Blogs

This week we ran into a problem. First we discovered that the function that id supposed to BLAST sequences for the user does not work on my machine. The problem is very deep within one of the packages that were imported into the application. This was a big setback because allowing the user to BLAST on their own machine is one of the main purposes of the application.

So today is Monday already! Last week was the final stretch of lab work for me and my project. The week (after our return from the labs at OHSU) was spent preparing a PCR of our samples to isolate and amplify DNA (including some colony isolates as well as three 9A1 samples). Most of the samples worked in the PCR and yielded good results, so some were chosen and the DNA was cleaned. On Friday, the cleaned DNA was concentrated down and taken to the primate center to be sequenced :)

We are almost home. Justin Roberts, a CMOP intern, wrote a song about our adventures aboard the R/V Wecoma. It is a fun look back at what life was like aboard a research vessel. It's not all chasing salinity and collecting marine microbes.

Today is the day we present the lesson plans to the whole group. Most groups had PowerPoints to aid them in presentation. The site is:

http://www.mbari.org/earth/2008/schedule.htm

The lessons and activities are listed under Friday.

Of the 30 people there, we now have an admirable selection of lessons from this workshop. The activities are using RTD or are about current microbes and how they affect the world.

Today we divided into groups to try and look at what we had learned all week to make into lesson plans that could be useable by teachers, using the info we got. The intention is to make them into Real Time Data lesson plans, but not all the lectures were based on that. So some teachers did that and some used other info.

We worked in partners and worked through lunch and dinner, some working as late as 9:30pm.

Today we had a lecture on how to use the HOT DOG Data sets. HOT DOG is the Hawaiian Ocean Time series and Data Organization and Graphing Series. It is fairly complicated, but there are simplified instructions on an educational site...http://www.mbari.org/earth/2008/schedule.htm#Wednesday

go to Friday >look under the names of Stephanie and Becky > look at HOT Data

You have to know which cruise to look up and what kind of data you want.

We also had a presentation on Satellite imagery, and the many ways it is being used today.

Today was another day of learning, lectures, and tours. We had a speaker from MBARI speak on ESP's, Environmental Sample Processors. They collect data from biological samples remotely and through DNA isolation and PCR, can identify the species and send back the information to a lab. CMOP is acquiring one soon! The data from these is not as readily available as some of the data from other sites for teachers and students to use.

Nirzwan gave Khalilha and I diagrams (scanned onto the computer) of the eustuary and sediment distribution. He instructed us to make the differences more apparent by adding color.

After finishing the maps, we were told to answer the following questions:
How many different types of sediments were found?
Seasonal Differences? Which seasons?
What does the generalized sediment distribution map show?
Overlay the north and south channels.
What sorts of sediments do you see in the north channel?
What sorts of sediments do you see in the south channel?

It is day nine aboard the cruise and Byron Crump has taken me up to the radioactive isotope lab to perform bacterial production measurements.

Yesterday evening we received waypoints/waytimes from Grant Law for today Feature Tracking Exercise. We did one of these on the 16th during the Spring Tide. Now that it is Neap Tide we are doing it again. We were not able to get to the first way-point in time after pulling the drifter at 08:30, so we started our series a little late. Grant updated the surface salinity forecast for the locations and times we did CTD casts, and the numbers improved.