Bernice:superM13: Difference between revisions
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{|border="1" '''Re-engineering the M13K07 Genome''' | #{|border="1" '''Re-engineering the M13K07 Genome''' | ||
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|align="center" |Gene | |align="center" |Gene | ||
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# | # M13's closest evolutionary relative is the bacteriophage fd. Their genomes are about the same length, around 6400 bases, and their nucleotide sequences differ by only about 3.0%. Because their differences occur most frequently in some genes rather than others, it is less risky to re-engineer those genes that the differences occur on, since they are probably less critical to the virus. | ||
#"BBa_M1307 is not a standard biological part and does not belong in the registry." | #"BBa_M1307 is not a standard biological part and does not belong in the registry." | ||
::*Response: Because BBa_M1307 is the entire genome of the M13K07 phage, it is more like a system than just a single part. According to the abstraction hierarchy, a "part" is a basic biological function that can be encoded as genetic material. BBa_M1307 is composed of numerous parts, such as the promoters, ribosome binding sites, and terminators for each gene. These parts come together to form devices that serve certain functions in the virus, such as proteins that enclose the system. Together, these devices sustain the virus and help it reproduce. However, the genome could be far more useful if its individual parts were broken down and biobricked, so that they could be studied individually or rearranged to create new systems. | ::*Response: Because BBa_M1307 is the entire genome of the M13K07 phage, it is more like a system than just a single part. According to the abstraction hierarchy, a "part" is a basic biological function that can be encoded as genetic material. BBa_M1307 is composed of numerous parts, such as the promoters, ribosome binding sites, and terminators for each gene. These parts come together to form devices that serve certain functions in the virus, such as proteins that enclose the system. Together, these devices sustain the virus and help it reproduce. However, the genome could be far more useful if its individual parts were broken down and biobricked, so that they could be studied individually or rearranged to create new systems. | ||
Revision as of 05:48, 14 September 2007
- {|border="1" Re-engineering the M13K07 Genome
|-style="background:lightgray; color:black" |align="center" |Gene |align="center" |Base Pairs |align="center" |Overlaps(bp's) |align="center" |Function |align="center" |Suggested Changes |-style="background:beige; color:black" |align="center" |I |3196-4242 |IV(4220-4242), XI(3916-4242) |assembly | |-style="background:beige; color:black" |align="center" |II |8268-831 |X(496-831) |replication of DNA+strand | |-style="background:beige; color:black" |align="center" |III |1579-2853 |BamHI(2220-2225) |phage tail protein (5 copies) | |-style="background:beige; color:black" |align="center" |IV |4220-5500 |I(4220-4242), XI(4220-4242) |assembly | |-style="background:beige; color:black" |align="center" |V |843-1106 | |binds ssDNA | |-style="background:beige; color:black" |align="center" |VI |2856-3194 | |phage tail protein (5 copies) | |-style="background:beige; color:black" |align="center" |VII |1108-1209 |IX(1207-1208) |phage head protein (5 copies) | |-style="background:beige; color:black" |align="center" |VIII |1304-1522 |IX(1302-1303) |phage coat protein (2700 copies) | |-style="background:beige; color:black" |align="center" |IX |1206-1304 |VII(1207-1208), VIII(1302-1303) |phage head protein (5 copies) | |-style="background:beige; color:black" |align="center" |X |496-831 |II(496-831) |DNA replication | |-style="background:beige; color:black" |align="center" |XI (I*) |3916-4242 |I(3916-4242), IV(4220-4242) |assembly | |}
- M13's closest evolutionary relative is the bacteriophage fd. Their genomes are about the same length, around 6400 bases, and their nucleotide sequences differ by only about 3.0%. Because their differences occur most frequently in some genes rather than others, it is less risky to re-engineer those genes that the differences occur on, since they are probably less critical to the virus.
- "BBa_M1307 is not a standard biological part and does not belong in the registry."
- Response: Because BBa_M1307 is the entire genome of the M13K07 phage, it is more like a system than just a single part. According to the abstraction hierarchy, a "part" is a basic biological function that can be encoded as genetic material. BBa_M1307 is composed of numerous parts, such as the promoters, ribosome binding sites, and terminators for each gene. These parts come together to form devices that serve certain functions in the virus, such as proteins that enclose the system. Together, these devices sustain the virus and help it reproduce. However, the genome could be far more useful if its individual parts were broken down and biobricked, so that they could be studied individually or rearranged to create new systems.
