User:Snix: Difference between revisions

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(New page: =Student Registration/Questionnaire= ==20.109 Spring 2007== ===Last Name=== Nix ===First Name=== Stephanie ===Preferred name=== whatever you feel like ===Course/Minor=== 20/8, 5...)
 
 
(9 intermediate revisions by the same user not shown)
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=Student Registration/Questionnaire=
===About Me===
==20.109 Spring 2007==


===Last Name===
*Email: snix at mit <br>
Nix
*Year: 2009 <br>
*Major: 20/8B <br>
*Minor: possibly 5 <br>


===First Name===
Stephanie


===Preferred name===
===Course Load===
whatever you feel like


===Course/Minor===
*[http://stellar.mit.edu/S/course/5/sp07/5.03/index.html 5.03] <br>
20/8, 5 minor?
*[http://web.mit.edu/6.00/www/ 6.00] <br>
*[http://web.mit.edu/8.044/www/ 8.044] <br>
*[http://openwetware.org/wiki/20.109 20.109] <br>
*[http://web.mit.edu/21f.502/www/index.html 21f.502] <br>


===Year of Graduation===
2009 (but at this rate, 2010?)


===Telephone #===
===Other Stuff===
uh


===Email===
*[http://web.mit.edu/taekwondo/ MIT Sport Taekwondo] <br>
snix at mit
*[http://web.mit.edu/mars/ MIT Mars Society (not recently updated)]


===Have you taken===
7.05/5.07 (Biochemistry)<br> no


7.06 (Cell Biology)<br> no
===20.109 M13 plans===


7.02 (General Biology Lab)<br> no


5.310 (General Chemistry Lab)<br> no
{| Border="1"
!Gene #!!Ideas
|-
| g1 || After another copy of g11 is made, edit the ATG sequence that starts g11 so that g1 and g11 can be modified independently. Once this has been done, modify parts of g11 while keeping g1 intact and vice versa to see how this affects replication.
|-
| g2 || After another copy of g10 is made, edit the ATG sequence that starts g10 so that g2 and g10 can be modified independently. Modify parts of g2 or g10 while keeping the other intact to see how the disparate sequences affect replication.
|-
| g3 || Make the sequence longer to see whether this makes the tail longer and more likely to grasp onto an E. coli cell. Could also change the sequence around to find out by what mechanism p3 works to enter and exit the cell. For example: exchanging charged amino acids for neutral, acidic for neutral or basic, etc. This would take a long time, but could be used to adapt M13 to other hosts for various reasons, since it doesn't kill its host.
|-
| g4 || After g11 has been removed, decouple from g1 to better manipulate g4. While doing so, keep various lengths of the sequence that was originally before g4 intact to find out if there is a promoter before g4 and, if there is, how long it is.
|-
| g5 || Modify parts of the genome systematically to find out how the interaction with p8 changes with these changes.
|-
| g6 || Edit the length of the protein and see what happens. (Does it bulk up under p8/p3, or does it leak out?)
|-
| g7 || Modify the last few codons so that there is no overlap with g9.
|-
| g8 || Insert a sequence that shifts g8 so there is no overlap with g9. Then, experiment with various tags to see how receptive the coat is to tagging. Also, could find out whether M13 has a particular predilection for a marker that would allow it to be used for building nanomaterials.
|-
| g9 || Modify beginning and end sequences so that g9 does not overlap with g7 and g8.
|-
| g10 || Make another copy of g10, then insert it in an area where there is no coding sequence. Put a tag on p10 and see what it binds to at various parts of replication. This will help to elucidate how it controls the amount of double stranded M13 genomes. See g2 entry for other details.
|-
| g11 || Make another copy of g11, then insert it in an area where there is no coding sequence. See g1 entry for other details.
|}


Do you have any experience culturing cells (mammalian, yeast or microbial)?<br>  no


Do you have any experience in molecular biology (electrophoresis, PCR, etc)?<br>  some
===Refactoring M13===


===Please briefly describe any previous laboratory experience===
[http://parts.mit.edu/r/parts/partsdb/part_info.cgi?id=8162 link to data]
typical high school stuff
 
===Anything else you would like us to know?===
<i>"Spit on a bat before using it for the 1st time to make it lucky,"</i> they say. Well, they don't specify that spitting on the bat makes it lucky in baseball, so I propose that the bat should be lucky in other areas of life. Thus, I propose that we gather 100 spitten bats and 100 unspitten bats (forgive my creative use of English), throw them out into traffic, and see how the bats fare. Of course, how the people in traffic fare is another matter - perhaps we could provide them with bats that may or may not have been spat upon as well.

Latest revision as of 09:55, 27 February 2007

About Me

  • Email: snix at mit
  • Year: 2009
  • Major: 20/8B
  • Minor: possibly 5


Course Load


Other Stuff


20.109 M13 plans

Gene # Ideas
g1 After another copy of g11 is made, edit the ATG sequence that starts g11 so that g1 and g11 can be modified independently. Once this has been done, modify parts of g11 while keeping g1 intact and vice versa to see how this affects replication.
g2 After another copy of g10 is made, edit the ATG sequence that starts g10 so that g2 and g10 can be modified independently. Modify parts of g2 or g10 while keeping the other intact to see how the disparate sequences affect replication.
g3 Make the sequence longer to see whether this makes the tail longer and more likely to grasp onto an E. coli cell. Could also change the sequence around to find out by what mechanism p3 works to enter and exit the cell. For example: exchanging charged amino acids for neutral, acidic for neutral or basic, etc. This would take a long time, but could be used to adapt M13 to other hosts for various reasons, since it doesn't kill its host.
g4 After g11 has been removed, decouple from g1 to better manipulate g4. While doing so, keep various lengths of the sequence that was originally before g4 intact to find out if there is a promoter before g4 and, if there is, how long it is.
g5 Modify parts of the genome systematically to find out how the interaction with p8 changes with these changes.
g6 Edit the length of the protein and see what happens. (Does it bulk up under p8/p3, or does it leak out?)
g7 Modify the last few codons so that there is no overlap with g9.
g8 Insert a sequence that shifts g8 so there is no overlap with g9. Then, experiment with various tags to see how receptive the coat is to tagging. Also, could find out whether M13 has a particular predilection for a marker that would allow it to be used for building nanomaterials.
g9 Modify beginning and end sequences so that g9 does not overlap with g7 and g8.
g10 Make another copy of g10, then insert it in an area where there is no coding sequence. Put a tag on p10 and see what it binds to at various parts of replication. This will help to elucidate how it controls the amount of double stranded M13 genomes. See g2 entry for other details.
g11 Make another copy of g11, then insert it in an area where there is no coding sequence. See g1 entry for other details.


Refactoring M13

link to data

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