Eisen Lab Blog

After spending the majority of our time collecting samples and doing water chemistry on site, we are all back in our lab ready to do DNA extractions and PCR galore. Unfortunately, the kim wipes we used to scrub microbes off the walls of the tanks are too large to fit into our tubes with the extraction beads. After about an hour of stressing and improvising, we were able to get a usable amount of supernatant…or so we hope. We will find out after we do our PCR.

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.

A couple of people have requested that I post information on the various kits and probes being used to assay water chemistry for our aquarium study.  Here’s the list, divided by type with a link to each item on Amazon.  Also various user complaints.

Probes:

pH  (worked fine, held calibration well)

Salinity (worked fine, held calibration well)

Temperature (annoying, a bit fiddly, I wouldn’t do this one again)

Titration-based kits:

Hardness, Alkalinity, Chloride, and Sulfide were all measured using this combo package  It also includes an iron assay that we didn’t use.  All of these kits are prone to error since they’re titration based.   But used very carefully (takes time!) they seemed to produce okay results.  I recommend using glass flasks instead of the plastic beakers supplied.

Colorimetric scanners:

Dissolved oxygen (this kit requires that you have a glass container capable of holding exactly 60 mls of water.. they don’t tell you this until you read the instructions.  Otherwise worked fine.  A bit hard to use but conversely you’ll learn new vocabulary from reading the instructions)

Ammonia (worked fine, but you have to be very careful to follow the instructions and mix between adding reagents or you’ll get a false high reading)

Nitrate (worked fine)

Nitrite (this one is pretty annoying; it’s hard to get the reagents into the tiny vial and these handheld meters turn themselves off after only 2 minute so if you get distracted you have to start over)

Phosphorus (see nitrite, but even worse.  As far as we can tell it’s not even possible to follow the instructions for this since it turns itself off before you finish mixing the reagents)

Since we’ve stopped sampling I went ahead and graphed out all the water chemistry data from Coral Pond #1.   Feeback, thoughts, comments etc. are welcome!