User:John M.L. Craven/Notebook/20.109 Mod 3, W/F Green Presentation

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
(Autocreated Lab Notebook name=User:John M.L. Craven/Notebook/20.109 Mod 3, W/F Green Presentation, content from MediaWiki:ProjectContentDefault)
Line 1: Line 1:
-
{|{{table}} width="800"
+
{{Rebuilding T7}}
-
|-
+
T7.2 is part of a larger project of [[Rebuilding T7]] to construct a more understandable model organism. T7.2 is the second iteration of our work in creating a more modelable organism, which began with [[T7.1]].
-
|style="background-color: #cdde95;" align="center"|
+
-
<!-- ## START calendar column -->
+
-
<LNCalendar></LNCalendar>
+
-
<!-- ## END calendar column -->
+
-
|align="center" style="background-color: #e5edc8;" |
+
-
<!-- ## START search column: Place your logo here. Try keep it below 200px in width and 150px in height. ##  -->
+
-
[[Image:owwnotebook_icon.png|128px]] <sitesearch>title=Search this Project</sitesearch>
+
-
<!-- ## END search column ## -->
+
-
|-
+
-
|colspan="2" style="background-color: #F2F2F2;" align="right"|[[{{FULLPAGENAME}}/Entry_Base|Customize your entry pages]] [[Help:Notebook/Project_Base/Customize_entry_page|<html><img src="/images/a/aa/Help.png" border="0" /></html>]]
+
-
|-
+
-
|colspan="2"|
+
-
==Project Description/Abstract==
+
-
* Place short description of project or notes regarding this project
+
-
* Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Donec porta commodo tellus. Nam a est eget libero mollis tincidunt. Aliquam purus. Quisque nulla ligula, facilisis in, pulvinar sed, molestie a, quam. Vestibulum at pede. In in sem eget odio eleifend placerat. Phasellus ultricies felis quis sapien. Etiam molestie volutpat quam. Praesent pulvinar scelerisque mi. Nam mi urna, fringilla eu, mattis sed, venenatis id, nunc. Maecenas velit eros, congue ut, placerat in, ornare vel, sem. Aenean porta enim sit amet felis gravida posuere. Phasellus faucibus nibh et orci.
+
==Background==
 +
The [[T7.1]] genome was more constrained by our initial uncertainty on the number of simultaneous changes T7 could tolerate than driven by our primary design goal – to construct a genetic system to help us understand how parts of a genetic system act in coordination to produce system-level behavior. While we will complete construction of [[T7.1]], and will make use of [[T7.1]] as an intermediate tool for comparison of wild type to T7.2, [[T7.1]] is not best suited for our proposed work.
-
==Notes==
+
==Goals==
-
* Place some notes here for visitors
+
The primary purpose of T7.2 is to construct a biological organism that is easier to model than the original biological isolate.  There are existing aspects of the natural isolate that make it particularly well suited to system-level analysis.  We want to make every effort to preserve these aspects, which include:
 +
#Viability -- Here viability refers to the ability to propagate the new species for practical experimental purposes.
 +
#Existing knowledge of the functional genetic elements -- We must continue to harness the tremendous amount of knowledge gained from genetic and biochemical experiments of T7 over the past 60 years.  To some extent, these studies are what allow our current models to as detailed as they are.
 +
#Relatively decoupled from host physiology -- T7 begins shutting off host transcription and solublizing the host genome within minutes of infection.  There are very few host proteins necessary for T7 infection.  We do not want to purposely or incidentally increase the dependency of the phage upon the host so that we can minimize modeling the intricacies of host physiology.
 +
#Coupling of entry and transcription -- This coupling leads to the natural organization of genes on the T7 genome.  In addition, the timing of genome entry, to some extent, makes modeling the phage easier.  In addition, any importance of the ordering of elements on the natural isolate will be more relevant to T7.2.
-
* Example: This project is currently on hold until further notice.
+
However, we feel the original biological isolate is not necessarily where we should begin to understand how system-behavior is produced.  Specifically, in designing T7.2, the following five goals will drive our design; the first three goals revisit or extend goals motivating the design of [[T7.1]]. 
 +
#Our design of T7.2 will enable the unique and selection-independent manipulation of each genetic element via restriction enzymes.
 +
#We will specify a genome that does not include any functions that might be encoded via the physical coupling of multiple genetic elements.
 +
#We will specify a genome that only includes elements that we believe contribute to phage gene expression.  Moving beyond our design of T7.1, we will actively erase or delete elements of unknown function.  In addition, efforts will be made to made to remove unknown genetic elements.
 +
##reduced gene sets?
 +
##codon shuffling?
 +
#To attempt to make our modeling of gene expression easier, we will use standard synthetic elements in place of the natural elements that regulate transcription and translation. 
 +
#We will make a genome that is more anemenable to measurements that are important to us, such as adding reporters of transcription and translation.  
 +
Taken together, our design of T7.2 should specify a genome that is simpler to model and manipulate, in which we have a putative function for each base pair of DNA involved in phage gene expression.  We hypothesize that as a result of the more parsimonious genome design, T7.2 will also encode a dynamic system that is easier to model and interact with, relative to the natural biological isolate.
-
|-
+
==Meta Considerations==
-
|colspan="2" style="background-color: #F2F2F2;"|
+
===Standardization===
-
{{LnNotebookRecentChanges2}}
+
We want to standardize certain functional genetic elements to make them easier to model.  For example, instead of further characterizing every different ribosome binding site and promoter, we can standardize on a set of that would take considerably less effort to characterize.
-
|}
+
===Measurement===
 +
We want to increase the ability to measure different aspects of phage biology.  This may including mRNA and protein reporters, and/or optimizing DpnI restriction sites to ease entry assays. 
 +
===Manipulability===
 +
We need to increase our ability to make selection-independent changes to the genome easily.  We will take the some of the lessons we learned in T7.1 about the types and distribution of restriction sites needed. 
 +
===Encoding===
 +
We want to reduce, to as large of an extent as possible, the number of genetic elements that are included in T7.2 that do not encode functions that we do not know about. 
-
__NOTOC__
+
==Designs==
 +
See the [[T7.2/Design|Designs Page]] for further information.

Revision as of 14:21, 4 May 2009

Project pages on
Rebuilding T7

T7.1
Reannotation
Specification
Construction
Evolution

T7.2
Design

back to Endy Lab

T7.2 is part of a larger project of Rebuilding T7 to construct a more understandable model organism. T7.2 is the second iteration of our work in creating a more modelable organism, which began with T7.1.

Contents

Background

The T7.1 genome was more constrained by our initial uncertainty on the number of simultaneous changes T7 could tolerate than driven by our primary design goal – to construct a genetic system to help us understand how parts of a genetic system act in coordination to produce system-level behavior. While we will complete construction of T7.1, and will make use of T7.1 as an intermediate tool for comparison of wild type to T7.2, T7.1 is not best suited for our proposed work.

Goals

The primary purpose of T7.2 is to construct a biological organism that is easier to model than the original biological isolate. There are existing aspects of the natural isolate that make it particularly well suited to system-level analysis. We want to make every effort to preserve these aspects, which include:

  1. Viability -- Here viability refers to the ability to propagate the new species for practical experimental purposes.
  2. Existing knowledge of the functional genetic elements -- We must continue to harness the tremendous amount of knowledge gained from genetic and biochemical experiments of T7 over the past 60 years. To some extent, these studies are what allow our current models to as detailed as they are.
  3. Relatively decoupled from host physiology -- T7 begins shutting off host transcription and solublizing the host genome within minutes of infection. There are very few host proteins necessary for T7 infection. We do not want to purposely or incidentally increase the dependency of the phage upon the host so that we can minimize modeling the intricacies of host physiology.
  4. Coupling of entry and transcription -- This coupling leads to the natural organization of genes on the T7 genome. In addition, the timing of genome entry, to some extent, makes modeling the phage easier. In addition, any importance of the ordering of elements on the natural isolate will be more relevant to T7.2.

However, we feel the original biological isolate is not necessarily where we should begin to understand how system-behavior is produced. Specifically, in designing T7.2, the following five goals will drive our design; the first three goals revisit or extend goals motivating the design of T7.1.

  1. Our design of T7.2 will enable the unique and selection-independent manipulation of each genetic element via restriction enzymes.
  2. We will specify a genome that does not include any functions that might be encoded via the physical coupling of multiple genetic elements.
  3. We will specify a genome that only includes elements that we believe contribute to phage gene expression. Moving beyond our design of T7.1, we will actively erase or delete elements of unknown function. In addition, efforts will be made to made to remove unknown genetic elements.
    1. reduced gene sets?
    2. codon shuffling?
  4. To attempt to make our modeling of gene expression easier, we will use standard synthetic elements in place of the natural elements that regulate transcription and translation.
  5. We will make a genome that is more anemenable to measurements that are important to us, such as adding reporters of transcription and translation.

Taken together, our design of T7.2 should specify a genome that is simpler to model and manipulate, in which we have a putative function for each base pair of DNA involved in phage gene expression. We hypothesize that as a result of the more parsimonious genome design, T7.2 will also encode a dynamic system that is easier to model and interact with, relative to the natural biological isolate.

Meta Considerations

Standardization

We want to standardize certain functional genetic elements to make them easier to model. For example, instead of further characterizing every different ribosome binding site and promoter, we can standardize on a set of that would take considerably less effort to characterize.

Measurement

We want to increase the ability to measure different aspects of phage biology. This may including mRNA and protein reporters, and/or optimizing DpnI restriction sites to ease entry assays.

Manipulability

We need to increase our ability to make selection-independent changes to the genome easily. We will take the some of the lessons we learned in T7.1 about the types and distribution of restriction sites needed.

Encoding

We want to reduce, to as large of an extent as possible, the number of genetic elements that are included in T7.2 that do not encode functions that we do not know about.

Designs

See the Designs Page for further information.

Personal tools