Team:British Columbia/Notebook/Labbook
From 2014.igem.org
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<a href="#oct_w2">Week 2</a><br> | <a href="#oct_w2">Week 2</a><br> | ||
<a href="#oct_w3">Week 3</a><br> | <a href="#oct_w3">Week 3</a><br> | ||
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<div id="collapseTwo" class="panel-collapse collapse"> | <div id="collapseTwo" class="panel-collapse collapse"> | ||
<div class="panel-body"> | <div class="panel-body"> | ||
- | <h4> | + | <h4>August</h4> |
- | <a href="# | + | <a href="#b_aug_w3">Week 3</a><br> |
- | <a href="# | + | <a href="#b_aug_w4">Week 4</a><br> |
+ | <h4>September</h4> | ||
+ | <a href="#b_sept_w1">Week 1</a><br> | ||
+ | <a href="#b_sept_w2">Week 2</a><br> | ||
+ | <a href="#b_sept_w3">Week 3</a><br> | ||
+ | <a href="#b_sept_w4">Week 4</a><br> | ||
</div> | </div> | ||
</div> | </div> | ||
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</div> | </div> | ||
- | <!-- =============== LAB NOTE BOOK STARTS ======================== --> | + | <!-- =============== ORTHOGONAL LAB NOTE BOOK STARTS ======================== --> |
<div class="col-md-8"> | <div class="col-md-8"> | ||
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</p> | </p> | ||
- | <h1 id=" | + | <h1 id="oct_w2"> October - Week 2 </h1> |
<h3> October 4th </h3> | <h3> October 4th </h3> | ||
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</p> | </p> | ||
- | <h1 id=" | + | <h1 id="oct_w3"> October - Week 3 </h1> |
<h3> October 14th </h3> | <h3> October 14th </h3> | ||
<p> | <p> | ||
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</p> | </p> | ||
- | |||
- | |||
- | |||
+ | <!-- ==== THIS IS WHERE BIOMINING STARTS ============= --> | ||
- | < | + | <h1 id="b_aug_w3"> August - Week 3</h1> |
+ | <h3> August 20th </h3> | ||
+ | <p> | ||
+ | <b> Experimenter </b>: Anna Müller, Joe Ho | ||
+ | </p><p> | ||
+ | <b> Aim </b>: Phosphorylate metal binding DNA sequence from Dunbar lab using Oligonucleotide Phosphorylation protocol prior to ligation. Double digest RsaA with PstI and BglII. | ||
+ | </p><p> | ||
+ | <b> Results </b>: NA. | ||
+ | </p> | ||
+ | <h3> August 22th </h3> | ||
+ | <p> | ||
+ | <b> Experimenter </b>: Anna Müller, Joe Ho | ||
+ | </p><p> | ||
+ | <b> Aim </b>: Ligate metal binding DNA sequence into RsaA expression vector. | ||
+ | </p><p> | ||
+ | <b> Results </b>: NA. | ||
+ | </p> | ||
+ | <h1 id="b_aug_w4"> August - Week 4</h1> | ||
- | + | <h3> August 27th </h3> | |
+ | <p> | ||
+ | <b> Experimenter </b>: Anna Müller, Joe Ho | ||
+ | </p><p> | ||
+ | <b> Aim </b>: Make electrocompetent Caulobacter cells using the electrocompetent cell production protocol. | ||
+ | </p><p> | ||
+ | <b> Results </b>: NA. | ||
+ | </p> | ||
- | </ | + | <h1 id="b_sept_w1"> September - Week 1</h1> |
+ | <h3> September 2nd </h3> | ||
+ | <p> | ||
+ | <b> Experimenter </b>: Anna Müller, Joe Ho | ||
+ | </p><p> | ||
+ | <b> Aim </b>: Transform expression vector into electrocompetent Caulobacter cells. | ||
+ | </p><p> | ||
+ | <b> Results </b>: Colonies successfully grew on PYE plate with chloramphenicol. | ||
+ | </p> | ||
+ | <h3> September 5th </h3> | ||
+ | <p> | ||
+ | <b> Experimenter </b>: Anna Müller, Joe Ho | ||
+ | </p><p> | ||
+ | <b> Aim </b>: Pick colonies and inoculate into PYE media | ||
+ | </p><p> | ||
+ | <b> Results </b>: NA. | ||
+ | </p> | ||
- | < | + | <h3> September 6th </h3> |
- | + | <p> | |
+ | <b> Experimenter </b>: Anna Müller, Joe Ho | ||
+ | </p><p> | ||
+ | <b> Aim </b>: Miniprep Caulobacter culture and send the plasmid for sequencing. | ||
+ | </p><p> | ||
+ | <b> Results </b>: NA. | ||
+ | </p> | ||
- | + | <h1 id="b_sept_w2"> September - Week 2</h1> | |
+ | <h3> September 10th </h3> | ||
+ | <p> | ||
+ | <b> Experimenter </b>: Anna Müller, Joe Ho | ||
+ | </p><p> | ||
+ | <b> Aim </b>: Miniprep Caulobacter culture and send the plasmid for sequencing. | ||
+ | </p><p> | ||
+ | <b> Results </b>: NA. | ||
+ | </p> | ||
+ | <h1 id="b_sept_w3"> September - Week 3</h1> | ||
- | + | <h3> September 15th </h3> | |
- | + | <p> | |
- | + | <b> Experimenter </b>: Anna Müller, Joe Ho | |
- | + | </p><p> | |
- | + | <b> Aim </b>: Analyse sequencing results | |
+ | </p><p> | ||
+ | <b> Results </b>: Sequencing result was positive. The metal binding DNA sequencing was successfully inserted into RsaA expression vector. | ||
+ | </p> | ||
- | + | <h3> September 18th </h3> | |
- | </ | + | <p> |
+ | <b> Experimenter </b>: Anna Müller, Joe Ho | ||
+ | </p><p> | ||
+ | <b> Aim </b>: To test effect of fucose on binding affinity to chalcopyrite by doing biopanning assay of fucose knockout and WT Caulobacter. | ||
+ | </p><p> | ||
+ | <b> Results </b>: There was no binding observed in fucose knockout and non-specific binding in WT Caulobacter. See Biomining results – Figure 8. | ||
+ | </p> | ||
+ | <h1 id="b_sept_w4"> September - Week 4</h1> | ||
+ | <h3> September 20th </h3> | ||
+ | <p> | ||
+ | <b> Experimenter </b>: Anna Müller, Joe Ho | ||
+ | </p><p> | ||
+ | <b> Aim </b>: Transform recombinant RsaA expression vector into fucose knockout Caulobacter cells. | ||
+ | </p><p> | ||
+ | <b> Results </b>: NA. | ||
+ | </p> | ||
+ | <h3> September 26th </h3> | ||
+ | <p> | ||
+ | <b> Experimenter </b>: Anna Müller, Joe Ho | ||
+ | </p><p> | ||
+ | <b> Aim </b>: Perform biomining assay on fucose knockout Caulobacter with recombinant RsaA expression vector to see if the presence of expression vector improves the binding efficiency. | ||
+ | </p><p> | ||
+ | <b> Results </b>: See Biomining results – Figure 9. | ||
+ | </p> | ||
+ | |||
+ | |||
+ | |||
+ | </div> | ||
+ | <!-- ========================== BIOMINING LAB NOTEBOOK ENDS ============================== --> | ||
+ | |||
+ | </div> | ||
+ | |||
+ | <a href="#top" class="scrollup"> | ||
+ | <img src="https://static.igem.org/mediawiki/parts/0/01/Arrow_up_2x.png"> | ||
+ | |||
+ | |||
+ | |||
+ | </div> | ||
+ | |||
+ | </div> | ||
Latest revision as of 03:57, 18 October 2014
June - Week 3
June 19th
Experimenter : Dan Korvin, Wenchen Zhao, Zeki Ekmekci
Aim : Amplify T7 RNA polymerase gene (RNAP) from T7 bacteriophage genome and terminator from part BBa_B0015 by PCR.
Result : PCR was successful. Target bands were seen on the agarose gel.
June - Week 4
June 23th
Experimenter : Zeki Ekmekci, Wenchen Zhao, Dan Korvin
Aim : Amplify T7 DNA polymerase (DNAP), primase/helicase (P/H), single strand binding protein (SSBP) genes from T7 bacteriophage genome by PCR. Digest terminator with EcoRI (E) and XbaI (X). Digest RNAP with E and SpeI (S).
Results : NA.
June 24th
Experimenter : Ariel Ragetli, Zeki Ekmekci
Aim : Verify DNAP, P/H, SSBP genes on agarose gel. Digest DNAP, P/H, SSBP amplicons with E and S. Ligate each digested T7 gene to digested terminator vector.
Results : DNAP, P/H, SSBP genes successfully amplified, but non-trivial amount of side products (mostly primer-dimer) appeared in DNAP and P/H lanes. Four T7 genes all digested and ligated with terminator.
June 28th
Experimenter : Wenchen Zhao
Aim : Verify the ligation results on agarose gel.
Results : Multiple bands observed (non-trivial amount of side products). Target SSBP+terminator fragment with distinctive amount observed (only one lane with decent result).
June 29th
Experimenter : Jeffrey Pea
Aim : Amplify the target gene/terminator ligated sequence using four different forward primers and same VF reversed primer. Verify the PCR products on a gel.
Results : No significant bands we were looking for observed on the gel.
June 30th
Experimenter : Tudor Lapuste
Aim : Amplify four T7 genes and terminator gene by PCR. Digest four genes using E and S.
Results : SSBP, DNAP and RNAP were amplified successfully. P/H and terminator PCR failed. PCR for P/H and terminator set up.
July - Week 1
July 2nd
Experimenter : Dan Korvin
Aim : Verify P/H + terminator PCR products on agarose gel.
Results : PCR failed for both. More PCR set up for primase/helicase.
July 3rd
Experimenter : Ariel Ragetli, Jeffrey Pea, Zeki Ekmekci
Aim : Verify PCR products for P/H on agarose gel. Amplify terminator by gradient PCR. Transform E.coli cells with terminator-containing plasmid.
Results : Terminator and P/H genes amplified.
July 4th
Experimenter : Dan Korvin
Aim : Digest terminator with E and X. Run PCR products of all four T7 genes on a gel, followed by gel extraction and purification.
Results : NA
July - Week 2
July 6th
Experimenter : Zeki Ekmekci, Wenchen Zhao, Jeffrey Pea
Aim : Double digest all four T7 genes with E and S. Run digested T7 genes and terminator on a gel, followed by gel extraction and purification. Ligate T7 genes with terminator. Transform all four constructs to E.coli
Results : NA
July - Week 3
July 10th
Experimenter : Wenchen Zhao, Zeki Ekmekci
Aim : Verify constructs by colony PCR.
Results : Colony PCR failed. No bands were observed.
July 17th
Experimenter : Jeffrey Pea
Aim : Double digest terminator plasmid with E and X. Ligate digested T7 genes to terminator. Transformed four constructs to E.coli
Results : NA
July - Week 4
July 20th
Experimenter : Tudor Lapuste
Aim : Verify constructs by colony PCR.
Results : SSBP and RNAP constructs (gene + terminator) confirmed.
July 24th
Experimenter : Ariel Ragetli, Jeffrey Pea
Aim : Re-amplify DNAP and P/H by PCR followed by gel check. Ligate two digested amplicons to digested terminator. Transform two constructs into E.coli.
Results : DNAP and P/H were successfully amplified.
August - Week 1
August 1st
Experimenter : Wenchen Zhao, Dan Korvin, Zeki Ekmekci
Aim : Verify DNAP and P/H constructs by colony PCR. Digest SSBP and RNAP constructs with E and S. Digest the plasmid containing Pbad promoter and RBS with E and X. Transform the ligation products to E.coli.
Results : Colony PCR failed.
August 6th
Experimenter : Wenchen Zhao, Jeffrey Pea, Zeki Ekmekci
Aim : Verify DNAP and P/H constructs (gene+terminator), SSBP and RNAP constructs (gene+terminator+RBS+promoter) using colony PCR.
Results : P/H and DNAP constructs confirmed. Bands with correct size were found on the gel after colony PCR of SSBP and RNAP constructs.
August - Week 2
August 12th
Experimenter : Wenchen Zhao, Zeki Ekmekci
Aim : Prepare SSBP and RNAP miniprep products and send them for sequencing. Double digest P/H and DNAP constructs with E and S. Ligate digested constructs into vector digested with E and X. Transform ligation products into E.coli.
Results : NA.
August - Week 3
August 19th
Experimenter : Ariel Ragetli, Zeki Ekmekci
Aim : Verify P/H and DNAP constructs using colony PCR. Analyze sequencing results of SSBP and RNAP complete constructs.
Results : Sequencing results are negative – no Pbad promoter/RBS found in SSBP and RNAP constructs. Colony PCR result was also negative.
September - Week 1
September 4th
Experimenter : Dan Korvin, Wenchen Zhao
Aim : Double digest DNAP, RNAP and SSBP constructs with X and PstI (P). Ligate three digested genes into RBS + Pbad Promoter plasmid digested with S and P. Miniprep P/H construct.
Results : NA.
September 5th
Experimenter : Wenchen Zhao
Aim : Transform all three constructs into E.coli. Site-directed mutagenize P/H construct and transform into E.coli.
Results : NA.
September 6th
Experimenter : Anna Müller
Aim : Verify DNAP, RNAP and SSBP constructs by colony PCR.
Results : Bands with correct size observed, need to send to sequencing for further verification.
September - Week 2
September 8th
Experimenter : Anna Müller
Aim : Miniprep all cultures including SDM P/H construct with terminator and complete DNAP, RNAP and SSBP constructs
Results : NA
September 9th
Experimenter : Wenchen Zhao, Zeki Ekmekci
Aim : Send DNAP, RNAP, SSBP constructs for sequencing. Double digest P/H constructs with X and P, followed by gel check. Double digest RNAP with E and X.
Results : Gel check result was negative. No target band was observed. P/H was not mutagenized.
September 10th
Experimenter : Ariel Ragetli, Jeffrey Pea
Aim : Double digest SSBP with E and S. Double digest RNAP with E and X, followed by gel check and extraction. Ligate digested SSBP into digested RNAP vector. Transform ligation product into E.coli.
Results : NA.
September - Week 3
September 15th
Experimenter : Wenchen Zhao
Aim : Colony PCR SSBP + RNAP construct. Repeat SDM of P/H construct.
Results : Colony PCR failed.
September 16th
Experimenter : Wenchen Zhao
Aim : Re-run colony PCR of SSBP and RNAP construct.
Results : Colony PCR result was positive.
September 17th
Experimenter : Wenchen Zhao
Aim : Miniprep SSBP + RNAP construct, double digest with E and S. Double digest DNAP with E and X, followed by gel verification and extraction. Ligate digested DNAP with digested SSBP + RNAP construct. Transform SDM P/H plasmid.
Results : NA.
September 18th
Experimenter : Wenchen Zhao
Aim : Colony PCR SDM P/H. Double digest P/H with X and P.
Results : Colony PCR failed.
September 19th
Experimenter : Wenchen Zhao
Aim : Repeat colony PCR of SDM P/H. Miniprep DNAP, RNAP for sequencing.
Results : Colony PCR results were positive.
September - Week 4
September 21st
Experimenter : Zeki Ekmekci
Aim : Double digest 3-gene assembly with E and P. Double digest SDM P/H with X and P. Ligate digested P/H to digested RBS plasmid. Transform ligation product to E.coli.
Results : NA.
September 23rd
Experimenter : Wenchen Zhao
Aim : Colony PCR P/H construct followed by gel check.
Results : Colony PCR result was positive.
September 24th
Experimenter : Wenchen Zhao
Aim : Analyze sequencing results for DNAP, SSBP and RNAP constructs. Miniprep SDM P/H and send it for sequencing.
Results : Sequencing results were positive. DNAP, SSBP and RNAP constructs were successfully assembled.
October - Week 1
October 1st
Experimenter : Wenchen Zhao
Aim : Analyze sequencing results for P/H construct. Digest P/H with E and S and digest 3-gene assembly with E and X. Ligate double digest P/H into double digested 3-gene vector. Transform the ligation product to E.coli.
Results : Sequencing result was negative. Pbad romoter/RBS was not present in the sequence. But XbaI restriction site was successfully mutated.
October 2nd
Experimenter : Wenchen Zhao
Aim : Double digest SDM P/H with X and P. Double digest promoter/RBS plasmid with S and P. Ligate digested P/H into digested promoter/RBS plasmid. Transform the ligation product into E.coli.
Results : NA
October 3rd
Experimenter : Wenchen Zhao
Aim : Verify P/H constructs by colony PCR.
Results : Colony PCR result was positive. Target band was observed on the gel.
October - Week 2
October 4th
Experimenter : Ariel Ragetli
Aim : Verify P/H constructs by colony PCR.
Results : Colony PCR result was positive. Target band was observed on the gel.
October 7th
Experimenter : Jeffrey Pea
Aim : Miniprep P/H plasmid and send it for sequencing.
Results : NA
October 8th
Experimenter : Jeffrey Pea
Aim : Double digest P/H with E and X. Double digest 3-gene assembly with E and S. Ligate digested P/H into digested 3-gene assembly. Transform the ligation product to E.coli.
Results : NA
October 9th
Experimenter : Jeffrey Pea
Aim : Verify 4-gene assembly by colony PCR followed by PCR.
Results : Colony PCR result was positive. 4-gene construct was assembled.
October 10th
Experimenter : Wenchen Zhao
Aim : Analyze sequencing result for P/H plasmid.
Results : Sequencing result was negative. There was a ~200bp deletion in the middle of P/H gene. Also there was a 2bp deletion at the beginning of the gene, causing a frameshift mutation
October - Week 3
October 14th
Experimenter : Wenchen Zhao
Aim : Verify protein expression of 4-gene assembly on SDS-PAGE.
Results : DNAP and SSBP protein was successfully expressed. P/H expression was not detected likely due to the mutation. RNAP expression was also not detected.
August - Week 3
August 20th
Experimenter : Anna Müller, Joe Ho
Aim : Phosphorylate metal binding DNA sequence from Dunbar lab using Oligonucleotide Phosphorylation protocol prior to ligation. Double digest RsaA with PstI and BglII.
Results : NA.
August 22th
Experimenter : Anna Müller, Joe Ho
Aim : Ligate metal binding DNA sequence into RsaA expression vector.
Results : NA.
August - Week 4
August 27th
Experimenter : Anna Müller, Joe Ho
Aim : Make electrocompetent Caulobacter cells using the electrocompetent cell production protocol.
Results : NA.
September - Week 1
September 2nd
Experimenter : Anna Müller, Joe Ho
Aim : Transform expression vector into electrocompetent Caulobacter cells.
Results : Colonies successfully grew on PYE plate with chloramphenicol.
September 5th
Experimenter : Anna Müller, Joe Ho
Aim : Pick colonies and inoculate into PYE media
Results : NA.
September 6th
Experimenter : Anna Müller, Joe Ho
Aim : Miniprep Caulobacter culture and send the plasmid for sequencing.
Results : NA.
September - Week 2
September 10th
Experimenter : Anna Müller, Joe Ho
Aim : Miniprep Caulobacter culture and send the plasmid for sequencing.
Results : NA.
September - Week 3
September 15th
Experimenter : Anna Müller, Joe Ho
Aim : Analyse sequencing results
Results : Sequencing result was positive. The metal binding DNA sequencing was successfully inserted into RsaA expression vector.
September 18th
Experimenter : Anna Müller, Joe Ho
Aim : To test effect of fucose on binding affinity to chalcopyrite by doing biopanning assay of fucose knockout and WT Caulobacter.
Results : There was no binding observed in fucose knockout and non-specific binding in WT Caulobacter. See Biomining results – Figure 8.
September - Week 4
September 20th
Experimenter : Anna Müller, Joe Ho
Aim : Transform recombinant RsaA expression vector into fucose knockout Caulobacter cells.
Results : NA.
September 26th
Experimenter : Anna Müller, Joe Ho
Aim : Perform biomining assay on fucose knockout Caulobacter with recombinant RsaA expression vector to see if the presence of expression vector improves the binding efficiency.
Results : See Biomining results – Figure 9.
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