Murray Wiki - User contributions [en]

RMM research meetings, Mar 2026

2026-03-15T18:48:52Z

Zmartine:

Please sign up for a time to meet.

18 Mar (Wed)
* 3:30 pm: Open
* 4:15 pm: Open
* 5:00 pm: Open

20 Mar (Fri)
* 2:00 pm: Miki
* 2:45 pm: Zach M.
* 3:30 pm: Open
* 4:15 pm: Open

RMM research meetings, Jan 2026

2026-01-07T18:42:43Z

Zmartine:

Please sign up for a slot below on both Mon and Tue (we'll meet on Mon unless I get called in for jury duty):

12 Jan (Mon):
* 9:00 am: Open
* 11:00 am: Sal
* 1:00 pm: Zach
* 2:00 pm: Han
* 3:00 pm: Nikos & Richard Andersen
* 4:00 pm: Leo & Markus Meister

RMM research meetings, Jul-Aug 2025

2025-07-28T00:24:00Z

Zmartine:

Please sign up for a slot below.

31 Jul (Thu):
* 9:00 am: Open
* 10:00 am: Open
* 11:00 am: Hold: Nuvia
* 1:30 pm: Miki
* 2:30 pm: Leo
* 3:30 pm: Matt
* 4:30 pm: Open

1 Aug (Fri)
* 10:00 am: Open
* 11:00 am: Zach M.
* 2:00 pm: Blade

RMM research meetings, May 2025

2025-04-28T16:44:09Z

Zmartine:

Please sign up for a slot below.

5 May (Mon):
* 8:30 am: Open
* 9:15 am: Open
* 3 pm: Josefine
* 3:45 pm: Open

11 May (Sun):
* 2:15 pm: Open
* 3 pm: Open
* 3:45 pm: Open
* 4:30 pm: Open

12 May (Mon):
* 10 am: Open
* 10:45 am: Zach M
* 3:30 pm: Open
* 4:15 pm: Open

SURF 2024: Towards a Minimal Model for Virus-Host Interactions

2023-12-18T04:02:18Z

Zmartine: Created page with "'''2024 SURF project description''' __NOTOC__ * Mentor: Richard Murray * Co-mentors: Zachary Martinez 600px Main Idea: Engineering a synthetic cell that can be infected by a natural virus. === Introduction === Viruses are abundant (~1031), ancient (> 4 bya), and evolve quickly (average of 10-3 - 10-8 mutation rate). Due to the immense diversity of viruses, between..."

'''[[SURF 2024|2024 SURF]] project description'''
__NOTOC__
* Mentor: Richard Murray
* Co-mentors: Zachary Martinez

[[Image:Phage_Infecting_Synthetic_Cell.png|right|600px]]

Main Idea: Engineering a synthetic cell that can be infected by a natural virus.

=== Introduction ===
Viruses are abundant (~1031), ancient (> 4 bya), and evolve quickly (average of 10-3 -
10-8 mutation rate). Due to the immense diversity of viruses, between 60-95% of
viruses are uncharacterized/unidentifiable.1,2,3 Viruses can have global impacts including carbon cycling in the oceans and the spread of deadly
disease during a pandemic. While most may consider viruses to be completely detrimental to
humanity, they have proven to be incredibly useful for biotechnological purposes. From tailored
phage therapy that can fight antibiotic resistant bacterial infections to the therapeutic delivery of base
editors to correct genetic mutations like hemophilia, viruses can be powerful tools.4 While viruses are
undoubtedly important to science, they can be extremely challenging to study. Complex
lifestyles, sheer diversity, host requirement, and numerous other factors contribute to the hurdles
that contemporary virology faces. Through the bottom-up construction of a synthetic host, we can hopefully exert greater control over our experimental design and allow for a more in-depth interrogation of the underlying viral biology. At the same time, with the advancement of synthetic biology, it would be useful to create a viral vector that can engage with synthetic cells. By allowing viruses to interface with synthetic cells, it opens up more complex engineering goals that might involve targeted delivery of genetic payloads (CRISPR/Cas9) to mixed populations of living and synthetic cells. The specificity and robustness of viruses might prove to be a valuable asset in our synthetic cell toolbox.

=== Project Overview ===
In order to build a minimal model for viral infection, we will be using synthetic cells for our hosts and
T4 phage for our virus. Our non-living synthetic cells are typically comprised of cell-free protein
synthesis extract that is encapsulated inside of a lipid vesicle. For this minimal model however, we
will be embedding E. coli protein OmpC into our liposome in order for T4 to recognize the vesicle as a
potential host. While we will first use RNA based toehold switches to determine if successful infection
occurs, the end goal is to use PURErep (platform for transcription-translation-coupled DNA
replication) inside of the vesicles which should allow for viral propagation after infection.5 Lastly, we will investigate whether the viruses are able to escape their host and what mechanism they use to lyse the liposome. If we are able to fully recapitulate the viral life cycle in a synthetic host, this will hopefully lead to a publication.

=== Preferred Skills ===
<ul>
<li> Background in basic molecular biology through coursework </li>
<li> Some experimental experience through coursework with a lab component or research </li>
</ul>
==== References ====
<ol>
<li>Microbiology by numbers. Nat Rev Microbiol. 2011 Aug. https://doi.org/10.1038/nrmicro2644 </li>
<li>Nasir A., et al. Investigating the Concept and Origin of Viruses. 2020 Dec. https://doi.org/10.1016/j.tim.2020.08.003 </li>
<li>Stern A. and Andino R. Viral Evolution. Viral Pathogenesis. 2016 Feb. https://doi.org/10.1016%2FB978-0-12-800964-2.00017-3 </li>
<li>Rosen S., et al. Activity of transgene-produced B-domain-deleted factor VIII in human plasma following AAV5 gene therapy. Blood. 2020 Nov. https://doi.org/10.1182/blood.2020005683 </li>
<li>Libicher K., et al. In vitro self-replication and multicistronic expression of large synthetic genomes. Nature Communications. 2020 Feb. https://doi.org/10.1038/s41467-020-14694-2 </li>
</ol>

SURF 2024

2023-12-18T04:01:16Z

Zmartine:

{{righttoc}}
This page is intended for students interested in working on SURF projects in the Summer of 2024. 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 and up to the start of classes. Please check back after that time for more information.

=== Applying for a SURF project in my group ===

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 1 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.
# If you are selected for a SURF, please be aware of the following information
#* All SURF projects in my group will start on 18 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.
#* Additional information on SURF available here: https://sfp.caltech.edu/undergraduate-research/programs/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|2024|Task-Relevant Metrics for Perception}}
| TBD
| Apurva Badithela
|
|-
| {{SURF|2024|Establish synthetic biology toolkits for Steinernema nematode transgene expression}}
| Carnegie Institution for Science
| TBD
| Mentor: Mengyi Cao (PI)
|-
| {{SURF|2024|Bioengineering toolkit development for genetic alterations in the entomopathogenic nematode symbiont Xenorhabdus griffiniae}}
| TBD
| Elin Larsson
|
|-
| {{SURF|2023|Genetically-Programmed Synthetic Cells and Multi-Cellular Machines}}
| [[NSF Cell Free]]
| TBD
| Multiple projects may be available; competitive selection
|-
| {{SURF|2024|Towards a Minimal Model for Virus-Host Interactions}}
| TBD
| Zachary Martinez
|
|}

Andras Gyorgy, Aug 2023

2023-08-07T06:21:10Z

Zmartine:

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

== Schedule ==

* 9:30 am: Richard, 109 Steele
* 10:00 am: Manisha, 138 Keck (?)
* 10:30 am: Zach Martinez, 138 Keck
* 11:00 am: Seminar, 111 Keck
* 12:15 pm: Lunch with graduate students (organized by John M)
* 1:30 pm: Matt K
* 2:15 pm: Yan, location TBD
* 3:00 pm: John M, location TBD
* 3:45 pm: Inigo, Annenberg 2nd floor lounge
* 4:30 pm: Richard, 109 Steele

Andras Gyorgy, Aug 2023

2023-08-03T15:51:12Z

Zmartine:

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: Zach Martinez, Red Door(?)
* 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: Inigo, Annenberg 2nd floor lounge
* 4:30 pm: Richard, 109 Steele

SURF discussions, Feb 2023

2023-01-23T02:39:04Z

Zmartine: /* 6 Feb (Mon) */

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/Zoom call. (For Zoom 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. It would be great to show up with a first draft of your GOTChA chart.

{| border=1 width=100%
|- valign=top
| width=50% |
==== 6 Feb (Mon) ====
* 8:00 am PST: open
* 8:30 am PST: open
<hr>
* 1:00 pm PST: open
* 1:30 pm PST: Phillipe and Zach
| width=50% |

==== 7 Feb (Tue) ====
* 8:00 am PST: open
* 8:30 am PST: open
<hr>
* 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, what you have read, variations to consider, etc
# Review of GOTChA chart and how we will use it
# Discussion of the format of the proposal
# Questions and discussion about the process

SURF 2023

2022-12-21T17:06:23Z

Zmartine:

{{righttoc}}
This page is intended for students interested in working on SURF projects in the Summer of 2023. 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 and up to the start of classes. 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 (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 9 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 18 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.
# If you are selected for a SURF, please be aware of the following information
#* All SURF projects in my group will start on 15 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.
#* Additional information on SURF available here: https://sfp.caltech.edu/programs/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|2023|Formal compositional design of electro-mechanical systems}}
| [[AFOSR T&E]]
| Inigo Incer
|
|-
| {{SURF|2023|Lysate Optimization to Extend Cell-Free Reaction Lifetime}}
| [[NSF Cell Free]]
| Yan Zhang
|
|-
| {{SURF|2023|Membrane Proteins}}
| [[NSF Cell Free]]
| Alex Johnson
|
|-
|-
| {{SURF|2023|Towards a Minimal Model for Virus-Host Interactions}}
| [[NSF Cell Free]]
| Zachary Martinez
|
|-
| {{SURF|2023|Genetically-Programmed Synthetic Cells and Multi-Cellular Machines}}
| [[NSF Cell Free]]
| None
| Multiple projects may be available; competitive selection
|}

SURF 2023: Towards a Minimal Model for Virus-Host Interactions

2022-12-21T17:02:09Z

Zmartine:

'''[[SURF 2023|2023 SURF]] project description'''
__NOTOC__
* Mentor: Richard Murray
* Co-mentors: Zachary Martinez

[[Image:Phage_Infecting_Synthetic_Cell.png|right|600px]]

Main Idea: Engineering a synthetic cell that can be infected by a natural virus.

=== Introduction ===
Viruses are abundant (~1031), ancient (> 4 bya), and evolve quickly (average of 10-3 -
10-8 mutation rate). Due to the immense diversity of viruses, between 60-95% of
viruses are uncharacterized/unidentifiable.1,2,3 Viruses can have global impacts including carbon cycling in the oceans and the spread of deadly
disease during a pandemic. While most may consider viruses to be completely detrimental to
humanity, they have proven to be incredibly useful for biotechnological purposes. From tailored
phage therapy that can fight antibiotic resistant bacterial infections to the therapeutic delivery of base
editors to correct genetic mutations like hemophilia, viruses can be powerful tools.4 While viruses are
undoubtedly important to science, they can be extremely challenging to study. Complex
lifestyles, sheer diversity, host requirement, and numerous other factors contribute to the hurdles
that contemporary virology faces. Through the bottom-up construction of a synthetic host, we can hopefully exert greater control over our experimental design and allow for a more in-depth interrogation of the underlying viral biology. At the same time, with the advancement of synthetic biology, it would be useful to create a viral vector that can engage with synthetic cells. By allowing viruses to interface with synthetic cells, it opens up more complex engineering goals that might involve targeted delivery of genetic payloads (CRISPR/Cas9) to mixed populations of living and synthetic cells. The specificity and robustness of viruses might prove to be a valuable asset in our synthetic cell toolbox.

=== Project Overview ===
In order to build a minimal model for viral infection, we will be using synthetic cells for our hosts and
T4 phage for our virus. Our non-living synthetic cells are typically comprised of cell-free protein
synthesis extract that is encapsulated inside of a lipid vesicle. For this minimal model however, we
will be embedding E. coli protein OmpC into our liposome in order for T4 to recognize the vesicle as a
potential host. While we will first use RNA based toehold switches to determine if successful infection
occurs, the end goal is to use PURErep (platform for transcription-translation-coupled DNA
replication) inside of the vesicles which should allow for viral propagation after infection.5 Lastly, we will investigate whether the viruses are able to escape their host and what mechanism they use to lyse the liposome. If we are able to fully recapitulate the viral life cycle in a synthetic host, this will hopefully lead to a publication.

=== Preferred Skills ===
<ul>
<li> Background in basic molecular biology through coursework </li>
<li> Some experimental experience through coursework with a lab component or research </li>
</ul>
==== References ====
<ol>
<li>Microbiology by numbers. Nat Rev Microbiol. 2011 Aug. https://doi.org/10.1038/nrmicro2644 </li>
<li>Nasir A., et al. Investigating the Concept and Origin of Viruses. 2020 Dec. https://doi.org/10.1016/j.tim.2020.08.003 </li>
<li>Stern A. and Andino R. Viral Evolution. Viral Pathogenesis. 2016 Feb. https://doi.org/10.1016%2FB978-0-12-800964-2.00017-3 </li>
<li>Rosen S., et al. Activity of transgene-produced B-domain-deleted factor VIII in human plasma following AAV5 gene therapy. Blood. 2020 Nov. https://doi.org/10.1182/blood.2020005683 </li>
<li>Libicher K., et al. In vitro self-replication and multicistronic expression of large synthetic genomes. Nature Communications. 2020 Feb. https://doi.org/10.1038/s41467-020-14694-2 </li>
</ol>

SURF 2023: Towards a Minimal Model for Virus-Host Interactions

2022-12-21T17:01:25Z

Zmartine:

'''[[SURF 2023|2023 SURF]] project description'''
__NOTOC__
* Mentor: Richard Murray
* Co-mentors: Zachary Martinez

[[Image:Phage_Infecting_Synthetic_Cell.png|right|800px]]

Main Idea: Engineering a synthetic cell that can be infected by a natural virus.

=== Introduction ===
Viruses are abundant (~1031), ancient (> 4 bya), and evolve quickly (average of 10-3 -
10-8 mutation rate). Due to the immense diversity of viruses, between 60-95% of
viruses are uncharacterized/unidentifiable.1,2,3 Viruses can have global impacts including carbon cycling in the oceans and the spread of deadly
disease during a pandemic. While most may consider viruses to be completely detrimental to
humanity, they have proven to be incredibly useful for biotechnological purposes. From tailored
phage therapy that can fight antibiotic resistant bacterial infections to the therapeutic delivery of base
editors to correct genetic mutations like hemophilia, viruses can be powerful tools.4 While viruses are
undoubtedly important to science, they can be extremely challenging to study. Complex
lifestyles, sheer diversity, host requirement, and numerous other factors contribute to the hurdles
that contemporary virology faces. Through the bottom-up construction of a synthetic host, we can hopefully exert greater control over our experimental design and allow for a more in-depth interrogation of the underlying viral biology. At the same time, with the advancement of synthetic biology, it would be useful to create a viral vector that can engage with synthetic cells. By allowing viruses to interface with synthetic cells, it opens up more complex engineering goals that might involve targeted delivery of genetic payloads (CRISPR/Cas9) to mixed populations of living and synthetic cells. The specificity and robustness of viruses might prove to be a valuable asset in our synthetic cell toolbox.

=== Project Overview ===
In order to build a minimal model for viral infection, we will be using synthetic cells for our hosts and
T4 phage for our virus. Our non-living synthetic cells are typically comprised of cell-free protein
synthesis extract that is encapsulated inside of a lipid vesicle. For this minimal model however, we
will be embedding E. coli protein OmpC into our liposome in order for T4 to recognize the vesicle as a
potential host. While we will first use RNA based toehold switches to determine if successful infection
occurs, the end goal is to use PURErep (platform for transcription-translation-coupled DNA
replication) inside of the vesicles which should allow for viral propagation after infection.5 Lastly, we will investigate whether the viruses are able to escape their host and what mechanism they use to lyse the liposome. If we are able to fully recapitulate the viral life cycle in a synthetic host, this will hopefully lead to a publication.

=== Preferred Skills ===
<ul>
<li> Background in basic molecular biology through coursework </li>
<li> Some experimental experience through coursework with a lab component or research </li>
</ul>
==== References ====
<ol>
<li>Microbiology by numbers. Nat Rev Microbiol. 2011 Aug. https://doi.org/10.1038/nrmicro2644 </li>
<li>Nasir A., et al. Investigating the Concept and Origin of Viruses. 2020 Dec. https://doi.org/10.1016/j.tim.2020.08.003 </li>
<li>Stern A. and Andino R. Viral Evolution. Viral Pathogenesis. 2016 Feb. https://doi.org/10.1016%2FB978-0-12-800964-2.00017-3 </li>
<li>Rosen S., et al. Activity of transgene-produced B-domain-deleted factor VIII in human plasma following AAV5 gene therapy. Blood. 2020 Nov. https://doi.org/10.1182/blood.2020005683 </li>
<li>Libicher K., et al. In vitro self-replication and multicistronic expression of large synthetic genomes. Nature Communications. 2020 Feb. https://doi.org/10.1038/s41467-020-14694-2 </li>
</ol>

File:Phage Infecting Synthetic Cell.png

2022-12-21T17:00:46Z

Zmartine: Zmartine uploaded a new version of File:Phage Infecting Synthetic Cell.png

File:Phage Infecting Synthetic Cell.png

2022-12-21T16:57:24Z

Zmartine: Zmartine uploaded a new version of File:Phage Infecting Synthetic Cell.png

File:Phage Infecting Synthetic Cell.png

2022-12-21T16:56:18Z

Zmartine:

SURF 2023: Towards a Minimal Model for Virus-Host Interactions

2022-12-21T16:35:44Z

Zmartine:

'''[[SURF 2023|2023 SURF]] project description'''
__NOTOC__
* Mentor: Richard Murray
* Co-mentors: Zachary Martinez

Main Idea: Engineering a synthetic cell that can be infected by a natural virus.

=== Introduction ===
Viruses are abundant (~1031), ancient (> 4 bya), and evolve quickly (average of 10-3 -
10-8 mutation rate). Due to the immense diversity of viruses, between 60-95% of
viruses are uncharacterized/unidentifiable.1,2,3 Viruses can have global impacts including carbon cycling in the oceans and the spread of deadly
disease during a pandemic. While most may consider viruses to be completely detrimental to
humanity, they have proven to be incredibly useful for biotechnological purposes. From tailored
phage therapy that can fight antibiotic resistant bacterial infections to the therapeutic delivery of base
editors to correct genetic mutations like hemophilia, viruses can be powerful tools.4 While viruses are
undoubtedly important to science, they can be extremely challenging to study. Complex
lifestyles, sheer diversity, host requirement, and numerous other factors contribute to the hurdles
that contemporary virology faces. Through the bottom-up construction of a synthetic host, we can hopefully exert greater control over our experimental design and allow for a more in-depth interrogation of the underlying viral biology. At the same time, with the advancement of synthetic biology, it would be useful to create a viral vector that can engage with synthetic cells. By allowing viruses to interface with synthetic cells, it opens up more complex engineering goals that might involve targeted delivery of genetic payloads (CRISPR/Cas9) to mixed populations of living and synthetic cells. The specificity and robustness of viruses might prove to be a valuable asset in our synthetic cell toolbox.

=== Project Overview ===
In order to build a minimal model for viral infection, we will be using synthetic cells for our hosts and
T4 phage for our virus. Our non-living synthetic cells are typically comprised of cell-free protein
synthesis extract that is encapsulated inside of a lipid vesicle. For this minimal model however, we
will be embedding E. coli protein OmpC into our liposome in order for T4 to recognize the vesicle as a
potential host. While we will first use RNA based toehold switches to determine if successful infection
occurs, the end goal is to use PURErep (platform for transcription-translation-coupled DNA
replication) inside of the vesicles which should allow for viral propagation after infection.5 Lastly, we will investigate whether the viruses are able to escape their host and what mechanism they use to lyse the liposome. If we are able to fully recapitulate the viral life cycle in a synthetic host, this will hopefully lead to a publication.

=== Preferred Skills ===
<ul>
<li> Background in basic molecular biology through coursework </li>
<li> Some experimental experience through coursework with a lab component or research </li>
</ul>
==== References ====
<ol>
<li>Microbiology by numbers. Nat Rev Microbiol. 2011 Aug. https://doi.org/10.1038/nrmicro2644 </li>
<li>Nasir A., et al. Investigating the Concept and Origin of Viruses. 2020 Dec. https://doi.org/10.1016/j.tim.2020.08.003 </li>
<li>Stern A. and Andino R. Viral Evolution. Viral Pathogenesis. 2016 Feb. https://doi.org/10.1016%2FB978-0-12-800964-2.00017-3 </li>
<li>Rosen S., et al. Activity of transgene-produced B-domain-deleted factor VIII in human plasma following AAV5 gene therapy. Blood. 2020 Nov. https://doi.org/10.1182/blood.2020005683 </li>
<li>Libicher K., et al. In vitro self-replication and multicistronic expression of large synthetic genomes. Nature Communications. 2020 Feb. https://doi.org/10.1038/s41467-020-14694-2 </li>
</ol>

SURF 2023: Towards a Minimal Model for Virus-Host Interactions

2022-12-20T16:13:13Z

Zmartine: /* Project Overview */

= Towards a minimal model for virus-host interactions =

'''[[SURF 2023|2023 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentors: Zachary Martinez

Main Idea:
Engineering a synthetic cell that can be infected by a natural virus.

=== Introduction ===
Viruses are abundant (~1031), ancient (> 4 billion years old), and evolve quickly (average of 10-3 -
10-8 mutation rate). Due to the immense diversity of viruses, between 60-95% of
viruses are uncharacterized/unidentifiable.1,2,3 Viruses can have global impacts including carbon cycling in the oceans and the spread of deadly
disease during a pandemic. While most may consider viruses to be completely detrimental to
humanity, they have proven to be incredibly useful for biotechnological purposes. From tailored
phage therapy that can fight antibiotic resistant bacterial infections to the therapeutic delivery of base
editors to correct genetic mutations like hemophilia, viruses can be powerful tools.4 While viruses are
undoubtedly important to science, they can be extremely challenging to study. Complex
lifestyles, sheer diversity, host requirement, and numerous other factors contribute to the hurdles
that contemporary virology faces. At the same time, with the advancement of synthetic biology, it would be useful to create a viral vector that can engage with synthetic cells. By allowing viruses to interface with synthetic cells, it opens up more complex engineering goals that might involve targeted delivery of genetic payloads (CRISPR/Cas9) to mixed populations of living and synthetic cells. The specificity and robustness of viruses might prove to be a valuable asset in our synthetic cell toolbox.

=== Project Overview ===
In order to build a minimal model for viral infection, we will be using synthetic cells for our hosts and
T4 phage for our virus. Our non-living synthetic cells are typically comprised of cell-free protein
synthesis extract that is encapsulated inside of a lipid vesicle. For this minimal model however, we
will be embedding E. coli protein OmpC into our liposome in order for T4 to recognize the vesicle as a
potential host. While we will first use RNA based toehold switches to determine if successful infection
occurs, the end goal is to use PURErep (platform for transcription-translation-coupled DNA
replication) inside of the vesicles which should allow for viral propagation after infection.5

==== References ====
<ol>
<li>Microbiology by numbers. Nat Rev Microbiol. 2011 Aug </li>
<li>Nasir A., et al. Investigating the Concept and Origin of Viruses. 2020 Dec </li>
<li>Stern A. and Andino R. Viral Evolution. Viral Pathogenesis. 2016 Feb </li>
<li>Rosen S., et al. Activity of transgene-produced B-domain-deleted factor VIII in human plasma following AAV5 gene therapy. Blood. 2020 Nov </li>
<li>Libicher K., et al. In vitro self-replication and multicistronic expression of large synthetic genomes. Nature Communications. 2020 Feb </li>
</ol>

SURF 2023: Towards a Minimal Model for Virus-Host Interactions

2022-12-20T16:12:47Z

Zmartine: Created page with "= Towards a minimal model for virus-host interactions = '''2023 SURF project description''' * Mentor: Richard Murray * Co-mentors: Zachary Martinez Main Idea: Engineering a synthetic cell that can be infected by a natural virus. === Introduction === Viruses are abundant (~1031), ancient (> 4 billion years old), and evolve quickly (average of 10-3 - 10-8 mutation rate). Due to the immense diversity of viruses, bet..."

= Towards a minimal model for virus-host interactions =

'''[[SURF 2023|2023 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentors: Zachary Martinez

Main Idea:
Engineering a synthetic cell that can be infected by a natural virus.

=== Introduction ===
Viruses are abundant (~1031), ancient (> 4 billion years old), and evolve quickly (average of 10-3 -
10-8 mutation rate). Due to the immense diversity of viruses, between 60-95% of
viruses are uncharacterized/unidentifiable.1,2,3 Viruses can have global impacts including carbon cycling in the oceans and the spread of deadly
disease during a pandemic. While most may consider viruses to be completely detrimental to
humanity, they have proven to be incredibly useful for biotechnological purposes. From tailored
phage therapy that can fight antibiotic resistant bacterial infections to the therapeutic delivery of base
editors to correct genetic mutations like hemophilia, viruses can be powerful tools.4 While viruses are
undoubtedly important to science, they can be extremely challenging to study. Complex
lifestyles, sheer diversity, host requirement, and numerous other factors contribute to the hurdles
that contemporary virology faces. At the same time, with the advancement of synthetic biology, it would be useful to create a viral vector that can engage with synthetic cells. By allowing viruses to interface with synthetic cells, it opens up more complex engineering goals that might involve targeted delivery of genetic payloads (CRISPR/Cas9) to mixed populations of living and synthetic cells. The specificity and robustness of viruses might prove to be a valuable asset in our synthetic cell toolbox.

=== Project Overview ===
In order to build a minimal model for viral infection, we will be using synthetic cells for our hosts and
T4 phage for our virus. Our non-living synthetic cells are typically comprised of cell-free protein
synthesis extract that is encapsulated inside of a lipid vesicle. For this minimal model however, we
will be embedding E. coli protein OmpC into our liposome in order for T4 to recognize the vesicle as a
potential host. While we will first use RNA based toehold switches to determine if successful infection
occurs, the end goal is to use PURErep (platform for transcription-translation-coupled DNA
replication) inside of the vesicles which should allow for viral propagation after infection.5

==== References ====
<ol>
<li>Microbiology by numbers. Nat Rev Microbiol. 2011 Aug </li>
<li>Nasir A., et al. Investigating the Concept and Origin of Viruses. 2020 Dec </li>
<li>Stern A. and Andino R. Viral Evolution. Viral Pathogenesis. 2016 Feb </li>
<li>Rosen S., et al. Activity of transgene-produced B-domain-deleted factor VIII in human plasma following AAV5 gene therapy. Blood. 2020 Nov </li>
<li>Libicher K., et al. In vitro self-replication and multicistronic expression of large synthetic genomes. Nature Communications. 2020 Feb </li>
</ol>