Murray Wiki - User contributions [en]

RMM research meetings, May 2025

2025-05-05T17:27:05Z

Dajohnso:

Please sign up for a slot below.

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

12 May (Mon):
* 10 am: Nikos
* 10:45 am: Zach M
* 12:30 pm: Alex J.
* 3:30 pm: David
* 4:15 pm: Yan
* 5:00 pm: Open

SURF discussions, Feb 2023

2023-01-24T22:50:56Z

Dajohnso: /* 7 Feb (Tue) */

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: Kelly & Yan
* 5:30 pm PST: Elna & Alex

|}

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: Membrane Proteins

2022-12-21T06:27:42Z

Dajohnso: /* Research overview */

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

[[Image:integrated-membrane.png|right|100px|frame|Integration of a membrane protein for extracellular interaction. Membrane proteins allow extracellular interactions through: viral targeting of cognate proteins, decoration of cell surface with a variety of external proteins, and identification and possibly import of environmental chemical species.]]
== Introduction ==
This SURF project aims to characterize membrane integrated protein expression in synthetic cells and leverage the results through design of a system to interact with the extracellular space. Taking synthetic biology out of the test tube and integrating it into our everyday life requires questioning the way in which cells interact with the world around them. Membrane integrated proteins provide a wide range of extracellular engagement such as information transmission and surface recognition and binding [[https://royalsocietypublishing.org/doi/10.1098/rstb.2015.0023 1]]. Up to 200 species of proteins are found in the typical bacterial membrane and comprise 70% of the membrane mass [[https://bionumbers.hms.harvard.edu/bionumber.aspx?id=106255 2]]. Traditional microbes, even those well characterized such as E. coli, make interrogating membrane proteins difficult. A recently published protocol suggest the use of synthetic cells, non-living encapsulates of cell-free solutions encased within lipid vesicles, to examine isolated membrane protein activity [[https://link.springer.com/protocol/10.1007/978-1-0716-1998-8_16 3]].

== Research overview ==

The 10–12-week project will be split into three stages The first stage will involve screening a selection of membrane proteins for ability to integrate within the membrane and carry out predicted functions. Ideally, this stage will be completed within 4 weeks and a library of characterized parts will be documents for use in the next stage. The second stage would involve coupling the project to a parallel project designed by another SURF team. 2 weeks are suggested to redesign genetic parts for compatibility and couple the projects. The third and final stage carries the coupled project through characterization and elaboration resulting in system designed from parts and capable of a predetermined goal. One arm of the campaign is laid out below:
* Viral infection of a synthetic cell. Synthetic cells maintain the capability to transcribe and translate genetic components but remain largely featureless on their membrane surface. Successful integration of cognate proteins to known viruses may enable viruses to engage synthetic cells and deliver viral payloads[[https://www.mdpi.com/1422-0067/23/20/12146#B53-ijms-23-12146 4]]. A project in this realm would consider minimum requirements for viral binding and delivery of payload. It would also necessitate a quantitative detection method for payload identification. Additionally, it may capitalize on the delivery of a genetic payload to enable the synthetic cell to expand its capabilities.

Preferred Skills: <br/>
Minimum one biology course with lab <br/>
General Python language experience to analyze results <br/>
Recombinant protein expression

'''References:'''
# Rollauer, S.E., Sooreshjani, M.A., Noinaj, N. and Buchanan, S.K. (2015). Outer membrane protein biogenesis in Gram-negative bacteria. Philosophical Transactions of the Royal Society B: Biological Sciences [https://doi.org/10.1098/rstb.2015.0023 https://doi.org/10.1098/rstb.2015.0023]
# BioNumbers ID [https://bionumbers.hms.harvard.edu/bionumber.aspx?id=106255 106255], "Fraction of cell membrane that is made of proteins by mass"
# Jacobs, M.L., Kamat, N.P. (2022). Cell-Free Membrane Protein Expression into Hybrid Lipid/Polymer Vesicles. In: Karim, A.S., Jewett, M.C. (eds) Cell-Free Gene Expression. Methods in Molecular Biology, vol 2433. Humana, New York, NY. [https://doi.org/10.1007/978-1-0716-1998-8_16 https://doi.org/10.1007/978-1-0716-1998-8_16]
# Taslem Mourosi, J.; Awe, A.; Guo, W.; Batra, H.; Ganesh, H.; Wu, X.; Zhu, J. Understanding Bacteriophage Tail Fiber Interaction with Host Surface Receptor: The Key “Blueprint” for Reprogramming Phage Host Range. Int. J. Mol. Sci. 2022, 23, 12146. [https://doi.org/10.3390/ijms232012146 https://doi.org/10.3390/ijms232012146]

SURF 2023: Membrane Proteins

2022-12-21T03:04:32Z

Dajohnso:

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

[[Image:integrated-membrane.png|right|100px|frame|Integration of a membrane protein for extracellular interaction. Membrane proteins allow extracellular interactions through: viral targeting of cognate proteins, decoration of cell surface with a variety of external proteins, and identification and possibly import of environmental chemical species.]]
== Introduction ==
This SURF project aims to characterize membrane integrated protein expression in synthetic cells and leverage the results through design of a system to interact with the extracellular space. Taking synthetic biology out of the test tube and integrating it into our everyday life requires questioning the way in which cells interact with the world around them. Membrane integrated proteins provide a wide range of extracellular engagement such as information transmission and surface recognition and binding [[https://royalsocietypublishing.org/doi/10.1098/rstb.2015.0023 1]]. Up to 200 species of proteins are found in the typical bacterial membrane and comprise 70% of the membrane mass [[https://bionumbers.hms.harvard.edu/bionumber.aspx?id=106255 2]]. Traditional microbes, even those well characterized such as E. coli, make interrogating membrane proteins difficult. A recently published protocol suggest the use of synthetic cells, non-living encapsulates of cell-free solutions encased within lipid vesicles, to examine isolated membrane protein activity [[https://link.springer.com/protocol/10.1007/978-1-0716-1998-8_16 3]].

== Research overview ==

The 10–12-week project will be split into three stages The first stage will involve screening a selection of membrane proteins for ability to integrate within the membrane and carry out predicted functions. Ideally, this stage will be completed within 4 weeks and a library of characterized parts will be documents for use in the next stage. The second stage would involve coupling the project to a parallel project designed by another SURF team. 2 weeks are suggested to redesign genetic parts for compatibility and couple the projects. The third and final stage carries the coupled project through characterization and elaboration resulting in system designed from parts and capable of a predetermined goal. One arm of the campaign is laid out below:
* Viral infection of a synthetic cell. Synthetic cells maintain the capability to transcribe and translate genetic components but remain largely featureless on their membrane surface. Successful integration of cognate proteins to known viruses may enable viruses to engage synthetic cells and deliver viral payloads[[https://www.mdpi.com/1422-0067/23/20/12146#B53-ijms-23-12146 4]]. A project in this realm would consider minimum requirements for viral binding and delivery of payload. It would also necessitate a quantitative detection method for payload identification. Additionally, it may capitalize on the delivery of a genetic payload to enable the synthetic cell to expand its capabilities.

'''References:'''
# Rollauer, S.E., Sooreshjani, M.A., Noinaj, N. and Buchanan, S.K. (2015). Outer membrane protein biogenesis in Gram-negative bacteria. Philosophical Transactions of the Royal Society B: Biological Sciences [https://doi.org/10.1098/rstb.2015.0023 https://doi.org/10.1098/rstb.2015.0023]
# BioNumbers ID [https://bionumbers.hms.harvard.edu/bionumber.aspx?id=106255 106255], "Fraction of cell membrane that is made of proteins by mass"
# Jacobs, M.L., Kamat, N.P. (2022). Cell-Free Membrane Protein Expression into Hybrid Lipid/Polymer Vesicles. In: Karim, A.S., Jewett, M.C. (eds) Cell-Free Gene Expression. Methods in Molecular Biology, vol 2433. Humana, New York, NY. [https://doi.org/10.1007/978-1-0716-1998-8_16 https://doi.org/10.1007/978-1-0716-1998-8_16]
# Taslem Mourosi, J.; Awe, A.; Guo, W.; Batra, H.; Ganesh, H.; Wu, X.; Zhu, J. Understanding Bacteriophage Tail Fiber Interaction with Host Surface Receptor: The Key “Blueprint” for Reprogramming Phage Host Range. Int. J. Mol. Sci. 2022, 23, 12146. [https://doi.org/10.3390/ijms232012146 https://doi.org/10.3390/ijms232012146]

File:Integrated-membrane.png

2022-12-21T03:02:27Z

Dajohnso: Dajohnso uploaded a new version of File:Integrated-membrane.png

SURF 2023: Membrane Proteins

2022-12-16T23:33:18Z

Dajohnso: Created page with "'''2023 SURF project description''' * Mentor: Richard Murray * Co-mentors: Alex Johnson Integration of a membrane protein for extracellular interaction. == Introduction == This SURF project aims to characterize membrane integrated protein expression in synthetic cells and leverage the results through design of a system to interact with the extracellular space. Taking synthetic biology out of the test tube..."

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

[[Image:integrated-membrane.png|right|100px|frame|Integration of a membrane protein for extracellular interaction.]]
== Introduction ==
This SURF project aims to characterize membrane integrated protein expression in synthetic cells and leverage the results through design of a system to interact with the extracellular space. Taking synthetic biology out of the test tube and integrating it into our everyday life requires questioning the way in which cells interact with the world around them. Membrane integrated proteins provide a wide range of extracellular engagement such as information transmission and surface recognition and binding. Up to 200 species of proteins are found in the typical bacterial membrane and comprise 70% of the membrane mass [[https://bionumbers.hms.harvard.edu/bionumber.aspx?id=106255 1]]. Traditional microbes, even those well characterized such as E. coli, make interrogating membrane proteins difficult. A current approach is the use of synthetic cells, non-living encapsulates of cell-free solutions encased within lipid vesicles. A recent method was published which guides implementation of membrane proteins in synthetic cell systems[[https://link.springer.com/protocol/10.1007/978-1-0716-1998-8_16 2]].

== Research overview ==

The 10–12-week project will be split into three stages The first stage will involve screening a selection of membrane proteins for ability to integrate within the membrane and carry out predicted functions. Ideally, this stage will be completed within 4 weeks and a library of characterized parts will be documents for use in the next stage. The second stage would involve coupling the project to a parallel project designed by another SURF team. 2 weeks are suggested to redesign genetic parts for compatibility and couple the projects. The third and final stage carries the coupled project through characterization and elaboration resulting in system designed from parts and capable of a predetermined goal. An example of a campaign is laid out below:
* Viral infection of a synthetic cell. Synthetic cells maintain the capability to transcribe and translate genetic components but remain largely featureless on their membrane surface. Successful integration of cognate proteins to known viruses may enable viruses to engage synthetic cells and deliver viral payloads. A project in this realm would consider minimum requirements for viral binding and delivery of payload. It would also necessitate a quantitative detection method for payload identification. Additionally, it may capitalize on the delivery of a genetic payload to enable the synthetic cell to expand its capabilities.

'''References:'''
# BioNumbers ID [https://bionumbers.hms.harvard.edu/bionumber.aspx?id=106255 106255], "Fraction of cell membrane that is made of proteins by mass"
# Jacobs, M.L., Kamat, N.P. (2022). Cell-Free Membrane Protein Expression into Hybrid Lipid/Polymer Vesicles. In: Karim, A.S., Jewett, M.C. (eds) Cell-Free Gene Expression. Methods in Molecular Biology, vol 2433. Humana, New York, NY. [https://doi.org/10.1007/978-1-0716-1998-8_16 https://doi.org/10.1007/978-1-0716-1998-8_16]

File:Integrated-membrane.png

2022-12-16T23:15:02Z

Dajohnso: Dajohnso uploaded a new version of File:Integrated-membrane.png

File:Integrated-membrane.png

2022-12-16T23:10:57Z

Dajohnso:

Manos Alexis, Oct 2022

2022-10-21T20:39:45Z

Dajohnso: /* 24 Oct (Mon) */

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

=== 24 Oct (Mon) ===

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

=== 25 Oct (Tue) ===

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

Manos Alexis, Oct 2022

2022-10-21T16:05:48Z

Dajohnso:

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

=== 24 Oct (Mon) ===

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

=== 25 Oct (Tue) ===

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

Nacho Gispert, 10 Aug 2022

2022-08-09T15:28:09Z

Dajohnso:

Ignacio (Nacho) Gispert, a postdoc with Yuval Elani at Imperial will visit on 10 Aug 2022 (Wed).

Schedule:
* 9:15 am: Richard Murray, 109 Steele
* 10:00 am: Group meeting (Nacho + summer students + lab updates)
* 12:00 pm: Lunch with Manisha and Zoila
* 1:30 pm: Zoila
* 2:15 pm: Manisha
* 3:00 pm: CDS Tea
* 3:45 pm: Alex
* 4:30 pm: open
* 5:30 pm: Richard, 109 Steele

Research interests: Nacho's research focuses on artificial/biological hybrid cells, specially on how to replicate cell characteristics and behavior in artificial cell-like entities.