Murray Wiki - User contributions [en]

Group Schedule, Winter 2024

2024-01-09T02:09:08Z

Jmarken: /* Week 4: 22-26 Jan */

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [[http:www.cds.caltech.edu/~murray/myschedule.html|Richard's calendar]]
| width=50% |
* [[Group Schedule, Fall 2023]]
|}

The schedule for group and subgroup meetings is given below. Contact Richard if you need to change the schedule. Unless otherwise noted, biocircuits meetings are in 111 Keck and NCS meetings are in 110 Steele Lab.

{| width=100% border=1
|- valign=top

| width=25% |
=== Week 1: 1-5 Jan ===
* Classes start on 3 Jan
* No group meetings

| width=25% |

=== Week 2: 8-12 Jan ===
'''Biocircuits: Tue, 10a-12p'''
* [[http:docs.google.com/presentation/d/1mfEkB7m2aSYY-CRQfikXd4v34akD3fAFwxkv1nXyTE0|Individual updates]]
'''NCS: Wed, ~3:45p-5p'''
* Nikos

| width=25% |

=== Week 3: 15-19 Jan ===
'''Biocircuits: Tue, 10a-12p'''
* Zach
'''NCS: <s>Wed, ~3:45p</s>Thu, 3:30-5p'''
* T&E

| width=25% |

=== Week 4: 22-26 Jan ===
'''Biocircuits: Tue, 10a-12p'''
* John
* Group meeting may move to Mon @ 9 am
'''NCS: Tue, 3:30p-5p'''
* Inigo

|- valign=top
| width=25% |

=== Week 5: 29 Jan - 2 Feb ===
'''Biocircuits: Tue, 10a-12p'''
* Group meeting may move to Mon @ 9 am
* Blade
'''NCS: Wed, ~3:45p-5p'''
* Apurva

| width=25% |

=== Week 6: 5-9 Feb ===
'''Biocircuits: Tue, 10a-12p'''
* Individual updates
* Group meeting may move to Mon @ 9 am
'''NCS: Wed, ~3:45p-5p'''
* Kellan

| width=25% |

=== Week 7: 12-16 Feb ===
'''Biocircuits: Wed, 9a-11a'''
* Alex
'''NCS: <s>Wed, ~3:45p</s>Thu, 3:30-5p'''
* T&E

| width=25% |

=== Week 8: 19-23 Feb ===
'''Biocircuits: Tue, 10a-12p'''
* TBD
'''NCS: Tue, 3:30p-5p'''
* Josefine

|- valign=top
| width=25% |

=== Week 9: 26 Feb - 1 Mar ===
'''Biocircuits: Mon, 9a-11a'''
* Rotation students
'''NCS: Wed, ~3:45p-5p'''
* Ioannis

| width=25% |

=== Week 10: 4-8 Mar ===
'''Biocircuits: Mon, 9a-11a'''
* Individual updates
* Meeting might shift to Wed
'''NCS: Wed, ~3:45p-5p'''
* Kimia

| width=25% |

=== Week 11: 11-16 Mar ===
'''Biocircuits: Tue, 10a-12p'''
* Manisha
* Meeting might shift to Wed
'''NCS: Wed, ~3:45p-5p'''
* TBD

| width=25% |

=== Week 12: 18-23 Mar ===
'''Biocircuits: Tue, 10a-12p'''
* TBD
'''NCS: Wed, ~3:45p-5p'''
* T&E
<hr>
* Meetings may get cancelled

|}

Andras Gyorgy, Aug 2023

2023-08-03T18:43:11Z

Jmarken: /* Schedule */

Andras Gyorgy from NYU Abu Dhabi will visit on 7 Aug (Mon).

== Schedule ==

* 9:30 am: Richard, 109 Steele
* 10:00 am: Manisha
* 10:30 am: Zach Martinez, Red Door(?)
* 11:00 am: Seminar, 111 Keck
* 12:15 pm: Lunch with graduate students
* 1:30 pm: open
* 2:15 pm: Yan, location TBD
* 3:00 pm: John, location TBD
* 3:45 pm: Inigo, Annenberg 2nd floor lounge
* 4:30 pm: Richard, 109 Steele

Andras Gyorgy, Aug 2023

2023-08-03T17:35:44Z

Jmarken: /* Schedule */

Andras Gyorgy from NYU Abu Dhabi will visit on 7 Aug (Mon).

== Schedule ==

* 9:30 am: Richard, 109 Steele
* 10:00 am: Manisha
* 10:30 am: Zach Martinez, Red Door(?)
* 11:00 am: Seminar, 111 Keck
* 12:15 pm: Lunch with graduate students
* 1:30 pm: open [potentially elowitz lab members?]
* 2:15 pm: Yan, location TBD
* 3:00 pm: John, location TBD
* 3:45 pm: Inigo, Annenberg 2nd floor lounge
* 4:30 pm: Richard, 109 Steele

Andras Gyorgy, Aug 2023

2023-08-03T17:35:19Z

Jmarken: /* Schedule */

Andras Gyorgy, Aug 2023

2023-08-03T17:22:24Z

Jmarken: /* Schedule */

Andras Gyorgy from NYU Abu Dhabi will visit on 7 Aug (Mon).

== Schedule ==

* 9:30 am: Richard, 109 Steele
* 10:00 am: Manisha
* 10:30 am: Zach Martinez, Red Door(?)
* 11:00 am: Seminar, 111 Keck
* 12:15 pm: Lunch with graduate students
* 1:30 pm: Jacob Parres-Gold (Elowitz Lab), Chen 2nd floor lobby
* 2:15 pm: Yan, location TBD
* 3:00 pm: John, location TBD
* 3:45 pm: Inigo, Annenberg 2nd floor lounge
* 4:30 pm: Richard, 109 Steele

Andras Gyorgy, Aug 2023

2023-08-03T17:16:53Z

Jmarken: /* Schedule */

Andras Gyorgy from NYU Abu Dhabi will visit on 7 Aug (Mon).

== Schedule ==

* 9:30 am: Richard, 109 Steele
* 10:00 am: Manisha
* 10:30 am: Zach Martinez, Red Door(?)
* 11:00 am: Seminar, 111 Keck
* 12:15 pm: Lunch with graduate students
* 1:30 pm: Jacob Parres-Gold (Elowitz Lab), location TBD
* 2:15 pm: Yan, location TBD
* 3:00 pm: John, location TBD
* 3:45 pm: Inigo, Annenberg 2nd floor lounge
* 4:30 pm: Richard, 109 Steele

Andras Gyorgy, Aug 2023

2023-08-03T17:16:42Z

Jmarken: /* Schedule */

Andras Gyorgy from NYU Abu Dhabi will visit on 7 Aug (Mon).

== Schedule ==

* 9:30 am: Richard, 109 Steele
* 10:00 am: Manisha
* 10:30 am: Zach Martinez, Red Door(?)
* 11:00 am: Seminar, 111 Keck
* 12:15 pm: Lunch with graduate students
* 1:30 pm: Jacob Parres-Gold, location TBD
* 2:15 pm: Yan, location TBD
* 3:00 pm: John, location TBD
* 3:45 pm: Inigo, Annenberg 2nd floor lounge
* 4:30 pm: Richard, 109 Steele

Andras Gyorgy, Aug 2023

2023-08-03T17:11:00Z

Jmarken: /* Schedule */

Andras Gyorgy, Aug 2023

2023-08-03T14:48:10Z

Jmarken: /* Schedule */

Andras Gyorgy from NYU Abu Dhabi will visit on 7 Aug (Mon).

== Schedule ==

* 9:30 am: Richard, 109 Steele
* 10:00 am: John Marken, location TBD
* 10:30 am: open
* 11:00 am: Seminar, 111 Keck
* 12:15 pm: Lunch with graduate students
* 1:30 pm: open
* 2:15 pm: open
* 3:00 pm: open
* 3:45 pm: open
* 4:30 pm: Richard, 109 Steele

Manos Alexis, Oct 2022

2022-10-21T15:14:34Z

Jmarken: /* 24 Oct (Mon) */

Manos Alexis, a PhD student at Cambridge interested in dynamical systems, control theory, synthetic biology and systems biology will visit our group the week of 24 Oct. You can sign up for a time to meet with him below:

=== 24 Oct (Mon) ===

* 9:00 am: Monica Nolasco, 107 Steele Lab
* 10:00 am: Richard Murray, 109 Steele Lab
* 10:45 am: open
* 11:30 am: open
* 12:00 pm: Lunch w/ soil syn bio students (tentative)
* 1:30 pm: John Marken
* 2:15 pm: open
* 3:00 pm: open
* 3:45 pm: open
* 4:30 pm: open

=== 25 Oct (Tue) ===

* 9:00 am: open
* 10:00 am: Biocircuits group meeting, 111 Keck
* 12:00 pm: Lunch w/ synthetic cell students (tentative)
* 1:30 pm: open
* 2:15 pm: open
* 3:00 pm: open
* 3:45 pm: open
* 4:30 pm: open

Yan Zhang, 28 Mar 2022

2022-03-25T05:31:08Z

Jmarken:

Yan Zhang, a PhD student at Georgia Tech will visit on 28 Mar 2022.

Schedule:
* 8:30 am: Richard Murray, 109 Steele
* 9:00 am: Open
* 10:00 am: Group meeting presentation
* 12:00 pm: Lunch with Chelsea, Michaelle
* 1:15 pm: Meet with John (wherever-- Red Door is fine. Or Chen tables if that's convenient coming from lunch?)
* 2:00 pm: Meet with Ayush at Red Door
* 2:45 pm: Meet with Manisha (at Red Door?)
* 3:30 pm: Meet with Zoila (meet at Red Door -> walk to Lake)
* 4:15 pm: Open
* 5:00 pm: Richard Murray, 109 Steele

Research interests:
* Developed a new diagnostic platform interfacing cell-free biosensors with biphasic polymer systems for simultaneous detection of diverse classes of analytes that are robust to human biofluids and field-deployable.
* Integrated cell-free biosensors to a personal glucose monitor for rapid and reliable biomarker quantification at the point of need
* Designed, characterized, and optimized cell-free bacterial biosensors to detect micronutrient deficiencies, pathogenic bacterial infections, and heavy metal environment contaminants

Yan Zhang, 28 Mar 2022

2022-03-25T05:30:15Z

Jmarken:

Yan Zhang, a PhD student at Georgia Tech will visit on 28 Mar 2022.

Schedule:
* 8:30 am: Richard Murray, 109 Steele
* 9:00 am: Open
* 10:00 am: Group meeting presentation
* 12:00 pm: Lunch with Chelsea, Michaelle
* 1:15 pm: Meet with John at Red Door
* 2:00 pm: Meet with Ayush at Red Door
* 2:45 pm: Meet with Manisha (at Red Door?)
* 3:30 pm: Meet with Zoila (meet at Red Door -> walk to Lake)
* 4:15 pm: Open
* 5:00 pm: Richard Murray, 109 Steele

Research interests:
* Developed a new diagnostic platform interfacing cell-free biosensors with biphasic polymer systems for simultaneous detection of diverse classes of analytes that are robust to human biofluids and field-deployable.
* Integrated cell-free biosensors to a personal glucose monitor for rapid and reliable biomarker quantification at the point of need
* Designed, characterized, and optimized cell-free bacterial biosensors to detect micronutrient deficiencies, pathogenic bacterial infections, and heavy metal environment contaminants

David Garcia, 13 Feb 2020

2020-02-13T19:43:53Z

Jmarken:

David Garcia, a PhD student working at Oak Ridge National Laboratory (ORNL) will visit Caltech on 13 Feb (Thu). If you would like to meet with him, sign up here (using your IMSS credentials).

=== Schedule ===
* 9:15 am: Richard (107 Steele Lab)
* 10:00 am: Seminar
* 11:00 am: Zoila
* 11:45 am: Lunch (Michaelle, Chelsea)
* 1:00 pm: Elin
* 1:45 pm: Chelsea
* 2:30 pm: John Marken
* 3:15 pm: Rory
* 4:00 pm: Ayush
* 4:45 pm: Wrap up meet with Richard

=== Seminar ===

Cell-Free Enabled Bioproduction and Biological Discovery 
David Garcia, The University of Tennessee, Knoxville and Oak Ridge National Laboratory 

13 Feb (Thu), 10a-11a, 114 Steele

As our understanding of the microbial world has progressed, so too has the backlog of information and open questions generated from the thousands uncharacterized proteins and metabolites with potential applications as biofuels, therapeutics, and biomaterials. To address this problem, new tools need to be developed in order to rapidly test and take advantage of uncharacterized proteins and metabolites. Cell-free systems have developed into a high-throughput and scalable tool for synthetic biology and metabolic engineering with applications across multiple disciplines. The work presented in this talk leverages cell-free systems as a conduit for the exploration of protein function and metabolite production using two complementary approaches. The first elucidates interaction networks associated with secondary metabolite production using a computationally assisted pathway description pipeline that employs bioinformatic searches of genome databases, structural modeling, and ligand-docking simulations to predict the gene products most likely to be involved in a metabolic pathway. In vitro reconstructions of the pathway are then modularly assembled and chemically verified in Escherichia coli lysates in order to differentiate between active and inactive pathways. The second takes a systems and synthetic biology approach to engineer E. coli extracts capable of directing flux towards specific metabolites. Using growth and genome engineering-based methods, we produced cell-free proteomes capable of creating unconventional metabolic states with minimal impact on the cell in vivo. As a result of this work, we have significantly expanded our ability to use cell extracts outside of their native context to solve metabolic engineering problems and provide engineers new tools that can rapidly explore the functions of proteins and test novel metabolic pathways.

David Garcia, 13 Feb 2020

2020-02-11T18:22:35Z

Jmarken: /* Schedule */

David Garcia, a PhD student working at Oak Ridge National Laboratory (ORNL) will visit Caltech on 13 Feb (Thu). If you would like to meet with him, sign up here (using your IMSS credentials).

=== Schedule ===
* 9:15 am: Richard (107 Steele Lab)
* 10:00 am: Seminar
* 11:00 am: Zoila
* 11:45 am: Lunch (Michaelle, Chelsea)
* 1:00 pm: Open
* 1:45 pm: Chelsea
* 2:30 pm: Open
* 3:15 pm: John Marken
* 4:00 pm: Open
* 4:45 pm: Wrap up meet with Richard

=== Seminar ===

Cell-Free Enabled Bioproduction and Biological Discovery 
David Garcia, The University of Tennessee, Knoxville and Oak Ridge National Laboratory 

13 Feb (Thu), 10a-11a, 114 Steele

As our understanding of the microbial world has progressed, so too has the backlog of information and open questions generated from the thousands uncharacterized proteins and metabolites with potential applications as biofuels, therapeutics, and biomaterials. To address this problem, new tools need to be developed in order to rapidly test and take advantage of uncharacterized proteins and metabolites. Cell-free systems have developed into a high-throughput and scalable tool for synthetic biology and metabolic engineering with applications across multiple disciplines. The work presented in this talk leverages cell-free systems as a conduit for the exploration of protein function and metabolite production using two complementary approaches. The first elucidates interaction networks associated with secondary metabolite production using a computationally assisted pathway description pipeline that employs bioinformatic searches of genome databases, structural modeling, and ligand-docking simulations to predict the gene products most likely to be involved in a metabolic pathway. In vitro reconstructions of the pathway are then modularly assembled and chemically verified in Escherichia coli lysates in order to differentiate between active and inactive pathways. The second takes a systems and synthetic biology approach to engineer E. coli extracts capable of directing flux towards specific metabolites. Using growth and genome engineering-based methods, we produced cell-free proteomes capable of creating unconventional metabolic states with minimal impact on the cell in vivo. As a result of this work, we have significantly expanded our ability to use cell extracts outside of their native context to solve metabolic engineering problems and provide engineers new tools that can rapidly explore the functions of proteins and test novel metabolic pathways.

David Garcia, 13 Feb 2020

2020-02-11T17:05:37Z

Jmarken: /* Schedule */

David Garcia, a PhD student working at Oak Ridge National Laboratory (ORNL) will visit Caltech on 13 Feb (Thu). If you would like to meet with him, sign up here (using your IMSS credentials).

=== Schedule ===
* 9:15 am: Richard (107 Steele Lab)
* 10:00 am: Seminar
* 11:00 am: Zoila
* 11:45 am: Lunch (Michaelle, Chelsea)
* 1:00 pm: John Marken
* 1:45 pm: Open
* 2:30 pm: Open
* 3:15 pm: Open
* 4:00 pm: Open
* 4:45 pm: Wrap up meet with Richard

=== Seminar ===

Cell-Free Enabled Bioproduction and Biological Discovery 
David Garcia, The University of Tennessee, Knoxville and Oak Ridge National Laboratory 

13 Feb (Thu), 10a-11a, 114 Steele

As our understanding of the microbial world has progressed, so too has the backlog of information and open questions generated from the thousands uncharacterized proteins and metabolites with potential applications as biofuels, therapeutics, and biomaterials. To address this problem, new tools need to be developed in order to rapidly test and take advantage of uncharacterized proteins and metabolites. Cell-free systems have developed into a high-throughput and scalable tool for synthetic biology and metabolic engineering with applications across multiple disciplines. The work presented in this talk leverages cell-free systems as a conduit for the exploration of protein function and metabolite production using two complementary approaches. The first elucidates interaction networks associated with secondary metabolite production using a computationally assisted pathway description pipeline that employs bioinformatic searches of genome databases, structural modeling, and ligand-docking simulations to predict the gene products most likely to be involved in a metabolic pathway. In vitro reconstructions of the pathway are then modularly assembled and chemically verified in Escherichia coli lysates in order to differentiate between active and inactive pathways. The second takes a systems and synthetic biology approach to engineer E. coli extracts capable of directing flux towards specific metabolites. Using growth and genome engineering-based methods, we produced cell-free proteomes capable of creating unconventional metabolic states with minimal impact on the cell in vivo. As a result of this work, we have significantly expanded our ability to use cell extracts outside of their native context to solve metabolic engineering problems and provide engineers new tools that can rapidly explore the functions of proteins and test novel metabolic pathways.

Group Schedule, Winter 2020

2019-12-19T15:40:37Z

Jmarken: /* Week 4: 27-31 Jan */

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [[Schedule|Richard's calendar (travel)]]
| width=50% |
* [[Group Schedule, Fall 2019]]
|}

The schedule for group and subgroup meetings is given below. Contact Richard if you need to change the schedule. Unless otherwise noted, biocircuits meetings are in 111 Keck and NCS meetings are in 110 Steele.

{| width=100% border=1
|- valign=top

| width=25% |
=== Week 1: 6-10 Jan ===
'''Biocircuits: Tue, 10a-12p'''
* Andrey
* James
* Meeting may shift to 9a-11a
'''NCS: Wed, 2p-3p'''
* Chuchu

| width=25% |

=== Week 2: 13-17 Jan===
'''Biocircuits: Tue, 10a-12p'''
* Individual updates
* Meeting may shift to 9a-11a
'''NCS: Wed, 2p-3p'''
* Francesca
* Meeting may shift to 1:30p-2:30p in Keck 111

| width=25% |

=== Week 3: 20-24 Jan ===
'''Biocircuits: Tue, 10a-12p'''
* TBD
'''NCS: Wed, 2p-3p'''
* Prithvi


| width=25% |

=== Week 4: 27-31 Jan ===
'''Biocircuits: Tue, 10a-12p'''
* John
* Leo
* Meeting may shift to 3p-5p
'''NCS: Wed, 2p-3p'''
* Sumanth

|- valign=top
| width=25% |

=== Week 5: 3-7 Feb ===
'''Biocircuits: Tue, 10a-12p'''
* Individual updates
'''NCS: Wed, 2p-3p'''
* Karena


| width=25% |

=== Week 6: 10-14 Feb ===
'''Biocircuits: Tue, 10a-12p'''
* TBD
* Meeting may shift to 9a-11a
'''NCS: Wed, 2p-3p'''
* Richard C


| width=25% |

=== Week 7: 17-21 Feb ===
'''Biocircuits: Tue, 10a-12p'''
* Reed
* Cindy
'''NCS: Wed, 2p-3p'''
* Tung

| width=25% |

=== Week 8: 24-28 Feb ===
'''Biocircuits: Tue, 10a-12p'''
* Individual updates
* Meeting may shift to 9a-11a
'''NCS: Wed, 2p-3p'''
* Reza


|- valign=top
| width=25% |

=== Week 9: 2-6 Mar ===
'''Biocircuits: Tue, 10a-12p'''
* Liana
* Sophie
'''NCS: Wed, 2p-3p'''
* UG/visitor

| width=25% |

=== Week 10: 9-13 Mar ===
'''Biocircuits: Tue, 10a-12p'''
* Ayush
* Sam
* Meeting may be cancelled
'''NCS: Wed, 2p-3p'''
* Yuxiao
* Meeting may be cancelled

| width=25% |

=== Week 11: 16-20 Mar ===
'''Biocircuits: Tue, 10a-12p'''
* Individual updates
* Meeting may be cancelled
'''NCS: Wed, 2p-3p'''
* Apurva
* Meeting may be cancelled


| width=25% |

=== Week 12: 23-27 Mar ===
* Spring break

|}

Group Schedule, Winter 2020

2019-12-19T15:40:28Z

Jmarken: /* Week 1: 6-10 Jan */

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [[Schedule|Richard's calendar (travel)]]
| width=50% |
* [[Group Schedule, Fall 2019]]
|}

The schedule for group and subgroup meetings is given below. Contact Richard if you need to change the schedule. Unless otherwise noted, biocircuits meetings are in 111 Keck and NCS meetings are in 110 Steele.

{| width=100% border=1
|- valign=top

| width=25% |
=== Week 1: 6-10 Jan ===
'''Biocircuits: Tue, 10a-12p'''
* Andrey
* James
* Meeting may shift to 9a-11a
'''NCS: Wed, 2p-3p'''
* Chuchu

| width=25% |

=== Week 2: 13-17 Jan===
'''Biocircuits: Tue, 10a-12p'''
* Individual updates
* Meeting may shift to 9a-11a
'''NCS: Wed, 2p-3p'''
* Francesca
* Meeting may shift to 1:30p-2:30p in Keck 111

| width=25% |

=== Week 3: 20-24 Jan ===
'''Biocircuits: Tue, 10a-12p'''
* TBD
'''NCS: Wed, 2p-3p'''
* Prithvi


| width=25% |

=== Week 4: 27-31 Jan ===
'''Biocircuits: Tue, 10a-12p'''
* James
* Leo
* Meeting may shift to 3p-5p
'''NCS: Wed, 2p-3p'''
* Sumanth

|- valign=top
| width=25% |

=== Week 5: 3-7 Feb ===
'''Biocircuits: Tue, 10a-12p'''
* Individual updates
'''NCS: Wed, 2p-3p'''
* Karena


| width=25% |

=== Week 6: 10-14 Feb ===
'''Biocircuits: Tue, 10a-12p'''
* TBD
* Meeting may shift to 9a-11a
'''NCS: Wed, 2p-3p'''
* Richard C


| width=25% |

=== Week 7: 17-21 Feb ===
'''Biocircuits: Tue, 10a-12p'''
* Reed
* Cindy
'''NCS: Wed, 2p-3p'''
* Tung

| width=25% |

=== Week 8: 24-28 Feb ===
'''Biocircuits: Tue, 10a-12p'''
* Individual updates
* Meeting may shift to 9a-11a
'''NCS: Wed, 2p-3p'''
* Reza


|- valign=top
| width=25% |

=== Week 9: 2-6 Mar ===
'''Biocircuits: Tue, 10a-12p'''
* Liana
* Sophie
'''NCS: Wed, 2p-3p'''
* UG/visitor

| width=25% |

=== Week 10: 9-13 Mar ===
'''Biocircuits: Tue, 10a-12p'''
* Ayush
* Sam
* Meeting may be cancelled
'''NCS: Wed, 2p-3p'''
* Yuxiao
* Meeting may be cancelled

| width=25% |

=== Week 11: 16-20 Mar ===
'''Biocircuits: Tue, 10a-12p'''
* Individual updates
* Meeting may be cancelled
'''NCS: Wed, 2p-3p'''
* Apurva
* Meeting may be cancelled


| width=25% |

=== Week 12: 23-27 Mar ===
* Spring break

|}

Group Schedule, Fall 2019

2019-12-03T03:09:52Z

Jmarken: /* Week 10: 2-6 Dec */

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [[Schedule|Richard's calendar (travel)]]
| width=50% |
* [[Group Schedule, Summer 2019]]
|}

The schedule for group and subgroup meetings is given below. Contact Richard if you need to change the schedule. Unless otherwise noted, biocircuits meetings are in 111 Keck and NCS meetings are in 243 Annenberg.

{| width=100% border=1
|- valign=top

| width=25% |
=== Week 1: 30 Sep - 4 Oct ===
'''Biocircuits: Tue, <s>10a-12p</s> 9a-11a'''
* Ayush
* Cindy
* Note: meeting will probably shift to start at 9 am
'''NCS: Wed, 10a-11:30a, BBB 181'''
* Thomas Mohren (visitor)

| width=25% |

=== Week 2: 7-11 Oct ===
'''Biocircuits: Tue, 10a-12p'''
* [[http:docs.google.com/presentation/d/18AQHdCkuT70Zm_3CqiODFfDa0sMmwADnzD4D6FhB22c/edit#slide=id.g4bc2dc3c11_0_0|Individual updates]]
'''NCS: Wed, 3:45p-5p'''
* Prithvi

| width=25% |

=== Week 3: 14-18 Oct ===
'''Biocircuits: Tue, 10a-12p'''
* Michaelle
* Zoila
'''NCS: Wed, 3:45p-5p'''
* Sumanth

| width=25% |

=== Week 4: 21-27 Oct ===
'''Biocircuits: Tue, 10a-12p'''
* [[http:/docs.google.com/presentation/d/1GBTVY5KnSAvFkMQxzHjOiWsIKTGFCpcu1GgURpqI-RI|Individual updates]]
'''NCS: Wed, 3:45p-5p'''
* Richard C

|- valign=top
| width=25% |

=== Week 5: 28 Oct - 1 Nov ===
'''NCS: <s>Wed, 3:45p-5p</s> Mon, 10a-11a'''
* Karena
'''Biocircuits: Tue, 10a-12p'''
* William
* Richard

| width=25% |

=== Week 6: 4-8 Nov ===
'''Biocircuits: Tue, 10a-12p'''
* [[http:docs.google.com/presentation/d/1nPgKyVJb6AF3o50YytEh9H6d8bHhQSHsUhGHYtDCKL8|Individual updates]]
'''NCS: Wed, 3:45p-5p'''
* Yuxiao

| width=25% |

=== Week 7: 11-15 Nov ===
'''Biocircuits: Tue, 10a-12p'''
* Chelsea
* Rory
'''NCS: Wed, 3:45p-5p'''
* Reza

| width=25% |

=== Week 8: 18-22 Nov ===
'''Biocircuits: <s>Tue</s> Mon, 10a-12p STL 114'''
* [[http:docs.google.com/presentation/d/14mJLdC-HjFLChMf_u8G2dzE9RrcN5XReypSQUP-J-Ys|Individual updates]]
'''NCS: Fri, 3-4pm ANB 121'''
* Tung

|- valign=top
| width=25% |

=== Week 9: 25-29 Nov ===
'''Biocircuits: Tue, <s>10a-12p</s> 9:30a-11:30a'''
* Liana
* Elin

| width=25% |

=== Week 10: 2-6 Dec ===
'''NCS: Mon, 4-5pm ANB 121'''
* Apurva
'''Biocircuits: Tue, 10a-12p'''
* [[http:docs.google.com/presentation/d/1PWd7tirvuWj3x9TTzehB7zvyfOfy2ucs2Ebxhgeqxxk|Individual updates]]
'''Biocircuits: Thu, 11a-12p'''
* Lab cleanup

| width=25% |

=== Week 11: 9-13 Dec ===
'''Biocircuits: Wed, 10a-12p'''
* Matthieu
* Manisha
'''NCS: Wed, 3:45p-5p'''
* Josefine

| width=25% |

=== Week 12: 16-20 Dec ===
* Winter recess

|}

Group Schedule, Fall 2019

2019-10-07T22:59:05Z

Jmarken: /* Week 2: 7-11 Oct */

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [[Schedule|Richard's calendar (travel)]]
| width=50% |
* [[Group Schedule, Summer 2019]]
|}

The schedule for group and subgroup meetings is given below. Contact Richard if you need to change the schedule. Unless otherwise noted, biocircuits meetings are in 111 Keck and NCS meetings are in 314 Annenberg.

{| width=100% border=1
|- valign=top

| width=25% |
=== Week 1: 30 Sep - 4 Oct ===
'''Biocircuits: Tue, <s>10a-12p</s> 9a-11a'''
* Ayush
* Cindy
* Note: meeting will probably shift to start at 9 am
'''NCS: Wed, 10a-11:30a, BBB 181'''
* Thomas Mohren (visitor)

| width=25% |

=== Week 2: 7-11 Oct ===
'''Biocircuits: Tue, 10a-12p'''
* [[http:docs.google.com/presentation/d/18AQHdCkuT70Zm_3CqiODFfDa0sMmwADnzD4D6FhB22c/edit#slide=id.g4bc2dc3c11_0_0|Individual updates]]
'''NCS: Wed, 3:45p-5p'''
* Prithvi

| width=25% |

=== Week 3: 14-18 Oct ===
'''Biocircuits: Tue, 10a-12p'''
* Michaelle
* Zoila
'''NCS: Wed, 3:45p-5p'''
* Sumanth

| width=25% |

=== Week 4: 21-27 Oct ===
'''Biocircuits: Tue, 10a-12p'''
* Meeting may shift to Mon, 3p-5p
* Individual updates
'''NCS: Wed, 3:45p-5p'''
* Karena
* Note: meeting may shift to 11a-12p

|- valign=top
| width=25% |

=== Week 5: 28 Oct - 1 Nov ===
'''Biocircuits: Tue, 10a-12p'''
* Open
* William
'''NCS: Wed, 3:45p-5p'''
* Richard C

| width=25% |

=== Week 6: 4-8 Nov ===
'''Biocircuits: Tue, 10a-12p'''
* Individual updates
'''NCS: Wed, 3:45p-5p'''
* Tung

| width=25% |

=== Week 7: 11-15 Nov ===
'''Biocircuits: Tue, 10a-12p'''
* Chelsea
* Rory
'''NCS: Wed, 3:45p-5p'''
* Reza

| width=25% |

=== Week 8: 18-22 Nov ===
'''Biocircuits: Tue, 10a-12p'''
* Individual updates
'''NCS: Wed, 3:45p-5p'''
* Yuxiao
* Note: meeting may shift to Fri, 3p-4p

|- valign=top
| width=25% |

=== Week 9: 25-29 Nov ===
'''Biocircuits: Tue, 10a-12p'''
* Elin
* Rotation/UG

| width=25% |

=== Week 10: 2-6 Dec ===
'''Biocircuits: Tue, 10a-12p'''
* Individual updates
'''NCS: Wed, 3:45p-5p'''
* Apurva
* Note: meeting may shift to Mon, 4p-5p

| width=25% |

=== Week 11: 9-13 Dec ===
'''Biocircuits: Wed, 10a-12p'''
* Rotation/UG
* Rotation/UG
'''NCS: Wed, 3:45p-5p'''
* Josefine

| width=25% |

=== Week 12: 16-20 Dec ===
* Winter recess

|}

Group Schedule, Fall 2019

2019-10-07T22:56:55Z

Jmarken: /* Week 2: 7-11 Oct */

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [[Schedule|Richard's calendar (travel)]]
| width=50% |
* [[Group Schedule, Summer 2019]]
|}

The schedule for group and subgroup meetings is given below. Contact Richard if you need to change the schedule. Unless otherwise noted, biocircuits meetings are in 111 Keck and NCS meetings are in 314 Annenberg.

{| width=100% border=1
|- valign=top

| width=25% |
=== Week 1: 30 Sep - 4 Oct ===
'''Biocircuits: Tue, <s>10a-12p</s> 9a-11a'''
* Ayush
* Cindy
* Note: meeting will probably shift to start at 9 am
'''NCS: Wed, 10a-11:30a, BBB 181'''
* Thomas Mohren (visitor)

| width=25% |

=== Week 2: 7-11 Oct ===
'''Biocircuits: Tue, 10a-12p'''
* [[https://docs.google.com/presentation/d/18AQHdCkuT70Zm_3CqiODFfDa0sMmwADnzD4D6FhB22c/edit#slide=id.g4bc2dc3c11_0_0|Individual updates]]
'''NCS: Wed, 3:45p-5p'''
* Prithvi

| width=25% |

=== Week 3: 14-18 Oct ===
'''Biocircuits: Tue, 10a-12p'''
* Michaelle
* Zoila
'''NCS: Wed, 3:45p-5p'''
* Sumanth

| width=25% |

=== Week 4: 21-27 Oct ===
'''Biocircuits: Tue, 10a-12p'''
* Meeting may shift to Mon, 3p-5p
* Individual updates
'''NCS: Wed, 3:45p-5p'''
* Karena
* Note: meeting may shift to 11a-12p

|- valign=top
| width=25% |

=== Week 5: 28 Oct - 1 Nov ===
'''Biocircuits: Tue, 10a-12p'''
* Open
* William
'''NCS: Wed, 3:45p-5p'''
* Richard C

| width=25% |

=== Week 6: 4-8 Nov ===
'''Biocircuits: Tue, 10a-12p'''
* Individual updates
'''NCS: Wed, 3:45p-5p'''
* Tung

| width=25% |

=== Week 7: 11-15 Nov ===
'''Biocircuits: Tue, 10a-12p'''
* Chelsea
* Rory
'''NCS: Wed, 3:45p-5p'''
* Reza

| width=25% |

=== Week 8: 18-22 Nov ===
'''Biocircuits: Tue, 10a-12p'''
* Individual updates
'''NCS: Wed, 3:45p-5p'''
* Yuxiao
* Note: meeting may shift to Fri, 3p-4p

|- valign=top
| width=25% |

=== Week 9: 25-29 Nov ===
'''Biocircuits: Tue, 10a-12p'''
* Elin
* Rotation/UG

| width=25% |

=== Week 10: 2-6 Dec ===
'''Biocircuits: Tue, 10a-12p'''
* Individual updates
'''NCS: Wed, 3:45p-5p'''
* Apurva
* Note: meeting may shift to Mon, 4p-5p

| width=25% |

=== Week 11: 9-13 Dec ===
'''Biocircuits: Wed, 10a-12p'''
* Rotation/UG
* Rotation/UG
'''NCS: Wed, 3:45p-5p'''
* Josefine

| width=25% |

=== Week 12: 16-20 Dec ===
* Winter recess

|}

Group Schedule, Fall 2019

2019-10-07T22:56:31Z

Jmarken: /* Week 2: 7-11 Oct */

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [[Schedule|Richard's calendar (travel)]]
| width=50% |
* [[Group Schedule, Summer 2019]]
|}

The schedule for group and subgroup meetings is given below. Contact Richard if you need to change the schedule. Unless otherwise noted, biocircuits meetings are in 111 Keck and NCS meetings are in 314 Annenberg.

{| width=100% border=1
|- valign=top

| width=25% |
=== Week 1: 30 Sep - 4 Oct ===
'''Biocircuits: Tue, <s>10a-12p</s> 9a-11a'''
* Ayush
* Cindy
* Note: meeting will probably shift to start at 9 am
'''NCS: Wed, 10a-11:30a, BBB 181'''
* Thomas Mohren (visitor)

| width=25% |

=== Week 2: 7-11 Oct ===
'''Biocircuits: Tue, 10a-12p'''
* I[[https://docs.google.com/presentation/d/18AQHdCkuT70Zm_3CqiODFfDa0sMmwADnzD4D6FhB22c|Individual updates]]
'''NCS: Wed, 3:45p-5p'''
* Prithvi

| width=25% |

=== Week 3: 14-18 Oct ===
'''Biocircuits: Tue, 10a-12p'''
* Michaelle
* Zoila
'''NCS: Wed, 3:45p-5p'''
* Sumanth

| width=25% |

=== Week 4: 21-27 Oct ===
'''Biocircuits: Tue, 10a-12p'''
* Meeting may shift to Mon, 3p-5p
* Individual updates
'''NCS: Wed, 3:45p-5p'''
* Karena
* Note: meeting may shift to 11a-12p

|- valign=top
| width=25% |

=== Week 5: 28 Oct - 1 Nov ===
'''Biocircuits: Tue, 10a-12p'''
* Open
* William
'''NCS: Wed, 3:45p-5p'''
* Richard C

| width=25% |

=== Week 6: 4-8 Nov ===
'''Biocircuits: Tue, 10a-12p'''
* Individual updates
'''NCS: Wed, 3:45p-5p'''
* Tung

| width=25% |

=== Week 7: 11-15 Nov ===
'''Biocircuits: Tue, 10a-12p'''
* Chelsea
* Rory
'''NCS: Wed, 3:45p-5p'''
* Reza

| width=25% |

=== Week 8: 18-22 Nov ===
'''Biocircuits: Tue, 10a-12p'''
* Individual updates
'''NCS: Wed, 3:45p-5p'''
* Yuxiao
* Note: meeting may shift to Fri, 3p-4p

|- valign=top
| width=25% |

=== Week 9: 25-29 Nov ===
'''Biocircuits: Tue, 10a-12p'''
* Elin
* Rotation/UG

| width=25% |

=== Week 10: 2-6 Dec ===
'''Biocircuits: Tue, 10a-12p'''
* Individual updates
'''NCS: Wed, 3:45p-5p'''
* Apurva
* Note: meeting may shift to Mon, 4p-5p

| width=25% |

=== Week 11: 9-13 Dec ===
'''Biocircuits: Wed, 10a-12p'''
* Rotation/UG
* Rotation/UG
'''NCS: Wed, 3:45p-5p'''
* Josefine

| width=25% |

=== Week 12: 16-20 Dec ===
* Winter recess

|}

Jake Beal, 1 Oct 2019

2019-09-26T20:37:10Z

Jmarken: /* Schedule */

Jake Beal will visit Caltech on 1 Oct 2019. If you would like to meet with him, please sign up below.

=== Schedule ===
* 10:00a: RMM group meeting, 111 Keck (if interested)
* 12:00p: Seminar, 111 Keck (abstract below)
* 1:00p: Lunch with Andrey Shur, Sam Clamons
* 1:45p: Lab tour and calibration discussion (Andrey, Sam, Mark, Miki)
* 2:30p: John Marken
* 3:15p: Open
* 4:00p: Open
* 4:45p: Wrap up with Richard

=== Talk abstract ===

Paths to Resilient Biological Information Processing 
Jake Beal (Raytheon BBN) 

1 October (Tue), 12-1 pm, 111 Keck

Engineered information processing in biological organisms has potential revolutionary implications across many application domains. A major barrier, however, has been the fragility of biological information processing devices to changes in their usage, genetic context, or operating environment. Engineering resilient information processing, however, is not just a biological challenge, but a three-way interplay between device performance, measurement quality, and model accuracy. In this talk, I will discuss how the interplay between these three aspects offer multiple paths for improving the resilience of biological information processing, giving examples of recent progress in reproducible and comparable measurement, the development of high-performance devices and insulators, and precision prediction of genetic circuits.

Dr. Jacob Beal is a Senior Scientist at Raytheon BBN Technologies, where he leads research on synthetic biology and distributed systems engineering. His work in synthetic biology includes development of methods for calibrated flow cytometry, precision analysis and design of genetic regulatory networks, engineering of biological information processing devices, standards for representation and communication of biological designs, and signature-based detection of pathogenic sequences.

Sara Molinari, 29 Jan 2019

2019-01-27T21:55:44Z

Jmarken: /* Schedule */

Sara Molinari will visit Caltech on 29-30 Jan 2019.

=== Schedule ===

{| width=100% border=1
|- valign=top
| width=50% |
29 Jan (Tue):
* 8:30 am: Richard, 109 Steele Lab
* 9:00 am: seminar
* 10:00 am: Andrey (meet after seminar)
* 10:45 am: open
* 11:30 am: open
* 12:00 pm: Lunch with postdocs John McManus, Leo Green
* 1:00 pm: ELM discussion (Richard, James, Rory, ERDC?)
* 2:00 pm: Andy (meet at Richard's office)
* 2:45 pm: open
* 3:30 pm: open
* 4:15 pm: open
* 5:00 pm: done for the day
* 6:00 pm (or other): dinner with grad students (John Marken) (TBD)

| width=50% |
30 Jan (Wed):
* 9:00 am: Biocircuits group meeting
* 11:00 am: Hold: Niles?
* 11:45 am: open
* 12:30 pm: working lunch with James and Rory
* 1:45 pm: John Marken (103 Steele)
* 2:30 pm: Richard, 109 Steele Lab
* 3:00 pm: depart campus
|}

=== Talk ===

'''Engineering asymmetrical cell division into Escherichia coli'''

Sara Molinari, Rice University 
29 Jan (Tue) @ 9 am, 111 Keck

Multicellularity, in eukaryotic organisms, is ultimately responsible for most of the tissues features, such as controlling its shape and size, distributing biochemical, structural and reproductive tasks. Multicellularity is reached through asymmetrical cell division in which progenitor cells create a differentiated daughter cell while retaining their original phenotype. Here, we describe a synthetic genetic circuit for controlling asymmetrical cell division in Escherichia coli. Specifically, we engineered an inducible system that can bind and segregate plasmid DNA to a single position in the cell. Upon division, the co-localized plasmids are kept by one and only one of the daughter cells. The other daughter cell receives no plasmid DNA and is hence irreversibly differentiated from its sibling. In this way, we achieved asymmetric cell division though asymmetric plasmid partitioning. We used this system to achieve physical separation of genetically different cells. We also characterized an orthogonal inducible circuit that enables the simultaneous asymmetric partitioning of two plasmid species – resulting in pluripotent cells that have four distinct differentiated states. These results point the way towards engineering multicellular systems from prokaryotic hosts.

Sara Molinari, 29 Jan 2019

2019-01-27T21:54:48Z

Jmarken: /* Schedule */

Sara Molinari will visit Caltech on 29-30 Jan 2019.

=== Schedule ===

{| width=100% border=1
|- valign=top
| width=50% |
29 Jan (Tue):
* 8:30 am: Richard, 109 Steele Lab
* 9:00 am: seminar
* 10:00 am: Andrey (meet after seminar)
* 10:45 am: open
* 11:30 am: open
* 12:00 pm: Lunch with postdocs John McManus, Leo Green
* 1:00 pm: ELM discussion (Richard, James, Rory, ERDC?)
* 2:00 pm: Andy (meet at Richard's office)
* 2:45 pm: open
* 3:30 pm: open
* 4:15 pm: open
* 5:00 pm: done for the day
* 6:00 pm (or other): dinner with grad students (John Marken) (TBD)

| width=50% |
30 Jan (Wed):
* 9:00 am: Biocircuits group meeting
* 11:00 am: Hold: Niles?
* 11:45 am: open
* 12:30 pm: working lunch with James and Rory
* 1:45 pm: John Marken (location)
* 2:30 pm: Richard, 109 Steele Lab
* 3:00 pm: depart campus
|}

=== Talk ===

'''Engineering asymmetrical cell division into Escherichia coli'''

Sara Molinari, Rice University 
29 Jan (Tue) @ 9 am, 111 Keck

Multicellularity, in eukaryotic organisms, is ultimately responsible for most of the tissues features, such as controlling its shape and size, distributing biochemical, structural and reproductive tasks. Multicellularity is reached through asymmetrical cell division in which progenitor cells create a differentiated daughter cell while retaining their original phenotype. Here, we describe a synthetic genetic circuit for controlling asymmetrical cell division in Escherichia coli. Specifically, we engineered an inducible system that can bind and segregate plasmid DNA to a single position in the cell. Upon division, the co-localized plasmids are kept by one and only one of the daughter cells. The other daughter cell receives no plasmid DNA and is hence irreversibly differentiated from its sibling. In this way, we achieved asymmetric cell division though asymmetric plasmid partitioning. We used this system to achieve physical separation of genetically different cells. We also characterized an orthogonal inducible circuit that enables the simultaneous asymmetric partitioning of two plasmid species – resulting in pluripotent cells that have four distinct differentiated states. These results point the way towards engineering multicellular systems from prokaryotic hosts.

Sara Molinari, 29 Jan 2019

2019-01-27T21:53:22Z

Jmarken: /* Schedule */

Sara Molinari will visit Caltech on 29-30 Jan 2019.

=== Schedule ===

{| width=100% border=1
|- valign=top
| width=50% |
29 Jan (Tue):
* 8:30 am: Richard, 109 Steele Lab
* 9:00 am: seminar
* 10:00 am: Andrey (meet after seminar)
* 10:45 am: open
* 11:30 am: open
* 12:00 pm: Lunch with postdocs John McManus, Leo Green
* 1:00 pm: ELM discussion (Richard, James, Rory, ERDC?)
* 2:00 pm: Andy (meet at Richard's office)
* 2:45 pm: open
* 3:30 pm: open
* 4:15 pm: open
* 5:00 pm: done for the day
* 6:00 pm (or other): dinner with grad students (TBD)

| width=50% |
30 Jan (Wed):
* 9:00 am: Biocircuits group meeting
* 11:00 am: Hold: Niles?
* 11:45 am: open
* 12:30 pm: working lunch with James and Rory
* 1:45 pm: John Marken (location)
* 2:30 pm: Richard, 109 Steele Lab
* 3:00 pm: depart campus
|}

=== Talk ===

'''Engineering asymmetrical cell division into Escherichia coli'''

Sara Molinari, Rice University 
29 Jan (Tue) @ 9 am, 111 Keck

Multicellularity, in eukaryotic organisms, is ultimately responsible for most of the tissues features, such as controlling its shape and size, distributing biochemical, structural and reproductive tasks. Multicellularity is reached through asymmetrical cell division in which progenitor cells create a differentiated daughter cell while retaining their original phenotype. Here, we describe a synthetic genetic circuit for controlling asymmetrical cell division in Escherichia coli. Specifically, we engineered an inducible system that can bind and segregate plasmid DNA to a single position in the cell. Upon division, the co-localized plasmids are kept by one and only one of the daughter cells. The other daughter cell receives no plasmid DNA and is hence irreversibly differentiated from its sibling. In this way, we achieved asymmetric cell division though asymmetric plasmid partitioning. We used this system to achieve physical separation of genetically different cells. We also characterized an orthogonal inducible circuit that enables the simultaneous asymmetric partitioning of two plasmid species – resulting in pluripotent cells that have four distinct differentiated states. These results point the way towards engineering multicellular systems from prokaryotic hosts.

SURF discussions, Jan 2019

2019-01-26T21:57:52Z

Jmarken: /* 31 Jan (Thu) */

Slots for talking with applicants and co-mentors about SURF projects. Please sign up for one of the slots below. All times are PST. __NOTOC__

In preparation for our conversation, please do the following:
* SURF students should work with their co-mentors to find a time the meeting/Skype call. (For Skype calls, co-mentors should initiate.)
* Please make sure you have read the material in the description of your project, so that you are prepared to talk about what the project is about and we can narrow in on the key ideas that will be the basis of your proposal
* Please take a look at the [[SURF GOTChA chart]] page, which is the format that we will use for the first iteration of your project proposal.

{| border=1 width=100%
|- valign=top
| width=25% |
==== 28 Jan (Mon) ====
* 5:00 pm PST: Victoria / Andy
* 5:30 pm PST: open
| width=25% |

==== 29 Jan (Tue) ====
* 12:00 pm PST: open
| width=25% |

==== 31 Jan (Thu) ====
* 12:00 pm PST: Isabelle / John
| width=25% |

==== 1 Feb (Fri) ====
* 11:00 am PST: Ludvig / Petter
<hr>
* 3:30 pm PST: open
* 4:00 pm PST: open
|}

The agenda for the phone call is (roughly):

# Description of the basic idea behind the project (based on applicant's understanding)
# Discussion about approaches, things to read, variations to consider, etc
# Discussion of the format of the proposal
# Questions and discussion about the process

Sara Molinari, 29 Jan 2019

2019-01-26T21:06:05Z

Jmarken: /* Schedule */

SURF 2019: Engineering a synthetic high-bandwidth intercellular communication system through plasmid conjugation

2018-12-10T23:12:23Z

Jmarken:

'''[[SURF 2019|2019 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: John Marken

'''Background'''

In order to realize many of synthetic biology's long-term goals, it is necessary to engineer populations of interacting cells rather than focusing on engineering individual cells alone. So far, work in this area has almost exclusively used quorum sensing systems to transfer information between cells, due to these systems' simplicity and modularity. However, because a quorum sensing system encodes its information in the concentration of a single signaling molecule, and because different systems exhibit a high degree of cross-talk with each other, quorum sensing is a low-bandwidth information transmission medium [1]. This makes quorum sensing a poor choice for implementing engineered populations with a high degree of complexity.

Plasmid conjugation is a common type of bacterial horizontal gene transfer where a plasmid in one cell transfers a copy of itself into another adjacent cell. Because entire synthetic circuits can be contained on the transferred plasmid, conjugation is an extremely high-bandwidth channel for intercellular information transfer. Furthermore, synthetic conjugation systems have already been developed where 'helper plasmids' encode all of the genes required for plasmid transfer but lack the ability to transfer themselves, thereby conferring on its host cell the ability to modularly send any plasmid that contains the appropriate 'origin of transfer' (oriT) sequence [2,3]. Such systems allow distinctions to be made between 'sender' and 'receiver' strains, which is an important prerequisite in the development of a flexible intercellular communication system.

Despite the advantages of plasmid conjugation, so far there has been no published work which uses it as the basis for a general synthetic intercellular communication system. To give just one example of the new capabilities which are made available by conjugation-based signaling, I am currently developing a 'message routing' framework that allows messages to be transferred only to designated recipients within a population (Fig. 1). In this system, the cells express Cas9 and a guide RNA which serves to identify their strain. The signal plasmid contains an 'address' region which includes binding sites for the guide RNAs. The signal plasmid can only be transferred to a strain which does not have a site on the address, as otherwise the plasmid will be immediately cleaved by Cas9 upon receipt. Integrase attachment sites flank the guide RNA binding sites in the address, allowing the cells to use integrase-mediated cassette exchange to dynamically swap out guide RNA binding sites within the address, editing the list of 'allowed' recipients of the signal plasmid. In this way one can construct a defined path of information flow through a population, such as the linear path shown in Fig. 1.

[[File:Message_Routing_Schematic.png|thumb|Fig. 1: (a) A 3-node linear signal path built with two guide RNAs and one integrase. The signal plasmid originally starts in Cell A, and cannot be sent to Cell C as the address contains the C gRNA binding site. However, once the signal plasmid enters Cell B, the TP901 integrase swaps the C binding site for an A binding site. The signal plasmid is now unable to return to Cell A, but is now able to proceed to cell C. (b) A 4-node linear signal path built with three guide RNAs and two integrases.]]

'''Project Goals'''

The aim of this SURF project is to make experimental and/or theoretical contributions to the development of a conjugation-based intercellular communication system. These contributions can encompass anything from improving the fundamental properties of the conjugation system itself, to implementing a new population circuit that uses conjugation, to exploring broader concepts about what can be enabled by high-bandwidth intercellular communication. Some examples for project directions are given below.

''Fruitful avenues for experimental work include:''
* Creating helper plasmids with externally-controllable 'dials' to dynamically tune the rate of conjugation.
** The regulatory architecture governing the genes associated with conjugation is well-understood [4]. By introducing inducible copies of the master transcription factors regulating transfer onto the helper plasmid, we should be able to modify existing synthetic conjugation systems to allow for more versatile control of the transfer dynamics.
* Implementing systems that allow cells to dynamically switch (and be switched) between sending and receiving states.
** Currently, synthetic conjugation systems distinguish between Senders and Receivers by having cells containing the helper plasmid be Senders and all other cells being Receivers. However, because the helper plasmid cannot transfer itself, there is no way to dynamically alter these distinctions without re-engineering the whole population. By deleting the master regulators of the transfer genes on the F plasmid and replacing them with inducible versions, it should be possible to create basally inert versions of the helper plasmid that can be switched on and off by external signals (and even by the cells themselves).
* Creating spatially-defined population-level circuits.
** One of the interesting properties of conjugation is that it can only occur between adjacent cells. This allows spatial circuits to be defined at the length scale of cell-cell contacts, rather than by the diffusion constant of a molecule. Can we build a spatial circuit that harnesses this distinction for a functional role?

''Interesting questions to address theoretically/computationally include:''
* Are there new ''types'' of population-level circuits which can be built when plasmids (instead of quorum sensing signals) are the medium of communication?
** In addition to the high bandwidth and the fact that signaling can only occur between adjacent cells, conjugation-based communication has many other properties that distinguish it from quorum-based communication. These include the fact that the messages (plasmids) can replicate semi-independently of their hosts and the fact that the message can propagate through different cells and update its content based on the conditions within each cell. Are these extra properties enough to distinguish conjugation-based communication as a qualitatively distinct form of communication from quorum signaling? If so, there should be population circuits which can be designed with conjugation to perform functions that equivalent quorum-based circuits could not perform. Do these circuits exist? If so, what do they look like? For further reading along these lines, see [5,6,7].
* Can we think of general schemes for information representation in plasmids that allow for the encoding and interpretation of arbitrary messages? What are the advantages and disadvantages of different schemes?
** Although an intercellular communication channel based on quorum sensing can only transfer information encodable into a single scalar variable, it does have the advantage of being able to easily map a continuous-valued input signal into a continuous-valued message. Because conjugation-based messaging is driven by the receipt of a plasmid into a cell, the simplest implementation of signaling is in representing a multi-dimensional binary message (where components of that message might either be present or absent from the signal plasmid). Although there are many ways to transfer continuous-valued information across a conjugation-based communication channel, it is not clear ''a priori'' whether there is an optimal molecular implementation (and if so, what it is).

'''Prerequisite Skills'''

''For Experimental Work''
* Familiarity with standard BSL-1 wetlab procedures
* Familiarity with molecular cloning techniques
* Familiarity with synthetic biology and genetic circuit design

''For Computational Work''
* Coding experience, preferably in Python
* Familiarity with differential equations
* Familiarity with synthetic biology and genetic circuit design

'''References'''
# Davis RM, Muller RY, Haynes KA. [https://www.frontiersin.org/articles/10.3389/fbioe.2015.00030/full Can the natural diversity of quorum-sensing advance synthetic biology?]. Frontiers in bioengineering and biotechnology. 2015 Mar 10;3:30.
# Dimitriu T, Lotton C, Bénard-Capelle J, Misevic D, Brown SP, Lindner AB, Taddei F. [https://www.pnas.org/content/pnas/111/30/11103.full.pdf Genetic information transfer promotes cooperation in bacteria]. Proceedings of the National Academy of Sciences. 2014 Jul 29;111(30):11103-8.
# Strand TA, Lale R, Degnes KF, Lando M, Valla S. [https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0090372&type=printable A new and improved host-independent plasmid system for RK2-based conjugal transfer]. PloS one. 2014 Mar 3;9(3):e90372.
# Zatyka M, Thomas CM. [https://watermark.silverchair.com/21-4-291.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAlMwggJPBgkqhkiG9w0BBwagggJAMIICPAIBADCCAjUGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMMPy4qq-YJNQmLAsHAgEQgIICBhvwOpoZlRotMutpdSQox-8fhWZh2IOVrjbrD1zal9K4Vbzy1wwwKzcdxGIQMhKQkOFfxwR51rH0o5HKVAIp-_qrfhI1_9KBZJlGU1bggkYs4bXWDuQMMe8du8oF3E9hxCFx2s49v4kQyXSpF7A_89uj_wJYsAa71tTMKo6wxm_Fdobodx_o8V2LFATHbeMU-A_7ViJy683UD4GUTrFdMJQydKbiZyLT4guFagPNJk9C-6U7qbAmWemrxSLEIOHLoTwPvLNwAOCSt28zcN1MIMfAa6ykivp-mQk3Ta3l1dIo6_eqiGNyv9dGQItZb265eh6N3OC7dMLrLmfISdCJzA36qqkkAyBjMUbps-1cDUvCX21RY7u8cxY74G6y8ekRtcMXyeVH3OfoXksplBPdWw5HH6DOE9x2dHVEQKOUyzKXnkvtYtdfX6KEySrEvU9EF_AjbfeOMS9h66vd5HzUQXzTJdLd62DxRnTksA-EeOgymVv7lWPgrpRNWNWjpMRmgFvyP0M4xBxe-UKDzJK9FMooR6-UETmuVpeDzk0GJYC8v1-2vWnC-sz4p5ZtB-BICVCRVkY3xB8u9e4MbHXl3QpvmLYQD9KZsEkTOdmRnEZ1W1_SKOtJW-JUH83a2mgeQtFaFpq7VdIThOULz5-eubcjn-OjazTsDjzY3h9eOczud5EUkVVh Control of genes for conjugative transfer of plasmids and other mobile elements]. FEMS microbiology reviews. 1998 Feb 1;21(4):291-319.
# Goñi-Moreno A, Amos M, de la Cruz F. [https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0065986&type=printable Multicellular computing using conjugation for wiring]. PLoS One. 2013 Jun 20;8(6):e65986.
# Beneš D, Rodríguez-Patón A, Sosík P. [https://link.springer.com/content/pdf/10.1007%2Fs11047-016-9595-9.pdf Directed evolution of biocircuits using conjugative plasmids and CRISPR-Cas9: design and in silico experiments]. Natural Computing. 2017 Sep 1;16(3):497-505.
# Goni-Moreno A, de la Cruz F, Rodriguez-Paton A, Amos M. [https://www.biorxiv.org/content/biorxiv/early/2018/11/27/479998.full.pdf Dynamical Task Switching in Cellular Computers]. bioRxiv. 2018 Jan 1:479998.

SURF 2019: Engineering a synthetic high-bandwidth intercellular communication system through plasmid conjugation

2018-12-10T23:10:50Z

Jmarken:

'''[[SURF 2019|2019 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: John Marken

'''Background'''

In order to realize many of synthetic biology's long-term goals, it is necessary to engineer populations of interacting cells rather than focusing on engineering individual cells alone. So far, work in this area has almost exclusively used quorum sensing systems to transfer information between cells, due to these systems' simplicity and modularity. However, because a quorum sensing system encodes its information in the concentration of a single signaling molecule, and because different systems exhibit a high degree of cross-talk with each other, quorum sensing is a low-bandwidth information transmission medium [1]. This makes quorum sensing a poor choice for implementing engineered populations with a high degree of complexity.

Plasmid conjugation is a common type of bacterial horizontal gene transfer where a plasmid in one cell transfers a copy of itself into another adjacent cell. Because entire synthetic circuits can be contained on the transferred plasmid, conjugation is an extremely high-bandwidth channel for intercellular information transfer. Furthermore, synthetic conjugation systems have already been developed where 'helper plasmids' encode all of the genes required for plasmid transfer but lack the ability to transfer themselves, thereby conferring on its host cell the ability to modularly send any plasmid that contains the appropriate 'origin of transfer' (oriT) sequence [2,3]. Such systems allow distinctions to be made between 'sender' and 'receiver' strains, which is an important prerequisite in the development of a flexible intercellular communication system.

Despite the advantages of plasmid conjugation, so far there has been no published work which uses it as the basis for a general synthetic intercellular communication system. To give just one example of the new capabilities which are made available by conjugation-based signaling, I am currently developing a 'message routing' framework that allows messages to be transferred only to designated recipients within a population (Fig. 1). In this system, the cells express Cas9 and a guide RNA which serves to identify their strain. The signal plasmid contains an 'address' region which includes binding sites for the guide RNAs. The signal plasmid can only be transferred to a strain which does not have a site on the address, as otherwise the plasmid will be immediately cleaved by Cas9 upon receipt. Integrase attachment sites flank the guide RNA binding sites in the address, allowing the cells to use integrase-mediated cassette exchange to dynamically swap out guide RNA binding sites within the address, editing the list of 'allowed' recipients of the signal plasmid. In this way one can construct a defined path of information flow through a population, such as the linear path shown in Fig. 1.

[[File:Message_Routing_Schematic.png|thumb|Fig. 1: (a) A 3-node linear signal path built with two guide RNAs and one integrase. The signal plasmid originally starts in Cell A, and cannot be sent to Cell C as the address contains the C gRNA binding site. However, once the signal plasmid enters Cell B, the TP901 integrase swaps the C binding site for an A binding site. The signal plasmid is now unable to return to Cell A, but is now able to proceed to cell C. (b) A 4-node linear signal path built with three guide RNAs and two integrases.]]

'''Project Goals'''

The aim of this SURF project is to make experimental and/or theoretical contributions to the development of a conjugation-based intercellular communication system. These contributions can encompass anything from improving the fundamental properties of the conjugation system itself, to implementing a new population circuit that uses conjugation, to exploring broader concepts about what can be enabled by high-bandwidth intercellular communication. Some examples for project directions are given below.

''Fruitful avenues for experimental work include:''
* Creating helper plasmids with externally-controllable 'dials' to dynamically tune the rate of conjugation.
** The regulatory architecture governing the genes associated with conjugation is well-understood [4]. By introducing inducible copies of the master transcription factors regulating transfer onto the helper plasmid, we should be able to modify existing synthetic conjugation systems to allow for more versatile control of the transfer dynamics.
* Implementing systems that allow cells to dynamically switch (and be switched) between sending and receiving states.
** Currently, synthetic conjugation systems distinguish between Senders and Receivers by having cells containing the helper plasmid be Senders and all other cells being Receivers. However, because the helper plasmid cannot transfer itself, there is no way to dynamically alter these distinctions without re-engineering the whole population. By deleting the master regulators of the transfer genes on the F plasmid and replacing them with inducible versions, it should be possible to create basally inert versions of the helper plasmid that can be switched on and off by external signals (and even by the cells themselves).
* Creating spatially-defined population-level circuits.
** One of the interesting properties of conjugation is that it can only occur between adjacent cells. This allows spatial circuits to be defined at the length scale of cell-cell contacts, rather than by the diffusion constant of a molecule. Can we build a spatial circuit that harnesses this distinction for a functional role?

''Interesting questions to address theoretically/computationally include:''
* Are there new ''types'' of population-level circuits which can be built when plasmids (instead of quorum sensing signals) are the medium of communication?
** In addition to the high bandwidth and the fact that signaling can only occur between adjacent cells, conjugation-based communication has many other properties that distinguish it from quorum-based communication. These include the fact that the messages (plasmids) can replicate semi-independently of their hosts and the fact that the message can propagate through different cells and update its content based on the conditions within each cell. Are these extra properties enough to distinguish conjugation-based communication as a qualitatively distinct form of communication from quorum signaling? If so, there should be population circuits which can be designed with conjugation to perform functions that equivalent quorum-based circuits could not perform. Do these circuits exist? If so, what do they look like? For further reading along these lines, see [].
* Can we think of general schemes for information representation in plasmids that allow for the encoding and interpretation of arbitrary messages? What are the advantages and disadvantages of different schemes?
** Although an intercellular communication channel based on quorum sensing can only transfer information encodable into a single scalar variable, it does have the advantage of being able to easily map a continuous-valued input signal into a continuous-valued message. Because conjugation-based messaging is driven by the receipt of a plasmid into a cell, the simplest implementation of signaling is in representing a multi-dimensional binary message (where components of that message might either be present or absent from the signal plasmid). Although there are many ways to transfer continuous-valued information across a conjugation-based communication channel, it is not clear ''a priori'' whether there is an optimal molecular implementation (and if so, what it is).

'''Prerequisite Skills'''

''For Experimental Work''
* Familiarity with standard BSL-1 wetlab procedures
* Familiarity with molecular cloning techniques
* Familiarity with synthetic biology and genetic circuit design

''For Computational Work''
* Coding experience, preferably in Python
* Familiarity with differential equations
* Familiarity with synthetic biology and genetic circuit design

'''References'''
# Davis RM, Muller RY, Haynes KA. [https://www.frontiersin.org/articles/10.3389/fbioe.2015.00030/full Can the natural diversity of quorum-sensing advance synthetic biology?]. Frontiers in bioengineering and biotechnology. 2015 Mar 10;3:30.
# Dimitriu T, Lotton C, Bénard-Capelle J, Misevic D, Brown SP, Lindner AB, Taddei F. [https://www.pnas.org/content/pnas/111/30/11103.full.pdf Genetic information transfer promotes cooperation in bacteria]. Proceedings of the National Academy of Sciences. 2014 Jul 29;111(30):11103-8.
# Strand TA, Lale R, Degnes KF, Lando M, Valla S. [https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0090372&type=printable A new and improved host-independent plasmid system for RK2-based conjugal transfer]. PloS one. 2014 Mar 3;9(3):e90372.
# Zatyka M, Thomas CM. [https://watermark.silverchair.com/21-4-291.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAlMwggJPBgkqhkiG9w0BBwagggJAMIICPAIBADCCAjUGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMMPy4qq-YJNQmLAsHAgEQgIICBhvwOpoZlRotMutpdSQox-8fhWZh2IOVrjbrD1zal9K4Vbzy1wwwKzcdxGIQMhKQkOFfxwR51rH0o5HKVAIp-_qrfhI1_9KBZJlGU1bggkYs4bXWDuQMMe8du8oF3E9hxCFx2s49v4kQyXSpF7A_89uj_wJYsAa71tTMKo6wxm_Fdobodx_o8V2LFATHbeMU-A_7ViJy683UD4GUTrFdMJQydKbiZyLT4guFagPNJk9C-6U7qbAmWemrxSLEIOHLoTwPvLNwAOCSt28zcN1MIMfAa6ykivp-mQk3Ta3l1dIo6_eqiGNyv9dGQItZb265eh6N3OC7dMLrLmfISdCJzA36qqkkAyBjMUbps-1cDUvCX21RY7u8cxY74G6y8ekRtcMXyeVH3OfoXksplBPdWw5HH6DOE9x2dHVEQKOUyzKXnkvtYtdfX6KEySrEvU9EF_AjbfeOMS9h66vd5HzUQXzTJdLd62DxRnTksA-EeOgymVv7lWPgrpRNWNWjpMRmgFvyP0M4xBxe-UKDzJK9FMooR6-UETmuVpeDzk0GJYC8v1-2vWnC-sz4p5ZtB-BICVCRVkY3xB8u9e4MbHXl3QpvmLYQD9KZsEkTOdmRnEZ1W1_SKOtJW-JUH83a2mgeQtFaFpq7VdIThOULz5-eubcjn-OjazTsDjzY3h9eOczud5EUkVVh Control of genes for conjugative transfer of plasmids and other mobile elements]. FEMS microbiology reviews. 1998 Feb 1;21(4):291-319.
# Goñi-Moreno A, Amos M, de la Cruz F. [https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0065986&type=printable Multicellular computing using conjugation for wiring]. PLoS One. 2013 Jun 20;8(6):e65986.
# Beneš D, Rodríguez-Patón A, Sosík P. [https://link.springer.com/content/pdf/10.1007%2Fs11047-016-9595-9.pdf Directed evolution of biocircuits using conjugative plasmids and CRISPR-Cas9: design and in silico experiments]. Natural Computing. 2017 Sep 1;16(3):497-505.
# Goni-Moreno A, de la Cruz F, Rodriguez-Paton A, Amos M. https://www.biorxiv.org/content/biorxiv/early/2018/11/27/479998.full.pdf Dynamical Task Switching in Cellular Computers]. bioRxiv. 2018 Jan 1:479998.

SURF 2019: Engineering a synthetic high-bandwidth intercellular communication system through plasmid conjugation

2018-12-10T22:57:16Z

Jmarken:

'''[[SURF 2019|2019 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: John Marken

'''Background'''

In order to realize many of synthetic biology's long-term goals, it is necessary to engineer populations of interacting cells rather than focusing on engineering individual cells alone. So far, work in this area has almost exclusively used quorum sensing systems to transfer information between cells, due to these systems' simplicity and modularity. However, because a quorum sensing system encodes its information in the concentration of a single signaling molecule, and because different systems exhibit a high degree of cross-talk with each other, quorum sensing is a low-bandwidth information transmission medium. This makes quorum sensing a poor choice for implementing engineered populations with a high degree of complexity.

Plasmid conjugation is a common type of bacterial horizontal gene transfer where a plasmid in one cell transfers a copy of itself into another adjacent cell. Because entire synthetic circuits can be contained on the transferred plasmid, conjugation is an extremely high-bandwidth channel for intercellular information transfer. Furthermore, synthetic conjugation systems have already been developed where 'helper plasmids' encode all of the genes required for plasmid transfer but lack the ability to transfer themselves, thereby conferring on its host cell the ability to modularly send any plasmid that contains the appropriate 'origin of transfer' (oriT) sequence. Such systems allow distinctions to be made between 'sender' and 'receiver' strains, which is an important prerequisite in the development of a flexible intercellular communication system.

Despite the advantages of plasmid conjugation, so far there has been no published work which uses it as the basis for a general synthetic intercellular communication system. To give just one example of the new capabilities which are made available by conjugation-based signaling, I am currently developing a 'message routing' framework that allows messages to be transferred only to designated recipients within a population (Fig. 1). In this system, the cells express Cas9 and a guide RNA which serves to identify their strain. The signal plasmid contains an 'address' region which includes binding sites for the guide RNAs. The signal plasmid can only be transferred to a strain which does not have a site on the address, as otherwise the plasmid will be immediately cleaved by Cas9 upon receipt. Integrase attachment sites flank the guide RNA binding sites in the address, allowing the cells to use integrase-mediated cassette exchange to dynamically swap out guide RNA binding sites within the address, editing the list of 'allowed' recipients of the signal plasmid. In this way one can construct a defined path of information flow through a population, such as the linear path shown in Fig. 1.

[[File:Message_Routing_Schematic.png|thumb|Fig. 1: (a) A 3-node linear signal path built with two guide RNAs and one integrase. The signal plasmid originally starts in Cell A, and cannot be sent to Cell C as the address contains the C gRNA binding site. However, once the signal plasmid enters Cell B, the TP901 integrase swaps the C binding site for an A binding site. The signal plasmid is now unable to return to Cell A, but is now able to proceed to cell C. (b) A 4-node linear signal path built with three guide RNAs and two integrases.]]

'''Project Goals'''

The aim of this SURF project is to make experimental and/or theoretical contributions to the development of a conjugation-based intercellular communication system. These contributions can encompass anything from improving the fundamental properties of the conjugation system itself, to implementing a new population circuit that uses conjugation, to exploring broader concepts about what can be enabled by high-bandwidth intercellular communication. Some examples for project directions are given below.

''Fruitful avenues for experimental work include:''
* Creating helper plasmids with externally-controllable 'dials' to dynamically tune the rate of conjugation.
** The regulatory architecture governing the genes associated with conjugation is well-understood. By introducing inducible copies of the master transcription factors regulating transfer onto the helper plasmid, we should be able to modify existing synthetic conjugation systems to allow for more versatile control of the transfer dynamics.
* Implementing systems that allow cells to dynamically switch (and be switched) between sending and receiving states.
** Currently, synthetic conjugation systems distinguish between Senders and Receivers by having cells containing the helper plasmid be Senders and all other cells being Receivers. However, because the helper plasmid cannot transfer itself, there is no way to dynamically alter these distinctions without re-engineering the whole population. By deleting the master regulators of the transfer genes on the F plasmid and replacing them with inducible versions, it should be possible to create 'inert' versions of the helper plasmid that can be switched on and off by external signals (and even by the cells themselves).
* Creating spatially-defined population-level circuits.
** One of the interesting properties of conjugation is that it can only occur between adjacent cells. This allows spatial circuits to be defined at the length scale of cell-cell contacts, rather than by the diffusion constant of a molecule. Can we build a spatial circuit that harnesses this distinction for a functional role?

''Interesting questions to address theoretically/computationally include:''
* Are there new ''types'' of population-level circuits which can be built when plasmids (instead of quorum sensing signals) are the medium of communication?
** In addition to the high bandwidth and the fact that signaling can only occur between adjacent cells, conjugation-based communication has many other properties that distinguish it from quorum-based communication. These include the fact that the messages (plasmids) can replicate semi-independently of their hosts and the fact that the message can propagate through different cells and update its content based on the conditions within each cell. Are these extra properties enough to distinguish conjugation-based communication as a qualitatively distinct form of communication from quorum signaling? If so, there should be population circuits which can be designed with conjugation to perform functions that equivalent quorum-based circuits could not perform. Do these circuits exist? If so, what do they look like? For further reading along these lines, see [ref, ref, ref].
* Can we think of general schemes for information representation in plasmids that allow for the encoding and interpretation of arbitrary messages? What are the advantages and disadvantages of different schemes?
** Although an intercellular communication channel based on quorum sensing can only transfer information encodable into a single scalar variable, it does have the advantage of being able to easily map a continuous-valued input signal into a continuous-valued message. Because conjugation-based messaging is driven by the receipt of a plasmid into a cell, the simplest implementation of signaling is in representing a multi-dimensional binary message (where components of that message might either be present or absent from the signal plasmid). Although there are many ways to transfer continuous-valued information across a conjugation-based communication channel, it is not clear ''a priori'' whether there is an optimal molecular implementation (and if so, what it is).

'''Prerequisite Skills'''

''For Experimental Work''
* Familiarity with standard BSL-1 wetlab procedures
* Familiarity with molecular cloning techniques
* Familiarity with synthetic biology and genetic circuit design

''For Computational Work''
* Coding experience, preferably in Python
* Familiarity with differential equations
* Familiarity with synthetic biology and genetic circuit design

'''References'''

SURF 2019: Engineering a synthetic high-bandwidth intercellular communication system through plasmid conjugation

2018-12-10T22:21:44Z

Jmarken:

SURF 2019: Engineering a synthetic high-bandwidth intercellular communication system through plasmid conjugation

2018-12-10T19:04:36Z

Jmarken:

SURF 2019: Engineering a synthetic high-bandwidth intercellular communication system through plasmid conjugation

2018-12-10T18:59:25Z

Jmarken:

File:Message Routing Schematic.png

2018-12-10T18:58:14Z

Jmarken: Fig. 1: (a) A 3-node linear signal path built with two guide RNAs and one integrase. The signal plasmid originally starts in Cell A, and cannot be sent to Cell C as the address contains the C gRNA binding site. However, once the signal plasmid enters C...

Fig. 1: (a) A 3-node linear signal path built with two guide RNAs and one integrase. The signal plasmid originally starts in Cell A, and cannot be sent to Cell C as the address contains the C gRNA binding site. However, once the signal plasmid enters Cell B, the TP901 integrase swaps the C binding site for an A binding site. The signal plasmid is now unable to return to Cell A, but is now able to proceed to cell C. (b) A 4-node linear signal path built with three guide RNAs and two integrases.

SURF 2019: Engineering a synthetic high-bandwidth intercellular communication system through plasmid conjugation

2018-12-10T18:57:43Z

Jmarken:

SURF 2019: Engineering a synthetic high-bandwidth intercellular communication system through plasmid conjugation

2018-12-10T18:33:55Z

Jmarken:

File:3-node Message Routing figure.png

2018-12-10T18:33:08Z

Jmarken: Schematic figure for John Marken's message routing circuit. For the 2019 SURF page.

Schematic figure for John Marken's message routing circuit. For the 2019 SURF page.

SURF 2019: Engineering a synthetic high-bandwidth intercellular communication system through plasmid conjugation

2018-12-10T18:29:23Z

Jmarken: Created page with "'''2019 SURF project description''' * Mentor: Richard Murray * Co-mentor: John Marken '''Background''' In order to realize many of synthetic biology's long-ter..."