Team:Cornell/testing/notebook/wetlab/3

From 2012.igem.org

(Difference between revisions)
Line 77: Line 77:
<div class="nine columns">
<div class="nine columns">
<h3>Week 2</h3>
<h3>Week 2</h3>
-
It has been said that astronomy is a humbling and character-building experience. There is perhaps no better demonstration of the folly of human conceits than this distant image of our tiny world. To me, it underscores our responsibility to deal more kindly with one another, and to preserve and cherish the pale blue dot, the only home we've ever known.
+
It was confirmed that RFP was successfully inserted downstream of mtrB in our arsenic reporter parts in Shewanella. Site-directed mutagenesis of the nah operon failed. We are still trying to insert the nah operon into the mobility backbone (OriT) to prepare for conjugation into Shewanella later on.
<a href="#" class="technical-desc" for="#technical-desc7" style="display:block;margin-top:20px;">Daily Details</a>
<a href="#" class="technical-desc" for="#technical-desc7" style="display:block;margin-top:20px;">Daily Details</a>
<div class="hide-me panel" style="background:white;margin-top: 20px;" id="technical-desc7">
<div class="hide-me panel" style="background:white;margin-top: 20px;" id="technical-desc7">
<h6>Daily Details:</h6>
<h6>Daily Details:</h6>
-
Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
+
<br><b>August 5th, Sunday </b></br><br> Swati yet again was saddled with a massive number of <a href="http://2012.igem.org/wiki/images/3/35/Ezna_Miniprep.pdf">minipreps </a>, since her magic fingers are able to cast yield-increasing spells on minipreps. She miniprepped: SAL2 from WM3064, p37-41k from JG700 (one arsenic reporter with cut sites flanking the RBS, another arsenic reporter without the cut sites, and three different Anderson series promoters with mRFP1 downstream on a pBBRBB backbone), oriT p29nah_p17c from DH5a, and nah_p31c from DH5a. And indeed her yields were impressive, massive, gargantuan! Good job Sorceress Swati.
 +
We will <a href="http://2012.igem.org/wiki/images/0/03/Sequencing_Preparation.pdf "> sequence </a> SAL2 and oriT p29nah_p17c to see if we should continue to conjugation, and sequence nah_p31c to see if we can start <a href=" http://2012.igem.org/wiki/images/a/a5/Site_Directed_Mutagenesis.pdf "> site-directed mutagenesis </a> to get a biobrick-compatible nah operon on the biobrick backbone. We will sequence or PCR to confirm p37k-p41k's conjugation into Shewanella.
 +
</br> <br> </br>
 +
 
 +
 
 +
<br><b> August 6th, Monday </b></br><br> Caleb and Dylan amplified the two different arsenic promoters (p37k and p38k) and ran them on a gel alongside p14 and p16 (the arsenic reporters without mRFP1 downstream) to confirm successful insertion of RFP downstream of mtrB in our arsenic reporter parts in Shewenella. Band lengths appeared in expected places. Dylan is worried that we will not be able to use PCR to definitely confirm that p39-41k worked, so we submitted these for <a href="http://2012.igem.org/wiki/images/0/03/Sequencing_Preparation.pdf "> sequencing </a>. Unfortunately, sequencing failed, perhaps because random gunk from Shewanella added noise to the process.
 +
Tina did a PCR cleanup of the nah operon PCR. Dylan also ran a gel of nah operon PCRs to make sure that there was no mispriming. The gel looked good, so he submitted the PCRs for sequencing.
 +
</br> <br> </br>
 +
 
 +
 
 +
<br><b> August 7th, Tuesday </b></br><br> JG1531 overnight culture didn't grow. We suspect that the plate Dylan picked from is dead. We'll have to go back to the glycerol stocks if we want to play with mtrE. Dylan set up a continuous flow M4 reactor in morning. Caleb started a liquid culture of MR-1 with which to inoculate the reactor. Checked sequencing results of nah stuff. oriT thing was bad. nah_p31c was good.
 +
Caleb and Dylan proceeded with <a href=" http://2012.igem.org/wiki/images/a/a5/Site_Directed_Mutagenesis.pdf "> site-directed mutagenesis </a> of nah_p31c, attempting to get rid of the first PstI cutsite in the nah operon. After digestion with DpnI, we purified using the E.Z.N.A. MicroElute kit and quantified. DNA was split into three directions: First, Danielle and Dylan set up another mutagenic PCR using the digestion product as template to get rid of the second internal cut site (we expect lower mutation efficiency because template DNA is not methylated). Second, we transformed DH5a with the mutated plasmid. Third, Danielle and Chie <a href="http://2012.igem.org/wiki/images/a/af/Double_Digest.pdf "> digested </a> both the purified – and hopefully mutated – plasmid and un-mutated plasmid with PstI. Dylan ran these digestions on a gel, along with supercoiled plasmid as a control. Unfortunately, the (hopefully) mutated plasmid never showed up on the gel.
 +
In the evening, we didn't observe growth in the MR-1 culture, so Dylan set up another culture just in case Shewanella was dead and not lazy.
 +
</br> <br> </br>
 +
 
 +
 
 +
<br><b> August 8th, Wednesday </b></br><br> Caleb and Dylan performed another <a href="http://2012.igem.org/wiki/images/a/af/Double_Digest.pdf "> digest </a> to check if the second <a href="http://2012.igem.org/wiki/images/a/a5/Site_Directed_Mutagenesis.pdf "> site-directed mutagenesis </a> (that was supposed to get rid of the second PstI internal cut site within the nah operon) worked. Unfortunately, there wasn't enough DNA to see anything when visualized on a gel. They decided to proceed with electroporation into DH5a just in case - however, to use Caleb's terminology, cells exploded - there were probably too many salts in the solution, which causing arcing and a PBBHTTTZZZ! of cells all over the cuvette.
 +
Dylan re-digested p29 nah and oriT p17c to redo a ligation that would allow for conjugation into Shewanella later on. Dylan also re-digested p27 (Anderson series promoter with RFP downstream) and SAL to redo a ligation to create a plasmid with SAL-RFP.
 +
Dylan also submitted several samples for <a href="http://2012.igem.org/wiki/images/0/03/Sequencing_Preparation.pdf "> sequencing </a> to make sure that three Anderson promoters with RFP downstream in JG700 and SAL2 (the salicylate reporter without the BAMHI cut site) in WN3064 and JG700 were in the correct sequence.
 +
</br> <br> </br>
 +
 
 +
 
 +
<br><b> August 9th, Thursday </b></br><br> Today Dylan chilled with his mom. Well, he tried to. :) Despite the eternal bonds that bind mother and son, plus the 3 billion miles she flew to see him, he still couldn't resist coming in to lab to open packages! And then got sucked into a long discussion of what had to be done for the rest of the day - scientific endeavors taking him away yet again from filial duties. Swati and Claire bonded over dry ice, and Caleb regaled us with tales of dry ice bombs gone awry.
 +
Swati and Caleb miniprepped the first mutagenesis of nah_p31c that had been transformed into DH5a yesterday. They then digested it with PstI-HF to see if the mutation was successful. Unfortunately the mutagenesis failed! We will start over from nah_p31c and lower the annealing temperature at 60degC. The Stratagene kit, which uses PFU ultra, asks for 60degC, but because we are using our own boot-leg protocol with Phusion we did the first try at 65degC, as Phusion usually calls for a higher annealing temperature than the theoretically calculated value. For this second try we will stick to the 60degC suggested by Stratagene and see if we get better results. Also, called NEB to find out if after PCR with Phusion, DpnI will still have activity in the following digestion step in Buffer 4, or if we need to clean up the PCR before digesting with DpnI - they said PCR clean up isn't needed.
 +
We also ran digestions for making the nah operon on a backbone with a mobility gene and the salicylate reporter (w/ BamHI cutsite) with RFP downstream. We cut our mobile backbone, OriT in p17c (pSB3C5), with EcoRI and XbaI, while cutting the nah operon (p29nah) with EcoRI and SpeI. The nah operon with mobility gene must be constructed so that we may conjugate into Shewy and start testing our salicylate reporter. The salicylate reporter and p27a (from the Anderson series), with RFP, were cut with SpeI and PstI. The salicylate/RFP part will be used for troubleshooting the salicylate reporter. Digestion products were run on a gel, extracted, and quantified. Swati then dephosphorylated backbones and ligated both parts.
 +
Sequencing for p39-41k didn't look good, and neither did the salicylate reporter w/BamHI cutsite miniprepped from JG700. The sequencing for salicylate reporter w/ BamHI in WM3064, however, looked good, suggesting that conjugation may not have been as efficient as we had hoped. After a pow-wow we decided not to sequence more colonies, as we are hoping some may be good, and more importantly that if we use qPCR to get quantitative characterization data, we won't need to use the RFP parts. The plates will stay in the fridge as a back-up plan.
 +
In other news: Claire cried because it was difficult to update the notebook with a week's worth of work. Mark's dedication to the notebook is laudable and impressive. Good job team for doing so much! My head can't even comprehend the magnitude of your endeavors.
 +
</br> <br> </br>
 +
 
 +
<br><b> August 10th, Friday </b></br><br> Caleb miniprepped a plasmid with mtrE from JG1531, and just for kicks, miniprepped from the "exploded cells" from August 8th. Suprisingly, he ended up getting decent yields for both, showing that the electroporation worked despite arcing. Caleb then digested the nah operon of the miniprep with PSTI and NotI to check if the mutagenesis was a success. It was run on a gel alongside a PCR of the Anderson series promoters with RFP downstream and SAL2 from Shewanella (to check if SAL2 and the promoters were sucessfully conjugated after sequencing on Monday failed). Unfortunately, bands did not appear where we expected them to.
 +
Steven and Spencer performed a PCR to get mtrE out of the Gralnick (JG700) plasmid. </br> <br> </br>
 +
 
 +
<br><b> August 11th, Saturday </b></br><br> Spencer and Steven checked the nah operon PstI and NotI digest (because yesterday's gel ran weirdly) and their mtrE PCR from the previous day on a gel. Unfortunately, bands did not appear where we expected them to.
 +
</br> <br> </br>
 +
 
</div>
</div>
</div>
</div>
Line 160: Line 194:
<div class="nine columns">
<div class="nine columns">
<h3>Week 2</h3>
<h3>Week 2</h3>
-
Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
+
<br><b>August 5th, Sunday </b></br><br> Swati yet again was saddled with a massive number of <a href="http://2012.igem.org/wiki/images/3/35/Ezna_Miniprep.pdf">minipreps </a>, since her magic fingers are able to cast yield-increasing spells on minipreps. She miniprepped: SAL2 from WM3064, p37-41k from JG700 (one arsenic reporter with cut sites flanking the RBS, another arsenic reporter without the cut sites, and three different Anderson series promoters with mRFP1 downstream on a pBBRBB backbone), oriT p29nah_p17c from DH5a, and nah_p31c from DH5a. And indeed her yields were impressive, massive, gargantuan! Good job Sorceress Swati.
 +
We will <a href="http://2012.igem.org/wiki/images/0/03/Sequencing_Preparation.pdf "> sequence </a> SAL2 and oriT p29nah_p17c to see if we should continue to conjugation, and sequence nah_p31c to see if we can start <a href=" http://2012.igem.org/wiki/images/a/a5/Site_Directed_Mutagenesis.pdf "> site-directed mutagenesis </a> to get a biobrick-compatible nah operon on the biobrick backbone. We will sequence or PCR to confirm p37k-p41k's conjugation into Shewanella.
 +
</br> <br> </br>
 +
 
 +
 
 +
<br><b> August 6th, Monday </b></br><br> Caleb and Dylan amplified the two different arsenic promoters (p37k and p38k) and ran them on a gel alongside p14 and p16 (the arsenic reporters without mRFP1 downstream) to confirm successful insertion of RFP downstream of mtrB in our arsenic reporter parts in Shewenella. Band lengths appeared in expected places. Dylan is worried that we will not be able to use PCR to definitely confirm that p39-41k worked, so we submitted these for <a href="http://2012.igem.org/wiki/images/0/03/Sequencing_Preparation.pdf "> sequencing </a>. Unfortunately, sequencing failed, perhaps because random gunk from Shewanella added noise to the process.
 +
Tina did a PCR cleanup of the nah operon PCR. Dylan also ran a gel of nah operon PCRs to make sure that there was no mispriming. The gel looked good, so he submitted the PCRs for sequencing.
 +
</br> <br> </br>
 +
 
 +
 
 +
<br><b> August 7th, Tuesday </b></br><br> JG1531 overnight culture didn't grow. We suspect that the plate Dylan picked from is dead. We'll have to go back to the glycerol stocks if we want to play with mtrE. Dylan set up a continuous flow M4 reactor in morning. Caleb started a liquid culture of MR-1 with which to inoculate the reactor. Checked sequencing results of nah stuff. oriT thing was bad. nah_p31c was good.
 +
Caleb and Dylan proceeded with <a href=" http://2012.igem.org/wiki/images/a/a5/Site_Directed_Mutagenesis.pdf "> site-directed mutagenesis </a> of nah_p31c, attempting to get rid of the first PstI cutsite in the nah operon. After digestion with DpnI, we purified using the E.Z.N.A. MicroElute kit and quantified. DNA was split into three directions: First, Danielle and Dylan set up another mutagenic PCR using the digestion product as template to get rid of the second internal cut site (we expect lower mutation efficiency because template DNA is not methylated). Second, we transformed DH5a with the mutated plasmid. Third, Danielle and Chie <a href="http://2012.igem.org/wiki/images/a/af/Double_Digest.pdf "> digested </a> both the purified – and hopefully mutated – plasmid and un-mutated plasmid with PstI. Dylan ran these digestions on a gel, along with supercoiled plasmid as a control. Unfortunately, the (hopefully) mutated plasmid never showed up on the gel.
 +
In the evening, we didn't observe growth in the MR-1 culture, so Dylan set up another culture just in case Shewanella was dead and not lazy.
 +
</br> <br> </br>
 +
 
 +
 
 +
<br><b> August 8th, Wednesday </b></br><br> Caleb and Dylan performed another <a href="http://2012.igem.org/wiki/images/a/af/Double_Digest.pdf "> digest </a> to check if the second <a href="http://2012.igem.org/wiki/images/a/a5/Site_Directed_Mutagenesis.pdf "> site-directed mutagenesis </a> (that was supposed to get rid of the second PstI internal cut site within the nah operon) worked. Unfortunately, there wasn't enough DNA to see anything when visualized on a gel. They decided to proceed with electroporation into DH5a just in case - however, to use Caleb's terminology, cells exploded - there were probably too many salts in the solution, which causing arcing and a PBBHTTTZZZ! of cells all over the cuvette.
 +
Dylan re-digested p29 nah and oriT p17c to redo a ligation that would allow for conjugation into Shewanella later on. Dylan also re-digested p27 (Anderson series promoter with RFP downstream) and SAL to redo a ligation to create a plasmid with SAL-RFP.
 +
Dylan also submitted several samples for <a href="http://2012.igem.org/wiki/images/0/03/Sequencing_Preparation.pdf "> sequencing </a> to make sure that three Anderson promoters with RFP downstream in JG700 and SAL2 (the salicylate reporter without the BAMHI cut site) in WN3064 and JG700 were in the correct sequence.
 +
</br> <br> </br>
 +
 
 +
 
 +
<br><b> August 9th, Thursday </b></br><br> Today Dylan chilled with his mom. Well, he tried to. :) Despite the eternal bonds that bind mother and son, plus the 3 billion miles she flew to see him, he still couldn't resist coming in to lab to open packages! And then got sucked into a long discussion of what had to be done for the rest of the day - scientific endeavors taking him away yet again from filial duties. Swati and Claire bonded over dry ice, and Caleb regaled us with tales of dry ice bombs gone awry.
 +
Swati and Caleb miniprepped the first mutagenesis of nah_p31c that had been transformed into DH5a yesterday. They then digested it with PstI-HF to see if the mutation was successful. Unfortunately the mutagenesis failed! We will start over from nah_p31c and lower the annealing temperature at 60degC. The Stratagene kit, which uses PFU ultra, asks for 60degC, but because we are using our own boot-leg protocol with Phusion we did the first try at 65degC, as Phusion usually calls for a higher annealing temperature than the theoretically calculated value. For this second try we will stick to the 60degC suggested by Stratagene and see if we get better results. Also, called NEB to find out if after PCR with Phusion, DpnI will still have activity in the following digestion step in Buffer 4, or if we need to clean up the PCR before digesting with DpnI - they said PCR clean up isn't needed.
 +
We also ran digestions for making the nah operon on a backbone with a mobility gene and the salicylate reporter (w/ BamHI cutsite) with RFP downstream. We cut our mobile backbone, OriT in p17c (pSB3C5), with EcoRI and XbaI, while cutting the nah operon (p29nah) with EcoRI and SpeI. The nah operon with mobility gene must be constructed so that we may conjugate into Shewy and start testing our salicylate reporter. The salicylate reporter and p27a (from the Anderson series), with RFP, were cut with SpeI and PstI. The salicylate/RFP part will be used for troubleshooting the salicylate reporter. Digestion products were run on a gel, extracted, and quantified. Swati then dephosphorylated backbones and ligated both parts.
 +
Sequencing for p39-41k didn't look good, and neither did the salicylate reporter w/BamHI cutsite miniprepped from JG700. The sequencing for salicylate reporter w/ BamHI in WM3064, however, looked good, suggesting that conjugation may not have been as efficient as we had hoped. After a pow-wow we decided not to sequence more colonies, as we are hoping some may be good, and more importantly that if we use qPCR to get quantitative characterization data, we won't need to use the RFP parts. The plates will stay in the fridge as a back-up plan.
 +
In other news: Claire cried because it was difficult to update the notebook with a week's worth of work. Mark's dedication to the notebook is laudable and impressive. Good job team for doing so much! My head can't even comprehend the magnitude of your endeavors.
 +
</br> <br> </br>
 +
 
 +
<br><b> August 10th, Friday </b></br><br> Caleb miniprepped a plasmid with mtrE from JG1531, and just for kicks, miniprepped from the "exploded cells" from August 8th. Suprisingly, he ended up getting decent yields for both, showing that the electroporation worked despite arcing. Caleb then digested the nah operon of the miniprep with PSTI and NotI to check if the mutagenesis was a success. It was run on a gel alongside a PCR of the Anderson series promoters with RFP downstream and SAL2 from Shewanella (to check if SAL2 and the promoters were sucessfully conjugated after sequencing on Monday failed). Unfortunately, bands did not appear where we expected them to.
 +
Steven and Spencer performed a PCR to get mtrE out of the Gralnick (JG700) plasmid. </br> <br> </br>
 +
 
 +
<br><b> August 11th, Saturday </b></br><br> Spencer and Steven checked the nah operon PstI and NotI digest (because yesterday's gel ran weirdly) and their mtrE PCR from the previous day on a gel. Unfortunately, bands did not appear where we expected them to.
 +
</br> <br> </br>
 +
 
</div>
</div>
<div class="three columns">
<div class="three columns">
Line 227: Line 295:
<div class="nine columns">
<div class="nine columns">
<h3>Week 2</h3>
<h3>Week 2</h3>
-
It has been said that astronomy is a humbling and character-building experience. There is perhaps no better demonstration of the folly of human conceits than this distant image of our tiny world. To me, it underscores our responsibility to deal more kindly with one another, and to preserve and cherish the pale blue dot, the only home we've ever known.
+
It was confirmed that RFP was successfully inserted downstream of mtrB in our arsenic reporter parts in Shewanella. Site-directed mutagenesis of the nah operon failed. We are still trying to insert the nah operon into the mobility backbone (OriT) to prepare for conjugation into Shewanella later on.
<div class="panel" style="background:white;margin-top: 20px;">
<div class="panel" style="background:white;margin-top: 20px;">
<h6>Daily Details:</h6>
<h6>Daily Details:</h6>
-
Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
+
<br><b>August 5th, Sunday </b></br><br> Swati yet again was saddled with a massive number of <a href="http://2012.igem.org/wiki/images/3/35/Ezna_Miniprep.pdf">minipreps </a>, since her magic fingers are able to cast yield-increasing spells on minipreps. She miniprepped: SAL2 from WM3064, p37-41k from JG700 (one arsenic reporter with cut sites flanking the RBS, another arsenic reporter without the cut sites, and three different Anderson series promoters with mRFP1 downstream on a pBBRBB backbone), oriT p29nah_p17c from DH5a, and nah_p31c from DH5a. And indeed her yields were impressive, massive, gargantuan! Good job Sorceress Swati.
 +
We will <a href="http://2012.igem.org/wiki/images/0/03/Sequencing_Preparation.pdf "> sequence </a> SAL2 and oriT p29nah_p17c to see if we should continue to conjugation, and sequence nah_p31c to see if we can start <a href=" http://2012.igem.org/wiki/images/a/a5/Site_Directed_Mutagenesis.pdf "> site-directed mutagenesis </a> to get a biobrick-compatible nah operon on the biobrick backbone. We will sequence or PCR to confirm p37k-p41k's conjugation into Shewanella.
 +
</br> <br> </br>
 +
 
 +
 
 +
<br><b> August 6th, Monday </b></br><br> Caleb and Dylan amplified the two different arsenic promoters (p37k and p38k) and ran them on a gel alongside p14 and p16 (the arsenic reporters without mRFP1 downstream) to confirm successful insertion of RFP downstream of mtrB in our arsenic reporter parts in Shewenella. Band lengths appeared in expected places. Dylan is worried that we will not be able to use PCR to definitely confirm that p39-41k worked, so we submitted these for <a href="http://2012.igem.org/wiki/images/0/03/Sequencing_Preparation.pdf "> sequencing </a>. Unfortunately, sequencing failed, perhaps because random gunk from Shewanella added noise to the process.
 +
Tina did a PCR cleanup of the nah operon PCR. Dylan also ran a gel of nah operon PCRs to make sure that there was no mispriming. The gel looked good, so he submitted the PCRs for sequencing.
 +
</br> <br> </br>
 +
 
 +
 
 +
<br><b> August 7th, Tuesday </b></br><br> JG1531 overnight culture didn't grow. We suspect that the plate Dylan picked from is dead. We'll have to go back to the glycerol stocks if we want to play with mtrE. Dylan set up a continuous flow M4 reactor in morning. Caleb started a liquid culture of MR-1 with which to inoculate the reactor. Checked sequencing results of nah stuff. oriT thing was bad. nah_p31c was good.
 +
Caleb and Dylan proceeded with <a href=" http://2012.igem.org/wiki/images/a/a5/Site_Directed_Mutagenesis.pdf "> site-directed mutagenesis </a> of nah_p31c, attempting to get rid of the first PstI cutsite in the nah operon. After digestion with DpnI, we purified using the E.Z.N.A. MicroElute kit and quantified. DNA was split into three directions: First, Danielle and Dylan set up another mutagenic PCR using the digestion product as template to get rid of the second internal cut site (we expect lower mutation efficiency because template DNA is not methylated). Second, we transformed DH5a with the mutated plasmid. Third, Danielle and Chie <a href="http://2012.igem.org/wiki/images/a/af/Double_Digest.pdf "> digested </a> both the purified – and hopefully mutated – plasmid and un-mutated plasmid with PstI. Dylan ran these digestions on a gel, along with supercoiled plasmid as a control. Unfortunately, the (hopefully) mutated plasmid never showed up on the gel.
 +
In the evening, we didn't observe growth in the MR-1 culture, so Dylan set up another culture just in case Shewanella was dead and not lazy.
 +
</br> <br> </br>
 +
 
 +
 
 +
<br><b> August 8th, Wednesday </b></br><br> Caleb and Dylan performed another <a href="http://2012.igem.org/wiki/images/a/af/Double_Digest.pdf "> digest </a> to check if the second <a href="http://2012.igem.org/wiki/images/a/a5/Site_Directed_Mutagenesis.pdf "> site-directed mutagenesis </a> (that was supposed to get rid of the second PstI internal cut site within the nah operon) worked. Unfortunately, there wasn't enough DNA to see anything when visualized on a gel. They decided to proceed with electroporation into DH5a just in case - however, to use Caleb's terminology, cells exploded - there were probably too many salts in the solution, which causing arcing and a PBBHTTTZZZ! of cells all over the cuvette.
 +
Dylan re-digested p29 nah and oriT p17c to redo a ligation that would allow for conjugation into Shewanella later on. Dylan also re-digested p27 (Anderson series promoter with RFP downstream) and SAL to redo a ligation to create a plasmid with SAL-RFP.
 +
Dylan also submitted several samples for <a href="http://2012.igem.org/wiki/images/0/03/Sequencing_Preparation.pdf "> sequencing </a> to make sure that three Anderson promoters with RFP downstream in JG700 and SAL2 (the salicylate reporter without the BAMHI cut site) in WN3064 and JG700 were in the correct sequence.
 +
</br> <br> </br>
 +
 
 +
 
 +
<br><b> August 9th, Thursday </b></br><br> Today Dylan chilled with his mom. Well, he tried to. :) Despite the eternal bonds that bind mother and son, plus the 3 billion miles she flew to see him, he still couldn't resist coming in to lab to open packages! And then got sucked into a long discussion of what had to be done for the rest of the day - scientific endeavors taking him away yet again from filial duties. Swati and Claire bonded over dry ice, and Caleb regaled us with tales of dry ice bombs gone awry.
 +
Swati and Caleb miniprepped the first mutagenesis of nah_p31c that had been transformed into DH5a yesterday. They then digested it with PstI-HF to see if the mutation was successful. Unfortunately the mutagenesis failed! We will start over from nah_p31c and lower the annealing temperature at 60degC. The Stratagene kit, which uses PFU ultra, asks for 60degC, but because we are using our own boot-leg protocol with Phusion we did the first try at 65degC, as Phusion usually calls for a higher annealing temperature than the theoretically calculated value. For this second try we will stick to the 60degC suggested by Stratagene and see if we get better results. Also, called NEB to find out if after PCR with Phusion, DpnI will still have activity in the following digestion step in Buffer 4, or if we need to clean up the PCR before digesting with DpnI - they said PCR clean up isn't needed.
 +
We also ran digestions for making the nah operon on a backbone with a mobility gene and the salicylate reporter (w/ BamHI cutsite) with RFP downstream. We cut our mobile backbone, OriT in p17c (pSB3C5), with EcoRI and XbaI, while cutting the nah operon (p29nah) with EcoRI and SpeI. The nah operon with mobility gene must be constructed so that we may conjugate into Shewy and start testing our salicylate reporter. The salicylate reporter and p27a (from the Anderson series), with RFP, were cut with SpeI and PstI. The salicylate/RFP part will be used for troubleshooting the salicylate reporter. Digestion products were run on a gel, extracted, and quantified. Swati then dephosphorylated backbones and ligated both parts.
 +
Sequencing for p39-41k didn't look good, and neither did the salicylate reporter w/BamHI cutsite miniprepped from JG700. The sequencing for salicylate reporter w/ BamHI in WM3064, however, looked good, suggesting that conjugation may not have been as efficient as we had hoped. After a pow-wow we decided not to sequence more colonies, as we are hoping some may be good, and more importantly that if we use qPCR to get quantitative characterization data, we won't need to use the RFP parts. The plates will stay in the fridge as a back-up plan.
 +
In other news: Claire cried because it was difficult to update the notebook with a week's worth of work. Mark's dedication to the notebook is laudable and impressive. Good job team for doing so much! My head can't even comprehend the magnitude of your endeavors.
 +
</br> <br> </br>
 +
 
 +
<br><b> August 10th, Friday </b></br><br> Caleb miniprepped a plasmid with mtrE from JG1531, and just for kicks, miniprepped from the "exploded cells" from August 8th. Suprisingly, he ended up getting decent yields for both, showing that the electroporation worked despite arcing. Caleb then digested the nah operon of the miniprep with PSTI and NotI to check if the mutagenesis was a success. It was run on a gel alongside a PCR of the Anderson series promoters with RFP downstream and SAL2 from Shewanella (to check if SAL2 and the promoters were sucessfully conjugated after sequencing on Monday failed). Unfortunately, bands did not appear where we expected them to.
 +
Steven and Spencer performed a PCR to get mtrE out of the Gralnick (JG700) plasmid. </br> <br> </br>
 +
 
 +
<br><b> August 11th, Saturday </b></br><br> Spencer and Steven checked the nah operon PstI and NotI digest (because yesterday's gel ran weirdly) and their mtrE PCR from the previous day on a gel. Unfortunately, bands did not appear where we expected them to.
 +
</br> <br> </br>
 +
 
</div>
</div>
</div>
</div>

Revision as of 03:08, 4 October 2012

Weekly Update
Daily Details
Both

Wet Lab - August

  • Week 1

    It has been said that astronomy is a humbling and character-building experience. There is perhaps no better demonstration of the folly of human conceits than this distant image of our tiny world. To me, it underscores our responsibility to deal more kindly with one another, and to preserve and cherish the pale blue dot, the only home we've ever known. Daily Details
    Daily Details:
    Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

    Week 2

    It was confirmed that RFP was successfully inserted downstream of mtrB in our arsenic reporter parts in Shewanella. Site-directed mutagenesis of the nah operon failed. We are still trying to insert the nah operon into the mobility backbone (OriT) to prepare for conjugation into Shewanella later on. Daily Details
    Daily Details:

    August 5th, Sunday

    Swati yet again was saddled with a massive number of minipreps , since her magic fingers are able to cast yield-increasing spells on minipreps. She miniprepped: SAL2 from WM3064, p37-41k from JG700 (one arsenic reporter with cut sites flanking the RBS, another arsenic reporter without the cut sites, and three different Anderson series promoters with mRFP1 downstream on a pBBRBB backbone), oriT p29nah_p17c from DH5a, and nah_p31c from DH5a. And indeed her yields were impressive, massive, gargantuan! Good job Sorceress Swati. We will sequence SAL2 and oriT p29nah_p17c to see if we should continue to conjugation, and sequence nah_p31c to see if we can start site-directed mutagenesis to get a biobrick-compatible nah operon on the biobrick backbone. We will sequence or PCR to confirm p37k-p41k's conjugation into Shewanella.



    August 6th, Monday

    Caleb and Dylan amplified the two different arsenic promoters (p37k and p38k) and ran them on a gel alongside p14 and p16 (the arsenic reporters without mRFP1 downstream) to confirm successful insertion of RFP downstream of mtrB in our arsenic reporter parts in Shewenella. Band lengths appeared in expected places. Dylan is worried that we will not be able to use PCR to definitely confirm that p39-41k worked, so we submitted these for sequencing . Unfortunately, sequencing failed, perhaps because random gunk from Shewanella added noise to the process. Tina did a PCR cleanup of the nah operon PCR. Dylan also ran a gel of nah operon PCRs to make sure that there was no mispriming. The gel looked good, so he submitted the PCRs for sequencing.



    August 7th, Tuesday

    JG1531 overnight culture didn't grow. We suspect that the plate Dylan picked from is dead. We'll have to go back to the glycerol stocks if we want to play with mtrE. Dylan set up a continuous flow M4 reactor in morning. Caleb started a liquid culture of MR-1 with which to inoculate the reactor. Checked sequencing results of nah stuff. oriT thing was bad. nah_p31c was good. Caleb and Dylan proceeded with site-directed mutagenesis of nah_p31c, attempting to get rid of the first PstI cutsite in the nah operon. After digestion with DpnI, we purified using the E.Z.N.A. MicroElute kit and quantified. DNA was split into three directions: First, Danielle and Dylan set up another mutagenic PCR using the digestion product as template to get rid of the second internal cut site (we expect lower mutation efficiency because template DNA is not methylated). Second, we transformed DH5a with the mutated plasmid. Third, Danielle and Chie digested both the purified – and hopefully mutated – plasmid and un-mutated plasmid with PstI. Dylan ran these digestions on a gel, along with supercoiled plasmid as a control. Unfortunately, the (hopefully) mutated plasmid never showed up on the gel. In the evening, we didn't observe growth in the MR-1 culture, so Dylan set up another culture just in case Shewanella was dead and not lazy.



    August 8th, Wednesday

    Caleb and Dylan performed another digest to check if the second site-directed mutagenesis (that was supposed to get rid of the second PstI internal cut site within the nah operon) worked. Unfortunately, there wasn't enough DNA to see anything when visualized on a gel. They decided to proceed with electroporation into DH5a just in case - however, to use Caleb's terminology, cells exploded - there were probably too many salts in the solution, which causing arcing and a PBBHTTTZZZ! of cells all over the cuvette. Dylan re-digested p29 nah and oriT p17c to redo a ligation that would allow for conjugation into Shewanella later on. Dylan also re-digested p27 (Anderson series promoter with RFP downstream) and SAL to redo a ligation to create a plasmid with SAL-RFP. Dylan also submitted several samples for sequencing to make sure that three Anderson promoters with RFP downstream in JG700 and SAL2 (the salicylate reporter without the BAMHI cut site) in WN3064 and JG700 were in the correct sequence.



    August 9th, Thursday

    Today Dylan chilled with his mom. Well, he tried to. :) Despite the eternal bonds that bind mother and son, plus the 3 billion miles she flew to see him, he still couldn't resist coming in to lab to open packages! And then got sucked into a long discussion of what had to be done for the rest of the day - scientific endeavors taking him away yet again from filial duties. Swati and Claire bonded over dry ice, and Caleb regaled us with tales of dry ice bombs gone awry. Swati and Caleb miniprepped the first mutagenesis of nah_p31c that had been transformed into DH5a yesterday. They then digested it with PstI-HF to see if the mutation was successful. Unfortunately the mutagenesis failed! We will start over from nah_p31c and lower the annealing temperature at 60degC. The Stratagene kit, which uses PFU ultra, asks for 60degC, but because we are using our own boot-leg protocol with Phusion we did the first try at 65degC, as Phusion usually calls for a higher annealing temperature than the theoretically calculated value. For this second try we will stick to the 60degC suggested by Stratagene and see if we get better results. Also, called NEB to find out if after PCR with Phusion, DpnI will still have activity in the following digestion step in Buffer 4, or if we need to clean up the PCR before digesting with DpnI - they said PCR clean up isn't needed. We also ran digestions for making the nah operon on a backbone with a mobility gene and the salicylate reporter (w/ BamHI cutsite) with RFP downstream. We cut our mobile backbone, OriT in p17c (pSB3C5), with EcoRI and XbaI, while cutting the nah operon (p29nah) with EcoRI and SpeI. The nah operon with mobility gene must be constructed so that we may conjugate into Shewy and start testing our salicylate reporter. The salicylate reporter and p27a (from the Anderson series), with RFP, were cut with SpeI and PstI. The salicylate/RFP part will be used for troubleshooting the salicylate reporter. Digestion products were run on a gel, extracted, and quantified. Swati then dephosphorylated backbones and ligated both parts. Sequencing for p39-41k didn't look good, and neither did the salicylate reporter w/BamHI cutsite miniprepped from JG700. The sequencing for salicylate reporter w/ BamHI in WM3064, however, looked good, suggesting that conjugation may not have been as efficient as we had hoped. After a pow-wow we decided not to sequence more colonies, as we are hoping some may be good, and more importantly that if we use qPCR to get quantitative characterization data, we won't need to use the RFP parts. The plates will stay in the fridge as a back-up plan. In other news: Claire cried because it was difficult to update the notebook with a week's worth of work. Mark's dedication to the notebook is laudable and impressive. Good job team for doing so much! My head can't even comprehend the magnitude of your endeavors.



    August 10th, Friday

    Caleb miniprepped a plasmid with mtrE from JG1531, and just for kicks, miniprepped from the "exploded cells" from August 8th. Suprisingly, he ended up getting decent yields for both, showing that the electroporation worked despite arcing. Caleb then digested the nah operon of the miniprep with PSTI and NotI to check if the mutagenesis was a success. It was run on a gel alongside a PCR of the Anderson series promoters with RFP downstream and SAL2 from Shewanella (to check if SAL2 and the promoters were sucessfully conjugated after sequencing on Monday failed). Unfortunately, bands did not appear where we expected them to. Steven and Spencer performed a PCR to get mtrE out of the Gralnick (JG700) plasmid.



    August 11th, Saturday

    Spencer and Steven checked the nah operon PstI and NotI digest (because yesterday's gel ran weirdly) and their mtrE PCR from the previous day on a gel. Unfortunately, bands did not appear where we expected them to.


    Week 3

    It has been said that astronomy is a humbling and character-building experience. There is perhaps no better demonstration of the folly of human conceits than this distant image of our tiny world. To me, it underscores our responsibility to deal more kindly with one another, and to preserve and cherish the pale blue dot, the only home we've ever known. Daily Details
    Daily Details:
    Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

    Week 4

    It has been said that astronomy is a humbling and character-building experience. There is perhaps no better demonstration of the folly of human conceits than this distant image of our tiny world. To me, it underscores our responsibility to deal more kindly with one another, and to preserve and cherish the pale blue dot, the only home we've ever known. Daily Details
    Daily Details:
    Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

    Week 5

    It has been said that astronomy is a humbling and character-building experience. There is perhaps no better demonstration of the folly of human conceits than this distant image of our tiny world. To me, it underscores our responsibility to deal more kindly with one another, and to preserve and cherish the pale blue dot, the only home we've ever known. Daily Details
    Daily Details:
    Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
  • Week 1

    Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

    Week 2


    August 5th, Sunday

    Swati yet again was saddled with a massive number of minipreps , since her magic fingers are able to cast yield-increasing spells on minipreps. She miniprepped: SAL2 from WM3064, p37-41k from JG700 (one arsenic reporter with cut sites flanking the RBS, another arsenic reporter without the cut sites, and three different Anderson series promoters with mRFP1 downstream on a pBBRBB backbone), oriT p29nah_p17c from DH5a, and nah_p31c from DH5a. And indeed her yields were impressive, massive, gargantuan! Good job Sorceress Swati. We will sequence SAL2 and oriT p29nah_p17c to see if we should continue to conjugation, and sequence nah_p31c to see if we can start site-directed mutagenesis to get a biobrick-compatible nah operon on the biobrick backbone. We will sequence or PCR to confirm p37k-p41k's conjugation into Shewanella.



    August 6th, Monday

    Caleb and Dylan amplified the two different arsenic promoters (p37k and p38k) and ran them on a gel alongside p14 and p16 (the arsenic reporters without mRFP1 downstream) to confirm successful insertion of RFP downstream of mtrB in our arsenic reporter parts in Shewenella. Band lengths appeared in expected places. Dylan is worried that we will not be able to use PCR to definitely confirm that p39-41k worked, so we submitted these for sequencing . Unfortunately, sequencing failed, perhaps because random gunk from Shewanella added noise to the process. Tina did a PCR cleanup of the nah operon PCR. Dylan also ran a gel of nah operon PCRs to make sure that there was no mispriming. The gel looked good, so he submitted the PCRs for sequencing.



    August 7th, Tuesday

    JG1531 overnight culture didn't grow. We suspect that the plate Dylan picked from is dead. We'll have to go back to the glycerol stocks if we want to play with mtrE. Dylan set up a continuous flow M4 reactor in morning. Caleb started a liquid culture of MR-1 with which to inoculate the reactor. Checked sequencing results of nah stuff. oriT thing was bad. nah_p31c was good. Caleb and Dylan proceeded with site-directed mutagenesis of nah_p31c, attempting to get rid of the first PstI cutsite in the nah operon. After digestion with DpnI, we purified using the E.Z.N.A. MicroElute kit and quantified. DNA was split into three directions: First, Danielle and Dylan set up another mutagenic PCR using the digestion product as template to get rid of the second internal cut site (we expect lower mutation efficiency because template DNA is not methylated). Second, we transformed DH5a with the mutated plasmid. Third, Danielle and Chie digested both the purified – and hopefully mutated – plasmid and un-mutated plasmid with PstI. Dylan ran these digestions on a gel, along with supercoiled plasmid as a control. Unfortunately, the (hopefully) mutated plasmid never showed up on the gel. In the evening, we didn't observe growth in the MR-1 culture, so Dylan set up another culture just in case Shewanella was dead and not lazy.



    August 8th, Wednesday

    Caleb and Dylan performed another digest to check if the second site-directed mutagenesis (that was supposed to get rid of the second PstI internal cut site within the nah operon) worked. Unfortunately, there wasn't enough DNA to see anything when visualized on a gel. They decided to proceed with electroporation into DH5a just in case - however, to use Caleb's terminology, cells exploded - there were probably too many salts in the solution, which causing arcing and a PBBHTTTZZZ! of cells all over the cuvette. Dylan re-digested p29 nah and oriT p17c to redo a ligation that would allow for conjugation into Shewanella later on. Dylan also re-digested p27 (Anderson series promoter with RFP downstream) and SAL to redo a ligation to create a plasmid with SAL-RFP. Dylan also submitted several samples for sequencing to make sure that three Anderson promoters with RFP downstream in JG700 and SAL2 (the salicylate reporter without the BAMHI cut site) in WN3064 and JG700 were in the correct sequence.



    August 9th, Thursday

    Today Dylan chilled with his mom. Well, he tried to. :) Despite the eternal bonds that bind mother and son, plus the 3 billion miles she flew to see him, he still couldn't resist coming in to lab to open packages! And then got sucked into a long discussion of what had to be done for the rest of the day - scientific endeavors taking him away yet again from filial duties. Swati and Claire bonded over dry ice, and Caleb regaled us with tales of dry ice bombs gone awry. Swati and Caleb miniprepped the first mutagenesis of nah_p31c that had been transformed into DH5a yesterday. They then digested it with PstI-HF to see if the mutation was successful. Unfortunately the mutagenesis failed! We will start over from nah_p31c and lower the annealing temperature at 60degC. The Stratagene kit, which uses PFU ultra, asks for 60degC, but because we are using our own boot-leg protocol with Phusion we did the first try at 65degC, as Phusion usually calls for a higher annealing temperature than the theoretically calculated value. For this second try we will stick to the 60degC suggested by Stratagene and see if we get better results. Also, called NEB to find out if after PCR with Phusion, DpnI will still have activity in the following digestion step in Buffer 4, or if we need to clean up the PCR before digesting with DpnI - they said PCR clean up isn't needed. We also ran digestions for making the nah operon on a backbone with a mobility gene and the salicylate reporter (w/ BamHI cutsite) with RFP downstream. We cut our mobile backbone, OriT in p17c (pSB3C5), with EcoRI and XbaI, while cutting the nah operon (p29nah) with EcoRI and SpeI. The nah operon with mobility gene must be constructed so that we may conjugate into Shewy and start testing our salicylate reporter. The salicylate reporter and p27a (from the Anderson series), with RFP, were cut with SpeI and PstI. The salicylate/RFP part will be used for troubleshooting the salicylate reporter. Digestion products were run on a gel, extracted, and quantified. Swati then dephosphorylated backbones and ligated both parts. Sequencing for p39-41k didn't look good, and neither did the salicylate reporter w/BamHI cutsite miniprepped from JG700. The sequencing for salicylate reporter w/ BamHI in WM3064, however, looked good, suggesting that conjugation may not have been as efficient as we had hoped. After a pow-wow we decided not to sequence more colonies, as we are hoping some may be good, and more importantly that if we use qPCR to get quantitative characterization data, we won't need to use the RFP parts. The plates will stay in the fridge as a back-up plan. In other news: Claire cried because it was difficult to update the notebook with a week's worth of work. Mark's dedication to the notebook is laudable and impressive. Good job team for doing so much! My head can't even comprehend the magnitude of your endeavors.



    August 10th, Friday

    Caleb miniprepped a plasmid with mtrE from JG1531, and just for kicks, miniprepped from the "exploded cells" from August 8th. Suprisingly, he ended up getting decent yields for both, showing that the electroporation worked despite arcing. Caleb then digested the nah operon of the miniprep with PSTI and NotI to check if the mutagenesis was a success. It was run on a gel alongside a PCR of the Anderson series promoters with RFP downstream and SAL2 from Shewanella (to check if SAL2 and the promoters were sucessfully conjugated after sequencing on Monday failed). Unfortunately, bands did not appear where we expected them to. Steven and Spencer performed a PCR to get mtrE out of the Gralnick (JG700) plasmid.



    August 11th, Saturday

    Spencer and Steven checked the nah operon PstI and NotI digest (because yesterday's gel ran weirdly) and their mtrE PCR from the previous day on a gel. Unfortunately, bands did not appear where we expected them to.


    Week 3

    Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

    Week 4

    Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

    Week 5

    Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
  • Week 1

    It has been said that astronomy is a humbling and character-building experience. There is perhaps no better demonstration of the folly of human conceits than this distant image of our tiny world. To me, it underscores our responsibility to deal more kindly with one another, and to preserve and cherish the pale blue dot, the only home we've ever known.
    Daily Details:
    Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

    Week 2

    It was confirmed that RFP was successfully inserted downstream of mtrB in our arsenic reporter parts in Shewanella. Site-directed mutagenesis of the nah operon failed. We are still trying to insert the nah operon into the mobility backbone (OriT) to prepare for conjugation into Shewanella later on.
    Daily Details:

    August 5th, Sunday

    Swati yet again was saddled with a massive number of minipreps , since her magic fingers are able to cast yield-increasing spells on minipreps. She miniprepped: SAL2 from WM3064, p37-41k from JG700 (one arsenic reporter with cut sites flanking the RBS, another arsenic reporter without the cut sites, and three different Anderson series promoters with mRFP1 downstream on a pBBRBB backbone), oriT p29nah_p17c from DH5a, and nah_p31c from DH5a. And indeed her yields were impressive, massive, gargantuan! Good job Sorceress Swati. We will sequence SAL2 and oriT p29nah_p17c to see if we should continue to conjugation, and sequence nah_p31c to see if we can start site-directed mutagenesis to get a biobrick-compatible nah operon on the biobrick backbone. We will sequence or PCR to confirm p37k-p41k's conjugation into Shewanella.



    August 6th, Monday

    Caleb and Dylan amplified the two different arsenic promoters (p37k and p38k) and ran them on a gel alongside p14 and p16 (the arsenic reporters without mRFP1 downstream) to confirm successful insertion of RFP downstream of mtrB in our arsenic reporter parts in Shewenella. Band lengths appeared in expected places. Dylan is worried that we will not be able to use PCR to definitely confirm that p39-41k worked, so we submitted these for sequencing . Unfortunately, sequencing failed, perhaps because random gunk from Shewanella added noise to the process. Tina did a PCR cleanup of the nah operon PCR. Dylan also ran a gel of nah operon PCRs to make sure that there was no mispriming. The gel looked good, so he submitted the PCRs for sequencing.



    August 7th, Tuesday

    JG1531 overnight culture didn't grow. We suspect that the plate Dylan picked from is dead. We'll have to go back to the glycerol stocks if we want to play with mtrE. Dylan set up a continuous flow M4 reactor in morning. Caleb started a liquid culture of MR-1 with which to inoculate the reactor. Checked sequencing results of nah stuff. oriT thing was bad. nah_p31c was good. Caleb and Dylan proceeded with site-directed mutagenesis of nah_p31c, attempting to get rid of the first PstI cutsite in the nah operon. After digestion with DpnI, we purified using the E.Z.N.A. MicroElute kit and quantified. DNA was split into three directions: First, Danielle and Dylan set up another mutagenic PCR using the digestion product as template to get rid of the second internal cut site (we expect lower mutation efficiency because template DNA is not methylated). Second, we transformed DH5a with the mutated plasmid. Third, Danielle and Chie digested both the purified – and hopefully mutated – plasmid and un-mutated plasmid with PstI. Dylan ran these digestions on a gel, along with supercoiled plasmid as a control. Unfortunately, the (hopefully) mutated plasmid never showed up on the gel. In the evening, we didn't observe growth in the MR-1 culture, so Dylan set up another culture just in case Shewanella was dead and not lazy.



    August 8th, Wednesday

    Caleb and Dylan performed another digest to check if the second site-directed mutagenesis (that was supposed to get rid of the second PstI internal cut site within the nah operon) worked. Unfortunately, there wasn't enough DNA to see anything when visualized on a gel. They decided to proceed with electroporation into DH5a just in case - however, to use Caleb's terminology, cells exploded - there were probably too many salts in the solution, which causing arcing and a PBBHTTTZZZ! of cells all over the cuvette. Dylan re-digested p29 nah and oriT p17c to redo a ligation that would allow for conjugation into Shewanella later on. Dylan also re-digested p27 (Anderson series promoter with RFP downstream) and SAL to redo a ligation to create a plasmid with SAL-RFP. Dylan also submitted several samples for sequencing to make sure that three Anderson promoters with RFP downstream in JG700 and SAL2 (the salicylate reporter without the BAMHI cut site) in WN3064 and JG700 were in the correct sequence.



    August 9th, Thursday

    Today Dylan chilled with his mom. Well, he tried to. :) Despite the eternal bonds that bind mother and son, plus the 3 billion miles she flew to see him, he still couldn't resist coming in to lab to open packages! And then got sucked into a long discussion of what had to be done for the rest of the day - scientific endeavors taking him away yet again from filial duties. Swati and Claire bonded over dry ice, and Caleb regaled us with tales of dry ice bombs gone awry. Swati and Caleb miniprepped the first mutagenesis of nah_p31c that had been transformed into DH5a yesterday. They then digested it with PstI-HF to see if the mutation was successful. Unfortunately the mutagenesis failed! We will start over from nah_p31c and lower the annealing temperature at 60degC. The Stratagene kit, which uses PFU ultra, asks for 60degC, but because we are using our own boot-leg protocol with Phusion we did the first try at 65degC, as Phusion usually calls for a higher annealing temperature than the theoretically calculated value. For this second try we will stick to the 60degC suggested by Stratagene and see if we get better results. Also, called NEB to find out if after PCR with Phusion, DpnI will still have activity in the following digestion step in Buffer 4, or if we need to clean up the PCR before digesting with DpnI - they said PCR clean up isn't needed. We also ran digestions for making the nah operon on a backbone with a mobility gene and the salicylate reporter (w/ BamHI cutsite) with RFP downstream. We cut our mobile backbone, OriT in p17c (pSB3C5), with EcoRI and XbaI, while cutting the nah operon (p29nah) with EcoRI and SpeI. The nah operon with mobility gene must be constructed so that we may conjugate into Shewy and start testing our salicylate reporter. The salicylate reporter and p27a (from the Anderson series), with RFP, were cut with SpeI and PstI. The salicylate/RFP part will be used for troubleshooting the salicylate reporter. Digestion products were run on a gel, extracted, and quantified. Swati then dephosphorylated backbones and ligated both parts. Sequencing for p39-41k didn't look good, and neither did the salicylate reporter w/BamHI cutsite miniprepped from JG700. The sequencing for salicylate reporter w/ BamHI in WM3064, however, looked good, suggesting that conjugation may not have been as efficient as we had hoped. After a pow-wow we decided not to sequence more colonies, as we are hoping some may be good, and more importantly that if we use qPCR to get quantitative characterization data, we won't need to use the RFP parts. The plates will stay in the fridge as a back-up plan. In other news: Claire cried because it was difficult to update the notebook with a week's worth of work. Mark's dedication to the notebook is laudable and impressive. Good job team for doing so much! My head can't even comprehend the magnitude of your endeavors.



    August 10th, Friday

    Caleb miniprepped a plasmid with mtrE from JG1531, and just for kicks, miniprepped from the "exploded cells" from August 8th. Suprisingly, he ended up getting decent yields for both, showing that the electroporation worked despite arcing. Caleb then digested the nah operon of the miniprep with PSTI and NotI to check if the mutagenesis was a success. It was run on a gel alongside a PCR of the Anderson series promoters with RFP downstream and SAL2 from Shewanella (to check if SAL2 and the promoters were sucessfully conjugated after sequencing on Monday failed). Unfortunately, bands did not appear where we expected them to. Steven and Spencer performed a PCR to get mtrE out of the Gralnick (JG700) plasmid.



    August 11th, Saturday

    Spencer and Steven checked the nah operon PstI and NotI digest (because yesterday's gel ran weirdly) and their mtrE PCR from the previous day on a gel. Unfortunately, bands did not appear where we expected them to.


    Week 3

    It has been said that astronomy is a humbling and character-building experience. There is perhaps no better demonstration of the folly of human conceits than this distant image of our tiny world. To me, it underscores our responsibility to deal more kindly with one another, and to preserve and cherish the pale blue dot, the only home we've ever known.
    Daily Details:
    Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

    Week 4

    It has been said that astronomy is a humbling and character-building experience. There is perhaps no better demonstration of the folly of human conceits than this distant image of our tiny world. To me, it underscores our responsibility to deal more kindly with one another, and to preserve and cherish the pale blue dot, the only home we've ever known.
    Daily Details:
    Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

    Week 5

    It has been said that astronomy is a humbling and character-building experience. There is perhaps no better demonstration of the folly of human conceits than this distant image of our tiny world. To me, it underscores our responsibility to deal more kindly with one another, and to preserve and cherish the pale blue dot, the only home we've ever known.
    Daily Details:
    Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.