PCR A, PCR A, and more PCR A…

I’ve spent the week doing PCR A! So far I’m up to 40+ PCR A reactions. I finished up the 20 remaining samples needing PCR A this morning. After losing track of where I was in the PCR A process on Tuesday (and having to restart half of them) I developed an extremely organized way to do today’s set of samples! I meant to take a picture of the chart I made and used and post it here, but I forgot 😦


We are almost done with our preliminary set of samples to be sequenced! Assuming all the PCR A’s work, we will have quite a bit of PCR B to do (which is a lot quicker than PCR A!) and then gel confirmation, quantification, and dilutions to 1 ul. Maybe we can get it done in the next week.. too optimistic? We’ll see!


On a side note, David and a few others get to go to the Kings vs. Spurs game in San Antonio to collect samples for their space project. What a cool opportunity! (Say hi to Tim Duncan for me!)

Organization plan of attack!

One thing I would like to do tomorrow is go through our boxes and organize all the DNA, PCR reactions, and final products by sample ID #. I also want to write on the boxes of DNA and PCR reactions which numbers are in that box. For example, we have two DNA boxes (and probably more to come), and it can be quite tedious finding a DNA sample when you don’t know which box it’s in and the ID #’s are written very small on the lids of the 2mL tubes. (You would feel the same way if you had my terrible vision!)  I also want to take the original samples out of the freezer and write on the box which samples are in that particular box. Those samples are in the negative 80 degree fridge and it can be quite painful sitting there opening and closing box after box looking for the write samples. Hopefully I get a chance to do that and hopefully it helps 🙂

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!

Lab presentation last Friday

Unfortunately I missed our lab meeting presentation last Friday, due to a doctor appointment taking longer than expected, but I did learn a huge amount of what’s to come in the data analysis portion of our project (basically everything that happens after sequencing). It’s going to be a lot of work, from assigning OTUs to building phylogenetic trees and much more!


For now we will be continuing our normal lab work. We have made a few modifications to speed up the process. For example, for PCR A, we are adding a more rough amount of DNA rather than calculating it all out, which takes a good amount of time. Note: this does not make our end results less accurate.


I’m excited to finish our first set of time intervals for Coral Pond 1 so we can get them sequenced and start analyzing!

Pipet or Pipette?! And some updates on our project :)

First of all, how do you spell the thing?? I’ve seen it both ways.. pipet and pipette. I’m thinking it’s pipette because it doesn’t have the red squiggly spelling error sign under it. Just wondering!


Now for the good stuff! We’ve been rocking and rolling in the lab. (Except for the week I came down with the flu) We have so many samples and it would be a bummer to do EVERYTHING (DNA extractions, PCR, Gel confirmation, etc) for every single sample and have disappointing results. While we are optimistic about our results, we are currently preparing samples from the first coral ponds at different time points for sequencing just so we can see how our results look in terms of succession of the microbial community in the pond. If we get cool results (crossing our fingers) we’ll go back to the pipettes and prepare the rest of the samples!


We’ve got a lot of work to do but we are making progress. We are presenting to the lab next Friday about our project. I am really excited to get feedback from experts who know a lot more than me!

Advice on asking for letters of recommendation (updated May 2013)

This is based off an e-mail I sent recently to a student and someone suggested I post it here:

Asking for letters of recommendation

In general I, and others are happy to write letters of recommendation for people… it’s part of our jobs after all.  However, there are some tips I would offer anyone soliciting letters at any stage of their career.

1)  Don’t ask me for a letter only a few days before it’s due.  This seems like such a simple concept but one that is violated so often.

2)  If you ask me for a letter, you need to send a copy of your CV.  No matter how long I’ve worked with you, there’s probably still information in there I didn’t know and this helps me write a letter that doesn’t sound like a form letter.

3) Send me a description of the program you’re applying for and why.  Again, this helps me write a better letter and doesn’t force me to have to trawl the internet for information

4) Make it as easy as possible for me to write the letter!  This is especially critical with professors.  If the letter needs to be mailed, you should hand me a stamped, already addressed envelope so all I have to do is drop in a letter and throw it in the outgoing mail.  If it’s an electronic form provide me with detailed instructions and links.

5) Don’t attempt to bribe me.  I’m not kidding… for example once I got a handwritten request for a letter of recommendation along with $50.  This is not a good idea!

(Updated with two more in May 2013)

6) Before asking a post-doc or a project scientist for a letter of recommendation make sure that you don’t actually need one from the professor.

7) Don’t list me as a reference for anything without at least asking first.

Finally back in the lab

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.

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.

Water Chemistry Sampling: Our kit list

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.


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)