Murray Wiki - User contributions [en]

SURF discussions, Jan 2024

2024-01-22T04:42:23Z

Elarsson: /* 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/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=33% |
==== 22 Jan (Mon) ====
* <s>10:15-10:45 am PST</s>: not available
* 3:00-3:30 pm PST: open
* 3:30-4:00 pm PST: Lovisa, Yan, Zach

| width=33% |

==== 23 Jan (Tue) ====
* 2:00-2:30 pm PST: open
* 2:30-3:00 pm PST: open
* 3:00-3:30 pm PST: open

| width=33% |

==== 24 Jan (Wed) ====
* 9:15-9:45 am PST: Olivia and Elin
* 12:45-1:15 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 2024: Bioengineering toolkit development for genetic alterations in the entomopathogenic nematode symbiont Xenorhabdus griffiniae

2023-12-11T12:02:20Z

Elarsson:

'''[[SURF 2024|SURF 2024]] project description''' __NOTOC__
* Mentor: Richard Murray
* Co-mentor: Elin Larsson

== Background ==

Nematodes are key players in the soil environment, where they feed on bacteria, fungi, insects and plant roots. Therefore, they affect decomposition of organic matter, cycling of nutrients and population size and distribution of other living organisms. Entomopathogenic nematodes (EPN, insect-parasitic) and their symbiotic bacteria are crucial to soil ecology (1,2). The bacterium Xenorhabdus griffiniae is the core symbiont that associates with Steinernema hermaphroditum, an EPN that seeks out and infects insects. The symbiotic pair kills the insect and uses the nutrient from the insect cadaver for reproduction (Fig. 1) (3). To smoothly transition and adapt to complex host environments including the nematode intestine, insect immune system, and decaying insect cadaver, Xenorhabdus bacteria must encode molecular mechanisms to sense the signals from each microenvironment, and regulate its gene expression accordingly. Therefore, it is crucial to characterize gene expression patterns within its relevant ecological niche to better understand and manipulate the bacterial behaviors, such as colonization of nematodes, virulence towards insects, and production of attractants, repellents, and nematicidal metabolites.

[[File:lifecycle.png|500px|thumb|right|Figure 1: The lifecycle of Steinernema hermaphroditum (blue) and its symbiont Xenorhabdus griffiniae (pink) harbored in the nematode receptacle during the host seeking phase.]]

In order to achieve this goal, tool development in both partners is necessary. Although basic genetic tools, such as conjugation and transformation, are available in Xenorhabdus bacteria (4), systematic and efficient toolkits in bioengineering are lacking, which has limited the basic research and application of these species. Current synthetic biology tools have been proven powerful in bioengineering, but are largely limited to bacterial model organisms like E. coli and B. subtilis, and the yeast S.cerevisiae. To understand ecologically relevant interactions among species, the same tools need to become available in non- and emerging model organisms. In this project, we are focusing on systematically establishing a part library (Murray lab expertise) in X. griffiniae to expand the capacity of bioengineering in this species. As a proof of concept, we will adapt a small-scale part library from E. coli in X. griffiniae for in vitro screening of bacterial gene expression. Relevant candidate bacterial strains will be tested further in vivo using its natural mutualistic host nematode (Cao lab expertise). The proposed effort in tool development will be crucial to elucidating signaling between the nematode and bacteria in this partnership and potentially expand its application to soil microbe engineering.

== Research overview ==

The SURF student will use molecular biology techniques to generate a genetic part library, a collection of promoters, ribosome binding sites, fluorescent proteins with different properties, for X. griffiniae, largely using the pre-existing part library available in the lab for E. coli. Even though genetic parts often function across species, there are many examples where they function differently or not at all. Therefore, it is important to characterize a range of the aforementioned parts in the genetic background of the species of interest, to be able to predictably build different variants of genetic constructs.

[[File:SURF2024_Fig2.png|500px|thumb|right|Figure 2: Schematic of Aim 1 and 2.]]

=== Aim 1: Creating a genetic part library for X. griffiniae ===

The first aim of the project is to generate a small part library that is compatible with the 3G cloning pipeline (5). First, Xenorhabdus vectors will be modified to fit into the E. coli cloning pipeline. The vectors can then be used to build a range of constructs using the parts already available in the Murray lab part library .
The plasmids will then be integrated on the X. griffiniae genome using conjugation (or trying to develop electroporation if this is preferable).

=== Aim 2: Characterization of parts in vitro ===

After creating a library of parts, these can be characterized in a plate reader assay. The strains will be grown in minimal medium (+/- inducers where appropriate). The functionality and rank order of the parts in this species can then be determined.

=== Aim 3: Characterization of parts in vivo ===

Last of all we want to see if the in vitro behavior can translate to an ecologically relevant context. To do this, a genetic construct will be designed for bacteria colonizing the worm receptacle. The in vitro performance can be determined using fluorescence microscopy or worm viability depending on the intended construct output.

'''SURF student qualifications:'''
* Prerequisite coursework: Bi1x, Bi8/9 (or similar introductory biology course that provides a basic foundation in molecular biology)
*Preferred: Familiarity with synthetic biology/circuit design
*Basic familiarity with coding in Python

'''References:'''

1. Abd-Elgawad MMM. spp.: An Overview of the Useful Facets of Mutualistic Bacteria of Entomopathogenic Nematodes. Life [Internet]. 2022 Aug 31;12(9). Available from: http://dx.doi.org/10.3390/life12091360

2. Kenney E, Eleftherianos I. Entomopathogenic and plant pathogenic nematodes as opposing forces in agriculture. Int J Parasitol. 2016 Jan;46(1):13–9.

3. Cao M, Schwartz HT, Tan CH, Sternberg PW. The entomopathogenic nematode Steinernema hermaphroditum is a self-fertilizing hermaphrodite and a genetically tractable system for the study of parasitic and mutualistic symbiosis. Genetics [Internet]. 2022 Jan 4;220(1). Available from: http://dx.doi.org/10.1093/genetics/iyab170

4. Alani OS, Cao M, Goodrich-Blair H, Heppert JK. Conjugation and transposon mutagenesis of HGB2511, the bacterial symbiont of the nematode (India). MicroPubl Biol [Internet]. 2023 Apr 25;2023. Available from: http://dx.doi.org/10.17912/micropub.biology.000772

5. Halleran AD, Swaminathan A, Murray RM. Single Day Construction of Multigene Circuits with 3G Assembly. ACS Synth Biol. 2018 May 18;7(5):1477–80.

File:SURF2024 Fig2.png

2023-12-11T11:59:12Z

Elarsson:

SURF 2024: Bioengineering toolkit development for genetic alterations in the entomopathogenic nematode symbiont Xenorhabdus griffiniae

2023-12-11T02:10:35Z

Elarsson: /* Background */

'''[[SURF 2024|SURF 2024]] project description''' __NOTOC__
* Mentor: Richard Murray
* Co-mentor: Elin Larsson

== Background ==

Nematodes are key players in the soil environment, where they feed on bacteria, fungi, insects and plant roots. Therefore, they affect decomposition of organic matter, cycling of nutrients and population size and distribution of other living organisms. Entomopathogenic nematodes (EPN, insect-parasitic) and their symbiotic bacteria are crucial to soil ecology (1,2). The bacterium Xenorhabdus griffiniae is the core symbiont that associates with Steinernema hermaphroditum, an EPN that seeks out and infects insects. The symbiotic pair kills the insect and uses the nutrient from the insect cadaver for reproduction (Fig. 1) (3). To smoothly transition and adapt to complex host environments including the nematode intestine, insect immune system, and decaying insect cadaver, Xenorhabdus bacteria must encode molecular mechanisms to sense the signals from each microenvironment, and regulate its gene expression accordingly. Therefore, it is crucial to characterize gene expression patterns within its relevant ecological niche to better understand and manipulate the bacterial behaviors, such as colonization of nematodes, virulence towards insects, and production of attractants, repellents, and nematicidal metabolites.

[[File:lifecycle.png|500px|thumb|right|Figure 1: The lifecycle of Steinernema hermaphroditum (blue) and its symbiont Xenorhabdus griffiniae (pink) harbored in the nematode receptacle during the host seeking phase.]]

In order to achieve this goal, tool development in both partners is necessary. Although basic genetic tools, such as conjugation and transformation, are available in Xenorhabdus bacteria (4), systematic and efficient toolkits in bioengineering are lacking, which has limited the basic research and application of these species. Current synthetic biology tools have been proven powerful in bioengineering, but are largely limited to bacterial model organisms like E. coli and B. subtilis, and the yeast S.cerevisiae. To understand ecologically relevant interactions among species, the same tools need to become available in non- and emerging model organisms. In this project, we are focusing on systematically establishing a part library (Murray lab expertise) in X. griffiniae to expand the capacity of bioengineering in this species. As a proof of concept, we will adapt a small-scale part library from E. coli in X. griffiniae for in vitro screening of bacterial gene expression. Relevant candidate bacterial strains will be tested further in vivo using its natural mutualistic host nematode (Cao lab expertise). The proposed effort in tool development will be crucial to elucidating signaling between the nematode and bacteria in this partnership and potentially expand its application to soil microbe engineering.

== Research overview ==

The SURF student will use molecular biology techniques to generate a genetic part library, a collection of promoters, ribosome binding sites, fluorescent proteins with different properties, for X. griffiniae, largely using the pre-existing part library available in the lab for E. coli. Even though genetic parts often function across species, there are many examples where they function differently or not at all. Therefore, it is important to characterize a range of the aforementioned parts in the genetic background of the species of interest, to be able to predictably build different variants of genetic constructs.

=== Aim 1: Creating a genetic part library for X. griffiniae ===

The first aim of the project is to generate a small part library that is compatible with the 3G cloning pipeline (5). First, Xenorhabdus vectors will be modified to fit into the E. coli cloning pipeline. The vectors can then be used to build a range of constructs using the parts already available in the Murray lab part library .
The plasmids will then be integrated on the X. griffiniae genome using conjugation (or trying to develop electroporation if this is preferable).

=== Aim 2: Characterization of parts in vitro ===

After creating a library of parts, these can be characterized in a plate reader assay. The strains will be grown in minimal medium (+/- inducers where appropriate). The functionality and rank order of the parts in this species can then be determined.

=== Aim 3: Characterization of parts in vivo ===

Last of all we want to see if the in vitro behavior can translate to an ecologically relevant context. To do this, a genetic construct will be designed for bacteria colonizing the worm receptacle. The in vitro performance can be determined using fluorescence microscopy or worm viability depending on the intended construct output.

'''SURF student qualifications:'''
* Prerequisite coursework: Bi1x, Bi8/9 (or similar introductory biology course that provides a basic foundation in molecular biology)
*Preferred: Familiarity with synthetic biology/circuit design
*Basic familiarity with coding in Python

'''References:'''

1. Abd-Elgawad MMM. spp.: An Overview of the Useful Facets of Mutualistic Bacteria of Entomopathogenic Nematodes. Life [Internet]. 2022 Aug 31;12(9). Available from: http://dx.doi.org/10.3390/life12091360

2. Kenney E, Eleftherianos I. Entomopathogenic and plant pathogenic nematodes as opposing forces in agriculture. Int J Parasitol. 2016 Jan;46(1):13–9.

3. Cao M, Schwartz HT, Tan CH, Sternberg PW. The entomopathogenic nematode Steinernema hermaphroditum is a self-fertilizing hermaphrodite and a genetically tractable system for the study of parasitic and mutualistic symbiosis. Genetics [Internet]. 2022 Jan 4;220(1). Available from: http://dx.doi.org/10.1093/genetics/iyab170

4. Alani OS, Cao M, Goodrich-Blair H, Heppert JK. Conjugation and transposon mutagenesis of HGB2511, the bacterial symbiont of the nematode (India). MicroPubl Biol [Internet]. 2023 Apr 25;2023. Available from: http://dx.doi.org/10.17912/micropub.biology.000772

5. Halleran AD, Swaminathan A, Murray RM. Single Day Construction of Multigene Circuits with 3G Assembly. ACS Synth Biol. 2018 May 18;7(5):1477–80.

SURF 2024: Bioengineering toolkit development for genetic alterations in the entomopathogenic nematode symbiont Xenorhabdus griffiniae

2023-12-11T02:09:40Z

Elarsson: /* Background */

'''[[SURF 2024|SURF 2024]] project description''' __NOTOC__
* Mentor: Richard Murray
* Co-mentor: Elin Larsson

== Background ==

Nematodes are key players in the soil environment, where they feed on bacteria, fungi, insects and plant roots. Therefore, they affect decomposition of organic matter, cycling of nutrients and population size and distribution of other living organisms. Entomopathogenic nematodes (EPN, insect-parasitic) and their symbiotic bacteria are crucial to soil ecology (1,2). The bacterium Xenorhabdus griffiniae is the core symbiont that associates with Steinernema hermaphroditum, an EPN that seeks out and infects insects. The symbiotic pair kills the insect and uses the nutrient from the insect cadaver for reproduction (Fig. 1) (3). To smoothly transition and adapt to complex host environments including the nematode intestine, insect immune system, and decaying insect cadaver, Xenorhabdus bacteria must encode molecular mechanisms to sense the signals from each microenvironment, and regulate its gene expression accordingly. Therefore, it is crucial to characterize gene expression patterns within its relevant ecological niche to better understand and manipulate the bacterial behaviors, such as colonization of nematodes, virulence towards insects, and production of attractants, repellents, and nematicidal metabolites.

[[File:lifecycle.png|200px|thumb|right|Caption]]

In order to achieve this goal, tool development in both partners is necessary. Although basic genetic tools, such as conjugation and transformation, are available in Xenorhabdus bacteria (4), systematic and efficient toolkits in bioengineering are lacking, which has limited the basic research and application of these species. Current synthetic biology tools have been proven powerful in bioengineering, but are largely limited to bacterial model organisms like E. coli and B. subtilis, and the yeast S.cerevisiae. To understand ecologically relevant interactions among species, the same tools need to become available in non- and emerging model organisms. In this project, we are focusing on systematically establishing a part library (Murray lab expertise) in X. griffiniae to expand the capacity of bioengineering in this species. As a proof of concept, we will adapt a small-scale part library from E. coli in X. griffiniae for in vitro screening of bacterial gene expression. Relevant candidate bacterial strains will be tested further in vivo using its natural mutualistic host nematode (Cao lab expertise). The proposed effort in tool development will be crucial to elucidating signaling between the nematode and bacteria in this partnership and potentially expand its application to soil microbe engineering.

== Research overview ==

The SURF student will use molecular biology techniques to generate a genetic part library, a collection of promoters, ribosome binding sites, fluorescent proteins with different properties, for X. griffiniae, largely using the pre-existing part library available in the lab for E. coli. Even though genetic parts often function across species, there are many examples where they function differently or not at all. Therefore, it is important to characterize a range of the aforementioned parts in the genetic background of the species of interest, to be able to predictably build different variants of genetic constructs.

=== Aim 1: Creating a genetic part library for X. griffiniae ===

The first aim of the project is to generate a small part library that is compatible with the 3G cloning pipeline (5). First, Xenorhabdus vectors will be modified to fit into the E. coli cloning pipeline. The vectors can then be used to build a range of constructs using the parts already available in the Murray lab part library .
The plasmids will then be integrated on the X. griffiniae genome using conjugation (or trying to develop electroporation if this is preferable).

=== Aim 2: Characterization of parts in vitro ===

After creating a library of parts, these can be characterized in a plate reader assay. The strains will be grown in minimal medium (+/- inducers where appropriate). The functionality and rank order of the parts in this species can then be determined.

=== Aim 3: Characterization of parts in vivo ===

Last of all we want to see if the in vitro behavior can translate to an ecologically relevant context. To do this, a genetic construct will be designed for bacteria colonizing the worm receptacle. The in vitro performance can be determined using fluorescence microscopy or worm viability depending on the intended construct output.

'''SURF student qualifications:'''
* Prerequisite coursework: Bi1x, Bi8/9 (or similar introductory biology course that provides a basic foundation in molecular biology)
*Preferred: Familiarity with synthetic biology/circuit design
*Basic familiarity with coding in Python

'''References:'''

1. Abd-Elgawad MMM. spp.: An Overview of the Useful Facets of Mutualistic Bacteria of Entomopathogenic Nematodes. Life [Internet]. 2022 Aug 31;12(9). Available from: http://dx.doi.org/10.3390/life12091360

2. Kenney E, Eleftherianos I. Entomopathogenic and plant pathogenic nematodes as opposing forces in agriculture. Int J Parasitol. 2016 Jan;46(1):13–9.

3. Cao M, Schwartz HT, Tan CH, Sternberg PW. The entomopathogenic nematode Steinernema hermaphroditum is a self-fertilizing hermaphrodite and a genetically tractable system for the study of parasitic and mutualistic symbiosis. Genetics [Internet]. 2022 Jan 4;220(1). Available from: http://dx.doi.org/10.1093/genetics/iyab170

4. Alani OS, Cao M, Goodrich-Blair H, Heppert JK. Conjugation and transposon mutagenesis of HGB2511, the bacterial symbiont of the nematode (India). MicroPubl Biol [Internet]. 2023 Apr 25;2023. Available from: http://dx.doi.org/10.17912/micropub.biology.000772

5. Halleran AD, Swaminathan A, Murray RM. Single Day Construction of Multigene Circuits with 3G Assembly. ACS Synth Biol. 2018 May 18;7(5):1477–80.

File:Lifecycle.png

2023-12-11T02:09:06Z

Elarsson:

SURF 2024: Bioengineering toolkit development for genetic alterations in the entomopathogenic nematode symbiont Xenorhabdus griffiniae

2023-12-11T02:02:00Z

Elarsson: /* Research overview */

'''[[SURF 2024|SURF 2024]] project description''' __NOTOC__
* Mentor: Richard Murray
* Co-mentor: Elin Larsson

== Background ==

Nematodes are key players in the soil environment, where they feed on bacteria, fungi, insects and plant roots. Therefore, they affect decomposition of organic matter, cycling of nutrients and population size and distribution of other living organisms. Entomopathogenic nematodes (EPN, insect-parasitic) and their symbiotic bacteria are crucial to soil ecology (1,2). The bacterium Xenorhabdus griffiniae is the core symbiont that associates with Steinernema hermaphroditum, an EPN that seeks out and infects insects. The symbiotic pair kills the insect and uses the nutrient from the insect cadaver for reproduction (Fig. 1) (3). To smoothly transition and adapt to complex host environments including the nematode intestine, insect immune system, and decaying insect cadaver, Xenorhabdus bacteria must encode molecular mechanisms to sense the signals from each microenvironment, and regulate its gene expression accordingly. Therefore, it is crucial to characterize gene expression patterns within its relevant ecological niche to better understand and manipulate the bacterial behaviors, such as colonization of nematodes, virulence towards insects, and production of attractants, repellents, and nematicidal metabolites.

[Figure 1]

In order to achieve this goal, tool development in both partners is necessary. Although basic genetic tools, such as conjugation and transformation, are available in Xenorhabdus bacteria (4), systematic and efficient toolkits in bioengineering are lacking, which has limited the basic research and application of these species. Current synthetic biology tools have been proven powerful in bioengineering, but are largely limited to bacterial model organisms like E. coli and B. subtilis, and the yeast S.cerevisiae. To understand ecologically relevant interactions among species, the same tools need to become available in non- and emerging model organisms. In this project, we are focusing on systematically establishing a part library (Murray lab expertise) in X. griffiniae to expand the capacity of bioengineering in this species. As a proof of concept, we will adapt a small-scale part library from E. coli in X. griffiniae for in vitro screening of bacterial gene expression. Relevant candidate bacterial strains will be tested further in vivo using its natural mutualistic host nematode (Cao lab expertise). The proposed effort in tool development will be crucial to elucidating signaling between the nematode and bacteria in this partnership and potentially expand its application to soil microbe engineering.

== Research overview ==

The SURF student will use molecular biology techniques to generate a genetic part library, a collection of promoters, ribosome binding sites, fluorescent proteins with different properties, for X. griffiniae, largely using the pre-existing part library available in the lab for E. coli. Even though genetic parts often function across species, there are many examples where they function differently or not at all. Therefore, it is important to characterize a range of the aforementioned parts in the genetic background of the species of interest, to be able to predictably build different variants of genetic constructs.

=== Aim 1: Creating a genetic part library for X. griffiniae ===

The first aim of the project is to generate a small part library that is compatible with the 3G cloning pipeline (5). First, Xenorhabdus vectors will be modified to fit into the E. coli cloning pipeline. The vectors can then be used to build a range of constructs using the parts already available in the Murray lab part library .
The plasmids will then be integrated on the X. griffiniae genome using conjugation (or trying to develop electroporation if this is preferable).

=== Aim 2: Characterization of parts in vitro ===

After creating a library of parts, these can be characterized in a plate reader assay. The strains will be grown in minimal medium (+/- inducers where appropriate). The functionality and rank order of the parts in this species can then be determined.

=== Aim 3: Characterization of parts in vivo ===

Last of all we want to see if the in vitro behavior can translate to an ecologically relevant context. To do this, a genetic construct will be designed for bacteria colonizing the worm receptacle. The in vitro performance can be determined using fluorescence microscopy or worm viability depending on the intended construct output.

'''SURF student qualifications:'''
* Prerequisite coursework: Bi1x, Bi8/9 (or similar introductory biology course that provides a basic foundation in molecular biology)
*Preferred: Familiarity with synthetic biology/circuit design
*Basic familiarity with coding in Python

'''References:'''

1. Abd-Elgawad MMM. spp.: An Overview of the Useful Facets of Mutualistic Bacteria of Entomopathogenic Nematodes. Life [Internet]. 2022 Aug 31;12(9). Available from: http://dx.doi.org/10.3390/life12091360

2. Kenney E, Eleftherianos I. Entomopathogenic and plant pathogenic nematodes as opposing forces in agriculture. Int J Parasitol. 2016 Jan;46(1):13–9.

3. Cao M, Schwartz HT, Tan CH, Sternberg PW. The entomopathogenic nematode Steinernema hermaphroditum is a self-fertilizing hermaphrodite and a genetically tractable system for the study of parasitic and mutualistic symbiosis. Genetics [Internet]. 2022 Jan 4;220(1). Available from: http://dx.doi.org/10.1093/genetics/iyab170

4. Alani OS, Cao M, Goodrich-Blair H, Heppert JK. Conjugation and transposon mutagenesis of HGB2511, the bacterial symbiont of the nematode (India). MicroPubl Biol [Internet]. 2023 Apr 25;2023. Available from: http://dx.doi.org/10.17912/micropub.biology.000772

5. Halleran AD, Swaminathan A, Murray RM. Single Day Construction of Multigene Circuits with 3G Assembly. ACS Synth Biol. 2018 May 18;7(5):1477–80.

SURF 2024: Bioengineering toolkit development for genetic alterations in the entomopathogenic nematode symbiont Xenorhabdus griffiniae

2023-12-11T02:01:43Z

Elarsson: /* Research overview */

'''[[SURF 2024|SURF 2024]] project description''' __NOTOC__
* Mentor: Richard Murray
* Co-mentor: Elin Larsson

== Background ==

Nematodes are key players in the soil environment, where they feed on bacteria, fungi, insects and plant roots. Therefore, they affect decomposition of organic matter, cycling of nutrients and population size and distribution of other living organisms. Entomopathogenic nematodes (EPN, insect-parasitic) and their symbiotic bacteria are crucial to soil ecology (1,2). The bacterium Xenorhabdus griffiniae is the core symbiont that associates with Steinernema hermaphroditum, an EPN that seeks out and infects insects. The symbiotic pair kills the insect and uses the nutrient from the insect cadaver for reproduction (Fig. 1) (3). To smoothly transition and adapt to complex host environments including the nematode intestine, insect immune system, and decaying insect cadaver, Xenorhabdus bacteria must encode molecular mechanisms to sense the signals from each microenvironment, and regulate its gene expression accordingly. Therefore, it is crucial to characterize gene expression patterns within its relevant ecological niche to better understand and manipulate the bacterial behaviors, such as colonization of nematodes, virulence towards insects, and production of attractants, repellents, and nematicidal metabolites.

[Figure 1]

In order to achieve this goal, tool development in both partners is necessary. Although basic genetic tools, such as conjugation and transformation, are available in Xenorhabdus bacteria (4), systematic and efficient toolkits in bioengineering are lacking, which has limited the basic research and application of these species. Current synthetic biology tools have been proven powerful in bioengineering, but are largely limited to bacterial model organisms like E. coli and B. subtilis, and the yeast S.cerevisiae. To understand ecologically relevant interactions among species, the same tools need to become available in non- and emerging model organisms. In this project, we are focusing on systematically establishing a part library (Murray lab expertise) in X. griffiniae to expand the capacity of bioengineering in this species. As a proof of concept, we will adapt a small-scale part library from E. coli in X. griffiniae for in vitro screening of bacterial gene expression. Relevant candidate bacterial strains will be tested further in vivo using its natural mutualistic host nematode (Cao lab expertise). The proposed effort in tool development will be crucial to elucidating signaling between the nematode and bacteria in this partnership and potentially expand its application to soil microbe engineering.

== Research overview ==

The SURF student will use molecular biology techniques to generate a genetic part library, a collection of promoters, ribosome binding sites, fluorescent proteins with different properties, for X. griffiniae, largely using the pre-existing part library available in the lab for E. coli. Even though genetic parts often function across species, there are many examples where they function differently or not at all. Therefore, it is important to characterize a range of the aforementioned parts in the genetic background of the species of interest, to be able to predictably build different variants of genetic constructs.

/Users/elinlarsson/Downloads/SURF proposal graphic.png

=== Aim 1: Creating a genetic part library for X. griffiniae ===

The first aim of the project is to generate a small part library that is compatible with the 3G cloning pipeline (5). First, Xenorhabdus vectors will be modified to fit into the E. coli cloning pipeline. The vectors can then be used to build a range of constructs using the parts already available in the Murray lab part library .
The plasmids will then be integrated on the X. griffiniae genome using conjugation (or trying to develop electroporation if this is preferable).

=== Aim 2: Characterization of parts in vitro ===

After creating a library of parts, these can be characterized in a plate reader assay. The strains will be grown in minimal medium (+/- inducers where appropriate). The functionality and rank order of the parts in this species can then be determined.

=== Aim 3: Characterization of parts in vivo ===

Last of all we want to see if the in vitro behavior can translate to an ecologically relevant context. To do this, a genetic construct will be designed for bacteria colonizing the worm receptacle. The in vitro performance can be determined using fluorescence microscopy or worm viability depending on the intended construct output.

'''SURF student qualifications:'''
* Prerequisite coursework: Bi1x, Bi8/9 (or similar introductory biology course that provides a basic foundation in molecular biology)
*Preferred: Familiarity with synthetic biology/circuit design
*Basic familiarity with coding in Python

'''References:'''

1. Abd-Elgawad MMM. spp.: An Overview of the Useful Facets of Mutualistic Bacteria of Entomopathogenic Nematodes. Life [Internet]. 2022 Aug 31;12(9). Available from: http://dx.doi.org/10.3390/life12091360

2. Kenney E, Eleftherianos I. Entomopathogenic and plant pathogenic nematodes as opposing forces in agriculture. Int J Parasitol. 2016 Jan;46(1):13–9.

3. Cao M, Schwartz HT, Tan CH, Sternberg PW. The entomopathogenic nematode Steinernema hermaphroditum is a self-fertilizing hermaphrodite and a genetically tractable system for the study of parasitic and mutualistic symbiosis. Genetics [Internet]. 2022 Jan 4;220(1). Available from: http://dx.doi.org/10.1093/genetics/iyab170

4. Alani OS, Cao M, Goodrich-Blair H, Heppert JK. Conjugation and transposon mutagenesis of HGB2511, the bacterial symbiont of the nematode (India). MicroPubl Biol [Internet]. 2023 Apr 25;2023. Available from: http://dx.doi.org/10.17912/micropub.biology.000772

5. Halleran AD, Swaminathan A, Murray RM. Single Day Construction of Multigene Circuits with 3G Assembly. ACS Synth Biol. 2018 May 18;7(5):1477–80.

SURF 2024

2023-12-11T01:59:27Z

Elarsson: /* List of available projects */

{{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|2023|Genetically-Programmed Synthetic Cells and Multi-Cellular Machines}}
| [[NSF Cell Free]]
| None
| Multiple projects may be available; competitive selection
|-
| {{SURF|2024|Bioengineering toolkit development for genetic alterations in the entomopathogenic nematode symbiont Xenorhabdus griffiniae}}
| None
| Elin Larsson
|
|}

SURF 2024: Bioengineering toolkit development for genetic alterations in the entomopathogenic nematode symbiont Xenorhabdus griffiniae

2023-12-11T01:56:56Z

Elarsson: /* Research overview */

'''[[SURF 2024|SURF 2024]] project description''' __NOTOC__
* Mentor: Richard Murray
* Co-mentor: Elin Larsson

== Background ==

Nematodes are key players in the soil environment, where they feed on bacteria, fungi, insects and plant roots. Therefore, they affect decomposition of organic matter, cycling of nutrients and population size and distribution of other living organisms. Entomopathogenic nematodes (EPN, insect-parasitic) and their symbiotic bacteria are crucial to soil ecology (1,2). The bacterium Xenorhabdus griffiniae is the core symbiont that associates with Steinernema hermaphroditum, an EPN that seeks out and infects insects. The symbiotic pair kills the insect and uses the nutrient from the insect cadaver for reproduction (Fig. 1) (3). To smoothly transition and adapt to complex host environments including the nematode intestine, insect immune system, and decaying insect cadaver, Xenorhabdus bacteria must encode molecular mechanisms to sense the signals from each microenvironment, and regulate its gene expression accordingly. Therefore, it is crucial to characterize gene expression patterns within its relevant ecological niche to better understand and manipulate the bacterial behaviors, such as colonization of nematodes, virulence towards insects, and production of attractants, repellents, and nematicidal metabolites.

[Figure 1]

In order to achieve this goal, tool development in both partners is necessary. Although basic genetic tools, such as conjugation and transformation, are available in Xenorhabdus bacteria (4), systematic and efficient toolkits in bioengineering are lacking, which has limited the basic research and application of these species. Current synthetic biology tools have been proven powerful in bioengineering, but are largely limited to bacterial model organisms like E. coli and B. subtilis, and the yeast S.cerevisiae. To understand ecologically relevant interactions among species, the same tools need to become available in non- and emerging model organisms. In this project, we are focusing on systematically establishing a part library (Murray lab expertise) in X. griffiniae to expand the capacity of bioengineering in this species. As a proof of concept, we will adapt a small-scale part library from E. coli in X. griffiniae for in vitro screening of bacterial gene expression. Relevant candidate bacterial strains will be tested further in vivo using its natural mutualistic host nematode (Cao lab expertise). The proposed effort in tool development will be crucial to elucidating signaling between the nematode and bacteria in this partnership and potentially expand its application to soil microbe engineering.

== Research overview ==

The SURF student will use molecular biology techniques to generate a genetic part library, a collection of promoters, ribosome binding sites, fluorescent proteins with different properties, for X. griffiniae, largely using the pre-existing part library available in the lab for E. coli. Even though genetic parts often function across species, there are many examples where they function differently or not at all. Therefore, it is important to characterize a range of the aforementioned parts in the genetic background of the species of interest, to be able to predictably build different variants of genetic constructs.

[Figure 2]

=== Aim 1: Creating a genetic part library for X. griffiniae ===

The first aim of the project is to generate a small part library that is compatible with the 3G cloning pipeline (5). First, Xenorhabdus vectors will be modified to fit into the E. coli cloning pipeline. The vectors can then be used to build a range of constructs using the parts already available in the Murray lab part library .
The plasmids will then be integrated on the X. griffiniae genome using conjugation (or trying to develop electroporation if this is preferable).

=== Aim 2: Characterization of parts in vitro ===

After creating a library of parts, these can be characterized in a plate reader assay. The strains will be grown in minimal medium (+/- inducers where appropriate). The functionality and rank order of the parts in this species can then be determined.

=== Aim 3: Characterization of parts in vivo ===

Last of all we want to see if the in vitro behavior can translate to an ecologically relevant context. To do this, a genetic construct will be designed for bacteria colonizing the worm receptacle. The in vitro performance can be determined using fluorescence microscopy or worm viability depending on the intended construct output.

'''SURF student qualifications:'''
* Prerequisite coursework: Bi1x, Bi8/9 (or similar introductory biology course that provides a basic foundation in molecular biology)
*Preferred: Familiarity with synthetic biology/circuit design
*Basic familiarity with coding in Python

'''References:'''

1. Abd-Elgawad MMM. spp.: An Overview of the Useful Facets of Mutualistic Bacteria of Entomopathogenic Nematodes. Life [Internet]. 2022 Aug 31;12(9). Available from: http://dx.doi.org/10.3390/life12091360

2. Kenney E, Eleftherianos I. Entomopathogenic and plant pathogenic nematodes as opposing forces in agriculture. Int J Parasitol. 2016 Jan;46(1):13–9.

3. Cao M, Schwartz HT, Tan CH, Sternberg PW. The entomopathogenic nematode Steinernema hermaphroditum is a self-fertilizing hermaphrodite and a genetically tractable system for the study of parasitic and mutualistic symbiosis. Genetics [Internet]. 2022 Jan 4;220(1). Available from: http://dx.doi.org/10.1093/genetics/iyab170

4. Alani OS, Cao M, Goodrich-Blair H, Heppert JK. Conjugation and transposon mutagenesis of HGB2511, the bacterial symbiont of the nematode (India). MicroPubl Biol [Internet]. 2023 Apr 25;2023. Available from: http://dx.doi.org/10.17912/micropub.biology.000772

5. Halleran AD, Swaminathan A, Murray RM. Single Day Construction of Multigene Circuits with 3G Assembly. ACS Synth Biol. 2018 May 18;7(5):1477–80.

SURF 2024: Bioengineering toolkit development for genetic alterations in the entomopathogenic nematode symbiont Xenorhabdus griffiniae

2023-12-11T01:56:36Z

Elarsson: /* Research overview */

'''[[SURF 2024|SURF 2024]] project description''' __NOTOC__
* Mentor: Richard Murray
* Co-mentor: Elin Larsson

== Background ==

Nematodes are key players in the soil environment, where they feed on bacteria, fungi, insects and plant roots. Therefore, they affect decomposition of organic matter, cycling of nutrients and population size and distribution of other living organisms. Entomopathogenic nematodes (EPN, insect-parasitic) and their symbiotic bacteria are crucial to soil ecology (1,2). The bacterium Xenorhabdus griffiniae is the core symbiont that associates with Steinernema hermaphroditum, an EPN that seeks out and infects insects. The symbiotic pair kills the insect and uses the nutrient from the insect cadaver for reproduction (Fig. 1) (3). To smoothly transition and adapt to complex host environments including the nematode intestine, insect immune system, and decaying insect cadaver, Xenorhabdus bacteria must encode molecular mechanisms to sense the signals from each microenvironment, and regulate its gene expression accordingly. Therefore, it is crucial to characterize gene expression patterns within its relevant ecological niche to better understand and manipulate the bacterial behaviors, such as colonization of nematodes, virulence towards insects, and production of attractants, repellents, and nematicidal metabolites.

[Figure 1]

In order to achieve this goal, tool development in both partners is necessary. Although basic genetic tools, such as conjugation and transformation, are available in Xenorhabdus bacteria (4), systematic and efficient toolkits in bioengineering are lacking, which has limited the basic research and application of these species. Current synthetic biology tools have been proven powerful in bioengineering, but are largely limited to bacterial model organisms like E. coli and B. subtilis, and the yeast S.cerevisiae. To understand ecologically relevant interactions among species, the same tools need to become available in non- and emerging model organisms. In this project, we are focusing on systematically establishing a part library (Murray lab expertise) in X. griffiniae to expand the capacity of bioengineering in this species. As a proof of concept, we will adapt a small-scale part library from E. coli in X. griffiniae for in vitro screening of bacterial gene expression. Relevant candidate bacterial strains will be tested further in vivo using its natural mutualistic host nematode (Cao lab expertise). The proposed effort in tool development will be crucial to elucidating signaling between the nematode and bacteria in this partnership and potentially expand its application to soil microbe engineering.

== Research overview ==

The SURF student will use molecular biology techniques to generate a genetic part library, a collection of promoters, ribosome binding sites, fluorescent proteins with different properties, for X. griffiniae, largely using the pre-existing part library available in the lab for E. coli. Even though genetic parts often function across species, there are many examples where they function differently or not at all. Therefore, it is important to characterize a range of the aforementioned parts in the genetic background of the species of interest, to be able to predictably build different variants of genetic constructs.

[Figure 2]

=== Aim 1: Creating a genetic part library for X. griffiniae ===

The first aim of the project is to generate a small part library that is compatible with the 3G cloning pipeline (5). First, Xenorhabdus vectors will be modified to fit into the E. coli cloning pipeline. The vectors can then be used to build a range of constructs using the parts already available in the Murray lab part library .
The plasmids will then be integrated on the X. griffiniae genome using conjugation (or trying to develop electroporation if this is preferable).

=== Aim 2: Characterization of parts in vitro ===

After creating a library of parts, these can be characterized in a plate reader assay. The strains will be grown in minimal medium (+/- inducers where appropriate). The functionality and rank order of the parts in this species can then be determined.

=== Aim 3: Characterization of parts in vivo ===

Last of all we want to see if the in vitro behavior can translate to an ecologically relevant context. To do this, a genetic construct will be designed for bacteria colonizing the worm receptacle. The in vitro performance can be determined using fluorescence microscopy or worm viability depending on the intended construct output.

'''SURF student qualifications:'''
* Prerequisite coursework: Bi1x, Bi8/9 (or similar introductory biology course that provides a basic foundation in molecular biology)
*Preferred: Familiarity with synthetic biology/circuit design
*Basic familiarity with coding in Python

'''References:'''

1. Abd-Elgawad MMM. spp.: An Overview of the Useful Facets of Mutualistic Bacteria of Entomopathogenic Nematodes. Life [Internet]. 2022 Aug 31;12(9). Available from: http://dx.doi.org/10.3390/life12091360

2. Kenney E, Eleftherianos I. Entomopathogenic and plant pathogenic nematodes as opposing forces in agriculture. Int J Parasitol. 2016 Jan;46(1):13–9.

3. Cao M, Schwartz HT, Tan CH, Sternberg PW. The entomopathogenic nematode Steinernema hermaphroditum is a self-fertilizing hermaphrodite and a genetically tractable system for the study of parasitic and mutualistic symbiosis. Genetics [Internet]. 2022 Jan 4;220(1). Available from: http://dx.doi.org/10.1093/genetics/iyab170

4. Alani OS, Cao M, Goodrich-Blair H, Heppert JK. Conjugation and transposon mutagenesis of HGB2511, the bacterial symbiont of the nematode (India). MicroPubl Biol [Internet]. 2023 Apr 25;2023. Available from: http://dx.doi.org/10.17912/micropub.biology.000772

5. Halleran AD, Swaminathan A, Murray RM. Single Day Construction of Multigene Circuits with 3G Assembly. ACS Synth Biol. 2018 May 18;7(5):1477–80.

SURF 2024: Bioengineering toolkit development for genetic alterations in the entomopathogenic nematode symbiont Xenorhabdus griffiniae

2023-12-11T01:56:08Z

Elarsson: /* Research overview */

'''[[SURF 2024|SURF 2024]] project description''' __NOTOC__
* Mentor: Richard Murray
* Co-mentor: Elin Larsson

== Background ==

Nematodes are key players in the soil environment, where they feed on bacteria, fungi, insects and plant roots. Therefore, they affect decomposition of organic matter, cycling of nutrients and population size and distribution of other living organisms. Entomopathogenic nematodes (EPN, insect-parasitic) and their symbiotic bacteria are crucial to soil ecology (1,2). The bacterium Xenorhabdus griffiniae is the core symbiont that associates with Steinernema hermaphroditum, an EPN that seeks out and infects insects. The symbiotic pair kills the insect and uses the nutrient from the insect cadaver for reproduction (Fig. 1) (3). To smoothly transition and adapt to complex host environments including the nematode intestine, insect immune system, and decaying insect cadaver, Xenorhabdus bacteria must encode molecular mechanisms to sense the signals from each microenvironment, and regulate its gene expression accordingly. Therefore, it is crucial to characterize gene expression patterns within its relevant ecological niche to better understand and manipulate the bacterial behaviors, such as colonization of nematodes, virulence towards insects, and production of attractants, repellents, and nematicidal metabolites.

[Figure 1]

In order to achieve this goal, tool development in both partners is necessary. Although basic genetic tools, such as conjugation and transformation, are available in Xenorhabdus bacteria (4), systematic and efficient toolkits in bioengineering are lacking, which has limited the basic research and application of these species. Current synthetic biology tools have been proven powerful in bioengineering, but are largely limited to bacterial model organisms like E. coli and B. subtilis, and the yeast S.cerevisiae. To understand ecologically relevant interactions among species, the same tools need to become available in non- and emerging model organisms. In this project, we are focusing on systematically establishing a part library (Murray lab expertise) in X. griffiniae to expand the capacity of bioengineering in this species. As a proof of concept, we will adapt a small-scale part library from E. coli in X. griffiniae for in vitro screening of bacterial gene expression. Relevant candidate bacterial strains will be tested further in vivo using its natural mutualistic host nematode (Cao lab expertise). The proposed effort in tool development will be crucial to elucidating signaling between the nematode and bacteria in this partnership and potentially expand its application to soil microbe engineering.

== Research overview ==

The SURF student will use molecular biology techniques to generate a genetic part library, a collection of promoters, ribosome binding sites, fluorescent proteins with different properties, for X. griffiniae, largely using the pre-existing part library available in the lab for E. coli. Even though genetic parts often function across species, there are many examples where they function differently or not at all. Therefore, it is important to characterize a range of the aforementioned parts in the genetic background of the species of interest, to be able to predictably build different variants of genetic constructs.

[Figure 2]

=== Aim 1: Creating a genetic part library for X. griffiniae ===

The first aim of the project is to generate a small part library that is compatible with the 3G cloning pipeline (5). First, Xenorhabdus vectors will be modified to fit into the E. coli cloning pipeline. The vectors can then be used to build a range of constructs using the parts already available in the Murray lab part library .
The plasmids will then be integrated on the X. griffiniae genome using conjugation (or trying to develop electroporation if this is preferable).

=== Aim 2: Characterization of parts in vitro ===

After creating a library of parts, these can be characterized in a plate reader assay. The strains will be grown in minimal medium (+/- inducers where appropriate). The functionality and rank order of the parts in this species can then be determined.

=== Aim 3: Characterization of parts in vivo ===

Last of all we want to see if the in vitro behavior can translate to an ecologically relevant context. To do this, a genetic construct will be designed for bacteria colonizing the worm receptacle. The in vitro performance can be determined using fluorescence microscopy or worm viability depending on the intended construct output.

'''SURF student qualifications:'''
* Prerequisite coursework: Bi1x, Bi8/9 (or similar introductory biology course that provides a basic foundation in molecular biology)
*Preferred: Familiarity with synthetic biology/circuit design
*Basic familiarity with coding in Python

'''References:'''
1. Abd-Elgawad MMM. spp.: An Overview of the Useful Facets of Mutualistic Bacteria of Entomopathogenic Nematodes. Life [Internet]. 2022 Aug 31;12(9). Available from: http://dx.doi.org/10.3390/life12091360

2. Kenney E, Eleftherianos I. Entomopathogenic and plant pathogenic nematodes as opposing forces in agriculture. Int J Parasitol. 2016 Jan;46(1):13–9.

3. Cao M, Schwartz HT, Tan CH, Sternberg PW. The entomopathogenic nematode Steinernema hermaphroditum is a self-fertilizing hermaphrodite and a genetically tractable system for the study of parasitic and mutualistic symbiosis. Genetics [Internet]. 2022 Jan 4;220(1). Available from: http://dx.doi.org/10.1093/genetics/iyab170

4. Alani OS, Cao M, Goodrich-Blair H, Heppert JK. Conjugation and transposon mutagenesis of HGB2511, the bacterial symbiont of the nematode (India). MicroPubl Biol [Internet]. 2023 Apr 25;2023. Available from: http://dx.doi.org/10.17912/micropub.biology.000772

5. Halleran AD, Swaminathan A, Murray RM. Single Day Construction of Multigene Circuits with 3G Assembly. ACS Synth Biol. 2018 May 18;7(5):1477–80.

SURF 2024

2023-12-11T01:55:43Z

Elarsson: /* List of available projects */

SURF 2024

2023-12-11T01:54:50Z

Elarsson: /* List of available projects */

{{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|2023|Genetically-Programmed Synthetic Cells and Multi-Cellular Machines}}
| [[NSF Cell Free]]
| None
| Multiple projects may be available; competitive selection
|-
| {{SURF|2023|Genetically-Programmed Synthetic Cells and Multi-Cellular Machines}}
| [[NSF Cell Free]]
| None
| Multiple projects may be available; competitive selection
|}

SURF 2024: Bioengineering toolkit development for genetic alterations in the entomopathogenic nematode symbiont Xenorhabdus griffiniae

2023-12-11T01:52:44Z

Elarsson: /* Research overview */

'''[[SURF 2024|SURF 2024]] project description''' __NOTOC__
* Mentor: Richard Murray
* Co-mentor: Elin Larsson

== Background ==

Nematodes are key players in the soil environment, where they feed on bacteria, fungi, insects and plant roots. Therefore, they affect decomposition of organic matter, cycling of nutrients and population size and distribution of other living organisms. Entomopathogenic nematodes (EPN, insect-parasitic) and their symbiotic bacteria are crucial to soil ecology (1,2). The bacterium Xenorhabdus griffiniae is the core symbiont that associates with Steinernema hermaphroditum, an EPN that seeks out and infects insects. The symbiotic pair kills the insect and uses the nutrient from the insect cadaver for reproduction (Fig. 1) (3). To smoothly transition and adapt to complex host environments including the nematode intestine, insect immune system, and decaying insect cadaver, Xenorhabdus bacteria must encode molecular mechanisms to sense the signals from each microenvironment, and regulate its gene expression accordingly. Therefore, it is crucial to characterize gene expression patterns within its relevant ecological niche to better understand and manipulate the bacterial behaviors, such as colonization of nematodes, virulence towards insects, and production of attractants, repellents, and nematicidal metabolites.

[Figure 1]

In order to achieve this goal, tool development in both partners is necessary. Although basic genetic tools, such as conjugation and transformation, are available in Xenorhabdus bacteria (4), systematic and efficient toolkits in bioengineering are lacking, which has limited the basic research and application of these species. Current synthetic biology tools have been proven powerful in bioengineering, but are largely limited to bacterial model organisms like E. coli and B. subtilis, and the yeast S.cerevisiae. To understand ecologically relevant interactions among species, the same tools need to become available in non- and emerging model organisms. In this project, we are focusing on systematically establishing a part library (Murray lab expertise) in X. griffiniae to expand the capacity of bioengineering in this species. As a proof of concept, we will adapt a small-scale part library from E. coli in X. griffiniae for in vitro screening of bacterial gene expression. Relevant candidate bacterial strains will be tested further in vivo using its natural mutualistic host nematode (Cao lab expertise). The proposed effort in tool development will be crucial to elucidating signaling between the nematode and bacteria in this partnership and potentially expand its application to soil microbe engineering.

== Research overview ==

The SURF student will use molecular biology techniques to generate a genetic part library, a collection of promoters, ribosome binding sites, fluorescent proteins with different properties, for X. griffiniae, largely using the pre-existing part library available in the lab for E. coli. Even though genetic parts often function across species, there are many examples where they function differently or not at all. Therefore, it is important to characterize a range of the aforementioned parts in the genetic background of the species of interest, to be able to predictably build different variants of genetic constructs.

[Figure 2]

=== Aim 1: Creating a genetic part library for X. griffiniae ===

The first aim of the project is to generate a small part library that is compatible with the 3G cloning pipeline (5). First, Xenorhabdus vectors will be modified to fit into the E. coli cloning pipeline. The vectors can then be used to build a range of constructs using the parts already available in the Murray lab part library .
The plasmids will then be integrated on the X. griffiniae genome using conjugation (or trying to develop electroporation if this is preferable).

=== Aim 2: Characterization of parts in vitro ===

After creating a library of parts, these can be characterized in a plate reader assay. The strains will be grown in minimal medium (+/- inducers where appropriate). The functionality and rank order of the parts in this species can then be determined.

=== Aim 3: Characterization of parts in vivo ===

Last of all we want to see if the in vitro behavior can translate to an ecologically relevant context. To do this, a genetic construct will be designed for bacteria colonizing the worm receptacle. The in vitro performance can be determined using fluorescence microscopy or worm viability depending on the intended construct output.

'''SURF student qualifications:'''
* Prerequisite coursework: Bi1x, Bi8/9 (or similar introductory biology course that provides a basic foundation in molecular biology)
*Preferred: Familiarity with synthetic biology/circuit design
*Basic familiarity with coding in Python

'''References:'''
1. Abd-Elgawad MMM. spp.: An Overview of the Useful Facets of Mutualistic Bacteria of Entomopathogenic Nematodes. Life [Internet]. 2022 Aug 31;12(9). Available from: http://dx.doi.org/10.3390/life12091360
2. Kenney E, Eleftherianos I. Entomopathogenic and plant pathogenic nematodes as opposing forces in agriculture. Int J Parasitol. 2016 Jan;46(1):13–9.
3. Cao M, Schwartz HT, Tan CH, Sternberg PW. The entomopathogenic nematode Steinernema hermaphroditum is a self-fertilizing hermaphrodite and a genetically tractable system for the study of parasitic and mutualistic symbiosis. Genetics [Internet]. 2022 Jan 4;220(1). Available from: http://dx.doi.org/10.1093/genetics/iyab170
4. Alani OS, Cao M, Goodrich-Blair H, Heppert JK. Conjugation and transposon mutagenesis of HGB2511, the bacterial symbiont of the nematode (India). MicroPubl Biol [Internet]. 2023 Apr 25;2023. Available from: http://dx.doi.org/10.17912/micropub.biology.000772
5. Halleran AD, Swaminathan A, Murray RM. Single Day Construction of Multigene Circuits with 3G Assembly. ACS Synth Biol. 2018 May 18;7(5):1477–80.

SURF 2024: Bioengineering toolkit development for genetic alterations in the entomopathogenic nematode symbiont Xenorhabdus griffiniae

2023-12-11T01:51:43Z

Elarsson: Created page with "'''SURF 2024 project description''' __NOTOC__ * Mentor: Richard Murray * Co-mentor: Elin Larsson == Background == Nematodes are key players in the soil environment, where they feed on bacteria, fungi, insects and plant roots. Therefore, they affect decomposition of organic matter, cycling of nutrients and population size and distribution of other living organisms. Entomopathogenic nematodes (EPN, insect-parasitic) and their symbiotic bacteria are crucial..."

'''[[SURF 2024|SURF 2024]] project description''' __NOTOC__
* Mentor: Richard Murray
* Co-mentor: Elin Larsson

== Background ==

Nematodes are key players in the soil environment, where they feed on bacteria, fungi, insects and plant roots. Therefore, they affect decomposition of organic matter, cycling of nutrients and population size and distribution of other living organisms. Entomopathogenic nematodes (EPN, insect-parasitic) and their symbiotic bacteria are crucial to soil ecology (1,2). The bacterium Xenorhabdus griffiniae is the core symbiont that associates with Steinernema hermaphroditum, an EPN that seeks out and infects insects. The symbiotic pair kills the insect and uses the nutrient from the insect cadaver for reproduction (Fig. 1) (3). To smoothly transition and adapt to complex host environments including the nematode intestine, insect immune system, and decaying insect cadaver, Xenorhabdus bacteria must encode molecular mechanisms to sense the signals from each microenvironment, and regulate its gene expression accordingly. Therefore, it is crucial to characterize gene expression patterns within its relevant ecological niche to better understand and manipulate the bacterial behaviors, such as colonization of nematodes, virulence towards insects, and production of attractants, repellents, and nematicidal metabolites.

[Figure 1]

In order to achieve this goal, tool development in both partners is necessary. Although basic genetic tools, such as conjugation and transformation, are available in Xenorhabdus bacteria (4), systematic and efficient toolkits in bioengineering are lacking, which has limited the basic research and application of these species. Current synthetic biology tools have been proven powerful in bioengineering, but are largely limited to bacterial model organisms like E. coli and B. subtilis, and the yeast S.cerevisiae. To understand ecologically relevant interactions among species, the same tools need to become available in non- and emerging model organisms. In this project, we are focusing on systematically establishing a part library (Murray lab expertise) in X. griffiniae to expand the capacity of bioengineering in this species. As a proof of concept, we will adapt a small-scale part library from E. coli in X. griffiniae for in vitro screening of bacterial gene expression. Relevant candidate bacterial strains will be tested further in vivo using its natural mutualistic host nematode (Cao lab expertise). The proposed effort in tool development will be crucial to elucidating signaling between the nematode and bacteria in this partnership and potentially expand its application to soil microbe engineering.

== Research overview ==

The SURF student will use molecular biology techniques to generate a genetic part library, a collection of promoters, ribosome binding sites, fluorescent proteins with different properties, for X. griffiniae, largely using the pre-existing part library available in the lab for E. coli. Even though genetic parts often function across species, there are many examples where they function differently or not at all. Therefore, it is important to characterize a range of the aforementioned parts in the genetic background of the species of interest, to be able to predictably build different variants of genetic constructs.

[Figure 2]

=== Aim 1: Creating a genetic part library for X. griffiniae ===

The first aim of the project is to generate a small part library that is compatible with the 3G cloning pipeline (5). First, Xenorhabdus vectors will be modified to fit into the E. coli cloning pipeline. The vectors can then be used to build a range of constructs using the parts already available in the Murray lab part library .
The plasmids will then be integrated on the X. griffiniae genome using conjugation (or trying to develop electroporation if this is preferable).

=== Aim 2: Characterization of parts in vitro ===

=== Aim 3: Characterization of parts in vivo ===

'''SURF student qualifications:'''
* Prerequisite coursework: Bi1x, Bi8/9 (or similar introductory biology course that provides a basic foundation in molecular biology)
*Preferred: Familiarity with synthetic biology/circuit design
*Basic familiarity with coding in Python

'''References:'''
1. Abd-Elgawad MMM. spp.: An Overview of the Useful Facets of Mutualistic Bacteria of Entomopathogenic Nematodes. Life [Internet]. 2022 Aug 31;12(9). Available from: http://dx.doi.org/10.3390/life12091360
2. Kenney E, Eleftherianos I. Entomopathogenic and plant pathogenic nematodes as opposing forces in agriculture. Int J Parasitol. 2016 Jan;46(1):13–9.
3. Cao M, Schwartz HT, Tan CH, Sternberg PW. The entomopathogenic nematode Steinernema hermaphroditum is a self-fertilizing hermaphrodite and a genetically tractable system for the study of parasitic and mutualistic symbiosis. Genetics [Internet]. 2022 Jan 4;220(1). Available from: http://dx.doi.org/10.1093/genetics/iyab170
4. Alani OS, Cao M, Goodrich-Blair H, Heppert JK. Conjugation and transposon mutagenesis of HGB2511, the bacterial symbiont of the nematode (India). MicroPubl Biol [Internet]. 2023 Apr 25;2023. Available from: http://dx.doi.org/10.17912/micropub.biology.000772
5. Halleran AD, Swaminathan A, Murray RM. Single Day Construction of Multigene Circuits with 3G Assembly. ACS Synth Biol. 2018 May 18;7(5):1477–80.

Group Schedule, Fall 2023

2023-09-13T21:24:00Z

Elarsson: /* Week 7: 6-10 Nov */

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

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

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

| width=25% |
=== Week 1: 25 Sep - 29 Sep ===
'''Biocircuits: Tue, 10a-12p'''
* Alex
'''NCS: Tue, 3:30p-5p'''
* Open

| width=25% |

=== Week 2: 2-6 Oct ===
'''Biocircuits: Mon, 10a-12p'''
* Manisha
'''NCS: Thu, 3:45p-5p'''
* Open

| width=25% |

=== Week 3: 9-13 Oct ===
'''Biocircuits: Tue, 10a-12p'''
* Synthetic Cell
'''NCS: Tue, 3:30p-5p'''
* Open

| width=25% |

=== Week 4: 16-20 Oct ===
'''Biocircuits: Tue, 10a-12p'''
* Individual updates
'''NCS: Wed, 3:45p-5p'''
* Open

|- valign=top
| width=25% |

=== Week 5: 23-27 Oct ===
'''Biocircuits: Tue, 10a-12p'''
* Matt
'''NCS: Wed, 3:45p-5p'''
* Open

| width=25% |

=== Week 6: 30 Oct - 3 Nov ===
'''Biocircuits: Tue, 10a-12p'''
* TBD
* Meeting might shift to Wed or Thu
'''NCS: Wed, 3:45p-5p'''
* Meeting might shift to Tue or Thu
* Open

| width=25% |

=== Week 7: 6-10 Nov ===
'''Biocircuits: Tue, 10a-12p'''
* Elin
* Meeting might shift to Wed
'''NCS: Wed, 3:45p-5p'''
* Open

| width=25% |

=== Week 8: 13-17 Nov ===
'''Biocircuits: Mon, 10a-12p'''
* Individual updates
'''NCS: Thu, 3:45p-5p'''
* Open

|- valign=top
| width=25% |

=== Week 9: 20-26 Nov ===
* Thanksgiving week, no meetings

| width=25% |

=== Week 10: 27 Nov - 1 Dec ===
'''Biocircuits: Tue, 10a-12p'''
* Yan
* Might shift to Wed
'''NCS: Wed, 3:45p-5p'''
* Open
'''Synthetic Cell: Thu, 10a-12p'''
* TBD

| width=25% |

=== Week 11: 4-8 Dec ===
'''Biocircuits: Wed, 10a-12p'''
* Zoila
'''NCS: Wed, 3:45p-5p'''
* Open

| width=25% |

=== Week 12: 11-15 Dec ===
'''Biocircuits: Tue, 10a-12p'''
* Individual updates
'''NCS: Wed, 3:45p-5p'''
* Open
<hr>
* CDC'23 this week
|}

Group Schedule, Fall 2023

2023-09-13T21:23:47Z

Elarsson: /* Week 10: 27 Nov - 1 Dec */

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

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

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

| width=25% |
=== Week 1: 25 Sep - 29 Sep ===
'''Biocircuits: Tue, 10a-12p'''
* Alex
'''NCS: Tue, 3:30p-5p'''
* Open

| width=25% |

=== Week 2: 2-6 Oct ===
'''Biocircuits: Mon, 10a-12p'''
* Manisha
'''NCS: Thu, 3:45p-5p'''
* Open

| width=25% |

=== Week 3: 9-13 Oct ===
'''Biocircuits: Tue, 10a-12p'''
* Synthetic Cell
'''NCS: Tue, 3:30p-5p'''
* Open

| width=25% |

=== Week 4: 16-20 Oct ===
'''Biocircuits: Tue, 10a-12p'''
* Individual updates
'''NCS: Wed, 3:45p-5p'''
* Open

|- valign=top
| width=25% |

=== Week 5: 23-27 Oct ===
'''Biocircuits: Tue, 10a-12p'''
* Matt
'''NCS: Wed, 3:45p-5p'''
* Open

| width=25% |

=== Week 6: 30 Oct - 3 Nov ===
'''Biocircuits: Tue, 10a-12p'''
* TBD
* Meeting might shift to Wed or Thu
'''NCS: Wed, 3:45p-5p'''
* Meeting might shift to Tue or Thu
* Open

| width=25% |

=== Week 7: 6-10 Nov ===
'''Biocircuits: Tue, 10a-12p'''
* Yan
* Meeting might shift to Wed
'''NCS: Wed, 3:45p-5p'''
* Open

| width=25% |

=== Week 8: 13-17 Nov ===
'''Biocircuits: Mon, 10a-12p'''
* Individual updates
'''NCS: Thu, 3:45p-5p'''
* Open

|- valign=top
| width=25% |

=== Week 9: 20-26 Nov ===
* Thanksgiving week, no meetings

| width=25% |

=== Week 10: 27 Nov - 1 Dec ===
'''Biocircuits: Tue, 10a-12p'''
* Yan
* Might shift to Wed
'''NCS: Wed, 3:45p-5p'''
* Open
'''Synthetic Cell: Thu, 10a-12p'''
* TBD

| width=25% |

=== Week 11: 4-8 Dec ===
'''Biocircuits: Wed, 10a-12p'''
* Zoila
'''NCS: Wed, 3:45p-5p'''
* Open

| width=25% |

=== Week 12: 11-15 Dec ===
'''Biocircuits: Tue, 10a-12p'''
* Individual updates
'''NCS: Wed, 3:45p-5p'''
* Open
<hr>
* CDC'23 this week
|}

Yan Zhang, 28 Mar 2022

2022-03-25T16:49:53Z

Elarsson:

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

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

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

Group Schedule, Fall 2021

2021-10-07T03:15:49Z

Elarsson:

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [[http:www.cds.caltech.edu/~murray/myschedule.html|Richard's calendar]]
| width=50% |
* [[Group Schedule, Summer 2021]]
|}

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 Jorgensen 109 and NCS meetings are in 111 Keck.

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

| width=25% |
=== Week 1: 27 Sep - 1 Oct ===
'''Biocircuits: Tue, 10a-12p'''
* Matt
* Open
'''NCS: Wed, ~3:30p-5p'''
* Kellan

| width=25% |

=== Week 2: 4-8 Oct ===
'''Biocircuits: Wed, 10a-12p'''
* Individual updates
'''T&E: Wed, ~3:30p-5p'''
* Individual updates and plans

| width=25% |

=== Week 3: 11-15 Oct ===
'''Biocircuits: Wed, 10a-12p'''
* Cindy
* Elin
'''NCS: Wed, ~3:30p-5p'''
* Apurva

| width=25% |

=== Week 4: 18-24 Oct ===
'''Biocircuits: Tue, 10a-12p'''
* TBD
'''AVP: Tue, 9a-10a'''

|- valign=top
| width=25% |

=== Week 5: 25-29 Oct ===
'''Biocircuits: Tue, 10a-12p'''
* Individual updates
'''NCS: TBD'''

| width=25% |

=== Week 6: 1-5 Nov ===
'''Biocircuits: Wed, 10a-12p'''
* Michaëlle
* Open
'''T&E: Wed, ~3:30p-5p'''

| width=25% |

=== Week 7: 8-12 Nov ===
'''Biocircuits: Tue, 10a-12p'''
* Chelsea
* Open
'''NCS: Wed, ~3:30p-5p'''
* Prithvi

| width=25% |

=== Week 8: 15-19 Nov ===
'''Biocircuits: Wed, 10a-12p'''
* TBD: Kaihang Wang
'''AVP: Wed, 9a-10a'''

|- valign=top
| width=25% |

=== Week 9: 22-26 Nov ===
* Thanksgiving week, no meetings

| width=25% |

=== Week 10: 29 Nov - 3 Dec ===
'''Biocircuits: Tue, 10a-12p'''
* Individual updates
'''NCS: Thu, 3:30p-5p'''
* Ersin

| width=25% |

=== Week 11: 6-10 Dec ===
'''Biocircuits: Wed, 10a-12p'''
* UG presentations (Victoria)
* Open
'''T&E: Wed, ~3:30p-5p'''

| width=25% |

=== Week 12: 13-17 Dec ===
'''Biocircuits: Tue, 10a-12p'''
* Open
* Meeting may get shifted/canceled
'''AVP: Mon, 9a-10a'''
* Meeting may get shifted
<hr>
* CDC'21 this week (remote)
|}

David Garcia, 13 Feb 2020

2020-02-12T13:48:21Z

Elarsson: /* 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: Open
* 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 <br>
David Garcia, The University of Tennessee, Knoxville and Oak Ridge National Laboratory<br>

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.

Jake Beal, 1 Oct 2019

2019-09-30T16:28:47Z

Elarsson:

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

=== Schedule ===
* 9:00a: RMM group meeting, 111 Keck (if interested)
* 11:00a: Open
* 11:45a: seminar setup
* 12:00p: Seminar, 111 Keck (abstract below)
* 1:00p: Lunch with Andrey Shur, Sam Clamons
* 1:45p: Lab tour and calibration discussion (Andrey, Sam, Mark, Miki)
* 2:30p: John Marken
* 3:15p: Elin Larsson
* 4:00p: Open
* 4:45p: Wrap up with Richard

=== Talk abstract ===

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

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

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

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