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Archive for April, 2012

Lab at Zzyzx

Lab Building at the Desert Research Station at Zzyzx Road, CA.

On this third day of our research project in the Mojave Desert, we did a series of tests on the biological soil crusts and soil samples we collected yesterday at three sites along Kelbaker Road near Baker, CA.

Parag and Rakesh

Parag and Rakesh demonstrate extraction protocols

The laboratory building at the Desert Research Station is set up with standard equipment for chemical and biological tests, including flasks, test tubes, Bunsen burners, sinks, a fume hood, etc. Most of the detailed equipment and supplies was brought by Rakesh Mogul and the other scientists working on this project, including a centrifuge, a spectrometer, pipettes and pumps, and test kits and reagents for the extractions and analyses we’d be doing.

Interior of lab

Inside the lab building at Zzyzx Road

The students and scientists had set up a series of protocols for the tests and a plan of attack for how to identify each sample. First, a group were taking samples of the crusts at each location and extracting the DNA from them. Each time, the scoop was sterilized with a Bunsen burner. The solution was then centrifuged to settle out the non-dissolved portions. Another group was at work using polymerase chain reaction techniques to increase the DNA yield so that the final sequencing could be done in a specialized lab. We’ll have the lab look at the specific species in the crusts, including the cyanobacteria, fungi, lichens, mosses, and archaea present in these symbiotic communities.

Extracting DNA

Extracting DNA from the biological soil crusts

Parag Vaishampayan worked with a group to extract ATP (adenosine triphosphate), which will give us a measure of metabolic rate in the crusts at each site. We sampled not only the crust itself but the soil directly underneath each sampled crust, and will look at ATP of the crust compared as a ratio to the ATP in the soil. The hypothesis is that the healthier crust will have a higher ratio.

Extracting ATP

Testing for ATP

Meanwhile, the soil itself was analyzed. Mary Beth Wilhelm and Liza Coe used a soil test kit to look for trace elements in the soil, such as aluminum, iron, chlorine, and magnesium. I helped do some of this analysis, since my background is in chemistry and geology. Rosalba Bonaccorsi, Ruben Hovanesian, and Leonard Bacon separated the soils using sieves to find the relative sizes of particles and materials at each site.

Soil tests

Testing the soils chemically

A final group of pre-math teachers developed a series of statistical tests to look at results of all these tests, including some ANOVA (analysis of variance) tests, which I vaguely remember from my masters degree program.

Pipette instruction

Instruction on pipette techniques

We got quite far with the tests today – it helps to have a group of people who are experienced and work well together. Although they come from all over the California State University system, the students are all in their second year in the program and know what to do and what each other’s strengths and weaknesses are. We all helped out where we had experitise. It was fun to see what college students can accomplish. We have one major remaining test for tomorrow: chlorophyll extraction and spectral analysis.

Statistical tests

Allison and Kristen working on statistical models

I also talked with Geoff Chu, Paul Mans, and Ryan Piaget from NASA Ames who are developing a prototype rover built from a commercial off-the-shelf RC car, with video camera provided by an Android phone controlled from a laptop over a local network. Motor servos are controlled by an Arduino brick. The point of this rover is to analyze the soil crusts remotely without having 20-odd people stomping around on them. The rover will be equipped with a stereoscopic IR camera that can read 3D depth, along with an RGB camera. My goal is to take the height data from the IR camera and convert it into a grayscale heightmap of the various crust locations, then turn the heightmap into a 3D model in Daz3D Bryce. The RGB photo will be mapped over the top of the model as a texture. Ultimately, the model can be uploaded to an online app where people can rotate and explore the crusts themselves.

Geoff and Paul

Geoff Chu and Paul Mans working on the RC rover

We had a preliminary results meeting after supper to look at what we have so far. The ATP analysis was not consistent across sites, possibly because the results changed as the day warmed up, but we’ll send the samples to labs for more accurate results.

Review session

Review session for today's results

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