1. Learning R
1.1. Dr. Koch wants to us R as our analysis tool for all our data.
1.2. He used the second set of data and R to show that spectroscopy readings we obtained with Stephen and the CHTM FTIR were in line with Seigelstein's 1981 data.
1.2.1. Dr. Koch's Code
1.2.1.1. https://github.com/stevekochscience/Deuterium-in-life-science/blob/master/Repeating%20Crumley/Water%20FTIR.R
1.2.2. https://github.com/stevekochscience/Deuterium-in-life-science/blob/master/Repeating%20Crumley/2011%20Dec%2028_three%20water%20abs%20compared%20seigelstein.png
1.2.3. My code
1.2.3.1. Installed Rcurl Package
1.2.3.2. Installed binom Package
1.2.3.3. Changed read.table to read.csv
2. Has life developed a Need for Deuterium?
2.1. links, qr codes
2.1.1. Unorthodox
2.2. Notebooks
2.2.1. http://research.iheartanthony.com/tag/ddw-effects-on-life/
2.2.2. http://alexhaddadnm.wordpress.com/
2.2.3. all my research is reproducible.
3. Next Steps
3.1. E. Coli
3.2. Yeast
3.3. Becoming fluent in R
3.4. Protein Stability
3.4.1. Study of Protein Stability Studies done this summer REU Kenji
3.4.1.1. http://research.iheartanthony.com/2011/08/29/ovalbumin-catalase-and-kinesin-aggregation-data/
3.4.1.2. 1. Ovalbumin aggregates at ~75 C in DI water but not in D2O.
3.4.1.2.1. https://docs.google.com/leaf?id=0B2DSwNF1eIqtYTE1MGI0MTYtNWI0ZS00NmYzLWI2ZWMtZDIwNmY5NTU1YTJj&hl=en_US
3.4.1.2.2. left is clear, right is aggregated
3.4.1.3. 2. Repeat of #1 with Catalase
3.4.1.4. So, stability is future work, but current work is related to the question "do cells specifically need deuterium?"
4. Question: Does life have a need for Deuterium? It's fairly abundant (more abundant than K and Ca). Very little information on how life forms manage without Deuterium.
4.1. Gilbert Lewis
4.1.1. Gilbert Lewis predicted in 1934 that deuterium may be essential for some life forms in his paper, The Biology of Heavy Water. He closed with, "It is not inconceivable that heavy hydrogen, which exists in small amounts in all natural water, may actually be essential to some plants or animals." However we have not been able to find any further experiments from Gilbert to support or contradict this question.
4.1.1.1. http://en.wikipedia.org/wiki/Gilbert_N._Lewis
4.1.1.2. Lewis, G. N. (1934). THE BIOLOGY OF HEAVY WATER. Science (New York, N.Y.), 79(2042), 151-153. doi: 10.1126/science.79.2042.151.
4.1.1.3. http://pubs.acs.org/doi/pdf/10.1021/ja01335a509
5. Understanding how water - particularly Hydrogen isotopes - affect biomolecular interactions and living cells
5.1. D2O studies
5.1.1. Repeating Crumley
5.1.1.1. Original Experiment
5.1.1.1.1. http://research.iheartanthony.com/2011/08/24/repeating-crumley-et-al-1950/
5.1.1.1.2. http://research.iheartanthony.com/wp-content/uploads/2011/08/figure3-crumley.png
5.1.1.2. RC4: Time-Lapse Growth
5.1.1.2.1. http://research.iheartanthony.com/2011/11/15/rc4-time-lapse-growth/
5.1.1.3. Graphs of RC on figshare
5.1.1.3.1. http://figshare.com/figures/index.php/Tobacco_Seed_Growth_in_D2O
5.2. DDW studies
5.2.1. Even though deuterium is toxic in large quantities, have some life forms developed a need for it?
5.2.1.1. Effect of Deuterium Depeleted Water on Life
5.2.1.1.1. Introduction
5.2.1.1.2. Project Outline Yeast and E.Coli
5.2.1.1.3. Havana Sample Pictures
5.2.1.1.4. Future Experiments
5.2.2. FTIR
5.2.2.1. The DDW experiment is sensitive. The DDW will exchange with the surrounding atmosphere and become regular H2O (SMOW) over a period of time. SMOW: Standard Mean Ocean Water Has 156ppm of H2/H1 or 15mM
5.2.2.1.1. Deuterium Exchange? What is the rate of exchange? How accurate are the results because of the exchange that is always going on?
5.2.2.1.2. Need to accurately measure the amounts of D2O in H2O.
5.2.2.2. Granted use by Dr. Sanjay Krishna courtesy of Stephen Myers
5.2.2.3. First try
5.2.2.3.1. Plastic cuvettes -- didn't work well at all
5.2.2.4. Second try
5.2.2.4.1. Quartz cuvettes -- Da Bomb!! Worked Great!!