Here comes the science, Part 2

This time around I'm going to dive down into a little more detail about what actually goes on in the process of making this optical maps of DNA samples. At a theoretical level, the process is fairly straight forward and sounds pretty basic. However, as I'm learning while working here, real life does not think very highly of our nice, simple, straight-forward theories. So the process has to be very robust, especially on the software side, which makes me very glad that I work with a lot of really smart people.

Making DNA lay down straight
The whole linchpin of this process is being able to measure the length of the strands of DNA (more accurately, the lengths of DNA fragments but we'll get to that shortly). In order for length to have any meaning, we need to have the subjects we're measuring be as close to a straight line as possible. In order to do that we use a glass surface (you remember those microscope slides you used in high school) and a cover slip that has microscopically small channels carved into it. The DNA is placed, in solution, onto this surface and, using a magical process I know nothing about, the DNA is stretched out along those channels which serve as guides for straightening out the molecules.

Cutting it up into fragments
In order to create meaningful maps that can be used to identify and compare organisms we need to break up the DNA molecules into fragments. It's these fragments that we measure to create that nice-looking barcode map. In order to create those maps you use what is called a "restriction enzyme", which are enzymes that actually cut DNA. A particular restriction enzyme always cuts in the same place, at a particular occurrence of base pairs in the DNA strand. For example, the enzyme BamHI cuts at restriction sites of GGATCC. As an aside, most restriction enzymes cut at sites that are palindromic.. there's no obvious reason that I know of why that is, but it sure is a neat coincidence. Due to the genetic makeup of different organisms, different enzymes will cut different numbers of fragments for each organism. Part of our process is picking an enzyme that will cut the "right number" of fragments, that is, enough to make a meaningful map. Too few fragments or too many fragments often make the maps indistinguishable from each other.

Measuring those fragments
As part of the preparation of the DNA, a stain is applied that will cause the fragments to light up or "fluoresce" when exposed to a laser. The glass slip containing the DNA solution is placed on a fluorescent microscope that has a camera attached to it and an automated software system moves the camera up and down the length of those channels and takes pictures through the microscope. Here's an example of what it looks like. Remember this is one tiny fraction of a single image from the microscope. You can see several broken strands of DNA. The colored one is one that has been picked out by the software as clean enough to be measured and recorded.


Hundreds of such images are acquired and finally fed through some image processing software that finds the nicest looking DNA molecules and it finds the fragments and measures their length in some unit of measure that is smaller than anything I can image. Finally those fragment lengths are recorded in order and they can be visually represented by that barcode-like display I showed last time. Here's an artists interpretation of how that looks:


Assembling the pieces
Here's where the real world comes in and whacks you in the head. DNA will almost never stay fully in tact throughout the process I just described. And even if it did, there are usually a lot of molecules and they tend to overlap each other or they don't straighten out exactly right (or sometimes at all). So what you end up with is lots and lots of small maps that represent just a chunk of the entire strand of DNA. And here is where some intense computing power is brought to bear on the problem as we take all of those smaller maps and try and determine how and where the overlap each other. It's kind of analogous to trying to put a piece of paper back together after it has been through a shredder. When this process is finally done (and everything worked out okay) you end up with a "consensus map", which is the amalgamation of all of those smaller map chunks.


Once you've got that consensus map, then the doors open to a wide range of things you can do with it and that's where the software that I'm working on comes into play. But I'll save that stuff for the third and final installment of this series. Thanks for reading!

Here comes the science, Part 1

I've been wanting for some time to make a post or two to try and explain the basics of the science that is the core of our company. The techniques described here are in the public domain so there's nothing secret here. I've been working here long enough that I now feel pretty confident that I understand the process at a fairly high level.. just the right amount to be able to describe it to someone else that might find it interesting. For part 1 here, I will just describe the basic premise and will cover more actual detail in later posts. I've really enjoyed learning this stuff and I hope that other people find it interesting too.

The "Op" stands for Optical
The company's name, OpGen, is based on the fact that the core scientific process behind the business is called "optical mapping" which is, in short, a technique for taking physical samples of DNA and creating a visual representation of it such that unique organisms can be easily differentiated from each other and similarities between other organisms can be easily spotted. The whole concept is that you can break up DNA into many fragments and then put those fragments together in a line and you get what we call a "map". What's useful about this is that similar organisms will consistently and repeatedly break up in the same way such that their maps are very similar. As you'll see later, these maps almost look like barcodes and you can actually think of them as such, or as a "fingerprint" which uniquely identifies an organism. Here's an example of what one might look like:


What's it for?
The most interesting applications for optical mapping that I am aware of are in the area of what we call "comparative genomics" (other people might call it something else). Basically, it's the practice of looking at a number of similar or related organisms and analyzing what's different about them. For instance, say you have maps of two isolates of the same species of bacteria that cause infections in humans. Furthermore, say that one of those isolates is known to be extremely nasty and hard to treat, while the other is easily killed off with a round of antibiotics. By comparing the maps of these two bugs, you can actually see where the two are genetically different. Those parts that are different most likely indicate where the nastiness of the bacteria is regulated and can point the way for researchers to know where to look when trying to figure out how to combat that strain.

Coming soon...
In future posts I'll tell you more detail about how we actually create those maps and talk about the software I'm working on and how it pertains to these maps.

Captain on the bridge

This week marks the first working week for our newly hired CEO. The board of directors and our executives spent quite some time looking for the right candidate, with an appropriate level of experience in the biotechnology field, and I think they've found a good one. I've just met him the once, but he seemed like a very personable person and even had some good technical questions to ask me. It remains to be seen what kind of direction he is going to be taking us in. I've always held the belief that the CEO really sets the "mood" of the company .. shaping the way that people relate with each other and the ways the things get done.

To start us off, we've got an all company meeting tomorrow... at the bowling alley! Sounds like a good way to get started. I hope I can still keep it out of the gutter. It's been a while since I last bowled. But in, seriousness, I like the fact that one of his first actions is to create an informal, fun environment for allowing us to get to know him and vice versa. That indicates to me that this is not your nose-to-the-grindstone, slave-driver type of person, but rather someone that acknowledges that employees need to have good relationships with each other in order to be productive.

I personally believe that good team chemistry (a combination of trust, respect, friendly competition, openness, and the ability to have fun) is of utmost importance when you need people to perform at their best. You can have an environment where people dislike, distrust, or disrespect each other and still get work done, but those people won't be as motivated or productive as people that feel at home when they're at work.

I'm working on developing that level of comfort with the people I immediately work with and I'm excited to see that our executives are actively working to encourage it, too.