Murray Wiki - User contributions [en]

David Garcia, 13 Feb 2020

2020-02-13T19:23:18Z

Rlwillia: /* 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: Elin
* 1:45 pm: Chelsea
* 2:30 pm: Rory
* 3:15 pm: John Marken
* 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.

SURF discussions, Jan 2020

2020-01-23T02:33:21Z

Rlwillia:

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.
* Please read through the [[http:sfp.caltech.edu/students/proposal/surf_and_amgen_proposals|SURF proposal information page]] to see what the SURF office requires (and when)

{| border=1 width=100%
|- valign=top
| width=25% |
==== 24 Jan (Fri) ====
* 2:00 pm PST: open
* 2:30 pm PST: Rory/Joe
<hr>
* 4:30 pm PST: open
* 5:00 pm PST: open
 
(Richard is off campus on Fri; all meetings via Skype)
| width=25% |

==== 28 Jan (Tue) ====
* 1:30 pm PST: open
<hr>
* 5:00 pm PST: Bruno and Francesca
* 5:30 pm PST: Ivy and Apurva
| width=25% |

==== 30 Jan (Thu) ====
* 9:00 am PST: open
* 9:30 am PST: Tom and Josefine
| width=25% |

==== 3 Feb (Mon, if needed) ====
* 9:00 am PST: Open
* 9:30 am PST: Chelsea, Katherine
<hr>
* 5:00 pm PST: Open
 
Please only use these slots of none of the others work (it is a bit late in the timeline for proposals)
|}

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

SURF 2020: Applications of synthetic differentiation

2019-12-22T22:07:38Z

Rlwillia:

'''[[SURF 2020|2020 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: Rory Williams

'''Applications of synthetic differentiation'''

In the Murray lab, we have demonstrated that the evolutionary stability of burdensome functions in E. coli can be improved by implementing tunable synthetic differentiation circuits utilizing serine integrases. Specifically, a population of progenitor cells which encodes, but does not express, the desired function, is able to replicate the DNA encoding the engineered function in the absence of its associated burden. An integrase-mediated genomic recombination event in a progenitor cell then both activates the engineered function by initiating the expression of T7RNAP, and starts a timer to limit the number of divisions differentiated cells are able to undergo. By appropriately tuning the differentiation rate through the inducible expression of degradation-tagged integrase protein, both the duration of circuit function and the total production achieved can be improved relative to the naïve implementation of the engineered function where all cells constitutively express the function. Though moderately effective, this strategy ultimately fails due to the selection of mutations which destroy the differentiation mechanism, and we are currently developing and testing circuits which will require two or more mutations to destroy the differentiation mechanism in order to improve its performance
[[File:2020_SURF_fig.png|600px|Image: 600 pixel]]

Figure 1: (A) Schematic of differentiation activated T7RNAP driven expression. Las AHL induces expression of pir protein, which is needed for replication of the R6K plasmid. Salicylate induces the expression of degradation-tagged Bxb1 integrase, which excises the pir expression cassette from the genome, and activates the expression of T7RNAP by bringing together two sections of the coding sequence. IPTG induces expression of full length T7RNAP in differentiated cells, allowing expression of sfYFP from the high-copy Cole1 plasmid. (B) Schematic of naïve inducible T7RNAP driven expression. Circuit is identical to a differentiated cell, but lacking the R6K plasmid. (C) Schematic for long-term differentiation experiments. (D-E) JS006 with differentiation circuit (A) above grown in M9CA + carbenicillin/3uM Las AHL, +/- chloramphenicol, 30uM IPTG, in varying concentrations of salicylate. Cells with naïve circuit (B) are grown in M9CA + carbenicillin/30uM IPTG. Cells diluted 50X into same media conditions into 300uL total volume every ~12 h for 8 total growths. (D) Cumulative total production plotted is the sum of endpoint fluorescence values from 12 h plate reader growth. (E) Samples taken immediately after growth were analyzed by flow cytometry, and fraction sfYFP positive cells is plotted. (D-E) Means of four total replicates from two independent experiments with standard deviation error bars.

We are interested in expanding the scope of differentiation architectures in a variety of ways, any of which could provide an opportunity for a SURF project.

'''1) Differentiation with reproductive and metabolic division of labor'''

While thus far we have been implementing differentiation in the context single-celled planktonically growing E. coli, naturally occurring examples of microbial differentiation are predominantly or exclusively found in species which form multicellular aggregates. In the context of multicellular aggregates, metabolic labor can be divided while allowing the benefits of this division of labor to be shared locally within the aggregate, and not with non-differentiating ‘cheaters’ or other competing microbes. We are currently exploring implementing differentiation in E. coli which form multicellular aggregates (through a combination of genetically controlled septation, and expression of pairs of cell-surface proteins facilitating cell-cell adhesion), and are interested in the potential of metabolic division of labor to increase the evolutionary stability of our differentiation architecture. This division of labor could take the form of amino acid cross-feeding, engineered nitrogen-fixation, etc.

'''2) Spatial patterning of multicellular E. coli'''

What types of spatial patterning can you achieve by combining synthetic differentiation with quorum-sensing/cell-cell communication, and the ability to genetically control cell lysis, septation and cell-cell adhesion? Can you make filamentous E. coli with regular patterns of distinct cell types? Can you genetically program the number of cells in these filamentous E. coli? Can you program the development of a hollow sphere of cells?

'''3) Production of burdensome or toxic proteins or metabolites using differentiation circuits'''

In the characterization of the capacity of differentiation circuits to improve the evolutionary stability of burdensome functions, we have exclusively used overproduction of a fluorescent protein. However, this circuit should be able to facilitate the production of any burdensome or even toxic protein or metabolite, particularly if the toxicity is specific to producer cells and not to all cells in the vessel. To explore this, a SURF student could identify useful/valuable protein(s) or metabolite(s) that currently are difficult to produce effectively in live cells, and evaluate their ability to be produced using differentiation circuits.

'''Useful previous experience'''
* molecular biology (pipetting, PCR, bacterial transformation, minipreps, etc.)
* coding (python preferred)
* mathematical modeling

'''Relevant publications'''
# Williams, R. L.; Murray, R. M. Tunable Integrase-Mediated Differentiation Facilitates Improved Output of Burdensome Functions in E. Coli. bioRxiv 2019. https://doi.org/10.1101/614529.
# Glass, D. S.; Riedel-Kruse, I. H. A Synthetic Bacterial Cell-Cell Adhesion Toolbox for Programming Multicellular Morphologies and Patterns. Cell 2018, 174 (3), 649-658.e16. https://doi.org/10.1016/j.cell.2018.06.041.
# Van Gestel, J.; Vlamakis, H.; Kolter, R. Division of Labor in Biofilms: The Ecology of Cell Differentiation. Microbiol. Spectr. 2015, 3 (2), 1–24. https://doi.org/10.1128/microbiolspec.mb-0002-2014.
# Wahl, M. E.; Murray, A. W. Multicellularity Makes Somatic Differentiation Evolutionarily Stable. Proc. Natl. Acad. Sci. U. S. A. 2016, 113 (30), 8362–8367. https://doi.org/10.1073/pnas.1608278113.

SURF 2020: Applications of synthetic differentiation

2019-12-16T18:32:33Z

Rlwillia: Created page with "'''2020 SURF project description''' * Mentor: Richard Murray * Co-mentor: Rory Williams '''Applications of synthetic differentiation''' In the Murray lab, we h..."

'''[[SURF 2020|2020 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: Rory Williams

'''Applications of synthetic differentiation'''

In the Murray lab, we have demonstrated that the evolutionary stability of burdensome functions in E. coli can be improved by implementing tunable synthetic differentiation circuits utilizing serine integrases. Specifically, a population of progenitor cells which encodes, but does not express, the desired function, is able to replicate the DNA encoding the engineered function in the absence of its associated burden. An integrase-mediated genomic recombination event in a progenitor cell then both activates the engineered function by initiating the expression of T7RNAP, and starts a timer to limit the number of divisions differentiated cells are able to undergo. By appropriately tuning the differentiation rate through the inducible expression of degradation-tagged integrase protein, both the duration of circuit function and the total production achieved can be improved relative to the naïve implementation of the engineered function where all cells constitutively express the function. Though moderately effective, this strategy ultimately fails due to the selection of mutations which destroy the differentiation mechanism, and we are currently developing and testing circuits which will require two or more mutations to destroy the differentiation mechanism in order to improve its performance
[[File:2020_SURF_fig.png|600px|Image: 600 pixel]]

Figure 1: (A) Schematic of differentiation activated T7RNAP driven expression. Las AHL induces expression of pir protein, which is needed for replication of the R6K plasmid. Salicylate induces the expression of degradation-tagged Bxb1 integrase, which excises the pir expression cassette from the genome, and activates the expression of T7RNAP by bringing together two sections of the coding sequence. IPTG induces expression of full length T7RNAP in differentiated cells, allowing expression of sfYFP from the high-copy Cole1 plasmid. (B) Schematic of naïve inducible T7RNAP driven expression. Circuit is identical to a differentiated cell, but lacking the R6K plasmid. (C) Schematic for long-term differentiation experiments. (D-E) JS006 with differentiation circuit (A) above grown in M9CA + carbenicillin/3M Las AHL, +/- chloramphenicol, 30M IPTG, in varying concentrations of salicylate. Cells with naïve circuit (B) are grown in M9CA + carbenicillin/30M IPTG. Cells diluted 50X into same media conditions into 300L total volume every ~12 h for 8 total growths. (D) Cumulative total production plotted is the sum of endpoint fluorescence values from 12 h plate reader growth. (E) Samples taken immediately after growth were analyzed by flow cytometry, and fraction sfYFP positive cells is plotted. (D-E) Means of four total replicates from two independent experiments with standard deviation error bars.

We are interested in expanding the scope of differentiation architectures in a variety of ways, any of which could provide an opportunity for a SURF project.

'''1) Differentiation with reproductive and metabolic division of labor'''

While thus far we have been implementing differentiation in the context single-celled planktonically growing E. coli, naturally occurring examples of microbial differentiation are predominantly or exclusively found in species which form multicellular aggregates. In the context of multicellular aggregates, metabolic labor can be divided while allowing the benefits of this division of labor to be shared locally within the aggregate, and not with non-differentiating ‘cheaters’ or other competing microbes. We are currently exploring implementing differentiation in E. coli which form multicellular aggregates (through a combination of genetically controlled septation, and expression of pairs of cell-surface proteins facilitating cell-cell adhesion), and are interested in the potential of metabolic division of labor to increase the evolutionary stability of our differentiation architecture. This division of labor could take the form of amino acid cross-feeding, engineered nitrogen-fixation, etc.

'''2) Spatial patterning of multicellular E. coli'''

What types of spatial patterning can you achieve by combining synthetic differentiation with quorum-sensing/cell-cell communication, and the ability to genetically control cell lysis, septation and cell-cell adhesion? Can you make filamentous E. coli with regular patterns of distinct cell types? Can you genetically program the number of cells in these filamentous E. coli? Can you program the development of a hollow sphere of cells?

'''3) Production of burdensome or toxic proteins or metabolites using differentiation circuits'''

In the characterization of the capacity of differentiation circuits to improve the evolutionary stability of burdensome functions, we have exclusively used overproduction of a fluorescent protein. However, this circuit should be able to facilitate the production of any burdensome or even toxic protein or metabolite, particularly if the toxicity is specific to producer cells and not to all cells in the vessel. To explore this, a SURF student could identify useful/valuable protein(s) or metabolite(s) that currently are difficult to produce effectively in live cells, and evaluate their ability to be produced using differentiation circuits.

'''Useful previous experience'''
* molecular biology (pipetting, PCR, bacterial transformation, minipreps, etc.)
* coding (python preferred)
* mathematical modeling

'''Relevant publications'''
# Williams, R. L.; Murray, R. M. Tunable Integrase-Mediated Differentiation Facilitates Improved Output of Burdensome Functions in E. Coli. bioRxiv 2019. https://doi.org/10.1101/614529.
# Glass, D. S.; Riedel-Kruse, I. H. A Synthetic Bacterial Cell-Cell Adhesion Toolbox for Programming Multicellular Morphologies and Patterns. Cell 2018, 174 (3), 649-658.e16. https://doi.org/10.1016/j.cell.2018.06.041.
# Van Gestel, J.; Vlamakis, H.; Kolter, R. Division of Labor in Biofilms: The Ecology of Cell Differentiation. Microbiol. Spectr. 2015, 3 (2), 1–24. https://doi.org/10.1128/microbiolspec.mb-0002-2014.
# Wahl, M. E.; Murray, A. W. Multicellularity Makes Somatic Differentiation Evolutionarily Stable. Proc. Natl. Acad. Sci. U. S. A. 2016, 113 (30), 8362–8367. https://doi.org/10.1073/pnas.1608278113.

File:SURF 2020 wahl murray.png

2019-12-16T18:27:16Z

Rlwillia:

File:2020 SURF fig.png

2019-12-16T18:25:09Z

Rlwillia:

SURF 2020

2019-12-16T12:15:55Z

Rlwillia: /* List of available projects */

{{righttoc}}
This page is intended for students interested in working on SURF projects in the Summer of 2020. It contains information about how to apply for a SURF project in my group along with a list of project areas.

'''Note:''' Projects will be posted here starting after finals week. Please check back after that time for more information.

=== 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 8 Jan (Wed) 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 10 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 2015 (Amgen applications are due a week earlier)..
# If you are selected for a SURF, please be aware of the following information
#* All SURF projects in my group will start on 16 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. 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 ===

Projects will be posted as they come available. I recommend waiting until near the deadline submission before submitting your project preferences.

{| border=1 width=100%
|-
| '''Title''' || '''Grant/Project''' || '''Co-Mentors''' || '''Comments'''
|-
|{{SURF|2020|Test and Evaluation for Autonomy}}
| [[Formal Methods for V&V and T&E of Autonomous Systems|AFOSR]]
| Apurva Badithela
|
|-
| {{SURF|2020|Rules of the Road--a top-down approach for guaranteeing correct behavior for self-driving cars}}
| [[NSF VeHICaL]]
| Karena Cai
|
|-
| {{SURF|2020|Modeling tools for design and analysis of synthetic biological circuits}}
| [[NSF Cell Free]]
| Ayush Pandey
|
|-
| {{SURF|2020|Hardware Implementation of Contract-Based Design for Automated Valet Parking System}}
| [[DENSO CPM]]
| Josefine Graebener
|
|-
| {{SURF|2020|Social-Aware Robot Navigation}}
| TBD
| Francesca Baldini
|
|-
| {{SURF|2020|Applications of synthetic differentiation}}
| TBD
| Rory Williams
|
|-
| {{SURF|2018|Genetically-Programmed Synthetic Cells and Multi-Cellular Machines}}
| [[NSF Cell Free]]
| None
| Multiple projects may be available; competitive selection
|}

Sara Molinari, 29 Jan 2019

2019-01-28T00:05:30Z

Rlwillia: /* 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: Joe (Keck 238)
* 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, Andy, Joe, Rory) (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.

Group Schedule, Fall 2018

2018-10-08T18:32:16Z

Rlwillia: Chelsea/Rory times switched

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 2018]]
|}

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 312 Annenberg.

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

| width=25% |
=== Week 1: 1-5 Oct ===
'''Biocircuits: Tue, 10a-12p
* [[http:docs.google.com/presentation/d/1iCRRMLL5ONt6SER9WEORths_63if78tHCm3idFo_AKg|Individual updates]]
'''NCS: Wed, 3:30-5 pm
* Karena Cai

| width=25% |

=== Week 2: 8-12 Oct ===
'''Biocircuits: Mon, 10a-12p
* William Poole
* Joe Meyerowitz
<hr>
* Richard out Tue-Thu

| width=25% |

=== Week 3: 15-19 Oct ===
'''Biocircuits: Mon, 10a-12p
* [[http:docs.google.com/presentation/d/12XSe2PqPQO6tVVi4-oe2TEzhSWhMb8K4ARfBeREsYnM|Individual updates]]
'''NCS: Mon, 3:30-5 pm
* Sumanth Dathathri


| width=25% |

=== Week 4: 22-26 Oct ===
'''Biocircuits: Tue, 9a-11a
* Zoila Jurado
* John McManus
'''NCS: Wed, 3:30-5 pm
* Richard Cheng


|- valign=top
| width=25% |

=== Week 5: 29 Oct - 2 Nov ===
'''Biocircuits: Tue, 1-3 pm
* [[http:docs.google.com/presentation/d/1vWp19lghWK1JylGJBoO0BEtMcrAyhh0efvYz0bV2Pa0|Individual updates]]
'''NCS: Wed, 3:30-5 pm
* Tung Phan


| width=25% |

=== Week 6: 5-9 Nov ===
'''Biocircuits: Tue, 1-3 pm
* Chelsea Hu
* Andy Halleran
'''NCS: Wed, 3:30-5 pm
* Hold: Mitch Ingham


| width=25% |

=== Week 7: 12-16 Nov ===
'''Biocircuits: Tue, 10a-12p
* [[http:docs.google.com/presentation/d/1D0IpbQp77uYaG00uB7VqS3qtJty2x45V11YLtrW4Wkw|Individual updates]]
Note: Meeting may shift to 12 Nov (Mon), 10a-12p
<hr>
* Richard out Wed-Thu

| width=25% |

=== Week 8: 19-23 Nov ===
'''Biocircuits: Tue, 1-3 pm
* Rory Williams
* Leo Green
'''NCS: Tue, 10:30a-12p
* Jin Ge


|- valign=top
| width=25% |

=== Week 9: 26-30 Nov ===
'''Biocircuits: Tue, 1-3 pm
* [[http:docs.google.com/presentation/d/1OJISoWIsDVtqVJPVLYH28Fo0ohyzpAfRTdOQYmtOemg|Individual updates]]
<hr>
* Domitilla Del Vecchio visiting on Wed, Thu

| width=25% |

=== Week 10: 3-7 Dec ===
'''Biocircuits: Tue, 1-3 pm
* Hold: rotation student
* Hold: rotation student
* Note: meeting may shift to Mon, 10a-12p
'''NCS: Wed, 3:30-5 pm
* Yuxiao Chen
* Note: meeting may get shifted to prior week


| width=25% |

=== Week 11: 10-14 Dec ===
'''Biocircuits: Tue, 1-3 pm
* [[http:docs.google.com/presentation/d/12mJfBndtE640Nufe7LDvdBpwKDFkQFJXHpg2UsZ0llE|Individual updates]]
'''NCS: Tue, 10:30a-12p
* Petter Nilsson

| width=25% |

=== Week 12: 17-21 Dec ===
* Winter recess

|}

John McManus, 5 Mar 2018

2018-03-02T22:38:50Z

Rlwillia:

[http://www.jbmcmanus.com John McManus] will be visiting Caltech on 5 Mar 2018. Sign up to meet with him below:

Schedule
* 9 am - meet with Richard for ~30 min
* 9:30 am - TX-TL discussion (Joe M, William P, Zoila J)
* 10:30a-12p - group meeting (including 15 min talk by John)
* 12p-1:30p - lunch with postdocs (Leo G, Michaelle M, Anandh S)
* 1:30p - lab tour (Leo and/or Anandh)
* 2:00p - Andrey
* 2:45p - James
* 3:00p - Azita Emami
* 3:45p - open
* 4:15p - Rory
* 5 pm - wrap up meeting with Richard for ~30 m

SURF discussions, Jan 2018

2018-01-22T19:45:36Z

Rlwillia: /* 24 Jan (Wed) */

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
|- valign=top
| width=30% |
==== 23 Jan (Tue) ====
* 1:00 pm PST: open
<hr>
* 4:00 pm PST: Andrey/ Sanjana
* 4:30 pm PST: open
<hr>
* 6:00 pm PST: open
* 6:30 pm PST: open
| width=30% |

==== 24 Jan (Wed) ====
* 7:30 am PST: open (hold for India/Europe)
* 8:00 am PST: Rory/Elin
<hr>
*12:15 pm PST: Filip / Jin
*12:45 pm PST: open (if needed)
<hr>
* 4:30 pm PST: Reed / Leah
* 5:00 pm PST: open
* 5:30 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

SURF 2018: Engineering metabolic cross-feeding relationships for robust microbial consortia

2017-12-18T09:26:11Z

Rlwillia: Created page with "'''2018 SURF project description''' * Mentor: Richard Murray * Co-mentor: Rory Williams '''Engineering metabolic cross-feeding relationships for robust microbia..."

'''[[SURF 2018|2018 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: Rory Williams

'''Engineering metabolic cross-feeding relationships for robust microbial consortia'''
Recent years have seen increased interest in both understanding the interactions governing the structure and dynamics of naturally occurring multi-species microbial communities, and implementing microbial consortia for bioremediation and bioprocessing. There are numerous potential advantages of using microbial consortia over a single species, including increased yield and efficiency through specialization of function, functional stability over a wider range of environmental conditions, and execution of metabolic functions not possible by a single organism alone. In selecting and designing microbial consortia, researches have harnessed existing microbial consortia, combined species with known metabolic function, and genetically engineered multiple species to cooperate in a single community. While more complex synthetic consortia may be more robust to environmental conditions, bottom-up design of many-membered consortia is yet challenging, in part due to our incomplete mechanistic understanding of natural complex consortia.

This SURF project will focus on the design and implementation of multi-species consortia which rely on metabolic cross-feeding. SURF students will model the dynamics of various community topologies across environmental conditions to characterize robustness, and utilize mutations inducing auxotrophy or overproduction of metabolites, and/or synthetic regulation of metabolite exchange to realize community structure(s). Communities may designed to be robust to variations of specific environmental conditions, and/or sensitive to variations in others. Through the identification of robust structures of metabolic interactions in multi-species communities, this project may help to elucidate consortia design principles, and to develop chassis for implementing circuits whose function is benefited or made possible through segregation across multiple distinct species.

'''Backround/skills''': Genetics/biology courses, general microbiology techniques, molecular biology (PCR, cloning, etc.), Python.

'''Relevent references''':

S. Widder et. al. (2016). Challenges in microbial ecology: building predictive understanding of community function and dynamics. ISMEJ.
OS Venturelli et. al. (2016). Towards Engineering Biological Systems in a Broader Context. J. Mol. Biol..
X Ren et. al. (2017). Population regulation in microbial consortia using dual feedback control. CDC.
TA Hoek et. al. (2016). Resource Availability Modulates the Cooperative and Competitive Nature of a Microbial Cross-Feeding Mutualism. PLoS Bio.
MT Mee et al. (2014). Syntrophic exchange in synthetic microbial communities. PNAS.

https://www.biorxiv.org/content/biorxiv/early/2017/12/03/228395.full.pdf

SURF 2018

2017-12-18T09:21:43Z

Rlwillia: /* List of available projects */

{{righttoc}}
This page is intended for students interested in working on SURF projects in the Summer of 2018. It contains information about how to apply for a SURF project in my group along with a list of project areas.

'''Note:''' Projects will be posted here starting after finals week. Please check back after that time for more information.

=== 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 (Wed) 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 2015 (Amgen applications are due a week earlier)..
# If you are selected for a SURF, please be aware of the following information
#* All SURF projects in my group will start on 19 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. 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 ===

Projects will be posted as they come available. I recommend waiting until near the deadline submission before submitting your project preferences.

{| border=1 width=100%
|-
| '''Title''' || '''Grant/Project''' || '''Co-Mentors''' || '''Comments'''
|-
| {{SURF entry|2018|Experimental verification of a semi-autonomous vehicle design based on human intention}}
| [[NSF VeHICaL]]
| Jin Ge
|
|-
| {{SURF entry|2018|Contract-based Design of Control Systems}}
| [[DENSO CPM]]
| Tung Phan
|
|-
| {{SURF entry|2018|Resource Usage in TX-TL}}
| [[NSF MPP2]]
| William Poole
|
|-
| {{SURF entry|2018|Integrase-based genetic circuits}}
| [[ARO ICB]]
| Andrey Shur
|
|-
| {{SURF entry|2018|Synthetic modules for regulation of bacterial growth}}
| [[DARPA BioCon]]
| Reed McCardell
|
|-
| {{SURF entry|2018|Evolutionary Stability of Genetic Circuits}}
| [[ARL Consortia]]
| Andy Halleran
|
|-
| {{SURF entry|2018|Test design for temporal logic controllers}}
| [[JPL PDF17]]
| Sofie Haesaert
|
|-
| {{SURF entry|2018|Modeling the Effect of Intracellular Signaling Mechanisms on Population Dynamic Behaviors in the Context of Paradoxical Signaling}}
| [[DARPA BioCon]]
| Michaelle Mayalu
|
|-
| {{SURF entry|2018|Engineering metabolic cross-feeding relationships for robust microbial consortia}}
|
| Rory Williams
|
|}

Mary Dunlop, Oct 2017

2017-10-18T22:56:45Z

Rlwillia: /* Topic #1: mutational robustness */

Mary Dunlop will visit Caltech on 19-20 Oct 2017. __NOTOC__

== Topics ==

Richard will organize a set of discussions with Mary on different topics. If you are interested in joining in the discussions, sign up below. You should put your name and any constraints on your time.

{| border=1
|- valign=top
| width=33% |
==== Topic #1: mutational robustness ====
* Richard - available 1-5 pm
* Anandh - 24/7/365
* Rory - 1-5pm (skype)
| width=33% |

==== Topic #2: feedback control of biological systems ====
* Richard - available 1-5 pm
* Ania - 1pm - 4pm
* Vipul - available 1-5p
* Name - availability
| width=33% |

==== Topic #3: TX-TL (modeling and experiments) ====
* Richard - available 1-5 pm
* William - busy 1-4 pm
* Vipul - available 1-5p
* Name - availability
|}

==== Additional topics ====
* If you have an additional topic you would like to discuss, but it here.

== Schedule ==
To be filled out later.

==== Thursday ====
* 11:00 am: Seminar in Gates-Thomas

=== Friday ===
* 8:45 am: Open
* 9:30 am: Ania
* 10:15 am: Vipul/Anandh (system ID etc)
* 11 am - 2 pm: off campus
* 2-5 pm: group discussions (sign up above)
* 5:00 pm: Done for the day

May 2017 meeting schedule

2017-05-10T06:26:38Z

Rlwillia: /* 21 May (Sun) */

Richard will be in town several different times in May. Please sign up for a time to meet below. Please note that these are likely the last "sabbatical" meetings until Richard returns to Pasadena in early July. __NOTOC__

{| border=1 width=100%
|- valign=top
| width=33% |
| width=33% |
==== 15 May (Mon) ====
* 9:30 am: Open
* 10:15 am: Open
* 11:00 am: Faculty meeting
* 11:30 am: Andy
* 12:15 pm: Lunch
* 1:30 pm: Sam
* 2:15 pm: Reed
* 3:00 pm: Vipul
* 3:45 pm: Break
* 4:00 pm: Namita
* 4:45 pm: Ania
* 5:30 pm: Anandh
* 6:15 pm: Done for the day

| width=33% |

==== 16 May (Tue)====
* 9:30 am: Yong
* 10:15 am: Tung
* 11:00 am: Faculty meeting
* 12:00 pm: Lunch
* 1:30 pm: Depart
* 12:00 pm: Lunch
* 1:30 pm: Depart

|- valign=top
| width=33% |

====21 May (Sun) ====
* 1:45 pm: Sofie
* 2:30 pm: Ioannis
* 3:15 pm: Karena
* 4:00 pm: Break
* 4:15 pm: Rory
* 5:00 pm: Open
* 5:45 pm: Open
* 6:30 pm: Done for the day

| width=33% |

==== 22 May (Mon) ====
* 10:15 am: Mark
* 11:00 am: Cindy
* 11:45 am: Lunch
* 12:00 pm: DARPA BioCon meeting
* 2:00 pm: Swati + Reed
* 2:45 pm: Off campus
* 4:15 pm: James
* 5:00 pm: Non-Caltech meetings
* 6:30 pm: Done for the day

| width=33% |

==== 23 May (Tue) ====
* 9:30 am: Faculty discussion
* 10:30 am: Hold (Susan)
* 11:30 am: Lunch
* 12:00 pm: Telecon
* 1:00 pm: Anu thesis defense
* 3:00 pm: Terri (?)
* 3:30 pm: Depart

|- valign=top
| width=33% |

====28 May (Sun) ====
* 1:45 pm: Richard C
* 2:30 pm: George
* 3:15 pm: Andy
* 4:00 pm: Done for the day
| width=33% |

====29 May (Mon) ====
* 1:45 pm: Open (if needed)
* 2:30 pm: Open (if needed)
* 3:15 pm: Sumanth
* 4:00 pm: Done for the day
| width=33% |

==== 30 May (Tue) ====
* 9:30 am: Shan
* 10:15 am: Shaobin
* 11:00 am: Stepan seminar
* 12:00 pm: Lunch
* 1:30 pm: Namita
* 2:15 pm: Andrey
* 3:00 pm: Depart
|}

SURF discussions, Jan 2017

2017-01-24T19:55:00Z

Rlwillia: /* 25 Jan (Wed) */

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.

{| width=100% border=1
|- valign=top
|
==== 25 Jan (Wed) ====
* 8:30 am PST: Kshitij Rai and Rory Williams
<hr>
* 11:00 am PST: open
<hr>
* 3:00 pm PST: open
* 3:30 pm PST: open
|

==== 26 Jan (Thu) ====
* 1:00 pm PST: open
* 1:30 pm PST: open
<hr>
* 6:30 pm PST: open
* 7:00 pm PST: open
|

==== 27 Jan (Fri) ====
* 9:00 am PST: Joy Doong and James Parkin
* 9:30 am PST: Swati Agrawal and Reed McCardell
* 10:00 am PST: open
* 10:30 am 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

Jan 2017 meeting schedule

2017-01-13T18:27:58Z

Rlwillia: /* 22 Jan (Sun) */

Richard will be in town 20-24 Jan. Please sign up for a time to meet below. __NOTOC__

{| border=1
|- valign=top
| width=25% |
==== 20 Jan (Fri) ====
* Richard arrives on campus ~9:45 am
* 10:15 am: Mark
* 11:00 am: Yong
* 11:45 am: Anandh
* 12:30 pm: Lunch
* 1:30 pm: Yong and Frances A
* 2:30 pm: Sumanth Dathathri
* 3:15 pm: Open
* 4:00 pm: Miki
* 4:45 pm: Break
* 5:00 pm: Cindy
* 5:45 pm: Open
* 6:30 pm: Done for the day

| width=25% |

==== 22 Jan (Sun) ====
* 1:45 pm: Open
* 2:30 pm: Open
* 3:15 pm: Rory
* 4:00 pm: Break
* 4:15 pm: Open
* 5:00 pm: Open
* 5:45 pm: Open
* 6:30 pm: Done for the day

| width=25% |

==== 23 Jan (Mon) ====
* 8:00 am: Michaelle
* 9:00 am: Hold: Jaymie
* 10:00 am: BioCon meeting
* 12:00 pm: Seminar ([[Michaëlle Mayalu, Jan 2017|Michaelle]])
* 1:00 pm: Hold until needed
* 1:45 pm: Open
* 2:30 pm: CDS faculty meeting
* 4:15 pm: Tony Fragoso
* 5:00 pm: Open
* 5:45 pm: Open
* 6:30 pm: Dinner with visitors

| width=25% |

==== 24 Jan (Tue) ====
* 9:45 am: Henrike
* 10:30 am: Karena
* 11:15 am: Tung
* 12:00 pm: Seminar ([[Henrike Niederholtmeyer, Jan 2017|Henrike]])
* 1:15 pm: [[Michaëlle Mayalu, Jan 2017|Michaelle]]
* 2:00 pm: Anu
* 2:45 pm: [[Henrike Niederholtmeyer, Jan 2017|Henrike]]
* 3:30 pm: Depart for airport
|}

SURF 2017: Integrase based circuits for sequential and temporal control of gene expression

2017-01-02T22:31:12Z

Rlwillia:

'''[[SURF 2017|2017 SURF]]: project description'''
* Mentor: Richard M. Murray
* Co-mentors: Rory Williams

Integrase based logic gates rely on the ability of integrases to invert, excise, or integrate functionally important sequences of DNA flanked by pairs of integrase recognition sites. Using both orthogonal integrases as well as multiple orthogonal integrase attachment sites per integrase, two-input one-output logic gates, two and three input state-machines, as well as temporal logic gates have been successfully demonstrated (Bonnet et al., 2013; Roquet et al., 2016; Hsiao et al., 2016). However, little has been done to harness integrase based logic for the control of gene expression in a sequential manner. This project would explore the utility of integrases for controlling sequential gene expression, and determine how to control the timing of steps in the cascade through tuning of promoter strength, mRNA stability, degradation tags, plasmid copy number, and/or other parameters. An example circuit for sequential gene expression is shown below to demonstrate the general principle, though the student may design a different circuit for this project. This project would involve modeling of the circuit to determine desirable characteristics and narrow the parameter space, and assembly and testing of the circuit(s) in vitro in TX-TL and in vivo in cells.

Recommended skills: Students interested in this project should have some basic laboratory skills (equivalent to Bi 1X, Bi 10 or ChE/BE 130) and have experience with either MATLAB, Python or a similar scientific programming package.

[[Image:Nsf_integrase_clock.png|Integrase clock cirucuit]]

Figure 1: (a) The circuit is constructed to have a single inducible promoter in front of an array of integrase genes. Each integrase coding sequence is followed by a transcriptional terminator and flanked by parallel attB/attP sites. Expression of the furthest upstream integrase results in the excision of its corresponding coding sequence, and allows expression of the subsequent integrase. (b) Incorporation of polycistronic transcripts in place of the single integrase allows sequential, non-overlapping expression of desired genes or operons (c).

==References==
J. Bonnet, P. Yin, M. E. Ortiz, P. Subsoontorn, and D. Endy. Amplifying genetic logic gates. Science, 340(6132):599–603, 2013.

V. Hsiao, Y. Hori, P. W. K. Rothemund, and R. M. Murray. A population-based temporal logic gate for timing and recording chemical events. Molecular Systems Biology, 12(5):869, 2016.

N. Roquet, A. P. Soleimany, A. C. Ferris, S. Aaronson, and T. K. Lu. Synthetic recombinasebased state machines in living cells. Science, 353(6297):aad8559, 2016.

SURF 2017: Integrase based circuits for sequential and temporal control of gene expression

2017-01-02T22:28:18Z

Rlwillia:

'''[[SURF 2017|2017 SURF]]: project description''
* Mentor: Richard M. Murray
* Co-mentors: Rory Williams

Integrase based logic gates rely on the ability of integrases to invert, excise, or integrate functionally important sequences of DNA flanked by pairs of integrase recognition sites. Using both orthogonal integrases as well as multiple orthogonal integrase attachment sites per integrase, two-input one-output logic gates, two and three input state-machines, as well as temporal logic gates have been successfully demonstrated (Bonnet et al., 2013; Roquet et al., 2016; Hsiao et al., 2016). However, little has been done to harness integrase based logic for the control of gene expression in a sequential manner. This project would explore the utility of integrases for controlling sequential gene expression, and determine how to control the timing of steps in the cascade through tuning of promoter strength, mRNA stability, degradation tags, plasmid copy number, and/or other parameters. An example circuit for sequential gene expression is shown below to demonstrate the general principle, though the student may design a different circuit for this project. This project would involve modeling of the circuit to determine desirable characteristics and narrow the parameter space, and assembly and testing of the circuit(s) in vitro in TX-TL and in vivo in cells.

Recommended skills: Students interested in this project should have some basic laboratory skills (equivalent to Bi 1X, Bi 10 or ChE/BE 130) and have experience with either MATLAB, Python or a similar scientific programming package.

[[Image:Nsf_integrase_clock.png|Integrase clock cirucuit]]

Figure 1: (a) The circuit is constructed to have a single inducible promoter in front of an array of integrase genes. Each integrase coding sequence is followed by a transcriptional terminator and flanked by parallel attB/attP sites. Expression of the furthest upstream integrase results in the excision of its corresponding coding sequence, and allows expression of the subsequent integrase. (b) Incorporation of polycistronic transcripts in place of the single integrase allows sequential, non-overlapping expression of desired genes or operons (c).

==References==
J. Bonnet, P. Yin, M. E. Ortiz, P. Subsoontorn, and D. Endy. Amplifying genetic logic gates. Science, 340(6132):599–603, 2013.

V. Hsiao, Y. Hori, P. W. K. Rothemund, and R. M. Murray. A population-based temporal logic gate for timing and recording chemical events. Molecular Systems Biology, 12(5):869, 2016.

N. Roquet, A. P. Soleimany, A. C. Ferris, S. Aaronson, and T. K. Lu. Synthetic recombinasebased state machines in living cells. Science, 353(6297):aad8559, 2016.

SURF 2017: Integrase based circuits for sequential and temporal control of gene expression

2017-01-02T22:24:52Z

Rlwillia: Created page with "'''2017 SURF: Integrase based circuits for sequential and temporal control of gene expression''' * Mentor: Richard M. Murray * Co-mentors: Rory Williams Integra..."

'''[[SURF 2017|2017 SURF]]: Integrase based circuits for sequential and temporal control of gene expression'''
* Mentor: Richard M. Murray
* Co-mentors: Rory Williams

Integrase based logic gates rely on the ability of integrases to invert, excise, or integrate functionally important sequences of DNA flanked by pairs of integrase recognition sites. Using both orthogonal integrases as well as multiple orthogonal integrase attachment sites per integrase, two-input one-output logic gates, two and three input state-machines, as well as temporal logic gates have been successfully demonstrated (Bonnet et al., 2013; Roquet et al., 2016; Hsiao et al., 2016). However, little has been done to harness integrase based logic for the control of gene expression in a sequential manner. This project would explore the utility of integrases for controlling sequential gene expression, and determine how to control the timing of steps in the cascade through tuning of promoter strength, mRNA stability, degradation tags, plasmid copy number, and/or other parameters. An example circuit for sequential gene expression is shown below to demonstrate the general principle, though the student may design a different circuit for this project. This project would involve modeling of the circuit to determine desirable characteristics and narrow the parameter space, and assembly and testing of the circuit(s) in vitro in TX-TL and in vivo in cells.

Recommended skills: Students interested in this project should have some basic laboratory skills (equivalent to Bi 1X, Bi 10 or ChE/BE 130) and have experience with either MATLAB, Python or a similar scientific programming package.

[[Image:Nsf_integrase_clock.png|Integrase clock cirucuit]]

Figure 1: (a) The circuit is constructed to have a single inducible promoter in front of an array of integrase genes. Each integrase coding sequence is followed by a transcriptional terminator and flanked by parallel attB/attP sites. Expression of the furthest upstream integrase results in the excision of its corresponding coding sequence, and allows expression of the subsequent integrase. (b) Incorporation of polycistronic transcripts in place of the single integrase allows sequential, non-overlapping expression of desired genes or operons (c).

==References==
J. Bonnet, P. Yin, M. E. Ortiz, P. Subsoontorn, and D. Endy. Amplifying genetic logic gates. Science, 340(6132):599–603, 2013.

V. Hsiao, Y. Hori, P. W. K. Rothemund, and R. M. Murray. A population-based temporal logic gate for timing and recording chemical events. Molecular Systems Biology, 12(5):869, 2016.

N. Roquet, A. P. Soleimany, A. C. Ferris, S. Aaronson, and T. K. Lu. Synthetic recombinasebased state machines in living cells. Science, 353(6297):aad8559, 2016.

File:Nsf integrase clock.png

2017-01-02T21:53:29Z

Rlwillia:

File:Integrase clock circuit.pdf

2017-01-02T16:31:09Z

Rlwillia:

SURF 2017

2017-01-02T15:40:10Z

Rlwillia: /* List of available projects */

{{righttoc}}
This page is intended for students interested in working on SURF projects in the Summer of 2015. It contains information about how to apply for a SURF project in my group along with a list of project areas.

=== 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 9 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 10 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 ~21 Feb 2015.
# If you are selected for a SURF, please be aware of the following information
#* All SURF projects in my group will start on 16 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 ===

Projects will be posted as they come available. I recommend waiting until near the deadline submission before submitting your project preferences.

{| border=1 width=100%
|-
| '''Title''' || '''Grant/Project''' || '''Co-Mentors''' || '''Comments'''
|-
|{{SURF entry|2017|Scalable Robust Synthesis from Temporal Logic Specifications}}
| [[SRC TerraSwarm]]
| Sumanth Dathathri
| Multiple projects may be available
|-
| {{SURF|2017|Integrase based circuits for sequential and temporal control of gene expression }}
|
| Rory Williams
|
|}

File:2017 integrase SURF RLW.pdf

2017-01-02T15:34:10Z

Rlwillia:

Nov 2016 meeting schedule

2016-11-07T01:45:23Z

Rlwillia: /* 16 Nov (Wed) */

Richard will be in town 13-16 Nov. Please sign up for a time to meet below.
__NOTOC__

{| border=1
|- valign=top
| width=25% |

==== 13 Nov (Sun) ====
 
 
<hr>
* 2:45 pm: Hold until needed
* 3:30 pm: Hold until needed
* 4:15 pm: Break
* 5:00 pm: Hold until needed
* 5:45 pm: Hold until needed
* 6:30 pm: Done for the day

| width=25% |

==== 14 Nov (Mon) ====
* 10:30 am: Andy Halleran
* 11:15 am: Tung
<hr>
* 1:30 pm: Vipul
* 2:15 pm: Andrey Shur
* 3:00 pm: Shaobin
* 3:45 pm: Break
* 4:00 pm: Miki
* 4:45 pm: Aryeh
* 5:30 pm: Anu
* 6:15 pm: Done for the day
| width=25% |

====15 Nov (Tue) ====
* 10:30 am: Mark
* 11:15 am: Reed
<hr>
* 1:30 pm: Sumanth
* 2:15 pm: Karena Cai
* 3:00 pm: Tony Fragoso
* 3:45 pm: Break
* 4:00 pm: Anandh
* 4:45 pm: Cindy
* 5:30 pm: Richard
* 6:15 pm: Done for the day
| width=25% |

==== 16 Nov (Wed) ====
* 9:30 am: Open
* 10:15 am: Ania
* 11:00 am: Telecon
* 12 pm: Ioannis
* 12:45 pm: Break
<hr>
* 1:30 pm: Sam
* 2:15 pm: Rory
* 3:00 pm: CDS tea
* Depart for airport at ~3:45 pm
|}

Sep/Oct 2016 meeting schedule

2016-09-21T18:24:01Z

Rlwillia:

Richard will be in town 29 Sept - 3 Oct 2016. Please sign up for a time to meet below.
__NOTOC__

{| border=1
|- valign=top
| width=25% |
==== 29 Sep (Thu) ====
* Flying in from SF in the morning
* 1:00 pm: George
* 1:45 pm: Andrey
* 2:30 pm: Tony Fragoso
* 3:15 pm: Break
* 3:30 pm: Richard C.
* 4:15 pm: Sam
* 5:00 pm: Mark
* 5:45 pm: Break
* 6:00 pm: Reed
* 6:45 pm: Rory
* 7:30 pm: Done for the day
| width=25% |

==== 30 Sep (Fri) ====
* Morning: busy with other meetings/phone calls
* 1:30-3:30 pm: Integrase project meeting (Victoria, Andrey, George, Sam, Ania, Cindy, Jining)
* 3:30 pm: Miki
* 4:30 pm: break
* 4:45 pm: Andrew
* 5:30 pm: Anandh
* 6:15 pm: Done for the day
| width=25% |

==== 2 Oct (Sun) ====
* 1:45 pm: YONG
* 2:30 pm: Open
* 3:15 pm: Karena
* 4:00 pm: Break
* 4:15 pm: Cindy
* 5:00 pm: Open
* 5:45 pm: Open
* 6:30 pm: Done for the day

| width=25% |

==== 3 Oct (Mon) ====
* 10 am - 12 pm: DARPA BioCon meeting
* 12:00 pm: Candidacy exam
* 1:45 pm: Jaymie
* 2:45 pm: Tung
* 3:30 pm: Shaobin
* 4:15 pm: Victoria
* 5:00 pm: Break
* 5:15 pm: Daniel N
* 6:00 pm: William
* 6:45 pm: Open
* 7:30 pm: Done for the day
|}