Murray Wiki - User contributions [en]

David Garcia, 13 Feb 2020

2020-02-11T17:30:25Z

Chelseah: /* 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: Chelsea
* 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.

SURF discussions, Jan 2020

2020-01-23T02:33:43Z

Chelseah: /* 24 Jan (Fri) */

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: Chelsea, Katherine
 
(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: Open
<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 discussions, Jan 2020

2020-01-23T02:33:30Z

Chelseah: /* 3 Feb (Mon, if needed) */

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: Open
<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 discussions, Jan 2020

2020-01-22T16:26:36Z

Chelseah: /* 3 Feb (Mon, if needed) */

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: open
<hr>
* 4:30 pm PST: open
* 5:00 pm PST: open
| width=25% |

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

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

==== 3 Feb (Mon, if needed) ====
* 9:00 am PST: Open
* 9:30 am PST: Chelsea, Katherine
<hr>
* 5:00 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

2019-01-28T02:03:20Z

Chelseah: /* 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: Zoila (Watson courtyard)
* 12:00 pm: Lunch with postdocs John McManus, Leo Green, Chelsea Hu
* 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: Chelsea (ANB lounge)
* 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.