I’m at a new internship

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So my REU internship ended in May. Thank you so very much Anthony Salvagno and Steve Koch for the experiences and opportunities you graciously shared with me over the past eight months.

I’m updating my blog/notebook to include my undergraduate and future experiences.

I was accepted for another NSF internship program for the summer. I’m working with some really great people at a UNM Research Center called COSMIAC. I’m updating FPGA/VHDL training materials and learning more about programing FPGAS. I’m really enjoying my time here, and here are some reasons why:

  • Last semester I took ECE 238 – Computer Logic and Design – and fell in love with VHDL and computer logic. This is the field I would eventually like to be working in, so the work I’m doing is really relevant for me.
  • My supervisors are supportive of me and really engaged in my success (just like Anthony and Steve were and still are).
  • I’m going on a little trip at the beginning of August to help train some people at a community college. What better way to learn more about a topic than to teach it.
  • I get to blog about my work.
  • (They also let me work 4 days a week, so I can have long weekends with my children for the summer! )

I’ll post updates about my experiences here.

Final Presentation for REU

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Yesterday afternoon I gave my final presentation for the NSF REU. I’ve posted it on Slideshare for you all to see. It wasn’t real obvious, until I started working on the presentation, how much Anthony and I have done over the last several months. We’ve gotten a lot accomplished!

I have had such a great experience this year that I volunteered to continue coming to the lab this summer. Thankfully Anthony and Dr. Koch aren’t tired of me and agreed to let me stay involved this summer. I hope to be able to work in Koch Lab at least 4 hours a week. I’m interested to see how the e.coli in D2O progresses.

Also, Anthony is really moving and shaking in the Open Notebook Science community. This is really exciting to me.  I’ll be taking my ONS experience with me to my next opportunity…

I’ve been given another NSF internship opportunity, the STEM Talent Expansion Program (STEP), for the summer. [I think that is the right link... the NSF site is down for maintenance until tomorrow night. Let me know if the link isn't correct]. I’ll be working part-time with Dr. Ramiro Jordan, who seemed open to me keeping an online notebook. Stay tuned for some information about VHDL and circuits.

I am indebted and full of gratitude for all the support and guidance that both Anthony and Dr. Koch gave me this past year. Thank you seems like not enough. Thank you both.

On growing e.coli and becoming an ONS scientist

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I’m guessing that growing e.coli might not be all that exciting to most of the world’s population. However, I’m excited because I’ve gotten the opportunity to learn how to do this and Anthony has put his trust in me to do it on my own.

Anthony posted a list of To-Dos for me this week. Today’s task was to start another batch of e.coli. Tomorrow we’ll use this batch to get spectroscopic absorbance readings on samples of 1:10 dilution in DI water, DDW, and 33% D2O. This is what I’ve been waiting for.

Just so you all know, with the exception of last week, everything I’ve done in the lab thus far was when Anthony was here. I’m not sure why, but I was a little nervous last week when I was actually on my own. I shouldn’t have been and I wasn’t today. I’ve taken, and posted, really good notes in my notebook. Today I was glad I did.

I got to the lab ready to start the next culture and discover that not only are we are out of LB broth, there are no autoclaved 50mL triangle beakers that we usually use to mix up this stuff. What we do have autoclaved is a few 150mL cylindrical beakers.

Anthony is busy working on his talk for this afternoon and I didn’t want to bother him and there isn’t enough time for me to autoclave beakers, start new broth (which also requires autoclaving), and make it to Anthony’s talk by 1.

So I improvised.

I used a 150mL beaker, and made 100mL of LB broth using 2g LB broth mixed with 100mL of Dbl processed water (twice the amount from my April 10th recipe).

I measured the LB powder pretty darn close, 2.0008g, poured it into the beaker, added the water and used the magnetic stirrer to get it all mixed up well. I had never actually used the stirrer before, but I watched Anthony and learned a little trick of moving the container around so that the magnet would hit the sides and get all the powder moving.

As I write this, the broth is in the autoclave. I used the same protocol as I wrote about on February 6. Since this is a liquid, it will cook at 250°F for 60 minutes.

I’ll start the broth after Anthony’s talk, before I run off to see Tom Petty and the Heartbreakers later tonight.

Monitoring e.coli growth

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Today Anthony and I are tracking e.coli growth over several hours. His post is detailed, so I wont repeat all the nitty-gritty here (I’ll add a link when he posts his notes).

First we took baseline readings using the Thermo Nanodrop 2000C. Then we made three new batches of diluted e.coli from the batch I ‘Koched’ up yesterday, diluted with LB broth in 1:2, 1:5, and 1:10 parts. Then we put the three batches in the incubator at 37º C and every hour took new spectroscopic readings.

During one of our in-between-spectroscopic-reading-times we ran out to lunch. We went to the Guava Tree Cafe… OMG… absolutely delicious. We both had a stuffed Arepa. I had La del Perro and Anthony had Arepa Pabellón. If you live in Albuquerque you have to try this place. If you don’t live here but get a chance to visit, make sure you eat here at least once. You wont regret it.

Growing e.coli on my own

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Anthony is teaching lab this afternoon and asked me to start a batch of e.coli… all by myself. At first I was thinking, “Sure, no big deal. I’ve done this several times with you.” Then I got to the lab and got all nervous. Silly me. :)

Here is the procedure I followed:

  1. put on gloves – very important not to contaminate myself.
  2. get supplies:
    • 10mL tube and pipette
    • inoculating loop, Green 10 x 1µL
    • autoclaved test tube
    • LB broth
    • agar plate with e.coli – LB Day 2 batch
  3. Remove cover from LB broth and pipette 10mL of broth into test tube.
  4. Re-cover test tube and broth.
  5. Dispose of pipette tube in bio-hazard bin.
  6. Remove parafilm from agar plate.
  7. Using inoculating loop, get a single colony of e.coli on loop.
  8. Put loop in test tube and swirl for a few seconds.
  9. Dispose of loop in bio-hazard bin.
  10. Recover test tube.
  11. Place test tube in incubator at 37 C.
  12. Re-cover agar plate and seal with new parafilm.
  13. Place agar plate and LB broth back in refrigerator.

Everything went smoothly. I didn’t spill or contaminate anything (this is so silly, I feel like the first time I got to ride my bike without my parents watching). We should have some new e.coli tomorrow to use for this week’s experiments.

See you all then!

Yeast, E.coli day 2

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After 12+ hours in the incubators we have growth… well almost. Neither one of the yeast agar plates grew anything. However, both the LB broth and LB agar plate grew e.coli, and the YPD broth grew yeast.

So today we did a few things:

  • We set up two new YPD agar plates using starter culture from the YPD broth that we grew last night. One agar plate is in the 24° C incubator and the other is at room temperature.
  • We decided to grow some more e.coli colonies on an additional LB agar plate using starter culture from the LB broth that we grew last night. It is now in the 37º C incubator.
  • We took spectroscopic readings of our samples using the Thermo Nanodrop 2000C. We used 2mL of the YPD and LB broth and then did the same with 2mL of each starter culture.

Baseline Spectroscopy of Yeast and E.Coli

Yeast Picture

E.Coli Picture

Anther round of yeast and e.coli

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Today Anthony and I started preparation for DDW and D2O experiments with yeast and e. coli.  Anthony has a few posts about our past growth experiments. Previously we were successful growing both organisms however, we didn’t get into the DDW or D2O phase of the experiments.

The yeast we are using is S. cerevisiae, g160/2d. We are growing three samples. One sample is being grown in YPD broth that is a mixture of 50mL SIGMA Db/processed water and 2.5g of USB YPD Broth (ultrapure). The other two samples are on 100mm YPD Agar plates from Teknova. One plate is in the incubator with the broth mixture at 24 degrees C. The other plate we are leaving out at room temperature.

We are growing two samples of  DH5α™ e. coli. The first sample on a 100mm LB Agar plate (also from Teknova). The second is in an LB broth mixture of 1g LB broth mixed with 50mL of Dbl processed water, both from SIGMA. Both samples are  in the incubator at 37 degrees C.

We made LB and YPD broth by carefully measuring the indicated amount of broth powder using the lab’s Ohause Adventurer SL balance and small weight boats. We then poured the powder from the weight boat into 50mL beakers and added 50mL of water. We then used magnetic stirrers and a hotplate/stirrer to mix both broths. The LB broth was autoclaved.

Tomorrow we should have some samples ready to go. We are planning on first seeing if we can grow deuterium resistant strains of both the yeast and e.coli. After that we will see how the resistant strains fair in DDW.

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