REU Tour of The National Museum of Nuclear Science & History and CINT

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Linda Bugge, our REU administrator coordinated a wonderful day for all of the REUs yesterday.

We all met at CHTM at 9:30 to carpool to our first destination, The National Museum of Nuclear Science & History. We arrived just in time to watch Modern Marvels, The Manhattan Project. I hadn’t seen the show before today, and was pretty impressed with the what I learned. A few key items that I recall (disclaimer: I am not making any kind of statement here, just recalling facts that I learned today):

  • The project was started in 1939 and cost over two billion dollars (over 30 billion in today’s dollars).
  • There were several, very large, sites built in a very short period of time to facilitate the building of the atomic bombs.The three main sites were Oak Ridge, Tennessee; Los Alamos, New Mexico; and Hanford, Washington. This map shows all the sites.
  • The three methods for obtaining Uranium 235 were all extremely difficult, time consuming, and labor intensive.
  • Most of the work done to obtain Uranium 235 was done in Oak Ridge.
  • Oak Ridge’s energy consumption was 10% of the total US energy consumption during it’s operation.
  • Since Uranium 235 was so difficult to obtain, there was only one bomb (Little Boy) made from this material… and no test bomb was made prior. The first Uranium 235 bomb to ever explode was the bomb dropped on Hiroshima.
  • Plutonium was easier to produce, and was made by a plutonium production reactor at the Hanford site.
  • Because they had plenty of plutonium, they exploded a test bomb on July 16, 1945. Fat Man was dropped on Nagasaki on August 9, 1945.
  • Since that time, war related deaths (U.S.) have declined exponentially.

After that we were free to view the exhibits of the museum at our leisure. At 12 we all got back together and went to Chili’s for a wonderful lunch. Next we headed over to CINT (The Center for Integrated Nanotechnologies) for a tour of the facilities and a few informative presentations by some of the staff.

2011/12 REUs outside of CINT

George Bachand was very kind, and took all of us around the facility and explained things as we were walking. The facility is quite large and there is a bunch of research being done. He was very informative, but to be honest, I understood only very little about what we initially saw. We then broke into two separate groups. One group went to tour microprocessors. I went with Wally Paxton’s group to take a look at his Soft and Biological Nanomaterials work.

Wally showed us his lab where he is “developing new strategies for efficient integration of functional molecules, including transmembrane transport proteins, and the means to characterize the action of these exotic molecules at interfaces.” Then we went into an adjoining lab and met another scientist, Nathan who showed us some video he had taken of microtubules.

Nathan had a lot of information for us about his current work and possible future applications for his research. If I understood him correctly, this could possibly, one day in the future, include repairing nerve damage and brain trauma. This was fascinating for me. It seemed similar to the work that Nadia Fernandez-Oropeza is working on. (Nadia is also one of Dr. Koch’s grad students. Anthony and I share a lab with her at CHTM.)

Next we all joined back up to hear from Mark Stevens, who told us about his work as a theorist. Finally Neal Shinn, the Co-Director of CINT, told us about the proposal submission process and life cycle. Basically it works like this:

Anyone who needs help with their research can submit a proposal for use of CINT’s facilities and/or scientists. There are two ways to submit proposals, during their twice a year “call for proposals,” which would provide access to CINT for up to 18 months, or as a “rapid access” submission for time sensitive or short term projects. The proposal should be no more than two pages. About 80% of the proposals submitted get approved. Once approved the only requirement is that the results of your research be published.

After that our day was over. I had a really good time and learned a lot. Many thanks to Linda for all of her efforts putting this day together for all of us.


Water Bears in the Lab


Wow, it’s been almost two weeks since my last post!  It’s almost spring break, and I’ve been studying like mad for midterms. I’ve been in the lab very little the past two weeks. <sad face>

Monday Anthony and I went on a little excursion to the Bosque looking for tardigrade habitats. Read his post here. It was an interesting experience. Anthony had mentioned tardigrades a few months ago. I did a Google search and found lots of interesting information about these little creatures:

Tardigrade (or water bear), the toughest creature on Earth.

  • They are found everywhere in the world, from the Himalayas to the Artic. They live in Hot Springs and Forests.
  • They can survive in extreme environments because they can pause their metabolism and enter a state of suspended animation, called cryptobiosis.When they are in this state they are in a tun.
  • They can survive without water for over 100 years while in tun.
  • They can withstand 1000 times more radiation than any other living creature known.
  • They can also survive in space (without space suites or spaceships).

All in all they are very impressive little critters.

So why were we looking for them? Well, since I’ve been here, all our research on D2O and DDW has been with tobacco and Arabidopsis seeds. We are now moving into the next phase of research, using yeast and e.coli. One day we were talking about this next phase, and Anthony mentioned that it would be cool to see what effects D2O and DDW have on other life forms. Since Tardigrades are so adaptable, we started looking into getting some for our experiments. Since they are found everywhere we decided to go on a Tardigrade hunt.

The following steps are how to find them (taken from Sarah Bordenstein’s page at Carleton College):

  1. Collect a clump of moss or lichen (dry or wet) and place in a shallow dish, such as a Petri dish.
  2. Soak in water (preferably rainwater or distilled water) for 3-24 hours.
  3. Remove and discard excess water from the dish.
  4. Shake or squeeze the moss/lichen clumps over another transparent dish to collect trapped water.
  5. Starting on a low objective lens, examine the water using a stereo microscope.
  6. Use a micropipette to transfer tardigrades to a slide, which can be observed with a higher power under a compound microscope.

Today we started step 2.

Bosque Samples in water, awaiting for Tardigrade extraction


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Today I ran FTIR spectroscopy on three ages of DDW, two ages of D2O and the four types of DI that Anthony is using in his current DDW5 experiments.

Many thanks to Stephen Myers for training me on the use of the FTIR, and Dr. Sanjay Krishna for providing me with access to the lab and machine. Stephen was in the lab today and was graciously helpful, as always.

As always I started with a scan of the empty cuvette for the background. Today I kept getting a really strange scan image. Stephen took a look and said confirmed that the scan didn’t look quite right. He changed the Bench Set Gain option to autogain, Anthony cleaned the cuvette, and the next scan came out as we expected it should. After we got a correct background we did a comparison of the previous FTIR background (2/2/2012), today’s background with no autogain correction, and the corrected autogain background. We used today’s autogain corrected background scan for all of our scans today.


Comparison background scans

For each of the following scans we used the same set up as my previous scans from 2/2/2012, using a quartz cuvette and 3µL of the specified water sample.

My first set of scans were three samples of DDW, each opened on a different date (9/6/2011, 1/17/2012, and 2/16/2012). I expected to see a difference because of possible atmospheric absorption of D2O. What I found was they were all pretty much the same the first scan that I ran. Unfortunately, I messed up the save process and had to re-scan the September and January samples. That scan produced a different result for January as shown in the following figure.

DDW second scan

DDW second scan

DDW (second scan) zoomed image

Next I scanned the four types of DI water Anthony is currently using in his current DDW5 experiment (see link). The four types of DI water are:

  1. DI from the Easypure RoDI (Thermohe) machine in our lab (Ro_DI – purple)
  2. CHTM’s DI (CHTM_DI – Red)
  3. Sigma molecular biology grade water (SMol_DI – light blue)
  4. Sigma double purified water (SDP_DI – green)

The results are surprising. The Sigma double purified water’s scan was slightly different than the other three, which were almost identical. This is certainly something to take a look at.

Deionized water scan

Deionized water - zoomed image

Next I scanned two samples of D2O:

  • a bottle opened on 2/16/2012 (red in the scan image)
  • a bottle opened on 11/1/2011 (blue in the scan image)

This scan also produced differing results, possibly from atmospheric absorption (what we had expected to see with the different aged DDW).

D2O scan

D2O scan zoomed

Finally just for comparison, I opened a new window and opened the scan of the February DDW and D2O, the Sigma double processed, and the Sigma molecular biology grade water just to see how the results compared. Interesting that the DDW and Sigma double purified water are identical. Hmmm…

Comparison of DDW, D2O and both of the Sigma DI scans

I’ve uploaded all the raw data onto FigShare with all the images.

My next project is to read up on water frequency and figure out what all the numbers mean. I’ve found a few papers and a website that will probably help shed some light on my very pretty graphs. I’ve ordered two of the papers from the library and the other information is available online.

Open Notebook Science — Taking what I’m Learning Outside


Some Background: I”ve got a full++ course load this semester, so I haven’t been in the Lab much this week to work on research related stuff. I’m a Computer Engineering major, hoping to get accepted into UNM’s 3+2 program and end up with a BS in Computer Engineering and an MBA in May 2015. My main motivation for working with Dr. Koch and Anthony was the Open Notebook Science portion of their work (and I just love the atmosphere of our lab — we’re the cool kids in our building).

So while I find all the stuff we do with D2O and protein studies really fascinating,my first love is with ONS. I truly believe that this is the way of future science and I’m so very grateful to get to be a part of it.

When I’m busy with all the engineering studies, in the back of my mind is a constant buzz … How can I take what I’m learning in school, the goals that I have, and marry all that with this exciting ONS movement — that I really want to continue to be a part of, even after my REU is over? :End Background

Here it comes… wait for it… wait for it… wait for it:

I had a really interesting experience today and I think that the marriage I want is going to arise.

In between classes this morning I ran into my Logic Design Prof (Marios Pattichis), and we started talking about the Lab portion of the class. He asked me what I thought, and I told him (truthfully) that VHDL is cool, but the supporting documentation for the lab really sucks. We then got into this discussion about my past experience (15 years as a technical writer, documentation manager, and trainer) and how I could maybe contribute to make the lab better.

I have been thinking about talking to him about this very thing, but was afraid that as an undergrad I wouldn’t qualify, I would be turned down, or whatever else the fear wanted to tell me for that day.

I said I would love to start a dialog with him about this over the rest of the semester. He then says, “Do everything (i.e., my lab work) open source.” I’m hoping that what I heard was what he really meant. Anyway, then I start to get really excited, and tell him about what I’m doing in the KochLab with Open Notebook Science.

 “OMG, this is really exciting,” I’m thinking. This is just the opportunity that I’ve been looking for. So that is my story.

I’m going to set up another blog for my Logic Lab Notebook in the next week (in my spare time LOL). Dr. Pattichis seemed to like that idea, and mentioned something about making it available to the class. So I need to get on it soon. I’m also hoping to start reworking the lab tutorials so that maybe I can be a TA or something next fall.

I’ll have to get really dedicated about blogging every day.  That is my weakness. My strength is my excitement about ONS.

E.coli – the morning after


Anthony checked the e.coli last night before he went home (after I went to class) and there wasn’t anything going on. He decided to leave the e.coli in the incubator shaker overnight at 150 RPM. This morning when I got into the lab, we checked the test tubes.

The P. Blue is cloudy which would indicate growth, yay!

P Blue e.coli... cloudy indicates that there was growth

The pALS is clear; probably no growth.

pALS e.coli - clear; probably no growth

Thermo Scientific Nanodrop 2000c SpectrophotometerTo accurately measure the number of cells we used a Thermo Scientific NanoDrop 2000c Spectrophotometer.  I’m new to spectroscopy, so for those of you who are also new:

“A spectrophotometer is a photometer (a device for measuring light intensity) that can measure intensity as a function of the light source wavelength. Important features of spectrophotometers are spectral bandwidth and linear range of absorption or reflectance measurement.” ~ Wikipedia – Spectrophotometry

Our method:

  1. Connect the nanodrop spectrophotometer to Anthony’s laptop and start the Nanodrop 2000 application.
  2. L to R: Growth Medium Only, GM & pALS, GM & P BluePrepare the three (3) sample cuvettes, with 1000 mL of LB Broth Growth medium.  The first cuvette has only the growth medium. This will serve as our blank reading (similar to the background reading we take for the Ft-IR).
  3. In the second cuvette we added 1000 mL of pALS to the growth medium.
  4. The third cuvette had an additional 1000 mL of P-Blue.

Now on to the scans:

  1. Click Cell Culture from the main screen of the nanodrop application.
  2. Starting with the “Blank” cuvette (the one with growth medium only), insert the cuvette into the cuvette holder of the nanodrop spectrometer.
    • Check (if not already) Add to Report and Use Cuvette. We used a 10 mm Path Length and no Stir Speed.
    • Click the Blank button (at top of screen).
    • Click the Measure button.
  3. Open the lid, remove the blank cuvette and insert the 2nd cuvette, pALS. Close the lid.
    • Enter a name (upper right of screen) for the new cuvette. We entered pALS.
    • Click the Measure button.
  4. Open the lid, remove the pALS cuvette and insert the 3rd cuvette, P Blue. Close the lid.
    • Enter a name for the new cuvette. We entered P_Blue.
    • Click the Measure button.
  5. Remove the last cuvette and dispose of all the cuvettes properly.

The nanodrop spectrometer software displayed a graph as we measured each sample. The A600 number for each sample was 0.001, -0.01, and 0.714 respectively.

Creation of E.Coli


Today we are making e.coli for our DDW experiments. The first step is to make the e.coli medium. We made up a small batch of LB Broth, using the instructions from the Sigma-Aldrich website.  We only made 100mL of LB Broth, instead of 1L, as follows:

  1. Mixed 2 g of LB Broth powder with 100mL of distilled water.
  2. Autoclave for 15 minutes at 121°C.

After the mixture cooled, we measured 10mL into two test tubes and mixed in a minute amount of e.coli.

Next we placed the test tubes in the New Brunswick Scientific Innova 4300 Incubator Shaker at 37° C. Our shaker’s thermostat is about .3°C – .4°C high , so we stuck a thermometer probe in the shaker to get an accurate temperature measurement.

We set the incubator shaker at 70 RPM for a few hours. I have to leave for class, and Anthony wasn’t sure if we needed to leave it longer or maybe even overnight. Please check his blog for the final details.

ToDo List – as of 2/7/2012

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While having lunch with Anthony I realized that I’ve been keeping my To Do list in my head. That’s a fairly dangerous place because of the high volume of traffic zipping around in there right now.

I’ve started a Google Docs Spreadsheet to help me keep better track of the stuff I have going on.

I’m using this list as a daily, “What do I want to accomplish today” type of list. Hopefully it will help me to better utilize my time in the lab (there is so much to learn about, I get distracted easily).

For instance, today, I was going through my email, logged into Google + and saw a post by Cameron Neylon about Zooniverse, Citizen Science and FigShare. I’m thinking that’s some cool stuff, let me take a quick peek. My “quick peek” turns into me creating a Zooniverse account and then proceeding to classify at least three stars and post a question – all to the tune of 20 minutes gone.

Nothing wrong with all of that, except I have a few other things to look over before I start worrying about which stars have planets. Although, it is super cool, and I want my sons to look for planets instead of playing MineCraft.

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