Difference between revisions of "Cumbers:notes"

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==Chassis Choice==
==Outline of MIT syn bio tea talk==
Research Article
1) Applications of syn bio to space
The Genome of the Diatom Thalassiosira Pseudonana: Ecology, Evolution, and Metabolism
E. Virginia Armbrust, John A. Berges, Chris Bowler, Beverley R. Green, Diego Martinez, Nicholas H. Putnam, Shiguo Zhou, Andrew E. Allen, Kirk E. Apt, Michael Bechner, Mark A. Brzezinski, Balbir K. Chaal, Anthony Chiovitti, Aubrey K. Davis, Mark S. Demarest, J. Chris Detter, Tijana Glavina, David Goodstein, Masood Z. Hadi, Uffe Hellsten, Mark Hildebrand, Bethany D. Jenkins, Jerzy Jurka, Vladimir V. Kapitonov, Nils Kröger, Winnie W. Y. Lau, Todd W. Lane, Frank W. Larimer, J. Casey Lippmeier, Susan Lucas, Mónica Medina, Anton Montsant, Miroslav Obornik, Micaela Schnitzler Parker, Brian Palenik, Gregory J. Pazour, Paul M. Richardson, Tatiana A. Rynearson, Mak A. Saito, David C. Schwartz, Kimberlee Thamatrakoln, Klaus Valentin, Assaf Vardi, Frances P. Wilkerson, and Daniel S. Rokhsar
Science 1 October 2004: 79-86. 
Diatoms, key members of marine and freshwater ecosystems, have genes for the urea cycle, for using lipids as an energy source, and for synthesizing their ornate, silica-based cell walls.          Abstract »|          Full Text »|                    PDF »|                    Supporting Online Material »| 
==[[photosynthetic Chassis Choice]]==
Research Article
Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for 20% of global carbon fixation. We report the 34 million–base pair draft nuclear genome of the marine diatom Thalassiosira pseudonana and its 129 thousand–base pair plastid and 44 thousand–base pair mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, use of a range of nitrogenous compounds, and a complete urea cycle, all attributes that allow diatoms to prosper in aquatic environments.
[[The Genome of the Diatom Thalassiosira Pseudonana: Ecology, Evolution, and Metabolism]]
==Fuels for space==
==Fuels for space==

Latest revision as of 10:51, 25 March 2008

Outline of MIT syn bio tea talk

1) Applications of syn bio to space

photosynthetic Chassis Choice


Research Article The Genome of the Diatom Thalassiosira Pseudonana: Ecology, Evolution, and Metabolism

Fuels for space

  • Notes from speaking to David Thompson
  • Oxygen - O2 as byproduct of photosynthesis
  • Hydrogen - via the biohydrogen route
  • nitrogenase, the enzyme that fixes N2 to NH3(amonia)ozene

, as a normal part of its function it produces H2 albeit at a much slower rate than NH3, its a side reaction. but if you force the reaction in an atmosphere with zero nitrogen, then you get H2 production exclusively. (Hydrogen-2, H-2, 2H (a.k.a. Deuterium), an isotope of Hydrogen (1 proton, 1 neutron, 1 electron))


  • Deep sea bacteria that make hydrazine as a free metabolic intermediate. (Hydrazine is used as a bipropellant in combination with O2 I (DT) believe,and some of its derivatives are used in combination with other liquid rocket fuels...)

http://www.anammox.com/ is a resource for research on those particular bacteria.


A strongly alkaline crystalline compound, NHC(NH2)2, formed by the oxidation of guanine and found in the urine as a normal product of protein metabolism. It is commonly used in the organic synthesis of plastics, resins, and explosives. (answers.com) Guanine production was hypothetical, it would involve tweaking the purine biosynthetic pathway, and i think i mentioned a purine efflux pump... http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=181001

making TAL for TATB production was from this paper http://www.chemeng.uiuc.edu/~zhaogrp/images/HZ24-JACS%20Fas-B%20Engineering%202004.pdf

phloroglucinol: http://pubs.acs.org/cgi-bin/sample.cgi/jacsat/2005/127/i15/pdf/ja042340g.pdf

ammonia, formaldehyde --> hexamine (fireproofing, plastics) --> hexogen/RDX

toluene, sulfuric acid, nitric acid --> trinitrotoluene

acetone, sulfuric acid, hydrogen peroxide --> acetone Peroxide/TATP

guanine --> nitroguanidine

malonyl-CoA --> triacetic acid lactone --> LCD's

side product is phloroglucinol (can make adhesives)

ammonia, formaldehyde