http://2010.igem.org/wiki/index.php?title=Special:Contributions/Mxu&feed=atom&limit=50&target=Mxu&year=&month=2010.igem.org - User contributions [en]2024-03-28T14:53:07ZFrom 2010.igem.orgMediaWiki 1.16.5http://2010.igem.org/Team:Caltech/Week_8Team:Caltech/Week 82010-08-10T20:16:30Z<p>Mxu: </p>
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<div>{{Caltech_iGEM_10|<br />
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==Monday 8/2==<br />
* Group meeting today!<br />
* Started lots more CPCR:<br />
** 2 colonies each of: L24, L22, HSP-Cm, L20, L31, L49, L48, L26, and M30109 using distribution DNA as template.<br />
** Successful: L24-1/-2, 20-4/-5, L22-1/-2, L48-4<br />
* Started ligations:<br />
** L49: HSP-Amp + L40 + pSB1T3<br />
** L54: HSP-Amp + K215000 + pSB1K3<br />
** L55: K215000 + I13504 + pSB1K3<br />
* Began 2 1mL LB-Kan cultures of 42-4/-5 & incubated @ 30&deg;C<br />
* Began 2 5mL LB-Kan cultures of 43-4/-5 & incubated @ 37&deg;C for sequencing tomorrow.<br />
<br />
==Tuesday 8/3==<br />
* Ligations all failed! (pos control fine)<br />
* Prepped 42-4/-5 & sent out for sequencing<br />
* Prepped 48-4, 20-4/-5, 22-1/-2, 24-1<br />
** Concentrations all over 200ng/&mu;L, so diluted all 2x with diH2O.<br />
* Began colony PCR to verify the contents of the lysis casette and lysis gene (K124017 & K124017)<br />
** After checking the Registry page, we decided that there may be some sort of problem with the DNA or error in its cataloging.<br />
** Also started colony PCR of M30109 cells and ran M30109 digest DNA in the gel to similarly try to verify the presence of the desired insert, after talking with the UNAM-Genomics_Mexico iGEM team.<br />
* Digested L23, L44, L22, L24, more Cm and Kan backbone, and a few other bricks<br />
* Began ligations:<br />
** L36: K215000 + L22 + pSB1K3<br />
** L38: L19 + L22 + pSB1A3<br />
** L37: L23 + L24 + pSB1K3<br />
** L56: K124017 + B0015 + pSB1C3 (will ligate Thurs)<br />
** L57: K124014 + B0015 + pSB1C3 (will ligate Thurs)<br />
<br />
==Wednesday 8/4==<br />
* All ligation plates were successful (even though they were 20 min only)<br />
** Began colony PCR (x3) on each: L37, L49, L54, L55<br />
<br />
==Thursday 8/5==<br />
<br />
==Friday 8/6==<br />
<br />
==Weekend 8/7-8/8==<br />
* Used ligation of HSP + GFP to test temperatures at which transcription occurs.<br />
** Tested fluorescences at 4˚C, 25˚C, 37˚C, 42˚C, and 45˚C.<br />
** Fluorescence measured increased as temperature increased - a sign that HSP works.<br />
** Even at the low temperature of 4˚C, there was a significant amount of fluorescence.<br />
<br />
&nbsp;<br />
}}</div>Mxuhttp://2010.igem.org/Team:Caltech/Week_6Team:Caltech/Week 62010-07-21T00:23:24Z<p>Mxu: </p>
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<div>{{Caltech_iGEM_10|<br />
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<br />
==Monday 7/19==<br />
* Group meeting!<br />
** Discussed issues with cloning and next week's focus. <br />
* Performed a digest (now for 2hr) and ligations (L18-23). Transformed into DH5&alpha;.<br />
* Ran gel of digest product to verify correct bands.<br />
[[Image:DigestsGel7-19.jpg|200px|thumb|right|Digest test gel with US and DS digested bricks. (7/19)]]<br />
<br />
==Tuesday 7/20==<br />
* All ligation transformations failed. Will try 16hr ligations and purifying digest products with a PCR purification kit.<br />
* Made new growth curves testing AIBN effect on cells in LB<br />
* Performed another live/dead assay<br />
** Had solutions of cells in glycerol and AIBN<br />
** Plated cells every hour for three hours<br />
** Combined glycerol solutions with LB and plated the solution<br />
<br />
<br />
==Wednesday 7/21==<br />
<br />
==Thursday 7/22==<br />
<br />
==Friday 7/23==<br />
<br />
==Weekend 7/24-25==<br />
&nbsp;<br />
}}</div>Mxuhttp://2010.igem.org/Team:Caltech/Week_5Team:Caltech/Week 52010-07-19T23:13:03Z<p>Mxu: </p>
<hr />
<div>{{Caltech_iGEM_10|<br />
Content=<br />
{{:Team:Caltech/WeekTemplate}}<br />
<br />
==Monday 7/12==<br />
* Group meeting today!<br />
* Sequencing results were really crappy (quality < 30% confidence), so began 2 5mL LB cultures of the light-lysis construct (picked from the original transformation plate).<br />
<br />
==Tuesday 7/13==<br />
* Sent off two new samples of the light-lysis construct for sequencing using the VF2 and VR primers. Results should be available tonight or tomorrow. <br />
* Used remaining cells to inoculate new cultures of each and to extract DNA for a test digest:<br />
** Digested each (ideally identical) sample with EcoRI-HF and PstI, both for 1hr and for 10min. <br />
** The digest appears inconclusive, as a smear is visible from the top to about 3Kb, while little or no DNA is visible in the insert range (~1.5Kb, see below). <br />
** Will run another gel tonight with other bricks to check efficacy of digests and will look forward to sequencing results soon.<br />
** Second digest can be found below. Lane 1: 4uL 100bp ladder (NEB); Lane 2: 5uL pSB1T3 digest; Lane 3: 10uL lysis gene downstream digest; Lane 4: 10uL GFP upstream digest; Lane 5: 4uL 1kb ladder (NEB). <br />
*** Lanes appear to have correct bands; digests and ligations appear to be working better now. (We now run digests for 60min at 37C and ligations for 30min at RT, contrary to the times suggested by NEB.)<br />
* Ordered more SpeI from NEB, since we're basically out.<br />
[[Image:PRlyTgel7-13.jpg|200px|thumb|right|Gel image for the light-lysis test digest. (7/13)]]<br />
[[Image:CIT7-13gel.jpg|200px|thumb|right|Digest test gel featuring digested backbone, US and DS digested bricks. (7/13)]]<br />
* Performed initial growth assay with cells in different solutions mixed with varying levels of AIBN and other conditions. <br />
<br />
==Wednesday 7/14==<br />
* Received bricks from the Registry of Standard Parts today.<br />
** [http://partsregistry.org/Part:BBa_K156012 K156012], [http://partsregistry.org/Part:BBa_K156013 K156013], and [http://partsregistry.org/Part:BBa_K156014 K156014]<br />
** Made plates and liquid cultures of the cells containing the bricks.<br />
* The light-lysis sequencing results could not be returned due to insufficient DNA concentration. Picked two new colonies from the original plate. Also made cultures of the previous ligations (PR aka Ligation1 and lyT aka Ligation2). Will prep tomorrow for sequencing.<br />
* Met with the Caltech Office of Technology Transfer (Drs. Hannah Dvorak-Carbone & Jennifer Hodas)<br />
** Discussed patent law and IP issues relevant to our project<br />
* Began designing primers for making glutamine & lysine peptides to experiment with transglutaminase (TGase).<br />
* Transformed pBAD18 into both DH5\alpha and V1012 to test competence & troubleshoot transformation failures. (Used 2uL DNA and 60uL cells.)<br />
* Prepared SOC from SOB and made 10mL aliquots to freeze.<br />
* Ran gel to test ligation products from today (and troubleshoot the light-lysis construct some more...)<br />
** Lanes 2 & 3 contain Ligation1 & 2 digests. They have bands, but they do not appear to be the right size - we'll hasve to look at these a bit more. The other lanes are raw ligation product from today's ligations.<br />
[[Image:CITLigation-tests7-14.jpg|200px|thumb|right|Gel of today's ligation products & light-lysis ligation digests. (7/14)]]<br />
<br />
==Thursday 7/15==<br />
* The V1012 transformation was successful, but the V1012 was not. Will troubleshoot V1012 further, but it appears that the DH5\alpha cells are competent. <br />
** May want to make more V1012 cells competent this weekend.<br />
** It appears that using at least 50uL of comp cells and 2uL of DNA works most effectively. We will also use SOC to rescue the transformations from now on.<br />
* The PR (Ligation1) and PRlyT (Ligation3) cultures grew, but the lyT (Ligation2) culture did not. This could indicate an issue with the lyT product (perhaps the colonies on the plate are contamination). <br />
** Will reperform the Ligation3 reaction and see if that helps. (The gel of the Ligation2 digest (above) looks correct, so there shouldn't be a problem with the ligation product.)<br />
** Prepped the cultures (to send for sequencing)<br />
*** PRlyT1 = 50.1 ng/uL; PRlyT2 = 34.5 ng/uL (will send 20uL of each for seq.)<br />
*** PR1 = 197.0 ng/uL; PR2 = 201.0 ng/uL (will send 10uL of each for seq.)<br />
* Team signed the OTT Invention Disclosure form and submitted a project description to the OTT. Provisional patent application will be filed tomorrow.<br />
* Designed primers for BBb_K112400 to change from Berkley standard to the correct BBa standard. <br />
** Will order these tomorrow so they are ready when the heat-shock promoter arrives.<br />
* Prepared 500mL 2YT media, 1L diH2O, 2 250mL Erlenmeyer flasks and 50mL 10% glycerol. Inoculated 1 5mL culture of 2YT with DH5alpha cells. <br />
** Will make more competent cells tomorrow.<br />
* Made minipreps of the bricks received on Wednesday.<br />
** [http://partsregistry.org/Part:BBa_K156012 K156012], [http://partsregistry.org/Part:BBa_K156013 K156013], and [http://partsregistry.org/Part:BBa_K156014 K156014]<br />
<br />
==Friday 7/16==<br />
* Lab clean-up scheduled for today.<br />
* All 11 ligation transformations failed (except the positive control). This seems like a DNA issue - we will try transforming more DNA today after our competent cells are ready.<br />
* Performed solubility and reactivity test on AIBN on soybean and linseed oil.<br />
* Performed live-dead assay on cells under different conditions with solutions of varying AIBN concentrations.<br />
* Ordered primers to fix a BioBrick part.<br />
* Ordered a synthesized BioBrick part encoding a poly-lysine and poly-glutamine polypeptide sequence.<br />
<br />
==Weekend 7/17-18==<br />
* DH5\alpha competence test: positive control grew cells, negative did not -> Cells are competent and not contaminated.<br />
* Transformation plates: L15 (light-lysis construct): failed; L4: >1000 colonies (will reculture to verify antibiotic resistance); L8: 2 colonies (will also reculture to verify that colonies aren't contamination)<br />
* Will also start cultures of K124017, as all digests of this brick appear incorrect. We want to try again with fresh DNA.<br />
* Live-dead assay results: All plates from the start point in time contained films of cells. The plates created an hour later from glycerol solutions kept at 4˚C showed little change in the amount of cells grown. Plates created from the room temperature solutions, showed either large colonies and/or less developed films. <br />
* Transformed 5uL ligation product for ligations L4-L14 (again). <br />
* Hydrolyzed soybean oil<br />
}}</div>Mxuhttp://2010.igem.org/Team:Caltech/Week_5Team:Caltech/Week 52010-07-16T18:56:16Z<p>Mxu: </p>
<hr />
<div>{{Caltech_iGEM_10|<br />
Content=<br />
[[Team:Caltech/Notebook|Back to Notebook]]<br />
<br />
==Monday 7/12==<br />
* Group meeting today!<br />
* Sequencing results were really crappy (quality < 30% confidence), so began 2 5mL LB cultures of the light-lysis construct (picked from the original transformation plate).<br />
<br />
==Tuesday 7/13==<br />
* Sent off two new samples of the light-lysis construct for sequencing using the VF2 and VR primers. Results should be available tonight or tomorrow. <br />
* Used remaining cells to inoculate new cultures of each and to extract DNA for a test digest:<br />
** Digested each (ideally identical) sample with EcoRI-HF and PstI, both for 1hr and for 10min. <br />
** The digest appears inconclusive, as a smear is visible from the top to about 3Kb, while little or no DNA is visible in the insert range (~1.5Kb, see below). <br />
** Will run another gel tonight with other bricks to check efficacy of digests and will look forward to sequencing results soon.<br />
** Second digest can be found below. Lane 1: 4uL 100bp ladder (NEB); Lane 2: 5uL pSB1T3 digest; Lane 3: 10uL lysis gene downstream digest; Lane 4: 10uL GFP upstream digest; Lane 5: 4uL 1kb ladder (NEB). <br />
*** Lanes appear to have correct bands; digests and ligations appear to be working better now. (We now run digests for 60min at 37C and ligations for 30min at RT, contrary to the times suggested by NEB.)<br />
* Ordered more SpeI from NEB, since we're basically out.<br />
[[Image:PRlyTgel7-13.jpg|200px|thumb|right|Gel image for the light-lysis test digest. (7/13)]]<br />
[[Image:CIT7-13gel.jpg|200px|thumb|right|Digest test gel featuring digested backbone, US and DS digested bricks. (7/13)]]<br />
<br />
==Wednesday 7/14==<br />
* Received bricks from the Registry of Standard Parts today.<br />
** [http://partsregistry.org/Part:BBa_K156012 K156012], [http://partsregistry.org/Part:BBa_K156013 K156013], and [http://partsregistry.org/Part:BBa_K156014 K156014]<br />
** Made plates and liquid cultures of the cells containing the bricks.<br />
* The light-lysis sequencing results could not be returned due to insufficient DNA concentration. Picked two new colonies from the original plate. Also made cultures of the previous ligations (PR aka Ligation1 and lyT aka Ligation2). Will prep tomorrow for sequencing.<br />
* Met with the Caltech Office of Technology Transfer (Drs. Hannah Dvorak-Carbone & Jennifer Hodas)<br />
** Discussed patent law and IP issues relevant to our project<br />
* Began designing primers for making glutamine & lysine peptides to experiment with transglutaminase (TGase).<br />
* Transformed pBAD18 into both DH5\alpha and V1012 to test competence & troubleshoot transformation failures. (Used 2uL DNA and 60uL cells.)<br />
* Prepared SOC from SOB and made 10mL aliquots to freeze.<br />
* Ran gel to test ligation products from today (and troubleshoot the light-lysis construct some more...)<br />
** Lanes 2 & 3 contain Ligation1 & 2 digests. They have bands, but they do not appear to be the right size - we'll hasve to look at these a bit more. The other lanes are raw ligation product from today's ligations.<br />
[[Image:CITLigation-tests7-14.jpg|200px|thumb|right|Gel of today's ligation products & light-lysis ligation digests. (7/14)]]<br />
<br />
==Thursday 7/15==<br />
* The V1012 transformation was successful, but the V1012 was not. Will troubleshoot V1012 further, but it appears that the DH5\alpha cells are competent. <br />
** May want to make more V1012 cells competent this weekend.<br />
** It appears that using at least 50uL of comp cells and 2uL of DNA works most effectively. We will also use SOC to rescue the transformations from now on.<br />
* The PR (Ligation1) and PRlyT (Ligation3) cultures grew, but the lyT (Ligation2) culture did not. This could indicate an issue with the lyT product (perhaps the colonies on the plate are contamination). <br />
** Will reperform the Ligation3 reaction and see if that helps. (The gel of the Ligation2 digest (above) looks correct, so there shouldn't be a problem with the ligation product.)<br />
** Prepped the cultures (to send for sequencing)<br />
*** PRlyT1 = 50.1 ng/uL; PRlyT2 = 34.5 ng/uL (will send 20uL of each for seq.)<br />
*** PR1 = 197.0 ng/uL; PR2 = 201.0 ng/uL (will send 10uL of each for seq.)<br />
* Team signed the OTT Invention Disclosure form and submitted a project description to the OTT. Provisional patent application will be filed tomorrow.<br />
* Designed primers for BBb_K112400 to change from Berkley standard to the correct BBa standard. <br />
** Will order these tomorrow so they are ready when the heat-shock promoter arrives.<br />
* Prepared 500mL 2YT media, 1L diH2O, 2 250mL Erlenmeyer flasks and 50mL 10% glycerol. Inoculated 1 5mL culture of 2YT with DH5alpha cells. <br />
** Will make more competent cells tomorrow.<br />
* Made minipreps of the bricks received on Wednesday.<br />
** [http://partsregistry.org/Part:BBa_K156012 K156012], [http://partsregistry.org/Part:BBa_K156013 K156013], and [http://partsregistry.org/Part:BBa_K156014 K156014]<br />
<br />
==Friday 7/16==<br />
* Lab clean-up scheduled for today.<br />
* All 11 ligation transformations failed (except the positive control). This seems like a DNA issue - we will try transforming more DNA today after our competent cells are ready.<br />
<br />
==Weekend 7/17-18==<br />
&nbsp;<br />
}}</div>Mxuhttp://2010.igem.org/Team:Caltech/Week_4Team:Caltech/Week 42010-07-12T23:50:19Z<p>Mxu: </p>
<hr />
<div>{{Caltech_iGEM_10|<br />
Content=<br />
[[Team:Caltech/Notebook|Back to Notebook]]<br />
<br />
==Monday 7/5==<br />
Note: Today was another Institute Holiday.<br />
<br />
==Tuesday 7/6==<br />
*Hydrolyzed linseed oil. The reaction solution will be characterized on Wednesday.<br />
<br />
==Wednesday 7/7==<br />
* Attempted to make [http://partsregistry.org/Part:BBa_V1012 V1012] (strain CP919, KanR, ''envZ'' deficient) electrocompetent:<br />
** Centrifuged overnight 3mL LB-Kan culture at 4C, 16000rcf for 10min.<br />
** Discarded supernatant. Resuspended pellet in 1.5mL ice-cold water. Centrifuged again.<br />
** Repeated with 0.75mL ice-cold water. <br />
** Resuspended pellet in 1.5mL ice-cold 10% glycerol.<br />
** Flash-froze 100uL aliquots in dry ice/ethanol.<br />
* Transformed light/lysis ligation product from last week into [http://partsregistry.org/Part:BBa_V1012 V1012] via electroporation. (Voltage: 2.5V; time constant: 4.5)<br />
** Plated 100uL on LB-Tet agar plate & inoculated a 5mL LB-Tet overnight culture.<br />
* Inoculated 5mL LB-Kan culture of purely [http://partsregistry.org/Part:BBa_V1012 V1012] in case we need to retry the competence procedure.<br />
* Tested pigment production of cells containing [http://partsregistry.org/Part:BBa_K274100 K274100] in various solutions.<br />
** Tested solutions of LB, LB without yeast extract added, 80% glycerol, 100% glycerol, and glycerol with different concentrations of agar.<br />
** Since the brick is under an arabinose-inducible promoter, two versions of each solution were made - one containing arabinose, and one without arabinose.<br />
** Pigment production was subjectively measured every hour for five hours. It seemed like there wasn't going to be much pigment produced so the solutions were left overnight in the shaker.<br />
<br />
==Thursday 7/8==<br />
* The [http://partsregistry.org/Part:BBa_V1012 V1012] transformation appears to have worked - the plate is covered in 1000+ colonies.<br />
** Made freezer stock from parallel liquid culture.<br />
* Miniprepped the DNA and prepared a sample for sequencing.<br />
* Started LB liquid culture of [http://partsregistry.org/Part:BBa_M30109 M30109] for assembly tomorrow, along with cultures of [http://partsregistry.org/Part:BBa_J04450 J04450] to perform a quick lysis test (in preparation for testing the lysis construct).<br />
* Prepared 2YT and SOB media in preparation for making electrocompetent DH5\alpha cells tomorrow. Also prepared all glassware and other supplies.<br />
* Completed schematics for our printing process, including a detailed gene network diagram. We will begin assembly of the 3D genetic constructs tomorrow.<br />
* Results of the pigment test with [http://partsregistry.org/Part:BBa_K274100 K274100]: None of the cells seemed to have created the red pigment we were looking for.<br />
** It seems likely that that all the cells died.<br />
** Did not have a visible pellet of cells in the glycerol and agar solutions after centrifugation. The solutions were probably too viscous. <br />
<br />
==Friday 7/9==<br />
* Digested bricks according to NEB BioBrick assembly kit protocol.<br />
** [http://partsregistry.org/Part:BBa_R0077 R0077] (both upstream and downstream)<br />
** [http://partsregistry.org/Part:BBa_C0077 C0077] (upstream)<br />
** [http://partsregistry.org/Part:BBa_C0076 C0076] (upstream)<br />
** [http://partsregistry.org/Part:BBa_M30109 M30109] (downstream)<br />
* Began ligation reactions<br />
** [http://partsregistry.org/Part:R0082 R0082]/[http://partsregistry.org/Part:BBa_R0077 R0077]/[http://partsregistry.org/Part:pSB1T3 pSB1T3]<br />
** [http://partsregistry.org/Part:C0077 C0077]/[http://partsregistry.org/Part:B0015 B0015] (previously digested)/[http://partsregistry.org/Part:pSB1T3 pSB1T3]<br />
** [http://partsregistry.org/Part:C0076 C0076]/[http://partsregistry.org/Part:B0015 B0015] (previously digested)/[http://partsregistry.org/Part:pSB1T3 pSB1T3]<br />
* Transformed ligation products into DH5alpha cells.<br />
* Created liquid cultures<br />
** ligation 1 product - [http://partsregistry.org/Part:C0076 C0076]/[http://partsregistry.org/Part:B0015 B0015] (previously digested)/[http://partsregistry.org/Part:pSB1T3 pSB1T3]<br />
** ligation 2 product - [http://partsregistry.org/Part:C0077 C0077]/[http://partsregistry.org/Part:B0015 B0015] (previously digested)/[http://partsregistry.org/Part:pSB1T3 pSB1T3]<br />
** ligation 3 product - [http://partsregistry.org/Part:R0082 R0082]/[http://partsregistry.org/Part:BBa_R0077 R0077]/[http://partsregistry.org/Part:pSB1T3 pSB1T3]<br />
** [http://partsregistry.org/Part:B0015 B0015]<br />
** [http://partsregistry.org/Part:K124017 K124017]<br />
<br />
==Weekend 7/10-11==<br />
* Made minipreps of [http://partsregistry.org/Part:B0015 B0015] and [http://partsregistry.org/Part:K124017 K124017]<br />
* Transformation results: Transformations failed.<br />
** There could be a problem with the antibiotic used or there could also be an issue with the digestions and/or ligations.<br />
<br />
&nbsp;<br />
}}</div>Mxuhttp://2010.igem.org/Team:Caltech/Week_4Team:Caltech/Week 42010-07-12T19:56:09Z<p>Mxu: </p>
<hr />
<div>{{Caltech_iGEM_10|<br />
Content=<br />
[[Team:Caltech/Notebook|Back to Notebook]]<br />
<br />
==Monday 7/5==<br />
Note: Today was another Institute Holiday.<br />
<br />
==Tuesday 7/6==<br />
*Hydrolyzed linseed oil. The reaction solution will be characterized on Wednesday.<br />
<br />
==Wednesday 7/7==<br />
* Attempted to make [http://partsregistry.org/Part:BBa_V1012 V1012] (strain CP919, KanR, ''envZ'' deficient) electrocompetent:<br />
** Centrifuged overnight 3mL LB-Kan culture at 4C, 16000rcf for 10min.<br />
** Discarded supernatant. Resuspended pellet in 1.5mL ice-cold water. Centrifuged again.<br />
** Repeated with 0.75mL ice-cold water. <br />
** Resuspended pellet in 1.5mL ice-cold 10% glycerol.<br />
** Flash-froze 100uL aliquots in dry ice/ethanol.<br />
* Transformed light/lysis ligation product from last week into [http://partsregistry.org/Part:BBa_V1012 V1012] via electroporation. (Voltage: 2.5V; time constant: 4.5)<br />
** Plated 100uL on LB-Tet agar plate & inoculated a 5mL LB-Tet overnight culture.<br />
* Inoculated 5mL LB-Kan culture of purely [http://partsregistry.org/Part:BBa_V1012 V1012] in case we need to retry the competence procedure.<br />
* Tested pigment production of cells containing [http://partsregistry.org/Part:BBa_K274100 K274100] in various solutions.<br />
** Tested solutions of LB, LB without yeast extract added, 80% glycerol, 100% glycerol, and glycerol with different concentrations of agar.<br />
** Since the brick is under an arabinose-inducible promoter, two versions of each solution were made - one containing arabinose, and one without arabinose.<br />
** Pigment production was subjectively measured every hour for five hours. It seemed like there wasn't going to be much pigment produced so the solutions were left overnight in the shaker.<br />
<br />
==Thursday 7/8==<br />
* The [http://partsregistry.org/Part:BBa_V1012 V1012] transformation appears to have worked - the plate is covered in 1000+ colonies.<br />
** Made freezer stock from parallel liquid culture.<br />
* Miniprepped the DNA and prepared a sample for sequencing.<br />
* Started LB liquid culture of [http://partsregistry.org/Part:BBa_M30109 M30109] for assembly tomorrow, along with cultures of [http://partsregistry.org/Part:BBa_J04450 J04450] to perform a quick lysis test (in preparation for testing the lysis construct).<br />
* Prepared 2YT and SOB media in preparation for making electrocompetent DH5\alpha cells tomorrow. Also prepared all glassware and other supplies.<br />
* Completed schematics for our printing process, including a detailed gene network diagram. We will begin assembly of the 3D genetic constructs tomorrow.<br />
* Results of the pigment test with [http://partsregistry.org/Part:BBa_K274100 K274100]: None of the cells seemed to have created the red pigment we were looking for.<br />
** It seems likely that that all the cells died.<br />
** Did not have a visible pellet of cells in the glycerol and agar solutions after centrifugation. The solutions were probably too viscous. <br />
<br />
==Friday 7/9==<br />
* Digested bricks according to NEB BioBrick assembly kit protocol.<br />
** [http://partsregistry.org/Part:BBa_R0077 R0077] (both upstream and downstream)<br />
** [http://partsregistry.org/Part:BBa_C0077 C0077] (upstream)<br />
** [http://partsregistry.org/Part:BBa_C0076 C0076] (upstream)<br />
** [http://partsregistry.org/Part:BBa_M30109 M30109] (downstream)<br />
* Began ligation reactions<br />
** [http://partsregistry.org/Part:R0082 R0082]/[http://partsregistry.org/Part:BBa_R0077 R0077]/[http://partsregistry.org/Part:pSB1T3 pSB1T3]<br />
** [http://partsregistry.org/Part:C0077 C0077]/[http://partsregistry.org/Part:B0015 B0015] (previously digested)/[http://partsregistry.org/Part:pSB1T3 pSB1T3]<br />
** [http://partsregistry.org/Part:C0076 C0076]/[http://partsregistry.org/Part:B0015 B0015] (previously digested)/[http://partsregistry.org/Part:pSB1T3 pSB1T3]<br />
* Transformed ligation products into DH5alpha cells.<br />
* Created liquid cultures<br />
** ligation 1 product - [http://partsregistry.org/Part:C0076 C0076]/[http://partsregistry.org/Part:B0015 B0015] (previously digested)/[http://partsregistry.org/Part:pSB1T3 pSB1T3]<br />
** ligation 2 product - [http://partsregistry.org/Part:C0077 C0077]/[http://partsregistry.org/Part:B0015 B0015] (previously digested)/[http://partsregistry.org/Part:pSB1T3 pSB1T3]<br />
** ligation 3 product - [http://partsregistry.org/Part:R0082 R0082]/[http://partsregistry.org/Part:BBa_R0077 R0077]/[http://partsregistry.org/Part:pSB1T3 pSB1T3]<br />
** [http://partsregistry.org/Part:B0015 B0015]<br />
** [http://partsregistry.org/Part:K124017 K124017]<br />
<br />
==Weekend 7/10-11==<br />
* Made minipreps of [http://partsregistry.org/Part:B0015 B0015] and [http://partsregistry.org/Part:K124017 K124017]<br />
* Transformation results: Transformations failed.<br />
** There could be a problem with the antibiotic used or there could also be an issue with the ligations.<br />
<br />
&nbsp;<br />
}}</div>Mxuhttp://2010.igem.org/Team:Caltech/Week_4Team:Caltech/Week 42010-07-12T19:51:45Z<p>Mxu: </p>
<hr />
<div>{{Caltech_iGEM_10|<br />
Content=<br />
[[Team:Caltech/Notebook|Back to Notebook]]<br />
<br />
==Monday 7/5==<br />
Note: Today was another Institute Holiday.<br />
<br />
==Tuesday 7/6==<br />
*Hydrolyzed linseed oil. The reaction solution will be characterized on Wednesday.<br />
<br />
==Wednesday 7/7==<br />
* Attempted to make [http://partsregistry.org/Part:BBa_V1012 V1012] (strain CP919, KanR, ''envZ'' deficient) electrocompetent:<br />
** Centrifuged overnight 3mL LB-Kan culture at 4C, 16000rcf for 10min.<br />
** Discarded supernatant. Resuspended pellet in 1.5mL ice-cold water. Centrifuged again.<br />
** Repeated with 0.75mL ice-cold water. <br />
** Resuspended pellet in 1.5mL ice-cold 10% glycerol.<br />
** Flash-froze 100uL aliquots in dry ice/ethanol.<br />
* Transformed light/lysis ligation product from last week into [http://partsregistry.org/Part:BBa_V1012 V1012] via electroporation. (Voltage: 2.5V; time constant: 4.5)<br />
** Plated 100uL on LB-Tet agar plate & inoculated a 5mL LB-Tet overnight culture.<br />
* Inoculated 5mL LB-Kan culture of purely [http://partsregistry.org/Part:BBa_V1012 V1012] in case we need to retry the competence procedure.<br />
* Tested pigment production of cells containing [http://partsregistry.org/Part:BBa_K274100 K274100] in various solutions.<br />
** Tested solutions of LB, LB without yeast extract added, 80% glycerol, 100% glycerol, and glycerol with different concentrations of agar.<br />
** Since the brick is under an arabinose-inducible promoter, two versions of each solution were made - one containing arabinose, and one without arabinose.<br />
** Pigment production was subjectively measured every hour for five hours. It seemed like there wasn't going to be much pigment produced so the solutions were left overnight in the shaker.<br />
<br />
==Thursday 7/8==<br />
* The [http://partsregistry.org/Part:BBa_V1012 V1012] transformation appears to have worked - the plate is covered in 1000+ colonies.<br />
** Made freezer stock from parallel liquid culture.<br />
* Miniprepped the DNA and prepared a sample for sequencing.<br />
* Started LB liquid culture of [http://partsregistry.org/Part:BBa_M30109 M30109] for assembly tomorrow, along with cultures of [http://partsregistry.org/Part:BBa_J04450 J04450] to perform a quick lysis test (in preparation for testing the lysis construct).<br />
* Prepared 2YT and SOB media in preparation for making electrocompetent DH5\alpha cells tomorrow. Also prepared all glassware and other supplies.<br />
* Completed schematics for our printing process, including a detailed gene network diagram. We will begin assembly of the 3D genetic constructs tomorrow.<br />
* Results of the pigment test with [http://partsregistry.org/Part:BBa_K274100 K274100]: None of the cells seemed to have created the red pigment we were looking for.<br />
** It seems likely that that all the cells died.<br />
** Did not have a visible pellet of cells in the glycerol and agar solutions after centrifugation. The solutions were probably too viscous. <br />
<br />
==Friday 7/9==<br />
* Digested bricks according to NEB BioBrick assembly kit protocol.<br />
** [http://partsregistry.org/Part:BBa_R0077 R0077] (both upstream and downstream)<br />
** [http://partsregistry.org/Part:BBa_C0077 C0077] (upstream)<br />
** [http://partsregistry.org/Part:BBa_C0076 C0076] (upstream)<br />
** [http://partsregistry.org/Part:BBa_M30109 M30109] (downstream)<br />
* Began ligation reactions<br />
** [http://partsregistry.org/Part:R0082 R0082]/[http://partsregistry.org/Part:BBa_R0077 R0077]/[http://partsregistry.org/Part:pSB1T3 pSB1T3]<br />
** [http://partsregistry.org/Part:C0077 C0077]/[http://partsregistry.org/Part:B0015 B0015 (previously digested)]/[http://partsregistry.org/Part:pSB1T3 pSB1T3]<br />
** [http://partsregistry.org/Part:C0076 C0076]/[http://partsregistry.org/Part:B0015 B0015 (previously digested)]/[http://partsregistry.org/Part:pSB1T3 pSB1T3]<br />
* Transformed ligation products into DH5alpha cells.<br />
* Created liquid cultures<br />
** ligation 1 product - [http://partsregistry.org/Part:C0076 C0076]/[http://partsregistry.org/Part:B0015 B0015] (previously digested)/[http://partsregistry.org/Part:pSB1T3 pSB1T3]<br />
** ligation 2 product - [http://partsregistry.org/Part:C0077 C0077]/[http://partsregistry.org/Part:B0015 B0015] (previously digested)/[http://partsregistry.org/Part:pSB1T3 pSB1T3]<br />
** ligation 3 product - [http://partsregistry.org/Part:R0082 R0082]/[http://partsregistry.org/Part:BBa_R0077 R0077]/[http://partsregistry.org/Part:pSB1T3 pSB1T3]<br />
** [http://partsregistry.org/Part:B0015 B0015]<br />
** [http://partsregistry.org/Part:K124017 K124017]<br />
<br />
==Weekend 7/10-11==<br />
* Made minipreps of [http://partsregistry.org/Part:B0015 B0015] and [http://partsregistry.org/Part:K124017 K124017]<br />
* Transformation results: Transformations failed.<br />
** There could be a problem with the antibiotic used or there could also be an issue with the ligations.<br />
<br />
&nbsp;<br />
}}</div>Mxuhttp://2010.igem.org/Team:Caltech/Week_4Team:Caltech/Week 42010-07-09T19:59:49Z<p>Mxu: </p>
<hr />
<div>{{Caltech_iGEM_10|<br />
Content=<br />
[[Team:Caltech/Notebook|Back to Notebook]]<br />
<br />
==Monday 7/5==<br />
Note: Today was another Institute Holiday.<br />
<br />
==Tuesday 7/6==<br />
*Hydrolyzed linseed oil. The reaction solution will be characterized on Wednesday.<br />
<br />
==Wednesday 7/7==<br />
* Attempted to make [http://partsregistry.org/Part:BBa_V1012 V1012] (strain CP919, KanR, ''envZ'' deficient) electrocompetent:<br />
** Centrifuged overnight 3mL LB-Kan culture at 4C, 16000rcf for 10min.<br />
** Discarded supernatant. Resuspended pellet in 1.5mL ice-cold water. Centrifuged again.<br />
** Repeated with 0.75mL ice-cold water. <br />
** Resuspended pellet in 1.5mL ice-cold 10% glycerol.<br />
** Flash-froze 100uL aliquots in dry ice/ethanol.<br />
* Transformed light/lysis ligation product from last week into [http://partsregistry.org/Part:BBa_V1012 V1012] via electroporation. (Voltage: 2.5V; time constant: 4.5)<br />
** Plated 100uL on LB-Tet agar plate & inoculated a 5mL LB-Tet overnight culture.<br />
* Inoculated 5mL LB-Kan culture of purely [http://partsregistry.org/Part:BBa_V1012 V1012] in case we need to retry the competence procedure.<br />
* Tested pigment production of cells containing [http://partsregistry.org/Part:BBa_K274100 K274100] in various solutions.<br />
** Tested solutions of LB, LB without yeast extract added, 80% glycerol, 100% glycerol, and glycerol with different concentrations of agar.<br />
** Since the brick is under an arabinose-inducible promoter, two versions of each solution were made - one containing arabinose, and one without arabinose.<br />
** Pigment production was subjectively measured every hour for five hours. It seemed like there wasn't going to be much pigment produced so the solutions were left overnight in the shaker.<br />
<br />
==Thursday 7/8==<br />
* The [http://partsregistry.org/Part:BBa_V1012 V1012] transformation appears to have worked - the plate is covered in 1000+ colonies.<br />
** Made freezer stock from parallel liquid culture.<br />
* Miniprepped the DNA and prepared a sample for sequencing.<br />
* Started LB liquid culture of [http://partsregistry.org/Part:BBa_M30109 M30109] for assembly tomorrow, along with cultures of [http://partsregistry.org/Part:BBa_J04450 J04450] to perform a quick lysis test (in preparation for testing the lysis construct).<br />
* Prepared 2YT and SOB media in preparation for making electrocompetent DH5\alpha cells tomorrow. Also prepared all glassware and other supplies.<br />
* Completed schematics for our printing process, including a detailed gene network diagram. We will begin assembly of the 3D genetic constructs tomorrow.<br />
* Results of the pigment test with [http://partsregistry.org/Part:BBa_K274100 K274100]: None of the cells seemed to have created the red pigment we were looking for.<br />
** It seems likely that that all the cells died.<br />
** Did not have a visible pellet of cells in the glycerol and agar solutions after centrifugation. The solutions were probably too viscous. <br />
<br />
==Friday 7/9==<br />
<br />
==Weekend 7/10-11==<br />
&nbsp;<br />
}}</div>Mxuhttp://2010.igem.org/Team:Caltech/Week_4Team:Caltech/Week 42010-07-09T19:30:56Z<p>Mxu: </p>
<hr />
<div>{{Caltech_iGEM_10|<br />
Content=<br />
[[Team:Caltech/Notebook|Back to Notebook]]<br />
<br />
==Monday 7/5==<br />
Note: Today was another Institute Holiday.<br />
<br />
==Tuesday 7/6==<br />
*Hydrolyzed linseed oil. The reaction solution will be characterized on Wednesday.<br />
<br />
==Wednesday 7/7==<br />
* Attempted to make [http://partsregistry.org/Part:BBa_V1012 V1012] (strain CP919, KanR, ''envZ'' deficient) electrocompetent:<br />
** Centrifuged overnight 3mL LB-Kan culture at 4C, 16000rcf for 10min.<br />
** Discarded supernatant. Resuspended pellet in 1.5mL ice-cold water. Centrifuged again.<br />
** Repeated with 0.75mL ice-cold water. <br />
** Resuspended pellet in 1.5mL ice-cold 10% glycerol.<br />
** Flash-froze 100uL aliquots in dry ice/ethanol.<br />
* Transformed light/lysis ligation product from last week into [http://partsregistry.org/Part:BBa_V1012 V1012] via electroporation. (Voltage: 2.5V; time constant: 4.5)<br />
** Plated 100uL on LB-Tet agar plate & inoculated a 5mL LB-Tet overnight culture.<br />
* Inoculated 5mL LB-Kan culture of purely [http://partsregistry.org/Part:BBa_V1012 V1012] in case we need to retry the competence procedure.<br />
* Tested pigment production of cells containing [http://partsregistry.org/Part:BBa_K274100 K274100] in various solutions.<br />
** Tested solutions of LB, LB without yeast extract added, 80% glycerol, 100% glycerol, and glycerol with different concentrations of agar.<br />
** Since the brick is under an arabinose-inducible promoter, two versions of each solution were made - one containing arabinose, and one without arabinose.<br />
** Pigment production was subjectively measured every hour for five hours. It seemed like there wasn't going to be much pigment produced so the solutions were left overnight in the shaker.<br />
<br />
==Thursday 7/8==<br />
* The [http://partsregistry.org/Part:BBa_V1012 V1012] transformation appears to have worked - the plate is covered in 1000+ colonies.<br />
** Made freezer stock from parallel liquid culture.<br />
* Miniprepped the DNA and prepared a sample for sequencing.<br />
* Started LB liquid culture of [http://partsregistry.org/Part:BBa_M30109 M30109] for assembly tomorrow, along with cultures of [http://partsregistry.org/Part:BBa_J04450 J04450] to perform a quick lysis test (in preparation for testing the lysis construct).<br />
* Prepared 2YT and SOB media in preparation for making electrocompetent DH5\alpha cells tomorrow. Also prepared all glassware and other supplies.<br />
* Completed schematics for our printing process, including a detailed gene network diagram. We will begin assembly of the 3D genetic constructs tomorrow.<br />
* Results of the pigment test with [http://partsregistry.org/Part:BBa_K274100 K274100]: None of the cells seemed to have created the red pigment we were looking for.<br />
<br />
==Friday 7/9==<br />
<br />
==Weekend 7/10-11==<br />
&nbsp;<br />
}}</div>Mxuhttp://2010.igem.org/Team:Caltech/Week_4Team:Caltech/Week 42010-07-08T19:54:31Z<p>Mxu: </p>
<hr />
<div>{{Caltech_iGEM_10|<br />
Content=<br />
[[Team:Caltech/Notebook|Back to Notebook]]<br />
<br />
==Monday 7/5==<br />
Note: Today was another Institute Holiday.<br />
<br />
==Tuesday 7/6==<br />
*Hydrolyzed linseed oil. The reaction solution will be characterized on Wednesday.<br />
<br />
==Wednesday 7/7==<br />
* Attempted to make [http://partsregistry.org/Part:BBa_V1012 V1012] (strain CP919, KanR, ''envZ'' deficient) electrocompetent:<br />
** Centrifuged overnight 3mL LB-Kan culture at 4C, 16000rcf for 10min.<br />
** Discarded supernatant. Resuspended pellet in 1.5mL ice-cold water. Centrifuged again.<br />
** Repeated with 0.75mL ice-cold water. <br />
** Resuspended pellet in 1.5mL ice-cold 10% glycerol.<br />
** Flash-froze 100uL aliquots in dry ice/ethanol.<br />
* Transformed light/lysis ligation product from last week into [http://partsregistry.org/Part:BBa_V1012 V1012] via electroporation. (Voltage: 2.5V; time constant: 4.5)<br />
** Plated 100uL on LB-Tet agar plate & inoculated a 5mL LB-Tet overnight culture.<br />
* Inoculated 5mL LB-Kan culture of purely [http://partsregistry.org/Part:BBa_V1012 V1012] in case we need to retry the competence procedure.<br />
* Tested pigment production of cells containing [http://partsregistry.org/Part:BBa_K274100 K274100] in various solutions.<br />
** Tested solutions of LB, LB without yeast extract added, 80% glycerol, 100% glycerol, and glycerol with different concentrations of agar.<br />
** Since the brick is under an arabinose-inducible promoter, two versions of each solution were made - one containing arabinose, and one without arabinose.<br />
** Pigment production was subjectively measured every hour for five hours.<br />
<br />
==Thursday 7/8==<br />
* The V1012 transformation appears to have worked - the plate is covered in 1000+ colonies.<br />
** Made freezer stock from parallel liquid culture.<br />
* Miniprepped the DNA for further modification and for sequencing.<br />
<br />
<br />
==Friday 7/9==<br />
<br />
==Weekend 7/10-11==<br />
&nbsp;<br />
}}</div>Mxuhttp://2010.igem.org/Team:Caltech/Week_3Team:Caltech/Week 32010-07-02T00:11:03Z<p>Mxu: </p>
<hr />
<div>{{Caltech_iGEM_10|<br />
Content=<br />
[[Team:Caltech/Notebook|Back to Notebook]]<br />
<br />
==Monday 6/28==<br />
* Tested the success of the construct we made using digest and gel electrophoresis.<br />
** Digested ligation product from [https://2010.igem.org/Team:Caltech/Week_2#Saturday_6.2F26 6/26] with EcoRI and PstI.<br />
** Ran digests on gel along with 1kb and 100kb molecular ladders.<br />
* Gel result: No bands were visible other than those of the ladders. Amount of DNA used was most likely too low and thus the ligation product could not be confirmed.<br />
[[Image:CIT6-28gel.jpg|thumb|Alt=An image of the test gel of our ligation product. The middle two lanes should have bands, but apparently have none. Lane 1: 100bp ladder, Lane 2: 3uL raw ligation product, Lane 3: 15uL ligation digest, Lane 4: 1kb ladder.|Image of a test gel of our third ligation product. Note that the middle two lanes are sadly empty.]]<br />
* Transformed additional BioBricks from 2010 Spring DNA Distribution into DH5alpha cells<br />
** [http://partsregistry.org/wiki/index.php?title=Part:BBa_K274100 K274100], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K274200 K274200], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K274002 K274002], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K274003 K274003], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K274004 K274004]<br />
<br />
==Tuesday 6/29==<br />
* Transformation results: Transformation of the ampicillin-resistant BioBricks seemed to be successful. However, no bacterial growth was present in the plates and liquid cultures with tetracyclin present. This seems to indicate a problem with the tetracyclin used.<br />
** Of the plates with bacterial growth ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K274100 K274100 (red)], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K274200 K274200 (orange)]), there was evidence of pigment production, indicating a successful transformation.<br />
* Transformed 7 more bricks (pigments & our AND gate components):<br />
** [http://partsregistry.org/wiki/index.php?title=Part:BBa_K274110 K274110], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K274210 K274210], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K274003 K274003], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K274004 K274004], [http://partsregistry.org/wiki/index.php?title=Part:BBa_C0076 C0076], [http://partsregistry.org/wiki/index.php?title=Part:BBa_C0077 C0077], [http://partsregistry.org/wiki/index.php?title=Part:BBa_R0077 R0077], [http://partsregistry.org/wiki/index.php?title=Part:BBa_I1765001 I1765001]<br />
<br />
==Wednesday 6/30==<br />
* Transformation results: Only two plates did not have colonies on them. <br />
** The liquid cultures of the red and orange dyes, [http://partsregistry.org/wiki/index.php?title=Part:BBa_K274110 K274110] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K274210 K274210], seemed to be different colors than the other cultures. When centrifuged down, the cells showed signs of pigment production.<br />
** Both the colonies and the liquid culture of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K274004 K274004 (light green)] were darkly colored. There was pigment production; however, the pigment did not appear to be a light green color.<br />
* Prepared glycerol stocks.<br />
* Retransformed three bricks and one new brick (GFP):<br />
** [http://partsregistry.org/wiki/index.php?title=Part:BBa_I765001 I765001] [http://partsregistry.org/wiki/index.php?title=Part:BBa_K274004 K274004] [http://partsregistry.org/wiki/index.php?title=Part:BBa_C0077 C0077] [http://partsregistry.org/wiki/index.php?title=Part:BBa_I13504 I13504]<br />
<br />
==Thursday 7/1==<br />
* Transformation results: All transformations were successful! There was no problem with the antibiotic used.<br />
** [http://partsregistry.org/wiki/index.php?title=Part:BBa_K274003 K274003 (dark green)] was a dark gray color - evidence of production of pigment.<br />
** The colonies of [http://partsregistry.org/wiki/index.php?title=Part:BBa_I13504 I13504 (GFP reporter gene)] did not fluoresce under UV light.<br />
* Performed minipreps and created glycerol stocks from the liquid cultures.<br />
* Received requested bricks from the Registry of Standard Parts. We plated and created liquid cultures of the cells containing the bricks.<br />
* Began digests of bricks according to the NEB BioBrick assembly kit protocol.<br />
** [http://partsregistry.org/wiki/index.php?title=Part:BBa_KI765001 KI765001] (upstream)<br />
** [http://partsregistry.org/wiki/index.php?title=Part:BBa_KI13504 KI13504] (downstream)<br />
** [http://partsregistry.org/wiki/index.php?title=Part:BBa_B0034 B0034] (upstream)<br />
** [http://partsregistry.org/wiki/index.php?title=Part:BBa_K274100 K274100] (downstream)<br />
** [http://partsregistry.org/Part:pSB1C3 pSB1C3] (plasmid backbone)<br />
<br />
<br />
<br />
==Friday 7/2==<br />
<br />
==Weekend 7/3-4==<br />
&nbsp;<br />
}}</div>Mxuhttp://2010.igem.org/Team:Caltech/Week_3Team:Caltech/Week 32010-06-29T20:19:47Z<p>Mxu: </p>
<hr />
<div>{{Caltech_iGEM_10|<br />
Content=<br />
[[Team:Caltech/Notebook|Back to Notebook]]<br />
<br />
==Monday 6/28==<br />
* Tested the success of the construct we made using digest and gel electrophoresis.<br />
** Digested ligation product from [https://2010.igem.org/Team:Caltech/Week_2#Saturday_6.2F26 6/26] with EcoRI and PstI.<br />
** Ran digests on gel along with 1kb and 100kb molecular ladders.<br />
* Gel result: No bands were visible other than those of the ladders. Amount of DNA used was most likely too low and thus the ligation product could not be confirmed.<br />
[[Image:CIT6-28gel.jpg|thumb|Alt=An image of the test gel of our ligation product. The middle two lanes should have bands, but apparently have none. Lane 1: 100bp ladder, Lane 2: 3uL raw ligation product, Lane 3: 15uL ligation digest, Lane 4: 1kb ladder.|Image of a test gel of our third ligation product. Note that the middle two lanes are sadly empty.]]<br />
* Transformed additional BioBricks from 2010 Spring DNA Distribution into DH5alpha cells<br />
** [http://partsregistry.org/wiki/index.php?title=Part:BBa_K274100 K274100], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K274200 K274200], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K274002 K274002], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K274003 K274003], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K274004 K274004]<br />
<br />
==Tuesday 6/29==<br />
* Transformation results: Transformation of the ampicillin-resistant BioBricks seemed to be successful. However, no bacterial growth was present in the plates and liquid cultures with tetracyclin present. This seems to indicate a problem with the tetracyclin used.<br />
** Of the plates with bacterial growth, there was evidence of dye production, indicating a successful transformation.<br />
<br />
==Wednesday 6/30==<br />
<br />
==Thursday 7/1==<br />
<br />
==Friday 7/2==<br />
<br />
==Weekend 7/3-4==<br />
&nbsp;<br />
}}</div>Mxuhttp://2010.igem.org/Team:Caltech/Week_3Team:Caltech/Week 32010-06-29T00:25:22Z<p>Mxu: </p>
<hr />
<div>{{Caltech_iGEM_10|<br />
Content=<br />
[[Team:Caltech/Notebook|Back to Notebook]]<br />
<br />
==Monday 6/28==<br />
* Tested the success of the construct we made using digest and gel electrophoresis.<br />
** Digested ligation product from [https://2010.igem.org/Team:Caltech/Week_2#Saturday_6.2F26 6/26] with EcoRI and PstI.<br />
** Ran digests on gel along with 1kb and 100kb molecular ladders.<br />
* Gel result: No bands were visible other than those of the ladders. Amount of DNA used was most likely too low and thus the ligation product could not be confirmed.<br />
* Transformed additional BioBricks from 2010 Spring DNA Distribution into DH5alpha cells<br />
** [http://partsregistry.org/wiki/index.php?title=Part:BBa_K274100 K274100], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K274200 K274200], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K274002 K274002], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K274003 K274003], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K274004 K274004]<br />
<br />
==Tuesday 6/29==<br />
<br />
==Wednesday 6/30==<br />
<br />
==Thursday 7/1==<br />
<br />
==Friday 7/2==<br />
<br />
==Weekend 7/3-4==<br />
&nbsp;<br />
}}</div>Mxuhttp://2010.igem.org/Team:Caltech/Week_3Team:Caltech/Week 32010-06-29T00:21:11Z<p>Mxu: </p>
<hr />
<div>{{Caltech_iGEM_10|<br />
Content=<br />
[[Team:Caltech/Notebook|Back to Notebook]]<br />
<br />
==Monday 6/28==<br />
* Tested the success of the construct we made using digest and gel electrophoresis.<br />
** Digested ligation product from 6/26 with EcoRI and PstI.<br />
** Ran digests on gel along with 1kb and 100kb molecular ladders.<br />
* Gel result: No bands were visible other than those of the ladders. Amount of DNA used was most likely too low and thus the ligation product could not be confirmed.<br />
* Transformed additional BioBricks from 2010 Spring DNA Distribution into DH5alpha cells<br />
** [http://partsregistry.org/wiki/index.php?title=Part:BBa_K274100 K274100], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K274200 K274200], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K274002 K274002], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K274003 K274003], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K274004 K274004]<br />
<br />
==Tuesday 6/29==<br />
<br />
==Wednesday 6/30==<br />
<br />
==Thursday 7/1==<br />
<br />
==Friday 7/2==<br />
<br />
==Weekend 7/3-4==<br />
&nbsp;<br />
}}</div>Mxuhttp://2010.igem.org/Team:Caltech/Week_2Team:Caltech/Week 22010-06-25T18:51:38Z<p>Mxu: </p>
<hr />
<div>{{Caltech_iGEM_10|<br />
Content=<br />
[[Team:Caltech/Notebook|Back to Notebook]]<br />
<br />
==Monday 6/21==<br />
* Transformed additional bricks from distribution with other antibiotic resistances onto plates & liquid culture.<br />
** [http://partsregistry.org/wiki/index.php?title=Part:BBa_I15008 I15008], [http://partsregistry.org/wiki/index.php?title=Part:BBa_I15009 I15009], [http://partsregistry.org/wiki/index.php?title=Part:BBa_I15010 I15010], [http://partsregistry.org/wiki/index.php?title=Part:BBa_E0033 E0033], [http://partsregistry.org/wiki/index.php?title=Part:BBa_M30109 M30109], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K112000 K112000], [http://partsregistry.org/wiki/index.php?title=Part:BBa_J09250 J09250]<br />
<br />
==Tuesday 6/22==<br />
* Transformation success is ambiguous - the plates are covered in a lawn of bacteria, apparently indicating an issue with the antibiotic selection. This implies either a problem with the stock solution of antibiotic (Kan/Strep), or the procedure of plating the antibiotics on the surface of the LB-agar plates. <br />
** To find out what happened, we set up a simple experiment:<br />
* Reperformed the transformations on two of the bricks & plated on LB-agar plates with the antibiotic incorporated. <br />
<br />
==Wednesday 6/23==<br />
* Transformation plates are still covered in a film of bacteria. The negative control for the kanamycin test grew bacteria, suggesting that there is an issue with the kanamycin stock. <br />
<br />
==Thursday 6/24==<br />
<br />
==Friday 6/25==<br />
<br />
==Weekend 6/26-27==<br />
&nbsp;<br />
}}</div>Mxuhttp://2010.igem.org/Team:Caltech/TeamTeam:Caltech/Team2010-06-21T22:50:56Z<p>Mxu: /* Who we are */</p>
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|[[Image:Caltech_logo.png|200px|right|frame]]<br />
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''Tell us more about your project. Give us background. Use this is the abstract of your project. Be descriptive but concise (1-2 paragraphs)''<br />
|[[Image:Caltech_team.png|right|frame|Your team picture]]<br />
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<!--- The Mission, Experiments ---><br />
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{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Caltech|Home]]<br />
!align="center"|[[Team:Caltech/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2010&team_name=Caltech Official Team Profile]<br />
!align="center"|[[Team:Caltech/Project|Project]]<br />
!align="center"|[[Team:Caltech/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Caltech/Modeling|Modeling]]<br />
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== '''Who we are''' ==<br />
{|border = "0"<br />
|-<br />
|rowspan="3"|<br />
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<br />
<br />
<br />
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'''Advisors:'''<br />
<br />
Pr. Richard Murray<br />
<br />
Pr. Rob Phillips<br />
<br />
<br />
'''Grad Students:'''<br />
<br />
Joseph Meyerowitz<br />
<br />
Emzo de los Santos<br />
<br />
Jerzy Szablowski<br />
<br />
<br />
'''Undergrads:'''<br />
<br />
Lucas Hartsough<br />
<br />
Brian Ma<br />
<br />
Yuehan Huang<br />
<br />
Alexandre Boulgakov<br />
<br />
Melissa Xu<br />
<br />
Paul Nguyen<br />
<br />
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|<br />
<gallery><br />
Image:Caltech_Team_member_1.png|Team member 1<br />
Image:Caltech_Team_member_2.png|Team member 2<br />
Image:Caltech_Team_member_3.png|Team member 3<br />
Image:Caltech_Team_member_4.png|Team member 4<br />
Image:Caltech_Team_member_5.png|Team member 5<br />
Image:Caltech_Team_member_6.png|Team member 6<br />
Image:Caltech_Team_member_7.png|Team member 7<br />
Image:Caltech_Team_member_8.png|Team member 8<br />
</gallery><br />
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== '''What we did''' ==<br />
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(Provide proper attribution for all work)<br />
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== '''Where we're from''' ==</div>Mxuhttp://2010.igem.org/Team:Caltech/TeamTeam:Caltech/Team2010-06-21T22:49:31Z<p>Mxu: </p>
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This is a template page. READ THESE INSTRUCTIONS.<br />
</div><br />
<div id="instructions" style="text-align: center; font-weight: normal; font-size: small; color: #f6f6f6; padding: 5px;"><br />
You are provided with this team page template with which to start the iGEM season. You may choose to personalize it to fit your team but keep the same "look." Or you may choose to take your team wiki to a different level and design your own wiki. You can find some examples <a href="https://2008.igem.org/Help:Template/Examples">HERE</a>.<br />
</div><br />
<div id="warning" style="text-align: center; font-weight: bold; font-size: small; color: #f6f6f6; padding: 5px;"><br />
You <strong>MUST</strong> have a team description page, a project abstract, a complete project description, a lab notebook, and a safety page. PLEASE keep all of your pages within your teams namespace. <br />
</div><br />
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<!-- *** End of the alert box *** --><br />
<br />
<br />
{|align="justify"<br />
|You can write a background of your team here. Give us a background of your team, the members, etc. Or tell us more about something of your choosing.<br />
|[[Image:Caltech_logo.png|200px|right|frame]]<br />
|-<br />
|<br />
''Tell us more about your project. Give us background. Use this is the abstract of your project. Be descriptive but concise (1-2 paragraphs)''<br />
|[[Image:Caltech_team.png|right|frame|Your team picture]]<br />
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|align="center"|[[Team:Caltech | Team Example]]<br />
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<!--- The Mission, Experiments ---><br />
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{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Caltech|Home]]<br />
!align="center"|[[Team:Caltech/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2010&team_name=Caltech Official Team Profile]<br />
!align="center"|[[Team:Caltech/Project|Project]]<br />
!align="center"|[[Team:Caltech/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Caltech/Modeling|Modeling]]<br />
!align="center"|[[Team:Caltech/Notebook|Notebook]]<br />
!align="center"|[[Team:Caltech/Safety|Safety]]<br />
|}<br />
<br />
<br />
<br />
== '''Who we are''' ==<br />
{|border = "0"<br />
|-<br />
|rowspan="3"|<br />
<br />
<br />
<br />
<br />
<br />
'''Advisors:'''<br />
<br />
Pr. Richard Murray<br />
<br />
Pr. Rob Phillips<br />
<br />
<br />
'''Grad Students:'''<br />
<br />
Joseph Meyerowitz<br />
<br />
Emzo de los Santos<br />
<br />
Jerzy Szablowski<br />
<br />
<br />
'''Undergrads:'''<br />
<br />
Lucas Hartsough<br />
<br />
Brian Ma<br />
<br />
Yuehan Huang<br />
<br />
Alexandre Boulgakov<br />
<br />
Melissa Xu<br />
<br />
Paul Nguyen<br />
<br />
<br />
|<br />
<gallery><br />
Image:Caltech_Team_member_1.png|Team member 1<br />
Image:Caltech_Team_member_2.png|Team member 2<br />
Image:Caltech_Team_member_3.png|Team member 3<br />
Image:Caltech_Team_member_4.png|Team member 4<br />
Image:Caltech_Team_member_5.png|Team member 5<br />
Image:Caltech_Team_member_6.png|Team member 6<br />
Image:Caltech_Team_member_7.png|Team member 7<br />
</gallery><br />
|}<br />
<br />
== '''What we did''' ==<br />
<br />
(Provide proper attribution for all work)<br />
<br />
<br />
== '''Where we're from''' ==</div>Mxu