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=Student Registration/Questionnaire=
Name: Jennifer Logan <br>
Please copy the source code from this page to your user page (click on the [[Image:EditButton.jpg]] button above, and copy everything inside the box to [[Special:Mypage|your user page]]).  Fill in the answers and print out a copy for next time. You do not need to keep the information on your user page once you've printed it out.
Email: jlogan at mit dot edu <br>
==20.109 Spring 2007==


===Last Name===  
==== M13 phage re-engineering ideas: ====
Logan
{| Border="1"
===First Name===
! Gene !! Ideas
Jennifer
|-
===Preferred name===
| I || Modify such that it is able to interact with multiple p4s and see how phage  secretion changes (this would affect the effectiveness of the channels).
Jen
|-
===Course/Minor===
| II || modify such that it not only nicks the double stranded form of the genome to initiate replication of the + strand, but also nicks the - strand to impede the formation of dsDNA (this would also help g5). Care should be taken when modifying because this is also linked to g10.
BE
|-
===Year of Graduation===
| III || Add myc or other tag to monitor how it affects time delay/progression of phage escape from host
2009
|-
===Telephone #===
| IV || modify to increase its affinity for p1 and p11--this would possibly increase the effectiveness of the channels
630 347 0418
|-
jlogan AT mit DOT edu
| V ||Modify such that it is able to sequester the positive stranded DNA more effectively, thus reducing the competition with dsDNA formation
|-
| VI || As an accessory protein to p3, modify such that p3 is more effective in its interaction with TolA protein
|-
| VII || Modify in such a way to allow for phage secretion speed to increase so the phage-host interaction time is decreased.
|-
| VIII || Add myc or alternative tag to possibly aid in targeting various qualities of host
|-
| IX ||Same principle as gene VII except that care must be taken with this modification because it overlaps with gene 8.
|-
| X || Modify such that + strands are not dependent on the presense of p10. This would work in conjuction with our modification of p2 (since they are linked).
|-
| XI || same as p1
|}


===Have you taken===
===M13.1 Section Design===
7.05/5.07 (Biochemistry)<br> concurrently
7.06 (Cell Biology)<br> no
7.02 (General Biology Lab)<br> no
5.310 (General Chemistry Lab)<br> no


Do you have any experience culturing cells (mammalian, yeast or microbial)?<br>    Yes   
{| Border="2"
! Modification/Limitation !! Description
|-
| gene VIII and promoter-g3 || These two overlapped so I separated and added in ecoRI (g/aattc)and XmaI (c/ccggg) restriction sites to create unique sticky ends. I also modified codons at the wobble positions so that the promoter for g3 can no longer exist within gene VIII but the amino acid sequence of gene VIII was maintained. (Portion of overlap in gene VIII is now 5' aattTacctcgaaagcaagTtga 3')
|-
| myc epitope within gene 3 || Myc epitope is known as a good tag, this way when gene 3 regulation occurs the myc tag will help locate this regulation. I had to add some bases on the ends of the myc epitope so that when I cut with the restriction site (NIaIII: ccatg/t)I was able to anneal my insert. However, I designed the insert such that when it anneals with our segment, the NIaIII site is destroyed. (Myc epitope top strand: 5' GAA CAG AAA CTG ATC TCT GAA GAA GAC CTG catg 3'
bottom strand: 5' CAG GTC TTC TTC AGA GAT CAG TTT CAG TTC catg 3')


Do you have any experience in molecular biology (electrophoresis, PCR, etc)?<br>  Yes   
|-
|-
|}


===Please briefly describe any previous laboratory experience===
The modifications that were necessary for me as a Discoverer (I choose to focus on gene 3) were mainly to unstuff the overlapping regions of gene VIII and the promoter of gene III. I did this by first copying over the region of overlap between gene VIII and the promoter of gene III and then modified two bases within the gene VIII overlap sequence (the wobble positions)so that gene III can no longer exist within it. However, care was take that the amino acid sequence was maintained. Also, two restriction sites (ecoRI and XmaI) were added to create unique sticky ends. I then found another restriction site (NIaIII) and cut open inbetween gene III so that I could insert a myc epitope that I modified by adding sticky ends (but upon insertion would destroy the NIaIII site). As the table above indicates, I hoped to insert the myc epitope because since it is known as a good tag, when regulation of gene III does occur, the myc epitope will help us pinpoint more exactly when this occurs. I hope that this will help me discover more about the regulation of gene III.
I am currently working in the Yaffe lab. I also researched at Northwestern University in a neuro lab as well as at University of Illinois-Chicago in a lab that dealt with ovarian cancer.
<br/>
 
[http://parts.mit.edu/r/parts/partsdb/part_info.cgi?part_name=BBa_M31517 My Redesigned Phage Section]
 
 
 
 
 
===Anything else you would like us to know?===
<i>Optional: As mentioned in lecture on 02.06.07, we would like you to consider how, as a biological engineer you might test the superstition "Spit on a bat before using it for the 1st time to make it lucky." </i>fill in your answer here
I think I would first take batters of all skill ranges and make sure to record their batting averages. I would then give them two identical bats and have them spit on one and not the other; then randomly give them one and then the other and record their batting averages. Also I would repeat a similar experiment except this time tell them if they were hitting with a 'lucky' bat or not and see if this created any significant changes.

Latest revision as of 10:41, 27 February 2007

Name: Jennifer Logan
Email: jlogan at mit dot edu

M13 phage re-engineering ideas:

Gene Ideas
I Modify such that it is able to interact with multiple p4s and see how phage secretion changes (this would affect the effectiveness of the channels).
II modify such that it not only nicks the double stranded form of the genome to initiate replication of the + strand, but also nicks the - strand to impede the formation of dsDNA (this would also help g5). Care should be taken when modifying because this is also linked to g10.
III Add myc or other tag to monitor how it affects time delay/progression of phage escape from host
IV modify to increase its affinity for p1 and p11--this would possibly increase the effectiveness of the channels
V Modify such that it is able to sequester the positive stranded DNA more effectively, thus reducing the competition with dsDNA formation
VI As an accessory protein to p3, modify such that p3 is more effective in its interaction with TolA protein
VII Modify in such a way to allow for phage secretion speed to increase so the phage-host interaction time is decreased.
VIII Add myc or alternative tag to possibly aid in targeting various qualities of host
IX Same principle as gene VII except that care must be taken with this modification because it overlaps with gene 8.
X Modify such that + strands are not dependent on the presense of p10. This would work in conjuction with our modification of p2 (since they are linked).
XI same as p1

M13.1 Section Design

Modification/Limitation Description
gene VIII and promoter-g3 These two overlapped so I separated and added in ecoRI (g/aattc)and XmaI (c/ccggg) restriction sites to create unique sticky ends. I also modified codons at the wobble positions so that the promoter for g3 can no longer exist within gene VIII but the amino acid sequence of gene VIII was maintained. (Portion of overlap in gene VIII is now 5' aattTacctcgaaagcaagTtga 3')
myc epitope within gene 3 Myc epitope is known as a good tag, this way when gene 3 regulation occurs the myc tag will help locate this regulation. I had to add some bases on the ends of the myc epitope so that when I cut with the restriction site (NIaIII: ccatg/t)I was able to anneal my insert. However, I designed the insert such that when it anneals with our segment, the NIaIII site is destroyed. (Myc epitope top strand: 5' GAA CAG AAA CTG ATC TCT GAA GAA GAC CTG catg 3'

bottom strand: 5' CAG GTC TTC TTC AGA GAT CAG TTT CAG TTC catg 3')

The modifications that were necessary for me as a Discoverer (I choose to focus on gene 3) were mainly to unstuff the overlapping regions of gene VIII and the promoter of gene III. I did this by first copying over the region of overlap between gene VIII and the promoter of gene III and then modified two bases within the gene VIII overlap sequence (the wobble positions)so that gene III can no longer exist within it. However, care was take that the amino acid sequence was maintained. Also, two restriction sites (ecoRI and XmaI) were added to create unique sticky ends. I then found another restriction site (NIaIII) and cut open inbetween gene III so that I could insert a myc epitope that I modified by adding sticky ends (but upon insertion would destroy the NIaIII site). As the table above indicates, I hoped to insert the myc epitope because since it is known as a good tag, when regulation of gene III does occur, the myc epitope will help us pinpoint more exactly when this occurs. I hope that this will help me discover more about the regulation of gene III.
My Redesigned Phage Section

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