintenance, and we'd like it to be rentable. Also some of our furniture, which did not fit in California, will fit in Erie. So we put them in a Uhaul to go to Erie.

There was black mold in the basement, and then guys roto-rooting the storm pipe. There was dust. There was humidity. There were lights out all over the place. It was not a fun day.

Also, I ordered a cake.

Aunt E, with whom I was staying, made spaghetti and meatballs for dinner and Uncle S and Aunt L showed up for desert and conversation! It was a pretty good end to an uncomfortably gross day.
[/flashback]

Symposium

Sep. 21st, 2013 08:08 pm
tanarill: (Science!)
In the original Greek, a symposium was rather like a Roman orgy - that is, you and some of your friends got together to eat a nice meal and drink some drinks and debate philosophy; in modern times, it would be called a "dinner party." But in Science!, symposiums means "when a bunch of scientists get together and tell each other about the cool things that they are doing." At my school, we have one each year, just before school starts, to welcome the incoming grad students. It was yesterday.

I will not bore you with the details, but here are some highlights:
1. Using embryonic stem cells to grow retinal cells, which are then implanted into the eyes of people suffering age-related macular degeneration. If it is done early enough, there is no degeneration.
2. Molecular motors that pump DNA into viral capsids. These are not the most efficient motors we have found, but they are among the strongest, exerting forces of of up to 70 pN. (For comparison, the motors that drive muscle cells can exert between 3 and 5 pN.) Also, they make things spin.
3. A 10-minute drug test that will enable police with the device to determine if someone has been doing meth (and in the future, other narcotics) from 20 uL of saliva. There are 1000 uL in each milliliter, so we are talking less than the volume of saliva that is in your mouth right now. Least invasive, fastest test.
4. A growing mass of cells is under both tension (at the edges) and compression (in the middle). When the forces balance, the cell mass stops growing. Unless it's cancer.

Today, for no good reason that I can tell, half the power in this house is out. I mean, half the circuits are not working, but which ones are not working seems kind of random and arbitrary. I can't find the fuse box, so I will have to wait until the landlady returns.

[flashbacky effects]
Sunday! The wedding! Yaakov and Caryn got married! I do not have much to say, aside from the fact that Yaakov was crying with joy as he walked to the Khuppa*. They are pretty much for each other, and everyone has known this forever. He did not propose until he finished his degree, which is a good and responsible thing to do.

The MC was Orthodox but not crazily so, as evidenced by his first statement, to whit: "Mawwige. Mawwige is what bwings us togevow today." The whole wedding was like that, which various people reading the Seven Blessings, and the drinking of the wine, and the smashing of the glass, and the (not-necessary in a functional sense) exchange of rings, and toasting.

Then we partied, and partied, and did the terrifying chair dance, and partied, and ate some food, and partied. It was pretty great.

Yes, the wedding is why I went to Michigan during Hell Month. But if your close good friend, your best-friend while you were in middle school, gets married . . . you go to the wedding :)
[flashbacky wavy effects]

*Marriage tent. Think altar, though, if you are Christian, functionally it works the same way.
tanarill: (Default)
Although, in my defense, the great and holy festival of Sukkot, blessed be it, has begun.

Sukkot it one of those week-long holidays that were, in the days before atomic clocks and instantaneous communication, lengthened to eight days. The reason was that the official calendar-keepers in the capitol would send out runners to announce the holiday, which works in a tiny country like Israel. Once you have a Diaspora going, you might not get your runner until the second day of the holiday, so you'd do the whole thing a day off unless you were given an extra day of leeway. Of course a two-year-old can spot the flaw in this plan, to whit: people are not stupid, and can keep calendars and just start the holiday on their own on the correct day. Nevertheless, in modern times the seven-day holidays are eight days long.

I went to Chabad, and also drove J. I do not like J much, because he is wrong on practically every issue is there is, but he has no other way to get to Chabad. In order to not argue, we have agreed that he is only allowed to talk about whatever book he has been reading lately while in my car. This works, if only because we have the same taste in sci-fi/fantasy novels.

Baby Israel (pronounced: Yees-raw-el) is officially a toddler now. He has figured out this walking thing and is toddling around on his own two legs.

[flashback wavy screen effects]

The Saturday next, which was August 10, my family and I went to the Aufruf (pronounced: oof-roof). We Jews have broken up the Torah in such a way that if you read a bit of it every week for a year, you get to the end and then rewind the whole thing and start again. Obviously this plan only works if you read the designated portion each week, and in general, that is what happens at Jewish services. There are certain blessings said in regards to reading the Torah, and then other optional blessings: the blessing for a woman who has just given birth, the blessing for a sick person, and of course, the blessing for people who are about to get married. This last is said only rarely, because, well, people do not get married that much. So the Aufruf refers to reading the Torah and then saying the blessing for people who are about to get married. And then throwing candy at the couple.

(There was this one kid, who was maybe four, and could not throw the candy. He waited until Yaakov was conveniently sitting down hold the Torah, which is a good thirty pounds worth of scroll, before walking up to him and beaning him in the head with a candy. It was cute.)

As an unexpected bonus, it turns out that my cousin A and his wife J go to that particular Shul, so we were able to see/talk to them at the bruncheon. It was nice.

Then I walked over to the house of the Boy, and spent basically all day there, or at least until after sunset at 9:30, when we went out for ice-cream at this place that makes delicious ice cream.

[flashback wavy screen effects

I will continue to report things that happened, and things that are happening.
tanarill: (Default)
So that was Thursday. Friday, I visited with Great-Aunt E, and then went out to late-lunch/movie date with my <>Rags. We saw Pacific Rim (it still being in a theatre at that time). I think she did not enjoy it as much as I did :/. In the future I shall keep the MST3K to a minimum :x.

Then Rags drove me off to the house of Anne W, who was hosting the rest of my family and also having us and JJ's friend A and A's family over to dinner. I spent hours catching up with everyone, and making relentless Monty Python references, and breaking into song at the same time, and eating Meat. It was pretty great.

Then Panda drove me back to Great-Aunt E's house, for another exciting night of fun!! Just kidding, it was beastly hot there sleeping was not fun at all.

Flashback of the day complete! [imagine wavy fading-out-of-flashback effects here]

Today, I biked the whole two miles to school. It's mostly uphill, and I am mostly anemic, and as it turns out, this is not a great combination. I will have fabulous legs later, if the biking doesn't kill me.

Then I came home and watched a livestream of Some Like It Hot. It is not my kind of movie, but great if you are into that kind of movie. And now I am online. Whoo!
tanarill: (Default)
I'm going to try marathon posting, posting every single day. If you see me and I have not posted yet that day, poke me to do so.

H'okay, so, we're doing this in chronological order until we catch up, but only once I have remarked upon the fact that Saturday was Yom Kippur, and this Wednesday night is the beginning of Sukkot*.

Also, I must first wish my brother JJ a very happy birthday, because it is his birthday and this year is the very special birthday which means he can legally buy alcohol and consume it in public places. Happy birthday, JJ!

So, after my aunt took me out for sushi, and we had a great time, it was time to fly to MI. I got up at ungodly early o'clock to be at the bus place at 8:00 so they could drive us to LAX for flyings. Due to traffic patterns, we did not take the 101 to I-405 and I-405 into the city. Instead, we drove south along the coast, through Malibu. Teeny tiny little million dollar closet-houses. (And Tony Stark's mansion, except it doesn't actually exist.) We got the airport ~11:30, and I got through security quickly before sitting down for an hour and a half waiting for my flight. Which was late, and got out of LAX late, but which got to Detroit half an hour early. Then Rags picked me up and we went over to my great-aunt's house, where I promptly fell into bed and went to sleep.

Basically, the whole day was travelling.

Okay, that's all for today.

*Jewish Thanksgiving.

Aunt

Aug. 7th, 2013 08:39 pm
tanarill: (Default)
So yesterday my Aunt N called, and said that she happened to be on this side of the country and we should get together. I mean, I hadn't known about the this-side-of-the-country-ness, but I was wiling to do a thing; this is an Aunt I have not seen since April, after all.

We ate dinner together. She told me about her life, I told her about my life, and we made each other laugh a lot with amusing stories and bad puns. (If you suddenly move to Rome, does your cell phone get Roming charges?) It was nice, and also a first because I had never done anything with only Aunt N and not my cousins as well.

Now I am happy, and also full of sushi, and I am loved.
tanarill: (Science!)
Often, the Boy will start a conversation by going, "You know what's annoying?" or "You know what's weird?"

And usually, the response is supposed to be "What?"

That is not my response. My responses are, for example, "mosquitoes" and "quantum mechanics." Because what did you think was going to happen, giving me such an open-ended question?
tanarill: (Default)
I live in the campus Chemistry building, and I am friendly with some other people who also live in the Chem building. One of my friends, who we shall call Arizona for the purposes of this post, is a hugging friend. On days when he is feeling sad, or I am feeling sad, we will go find each other and demand hugs. Arizona will also do that thing that is like a backwards piggy back ride and is focused on spinal squeezing and which alleviates back pains.

Anyway. We were walking opposite directions down the hallway, and noticed each other. It would not have been difficult to change courses and avoid each other, but instead we just sort of walked into a hug. No actual words were spoken. Just hug, okay, back to lab.

Upon reflection, this makes me happy. Not just that I have good friends, but that I know my good friends well enough that we can just decide, completely nonverbally, to have a hug in the hallway.

My life is good.
tanarill: (Jewish)
I was just at the hair-cutting ceremony of the local rabbi's second-youngest son. (The youngest hasn't figured out walking yet, although he is pretty solid on crawling.) I had never been to one of these before, and it was, to my not-entirely-religious eye, bizarre. But I shall record the logic behind it for purposes of cross-cultural talking.

Weird Jewish Thing )

Jul. 19th, 2013 11:24 pm
tanarill: (Default)
So. Good news IRL: although the Scottish Scientist has patented the use of HOT (hydroxyacid-oxoacid transhydrogenase, my protein) as a detector of GHB, she has not actually cloned it successfully. They can get a peptide, sure, but it is inactive. They could not reactivate it. We can still be the first group to successfully express active HOT. So that's good.

I have been reading Pacific Rim fic. I mean, the ones set during the movie kind of suck, because most of the movie took place over just a couple of days. But futurefic? I could read people writing about what the heroes do after the world doesn't end forever.

But also, Homestuck. The way that webcomic changes how people read relationships ought to be a crime. With that in mind, flawless kismesissitude. I don't even particularly ship those two, but rarely have I ever seen anyone write black romance as well as that. So even if you aren't a Homestuck and just like candlelit hate dates, read this fic.
tanarill: (Glee!)
I went to see this movie! This movie was ridiculous and awesome in all of the right ways.

more review under here )

TL;DR: If you liked Independence Day, Avengers, or even superhero cartoons as a child, you will enjoy this movie.

Ho-Hum

Jul. 8th, 2013 08:16 pm
tanarill: (Science!)
So I successfully deplated the silver. I no longer have a mirrored Erlynmeyer flask, boo. Also, I discovered why we hate silver staining so much: not that it is not functionally better than the blue, but that cleaning up after it is a pain in the ass.

Now I am trying to see if my bacteria that grow after induction are doing so by mutating, and also if media makes a difference. So there is that.

An unrelated thing that happened that I didn't mention on this blog because I had fallen off the planet: there was an earthquake. This happened about a month ago, but the point was I had never been in an earthquake so it was a new and interesting experience. Also not scary. I mean, if it were more violent (it was only a 4.7) I can see how it would be, but I literally went, 'grumble stupid earthquake waking me up grumble' and turned over to sleep for another hour or so. I kind of liked it, actually. Score for geology! :D
tanarill: (Science!)
So, do you guys remember that one time I gold plated my magnetic stir bar? Today, I managed to duplicate the feat . . . in silver. So obviously the next thing to do is do it again in bronze, and then I can have a full set.

Actually, it wasn't just the stir-bar. Today I was doing silver staining, which is what you do when you have so little protein that the standard blue dye won't work. The thing is, at the end you have a solution full of silver and a slow-release reducing agent. This causes the silver to plate itself out on basically anything involved, and it will continue to do so for a couple of days. So in addition to a silver-plated magnetic stir-bar, I have a silver-plated glass stirring rod, a silver-plated protein staining bath, and a silver-plated erlynmeyer flask. The glass ones are particularly interesting, because glass + silver coating = mirror. I can see my reflection in them.

I will try deplating everything on Friday. It will involve strong acid. I can't do it now because strong acid + organic solvent (like is in the staining solution) = explosion. I have to wait until all the silver exits solution, pour off the solution, and then try with the strong acid. Wish me luck :D