Murray Wiki - User contributions [en]

May 2017 meeting schedule

2017-05-08T15:16:26Z

Yywu: /* 16 May (Tue) */

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

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==== 15 May (Mon) ====
* 9:30 am: Open
* 10:15 am: Open
* 11:00 am: Faculty meeting
* 11:30 am: Open
* 12:15 pm: Lunch
* 1:30 pm: Open
* 2:15 pm: Open
* 3:00 pm: Open
* 3:45 pm: Break
* 4:00 pm: Namita
* 4:45 pm: Open
* 5:30 pm: Open
* 6:15 pm: Done for the day

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

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

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

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

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====28 May (Sun) ====
* 1:45 pm: Open
* 2:30 pm: Open
* 3:15 pm: Open
* 4:00 pm: Done for the day
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====29 May (Mon) ====
* 1:45 pm: Open (if needed)
* 2:30 pm: Open (if needed)
* 3:15 pm: Open (if needed)
* 4:00 pm: Done for the day
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==== 30 May (Tue) ====
* 9:30 am: Open
* 10:15 am: Shaobin
* 11:00 am: Stepan seminar
* 12:00 pm: Lunch
* 1:30 pm: Namita
* 2:15 pm: Andrey
* 3:00 pm: Depart
|}

Apr 2017 meeting schedule

2017-04-12T16:42:10Z

Yywu: /* 19 Apr (Wed) */

Richard will be in town 19-21 Apr. Please sign up for a time to meet below. __NOTOC__

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==== 19 Apr (Wed) ====
* 9:30 am: Hold (Sofie or Leo)
* 10:30 am: Admin meeting (SP, MC)
* 11:15 am: Shaobin
* 12:00 pm: DARPA BioCon meeting
* 2:00 pm: Candidacy exam
* 3:00 pm: CDS tea
* 3:45 pm: Yong
* 4:30 pm: Admin meeting (LL)
* 5:00 pm: Open (tentative)
* 5:45 pm: Associates event

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==== 20 Apr (Thu) ====
* 9:30 am: Hold (Sofie or Leo)
* 10:30 am: Mark
* 11:15 am: Tony Fragoso
* 12:00 pm: Lunch
* 1:30 pm: EBRC telecon
* 2:30 pm: Open
* 3:15 pm: Open
* 4:00 pm: Vipul
* 4:45 pm: Break
* 5:00 pm: Tung
* 5:45 pm: Sam
* 6:00 pm: Open (if needed)
* 6:45 pm: Open (if needed)
* 7:30 pm: Done for the day

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==== 21 Apr (Fri) ====
* 9:15 am: Open
* 10:00 am: JPL CIF meeting
* 11:15 am: Karena
* 12:00 pm: Lunch
* 12:45 pm: Open
* 1:30 pm: Open
* 2:15 pm: Open
* 3:00 pm: Break
* 3:15 pm: Open
* 4:00 pm: Miki
* 4:45 pm: Open
* 5:30 pm: Done for the day

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==== 23 Apr (Sun) ====
* 1:45 pm: Open
* 2:30 pm: Open
* 3:15 pm: Open
* 4:00 pm: Break
* 4:15 pm: Open
* 5:00 pm: Open
* 5:45 pm: Shan
* 6:30 pm: Done for the day
|}

Group Schedule, Spring 2017

2017-03-21T23:59:34Z

Yywu: /* Week 3: 17 Apr - 21 Apr */

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
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* {{RMM public schedule|Richard's calendar (travel)}}
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* [[Group Schedule, Winter 2017]]
|}

The schedule for group and subgroup meetings is given below. Contact Anandh if you need to change the schedule. Unless otherwise noted, here are the locations of the meetings:

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* Group meetings - 213 ANB
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* Biocircuits subgroup - Keck 111
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* NCS subgroup - 243 ANB
|}

{| width=100% border=1

|- valign=top
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=== Week 1: 3 Apr - 7 Apr ===
'''Biocircuits: Mon, 10a-12p'''
* Leo Green
* Ania Baetica

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=== Week 2: 10 Apr - 14 Apr ===
'''Biocircuits: Mon, 10a-12p'''
* Vipul Singhal
* George Artavanis

'''Biocircuits: Wed, 11a-12p'''
* Lab cleanup

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=== Week 3: 17 Apr - 21 Apr ===
'''Biocircuits: Mon, 10a-12p'''
* Yong Wu
* Mark Prator

'''DARPA Biocon: Wed, 12p-2p'''

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=== Week 4: 24 Apr - 28 Apr ===
'''Biocircuits: Mon, 10a-12p'''
* James Parkin
* Shaobin Guo (Pre-defense talk)

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=== Week 5: 1 May - 5 May ===
'''Biocircuits: Mon, 10a-12p'''
* Sam Clamons
* Andrey Shur

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=== Week 6: 8 May - 12 May===
'''Biocircuits: Mon, 10a-12p'''
* Anandh Swaminathan
* Cindy Ren

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=== Week 7: 15 May - 19 May ===
'''Biocircuits: Mon, 10a-12p'''
* Reed McCardell
* William Poole
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=== Week 8: 22 May - 26 May ===
* RMM in town, no group meeting

'''DARPA Biocon: Wed, 12p-2p'''

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=== Week 9: 29 May - 2 Jun ===
'''Happy Memorial Day!'''

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=== Week 10: 5 Jun - 9 Jun ===
'''Biocircuits: Mon, 10a-12p'''
* Rotation student
* Rotation student

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=== Week 11: 12 Jun - 16 Jun ===
'''Biocircuits: Mon, 10a-12p'''
* Rotation student
* Rotation student
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=== Week 12: 19 Jun - 23 Jun ===
'''Summer'''
|}

Mar 2017 meeting schedule

2017-03-05T18:34:08Z

Yywu: /* 6 Mar (Mon) */

Richard will be in town 3-7 Mar. Please sign up for a time to meet below. __NOTOC__

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==== 3 Mar (Fri) ====
* 10:00 am: DENSO CPM telecon
* 11:00 am: Reed
* 11:45 am: Andrey
* 12:30 pm: Lunch
* 1:15 pm: George
* 2:00 pm: Shaobin
* 2:45 pm: Mark
* 3:30 pm: SBIR telecon (w/ Mark P)
* 4:00 pm: Faculty meeting
* 5:45 pm: William
* 6:30 pm: Done for the day

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==== 5 Mar (Sun) ====
* 1:45 pm: Anandh
* 2:30 pm: Anu
* 3:15 pm: Sam
* 4:00 pm: Break
* 4:15 pm: Ioannis
* 5:00 pm: Shan
* 5:45 pm: Sumanth Dathathri
* 6:30 pm: Done for the day

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==== 6 Mar (Mon) ====
* 9:30 am: AFOSR BRI telecon
* 10:30 am: Open
* 11:15 am: Fragoso
* 12:00 pm: Lunch
* 12:45 pm: Vipul?
* 1:30 pm: DARPA telecon
* 2:30 pm: Richard C?
* 3:00 pm: Miki
* 3:45 pm: Break
* 4:00 pm: James
* 4:45 pm: Karena
* 5:30 pm: Ania
* 6:15 pm: Done for the day

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==== 7 Mar (Tue) ====
* 9:30 am: Busy
* 10:30 am: Tung
* 11:15 am: Yong
* 12:00 pm: Lunch
* 1:15 pm: Andrew M
* 2:00 pm: Andy Halleran
* 2:45 pm: Depart for airport
|}

Mar 2017 meeting schedule

2017-03-05T18:33:51Z

Yywu: /* 7 Mar (Tue) */

Richard will be in town 3-7 Mar. Please sign up for a time to meet below. __NOTOC__

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==== 3 Mar (Fri) ====
* 10:00 am: DENSO CPM telecon
* 11:00 am: Reed
* 11:45 am: Andrey
* 12:30 pm: Lunch
* 1:15 pm: George
* 2:00 pm: Shaobin
* 2:45 pm: Mark
* 3:30 pm: SBIR telecon (w/ Mark P)
* 4:00 pm: Faculty meeting
* 5:45 pm: William
* 6:30 pm: Done for the day

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==== 5 Mar (Sun) ====
* 1:45 pm: Anandh
* 2:30 pm: Anu
* 3:15 pm: Sam
* 4:00 pm: Break
* 4:15 pm: Ioannis
* 5:00 pm: Shan
* 5:45 pm: Sumanth Dathathri
* 6:30 pm: Done for the day

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==== 6 Mar (Mon) ====
* 9:30 am: AFOSR BRI telecon
* 10:30 am: Yong
* 11:15 am: Fragoso
* 12:00 pm: Lunch
* 12:45 pm: Vipul?
* 1:30 pm: DARPA telecon
* 2:30 pm: Richard C?
* 3:00 pm: Miki
* 3:45 pm: Break
* 4:00 pm: James
* 4:45 pm: Karena
* 5:30 pm: Ania
* 6:15 pm: Done for the day

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==== 7 Mar (Tue) ====
* 9:30 am: Busy
* 10:30 am: Tung
* 11:15 am: Yong
* 12:00 pm: Lunch
* 1:15 pm: Andrew M
* 2:00 pm: Andy Halleran
* 2:45 pm: Depart for airport
|}

Mar 2017 meeting schedule

2017-02-26T20:53:51Z

Yywu: /* 6 Mar (Mon) */

Richard will be in town 3-7 Mar. Please sign up for a time to meet below. __NOTOC__

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==== 3 Mar (Fri) ====
* 10:00 am: DENSO CPM telecon
* 11:00 am: Open
* 11:45 am: Shaobin
* 12:30 pm: Lunch
* 1:00 pm: Hold: DARPA telecon
* 2:00 pm: Open
* 2:45 pm: Open
* 3:30 pm: SBIR telecon (w/ Mark P)
* 4:00 pm: Faculty meeting
* 5:45 pm: Open
* 6:30 pm: Done for the day

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

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==== 6 Mar (Mon) ====
* 9:30 am: AFOSR BRI telecon
* 10:30 am: Yong
* 11:15 am: Fragoso
* 12:00 pm: Lunch
* 12:30 pm: Hold: DARPA telecon
* 1:30 pm: Open
* 2:15 pm: Open
* 3:00 pm: Open
* 3:45 pm: Break
* 4:00 pm: Open
* 4:45 pm: Open
* 5:30 pm: Open
* 6:15 pm: Done for the day

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==== 7 Mar (Tue) ====
* 9:30 am: Busy
* 10:15 am: Open
* 11:00 am: Hold: DARPA telecon
* 12:00 pm: Lunch
* 12:45 pm: Hold
* 1:15 pm: Andrew M
* 2:00 pm: Andy Halleran
* 2:45 pm: Depart for airport
|}

Henrike Niederholtmeyer, Jan 2017

2017-01-24T21:13:41Z

Yywu: /* 24 Jan (Tue) */

Henrike Niederholtmeyer will visit Caltech on 23-24 January 2017 to help us out with some microfluidics work we are doing. If you would like to meet with her, please sign up below. __NOTOC__

=== Schedule ===
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==== 23 Jan (Mon) ====
* Arrive sometime before noon
* 12 pm: Michaelle Mayalu seminar, 121 Annenberg (lunch)
* 1 pm: meet with Mark Prator and Reed McCardell
* 3 pm: TX-TL extract prep discussion: Miki, Yong, Sam
* 4 pm: Open
* 4:45 pm: Open
<hr>
* 6:30 pm: Meet Richard in 107 Steele. Walk to dinner.

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==== 24 Jan (Tue) ====
* Morning: work with Mark and Reed
* 12 pm: Seminar in 121 Annenberg (abstract below)
* 1 pm: Lunch with Mark and Reed
* 2 pm: Yong
* 2:45 pm: [[Jan 2017 meeting schedule|Richard]]
* 3:30 pm: Will
* 4:15 pm: Vipul
* 5:00 pm: Done for the day
|}

=== Seminar info ===
<center>
'''Gene expression in a synthetic tissue of artificial cells'''

Henrike Niederholtmeyer and Neal K. Devaraj 
Department of Chemistry and Biochemistry, University of California, San Diego, USA

Tuesday, January 24, 2017 
12:00 pm, 121 Annenberg
</center>

Living cells in tissues or biofilms communicate with neighboring cells through chemical and mechanical signals allowing them to organize spatially. To reduce the complexity of these natural systems we create synthetic tissues of non-living artificial cells. We use a microfluidic method to produce porous capsules with an artificial “nucleus” where DNA is immobilized. Upon addition of transcription and translation reagents capsules synthesize proteins, which localize to nuclei containing binding sites. Neighboring capsules communicate by producing transcription factors that diffuse through the artificial tissue suggesting that it can serve as a model system to study pattern formation.

Henrike Niederholtmeyer, Jan 2017

2017-01-16T17:00:15Z

Yywu: /* 24 Jan (Tue) */

Henrike Niederholtmeyer will visit Caltech on 23-24 January 2017 to help us out with some microfluidics work we are doing. If you would like to meet with her, please sign up below.

=== Schedule ===
{| border=1
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==== 23 Jan (Mon) ====
* Arrive sometime before noon
* 12 pm: Michaelle Mayalu seminar, 121 Annenberg (lunch)
* 1 pm: meet with Mark Prator and Reed McCardell
* 3 pm: TX-TL extract prep discussion: Miki, Yong, Sam
* 4 pm: Open
* 4:45 pm: Open
* 5:30 pm: Meet Richard in 107 Steele. Walk to dinner.

| width=50% |
==== 24 Jan (Tue) ====
* Morning: work with Mark and Reed
* 12 pm: Seminar in 121 Annenberg (abstract below)
* 1 pm: Lunch with Mark and Reed
* 2 pm: Open
* 2:45 pm: [[Jan 2017 meeting schedule|Richard]]
* 3:30 pm: Yong
* 4:15 pm: Open
* 5:00 pm: Done for the day
|}

=== Seminar info ===
<center>
'''Gene expression in a synthetic tissue of artificial cells'''

Henrike Niederholtmeyer and Neal K. Devaraj 
Department of Chemistry and Biochemistry, University of California, San Diego, USA

Tuesday, January 24, 2017 
12:00 pm, 121 Annenberg
</center>

Living cells in tissues or biofilms communicate with neighboring cells through chemical and mechanical signals allowing them to organize spatially. To reduce the complexity of these natural systems we create synthetic tissues of non-living artificial cells. We use a microfluidic method to produce porous capsules with an artificial “nucleus” where DNA is immobilized. Upon addition of transcription and translation reagents capsules synthesize proteins, which localize to nuclei containing binding sites. Neighboring capsules communicate by producing transcription factors that diffuse through the artificial tissue suggesting that it can serve as a model system to study pattern formation.

Jan 2017 meeting schedule

2017-01-13T16:31:05Z

Yywu: /* 20 Jan (Fri) */

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

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==== 20 Jan (Fri) ====
* Richard arrives on campus ~9:45 am
* 10:15 am: Mark
* 11:00 am: Yong
* 11:45 am: Open
* 12:30 pm: Lunch
* 1:30 pm: Yong and Frances A
* 2:30 pm: Open
* 3:15 pm: Open
* 4:00 pm: Open
* 4:45 pm: Break
* 5:00 pm: Open
* 5:45 pm: Open
* 6:30 pm: Done for the day

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

| width=25% |

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

| width=25% |

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

Sep/Oct 2016 meeting schedule

2016-09-18T00:01:30Z

Yywu: /* 2 Oct (Sun) */

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

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

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

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

| width=25% |

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

Aug 2016 meeting schedule

2016-08-01T18:30:55Z

Yywu: /* 7 Aug (Sun) */

Richard will be in town 7-10 August 2016. Please sign up for a time to meet below.
__NOTOC__

{| border=1
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==== 7 Aug (Sun) ====
* 2:15 pm: Open
* 3:00 pm: Open
* 3:45 pm: Yong
* 4:00 pm: Break
* 4:45 pm: Sam
* 5:30 pm: Open
* 6:30 pm: Open
| width=25% |

==== 8 Aug (Mon) ====
* 9-11 am: Integrase project meeting (Victoria, Andrey, Sam, Ania, Cindy)
<hr>
* 12:45 pm: Anandh
* 1:30 pm: Shaobin (if TXTL meeting changed to today)
* 2:15 pm: Richard C
* 3:00 pm: Open
* 3:45 pm: Break
* 4:00 pm: Open
* 4:45 pm: Anu
| width=25% |

==== 9 Aug (Tue) ====
* 8:30 am: Open
* 9:15 am: Mark
* 10:00 am: Jaymie
* 11 am - 2 pm: DARPA Biological Control project meeting (Anandh, Ania, Cindy, James, Reed, Andrey, Sam?)
* 1:00 pm: Tung
* 1:45 pm: Hold: James
* 2:30 pm: Tony Fragoso
* 3:15 pm: Break
* 3:30 pm: Vipul
* 4:15 pm: Ioannis
* 5:00 pm: Ania
* 5:45 pm: Break
| width=25% |

==== 10 Aug (Wed) ====
* 9-11 am: TX-TL project meeting (Clare, Mark, Shaobin, Yong, Vipul, Sam, Miki)
* 11:00 am: Shaobin
* 11:45 am: Unavailable
* 12:45 pm: Miki
* 1:45 pm: Open
* 2:30 pm: Leave for airport
|}

Aug 2016 meeting schedule

2016-07-31T18:05:59Z

Yywu: /* 10 Aug (Wed) */

Richard will be in town 7-10 August 2016. Please sign up for a time to meet below.
__NOTOC__

{| border=1
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| width=25% |
==== 7 Aug (Sun) ====
* 2:15 pm:
* 3:00 pm: Open
* 3:45 pm: Yong
* 4:00 pm: Break
* 4:45 pm: Open
* 5:30 pm: Open
* 6:30 pm: Open
| width=25% |

==== 8 Aug (Mon) ====
* 9-11 am: Integrase project meeting (Victoria, Andrey, Sam, Ania, Cindy)
<hr>
* 12:45 pm: Anandh
* 1:30 pm: Shaobin (if TXTL meeting changed to today)
* 2:15 pm: Richard C
* 3:00 pm: Open
* 3:45 pm: Break
* 4:00 pm: Open
* 4:45 pm: Open
| width=25% |

==== 9 Aug (Tue) ====
* 8:30 am: Open
* 9:15 am: Open
* 10:00 am: Jaymie
* 11 am - 2 pm: DARPA Biological Control project meeting (Anandh, Ania, Cindy, James, Reed, Andrey, Sam?)
* 1:00 pm: Tung
* 1:45 pm: Hold: James
* 2:30 pm: Tony Fragoso
* 3:15 pm: Break
* 3:30 pm: Vipul
* 4:15 pm: Ioannis
* 5:00 pm: Open
* 5:45 pm: Break
| width=25% |

==== 10 Aug (Wed) ====
* 9-11 am: TX-TL project meeting (Clare, Mark, Shaobin, Yong, Vipul, Sam, Miki)
* 11:00 am: Shaobin
* 11:45 am: Unavailable
* 12:45 pm: Miki
* 1:45 pm: Open
* 2:30 pm: Leave for airport
|}

Aug 2016 meeting schedule

2016-07-31T18:05:39Z

Yywu: /* 7 Aug (Sun) */

Aug 2016 meeting schedule

2016-07-31T15:57:23Z

Yywu: /* 7 Aug (Sun) */

Richard will be in town 7-10 August 2016. Please sign up for a time to meet below.
__NOTOC__

{| border=1
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| width=25% |
==== 7 Aug (Sun) ====
* 2:15 pm: YONG?
* 3:00 pm: Open
* 3:45 pm: Open
* 4:00 pm: Break
* 4:45 pm: Open
* 5:30 pm: Open
* 6:30 pm: Open
| width=25% |

==== 8 Aug (Mon) ====
* 9-11 am: Integrase project meeting (Victoria, Andrey, Sam, Ania, Cindy)
<hr>
* 12:45 pm: Anandh
* 1:30 pm: Open
* 2:15 pm: Open
* 3:00 pm: Open
* 3:45 pm: Break
* 4:00 pm: Open
* 4:45 pm: Open
| width=25% |

==== 9 Aug (Tue) ====
* 8:30 am: Open
* 9:15 am: Open
* 10:00 am: Jaymie
* 11 am - 2 pm: DARPA Biological Control project meeting (Anandh, Ania, Cindy, James, Reed, Andrey, Sam?)
* 1:00 pm: Tung
* 1:45 pm: Hold: James
* 2:30 pm: Tony Fragoso
* 3:15 pm: Break
* 3:30 pm: Vipul
* 4:15 pm: Ioannis
* 5:00 pm: Open
* 5:45 pm: Break
| width=25% |

==== 10 Aug (Wed) ====
* 9-11 am: TX-TL project meeting (Clare, Mark, Shaobin, Yong, Vipul, Sam, Miki)
* 11:00 am: Shaobin
* 11:45 am: Unavailable
* 12:45 pm: Miki
* 1:45 pm: YONG?
* 2:30 pm: Leave for airport
|}

Aug 2016 meeting schedule

2016-07-31T15:57:04Z

Yywu: /* 10 Aug (Wed) */

Richard will be in town 7-10 August 2016. Please sign up for a time to meet below.
__NOTOC__

{| border=1
|- valign=top
| width=25% |
==== 7 Aug (Sun) ====
* 2:15 pm: Open
* 3:00 pm: Open
* 3:45 pm: Open
* 4:00 pm: Break
* 4:45 pm: Open
* 5:30 pm: Open
* 6:30 pm: Open
| width=25% |
==== 8 Aug (Mon) ====
* 9-11 am: Integrase project meeting (Victoria, Andrey, Sam, Ania, Cindy)
<hr>
* 12:45 pm: Anandh
* 1:30 pm: Open
* 2:15 pm: Open
* 3:00 pm: Open
* 3:45 pm: Break
* 4:00 pm: Open
* 4:45 pm: Open
| width=25% |

==== 9 Aug (Tue) ====
* 8:30 am: Open
* 9:15 am: Open
* 10:00 am: Jaymie
* 11 am - 2 pm: DARPA Biological Control project meeting (Anandh, Ania, Cindy, James, Reed, Andrey, Sam?)
* 1:00 pm: Tung
* 1:45 pm: Hold: James
* 2:30 pm: Tony Fragoso
* 3:15 pm: Break
* 3:30 pm: Vipul
* 4:15 pm: Ioannis
* 5:00 pm: Open
* 5:45 pm: Break
| width=25% |

==== 10 Aug (Wed) ====
* 9-11 am: TX-TL project meeting (Clare, Mark, Shaobin, Yong, Vipul, Sam, Miki)
* 11:00 am: Shaobin
* 11:45 am: Unavailable
* 12:45 pm: Miki
* 1:45 pm: YONG?
* 2:30 pm: Leave for airport
|}

Frank Bernhard, April 2016

2016-04-21T06:07:53Z

Yywu: /* Schedule */

Frank Bernhard will visit Caltech on 22 April 2016 (Fri). Please sign up below if you would like to meet with him:

=== Schedule ===

22 April 2016 (Friday):
* 9-11 am: Caltech/Amgen project discussion
* 11 am: Talk (room TBD)
* 12 pm: Lunch with Richard, Ching, Amit, Shaobin
* 1:30 pm: Yong (more flexible after 3 pm)
* 2:00 pm: Open
* 2:45 pm: Open
* 3:30 pm: Open
* 4:15 pm: Open
* 5:00 pm: Done for the day

=== Talk abstract ===

'''Frank Bernhard''' 
Institute of Biophysical Chemistry 
Center for Biomolecular Magnetic Resonance 
INSTRUCT Core Center for Cell-Free Expression 
J.W. Goethe-University, Frankfurt-am-Main 60438, Germany

Cell-free expression technologies represent a continuously growing central platform in the emerging field of synthetic biology. Core applications are the synthesis of difficult biomolecules that cannot be obtain in cellular production systems due to toxic effects, absence of proper folding environments or other limitations. Bacterial lysates of certain E. coli strains combine high production efficiencies with considerable tolerance for a wide range of supplied compounds such as stabilizer, cofactors or ligands. Cell-free expression environments can therefore be adjusted according to the individual requirements of synthesized target proteins. We have analyzed the proteome background of lysates processed for high expression efficiency by detailed proteomics studies. Effects of lysate modifications on proteome composition and quality of synthesized targets was further analyzed. In addition, we exemplify the screening of beneficial additives such as chemical chaperones.

Membrane proteins are key targets of current drug and antibody development and often difficult to synthesize in sufficient amounts and quality by using conventional cell-based production systems. Cell-free systems reduce complexity of membrane protein production to the central translation process and basic production protocols can be standardized. The open nature of cell-free systems furthermore allows to create customized and well-defined hydrophobic environments composed out of detergents, lipids or amphipols. Cell-free expression therefore completely re-designs natural targeting and folding pathways of membrane proteins. By using preformed membrane-like particles such as nanodiscs, even detergent sensitive membrane proteins can be synthesized and subsequently characterized at the molecular level. We exemplify the expression tuning of a variety of membrane proteins comprising G-protein coupled receptors, transporters or large complexes.

Frank Bernhard, April 2016

2016-04-21T05:09:30Z

Yywu: /* Schedule */

Frank Bernhard will visit Caltech on 22 April 2016 (Fri). Please sign up below if you would like to meet with him:

=== Schedule ===

22 April 2016 (Friday):
* 9-11 am: Caltech/Amgen project discussion
* 11 am: Talk (room TBD)
* 12 pm: Lunch with Richard, Ching, Amit, Shaobin
* 1:30 pm: Yong (more flexible aber 3 pm)
* 2:00 pm: Open
* 2:45 pm: Open
* 3:30 pm: Open
* 4:15 pm: Open
* 5:00 pm: Done for the day

=== Talk abstract ===

'''Frank Bernhard''' 
Institute of Biophysical Chemistry 
Center for Biomolecular Magnetic Resonance 
INSTRUCT Core Center for Cell-Free Expression 
J.W. Goethe-University, Frankfurt-am-Main 60438, Germany

Cell-free expression technologies represent a continuously growing central platform in the emerging field of synthetic biology. Core applications are the synthesis of difficult biomolecules that cannot be obtain in cellular production systems due to toxic effects, absence of proper folding environments or other limitations. Bacterial lysates of certain E. coli strains combine high production efficiencies with considerable tolerance for a wide range of supplied compounds such as stabilizer, cofactors or ligands. Cell-free expression environments can therefore be adjusted according to the individual requirements of synthesized target proteins. We have analyzed the proteome background of lysates processed for high expression efficiency by detailed proteomics studies. Effects of lysate modifications on proteome composition and quality of synthesized targets was further analyzed. In addition, we exemplify the screening of beneficial additives such as chemical chaperones.

Membrane proteins are key targets of current drug and antibody development and often difficult to synthesize in sufficient amounts and quality by using conventional cell-based production systems. Cell-free systems reduce complexity of membrane protein production to the central translation process and basic production protocols can be standardized. The open nature of cell-free systems furthermore allows to create customized and well-defined hydrophobic environments composed out of detergents, lipids or amphipols. Cell-free expression therefore completely re-designs natural targeting and folding pathways of membrane proteins. By using preformed membrane-like particles such as nanodiscs, even detergent sensitive membrane proteins can be synthesized and subsequently characterized at the molecular level. We exemplify the expression tuning of a variety of membrane proteins comprising G-protein coupled receptors, transporters or large complexes.

Frank Bernhard, April 2016

2016-04-21T04:55:25Z

Yywu: /* Schedule */

Frank Bernhard will visit Caltech on 22 April 2016 (Fri). Please sign up below if you would like to meet with him:

=== Schedule ===

22 April 2016 (Friday):
* 9-11 am: Caltech/Amgen project discussion
* 11 am: Talk (room TBD)
* 12 pm: Lunch with Richard, Ching, Amit, Shaobin
* 1:30 pm: Yong
* 2:00 pm: Open
* 2:45 pm: Open
* 3:30 pm: Open
* 4:15 pm: Open
* 5:00 pm: Done for the day

=== Talk abstract ===

'''Frank Bernhard''' 
Institute of Biophysical Chemistry 
Center for Biomolecular Magnetic Resonance 
INSTRUCT Core Center for Cell-Free Expression 
J.W. Goethe-University, Frankfurt-am-Main 60438, Germany

Cell-free expression technologies represent a continuously growing central platform in the emerging field of synthetic biology. Core applications are the synthesis of difficult biomolecules that cannot be obtain in cellular production systems due to toxic effects, absence of proper folding environments or other limitations. Bacterial lysates of certain E. coli strains combine high production efficiencies with considerable tolerance for a wide range of supplied compounds such as stabilizer, cofactors or ligands. Cell-free expression environments can therefore be adjusted according to the individual requirements of synthesized target proteins. We have analyzed the proteome background of lysates processed for high expression efficiency by detailed proteomics studies. Effects of lysate modifications on proteome composition and quality of synthesized targets was further analyzed. In addition, we exemplify the screening of beneficial additives such as chemical chaperones.

Membrane proteins are key targets of current drug and antibody development and often difficult to synthesize in sufficient amounts and quality by using conventional cell-based production systems. Cell-free systems reduce complexity of membrane protein production to the central translation process and basic production protocols can be standardized. The open nature of cell-free systems furthermore allows to create customized and well-defined hydrophobic environments composed out of detergents, lipids or amphipols. Cell-free expression therefore completely re-designs natural targeting and folding pathways of membrane proteins. By using preformed membrane-like particles such as nanodiscs, even detergent sensitive membrane proteins can be synthesized and subsequently characterized at the molecular level. We exemplify the expression tuning of a variety of membrane proteins comprising G-protein coupled receptors, transporters or large complexes.

Research meetings, Jan/Feb 2016

2016-01-18T22:56:18Z

Yywu: /* 2 Feb 2016 (Tue) */

Please sign up for a slot below. __NOTOC__

{| border=1 width=100%
|- valign = top
|
=== 25 Jan 2016 (Mon) ===
* Richard in SF
|
=== 26 Jan 2016 (Tue) ===
* 1-2 pm: Andrey Shur
* 2-3 pm: Anders Knight
* 3-4 pm: Reed McCardell
* 5:30-6:30 pm: Ania Baetica
|

=== 27 Jan 2016 (Wed) ===
* 8:30-9:30 am: open
* 9:30-10:30 am: open
* 4-5 pm: open
* 5-6 pm: open
|
=== 28 Jan 2016 (Thu) ===
* 5:30-6:30 pm: open
* 6:30-7:30 pm: open
|
=== 29 Jan 2016 (Fri) ===
* 2-3 pm: open
* 3-4 pm: open
* 4:30-5:30 pm: Ioannis Filippidis
* 5:30-6:30 pm: open
|- valign = top
|

=== 25 Jan 2016 (Mon) ===
* Richard in Hartford
|
=== 2 Feb 2016 (Tue) ===
* 9-10 am: Yong W.
* 2-3 pm: Tony Fragoso
* 3-4 pm: open
* 4-5 pm: open
* 5:30-6:30 pm: open
* 6:30-7:30 pm: open
|

=== 3 Feb 2016 (Wed) ===
* 8:30-9:30 am: open
* 9:30-10:30 am: open
|
=== 4 Feb 2016 (Thu) ===
* Richard in SF
|
=== 5 Feb 2016 (Fri) ===
* BE visiting day
|}

Tom Ellis, May 2015

2015-05-04T22:59:19Z

Yywu: /* Schedule: 18 May (Mon) */

Tom Ellis from Imperial College will be visiting on 18 May (Mon). If you would like to meet with him, please sign up for a slot below.

=== Schedule: 18 May (Mon) ===

{{agenda begin}}
{{agenda item|12:00 pm|Lunch with Richard}}
{{agenda item|1:15 pm|Open}}
{{agenda item|2:00 pm|Open}}
{{agenda item|2:45 pm|Open}}
{{agenda item|3:30 pm|Open}}
{{agenda item|4:15 pm|Yong,}}
{{agenda item|5:00 pm|Richard}}
{{agenda item|5:30 pm|Done for the day}}
{{agenda end}}

SURF 2015: Design space exploration of the violacein pathway in TX-TL

2014-12-23T00:44:35Z

Yywu:

'''[[SURF 2015|2015 SURF]] project description'''
*Mentor: Richard Murray
*Co-mentor: Shaobin Guo and Yong Wu

[[File:Violacein.jpg|300px|thumb|Figure 1. Violacein Pathway (Balibar, 2006).]]
===Project Description===
This project aims to explore the possibilities of utilizing cell-free systems to resolve some of the challenges and difficulties in metabolic engineering. Challenges in studying metabolic pathway include feedback loop, bifunctional enzymes, and parallel reactions (Woolston, 2012). Furthermore, the precise control of enzyme expressions and activities in complex pathway is difficult to achieve. On the other hand, cell-free systems simulate controlled cell environment. Several key benefits of using cell-free systems as biomolecular breadboard include small reaction volume, protein expressions from linear pieces of DNAs, and simultaneous protein expressions of multiple pieces of DNAs (Sun, 2013). These unique properties open up the possibilities of modulating concentrations of DNA encoding individual pathway enzymes, testing the related effect on metabolite production, and exploring pathway design space.

Violacein is a water-insoluble violet pigment that naturally exists in a few bacteria (Jiang, 2010 & Pantanella, 2007). Violacein has the potential applications in antibacterial, anti-trypanocidal, anti-ulcerogenic, and anticancer drugs (Balibar, 2006). The various enzymes involved in the pathway can lead to the production of byproducts that might interfere with quantification of violacein. The goal of the project is to characterize the violacein pathway using cell-free transcription and translational (TX-TL) system. Students will need to clone pathway enzymes under desired promoters and RBSes (ribosomal binding sites). Students will develop reliable quantification methods for violacein. Students will take advantages of the TX-TL system to explore ways to improve violacein production.

''Skills:'' Students are required to be flexible and have the willingness to learn new things. Background in organic chemistry (Ch 41abc or equivalent) and experience with analytical techniques or separation methods (Ch 4a, Ch/ChE 9, Ch 24, ChE 62, or equivalent) is recommended, but not required. Students interested in this project might need some basic microbiology laboratory experience( Bi 1X, Bi 10, ChE/BE 130, or equivalent), but not required.
===References: ===

Balibar, C. J. and C. T. Walsh (2006). "[http://pubs.acs.org/doi/full/10.1021/bi061998z In Vitro Biosynthesis of Violacein from l-Tryptophan by the Enzymes VioA−E from Chromobacterium violaceum]." Biochemistry 45(51): 15444-15457. [http://pubs.acs.org/doi/full/10.1021/bi061998z]

Jiang, P.-x., et al. (2010). "[http://link.springer.com/article/10.1007%2Fs00253-009-2375-z Reconstruction of the violacein biosynthetic pathway from Duganella sp. B2 in different heterologous hosts]." Applied Microbiology and Biotechnology 86(4): 1077-1088.

Pantanella, F., et al. (2007). "[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2672.2006.03155.x/full Violacein and biofilm production in Janthinobacterium lividum]." Journal of Applied Microbiology 102(4): 992-999.

Sun, Z. Z., et al. (2013). "[http://www.jove.com/video/50762/protocols-for-implementing-an-escherichia-coli-based-tx-tl-cell-free Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology]." (79): e50762.

Sun, Z. Z., et al. (2013). "[http://pubs.acs.org/doi/abs/10.1021/sb400131a Linear DNA for Rapid Prototyping of Synthetic Biological Circuits in an Escherichia coli Based TX-TL Cell-Free System]." ACS Synthetic Biology.

Woolston, B. M., et al. (2013). "[http://www.annualreviews.org/doi/abs/10.1146/annurev-chembioeng-061312-103312 Metabolic Engineering: Past and Future]." Annual Review of Chemical and Biomolecular Engineering 4(1): 259-288.

SURF 2015: Design space exploration of the violacein pathway in TX-TL

2014-12-23T00:33:35Z

Yywu:

'''[[SURF 2015|2015 SURF]] project description'''
*Mentor: Richard Murray
*Co-mentor: Shaobin Guo and Yong Wu

[[File:Violacein.jpg|300px|thumb|Figure 1. Violacein Pathway (Balibar, 2006).]]
===Project Description===
This project aims to explore the possibilities of utilizing cell-free systems to resolve some of the challenges and difficulties in metabolic engineering. Challenges in studying metabolic pathway include feedback loop, bifunctional enzymes, and parallel reactions (Woolston, 2012). Furthermore, the precise control of enzyme expressions and activities in complex pathway is difficult to achieve. On the other hand, cell-free systems simulate controlled cell environment. Several key benefits of using cell-free systems as biomolecular breadboard include small reaction volume, protein expressions from linear pieces of DNAs, and simultaneous protein expressions of multiple pieces of DNAs (Sun, 2013). These unique properties open up the possibilities of modulating concentrations of DNA encoding individual pathway enzymes, testing the related effect on metabolite production, and exploring pathway design space.

Violacein is a water-insoluble violet pigment that naturally exists in a few bacteria (Jiang, 2010 & Pantanella, 2007). Violacein has the potential applications in antibacterial, anti-trypanocidal, anti-ulcerogenic, and anticancer drugs (Balibar, 2006). The various enzymes involved in the pathway can lead to the production of byproducts that might interfere with quantification of violacein. The goal of the project is to characterize the violacein pathway using cell-free transcription and translational (TX-TL) system. Students will need to clone pathway enzymes under desired promoters and RBSes (ribosomal binding sites). Students will develop reliable quantification methods for violacein. Students will take advantages of the TX-TL system to explore ways to improve violacein production.

''Skills:'' Background in organic chemistry (Ch 41abc or equivalent) and experience with analytical techniques or separation methods (Ch 4a, Ch/ChE 9, Ch 24, ChE 62, or equivalent) is recommended.
Students interested in this project might need some basic microbiology laboratory experience ( Bi 1X, Bi 10, ChE/BE 130, or equivalent).
===References: ===

Balibar, C. J. and C. T. Walsh (2006). "[http://pubs.acs.org/doi/full/10.1021/bi061998z In Vitro Biosynthesis of Violacein from l-Tryptophan by the Enzymes VioA−E from Chromobacterium violaceum]." Biochemistry 45(51): 15444-15457. [http://pubs.acs.org/doi/full/10.1021/bi061998z]

Jiang, P.-x., et al. (2010). "[http://link.springer.com/article/10.1007%2Fs00253-009-2375-z Reconstruction of the violacein biosynthetic pathway from Duganella sp. B2 in different heterologous hosts]." Applied Microbiology and Biotechnology 86(4): 1077-1088.

Pantanella, F., et al. (2007). "[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2672.2006.03155.x/full Violacein and biofilm production in Janthinobacterium lividum]." Journal of Applied Microbiology 102(4): 992-999.

Sun, Z. Z., et al. (2013). "[http://www.jove.com/video/50762/protocols-for-implementing-an-escherichia-coli-based-tx-tl-cell-free Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology]." (79): e50762.

Sun, Z. Z., et al. (2013). "[http://pubs.acs.org/doi/abs/10.1021/sb400131a Linear DNA for Rapid Prototyping of Synthetic Biological Circuits in an Escherichia coli Based TX-TL Cell-Free System]." ACS Synthetic Biology.

Woolston, B. M., et al. (2013). "[http://www.annualreviews.org/doi/abs/10.1146/annurev-chembioeng-061312-103312 Metabolic Engineering: Past and Future]." Annual Review of Chemical and Biomolecular Engineering 4(1): 259-288.

SURF 2015: Design space exploration of the violacein pathway in TX-TL

2014-12-22T19:50:09Z

Yywu:

'''[[SURF 2015|2015 SURF]] project description'''
*Mentor: Richard Murray
*Co-mentor: Shaobin Guo and Yong Wu

[[File:Violacein.jpg|300px|thumb|Figure 1. Violacein Pathway (Balibar, 2006).]]
===Project Description===
This project aims to explore the possibilities of utilizing cell-free systems to resolve some of the challenges and difficulties in metabolic engineering. Challenges in studying metabolic pathway include feedback loop, bifunctional enzymes, and parallel reactions (Woolston, 2012). Furthermore, the precise control of enzyme expressions and activities in complex pathway is difficult to achieve. On the other hand, cell-free systems simulate controlled cell environment. Several key benefits of using cell-free systems as biomolecular breadboard include small reaction volume, protein expressions from linear pieces of DNAs, and simultaneous protein expressions of multiple pieces of DNAs (Sun, 2013). These unique properties open up the possibilities of modulating concentrations of DNA encoding individual pathway enzymes, testing the related effect on metabolite production, and exploring pathway design space.

Violacein is a water-insoluble violet pigment that naturally exists in a few bacteria (Jiang, 2010 & Pantanella, 2007). Violacein has the potential applications in antibacterial, anti-trypanocidal, anti-ulcerogenic, and anticancer drugs (Balibar, 2006). The various enzymes involved in the pathway can lead to the production of byproducts that might interfere with quantification of violacein. The goal of the project is to characterize the violacein pathway using cell-free transcription and translational (TX-TL) system. Students will need to clone pathway enzymes under desired promoters and RBSes (ribosomal binding sites). Students will develop reliable quantification methods for violacein. Students will take advantages of the TX-TL system to explore ways to improve violacein production.

''Skills:'' Students interested in this project is required to have some basic microbiology laboratory experience ( Bi 1X, Bi 10, ChE/BE 130, or equivalent). Experience with either MATLAB, Python or a similar scientific programming package is strongly recommended. Other desired qualities include background in organic chemistry (Ch 41abc or equivalent) and experience with analytical techniques or separation methods (Ch 4a, Ch/ChE 9, Ch 24, ChE 62, or equivalent).

===References: ===

Balibar, C. J. and C. T. Walsh (2006). "[http://pubs.acs.org/doi/full/10.1021/bi061998z In Vitro Biosynthesis of Violacein from l-Tryptophan by the Enzymes VioA−E from Chromobacterium violaceum]." Biochemistry 45(51): 15444-15457. [http://pubs.acs.org/doi/full/10.1021/bi061998z]

Jiang, P.-x., et al. (2010). "[http://link.springer.com/article/10.1007%2Fs00253-009-2375-z Reconstruction of the violacein biosynthetic pathway from Duganella sp. B2 in different heterologous hosts]." Applied Microbiology and Biotechnology 86(4): 1077-1088.

Pantanella, F., et al. (2007). "[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2672.2006.03155.x/full Violacein and biofilm production in Janthinobacterium lividum]." Journal of Applied Microbiology 102(4): 992-999.

Sun, Z. Z., et al. (2013). "[http://www.jove.com/video/50762/protocols-for-implementing-an-escherichia-coli-based-tx-tl-cell-free Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology]." (79): e50762.

Sun, Z. Z., et al. (2013). "[http://pubs.acs.org/doi/abs/10.1021/sb400131a Linear DNA for Rapid Prototyping of Synthetic Biological Circuits in an Escherichia coli Based TX-TL Cell-Free System]." ACS Synthetic Biology.

Woolston, B. M., et al. (2013). "[http://www.annualreviews.org/doi/abs/10.1146/annurev-chembioeng-061312-103312 Metabolic Engineering: Past and Future]." Annual Review of Chemical and Biomolecular Engineering 4(1): 259-288.

SURF 2015: Design space exploration of the violacein pathway in TX-TL

2014-12-22T19:45:10Z

Yywu:

'''[[SURF 2015|2015 SURF]] project description'''
*Mentor: Richard Murray
*Co-mentor: Shaobin Guo and Yong Wu

[[File:Violacein.jpg|300px|thumb|Figure 1. Violacein Pathway (Balibar, 2006).]]
===Project Description===
This project aims to explore the possibilities of utilizing cell-free systems to resolve some of the challenges and difficulties in metabolic engineering. Challenges in studying metabolic pathway include feedback loop, bifunctional enzymes, and parallel reactions (Woolston, 2012). Furthermore, the precise control of enzyme expressions and activities in complex pathway is difficult to achieve. On the other hand, cell-free systems simulate controlled cell environment. Several key benefits of using cell-free systems as biomolecular breadboard include small reaction volume, protein expressions from linear pieces of DNAs, and simultaneous protein expressions of multiple pieces of DNAs (Sun, 2013). These unique properties open up the possibilities of modulating concentrations of DNA encoding individual pathway enzymes, testing the related effect on metabolite production, and exploring pathway design space.

Violacein is a water-insoluble violet pigment that naturally exists in a few bacteria (Jiang, 2010 & Pantanella, 2007). Violacein has the potential applications in antibacterial, anti-trypanocidal, anti-ulcerogenic, and anticancer drugs (Balibar, 2006). The various enzymes involved in the pathway can lead to the production of byproducts that might interfere with quantification of violacein. The goal of the project is to characterize the violacein pathway using cell-free transcription and translational (TX-TL) system. Students will develop reliable quantification methods for violacein and take advantages of the TX-TL system to explore ways to improve violacein production.

''Skills:'' Students interested in this project is required to have some basic microbiology laboratory experience ( Bi 1X, Bi 10, ChE/BE 130, or equivalent). Experience with either MATLAB, Python or a similar scientific programming package is strongly recommended. Other desired qualities include background in organic chemistry (Ch 41abc or equivalent) and experience with analytical techniques or separation methods (Ch 4a, Ch/ChE 9, Ch 24, ChE 62, or equivalent).

===References: ===

Balibar, C. J. and C. T. Walsh (2006). "[http://pubs.acs.org/doi/full/10.1021/bi061998z In Vitro Biosynthesis of Violacein from l-Tryptophan by the Enzymes VioA−E from Chromobacterium violaceum]." Biochemistry 45(51): 15444-15457. [http://pubs.acs.org/doi/full/10.1021/bi061998z]

Jiang, P.-x., et al. (2010). "[http://link.springer.com/article/10.1007%2Fs00253-009-2375-z Reconstruction of the violacein biosynthetic pathway from Duganella sp. B2 in different heterologous hosts]." Applied Microbiology and Biotechnology 86(4): 1077-1088.

Pantanella, F., et al. (2007). "[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2672.2006.03155.x/full Violacein and biofilm production in Janthinobacterium lividum]." Journal of Applied Microbiology 102(4): 992-999.

Sun, Z. Z., et al. (2013). "[http://www.jove.com/video/50762/protocols-for-implementing-an-escherichia-coli-based-tx-tl-cell-free Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology]." (79): e50762.

Sun, Z. Z., et al. (2013). "[http://pubs.acs.org/doi/abs/10.1021/sb400131a Linear DNA for Rapid Prototyping of Synthetic Biological Circuits in an Escherichia coli Based TX-TL Cell-Free System]." ACS Synthetic Biology.

Woolston, B. M., et al. (2013). "[http://www.annualreviews.org/doi/abs/10.1146/annurev-chembioeng-061312-103312 Metabolic Engineering: Past and Future]." Annual Review of Chemical and Biomolecular Engineering 4(1): 259-288.

SURF 2015: Design space exploration of the violacein pathway in TX-TL

2014-12-22T19:44:07Z

Yywu:

'''[[SURF 2015|2015 SURF]] project description'''
*Mentor: Richard Murray
*Co-mentor: Shaobin Guo and Yong Wu

[[File:Violacein.jpg|300px|thumb|Figure 1. Violacein Pathway (Balibar, 2006).]]
===Project Description===
This project aims to explore the possibilities of utilizing cell-free systems to resolve some of the challenges and difficulties in metabolic engineering. Challenges in studying metabolic pathway include feedback loop, bifunctional enzymes, and parallel reactions (Woolston, 2012). Furthermore, the precise control of enzyme expressions and activities in complex pathway is difficult to achieve. On the other hand, cell-free systems simulate controlled cell environment. Several key benefits of using cell-free systems as biomolecular breadboard include small reaction volume, protein expressions from linear pieces of DNAs, and simultaneous protein expressions of multiple pieces of DNAs (Sun, 2013). These unique properties open up the possibilities of modulating concentrations of DNA encoding individual pathway enzymes, testing the related effect on metabolite production, and exploring pathway design space.

Violacein is a water-insoluble violet pigment that naturally exists in a few bacteria (Jiang, 2010 & Pantanella, 2007). Violacein has the potential applications in antibacterial, anti-trypanocidal, anti-ulcerogenic, and anticancer drugs (Balibar, 2006). The various enzymes involved in the pathway can lead to the production of byproducts that might interfere with quantification of violacein. The goal of the project is to characterize the violacein pathway using cell-free transcription and translational (TX-TL) system. Students will develop reliable quantification methods for violacein and take advantages of the TX-TL system to explore ways to improve violacein production.

''Skills:'' Students interested in this project is required to have some basic microbiology laboratory experience ( Bi 1X, Bi 10, ChE/BE 130, or equivalent). Experience with either MATLAB, Python or a similar scientific programming package is strongly recommended. Other desired qualities include background in organic chemistry (Ch 41abc or equivalent) and experience with analytical techniques or separation methods (Ch 4a, Ch/ChE 9, Ch 24, ChE 62, or equivalent).

===References: ===

Balibar, C. J. and C. T. Walsh (2006). "[http://pubs.acs.org/doi/full/10.1021/bi061998z In Vitro Biosynthesis of Violacein from l-Tryptophan by the Enzymes VioA−E from Chromobacterium violaceum]." Biochemistry 45(51): 15444-15457. [http://pubs.acs.org/doi/full/10.1021/bi061998z]

Hoshino, T. (2011). "[http://link.springer.com/article/10.1007%2Fs00253-011-3468-z Violacein and related tryptophan metabolites produced by Chromobacterium violaceum: biosynthetic mechanism and pathway for construction of violacein core]." Applied Microbiology and Biotechnology 91(6):1463-1475.

Jiang, P.-x., et al. (2010). "[http://link.springer.com/article/10.1007%2Fs00253-009-2375-z Reconstruction of the violacein biosynthetic pathway from Duganella sp. B2 in different heterologous hosts]." Applied Microbiology and Biotechnology 86(4): 1077-1088.

Pantanella, F., et al. (2007). "[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2672.2006.03155.x/full Violacein and biofilm production in Janthinobacterium lividum]." Journal of Applied Microbiology 102(4): 992-999.

Sun, Z. Z., et al. (2013). "[http://www.jove.com/video/50762/protocols-for-implementing-an-escherichia-coli-based-tx-tl-cell-free Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology]." (79): e50762.

Sun, Z. Z., et al. (2013). "[http://pubs.acs.org/doi/abs/10.1021/sb400131a Linear DNA for Rapid Prototyping of Synthetic Biological Circuits in an Escherichia coli Based TX-TL Cell-Free System]." ACS Synthetic Biology.

Woolston, B. M., et al. (2013). "[http://www.annualreviews.org/doi/abs/10.1146/annurev-chembioeng-061312-103312 Metabolic Engineering: Past and Future]." Annual Review of Chemical and Biomolecular Engineering 4(1): 259-288.

SURF 2015: Design space exploration of the violacein pathway in TX-TL

2014-12-22T18:38:37Z

Yywu:

'''[[SURF 2015|2015 SURF]] project description'''
*Mentor: Richard Murray
*Co-mentor: Shaobin Guo and Yong Wu

[[File:Violacein.jpg|300px|thumb|Figure 1. Violacein Pathway (Balibar, 2006).]]
===Project Description===
Violacein is a water-insoluble violet pigment that naturally exists in a few bacteria (Jiang, 2010 & Pantanella, 2007). Violacein has the potential applications in antibacterial, anti-trypanocidal, anti-ulcerogenic, and anticancer drugs (Balibar, 2006). The pathway to produce violacein from tryptophan consists of five enzymes vioA-E (Hoshino, 2011). The pathway is NADPH dependent and consumes oxygen. The various enzymes involved in the pathway could also lead to the production of a few colorful byproducts, which might interfere with fluorescence signals when plate reader is used. The goal of the project is to characterize the violacein pathway using cell-free transcription and translational (TX-TL) system (Sun, 2013). Student will take advantage of the TX-TL system to explore ways to improve violacein production.

''Skills:'' Students interested in this project is required to have some basic microbiology laboratory experience ( Bi 1X, Bi 10, ChE/BE 130, or equivalent). Experience with either MATLAB, Python or a similar scientific programming package is strongly recommended. Other desired qualities include background in organic chemistry (Ch 41abc or equivalent) and experience with analytical techniques or separation methods (Ch 4a, Ch/ChE 9, Ch 24, ChE 62, or equivalent).

===References: ===

Balibar, C. J. and C. T. Walsh (2006). "[http://pubs.acs.org/doi/full/10.1021/bi061998z In Vitro Biosynthesis of Violacein from l-Tryptophan by the Enzymes VioA−E from Chromobacterium violaceum]." Biochemistry 45(51): 15444-15457. [http://pubs.acs.org/doi/full/10.1021/bi061998z]

Hoshino, T. (2011). "[http://link.springer.com/article/10.1007%2Fs00253-011-3468-z Violacein and related tryptophan metabolites produced by Chromobacterium violaceum: biosynthetic mechanism and pathway for construction of violacein core]." Applied Microbiology and Biotechnology 91(6):1463-1475.

Jiang, P.-x., et al. (2010). "[http://link.springer.com/article/10.1007%2Fs00253-009-2375-z Reconstruction of the violacein biosynthetic pathway from Duganella sp. B2 in different heterologous hosts]." Applied Microbiology and Biotechnology 86(4): 1077-1088.

Pantanella, F., et al. (2007). "[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2672.2006.03155.x/full Violacein and biofilm production in Janthinobacterium lividum]." Journal of Applied Microbiology 102(4): 992-999.

Sun, Z. Z., et al. (2013). "[http://www.jove.com/video/50762/protocols-for-implementing-an-escherichia-coli-based-tx-tl-cell-free Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology]." (79): e50762.

Sun, Z. Z., et al. (2013). "[http://pubs.acs.org/doi/abs/10.1021/sb400131a Linear DNA for Rapid Prototyping of Synthetic Biological Circuits in an Escherichia coli Based TX-TL Cell-Free System]." ACS Synthetic Biology.

SURF 2015: Design space exploration of the violacein pathway in TX-TL

2014-12-22T18:37:33Z

Yywu:

'''[[SURF 2015|2015 SURF]] project description'''
*Mentor: Richard Murray
*Co-mentor: Shaobin Guo and Yong Wu

[[File:Violacein.jpg|300px|thumb|Figure 1. Violacein Pathway (Balibar, 2006).]]
===Project Description===
Violacein is a water-insoluble violet pigment that naturally exists in a few bacteria (Jiang, 2010 & Pantanella, 2007). Violacein has the potential applications in antibacterial, anti-trypanocidal, anti-ulcerogenic, and anticancer drugs (Balibar, 2006). The pathway to produce violacein from tryptophan consists of five enzymes vioA-E (Hoshino, 2011). The pathway is NADPH dependent and consumes oxygen. The various enzymes involved in the pathway could also lead to the production of a few colorful byproducts, which might interfere with fluorescence signals when plate reader is used. The goal of the project is to characterize the violacein pathway using cell-free transcription and translational (TX-TL) system (Sun, 2013). Student will take advantage of the TX-TL system to explore ways to improve violacein production.

Students interested in this project is required to have some basic microbiology laboratory skills ( Bi 1X, Bi 10, ChE/BE 130, or equivalent). Experience with either MATLAB, Python or a similar scientific programming package is strongly recommended. Other desired qualities include background in organic chemistry (Ch 41abc or equivalent) and experience with analytical techniques or separation methods (Ch 4a, Ch/ChE 9, Ch 24, ChE 62, or equivalent).

===References: ===

Balibar, C. J. and C. T. Walsh (2006). "[http://pubs.acs.org/doi/full/10.1021/bi061998z In Vitro Biosynthesis of Violacein from l-Tryptophan by the Enzymes VioA−E from Chromobacterium violaceum]." Biochemistry 45(51): 15444-15457. [http://pubs.acs.org/doi/full/10.1021/bi061998z]

Hoshino, T. (2011). "[http://link.springer.com/article/10.1007%2Fs00253-011-3468-z Violacein and related tryptophan metabolites produced by Chromobacterium violaceum: biosynthetic mechanism and pathway for construction of violacein core]." Applied Microbiology and Biotechnology 91(6):1463-1475.

Jiang, P.-x., et al. (2010). "[http://link.springer.com/article/10.1007%2Fs00253-009-2375-z Reconstruction of the violacein biosynthetic pathway from Duganella sp. B2 in different heterologous hosts]." Applied Microbiology and Biotechnology 86(4): 1077-1088.

Pantanella, F., et al. (2007). "[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2672.2006.03155.x/full Violacein and biofilm production in Janthinobacterium lividum]." Journal of Applied Microbiology 102(4): 992-999.

Sun, Z. Z., et al. (2013). "[http://www.jove.com/video/50762/protocols-for-implementing-an-escherichia-coli-based-tx-tl-cell-free Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology]." (79): e50762.

Sun, Z. Z., et al. (2013). "[http://pubs.acs.org/doi/abs/10.1021/sb400131a Linear DNA for Rapid Prototyping of Synthetic Biological Circuits in an Escherichia coli Based TX-TL Cell-Free System]." ACS Synthetic Biology.

SURF 2015: Design space exploration of the violacein pathway in TX-TL

2014-12-19T20:23:55Z

Yywu:

'''[[SURF 2015|2015 SURF]] project description'''
*Mentor: Richard Murray
*Co-mentor: Shaobin Guo and Yong Wu

[[File:Violacein.jpg|300px|thumb|Figure 1. Violacein Pathway (Balibar, 2006).]]
===Project Description===
Violacein is a water-insoluble violet pigment that naturally exists in a few bacteria (Jiang, 2010 & Pantanella, 2007). Violacein has the potential applications in antibacterial, anti-trypanocidal, anti-ulcerogenic, and anticancer drugs (Balibar, 2006). The pathway to produce violacein from tryptophan consists of five enzymes vioA-E (Hoshino, 2011). The pathway is NADPH dependent and consumes oxygen. The various enzymes involved in the pathway could also lead to the production of a few colorful byproducts, which might interfere with fluorescence signals when plate reader is used. The goal of the project is to characterize the violacein pathway using cell-free transcription and translational (TX-TL) system (Sun, 2013). Student will take advantage of the TX-TL system to explore ways to improve violacein production.

===References: ===

Balibar, C. J. and C. T. Walsh (2006). "[http://pubs.acs.org/doi/full/10.1021/bi061998z In Vitro Biosynthesis of Violacein from l-Tryptophan by the Enzymes VioA−E from Chromobacterium violaceum]." Biochemistry 45(51): 15444-15457. [http://pubs.acs.org/doi/full/10.1021/bi061998z]

Hoshino, T. (2011). "[http://link.springer.com/article/10.1007%2Fs00253-011-3468-z Violacein and related tryptophan metabolites produced by Chromobacterium violaceum: biosynthetic mechanism and pathway for construction of violacein core]." Applied Microbiology and Biotechnology 91(6):1463-1475.

Jiang, P.-x., et al. (2010). "[http://link.springer.com/article/10.1007%2Fs00253-009-2375-z Reconstruction of the violacein biosynthetic pathway from Duganella sp. B2 in different heterologous hosts]." Applied Microbiology and Biotechnology 86(4): 1077-1088.

Pantanella, F., et al. (2007). "[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2672.2006.03155.x/full Violacein and biofilm production in Janthinobacterium lividum]." Journal of Applied Microbiology 102(4): 992-999.

Sun, Z. Z., et al. (2013). "[http://www.jove.com/video/50762/protocols-for-implementing-an-escherichia-coli-based-tx-tl-cell-free Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology]." (79): e50762.

Sun, Z. Z., et al. (2013). "[http://pubs.acs.org/doi/abs/10.1021/sb400131a Linear DNA for Rapid Prototyping of Synthetic Biological Circuits in an Escherichia coli Based TX-TL Cell-Free System]." ACS Synthetic Biology.

SURF 2015: Design space exploration of the violacein pathway in TX-TL

2014-12-19T20:23:17Z

Yywu:

'''[[SURF 2015|2015 SURF]] project description'''
*Mentor: Richard Murray
*Co-mentor: Shaobin Guo and Yong Wu

[[File:Violacein.jpg|300px|thumb|Figure 1. Violacein Pathway (Balibar, 2006).]]
===Project Description===
Violacein is a water-insoluble violet pigment that naturally exists in a few bacteria (Jiang, 2010 & Pantanella, 2007). Violacein has the potential applications in antibacterial, anti-trypanocidal, anti-ulcerogenic, and anticancer drugs (Balibar, 2006). The pathway to produce violacein from tryptophan consists of five enzymes vioA-E (Hoshino, 2011). The pathway is NADPH dependent and consumes oxygen. The various enzymes involved in the pathway could also lead to the production of a few colorful byproducts, which might interfere with fluorescence signals when plate reader is used. The goal of the project is to characterize the violacein pathway using cell-free transcription and translational (TX-TL) system (Sun, 2013). Student will take advantage of the TX-TL system to explore ways to improve violacein production.

===References: ===

Balibar, C. J. and C. T. Walsh (2006). "[http://pubs.acs.org/doi/full/10.1021/bi061998z In Vitro Biosynthesis of Violacein from l-Tryptophan by the Enzymes VioA−E from Chromobacterium violaceum]." Biochemistry 45(51): 15444-15457. [http://pubs.acs.org/doi/full/10.1021/bi061998z]

Hoshino, T. (2011). "[http://link.springer.com/article/10.1007%2Fs00253-011-3468-z Violacein and related tryptophan metabolites produced by Chromobacterium violaceum: biosynthetic mechanism and pathway for construction of violacein core]." Applied Microbiology and Biotechnology 91(6):1463-1475.

Jiang, P.-x., et al. (2010). "[http://link.springer.com/article/10.1007%2Fs00253-009-2375-z Reconstruction of the violacein biosynthetic pathway from Duganella sp. B2 in different heterologous hosts]." Applied Microbiology and Biotechnology 86(4): 1077-1088.

Pantanella, F., et al. (2007). "[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2672.2006.03155.x/full Violacein and biofilm production in Janthinobacterium lividum]." Journal of Applied Microbiology 102(4): 992-999.

Sun, Z. Z., et al. (2013). "[http://www.jove.com/video/50762/protocols-for-implementing-an-escherichia-coli-based-tx-tl-cell-free Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology]." (79): e50762.

Sun, Z. Z., et al. (2013). "[http://pubs.acs.org/doi/abs/10.1021/sb400131a Linear DNA for Rapid Prototyping of Synthetic Biological Circuits in an Escherichia coli Based TX-TL Cell-Free System]." ACS Synthetic Biology.

SURF 2015: Design space exploration of the violacein pathway in TX-TL

2014-12-19T20:22:51Z

Yywu:

*Mentor: Richard Murray
*Co-mentor: Shaobin Guo and Yong Wu

[[File:Violacein.jpg|300px|thumb|Figure 1. Violacein Pathway (Balibar, 2006).]]
===Project Description===
Violacein is a water-insoluble violet pigment that naturally exists in a few bacteria (Jiang, 2010 & Pantanella, 2007). Violacein has the potential applications in antibacterial, anti-trypanocidal, anti-ulcerogenic, and anticancer drugs (Balibar, 2006). The pathway to produce violacein from tryptophan consists of five enzymes vioA-E (Hoshino, 2011). The pathway is NADPH dependent and consumes oxygen. The various enzymes involved in the pathway could also lead to the production of a few colorful byproducts, which might interfere with fluorescence signals when plate reader is used. The goal of the project is to characterize the violacein pathway using cell-free transcription and translational (TX-TL) system (Sun, 2013). Student will take advantage of the TX-TL system to explore ways to improve violacein production.

===References: ===

Balibar, C. J. and C. T. Walsh (2006). "[http://pubs.acs.org/doi/full/10.1021/bi061998z In Vitro Biosynthesis of Violacein from l-Tryptophan by the Enzymes VioA−E from Chromobacterium violaceum]." Biochemistry 45(51): 15444-15457. [http://pubs.acs.org/doi/full/10.1021/bi061998z]

Hoshino, T. (2011). "[http://link.springer.com/article/10.1007%2Fs00253-011-3468-z Violacein and related tryptophan metabolites produced by Chromobacterium violaceum: biosynthetic mechanism and pathway for construction of violacein core]." Applied Microbiology and Biotechnology 91(6):1463-1475.

Jiang, P.-x., et al. (2010). "[http://link.springer.com/article/10.1007%2Fs00253-009-2375-z Reconstruction of the violacein biosynthetic pathway from Duganella sp. B2 in different heterologous hosts]." Applied Microbiology and Biotechnology 86(4): 1077-1088.

Pantanella, F., et al. (2007). "[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2672.2006.03155.x/full Violacein and biofilm production in Janthinobacterium lividum]." Journal of Applied Microbiology 102(4): 992-999.

Sun, Z. Z., et al. (2013). "[http://www.jove.com/video/50762/protocols-for-implementing-an-escherichia-coli-based-tx-tl-cell-free Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology]." (79): e50762.

Sun, Z. Z., et al. (2013). "[http://pubs.acs.org/doi/abs/10.1021/sb400131a Linear DNA for Rapid Prototyping of Synthetic Biological Circuits in an Escherichia coli Based TX-TL Cell-Free System]." ACS Synthetic Biology.

File:Violacein.jpg

2014-12-19T20:21:42Z

Yywu:

SURF 2015: Design space exploration of the violacein pathway in TX-TL

2014-12-19T20:20:03Z

Yywu:

*Mentor: Richard Murray
*Co-mentor: Shaobin Guo and Yong Wu

[[File:Violacein.jpg|300px|thumb|Figure 1. Violacein Pathway (Balibar, 2006).]]

Violacein is a water-insoluble violet pigment that naturally exists in a few bacteria (Jiang, 2010 & Pantanella, 2007). Violacein has the potential applications in antibacterial, anti-trypanocidal, anti-ulcerogenic, and anticancer drugs (Balibar, 2006). The pathway to produce violacein from tryptophan consists of five enzymes vioA-E (Hoshino, 2011). The pathway is NADPH dependent and consumes oxygen. The various enzymes involved in the pathway could also lead to the production of a few colorful byproducts, which might interfere with fluorescence signals when plate reader is used. The goal of the project is to characterize the violacein pathway using cell-free transcription and translational (TX-TL) system (Sun, 2013). Student will take advantage of the TX-TL system to explore ways to improve violacein production.

References:

Balibar, C. J. and C. T. Walsh (2006). "[http://pubs.acs.org/doi/full/10.1021/bi061998z In Vitro Biosynthesis of Violacein from l-Tryptophan by the Enzymes VioA−E from Chromobacterium violaceum]." Biochemistry 45(51): 15444-15457. [http://pubs.acs.org/doi/full/10.1021/bi061998z]

Hoshino, T. (2011). "[http://link.springer.com/article/10.1007%2Fs00253-011-3468-z Violacein and related tryptophan metabolites produced by Chromobacterium violaceum: biosynthetic mechanism and pathway for construction of violacein core]." Applied Microbiology and Biotechnology 91(6):1463-1475.

Jiang, P.-x., et al. (2010). "[http://link.springer.com/article/10.1007%2Fs00253-009-2375-z Reconstruction of the violacein biosynthetic pathway from Duganella sp. B2 in different heterologous hosts]." Applied Microbiology and Biotechnology 86(4): 1077-1088.

Pantanella, F., et al. (2007). "[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2672.2006.03155.x/full Violacein and biofilm production in Janthinobacterium lividum]." Journal of Applied Microbiology 102(4): 992-999.

Sun, Z. Z., et al. (2013). "[http://www.jove.com/video/50762/protocols-for-implementing-an-escherichia-coli-based-tx-tl-cell-free Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology]." (79): e50762.

Sun, Z. Z., et al. (2013). "[http://pubs.acs.org/doi/abs/10.1021/sb400131a Linear DNA for Rapid Prototyping of Synthetic Biological Circuits in an Escherichia coli Based TX-TL Cell-Free System]." ACS Synthetic Biology.

SURF 2015: Design space exploration of the violacein pathway in TX-TL

2014-12-19T20:17:01Z

Yywu:

*Mentor: Richard Murray
*Co-mentor: Shaobin Guo and Yong Wu

Violacein is a water-insoluble violet pigment that naturally exists in a few bacteria (Jiang, 2010 & Pantanella, 2007). Violacein has the potential applications in antibacterial, anti-trypanocidal, anti-ulcerogenic, and anticancer drugs (Balibar, 2006). The pathway to produce violacein from tryptophan consists of five enzymes vioA-E (Hoshino, 2011). The pathway is NADPH dependent and consumes oxygen. The various enzymes involved in the pathway could also lead to the production of a few colorful byproducts, which might interfere with fluorescence signals when plate reader is used. The goal of the project is to characterize the violacein pathway using cell-free transcription and translational (TX-TL) system (Sun, 2013). Student will take advantage of the TX-TL system to explore ways to improve violacein production.

References:

Balibar, C. J. and C. T. Walsh (2006). "[http://pubs.acs.org/doi/full/10.1021/bi061998z In Vitro Biosynthesis of Violacein from l-Tryptophan by the Enzymes VioA−E from Chromobacterium violaceum]." Biochemistry 45(51): 15444-15457. [http://pubs.acs.org/doi/full/10.1021/bi061998z]

Hoshino, T. (2011). "[http://link.springer.com/article/10.1007%2Fs00253-011-3468-z Violacein and related tryptophan metabolites produced by Chromobacterium violaceum: biosynthetic mechanism and pathway for construction of violacein core]." Applied Microbiology and Biotechnology 91(6):1463-1475.

Jiang, P.-x., et al. (2010). "[http://link.springer.com/article/10.1007%2Fs00253-009-2375-z Reconstruction of the violacein biosynthetic pathway from Duganella sp. B2 in different heterologous hosts]." Applied Microbiology and Biotechnology 86(4): 1077-1088.

Pantanella, F., et al. (2007). "[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2672.2006.03155.x/full Violacein and biofilm production in Janthinobacterium lividum]." Journal of Applied Microbiology 102(4): 992-999.

Sun, Z. Z., et al. (2013). "[http://www.jove.com/video/50762/protocols-for-implementing-an-escherichia-coli-based-tx-tl-cell-free Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology]." (79): e50762.

Sun, Z. Z., et al. (2013). "[http://pubs.acs.org/doi/abs/10.1021/sb400131a Linear DNA for Rapid Prototyping of Synthetic Biological Circuits in an Escherichia coli Based TX-TL Cell-Free System]." ACS Synthetic Biology.

SURF 2015: Design space exploration of the violacein pathway in TX-TL

2014-12-19T20:14:55Z

Yywu:

*Mentor: Richard Murray
*Co-mentor: Shaobin Guo and Yong Wu

Violacein is a water-insoluble violet pigment that naturally exists in a few bacteria (Jiang, 2010 & Pantanella, 2007). Violacein has the potential applications in antibacterial, anti-trypanocidal, anti-ulcerogenic, and anticancer drugs (Balibar, 2006). The pathway to produce violacein from tryptophan consists of five enzymes vioA-E (Hoshino, 2011). The pathway is NADPH dependent and consumes oxygen. The various enzymes involved in the pathway could also lead to the production of a few colorful byproducts, which might interfere with fluorescence signals when plate reader is used. The goal of the project is to characterize the violacein pathway using cell-free transcription and translational (TX-TL) system. Student will take advantage of the TX-TL system to explore ways to improve violacein production.

References:

Balibar, C. J. and C. T. Walsh (2006). "[http://pubs.acs.org/doi/full/10.1021/bi061998z In Vitro Biosynthesis of Violacein from l-Tryptophan by the Enzymes VioA−E from Chromobacterium violaceum]." Biochemistry 45(51): 15444-15457. [http://pubs.acs.org/doi/full/10.1021/bi061998z]

Hoshino, T. (2011). "[http://link.springer.com/article/10.1007%2Fs00253-011-3468-z Violacein and related tryptophan metabolites produced by Chromobacterium violaceum: biosynthetic mechanism and pathway for construction of violacein core]." Applied Microbiology and Biotechnology 91(6):1463-1475.

Jiang, P.-x., et al. (2010). "Reconstruction of the violacein biosynthetic pathway from Duganella sp. B2 in different heterologous hosts." Applied Microbiology and Biotechnology 86(4): 1077-1088.
[http://link.springer.com/article/10.1007%2Fs00253-009-2375-z]

Pantanella, F., et al. (2007). "Violacein and biofilm production in Janthinobacterium lividum." Journal of Applied Microbiology 102(4): 992-999.
http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2672.2006.03155.x/full

Sun, Z. Z., et al. (2013). "Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology." (79): e50762.
http://www.jove.com/video/50762/protocols-for-implementing-an-escherichia-coli-based-tx-tl-cell-free

Sun, Z. Z., et al. (2013). "Linear DNA for Rapid Prototyping of Synthetic Biological Circuits in an Escherichia coli Based TX-TL Cell-Free System." ACS Synthetic Biology.
http://pubs.acs.org/doi/abs/10.1021/sb400131a

SURF 2015: Design space exploration of the violacein pathway in TX-TL

2014-12-19T20:14:25Z

Yywu:

===Mentor: Richard Murray===
===Co-mentor: Shaobin Guo and Yong Wu===

Violacein is a water-insoluble violet pigment that naturally exists in a few bacteria (Jiang, 2010 & Pantanella, 2007). Violacein has the potential applications in antibacterial, anti-trypanocidal, anti-ulcerogenic, and anticancer drugs (Balibar, 2006). The pathway to produce violacein from tryptophan consists of five enzymes vioA-E (Hoshino, 2011). The pathway is NADPH dependent and consumes oxygen. The various enzymes involved in the pathway could also lead to the production of a few colorful byproducts, which might interfere with fluorescence signals when plate reader is used. The goal of the project is to characterize the violacein pathway using cell-free transcription and translational (TX-TL) system. Student will take advantage of the TX-TL system to explore ways to improve violacein production.

References:

Balibar, C. J. and C. T. Walsh (2006). "[http://pubs.acs.org/doi/full/10.1021/bi061998z In Vitro Biosynthesis of Violacein from l-Tryptophan by the Enzymes VioA−E from Chromobacterium violaceum]." Biochemistry 45(51): 15444-15457. [http://pubs.acs.org/doi/full/10.1021/bi061998z]

Hoshino, T. (2011). "[http://link.springer.com/article/10.1007%2Fs00253-011-3468-z Violacein and related tryptophan metabolites produced by Chromobacterium violaceum: biosynthetic mechanism and pathway for construction of violacein core]." Applied Microbiology and Biotechnology 91(6):1463-1475.

Jiang, P.-x., et al. (2010). "Reconstruction of the violacein biosynthetic pathway from Duganella sp. B2 in different heterologous hosts." Applied Microbiology and Biotechnology 86(4): 1077-1088.
[http://link.springer.com/article/10.1007%2Fs00253-009-2375-z]

Pantanella, F., et al. (2007). "Violacein and biofilm production in Janthinobacterium lividum." Journal of Applied Microbiology 102(4): 992-999.
http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2672.2006.03155.x/full

Sun, Z. Z., et al. (2013). "Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology." (79): e50762.
http://www.jove.com/video/50762/protocols-for-implementing-an-escherichia-coli-based-tx-tl-cell-free

Sun, Z. Z., et al. (2013). "Linear DNA for Rapid Prototyping of Synthetic Biological Circuits in an Escherichia coli Based TX-TL Cell-Free System." ACS Synthetic Biology.
http://pubs.acs.org/doi/abs/10.1021/sb400131a

SURF 2015: Design space exploration of the violacein pathway in TX-TL

2014-12-19T20:13:54Z

Yywu: /* Design space exploration of the violacein pathway in TX-TL */

== Design space exploration of the violacein pathway in TX-TL ==
=Mentor: Richard Murray=
=Co-mentor: Shaobin Guo and Yong Wu=

Violacein is a water-insoluble violet pigment that naturally exists in a few bacteria (Jiang, 2010 & Pantanella, 2007). Violacein has the potential applications in antibacterial, anti-trypanocidal, anti-ulcerogenic, and anticancer drugs (Balibar, 2006). The pathway to produce violacein from tryptophan consists of five enzymes vioA-E (Hoshino, 2011). The pathway is NADPH dependent and consumes oxygen. The various enzymes involved in the pathway could also lead to the production of a few colorful byproducts, which might interfere with fluorescence signals when plate reader is used. The goal of the project is to characterize the violacein pathway using cell-free transcription and translational (TX-TL) system. Student will take advantage of the TX-TL system to explore ways to improve violacein production.

References:

Balibar, C. J. and C. T. Walsh (2006). "[http://pubs.acs.org/doi/full/10.1021/bi061998z In Vitro Biosynthesis of Violacein from l-Tryptophan by the Enzymes VioA−E from Chromobacterium violaceum]." Biochemistry 45(51): 15444-15457. [http://pubs.acs.org/doi/full/10.1021/bi061998z]

Hoshino, T. (2011). "[http://link.springer.com/article/10.1007%2Fs00253-011-3468-z Violacein and related tryptophan metabolites produced by Chromobacterium violaceum: biosynthetic mechanism and pathway for construction of violacein core]." Applied Microbiology and Biotechnology 91(6):1463-1475.

Jiang, P.-x., et al. (2010). "Reconstruction of the violacein biosynthetic pathway from Duganella sp. B2 in different heterologous hosts." Applied Microbiology and Biotechnology 86(4): 1077-1088.
[http://link.springer.com/article/10.1007%2Fs00253-009-2375-z]

Pantanella, F., et al. (2007). "Violacein and biofilm production in Janthinobacterium lividum." Journal of Applied Microbiology 102(4): 992-999.
http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2672.2006.03155.x/full

Sun, Z. Z., et al. (2013). "Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology." (79): e50762.
http://www.jove.com/video/50762/protocols-for-implementing-an-escherichia-coli-based-tx-tl-cell-free

Sun, Z. Z., et al. (2013). "Linear DNA for Rapid Prototyping of Synthetic Biological Circuits in an Escherichia coli Based TX-TL Cell-Free System." ACS Synthetic Biology.
http://pubs.acs.org/doi/abs/10.1021/sb400131a

SURF 2015: Design space exploration of the violacein pathway in TX-TL

2014-12-19T20:13:31Z

Yywu: Created page with " == Design space exploration of the violacein pathway in TX-TL == Mentor: Richard Murray Co-mentor: Shaobin Guo and Yong Wu Violacein is a water-insoluble violet pigment that..."

== Design space exploration of the violacein pathway in TX-TL ==
Mentor: Richard Murray
Co-mentor: Shaobin Guo and Yong Wu

Violacein is a water-insoluble violet pigment that naturally exists in a few bacteria (Jiang, 2010 & Pantanella, 2007). Violacein has the potential applications in antibacterial, anti-trypanocidal, anti-ulcerogenic, and anticancer drugs (Balibar, 2006). The pathway to produce violacein from tryptophan consists of five enzymes vioA-E (Hoshino, 2011). The pathway is NADPH dependent and consumes oxygen. The various enzymes involved in the pathway could also lead to the production of a few colorful byproducts, which might interfere with fluorescence signals when plate reader is used. The goal of the project is to characterize the violacein pathway using cell-free transcription and translational (TX-TL) system. Student will take advantage of the TX-TL system to explore ways to improve violacein production.

References:

Balibar, C. J. and C. T. Walsh (2006). "[http://pubs.acs.org/doi/full/10.1021/bi061998z In Vitro Biosynthesis of Violacein from l-Tryptophan by the Enzymes VioA−E from Chromobacterium violaceum]." Biochemistry 45(51): 15444-15457. [http://pubs.acs.org/doi/full/10.1021/bi061998z]

Hoshino, T. (2011). "[http://link.springer.com/article/10.1007%2Fs00253-011-3468-z Violacein and related tryptophan metabolites produced by Chromobacterium violaceum: biosynthetic mechanism and pathway for construction of violacein core]." Applied Microbiology and Biotechnology 91(6):1463-1475.

Jiang, P.-x., et al. (2010). "Reconstruction of the violacein biosynthetic pathway from Duganella sp. B2 in different heterologous hosts." Applied Microbiology and Biotechnology 86(4): 1077-1088.
[http://link.springer.com/article/10.1007%2Fs00253-009-2375-z]

Pantanella, F., et al. (2007). "Violacein and biofilm production in Janthinobacterium lividum." Journal of Applied Microbiology 102(4): 992-999.
http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2672.2006.03155.x/full

Sun, Z. Z., et al. (2013). "Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology." (79): e50762.
http://www.jove.com/video/50762/protocols-for-implementing-an-escherichia-coli-based-tx-tl-cell-free

Sun, Z. Z., et al. (2013). "Linear DNA for Rapid Prototyping of Synthetic Biological Circuits in an Escherichia coli Based TX-TL Cell-Free System." ACS Synthetic Biology.
http://pubs.acs.org/doi/abs/10.1021/sb400131a

September 2013 Meetings

2013-08-27T06:20:45Z

Yywu: /* Wed, 11 Sep */

The list below has times that I am available to meet between 3 and 13 September. Please pick a time that works and fill in your name. If none of the times work, send me e-mail (or find someone else who has a slot that does work and figure out how much of a bribe is required to get them to switch). __NOTOC__

{| border=1 width=100%
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2 Sep - Labor Day
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==== Tue, 3 Sep ====
{{agenda begin}}
{{agenda item|2:00p|Emzo}}
{{agenda item|3:00p|Joe Levine}}
{{agenda item| | }}
{{agenda item|4:30|Enoch}}
{{agenda item|5:30|Zach}}
{{agenda end}}
| width=20% |

==== Wed, 4 Sep ====
{{agenda begin}}
{{agenda item| | }}
{{agenda item| | }}
{{agenda item| | }}
{{agenda item|4:30|Joe}}
{{agenda item|5:30|Jongmin}}
{{agenda end}}
| width=20% |

==== Thu, 5 Sep ====
{{agenda begin}}
{{agenda item|2:00p|Open}}
{{agenda item|3:00p|Open}}
{{agenda item| | }}
{{agenda item|4:30|Open}}
{{agenda item|5:30|Ioannis}}
{{agenda end}}
| width=20% |
6 Sep - Richard out of town
|- valign=top
| colspan=2 width=40% |

==== Mon, 9 Sep / Tue, 10 Sep ====
{| cellspacing=0 cellpadding=0
|- valign=top
| width=50% |
{{agenda begin}}
{{agenda item|2:00p|dsg}}
{{agenda item|3:00p|Scott Livingston}}
{{agenda item| | }}
{{agenda item|4:30|Ivan Papusha}}
{{agenda item|5:30|Zoltan}}
{{agenda end}}
| width=50% |
Note: I may need to travel on either Mon or Tue {{implies}} please only sign up for a slot if you can make that time on both days.
|}
| width=20% |

==== Wed, 11 Sep ====
{{agenda begin}}
{{agenda item|1:00p|Clare}}
{{agenda item|2:00p|Yong}}
{{agenda item| | }}
{{agenda item|4:00|Anandh}}
{{agenda item|5:00|Anu}}
{{agenda end}}
| width=20% |

==== Thu, 12 Sep ====
{{agenda begin}}
{{agenda item|2:00p|Stephanie}}
{{agenda item|3:00p|Victoria}}
{{agenda item| | }}
{{agenda item|4:30|Open}}
{{agenda item|5:30|Open}}
{{agenda end}}
| width=20% |

==== Fri, 13 Sep ====
{{agenda begin}}
{{agenda item|1:00p|Vanessa}}
{{agenda item|2:00p|Open}}
{{agenda end}}
|}