Murray Wiki - User contributions [en]

File:Expression @ 30C and 37C pelleted.png

2014-06-10T08:37:29Z

Rsatija: Pelleted cultures with different RNA Thermometers grown overnight at different temperatures

Pelleted cultures with different RNA Thermometers grown overnight at different temperatures

File:U9.PNG

2014-06-10T08:34:30Z

Rsatija: OD and GFP Expression Profiles of U9 during first expression experiment @ 30C and 37C.

OD and GFP Expression Profiles of U9 during first expression experiment @ 30C and 37C.

File:U8.PNG

2014-06-10T08:34:13Z

Rsatija: OD and GFP Expression Profiles of U8 during first expression experiment @ 30C and 37C.

OD and GFP Expression Profiles of U8 during first expression experiment @ 30C and 37C.

File:U6.PNG

2014-06-10T08:33:18Z

Rsatija: OD and GFP Expression Profiles of U6 during first expression experiment @ 30C and 37C.

OD and GFP Expression Profiles of U6 during first expression experiment @ 30C and 37C.

File:U2.PNG

2014-06-10T08:31:36Z

Rsatija: OD and GFP Expression Profiles of U2 during first expression experiment @ 30C and 37C.

OD and GFP Expression Profiles of U2 during first expression experiment @ 30C and 37C.

File:U0.PNG

2014-06-10T08:28:31Z

Rsatija: OD and GFP Expression Profiles of U0 during first expression experiment @ 30C and 37C.

OD and GFP Expression Profiles of U0 during first expression experiment @ 30C and 37C.

SURF 2014: Fabricating a Toolbox of RNA Thermometers

2014-06-10T06:31:53Z

Rsatija:

'''[[SURF 2014|2014 SURF]] project description'''

* Mentor: Richard Murray
* Co-mentor: Shaunak Sen

[[File:Zipper%2BSwitch_image.png‎|frame|Fig. 1. a) The RNA thermometer structure melts at higher temperature (open configuration) and re-natures to a closed configuration on again reducing the temperature (like a zipper). b) A switch-like RNA thermometer has two mutually exclusive secondary structures that switch between the two states based on temperature.]]
 
'''Overview:''' RNA Thermometers (RNATs) are mRNA sequences that change their secondary structures on the basis of temperature. Natural RNATs are usually present upstream of genes and regulate their rate of translation by revealing or hiding the Ribosome Binding Site (RBS) at different temperatures. Two common types of RNATs [4] are:
 a) Switch-type: These RNATs ‘switch’ between two mutually exclusive secondary structures at different temperatures. One example is the cIII switch found in λ phage viruses.
 b) Zipper-like: These are simple stem-loop structures which melt at higher temperatures and re-anneal at lower temperature. Examples include the ROSE (Repression Of heat Shock gene Expression) elements in many bacteria.
 Previous studies [1] [3] have shown how simple ‘zipper-like’ RNATs can be synthesized de novo. It is possible to alter the structures of these RNATs and observe temperature sensitivity of gene expression with respect to these changes. I will be working on developing a toolkit of RNATs with different threshold values of gene expression in relation to changes in temperature. Further, I will be demonstrating the utility of our toolkit through a simple gene circuit.
 
'''Goals:'''
 1. Validating putative synthetic RNATs [1] in vitro using the Transcription-Translation toolkit (TXTL) [5] and coming up with new designs based on free energy estimation using Mfold [2] as well as testing them in vitro
 2. Testing these novel RNAT designs in vivo
 3. Application of the toolkit in construction of a gene circuit that gives a temperature-compensated output for a given input

'''Required Skills:''' This project requires experience in molecular biology techniques and cloning. Also, understanding of as well as interest in synthetic biology and computation modeling is a pre-requisite.

=== References ===

[1] J. Neupert, D. Karcher, R. Bock. “Design of simple synthetic RNA thermometers for temperature-controlled gene expression in Escherichia coli.” Nucleic Acids Res. (2008): 36(19).

[2] http://mfold.rna.albany.edu/?q=mfold (accessed date: 05-30-14).

[3] J. Neupert, R. Bock. "Designing and using synthetic RNA thermometers for temperature-controlled gene expression in bacteria." Nature protocols 4.9 (2009): 1262-1273.

[4] J. Kortmann, F. Narberhaus. “Bacterial RNA thermometers: molecular zippers and switches.” Nature Reviews Microbiology 10 (2012): 255-265.

[5] ZZ. Sun, CA. Hayes, J. Shin, F. Caschera, RM. Murray, V. Noireaux. "Protocols for implementing an Escherichia coli based TX-TL cell-free expression system for synthetic biology." JoVE (Journal of Visualized Experiments) 79 (2013): e50762-e50762.

SURF 2014: Fabricating a Toolbox of RNA Thermometers

2014-06-10T06:31:09Z

Rsatija: Created page with "'''2014 SURF project description''' * Mentor: Richard Murray * Co-mentor: Shaunak Sen [[File:Zipper%2BSwitch_image.png‎|frame|Fig. 1. a) The RNA thermometer ..."

'''[[SURF 2014|2014 SURF]] project description'''

* Mentor: Richard Murray
* Co-mentor: Shaunak Sen

[[File:Zipper%2BSwitch_image.png‎|frame|Fig. 1. a) The RNA thermometer structure melts at higher temperature (open configuration) and re-natures to a closed configuration on again reducing the temperature (like a zipper). b) A switch-like RNA thermometer has two mutually exclusive secondary structures that switch between the two states based on temperature.]]

'''Overview:''' RNA Thermometers (RNATs) are mRNA sequences that change their secondary structures on the basis of temperature. Natural RNATs are usually present upstream of genes and regulate their rate of translation by revealing or hiding the Ribosome Binding Site (RBS) at different temperatures. Two common types of RNATs [4] are:
 a) Switch-type: These RNATs ‘switch’ between two mutually exclusive secondary structures at different temperatures. One example is the cIII switch found in λ phage viruses.
 b) Zipper-like: These are simple stem-loop structures which melt at higher temperatures and re-anneal at lower temperature. Examples include the ROSE (Repression Of heat Shock gene Expression) elements in many bacteria.
 Previous studies [1] [3] have shown how simple ‘zipper-like’ RNATs can be synthesized de novo. It is possible to alter the structures of these RNATs and observe temperature sensitivity of gene expression with respect to these changes. I will be working on developing a toolkit of RNATs with different threshold values of gene expression in relation to changes in temperature. Further, I will be demonstrating the utility of our toolkit through a simple gene circuit.
 
'''Goals:'''
 1. Validating putative synthetic RNATs [1] in vitro using the Transcription-Translation toolkit (TXTL) [5] and coming up with new designs based on free energy estimation using Mfold [2] as well as testing them in vitro
 2. Testing these novel RNAT designs in vivo
 3. Application of the toolkit in construction of a gene circuit that gives a temperature-compensated output for a given input

'''Required Skills:''' This project requires experience in molecular biology techniques and cloning. Also, understanding of as well as interest in synthetic biology and computation modeling is a pre-requisite.

=== References ===

[1] J. Neupert, D. Karcher, R. Bock. “Design of simple synthetic RNA thermometers for temperature-controlled gene expression in Escherichia coli.” Nucleic Acids Res. (2008): 36(19).

[2] http://mfold.rna.albany.edu/?q=mfold (accessed date: 05-30-14).

[3] J. Neupert, R. Bock. "Designing and using synthetic RNA thermometers for temperature-controlled gene expression in bacteria." Nature protocols 4.9 (2009): 1262-1273.

[4] J. Kortmann, F. Narberhaus. “Bacterial RNA thermometers: molecular zippers and switches.” Nature Reviews Microbiology 10 (2012): 255-265.

[5] ZZ. Sun, CA. Hayes, J. Shin, F. Caschera, RM. Murray, V. Noireaux. "Protocols for implementing an Escherichia coli based TX-TL cell-free expression system for synthetic biology." JoVE (Journal of Visualized Experiments) 79 (2013): e50762-e50762.

File:Zipper+Switch image.png

2014-06-10T06:15:52Z

Rsatija: a) The RNA thermometer structure melts at higher temperature (open configuration) and re-natures to a closed configuration on again reducing the temperature (like a zipper). b) A switch-like RNA thermometer has two mutually exclusive secondary structur...

a) The RNA thermometer structure melts at higher temperature (open configuration) and re-natures to a closed configuration on again reducing the temperature (like a zipper). b) A switch-like RNA thermometer has two mutually exclusive secondary structures that switch between the two states based on temperature.

SURF 2014

2014-06-10T04:58:22Z

Rsatija:

This page is intended for students interested in working on SURF projects in the Summer of 2014. It contains a list of project areas where I will be supervising projects this year along with information about how to apply for a SURF project in my group. __NOTOC__

=== Meetings on 17-20 June ===
{| border=1 width=100%
|- valign=top
| width=25% |
===== Tue (17 Jun) =====
* SURF orientation
| width=25% |
===== Wed (18 Jun) =====
* 10:00 - Meeting with co-mentors, 114 Steele Lab
** Biocircuits: lab orientation/cleanup
* 12:00 - SURF seminar
* 1:30 - Caltech safety briefing (mandatory)
| width=25% |
===== Thu (19 Jun) =====
* First full day with co-mentors
| width=25% |
===== Fri (20 Jun) =====
* 1:00-3:00 - SURF group meeting with Richard and co-mentors, 114 Steele
** 1 chart overviews (5 min each)
|}

== Students ==
{| width=100% border=1
|-
| Student
| Subgroup
| Co-mentor(s)
| Project
|-
| Mattias Falt || NCS || Vasu || {{SURF entry|2014|Invariant Refinement for Receding Horizon Temporal Logic Planning}}
|-
| Anton Frisk || Biocircuits || Clare, Vipul || {{SURF entry|2014|Rapid prototyping of moderate complexity biomolecular circuits}}
|-
| Joaquin Gabaldon || NCS || Ioannis || {{SURF entry|2014|Symbolic Verification of Nonlinear Hybrid Systems using Theorem Provers}}
|-
| Joon Sik (David) Kim [starts in Jul] || NCS || Vasu || {{SURF entry|2014|Invariant Refinement for Receding Horizon Temporal Logic Planning}}
|-
| Pulkit Malik || Biocircuits || Clare, Vipul || {{SURF entry|2014|Rapid prototyping of moderate complexity biomolecular circuits}}
|-
| Robert Mattila || NCS || Yilin || {{SURF entry|2014|Improved methods of discretization for temporal logic planning}}
|-
| Linnea Persson || NCS || Scott || {{SURF entry|2014|Switching control synthesis in the presence of uncertainty and general loads for an aircraft electric power system testbed}}
|-
| Rohit Satija || Biocircuits || S. Sen || {{SURF entry|2014|Fabricating a Toolbox of RNA Thermometers}}
|-
| Samriddhi Sharma || NCS || Ioannis || {{SURF entry|2014|Symbolic Verification of Nonlinear Hybrid Systems using Theorem Provers}}
|-
| Tiffany Zhou || Biocircuits || Clare, Vipul || {{SURF entry|2014|Rapid prototyping of moderate complexity biomolecular circuits}}
|}

=== Applying for a SURF project ===

Because I get many students interested in doing SURFs in my group and because we have several projects available, we use the first few weeks in January to sort out who we will work with in writing proposals. We only submit one proposal per project area and so we often can't accommodate everyone who wants to work in my group over the summer.

# A list of SURF project descriptions is given in the table below. Due to the number of SURF projects that we support, we are only able to support students who select from among these projects. Please make sure to read the project descriptions, required skills (if any) and skim a few of the listed references before contacting me about doing a SURF project.
# Students interested in writing proposals for SURF projects should contact me via e-mail by 10 Jan (Fri) and provide the following information:
#* A list of up to three SURF projects from the list below that you are interested in working on
#* A one page resume listing relevant experience and coursework
#* If you are not a Caltech student, I will also need the following additional information:
#** An unofficial copy of your academic transcript
#** Names of two faculty members at your current institution that I can contact for a reference
# Starting on 11 January, I will go through all applications and work with my group to identify who is a possible fit for each project. We will then contact you and ask for you to meet (or talk with) possible co-mentors so that we can eventually work out who we will work with in writing up a proposal.
# We hope to make final decisions on projects by about 20 Jan, at which point we will start working with students on writing up proposals.
# All applications should go through the normal SURF application process, described at www.surf.caltech.edu. SURF applications are due on 22 Feb 2014.
# If you are selected for a SURF, please be aware of the following information
#* All SURF projects in my group will start on 17 Jun (Tue). If you can't start on that date, please make sure that you indicate this when you contact me
#* All SURF projects are for a minimum of 10 weeks, although I usually recommend that you try to stay for 12 weeks if possible (at no additional pay). It's hard to complete a project in just 10 weeks and spending a few extra weeks can greatly improve the project.
#* All SURF students in my group will be expected to devote full-time effort to their SURF project, so you cannot have a second job in addition to your SURF.

=== List of available projects ===

{| border=1 width=100%
|-
| '''Title''' || '''Grant/Project''' || '''Co-Mentors''' || '''Comments'''
|-
| {{SURF entry|2014|Switching control synthesis in the presence of uncertainty and general loads for an aircraft electric power system testbed}}
| [[ICyPhy:_Industrial_Cyber-Physical_Systems|iCyPhy]]
| [http://scottman.net Scott C. Livingston]
|
|-
| {{SURF entry|2014|Improved methods of discretization for temporal logic planning}}
| [[ICyPhy:_Industrial_Cyber-Physical_Systems|iCyPhy]]
| Yilin Mo
|
|-
| {{SURF entry|2014|Symbolic Verification of Nonlinear Hybrid Systems using Theorem Provers}}
| [[The_TerraSwarm_Research_Center|TerraSwarm]]
| [http://www.cds.caltech.edu/~ifilippi/ Ioannis Filippidis]
|
|-
| {{SURF entry|2014|Rapid prototyping of moderate complexity biomolecular circuits}}
| [[Biomolecular_Breadboards_for_Prototyping_and_Debugging_Synthetic_Biocircuits|DARPA Breadboards]]
| Richard Murray, Clare Hayes
| Multiple positions available (2-4)
|
|-
| {{SURF entry|2014|Invariant Refinement for Receding Horizon Temporal Logic Planning}}
| [[The_TerraSwarm_Research_Center|TerraSwarm]]
| [http://users.cms.caltech.edu/~vasu/ Vasu Raman]
|
|}