Updates about the Undergraduate Research Conference

Hello Everyone,

I have a few updates with regard to the Undergraduate Research Conference.

The abstract that I turned in originally had a few mistakes, so I made sure to contact the Undergraduate Research office at the Student Community Center. Initially, they said that they wouldn’t allow any corrections upon submission of the abstract, but I was slightly insistent, so they agreed.

The updated abstract has been developed after considering everyone’s inputs and modifying the original abstract as necessary. As of now, it reads as below:

Aquarium Biogeography and Succession of Microbial Communities in Aquatic Environments

The biological sciences teaching laboratory for UC Davis maintains a wide variety of large aquaria, including freshwater and marine tanks, designed to mimic both temperate and tropical ecosystems. In this study, we seek to better understand the biogeography of microbial communities associated with these tanks. Using a culture-independent, DNA-based community census approach (i.e., 16S rRNA PCR surveys), we tackle two main questions: 1) how do microbial communities vary with respect to various environmental parameters (temperature, salinity, pH, oxygen and nitrogen concentrations) both within and across tanks; and 2) how does the structure of microbial communities change in response to ecosystem disturbance. To address this second question, we coincided our data collection with the establishment of two new aquarium systems (coral ponds).  We use high-throughput DNA sequencing of the 16S rRNA gene to generate a microbial community profile from hundreds of samples. These microbial community profiles are then compared across tanks (marine vs. fresh water, warm vs. cold) and in response to disturbances introduced during the establishment of the coral ponds.

I hope this acts as an almost accurate summary of what we are doing. The abstract was accepted, reviewed and approved by the URC people, so we are all set as far as that is concerned.

I need to also come up with a poster to represent our lab and the kind of work we do, and I get access to free poster printing services for that, so yay! This work is going to start next quarter, and I’m hoping that some of you will pitch in and help me out to make a good job of it and represent our lab in the way it deserves to be showcased. Also, I don’t know if others are allowed to co-present with me. If you are interested, do contact the URC office, I think it’s a great opportunity.

I attended the mandatory meeting for all participants of the conference. It was hosted by Tammy Hoyer of the Undergraduate Research Office today. It was pretty informative in the sense it gave me information on all the resources that were made available to me and what I could expect at the Undergraduate Research Conference.

Also, Tammy mentioned about the Undergraduate Research Journal, Explorations. They are currently taking papers, and I believe the deadline is 6th June, if I heard correctly. I know we wouldn’t have completed all of our research by then, but just letting you know of the opportunity.

Well, that’s all for now.

Also, starting next quarter, I will try my best to do the 8 hour a week thing, will be coming in on Mondays and Fridays, a 4+4. I hope to work with most of you during that time.

Good luck for finals!

My progress with the Aquarium Project

Hello everybody, 

Thought I’d do a quick log/blog entry of what I have been doing in the lab for the past couple of days. I just got a brief introduction to sampling the first few times I was in the lab. I didn’t do too much of hands on sampling, but developed a fair idea of how it was done before it all ended.

And now we are moving on to do PCR’s and DNA extractions.  This is what I consider to be the core of the project and I truly hope to learn a great deal from it. I’ve never been exposed to all these techniques in this particular way and that makes it really exciting to learn all these things! I was really happy to see magnetic beads, cytometers and micro pipettes the first time I entered the Genome Center. 

The last time I was in the lab, I was introduced to the basics of analysis, and I learnt how to handle the micro-pipettes. I look forward to performing PCR this week.

Another important update: Currently, I am looking for people in the lab to work with me on the Undergraduate Research Conference. It is something I am really interested in because I love making posters and talking about research and also learning about research. If anyone is interested in doing this, I am willing to help out in any way possible.

The link to the conference page is here: http://undergraduateresearch.ucdavis.edu/urcConf/

I think it’s a good opportunity for the Eisen lab to talk about its achievements! 

If anyone is interested, please let David Coil know, and if you need help, please do ask me. I’d love to do my bit! I hope to hear back on this.

Introduction and my first day of sampling: Undergraduate Aquarium Project

Hello Everyone!

Since I am new to the lab and not many of you know me, I thought of positing a quick introduction along with my first day experiences with sampling.

My name is Lakshmi Bharadwaj, you’ll probably see a lot of me this quarter.


(That is how I look like if you find me walking into the lab, you can say hello!)

I hope that I get to work in the lab with all of you at least once. Here’s a little bit about me:

I am a senior Biomedical Engineering major and I love photography, writing, swimming and microbes! Currently, I am extremely curious about bacteria, and my senior design project is all about how they infect your bloodstream, their clinical relevance and detection. I haven’t really dealt with a lot of microbial procedures: my time in engineering lab has been mostly machine work. So I’m really excited to learn from all of you and also observe how things work in a biology lab!

My first day in the lab was exciting because I hadn’t really seen anything like it before. I got introduced to the basics. I learnt how to correctly obtain the water, sediment and wipe samples. I learnt of the rate-limiting step in the procedure, proper techniques etc. Then, David taught me some lab protocols that I needed to follow. I was really glad with the pipettes that the lab uses because I find it extremely convenient. The only one time I have used micropipettes before involved stops and was slightly confusing. I find our pipettes so much easier to use.

I also got a basic understanding of what water chemistry involved. I learnt about how there were different tests for different chemicals and all of them required a different procedure. Although I couldn’t perform all the procedures, I got a pH reading and observed how oxygen levels were tested for.  I hope to perform each test individually and learn it in greater detail next time.

I was half-way through testing, but I had to abandon it last minute because of incorrect dilution. I did obtain a fair understanding of how this should be done in my two and a half hours in the laboratory though.

During my time in the lab and with the genome project, I hope to use this blogging space to document my observations and have it act as my notes/log book. You should expect a blogpost from me weekly.

I wish to come in every week, probably on Tuesdays or Wednesday mornings and I look forward to meeting everybody.