Category Archives: Undergraduate Aquarium Project

Photos from the now-thriving aquarium project tanks.

Just got these photos of a couple organisms that are thriving in the aquarium tanks that we helped set up as part of the Aquarium Project.  Stay tuned for sequence data one of these days…  

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Final Presentation of Aquarium Project

Today was the final presentation by the students working on the aquarium research project. Alex, Lakshmi, Sabreen, Andrew, and Kevin all talked about their recent work using QIIME to analyze the 16S sequence data from the project. Their presentations, along … Continue reading

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Learning How to Work Qiime

So we’ve done our data collection, we’ve done more PCR than we could ever imagine, and we finally got our sequences. Now what? We analyze our data using Qiime, a software that will help us see connections between our microbe … Continue reading

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Aquarium 16S library submitted today

Seven months after starting the sample collections we finally submitted our pooled 16S library today for sequencing.  We have somewhere around 90 samples from a few different types of aquariums and our community succession experiment.  Now time for everyone to … Continue reading

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Sitting in the lab

I’m sitting here in the lab looking at our google doc and it’s looking pretty good! We only have a few final dilutions to do and we’ll be on our way to sequencing! I’m waiting for David to come back … Continue reading

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We are getting close to sequencing!

A few of the PCRs last week didn’t work so I’m finishing up the last PCR B’s right now that we’ve had to redo and then all we have to do is Gel confirmations. If I counted correctly there are … Continue reading

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Aquarium project poster at the UCD Undergraduate Research Conference

Here’s the poster that Lakshmi prepared for the conference.   The presentation went well!  Thanks to everyone who helped out.

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Amazon Research Grant for Aquarium Project

Just an FYI that Holly and I received a grant from Amazon for a bunch of cloud computing credits for the aquarium project.   This will allow us to run all of our various 16S analyses for free on their servers. … Continue reading

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PCR B

Today I did 32 PCR B’s. It may sound like a lot but PCR B’s are extremely easy so it went by pretty quick. I also messed up on updating the google doc and had to throw away three PCR … Continue reading

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Today in the lab

Today I primarily focused on reorganizing some of our stuff. First, I went through our two boxes of extracted DNA and put them in numerical order by sample ID. I think at one point they were in order but with … Continue reading

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