30 March, 2009

Who's Got the Giggly Munchies?

I have no comment on this figure as I was far too busy laughing. Click to open a larger version.

Central and Peripheral Signaling Mechanisms Involved in Endocannabinoid Regulation of Feeding: A Perspective on the Munchies
Keith A. Sharkey* and Quentin J. Pittman
Sci. STKE, 29 March 2005
Vol. 2005, Issue 277, p. pe15
[DOI: 10.1126/stke.2772005pe15]


28 March, 2009

Pretty Pictures That Toaster Takes (SFW?)

Immunofluoresence microscopy is one of my absolute favorite laboratory techniques. The method I use takes about 4 days and time for the slides to "cure", and during that entire time there is absolutely nothing I can do to tell whether or not the technique is even working at all. So I always seat myself in front of the microscope with bated breath, peering in hoping desperately that I haven't just wasted so much time and effort for no results. But, unlike an ELISA, which also takes lots of little invisible steps, the results of immunofluorescence microscopy are often absolutely stunning. I sit in that darkened room alone with these brilliant snapshots of life itself glowing below me as I feebly try to capture their gorgeousness with a camera. Compared to everything I've done so far in science, this is molecular biology at it's most palpable, it's most real. So much of my job consists of moving tiny amounts of one solution to another suspension and spinning it down and waiting and repeating and counting...all invisible stuff. I feel so often like I'm trying to find truth at the bottom of a dark chest with my eyes blindfolded, ears muffled, nose plugged, and hands encased in bubble wrap. When I do find something there it's like touching a loose vacuum tube* and that victory sings along my nerves electric, reawakening out of poor data's despair and repetitive boredom that fundamental hunger for discovery, a thrill of small but bottomless adventures. I study molecular biology not just because I'm an easily captivated nerd in search of shiny things, but because molecular biology is life itself vivisected out in all of its wonder and glory. It's not just difficult and complex, it's the biggest puzzle humankind has yet found and by doing science I am hewing the pieces of that puzzle out of raw ignorance and curiosity into elegance and grace.

Immunofluorescence microscopy, for me at least, bypasses all the trudgy serial dilutions and quantitative cell culture and patches me directly into that holy place of rare wonder and quintessential awe.

Below are a few of the hundreds of pictures I have taken over the past several months. These are all scientifically useless: control slides and slides where the concentrations weren't quite right or just not good enough for inclusion in practicable data. I've loaded each of these as large .jpegs, so if you'd like to download them I can assure you they make for excellent desktop backgrounds.

This is a frozen section of mouse stomach at 100X. The mouse was a germ-free C57/B6 infected with H. pylori and a unique microbiota that we're studying. The picture is at 100X. This is from a test-run I did on stomach tissue to make sure the same immunofluorescence staining protocol I use for mouse ceca works in this tissue type. We can't use this picture in any kind of data or results because it is, by and large, a mistake (pretty nonetheless, though). The red is an APC-labeled anti-mouse CD11c antibody and the blue is just the DAPI (therefore showing DNA) that came mixed in with the Promega Gold Anti-Fade Reagent.

So why is CD11c showing up so well on stomach parietal and smooth muscle cells when it's primarily a marker for dendritic cells?

There're a couple of reasons. First, according to other labs in our working group, CD11c antibodies have to be at a really high concentration to detect dendritic cells well (e.g., 1:10 instead of the 1:400 shown above). Secondly, Fc receptors bind antibodies. Fc receptors are most commonly associated with innate immune effector cells such as dendritic cells, macrophages, natural killer cells, and neutrophils; however, Fc-gamma receptors are widely expressed by several different cell types in diverse tissues. I didn't use any Fc blockers in this particular slide, so the Fc-gamma receptors likely present on the parietal and smooth muscle cells probably bound up my mouse IgG antibody (reason #1 there's high background). Thirdly, I used a mouse antibody in mouse tissue (reason #2 there's high background, also a stupid move on my part). Fourthly, I pulled out my old IF blocking buffer and used it without remembering that it contains normal goat serum instead of normal mouse serum (reason #3 there's high background). I might as well have not bothered blocking at all. Fifthly, these antibodies have only been tested, in the literature and our lab, for flow cytometry and not immunofluorescence microscopy. This last point is the win for the picture as it demonstrates we can use flow cytometry antibodies for this project, which is really really really convenient as it standardizes our data. That being said, however, I recently found out that rabbit anti-mouse monoclonals are coming onto the market for several CDs and if I hear that they do a better job than mouse anti-mouse CD antibodies I will not hesitate to use them instead (although if i do I'll probably wind up doing a direct comparison of the two by flow cytometry).

This is a section of mouse cecal wall. In this one the red is an AlexaFluor 597 phalloidin that binds to actin. Blue is DAPI again. This is a control slide where I was trying to find the optimal concentration of the phalloidin to label actin in cecal epithelial cells. Here the concentration was too low and only clearly labeled the actin in the smooth muscle that lies under the cecal epithelium. The DAPI to the left of the smooth muscle shows where the epithelial cells should be.

Same thing, different field.

Here I got the phalloidin concentration just about right to stain the epithelium. Also, a different person cut these blocks into slides and got much nicer sections without destroying the tissue architecture (it helps when the person operating the cryostat doesn't melt down the OCT and rearrange the tissues to their liking). When we took this tissue from a mouse infected with E. coli O157:H7, we cut along the inferior curvature of the cecum, spread it flat open, washed with 1X PBS three times to wash away food gunk (because that shit autofluoresces) and unadhered bacteria, and cut a ~2mm wide strip of cecum down the length with a scalpel. Then we took a Q-tip swab and rolled the tissue around the end like a cinnamon bun (my boss calls them "Swiss rolls") before embedding it in OCT (like clear syrup that keeps cells from bursting when they freeze) and slow freezing in a -20C freezer (as opposed to snap freezing in liquid nitrogen). The green in the picture above is from a poly-clonal goat anti-E. coli O157:H7 lipolysaccharide. The little green dots along the thicker actin lines (tight epithelial junctions) are enterohemorrhagic E. coli O157:H7 that have stuck themselves to the cecal epithelium (the mechanics of which are discussed here).

*I've done that, once. I was testing out an old Fender bass amp. It was a beautiful amp, 4 10" speakers with a tweeter, sounded great on a 4-string bass, tight and punchy where you can feel the rumble right in your diaphragm. But I play a 5-string bass and it lacked good low-end definition; also, I prefer to run my rig at settings that place the bass rumble firmly in one's duodenum. The vacuum tubes of the amplifier were placed right next to the on-off switch on the back of the amp head where I could see it, so when I went to turn it off I groped too far to the right and wound up feeling up the vacuum tubes' loose connections. I was knocked flat on my ass.

27 March, 2009

Fragments of Toaster's Mind Blather

1) Debating ethical-ness of studying non-work stuff at work. I already carry around my Janeway's Immunobiology with me, so why not my Llama Book as well?

2) Finished -80C freezer inventory. No one had ever done so and my PI has had the freezer for ~15-20 years. I found tubes that contained the entire GI tract of mice in there, not to mention the many other unidentifiable things floating around (take note: if you're putting it in long term storage, clearly label what it is. "17" is not a valid label!) Now, unfortunately, I'm sorta bored.

3) I only have 2 projects right now, and they're both sidelined waiting on reagents/supplies. The lab is rather clean, too. See Fragment #1.

4) Does anyone have any wise tricks for dealing with student loan companies?

5) I'm going to go see Monsters vs. Aliens tonight!

6) I tried stopping eating cookies and burritos for 2 weeks not long ago and promptly lost 5 pounds. I promptly introduced doughnuts, pie, and pie into my diet and have managed to get 3 back. I'm becoming resigned to the idea that my ribs and hip bones will always be highly visible until I hit the mid-forties.

7) Sooner or later I'm going to wind up shanking a jogger. Not because I want to, mind you, but because that's what you get when you manage to sneak up on Toaster. Normally I can hear them coming many yards away (and smell them; for some reason many of the female joggers spray themselves with some kind of flowery scent before they leave, which I suppose is better than poop), but there's one part of my plod home that's really traffic noisy and I can't hear them when they're running on the grass. One surprised me recently and I had my umbrella out of my coat pockets ready to take out his knees before I realized what exactly was going on.

8) I realize that I've come to the age where little children no longer regard me as being just a big kid and now think of me as an ominous adult. Maybe it's just that children are inherently wise enough to avoid asking a Mad Scientist what's in his backpack.

9) OK, honestly I don't know what's in there anymore either. Let's investigate:
2 mechanical pencils
1 tattered index card with the word "gonads" written on front
1/2 bottle Pepto Bismol
8 chewable doses of ivermectin
1 green hair Scrunchie
1 blue hair Scrunchie
1 pair black and grey striped fistwarmers
1 pair blue striped knee socks
lots of batteries
Everlast brand fisticuffs
1 dirty Tupperware container from several months ago
several plastic bags (dog poop bags?)
1 empty envelope
1 burned copy of the Big Lebowski (unwatched and unlikely to be)
5 official transcripts
1 Janeway's Immunobiology, 7th ed.
1 old sketchbook from cartooning job containing various obscenities and stick figures
1 ream of unread papers
2 bars of graphite
3 1m-long high-tension rubber bands

10) Mercifully self-censored complaint about the fit of my underwear.

11) I need to write myself a Perl app and install it on all the computers I use to remind me to eat. Due to a self-experiment that I've not yet blogged, I have developed a rather extreme tolerance for hunger. I have caught myself going 14+ hours without food before realizing that I actually am hungry. Often I don't remember that I haven't eaten in quite a while until I have real hunger pains. And before you tell me that maybe that is why I am scrawny, it should be noted that when I eat it is usually best measured in kilograms and what it is would make a nutritionist cry (e.g., just the other day I discovered how delicious chocolate chip peanut butter sandwiches can be).

26 March, 2009

Luciferase Shampoo

I just attended a departmental seminar where the guest lecturer presented data showing that transcutaneous vaccination works from DNA vaccines. Apparently, if you abrade the skin to remove the stratum corneum and rub on a transfection plasmid with your desired DNA (best to use a fusion protein, methinks) that has been stuck inside liposomes, the hair follicles will take up the DNA and use it. This apparently produces antigens inside the body and activates dendritic cells to take it up, process it, and go activate T cells to start a humoral immunity response. This has been demonstrated in mice.

Previously I had had no idea that mouse hair follicles are much smaller than human hair follicles. Nor did I know that ~80-90% of hair follicles on a human scalp are usually in growth phase at any given point. DNA vaccines have so far been shown to work best when they're applied to skin in which the hair follicles are in anagen (growth) phase. Therefore, it stands to reason that the human scalp would be a convenient portal for localized transfection.

As such, I need volunteers for 2 experiments.

1) Balding. There are demonstrated links between testosterone and alopecia. It is thought that testosterone is somehow acting upon hair follicles in middle age to cause them to somehow stop growing. But if we could make a fusion gene for the testosterone receptor coupled to nonfunctionality, we could theoretically block that signal and prevent testosterone-associated baldness at the scalp. However, in the interest of transparency, it should be acknowledged that there is a small chance that the testosterone knockout genetic construct will get into more places than just one's scalp, but also possibly other rapidly dividing cells. Other rapidly dividing cells include those in the skin and gut epithelium, where a loss of testosterone receptivity wouldn't do much, but also Sertoli cells, which could indeed cause infertility. However, as Leydig cells produce testosterone itself in response to luteinizing hormone and follicle-stimulating hormone, systemic testosterone shouldn't be affected and no loss of virilization should occur.

2) Luciferase Shampoo. I don't know about you, but I think I'd look quite nice with glowing bright red hair. If adding the luciferase gene to a liposome and getting that to hair follicles could result in expression of luciferase, then great, we'd be able to get glowy hair! However, there is a very real possibility that doing this would only result in glowy hair follicles, which could still be kind of cool (light tends to shine through and off of my blonde hair, so in effect it might look like a translucent pink cloud, like fiber optics).
1. Luciferase transfection vector inside liposomes.
2. CaCl2
3. HEPES buffer
4. Glycerin (might as well make functioning shampoo whilst we're at it, no?)
5. Fragrance (anyone know how to synthesize the scent of melting lemon drops?)
But first, I need volunteers! Mad Science Law #9 may be waived if I get volunteers. Or maybe I should just get the DIY-Bio people to do this for me.

25 March, 2009

Not-So-Mad Science: IL-13 vs. IL-4 In The Battle For Asthma!

ResearchBlogging.org(Previous asthma research-blogging here)

Marsha Wills-Karp, Jackie Luyimbazi, Xueying Xu, Brian Schofield, Tamlyn Y. Neben, Christopher L. Karp, Debra D. Donaldson (1998). Interleukin-13: Central Mediator of Allergic Asthma Science, 282, 2258-2261

The worldwide incidence, morbidity, and mortality of allergic asthma are increasing. The pathophysiological features of allergic asthma are thought to result from the aberrant expansion of CD4(+) T cells producing the type 2 cytokines interleukin-4 (IL-4) and IL-5, although a necessary role for these cytokines in allergic asthma has not been demonstrable. The type 2 cytokine IL-13, which shares a receptor component and signaling pathways with IL-4, was found to be necessary and sufficient for the expression of allergic asthma. IL-13 induces the pathophysiological features of asthma in a manner that is independent of immunoglobulin E and eosinophils. Thus, IL-13 is critical to allergen-induced asthma but operates through mechanisms other than those that are classically implicated in allergic responses.

There are many morbidly fascinating pathological changes associated with onset and clinical asthma. To wit, these include eosinophilia, mucus overproduction, mast cell/other inflammatory cell airway infiltration, and increased smooth muscle. There may also be scarring of the airways.

From what I currently understand about it, airway hypersensitivity generally happens after immune effector cells have infiltrated the underlying airway tissues. When these effector cells, which can include allergen-specific T-cells, mast cells, eosinophils, basophils, and even macrophages, are activated by an irritant (the allergen) they more or less cut loose and let wild with the localized inflammation. The localized inflammation, in turn, leads to more immune cell infiltration over time and concurrently the tissue itself undergoes histopathologically apparent changes, including thickening of the base layer of smooth muscle.

For example of immune effector cells getting activated, let's consider the most dramatic case: the mast cell. Mast cells are a type of white blood cell that expresses Fc receptors for IgE (IgE is the immunoglobulin most associated with allergic and anti-parasite responses) on it's surface. The Fc-bound IgE act as allergen-specific receptors that, when bound to their ligand, send a signal into the cell to degranulate. Mast cells store relatively massive amounts of inflammatory cytokines and peptides in large granules (e.g., histamines, prostaglandins, and leukotrienes) and they can, effectively, disgorge them all at once. This can lead to a very rapid spike in the systemic concentration of inflammatory effector molecules and subsequently extremely rapid onset of asthmatic symptoms. The same process is at work in acute food allergies.

Figure A: The mast cell is the one with the big lumpy nucleus in the center. The black dots surrounding it are granules packed with inflammatory molecules, just waiting to be released and wreak havoc. Those other 2 cells to the right are lymphocytes (according to the original caption on this TEM).

But what inflammatory molecules are required to invoke and/or sustain a hypersensitive airway response?

This paper examined the role of IL-13 in allergic asthma. According to Janeway's Immunobiology, IL-13 is involved in the differentiation of naive CD4+ T-cells into TH2 cells, which have been shown to be more involved in allergy than TH1 cells. IL-13 is also secreted by TH2 cells, apparently, and has been shown to have a direct effect on airway epithelial cells by which their proliferation in increased and differentiation into goblet cells (goblet cell metaplasia) is increased, which in turn leads to the increased mucus production seen in allergy and asthma. And when your organs are infected with multicellular parasites, IL-13 is there to help the organs make the changes they need to get rid of those parasites. And as if that weren't enough, IL-13 also increases smooth muscle contractility.

But IL-13 doesn't really do anything without the context of a TH2 immune response. Th2 cells are characterized by secretion of IL-4, and it should be noted that IL-4 and IL-13 share a subunit in their receptors.

Figure B: The left column has a normal lung biopsy (top) and a normal airway (bottom) from a Tbet+/+ mouse. The right column has the same measurements, but showing airway inflammation with lymphocyte and eosinophil infiltration (top) and remodeled airway with increased collagen (bottom) from a Tbet-/- mouse. The picture is blurry because I took it with my phone. It is from Janeway's Immunobiology, 7th ed., page 575. Tbet is a transcription factor that is necessary for the development of TH1 cells, so its abscence will invariably result in a TH2 inflammatory response (right column). Tbet is analogous to GATA3 in TH2 cells.

Allow me to explain T-cell differentiation really briefly:
1) Naive T-cells arrive in thymus.
2) Naive T-cells have to decide whether or not to be CD4+ or CD8+, which will result in being able to recognize MHCII or MHCI, respectively.
3) CD4+ T-cells get stimulated by DCs or stuff, and the resulting cytokine mileau determines whether they become TH1, TH2, Treg (also refered to as TH3), or TH17. They can also become memory T-cells of any of those variety later on in. Respectively, these cell types are characterized by secretion of IFNg, IL-4/IL-5, IL-10, and IL-17.
4) TH1, TH2, Treg, and TH17 all more or less have distinct biological roles, although the cytokine soup that gives rise to different types is messy (e.g., IL-2 just drives T-cell proliferation irrespective of subset) and often overlaps, and they'll even compete against each other (IL-12 drives TH1 proliferation but inhibits TH2 proliferation while IL-4 does the same for TH2 cells).
So, anyway, the group behind this paper found that while IL-4 is sufficient to initiate asthmatic events, IL-13 is required for the development of the airway hypersensitivity response (AHR). They used the standard ovalbumin (OVA) induced model of AHR and found that blocking IL-13 with an neutralizing fusion protein prevents the development of AHR. Apparently blocking IL-13 in mice who already have AHR results in their measures of AHR decreasing (specifically goblet cell metaplasia and mucus production). However, with all of this, blocking IL-13 had no effect whatsoever on net circulating IgE or eosinophilia.

These findings prove that IL-13 has a significant role in asthma. But they also imply that IL-13 does not play this role through classical allergy pathways, as IL-13 is found to be elevated in patients with both allergic and non-allergic asthma. This is further supported by the group's finding that daily intratracheally administration of IL-13 is sufficient to induce asthmatic pathology even in the abscence of antigen sensitization.

What I wonder about here is: how does it make biological sense for a molecule involved heavily in the production of allergen-specific TH2 cells to also operate completely independently of that cellular phenotype?

But what is important to human health is that this paper demonstrates that adminstration of IL-13 agonists or blockers may be of great therapeutic value to human asthmatics. This paper is 11 years old, and I don't currently know if anything has come of their findings, but still, it'd be cool if this really did have therapeutic value because, as my last post on asthma discussed (link up top), inhaled acute anti-inflammatories may only be getting to the pieces of lung that need it least (because they're the pieces that can still pump air, and if reacting tissue isn't pumping tidal volume, how can inhaled medicine get to it?). If this could be used daily as a preventative, I think it could greatly improve the quality of life for asthmatics everywhere.

24 March, 2009

Actual Action Ranty Rant #1

As a Mad Scientist, the temptation to unleash my wrath upon those who annoy or piss me off is sometimes very great indeed. As such, I usually try to sleep on it when my spleen feels to need exploding, and if I'm still a handsome kettle of seething rage in the morning I figure it's worth letting fly (zeppelin!). I've even had 3 donuts and a burger and a half (unfortunately I didn't have the donuts when I had the burgers, so I couldn't use them as a bun. That would've been delicious!) to make absolutely sure I wasn't just cranky from low blood sugar or some such crap like that.

However, the thing that currently has me so pissed off is rather too public for actual action, so I'm going to have to let the following Ranty Rant suffice.

This rant regards the overpriced and overpretentious grocery store Whole Foods. I will begin by disclosing that I do go to Whole Foods to buy turkey sausages (Toaster doesn't eat cows because they never did anything to him, nor pork because it didn't deserve the ill fate of being so tasty; venison, however, is fair game) because they are the same price as Trader Joe's, and they have chorizo, which is delicious. I also buy bulk grains there. With that in hand, I am going to tint this window with a slight hue of hypocrisy.

As I was leaving Whole Foods with a paper bag loudly telling me how it's 100% recycled and that I should definitely recycle it as soon as I possibly could (green-washing, anyone?), I noticed that they were selling canvas grocery bags with the (paraphrased) words: "FEED THE CHILDREN OF THE WORLD!"

For real. Now, first note that I don't have a problem with the message emblazoned on the bag, because yes, the children of the world should be fed, and so should the adults and geezers. However, note secondly that I have a huge problem with this kind of fake socioenvironmentalist bullshit. Thirdly, I also have a problem with the kind of bougie asshat who buys that kind of shit and then prances around like the sun shining out their ass has given them an orgasmic wedgie*. They are a bunch of plinking facile douchebag noodley rotten overtan lardass colostomy bags.

Some bougie motherfucker who has never really been truly hungry** is going to go to Whole Foods, which specializes in petroleum-drenched, overpriced, overproduced food flown in from developing countries all over the world, pay a premium on their groceries so that they can feel better about the rest of their wastefulness, and then on their way out to their newer model SUV note that they shop there often enough to need a canvas bag. So they buy the one with the socially aware message that gives $2 to some humanitarian aid organization so that they can feel additionally special and like they're saving the world when in reality, if they'd walked their fat asses to Trader Joe's or Kroger they could have helped a hell of a lot more hungry children by donating the money they'd saved directly to the same organization.

This is fake concern at it's worst. These bougie asshats are the very same who patronize bullshit coffeehouses and walk around with their thumbs firmly lodged up their asses, listening to their iPods and looking down their nose at everyone around them (seriously, the next person who tries to talk to me with one or both of their earbuds still in their ears is going to have to extract said earbuds from his sinuses). I've listened to their shallow bullshit conversations in the past and I avoid overhearing them anymore because I inevitably feel a strong urge to kick them in the throats because all it is is a bunch of sophmoric swaddle about how each of them is hipper than the last ("OMG [wait, remember you're too hip for that, but play it cool like you're being ironic], check out these new shoes [puff on cloves cigarette], they cost, like, $100 [it's OK, daddy gave me a credit card] but they were fair trade [adjust boutique vintage hat] and made with organic cotton!" like it's pixie unicorn dust magic). People who bitch and moan that they're starving when all they've had is a motherfucking latte in the past 4 hours and now they need some motherfucking hummus and organic whole wheat crackers. The people who buy a bag saying "FEED THE CHILDREN OF THE WORLD" and fill it with food taken from those children's countries***. Not to mention that they're buying this shit while children starve right here in this country.

This isn't coming across nearly as angry as I feel it. I tried not to resort to unbroken streams of cursing and eleventies. Hmm...maybe /RANTFAIL.

*Wonder what kind of search terms that's going to get me. Here's a chaser for your mental image.
**What I mean here is the kind of hungry that you get when you don't have food and can't afford it and can smell someone else's tasty lunch and your stomach has absolutely nothing in it at all and is knotted up and chewing on itself. I mean the kind of hungry you get after weeks of watered-down food. I'd like to see one of these bougie bastards try to make it just 24h with no food at all, and no motherfucking replacement power shakes or other such bullshit. Maybe then they wouldn't have such stupid ideals for skinniness.
***Look at many tropical countries that grow commodity foods such as plantains, pomegranite, etc. to export to post-industrial countries that then have to import essential foods from industrial agriculture in those post-industrial countries. A good example of this may be El Salvador and the U.S..

23 March, 2009


Figure A: Toaster would rather be here than where he is.

The picture above is of the Current River in the Ozarks. This river is generally noted for its clear water and gravel bed, and it's fed by lots of springs that have carved floatable caves out of the bluffs. I would currently rather be there on a kayak than here in the lab starting another week's toil. Alternatively, it'd be nice to be breaking my ribs on the St. Francis River spring shut-ins*.

*Shut-ins = Ozark colloquialism referring to sections of streams or rivers that run rapids through narrow gorges (~<1m wide), usually occur in parallel sets and often have chutes and drops. Also used as early water slides.

20 March, 2009

Audio Monstrosity #2

Toaster has been up to nefariousness for the past couple of hours (2.5h, to be exacter). This is what inevitably happens when he's left up to his own devices. You see, I have created yet another Audio Monstrosity! But this one is better. Much better! Although it's not finished yet, either...


In this track, I programmed the drum machine myself (I generally don't like using loops), played the guitar myself (which is why it's so bad) and the bass guitar myself (which is why it's so good). I know, there is a buzzing, but I wasn't able to process that out as it seemed to be part of the feedback from the distortion I was using on the guitar. My equipment is rather limited, so I do the best I can.

Here is the track: Mad Scientist Personal Ad!

Here are the lyrics:

Toaster Sunshine, Personal Ad, Take 9

The life of a mad scientist is so sad and lonely
All of my best friends live in formalin jars, you see

So I took out this personal ad
As an appeal to all the hot science ladies
You know, I might be mad
But that doesn't mean I'm all bad
At least not for you, baby
I'm about six feet tall
With a slightly hunched back
Uh, my hair's pretty wild
But, you know, I know that
I enjoy long walks
Through the city ruins
After I've destroyed it
Um, I love the smell of Tesla coil in the morning
Um, my hobbies include orchestrating my enemies' doom
And, building weird devices
The more devices I can fit into one chassis, the better
So I really hope you like electronics
And if you know how to solder, it's a plus

Did I mention I have a zeppelin?
Because it's a really cool zeppelin!

I'm a mad scientist
Lookin' for love
Your legs need to be as sexy as your brain
I'm a mad scientist
Just looking lookin' for love
Want brains so full and curvy
I want your brains wrinkly
I want your brains smart
I want your brains so juicy
I want you in my heart

I'm a mad scientist
Lookin' for love
Your brains gotta be as hot as your legs

Call me.

This one is downloadable!

I have also uploaded a couple of older tracks, "Zombie Cookie" (lyrics: "I am a zombie, give me a cookie!") and "Dishware Flossery".

Story of Toaster: Self Experimentation #1

Looking back, even though I sometimes wanted to be an astronaut or an architect, it becomes apparent that I was fated to become a scientist. And it manifested rather early. For evidence of that, here is the story of Toaster's First Experiment.

Or, well, at least the first experiment that I clearly remember doing. There may have been others before that, but as I was a child prodigy at dropping heavy things onto my own head I don't remember them.

Young Toaster, aged ~5. Hot Southern summer*, I was left to play alone in the backyard. I was very good at this, busily digging holes, hoarding things in the shed, and collecting pillbugs. I had recently tried to dig a tunnel under our neighbors' yards (this failed).

So I was casting around for something to do when I noticed that it was difficult to breathe in the very hot humid summer air (typically >40C + 70%+ humidity). I noted that air was coming out of my mouth and my nose, but not the other holes in my head.

Because the holes for my eyes are already filled up with my eyes, I logically cannot breathe through them. However, there is nothing filling up my ears, so I should be able to breathe through them.

Test 1:
I held my breath very tightly and even closed my eyes to make sure no air leaked out (just in case). I pinched my nose shut and tried to force air out my ears.

Result 1:
No air went through my ears.

OK, it's not easy, but that doesn't mean it's not possible.

Revision Tool:
Piston-style air pump found in shed**!

Test 2:
I held my breath again like before. And I held the air pump to my right ear and tried to pump air in mechanically.

Result 2:
Young Toaster runs into the house trying to scream over the sudden painful ringing in his ears. A visit to the doctor revealed that I had managed to puncture my eardrum membrane when I didn't account for the pointy tip of the air pump moving toward my ear when I pushed down on the plunger. The tinnitus lasted for 2 weeks and thankfully my eardrum healed. Interestingly, my balance was off during the entire acute phase of the tinnitus. Incredibly (because walking was [and is still sometimes at any level of sobriety] a dangerous undertaking for me), I managed to not further injure myself, I think. Sometimes I still get transient tinnitus.

Once cannot breathe through their ears, either unassisted or with mechanical help, no matter how much they may wish to.

**One of the few days where we weren't inside hiding from these.
*At this point you probably already knew how this was going to end: Badly.

18 March, 2009

Not-So-Mad Science: STEM Education

In lieu of your normal Wednesday Cyber Journal Club Science Blogging, I offer you the following:

Most everyone agrees that Science, Technology, Engineering, and Mathematics education in the U.S.A generally sucks. We often rail against Teh Stupidz of the masses and their ignorance of basic scientific concepts and principles and in doing so we frequently make the masses out to be lazy. I don't think they're lazy necessarily, I think the public school system and society as a whole have failed them. And to a degree, by extension, we as scientists have failed them.

Certainly, we can spend our time debating the global warming deniers and proponents of creationism or the vaccine-autism link. A vigorous debate is necessary to discredit the dishonest irrationality of the opponents of scientific knowledge and progress. However, I posit that directing the bulk of our attentions and energy to this task is stupid. Stupid because it is ineffective, like waiting in the wings with a tourniquet and bone saw as we watch clumsy children try to juggle chainsaws. When we spend so much time interfacing with and disproving the few loud idiot voices in the crowd, we are doing a disservice to that crowd by ignoring it. In effect, we are fighting the flawed output instead of striving to better the input. Doing so would stem the tide of ignorance and intellectual laziness.

I'm not saying that this is all on us scientists' shoulders per se, at least not exclusively. We're a busy profession, trying to conquer save the world by engaging in deeply imaginative and technically practicable play. The worlds inside our labs, our offices, our Ivory Towers are our cherished sandboxes, and as such we are reluctant to leave them and face the bitter reality that we cannot well communicate with...well, anyone who isn't also a scientist. We are a deeply insular and idiosyncratic culture and to a degree this is why we thrive in the right settings. But we need to come out of this shell and start real dialogues with interested citizens, nosy neighbors, and especially students.

Our society has forgotten the value of independent, creative, critical thought and replaced it with iPods and whatever clothing brand is popular today (Baby Phat?). We make public school students jump through the flaming hoops of standardized tests of regurgitated facts and teach through prime-time TV advertisements that instant gratification and consumerism are far more valuable than meaningful education or thoughtful pondering. We teach the dates of the important battles of the War of Roses or the American Civil War, but we neglect the causes of why those factions marched on each other in the first place and we fail to examine the consequences of those battles and wars. We teach the DNA is a double helix with 4 different nucleotides that pair specifically, but we don't talk very well about why a double helix is optimal or what difficulties it might pose. We teach physics as ballistics fun fun time and don't talk about how the application of electromagnetism has revolutionized the entire world.

Ultimately, we are substituting meaningful discourse on the Whys, the Hows, the What Ifs, and most importantly the Why Nots, for boiled-meat-and-potatoes Whats and Whens.

This represents a deep and disturbing failure to teach Critical Thinking and to foster Curiosity.

Society: FAIL.

We as scientists, ostensibly working for society, have an obligation to make that society smarter, or at least more curious. Why aren't more of us out there on lecture circuits in local libraries and community centers giving layman's presentations on basic scientific concepts, such as the nature of electromagnetism or what a gene actually is and how it works? Yes, we are nerds, but we are damn sexy smart nerds, and if we can figure out which molecules bind what cells or how to make a 100ton metal airplane fly through air, then we can damn well figure out how to talk to normal people!

We should be! So get to it!


I believe that TV is a useful barometer of cultural conditions, especially children's TV. I still watch cartoons, and I have noticed that the science content in cartoons has sharply declined over the past 10 years. 10 years ago we had Dexter's Lab, Pinky and the Brain, and Bill Nye reruns. Then for a couple years there was Jimmy Neutron. And now all that remains is Johnny Test, who is the favorite guinea pig of his twin scientist big sisters, and the "science" in these episodes is just plain stupid. I mean, even stupider than Dexter's Lab, which was at least entertaining. So do you think that maybe the absolute decline of children's science programming is reflective of a devaluation of the place of science in society?

17 March, 2009

How Deeply Do You Focus the Lens?

I have another post brewing, basically the other shitkettle that's stinking up my life at the moment. It's even written. However, it's dark and deeply personal, and I'm still trying to figure out just how much one can/should let leak from behind the mask of their blogonymity.

So, dear apprentices, how do you balance connecting with your readers as more than a witting wordy pontiff and feeling exposed?

I'm aware that each of us must choose how much of our real lives to reveal. I intend to write more than mere Mad Science Lulz, but at the same time, do I want to invite you all to examine the light at the end of the tunnel between my ears? This is the question I am currently wrestling with, and perhaps your experienced wisdom/bidness could lend me a hand.

15 March, 2009

Useful Uses for Anger

I have been rejected by all the institutions to which I applied for graduate studies.

Family and friends keep asked me if I was OK about it, and I told them that yes, I'm just peachy because there's always next year (there is, right?). But I'm not. I guess in reality I'm kind of torn up by this, as well as mightily pissed off, but I don't tell them this because I don't want them to worry and I don't want them to see just how much I care because then I think they'd share in my disappointment. I have an uncle or two in Scandinavia that I think went to graduate school, but I'm fairly sure that they went for professional degrees. But of the family that I grew up with here in the States, no one else has ever gone to grad school. And they're all looking at me expectantly smiling and prodding me on, expecting me to set a gleaming example for the younglings of my generation (I'm the eldest of the current generation). And in addition to this pressure, I put myself under more, muttering fervently the exhausting mantra: "Do more, be better!"

Failing to get into grad school, failing to even get so much as an interview, is not doing more or being better. And because of this I'm not so much pissed off at the institutions (they had very few spots, I understand) as I'm angry at myself. Angry at not selling myself better. Disappointed that I didn't find the wonderful advice that Eppendork, Dr. Isis, PhysioProf, Ambivalent Academic, et al have shared with the world via their blogs.

Part of this, I know, is that I am sick of being stuck in small-city Midwest, sick of the same grey weather, sick of the same fucking patterns of everyfuckingthing. Especially sick of the bougie locals who think science is just cute. But it's also largely that I'm restless, I want to move on, and as far as I am willing to see, the only direction to move on in is up.

But a larger part of it is that I am having a hard time separating my self-worth as an aspirant scientist from being rejected.

I want so badly to tear through some new applicable literature*, to sink my teeth into a new set of experimental skills and shake the living shit out of them until they splatter beautiful data everywhere, to learn further and deeper and have peers with whom I can discuss it all, to design and fail and design and fail again and again until I have hammered out elegance! Most of all, I want to be challenged!

The anger I currently hold is of a useful sort. I can use it as fuel. It was anger at being trapped in an endless surburban tract with people who cared more about their lawns' green-ness than the dynamics of molecular orbitals that motivated me to do well in high school so I could get the fuck out of the South**. It was anger at national politics that caused me to harrass the university newspaper's cartoonists until they let me into their club, and that later got me condemned by Catholics, fundamentalists, and Republicans across campus.

So it is this anger, me being mad at being mediocre, that will have me kicking in doors this coming summer and contacting specific professors instead of relying on the sparkliness of specific programs. It is this anger that will have me dissecting my essays several more times, and maybe even being more careful with whom I ask to write letters on my behalf. I am going to beat down the door to academia, even if I'm not sure I want a post-postdoc career in it, with manners and all the charisma*** I can muster. I'll keep the anger to myself, but I'm sure as hell going to bend it to a useful use.

*I frequently read papers on topics other than my projects, but it's always kind of bittersweet because I don't get to use them for anything.

**At the time I thought that I was getting out of the Midwestern mindset (I lived in the interface of Midwest and South) when I came to Michigan, but it turns out that Michigan was just as dopey and the food wasn't even nearly as good. Seriously, why do Michigan tomatoes taste like nothing?

***Note to self: get charisma. Best strategy likely to be attaching my name to a celebrity like a male anglerfish, but much handsomer.

Even Toaster's anger contains polka.

13 March, 2009

Poll! Vanity! Toaster's Face!

Figure A: Toaster (after combing his hair).

For the boosting of my own ego and infrequent vanity, I included a response for "I'm only here because I think Toaster is hot" in the poll to your left. I didn't expect much of a response, but I did not expect to be beaten 10 to motherfucking 1 (whoever that 1 is, thank you) by motherfucking bunnies! I guess, honestly, I should have known better than to tempt the Internet with bunnies. But still, I looked at the picture of me that was attached to this blog, with full PPE and fresh haircut on, and realized that maybe this disparity is because that photo looks like a pile of blue with some hair sticking out.

Figure B: Toaster models most of the PPE in the lab (also: prepared for zombie apocalypse).

So I provide for you this picture above (very top, not immediately above), of myself, to influence your opinions. Don't vote for the sake of my ego or vanity; don't vote because of my mild ranting; no, vote for my creepy lopsided stare and week-long invisible stubble!

Vote early!

Vote now!

Vote multiple times!

I'll find some connection to science here somehow sometime later (feel free to do so yourself, though).

12 March, 2009


I gave my lab computer a face.

Now it won't turn on.

Granted, it has had a face for 6 months (at least), so I can't definitively say that this is what caused it to fizzle, but still. It has been freezing once a day for the past couple of months, which has necessitated that I force a shut down and reboot. But now I'm not even getting anything and it's overheating.

Seriously, computer, what the fuck? I'm nice to you. I keep your hard drive relatively organized, I keep my data in the cloud instead of making you carry it. I turn you off every night so you can rest. Yes, I play a lot of music with you since the other other computer blew some capacitors, but that doesn't mean you're just a dressed up jukebox! So what is it then, computer? Has it been the electrical work the plant crew has been doing around here lately with the frequent blackouts at odd hours of the night? Did I dress you with too many Post-It notes that you sweated yourself into exhaustion? Did you want a prettier face? You should have told me, because, frankly, this is a shitty way to get my attention.

And this CRT monitor is already giving me a headache.

Therefore, computer, I ask of you: why?

11 March, 2009

Not-So-Mad Science: Shiga Toxin Increases EHEC Intestinal Colonization

This post is part of Cyber Journal Club with Science Bear and R.E.S.E.A.R.C.H.E.R.S..

Figure A: EHEC + other stuff on sorbitol MacConkey Agar. Most EHEC cannot ferment sorbitol and on SMAC agar it will grow translucent. Other stuff pictured here can ferment sorbitol and as such is pink because it has raised the local pH and tripped the pH indicator in MacConkey plates.

(For background, I've discussed Shiga toxin and EHEC in greater detail before.)

EHEC = enterohemorrhagic Escherichia coli O157:H7
Stx = Shiga toxin

ResearchBlogging.orgBriefly, EHEC is a food-borne enteric pathogen that has been evolving over the past 2 decades from a minor poop-tainted beef-borne pathogen to a more severe and flexible pathogen that is still found in beef, but now also on spinach (even growing inside the spinach). Primary sequalae of EHEC infection are intestinal cramping and diarrhea progressing to hemorrhagic colitis. This may usually be resolved with careful and selective use of antibiotics (antibiotics that cause any DNA stress will just make it worse). However, in some cases EHEC infection progresses to hemolytic uremic syndrome (HUS), which includes hemolytic anemia (lysed RBCs), uremia (acute renal failure), and thrombocytopenia (low platelet count). HUS can involve microangiopathic inflammation of the kidneys, bowels, and CNS, which can result in long-term dysfunction.

Epidemiologically, HUS is closely associated with infection by Stx-producing E. colis. As such, and because Stx is directly cytotoxic to in vitro renal cell cultures, Stx has been implicated as a primary causative agent of HUS. Stx is a AB5 N-glycosidase that shuts down protein synthesis by binding to and disabling ribosomes. Stx is encoded by a lambdoid prophage integrated into the EHEC chromosome that is inducible by DNA stress, specifically RecA in the SOS response. RecA cleaves the cI/LexA repressor on the lambdoid genes and allows transcription. Shiga toxin is thought to be released primarily when the induced host cell is lysed by prophage proteins. It has been observed that Stx+ EHEC results in more severe pathologies than Stx- EHEC.

Robinson et al (below) has found that EHEC adherence (in vitro) and colonization (in vivo) are increased in the prescence of Stx2. They used the Relatively Straightforward Common Biotech Method:
Step 1: Break it and compare that to that that ain't broke, then supplement the broken stuff to the level of that which ain't broke and compare again. If breaking it resulted in nothing, or less, happening, then what you broke might be causing that effect to happen in the first place and you may develop sweaty palms.
Step 2: If supplementing what's broken to non-broken levels restores the effect, then what you broke is probably causing that effect and you may start fidgeting uncontrollable.
Step 3: But, if you've also broken other related stuff and not seen the same pattern, then you can say that what you broke is causing it to happen (to the best of our current knowledge!) and you may then do a happy marshmallow dance of victory.
So Robinson et al took a normal Stx+ EHEC (strain 86-24) and made a mutant Stx- EHEC (strain TUV86-2, checked culture supernatant for cytotoxin activity: negative), then made them both into glowy mutants by adding constitutive GFP (this was smart for reasons we'll come to shortly). Then they grew up some HEp-2 cells in culture and let both strains loose on it in separate wells, which resulted in more 86-24 sticking than TUV86-2 (step 1). This same pattern was also observed in mice infected with both strains: 86-24 colonized the gut better than TUV86-2. They also checked microcolony formation and the degree of actin condensation (both characteristics of EHEC adherence), which was important because it demonstrates that TUV86-2 wasn't fundamentally different than 86-24 and so could be compared. So naturally, Robinson et al's next logical step was to add some Stx2 to the TUV86-2 to see if it could restore 86-24 adherence and colonization. It worked (step 2). Interestingly, in TUV86-2 + Stx2 groups, the proportion of HEp-2 cells to which the bacteria adhered remained the same, but the bacteria/cell increased (not significantly). And to prove that step 2 worked, they also repeated this with a neutralizing anti-Stx2 mAb and compared that to normal mouse serum. The TUV86-2 + Stx2 + anti-Stx2 mAb had similar adherence and colonization patterns to TUV86-2 alone. The normal mouse serum had no effect on the effect of Stx2.

So what was the Stx2 doing in the lumen that was causing increased adhesion? They looked at bacterial adhesion factors (Tir, intimin, et al) after incubation with Stx2 and found no change (however, they used Western blot for this; I'd have accepted this more readily if they'd also done a bacterial mRNA profile as it is possible that the incubation time was not long enough for a signal change in transcription to become evident at the level of proteins; also: step 3). So they looked at putative adhesion factors on the host HEp-2 cells, namely: nucleolin. Incubation of HEp-2 cells with Stx2 resulted in a dose- (and, kinda, time-) dependent increase in the cell surface expression of nucleolin, which was statistically significant even with just 10ng/ml Stx2 for 2h (for contrast, 100ng/ml Stx2 for 2h resulted in a significant increase of nucleolin). However, I would have again have preferred to see some mRNA analysis of the host cells. Not because I suspect there could be a significant effect from an incubation time artifact (at least, not after 24h), but because the data would have been very interesting. Is Stx2 increasing transcription of nucleolin or just an increase in the surface display thereof? mRNA data could have answered that. Also, why not wash the crap out of the cells to remove any residual media-borne Stx2 and check to see if there is any Stx2 inside the cells (either with a GFP-tagged Stx2 or ELISA on cell lysate)? Stx2 has been shown to enter gastrointestinal epithelial cells (in culture) nonspecifically through macropinocytosis, but is it doing something specific once its in there, if it's even getting in (because the macropinocytosis has only been observed to happen in some specific cell culture lines)? Is Stx2 reacting with a surface HEp-2 receptor or is it some internal effect? Is Stx2 binding nucleolin itself and causing autoaggregation at the surface (FRET!)?

All in all, an interesting paper, but for me it raised many more questions than it answered.
Robinson, C. (2006). Shiga toxin of enterohemorrhagic Escherichia coli type O157:H7 promotes intestinal colonization Proceedings of the National Academy of Sciences, 103 (25), 9667-9672 DOI: 10.1073/pnas.0602359103

10 March, 2009

How Do Mad Scientists Grill?

Figure A: Like this.

I am Toaster, and I enjoy barbecue immensely. If it's been fried and then barbecued, it's even better (can Toaster has OKRA and CORNBREADS?). However, I am also a Mad Scientist, and connoisseurs of barbecue are generally known as rednecks. These labels are not exactly compatible. While it is true that I will quickly and invariably develop a red neck if left out in the sun for too long, I do not drive a pick-up truck or think that country music is palatable. I have never gone turtle stomping, square dancing (although my high school required us to learn how to do so in gym class), slough hollerin', swamp boating, or had a moustache. However, in the interests of disclosure, I must admit that I have occasionally been known to let slip a "ya'll" or an "ain't", sometimes even a "y'all'rnt".

Ahem. Don't judge.

Anyway, given the above conflict of labels, I of course started to ponder how I might prepare barbecue and retain my Mad Scientist Street Cred. The answer, of course, is to build an overly complicated device to barbecue for me. Naturally, the answer is a Tesla coil:

However, this Tesla coil is cooking hot dogs in a row. That's the voltage arcing between the hot dogs that you can see flashing in the lower right quadrant of that video. I also remember that in the hometown of Dumpling Toaster (i.e., Young Toaster) there was a hot dog stand guy who electro-cooked the hot dogs he sold. He had a little breadboard set up with exposed metal pegs spaced a little less than the length of a hot dog. He'd impale each end of a hot dog on those pegs and run current through it until it was cooked and somewhat singed. It worked well and the end result was somewhat tasty, I mean, about as tasty as a hot dog can be.

But I don't want to Teslacue hot dogs. I want to barbecue whole motherfucking chickens and turkey breasts at once! So this brings up some practical considerations:

1) In order to cook the flesh, I'll need a complete circuit. Most of the time with Tesla coils one can come into contact with 1000s of volts because the amps are low and the circuit isn't complete. This means I'll need not just one, but two Tesla coils! However, this means that I can't just stand between them and hold the meat, because then I'd either a) get cooked as well, which I do not wish to do or b) have tachycardia and possibly cardiac arrest, neither of which seem particularly pleasant. This is somewhat disappointing, but understandable.

2) Hot dogs are made from chopped up processed meat, usually beef, pork, or turkey (fish dogs?), that has been pressed into a mold. What muscle fibers remain in hot dogs has been completely chaos-ified and as such no contractions will occur. But in a whole chicken, muscle fibers remain in their original orientation. As such, is it possible that, when zapped with thousands of volts, they'll twitch and spasm horribly and cause everyone buy me to lose their appetite, and maybe even spatter delicious barbecue sauce everywhere?

Figure B: Luigi Galvani beat me to it. But he was Italian and this was 1771, so I don't think he had barbecue in mind when he conducted these experiments. His frog legs twitched and he figured out that nerves are electrical.

I searched the Internets for information on this in barbecue, but to no avail. Based on the experiments of Luigi Galvani (above), it looks likely that they will. Gross as it may be to think of, this isn't much of a disincentive for me.

3) What is the probability that the flesh I intend to be barbecue will instead be reanimated into horrific, yet tasty, zombie barbecue chickens? I think that, so long as the flesh has been deceased for a sufficiently long time, say, a week refrigerated, that no reanimation would occur because the cells of the flesh would be far too degraded to jump up and wreak evil. However, it is also possible that this effect could be desirable, especially should I wish to ever conquer Kentucky (which is unlikely in any event).

4) Cornflower + cayenne = purple barbecue!

5) Who wants to come to a barbecue? I'll even make some without heat (= only 1% cayenne powder) for the wusses out there.

09 March, 2009

Verrückte Wissenschaft im Weltraum!

Natürlich folgt es, dass, wenn mann einer verrückte Wissenschaftler werden will, mann auch eine grosse Intresse an die Kraft und den Macht des Weltraums, so lang als mann die kontrollieren und nützen könnt, haben wird! So ich finde es nun sehr gut, dass die ESA eine Mondbasis bauen will. Verrückte Wissenschaft ist natürlich immer ein bisschen weiter fortgeschritten als normale Wissenschaft, aber zum besten meines jetzige Wissen sind keine verrückte Wissenschaftler auf dem Mond für forschung, leisen, oder Sonnensystemherrschaft (es gab einen Versuch in 1987 bei Drs. Rosrt, Klage, und Lollipop, um zu nach Mars zu reisen und dann dort wohnen. Wir hörten nichts von ihnen seit dann). Bei Moment bin ich nicht sicher, ob ich enttäuscht von verrückter Wissenschaft bin, oder stolz auf normaler Wissenschaft bin...

...ach, warum nicht? Ich bin Wissenschaftler, so ich werde immer stolz auf meinen Wissenschaftkameraden, auch wenn sie forschen irgendanders als mich, scheissegal ob sie verrückte oder nicht sind.

Convenient Translation:
Mad Science in Space!

It naturally follows that, when one wants to be a Mad Scientist, that they will also have a great interest in the power and force, so long as they can control and use them, of outer space. So I find it excellent that the ESA wants to build a moon base. Mad Science is naturally always a bit father progressed than normal science, but to the best of my current knowledge there are no Mad Scientists on the Moon for research, leisure, or solar system domination (there was an attempt in 1987 by Drs. Rosrt, Klage, and Lollipop to travel to Mars than then live there. We haven't heard from then since then). At the moment I am not sure whether I am disappointed in Mad Science or proud of normal science...

...oh, why not? I am a scientist, so I will always be proud of my fellow scientists, even when then research different stuff than me, and I don't give a fuck whether they're Mad or not.

05 March, 2009

Not-So-Mad Science: Patchiness in Asthma

ResearchBlogging.orgIt’s a beautiful spring day, the first warm and sunny day of the year and the snow has finally melted. So naturally, you’re outside, enjoying it. The birds have reemerged from their hiding places, and all the plants are heavy with green and bloom. The whole earth smells clean, as though the snow and sleet somehow scrubbed the very grass and have made it shine, even if it is still brown and crinkles underfoot. Off in the birdsong distance, you can see the tree boughs tossing in the breeze. After so long cooped up inside with nothing but TV and the Internet, you ignore it. But then you suddenly notice that you’re struggling to pull air into your lungs while the air trapped deep inside is beginning to burn. You try to form words for help, yet nothing but a faint wheezing gasp comes out as you can literally feel your throat closing around your words like a wet, desperate fist. At this point you’re hunched over, chest heaving, desperate to yank the slightest bit of oxygen into your lungs that feel like a wet towel tightening slowly around your wildly beating heart. You clutch at your throat and a detached piece of your rapidly dizzying mind notices that your hands are shockingly cold. The crinkly grass rushes up and catches you as you strain, tendons taut and eyes watering, for any breath at all, barely enough of you left to wonder where you left your inhaler. But it’s there, digging into your hip in the pocket of your coat. Your lizard brain swats what remains of consciousness aside, manages to feebly flop you over, dig the inhaler out, and jam it between bluing lips. That first puff hits your throat cold and gritty, but it opens a little, just a bit, enough for the tiniest of breaths, which stings like salt. The second puff gets you going a bit more, and finally a third puff gets at least 1 bronchiole knocked wide open. Spreadeagled and panting hard on the grass, you watch the clouds scud above and silently curse the Ur-flower that first thought to make pollen. What a motherfucker that little bitch was. But at least you’re alive to even curse it.


Although we know quite a bit about the gross pathophysiology of asthma and, in most cases, how to treat it (acute and prophylactic), there remains quite a bit we do not know*. And there have been several well publicized epidemiological studies over the past 2 decades that indicate that asthma and allergy are increasing in prevalence across all socioeconomic lines. And the challenging and perhaps most frustrating part (and this, to me at least, is what makes it so intriguing) is that no one really knows why asthma and allergy (referred to together as atopy) are increasing, although we have hypothesizes ranging from diet, the hygiene hypothesis, perturbed gut microbial ecology, and general organic and synthetic chemical pollution.

First, let’s talk about the structural physiology of lungs. Anyone who has ever dissected a mouse knows that the lungs collapse into a wet pink mess pretty much as soon as the organism dies. This is because mice have spongy lungs (as opposed to “simpler” bag-like lungs in many animals) like humans. This is also because lungs are mostly soft tissue with air-filled tubes running throughout, somewhat analogous to Jello with holes drilled through it (though I don’t know why anyone would drill holes in Jello, if it’s even drillable [I may need to empirically test this]). The trachea branches off into the main bronchi, which each branch into lobar bronchi. These then branch into tertiary bronchi and form bronchopulmonary segments separated by connective tissue (lobes, essentially). Inside the bronchopulmonary segments the bronchi are called segmental bronchi, which then divide into primary bronchioles before dividing further into terminal bronchioles. And because this isn’t yet enough (think about it: each stage of segmentation increases the surface area per given unit volume quite efficiently, like a Sierpinski triangle), the terminal bronchioles branch into respiratory bronchioles branch into alveolar ducts end in alveolar sacs that contain the alveoli. Alveoli are where gas exchange happens via the blood vessels that cover most of their surface area. As the airways branch further out, rigid supporting cartilage decreases and smooth muscle increases. This is important to note for later, as are the observations that each lung does not branch perfectly symmetrically.

Figure A: 2 ways to visualize the branching of the bronchi. Mandelbrot set visualization (top) and fractal tree (bottom).

Second, let’s talk about the pathophysiology of asthma. The possible causes and/or triggers of asthma warrant an entire series of posts by themselves, so they won’t be discussed here. Asthma occurs when the lungs aren’t providing adequate respiratory exchange due to constricted air flow volume (also referred to as tidal volume) and the levels of oxygen in the blood begin to fall; asthma is generally treatable with drugs, this is what clinically differentiates asthma from COPD and/or some ARDS. Reduced tidal volume is primarily thought to be a direct consequence of increased smooth muscle activation. Smooth muscles can be triggered by a wide variety of extrinsic factors and the resulting asthma attack can range from mild wheezing to complete respiratory failure and death. Long-term pathophysiological manifestations include scarring of the lung airway epithelium, localized sustained inflammation, and a reduced baseline tidal capacity, which are thought to be due to recruitment of immune system effector cells into the underlying tissues (which in turn cyclically drives more inflammation).

Figure B: Like that (although this .png has been squished a bit).

Finally, then, to the paper. A computational model of a single terminal bronchiole that included the physics of positive airway pressure inside the lumen space, the tension of underlying parenchymal upon bronchioles, and the constriction caused by smooth muscle activation was integrated to simulate a whole lung by using a Mandelbrot-like structure that reflects the serial branching of airways. This model assumes constant tidal volume and rate and neglects gravity-dependent lung effects as would occur in the deeper lungs. It also ignores the effect of diaphragm muscles on lung function. Obviously, in real life we breathe harder when we’re winded and the air deep in our lungs has to contend with gravity more than air in our upper lungs, and we also use muscles to breathe, but simplifications are necessary to make modeling a sane endeavor.
And now for the metaphorical vehicle: Imagine you’re standing on a tightrope with someone else at some distance away from you, say, farther than you could throw a tuba. If you lose your balance, you’ll swing about to try to regain it, and doing so will move the rope you’re standing on, which will then result in the other person having to move to keep their balance. If you don’t quickly recover your balance and steady the rope, either you’ll fall or the other person will have to work harder to stay on the rope and continue to amplify your instability.

Figure C: Don't try this at home. Go somewhere more dangerous first.

Unfortunately, falling off the rope doesn’t really happen in asthma attacks (unless you think of that as a piece of lung shutting down). Sure, whole chunks of lung seize up and stop providing adequate ventilation, but this is patchy and even then those patches still contain smaller bits that still work as they’re supposed to. But it is the amplification of instability that leads to the progressive and terrifyingly fast clamping shut of airways in an asthma attack. Section A shuts down, so Sections B, C, and D will have to work harder to compensate. Compensation will involve greater intrabronchial airway pressure, which the normally functioning lung interprets as bad and tries to compensate for in the opposite direction by activating smooth muscle, so smooth muscle activation and airway constriction can spread rapidly from Section A to B to C in sudden and catastrophic sequence even if only a little tiny bit of Section A started the whole thing.

The computational model used in this paper found that catastrophic shifts as described above don’t really happen unless some degree (~1%) of heterogeneity in lung response to constriction/smooth muscle activation is included. If the computational model was allowed to be completely symmetrical and if all lung tissue responded in exactly the same way, then nothing spectacular happened.

While I find the computational modeling stuff to be fascinatingly awesome, that’s not all they did. They also got mild to moderate asthmatic volunteers to inhale isotopic nitrogen gas inside of a PET machine during a chemically induced asthma attack to map where the gas was going (those were very brave asthmatics). In poorly functioning lung, iN2 would be trapped and remain visible on the PET while normally functioning, or lung hyper-functioning to compensate, lung would clear it quickly. These PET results validated their modeling outcomes in that asthmatic events are patchy in that neighboring bronchioles are more likely to become distressed than distant bronchioles, though not absolutely in that the patchiness of poorly ventilated lung was itself patchy (mirroring computationally induced heterogeneity). Furthermore, these findings were clinically relevant because only normal- or hyper-functioning lung remained open during the asthmatic event, which suggests that inhaled anti-inflammatories may be being delivered primarily to the lung epithelium that needs it least.

Research Cited:
Jose G. Venegas, Tilo Winkler, Guido Musch, Marcos F. Vidal Melo, Dominick Layfield, Nora Tgavalekos, Alan J. Fischman, Ronald J. Callahan, Giacomo Bellani, R. Scott Harris (2005). Self-organized patchiness in asthma as a prelude to catastrophic shifts Nature, 434 (7034), 777-782 DOI: 10.1038/nature03490

*From my perspective as someone who doesn't actually do atopy research...yet, anyway. Therefore, if I am flatulating ignorance and posing it as wisdom, feel free to correct my mistakes in comments.

NOTE: This is my first post for the Cyber Journal Club that Science Bear is organizing. R.E.S.E.A.R.C.H.E.R.S are also participating. My goal is to post every Wednesday and apparently Science Bear is going to be posting 2 Wednesdays a month. Feel free to join in by commenting or posting your own (we'll ping you).

03 March, 2009

Mad Scientist Etiquette

[There will be more Not-So-Mad Science {aka, Real Science} tomorrow!]

Naturally, since Mad Scientists have Laws, it follows that we will also have a semi-standardized guidebook for Mad Scientist Etiquette. This guidebook is not about rules or standards per se, it's more of an orientation pamphlet for aspiring Mad Scientists. I present some selections from the Etiquette Brassiere below. Suggestions are welcomed, but stupid questions will be shot (the questioners will just be chased about by robots specially built for that task). Composite-numbered items have been banned.

Tip #7:
A proper Mad Scientist never merely orchestrates the downfall or demise of their enemies. Instead, they compose a whole motherfucking* symphony with multiple thematic overtures and movements.

Tip #11:
A proper Mad Scientist laugh is indistinguishable from an Evil Genius guffaw to unpracticed ears, but the two are distinct to a practiced ear, although it is physically possible to produce both at the same time. Recordings of both can be provided to you upon request.

Tip #13:
Remember your assistant's birthday, especially if you have accidentally horrifically scarred or maimed him/her in the last year.

Tip #23:
It is both wise and polite to maintain a ready supply of spare parts for assistants and guests.

Tip #71:
Flip-flops are an excellent shoe for Mad Scientists in tropical climates because they can be used to swat mosquitoes, assistants, and malfunctioning machinery.

Tip #83:
Wipe your feet when coming inside from out.

Tip #97:
If you must pass gas, please do so away from Bunsen burners.


02 March, 2009

Wacklegrot + Whuzzafux

Today, I have not just one, but two (!) additions to the English language for your grokking pleasure (which somehow sounds like something one would have to pay to watch, but that's not how I mean it, I think): Wacklegrot and whuzzafux.

1) noun; category of very shiny objects of a puzzling and vague nature that can and invariably do distract the easily distracted for hours on end to the exclusion of all other attentions.
2) noun; legendary fabled focuser of attention for the easily distracted, for whom it will make concentration easy if its puzzling nature is solved.
3) noun; derogatory term used to describe those easily distracted by shiny objects.

1) noun; disappointing lulz
2) verb; to be surprised by something very shocking and random

Once again, English language, you are welcome. Now I am going to run away before you blurf me for being so irreverent.