Value

We use a lot of stuff here. Everything is "disposable," and should be disposed of. Alright, not everything, but it sure feels that way. There is a lot of glass that is one time use. Glass is expensive right?

Two types of pipettes (only two that I am aware of!) are used for measuring small volumes. A pipette is basically a turkey baster but much more accurate and precise. The first type has a dial that you use to tell the device how much it should suction. This type works mostly in microliters. Do you have any idea how small a microliter is? There are about 40-50 microliters to a drop of water (depending on pressure, temperature, etc.). So we pull up 10 (or some such number) microliters in this pipette and put it in a different container, like a tube. Every time that we are introducing a new reagent (ree-agent. Fancy word for ingredient), we need a new tip for the pipette. You draw up a bit in that tip, eject the tip in the disposal container, and grab a new tip. We go through at least 10 of these tips a day, and as much as 50.

The second type of pipette is for larger volumes. For amounts of liquid that are larger than 1 milliliter (ml), we use this second type. There is a handle that is sort of like a hand-gun. It has two triggers. One pulls liquid up, and the other pushes liquid down. This is done by way of a pump mechanism in the handle. This pipette also has tips. However, each tip is a long glass tube of at least 10 inches in length. These are marked along the side with ticks for varying amounts of volume. You could put in a 50 ml tip or a 10 ml tip or anything between. These are not nearly as accurate as the smaller volume pipettes because you are using your eyes rather than calibrated machinery. These are used when it is OK to be approximate. Whenever a "recipe" calls for 10 ml of this reagent, it means around 10 ml. These tips that are specially calibrated and marked (and have a filter at the top to make it harder to destroy the handle by pulling up too much liquid) get disposed of after each use as well. I imagine they are the more expensive type as they are glass.

We also use a type of non-calibrated, non-filtered glass tip. This is to get rid of waste liquid. You attach it to a vacuum tube and it sucks away liquid stuff. Each of these has to be disposed of after use or if you change the type of liquid you are vacuuming.

These latter types get used whenever you are doing tissue culture, as you are working with "large" amounts of liquid, and have plenty of waste.

There is also the issue of gloves. Every time you enter a lab it's a new pair of gloves. When you leave (even if you are coming back), you throw them away.

Then the cost of reagents. A lot of things are for general use and come in large quantities. Sometimes you get something that is at a high concentration and you only use it at low concentrations. It lasts a while. Sometimes however, you need something that is very particular or of particularly high quality. A little vial that has 1 ml (20 drops of water worth) in it can sometimes cost as much as $300 (probably even more than that). Even the more common, bulk ones are not so cheap. A half-liter of PBS (Phosphate Buffered Saline), a reagent that we use quite often, is more than $30. We generally use 10 ml per plate. If we are doing 20 plates, that is 2/5 of a bottle. Trypsin, which is used in pretty much everything, is $40-$100 for 100 micrograms, depending on the grade (the lower grade can be used for many things).

Gels, which are used to see whether the proteins or DNA you were looking for are actually present, run upwards of $40 each. Ones that are actually useful for what we do run upwards of $60 each.

I have not gone into any of the one time costs such as the initial investment in a piece of machinery. Nor have I gone into utility cost (I'll let you guess; hint- it's astronomical).

What I am trying to get at here is that science is expensive. I probably think about the cost too often. I am afraid of how much I cost, in that I am not experienced and therefore my work is not as efficient or correct as a more-well-trained individual. I will keep on trying and spending your tax-dollars though!

Goals

The lab I am with is the Laboratory of Proteomics and Analytical Technologies. Particularly the proteomics part. If the genome is the sum of all DNA and gene interactions, the proteome is the sum of all protein interactions.

DNA is the code that tells the cell (and further, the body or organism) how to make proteins. Proteins are vastly complicated. There are only 20 amino acids, which act as the base units for making protein. A protein is just a string of amino acids folded into a particular way. Proteins can be strung together in interesting ways to make protein machines. All of the action, anything that is dynamic, in a biological system can be traced to proteins. For example, digestive enzymes are type of protein that breaks apart food stuff so that it can be digested better. Lipase is a digestive enzyme that breaks fats down into triglycerides, which is how the body utilizes fats. Lipase is a protein with a special function. By educated estimates, there are thought to be over 50,000 proteins involved in making humans work properly (and improperly).

There are proteins that stay in the cell nucleus (where DNA is located). Some of these help with DNA copying, or in making other proteins. Many of them bind to DNA at certain locations. That is what we are currently studying.

There are about 10,000 employees of the NIH on this base, so my group (less than 10 people) is studying a very particular piece of the pie.

Proteins are very small. You can't see/identify particular proteins in a microscope. The best method we have currently for looking at proteins is very indirect. It is called mass spectrometry. For this method to work, you need to have a sample of proteins. These are given an electrical charge. They are also cut up. These charged pieces are sent through a constant electrical current from one electrode to another that has a sensor. We are then able to tell the size and mass of these pieces by seeing how long it took them to get through the current. By putting them all together, we are then able to see which proteins were in the sample.

While we are a mass spectrometry lab, we sort of out-source the mass spec to the experts. We design and do the experiments that get the proteins ready to be looked at in the mass spec.

So what are we looking at? We are particularly interested in chromatin and the proteins that bind to it. Chromatin is the fibers that DNA is supported on. When I say DNA, you think double-helix, right? The DNA itself is the rungs on that ladder. The actual structure, helical part is chromatin. So, the long term goal is to develop a way to look at a specific part of chromatin, and the proteins that bind to it. Current research generally looks at the protein complex without DNA, but that is likely an important part of the picture. It seems that some proteins identify where to bind because of the DNA sequence at that location, and that part of its ability to bind is based on DNA as well. This can be illustrated by thinking of a house you want to visit. You find the particular house by its address, but you don't know where to enter until you find the door. By looking at chromatin and the proteins without the DNA, it is as though you visit a house (you've followed very detailed directions to get there) and are inside, but someone studying you from above makes the house invisible to see you standing there in what was the kitchen. If you are holding a frying pan, it might be clear as to where you are. If you are simply sitting down, you might be at the kitchen table, in the living room, or even on the toilet.

Looking at protein-binding on chromatin out of context is like this. We don't know whether that is the location that the protein would normally be if the DNA was still intact or whether the interactions are more or less as complex in vivo.

The intermediate goal is to be able to understand some or all protein interactions through a model system. Also, to learn novel things about proteins that we already think we know about. One issue is what is called "background." If we are studying p53 (a human protein that we are actually studying), there are bound to be tons of other stuff that just happened to be chilling around there at the time that we harvested the sample. How much of it is supposed to be there and how much is non-specific? In the past, background has been washed away, but then you also lose some of your sample. And it's hard to know how this affects the way you would find interactions in vivo. I don't know how we are trying to get around that.

Those are some of the goals of the group I am working with. It's hard to know how to actually get there, but basically you change little things until it gets you closer.

If you want to learn a bit more, the wikipedia post on protemics is pretty helpful as is the proteopedia.

science

I realize that up until this point, I have not really mentioned much about science or even that I have started working in the lab. I started working in the lab on Monday. This is the end of my first full week. It has been such a learning experience.

I have not really mentioned anything about the science for fear of not being able to make myself understood. Here is my charge to you: if you don't understand, please let me know! I will not get better at making science accessible unless you tell me where I have assumed things that are not true.

Also, bear with me. I don't totally understand it either. I would ask questions, but I am not sure what questions will make things clearer. My next post will be all sciency. Please help me to explain it better by asking about things you don't understand. Thanks!

JK comes out of his shell

Apparently, JK is quite a character. He asked me last night whether I had plans for the evening, I didn't so he invited me out to a local brewery with a friend.

The brewery has a deal on weeknights that from 8-12 beers are half off. They also put out a free wings buffet. SH, whom I have met on a couple of occasions, was there when we arrived. He had managed to get us a table (I have never seen a bar so busy on a weeknight!)

It turns out that both of them are politically liberal, which I had not known until this point. We discussed the healthcare overhaul mostly. SH does not stay too on top of the news. He did not know most of the details of the new law. For instance, he thought that health care would now be free. JK and I made it all clear to him.

Another big topic was eating contests. JK told us about a burger place in PA where you can get a 1, 2, 3, 10, or 30 pound burger. The two and three pounders were contests. You have an hour to eat it and if you do, the meal is comped, you get a gift certificate, and a little plaque on the wall.

A couple of years ago, JK gained about 10 pounds. He started this off by saying that he gained a bit of weight, to which SH responded incredulously, "A little?!" JK's response to the situation was, "Fuck it, I'm gonna eat what I want." It was a few month's until New Years, and JK wanted to gain as much weight as possible before the New Year. He was about 185 (whereas previously he had been about 175). He wanted to pass the 200 mark before the New Year. He would eat until it hurt. All the time. On New Years eve, he finished it off with 5 junior bacon cheeseburgers and a four pack of chicken nuggets from Burger King. His weight was 203. He then went on a diet and started working out. He is now in pretty good shape and goes to the gym (with SH or his girlfriend or both) two to three times a week.

It seems that a bar is JK's natural habitat. Previously I had thought he was kind of insecure and without much character. He totally opened up, and it was great.

Parking v2

Apparently the decal just works. I drove on to the base this morning, handed over my ID, and he handed it back and told me that I should have a good day. Much easier and quicker.

Parking

I lied a little when I said that the bureaucracy was finished. Only this morning did I get a parking decal for my car. Previously, I could only enter at one gate of the base, come at least 15 minutes early, and get in the non-decal line of the security checkpoint. When it was finally my turn, they would take my license, and write down a lot of information. They would ask me to open up everything in my car. This includes center console, glovebox, all doors, trunk, and apparently the fold-down arm rest in the back. Then, they go around the car with this funny mirror that is basically a much larger version of a dentist's mirror. It allows them to see the entire under-carriage of the car. They reach under the seats, and feel around. Then they tell me that I can close everything up, present me with a dashboard pass, and I can then find parking. Now I have a decal. I can enter any of three gates, I drive right up, they ask to see my NIH ID, and that's it. Theoretically speaking. I'll let you know if that works tomorrow.

A dip of the toes

When I went in on Tuesday, I was not expecting to stay there for a whole work day. In fact, I thought I would do my blood test and get my ID, then go home. I got to stay the whole day and it was great.

TA and AB collaborated in creating a list of papers for me to read. They gave me 12. I don't know if you have ever read a scientific paper, but there are really two types: easy to read/understand or is-this-English-it-is-not-comprehensible-at-all. They were all the latter type. Unfortunately, very few of the classes that I have taken at Hampshire were of any use to me in making heads or tails. I thought that maybe if I just read them, it would eventually click. Sort of like immersion in another language. So I just kept chugging through. I would finish a paper and think, 'I have no idea what their goal was, or if they accomplished it!'

For the past few months (since the beginning of January), I have been teaching myself Cell Biology out of a textbook. CJ told me which chapters I should definitely cover, and which I could skip. Unfortunately, he told me I could skip a lot of the protein and DNA stuff, which is all that these papers were about. I did preempt this though. I was interested in the protein and DNA stuff, so I did not skip that much of it. CJ, I know you meant well, and I don't hold it against you.

I wrote down questions I had about the papers. I was not sure that any of them would be particularly helpful, but I asked things about what a certain technique did, or why was it important to do such-and-such? I spent the entirety of Wednesday reading papers (I had spent some time reading papers on Tuesday as well, in between bureaucratic nonsenses). TA said that tomorrow (Thursday), I would meet with AB and him to ask questions and have a learning session. He set aside 1.5 hours, and I got nervous. We would meet at 11.

I came in on Thursday, and sat down to go over papers. And it clicked. I was not reading jargon, but I mostly understood what was going on! I finished that paper in probably half the time it had taken me to do earlier ones. [If anyone ever tells you that the human brain is not good at adapting, you should laugh at them...]

I finished the other papers I had left pretty easily, and went in for my meeting. I brought a sheet of questions, and even took notes. I did not need to ask half of the questions at that point. I think that TA and AB were impressed with my grasp of the material (they had not intended that I finish all the papers before Friday). They told me what they intended for next week, but they were in between experiments, so there was nothing for me to do in the lab until Monday. I asked if there was any reason for me to come in on Friday, and they could not see any (I am paid salary, not hourly, so if they said I could be off, I was still paid for it). It was not even lunch yet, so I went home and made lunch.

AK and I then went out to a park, and went on the swings a bit. I got to hang out with her for the rest of the weekend too! It was great. We went to a mega-church on Sunday morning. AK is studying fundamentalist Christianity, so it was a real treat for her. She really enjoyed it. I enjoyed it too. It is a really well-oiled machine! They gave us some really great travel mugs because it was our first time there.

AK had to leave shortly after the service so that she could be back at Camp Hamp before the vampires came out. I miss her already.