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. 

Singing Sinatra

This year's MPI-CBG Christmas party was a bigger hit than usual, and I think most people agreed it was due to a new format, which was basically much more informal, and with lots of live music, spearheaded by Tim Cross. Several months prior, Tim sent out an email calling for anybody with any sort of musical talent to sign up to play at the Christmas party. I sent an email back saying I'd always dreamed of singing Sinatra with a band, but had never sung before an audience, nor had been trained in any way. I did not expect Tim's response, which was "RIGHT FUCKING ON!!!", and a promise to assemble a band. I then attempted to back out several times over the next couple months, thinking I was in over my head, but Tim wouldn't have it. And so a band was assembled, and with a handful of rehearsals, but never with the entire ensemble present, we pulled off a number of tunes that night:









Tim is on bass, Per's on guitar, Coleman on the drums, Guillaume on paino, and Veikko on violin. These guys basically pulled this off without really practicing, and with me asking for stupid things like changing the key up a couple steps cause it was more familiar that way. It was quite impressive.

I don't have videos of any of the many many other acts from the night, but they were
quite phenomenal, sometimes to a jaw-dropping degree. It's amazing to see your colleagues really jam and wail.

And the results are in.....

Sächsisch Beer vs. Czech Beer at the MPI beer hour. I think the picture speaks for itself.

Making a Gingerbread House in Germany

As usual this is about a month late, but had to post some pictures to show that while in Germany I actually helped make a gingerbread house during Christmas-time. There was a cookie competition at work as part of the Christmas party and our lab decided we would make a gingerbread house as our entry....

The walls go up. Not looking like a standard house

Jenn was the master-coordinator of the project, and supervised the American postdocs



A sidewalk and street, and pedestrians go down...

Final touches included a speed bump and smokers outside in the cold. (Gummibärchen, of course)

And BAM! The MPI-CBG in the snow. Complete with funky awning, trees, speed bumps, smokers, benches, pond, and even some little guys playing kicker up on the roof.

First place! And this contest was no joke, as evidenced by the mean looking cookie on the certificate. Notice Till lurking in the background. He was cherry-picking the candy when eyes were turned.

Soon everybody got into the act. It didn't last very long. But tasted pretty good.

Dress like a Scientist Day

Today was "Dress Like a Scientist Day" here in the MPI-CBG. Also known as as genetic engineering inspection by the Saxon Ministry of Environment and Agriculture. We've been getting reminders and warnings for over a week now that today inspectors will be in the building to check that we are meeting safety regulations. So we've had a week to prepare - which means removing coke bottles from lab desks, taking empty beer cases out of cold rooms, buying lab coats so that we can actually wear them while the inspectors are here, closing and locking doors to "Gentechnik Arbeitsbereich S2" rooms that have been open since, well, the last inspection. The fun part is everybody is walking around all day in sterile white full-length lab coats and you feel like you are in the movies. It lasts a whole day. At about 6pm people started opening doors back up, bringing their snacks back to their desks, and removing their labcoats and hanging them back on their hooks, where they will sit until the next inspection (complete with one-week warning) comes around. That we are are told about these inspections in advance of course renders them pointless, and the fact that we ARE told about them must mean that the inspecting agency knows that the regulations are in fact a bit of overkill, and it's all just a big song and dance for the people who don't know how science is done to feel good about health safety and etcetera.

More beauty in science

I just really like this picture. The colors.
What it is is the inside of a centrifuge that was damaged due to a user failing to clean out extra liquid that leaked out during a run. 6000euros of damage apparently. This was posted on a big screen in the institute lobby as a scolding to the anonymous user.

Somehow I find pictures of old metals and rust fascinating. I need to explore that again.

Weeeeee are the Champiuuuuuuns my Friiiiieeeennnd.........in Beautiful Chemnitz

Last weekend the MPI-CBG and friends ultimate frisbee team Ring of Fire competed in a tournament in Chemnitz (more on Chemnitz below).

This was our first tournament as a team, and I have to say, we had especially low expectations. Mainly stemming from a combination of the facts that a)we "practice" on a field about half-regulation size b)we are usually out there for fun and don't spend alot of time on rules and strategy and c) we've never actually played all together on a full size team. So to our amazement we went out there and gave a good show. Actually from the beginning we were winning convincingly. Like 6-3, 7-1, 5-2 types of scores. In fact we didn't lose a game and took the championship with a closely fought and dramatic comeback (against another Dresden team) in the last game. Down 2-4 with 5 minutes left, reeled off 3 scores to take it. It was a great sports moment.


Now there were only 8 teams at this tourney. And this clearly wasn't the best Germany had to offer as far as ultimate. But people were traveling from as far away as Munich to participate. And we actually did a very good job as coming together as a team, sticking to our game plans, remaining calm, playing tough defense, and going close to 100% all the time with frequent substitutions.
Our rewards included a couple of bottles of Sekt, which Sanni and Albrecht quickly made good use of at the awards ceremony:

And a small trophy in the shape of the head of Karl Marx:

Which brings me back to Chemnitz. Chemnitz is a city of about 250,000 about 45 minutes southwest of Dresden. I'd never been there before, but heard things about it, all of it bad. As in, basically a crappy place nobody would ever want to go. During East German times Chemnitz was named "Karl-Marx-Stadt" and was basically the quintessential communist DDR city. The trophy above is a replica of a giant stone head in the city:

As you can see, it's freakin' huge (see person at base). If this scene isn't communist, I don't know what is. Unfortunately, Chemnitz hasn't come a long way since reunification. My first impression was that is was a quite green city. Then I realized that was from trees and grass growing up through run down, abandoned buildings. Communist type buildings are everywhere, and most streets and buildings remain in a state of disrepair. Unemployment in Chemnitz is among the highest in Germany, and birth rate is the lowest. There are ongoing plans to restore the city center, but it will be a slow process.

but back to ultimate. Which I will never get used to saying. I don't know what hippie came up with this name, but I still cringe to say we're playing "ultimate frisbee". One nice thing is that it offers a nice chance to practice some sports photography:

These are from our regular Sunday games in the Grosse Garten. More pics are here.
Wow, long post....So I'll leave you with the aftermath of a long Saturday