User:Pakpoom Subsoontorn/Notebook/general reading/2008/11/09: Difference between revisions
From OpenWetWare
Line 21: | Line 21: | ||
***Data representation: after all, whatever we did will be useful only if those who come after can use it. There are many ways to represent the collective information about part that we know. Again, I believe that the very important features of our presenting schema is the capability to compare and contrast thing in the same category (like comparing one DNA polymerase to another DNA polymerase.. comparing one transcription inhibition system to another transcription inhibiting system) and same attribute (compare the speed of all DNAP in catalog... compare inhibiting kinetic of all transcriptional inhibitors in the catalog) | ***Data representation: after all, whatever we did will be useful only if those who come after can use it. There are many ways to represent the collective information about part that we know. Again, I believe that the very important features of our presenting schema is the capability to compare and contrast thing in the same category (like comparing one DNA polymerase to another DNA polymerase.. comparing one transcription inhibition system to another transcription inhibiting system) and same attribute (compare the speed of all DNAP in catalog... compare inhibiting kinetic of all transcriptional inhibitors in the catalog) | ||
***Synthetic studies: it's important to demonstrate that the collection of data we present can facilitate the process of engineering a cells. In reverse, the result from an engineering project will also help us modify the methods and the management of the library of parts. Note that there can be many level of synthetic studies. Let's say we get the collection of information about DNA polymerase, that could help the protein engineering project on DNA polymerase..it could also help the circuit level projects that require DNA polymerase with specific properties. | ***Synthetic studies: it's important to demonstrate that the collection of data we present can facilitate the process of engineering a cells. In reverse, the result from an engineering project will also help us modify the methods and the management of the library of parts. Note that there can be many level of synthetic studies. Let's say we get the collection of information about DNA polymerase, that could help the protein engineering project on DNA polymerase..it could also help the circuit level projects that require DNA polymerase with specific properties. | ||
*Specific projects: Genetically encoded memory and site-specific recombinases | *Specific projects: Genetically encoded memory and site-specific recombinases | ||
Line 27: | Line 28: | ||
**Starting with some reading on invertase and other related enzymes in site-specific recombinase enzyme family, I realized that these classes of enzymes have a great potential of being our writing tools. Hundreds of these enzymes have been identified even though only about ten have been heavily studied. Their capability to cut-and-exchange pieces of DNA has been widely exploited in construction transgenic organisms, genetic knock out and possibly gene therapy. Surprisingly, I haven' seen any public database that store the whole collections and reaction profiles of these enzyme, not that I saw any large scales study that compare and contrast their activity profiles. I imagine that it would be very useful to have the extensive database and the large scale studies of this class of enzymes, not only for our genetically encoded memory project but also for many other biotechnology that based on site-specific DNA recombination. | **Starting with some reading on invertase and other related enzymes in site-specific recombinase enzyme family, I realized that these classes of enzymes have a great potential of being our writing tools. Hundreds of these enzymes have been identified even though only about ten have been heavily studied. Their capability to cut-and-exchange pieces of DNA has been widely exploited in construction transgenic organisms, genetic knock out and possibly gene therapy. Surprisingly, I haven' seen any public database that store the whole collections and reaction profiles of these enzyme, not that I saw any large scales study that compare and contrast their activity profiles. I imagine that it would be very useful to have the extensive database and the large scale studies of this class of enzymes, not only for our genetically encoded memory project but also for many other biotechnology that based on site-specific DNA recombination. | ||
**(More) Specific goal: Therefore, I planed to use "site-specific recombinases" as a specific study case for my general interest I mentioned above. In the project, "Parts" to be standardized in the whole collections of site-specific recombinase enzyme, natural or synthetic. I will be developing methods and managing guideline for discovering, characterizing, standardizing and presenting biological this class of enzyme. | **(More) Specific goal: Therefore, I planed to use "site-specific recombinases" as a specific study case for my general interest I mentioned above. In the project, "Parts" to be standardized in the whole collections of site-specific recombinase enzyme, natural or synthetic. I will be developing methods and managing guideline for discovering, characterizing, standardizing and presenting biological this class of enzyme. | ||
*Specific project in detail, current progress and plan | |||
** As I mention above, I hope that this project will have five related components | |||
***Prioritizing Questions and information | |||
***Database and literature mining | |||
***Developing higher throughput assay/ better measurement for characterizing recombinase enzymes | |||
***Constructing custom integrative database..combing our assay results and existing data we have dug out other studies | |||
***Synthetic studies: constructing genetically encoded memory system...at least the basic one. | |||
== Bacterial Cell shape== | == Bacterial Cell shape== |
Revision as of 19:48, 9 November 2008
Project name | <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page <html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>Previous entry<html> </html>Next entry<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html> |
Strategic Summary: week of 11/09/08
Genetically Encoded Memory
Bacterial Cell shape |