Template:Team:Uppsala/JS/notebook

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ds = '<div id="dairy-text"><h1>Friday 2013-07-05</h1> Name of participants: Kristoffer L, Emil M, Marcus H, Karl H, Peter C, Ken B.-A., Christoffer Ahlström (CA), Anton Berglund (AB), Stephanie Herman (SH), Mikael Strandgren (MS), Viktor Blomkvist (VB), Nafisa Bashir (NB), Magnus, Thorsteinn, Alexander, Nils, Christoffer <h2>Ongoing constructs:</h2> 15. pSB4K5-RBS-TAL-Linker-Zif268-RBS-4cl-Linker-PBSII-STS-OMT 43. pSB1C3-B0034-TAL 44. pSB1C3-B0034-His-TAL 45. pSB1C3-B0034-4CL 46. pSB1C3-B0034-His-4CL 47. pSB1C3-B0034-STS 61. pSB1C3-CP1 62. pSB1C3-CP8 63. pSB1C3-CP11 64. pSB1C3-CP29 65. pSB1C3-CP30 66. pSB1C3-CP41 67. pSB1C3-CP44 57. pSB1C3-B0034-Idi 58. pSB1C3-B0034-ispA L. reuteri Lb4. 100-23 no plasmid Lb12. DSM 20016 no plasmid L. plantarum: Lb10. 256 no plasmid Lb11. 36E no plasmid L. thermophilus: Lb19. L.thermophilus Todays work Screening PCR & gel analysis of constructs: 43. pSB1C3-B0034-TAL 44. pSB1C3-B0034-His-TAL 45. pSB1C3-B0034-4CL 46. pSB1C3-B0034-His-4CL 47. pSB1C3-B0034-STS 61.1 pSB1C3-CP1 61.2 pSB1C3-CP1 62.1 pSB1C3-CP8 62.2 pSB1C3-CP8 62.3 pSB1C3-CP8 62.4 pSB1C3-CP8 63.1 pSB1C3-CP11 63.2 pSB1C3-CP11 63.3 pSB1C3-CP11 63.4 pSB1C3-CP11 64.1.1 pSB1C3-CP29 64.1.2 pSB1C3-CP29 64.1.3 pSB1C3-CP29 64.1.4 pSB1C3-CP29 65.1.1 pSB1C3-CP30 65.1.2 pSB1C3-CP30 65.2.1 pSB1C3-CP30 65.2.2 pSB1C3-CP30 66.5 pSB1C3-CP41 66.6 pSB1C3-CP41 66.7 pSB1C3-CP41 66.8 pSB1C3-CP41 67.1.1 pSB1C3-CP44 67.1.2 pSB1C3-CP44 67.2.1 pSB1C3-CP44 67.2.2 pSB1C3-CP44 Plasmid prep & glycerol stock: 48. pSB1C3-B0034-His-STS O/N: 57. pSB1C3-B0034-Idi 58. pSB1C3-B0034-ispA 61. pSB1C3-CP1 62. pSB1C3-CP8 63. pSB1C3-CP11 64. pSB1C3-CP29 65. pSB1C3-CP30 66. pSB1C3-CP41 67. pSB1C3-Cp44 47.(9, 20) pSB1C3-B0034-STS Lb4. reuteri 100-23 no plasmid Lb10. plantarum 256 no plasmid Lb11. plantarum 36E no plasmid Lb12. reuteri DSM 20016 no plasmid Re-streaks: Lb19. L.thermophilus <h2>Results</h2> The O/N on 42. pSB4S15-red was done improperly in 15 ml falcon tubes and the lids were screwed on too tightly. A new O/N was done on 42. pSB4S15-red by NB. PCR screen and gel electrophoresis: 61.1 pSB1C3-CP1 61.2 pSB1C3-CP1 62.1 pSB1C3-CP8 62.2 pSB1C3-CP8 62.3 pSB1C3-CP8 62.4 pSB1C3-CP8 63.1 pSB1C3-CP11 63.2 pSB1C3-CP11 63.3 pSB1C3-CP11 63.4 pSB1C3-CP11 64.1.1 pSB1C3-CP29 64.1.2 pSB1C3-CP29 64.1.3 pSB1C3-CP29 64.1.4 pSB1C3-CP29 65.1.1 pSB1C3-CP30 65.1.2 pSB1C3-CP30 65.2.1 pSB1C3-CP30 65.2.2 pSB1C3-CP30 66.5 pSB1C3-CP41 66.6 pSB1C3-CP41 66.7 pSB1C3-CP41 66.8 pSB1C3-CP41 67.1.1 pSB1C3-CP44 67.1.2 pSB1C3-CP44 67.2.1 pSB1C3-CP44 67.2.2 pSB1C3-CP44 *The gel only showed smudgy bands. succesful 47.9 pSB1C3-B0034-STS 47.20 pSB1C3-B0034-STS failed 43. pSB1C3-B0034-TAL 46. pSB1C3-B0034-His-4CL No contamination in negative control -_- Religation from yesterday failed. No colonies, only a few at 76, both red and white. <h2>ther experiments</h2> Contamination control: CA * *Contamination control of growth medium for Lc.lactis and Lb.reuteri. Two test from both bottles. E.coli growth test: CA * *To see if strain 1 of e.coli in strain database 13 grow on M17 and MRS plates as well. </div>';

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ds = '<div id="dairy-text"><h1>Thursday 2013-07-04</h1>Name of participants: Lovisa P, Kristoffer L, Emil M, Marcus H, Karl H, Peter C, Ken B.-A., Christoffer Ahlström (CA), Nafisa Bashir (NB), Mikael Strandgren (MS), Anton Berglund (AB), Magnus, Thorsteinn, Alexander, Nils, Christoffer <h2>Ongoing constructs</h2>E.coli (strain D5α): 15. pSB4K5-RBS-TAL-Linker-Zif268-RBS-4cl-Linker-PBSII-STS-OMT 43. pSB1C3-B0034-TAL 44. pSB1C3-B0034-His-TAL 45. pSB1C3-B0034-4CL 46. pSB1C3-B0034-His-4CL 47. pSB1C3-B0034-STS 48. pSB1C3-B0034-His-STS 57. pSB1C3-B0034-Idi 58. pSB1C3-B0034-ispA 42. pSB4S15-red 62. pSB1C3-CP8 63. pSB1C3-CP11 64. pSB1C3-CP29 65. pSB1C3-CP30 67. pSB1C3-CP44 68. pSB3K3-CP1-B0032-BFP 69.pSB3K3-CP8-B0032-BFP 70. pSB3K3-CP11-B0032-BFP 72. pSB3K3-CP30-B0032-BFP L. lactis: Lb13. MG1363-pJP059 Lb15. unknown-pGus E. faecalis: Lb9. JH2-2 pAMβ1 <h2>Todays work</h2>Frozen stock and plasmid preparation: Lb9.7. faecalis JH2-2 pAMβ1 clone 7 (erythromycin) Lb9.8. faecalis JH2-2 pAMβ1 clone 8 (no-antibiotic) Lb9.9. faecalis JH2-2 pAMβ1 clone 9 (erythromycin) Lb9.10. faecalis JH2-2 pAMβ1 clone 10 (no-antibiotic) Lb13.5. Lc. lactis MG1363 pJP059 clone 5 Lb13.6. Lc. lactis MG1363 pJP059 clone 6 Lb13.7. Lc. lactis MG1363 pJP059 clone 7 Lb13.8. Lc. lactis MG1363 pJP059 clone 8 Lb15.5. Lc. lactis MG1363 pGus clone 5 Lb15.6. Lc. lactis MG1363 pGus clone 6 Lb15.7. Lc. lactis MG1363 pGus clone 7 Lb15.8. Lc. lactis MG1363 pGus clone 8 Touchdown PCR: Lb13.2.2 Lc. lactis MG1363 pJP059 Lb13.2.3 Lc. lactis MG1363 pJP059 Lb13.3 Lc. lactis MG1363 pJP059 Lb13.4 Lc. lactis MG1363 pJP059 Screening PCR: 62.1 pSB1C3-CP8 62.2 pSB1C3-CP8 63.1 pSB1C3-CP11 63.2 pSB1C3-CP11 63.3 pSB1C3-CP11 63.4 pSB1C3-CP11 64.1.1 pSB1C3-CP29 64.1.2 pSB1C3-CP29 64.1.3 pSB1C3-CP29 64.1.4 pSB1C3-CP29 65.1.1 pSB1C3-CP30 65.1.2 pSB1C3-CP30 65.2.1 pSB1C3-CP30 65.2.2 pSB1C3-CP30 67.1.1 pSB1C3-CP44 67.1.2 pSB1C3-CP44 67.2.1 pSB1C3-CP44 67.2.2 pSB1C3-CP44 Gel electrophoresis: Lb13.2.2 lactis MG1363 pJP059 (PCR with DMSO done yesterday) Lb13.2.3 lactis MG1363 pJP059 (PCR with DMSO done yesterday) Lb13.3 lactis MG1363 pJP059 (PCR with DMSO done yesterday) Lb13.4 Lc. lactis MG1363 pJP059 (PCR with DMSO done yesterday) Lb13.2.2 Lc. lactis MG1363 pJP059 (Touchdown-PCR today) Lb13.2.3 Lc. lactis MG1363 pJP059 (Touchdown-PCR today) Lb13.3 Lc. lactis MG1363 pJP059 (Touchdown-PCR today) Lb13.4 Lc. lactis MG1363 pJP059 (Touchdown-PCR today) 62.1 pSB1C3-CP8 (Screening-PCR today, was run two times) 62.2 pSB1C3-CP8 (Screening-PCR today, was run two times) 63.1 pSB1C3-CP11 (Screening-PCR today, was run two times) 63.2 pSB1C3-CP11 (Screening-PCR today, was run two times) 63.3 pSB1C3-CP11 (Screening-PCR today, was run two times) 63.4 pSB1C3-CP11 (Screening-PCR today, was run two times) 64.1.1 pSB1C3-CP29 (Screening-PCR today, was run two times) 64.1.2 pSB1C3-CP29 (Screening-PCR today, was run two times) 64.1.3 pSB1C3-CP29 (Screening-PCR today, was run two times) 64.1.4 pSB1C3-CP29 (Screening-PCR today, was run two times) 65.1.1 pSB1C3-CP30 (Screening-PCR today, was run two times) 65.1.2 pSB1C3-CP30 (Screening-PCR today, was run two times) 65.2.1 pSB1C3-CP30 (Screening-PCR today, was run two times) 65.2.2 pSB1C3-CP30 (Screening-PCR today, was run two times) 67.1.1 pSB1C3-CP44 (Screening-PCR today, was run two times) 67.1.2 pSB1C3-CP44 (Screening-PCR today, was run two times) 67.2.1 pSB1C3-CP44 (Screening-PCR today, was run two times) 67.2.2 pSB1C3-CP44 (Screening-PCR today, was run two times) 1. pSB1C3-red (digest used in transformation, cut with E and S) 7. pSB3K3-red (digest used in transformation, cut with E and P) 22. pSB1C3-B0032-BFP (digest used in transformation, cut with X and P) 42. pSB4S15 (digest used in transformation, cut with SalI and SacI) pSB3C17-BFP (digest used in transformation, cut with SalI and SacI) PCR purification: 13.2.2 Lc. lactis MG1363-pJP059 Re-streaks: 42. pSB4S15-red 61. pSB1C3-CP1, clone 1-8 (spread out 2/7) 62. pSB1C3-CP8, clone 4-8 (spread out yesterday) 63. pSB1C3-CP11, clone 4-8 (spread out yesterday) 64. pSB1C3-CP29, clone 4-8 (spread out yesterday) 65. pSB1C3-CP30, clone 4-8 (spread out yesterday) 66. pSB1C3-CP41, clone 1-8 (spread out 2/7) 67. pSB1C3-Cp44, clone 4-8 (spread out yesterday) 68. pSB3K3-CP1-B0032-BFP 69.pSB3K3-CP8-B0032-BFP 70. pSB3K3-CP11-B0032-BFP 72. pSB3K3-CP30-B0032-BFP Lb1. reuteri CF48 pLR581 Lb2. reuteri 1063 pLUL631 Lb3. reuteri DSM 20016 pVS2 Lb4. reuteri 100-23 no plasmid Lb6. reuteri DSM 20016 pLUL63TsA8 Lb7. reuteri DSM 20016 pGFP Lb8. reuteri 100-23 pGT232 Lb12. reuteri DSM 20016 no plasmid Lb14. reuteri DSM 20016 pLUL631(B?) Lb5. plantarum 256 rifR pAMβ1 Lb10. plantarum 256 no plasmid Lb11. plantarum 36E no plasmid 43. pSB1C3-B0034-TAL 44. pSB1C3-B0034-His-TAL 45. pSB1C3-B0034-4CL 46. pSB1C3-B0034-His-4CL 47. pSB1C3-B0034-STS Screening PCR and gel analysis: 45. pSB1C3-B0034-4CL 46. pSB1C3-B0034-His-4CL 47. pSB1C3-B0034-STS 48. pSB1C3-B0034-His-STS Overnight culture: 48. pSB1C3-B0034-His-STS 42. pSB4S15-red Gel of Crt Z Ligation of 38(religation of digest), 27(religation of digest), 51(religation of digest), 75, 76, 78 Transformation of 38(religated), 38, 27(religated), 27, 51(religated), 51, 75, 76, 78 O/N of 57. and 58. <h2>Results</h2> Screening PCR and gel analysis: 48.1 pSB1C3-B0034-His-STS, was successful 45. pSB1C3-B0034-4CL 47. pSB1C3-B0034-STS, failed. Gel of CrtZ was blank. PCR fail. Think up a new method. Transformation of 75, 76 and 78(from yesterday) failed. Redo with negative controll of both ligation(by religating the digested pEL-plasmids) and plasmids(from plasmidprepp). Negative controll of O/N 57. and 58. contaminated. O/N: Lb10.1. plantarum 256: NC ok, but weirdly looking pellets and supernatants. Lb11.1. plantarum 36E: NC ok, but weirdly looking pellets and supernatants. Lb12.1 reuteri DSM 20016: NC ok, but weirdly looking pellets and supernatants. → Look in microscope to see if contaminated. Assembly and transformation: 1. pSB1C3-red, as NC: Good growth 7. pSB3K3-red, as NC: No growth 42. pSB4S15-red, as NC: No growth 61. pSB1C3-CP1: Growth, discernable red and white colonies 62. pSB1C3-CP8: Growth, discernable red and white colonies 63. pSB1C3-CP11: Growth, discernable red and white colonies 64. pSB1C3-CP29: Growth, discernable red and white colonies 65. pSB1C3-CP30: Growth, discernable red and white colonies 66. pSB1C3-CP41: Growth, discernable red and white colonies 67. pSB1C3-Cp44: Growth, discernable red and white colonies 77 pSB4C15-red: Growth, but only white and blue colonies* *E. coli with the right plasmid should have become red. → Most seem ok, do restreaks! Test fluorescence of BFP-colonies from 2/7, get new 42’s from Erik Gullberg since not even our frozen stocks are red (as they should be). Gel electrophoresis: Lb13.2.2 lactis MG1363 pJP059 (yesterday) No bands Lb13.2.3 lactis MG1363 pJP059 (yesterday) --”-- Lb13.3 lactis MG1363 pJP059 (yesterday) --”-- Lb13.4 Lc. lactis MG1363 pJP059 (yesterday) --”-- Lb13.2.2 Lc. lactis MG1363 pJP059 (Touchdown) Right band (~2000) Lb13.2.3 Lc. lactis MG1363 pJP059 (Touchdown) No bands Lb13.3 Lc. lactis MG1363 pJP059 (Touchdown) --”-- Lb13.4 Lc. lactis MG1363 pJP059 (Touchdown) --”-- 62.1 pSB1C3-CP8 (Screening) * (see below) 62.2 pSB1C3-CP8 (Screening) * (see below) 63.1 pSB1C3-CP11 (Screening) * (see below) 63.2 pSB1C3-CP11 (Screening) * (see below) 63.3 pSB1C3-CP11 (Screening) * (see below) 63.4 pSB1C3-CP11 (Screening) * (see below) 64.1.1 pSB1C3-CP29 (Screening) * (see below) 64.1.2 pSB1C3-CP29 (Screening) * (see below) 64.1.3 pSB1C3-CP29 (Screening) * (see below) 64.1.4 pSB1C3-CP29 (Screening) * (see below) 65.1.1 pSB1C3-CP30 (Screening) * (see below) 65.1.2 pSB1C3-CP30 (Screening) * (see below) 65.2.1 pSB1C3-CP30 (Screening) * (see below) 65.2.2 pSB1C3-CP30 (Screening) * (see below) 67.1.1 pSB1C3-CP44 (Screening) * (see below) 67.1.2 pSB1C3-CP44 (Screening) * (see below) 67.2.1 pSB1C3-CP44 (Screening) * (see below) 67.2.2 pSB1C3-CP44 (Screening) * (see below) 1. pSB1C3-red (cut with E and S): Clear bands (safe to use) 7. pSB3K3-red (cut with E and P): Clear bands (safe to use) 22. pSB1C3-B0032-BFP (cut with X and P) No bands (get more data) 42. pSB4S15 (cut with SalI and SacI) No bands (get more data) pSB3C17-BFP (cut with SalI and SacI) Faint bands (likely safe) *Neither of the two runs on gel showed anything but weak, smudgy bands. Try again. PCR purification: Lb13.2.2 Lc. lactis MG1363-pJP059: 25.9 ng/µl Plasmid preparation: Lb9.7.1 faecalis JH2-2 pAMβ1 clone 7.1 (erythromycin): 140.5 ng/µl → Throw away other low concentration clones and replace with this one in the -80o C freezer. Lb9.7.2 faecalis JH2-2 pAMβ1 clone 7.2 (erythromycin): 116.0 ng/µl → Throw away other low concentration clones and replace with this one in the -80o C freezer. Lb9.8.1 faecalis JH2-2 pAMβ1 clone 8.1 (no-antibiotic): 76.6 ng/µl → Throw away other low concentration clones and replace with this one in the -80o C freezer. Lb9.8.2 faecalis JH2-2 pAMβ1 clone 8.2 (no-antibiotic): 55.5 ng/µl → Throw away other low concentration clones and replace with this one in the -80o C freezer. Lb9.9.1 faecalis JH2-2 pAMβ1 clone 9.1 (erythromycin): 231.9 ng/µl → Throw away other low concentration clones and replace with this one in the -80o C freezer. Lb9.9.2 faecalis JH2-2 pAMβ1 clone 9.2 (erythromycin): 96.5 ng/µl → Throw away other low concentration clones and replace with this one in the -80o C freezer. Lb9.10.1 faecalis JH2-2 pAMβ1 clone 10.1 (no-antibiotic): 113.2 ng/µl → Throw away other low concentration clones and replace with this one in the -80o C freezer. Lb9.10.2 faecalis JH2-2 pAMβ1 clone 10.2 (no-antibiotic): 107.5 ng/µl → Throw away other low concentration clones and replace with this one in the -80o C freezer. Lb13.5. Lc. lactis MG1363 pJP059 clone 5: 13.8 ng/µl → Dispose & don’t save in freezer. Lb13.6. Lc. lactis MG1363 pJP059 clone 6: 34.8 ng/µl → Throw away other low concentration clones and replace with this one in the -80o C freezer. Lb13.7. Lc. lactis MG1363 pJP059 clone 7: 25.9 ng/µl → Throw away other low concentration clones and replace with this one in the -80o C freezer. Lb13.8. Lc. lactis MG1363 pJP059 clone 8: 34.3 ng/µl → Throw away other low concentration clones and replace with this one in the -80o C freezer. Lb15.5. Lc. lactis MG1363 pGus clone 5: 5.9 ng/µl → Dispose & don’t save in freezer. Lb15.6. Lc. lactis MG1363 pGus clone 6: 9.7 ng/µl → Dispose & don’t save in freezer. Lb15.7. Lc. lactis MG1363 pGus clone 7: 15.7 ng/µl → Throw away other low concentration clones and replace with this one in the -80o C freezer. Lb15.8. Lc. lactis MG1363 pGus clone 8: 16.7 ng/µl → Throw away other low concentration clones and replace with this one in the -80o C freezer. <h2>Other experiments</h2>TBE-mix Agarose gel mix EDTA mix Microscoping: *To see if the overnights from yesterday on strains 10 → 12 were contaminated. They showed to be that and the source are thought to be from a time ago, before frozen stock, since NC checked good for these overnights. </div>';

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    ds = '<div id="dairy-text"><h1>Friday 2013-07-05</h1><br><b>Name of participants:</b> Kristoffer L, Emil M, Marcus H, Karl H, Peter C, Ken B.-A., Christoffer Ahlström (CA), Anton Berglund (AB), Stephanie Herman (SH), Mikael Strandgren (MS), Viktor Blomkvist (VB), Nafisa Bashir (NB), Magnus, Thorsteinn, Alexander, Nils, Christoffer<br><br><h2>Ongoing constructs:</h2><br>15. pSB4K5-RBS-TAL-Linker-Zif268-RBS-4cl-Linker-PBSII-STS-OMT<br>43. pSB1C3-B0034-TAL<br>44. pSB1C3-B0034-His-TAL<br>45. pSB1C3-B0034-4CL<br>46. pSB1C3-B0034-His-4CL<br>47. pSB1C3-B0034-STS<br>61. pSB1C3-CP1<br>62. pSB1C3-CP8<br>63. pSB1C3-CP11<br>64. pSB1C3-CP29<br>65. pSB1C3-CP30<br>66. pSB1C3-CP41<br>67. pSB1C3-CP44<br>57. pSB1C3-B0034-Idi<br>58. pSB1C3-B0034-ispA<br><br><b>L. reuteri</b><br>Lb4. 100-23 no plasmid<br>Lb12. DSM 20016 no plasmid<br><br><b>L. plantarum:</b><br>Lb10. 256 no plasmid<br>Lb11. 36E no plasmid<br><br><b>L. thermophilus:</b><br>Lb19. L.thermophilus<br><br><b>Todays work</b><br>Screening PCR & gel analysis of constructs:<br>43. pSB1C3-B0034-TAL<br>44. pSB1C3-B0034-His-TAL<br>45. pSB1C3-B0034-4CL<br>46. pSB1C3-B0034-His-4CL<br>47. pSB1C3-B0034-STS<br>61.1 pSB1C3-CP1<br>61.2 pSB1C3-CP1<br>62.1 pSB1C3-CP8<br>62.2 pSB1C3-CP8<br>62.3 pSB1C3-CP8<br>62.4 pSB1C3-CP8<br>63.1 pSB1C3-CP11<br>63.2 pSB1C3-CP11<br>63.3 pSB1C3-CP11<br>63.4 pSB1C3-CP11<br>64.1.1 pSB1C3-CP29<br>64.1.2 pSB1C3-CP29<br>64.1.3 pSB1C3-CP29<br>64.1.4 pSB1C3-CP29<br>65.1.1 pSB1C3-CP30<br>65.1.2 pSB1C3-CP30<br>65.2.1 pSB1C3-CP30<br>65.2.2 pSB1C3-CP30<br>66.5 pSB1C3-CP41<br>66.6 pSB1C3-CP41<br>66.7 pSB1C3-CP41<br>66.8 pSB1C3-CP41<br>67.1.1 pSB1C3-CP44<br>67.1.2 pSB1C3-CP44<br>67.2.1 pSB1C3-CP44<br>67.2.2 pSB1C3-CP44<br><br><b>Plasmid prep & glycerol stock:</b><br>48. pSB1C3-B0034-His-STS<br><br><b>O/N:</b> <br>57. pSB1C3-B0034-Idi<br>58. pSB1C3-B0034-ispA<br>61. pSB1C3-CP1<br>62. pSB1C3-CP8<br>63. pSB1C3-CP11<br>64. pSB1C3-CP29<br>65. pSB1C3-CP30<br>66. pSB1C3-CP41<br>67. pSB1C3-Cp44<br>47.(9, 20) pSB1C3-B0034-STS<br>Lb4. reuteri 100-23 no plasmid<br>Lb10. plantarum 256 no plasmid<br>Lb11. plantarum 36E no plasmid<br>Lb12. reuteri DSM 20016 no plasmid<br><br><b>Re-streaks:</b><br>Lb19. L.thermophilus<br><br><h2>Results</h2><br>The O/N on 42. pSB4S15-red was done improperly in 15 ml falcon tubes and the lids were screwed on too tightly. A new O/N was done on 42. pSB4S15-red by NB.<br><br><b>PCR screen and gel electrophoresis:</b><br>61.1 pSB1C3-CP1<br>61.2 pSB1C3-CP1<br>62.1 pSB1C3-CP8<br>62.2 pSB1C3-CP8<br>62.3 pSB1C3-CP8<br>62.4 pSB1C3-CP8<br>63.1 pSB1C3-CP11<br>63.2 pSB1C3-CP11<br>63.3 pSB1C3-CP11<br>63.4 pSB1C3-CP11<br>64.1.1 pSB1C3-CP29<br>64.1.2 pSB1C3-CP29<br>64.1.3 pSB1C3-CP29<br>64.1.4 pSB1C3-CP29<br>65.1.1 pSB1C3-CP30<br>65.1.2 pSB1C3-CP30<br>65.2.1 pSB1C3-CP30<br>65.2.2 pSB1C3-CP30<br>66.5 pSB1C3-CP41<br>66.6 pSB1C3-CP41<br>66.7 pSB1C3-CP41<br>66.8 pSB1C3-CP41<br>67.1.1 pSB1C3-CP44<br>67.1.2 pSB1C3-CP44<br>67.2.1 pSB1C3-CP44<br>67.2.2 pSB1C3-CP44<br><br>*The gel only showed smudgy bands.<br><br><b>succesful</b><br>47.9 pSB1C3-B0034-STS<br>47.20 pSB1C3-B0034-STS<br><br><b>failed</b><br>43. pSB1C3-B0034-TAL<br>46. pSB1C3-B0034-His-4CL<br><br>No contamination in negative control -_-<br>Religation from yesterday failed. No colonies, only a few at 76, both red and white. <br><br><h2>ther experiments</h2><br><b>Contamination control:</b> CA *<br><br><i>*Contamination control of growth medium for Lc.lactis and Lb.reuteri.<br> Two test from both bottles. </i><br><br><b>E.coli growth test:</b> CA *<br><br><i>*To see if strain 1 of e.coli in strain database 13 grow on M17 and MRS plates as well. </i></div>';
   }
-   else if(id == 'd201372')
+   else if(id == 'd201374')
   {
-ds = '<div id="dairy-text"></div>';
+  ds = '<div id="dairy-text"><h1>Thursday 2013-07-04</h1><b>Name of participants:</b> Lovisa P, Kristoffer L, Emil M, Marcus H, Karl H, Peter C, Ken B.-A., Christoffer Ahlström (CA), Nafisa Bashir (NB), Mikael Strandgren (MS), Anton Berglund (AB),  Magnus, Thorsteinn, Alexander, Nils, Christoffer<br><br><h2>Ongoing constructs</h2><b>E.coli (strain D5α):</b> <br>15. pSB4K5-RBS-TAL-Linker-Zif268-RBS-4cl-Linker-PBSII-STS-OMT<br>43. pSB1C3-B0034-TAL<br>44. pSB1C3-B0034-His-TAL<br>45. pSB1C3-B0034-4CL<br>46. pSB1C3-B0034-His-4CL<br>47. pSB1C3-B0034-STS<br>48. pSB1C3-B0034-His-STS<br>57. pSB1C3-B0034-Idi<br>58. pSB1C3-B0034-ispA<br>42. pSB4S15-red<br>62. pSB1C3-CP8<br>63. pSB1C3-CP11<br>64. pSB1C3-CP29<br>65. pSB1C3-CP30<br>67. pSB1C3-CP44<br>68. pSB3K3-CP1-B0032-BFP<br>69.pSB3K3-CP8-B0032-BFP<br>70. pSB3K3-CP11-B0032-BFP<br>72. pSB3K3-CP30-B0032-BFP<br><br><b>L. lactis:</b><br>Lb13. MG1363-pJP059<br>Lb15. unknown-pGus<br><br><b>E. faecalis:</b><br>Lb9. JH2-2 pAMβ1<br><br><h2>Todays work</h2><b>Frozen stock and plasmid preparation:</b> <br>Lb9.7. faecalis JH2-2 pAMβ1 clone 7 (erythromycin) <br>Lb9.8. faecalis JH2-2 pAMβ1 clone 8 (no-antibiotic)<br>Lb9.9. faecalis JH2-2 pAMβ1 clone 9 (erythromycin)<br>Lb9.10. faecalis JH2-2 pAMβ1 clone 10 (no-antibiotic) <br>Lb13.5. Lc. lactis MG1363 pJP059 clone 5<br>Lb13.6. Lc. lactis MG1363 pJP059 clone 6<br>Lb13.7. Lc. lactis MG1363 pJP059 clone 7<br>Lb13.8. Lc. lactis MG1363 pJP059 clone 8<br>Lb15.5. Lc. lactis MG1363 pGus clone 5<br>Lb15.6. Lc. lactis MG1363 pGus clone 6<br>Lb15.7. Lc. lactis MG1363 pGus clone 7<br>Lb15.8. Lc. lactis MG1363 pGus clone 8<br><br><b>Touchdown PCR: </b><br>Lb13.2.2 Lc. lactis MG1363 pJP059<br>Lb13.2.3 Lc. lactis MG1363 pJP059<br>Lb13.3 Lc. lactis MG1363 pJP059<br>Lb13.4 Lc. lactis MG1363 pJP059<br><br><b>Screening PCR: </b><br>62.1 pSB1C3-CP8<br>62.2 pSB1C3-CP8<br>63.1 pSB1C3-CP11<br>63.2 pSB1C3-CP11<br>63.3 pSB1C3-CP11<br>63.4 pSB1C3-CP11<br>64.1.1 pSB1C3-CP29<br>64.1.2 pSB1C3-CP29<br>64.1.3 pSB1C3-CP29<br>64.1.4 pSB1C3-CP29<br>65.1.1 pSB1C3-CP30<br>65.1.2 pSB1C3-CP30<br>65.2.1 pSB1C3-CP30<br>65.2.2 pSB1C3-CP30<br>67.1.1 pSB1C3-CP44<br>67.1.2 pSB1C3-CP44<br>67.2.1 pSB1C3-CP44<br>67.2.2 pSB1C3-CP44<br><br><b>Gel electrophoresis:</b> <br>Lb13.2.2 lactis MG1363 pJP059 (PCR with DMSO done yesterday)<br>Lb13.2.3 lactis MG1363 pJP059 (PCR with DMSO done yesterday)<br>Lb13.3 lactis MG1363 pJP059 (PCR with DMSO done yesterday)<br>Lb13.4 Lc. lactis MG1363 pJP059 (PCR with DMSO done yesterday)<br>Lb13.2.2 Lc. lactis MG1363 pJP059 (Touchdown-PCR today)<br>Lb13.2.3 Lc. lactis MG1363 pJP059 (Touchdown-PCR today)<br>Lb13.3 Lc. lactis MG1363 pJP059 (Touchdown-PCR today)<br>Lb13.4 Lc. lactis MG1363 pJP059 (Touchdown-PCR today)<br>62.1 pSB1C3-CP8 (Screening-PCR today, was run two times)<br>62.2 pSB1C3-CP8 (Screening-PCR today, was run two times)<br>63.1 pSB1C3-CP11 (Screening-PCR today, was run two times)<br>63.2 pSB1C3-CP11 (Screening-PCR today, was run two times)<br>63.3 pSB1C3-CP11 (Screening-PCR today, was run two times)<br>63.4 pSB1C3-CP11 (Screening-PCR today, was run two times)<br>64.1.1 pSB1C3-CP29 (Screening-PCR today, was run two times)<br>64.1.2 pSB1C3-CP29 (Screening-PCR today, was run two times)<br>64.1.3 pSB1C3-CP29 (Screening-PCR today, was run two times)<br>64.1.4 pSB1C3-CP29 (Screening-PCR today, was run two times)<br>65.1.1 pSB1C3-CP30 (Screening-PCR today, was run two times)<br>65.1.2 pSB1C3-CP30 (Screening-PCR today, was run two times)<br>65.2.1 pSB1C3-CP30 (Screening-PCR today, was run two times)<br>65.2.2 pSB1C3-CP30 (Screening-PCR today, was run two times)<br>67.1.1 pSB1C3-CP44 (Screening-PCR today, was run two times)<br>67.1.2 pSB1C3-CP44 (Screening-PCR today, was run two times)<br>67.2.1 pSB1C3-CP44 (Screening-PCR today, was run two times)<br>67.2.2 pSB1C3-CP44 (Screening-PCR today, was run two times)<br>1. pSB1C3-red (digest used in transformation, cut with E and S)<br>7. pSB3K3-red (digest used in transformation, cut with E and P)<br>22. pSB1C3-B0032-BFP (digest used in transformation, cut with X and P)<br>42. pSB4S15 (digest used in transformation, cut with SalI and SacI)<br>pSB3C17-BFP (digest used in transformation, cut with SalI and SacI)<br><br><b>PCR purification: </b><br>13.2.2 Lc. lactis MG1363-pJP059<br><br><b>Re-streaks: </b><br>42. pSB4S15-red<br>61. pSB1C3-CP1, clone 1-8 (spread out 2/7)<br>62. pSB1C3-CP8, clone 4-8 (spread out yesterday)<br>63. pSB1C3-CP11, clone 4-8 (spread out yesterday)<br>64. pSB1C3-CP29, clone 4-8 (spread out yesterday)<br>65. pSB1C3-CP30, clone 4-8 (spread out yesterday)<br>66. pSB1C3-CP41, clone 1-8 (spread out 2/7)<br>67. pSB1C3-Cp44, clone 4-8 (spread out yesterday)<br>68. pSB3K3-CP1-B0032-BFP<br>69.pSB3K3-CP8-B0032-BFP<br>70. pSB3K3-CP11-B0032-BFP<br>72. pSB3K3-CP30-B0032-BFP<br>Lb1. reuteri CF48 pLR581<br>Lb2. reuteri 1063 pLUL631<br>Lb3. reuteri DSM 20016 pVS2<br>Lb4. reuteri 100-23 no plasmid<br>Lb6. reuteri DSM 20016 pLUL63TsA8<br>Lb7. reuteri DSM 20016 pGFP<br>Lb8. reuteri 100-23 pGT232<br>Lb12. reuteri DSM 20016 no plasmid<br>Lb14. reuteri DSM 20016 pLUL631(B?)<br>Lb5. plantarum 256 rifR pAMβ1<br>Lb10. plantarum 256 no plasmid<br>Lb11. plantarum 36E no plasmid<br>43. pSB1C3-B0034-TAL<br>44. pSB1C3-B0034-His-TAL<br>45. pSB1C3-B0034-4CL<br>46. pSB1C3-B0034-His-4CL<br>47. pSB1C3-B0034-STS<br><br><b>Screening PCR and gel analysis:</b><br>45. pSB1C3-B0034-4CL<br>46. pSB1C3-B0034-His-4CL<br>47. pSB1C3-B0034-STS<br>48. pSB1C3-B0034-His-STS<br><br><b>Overnight culture:</b><br>48. pSB1C3-B0034-His-STS<br>42. pSB4S15-red<br><br><b>Gel</b> of Crt Z<br>Ligation of 38(religation of digest), 27(religation of digest), 51(religation of digest), 75, 76, 78<br>Transformation of 38(religated), 38, 27(religated), 27, 51(religated), 51, 75, 76, 78<br>O/N of 57. and 58.<br><br><h2>Results</h2><br><b>Screening PCR and gel analysis:</b><br>48.1 pSB1C3-B0034-His-STS, was successful<br>45. pSB1C3-B0034-4CL<br>47. pSB1C3-B0034-STS, failed.<br><br><b>Gel</b> of CrtZ was blank. PCR fail. Think up a new method. <br>Transformation of 75, 76 and 78(from yesterday) failed. Redo with negative controll of both ligation(by religating the digested pEL-plasmids) and plasmids(from plasmidprepp).<br>Negative controll of O/N 57. and 58. contaminated.<br><br><b>O/N:</b> <br>Lb10.1. plantarum 256: NC ok, but weirdly looking pellets and supernatants. <br>Lb11.1. plantarum 36E: NC ok, but weirdly looking pellets and supernatants. <br>Lb12.1 reuteri DSM 20016: NC ok, but weirdly looking pellets and supernatants. <br>→ Look in microscope to see if contaminated. <br><br><b>Assembly and transformation:</b> <br>1. pSB1C3-red, as NC: Good growth<br>7. pSB3K3-red, as NC: No growth<br>42. pSB4S15-red, as NC: No growth<br>61. pSB1C3-CP1: Growth, discernable red and white colonies<br>62. pSB1C3-CP8: Growth, discernable red and white colonies<br>63. pSB1C3-CP11: Growth, discernable red and white colonies<br>64. pSB1C3-CP29: Growth, discernable red and white colonies<br>65. pSB1C3-CP30: Growth, discernable red and white colonies<br>66. pSB1C3-CP41: Growth, discernable red and white colonies<br>67. pSB1C3-Cp44: Growth, discernable red and white colonies<br>77 pSB4C15-red: Growth, but only white and blue colonies*<br>*E. coli with the right plasmid should have become red.<br>→ Most seem ok, do restreaks! Test fluorescence of BFP-colonies from 2/7, get new 42’s from Erik Gullberg since not even our frozen stocks are red (as they should be).<br><br><b>Gel electrophoresis:</b> <br>Lb13.2.2 lactis MG1363 pJP059 (yesterday)		No bands<br>Lb13.2.3 lactis MG1363 pJP059 (yesterday)		--”--<br>Lb13.3 lactis MG1363 pJP059 (yesterday)		--”--<br>Lb13.4 Lc. lactis MG1363 pJP059 (yesterday)		--”--<br>Lb13.2.2 Lc. lactis MG1363 pJP059 (Touchdown)	Right band (~2000)<br>Lb13.2.3 Lc. lactis MG1363 pJP059 (Touchdown)	No bands<br>Lb13.3 Lc. lactis MG1363 pJP059 (Touchdown)	--”--<br>Lb13.4 Lc. lactis MG1363 pJP059 (Touchdown)	--”--<br>62.1 pSB1C3-CP8 (Screening)				* (see below)<br>62.2 pSB1C3-CP8 (Screening)				* (see below)<br>63.1 pSB1C3-CP11 (Screening)				* (see below)<br>63.2 pSB1C3-CP11 (Screening)				* (see below)<br>63.3 pSB1C3-CP11 (Screening)				* (see below)<br>63.4 pSB1C3-CP11 (Screening)				* (see below)<br>64.1.1 pSB1C3-CP29 (Screening)			* (see below)<br>64.1.2 pSB1C3-CP29 (Screening)			* (see below)<br>64.1.3 pSB1C3-CP29 (Screening)			* (see below)<br>64.1.4 pSB1C3-CP29 (Screening)			* (see below)<br>65.1.1 pSB1C3-CP30 (Screening)			* (see below)<br>65.1.2 pSB1C3-CP30 (Screening)			* (see below)<br>65.2.1 pSB1C3-CP30 (Screening)			* (see below)<br>65.2.2 pSB1C3-CP30 (Screening)			* (see below)<br>67.1.1 pSB1C3-CP44 (Screening)			* (see below)<br>67.1.2 pSB1C3-CP44 (Screening)			* (see below)<br>67.2.1 pSB1C3-CP44 (Screening)			* (see below)<br>67.2.2 pSB1C3-CP44 (Screening)			* (see below)<br>1. pSB1C3-red (cut with E and S): 			Clear bands (safe to use)<br>7. pSB3K3-red (cut with E and P): 			Clear bands (safe to use)<br>22. pSB1C3-B0032-BFP (cut with X and P)		No bands (get more data)<br>42. pSB4S15 (cut with SalI and SacI)			No bands (get more data)<br>pSB3C17-BFP (cut with SalI and SacI)			Faint bands (likely safe)<br><br>*Neither of the two runs on gel showed anything but weak, smudgy bands. Try again.<br><br><b>PCR purification: </b><br>Lb13.2.2 Lc. lactis MG1363-pJP059: 25.9 ng/µl<br><br><b>Plasmid preparation: </b><br>Lb9.7.1 faecalis JH2-2 pAMβ1 clone 7.1 (erythromycin): 140.5 ng/µl → Throw away other low concentration clones and replace with this one in the -80o C freezer.<br>Lb9.7.2 faecalis JH2-2 pAMβ1 clone 7.2 (erythromycin): 116.0 ng/µl → Throw away other low concentration clones and replace with this one in the -80o C freezer.<br>Lb9.8.1 faecalis JH2-2 pAMβ1 clone 8.1 (no-antibiotic): 76.6 ng/µl → Throw away other low concentration clones and replace with this one in the -80o C freezer.<br>Lb9.8.2 faecalis JH2-2 pAMβ1 clone 8.2 (no-antibiotic): 55.5 ng/µl → Throw away other low concentration clones and replace with this one in the -80o C freezer.<br>Lb9.9.1 faecalis JH2-2 pAMβ1 clone 9.1 (erythromycin): 231.9 ng/µl → Throw away other low concentration clones and replace with this one in the -80o C freezer.<br>Lb9.9.2 faecalis JH2-2 pAMβ1 clone 9.2 (erythromycin): 96.5 ng/µl → Throw away other low concentration clones and replace with this one in the -80o C freezer.<br>Lb9.10.1 faecalis JH2-2 pAMβ1 clone 10.1 (no-antibiotic): 113.2 ng/µl → Throw away other low concentration clones and replace with this one in the -80o C freezer.<br>Lb9.10.2 faecalis JH2-2 pAMβ1 clone 10.2 (no-antibiotic): 107.5 ng/µl → Throw away other low concentration clones and replace with this one in the -80o C freezer.<br>Lb13.5. Lc. lactis MG1363 pJP059 clone 5: 13.8 ng/µl → Dispose & don’t save in freezer. <br>Lb13.6. Lc. lactis MG1363 pJP059 clone 6: 34.8 ng/µl → Throw away other low concentration clones and replace with this one in the -80o C freezer.<br>Lb13.7. Lc. lactis MG1363 pJP059 clone 7: 25.9 ng/µl → Throw away other low concentration clones and replace with this one in the -80o C freezer.<br>Lb13.8. Lc. lactis MG1363 pJP059 clone 8: 34.3 ng/µl → Throw away other low concentration clones and replace with this one in the -80o C freezer.<br>Lb15.5. Lc. lactis MG1363 pGus clone 5: 5.9 ng/µl → Dispose & don’t save in freezer. <br>Lb15.6. Lc. lactis MG1363 pGus clone 6: 9.7 ng/µl → Dispose & don’t save in freezer. <br>Lb15.7. Lc. lactis MG1363 pGus clone 7: 15.7 ng/µl → Throw away other low concentration clones and replace with this one in the -80o C freezer.<br>Lb15.8. Lc. lactis MG1363 pGus clone 8: 16.7 ng/µl → Throw away other low concentration clones and replace with this one in the -80o C freezer.<br><br><h2>Other experiments</h2>TBE-mix<br>Agarose gel mix<br>EDTA mix<br><br><b>Microscoping:</b> *To see if the overnights from yesterday on strains 10 → 12 were contaminated.<br>They showed to be that and the source are thought to be from a time ago, before frozen stock, since NC checked good for these overnights. </div>';
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