Friday, December 9, 2011


I'm back in my experimental lab, and it's been a rough landing. I cut my hair before I left for my simulation rotation, and the new haircut has bangs. Bangs + microscopes = not seeing. Today I finally brought a hairclip. There is no way to tilt your head forward and look through a microscope without getting hair in your face!

I have three weeks to collect some much needed data for a grant, and while I had started some of this type of work before I left, I only did it for a few weeks. Now I'm trying to get set up again and it's HARD! Two nitrogen tanks had run out, someone let my cells (that they were supposed to be care-taking) get to passage 40 without thawing new ones, we didn't have the kind of glass capillaries I needed, the incubator water levels were low and I had to remake solutions. Needless to say, I did not get started on the actual work as fast as I wanted.

I'm trying to be patient about how long it's taking to ramp back up to my normal experimental output level, but given the grant deadline patience is hard to come by!

Saturday, November 26, 2011

Finally legal!

Yup - it's time for Christmas music without remorse! We've been listening to 8-Bit ChristmasMannheim Steamroller and Enya Christmas albums all day while we decorate. The dog is confused about why we put a tree in the living room. He spends a lot of time looking at it.

Sunday, November 20, 2011


I needed to calculate a free energy today. I knew the equation I needed to use. And it involved Faraday's constant. I looked at a table of F values (with various units) and none of them seemed to make sense. I figured out how to get free energy in units of (mv*C*kcal)/mol, which seemed fairly unreasonable. So finally, after thinking through several possible values/units of F, I gave up and e-mailed my PI. Turns out the solution to my problems is knowing that volt=joule/coulomb. Somehow I don't think I EVER knew this.

So of course, I head to Wikipedia, where I find out that not only can joules be defined as kg*m2/s2 i.e. Newton meters,  they can also be defined as the work required to move a charge of one coulomb through one volt potential difference! Obviously my physics teachers failed to prepare me for real life, because I swear I've only ever heard the Newton meter definition.

Wednesday, November 16, 2011

Best Poster Title Ever

The best poster I saw at SfN:

331.06 How does galactic cosmic radiation alter adult hippocampal neurogenesis? J. A. LEBLANC*; M. COLE; P. RIVERA; H. SHIH; B. P. C. CHEN; A. J. EISCH. UT Southwestern Med. Ctr., UT Southwestern Med. Ctr., UT Southwestern Med. Ctr. 

I actually laughed out loud when I walked by it, but they had a big crowd so maybe they're on to something!

Saturday, November 12, 2011

SfN 2011 - Neurobiology and the Law

Went to a GREAT symposium at SfN today: The Fred Kavli Public Symposium, which was titled "The Brain on Trial: Neurobiology and the Law." This symposium had speakers addressing 4 issues
  1. Memory and the courts - C.E. Stark, UC Irvine
  2. The biology of violence and the law - A. Raine, U Penn
  3. The adolescent brain and implications for the juvenile justice system - A Baird, Vassar
  4. Addiction and the control of behavior - S. E. Hyman, Harvard
There were so many great issues and I could recap the whole entire thing from my 7 pages of handwritten notes but I'll spare you. Instead, I'd like to pose a series of questions based on the lectures with some small anecdotes...

Can eyewitnesses pick out suspects?
  • Dr. Hyman points out that we best recognize people we know, and showed that people of similar ages and races can more accurately pick out someone they've seen only briefly in a line-up. 
Is eyewitness testimony reliable?
  • Our memories not only fade, but we fill them in with false memories (unconsciously). 
  • Some people believe that memories created in highly emotional situations are more accurate and less forgettable, such as where you were you when you heard about the World Trade Center on 9/11. But this seems unlikely, and two cases were presented
    • >200 college students were interviewed  immediately after the OJ Simpson verdict and again at 15 and 32 months. At the later timepoints, elements of their stories were classified as accurate, minorly distorted, majorly distorted relative to their original sotry, or they simply said that they didn't know certain detail. At 15 months, 40% of details/stories were accurate and a similar percentage had only minor distortions and a significant percentage of students admitted to not knowing some details. However at 32 months, most details were majorly distorted and NO ONE admitted to not knowing something. Not only were they less accurate, they were more confident!
    • In a simulated POW situation, soldiers were confined and subjected to harsh interrogation. Two days later, each soldier was given a packet of pictures and asked to identify their interrogator. Some packets had a picture of their interrogator, but others had no picture of that soldiers interrogator. Yet ~70% of soldiers chose a picture that they said was their interrogator in either case.
Can we predict violent behavior? Is it ethical to do so? Will it stigmatize individuals into crime? Or is early intervention necessary and responsible to avert violence?
  • Psychopaths have been shown to have a reduced volume in the amygdala (which controls the "4 F's:" fight, flight, feeding and sex). Their main reduction is in areas that control the fear response/conditioning system. In a study of 1800 3-year-olds, their fear responses (a proxy for amygdala function) were measured and the children were followed for 20 years. After 20 years, 137 of them had been convicted of a crime, and (as a group) they had shown reduced fear responses at the age of 3. 
If neurobiology plays such a big role in criminal behavior, how do we define responsibility?

  • A study imaged the brains of psychopaths and controls as they answered a "moral dilemma" question. 80% of people answer the question the same way, including psychopaths. But the areas of the brain used to answer the question are different between psychopaths and controls. In normal subjects, their emotional circuits and amygdala light up. In psychopaths, their cognitive areas light up. This (and other data) implies that while psychopaths know right from wrong, they don't have a feeling of right and wrong. In situations that also show that they have reduced empathy and impulse control, how much control over their behavior do they have relative to a control subject?
  • A more extreme case presented was a case of acquired pedophilia. A man with no criminal or abnormal psychological history began to collect child pornography and made sexual advances to his minor stepdaughter. He was reported and sentenced to rehabilitation or prison and picked rehab. He entered treatment, where he made sexual advances to the staff and was expelled from the program and headed to prison. Right before heading to prison he had intense headaches and suicidal ideation and was hospitalized (where he made sexual advances to medical personnel). Due to his intense headaches, he receive a brain scan where they found a large tumor! After resection of the tumor, he completed rehab successfully and returned home without issue. A few years later, he had intense headaches again and his wife found pornography on his computer. He immediately had a brain scan - and the tumor had grown again! After a second surgery, his life returned to normal. How responsible was he for his actions?
Are teenagers dealt a fair hand in sentencing in the juvenile justice system? Are they judged by juries "of their peers" who can really understand their behavior patterns?

  • Adolescents have immense development in the prefrontal cortex as they learn social behavior. Adult and adolescent brains were imaged as they answered whether a choice was good or bad. Adults had automatic responses (in the amygdala) very quickly. Swimming with sharks - bad. Lighting your hair on fire - bad! Adolescents mostly got the same answers, but much more slowly. And the areas of their brain involved in answering were cognitive areas, as they actually had to consider whether lighting your hair on fire is a good idea or not. As they mature, these responses become faster/more automatic.
  • Additionally, juveniles are hugely influence by peer  pressure. In an imaging study where some adolescents were told that their data would be visible to peers, they make worse decisions more automatically!
  • Social development during adolescence lasts for life. When teenagers are incarcerated, they are socialized as prisoners, which is evident in the correlation between re-incarceration and age.
Do drug courts and rehab programs actually help addicts reform?

  • Substance addiction overloads reward circuits and is classified as "highly valuable" by the brain, making drugs the highest reward. In rat studies, electrical stimulus of reward areas is prioritized even over food and sleep and rats can kill themselves self stimulating these pathways with a lever! Imaging of addicts shows reduced prefrontal cortex action (as in psychopaths). This means that an addict is physiologically incapable of adequately prioritizing at certain stages of drug use. Their ability to prioritize fluctuates with time since last drug dose, and a decision made at one time may not carry over to the next phase of their drug experience.
  • Addiction causes permanent changes in brain structure and reward systems, which makes even recovered addicts subject to relapse in response to cues and stress.
Obviously, there are no easy answers! However, neuroscience data is likely to play a role in dictating sentencing and perhaps should even prompt fundamental changes in the criminal justice system as we gain a more nuanced understanding of human capacity for responsibility and control of behavior.

BONUS EDIT: For further lay reading, check out this article from the Atlantic.

Friday, November 11, 2011

Not science - still dorky

Apparently working on computers all the time has made me pine for manual labor - I actually made a stuffed toy! By hand! during my train commute! I must be crazy. 

Lesson learned: threading a needle while standing on a swaying train = blood letting

Fig 1: Cute little stuffed Minecraft creeper

I'm sure this will be cured when I go back to my lab and start swearing at minute tubing that won't thread onto connectors and tiny glass pipettes that melt into globs when I've barely heated them at all.

Disclaimer: I do not play Minecraft. This was a gift to Mr. Alethea.

Wednesday, November 9, 2011

How did I become a graphic designer?

The public perception seems to be that grad students and other academic types are smart. You know, abstractly brainy, maybe good at math... What no one seems to realize is that in science not only are we supposed to be able to comprehend abstract concepts, to be successful we need to:

  • Write well
  • Be good at public speaking and presentation
  • Fix equipment (in my area, this means I can duct tape stuff, fix plumbing, wire things, solder, super-glue, etc.)
  • Create what you need from scratch out of stuff you find around the lab or buy cheap
  • Negotiate with product vendors to get good quotes on stuff
  • Be proficient with data analysis and graphing software
  • Be a graphic designer
It's this last one that trips me up (ok, that and the fact that I have wretched eye-hand coordination). I used to complain about this in my experimental lab, where all I had to generate was graphs. I love a good graph, it's always great when you graph something and suddenly a pattern is clear. But then you have to get these things ready for publication/presentation. I'd make a (simply dazzling) figure, and my PI would say, "Hmmm, maybe increase the axis line weights, add minor tick marks, change the color of the one line to a darker red and don't have little serifs on the scale bar." I would do all that, he'd look again and say, "What if we used open circles instead of filled circles? Let's show the correlation with a dashed line, not a solid one. Also, how about swapping panel C with panel F?" And so on.

But little did I know - it could be so much worse. Dun dun dun.

I'm getting preparing my first manuscript in the computational lab that I've been working in. I've got some really cool structural simulation data, and now I have to find the perfect way to display each aspect with 2D images. Really, it's all best shown with movies, but you can't publish a movie. So here I am in my program (called VMD - visual molecular dynamics) sitting on a pile of choices.

  • Do I use depth cuing? What perspective? Which frame of the movie? 
  • Then there are all the ways of showing a protein structure. Do I want my helix to look like a cartoon twisty? A cylinder? van der Waals radii of all atoms? Sticks? Ball and stick? Only show the protein surface? Implausible things, like licorice and paper chains? 
  • Then I can choose how to color: by atom name, residue name, secondary structure, subunit, charge, conformation... 
  • I also have a choice of "material" which is what the representation I've chosen is "made of" in the program. These choices have some obvious ones, like opaque, transparent, shiny and also some weirder ones like ghost, glass, brushed metal and chalk
  • Don't like the preset red? You can adjust it with the color manipulator. How opaque is opaque? There's a slider for that too!
Worse still, I'm often superimposing structures, or showing ligand molecules with the structure, so I may have two cartoon helices superimposed in different transparent colors with a ghostly surface representation of the rest of the protein and the drug molecule colored by atom name in licorice representation.

All of these parameters take ages to tweak so that my awesome discoveries are shown looking their best. I will never again criticize structure figures in any paper. And my advice is, if you're looking at a structure paper and they have a supplementary movie, save yourself some squinting and download it already!

An explanation

Last month was rough. As demonstrated by my total lack of posts. My husband had two close family members pass away three weeks apart, and my time and energy has been completely consumed with supporting him and being with family. His family lives about an hour away, so being at hospitals, houses, funerals, etc. kept me on the road most evenings and weekends.

Amazingly, both of us kept up with our respective graduate work all month, but boy did our home life suffer. Our wastebaskets overflowed, we ran out of milk twice because no one went shopping for most of the month, and when we did go shopping it was because we had no milk, all invitations were met with a stock "sorry, we can't make any commitments right now" response, we hadn't had a sit-down meal together at home in a month (I don't think I've alternated between starvation and fast-food that much in my whole life) and I seriously need a haircut before I go to SfN (in two days!).

In the last week we've been slowly returning to normal. And thus I will be returning to my normal (which is still seldom!) posting rate. Coming soon: figure-making - did I sign up to be a graphic designer?

Tuesday, October 4, 2011

Science: so easy a child can do it

A few days ago, a coworker and I were mourning the fact that huge chunks of our work could be done by a well-trained middle-schooler.

This is remarkable, because I've felt like this for years in an experimental lab. In fact, I started interning in an experimental lab at twelve, so apparently, microbiology is so easy a twelve-year-old can do it. And as I've seen more and more techniques I continue to discover that a kid could do it.

  • Making solutions - check
  • Western blotting - check
  • Flow cytometry - check
  • Cell culture - check
  • Pipetting - check
  • Minipreps - check
Now, I will say that kids (myself included) are not as good at troubleshooting, but given their lack of understanding of the process and terror of bigger people, they also make fewer careless mistakes. (Anecdata: I've had two summer students, a fourteen-year-old high-schooler and a thirty-something anesthesiologist. Guess who made more mistakes, because he thought he knew everything? Yeah. Not the highschooler.) And of course, all us grown-up geniuses are needed to actually plan research projects and interpret data meaningfully.

But I always assumed this was the way of the world in experimental work, and one day we'll all be replaced by robots anyway. In fact, our robot overlords are on their way, at conferences I've seen automated western blotting systems, pharma already has automated cell culture, automated patch clamp and high-throughput automated everything. What I did not know is that this is true of computational work as well!

I'm doing a three-month rotation in a molecular dynamics simulation lab, no wet bench work at all. But still, a big chunk of time is spent doing things like labeling components of text files, counting atoms and labeling/graphing bond distances in 3D graphics. My lamenting coworker spent three hours counting atoms in an attempt to match the number of atoms from one protein to the number of atoms in another. So even when everything is already run by computers, there's still low-skilled gruntwork to be done.

Once upon a time, I thought I'd always want to do benchwork, forever, for the joy of it. Now I've seen the light, so one day, I'll be a PI and only do the fun benchwork and spend the rest of the time thinking deep sciency thoughts. And I hope I don't come back in twenty years to describe my discovery that 50% of what PIs do could be done by a twelve-year-old too!

Wednesday, September 28, 2011

I'm gonna be a first author! (with bonus rant)

First order of business: yay for me! My first-author paper was finally accepted for publication by a pretty good journal and it's coming out next month! I'm so proud of it, and it's so adorable!

However, I have to say, my first foray into publishing has thoroughly disillusioned me concerning how review, publishing etc. works (not that I was all that illusioned to begin with).

One of the scammy things is the money (of course). You (and I) pay taxes. Some of these go to the NIH. The NIH funds my research with our tax money. In order to keep getting NIH funding and to advance my career, I have to publish the work I do with the NIH money. To publish, I have to pay the journal money (page/figure charges). Then if you, who payed the taxes that pay for my research, want to see what I did within a year of publication you have to pay the journal to access the content. Somehow the publishers are winning here.

And the winning keeps happening – because scientific journals are “peer-reviewed.” The people who review papers are other scientists who (in the vast majority of cases) are not being paid for their review work. In some cases, most of the editors are also unpaid scientists. While journal editing may give a bit of a resume boost, as far as I can tell, reviewing mostly doesn’t.

Now, the non-payment of reviewers makes the review process rather annoying. For this journal, I got to suggest 4 reviewers I wanted and 3 that I did not want. The journal may ask these people, but they might be too busy. So then they keep trying to find someone else competent and available to review. Once a reviewer accepts a paper, it’s probably not at the top of their to-do list, because they have their real job. So sometimes this takes a while and the results may be less than stellar.

Take my first set of reviews (which got the paper rejected)
·      Reviewer 1: Liked the paper, had a few questions/suggestions, about 1.5 pages
·      Reviewer 2: did not read the legend for the graphs in figure 1, consequently drew totally erroneous conclusions about our data vs. conclusions. Hated the paper. All this in half a page of comments.
·      Reviewer 3: Thought the paper was ok. But really wanted us to play up the specifics of another paper that was barely relevant. We suspect this reviewer was the author of said paper, given how specific he/she got about it. We had cited this paper, mainly to say that they did their experiments under non-physiological conditions, which prevented direct comparison to our work.

Happily, pointing out the reviewer 2 hadn’t even read the legend to figure 1 allowed us to resubmit to the same journal. We did one additional experiment based on comments from reviewers 2 and 3, and our resubmission was accepted (yay!). And on a positive note, it really is a better paper thanks to some of the revisions and the additional experiment (so thanks, reviewers 1 and 3!).

However, even before submission, there was an experiment I KNEW we should have done. In fact, while we waited for review, I slaved away trying to make this additional experiment work, certain that at least one reviewer would see this hole and want it addressed. Not one reviewer noticed. (N.B. I still think it matters, and I’m still working on the experiment, my initial attempts failed, but I have now taken a different approach to testing the same hypothesis).

Monday, September 26, 2011

How drugs you don't take can hurt you

Most of us have heard of the placebo effect: something makes you feel better because you think it will. Like how that first sip of coffee wakes you up in the morning, though the caffeine hasn’t hit your bloodstream. And how your headache feels better 10 minutes after popping some Advil, even though the biochemical effect won’t set in for another 20 minutes. What you might not know as much about is the nocebo effect - or how drugs you didn't take can cause side effects and even death!

The Placebo Effect
The placebo effect (Latin for "I will please") is extensively used in clinical trials. The most common setup for testing  a drug is to divide subjects into two groups, one of which gets the test drug for their condition, the other of which gets a sugar pill. The individual patients and the doctors monitoring the trial don’t know which people got which treatment.

The efficacy of placebos is sometimes called the “expectancy effect.” I.e., if a patient really believes it will work, it does (at least for a while). Researchers have shown that you can give the same placebo to two groups, telling one group that it will have one effect (such as muscle relaxation) and the other group that it will have the opposite effect (muscle tension) and you will observe relaxation in the first group and tension in the second. Another contributor to expectation is size and cost of placebo drugs – the more a patient pays for a placebo, they better it will work!

How does this work? An interesting hint comes from a study showing that the placebo painkiller effect can be blocked by using an opioid antagonist. This suggests that endogenous (i.e. genetically produced) opioids like endorphins are released because you  expect pain relief, but this effect tends to wear off over time, because you’re not receiving real drug to relieve pain.

The placebo effect can last for a long time, depending on the condition. Placebo painkillers have been reported to last as long as 8 weeks, and placebos for rheumatoid arthritis for as long as 2 years!

The Nocebo Effect: 
But the flip side of the expectancy effect is the “nocebo” effect (Latin for "I will harm"). In a clinical trial for painkillers, for example, the placebo group will often display side effect from the drug as well as pain relief – even though they only took a sugar pill!

A retrospective study in Pain looked at 73 studies of painkiller vs. placebo trials for migrains that used three classes of pain drugs (NSAIDS, triptans and anticonvulsants). This study analyzed side effects experienced by placebo patients in all trials, and found that the side effects they experienced matched the drug they believed they were receiving!

Another nocebo study assessed subjects who believed they got headaches from cell phone radio frequencies. Subjects were then allowed to watch TV and received calls from researchers on a cell phone. Some subjects had a phone that output normal cell phone radio waves, while others had a sham phone that did not emit radio waves. In fact, subjects with sham phones reported worse side effects than people with the real phones!

Yet another nocebo effect is “MSG sensitivity.” Certain people reported migraines, hyperactivity and other symptoms in connection with MSG consumption. However, a double-blind placebo-controlled study found only one reaction to MSG – but wait! That patient had eaten placebo! Expectations strike again!

The nocebo effect can be more sinister, for example patients who know they are diagnosed as terminal may die faster than those who don’t know. Some researchers believe that the nocebo effect may also explain why curses from black magic can adversely effect those who believe in it and know they have been cursed.

Friday, August 26, 2011

Should evolution be taught in schools?

I almost cried watching the Miss USA contestants address whether evolution should be taught in schools. The predominant answer are "No!" and "Children should be exposed to all belief systems and theories about how life arose." Because, of course, "Students should be knowledged about different options."

Why teach only two sides of the creation story? The world may have hatched out of an egg! So I guess biology class will soon become mythology class.

Personal favorites: California, Indiana, Kentucky, Maryland, Nevada (OK, I kind of <3 New Mexico!), and what is Miss Washington even saying?

Note: Candidates are in alphabetical order by state if you want to hit the highlights.

After you've seen all you can stomach of the first video, watch the parody!

Wednesday, August 24, 2011

White privilege

I enthusiastically agreed to go with my husband to an a capella gospel concert at the church he attended as a child. I love a capella, I love gospel. It's gonna be great!

Then, as I looked at the Facebook event page, I thought, "I wonder if I'll be the only white person there..." Then I realized that the converse is my husband's situation at least 80% of his life, if not more. And I kept my mouth shut.

Tuesday, August 23, 2011

I heart our tech

Subtitle: "How I ended up doing surgery with a shoe-cover on my head."

Our tech/lab manager type person is away this week. Our tech is a 20-something who didn't get into pharmacy school and makes beer in his parents' basement. I didn't like him at first. But he is astonishingly long-suffering and good-natured, and even though I don't think he gives a darn about the science we do, everything always runs smoothly.

But, as previously stated, he is away. So is one of the other grad students and our research assistant is sick. Thus, I am somehow in charge. In charge of ordering. In charge of the frogs. In charge of making my own solutions and electrodes. And stuck with frog surgery.

So, I go up to anesthetize the frog. This rarely works in the time-frame described in our protocol. 45 minutes later the frog is still kicking. At an hour it's not. But then I flip it over, and I can see it's throat pulsing. Back in the anesthetic. Meanwhile, my surgery suite reservation is running out of time. (N.B.: I did not reserve the suite, our blessed lab manager did, I didn't even know we needed to reserve it!). Finally, the frog is out. I realize I have no gauze for dabbing blood. I figure, oh well, I'll just deal. I start the surgery.

As soon as I start extracting eggs, the person who had the surgery room reserved starting 5 minutes before pokes her head in. I say I need 15 more minutes, she says no problem, she'll use a different room. It's all good. Then I go to stitch the frog back up. I swear to goodness, that thing had HIDDEN the other side of the muscle layer (it could have been all the blood that I couldn't mop up sans gauze). I was stressing. My new (very professional hair) was in my face and sticky. This is because I had no hairnet (they're not required in this situation, but are helpful for hair restraint). For some reason, the little supply station on this floor was out of hair nets. Finally, in extreme frustration, I leave the suite in search of a hair retainer. The little supply station is just outside the door. I grab a shoe cover and stick it over my head and return to fishing around for the muscle layer. When I eventually put the frog back together and start hauling all my supplies (and the frog) back to where they belong, I get strange looks in the hall. This is when I realize I still have a bright blue, waterproof shoe-cover on my head.

Thank heavens he's only gone a week. I will remember to be extra-nice to him when he comes back (until I forget).

Thursday, August 18, 2011

Race bias in science funding

It's a fairly well accepted fact that there are pipeline issues in getting racial minorities into STEM (Science, Technology, Engineering and Math) careers in the US. But it turns out that even once you get there, there are still hurdles.

A recent study published in Science (see the News and Views here) found that black PhDs have lower R01 funding rates than any other ethnic group (they note that there was also a disparity in NSF funding). While there are (due to the above mentioned pipeline issues) many fewer black applicants, 29% of white applicants were funded, 25% of Asian applicants were funded and only 16% of black applicants were funded. When only US citizens are included (to minimize language barrier bias), the funding gap between Asian and white applicants disappears, but the funding rate for black applicants was still 10% lower.

Why the disparity? They controlled for as many variables as possible (training, publication record, etc), but the gap remained. One theory was that better mentoring allowed whites and Asians to submit higher quality applications, but one would then expect a lower funding success rate for Hispanic applicants as well, but this was not observed.

Obviously, the NIH is working to determine what is causing this gap so that it can be closed. Reviewers do not have access to information about an applicant's ethnicity, but perhaps it is being inferred from the name, location, or college attended. My personal guess is that there's a bit of an old-boys-club effect going on, in addition to other factors such as not having access to high-quality mentoring and grant-writing training in their early career.

PS - There are also programs that try to address the minority pipeline issues by supporting STEM students from a very young age with high-quality mentoring and research opportunities. I recently became aware of the extremely rigorous physician-scientist training program, and there are many others.

Wednesday, August 10, 2011


This seems to be entirely accurate at all levels with which I am familiar (click to enlarge).

Had some viewing problems, hopefully fixed. If you still can't see it, try clicking here.

Tuesday, August 2, 2011

This guy is cooler than me

He DIY'd a scanning electron microscope! And just yesterday I was lamenting the state of science education, cuz I'm pretty sure no teenagers today could figure out how to build a nuclear reactor in their backyard. (Not that kids should use their science-smarts to build nuclear reactors, of course.)

Engineering HIV resistance

You may have heard in the news of people who are “immune” to HIV. This is because in order to infect cells, HIV needs to bind to a primary cell-surface receptor called CD4 and a co-receptor. HIV can use two kinds of co-receptors, CXCR4 and CCR5; X4 strains use only CXCR4, R5 strains use only CCR5 and X4R5 strains can use either one.  Some people are born with a mutation in the CCR5 receptor that makes it unrecognizable to HIV. This means that they’re not susceptible to infection from R5 viruses, but could still get HIV from X4 or X4R5 viruses.

Can we use a similar strategy to treat/prevent HIV infection? Maybe. There is a drug on the market (maraviroc) that blocks CCR5 so that HIV can’t recognize it. While this drug slows down infection, it usually comes back. First, because there is now a selective pressure for proliferation of any X4 or X4R5 viruses the patient might be harboring.  Second, because in some cases the virus mutates to recognize even the blocked receptor. (HIV has very little proofreading, so mutations accumulate very rapidly. One talk I went to estimated that every base is mutated to every other base every day in every patient.)

What if we could find a way to block both receptors at once in such a way that the virus couldn’t mutate to recognize them? Enter the zinc finger nucleases (ZFNs)!

ZFNs are engineered enzymes that use a zinc-finger domain to bind to a targeted DNA sequence and an endonuclease cleavage domain to cut the DNA at the binding site. The cleavage domains often need to function as dimers, so to edit DNA you need a pair of ZFNs that bind to adjacent regions. ZFNs can be used to edit genes, since after they cut DNA, it will be stuck back together in a process called non-homologous end joining (NHEJ) which will induce insertions or deletions that make the gene non-functional.

Scientists have tried this in cell cultures and found that they can indeed use ZFNs to edit both CCR5 and CXCR4 and these edited cells are resistant to HIV infection. Even more promisingly, this strategy also protects humanized mice which are immunodeficient mice that have human CD4+ T cells engrafted into them. When a portion of the T-cells are ZFN-edited, the mice show significant reduction in viral load and edited T-cells can be recovered, suggesting that they have a selective advantage.

Currently, clinical trials are underway. In these trials, a sample of CD+ T-cells is removed from the patient and edited with ZFNs and returned to the body. The hope is that these cells will create a virus-resistant reservoir that will preserve immune function. Of course, this therapy only applies to CD4+ T-cells and these cells won’t live forever, but extending immune function may prevent opportunistic infections and progression to AIDS in HIV infected patients.

ZFNs are already used for editing in a variety of research applications and scientists believe they show promise as a therapy for a variety of single-gene diseases.  Maybe ZFN editing will one day allow me to have permanently blue hair! I can only hope.


Alas, I have been too long absent. Seriously, my poor neglected blog, I haven't forgotten you.

I came back from vacation just in time to revise a paper, draft another paper and resubmit my F31. After all that serious science-writing, I couldn't summon the willpower to do more than whimper about science.

Now, however, various entities are casting their blood-curdling gaze upon my other work, so I have time to write here again. Cool science is on its way!

Monday, July 4, 2011

I'm a thinker, not a doer

Part 1:

Mr. Alethea, despite being twenty-something, had high cholesterol. I made him start running. Then I felt like a jerk for making him exercise while I never do. So, I started too, with Zumba and a Jillian Michaels DVD. (Parenthetical remark: I feel like an absolute fool doing Zumba, but it sure is fun, as long as I'm not in front of the mirror!)

Part 2: 

While home alone over a long weekend, I thought, "OK, I really need to release some endorphins and I've been on level 1 for like a month. I should try level 2." Yeaaaah. I'm pretty sure I will just ride my rolly chair around the lab tomorrow instead of walking.

Friday, July 1, 2011

Happy Dance

Today, I literally did a happy dance around the lab with my laptop (after I left my PI's office and closed the door). My data look super great and novel and all those good jargon-y words, even after averaging and showing them to my PI (who has an unnatural gift for popping my happy-bubble with requests for bigger Ns, more analysis, etc).

Now to get it published before I get scooped!

Thursday, June 30, 2011

No such thing as a dumb question

OK, at the time I was somewhat staggered by the dumbness of this question. I gave a talk about my work, in which I described how various ion channels could be inhibited and potentiated by a selection of anesthetics. Then someone asked, essentially: If a drug has the capability to depolarize a neuron, potentially leading to increased firing, it can't act as an anesthetic, can it?

Now, this dude, given that he must be in anesthesiology research if he was at my talk, should have known better. And definitely should have known better than to ask it as if he had stumbled across a trick question that would unravel all my research, because that's just jerk-y.

But it actually isn't a dumb question. Unconsciousness is much more complicated than simple suppression of all neuronal activity. During anesthesia, some neurons fire more and some neurons fire less. And the hard truth is - we're not totally sure which neurons do what or how that leads to anesthetic endpoints. In general what changes is firing PATTERN, which causes changes in how neurons talk to each other ("integration" for those wanting a more technically accurate term).

Consciousness and anesthesia are so much more complicated than simple reduction in total brain activity, but that's what makes it fun!

Tuesday, June 28, 2011

Federal regulations (a.k.a why your IACUC seems totally unreasonable)

It is a generally accepted belief that IACUCs as a whole and as individuals thrive on making animal use as annoying and difficult as possible, and derive great pleasure from rejecting, revising, rehousing and otherwise annoying animal users. I can assure you that, with rare exceptions, this is not the case.

Now, don’t get me wrong, there are a few animal users I’d like to have a little chat with. Like the pompous nitwit last month who sent me a one page “rebuttal” to my request for modification. I totted up his animal numbers, came up with 517, looked at his total of 617 and requested that he review his numbers. I got this >500 word rebuttal full of tables and equations and needlessly snotty language, I added them up again, still got 517.  I re-requested modification stating that his total was 517, the total on the rebuttal was 517 and the total on the protocol still said 617. Total waste of my time, total waste of his time, and totally his fault.

*Sidenote rant concluded*

The real reason our procedures are so darn convoluted is that we have to enforce federal regulations from multiple agencies, and they don’t always match. A priceless example of this emerged today.

1)   Animal users use gamma irradiators on some protocols. We are required to know where all animals go when they leave the animal facility, and to inspect all these places twice a year.
2)   Gamma irradiators are subject to increased controls, such that no one except for those certified as “Trustworthy and Reliable” (T&R) are allowed to know where the irradiators are, or who is certified to use them.

Long and the short of it, to uphold their laws, radiation safety wants us to permit irradiation users to avoid stating room locations and transit paths and to avoid inspection of these areas. We said no.

They said, OK, you can just let them not list the rooms. But then we still know who they are. And we have to inspect the rooms – without knowing where they are? They also said, fine, how ‘bout you have designated reviewers for irradiation protocols and we’ll just T&R a few people. We said sorry, we all have to have protocol access and the ability to conduct full committee review. Final answer: T&R the whole committee. And check up on the T&Rs every year. Honestly.

Also in our future – isoflurane badges? Does anyone else have halogenated-ether anesthetic monitoring for animal use? These drugs have hepatoxicity, the concern is that frequent use of anesthetics may expose humans to high levels of the drug. But honestly – we use these drugs on PEOPLE! To the point of unconsciousness! Is knocking out mice a few days a week really going to stack up to actual anesthesia?

The “Age of Enforcement” is going to be the death of me – the worst part is that it seems the majority of this enforcement is not directly about animal welfare.

Tuesday, June 21, 2011

Loaded Topic

I have the world’s most adorable little doggie at home, and I’m totally crazy about him. I am on my university’s IACUC (Institutional Animal Care and Use Committee), which I’m sure I’ll rant more about later. I use animals in my research. If I could eliminate the use of animals in research, I would.

In all likelihood, animal research is going to come up pretty frequently here, given my involvement. It’s a complicated issue, and easier not to engage, but it is ethically important for scientists to know what they think and continually evaluate to ensure they’re following best ethical practices.

I know that some extremist animal rights groups think that animal research can and should be stopped short, right this minute. Unfortunately, their arguments are pretty flawed.

Argument 1:

One big argument is that animal research hasn’t discovered anything beneficial to humans, or that all these things could have been discovered another way. This is simply untrue. Many important breakthroughs in disease treatment have been made in animal models. Farm animals, pets and endangered animals are also beneficiaries of animal research. Just Google it.

Argument 2:

Another major argument is that animals are not good models for humans and consequently research done in animals will have little relevance to human disease. Some such groups advocate for using cell culture or computer models only, instead of animals models. There’s a reason all these things are called models: they only approximate the human situation in key respects.

I’m pretty sure there isn’t a scientist alive who wouldn’t rather use a cell or a computer instead of an animal. Animals are expensive, require constant care, enormous amounts of paperwork, and specialized training. But sometimes they’re just better than a computer or a cell. The problem with creating a cell-culture or computer model is that you can only recapitulate the aspects of your system that you completely understand. But the whole problem is that we don’t completely understand most tissues or disease processes. So if you make a computer model that tells you everything we know about liver cancer, you won’t be able to cure liver cancer. The good thing about an animal model is that it’s a real tissue, that will act like a real tissue does, even in the ways we don’t understand. Unfortunately, it is true that animal systems aren’t exactly like human ones. This can sometimes be optimized by choosing the right animal, or creating a transgenic animal to better mimic key features of the human system, but even so, it isn’t perfect. That’s why it’s a model. The best science utilizes multiple modeling systems to eventually develop hypotheses that can safely be tested in humans.

Argument 3:

The hardest argument to answer, though, is the ethical/moral argument. Is it “species-ist” to treat a living thing from another species in ways that would be unacceptable to treat humans? Research makes it clear that vertebrate animals have experiences analogous to human pain, fear, pleasure and other emotional states. Rights advocates claim that these emotional and cognitive faculties make animal eligible for membership in the moral community with equal or near-equal rights to humans. This argument can’t be answered with facts or a utilitarian argument, it is about what an individual believes about the rights of non-human species. Even among anti-species-ist advocates, you can find dissent about which animals deserve what rights from worms to mice to monkeys.

Where I am:

I fall on the utilitarian end of the spectrum. Though I strongly support alternatives to animal use and sticking to the 3Rs when animals are necessary, in the end I conclude that the potential benefits of animal research outweigh the harm to animal research subjects. I think this campaign sums it up for me:

I chose to serve on my university IACUC to learn more about federal regulations concerning animal research. I got much more than I bargained for as I hear from many sides: from researchers, from regulators and from rights activists about balancing animal welfare with human welfare. There are never easy answers.

Scientists often feel pressure to justify animal research in the face of extremists who bomb, poison and mail razorblades to researchers, but most scientists will confess that it’s not a black-and-white issue. Respect for life at all levels, from proteins to cells to organisms, is central to biomedical research, and engaging with animal rights issues is important for animal users as we work to preserve the welfare of animals as best we can.

Monday, June 20, 2011

Reality - more magical than anticipated.

Piezoelectricity - a concept that is so cool I cannot believe I hadn’t heard of it until two weeks ago! I work with electricity, and figured I knew it all, but then the universe went and surprised me.

It didn’t start well. I was trying to set up a piezoelectric translator, which apparently someone used about 10 years ago, and it’s still kicking around the lab. it’s OLD, like the manual is type-written and comb-bound old. I read the (nearly useless) manual, and tried to set it up. It did not go well. Various parameters and parts did not function as anticipated. I finally diagnosed some of my issues, but my switching time was still much too long. So I thought, “I’m not a man, I’ll just call tech support.” Well, it turns out the thing is SO old that the company that made it doesn’t exist anymore, and the company they sold the manufacturing rights to doesn’t make this device anymore, and their tech support director was in China. But, you’ll be relieved to know that this story has two happy endings: First, I fixed the switching time after looking at pictures in a book about single channel recording (good news, reading is becoming obsolete!), second, I decided to look up PZT.

Throughout the (nearly useless) manual, they kept yapping about the PZT this and PZT that. Never mind that they never spell out this abbreviation anywhere in the entire manual. So I finally looked it up on Wikipedia, and it turns out to stand for “lead zirconium titanate,” and pointed me back to a page on piezoelectricity, and I was hooked.

So, here’s the basic deal – reality is more magical than anticipated. Tension and compression causes charge accumulation (measured as voltage). Turns out, the reverse is true too, application of voltage to said crystals causes changes in length. Piezoelectricity literally means “electricity from pressure.”
Crystals are made of atoms arranged in repeating blocks called “unit cells,” where the atoms in each repeating block are arranged the same way. Piezoelectric crystals have asymmetric arrangements of atoms in each unit cell. At rest, these crystals are electrically neutral, because the charges of the atoms are arranged such that each positive charge is balanced by a negative charge (really this has to do with dipole moments, if you’re into that level of detail). But when you squeeze or stretch the crystal, you upset this delicate balance of cancelling charges as you move atoms out of place, causing the crystal to have net charge on its faces. Same deal if you apply charge: you apply electrical force that makes the atoms rearrange in an attempt to cancel the charge, causing the shape of the crystal to change. This effect can be pretty large: applying 500 foot-pounds of force to a cubic centimeter of quartz can produce 12500 volts!

Not all asymmetric crystals exhibit piezoelectricity. Some naturally occurring crystals do, like cane sugar, quartz and topaz. Later, scientists began to create manmade crystals for commercial use, like my good friend PZT, which is a manmade ceramic.

Piezoelectricity – practically magic – but what is it good for? Turns out it’s everywhere, not just in science-y sounding equipment. In cigarette lighters, pressing the button makes a little hammer hit a piezoelectric crystal, which generates a high enough voltage that current flows across a spark gap to ignite the gas. You can also find piezoelectricity used in loudspeakers, inkjet printers, clocks, MRI machines and anywhere a cool little crystal motor might come in handy.

It makes me wonder how many other things I use operate on near-miraculous science!

Thursday, June 16, 2011

The origin of particular things

"Naming is the origin of particular things," said Lao Tzu, who obviously knew a thing or two, or people wouldn't quote him so much. There were many hurdles to actually starting a blog (which I have been idly contemplating for about a year). The obvious one, is of course inertia. But one of the most intractable was picking a name. I agonize over names, and like to name everything. My patch clamp rig still needs a name, but I haven't found one that encapsulates pure evil, capricious whimsy and occasional subservience.

Anyway, having finally determined the absolute best name, I would hate for it to be wasted on those who didn't grow up on gory mythology tales. (Seriously, every kid should be given mythology books! Murder, revenge, conspiracy, people with awesome powers and horrible disfigurements...) Thus, you shall be subjected to a short mythological explanation of my choices:

In Greek mythology, Mnemosyne was a Titaness, the goddess of memory, who is credited with discovering reason and language. The most well-known fact about her is that she slept with Zeus (after all, who didn’t?) and begot the nine muses. What is often forgotten is that she also presided over a river (or pool/well/spring) in Hades. The river of Mnemosyne was the opposite of the river of Lethe. Upon arriving in Hades, one would supposedly have to choose to drink either from Lethe or Mnemosyne. Choosing Lethe, the river of forgetfulness, would erase your memory of your past life and allow you to reincarnate. Choosing Mnemosyne, however, would make you omniscient.

My name, Alethea, again plays on the Mnemosyne-Lethe dichotomy. The Greek word Lethe means “oblivion” or “forgetfulness”, while Alethea is derived from the Greek word for “truth” or “un-forgetfulness.” I hope it’s obvious which Kool-Aid I drank! J

N.B. I love parenthetical statements. I know it's bad English. And I don't care.

Wednesday, June 15, 2011

I'm a grad student

This is what it's like. Today I peeled frog eggs with tweezers, then sat in what used to be a closet (now "renovated") full of patch clamp rigs, in the dark, with two other grad students, for most of the day. It's no wonder we lack balance.

Why hello!

Dear Internetz,

I'm a 4th year PhD student at a research university. As such, I am naturally possessed of an abundance of both angst and opinions.

Last night I had a total meltdown about my life, because let me tell you, even if you don't have kids, there is no such thing as work-life balance when you're in grad school (or probably if you're in academia at all)! Then today, as I watch my seal resistance aimlessly climb to 900 megaohms and hover there without getting a gigaseal for about the millionth time this week(I do patch clamp electrophysiology), I realized that I needed a better outlet for my rage than my poor husband.

Hence, I am officially "on the internet." Here, I will tell you what life is like as a female grad student in an all-male biophysics lab, rant about my life in general, and post the cool stuff (research, comics, videos) that helps me remember why being a scientist is worth it.

So, if you like blue-haired snarky biophysicists, you want to hear what science I think is awesome, or you just wonder why grad students are such basket cases, I hope you'll stick around!

Alethea (not my real name)