Monday, November 27, 2006

Monday Micro: Viruses Save Us from Evil Bacteria

Viruses are probably the most misunderstood creatures on the planet. Ask someone on the street what a virus is, what a virus does-- and theyll universally say "Viruses make us sick."

UGH! Not ALL of them! Bacteria have better PR. More people know that there are good bacteria that live in your digestive tract, eyes, skin, etc and keep us healthy and keep the yeast out of our vaginae. Well viruses do similar things! There are viruses called 'phages' whos natural habitat is your digestive tract (no, youre not special, theyre in all mammals' digestive tracts) that kill bad E. coli. You know, those 'bad' E. coli that were in the news a while back, hiding in spinach? That 'bad' E. coli that makes you poop all over the place when you drink the water in Mexico? The 'bad' E. coli that kills a few million kids a year.

Phages are the sweet lunar-lander viruses:

Sweet. Anyway, they only effect bacteria. They dont hurt you. Theyre a natural part of your bodys ecosystem. Hmm. Can we use these 'phage' things to our advantage? Can we use phages to treat antibiotic resistant bacteria??

Yes! Heres a nice little review I found, and its available free online!
'Phage therapy: the Escherichia coli experience'

I like this review because it covers the basics that any scientist or lay person would want to know:
1. Why do we want to use phages as antibacterials?
2. Is phage therapy safe?
3. What organisms have we tried phage therapy on? Humans? What happened?
4. What are the pharmacokinetics of phage therapies?
5. Will the phages hurt 'good' bacteria? I dont want an itchy vagina.
6. Why wont bacteria just develop resistance to phages, just like they did to our antibiotics?

Its an old idea, but its been gaining ground again lately because of the emergence of so many bacteria strains that are resistant to antibiotics. Resistant and deadly. Cant wait to see what we can do to a 70 year old idea with the molecular genetic technology of today!

Monday, November 13, 2006

A Sane Persons Guide to Creationism – Apollos Chariot

Too often, normal, sane people don’t think they can speak up when confronted with Creationism in every day life. Aunt Polly says something that just doesn’t sound right. Billys teacher says something fishy. But Sane Person doesn’t feel they have the ability to stand up against Creationist behavior because they don’t have a PhD in biology. Luckily, all you need is common sense.

I got to see Richard Dawkins presentation on ‘The God Delusion’ on CSPAN2 this weekend. The Liberty University kids thought it would be cute to bum-rush him, but alas, theyre retarded, and Dawkins patiently trounced them with classical British manners. But I think he missed one big point, and its one of my favorites—Apollos Chariot.

Huh? There are Greek Creationists too? No, but modern Creationists are using similar logic regarding various topics, and I think its an effective example for the silliness of a Creationists prized argument: “Well how does evolution explain ____????” Insert whatever you want in the blank. Consciousness. Altruism. ‘Morals.’ Origin of life. Origin of the Universe. Eyes. Immune systems. Whatever gap in our current knowledge some Creationist thinks he/she cleverly discovered.

Lets pick one—How about, “How does evolution explain the origin of life????” Well, weve got some ideas, but we don’t know what happened for sure on Earth 4.5 billion years ago. “AH HA!” says Creationist “Well how do you KNOW my god didn’t do it then???” Easy. When has a supernatural explanation been right? Thor doesn’t control lightning. Mental illness isn’t caused by demons. Miscarriages aren’t caused by witches’ hexes. The sun isn’t pulled across the sky by Apollos chariot.

Making up supernatural explanations for natural phenomena is what ancient civilizations do. They didn’t have the technology, they didn’t have the math, they didn’t have the foundation to understand what caused lightning, mental illness, miscarriages, or why the sun appears to move across the sky. Humanity has worked hard to improve chemistry, physics, biology, and medicine over the course of our history. Pathetic, to think weve made it this far, only to give up at ‘our eye.’ Why should we give up? When has the supernatural explanation been the right answer? When has giving up been the right action?


Sunday, November 05, 2006

Election 2006

November 2, 2004 was one of the worst days of my life. Im a cynical optimist, but I let myself get my hopes up that wed get rid of the Retard Death Squad. Fucking PA-- the race was supposed to be neck-in-neck there, and Kerry blew Bush out of the water.... I thought we were going to win.

I drank a LOT of rum and ate a LOT of gummi bears that night.

And I think everyone in the biology department had depression for at least a month.


So Im trying SOOOOOOOO hard not to get my hopes up again. Know whats not helping? This fucking site. Electoral-Vote got my hopes up in 2004 and they were dead wrong. Now what are they projecting? Dems taking the Senate, Dems killing in the House. Ive heard the 'algorithms' have been improved, whatever the hell that means, but its still getting my hopes up, and I know Im going to get crushed again, because Americans are idiots....

Ugh I cant take this shit every two years for the rest of my life!

Saturday, November 04, 2006

I Guess its Official: God Hates Fundies

I am a lucky, lucky little bitch. I grew up under very anti-girl-growing-up-to-be-a-scientist conditions, yet because I had wonderfully supportive family, friends, teachers, etc, I have grown up to be just that. Im healthy, have a well paying job, bright future... and Im an atheist. I love to tease the anti-female Islamic posters on a message board I frequent that their god has a boner for me. Seriously- If their god exists, it obviously doesnt give a crap that I dont believe in it. It doesnt care that I dont pray to it every night. It doesnt care that I do a LOT of stuff that its holy book forbids. It looks like he LIKES the fact Im playing hard-to-get-atheist.

Their response is normally along the lines of "Sure you think your life is great now, but OOOOOOOOOONE DAAAAAAAAAY your going to be begging our god for help." Awwwwww I love those loving gods! The ones that arent happy unless your groveling at their feet. But theres just one problem. It doesnt seem the True Believers are any better at holding back their gods wrath than I have been:
Kent Hovind is going to jail for a really long time.
Ann Coulter is being charged with felony voter fraud.
Ted Haggard is just a meth snorting hypocritical fag. (and I hope he shoots himself in the head)

Yup. Im sure gonna run to some god begging for something. He sure watches out for his own!

Thursday, November 02, 2006

In Honor of Haggard: PERVs

PERVs: Porcine Endogenous Retroviruses. hehehehe

This months Journal of Virology has a cool article on pigs version of HERVs:

Porcine endogenous retrovirus integration sites in the human genome: features in common with those of murine leukemia virus.

Im sure its not news to you, but theres an organ shortage in the US. And since George W wont let us clone humans just to harvest their organs (lol!), we have to look other places. Technically our closest primate relatives would be a good choice, but people (including me) think its weird to harvest their organs too. Turns out pigs arent a bad choice! Unless youre Jewish or Muslim... Anyway, even after creating transgenic organs in pigs (pig organ that expresses human proteins, so its less likely to be rejected), there are still more obstacles to cross before they can be a viable solution. One obstacle? PERVs.

PERVs (and ERVs in general in other organisms) are more active than our HERVs. You cant just put a pig liver in someone who is immunocompromised and not expect the 50 identified PERVs to start infecting other cells. Now pig PERvs dont hurt pigs, and human HERVs dont hurt humans... but what if you put a PERV in a human? Its not an ERV anymore-- its a retrovirus. Where is it going to land in the human genome?

These researchers found that when you put PERVS in human cells, they like to insert themselves near transcriptional start sites (right in front of a gene). Just like murine leukemia viruses. Like the MLV that was used in the disastrous gene therapy trials that gave some kids leukemia. Ugh. Crap.

As always, we have 'further avenues of research.'

Better than Pinkeye...

... But not better than Worcestershire sauce zombies.

The 'big' 'South Park' episode on 'atheism' was on last night. Looks like we get a part two too.

Meh, there were a couple good jokes-- Ms Garrisons description of evolution had me ROLFing. And some of the sticks to atheism were funny. Like when Dawkins had a crush on Ms Garrison, but wouldnt fuck her unless she was an atheist. Damn straight I wont fuck a theist! LOL Gawd gross! And saying 'Oh Science!' instead of 'Oh God!' was kinda funny. OH! And when Stan got put in the corner with a dunce cap that said 'I have faith'. hehehehe

I thought it was more funny that SP was trying so hard to have a 'big atheism show', but the best they could do was pull 'LOOK! SCIENCE IS A RELIGION!' and 'IF PEOPLE DIDNT KILL OVER RELIGION THEYD KILL OVER SOMETHING ELSE!'


Again, I could have written a better episode.

Whats REALLY funny about this episode is that the tards at Uncommon Descent were Super Excited about DAWKINS finally getting what he deserves! YEAH! They had him doing Ms Garrison! HAHAHAHAHAHAHAHAHAHA! Oh wait, Dawkins is really married to a hot, intelligent actress.

And whos really getting what he deserves is Ted Haggerd of 'Root of Evil' and 'Jesus Camp' infamy. He has allegedly been fucking dudes and shooting meth while encouraging his flock to hate gay people. There should be a word for this sort of thing. It happens so often.

Sunday, October 29, 2006

Queen of Acrylamide Gels

One of my favorite protocols in the lab is running SDS-Page gels. Boss thinks Im nuts (I guess other people hate running them), but I kick ass at them so he lets me be giddy.

The all knowing Wiki proclaims that SDS-Page is: a technique used in biochemistry, genetics and molecular biology to separate proteins according to their size (length of polypeptide chain or molecular weight).

We're trying to separate out three proteins HIV makes-- gp160, gp120, and gp41. Gp160 is just a precursor protein, it gets chopped into the two bits that HIV really wants: a transmembrane protein gp41, and gp120, which noncovalently bonds to gp41 to create the spikes that stick out of HIV that attach to your cells.

(from 'Molecules of HIV')

The thing is, when we blow up the cells in our Pulse Chase experiment, we collect all the proteins the cells make, not just the HIV proteins. So we do something cool called an immunoprecipitation-- we add HIV antibodies to the cell goo, the Ab stick to the HIV proteins, and we add beads to the goo that stick to the Ab. When we wash everything off, only the beads, the Ab, and the HIV proteins are left! Then we boil the samples to denature the proteins (they need to be linear to run in a gel) and BAM! Pretty gel time!


Thursday, October 26, 2006

The Only Thing Better than Syncytia:

Infectious viruses that express GFP and dsRED:

Those little dudes might revolutionize the way we study HIV. Talk to me in a year :)

Wednesday, October 25, 2006

Just in Time for Halloween!

I love my syncytia. There is only one thing better than blue syncytia. GLOWING SYNCYTIA YEAH!!!

I MADE those bad-boys myself! LOL I havent seen Boss this happy in a while. Look at those nuclei in that last one! WHOOO!!!

Monday, October 23, 2006

Monday Micro: Strep on Steroids

This weeks paper covers Streptococcus—the bacteria that gives little kids alllll over the world strep throat every winter. It likes to invade your tonsil cells, or sometimes cuts and wounds. They like epithelial cells. Well bacterial infections in your flesh are never a good thing, but in the mid 1980’s, something strange happened. No, not just the rise of fundamentalist Christianity in the US, strep infections were killing people, through a different kind of toxic shock syndrome, and through necrotic fasciitis. Do NOT Google necrotic fasciitis after you eat. Or before you want to eat. Seriously.

So what happened? A sweet, sweet lesson in evolution. Strep stole a gene from a phage (yes, a bacteria stole a gene from a virus), and it learned a new trick:

Emergence of a bacterial clone with enhanced virulence by acquisition of a phage encoding a secreted phospholipase A2

M3 strep infections have a higher death rate than other strains of strep. So these guys compared genomes of strep collected over the past 60 years, trying to find out what was so different, so deadly about M3. They found that M3 had stolen a phospholipase A2 gene from a phage virus (arch enemy of the bacteria) called SlaA. SlaA is the same stuff that you find in Australian brown snake venom. Yeah. They aren’t connected, but its still cool. Hehehe!

So these guys wanted to be sure they found the ‘right’ different gene in M3. So they went through a series of simple experiments to answer some basic questions:
1—What does SlaA do if you put it on tonsil cells?
Okay, easy enough to answer! Put some purified SlaA proteins on a culture dish of cells, watch what happens!
….. Nothing happened.

2—Okay… So what happens to the bacteria if you take away its SlaA gene?
They took away the M3s SlaA gene by making a delta-SlaA mutant and threw it on some cells! The bacteria behaved ‘normally’—they infected the cells, but not crazy nuts killing everything like the wild-type M3. So they were on to something! More experiments!
2A—Take a wt M3, but add SlaA antibodies to block it from doing anything. The ‘wt’ M3 acted more like a delta-SlaA mutant (missing SlaA)!
2B—Take a delta-SlaA mutant, and add exogenous SlaA to see if you can restore its phenotype. Sure enough, mutants complemented with SlaA proteins started killing more cells!

3—Well what the hell is going on??
When M3 strep hits saliva or tonsil cells, it starts secreting SlaA and gets it into the cells (remember, exogenous SlaA on its own didn’t do anything, it must act within the cells). SlaA works inside the cell to increase M3s ability to adhere to cells, and it itself toxic. They still need to work out the details (how, exactly, does SlaA get in? what does it do when it gets there?), but they’ve got a good case that in one fell swoop, this strain of bacteria stole a gene from a virus and became more virulent. This isn’t the *first* time this has happened (look at your own genome!) and evidently has had a huge impact on the evolution of life on this planet.

Tuesday, October 17, 2006

Staph in the Brain: Part 2

Well, that headache went away. I guess that means I dont have a colony of Staph eating my brain. **sigh** Oh well. hehehehehe!

As promised, I read through one of Dr. Kielians papers:

The role of Toll-like receptors in CNS response to microbial challenge

Sure they do a better job of explaining their research than I can, but heres my summary anyway--
There are these great cells in your brain-- astrocytes and microglia, that act as 'gatekeepers.' They keep bad stuff out. But sometimes, despite their best efforts, something does get through. So theyve got these receptors in their membrane that detect 'bad' stuff floating around called 'Toll like receptors.' Lots of families and lots of kinds of these receptors that non-specifically detect foreign stuff floating around your brain: Double stranded RNA (a virus got in!), PGN (a bacteria got in!), that sort of thing.

They then proceed to freak out.

When they detect something foreign has gotten past the blood-brain barrier, they start the inflammatory response, releasing cellular messengers that call white blood cells to the brain (thats why the ball of bacteria in your brain will also be filled with puss. YEAH!). One of the problems with a Staph infection in the brain (other than the fact Staph is in your brain), is that long after the bacteria are dead, their body parts are still floating around. The astrocytes and glial cells think that means there is still bacteria eating your brain, and they call up MORE white blood cells. This causes 'bystander injury,' where normal neurons are killed because of an over-active inflammatory response.

Dr. Kielian is hoping that their characterization of this pathway with Staph can help us better understand other diseases like HIV dementia and MS, which might be caused or propogated by this Toll receptor response.

Im going to think of this every time I get a headache now. Ugh.

Monday, October 16, 2006

Monday Microbiology—I am such a hypochondriac

Im going to be a PhD student in microbiology next year. Weird problem—Ive never taken a course in microbiology. Really! It was a low level course in college, and I didn’t want to take it for an elective when I could take a higher level (aka more interesting) course instead. So I just went straight from general bio courses to virology. I kinda suck when it comes to bacteria, or fungi, or amoebas, or any of the other cool critters out there.

So once a week I want to talk about something that’s not viruses. Very, very hard for me :) But I got to hear this speaker today that was SOOO COOL: Tammy Kielian!

First of all, she was just a kick ass chick—she had a family, a ton of $$$ in grants, and she was a great speaker too. But what pushed her into a whole new level of cool was her research on Staphylococcus aureus. You might have heard it referred to as ‘Staph’ before from a news program—‘Staph’ is infamous for being a problem in hospitals, causing ~12,000 deaths a year. If I recall correctly, that was the official cause of death of one of my grandmothers. Dr. Kielian studies a really weird thing Staph will do… Get into your brain, kill some tissue, and form a big, puss filled abscess.


Yeah. It doenst just get in your brain an obvious way, like a dagger to the forehead—it can contaminate the brain from a dental infection or a sinus infection, or it can spread if a chunk of bacteria dislodge from a main infection site (in the lungs, wherever) and gets stuck in the tiny blood vessels in your brain. Im going to try to read one of her papers tomorrow to give you all the gory details, but one of the major problems of this kind of infection is that its hard to diagnose. Symptoms don’t show until enough brain tissue dies to screw up your motor skills/memory/speech/etc. And the thing is, its not 'that' uncommon. Its not really common like the flu, but evidently a big ball of bacteria in your brain isnt all that rare either! AAAHHH!! **shudder** But one of the few ‘first signs’ is headaches… and Ive got a killer headache today. And Ive had a runny nose since I moved down here. Sure Ive never had a sinus infection, but still, I just know I have a hole in my brain filled with staph and white blood cells and blown up neurons. I just know it.


More to come!

Wednesday, October 11, 2006

Candles in the Dark

Ugh this post is really not going to be honorable enough or eloquent enough to warrant the Sagan reference in the title, but I think its appropriate.

When I was little, I wanted to be an astronaut. I loved Star Trek, I loved Star Wars, I wanted to explore new worlds, and I thought space was the only place I could go for that. I went to Space Camp a couple times, took a course on astronomy, just in love with all of it. The idea of doing things and seeing things that no one had seen before.

I decided my path to space was going to be through the Air Force Academy. If most astronauts were in the military, then I was going to join the military. I worked my ass off to get into their ‘Summer Scientific Seminar’—if you got into that camp, you were for all intents and purposes guaranteed a spot in the Academy for college. I got in. Only two people from every state got to go, and I got in. The path was laid for ERV to be an astronaut!!! WHOOO!!!

So what happened? I dunno. Through a series of fortunate events, I grew disillusioned with the USAFA. I didn’t fit in with the other students. I didn’t fit in with the atmosphere of the university. It wasn’t ‘right.’ I grew disillusioned with astronomy. Nebulas are amazing, but I was never going to get to fly near one. I was never going to put my feet on another planet. All space could offer me was cold. By the time this all hit me I was graduating high school and I needed to make some decisions about my future, so I decided to go into biology. I was meh about it at first. Honestly, I just did it for med school. What else could you do with a degree in biology?


BWAHAHAHAHA! Again, though a series of fortunate and completely unintentional events—I found a way to explore new worlds! I realized a couple days ago that the reason why I love my job so much is that Im getting to live out my childhood dreams, though I thought they were killed years ago by impossibility. No one else on the planet is doing what Im doing (well, except my boss)—Im exploring a part of this universe that none of us have seen before! People are depending on my observations to make a map to explore other parts of the universe! And to be completely trite—this universe is right in front of our faces, not far far away.

And Im not the only one doing this! Scientists all over the planet are busy exploring, discovering, observing things no one has seen or understood before! As Sagan put it, we’re candles lighting the dark of the universe. And right now I friggen feel like Im dancing around a bon fire (sure we’re still surrounded by darkness, but all of our candles put together looks real bright right now). I know I suck at explaining what I do to my friends. My parents don’t even ask what I do any more—its just “Are you enjoying work? Gooood!”. But I really really do try to light other peoples candles. I try to get them excited about science, whatever theyre interested in.

Yet some people don’t want their wicks lit. They want to live in the dark, or at least they think they do. I cant say why, I cant even imagine. But a group of the leaders of the Dark are most definitely the Creationists. They work so hard to keep their followers in the dark, some spending their lives dedicated to extinguishing candles. They teach those with extinguished flames to fear the light of science. Or delude themselves into thinking their ignorance is a camp fire. But I think this methodology is finally catching up to the leaders of the Creationist movement.

Recently, as I posted about, the discovery of RNAi won the Nobel Prize in Medicine… Go to Answers in Genesis, the YEC go-to site. Search for RNAi. Go to Harun Yahya, the Islamic counterpart. Search for RNAi. Go to ICR. Go to ARN. Go to DI.


Im about to start using siRNA myself—its absolutely necessary for my PhD project. Im dancing RIGHT up against the flames of science right now, and using siRNA and evolution. The leaders of Creationism are so scared of science that they cant address modern science! Second law of thermodynamics, they feel safe with. Evolutionists are evil, they feel safe with. Eyes are too complex, they feel safe with. But mention some new world that they haven’t even imagined, some fantastic mechanism they didn’t even know existed, and theyre scared to death to even address it.

Just a very strange observation.

Tuesday, October 10, 2006

I love COX

Sorry-- No internet the past few days, thanks to the great internet monopoly in this town. Posts will resume tomorrow.


Wednesday, October 04, 2006

The 12hr Time-Point

Its weird—what Im doing right now in the lab is exactly what I was doing this time last year. But this time last year I was a retard that didn’t know how to pour an 0.8% agarose gel. Seriously, my boss had to show me how to do that (and he was very sweet about it, btw. Didn’t even laugh when I tried to ‘write down the protocol.’ **blush**). Now Im doing these insane experiments by myself.

Including the dreaded 12hr time-point. Ugh. No matter how early you start this protocol, the 12hr point is always in the middle of the night!! ARRRG! I go to sleep 30 minutes ago!

So Im typing this blog entry to keep me awake until I have to drive to work and blow stuff up for 45 minutes. Yes, blow stuff up. Blow radioactive stuff up. I said these experiments are insane!

I infected some cells with a virus a couple days ago. Let the viruses get real comfy—let them set up shop, getting the cell to make its proteins for it. Hehehe But this morning, I took away all the cells’ food. I starved those bastards so they couldn’t make any proteins. Hehehe Then I gave them food, laced with radioactive Methionine and Cysteine amino acids!! Methionine and Cysteine are the only amino acids that contain sulfur, so we just exchanged a regular sulfur atom with a radioactive S35 atom—that way we could find out exactly what proteins the cells were making, because all the proteins they make will be radioactive! And those cells are making viral proteins :) We wanna know how much of a certain viral protein is getting made, and how fast its getting chopped into two pieces that the virus really needs to stay infectious.

Well we can collect all the proteins the cells make by blowing them up and collecting their innards (my favorite part, personally hehe). We blow them up right after we give them radioactive food, an identical batch of cells 2 hours later, another one 4 hours later, etc etc etc up to 24 hours. Again, we want to know how fast this protein were interested in gets chopped into two, so we take a snap-shot every couple of hours.

We can pull out the viral proteins we are interested in by making them stick to beads with special antibodies. These proteins get run out in a gel to separate them out by size—put a piece of film on the gel, let it set for a while, and the S35 excites the film when exposed to light, and you get a sweet ass gel that you can get lots of AWESOME data from!

… But that will be like, a few weeks from now. Sorry. :(

Monday, October 02, 2006

Discoverers of cellular “SHUT UP!” signals win Nobel!

Sweet! I remember when I first learned about siRNA—Fall of my senior year of college—Molecular Genetics—‘Control of Leaf Morphogenesis by microRNAs’.

As hard as my professor tried, I just didnt 'get' it at first. RISCs, Dicers, Pri-miRNA, Pre-miRNA-- The whole process is elegantly insane! Single stranded siRNA goes out into the cell and binds to its exact complement creating a double-stranded RNA. Double-stranded RNA is a magnent for this complex that rips the dsRNA apart. Its one of the ways your genome keeps all those endogenous retroviruses quiet ;)

This animation explains it much better than I can!

Isnt it nuts!! No wonder it took us so long to find it!

Its turned out to be not just an interesting process, but an absurdly useful tool as well. Plants, animals, insects, fungi, viruses, everybody has non-protein-coding sequences in their DNA that code for silencing RNA-- so that means that we can design an artificial 'siRNA' for a gene we're interested in, in basically any organism, and see what happens when we make the gene shut up!

Its so much more practical than mutating a gene so its not expressed all to see what happens. Sometimes when you totally knock out a gene, the organism cant even develop right, so youre no closer to understanding the gene fuction than you were before. But again, with siRNA, you can let the organism grow up and only silence a gene to see what happens, and then when all the siRNA is degraded, you can see what happens when the gene fuction is restored! Its a natural process that we can harness.

But Im kinda sad my pick didn’t win. I was partial to Roger Tsien because one of my research projects is all about making things glow. Tsiens lab made a billion new fluorescent proteins:

Well, I appreciate the ability to make my viruses in Skittles colors.

Sunday, October 01, 2006



Bro picked Baby Duke up at a Humane Society adoption drive! 10 month old yellow lab, sweet disposition, and at a shelter. **sigh** My family cant go to adoption drives/shelters/etc without bringing 12 dogs home, but for some reason my bro thought he outgrew that. He didnt. hehehehehehe!

The thing is, bro already has a dog-- Miss Speckles. Miss Speckles was a street dog before she found bro. She doesnt *like* other people. She doesnt *like* other dogs. Luckily bros house is like 8,000 square feet, so the two pups have avoided confrontation so far.


Saturday, September 30, 2006

The Zen of Cloning

Ugh. Loooong week. Ive been trying to get that last construct (the uninfectious bastard from Tuesday). I make these guys by cloning—not the half man/half cow clones George W has nightmares about at night, but molecular cloning.

I cut and paste lots of bits of DNA together into a plasmid, pop the plasmid into some bacteria, and give the bacteria lots of food so they will cheerfully make billions of copies of my plasmid. Just when the bacteria are getting comfy in their warm soup… I blow them up and harvest their innards!!! BWAHAHAHAHAHAHAHAHA!

Anyway, I cant get a good plasmid for that last construct. By *good* I mean one that doesnt have any weird random mutations, one that will make all the proteins I want when I put it in mammalian cells, one that actually makes infectious viruses, etc. But all of these procedures take forever, so I don’t know Ive got a bad one until Ive wasted three days. After ranting to my boss a bit yesterday—he said something very Zen:
“You are trying to make three pieces of DNA that might be 'bad' come together and make a 'good' construct. Why don’t you take parts from constructs you know are good and put them together? Use the good fragments to make a good whole.”

Of course, this is just common sense, and I don’t know why I didn’t think of it—but it just sounded very Zen to me.

Thursday, September 28, 2006

More Syncytia Sweetness

Syncytia formation is a fun technique I use in the lab to see if the viruses Ive made are infectious. But theyre important in vivo too— you wouldn’t be alive without retroviruses and their syncytia trick.

During embryological development, your first cells made a viral protein. No, you cant use ‘early embryological viral infection’ as an excuse for why youre so messed up. A functional viral env gene is in all of our genomes, and its still there right now. But this endogenous retrovirus is only actively transcribed and translated in embryos—Its env is expressed on the surface of embryo cells, and they use the syncytia trick to build you a placenta! When experimenters used siRNA ** to knock down this endogenous retrovirus, the embryo freaks out and wont make a placenta!

Its not exactly *ethical* to try this on a real baby—so the same group that found this ERV looked in mice to see if they could find something similar. They did! Another group found an ERV with the same function in sheep! The sheep guys went so far as to knockdown the expression of the sheep embryo ERV in actual embryos in a mommy sheep… and the embryos died. So that pretty much clenches the fact we need this endogenous retrovirus to survive.

Okay, so that makes sense. All mammals need placentas, I bet this retrovirus helped us ‘kingdomate.’ Not quite—this gets weirder. So far we know humans, mice, and sheep have ERVs that perform the same function… but all of them are different! Syncytin-1 and Syncytin-2 in humans are different from Syncytin-A and Syncytin-B in mice, which are different from enJSRV in sheep! Each of these species independently acquired a retrovirus that became endogenous and performs the same function! Kinda like how ‘eyes’ all perform similar functions, but eyes independently evolved at least 40-60 times! Or how bats and birds and insects have wings, but they all evolved them a different way! Convergent evolution!!

We don’t have the whole story on the origin of these ERVs, or whether there was a common mammalian embryo ERV that got replaced by ‘better’ embryo ERVs in each species over the course of time… I love it when we find tips of icebergs!

**(Instead of finding out what a gene does by irreversibly screwing it up and seeing what happens to the cell, siRNA lets you just make the gene shut up for a minute, you can see what happens when the gene isn’t translated. When the siRNA gets degraded, the gene gets expressed again and you can watch what happens then.)

Human paper

Mouse paper

Sheep paper

Wednesday, September 27, 2006

I suppose ‘Manbearpig’ should have been a clue.

South Park’ is starting their tenth season this fall. There have been a few stinkers over the years (Jackovasaurus, Crab People, Cancelled), but it has mainly been a fun show that Ive enjoyed since The Spirit of Christmas. That’s why I was disappointed to read this:

But Parker says atheism is more ludicrous to him than anything else.

"Out of all the ridiculous religion stories — which are greatly, wonderfully ridiculous — the silliest one I've ever heard is, 'Yeah, there's this big, giant universe and it's expanding and it's all going to collapse on itself and we're all just here, just 'cuz. Just 'cuz. That to me, is the most ridiculous explanation ever," he says. "So I think we have a big atheism show coming."

Great. South Park’ is taking the Poo-Choo-Train straight to Shitsville. A ‘big atheism show’? 22.5 minutes of ‘I don’t believe in a god. Do you believe in a god?’ ‘No. You wanna go get nachos?’

Look, Im all for making fun of atheists. I think I could write an awesome episode making fun of atheists—like the Jews did a better job making fun of the Holocaust than the Muslims. But considering SPs unempathetic attitude towards the Problem of Evil in Red Hot Catholic Love, and the stupid comment quoted above, Im not hopeful that this episode will be an accurate portrayal of atheism in America.

I also think its funny that Parker thinks scientific explanations of the universe are ‘the silliest’ things hes ever heard. Heres the deal, Parker—the leaders of the scientific community, the members of the National Academy of Science, are nearly exclusively atheists/agnostics/nontheists. Though Im still very young, Ive never worked with a True-Believer. Everyone is atheist/agnostic/apathetic/secular Jewish/etc. Why? Because reality is soooooo much cooler than any of those ‘wonderfully ridiculous’ myths people like. ‘Wonderfully ridiculous’ explanations of the universe cease to be 'wonderful' when you understand physics, chemistry, and biology. How can you compare this to ‘yeah, theres this big, giant universe and its expanding blah blah.’ Ugh. Ill say it again—Poo-Choo Train.

Tuesday, September 26, 2006

At Least Theyve Got Booze in Casinos...

My job is so damn addicting. Its like playing the slots—you can plug in quarters forever thinking “Maybe this time Ill win! I can feel it! One more spin!” And just when you’re starting to give up—BAM! Jackpot!!! Today was almost a jackpot:



AWWWWWWWWW!! Non-infectious construct! God dammit!

Ugh. 6 months of work. One more week and Ill get that last construct. I can do it.

What youre looking at:
My job is to make various laboratory strains of HIV to help us understand exactly how HIV attaches to our cells, so we can design vaccines in a more logical manner. I take those viruses and infect TZM-bl cells.

TZM-bls are ‘indicator cells.’ That means that some genes have been introduced into their genome-- luciferase and B-galactosidase, attached to the HIV promoter region. If the viruses are infectious, they will infect the TZMs, and bring along with them a gene called ‘tat’, which helps transcribe the infectious viruses genome, and also the artificially inserted genes. You can either do a ‘luciferase assay’, or a ‘beta-gal staining assay’ to see if you got any infected indicator cells. Those blue globs you see in the pics are infected cells.

Another cool thing about these indicator cells is that when they are infected with HIV, they will form ‘syncytia.’ The envelope gene is expressed on the surface of the cells. HIV will normally steal the cells membranes, and their env, when they bud off from the infected cell. When the env on the surface of the cells comes into contact with receptors on uninfected cells, they will fuse together, forming multinucleated blobs!


Monday, September 25, 2006

Irritating the CDC

Hehehehehehe Okay, Creationists always like to complain about how those meany scientists are peeeeeeeeeersecuting them. They have all this awesome evidence that not only PROVES their creationism myth is true, but ergo PROVES their god exists! But those EVILutionists wont let them publish their research! Well, ignoring the fact that they don’t, you know, do any research—how does the scientific community deal with ideas that go against the grain?

There is only one question we ask when hearing an ‘alternative’ idea—Where’s your research? Bad news for the Creationists, but good news for people who have discovered something interesting. You can use your research to convince others you are right, and they can review your work—maybe even go on to use your research as a foundation for more novel research of their own. Eventually, your ‘alternative’ idea can become mainstream! Hell, you may even win a Nobel!

But as we learn in Mooney’s ‘Republican War on Science’—the scientific community and governmental ‘scientific’ organizations don’t always see eye to eye. That brings us to todays paper:

Factors Associated with HIV Prevalence in a Pre-Partum Cohort of Zambian Women

The cohort Im working with is in Zambia too. What Ive learned over the past 3 years is that most women are infected through heterosexual contact. Their husbands run off to whores, get infected, come home, infect their wives. That’s even been the basis of some research, trying to explain why HIV Subtype C has outcompeted other subtypes, despite its lack of virulence in a Petri dish. Somehow, Subtype C has evolved to be the most efficient transmitter through heterosexual contact (example)

But this paper found something… different:

Even after accounting for the proportion of HIV infections associated with the domains listed above ( Demographics, Sexual behaviour, Alcohol and substance use, Cultural practices, STDs), medical injections emerged as the single most powerful predictor of HIV seropositivity.

Their idea isn’t totally new, which they mention in the intro. Gisselquist published several papers that reached a similar conclusion, but his analyses were all theoretical mathematical models. The authors of this paper simply did a retrospective study with data they collected for other reasons (KSHV transmission patterns). And they got evidence to support the claim that HIV transmission through contaminated needles in hospitals is gravely underestimated in Zambia, and probably all of Africa.

Well, great! Now we know another place to focus our efforts to prevent new infections, right? Hehehe Nope! *Word has it* the CDC is pissed at this paper because it makes them look stupid. The CDC hadn’t focused on this issue, and they should have. It’s not exactly a shocking conclusion. But, whether the CDC liked it or not, the paper got published. This was just a little battle in the War on Science, but it’s a victory none the less.

Sunday, September 24, 2006

Mobile Elements: Drivers of Genome Evolution

This spring I sat in on a course in Viral Evolution. I quickly fell madly in love with Patrick Forterre hypothesis: that everything on Earth now evolved from and because of—viruses.

Of course, one of the booby-traps that scientists need to watch out for is… falling madly in love with a hypothesis. You have to look at the data objectively—regardless of how much you might like or dislike an idea.

So even though I cant get into a time machine, go back a few billion years, and watch what happened myself, we can look at our (and other organisms’ genomes) to see if we can find any clues. And that’s the topic of this first paper: Mobile Elements: Drivers of Genome Evolution.

Approximately half of the mammalian genome is composed of mobile elements, cousins of retroviruses. Mobile elements can be in the form of:

DNA transposons: Cut and paste themselves into DNA, normally staying close to the original insertion (‘Local Hopping’), but can move to a distant site in the genome

LTR retrotransposons: Duplicate themselves, rather than cut/paste. They do this by being transcribed into RNA, reverse transcribed into DNA, then inserted into DNA. They are very similar to retroviruses (have gag and pol) but lack a functional env. Endogenous retroviruses fall into this category.

Non-LTR retrotransposons: LINE-1s, or L1s. Only encode a nucleic acid binding protein, endonuclease, and RT. They are reverse transcribed right on the genomic DNA, not in a viral-like particle in the cytoplasm like LTR retrotransposons.

Oddballs: Look like bits from the other groups, but lack all of the genes necessary to be autonomous. They might be missing a protease/integrase/RT/etc.

Okay, well, that’s neat—but what do these bits of DNA have to do with the evolution of genomes? Well, these little guys can really screw around with your chromosomes. Humans have about 80-100 L1s, and about 1 in 50 people have a novel L1. These L1s can plop themselves in the middle of a gene. They can repair breaks in your DNA. Increase/Decrease the transcription of genes. And they (potentially) control X-chromosome inactivation in women! Trust me, that’s a good thing.

L1s also act in trans to activate Alu sequences, or SINES. Alus are only ~300 base pairs long, but they make up 11% of our genome! 1 in 30 people has a *new* Alu. Alus really have the ability to screw around with genomes—they can cause unequal crossovers (instead of two identical chromosomes splitting into two eggs/sperm, one is chromosome is larger, one is smaller), rearrange coding regions, and duplicating portions of chromosomes. And, L1s can do some rearranging of their own, as well.

So what are the effects of these chromosomal rearrangements? Obviously, screwing around with genes can lead to diseases. Alu insertions are the cause of over 20 diseases, and L1s cause some as well. Obviously, there can also be problems with chromosomal deletions, and L1s changing the transcription levels of genes can also have negative consequences.

But, changing transcription levels can also have evolutionarily beneficial consequences. After comparing our genome to the recently finished chimpanzee genome, we noticed that it wasn’t so much our genes that make us different from our chimpanzee cousins, but the transcription levels of the genes we share. Chromosomal duplications can also have a benefit—if you have two copies of a gene, then one of those genes is no longer under any evolutionary pressure. Its free to mutate, potentially creating a new useful gene, or mutate into a pseudogene.

So maybe I cant completely agree with Forterre yet, but obviously, viral elements have played a huge role in the evolution of our genome, and every other organism on this planet.

Saturday, September 23, 2006

DI: A Day Late and a Dollar Short

I dont suppose *news* that the Discovery Institute is a little slow on the uptake, but a couple weeks ago, Casey Luskin finally got around to 'criticising' Chris Mooneys take on ID Creationism in The Republican War on Science. A book that came out over a year ago. While Im sure Casey was a little more concerned about controlling the damage from the Dover Trial last fall/winter, this still seems a little silly to me, but lets see what he has to say:

In its entirety

#1-- Mr. Mooney overpraises Darwin.
#2-- Mr. Mooney claims ID traces itself to the theological arguments of William Paley.
#3-- Mr. Mooney critiques a blatantly false, straw-man version of intelligent design.
#4-- Mr. Mooney implies there are no peer-reviewed scientific publications supporting ID.
#5-- Mr. Mooney alleges that the controversy over evolution is "manufactured".
#6-- Mr. Mooney insinuates that Discovery Institute opposed Dover's ID Policy because Discovery Institute allegedly believes ID is unconstitutional.
#7-- Mr. Mooney implies it is inappropriate to "teach the controversy" over evolution.
#8-- Mr. Mooney insinuates the Santorum Amendment inappropriately "singles out" evolution.
#9-- Mr. Mooney argues that intelligent design is not science because some
of its proponents have Christian religious beliefs and motives.
#10-- Mr. Mooney argues that Discovery Institute is "disingenuously pretending that modern science basically amounts to institutionalized atheism".
#11-- Mr. Mooney appeals to authority as a valid argument against ID.
#12-- Mr. Mooney's misrepresents Stephen Meyer's peer-reviewed pro-ID science article.
#13-- Mr. Mooney claims the Kitzmiller v. Dover case is the "death knell" of ID.
#14-- An Error of Omission--Mr. Mooney ignores the real "war"--the attack upon the academic freedom of scientists who support intelligent design in science and the media.
See? Its just the usual DI dreck! (If you dont know why these 'arguments' are retarded, Chris gives this garbage the attention it deserves here) It took Casey a year to pull this together? Ugh.

Evidently Casey is actually pissed off that all those darn 'scientists' are listening to Chris:
"Why do so many people eagerly listen to a journalist with neither scientific nor legal training discuss a complex scientific and legalissue like intelligent design?" asks Casey Luskin, an attorney with a science background, working with Discovery Institute's Center for Science & Culture (CSC).
Gee Casey, dont ya think its weird that a lot of people with credentials agree with Chris, and virtually everyone with credentials doesnt buy your Creationism bullshit? If you want to play the 'credentials' card, youre still neck-in-neck with the astrologers and faith healers. But fine, want me to disagree with Chris on something? Sure!

I dont mind Chris's lack of scientific credentials. He cited his sources and consulted appropriate experts and documents of the topics he addressed. What I have a problem with is his naive (hopefully not pretentious) attitude about how it is to be a scientist in the real world. There was one sentence in the new epilogue that pissed me off:
"But scientists have too often failed to counter creationist efforts ar a local level, preferring to remain in their ivory towers."

Bull. Shit.

I am still just a 'kid', yet I try to be as active as possible on the local Anti-Creationism front. Right after I moved down to OKC, I attended a local church to hear a Creationist speak (just a bottom feeder-- Brad Harrub . No one 'cool'). After sitting through a 2 hour hate speech - and I do mean hate speech - against science, reason, atheists, etc, the audience was invited to ask questions of Mr. Harrub. Questions written on a piece of paper, filtered through the ministers/elders, and finally to Harrub to answer or not answer. However I was allowed to ask as many questions of Harrub as I liked... as I was shepherded away from the rest of the church, so they wouldnt be tainted with my evil questions. I returned to the church a few days later and asked to give a presentation about evolution to anyone was interested. The ministers humored me for a bit, but then they suddenly were unable to return my emails and messages.

This is what you come up against being a science advocate in the real world. These people have absolutely no interest in 'teaching both sides.' They want to teach their side, their creation myth, nothing else. They blockade themselves in their churches and their religious schools and religious camps and nobody gets through with an outside opinion. Filtering questions?? Common!! I would ask Chris, why hasnt he promoted his book on 'The 700 Club'? He says we need to plead with the Religious Right to come back to reality, so why doesnt he go on 'The 700 Club' and do just that? Well, the same reason why I cant leave my 'ivory tower' to speak at local anti-evolution churches. I might want to go, but theyarent letting me in.

The answer is not to further condemn frustrated science activists, but to properly condemn the evil individuals that would rather keep their flocks ignorant than lose their tithes. Evil little twits like Casey who continue the religious mental abuse of teenagers and young adults with their IDEA clubs. Dont bitch to me about staying in my 'ivory tower' when youve never been in the dark trenches of the Bible Belt.

There, Casey. Feel better?

All the cool kids have blogs.

Thats it. After being a long time fan of ScienceBlogs, I want to join the cool-kids-club too.

Im going to (attempt) to keep the personal stuff to a minimum, and focus on science. While there are lots of great microbiologists around (Aetiology is great, Respectful Insolence gets into immunizations and such a bit), Ive yet to find a virology blog, so I want to fill that gap. Taking papersIm reading and transferring them into blog posts will hopefully help me understand the material better myself.

Of course, seeing as I live in Oklahoma, and seeing as my research relies on the validity of evolution, Im probably going to jump into that fray as well (even though everybody at ScienceBlogs is probably better qualified to address that issue).

Thanks for humoring me as I awkwardly start. I shouldnt be that bad. I did go to a liberal arts university :P