Team:Purdue/SandPit

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Latest revision as of 23:55, 29 May 2010

Our Sand Pit page is a place for our team to jot down ideas, share cool websites, and post important references that we think our other teammates should see

Sea Slug Inspiration

Cool U Maine Site on kleptoplasty - how some sea slugs steal and use chloroplasts from algae to capture energy from sunlight. [http://biology.umaine.edu/symbio/index.html]

Standard Assembly Methods for assembling dna

remember that we are supposed to use a standard assembly method for construction of our parts. if we do not use the BioBricks iGEM standard assembly then we must get approval for the method we choose. many teams have moved away from the original BioBricks iGEM assembly to more robust methods

Berkeley. "BglBricks: A flexible standard for biological part assembly" J. Biological Engineering. [http://www.jbioleng.org/content/4/1/1]
Venter. "Enzymatic assembly of DNA molecules up to several hundred kilobases" Nat Methods. 2009 May;6(5):343-5. Epub 2009 Apr 12.[http://www.nature.com/nmeth/journal/v6/n5/full/nmeth.1318.html]
Howard Hughes. "Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC".
Univ. of Illinois. "DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways" Nucleic Acids Res. 2009 Feb;37(2):e16. Epub 2008 Dec 12. [http://nar.oxfordjournals.org/cgi/content/abstract/gkn991]

How to Edit a Wiki

simple formating [http://openwetware.org/wiki/OpenWetWare:Getting_started_2]
the wikipedia wiki editing tutorial [http://en.wikipedia.org/wiki/Wikipedia:Tutorial]

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 '''Our Sand Pit page is a place for our team to jot down ideas, share cool websites, and post important references that we think our other teammates should see'''
+==Sea Slug Inspiration==
-==Oxygen sequestration to inhibit photorespiration in C3 plants==
-===The problem===
-Photorespiration is an unwanted chemical process that occurs in C3 plants that wastes ATP and organic nitrogen.  While many species have evolved to avoid photorespiration (C4 and CAM plants), attempts to transfer these methods to C3 plants have been unsuccessful due to the drastic physiological differences between species.  Photorespiration occurs when O2 concentrations increase relative to CO2.  In relatively dry conditions, the stomata of plants close to preserve moisture.  Unfortunately, these stomata are used for the exchange of atmospheric CO2 with photosynthetically-derived O2.  When the stomata close, the light-independent reactions of photosynthesis, notably the Calvin cycle, continue.  The Calvin cycle's purpose is to fix inorganic carbon (CO2) to generate a three-carbon sugar (G3P).  The key enzyme in the carbon-fixation process is RuBisCO.  Normally, RuBisCO directly fixes the CO2 to RuBP (an intermediate of the Calvin cycle) to produce G3P.  However, RuBisCO also has a significant affinity for O2, and can oxygenate RuBP instead.  This generates less G3P and produces a toxic intermediate.  Eliminating this toxic intermediate requires 1 ATP and causes the formation of NH3, which diffuses out of the plant.
-===The solution===
-Hemoproteins (such as hemoglobin and leghemoglobin) are capable of binding O2 with various affinities.  By combining a hemoprotein with a sequence that codes for protein import into the stroma of the chloroplast (a sequence found in the RuBisCO protein), excess oxygen produced during photosynthesis can be sequestered.  In theory, this would reduce oxygen concentrations and inhibit photorespiration.  A promoter for high dissolved oxygen concentrations could increase production of the hemoprotein during times that photorespiration is likely to occur in excess.
-===Resources===
-====Photorespiration and Calvin cycle review====
-[http://khanexercises.appspot.com/video?v=EQvTEFCANTM Khan Academy video lecture]
-====Potentially useful articles====
-[http://www3.interscience.wiley.com/cgi-bin/fulltext/121356215/HTMLSTART Changes in gene expression in Arabidopsis due to available oxygen]
-==Cancer and Metabolism==
-===Resources===
-====Potentially useful articles====
-#[http://www.molecular-cancer.com/content/2/1/12 Hypoxia, Neoangiogenesis Pancreatic Cancer]
-#[http://www.nature.com/nrc/journal/v2/n1/abs/nrc704.html Hypoxia as regulatory factor in tumor growth]
-#[http://genesdev.cshlp.org/content/18/17/2095 Hypoxia driving tumorigenesis]
-==Other Ideas==
-===Sea Slug Inspiration===
 #Cool U Maine Site on kleptoplasty - how some sea slugs steal and use chloroplasts from algae to capture energy from sunlight.  [http://biology.umaine.edu/symbio/index.html]