https://murray.cds.caltech.edu/api.php?action=feedcontributions&feedformat=atom&user=Jmeyerow 2026-05-08T06:06:53Z User contributions MediaWiki 1.44.2 https://murray.cds.caltech.edu/index.php?title=Sara_Molinari,_29_Jan_2019&diff=22555 2019-01-27T23:00:13Z

<p>Jmeyerow: /* Schedule */</p> <hr /> <div>Sara Molinari will visit Caltech on 29-30 Jan 2019.<br /> <br /> === Schedule ===<br /> <br /> {| width=100% border=1<br /> |- valign=top<br /> | width=50% |<br /> 29 Jan (Tue):<br /> * 8:30 am: Richard, 109 Steele Lab<br /> * 9:00 am: seminar<br /> * 10:00 am: Andrey (meet after seminar)<br /> * 10:45 am: Joe (Keck 238)<br /> * 11:30 am: open<br /> * 12:00 pm: Lunch with postdocs John McManus, Leo Green<br /> * 1:00 pm: ELM discussion (Richard, James, Rory, ERDC?)<br /> * 2:00 pm: Andy (meet at Richard's office)<br /> * 2:45 pm: open<br /> * 3:30 pm: open<br /> * 4:15 pm: open<br /> * 5:00 pm: done for the day<br /> * 6:00 pm (or other): dinner with grad students (John Marken, Andy, Joe) (TBD)<br /> <br /> | width=50% |<br /> 30 Jan (Wed):<br /> * 9:00 am: Biocircuits group meeting<br /> * 11:00 am: Hold: Niles?<br /> * 11:45 am: open<br /> * 12:30 pm: working lunch with James and Rory<br /> * 1:45 pm: John Marken (103 Steele)<br /> * 2:30 pm: Richard, 109 Steele Lab<br /> * 3:00 pm: depart campus<br /> |}<br /> <br /> === Talk ===<br /> <br /> '''Engineering asymmetrical cell division into Escherichia coli'''<br /> <br /> Sara Molinari, Rice University&lt;br&gt;<br /> 29 Jan (Tue) @ 9 am, 111 Keck<br /> <br /> Multicellularity, in eukaryotic organisms, is ultimately responsible for most of the tissues features, such as controlling its shape and size, distributing biochemical, structural and reproductive tasks. Multicellularity is reached through asymmetrical cell division in which progenitor cells create a differentiated daughter cell while retaining their original phenotype. Here, we describe a synthetic genetic circuit for controlling asymmetrical cell division in Escherichia coli. Specifically, we engineered an inducible system that can bind and segregate plasmid DNA to a single position in the cell. Upon division, the co-localized plasmids are kept by one and only one of the daughter cells. The other daughter cell receives no plasmid DNA and is hence irreversibly differentiated from its sibling. In this way, we achieved asymmetric cell division though asymmetric plasmid partitioning. We used this system to achieve physical separation of genetically different cells. We also characterized an orthogonal inducible circuit that enables the simultaneous asymmetric partitioning of two plasmid species – resulting in pluripotent cells that have four distinct differentiated states. These results point the way towards engineering multicellular systems from prokaryotic hosts.</div>

Jmeyerow https://murray.cds.caltech.edu/index.php?title=Chelsea_Hu,_Apr_2018&diff=21902 2018-04-06T05:50:35Z

<p>Jmeyerow: /* Monday */</p> <hr /> <div>Chelsea Hu, a PhD student working with Julius Lucks at Northwestern, is going to be visiting on 9-10 Apr. Sign up below for a time to meet with her.<br /> <br /> === Monday ===<br /> * ~9:15 am: Richard, 107 Steele<br /> * 10 am: Biocircuits group meeting<br /> * 12 pm: Lunch with current postdocs<br /> * 1:30 pm: Andy<br /> * 2:15 pm: Joe<br /> * 3:00 pm: Sam<br /> * 3:45 pm: Open<br /> * 4:30 pm: Open<br /> <br /> === Tuesday ===<br /> * 9:30 am: Pradeep Ramesh &lt;pramesh@caltech.edu&gt;<br /> * 10:15 am: Open<br /> * 11:00 am: Open<br /> * 12:00 pm: IST lunch bunch or lunch on your own<br /> * Leave afternoon open for now<br /> * 4:00 pm: Hold for BBE seminar<br /> * 5:00 pm: Niles Pierce, 165 Broad<br /> * 5:30 pm: Richard, 107 Steele</div>

Jmeyerow https://murray.cds.caltech.edu/index.php?title=Tom_Ellis,_September_2013&diff=16360 2013-09-12T18:00:37Z

<p>Jmeyerow: /* Schedule: 12 Sep (Thu) */</p> <hr /> <div>Tom Ellis from Imperial College will be visiting on 12 Sep (Thu). If you would like to meet with him, please sign up for a slot below.<br /> <br /> === Schedule: 12 Sep (Thu) ===<br /> <br /> {{agenda begin}}<br /> {{agenda item|10:00 am|Richard and Dan S-G, 109 Steele Lab}}<br /> {{agenda item|11:00 am|Continued discussion with Dan S-G [and others?]}}<br /> {{agenda item|11:45 am|Grab lunch (Chandler or Annenberg)}}<br /> {{agenda item|12:15 pm|Lunch seminar: 243 Annenberg}}<br /> {{agenda item|1:15 pm|Zach Sun (meet in 243 ANB)}}<br /> {{agenda item|2:00 pm|John Doyle, 210 ANB}}<br /> {{agenda item|2:45 pm|Joe M (Steele 110)}}<br /> {{agenda item|3:30 pm|Emzo (Steele 110)}}<br /> {{agenda item|4:15 pm|Victoria H (Steele 110)}}<br /> {{agenda item|5:00 pm|Wrap up meeting with Richard}}<br /> {{agenda item|5:30 pm|Done for the day}}<br /> {{agenda end}}<br /> <br /> === Seminar ===<br /> <br /> &lt;center&gt;<br /> Characterising, modelling and rewiring the effect synthetic genetic circuits have on the capacity of their host chassis<br /> &lt;br&gt;<br /> Tom Ellis, Imperial College, London &lt;br&gt;<br /> 12 Sep (Thu), 12-1:15, 243 ANB<br /> &lt;/center&gt;<br /> <br /> Characterisation and understanding of genetic components is a key part of both synthetic biology and systems biology. Quantitative knowledge of how DNA parts encode function allows parts to be predictably constructed into synthetic gene circuits. Less understood is how the expression of a synthetic gene circuit can have a detrimental effect on its host cell (the chassis) and how these effects can feedback to the behaviour of the circuit. We investigate how synthetic circuits use cellular resources (e.g. DNA polymerase, RNA polymerase, ribosomes, tRNA, etc.) to replicate and express and we quantify these effects and model gene expression in a way that accounts for this. This is done by considering this shared 'resource pool' as an interface between the host cell and the synthetic circuit. Through genetic engineering and synthetic biology, we have created a system that monitors the availability of shared resources in E. coli, thus enabling the quantification of the burden a synthetic circuit places on the cell's resources. We then measure the burden of a combinatorial library of different designs to examine how different genetic components influence the magnitude of burden. This is accompanied by a mathematical model. Through this method we work towards a system that will enable the prediction of how to optimise the design of a synthetic circuit with regards to its output and the levels of burden it places on a cell.</div>

Jmeyerow https://murray.cds.caltech.edu/index.php?title=Tom_Ellis,_September_2013&diff=16354 2013-09-09T23:02:11Z

<p>Jmeyerow: /* Schedule: 12 Sep (Thu) */</p> <hr /> <div>Tom Ellis from Imperial College will be visiting on 12 Sep (Thu). If you would like to meet with him, please sign up for a slot below.<br /> <br /> === Schedule: 12 Sep (Thu) ===<br /> <br /> {{agenda begin}}<br /> {{agenda item|10:00 am|Richard and Dan S-G, 109 Steele Lab}}<br /> {{agenda item|11:00 am|Continued discussion with Dan S-G [and others?]}}<br /> {{agenda item|11:45 am|Grab lunch (Chandler or Annenberg)}}<br /> {{agenda item|12:15 pm|Lunch seminar: 243 Annenberg}}<br /> {{agenda item|1:15 pm|Zach Sun (meet in 243 ANB)}}<br /> {{agenda item|2:00 pm|John Doyle, 210 ANB}}<br /> {{agenda item|2:45 pm|Open}}<br /> {{agenda item|3:30 pm|Open}}<br /> {{agenda item|4:15 pm|Joe M (Steele 110?)}}<br /> {{agenda item|5:00 pm|Wrap up meeting with Richard}}<br /> {{agenda item|5:30 pm|Done for the day}}<br /> {{agenda end}}<br /> <br /> === Seminar ===<br /> <br /> &lt;center&gt;<br /> Characterising, modelling and rewiring the effect synthetic genetic circuits have on the capacity of their host chassis<br /> &lt;br&gt;<br /> Tom Ellis, Imperial College, London &lt;br&gt;<br /> 12 Sep (Thu), 12-1:15, 243 ANB<br /> &lt;/center&gt;<br /> <br /> Characterisation and understanding of genetic components is a key part of both synthetic biology and systems biology. Quantitative knowledge of how DNA parts encode function allows parts to be predictably constructed into synthetic gene circuits. Less understood is how the expression of a synthetic gene circuit can have a detrimental effect on its host cell (the chassis) and how these effects can feedback to the behaviour of the circuit. We investigate how synthetic circuits use cellular resources (e.g. DNA polymerase, RNA polymerase, ribosomes, tRNA, etc.) to replicate and express and we quantify these effects and model gene expression in a way that accounts for this. This is done by considering this shared 'resource pool' as an interface between the host cell and the synthetic circuit. Through genetic engineering and synthetic biology, we have created a system that monitors the availability of shared resources in E. coli, thus enabling the quantification of the burden a synthetic circuit places on the cell's resources. We then measure the burden of a combinatorial library of different designs to examine how different genetic components influence the magnitude of burden. This is accompanied by a mathematical model. Through this method we work towards a system that will enable the prediction of how to optimise the design of a synthetic circuit with regards to its output and the levels of burden it places on a cell.</div>

Jmeyerow https://murray.cds.caltech.edu/index.php?title=September_2013_Meetings&diff=16262 2013-08-26T21:14:53Z

<p>Jmeyerow: /* Wed, 4 Sep */</p> <hr /> <div>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__<br /> <br /> {| border=1 width=100%<br /> |- valign=top<br /> | width=20% |<br /> 2 Sep - Labor Day<br /> | width=20% |<br /> ==== Tue, 3 Sep ====<br /> {{agenda begin}}<br /> {{agenda item|2:00p|Emzo}}<br /> {{agenda item|3:00p|Joe Levine}}<br /> {{agenda item|&amp;nbsp;|&amp;nbsp;}}<br /> {{agenda item|4:30|Enoch}}<br /> {{agenda item|5:30|Zach}}<br /> {{agenda end}}<br /> | width=20% |<br /> <br /> ==== Wed, 4 Sep ====<br /> {{agenda begin}}<br /> {{agenda item|&amp;nbsp;|&amp;nbsp;}}<br /> {{agenda item|&amp;nbsp;|&amp;nbsp;}}<br /> {{agenda item|&amp;nbsp;|&amp;nbsp;}}<br /> {{agenda item|4:30|Joe}}<br /> {{agenda item|5:30|Open}}<br /> {{agenda end}}<br /> | width=20% |<br /> <br /> ==== Thu, 5 Sep ====<br /> {{agenda begin}}<br /> {{agenda item|2:00p|Open}}<br /> {{agenda item|3:00p|Open}}<br /> {{agenda item|&amp;nbsp;|&amp;nbsp;}}<br /> {{agenda item|4:30|Open}}<br /> {{agenda item|5:30|Ioannis}}<br /> {{agenda end}}<br /> | width=20% |<br /> 6 Sep - Richard out of town<br /> |- valign=top<br /> | colspan=2 width=40% |<br /> <br /> ==== Mon, 9 Sep / Tue, 10 Sep ====<br /> {| cellspacing=0 cellpadding=0<br /> |- valign=top<br /> | width=50% |<br /> {{agenda begin}}<br /> {{agenda item|2:00p|dsg}}<br /> {{agenda item|3:00p|Scott Livingston}}<br /> {{agenda item|&amp;nbsp;|&amp;nbsp;}}<br /> {{agenda item|4:30|Ivan Papusha}}<br /> {{agenda item|5:30|Open}}<br /> {{agenda end}}<br /> | width=50% |<br /> 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.<br /> |}<br /> | width=20% |<br /> <br /> ==== Wed, 11 Sep ====<br /> {{agenda begin}}<br /> {{agenda item|1:00p|Open}}<br /> {{agenda item|2:00p|Open}}<br /> {{agenda item|&amp;nbsp;|&amp;nbsp;}}<br /> {{agenda item|4:00|Anandh}}<br /> {{agenda item|5:00|Anu}}<br /> {{agenda end}}<br /> | width=20% |<br /> <br /> ==== Thu, 12 Sep ====<br /> {{agenda begin}}<br /> {{agenda item|2:00p|Stephanie}}<br /> {{agenda item|3:00p|Victoria}}<br /> {{agenda item|&amp;nbsp;|&amp;nbsp;}}<br /> {{agenda item|4:30|Open}}<br /> {{agenda item|5:30|Open}}<br /> {{agenda end}}<br /> | width=20% |<br /> <br /> ==== Fri, 13 Sep ====<br /> {{agenda begin}}<br /> {{agenda item|1:00p|Vanessa}}<br /> {{agenda item|2:00p|Open}}<br /> {{agenda end}}<br /> |}</div>

Jmeyerow https://murray.cds.caltech.edu/index.php?title=March_2013_meeting_schedule&diff=15547 2013-03-05T03:27:06Z

<p>Jmeyerow: /* 12 Mar (Tue) */</p> <hr /> <div>The list below has times that I am available to meet between 4 March and 13 March. 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). Please only sign up for one time slot. __NOTOC__<br /> <br /> {| width=100% border=1<br /> |- valign=top<br /> | width=30% |<br /> ==== 6 Mar (Wed) ====<br /> {{agenda begin}}<br /> {{agenda item|8:45-9:45|Ophelia}}<br /> {{agenda item||}}<br /> {{agenda item|1:15-2:00|Stephanie}}<br /> {{agenda item||}}<br /> {{agenda item|5:00-5:45|Shuo}}<br /> {{agenda item|5:45-6:00|UG advisee}}<br /> {{agenda item|6:00-6:45|Jongmin}}<br /> {{agenda item|6:45-7:30|Zoltan}}<br /> {{agenda end}}<br /> | width=30% |<br /> <br /> ==== 7 Mar (Thu) ====<br /> {{agenda begin}}<br /> {{agenda item|2:00-3:30|DARPA breadboards}}<br /> {{agenda item|4:00-4:15|UG advisee}}<br /> {{agenda item|4:15-5:00|Unavailable}}<br /> {{agenda item|5:00-5:45|Chris Kempes}}<br /> {{agenda item|5:45-6:00|UG advisee}}<br /> {{agenda item|6:00-6:45|Anandh}}<br /> {{agenda item|6:45-7:30|Ivan}}<br /> {{agenda end}}<br /> | width=30% |<br /> <br /> ==== 8 Mar (Fri) ====<br /> {{agenda begin}}<br /> {{agenda item|11:00-11:45|ALL telecon (Enoch, Joe M)}}<br /> {{agenda item||}}<br /> {{agenda item|12:00-1:15|NCS group meeting}}<br /> {{agenda item|1:15-2:00|Nadine (might get shortened)}}<br /> {{agenda item||}}<br /> {{agenda item|5:00-5:45|Eric}}<br /> {{agenda item|5:45-6:30|Scott Livingston}}<br /> {{agenda item|6:30-7:15|Enoch Yeung}}<br /> {{agenda end}}<br /> <br /> |- valign=top<br /> |<br /> <br /> ==== 10 Mar (Sun) ====<br /> {{agenda begin}}<br /> {{agenda item|2:30-2:45|UG advisee}}<br /> {{agenda item|2:45-3:00|UG advisee}}<br /> {{agenda item|3:00-4:00|dan}}<br /> {{agenda item|4:00-5:00|Open}}<br /> {{agenda item|5:00-6:00|Open}}<br /> {{agenda item|6:00-6:15|UG advisee}}<br /> {{agenda item|6:15-6:30|UG advisee}}<br /> {{agenda end}}<br /> |<br /> <br /> ==== 11 Mar (Mon) ====<br /> {{agenda begin}}<br /> {{agenda item|12:30-1:15|Hold}}<br /> {{agenda item||}}<br /> {{agenda item|3:30-4:15|Mumu}}<br /> {{agenda item|4:15-5:00|Shaobin}}<br /> {{agenda item|5:00-5:15|UG advisee}}<br /> {{agenda item|5:15-6:00|Marcella}}<br /> {{agenda item|6:00-6:45|Victoria}}<br /> {{agenda item|6:45-7:30|Open}}<br /> {{agenda end}}<br /> |<br /> <br /> ==== 12 Mar (Tue) ====<br /> {{agenda begin}}<br /> {{agenda item|11:00-11:45|Emzo}}<br /> {{agenda item||}}<br /> {{agenda item|1:00-3:00|Biocircuits meeting}}<br /> {{agenda item||}}<br /> {{agenda item|3:30-4:15|Nathan Belliveau}}<br /> {{agenda item|4:15-5:00|Vipul}}<br /> {{agenda item|5:00-5:15|UG advisee}}<br /> {{agenda item|5:15-6:00|Joe}}<br /> {{agenda item|6:00-6:45|Anu}}<br /> {{agenda item|6:45-7:30|Zach}}<br /> {{agenda end}}<br /> |}</div>

Jmeyerow https://murray.cds.caltech.edu/index.php?title=Group_Schedule,_Winter_2012&diff=13335 2011-12-12T15:34:55Z

<p>Jmeyerow: </p> <hr /> <div>This page contains information about various upcoming events that are of interest to the group. __NOTOC__<br /> {| width=60%<br /> |- valign=top<br /> | width=50% |<br /> * [http://www.cds.caltech.edu/~murray/calendar.html Richard's calendar (travel)]<br /> | width=50% |<br /> * [[Group Schedule, Fall 2011]]<br /> |}<br /> <br /> The schedule for group and subgroup meetings is given below. Everyone should sign up for times to talk in the subgroup meetings.<br /> <br /> &lt;font color=red&gt;<br /> ==== Directions: ====<br /> * '''Biocircuits (Tue or Thu, 3-5 pm)''': graduate students should give 1 longer presentation per term + 1-2 additional research updates; postdocs, undergrads should give 1-2 research updates.<br /> * '''NCS (Wed, 4-6 pm)''': grad students should speak 2 times per term for 15-20 min (+ discussion), postdocs and undergrads at least once<br /> * '''Robotics (Wed, 4-6 pm)''': grad students and postdocs should speak 2 times per term for 15-20 min (+ discussion), undergrads at least once; will also do ad hoc updates<br /> * '''Group meeting talks (WThF, 12-1:15)''': postdocs and senior grad students (G4+) should feel free to sign up for a group meeting talk (biocircuit grad students: this can be in place of longer subgroup talk)<br /> &lt;/font&gt;<br /> <br /> &lt;center&gt;<br /> '''Please sign up for at least one presentation in the first six weeks of the term.'''<br /> &lt;/center&gt;<br /> <br /> &lt;font color=blue&gt;Note that some of the meetings might need to shift, as noted; only sign up for those slots if you can make both times listed&lt;/font&gt;<br /> &lt;br&gt;<br /> <br /> {| width=100% border=1<br /> |- valign=top<br /> | width=30% |<br /> <br /> === Week 1: 4-6 Jan ===<br /> '''NCS: 4 Jan (Wed), 4-6 pm'''<br /> * Jun Liu (15-20 min)<br /> * Joseph Meyerowitz (15-20 min)<br /> * Project updates<br /> '''Group meeting: 5 Jan (Thu), 12-1:15'''<br /> * Ophelia<br /> '''Biocircuits: 5 Jan (Thu), 3-5 pm'''<br /> * Safety briefing (30-40 min) <br /> * Research update (10-15 min)<br /> * Research update (10-15 min)<br /> * Lab updates<br /> &lt;hr&gt;<br /> Academic holiday, 2-3 Jan&lt;br&gt;<br /> CDS quals, 6 Jan (RMM busy all day)<br /> | width=30% |<br /> <br /> === Week 2: 9-13 Jan ===<br /> '''Robotics: 11 Jan (Wed), 4-6 pm'''<br /> * Shuo (15-20 min)<br /> * Open (15-20 min)<br /> * Short research updates (5 min each)<br /> * &lt;font color=blue&gt;Might shift to Fri, 1-3 pm&lt;/font&gt;<br /> '''Biocircuits: 12 Jan (Thu), 3-5 pm'''<br /> * Marcella (30-40 min) <br /> * Research update (10-15 min)<br /> * Research update (10-15 min)<br /> * Lab updates<br /> '''Group meeting: 13 Jan (Fri), 12-1:15 pm'''<br /> * Domitilla Del Vecchio (MIT)<br /> | width=30% |<br /> <br /> === Week 3: 16-20 Jan ===<br /> '''Biocircuits: 17 Jan (Tue), 2-4 pm'''<br /> * Research presentation (30-40 min) <br /> * Dan (10-15 min)<br /> * Shaunak (10-15 min)<br /> * Lab updates<br /> * &lt;font color=blue&gt;Note time shift in day (to &quot;regular&quot; day)&lt;/font&gt;<br /> '''NCS: 18 Jan (Wed), 4-6 pm'''<br /> * Eric (15-20 min)<br /> * Necmiye (15-20 min)<br /> * Project updates<br /> '''Group meeting: 19 Jan (Thu), 12-1:15'''<br /> * Naira Hovakimyan (UIUC)<br /> |- valign=top<br /> |<br /> <br /> === Week 4: 23-27 Jan ===<br /> '''Biocircuits: 24 Jan (Tue), 3-5 pm'''<br /> * Research presentation (30-40 min) <br /> * Emzo (10-15 min)<br /> * Enoch (10-15 min)<br /> * Lab updates<br /> '''Group meeting: 25 Jan (Wed), 12-1:15'''<br /> * Necmiye<br /> '''Robotics: 25 Jan (Wed), 4-6 pm'''<br /> * Stephanie (15-20 min)<br /> * Pete (15-20 min)<br /> * Short research updates (5 min each)<br /> * &lt;font color=blue&gt;Might shift to Fri, 1-3 pm&lt;/font&gt;<br /> |<br /> <br /> === Week 5: 30 Jan - 3 Feb ===<br /> '''Biocircuits: 31 Jan (Tue), 3-5 pm'''<br /> * Research presentation (30-40 min) <br /> * Nikki(10-15 min)<br /> * Zach (10-15 min)<br /> * Lab updates<br /> '''NCS: 1 Feb (Wed), 4-6 pm'''<br /> * Marcella (15-20 min)<br /> * Ufuk (15-20 min)<br /> * Project updates<br /> '''Group meeting: 2 Feb (Thu), 12-1:15'''<br /> * Jongmin<br /> |<br /> <br /> === Week 6: 6 Feb - 10 Feb ===<br /> '''Biocircuits: 7 Feb (Tue), 3-5 pm'''<br /> * Research presentation (30-40 min) <br /> * Paul (10-15 min)<br /> * Victoria (10-15 min)<br /> * Lab updates<br /> '''Group meeting: 8 Feb (Wed), 12-1:15'''<br /> * Andrea<br /> '''Robotics: 8 Feb (Wed), 4-6 pm'''<br /> * Open (15-20 min)<br /> * Open (15-20 min)<br /> * Short research updates (5 min each)<br /> <br /> |- valign=top<br /> |<br /> <br /> === Week 7: 13-17 Feb ===<br /> '''NCS: 15 Feb (Wed), 4-6 pm'''<br /> * Open (15-20 min)<br /> * Open (15-20 min)<br /> * Project updates<br /> '''Group meeting: 16 Feb (Thu), 12-1:15'''<br /> * Open<br /> '''Biocircuits: 16 Feb (Thu), 3-5 pm'''<br /> * Research presentation (30-40 min) <br /> * Marcella (10-15 min)<br /> * Research update (10-15 min)<br /> * Lab updates<br /> * &lt;font color=blue&gt;Note change in day&lt;/font&gt;<br /> |<br /> <br /> === Week 8: 20-24 Feb ===<br /> '''Biocircuits: 21 Feb (Tue), 3-5 pm'''<br /> * Emzo (30-40 min) <br /> * Research update (10-15 min)<br /> * Research update (10-15 min)<br /> * Lab updates<br /> '''Robotics: 22 Feb (Wed), 4-6 pm'''<br /> * Shuo (15-20 min)<br /> * Eric (15-20 min)<br /> * Short research updates (5 min each)<br /> '''Group meeting: 23 Feb (Thu), 12-1:15'''<br /> * Hold: possible job talk<br /> |<br /> <br /> === Week 9: 27 Feb - 2 Mar ===<br /> '''Biocircuits: 28 Feb (Tue), 3-5 pm'''<br /> * Dan (30-40 min) <br /> * Research update (10-15 min)<br /> * Research update (10-15 min)<br /> * Lab updates<br /> * &lt;font color=blue&gt;Will probably shift to 2 Mar, 3-5 pm&lt;/font&gt;<br /> '''NCS: 29 Feb (Wed), 4-6 pm'''<br /> * Open (15-20 min)<br /> * Open (15-20 min)<br /> * Project updates<br /> * &lt;font color=blue&gt;Will probably shift to 2 Mar, 1-3 pm&lt;/font&gt;<br /> '''Group meeting: 2 Mar (Fri), 12-1:15'''<br /> * Shaunak<br /> |- valign=top<br /> |<br /> <br /> === Week 10: 5-9 Mar ===<br /> '''Biocircuits: 6 Mar (Tue), 3-5 pm'''<br /> * Enoch (30-40 min) <br /> * Research update (10-15 min)<br /> * Research update (10-15 min)<br /> * Lab updates<br /> '''Robotics: 7 Mar (Wed), 4-6 pm'''<br /> * Pete (15-20 min)<br /> * Open (15-20 min)<br /> * Short research updates (5 min each)<br /> '''Group meeting: 9 Mar (Fri), 12-1:15'''<br /> * Hold: possible job talk<br /> |<br /> <br /> === Week 11: 12-16 Mar ===<br /> Finals week; Richard out of town<br /> |<br /> === Week 12: 19-23 Mar ===<br /> Spring break; Richard out of town<br /> |}</div>

Jmeyerow https://murray.cds.caltech.edu/index.php?title=Group_Schedule,_Summer_2011&diff=12719 2011-06-20T03:36:47Z

<p>Jmeyerow: /* Summer Schedule */</p> <hr /> <div>__NOTOC__<br /> This page contains information about various upcoming events that are of interest to the group.<br /> {| width=60%<br /> |- valign=top<br /> | width=50% |<br /> * [http://www.cds.caltech.edu/~murray/calendar.html Richard's calendar (travel)]<br /> | width=50% |<br /> * [[Group Schedule, Spring 2011]]<br /> |}<br /> <br /> === Summer Schedule ===<br /> <br /> {| border=1 width=100%<br /> |- valign=top<br /> | '''Week'''<br /> | '''Mini-group meetings'''<br /> | '''Group meeting'''<br /> | '''Other'''<br /> |- valign=top<br /> |<br /> ===== 13-17 Jun =====<br /> |<br /> None<br /> | <br /> None<br /> | <br /> RMM out all week<br /> |- valign=top<br /> |<br /> ===== 20-24 Jun =====<br /> |<br /> * iGEM: Mon @ 9:30<br /> * SURF meetings, cycle 0: (sign on at [[SURF 2011]] page)<br /> * NCS: Tue, 1-2:30 pm<br /> ** Speaker 1: Necmiye (discussion)<br /> ** Speaker 2: open<br /> |<br /> Tue @ 12: Necmiye<br /> |<br /> RMM out 22-24 Jun<br /> |- valign=top<br /> |<br /> <br /> ===== 27 Jun - 1 Jul =====<br /> |<br /> * Robotics: Mon, 1-3 pm<br /> ** Speaker 1: open<br /> ** Speaker 2: open<br /> * Biocircuits: Tue, 9a-2p<br /> ** Overview presentations (all; 10 min each)<br /> ** Lunch will be provided<br /> * SURF meetings, cycle 1: Tue pm<br /> ** 4:00 pm: open<br /> ** 4:30 pm: open<br /> ** 5:00 pm: open<br /> ** 5:30 pm: open<br /> ** 6:00 pm: open<br /> | <br /> Mon @ 12: Nils Napp<br /> |<br /> * Nils Napp visiting<br /> * RMM out 29 Jun-1 Jul (ACC)<br /> |- valign=top<br /> |<br /> <br /> ===== 4-8 Jul =====<br /> |<br /> * Biocircuits: Tue, 10-12<br /> ** Speaker 1: Marcella<br /> ** Speaker 2: Joe<br /> ** Speaker 3: open<br /> * NCS: Thu, 1-3 pm<br /> ** Speaker 3: Scott Livingston<br /> ** Speaker 4: Linlin<br /> * SURF meetings, cycle 1: Thu pm<br /> ** 3:00 pm: open<br /> ** 3:30 pm: open<br /> ** 4:00 pm: Klavdia and Sawyer<br /> ** 4:30 pm: open<br /> ** 5:00 pm: open<br /> <br /> | <br /> Tue @ 12: Henrik Sandberg<br /> |<br /> * Institute holiday on Mon<br /> * Eric Colinet visiting on 5 Jul<br /> * Henrik Sandberg visiting 3-9 Jul<br /> |- valign=top<br /> |<br /> <br /> ===== 11-15 Jul =====<br /> |<br /> * Robotics: &lt;font color=blue&gt;Wed&lt;/font&gt;, 1p-3p<br /> ** Speaker 3: Shuo<br /> ** Speaker 4: Sandeep<br /> * Biocircuits: &lt;font color=blue&gt;Thu&lt;/font&gt;, 10a-12p<br /> ** Speaker 4: Ophelia<br /> ** Speaker 5: open<br /> ** iGEM presentation (30 min)<br /> * SURF meetings, cycle 2: Thu, pm<br /> ** 3:00 pm: open<br /> ** 3:30 pm: open<br /> ** 4:00 pm: open<br /> ** 4:30 pm: open<br /> * iGEM: &lt;font color=blue&gt;Thu&lt;/font&gt; @ 5 pm? <br /> | <br /> &lt;font color=blue&gt;Thu&lt;/font&gt; @ 12: Speaker TBD <br /> |<br /> |- valign=top<br /> |<br /> <br /> ===== 18-22 Jul =====<br /> |<br /> * SURF meetings, cycle 2: Thu pm<br /> ** 2:30p: open<br /> ** 3:00p: open<br /> ** 3:30p: open<br /> ** 4:00p: Klavdia and Sawyer<br /> ** 4:30p: open<br /> * iGEM: Thu, 5-6p?<br /> * Biocircuits: Fri, 10a-12p<br /> ** Speaker 6: Ye Yuan<br /> ** Speaker 7: Dionysios<br /> ** SURF 1: Paul<br /> * Robotics: Fri, 1p-3p<br /> ** Speaker 5: pete<br /> ** SURF 1: Magnus<br /> ** SURF 2: Stephanie<br /> * NCS: Fri, 3p-5p<br /> ** Speaker 5: Mumu<br /> ** Speaker 6: Ufuk<br /> ** SURF 1: Petter<br /> | <br /> Fri @ 12: Josh Michener<br /> |<br /> * RMM out 18-21 Jul am<br /> * Josh Michener visiting 22 Jul<br /> |- valign=top<br /> |<br /> <br /> ===== 25-29 Jul =====<br /> |<br /> | <br /> |<br /> * RMM out 25-29 Jul<br /> |- valign=top<br /> |<br /> <br /> ===== 1-5 Aug =====<br /> |<br /> * iGEM: 5-6p?<br /> * Biocircuits: Fri, 10a-12p<br /> ** Speaker 8: Marcella<br /> ** SURF 2: Ishan<br /> ** SURF 3: Arjun<br /> * NCS: Fri, 1p-3p<br /> ** Speaker 7: Scott Livingston<br /> ** Speaker 8: Eric<br /> ** SURF 2: Yuchen<br /> * SURF meetings, cycle 3: Fri, pm<br /> ** 3:00p: Klavdia and Sawyer<br /> ** 3:30p: open<br /> ** 4:00p: open<br /> ** 4:30p: open<br /> ** 5:00p: open<br /> | <br /> Fri @ 12: speaker TBD<br /> |<br /> * RMM out 1-4 Aug<br /> |- valign=top<br /> |<br /> <br /> ===== 8-12 Aug =====<br /> |<br /> * Robotics: Tue, 1p-3p<br /> ** Speaker 6: open<br /> ** SURF 3: Klavdia<br /> * SURF meetings, cycle 3: Tue, pm<br /> ** 3:00p: open<br /> ** 4:30p: open<br /> ** 4:00p: open<br /> ** 5:30p: open<br /> ** 6:00p: open<br /> * Biocircuits: Thu, 10a-12p<br /> ** Speaker 9: Jongmin<br /> ** Speaker 10: Shaunak<br /> ** SURF 4: Keshav<br /> * iGEM: 5p-6p<br /> | <br /> Thu @ 12: speaker TBD<br /> |<br /> |- valign=top<br /> |<br /> <br /> ===== 15-19 Aug =====<br /> |<br /> | <br /> |<br /> RMM out 15-19 Aug<br /> |- valign=top<br /> |<br /> <br /> ===== 22-26 Aug =====<br /> |<br /> * Biocircuits: Mon, 10a-12p<br /> ** Speaker 11: open<br /> ** Speaker 12: Enoch Yeung<br /> ** Speaker 13: open<br /> * Robotics: Mon, 1p-3p<br /> ** Speaker 7: open<br /> ** Speaker 8: open<br /> * NCS: Mon, 3p-5p<br /> ** Speaker 9: Linlin<br /> ** Speaker 10: Necmiye<br /> * iGEM: 5p-6p<br /> | <br /> Tue @ 12: speaker TBD<br /> |<br /> RMM out: 25 Aug (pm) - 1 Sep (pm)<br /> |- valign=top<br /> |<br /> <br /> ===== 29 Aug - 2 Sep =====<br /> |<br /> * Robotics: Thu, 1-3p<br /> ** Speaker 9: Shuo<br /> ** Speaker 10: Pete<br /> * NCS: Thu, 3-5p<br /> ** Speaker 11: Asghar<br /> ** Speaker 12: Eric<br /> * iGEM: Thu, 5p-6p<br /> * Biocircuits; Fri, 10a-12p<br /> ** Speaker 14: Ophelia<br /> ** Speaker 15: open<br /> ** Speaker 16: open<br /> <br /> | <br /> Fri @ 12p (tentative): speaker TBD <br /> |<br /> * RMM out: 25 Aug (pm) - 1 Sep (pm)<br /> |- valign=top<br /> |<br /> <br /> ===== 5-9 Sep =====<br /> |<br /> | <br /> |<br /> * RMM out, 5-9 Sep<br /> |- valign=top<br /> |<br /> ===== 12-16 Sep =====<br /> |<br /> * Biocircuits: Tue, 10a-12p<br /> ** Speaker 17: open<br /> ** Speaker 18: open<br /> ** Speaker 19: open<br /> * NCS: Wed, 1p-3p<br /> ** Speaker 13: Mumu<br /> ** Speaker 14: Ufuk<br /> | <br /> Tue @ 12p: speaker TBD<br /> |<br /> |- valign=top<br /> |<br /> <br /> ===== 19-23 Sep =====<br /> |<br /> * Robotics: Mon, 1p-3p<br /> ** Speaker 11: Asghar<br /> ** Speaker 12: Andrea<br /> * Biocircuits: Tue, 10a-12p<br /> ** Speaker 20: open<br /> ** Speaker 21: Enoch Yeung<br /> ** Speaker 22: open<br /> | <br /> Tue @ 12p: speaker TBD<br /> |<br /> RMM out, 20 Sep (pm) to 23 Sep<br /> |}</div>

Jmeyerow https://murray.cds.caltech.edu/index.php?title=June_2011_meetings&diff=12570 2011-05-31T19:40:46Z

<p>Jmeyerow: /* 7 Jun (Tue) */</p> <hr /> <div>__NOTOC__<br /> {| border=1 width=100%<br /> |- valign=top<br /> | width=20% |<br /> <br /> | width=20% |<br /> <br /> | width=20% |<br /> ==== 1 Jun (Wed) ====<br /> * 9:15a - Ye <br /> * 10:00a - Matanya<br /> * 11:00a - Marcella<br /> * 1:00p - Anu<br /> * 3:00p - CDS tea<br /> * 4:00p - Fei Y<br /> * 5:00p - (Shuo; lab stuff)<br /> * 5:30p - Dionysios<br /> * 6:30p - Shaunak<br /> | width=20% |<br /> ==== 2 Jun (Thu) ====<br /> * 10:00a - Biocircuits<br /> * 12:00p - Group meeting<br /> * 5:30p - Necmiye<br /> | width=20% |<br /> ==== 3 Jun (Fri) ====<br /> * UCLA<br /> * BE BBQ<br /> |- valign=top<br /> | width=20% |<br /> ==== 6 Jun (Mon) ====<br /> * 10:00a - Vanessa<br /> * 11:00a - Henry J<br /> * 12:30p - Robotics<br /> * 5:30p - Andrea<br /> * 6:30p - Ophelia<br /> | width=20% |<br /> <br /> ==== 7 Jun (Tue) ====<br /> * 10:00a - NCS<br /> * 12:00p - Group meeting<br /> * 3:30p - Scott Livingston<br /> * 4:30p - Aneesh<br /> * 5:30p - Ufuk<br /> * 6:30p - Joe<br /> | width=20% |<br /> <br /> ==== 8 Jun (Wed) ====<br /> * 9:30a - Eric<br /> * 10:30a - Mumu<br /> * 11:30a - Open<br /> * 1:00p - Jongmin<br /> * 2:00p - Emzo<br /> * 3:00p - CDS tea<br /> * 5:30p - Jun Liu<br /> * 6:30p - Open<br /> * 7:30p - Open<br /> | width=20% |<br /> <br /> ==== 9 Jun (Thu) ====<br /> * 11:30a - Open<br /> * 1:00p - Open<br /> * 2:00p - Open<br /> * 3:00p - CDS 90 <br /> * 4:30p - Enoch Yeung <br /> * 5:30p - Shuo<br /> * 6:30p - Open<br /> | width=20% |<br /> <br /> ==== 10 Jun (Fri) ====<br /> * 5:30p - Open<br /> |}</div>

Jmeyerow https://murray.cds.caltech.edu/index.php?title=Group_Schedule,_Spring_2011&diff=12394 2011-04-18T16:46:25Z

<p>Jmeyerow: /* Group Meetings */</p> <hr /> <div>{{righttoc}} <br /> This page contains information about various upcoming events that are of interest to the group.<br /> {| width=60%<br /> |- valign=top<br /> | width=50% |<br /> * [http://www.cds.caltech.edu/~murray/calendar.html Richard's calendar (travel)]<br /> | width=50% |<br /> * [[Group Schedule, Winter 2011]]<br /> |}<br /> <br /> == Group Meetings ==<br /> Group meetings are at noon in 114 Steele. Visitors are welcome (but be prepared to get signed up to give a talk!).<br /> {| width=100% border=1<br /> |- valign=top<br /> | <br /> {{agenda begin}}<br /> {{agenda item|Date|Speaker}}<br /> {{agenda item|22 Apr (Fri)|Open}}<br /> {{agenda item|27 Apr (Wed)|Open}}<br /> {{agenda item|2 May (Mon)|Open}}<br /> {{agenda end}}<br /> | <br /> {{agenda begin}}<br /> {{agenda item|Date|Speaker}}<br /> {{agenda item|11 May (Wed)|Joseph T. Meyerowitz}}<br /> {{agenda item|16 May (Mon)|Open}}<br /> {{agenda item|26 May (Thu)|Open}}<br /> {{agenda end}}<br /> | <br /> {{agenda begin}}<br /> {{agenda item|Date|Speaker}}<br /> {{agenda item|2 Jun (Thu)|Open}}<br /> {{agenda item|7 Jun (Tue)|Open}}<br /> {{agenda end}}<br /> |}<br /> <br /> == Mini-group meetings ==<br /> <br /> Below are the ''tentative'' times for mini-group meetings. Updates to times are likely to accommodate scheduling conflicts. Changes from the original schedule are highlighted in blue.<br /> <br /> {| width=100% border=1<br /> |- valign=top<br /> | <br /> ==== Biocircuits ====<br /> * TBD<br /> |<br /> <br /> ==== Robotics ====<br /> * TBD<br /> |<br /> <br /> ==== NCS ====<br /> * TBD<br /> |}<br /> <br /> == Events and talks ==<br /> * 7 Apr - [[Cedric Langbort, April 2011|Cendric Langbort]]</div>

Jmeyerow https://murray.cds.caltech.edu/index.php?title=Mini-bootcamp_2011&diff=12225 2011-03-07T22:36:27Z

<p>Jmeyerow: /* Quick Links */</p> <hr /> <div>This page contains a description of the mini-bootcamp run in Feb 2011. __NOTOC__<br /> <br /> === Quick Links ===<br /> <br /> [[Cloning - high level timeline]]<br /> <br /> === Group ===<br /> &lt;center&gt;<br /> {| width=90%<br /> |- valign=top<br /> | width=25% |<br /> ===== Students =====<br /> * Jorge Goncalves<br /> * Jun Liu<br /> * Yuan Ye<br /> * Enoch Yeung<br /> | width=25% |<br /> <br /> ===== Part-time students =====<br /> * Elisa Franco<br /> * Richard Murray<br /> | width=25% |<br /> ===== Instructors =====<br /> * Emzo de los Santos<br /> * Joe Meyerowitz<br /> * Ophelia Venturelli<br /> * Vanessa Jonsson<br /> * Jongmin Kim<br /> | width=25% |<br /> <br /> ===== Project advisor =====<br /> * Richard Murray<br /> |}<br /> &lt;/center&gt;<br /> <br /> === Bootcamp description ===<br /> <br /> {| width=100% border=1<br /> |- valign=top<br /> | rowspan=3 |<br /> The goal of this bootcamp is to measure variability in gene expression that is relevant for synthetically designed circuits. The issue that we are trying to understand is now much variability arises for the expression of a given circuit under degrees of freedom that are typically not controlled in synthetic designs:<br /> * Location and orientation of circuit elements in the plasmid<br /> * Vectors used for expressing the circuit, including copy number and antibiotic resistance<br /> * Growth conditions (temperature, oxygen, media, growth phase)<br /> To understand how these (and other) factors will affect circuit operation, a simple genetic circuit consisting of 2 reporters will be built using different DNA locations and directions, and characterized in a variety of conditions. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry and microscopy).<br /> <br /> Bootcamp objectives:<br /> * Project 1: Construct a simple genetic circuit that tests the effects of putting different reporters in different configurations in a plasmid. Characterize the differences (if any) in mean expression level of the circuits, possibly in multiple growth conditions, using a plate reader<br /> * Project 2: Characterize differences in expression distributions using flow cytometry (FACS Calibur) and fluorescent microscopy<br /> * Project 3: Perform in vitro testing of the constructs using the PURExpress kit and spectrofluorometer to check for differences in mean expression level<br /> |<br /> [[Image:lambda_switch.png|300px]]<br /> * Circuit layout: directions, ordering<br /> |-<br /> | <br /> [[Image:biobrick_plasmid.png|300px]]<br /> * Copy number<br /> * Origin of replication<br /> * Antibiotic resistance<br /> * [[http:partsregistry.org/Plasmid_backbones|Biobrick plasmids]]<br /> |-<br /> | <br /> * (Cell strain)<br /> * Growth media: LB, M9/glycerol, M9/glucose<br /> * Induction level<br /> * Temperature<br /> |}<br /> <br /> === Schedule ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=20% | 14 Feb: 2-4<br /> * Biocircuits mini-group meeting - planning<br /> * Richard<br /> | width=20% | 15 Feb<br /> | width=20% | 16 Feb: <br /> * [[#Session 0: project discussion and lab tour|Session 0: project discussion and lab tour]]<br /> * Richard, Ophelia<br /> * Joe, Elisa<br /> | width=20% | 17 Feb: 2:30-6<br /> * [[Mini-bootcamp_2011/Session 1: lab techniques|Session 1: lab techniques]]<br /> * Emzo, Jongmin<br /> | width=20% | 18 Feb<br /> |- valign=top<br /> | width=20% | 21 Feb: 1-6<br /> * [[#Session 2: cloning|Session 2: cloning]]<br /> * Joe, Emzo<br /> | width=20% | 22 Feb<br /> | width=20% | 23 Feb: 1-6<br /> * [[#Session 3: plate reader|Session 3: plate reader]]<br /> * Ophelia, Richard<br /> | width=20% | 24 Feb<br /> * Project #1<br /> | width=20% | 25 Feb<br /> * Project #1<br /> <br /> |- valign=top<br /> | width=20% | 28 Feb<br /> * Project #1<br /> | width=20% | 1 Mar<br /> * Project #1<br /> | width=20% | 2 Mar: TBD<br /> * [[#Session 4: microscopy|Session 4: microscopy]]<br /> * Ophelia, Joe<br /> | width=20% | 3 Mar<br /> *Project #1<br /> | width=20% | 4 Mar<br /> *Project #1<br /> |- valign=top<br /> | width=20% | 7 Mar: TBD<br /> * [[#Session 5: flow cytometry|Session 5: flow cytometry]]<br /> * Joe, Vanessa<br /> | width=20% | 8 Mar: TBD<br /> * [[#Session 6: spectrofluorometer|Session 6: spectrofluorometer]]<br /> * Jongmin, Elisa<br /> | width=20% | 9 Mar<br /> * Project #3<br /> | width=20% | 10 Mar<br /> * Project #3<br /> | width=20% | 11 Mar<br /> * Project #3<br /> |}<br /> &amp;nbsp;<br /> &lt;hr&gt;<br /> ==== Session 0: project discussion and lab tour ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * Overview of project goals<br /> * Tour of 040 Keck<br /> * Lab safety<br /> ===== Instructors: =====<br /> * Richard Murray, Ophelia Venturelli<br /> * Joe Meyerowitz, Elisa Franco (lab tour, safety)<br /> &lt;hr&gt;<br /> ==== [[Mini-bootcamp_2011/Session 1: lab techniques|Session 1: lab techniques]] ====<br /> This lab session will teach some of the basic techniques that will be used throughout the bootcamp. We assume no background in molecular biology laboratory techniques. By the end of this session, students will be able to transform a plasmid into cells, pick colonies containing the plasmid, grow the cells up to a given optical density, extract the plasmids, and quantify them.<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * Lab safety<br /> * Laboratory techniques: gloves, pipetting, disposal<br /> * Transforming plasmids into cells, growing, extracting<br /> * Clean up: benches, glassware<br /> <br /> ===== Instructors: =====<br /> * Emzo<br /> * Jongmin <br /> | width=50% |<br /> ===== Techniques and equipment: =====<br /> * Pipetting<br /> * Transformation, selection, growth<br /> * Optical density (OD) measurements (nanodrop?)<br /> * Mini-preps<br /> * Quantification (nanodrop)<br /> * Autoclave<br /> |}<br /> &lt;hr&gt;<br /> <br /> ==== [[Mini-bootcamp_2011/Session 2: cloning|Session 2: cloning]] ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * Discussion of PCR, primer design, Gibson assembly, gels<br /> * Demonstration of PCR<br /> * Demonstration of Gibson assembly<br /> * Demonstration of electrophoresis, restriction digestion, mapping<br /> * Transform Gibson product<br /> <br /> ===== Instructors: =====<br /> * Joe<br /> * Emzo<br /> | width=50% |<br /> <br /> ===== Techniques and equipment: =====<br /> * PCR<br /> * Restriction digests<br /> * Gels<br /> * Gibson assembly<br /> |}<br /> &lt;hr&gt;<br /> <br /> ==== Session 3: [[plate reader]] ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * Set up dose response with E. coli strains using serial dilution method<br /> * Learn strategies for measuring dynamics in plate reader<br /> :*Growth in shaker (manual time points)<br /> :*Growth in VictorX3 (automated measurements)<br /> * Measure gene expression (GFP) and OD (cell mass) using VictorX3 over a period of time<br /> <br /> ===== Instructors: =====<br /> * Ophelia<br /> * Richard<br /> | width=50% |<br /> <br /> ===== Techniques and equipment: =====<br /> * Victor X3 plate reader<br /> |}<br /> &lt;hr&gt;<br /> <br /> ==== Session 4: [[microscope]] ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * Learn basic principles and design of the Olympus IX-81 light microscope<br /> * Learn how to make agarose pads for imaging E coli<br /> * Basics of Micro-Manager software<br /> * Discuss image analysis<br /> <br /> ===== Instructors: =====<br /> * Ophelia<br /> * Joe<br /> | width=50% |<br /> ===== Techniques and equipment: =====<br /> * Olympus IX-81 microscope<br /> * MATLAB tools for image analysis<br /> |}<br /> &lt;hr&gt;<br /> <br /> ==== Session 5: flow cytometer ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * <br /> ===== Instructors: =====<br /> * Joe<br /> * Vanessa<br /> | width=50% |<br /> ===== Techniques and equipment: =====<br /> * FACS Calibur flow cytometer<br /> * MaxQuant (?)<br /> |}<br /> &lt;hr&gt;<br /> <br /> ==== Session 6: [[Mini-bootcamp_2011/Session_6:_Spectrofluorometer|spectrofluorometer]] ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * Learn basic principles of the Fluorolog 3 spectrofluorometer<br /> * Learn how to run protein gels<br /> * Basics of the PURExpress protein expression kit<br /> * Basics of spectrofluorometer software<br /> ===== Instructors: =====<br /> * Jongmin<br /> * Elisa<br /> | width=50% |<br /> <br /> ===== Techniques and equipment: =====<br /> * PURExpress protein expression kit<br /> * Protein gels <br /> * Fluorolog 3 spectrofluorometer<br /> |}</div>

Jmeyerow https://murray.cds.caltech.edu/index.php?title=Mini-bootcamp_2011&diff=12224 2011-03-07T22:36:18Z

<p>Jmeyerow: </p> <hr /> <div>This page contains a description of the mini-bootcamp run in Feb 2011. __NOTOC__<br /> <br /> === Quick Links ===<br /> <br /> [Cloning - high level timeline]<br /> <br /> === Group ===<br /> &lt;center&gt;<br /> {| width=90%<br /> |- valign=top<br /> | width=25% |<br /> ===== Students =====<br /> * Jorge Goncalves<br /> * Jun Liu<br /> * Yuan Ye<br /> * Enoch Yeung<br /> | width=25% |<br /> <br /> ===== Part-time students =====<br /> * Elisa Franco<br /> * Richard Murray<br /> | width=25% |<br /> ===== Instructors =====<br /> * Emzo de los Santos<br /> * Joe Meyerowitz<br /> * Ophelia Venturelli<br /> * Vanessa Jonsson<br /> * Jongmin Kim<br /> | width=25% |<br /> <br /> ===== Project advisor =====<br /> * Richard Murray<br /> |}<br /> &lt;/center&gt;<br /> <br /> === Bootcamp description ===<br /> <br /> {| width=100% border=1<br /> |- valign=top<br /> | rowspan=3 |<br /> The goal of this bootcamp is to measure variability in gene expression that is relevant for synthetically designed circuits. The issue that we are trying to understand is now much variability arises for the expression of a given circuit under degrees of freedom that are typically not controlled in synthetic designs:<br /> * Location and orientation of circuit elements in the plasmid<br /> * Vectors used for expressing the circuit, including copy number and antibiotic resistance<br /> * Growth conditions (temperature, oxygen, media, growth phase)<br /> To understand how these (and other) factors will affect circuit operation, a simple genetic circuit consisting of 2 reporters will be built using different DNA locations and directions, and characterized in a variety of conditions. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry and microscopy).<br /> <br /> Bootcamp objectives:<br /> * Project 1: Construct a simple genetic circuit that tests the effects of putting different reporters in different configurations in a plasmid. Characterize the differences (if any) in mean expression level of the circuits, possibly in multiple growth conditions, using a plate reader<br /> * Project 2: Characterize differences in expression distributions using flow cytometry (FACS Calibur) and fluorescent microscopy<br /> * Project 3: Perform in vitro testing of the constructs using the PURExpress kit and spectrofluorometer to check for differences in mean expression level<br /> |<br /> [[Image:lambda_switch.png|300px]]<br /> * Circuit layout: directions, ordering<br /> |-<br /> | <br /> [[Image:biobrick_plasmid.png|300px]]<br /> * Copy number<br /> * Origin of replication<br /> * Antibiotic resistance<br /> * [[http:partsregistry.org/Plasmid_backbones|Biobrick plasmids]]<br /> |-<br /> | <br /> * (Cell strain)<br /> * Growth media: LB, M9/glycerol, M9/glucose<br /> * Induction level<br /> * Temperature<br /> |}<br /> <br /> === Schedule ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=20% | 14 Feb: 2-4<br /> * Biocircuits mini-group meeting - planning<br /> * Richard<br /> | width=20% | 15 Feb<br /> | width=20% | 16 Feb: <br /> * [[#Session 0: project discussion and lab tour|Session 0: project discussion and lab tour]]<br /> * Richard, Ophelia<br /> * Joe, Elisa<br /> | width=20% | 17 Feb: 2:30-6<br /> * [[Mini-bootcamp_2011/Session 1: lab techniques|Session 1: lab techniques]]<br /> * Emzo, Jongmin<br /> | width=20% | 18 Feb<br /> |- valign=top<br /> | width=20% | 21 Feb: 1-6<br /> * [[#Session 2: cloning|Session 2: cloning]]<br /> * Joe, Emzo<br /> | width=20% | 22 Feb<br /> | width=20% | 23 Feb: 1-6<br /> * [[#Session 3: plate reader|Session 3: plate reader]]<br /> * Ophelia, Richard<br /> | width=20% | 24 Feb<br /> * Project #1<br /> | width=20% | 25 Feb<br /> * Project #1<br /> <br /> |- valign=top<br /> | width=20% | 28 Feb<br /> * Project #1<br /> | width=20% | 1 Mar<br /> * Project #1<br /> | width=20% | 2 Mar: TBD<br /> * [[#Session 4: microscopy|Session 4: microscopy]]<br /> * Ophelia, Joe<br /> | width=20% | 3 Mar<br /> *Project #1<br /> | width=20% | 4 Mar<br /> *Project #1<br /> |- valign=top<br /> | width=20% | 7 Mar: TBD<br /> * [[#Session 5: flow cytometry|Session 5: flow cytometry]]<br /> * Joe, Vanessa<br /> | width=20% | 8 Mar: TBD<br /> * [[#Session 6: spectrofluorometer|Session 6: spectrofluorometer]]<br /> * Jongmin, Elisa<br /> | width=20% | 9 Mar<br /> * Project #3<br /> | width=20% | 10 Mar<br /> * Project #3<br /> | width=20% | 11 Mar<br /> * Project #3<br /> |}<br /> &amp;nbsp;<br /> &lt;hr&gt;<br /> ==== Session 0: project discussion and lab tour ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * Overview of project goals<br /> * Tour of 040 Keck<br /> * Lab safety<br /> ===== Instructors: =====<br /> * Richard Murray, Ophelia Venturelli<br /> * Joe Meyerowitz, Elisa Franco (lab tour, safety)<br /> &lt;hr&gt;<br /> ==== [[Mini-bootcamp_2011/Session 1: lab techniques|Session 1: lab techniques]] ====<br /> This lab session will teach some of the basic techniques that will be used throughout the bootcamp. We assume no background in molecular biology laboratory techniques. By the end of this session, students will be able to transform a plasmid into cells, pick colonies containing the plasmid, grow the cells up to a given optical density, extract the plasmids, and quantify them.<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * Lab safety<br /> * Laboratory techniques: gloves, pipetting, disposal<br /> * Transforming plasmids into cells, growing, extracting<br /> * Clean up: benches, glassware<br /> <br /> ===== Instructors: =====<br /> * Emzo<br /> * Jongmin <br /> | width=50% |<br /> ===== Techniques and equipment: =====<br /> * Pipetting<br /> * Transformation, selection, growth<br /> * Optical density (OD) measurements (nanodrop?)<br /> * Mini-preps<br /> * Quantification (nanodrop)<br /> * Autoclave<br /> |}<br /> &lt;hr&gt;<br /> <br /> ==== [[Mini-bootcamp_2011/Session 2: cloning|Session 2: cloning]] ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * Discussion of PCR, primer design, Gibson assembly, gels<br /> * Demonstration of PCR<br /> * Demonstration of Gibson assembly<br /> * Demonstration of electrophoresis, restriction digestion, mapping<br /> * Transform Gibson product<br /> <br /> ===== Instructors: =====<br /> * Joe<br /> * Emzo<br /> | width=50% |<br /> <br /> ===== Techniques and equipment: =====<br /> * PCR<br /> * Restriction digests<br /> * Gels<br /> * Gibson assembly<br /> |}<br /> &lt;hr&gt;<br /> <br /> ==== Session 3: [[plate reader]] ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * Set up dose response with E. coli strains using serial dilution method<br /> * Learn strategies for measuring dynamics in plate reader<br /> :*Growth in shaker (manual time points)<br /> :*Growth in VictorX3 (automated measurements)<br /> * Measure gene expression (GFP) and OD (cell mass) using VictorX3 over a period of time<br /> <br /> ===== Instructors: =====<br /> * Ophelia<br /> * Richard<br /> | width=50% |<br /> <br /> ===== Techniques and equipment: =====<br /> * Victor X3 plate reader<br /> |}<br /> &lt;hr&gt;<br /> <br /> ==== Session 4: [[microscope]] ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * Learn basic principles and design of the Olympus IX-81 light microscope<br /> * Learn how to make agarose pads for imaging E coli<br /> * Basics of Micro-Manager software<br /> * Discuss image analysis<br /> <br /> ===== Instructors: =====<br /> * Ophelia<br /> * Joe<br /> | width=50% |<br /> ===== Techniques and equipment: =====<br /> * Olympus IX-81 microscope<br /> * MATLAB tools for image analysis<br /> |}<br /> &lt;hr&gt;<br /> <br /> ==== Session 5: flow cytometer ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * <br /> ===== Instructors: =====<br /> * Joe<br /> * Vanessa<br /> | width=50% |<br /> ===== Techniques and equipment: =====<br /> * FACS Calibur flow cytometer<br /> * MaxQuant (?)<br /> |}<br /> &lt;hr&gt;<br /> <br /> ==== Session 6: [[Mini-bootcamp_2011/Session_6:_Spectrofluorometer|spectrofluorometer]] ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * Learn basic principles of the Fluorolog 3 spectrofluorometer<br /> * Learn how to run protein gels<br /> * Basics of the PURExpress protein expression kit<br /> * Basics of spectrofluorometer software<br /> ===== Instructors: =====<br /> * Jongmin<br /> * Elisa<br /> | width=50% |<br /> <br /> ===== Techniques and equipment: =====<br /> * PURExpress protein expression kit<br /> * Protein gels <br /> * Fluorolog 3 spectrofluorometer<br /> |}</div>

Jmeyerow https://murray.cds.caltech.edu/index.php?title=Mini-bootcamp_2011&diff=12183 2011-03-03T05:08:29Z

<p>Jmeyerow: </p> <hr /> <div>This page contains a description of the mini-bootcamp run in Feb 2011. __NOTOC__<br /> <br /> === Group ===<br /> &lt;center&gt;<br /> {| width=90%<br /> |- valign=top<br /> | width=25% |<br /> ===== Students =====<br /> * Jorge Goncalves<br /> * Jun Liu<br /> * Yuan Ye<br /> * Enoch Yeung<br /> | width=25% |<br /> <br /> ===== Part-time students =====<br /> * Elisa Franco<br /> * Richard Murray<br /> | width=25% |<br /> ===== Instructors =====<br /> * Emzo de los Santos<br /> * Joe Meyerowitz<br /> * Ophelia Venturelli<br /> * Vanessa Jonsson<br /> * Jongmin Kim<br /> | width=25% |<br /> <br /> ===== Project advisor =====<br /> * Richard Murray<br /> |}<br /> &lt;/center&gt;<br /> <br /> === Bootcamp description ===<br /> <br /> {| width=100% border=1<br /> |- valign=top<br /> | rowspan=3 |<br /> The goal of this bootcamp is to measure variability in gene expression that is relevant for synthetically designed circuits. The issue that we are trying to understand is now much variability arises for the expression of a given circuit under degrees of freedom that are typically not controlled in synthetic designs:<br /> * Location and orientation of circuit elements in the plasmid<br /> * Vectors used for expressing the circuit, including copy number and antibiotic resistance<br /> * Growth conditions (temperature, oxygen, media, growth phase)<br /> To understand how these (and other) factors will affect circuit operation, a simple genetic circuit consisting of 2 reporters will be built using different DNA locations and directions, and characterized in a variety of conditions. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry and microscopy).<br /> <br /> Bootcamp objectives:<br /> * Project 1: Construct a simple genetic circuit that tests the effects of putting different reporters in different configurations in a plasmid. Characterize the differences (if any) in mean expression level of the circuits, possibly in multiple growth conditions, using a plate reader<br /> * Project 2: Characterize differences in expression distributions using flow cytometry (FACS Calibur) and fluorescent microscopy<br /> * Project 3: Perform in vitro testing of the constructs using the PURExpress kit and spectrofluorometer to check for differences in mean expression level<br /> |<br /> [[Image:lambda_switch.png|300px]]<br /> * Circuit layout: directions, ordering<br /> |-<br /> | <br /> [[Image:biobrick_plasmid.png|300px]]<br /> * Copy number<br /> * Origin of replication<br /> * Antibiotic resistance<br /> * [[http:partsregistry.org/Plasmid_backbones|Biobrick plasmids]]<br /> |-<br /> | <br /> * (Cell strain)<br /> * Growth media: LB, M9/glycerol, M9/glucose<br /> * Induction level<br /> * Temperature<br /> |}<br /> <br /> === Schedule ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=20% | 14 Feb: 2-4<br /> * Biocircuits mini-group meeting - planning<br /> * Richard<br /> | width=20% | 15 Feb<br /> | width=20% | 16 Feb: <br /> * [[#Session 0: project discussion and lab tour|Session 0: project discussion and lab tour]]<br /> * Richard, Ophelia<br /> * Joe, Elisa<br /> | width=20% | 17 Feb: 2:30-6<br /> * [[Mini-bootcamp_2011/Session 1: lab techniques|Session 1: lab techniques]]<br /> * Emzo, Jongmin<br /> | width=20% | 18 Feb<br /> |- valign=top<br /> | width=20% | 21 Feb: 1-6<br /> * [[#Session 2: cloning|Session 2: cloning]]<br /> * Joe, Emzo<br /> | width=20% | 22 Feb<br /> | width=20% | 23 Feb: 1-6<br /> * [[#Session 3: plate reader|Session 3: plate reader]]<br /> * Ophelia, Richard<br /> | width=20% | 24 Feb<br /> * Project #1<br /> | width=20% | 25 Feb<br /> * Project #1<br /> <br /> |- valign=top<br /> | width=20% | 28 Feb<br /> * Project #1<br /> | width=20% | 1 Mar<br /> * Project #1<br /> | width=20% | 2 Mar: TBD<br /> * [[#Session 4: microscopy|Session 4: microscopy]]<br /> * Ophelia, Joe<br /> | width=20% | 3 Mar<br /> *Project #1<br /> | width=20% | 4 Mar<br /> *Project #1<br /> |- valign=top<br /> | width=20% | 7 Mar: TBD<br /> * [[#Session 5: flow cytometry|Session 5: flow cytometry]]<br /> * Joe, Vanessa<br /> | width=20% | 8 Mar: TBD<br /> * [[#Session 6: spectrofluorometer|Session 6: spectrofluorometer]]<br /> * Jongmin, Elisa<br /> | width=20% | 9 Mar<br /> * Project #3<br /> | width=20% | 10 Mar<br /> * Project #3<br /> | width=20% | 11 Mar<br /> * Project #3<br /> |}<br /> &amp;nbsp;<br /> &lt;hr&gt;<br /> ==== Session 0: project discussion and lab tour ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * Overview of project goals<br /> * Tour of 040 Keck<br /> * Lab safety<br /> ===== Instructors: =====<br /> * Richard Murray, Ophelia Venturelli<br /> * Joe Meyerowitz, Elisa Franco (lab tour, safety)<br /> &lt;hr&gt;<br /> ==== [[Mini-bootcamp_2011/Session 1: lab techniques|Session 1: lab techniques]] ====<br /> This lab session will teach some of the basic techniques that will be used throughout the bootcamp. We assume no background in molecular biology laboratory techniques. By the end of this session, students will be able to transform a plasmid into cells, pick colonies containing the plasmid, grow the cells up to a given optical density, extract the plasmids, and quantify them.<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * Lab safety<br /> * Laboratory techniques: gloves, pipetting, disposal<br /> * Transforming plasmids into cells, growing, extracting<br /> * Clean up: benches, glassware<br /> <br /> ===== Instructors: =====<br /> * Emzo<br /> * Jongmin <br /> | width=50% |<br /> ===== Techniques and equipment: =====<br /> * Pipetting<br /> * Transformation, selection, growth<br /> * Optical density (OD) measurements (nanodrop?)<br /> * Mini-preps<br /> * Quantification (nanodrop)<br /> * Autoclave<br /> |}<br /> &lt;hr&gt;<br /> <br /> ==== [[Mini-bootcamp_2011/Session 2: cloning|Session 2: cloning]] ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * Discussion of PCR, primer design, Gibson assembly, gels<br /> * Demonstration of PCR<br /> * Demonstration of Gibson assembly<br /> * Demonstration of electrophoresis, restriction digestion, mapping<br /> * Transform Gibson product<br /> <br /> ===== Instructors: =====<br /> * Joe<br /> * Emzo<br /> | width=50% |<br /> <br /> ===== Techniques and equipment: =====<br /> * PCR<br /> * Restriction digests<br /> * Gels<br /> * Gibson assembly<br /> |}<br /> &lt;hr&gt;<br /> <br /> ==== Session 3: [[plate reader]] ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * Set up dose response with E. coli strains using serial dilution method<br /> * Learn strategies for measuring dynamics in plate reader<br /> :*Growth in shaker (manual time points)<br /> :*Growth in VictorX3 (automated measurements)<br /> * Measure gene expression (GFP) and OD (cell mass) using VictorX3 over a period of time<br /> <br /> ===== Instructors: =====<br /> * Ophelia<br /> * Richard<br /> | width=50% |<br /> <br /> ===== Techniques and equipment: =====<br /> * Victor X3 plate reader<br /> |}<br /> &lt;hr&gt;<br /> <br /> ==== Session 4: [[microscope]] ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * Learn basic principles and design of the Olympus IX-81 light microscope<br /> * Learn how to make agarose pads for imaging E coli<br /> * Basics of Micro-Manager software<br /> * Discuss image analysis<br /> <br /> ===== Instructors: =====<br /> * Ophelia<br /> * Joe<br /> | width=50% |<br /> ===== Techniques and equipment: =====<br /> * Olympus IX-81 microscope<br /> * MATLAB tools for image analysis<br /> |}<br /> &lt;hr&gt;<br /> <br /> ==== Session 5: flow cytometer ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * <br /> ===== Instructors: =====<br /> * Joe<br /> * Vanessa<br /> | width=50% |<br /> ===== Techniques and equipment: =====<br /> * FACS Calibur flow cytometer<br /> * MaxQuant (?)<br /> |}<br /> &lt;hr&gt;<br /> <br /> ==== Session 6: spectrofluorometer ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * <br /> ===== Instructors: =====<br /> * Jongmin<br /> * Elisa<br /> | width=50% |<br /> <br /> ===== Techniques and equipment: =====<br /> * PURExpress protein expression kit<br /> * Protein gels (?)<br /> * Fluorilog 3 spectrofluorometer<br /> |}</div>

Jmeyerow https://murray.cds.caltech.edu/index.php?title=Mini-bootcamp_2011&diff=12168 2011-02-28T22:20:53Z

<p>Jmeyerow: </p> <hr /> <div>This page contains a description of the mini-bootcamp run in Feb 2011. __NOTOC__<br /> <br /> === Group ===<br /> &lt;center&gt;<br /> {| width=90%<br /> |- valign=top<br /> | width=25% |<br /> ===== Students =====<br /> * Jorge Goncalves<br /> * Jun Liu<br /> * Yuan Ye<br /> * Enoch Yeung<br /> | width=25% |<br /> <br /> ===== Part-time students =====<br /> * Elisa Franco<br /> * Richard Murray<br /> | width=25% |<br /> ===== Instructors =====<br /> * Emzo de los Santos<br /> * Joe Meyerowitz<br /> * Ophelia Venturelli<br /> * Vanessa Jonsson<br /> * Jongmin Kim<br /> | width=25% |<br /> <br /> ===== Project advisor =====<br /> * Richard Murray<br /> |}<br /> &lt;/center&gt;<br /> <br /> === Bootcamp description ===<br /> <br /> {| width=100% border=1<br /> |- valign=top<br /> | rowspan=3 |<br /> The goal of this bootcamp is to measure variability in gene expression that is relevant for synthetically designed circuits. The issue that we are trying to understand is now much variability arises for the expression of a given circuit under degrees of freedom that are typically not controlled in synthetic designs:<br /> * Location and orientation of circuit elements in the plasmid<br /> * Vectors used for expressing the circuit, including copy number and antibiotic resistance<br /> * Growth conditions (temperature, oxygen, media, growth phase)<br /> To understand how these (and other) factors will affect circuit operation, a simple genetic circuit consisting of 2 reporters will be built using different DNA locations and directions, and characterized in a variety of conditions. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry and microscopy).<br /> <br /> Bootcamp objectives:<br /> * Project 1: Construct a simple genetic circuit that tests the effects of putting different reporters in different configurations in a plasmid. Characterize the differences (if any) in mean expression level of the circuits, possibly in multiple growth conditions, using a plate reader<br /> * Project 2: Characterize differences in expression distributions using flow cytometry (FACS Calibur) and fluorescent microscopy<br /> * Project 3: Perform in vitro testing of the constructs using the PURExpress kit and spectrofluorometer to check for differences in mean expression level<br /> |<br /> [[Image:lambda_switch.png|300px]]<br /> * Circuit layout: directions, ordering<br /> |-<br /> | <br /> [[Image:biobrick_plasmid.png|300px]]<br /> * Copy number<br /> * Origin of replication<br /> * Antibiotic resistance<br /> * [[http:partsregistry.org/Plasmid_backbones|Biobrick plasmids]]<br /> |-<br /> | <br /> * (Cell strain)<br /> * Growth media: LB, M9/glycerol, M9/glucose<br /> * Induction level<br /> * Temperature<br /> |}<br /> <br /> === Schedule ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=20% | 14 Feb: 2-4<br /> * Biocircuits mini-group meeting - planning<br /> * Richard<br /> | width=20% | 15 Feb<br /> | width=20% | 16 Feb: <br /> * [[#Session 0: project discussion and lab tour|Session 0: project discussion and lab tour]]<br /> * Richard, Ophelia<br /> * Joe, Elisa<br /> | width=20% | 17 Feb: 2:30-6<br /> * [[Mini-bootcamp_2011/Session 1: lab techniques|Session 1: lab techniques]]<br /> * Emzo, Jongmin<br /> | width=20% | 18 Feb<br /> |- valign=top<br /> | width=20% | 21 Feb: 1-6<br /> * [[#Session 2: cloning|Session 2: cloning]]<br /> * Joe, Emzo<br /> | width=20% | 22 Feb<br /> | width=20% | 23 Feb: 1-6<br /> * [[#Session 3: plate reader|Session 3: plate reader]]<br /> * Ophelia, Richard<br /> | width=20% | 24 Feb<br /> * Project #1<br /> | width=20% | 25 Feb<br /> * Project #1<br /> <br /> |- valign=top<br /> | width=20% | 28 Feb<br /> * Project #1<br /> | width=20% | 1 Mar<br /> * Project #1<br /> | width=20% | 2 Mar: TBD<br /> * [[#Session 4: microscopy|Session 4: microscopy]]<br /> * Ophelia, Joe<br /> | width=20% | 3 Mar: TBD<br /> *Project #1.5<br /> | width=20% | 4 Mar: 1:30p-Z<br /> * [[#Session 5: flow cytometry|Session 5: flow cytometry]]<br /> * Joe, Vanessa<br /> |- valign=top<br /> | width=20% | 7 Mar<br /> * Project #2<br /> | width=20% | 8 Mar: TBD<br /> * [[#Session 6: spectrofluorometer|Session 6: spectrofluorometer]]<br /> * Jongmin, Elisa<br /> | width=20% | 9 Mar<br /> * Project #3<br /> | width=20% | 10 Mar<br /> * Project #3<br /> | width=20% | 11 Mar<br /> * Project #3<br /> |}<br /> &amp;nbsp;<br /> &lt;hr&gt;<br /> ==== Session 0: project discussion and lab tour ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * Overview of project goals<br /> * Tour of 040 Keck<br /> * Lab safety<br /> ===== Instructors: =====<br /> * Richard Murray, Ophelia Venturelli<br /> * Joe Meyerowitz, Elisa Franco (lab tour, safety)<br /> &lt;hr&gt;<br /> ==== [[Mini-bootcamp_2011/Session 1: lab techniques|Session 1: lab techniques]] ====<br /> This lab session will teach some of the basic techniques that will be used throughout the bootcamp. We assume no background in molecular biology laboratory techniques. By the end of this session, students will be able to transform a plasmid into cells, pick colonies containing the plasmid, grow the cells up to a given optical density, extract the plasmids, and quantify them.<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * Lab safety<br /> * Laboratory techniques: gloves, pipetting, disposal<br /> * Transforming plasmids into cells, growing, extracting<br /> * Clean up: benches, glassware<br /> <br /> ===== Instructors: =====<br /> * Emzo<br /> * Jongmin <br /> | width=50% |<br /> ===== Techniques and equipment: =====<br /> * Pipetting<br /> * Transformation, selection, growth<br /> * Optical density (OD) measurements (nanodrop?)<br /> * Mini-preps<br /> * Quantification (nanodrop)<br /> * Autoclave<br /> |}<br /> &lt;hr&gt;<br /> <br /> ==== [[Mini-bootcamp_2011/Session 2: cloning|Session 2: cloning]] ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * Discussion of PCR, primer design, Gibson assembly, gels<br /> * Demonstration of PCR<br /> * Demonstration of Gibson assembly<br /> * Demonstration of electrophoresis, restriction digestion, mapping<br /> * Transform Gibson product<br /> <br /> ===== Instructors: =====<br /> * Joe<br /> * Emzo<br /> | width=50% |<br /> <br /> ===== Techniques and equipment: =====<br /> * PCR<br /> * Restriction digests<br /> * Gels<br /> * Gibson assembly<br /> |}<br /> &lt;hr&gt;<br /> <br /> ==== Session 3: [[plate reader]] ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * Set up dose response with E. coli strains using serial dilution method<br /> * Learn strategies for measuring dynamics in plate reader<br /> :*Growth in shaker (manual time points)<br /> :*Growth in VictorX3 (automated measurements)<br /> * Measure gene expression (GFP) and OD (cell mass) using VictorX3 over a period of time<br /> <br /> ===== Instructors: =====<br /> * Ophelia<br /> * Richard<br /> | width=50% |<br /> <br /> ===== Techniques and equipment: =====<br /> * Victor X3 plate reader<br /> |}<br /> &lt;hr&gt;<br /> <br /> ==== Session 4: [[microscope]] ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * Learn basic principles and design of the Olympus IX-81 light microscope<br /> * Basics of Micro-Manager software<br /> * Learn how to make agarose pads for imaging E coli<br /> * Discuss image analysis<br /> <br /> ===== Instructors: =====<br /> * Ophelia<br /> * Joe<br /> | width=50% |<br /> ===== Techniques and equipment: =====<br /> * Olympus IX-81 microscope<br /> * MATLAB tools for image analysis<br /> |}<br /> &lt;hr&gt;<br /> <br /> ==== Session 5: flow cytometer ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * <br /> ===== Instructors: =====<br /> * Joe<br /> * Vanessa<br /> | width=50% |<br /> ===== Techniques and equipment: =====<br /> * FACS Calibur flow cytometer<br /> * MaxQuant (?)<br /> |}<br /> &lt;hr&gt;<br /> <br /> ==== Session 6: spectrofluorometer ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * <br /> ===== Instructors: =====<br /> * Jongmin<br /> * Elisa<br /> | width=50% |<br /> <br /> ===== Techniques and equipment: =====<br /> * PURExpress protein expression kit<br /> * Protein gels (?)<br /> * Fluorilog 3 spectrofluorometer<br /> |}</div>

Jmeyerow https://murray.cds.caltech.edu/index.php?title=Mini-bootcamp_2011&diff=12105 2011-02-20T22:21:46Z

<p>Jmeyerow: /* Session 2: cloning */</p> <hr /> <div>This page contains a description of the mini-bootcamp run in Feb 2011. __NOTOC__<br /> <br /> === Group ===<br /> &lt;center&gt;<br /> {| width=90%<br /> |- valign=top<br /> | width=25% |<br /> ===== Students =====<br /> * Jorge Goncalves<br /> * Jun Liu<br /> * Yuan Ye<br /> * Enoch Yeung<br /> | width=25% |<br /> <br /> ===== Part-time students =====<br /> * Elisa Franco<br /> * Richard Murray<br /> | width=25% |<br /> ===== Instructors =====<br /> * Emzo de los Santos<br /> * Joe Meyerowitz<br /> * Ophelia Venturelli<br /> * Vanessa Jonsson<br /> * Jongmin Kim<br /> | width=25% |<br /> <br /> ===== Project advisor =====<br /> * Richard Murray<br /> |}<br /> &lt;/center&gt;<br /> <br /> === Bootcamp description ===<br /> <br /> {| width=100% border=1<br /> |- valign=top<br /> | rowspan=3 |<br /> The goal of this bootcamp is to measure variability in gene expression that is relevant for synthetically designed circuits. The issue that we are trying to understand is now much variability arises for the expression of a given circuit under degrees of freedom that are typically not controlled in synthetic designs:<br /> * Location and orientation of circuit elements in the plasmid<br /> * Vectors used for expressing the circuit, including copy number and antibiotic resistance<br /> * Growth conditions (temperature, oxygen, media, growth phase)<br /> To understand how these (and other) factors will affect circuit operation, a simple genetic circuit consisting of 2 reporters will be built using different DNA locations and directions, and characterized in a variety of conditions. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry and microscopy).<br /> <br /> Bootcamp objectives:<br /> * Project 1: Construct a simple genetic circuit that tests the effects of putting different reporters in different configurations in a plasmid. Characterize the differences (if any) in mean expression level of the circuits, possibly in multiple growth conditions, using a plate reader<br /> * Project 2: Characterize differences in expression distributions using flow cytometry (FACS Calibur) and fluorescent microscopy<br /> * Project 3: Perform in vitro testing of the constructs using the PURExpress kit and spectrofluorometer to check for differences in mean expression level<br /> |<br /> [[Image:lambda_switch.png|300px]]<br /> * Circuit layout: directions, ordering<br /> |-<br /> | <br /> [[Image:biobrick_plasmid.png|300px]]<br /> * Copy number<br /> * Origin of replication<br /> * Antibiotic resistance<br /> * [[http:partsregistry.org/Plasmid_backbones|Biobrick plasmids]]<br /> |-<br /> | <br /> * (Cell strain)<br /> * Growth media: LB, M9/glycerol, M9/glucose<br /> * Induction level<br /> * Temperature<br /> |}<br /> <br /> === Schedule ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=20% | 14 Feb: 2-4<br /> * Biocircuits mini-group meeting - planning<br /> * Richard<br /> | width=20% | 15 Feb<br /> | width=20% | 16 Feb: <br /> * [[#Session 0: project discussion and lab tour|Session 0: project discussion and lab tour]]<br /> * Richard, Ophelia<br /> * Joe, Elisa<br /> | width=20% | 17 Feb: 2:30-6<br /> * [[Mini-bootcamp_2011/Session 1: lab techniques|Session 1: lab techniques]]<br /> * Emzo, Jongmin<br /> | width=20% | 18 Feb<br /> |- valign=top<br /> | width=20% | 21 Feb: 1-6<br /> * [[#Session 2: cloning|Session 2: cloning]]<br /> * Joe, Emzo<br /> | width=20% | 22 Feb<br /> | width=20% | 23 Feb: 1-6<br /> * [[#Session 3: plate reader|Session 3: plate reader]]<br /> * Ophelia, Richard<br /> | width=20% | 24 Feb<br /> * Project #1<br /> | width=20% | 25 Feb<br /> * Project #1<br /> <br /> |- valign=top<br /> | width=20% | 28 Feb<br /> * Project #1<br /> | width=20% | 1 Mar<br /> * Project #1<br /> | width=20% | 2 Mar: TBD<br /> * [[#Session 4: microscopy|Session 4: microscopy]]<br /> * Ophelia, Joe<br /> | width=20% | 3 Mar: TBD<br /> * [[#Session 5: flow cytometry|Session 5: flow cytometry]]<br /> * Joe, Vanessa<br /> | width=20% | 4 Mar<br /> * Project #2<br /> |- valign=top<br /> | width=20% | 7 Mar<br /> * Project #2<br /> | width=20% | 8 Mar: TBD<br /> * [[#Session 6: spectrofluorometer|Session 6: spectrofluorometer]]<br /> * Jongmin, Elisa<br /> | width=20% | 9 Mar<br /> * Project #3<br /> | width=20% | 10 Mar<br /> * Project #3<br /> | width=20% | 11 Mar<br /> * Project #3<br /> |}<br /> &amp;nbsp;<br /> &lt;hr&gt;<br /> ==== Session 0: project discussion and lab tour ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * Overview of project goals<br /> * Tour of 040 Keck<br /> * Lab safety<br /> ===== Instructors: =====<br /> * Richard Murray, Ophelia Venturelli<br /> * Joe Meyerowitz, Elisa Franco (lab tour, safety)<br /> &lt;hr&gt;<br /> ==== [[Mini-bootcamp_2011/Session 1: lab techniques|Session 1: lab techniques]] ====<br /> This lab session will teach some of the basic techniques that will be used throughout the bootcamp. We assume no background in molecular biology laboratory techniques. By the end of this session, students will be able to transform a plasmid into cells, pick colonies containing the plasmid, grow the cells up to a given optical density, extract the plasmids, and quantify them.<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * Lab safety<br /> * Laboratory techniques: gloves, pipetting, disposal<br /> * Transforming plasmids into cells, growing, extracting<br /> * Clean up: benches, glassware<br /> <br /> ===== Instructors: =====<br /> * Emzo<br /> * Jongmin <br /> | width=50% |<br /> ===== Techniques and equipment: =====<br /> * Pipetting<br /> * Transformation, selection, growth<br /> * Optical density (OD) measurements (nanodrop?)<br /> * Mini-preps<br /> * Quantification (nanodrop)<br /> * Autoclave<br /> |}<br /> &lt;hr&gt;<br /> <br /> ==== [[Mini-bootcamp_2011/Session 2: cloning|Session 2: cloning]] ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * Discussion of PCR, primer design, Gibson assembly, gels<br /> * Demonstration of PCR<br /> * Demonstration of Gibson assembly<br /> * Demonstration of electrophoresis, restriction digestion, mapping<br /> * Transform Gibson product<br /> <br /> ===== Instructors: =====<br /> * Joe<br /> * Emzo<br /> | width=50% |<br /> <br /> ===== Techniques and equipment: =====<br /> * PCR<br /> * Restriction digests<br /> * Gels<br /> * Gibson assembly<br /> |}<br /> &lt;hr&gt;<br /> <br /> ==== Session 3: plate reader ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * <br /> ===== Instructors: =====<br /> * Ophelia<br /> * Richard<br /> | width=50% |<br /> <br /> ===== Techniques and equipment: =====<br /> * Victor X3 plate reader<br /> |}<br /> &lt;hr&gt;<br /> <br /> ==== Session 4: microscope ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * <br /> ===== Instructors: =====<br /> * Ophelia<br /> * Joe<br /> | width=50% |<br /> ===== Techniques and equipment: =====<br /> * Olympus IX-81 microscope<br /> * MATLAB tools for image analysis<br /> |}<br /> &lt;hr&gt;<br /> <br /> ==== Session 5: flow cytometer ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * <br /> ===== Instructors: =====<br /> * Joe<br /> * Vanessa<br /> | width=50% |<br /> ===== Techniques and equipment: =====<br /> * FACS Calibur flow cytometer<br /> * MaxQuant (?)<br /> |}<br /> &lt;hr&gt;<br /> <br /> ==== Session 6: spectrofluorometer ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * <br /> ===== Instructors: =====<br /> * Jongmin<br /> * Elisa<br /> | width=50% |<br /> <br /> ===== Techniques and equipment: =====<br /> * PURExpress protein expression kit<br /> * Protein gels (?)<br /> * Fluorilog 3 spectrofluorometer<br /> |}</div>

Jmeyerow https://murray.cds.caltech.edu/index.php?title=Mini-bootcamp_2011&diff=12103 2011-02-20T21:41:56Z

<p>Jmeyerow: /* Session 2: cloning */</p> <hr /> <div>This page contains a description of the mini-bootcamp run in Feb 2011. __NOTOC__<br /> <br /> === Group ===<br /> &lt;center&gt;<br /> {| width=90%<br /> |- valign=top<br /> | width=25% |<br /> ===== Students =====<br /> * Jorge Goncalves<br /> * Jun Liu<br /> * Yuan Ye<br /> * Enoch Yeung<br /> | width=25% |<br /> <br /> ===== Part-time students =====<br /> * Elisa Franco<br /> * Richard Murray<br /> | width=25% |<br /> ===== Instructors =====<br /> * Emzo de los Santos<br /> * Joe Meyerowitz<br /> * Ophelia Venturelli<br /> * Vanessa Jonsson<br /> * Jongmin Kim<br /> | width=25% |<br /> <br /> ===== Project advisor =====<br /> * Richard Murray<br /> |}<br /> &lt;/center&gt;<br /> <br /> === Bootcamp description ===<br /> <br /> {| width=100% border=1<br /> |- valign=top<br /> | rowspan=3 |<br /> The goal of this bootcamp is to measure variability in gene expression that is relevant for synthetically designed circuits. The issue that we are trying to understand is now much variability arises for the expression of a given circuit under degrees of freedom that are typically not controlled in synthetic designs:<br /> * Location and orientation of circuit elements in the plasmid<br /> * Vectors used for expressing the circuit, including copy number and antibiotic resistance<br /> * Growth conditions (temperature, oxygen, media, growth phase)<br /> To understand how these (and other) factors will affect circuit operation, a simple genetic circuit consisting of 2 reporters will be built using different DNA locations and directions, and characterized in a variety of conditions. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry and microscopy).<br /> <br /> Bootcamp objectives:<br /> * Project 1: Construct a simple genetic circuit that tests the effects of putting different reporters in different configurations in a plasmid. Characterize the differences (if any) in mean expression level of the circuits, possibly in multiple growth conditions, using a plate reader<br /> * Project 2: Characterize differences in expression distributions using flow cytometry (FACS Calibur) and fluorescent microscopy<br /> * Project 3: Perform in vitro testing of the constructs using the PURExpress kit and spectrofluorometer to check for differences in mean expression level<br /> |<br /> [[Image:lambda_switch.png|300px]]<br /> * Circuit layout: directions, ordering<br /> |-<br /> | <br /> [[Image:biobrick_plasmid.png|300px]]<br /> * Copy number<br /> * Origin of replication<br /> * Antibiotic resistance<br /> * [[http:partsregistry.org/Plasmid_backbones|Biobrick plasmids]]<br /> |-<br /> | <br /> * (Cell strain)<br /> * Growth media: LB, M9/glycerol, M9/glucose<br /> * Induction level<br /> * Temperature<br /> |}<br /> <br /> === Schedule ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=20% | 14 Feb: 2-4<br /> * Biocircuits mini-group meeting - planning<br /> * Richard<br /> | width=20% | 15 Feb<br /> | width=20% | 16 Feb: <br /> * [[#Session 0: project discussion and lab tour|Session 0: project discussion and lab tour]]<br /> * Richard, Ophelia<br /> * Joe, Elisa<br /> | width=20% | 17 Feb: 2:30-6<br /> * [[Mini-bootcamp_2011/Session 1: lab techniques|Session 1: lab techniques]]<br /> * Emzo, Jongmin<br /> | width=20% | 18 Feb<br /> |- valign=top<br /> | width=20% | 21 Feb: 1-6<br /> * [[#Session 2: cloning|Session 2: cloning]]<br /> * Joe, Emzo<br /> | width=20% | 22 Feb<br /> | width=20% | 23 Feb: 1-6<br /> * [[#Session 3: plate reader|Session 3: plate reader]]<br /> * Ophelia, Richard<br /> | width=20% | 24 Feb<br /> * Project #1<br /> | width=20% | 25 Feb<br /> * Project #1<br /> <br /> |- valign=top<br /> | width=20% | 28 Feb<br /> * Project #1<br /> | width=20% | 1 Mar<br /> * Project #1<br /> | width=20% | 2 Mar: TBD<br /> * [[#Session 4: microscopy|Session 4: microscopy]]<br /> * Ophelia, Joe<br /> | width=20% | 3 Mar: TBD<br /> * [[#Session 5: flow cytometry|Session 5: flow cytometry]]<br /> * Joe, Vanessa<br /> | width=20% | 4 Mar<br /> * Project #2<br /> |- valign=top<br /> | width=20% | 7 Mar<br /> * Project #2<br /> | width=20% | 8 Mar: TBD<br /> * [[#Session 6: spectrofluorometer|Session 6: spectrofluorometer]]<br /> * Jongmin, Elisa<br /> | width=20% | 9 Mar<br /> * Project #3<br /> | width=20% | 10 Mar<br /> * Project #3<br /> | width=20% | 11 Mar<br /> * Project #3<br /> |}<br /> &amp;nbsp;<br /> &lt;hr&gt;<br /> ==== Session 0: project discussion and lab tour ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * Overview of project goals<br /> * Tour of 040 Keck<br /> * Lab safety<br /> ===== Instructors: =====<br /> * Richard Murray, Ophelia Venturelli<br /> * Joe Meyerowitz, Elisa Franco (lab tour, safety)<br /> &lt;hr&gt;<br /> ==== [[Mini-bootcamp_2011/Session 1: lab techniques|Session 1: lab techniques]] ====<br /> This lab session will teach some of the basic techniques that will be used throughout the bootcamp. We assume no background in molecular biology laboratory techniques. By the end of this session, students will be able to transform a plasmid into cells, pick colonies containing the plasmid, grow the cells up to a given optical density, extract the plasmids, and quantify them.<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * Lab safety<br /> * Laboratory techniques: gloves, pipetting, disposal<br /> * Transforming plasmids into cells, growing, extracting<br /> * Clean up: benches, glassware<br /> <br /> ===== Instructors: =====<br /> * Emzo<br /> * Jongmin <br /> | width=50% |<br /> ===== Techniques and equipment: =====<br /> * Pipetting<br /> * Transformation, selection, growth<br /> * Optical density (OD) measurements (nanodrop?)<br /> * Mini-preps<br /> * Quantification (nanodrop)<br /> * Autoclave<br /> |}<br /> &lt;hr&gt;<br /> <br /> ==== Session 2: cloning ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * Discussion of PCR, primer design, Gibson assembly, gels<br /> * Demonstration of PCR<br /> * Demonstration of Gibson assembly<br /> * Demonstration of electrophoresis, restriction digestion, mapping<br /> * Transform Gibson product<br /> <br /> ===== Instructors: =====<br /> * Joe<br /> * Emzo<br /> | width=50% |<br /> <br /> ===== Techniques and equipment: =====<br /> * PCR<br /> * Restriction digests<br /> * Gels<br /> * Gibson assembly<br /> |}<br /> &lt;hr&gt;<br /> <br /> ==== Session 3: plate reader ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * <br /> ===== Instructors: =====<br /> * Ophelia<br /> * Richard<br /> | width=50% |<br /> <br /> ===== Techniques and equipment: =====<br /> * Victor X3 plate reader<br /> |}<br /> &lt;hr&gt;<br /> <br /> ==== Session 4: microscope ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * <br /> ===== Instructors: =====<br /> * Ophelia<br /> * Joe<br /> | width=50% |<br /> ===== Techniques and equipment: =====<br /> * Olympus IX-81 microscope<br /> * MATLAB tools for image analysis<br /> |}<br /> &lt;hr&gt;<br /> <br /> ==== Session 5: flow cytometer ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * <br /> ===== Instructors: =====<br /> * Joe<br /> * Vanessa<br /> | width=50% |<br /> ===== Techniques and equipment: =====<br /> * FACS Calibur flow cytometer<br /> * MaxQuant (?)<br /> |}<br /> &lt;hr&gt;<br /> <br /> ==== Session 6: spectrofluorometer ====<br /> {| width=100%<br /> |- valign=top<br /> | width=50% |<br /> ===== Session goals: =====<br /> * <br /> ===== Instructors: =====<br /> * Jongmin<br /> * Elisa<br /> | width=50% |<br /> <br /> ===== Techniques and equipment: =====<br /> * PURExpress protein expression kit<br /> * Protein gels (?)<br /> * Fluorilog 3 spectrofluorometer<br /> |}</div>

Jmeyerow https://murray.cds.caltech.edu/index.php?title=SURF_2011&diff=11902 2011-01-24T02:53:37Z

<p>Jmeyerow: </p> <hr /> <div>{{righttoc}}<br /> This page is intended for students interested in working on SURF projects in the Summer of 2011. It contains a list of project areas where I will be supervising projects this year. Students interested in writing proposals for SURF projects should contact me via e-mail to discuss what areas they are interested in and talk through possible SURF proposal topics. All applications should go through the normal SURF application process, described at www.surf.caltech.edu.<br /> <br /> {| border=1 width=100%<br /> |-<br /> | '''Title''' || '''Grant/Project''' || '''Co-Mentors''' || '''Comments'''<br /> |-<br /> | [[SURF 2011: Synthetic biology in a cell-free expression system|Synthetic biology in a cell-free expression system]]<br /> | [[Molecular Programming Project|MPP]]<br /> | Jongmin Kim<br /> |<br /> |-<br /> | [[SURF 2011: Design of Biomolecular Circuits Using Programmable Protein Scaffolds|Design of Biomolecular Circuits Using Programmable Protein Scaffolds]]<br /> | [[Biomolecular Feedback Circuits for Modular, Robust and Rapid Response|ICB]]<br /> | Emzo de los Santos<br /> |<br /> |-<br /> | [[SURF 2011: Effects of Topology on DNA Transcription|Effects of Topology on DNA Transcription]]<br /> | [[Biomolecular Feedback Circuits for Modular, Robust and Rapid Response|ICB]]<br /> | Joseph T. Meyerowitz<br /> |<br /> |-<br /> | [[SURF 2011: Receding Horizon Temporal Logic Planning Toolbox|Receding Horizon Temporal Logic Planning Toolbox]]<br /> | [[Distributed_Sense_and_Control_Systems|MuSyC]]<br /> | Ufuk Topcu<br /> |<br /> |-<br /> | [[SURF 2011: Implementation of Control Protocols for Camera Networks|Implementation of Control Protocols for Camera Networks]]<br /> | [[Distributed_Sense_and_Control_Systems|MuSyC]]<br /> | Necmiye Ozay<br /> |<br /> |}</div>

Jmeyerow https://murray.cds.caltech.edu/index.php?title=SURF_2011:_Effects_of_Topology_on_DNA_Transcription&diff=11901 2011-01-24T02:51:39Z

<p>Jmeyerow: Created page with &#039;&#039;&#039;&#039;2011 SURF project description&#039;&#039;&#039; * Mentor: Richard Murray * Co-mentor: [http://openwetware.org/wiki/User:Joseph_T._Meyerowitz Joseph T. Meyerowitz] A goal of synthetic biolog…&#039;</p> <hr /> <div>'''2011 SURF project description'''<br /> * Mentor: Richard Murray<br /> * Co-mentor: [http://openwetware.org/wiki/User:Joseph_T._Meyerowitz Joseph T. Meyerowitz]<br /> <br /> A goal of synthetic biology is to predict the operation of a designed biological circuit in a cell. However, there are a number of cellular effects for which we have few/no accurate predictive models, including the change in gene translation that results from topological changes in DNA. Circular &quot;plasmid&quot; DNA takes on a number of [http://en.wikipedia.org/wiki/DNA_supercoil distinct topological states as it supercoils]. Previous work has shown that the distribution of topological states occupied by the DNA in cells can impact the expression of different genes, and that the distribution of topological states over time.<br /> <br /> This project will focus on developing a physical model for the relationship between DNA topological state and transcription. This may involve engineering biological circuits that rely on coiling effects for their operation as a proof-of-concept. There are commercially available enzymes to coil, uncoil, and cut DNA outside of cells, and experimental tools to measure the rate of translation from DNA and to measure the distribution of topological states for the DNA.<br /> <br /> Students interested in this project must be proactive and willing to work with both experiment and theory. Lab experience is not necessary but very helpful.<br /> <br /> '''References'''<br /> # [http://www.uic.edu/com/bcmg/mirkin_pdf/k_p.pdf Krasilnikov et al, Large-scale Effects of Transcriptional DNA Supercoiling in Vivo, Journal of Molecular Biology, 1999]<br /> # [http://www.pnas.org/content/106/52/22564.full Vijayan et al, Oscillations in supercoiling drive circadian gene expression in cyanobacteria, PNAS, 2009]<br /> # [http://dx.doi.org/10.1016/j.cell.2010.08.001 Koster et al, Cellular Strategies for Regulating DNA Supercoiling: A Single-Molecule Perspective, Cell, 2010]</div>

Jmeyerow https://murray.cds.caltech.edu/index.php?title=BFS_GOTChAs,_April_2010&diff=10677 2010-04-30T11:18:11Z

<p>Jmeyerow: /* Device Projects */</p> <hr /> <div>This page contains some [[GOTChA Chart|GOTChA charts]] for possible rotation projects in the lab this summer. __NOTOC__<br /> <br /> == Device Projects ==<br /> <br /> The following GOTChAs are for projects that involve building new device technologies that can be used to push biological circuit design forward.<br /> <br /> === Integrated Load and Context Compensation (RMM) ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=50% |<br /> ==== Goals ====<br /> * Design a transcriptional regulator that uses feedback to compensate for changes in load and changes in context and thus provides consistent performance independent of downstream loading or cellular context (cell strain, growth media)<br /> * Example: &lt;nowiki&gt;A -| B&lt;/nowiki&gt;, designed so that transfer curve is maintained across changes in downstream reactions involving B, cell strain, growth media<br /> | width=50% |<br /> ==== Technical Challenges ====<br /> |-valign=top<br /> | width=50% |<br /> ==== Objectives ====<br /> * Characterize the performance of existing transcriptional regulators across 3 cell strains, 3 growth media and 3 loading conditions.<br /> * Design a compensation circuit that measures output level and regulates device performance to compensate for uncertainty<br /> ** Idea: use RNA-based feedback in 5' UTR sequences to measure transcription and compensate<br /> ** Note: feedback dynamics should be 5-10X regulatory dynamics to allow for use in non-equilibrium circuits<br /> * Measure the performance of one or more compensation circuits and compare to existing regulators<br /> * Regulation circuitry should be &quot;internal&quot; to device, so that inputs and outputs are the same as traditional regulator<br /> |<br /> <br /> ==== Approach ====<br /> |}<br /> <br /> &lt;br&gt;<br /> === Fast Mechanisms for Biomolecular Feedback (RMM) ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=50% |<br /> ==== Goals ====<br /> * Design a set of devices for implementing feedback circuits that have timescales measured in seconds instead of minutes<br /> |<br /> ==== Technical Challenges ====<br /> |- valign = top<br /> | width=50% |<br /> ==== Objectives ====<br /> * Identify the mechanisms and timescales of various feedback mechanisms in natural systems<br /> ** Example: feedback mechanisms involved in chemotaxis<br /> * Use models to estimate the bandwidth of regulators based on transcriptional feedback, post-transcriptional feedback, translational feedback, post-translational feedback, and covalent modifications<br /> * Formulate a test setup that can be used to characterize the speed of response of one or more circuits using different mechanisms<br /> * Implement a fast-feedback mechanism using one of the following methods:<br /> ** RNA-based feedback using anti-sense interference<br /> ** RNA-based feedback using secondary structure<br /> ** Programmable scaffolds for phosphorylation cascades<br /> * Measure the response speed of one or more regulation mechanisms and demonstrate seconds-timescale response<br /> |<br /> ==== Approach ====<br /> |}<br /> <br /> &lt;br&gt;<br /> === Cell Division Tracker (ES) ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=50% |<br /> ==== Goals ====<br /> * Design a genetic construct that changes state upon cell division (i.e. Cells start expressing GFP, after cellular division cells now express YFP)<br /> |<br /> ==== Technical Challenges ====<br /> * Frequency of recombinases not well characterized<br /> * Might need to use a combination between two irreversible recombinases or a reversible recombinase and an irreversible one<br /> * If recognition sequences are not compatible may need to evolve recombinases to recognize different sequences that are compatible<br /> |-valign=top<br /> | width=50% |<br /> ==== Objectives ====<br /> * Characterize different recombinases<br /> ** (example: reversible vs. irreversible, frequency of recombinase activity)<br /> * Find a cell-cycle dependent promoter to use<br /> * Organize recognition sites and proteins of interest in an operon<br /> * Test the operon in cells (E coli or Yeast)<br /> * Measure system characteristics such as % errors <br /> |<br /> ==== Approach ====<br /> * Use recombinases<br /> ** The simplest approach would be to use a reversible recombinase (like fin and hin [http://jb.asm.org/cgi/content/full/188/3/950]) under a cell cycle dependent promoter<br /> ** If we see too many double inversions need to device a more complex mechanism using a combination of recombinases<br /> |}<br /> <br /> &lt;br&gt;<br /> === Stoichiometric Protein Expression (JTM) ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=50% |<br /> ==== Goals ====<br /> * Design a modular genetic construct that allows proteins to be maintained at a precise relative stoichiometry <br /> ** Allowing variable absolute expression, perhaps?<br /> ** A faculty member here once said that this might be useful for membrane protein crystallography<br /> |<br /> ==== Technical Challenges ====<br /> * Western blots/ELISA are time-consuming, require certain equipment<br /> * Expression may vary too much for modularity to work<br /> * Variable degradation rates may make this difficult<br /> |-valign=top<br /> | width=50% |<br /> ==== Objectives ====<br /> * Review existing literature<br /> * Investigate gene fusions and degradation control<br /> ** Are there paths in degradation that could connect the rate of degradation to expression in a specific way?<br /> ** Could some signaling peptide be integrated into the protein such that it's released upon degradation via a non-processive protease?<br /> ** For a 1:1 stoichiometry, one could imagine simply fusing the two proteins and then also expressing a protease to separate them after translation<br /> |<br /> ==== Approach ====<br /> * TBD<br /> |}<br /> <br /> &lt;br&gt;<br /> === Use of photoactive proteins to access multiple time-scale control (JTM) ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=50% |<br /> ==== Goals ====<br /> * Photoactive yellow protein (PYP) has multiple states, actuated by light<br /> ** Upon being hit by a photon of appropriate energy, a picosecond-scale transition occurs, followed by a millisecond-scale reversible photobleaching, then a second-scale reversion.<br /> ** There are fast-recovery and slow-recovery PYPs [ref:http://pubs.acs.org/doi/full/10.1021/bi020690e]<br /> ** PYP typically mediates negative phototaxis<br /> * Want to take Ppr-PYP (a PYP attached to a histidine kinase from Rc. centenum) and...<br /> |<br /> ==== Technical Challenges ====<br /> * TBD<br /> |-valign=top<br /> | width=50% |<br /> ==== Objectives ====<br /> * TBD<br /> |<br /> ==== Approach ====<br /> * TBD<br /> |}<br /> <br /> &lt;br&gt;<br /> === Manipulation of the integral controller in photo/chemotaxis (JTM) ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=50% |<br /> ==== Goals ====<br /> * Substitute heterologous che-like signal transducers between organisms such as H. salinarum, E. coli, and others<br /> * Observe preservation or destruction of integral controller after recombination and after evolution<br /> * TBD<br /> |<br /> ==== Technical Challenges ====<br /> * TBD<br /> |-valign=top<br /> | width=50% |<br /> ==== Objectives ====<br /> * Put che-like transducers in mutator plasmid and observe recovery of integral control if damaged after recombination<br /> |<br /> ==== Approach ====<br /> * TBD<br /> |}<br /> <br /> == Robustness Projects ==<br /> <br /> === CAGEN (RMM) ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=50% |<br /> ==== Goals ====<br /> * Design, synthesize and characterize a circuit that provides robust transcriptional regulation<br /> * Win the 2011 [[CAGEN]] competition<br /> |<br /> ==== Technical Challenges ====<br /> |-<br /> | width=50% |<br /> ==== Objectives ====<br /> |<br /> ==== Approach ====<br /> |}<br /> <br /> === Consistent Gene Expression Level (ES and JTM) ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=50% |<br /> ==== Goals ====<br /> * Design, synthesize and characterize an inducible gene circuit that will express a constant level of a protein regardless of inducer concentration<br /> |<br /> ==== Technical Challenges ====<br /> * Might have issues designing an ACR circuit synthetically<br /> * Getting an inducible circuit might be difficult, may start with the simpler problem of just expressing a protein at a constant level<br /> |-<br /> | width=50% |<br /> ==== Objectives ====<br /> * Design a circuit that exhibits a constant concentration of gene of interest (probably an xFP at steady state) we might be able to use ACR theory [http://www.sciencemag.org/cgi/content/abstract/327/5971/1389?ijkey=c777f236d838b71911625aae954a625090cf51ca&amp;keytype2=tf_ipsecsha]<br /> * Construct and characterize designed circuit<br /> |<br /> ==== Approach ====<br /> * Incorporate feedback into current inducer systems, possibly tie into a gene that is known to be tightly controlled<br /> * Design theoretical circuit, then use canonical examples of reactions<br /> * Try the a fusion protein with the circuit that is tightly regulated in paper as a crutch<br /> |}<br /> <br /> === State Transition Modeling in Chemical Reaction Networks (JTM) ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=50% |<br /> ==== Goals ====<br /> * Develop an enumeration algorithm to find distinct &quot;states&quot; for a chemical reaction network<br /> * Look at transition criteria between states<br /> * Test analysis on simple circuits and biological networks<br /> * Use transition criteria to develop robustness metrics<br /> |<br /> ==== Technical Challenges ====<br /> * Not immediately clear how to classify/cluster output<br /> * Not sure how to deal with continuous relationships vs. more discrete relationships (thresholding?)<br /> * May be useful to use analytical techniques () in addition to blind sampling<br /> |-<br /> | width=50% |<br /> ==== Objectives ====<br /> * Program a library of well-characterized reaction circuits (bi-stable flipflops, oscillators, etc)<br /> * Demonstrate proper time-evolution of circuits via numerical analysis<br /> * Run each circuit with a variety of initial conditions and mid-time-course perturbations<br /> * Cluster end states, evaluate quality of clustering, and match to known circuit behavior<br /> * Measure transition criteria between states<br /> |<br /> ==== Approach ====<br /> * Attempt naive exhausive approach to evaluation - sweep through all plausible initial conditions and cluster results (fuzzy c-means?)<br /> * Attempt theorem/network solver approach to evaluation - sweep through initial conditions and use Bayesian network analysis and/or theorem postulators (eureqa) to enumerate states<br /> |}</div>

Jmeyerow https://murray.cds.caltech.edu/index.php?title=BFS_GOTChAs,_April_2010&diff=10676 2010-04-30T10:54:56Z

<p>Jmeyerow: </p> <hr /> <div>This page contains some [[GOTChA Chart|GOTChA charts]] for possible rotation projects in the lab this summer. __NOTOC__<br /> <br /> == Device Projects ==<br /> <br /> The following GOTChAs are for projects that involve building new device technologies that can be used to push biological circuit design forward.<br /> <br /> === Integrated Load and Context Compensation (RMM) ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=50% |<br /> ==== Goals ====<br /> * Design a transcriptional regulator that uses feedback to compensate for changes in load and changes in context and thus provides consistent performance independent of downstream loading or cellular context (cell strain, growth media)<br /> * Example: &lt;nowiki&gt;A -| B&lt;/nowiki&gt;, designed so that transfer curve is maintained across changes in downstream reactions involving B, cell strain, growth media<br /> | width=50% |<br /> ==== Technical Challenges ====<br /> |-valign=top<br /> | width=50% |<br /> ==== Objectives ====<br /> * Characterize the performance of existing transcriptional regulators across 3 cell strains, 3 growth media and 3 loading conditions.<br /> * Design a compensation circuit that measures output level and regulates device performance to compensate for uncertainty<br /> ** Idea: use RNA-based feedback in 5' UTR sequences to measure transcription and compensate<br /> ** Note: feedback dynamics should be 5-10X regulatory dynamics to allow for use in non-equilibrium circuits<br /> * Measure the performance of one or more compensation circuits and compare to existing regulators<br /> * Regulation circuitry should be &quot;internal&quot; to device, so that inputs and outputs are the same as traditional regulator<br /> |<br /> <br /> ==== Approach ====<br /> |}<br /> <br /> &lt;br&gt;<br /> === Fast Mechanisms for Biomolecular Feedback (RMM) ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=50% |<br /> ==== Goals ====<br /> * Design a set of devices for implementing feedback circuits that have timescales measured in seconds instead of minutes<br /> |<br /> ==== Technical Challenges ====<br /> |- valign = top<br /> | width=50% |<br /> ==== Objectives ====<br /> * Identify the mechanisms and timescales of various feedback mechanisms in natural systems<br /> ** Example: feedback mechanisms involved in chemotaxis<br /> * Use models to estimate the bandwidth of regulators based on transcriptional feedback, post-transcriptional feedback, translational feedback, post-translational feedback, and covalent modifications<br /> * Formulate a test setup that can be used to characterize the speed of response of one or more circuits using different mechanisms<br /> * Implement a fast-feedback mechanism using one of the following methods:<br /> ** RNA-based feedback using anti-sense interference<br /> ** RNA-based feedback using secondary structure<br /> ** Programmable scaffolds for phosphorylation cascades<br /> * Measure the response speed of one or more regulation mechanisms and demonstrate seconds-timescale response<br /> |<br /> ==== Approach ====<br /> |}<br /> <br /> &lt;br&gt;<br /> === Cell Division Tracker (ES) ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=50% |<br /> ==== Goals ====<br /> * Design a genetic construct that changes state upon cell division (i.e. Cells start expressing GFP, after cellular division cells now express YFP)<br /> |<br /> ==== Technical Challenges ====<br /> * Frequency of recombinases not well characterized<br /> * Might need to use a combination between two irreversible recombinases or a reversible recombinase and an irreversible one<br /> * If recognition sequences are not compatible may need to evolve recombinases to recognize different sequences that are compatible<br /> |-valign=top<br /> | width=50% |<br /> ==== Objectives ====<br /> * Characterize different recombinases<br /> ** (example: reversible vs. irreversible, frequency of recombinase activity)<br /> * Find a cell-cycle dependent promoter to use<br /> * Organize recognition sites and proteins of interest in an operon<br /> * Test the operon in cells (E coli or Yeast)<br /> * Measure system characteristics such as % errors <br /> |<br /> ==== Approach ====<br /> * Use recombinases<br /> ** The simplest approach would be to use a reversible recombinase (like fin and hin [http://jb.asm.org/cgi/content/full/188/3/950]) under a cell cycle dependent promoter<br /> ** If we see too many double inversions need to device a more complex mechanism using a combination of recombinases<br /> |}<br /> <br /> &lt;br&gt;<br /> === Stoichiometric Protein Expression (JTM) ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=50% |<br /> ==== Goals ====<br /> * Design a modular genetic construct that allows proteins to be maintained at a precise relative stoichiometry <br /> ** Allowing variable absolute expression, perhaps?<br /> ** A faculty member here once said that this might be useful for membrane protein crystallography<br /> |<br /> ==== Technical Challenges ====<br /> * Western blots/ELISA are time-consuming, require certain equipment<br /> * Expression may vary too much for modularity to work<br /> * Variable degradation rates may make this difficult<br /> |-valign=top<br /> | width=50% |<br /> ==== Objectives ====<br /> * Review existing literature<br /> * Investigate gene fusions and degradation control<br /> ** Are there paths in degradation that could connect the rate of degradation to expression in a specific way?<br /> ** Could some signaling peptide be integrated into the protein such that it's released upon degradation via a non-processive protease?<br /> ** For a 1:1 stoichiometry, one could imagine simply fusing the two proteins and then also expressing a protease to separate them after translation<br /> |<br /> ==== Approach ====<br /> * TBD<br /> |}<br /> <br /> &lt;br&gt;<br /> === Manipulation of the integral controller in photo/chemotaxis (JTM) ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=50% |<br /> ==== Goals ====<br /> * Substitute heterologous che-like signal transducers between organisms such as H. salinarum, E. coli, and others<br /> * Observe preservation or destruction of integral controller after recombination and after evolution<br /> * TBD<br /> |<br /> ==== Technical Challenges ====<br /> * TBD<br /> |-valign=top<br /> | width=50% |<br /> ==== Objectives ====<br /> * Put che-like transducers in mutator plasmid and observe recovery of integral control if damaged after recombination<br /> |<br /> ==== Approach ====<br /> * TBD<br /> |}<br /> <br /> == Robustness Projects ==<br /> <br /> === CAGEN (RMM) ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=50% |<br /> ==== Goals ====<br /> * Design, synthesize and characterize a circuit that provides robust transcriptional regulation<br /> * Win the 2011 [[CAGEN]] competition<br /> |<br /> ==== Technical Challenges ====<br /> |-<br /> | width=50% |<br /> ==== Objectives ====<br /> |<br /> ==== Approach ====<br /> |}<br /> <br /> === Consistent Gene Expression Level (ES and JTM) ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=50% |<br /> ==== Goals ====<br /> * Design, synthesize and characterize an inducible gene circuit that will express a constant level of a protein regardless of inducer concentration<br /> |<br /> ==== Technical Challenges ====<br /> * Might have issues designing an ACR circuit synthetically<br /> * Getting an inducible circuit might be difficult, may start with the simpler problem of just expressing a protein at a constant level<br /> |-<br /> | width=50% |<br /> ==== Objectives ====<br /> * Design a circuit that exhibits a constant concentration of gene of interest (probably an xFP at steady state) we might be able to use ACR theory [http://www.sciencemag.org/cgi/content/abstract/327/5971/1389?ijkey=c777f236d838b71911625aae954a625090cf51ca&amp;keytype2=tf_ipsecsha]<br /> * Construct and characterize designed circuit<br /> |<br /> ==== Approach ====<br /> * Incorporate feedback into current inducer systems, possibly tie into a gene that is known to be tightly controlled<br /> * Design theoretical circuit, then use canonical examples of reactions<br /> * Try the a fusion protein with the circuit that is tightly regulated in paper as a crutch<br /> |}<br /> <br /> === State Transition Modeling in Chemical Reaction Networks (JTM) ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=50% |<br /> ==== Goals ====<br /> * Develop an enumeration algorithm to find distinct &quot;states&quot; for a chemical reaction network<br /> * Look at transition criteria between states<br /> * Test analysis on simple circuits and biological networks<br /> * Use transition criteria to develop robustness metrics<br /> |<br /> ==== Technical Challenges ====<br /> * Not immediately clear how to classify/cluster output<br /> * Not sure how to deal with continuous relationships vs. more discrete relationships (thresholding?)<br /> * May be useful to use analytical techniques () in addition to blind sampling<br /> |-<br /> | width=50% |<br /> ==== Objectives ====<br /> * Program a library of well-characterized reaction circuits (bi-stable flipflops, oscillators, etc)<br /> * Demonstrate proper time-evolution of circuits via numerical analysis<br /> * Run each circuit with a variety of initial conditions and mid-time-course perturbations<br /> * Cluster end states, evaluate quality of clustering, and match to known circuit behavior<br /> * Measure transition criteria between states<br /> |<br /> ==== Approach ====<br /> * Attempt naive exhausive approach to evaluation - sweep through all plausible initial conditions and cluster results (fuzzy c-means?)<br /> * Attempt theorem/network solver approach to evaluation - sweep through initial conditions and use Bayesian network analysis and/or theorem postulators (eureqa) to enumerate states<br /> |}</div>

Jmeyerow https://murray.cds.caltech.edu/index.php?title=BFS_GOTChAs,_April_2010&diff=10675 2010-04-30T10:31:13Z

<p>Jmeyerow: /* Device Projects */</p> <hr /> <div>This page contains some [[GOTChA Chart|GOTChA charts]] for possible rotation projects in the lab this summer. __NOTOC__<br /> <br /> == Device Projects ==<br /> <br /> The following GOTChAs are for projects that involve building new device technologies that can be used to push biological circuit design forward.<br /> <br /> === Integrated Load and Context Compensation (RMM) ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=50% |<br /> ==== Goals ====<br /> * Design a transcriptional regulator that uses feedback to compensate for changes in load and changes in context and thus provides consistent performance independent of downstream loading or cellular context (cell strain, growth media)<br /> * Example: &lt;nowiki&gt;A -| B&lt;/nowiki&gt;, designed so that transfer curve is maintained across changes in downstream reactions involving B, cell strain, growth media<br /> | width=50% |<br /> ==== Technical Challenges ====<br /> |-valign=top<br /> | width=50% |<br /> ==== Objectives ====<br /> * Characterize the performance of existing transcriptional regulators across 3 cell strains, 3 growth media and 3 loading conditions.<br /> * Design a compensation circuit that measures output level and regulates device performance to compensate for uncertainty<br /> ** Idea: use RNA-based feedback in 5' UTR sequences to measure transcription and compensate<br /> ** Note: feedback dynamics should be 5-10X regulatory dynamics to allow for use in non-equilibrium circuits<br /> * Measure the performance of one or more compensation circuits and compare to existing regulators<br /> * Regulation circuitry should be &quot;internal&quot; to device, so that inputs and outputs are the same as traditional regulator<br /> |<br /> <br /> ==== Approach ====<br /> |}<br /> <br /> &lt;br&gt;<br /> === Fast Mechanisms for Biomolecular Feedback (RMM) ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=50% |<br /> ==== Goals ====<br /> * Design a set of devices for implementing feedback circuits that have timescales measured in seconds instead of minutes<br /> |<br /> ==== Technical Challenges ====<br /> |- valign = top<br /> | width=50% |<br /> ==== Objectives ====<br /> * Identify the mechanisms and timescales of various feedback mechanisms in natural systems<br /> ** Example: feedback mechanisms involved in chemotaxis<br /> * Use models to estimate the bandwidth of regulators based on transcriptional feedback, post-transcriptional feedback, translational feedback, post-translational feedback, and covalent modifications<br /> * Formulate a test setup that can be used to characterize the speed of response of one or more circuits using different mechanisms<br /> * Implement a fast-feedback mechanism using one of the following methods:<br /> ** RNA-based feedback using anti-sense interference<br /> ** RNA-based feedback using secondary structure<br /> ** Programmable scaffolds for phosphorylation cascades<br /> * Measure the response speed of one or more regulation mechanisms and demonstrate seconds-timescale response<br /> |<br /> ==== Approach ====<br /> |}<br /> <br /> &lt;br&gt;<br /> === Cell Division Tracker (ES) ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=50% |<br /> ==== Goals ====<br /> * Design a genetic construct that changes state upon cell division (i.e. Cells start expressing GFP, after cellular division cells now express YFP)<br /> |<br /> ==== Technical Challenges ====<br /> * Frequency of recombinases not well characterized<br /> * Might need to use a combination between two irreversible recombinases or a reversible recombinase and an irreversible one<br /> * If recognition sequences are not compatible may need to evolve recombinases to recognize different sequences that are compatible<br /> |-valign=top<br /> | width=50% |<br /> ==== Objectives ====<br /> * Characterize different recombinases<br /> ** (example: reversible vs. irreversible, frequency of recombinase activity)<br /> * Find a cell-cycle dependent promoter to use<br /> * Organize recognition sites and proteins of interest in an operon<br /> * Test the operon in cells (E coli or Yeast)<br /> * Measure system characteristics such as % errors <br /> |<br /> ==== Approach ====<br /> * Use recombinases<br /> ** The simplest approach would be to use a reversible recombinase (like fin and hin [http://jb.asm.org/cgi/content/full/188/3/950]) under a cell cycle dependent promoter<br /> ** If we see too many double inversions need to device a more complex mechanism using a combination of recombinases<br /> |}<br /> <br /> &lt;br&gt;<br /> === Stoichiometric Protein Expression (JTM) ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=50% |<br /> ==== Goals ====<br /> * Design a modular genetic construct that allows proteins to be maintained at a precise relative stoichiometry <br /> ** Allowing variable absolute expression, perhaps?<br /> ** A faculty member here once said that this might be useful for membrane protein crystallography<br /> |<br /> ==== Technical Challenges ====<br /> * Western blots/ELISA are time-consuming, require certain equipment<br /> * Expression may vary too much for modularity to work<br /> * Variable degradation rates may make this difficult<br /> |-valign=top<br /> | width=50% |<br /> ==== Objectives ====<br /> * Review existing literature<br /> * Investigate gene fusions and degradation control<br /> ** Are there paths in degradation that could connect the rate of degradation to expression in a specific way?<br /> ** Could some signaling peptide be integrated into the protein such that it's released upon degradation via a non-processive protease?<br /> ** For a 1:1 stoichiometry, one could imagine simply fusing the two proteins and then also expressing a protease to separate them after translation<br /> |<br /> ==== Approach ====<br /> * TBD<br /> |}<br /> <br /> == Robustness Projects ==<br /> <br /> === CAGEN (RMM) ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=50% |<br /> ==== Goals ====<br /> * Design, synthesize and characterize a circuit that provides robust transcriptional regulation<br /> * Win the 2011 [[CAGEN]] competition<br /> |<br /> ==== Technical Challenges ====<br /> |-<br /> | width=50% |<br /> ==== Objectives ====<br /> |<br /> ==== Approach ====<br /> |}<br /> <br /> === Consistent Gene Expression Level (ES and JTM) ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=50% |<br /> ==== Goals ====<br /> * Design, synthesize and characterize an inducible gene circuit that will express a constant level of a protein regardless of inducer concentration<br /> |<br /> ==== Technical Challenges ====<br /> * Might have issues designing an ACR circuit synthetically<br /> * Getting an inducible circuit might be difficult, may start with the simpler problem of just expressing a protein at a constant level<br /> |-<br /> | width=50% |<br /> ==== Objectives ====<br /> * Design a circuit that exhibits a constant concentration of gene of interest (probably an xFP at steady state) we might be able to use ACR theory [http://www.sciencemag.org/cgi/content/abstract/327/5971/1389?ijkey=c777f236d838b71911625aae954a625090cf51ca&amp;keytype2=tf_ipsecsha]<br /> * Construct and characterize designed circuit<br /> |<br /> ==== Approach ====<br /> * Incorporate feedback into current inducer systems, possibly tie into a gene that is known to be tightly controlled<br /> * Design theoretical circuit, then use canonical examples of reactions<br /> * Try the a fusion protein with the circuit that is tightly regulated in paper as a crutch<br /> |}<br /> <br /> === State Transition Modeling in Chemical Reaction Networks (JTM) ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=50% |<br /> ==== Goals ====<br /> * Develop an enumeration algorithm to find distinct &quot;states&quot; for a chemical reaction network<br /> * Look at transition criteria between states<br /> * Test analysis on simple circuits and biological networks<br /> * Use transition criteria to develop robustness metrics<br /> |<br /> ==== Technical Challenges ====<br /> * Not immediately clear how to classify/cluster output<br /> * Not sure how to deal with continuous relationships vs. more discrete relationships (thresholding?)<br /> * May be useful to use analytical techniques () in addition to blind sampling<br /> |-<br /> | width=50% |<br /> ==== Objectives ====<br /> * Program a library of well-characterized reaction circuits (bi-stable flipflops, oscillators, etc)<br /> * Demonstrate proper time-evolution of circuits via numerical analysis<br /> * Run each circuit with a variety of initial conditions and mid-time-course perturbations<br /> * Cluster end states, evaluate quality of clustering, and match to known circuit behavior<br /> * Measure transition criteria between states<br /> |<br /> ==== Approach ====<br /> * Attempt naive exhausive approach to evaluation - sweep through all plausible initial conditions and cluster results (fuzzy c-means?)<br /> * Attempt theorem/network solver approach to evaluation - sweep through initial conditions and use Bayesian network analysis and/or theorem postulators (eureqa) to enumerate states<br /> |}</div>

Jmeyerow https://murray.cds.caltech.edu/index.php?title=BFS_GOTChAs,_April_2010&diff=10674 2010-04-30T10:23:12Z

<p>Jmeyerow: /* Robustness Projects */</p> <hr /> <div>This page contains some [[GOTChA Chart|GOTChA charts]] for possible rotation projects in the lab this summer. __NOTOC__<br /> <br /> == Device Projects ==<br /> <br /> The following GOTChAs are for projects that involve building new device technologies that can be used to push biological circuit design forward.<br /> <br /> === Integrated Load and Context Compensation (RMM) ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=50% |<br /> ==== Goals ====<br /> * Design a transcriptional regulator that uses feedback to compensate for changes in load and changes in context and thus provides consistent performance independent of downstream loading or cellular context (cell strain, growth media)<br /> * Example: &lt;nowiki&gt;A -| B&lt;/nowiki&gt;, designed so that transfer curve is maintained across changes in downstream reactions involving B, cell strain, growth media<br /> | width=50% |<br /> ==== Technical Challenges ====<br /> |-valign=top<br /> | width=50% |<br /> ==== Objectives ====<br /> * Characterize the performance of existing transcriptional regulators across 3 cell strains, 3 growth media and 3 loading conditions.<br /> * Design a compensation circuit that measures output level and regulates device performance to compensate for uncertainty<br /> ** Idea: use RNA-based feedback in 5' UTR sequences to measure transcription and compensate<br /> ** Note: feedback dynamics should be 5-10X regulatory dynamics to allow for use in non-equilibrium circuits<br /> * Measure the performance of one or more compensation circuits and compare to existing regulators<br /> * Regulation circuitry should be &quot;internal&quot; to device, so that inputs and outputs are the same as traditional regulator<br /> |<br /> <br /> ==== Approach ====<br /> |}<br /> <br /> &lt;br&gt;<br /> === Fast Mechanisms for Biomolecular Feedback (RMM) ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=50% |<br /> ==== Goals ====<br /> * Design a set of devices for implementing feedback circuits that have timescales measured in seconds instead of minutes<br /> |<br /> ==== Technical Challenges ====<br /> |- valign = top<br /> | width=50% |<br /> ==== Objectives ====<br /> * Identify the mechanisms and timescales of various feedback mechanisms in natural systems<br /> ** Example: feedback mechanisms involved in chemotaxis<br /> * Use models to estimate the bandwidth of regulators based on transcriptional feedback, post-transcriptional feedback, translational feedback, post-translational feedback, and covalent modifications<br /> * Formulate a test setup that can be used to characterize the speed of response of one or more circuits using different mechanisms<br /> * Implement a fast-feedback mechanism using one of the following methods:<br /> ** RNA-based feedback using anti-sense interference<br /> ** RNA-based feedback using secondary structure<br /> ** Programmable scaffolds for phosphorylation cascades<br /> * Measure the response speed of one or more regulation mechanisms and demonstrate seconds-timescale response<br /> |<br /> ==== Approach ====<br /> |}<br /> <br /> &lt;br&gt;<br /> === Cell Division Tracker (ES) ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=50% |<br /> ==== Goals ====<br /> * Design a genetic construct that changes state upon cell division (i.e. Cells start expressing GFP, after cellular division cells now express YFP)<br /> |<br /> ==== Technical Challenges ====<br /> * Frequency of recombinases not well characterized<br /> * Might need to use a combination between two irreversible recombinases or a reversible recombinase and an irreversible one<br /> * If recognition sequences are not compatible may need to evolve recombinases to recognize different sequences that are compatible<br /> |-valign=top<br /> | width=50% |<br /> ==== Objectives ====<br /> * Characterize different recombinases<br /> ** (example: reversible vs. irreversible, frequency of recombinase activity)<br /> * Find a cell-cycle dependent promoter to use<br /> * Organize recognition sites and proteins of interest in an operon<br /> * Test the operon in cells (E coli or Yeast)<br /> * Measure system characteristics such as % errors <br /> |<br /> ==== Approach ====<br /> * Use recombinases<br /> ** The simplest approach would be to use a reversible recombinase (like fin and hin [http://jb.asm.org/cgi/content/full/188/3/950]) under a cell cycle dependent promoter<br /> ** If we see too many double inversions need to device a more complex mechanism using a combination of recombinases<br /> |}<br /> <br /> == Robustness Projects ==<br /> <br /> === CAGEN (RMM) ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=50% |<br /> ==== Goals ====<br /> * Design, synthesize and characterize a circuit that provides robust transcriptional regulation<br /> * Win the 2011 [[CAGEN]] competition<br /> |<br /> ==== Technical Challenges ====<br /> |-<br /> | width=50% |<br /> ==== Objectives ====<br /> |<br /> ==== Approach ====<br /> |}<br /> <br /> === Consistent Gene Expression Level (ES and JTM) ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=50% |<br /> ==== Goals ====<br /> * Design, synthesize and characterize an inducible gene circuit that will express a constant level of a protein regardless of inducer concentration<br /> |<br /> ==== Technical Challenges ====<br /> * Might have issues designing an ACR circuit synthetically<br /> * Getting an inducible circuit might be difficult, may start with the simpler problem of just expressing a protein at a constant level<br /> |-<br /> | width=50% |<br /> ==== Objectives ====<br /> * Design a circuit that exhibits a constant concentration of gene of interest (probably an xFP at steady state) we might be able to use ACR theory [http://www.sciencemag.org/cgi/content/abstract/327/5971/1389?ijkey=c777f236d838b71911625aae954a625090cf51ca&amp;keytype2=tf_ipsecsha]<br /> * Construct and characterize designed circuit<br /> |<br /> ==== Approach ====<br /> * Incorporate feedback into current inducer systems, possibly tie into a gene that is known to be tightly controlled<br /> * Design theoretical circuit, then use canonical examples of reactions<br /> * Try the a fusion protein with the circuit that is tightly regulated in paper as a crutch<br /> |}<br /> <br /> === State Transition Modeling in Chemical Reaction Networks (JTM) ===<br /> {| width=100% border=1<br /> |- valign=top<br /> | width=50% |<br /> ==== Goals ====<br /> * Develop an enumeration algorithm to find distinct &quot;states&quot; for a chemical reaction network<br /> * Look at transition criteria between states<br /> * Test analysis on simple circuits and biological networks<br /> * Use transition criteria to develop robustness metrics<br /> |<br /> ==== Technical Challenges ====<br /> * Not immediately clear how to classify/cluster output<br /> * Not sure how to deal with continuous relationships vs. more discrete relationships (thresholding?)<br /> * May be useful to use analytical techniques () in addition to blind sampling<br /> |-<br /> | width=50% |<br /> ==== Objectives ====<br /> * Program a library of well-characterized reaction circuits (bi-stable flipflops, oscillators, etc)<br /> * Demonstrate proper time-evolution of circuits via numerical analysis<br /> * Run each circuit with a variety of initial conditions and mid-time-course perturbations<br /> * Cluster end states, evaluate quality of clustering, and match to known circuit behavior<br /> * Measure transition criteria between states<br /> |<br /> ==== Approach ====<br /> * Attempt naive exhausive approach to evaluation - sweep through all plausible initial conditions and cluster results (fuzzy c-means?)<br /> * Attempt theorem/network solver approach to evaluation - sweep through initial conditions and use Bayesian network analysis and/or theorem postulators (eureqa) to enumerate states<br /> |}</div>

Jmeyerow