Week 4 at Chandran Laboratory

My name is Anna, and I'm working at Dr. Kartik Chandran's Laboratory at Columbia University in Earth & Environmental Engineering.

So this week was mostly defined by transitions. Our batch reactor's finally reached their stable population so we took them and put the reactor into chemostat. Where batch reactor's have nothing going in or out (technically) and are used to watch change over time, chemostat reactors have influent and effluent moving at the same rate. This means that nothing changes: the population is constant, as is the amount of ammonia, nitrite, etc. The reactor is going to spend two weeks stabilizing in chemostat and then the real interesting stuff will begin. Even though I won't be there for it, the next step will be disturbance, or increased feed chemostat. In this phase, the bacteria will be subject to one hour of ammonia loading. Our strain, Nitrosomonas eutropha, is known to prefer larger quantities of ammonia as compared to its N. europa cousins, and hopefully this means that it produces NO and N20 gases differently (i.e. less of them.) However, this ammonia loading will require hourly testing for 12-15 hours every day, so I'm not completely heartbroken to be missing it. After those two weeks, tests will be done to see if the bacteria retained any of the previous traits.

We will be testing for the next few days to get baselines for ammonia, nitrite, hydroxalimine, and some mRNA stuff as well. We will also be creating our own standard curves for the aforementioned chemicals because we are finally getting into work that could be publish-able. Next week I will also be working on some poster drafts to present to Medini and Dr. Chandran.

In the past week, there has been an influx of people coming to the lab, including high school students, and new grad students. (Very thankful that I've had my own desk this whole time.)  

Although I can't stick around any longer, I look forward to periodically seeing how this project develops and maybe working with Medini again.

Week 2 and 3: Reactors and Reacting

My name is Anna Piwowar, and I am currently working at Dr. Kartik Chandran's lab at Columbia University, working with ammonia oxidzing bacteria in batch reactors and studying their kinetics.

This week began with Medini and I cleaning out the reactors and setting them up for a new cycle. Between rinsing and autoclaving, it was a lengthy process. We had to overcome many problems (pieces that didn't fit, screws that had to be unscrewed, and everything in between). Finally, we thought we would be ready to inoculate our sparkling clean reactors and begin looking at cell growth. However, problems kept cropping up, and Murphy's Law held true: everything that could go wrong did. *(Not everything did go wrong, yet. So I don't want to jinx anything but we are still able to move forward with the process.) The DO (Dissolved Oxygen) probe on one of the reactors was found to be defunct, so now we are in the process of ordering a new one (and they do not come cheap). We do have the one reactor working properly enough for the time being, and hopefully we'll start collecting data on cell growth and nitrite formation.

While the process goes, I have a lot of time to read. Medini has many textbooks to offer me, and on Tuesday it was all about studying reactors, all the types and the equations. Sadly, I lack the Calculas to understand some of the things, but after an arduous tutoring session with Medini, I understand what the kinetics are and what we need and why.

By the end of the week we decided to go forward with the second reactor without the DO probe, and instead opting to manually find the dissolved oxygen. Even though we can't have simultaneous growth, we will at least have two sets of data.

The third week was all about data collection. We went forward with the second reactor, and now we're just working on maintaining the reactors and improving my laboratory skills. My PI is out a lot, but I will be meeting with him soon to talk about other things I might pursue for my last few weeks here.

Other than that, Columbia is beautiful, especially with the cooler weather, and having the chance to travel around Manhatten is wonderful.

Chandran Laboratory Week 1: Dawn in Morningside Hights

So unlike my peers, who are mostly finishing up their lab work, I have only just begun my work at the Chandran Laboratory at Columbia University, working with a graduate student studying ammonia oxidizing bacteria and nitrous oxide and nitric oxide emissions.

 My new role as a commuter began when I was dropped off at the PATH station, gearing up for what I assumed to be a 2 hour commute to upper Manhattan. To my delight, everything went much faster than expected. I arrived and with only minimal trouble, found the correct building, and met my mentor, Medini, who is a first year graduate student and whose research I'm helping with. My PI, Dr. Chandran, was doing "field research" with another graduate student, and I would soon learn that he is often out of the office and very busy (although we did get a chance to meet to talk about the lab goals).

The first few days I passed the time observing Medini and her pure-culture batch reactor. Thus far all that she had been doing is observing the cell growth and troubleshooting reactor problems. The machinery is pretty cool, with the tub full of the media and cells connected via all these tubs to a fancy machine that regulates everything and shows all the things happening for you, except cell growth and product formation, which would be our job to track. Basically, her work involves Nitrosonomas eutropha, which is an ammonia oxidizing bacteria vital in nitrification, which is the change of ammonia into nitrate (via a few intermediate steps). Because the batch is a pure culture, meaning that no other bacteria are growing in it, this means that every piece of equipment and everything around it has to be extremely sterilized. Right off the bat, in order to retrieve a sample from the reactor, Medini had to use a Bunsen burner to switch out the tubing. Until my safety training, I could only observe, take notes, and hopefully absorb some skills.

Friday came quickly, and just in time for a new cycle of cell growth to begin. We had to make new media and autoclave many things and will soon be inoculating the reactor. While the cells grow in the reactor, we will be first observing their batch growth curve, which will involve lots of cell counting. Then we will be looking at product formation, in this case nitrite, using a spectrophotometer. Once the cell population stabilizes, then the real experimentation can begin.

 Fortunately, the heat wave is subsiding and I am particularly grateful seeing as I'd have to walk through the heat in my lab-appropriate long pants and cardigans. Today I met another high school student who is beginning a two year stint in the lab for INTEL and other lab research work, so it's good to see a familiar unsure face. The rest of the lab is graduate students and post-doc's from all over the world. According to Medini, it's one of the most diverse group of people around. From China to Brazil to New Jersey, the lab guarantees a lot of learning experience.