Poop's Lessons

"A parasitologist is a quaint individual who spends all day on a stool looking at another one."

This was one of the first things that greeted us upon entering the parasitology lab, which, although since my department consists of only one floor and this lab being the only one on the floor, is the same laboratory  I have all my labs in these days, we all knew that it would be different.

Our professor introduced herself as "the Poop Queen." All fecal matter aside, there would be no Parasitology lab.

And this is the main gist of it. I grew up thinking I was so interested in parasitology, aweing and gawking at countless colorful pictures of deformed and misshapen extremities. I heard tales of the origins of the physician's staff symbol (look it up) and loved taking my pets to the vet because it meant I got to see a dog's heart-worm infected heart preserved in formalin upon his desk. I thought I loved parasitology, and when I found out I would be taking it this semester I was ecstatic. The laboratory and the lecture! How awesome!

His name is Cadaceus. Awe at him.

So when my professor greeted us with those words, I felt it must be truly in jest. Surely, a parasitologist's job involves more than just gazing at poop. But from the beginning of lab, I knew I was mistaken.

We began the lecture by discussing the proper collection and preservation techniques for "formed" and "diarrhetic" stool, and just dove deeper and deeper into the subject. Stool samples, especially fresh diarrhetic ones, must be examined quickly. Diarrhetic samples must never be allowed to cool. And did you know: oftentimes the infective form of a parasite is only in formed stool, and not present in diarrhea?   Throws off that evolutionary theory that pathogens always cause symptoms that help progress their reproduction and spread, now, doesn't it?

We then spent thirty minutes going over pictures of all of the crap that can be found in crap. Hair that suspiciously resembled worms, fibers that looked astonishingly like larva, animal, vegetable, and plant cells that just looked creepy, and of course, the ever present ubiquitous "fecal debris." All normal. And then, the abnormal. Amoebic trophozoites (the form you see when you think amoeba) and cysts, roundworm and hookworm larvae and eggs.

Formed specimens can be kept in formalin and refrigerated for up to 24 hours. The most common stool sample stain is a simple iodine wet prep. So on and so forth. And then we did it.

The samples of stool were small enough not to smell badly, but were large enough to constantly remind you what exactly they were. A caramel brown color, they consisted of about ten milliliters of liquid in yellow-lidded sample tubes. We had to place a tiny drop of iodine upon a large microscope slide, and then place an even smaller drop of stool right on top of it, then mixing it. We placed a coverslip gently over. If any of the mixture seeped outside the range of the coverslip, we had to do the procedure all over again. If it did not, we were free to use nail polish - yes, nail polish - to seal the edges of the coverslip to the microscope slide, in order to prevent the sample from drying out.

We allowed the nail polish to dry, setting up Koehler Illumination as we did so (a whole other blog post), and then checked out our "stuff."

Immediately, I was struck by the amount of crap that was in crap. Granted, we'd spent the past hour and a half discussing it, but to actually see it was an entirely different. I was assaulted by all forms and shapes of various sizes but generally of a brown color. Being by nature a microbiology nerd, I noticed first the various rod-shaped and round bacteria Brownianly floating and squirming by, and would have like to oil-immersion those buddies and check them out.

However, being a wet prep, we were expressly forbidden to use oil immersion and were limited to using the 40x objective. The reason was that before we left lab that day, we had to find some sort of parasitic remnant in our stool sample. So systemically, I looked and looked and looked.

I found a whole bunch of wormy-looking fibers, some of disturbingly bright colors, round things that were too small to be anything and contained nothing of importance, and as always and forever - fecal debris.

Finally, after thirty minutes of looking, I found a cyst. It was a harmless looking thing, perfectly round with little dark circles inside (nuclei).  Yet however friendly this guy might appear, he wasn't messing around. He was the infective form of Entamoeba coli. OK, not strictly a pathogen, but definitely a guy you didn't want floating around in your food or water. He was a valuable indicator of fecal contamination, meaning where he was hanging out, poop wasn't far from him.

Entemoeba histolytica/dispar cyst. NOT something you want floating around in your drinking water.

We'd spent a good two solid hours looking at these stool samples, and by the end of it I came to realize something. Sure, there's the obviously trite and cute lesson of "one man's trash is another man's treasure," but there's also the deeper lesson of how all-expansive life is.

Here we were, staring at life forms whose entire existence revolved around stool, something we consider nothing more than to be "dumped" and flushed away. An entire existence was going on in something we never ever take a moment to think about, unless we're sick, and then it's only in terms of its shocking volume or lack thereof.

And there are plenty of things like this, existences going on in long hidden (maybe forever hidden) worlds, microbiology being a perfect example of a once-hidden world that was revealed to contain so much with the advent of the microscope. We think that such existences are insignificant, not because they are but because we do not understand them or fail to notice them. Our existence is surely among them, a world that makes little to no impression upon other worlds around it, worlds that exist outside our sphere of influence, or far too inside to ever become noticeable.

And other worlds may interact with ours, worlds that govern our every interaction and every moment of our being but are too intrinsic and basically a part of it that we have and will continue to fail to notice them.

All this, from a stool sample.

Gel Electrophoresis, or the Electrical Seaweed

Today I had my first lab in the Clinical Laboratory Science program, my first professional program, and I also created my own agarose gel! It was so exciting!

So, once upon a time there was an ocean, and it supported different types of life. One of these life forms, in fact, one of the first to emerge out of this hotbed of biological activity was seaweed, which while it resembles modern day plants is actually a type of algae, and predates plants as we know it by thousands of years.

Do not let the name or appearance fool you! This is a nasty group of unicellular algae working together as one biological unit.

This seaweed, quickly becoming a source of food for many other forms of life springing up in the ocean, also possessed certain qualities which make it useful for specific groups of individuals for specific reasons. The polysaccharide walls of red algae seaweed contains something called agar, which besides being one of the hardest words to rhyme also is a polymer made up of the sugar galactose.

The reason why agar is in the walls of algae is because it provides excellent structural support with flexibility. This same quality makes it valuable to chefs with molecular gastronomic intents, who must use it sparingly because it also acts as a laxative. Vegetarians use it as a beef-free alternative to gelatin, and for this reason it's increasingly used by companies as a thickener for soups, jellies, and ice cream. Did I mention it is completely non-toxic?

Tasty, tasty seaweed.

For us rats who reside in the darker, flourescent-lit and often horrendously smelly laboratories, agar proves of interest because of its quality as a medium. In microbiology labs, agar is mixed with variable concentrations of solvents to produce solid or semi-solid medium. Its ability to provide an oxygen gradient is invaluable to scientists growing anaerobic bacteria, and unlike vegans and vegetarians across the country, bacteria will not eat agar and instead simply set up shop upon it.

An agar plate, upon which bio-luminescent bacteria apparently unanimously decided to grow in a scenic pattern. Note: there is no eating going on here.

In molecular biology and genetics, agar is encountered in the process of gel electrophoresis. The basics of this technique are very simple. Opposite charges attract - negative attracts positive, and positive attracts negative. In gel electrophoresis, a gel medium is placed inside a buffer solution inside housing that is connected to an electrical source. One side of the housing is connected to the cathode, the other side of the housing is connected to the anode. Samples of different substances, primarily DNA, are placed inside wells in the gel and the device is turned on. Once that happens, the charged samples move to their respective "opposite" sides. The movement of these particles therefore depends on their size, shape, and charge. Bigger particles move slower, and the more charged a particle is, the faster it will move to it's oppositely charged side.

Gel electrophoresis apparatus. Observe the disparity between the coolness of the name and the visual of the device.

Agar is chosen as a gel medium because when its placed in solution, depending on its concentration it will form pores of various sizes. The particles in the samples move through these various sizes, thus by adjusting the concentration of the agar in the agarose gel medium you can select how fast the particles move and how much they become separated. Another quality of agar that makes it the molecular diagnostician's wet dream is the same one that makes it a chef's bee's knees - it's lack of toxicity. There is another gel medium used in electrophoresis, by the ugly and smart-sounding long name of polyacrylamide, which is so ridiculously toxic it kills neurons. You can automatically tell who the favorite is here.

Why is gel electrophoresis useful? Well, DNA is negatively charged. This makes gel electrophoresis a great tool for separating DNA from other components, and separating differently sized and charged particles from each other for isolation.

Yet another example of the incredible, edible seaweed!