Friday, December 30, 2011

Tubulin Prep and Meeting My Meat. 

Most of what I do in the lab involves manipulating DNA in little tubes, growing cells in culture dishes, and taking images of them with fancy microscopes.   The most striking images are inevitably those where microtubules are labelled (in the image below in white).

These filamentous structures are not only beautiful but extremely functional in the cell, and myself and thousands of other scientists around the world spend a lot of time studying how the cell uses them to carry out a variety of essential functions.

Several people I work with use purified microtubules outside the cell to study how other proteins interact with them and modulate their physical characteristics.   Microtubules are made of small proteins called 'tubulin', which stick together in an ordered way to eventually generate the long skinny structure.  Getting reasonably pure tubulin is not trivial.  It's just not as easy to generate and purify as some other proteins.  So the best way to get lots of tubulin has been to get it out of cells that have already made it naturally.  The most tubulin is in nerve cells, and the most nerve cells are in the brain.    So the best way to get tubulin is from brains.  And the best way to get lots of tubulin is from lots of brains, and the bigger the better. 

My friends Simone and Per, who are expert tubulin biochemists, recently decided to organize a large tubulin purification.  And until some brilliant person comes up with a way to purify large usable amounts of tubulin without brains, this means acquiring lots of brains.  Of course I jumped at the opportunity to help.  This sounds like real science. 

Now, it turns out that tubulin in brains doesn't freeze well, so the best way to get tubulin is actually from lots of big fresh brains.   It also turns out that thousands of big fresh brains are simply trashed in these parts each day in an effort to satisfy the German craving for Schwein.    The mission, then, was to go to a slaughterhouse in the wee hours of the morning, and get 100 fresh, warm pig brains, right out of the pigs.  

Coincidentally, at that time I was going pseudo-vegetarian, after reading the moving book 'Eating Animals' by Jonathan Safran Foer, and felt this would be a good opportunity to see the inner workings of a slaughterhouse.  Since I knew I would not realistically be able to cut out all meat forever, I thought I should at least know first-hand how it got to my plate. And who knows, maybe it would have some sort of impact.  I was starting to fall of the wagon. 

So Per and I got up one morning before sunrise to drive to the slaughterhouse, collect brains, and be back in the lab with enough time for all the biochemical processing to get the tubulin.  I think we were in the lab around 5am to get the supplies, where we found a friendly note from Simone:

She had arranged a chocolate basket and note for us to bring all the guys down at the slaughterhouse as a thank-you for all the brains.   

I don't have any photos from the slaughterhouse, I didn't even bother trying to take my camera in there.  As Per and I arrived in the dark the entrance looked like the registration lobby of a hospital: clean, white, cold, sparse, open.  After we explained we were the scientists there for the brains, our contact guy came out to greet us wearing a full body lab coat.  He then gave us each protective wear, including shoe-covers and hair nets.  We had several heavy containers of ice that the three of us then had to carry all the way to the slaughterhouse floor, which was a long trip though a maze of cool, white, fluorescently lighted corridors and locked doors, even more emphasizing the hospital feel.  Except that at with each door we crossed, a distinct scent registered stronger in my nose, undetectable at first, and overbearing by the last door.    At the last room before the slaughter floor, we passed over a machine that scrubbed our feet, and then through a door, where we were instantly confronted with a large, loud, crowded room with a thick suffocating stench, and absolutely buzzing with activity.  Dozens of workers, men and women, and hundreds of pig carcasses where whizzing around.  There was a long assembly line, which came in the room beyond our vision, twisted throughout, and back on itself, and then exited on the opposite side.  Our contact, probably younger than both of us, very matter-of-factly took us to the place on the line where the brains were removed, and then asked me a question.  With all the noise, and the guy's thick Saxon accent, I could just not understand what he was asking, but eventually gathered he wanted me to follow him to the other side of the room.  He very adeptly navigated across assembly lines of hanging carcasses being whisked through stations.  I had to pause often to get the timing right for fear of getting whacked with a carcass, but more so of somehow screwing up the whole operation.   Eventually he took me to another guy, high up on a metal grating, seemingly overseeing all the operations of the floor with a panel of knobs and phones. I was to come back to this guy when we were finished getting brains so that we could be led out of the floor.  

Once back at the de-braining station Per and I decided to dive into collecting.  We then realized that with all this protective gear, we were never given any gloves.  As we glanced around, we only then noticed that in fact nobody on the floor had gloves.   To ask for gloves would mean bothering three more people, interrupting the whole operation, and potentially receiving the scorn of the people in the room that were already looking at us with annoyance.  So we dug in with bare hands.   From our position, pigs came by cut in half.  They were whole about 30 meters to the left of us, where a guy stood with what essentially looked like a giant chainsaw with a firehose integrated. He cut the pigs, hung by their forelegs, perfectly in half, head to tail.  When the half pigs came by us, a woman was grabbing the brains and kidneys, and tossing them into separated cartons.  We then grabbed the half-brains, about 3 seconds out of the pig, and still quite warm, and tossed them into an ice-cold saline solution.   Occasionally a kidney would accidentally fly into our carton.  It probably took us 15 minutes to collect 200 half-brains. 
After we had packed all the brains in the car and ready to go, we were blocked in for several minutes by a huge semi truck - with a trailer containing dozens of pigs sticking their little snouts out through grates in the side of the truck, eyeing us in confusion.  If we had come 30 minutes later we would have had their brains in the trunk. 

Back in Dresden the sun had come up and a small team had assembled to process the brains as fast as possible.  The first step was to clean them up.  A cold room was set up to process them.

It was a cheerful environment as the team whistles while they work:

Ultimately the brains were liquified in a giant blender for further processing.  The official protocol says they should be blended until the consistency of a nice strawberry milkshake. 

More milkshake action, in the 4 degrees C room.  10 liters of brains in the end.

The rest of the purification consisted mostly of hours and hours of centrifugation steps and running protein over columns until reasonably pure tubulin was isolated.  One thing I did not foresee was that the incredible penetrating stench of the slaughterhouse would stay in in my clothes and skin.

Here Per and I had changed clothes from the slaughterhouse, but the stench of the worn clothes were so great we had to wrap them in plastic bags.  And were only in there for 30 minutes!  My skin even smelled for a day.  I can't imagine working 40 hours a week in that place.  I guess you get used to it, but that smell must be permanently attached to you. 

In the end the prep was a success, but we slightly underestimated our brain capacity and could have collected more in the beginning.  By making tubulin ourselves, we saved literally tens to hundreds of thousands of euros compared to buying it pure. 

As for the experience of seeing a slaughterhouse in action, and my newly found pseudo-vegetarianism, I was glad for the opportunity to visit.  It wasn't really all that disturbing to me while inside, as the pigs were already partially processed by the time they came in our room (dead, with no hair or skin, more like being in a giant meat locker).  It did kind put some things in perspective when the truckload of live ones showed up as we were leaving.  These are intelligent fully-aware individuals being processed.  And the sheer number was astounding.  

Our expectations for having meat for every meal really doesn't make sense when you sit down and think about it.  It's not sustainable, it's not in anyway necessary for health reasons, and as I've found out, meat actually tastes a whole lot better when you eat it on rare occasions, and when it's of the highest quality. I've gone from about 10 meals a week containing meat, to less than one a week on average.  I don't miss it, because if I really have a craving, or if I'm in a nice restaurant, or traveling, I go ahead and have some, preferably of free-range origin.   I'll never give up an occasional BBQ brisket or fresh homemade bratwurst, but I'm happy to give up cold-cut turkey (I cut out turkey, cold-turkey, so to speak, going from 4 sandwiches a week for the last 10 years to zero since I stopped), low grade hamburgers, canned tuna, and tasteless steaks that you just stuff in your face to make you full. 


Anonymous said...

Very nice blog. I had a similar experience, when we were collecting sheep blood for preparing some special lipids they have. It was at a small shepherd in Dippoldiswalde and we did see the full process. I was quite impressive seeing the sheep go from alive to hanging there, as you see them at the butchers, in about 15 min. It made a lasting impression on me.

Somehow, I also turned semi vegetarian, however this experience was only a piece in the puzzle. Best wishes from Heidelberg. Mathias

Alex said...

Thanks, Matthias. Yeah, I think everybody should be able to go have a look how their nice shiny steaks and deli meats wrapped in plastic get to the store. Sure, we all know. But it's another thing to see it, smell it.