Template:Team:Uppsala/JS/notebook

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   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>';  
   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>';  
  }
  }
-
   
+
  else if(id == 'd2013722')
 +
{
 +
  ds = '<div id="dairy-text"><h1>Monday 2013-07-22</h1><br><b>Name of participants:</b> Hampus.E, Karl H, Ken B, Kristoffer L, Victor S, Marcus H, Theodor L., Nils, Christoffer, Malin, Magnus, Niclas, Pontus, Christoffer Ahlström (CA), Stephanie Herman (SH), Alona Nyberg (AN), Mikael Strandgren (MS)<br><br><h2>Ongoing constructs</h2><br>104. pSB1C3-B0034-4CL-B0034-STS<br>105. pSB3T5-J23101-B0034-TAL<br>106. pSB3T5-J23110-B0034-TAL<br>107. pSB3T5-CP1-B0034-TAL<br>115. pSB3T5-J23101-B0034-His-TAL<br>116. pSB3T5-J23110-B0034-His-TAL<br>117. pSB3T5-CP1-B0034-His-TAL<br>119.pSB1C3-B0034-4CL<br>120.pSB1C3-B0034-HIS-4CL<br>121.pSB1C3-B0034-STS<br>121.pSB1C3-B0034-His-STS<br>137. pSB3K3-CP8-B0034-TAL<br>138. pSB3K3-CP8-B0034-His-TAL<br>139. pSB3K3-J23101-B0034-BFP<br>57.pSB1C3-B0034-Idi<br>99. pSB1C3-CrtO<br>108. pSB4A15-J23106-B0034-IspA<br>109. pSB4A15-K206000-B0034-IspA<br>110. pSB4A15-K206001-B0034-IspA<br>127. pSB1A3-B0034-UGTCs2-His<br>21. CrtE~I /w RBS, Zinc finger (PCR prod)<br>128. pSIM5-tet(Nissle)<br>130. pSB1C3-CrtE~I /w RBS, Zinc Finger<br>131. pSB4A15-J23101-CrtE~I /w RBS, Zinc Finger<br>132. pSB4A15-J23106-CrtE~I /w RBS, Zinc Finger<br>133. pSB4A15 -J23110-CrtE~I /w RBS, Zinc Finger<br>75 . pEL3A15 - CrtB (LR) <br>76.pEL3K16-CrtI (LR) <br>79.pEL3K16- CrtE (LR) <br>140.pSB3T5-J23110-B0034-UGTCs2-6xHis<br>141.pSB3T5-J23101-B0034-UGTCs2-6xHis<br>142.pSB3T5-CP1-B0034-UGTCs2-6xHis<br>143.pSB3T5-CP8-B0034-UGTCs2-6xHis<br>144.pSB1C3-B0034-UGTCs2-His<br>68. pSB3K3-CP1-B0032-BFP<br>73. pSB3K3-CP41-B0032-BFP<br>81. pSB4S15-CP41-B0032-BFP<br>82. pSB4S15-CP29-B0032-BFP<br>83. pSB4S15-CP30-B0032-BFP<br>85. pSB4S15-CP25<br>84. pSB4S15-CP6<br>86. pSB4S15-CP6-B0032-BFP<br>87. pSB4S15-CP25-B0032-BFP<br>88. pSB4S15-CP1-B0032-BFP<br>89. pSB4S15-CP44-B0032-BFP<br>97. pSB4S15-CP8-B0032-BFP<br>98. pSB4S15-CP11-B0032-BFP<br>134.1 pSB1C3-CBP<br><br><h2>Todays work</h2><br><b>Restreaks:</b><br>115. pSB3T5-J23101-B0034-His-TAL*<br>116. pSB3T5-J23110-B0034-His-TAL*<br>117. pSB3T5-CP1-B0034-His-TAL*<br>137. pSB3K3-CP8-B0034-TAL*<br>138. pSB3K3-CP8-B0034-His-TAL*<br>139. pSB3K3-J23101-B0034-BFP*<br><i>-*Restreaks from the transformation, that was done the day before</i><br><br><b>Mutagenisis:</b><br>57.pSB1C3-B0034-Idi -> 129. pSB1C3-B0034-Idi (mut)<br>136.1 pSB1C3-usp45<br>136.2 pSB1C3-usp45<br>136.3 pSB1C3-usp45<br><i>→ Run PCR-products on gel to see if correct and then PCR clean it and prepare for sequencing. </i><br><br><b>Phosphorylation of primers: </b><br>usp45_mut_R<br>usp45_mut_F<br><br><b>Overnight:</b><br>127.1.pSB1A3-B0034-UGTCs2-His <br>127.2.pSB1A3-B0034-UGTCs2-His <br>86. pSB4S15-CP6-B0032-BFP<br>97. pSB4S15-CP8-B0032-BFP<br>98. pSB4S15- CP11-B0032-BFP<br>134.1 pSB1C3-CBP<br>134.2 pSB1C3-CBP<br>134.3 pSB1C3-CBP<br>134.4 pSB1C3-CBP<br><br><b>Transformation: </b><br>68. pSB3K3-CP1-B0032-BFP<br>73. pSB3K3-CP41-B0032-BFP<br>81. pSB4S15-CP41-B0032-BFP<br>82. pSB4S15-CP29-B0032-BFP<br>83. pSB4S15-CP30-B0032-BFP<br>85. pSB4S15-CP25<br><br><b>Fluorescence(BFP) experiment with UV:</b><br>84. pSB4S15-CP6<br>86. pSB4S15-CP6-B0032-BFP<br>87. pSB4S15-CP25-B0032-BFP<br>88. pSB4S15-CP1-B0032-BFP<br>89. pSB4S15-CP44-B0032-BFP<br>97. pSB4S15-CP8-B0032-BFP<br>98. pSB4S15-CP11-B0032-BFP<br><br><b>Screening:</b><br>131.  pSB4A15-BBa-J61002-J23106-CrtE~I /w RBS, Zinc finger <br>132.  pSB4A15-BBa-J61002-J23110-CrtE~I /w RBS, Zinc finger <br>133.  pSB4A15-BBa-J61002-J23101-CrtE~I /w RBS, Zinc finger<br>75.  pEL3A15 - CrtB <br>76.  pEL3K16- CrtI <br>79.  pEL3K16 - CrtE <br><br><b>Digest</b><br>3.pSB3T5-red<br>92.BBa_J61002-J23110<br>90.BBa_J61002-J23101<br>127.pSB1A3-B0034-UGTCs2-His<br>51.pEL3C18-CP1<br>51.pEL3C18-CP8<br>58.pSB1C3-B0034-IspA<br>11.pSB4A15-red<br>91.BBa_J61002-J23106<br>94.pSB1C3-K206000<br>1.pSB1C3-red<br>CSP_3<br>Plasmid 1.1 (from strain database 2013)<br><br><b>Ligation:</b><br>3.pSB3T5-red, 127.pSB1A3-B0034-UGTCs2-His, 92.BBa_J61002-J23110 --> 140.pSB3T5-J23110-B0034-UGTCs2-6xHis<br>3.pSB3T5-red, 127.pSB1A3-B0034-UGTCs2-His, 92.BBa_J61002-J23101 --> 141.pSB3T5-J23101-B0034-UGTCs2-6xHis<br>3.pSB3T5-red, 127.pSB1A3-B0034-UGTCs2-His, 51.pEL3C18-CP1      --> 142.pSB3T5-CP1-B0034-UGTCs2-6xHis<br>3.pSB3T5-red, 127.pSB1A3-B0034-UGTCs2-His, 51.pEL3C18-CP8      --> 143.pSB3T5-CP8-B0034-UGTCs2-6xHis<br>58.pSB1C3-B0034-IspA, 11.pSB4A15-red, 91.BBa_J61002-J23106      --> 108.pSBA15-J23106-B0034-IspA<br>58.pSB1C3-B0034-IspA, 11.pSB4A15-red, 94.pSB1C3-K206000        --> 109.pSBA15-K206000-B0034-IspA<br>58.pSB1C3-B0034-IspA, 11.pSB4A15-red, 95.pSB1C3-K206001        --> 110.pSBA15-K206001-B0034-IspA<br>127.pSB1A3-B0034-UGTCs2-His, 1.pSB1C3-red                      --> 144.pSB1C3-B0034-UGTCs2-His<br>CSP_3 <i>-Ligated with strain 1.1 (from strain database 2013) <br>    Let ligate in room temperature overnight.</i> <br> <br><b>Frozen stock: (plasmid prep. tomorrow)</b><br>111.6 pSBLb4C15<br>111.7 pSBLb4C15<br><br><h2>Results</h2><br><b>Gel electrophoresis: </b><br>79.pEL3K16 - CrtE looked ok on gel, but there was primer dimer contamination. <br>75.pEL3A15 - CrtB had several bands around 1500-3000. <br>76.pEL3K16-CrtI displayed no band except primer dimers. <br>Digests looks good on gel<br><br><b>Overnights </b><br>127.1* pSB1A3-B0034-UGTCs2-His<br>127.2* pSB1A3-B0034-UGTCs2-His<br><i>-*did not grow.</i></div>';
 +
}
 +
else if(id == 'd2013723')
 +
{
 +
  ds = '<div id="dairy-text"><h1>Tuesday 2013-07-23</h1><br><b>Name of participants:</b> Nils, Christoffer, Malin, Magnus, Niclas, Pontus, Hampus.E, Karl H, Ken B, Kristoffer L, Victor S, Marcus H, Theodor L., Christoffer Ahlström (CA), Nafisa Bashir (NB), Mikael Strandgren (MS), Stephanie Herman (SH), Alona Nyberg (AN)<br><br><h2>Ongoing constructs:</h2><br>129. pSB1C3-B0034-Idi (mut)<br>108. pSB4A15-J23106-B0034-IspA<br>109. pSB4A15-K206000-B0034-IspA<br>110. pSB4A15-K206001-B0034-IspA<br>127. pSB1A3-B0034-UGTCs2-His<br>140.pSB3T5-J23110-B0034-UGTCs2-6xHis<br>141.pSB3T5-J23101-B0034-UGTCs2-6xHis<br>142.pSB3T5-CP1-B0034-UGTCs2-6xHis<br>143.pSB3T5-CP8-B0034-UGTCs2-6xHis<br>144.pSB1C3-B0034-UGTCs2-His<br>147. pSB1C3-B0034-Thioredoxin<br>152. pUC57 (amp)-B0034-Exp-Linker-Miraculin-Linker-His<br>75.pEL3A15 - CrtB (LR) <br>76.pEL3K16-CrtI (LR) <br>79.pEL3K16 - CrtE (LR) <br>104. pSB1C3-B0034-4CL-B0034-STS<br>105. pSB3T5-J23101-B0034-TAL<br>106. pSB3T5-J23110-B0034-TAL<br>107. pSB3T5-CP1-B0034-TAL<br>115. pSB3T5-J23101-B0034-His-TAL<br>116. pSB3T5-J23110-B0034-His-TAL<br>117. pSB3T5-CP1-B0034-His-TAL<br>119.pSB1C3-B0034-4CL<br>120.pSB1C3-B0034-HIS-4CL<br>121.pSB1C3-B0034-STS<br>121.pSB1C3-B0034-His-STS<br>137. pSB3K3-CP8-B0034-TAL<br>138. pSB3K3-CP8-B0034-His-TAL<br>139. pSB3K3-J23101-B0034-BFP<br>134. pSB1C3-CBP<br>111. pSBLb4C15<br>86. pSB4S15-CP6-B0032-BFP<br>97. pSB4S15-CP8-B0032-BFP<br>98. pSB4S15-CP11-B0032-BFP<br>136. pSB1C3-usp45<br><br>Lb9. faecalis JH2-2-pAMβ1<br><br><h2>Todays work</h2><br><b>Plasmid preparation:</b><br>86. pSB4S15-CP6-B0032-BFP<br>97. pSB4S15-CP8-B0032-BFP<br>98. pSB4S15-CP11-B0032-BFP<br>111.6 pSBLb4C15<br>111.7 pSBLb4C15<br>134.1 pSB1C3-CBP<br>134.2 pSB1C3-CBP<br>134.3 pSB1C3-CBP<br>134.4 pSB1C3-CBP<br>84. pSB4S15-CP6<br>87. pSB4S15-CP25-B0032-BFP<br>88. pSB4S15-CP1-B0032-BFP<br>89. pSB4S15-CP44-B0032-BFP<br><br><br><b>Mutagenesis:</b><br>136.1 pSB1C3-usp45<br>136.2 pSB1C3-usp45<br>136.3 pSB1C3-usp45<br>136.4 pSB1C3-usp45<br><br><b>PCR:</b><br>115. pSB3T5-J23101-B0034-His-TAL<br>116. pSB3T5-J23110-B0034-His-TAL<br>117. pSB3T5-CP1-B0034-His-TAL<br>137. pSB3K3-CP8-B0034-TAL<br>138. pSB3K3-CP8-B0034-His-TAL<br>139. pSB3K3-J23101-B0034-BFP<br>Lb9. faecalis JH2-2-pAMβ1 clone 10.1*<br>Lb9. faecalis JH2-2-pAMβ1 clone 10.2*<br><i>-*With primers pAM-M1_F, pAM-s-X1_R and pAM-d-M1_R. To isolate ori.</i><br><br><b>Digest:</b><br>B0034-Thioredoxin, 1. pSB1C3-red (E, P) -> 147. pSB1C3-B0034-Thioredoxin<br><br><b>Ligation:</b><br>pSB1C3-B0034-Thioredoxin<br><br><b>Restreak: </b><br>139. pSB3K3-J23101-B0032-BFP<br><br><b>Transformation:</b><br>108.pSBA15-J23106-B0034-IspA<br>109.pSBA15-K206000-B0034-IspA<br>110.pSBA15-K206001-B0034-IspA<br>140.pSB3T5-J23110-B0034-UGTCs2-6xHis<br>141.pSB3T5-J23101-B0034-UGTCs2-6xHis<br>142.pSB3T5-CP1-B0034-UGTCs2-6xHis<br>143.pSB3T5-CP8-B0034-UGTCs2-6xHis<br>144.pSB1C3-B0034-UGTCs2-His<br>152. pUC57 (amp)-B0034-Exp-Linker-Miraculin-Linker-His<br>135. pSB1C3-CSP*<br>148. pSB1C3-gfas purple<br>149. pSB1C3-meffred<br>150. pSB1C3-spispink<br>151. pSB1C3-meffblue<br><i>-*Transformed into D5(alpha) competent cells. </i><br><br><b>Gel electrophoresis: </b><br>136.1 pSB1C3-usp45<br>136.2 pSB1C3-usp45<br>136.3 pSB1C3-usp45<br><br><b>Screening:</b><br>129. pSB1C3-B0034-Idi (mut)<br>75.pEL3A15 - CrtE <br>76.pEL3K16 - CrtI <br>79.pEL3K16 - CrtB <br><br><b>Overnight:</b><br>127.1.pSB1A3-B0034-UGTCs2-His <br>127.2.pSB1A3-B0034-UGTCs2-His<br>84. pSB4S15-CP6<br>87. pSB4S15-CP25-B0032-BFP<br>88. pSB4S15-CP1-B0032-BFP<br>89. pSB4S15-CP44-B0032-BFP<br><br><b>Spreading of strains:</b><br>135. pSB1C3-CSP*<br><i>-*Two 1x dilutions were performed.</i><br><br><b>Phosphorylation of primers: </b><br>usp45_mut_R<br>usp45_mut_F<br><br><b>Frozen stock: </b><br>134.1 pSB1C3-CBP<br>134.2 pSB1C3-CBP<br>134.3 pSB1C3-CBP<br>134.4 pSB1C3-CBP<br><br><h2>Results</h2><br><b>Previous day: </b><br><b>O/N: </b><br>134.1 pSB1C3-CBP: NC ok!<br>134.2 pSB1C3-CBP: NC ok!<br>134.3 pSB1C3-CBP: NC ok!<br>134.4 pSB1C3-CBP: NC ok!<br><br><b>Today:</b><br><b>Gel electrophoresis: </b><br>136.1 pSB1C3-usp45: Possible primer-dimer!<br>136.2 pSB1C3-usp45: Possible primer-dimer!<br>136.3 pSB1C3-usp45: Possible primer-dimer!<br><i>→ Re-do PCR mutagenesis with some edits.</i><br>129. pSB1C3-B0034-Idi  (mut) did not show on gel<br>76.pEL3K16-CrtI displayed no band on gel. <br>75.pEL3A15 - CrtB displayed a band, lager than expected. <br>79.pEL3K16 - CrtE displayed a band at the right size (screened without dmso) and a good band with some contamination when screened with 7% dmso. <br><br><b>Plasmid preparation: </b><br>134.1 pSB1C3-CBP: 126.0 ng/µl → Do a sequencing preparation.<br>134.2 pSB1C3-CBP: 124.9 ng/µl<br>134.3 pSB1C3-CBP: 126.6 ng/µl<br>134.4 pSB1C3-CBP: 126.2 ng/µl<br>111.6 pSBLb4C15: 33.7 ng/µl<br>111.7 pSBLb4C15: 52.2 ng/µl<br><br><b>Transformation: </b><br>109.pSBA15-K206000-B0034-IspA - did not grow<br>147. pSB1C3-B0034-Thioredoxin - did not grow<br><br><h2>Other experiments</h2><br>10x TBE-Buffer<br>10% Glycerol solution<br><br><b>Sequencing preparation:</b><br>111.6. pSBLb4C15-red<br>111.7. pSBLb4C15-red<br>134.1 pSB1C3-CBP<br><br><b>Primer dilution (from 100 µM to 5 µM):</b><br>Ori-scr_F<br>pL1-scr_F2<br>pL1-scr_F3<br>pL3-scr_F2<br>pL3-scr_F3<br>pAM-M1_F<br>pAM-s-X1_R<br>pAM-d-M1_R</div>';
 +
}
 +
else if(id == 'd2013724')
 +
{
 +
  ds = '<div id="dairy-text"><h1>Wednesday 2013-07-24</h1><br><b>Name of participants:</b> Christoffer Ahlström (CA), Stephanie Herman (SH), Alona Nyberg (AN), Nafisa Bashir (NB), Mikael Strandgren (MS), Jens Isaksson (JI), Malin, Magnus, Pontus, Nils, Niclas, Hampus.E, Karl H, Ken B, Kristoffer L, Victor S, Marcus H.<br><br><h2>Ongoing constructs:</h2><br>127.1.pSB1A3-B0034-UGTCs2-His <br>127.2.pSB1A3-B0034-UGTCs2-His<br>108. pSBA15-J23106-B0034-IspA<br>110. pSBA15-K206001-B0034-IspA<br>140. pSB3T5-J23110-B0034-UGTCs2-6xHis<br>141. pSB3T5-J23101-B0034-UGTCs2-6xHis<br>142. pSB3T5-CP1-B0034-UGTCs2-6xHis<br>143. pSB3T5-CP8-B0034-UGTCs2-6xHis<br>144. pSB1C3-B0034-UGTCs2-His<br>152. pUC57 (amp)-B0034-Exp-Linker-Miraculin-Linker-His<br>163.pSB3T5-ZCD-His-B0034-UGTCs2-His<br>165.pSB1C3-tsPurple<br>166.pSB1C3-scOrange<br>167.pSB1C3-fwYellow<br>68. pSB3K3-CP1-B0032-BFP<br>73. pSB3K3-CP41-B0032-BFP<br>90. BBa_J61002-J23101<br>153. pSB1C3-J23110-meffBlue<br>154. pSB1C3-J23106-meffBlue<br>155. pSB1C3-J23110-meffRed<br>156. pSB1C3-J23106-meffRed<br>157. pSB1C3-J23110-spisPink<br>158. pSB1C3-J23106-spisPink<br>159. pSB1C3-J23110-gfasPurple<br>160. pSB1C3-J23106-gfasPurple<br>66. pSB1C3-CP41<br>98. pSB4S15-CP11-B0032-BFP<br>22. pSB1C3-B0032-BFP<br>87. pSB4S15-CP25-B0032-BFP<br>84. pSB4S15-CP6<br>88. pSB4S15-CP1-B0032-BFP<br>89. pSB4S15-CP44-B0032-BFP<br>104. pSB1C3-B0034-4CL-B0034-STS<br>105. pSB3T5-J23101-B0034-TAL<br>106. pSB3T5-J23110-B0034-TAL<br>107. pSB3T5-CP1-B0034-TAL<br>115. pSB3T5-J23101-B0034-His-TAL<br>116. pSB3T5-J23110-B0034-His-TAL<br>117. pSB3T5-CP1-B0034-His-TAL<br>119. pSB1C3-B0034-4CL<br>120. pSB1C3-B0034-HIS-4CL<br>121. pSB1C3-B0034-STS<br>121. pSB1C3-B0034-His-STS<br>137. pSB3K3-CP8-B0034-TAL<br>138. pSB3K3-CP8-B0034-His-TAL<br>139. pSB3K3-J23101-B0034-BFP<br><br><h2>Todays work</h2><br><b>Overnight culture: </b><br>68. pSB3K3-CP1-B0032-BFP<br>73. pSB3K3-CP41-B0032-BFP<br><br><b>Ligation:</b><br>139. pSB3K3-J23101-B0032-BFP<br>162. pSB1C3-J23101<br>B0034-Thioredoxin, 1. pSB1C3-red (E, P) -> 147. pSB1C3-B0034-Thioredoxin<br><br>125.1.pSB1C3-ZCD-His, 127.4.pSB1A3- B0034-UGTCs2-His -> 163.pSB3T5-ZCD-His-B0034-UGTCs2-His<br><br><b>Lambda Red:</b><br>164.E-coli Nissle-CrtY<br><br><b>Transformation: </b><br>90. BBa_J61002-J23101<br>153. pSB1C3-J23110-meffBlue<br>154. pSB1C3-J23106-meffBlue<br>155. pSB1C3-J23110-meffRed<br>156. pSB1C3-J23106-meffRed<br>157. pSB1C3-J23110-spisPink<br>158. pSB1C3-J23106-spisPink<br>159. pSB1C3-J23110-gfasPurple<br>160. pSB1C3-J23106-gfasPurple<br>147. pSB1C3-B0034-Thioredoxin<br>165.pSB1C3-tsPurple<br>166.pSB1C3-scOrange<br>167.pSB1C3-fwYellow<br><br><b>Sequencing preparation: </b><br>66. pSB1C3-CP41<br>98. pSB4S15-CP11-B0032-BFP<br>127.1.pSB1A3-B0034-UGTCs2-His <br><br><b>Digestion: </b><br>22. pSB1C3-B0032-BFP<br>90. BBa_J61002(amp)-J23101<br>125.1 pSB1C3-ZCD-His<br><br><b>Gel electrophoresis: </b><br>Lb9. faecalis JH2-2 pAMβ1<br>136.1 pSB1C3-usp45<br>136.2 pSB1C3-usp45<br>136.3 pSB1C3-usp45<br>136.4 pSB1C3-usp45<br><br><b>Re-streak:</b><br>108. pSBA15-J23106-B0034-IspA<br>110. pSBA15-K206001-B0034-IspA<br>140. pSB3T5-J23110-B0034-UGTCs2-6xHis<br>141. pSB3T5-J23101-B0034-UGTCs2-6xHis<br>142. pSB3T5-CP1-B0034-UGTCs2-6xHis<br>143. pSB3T5-CP8-B0034-UGTCs2-6xHis<br>144. pSB1C3-B0034-UGTCs2-His<br>152. pUC57 (amp)-B0034-Exp-Linker-Miraculin-Linker-His <br>135.1 pSB1C3-CSP<br>135.2 pSB1C3-CSP<br>135.3 pSB1C3-CSP<br>135.4 pSB1C3-CSP<br><br><b>Mutagenesis: </b><br>136.1 pSB1C3-usp45<br>136.2 pSB1C3-usp45<br>136.3 pSB1C3-usp45<br>136.4 pSB1C3-usp45<br><br><b>PCR: </b><br>Lb9. faecalis JH2-2-pAMβ1 clone 9.9.1<br>Lb9. faecalis JH2-2-pAMβ1 clone 9.9.2<br><i>-New temperatures (-3*C), new polymerase and new primer dilutions. With primers pAM-M1_F, pAM-s-X1_R and pAM-d-M1_R. To isolate ori.</i><br><br><b>Plasmid Prep: </b><br>84.1 pSB4S15-CP6<br>84.2 pSB4S15-CP6<br>87.1 pSB4S15-CP25-B0032-BFP<br>87.2 pSB4S15-CP25-B0032-BFP<br>88.1 pSB4S15-CP1-B0032-BFP<br>88.2 pSB4S15-CP1-B0032-BFP<br>89.1 pSB4S15-CP44-B0032-BFP<br>89.2 pSB4S15-CP44-B0032-BFP<br>127.1.pSB1A3-B0034-UGTCs2-His <br>127.2.pSB1A3-B0034-UGTCs2-His<br><br><b>Screening PCR and gel electrophoresis on:</b><br>115. pSB3T5-J23101-B0034-His-TAL clone: 1, 2, 3 ,4<br>116. pSB3T5-J23110-B0034-His-TAL clone: 1, 2, 3, 4<br>117. pSB3T5-CP1-B0034-His-TAL clone: 1, 2, 3, 4<br>137. pSB3K3-CP8-B0034-TAL clone: 1, 2, 3, 4<br>138. pSB3K3-CP8-B0034-His-TAL clone: 1, 2, 3, 4<br>139. pSB3K3-J23101-B0034-BFP clone: 1, 2, 3, 4<br>Sequence prep on: <br>116. pSB3T5-J23110-B0034-His-TAL clone: 3, 4<br>137. pSB3K3-CP8-B0034-TAL clone: 1, 4<br>Overnight culture on: <br>116. pSB3T5-J23110-B0034-His-TAL clone: 3, 4<br>137. pSB3K3-CP8-B0034-TAL: 1, 4<br>Measurement of standards of p-coumaric acid in the shimadzu UV160, plotting of a standard graph.<br><br><h2>Results</h2><br><b>Previous day:</b><br><b>Spreading of strains: </b><br>135. pSB1C3-CSP: Both white and red colonies.<br><i>*Two 1x dilutions were performed.<br>→ Re-streak with 4 colonies.</i><br><br><b>PCR:</b> <br>One of the PCR-machines (with 2x MluI-pAM)  <br><i>-were accidentally paused right after start last night, and so it had to be re-done this morning. Since the samples stood in room temperature for about 15 hour the polymerase may have lost it’s activity, a gel will tell.</i><br><br><b>Today:</b><br><b>Gel electrophoresis: </b><br>Lb9.10.1 faecalis  JH2-2 pAMβ1 with XbaI and MluI: Not even primer-bands<br>Lb9.10.2 faecalis  JH2-2 pAMβ1 with 2x MluI: -”-<br>Lb9.10.1 faecalis  JH2-2 pAMβ1 with XbaI and MluI: -”-<br>Lb9.10.2 faecalis  JH2-2 pAMβ1 with 2x MluI: -”-<br>136.1 pSB1C3-usp45: Possible primer-dimer and a mark at ~1000bp.<br>136.2 pSB1C3-usp45: Possible primer-dimer.<br>136.3 pSB1C3-usp45: Possible primer-dimer.<br>136.4 pSB1C3-usp45: Possible primer-dimer.<br><i>→ Re-do PCR with other temperatures!</i><br><br><b>Plasmid Prepp: </b><br>84.1 pSB4S15-CP6:            59.3 ng/µl<br>84.2 pSB4S15-CP6:            66.7 ng/µl<br>87.1 pSB4S15-CP25-B0032-BFP: 12.6 ng/µl                                              <br>87.2 pSB4S15-CP25-B0032-BFP: 52.0 ng/µl<br>88.1 pSB4S15-CP1-B0032-BFP:  508.2 ng/µl    <br>88.2 pSB4S15-CP1-B0032-BFP:  489.7 ng/µl<br>89. pSB4S15-CP44-B0032-BFP:  7.4 ng/µl<br><br><b>digest</b> of B0034-Thioredoxin (Synthetic construct) looks good on gel<br><br><b>Restreak</b> of 143. pSB3T5-CP8-B0034-UGTCs2-6xHis did not grow<br><br><b>ligation</b> of 141. pSB3T5-J23101-B0034-UGTCs2-6xHis is wrong, since 92.BBa_J61002-J23101 was digested wrong<br><br>Construct 116.3, 116.4, 137.1, 137.4 successfull.<br><br><h2>Other experiments</h2><br><b>Primer dilutions (from 100µM to 5 µM): </b><br>pAM-M1_F<br>pAM-M1_R<br>pAM-X1_R<br></div>';
 +
}
 +
else if(id == 'd2013725')
 +
{
 +
  ds = '<div id="dairy-text"><h1>Thursday 2013-07-25</h1><br><b>Name of participants:</b> Malin, Magnus, Niclas, Pontus, Nils, Nafisa Bashir (NB), Viktor Blomkvist (VB), Jens Isaksson (JI), Mikael Strandgren (MS), Hampus.E, Kristoffer L, Victor S, Marcus H, Karl H, Theodor L<br><br><h2>Ongoing constructs</h2><br><b>E. coli:</b><br>108.pSBA15-J23106-B0034-IspA<br>110.pSBA15-K206001-B0034-IspA<br>140.pSB3T5-J23110-B0034-UGTCs2-6xHis<br>141.pSB3T5-J23101-B0034-UGTCs2-6xHis <br>142.pSB3T5-CP1-B0034-UGTCs2-6xHis<br>143.pSB3T5-CP8-B0034-UGTCs2-6xHis<br>144.pSB1C3-B0034-UGTCs2-His<br>147.pSB1C3-B0034-Thioredoxin<br>152.pUC57 (amp)-B0034-Exp-Linker-Miraculin-Linker-His<br>163.pSB3T5-ZCD-His-B0034-UGTCs2-His<br>164.E-coli Nissle-CrtY<br>165.pSB1C3-tsPurple<br>166.pSB1C3-scOrange<br>167.pSB1C3-fwYellow<br>135. pSB1C3-CSP<br>136.1 pSB1C3-usp45<br>148. pSB1C3-gfas purple<br>149. pSB1C3-meffred<br>150. pSB1C3-spispink<br>151. pSB1C3-meffblue<br>162. pSB1C3-J23101<br>104. pSB1C3-B0034-4CL-B0034-STS<br>105. pSB3T5-J23101-B0034-TAL<br>106. pSB3T5-J23110-B0034-TAL<br>107. pSB3T5-CP1-B0034-TAL<br>115. pSB3T5-J23101-B0034-His-TAL<br>116. pSB3T5-J23110-B0034-His-TAL<br>117. pSB3T5-CP1-B0034-His-TAL<br>119.pSB1C3-B0034-4CL<br>120.pSB1C3-B0034-HIS-4CL<br>121.pSB1C3-B0034-STS<br>121.pSB1C3-B0034-His-STS<br>137. pSB3K3-CP8-B0034-TAL<br>138. pSB3K3-CP8-B0034-His-TAL<br>139. pSB3K3-J23101-B0034-BFP<br><br><b>E. faecalis:</b><br>9. JH2-2-pAMβ1 clone<br><br><h2>Todays work</h2><br><b>O/N:</b> <br>135. pSB1C3-CSP<br><br><b>Transformation:</b><br>163.pSB3T5-ZCD-His-B0034-UGTCs2-His<br>143. pSB3T5-CP8-B0034-UGTCs2-6xHis<br>162. pSB1C3-J23101<br><br><b>Restreak:</b><br>139. pSB3K3-J23101-B0032-BFP<br>148. pSB1C3-gfas purple<br>149. pSB1C3-meffred<br>150. pSB1C3-spispink<br>151. pSB1C3-meffblue<br>147. pSB1C3-B0034-Thioredoxin<br>164.E-coli Nissle-CrtY<br>165.pSB1C3-tsPurple<br>166.pSB1C3-scOrange<br>167.pSB1C3-fwYellow<br><br><b>Plasmid prep on:</b><br>116. pSB3T5-J23110-B0034-His-TAL clone: 3, 4<br>137. pSB3K3-CP8-B0034-TAL clone: 1, 4<br><br><br><b>Gel electrophoresis of PCR products: </b><br>Lb9. faecalis JH2-2-pAMβ1 clone 9.9.1*<br>Lb9. faecalis JH2-2-pAMβ1 clone 9.9.2*<br>136.1 pSB1C3-usp45<br>136.2 pSB1C3-usp45<br>136.3 pSB1C3-usp45<br>136.4 pSB1C3-usp45<br><i>-*(With primers pAM-M1_F, pAM-s-X1_R and pAM-d-M1_R)</i><br><br><b>PCR-purification: </b><br>Lb9. faecalis JH2-2-pAMβ1 clone 9.9.1*<br>Lb9. faecalis JH2-2-pAMβ1 clone 9.9.2*<br><i>*With primers pAM-M1_F, pAM-s-X1_R and pAM-d-M1_R</i><br><br><b>Screening:</b><br>108.3 pSBA15-J23106-B0034-IspA<br>108.4 pSBA15-J23106-B0034-IspA<br>110.1 pSBA15-K206001-B0034-IspA<br>140.1 pSB3T5-J23110-B0034-UGTCs2-6xHis<br>140.2 pSB3T5-J23110-B0034-UGTCs2-6xHis<br>140.3 pSB3T5-J23110-B0034-UGTCs2-6xHis<br>140.4 pSB3T5-J23110-B0034-UGTCs2-6xHis<br>142.1 pSB3T5-CP1-B0034-UGTCs2-6xHis<br>142.2 pSB3T5-CP1-B0034-UGTCs2-6xHis<br>142.3 pSB3T5-CP1-B0034-UGTCs2-6xHis<br>142.4 pSB3T5-CP1-B0034-UGTCs2-6xHis<br>144.1 pSB1C3-B0034-UGTCs2-His<br>144.2 pSB1C3-B0034-UGTCs2-His<br>144.3 pSB1C3-B0034-UGTCs2-His<br>144.4 pSB1C3-B0034-UGTCs2-His<br><br><b>Overnight:</b><br>144.1 pSB1C3-B0034-UGTCs2-His<br>144.2 pSB1C3-B0034-UGTCs2-His<br>144.3 pSB1C3-B0034-UGTCs2-His<br>144.4 pSB1C3-B0034-UGTCs2-His<br>152.1 pUC57 (amp)-B0034-Exp-Linker-Miraculin-Linker-His<br>152.2 pUC57 (amp)-B0034-Exp-Linker-Miraculin-Linker-His<br>152.3 pUC57 (amp)-B0034-Exp-Linker-Miraculin-Linker-His<br>152.4 pUC57 (amp)-B0034-Exp-Linker-Miraculin-Linker-His<br><br><b>Ligation:</b><br>3.pSB3T5-red, 127.pSB1A3-B0034-UGTCs2-His, 103.pSB1K3-J23101--> 141.pSB3T5-J23101-B0034-UGTCs2-6xHis <br><br><b>Digest and assembly:</b><br>pL3E1 (pAMβ1 double)<br>pL3 (pAMβ1 single)<br>105. pSB3T5-J23101-B0034-TAL<br>115. pSB3T5-J23101-B0034--His-TAL<br><br><b>Transformation on construct:</b><br>105. pSB3T5-J23101-B0034-TAL<br>115. pSB3T5-J23101-B0034--His-TAL<br><br><h2>Results</h2><br><b>Screening of all clones failed except for:</b><br>144.1 pSB1C3-B0034-UGTCs2-His<br>144.2 pSB1C3-B0034-UGTCs2-His<br>144.3 pSB1C3-B0034-UGTCs2-His<br>144.4 pSB1C3-B0034-UGTCs2-His<br><br><b>Today:</b><br><b>Gel electrophoresis: </b><br>Lb9. faecalis JH2-2-pAMβ1 clone 9.9.1: Clear and correct bands, at ~1700 bp.*<br>Lb9. faecalis JH2-2-pAMβ1 clone 9.9.2: Clear and correct bands, at ~1700 bp.*<br>136.1 pSB1C3-usp45: Big smudge between approx. 2500 and 200 bp<br>136.2 pSB1C3-usp45: Empty<br>136.3 pSB1C3-usp45: Empty<br>136.4 pSB1C3-usp45: Empty<br> <i>*(With primers pAM-M1_F, pAM-s-X1_R and pAM-d-M1_R)</i><br><br><h2>Other experiments</h2><br>75. Digest to check for wrong bindings<br>Making LB-agar plates<br><br>Spectrophotomertry of 106.5, 106.6 and 43.7, using the shimadzu UV160.<br><i>-Inconclusive spectrophotometry results.</i></div>';
 +
}
 +
else if(id == 'd2013726')
 +
{
 +
  ds = '<div id="dairy-text"><h1>Friday 2013-07-26</h1><br><b>Name of participants:</b> Nafisa Bashir (NB), Christoffer Ahlström (CA), Stephanie Herman (SH), Alona Nyberg (AN), Mikael Strandgren (MS), Viktor Blomkvist (VB), Jens Isaksson (JI), Malin, Magnus, Niclas, Pontus, Nils, Hampus.E, Kristoffer L, Viktor @, Marcus H. Ken B-A, Karl H, Theodor L<br><br><h2>Ongoing constructs</h2><br>148. pSB1C3-gfas purple<br>149. pSB1C3-meffred<br>150. pSB1C3-spispink<br>151. pSB1C3-meffblue<br>90. BBa_J61002-J23101<br>153. pSB1C3-J23110-meffBlue<br>154. pSB1C3-J23106-meffBlue<br>155. pSB1C3-J23110-meffRed<br>156. pSB1C3-J23106-meffRed<br>157. pSB1C3-J23110-spisPink<br>158. pSB1C3-J23106-spisPink<br>159. pSB1C3-J23110-gfasPurple<br>160. pSB1C3-J23106-gfasPurple<br>162. pSB1C3-J23101<br>168. pSBLbC2 (working name)<br>169. pSBLbEcC2 (working name)<br>143. pSB3T5-CP8-B0034-UGTCs2-6xHis<br>144.pSB1C3-B0034-UGTCs2-His<br>152.pUC57 (amp)-B0034-Exp-Linker-Miraculin-Linker-His<br>147. pSB1C3-B0034-Thioredoxin<br>164.E-coli Nissle-CrtY<br>165.pSB1C3-tsPurple<br>166.pSB1C3-scOrange<br>167.pSB1C3-fwYellow<br>104. pSB1C3-B0034-4CL-B0034-STS<br>105. pSB3T5-J23101-B0034-TAL<br>106. pSB3T5-J23110-B0034-TAL<br>107. pSB3T5-CP1-B0034-TAL<br>115. pSB3T5-J23101-B0034-His-TAL<br>116. pSB3T5-J23110-B0034-His-TAL<br>117. pSB3T5-CP1-B0034-His-TAL<br>119.pSB1C3-B0034-4CL<br>120.pSB1C3-B0034-HIS-4CL<br>121.pSB1C3-B0034-STS<br>121.pSB1C3-B0034-His-STS<br>137. pSB3K3-CP8-B0034-TAL<br>138. pSB3K3-CP8-B0034-His-TAL<br>139. pSB3K3-J23101-B0034-BFP<br><br><h2>Todays work</h2><br>Screening:<br>108.3 pSBA15-J23106-B0034-IspA<br>108.4 pSBA15-J23106-B0034-IspA<br>110.1 pSBA15-K206001-B0034-IspA<br>140.1 pSB3T5-J23110-B0034-UGTCs2-6xHis<br>140.2 pSB3T5-J23110-B0034-UGTCs2-6xHis<br>140.3 pSB3T5-J23110-B0034-UGTCs2-6xHis<br>140.4 pSB3T5-J23110-B0034-UGTCs2-6xHis<br>142.1 pSB3T5-CP1-B0034-UGTCs2-6xHis<br>142.2 pSB3T5-CP1-B0034-UGTCs2-6xHis<br>142.3 pSB3T5-CP1-B0034-UGTCs2-6xHis<br>142.4 pSB3T5-CP1-B0034-UGTCs2-6xHis<br>147. pSB1C3-B0034-Thioredoxin<br>165.pSB1C3-tsPurple<br>166.pSB1C3-scOrange<br>167.pSB1C3-fwYellow<br><br></b>Re-streak: </b><br>163.pSB3T5-ZCD-His-B0034-UGTCs2-His<br>143. pSB3T5-CP8-B0034-UGTCs2-6xHis<br>105. pSB3T5-J23101-B0034-TAL<br>115. pSB3T5-J23101-B0034--His-TAL<br><br>Plasmid prep:<br>144.1 pSB1C3-B0034-UGTCs2-His<br>144.2 pSB1C3-B0034-UGTCs2-His<br>144.3 pSB1C3-B0034-UGTCs2-His<br>144.4 pSB1C3-B0034-UGTCs2-His<br>152.1 pUC57 (amp)-B0034-Exp-Linker-Miraculin-Linker-His<br>152.2 pUC57 (amp)-B0034-Exp-Linker-Miraculin-Linker-His<br>152.3 pUC57 (amp)-B0034-Exp-Linker-Miraculin-Linker-His<br>152.4 pUC57 (amp)-B0034-Exp-Linker-Miraculin-Linker-His<br><br><b>Transformation*:</b><br>168. pSBLbC2 (ori from pSB4C15 replaced with ori from pAMβ1)<br>169. pSBLbEcC2 (ori from pAMβ1 added to pSB4C15)<br><i>* Not spread.</i><br><br><b>Ligation:</b><br>3.pSB3T5-red, 127.pSB1A3-B0034-UGTCs2-His, 103.pSB1K3-J23101--> 141.pSB3T5-J23101-B0034-UGTCs2-6xHis <br><br><h2>Results:</h2><br>Screening showed incorrect results on all constructs, but possible sources for error in the analysis made these results inconclusive. A new screening was set to run overnight.<br><br><h2>Other experiments</h2><br>Organization of frozen stock<br><br>75. Digest to check for wrong bindings<br><br>Two phase separation of p-coumaric acid with heptane. Spectrophotometry.<br><i>--Heptane proved not to be so good for the separation.</i></div>';
 +
}
 +
else if(id == 'd2013727')
 +
{
 +
  ds = '<div id="dairy-text"><h1>Saturday 2013-07-27</h1><br><b>Name of participants:</b> Kristoffer L, Marcus H., Stephanie Herman (SH), Nafisa Bashir (NB), Malin, Magnus, Pontus, Nils<br><br><h2>Ongoing constructs</h2><br>104. pSB1C3-B0034-4CL-B0034-STS<br>105. pSB3T5-J23101-B0034-TAL<br>106. pSB3T5-J23110-B0034-TAL<br>107. pSB3T5-CP1-B0034-TAL<br>115. pSB3T5-J23101-B0034-His-TAL<br>116. pSB3T5-J23110-B0034-His-TAL<br>117. pSB3T5-CP1-B0034-His-TAL<br>119.pSB1C3-B0034-4CL<br>120.pSB1C3-B0034-HIS-4CL<br>121.pSB1C3-B0034-STS<br>121.pSB1C3-B0034-His-STS<br>137. pSB3K3-CP8-B0034-TAL<br>138. pSB3K3-CP8-B0034-His-TAL<br>139. pSB3K3-J23101-B0034-BFP<br>170. pSB3T5-J23110-B0034-TAL-B0034-4CL-B0034-STS<br>171. pSB3T5-J23110-B0034-4CL-B0034-STS<br>90. BBa_J61002-J23101<br>148. pSB1C3-gfas purple<br>149. pSB1C3-meffred<br>150. pSB1C3-spispink<br>151. pSB1C3-meffblue<br>153. pSB1C3-J23110-meffBlue<br>154. pSB1C3-J23106-meffBlue<br>155. pSB1C3-J23110-meffRed<br>156. pSB1C3-J23106-meffRed<br>157. pSB1C3-J23110-spisPink<br>158. pSB1C3-J23106-spisPink<br>159. pSB1C3-J23110-gfasPurple<br>160. pSB1C3-J23106-gfasPurple<br>162. pSB1C3-J23101<br><br><h2>Todays work</h2><br><b>Digest on construct:</b><br>106. pSB3T5-J23110-B0034-TAL<br>104. pSB1C3-B0034-4CL-B0034-STS<br><br><b>Assembly on cnstruct:</b><br>170. pSB3T5-J23110-B0034-TAL-B0034-4CL-B0034-STS<br>171. pSB3T5-J23110-B0034-4CL-B0034-STS<br>Transformation on construct:<br>170. pSB3T5-J23110-B0034-TAL-B0034-4CL-B0034-STS<br>171. pSB3T5-J23110-B0034-4CL-B0034-STS<br><br><b>Plasmid Preperation: </b><br>148.1 pSB1C3-gfas purple<br>148.2 pSB1C3-gfas purple<br>149.1 pSB1C3-meffred<br>149.4 pSB1C3-meffred<br>150.1 pSB1C3-spispink<br>150.2 pSB1C3-spispink<br>151.2 pSB1C3-meffblue<br><br><b>Overnight culture:</b> <br>90. BBa_J61002-J23101<br>153. pSB1C3-J23110-meffBlue<br>154. pSB1C3-J23106-meffBlue<br>155. pSB1C3-J23110-meffRed<br>156. pSB1C3-J23106-meffRed<br>157. pSB1C3-J23110-spisPink<br>158. pSB1C3-J23106-spisPink<br>159. pSB1C3-J23110-gfasPurple<br>160. pSB1C3-J23106-gfasPurple<br>162. pSB1C3-J23101<br><br><h2>Result</h2><br><b>Transformation on construct:</b><br>170. pSB3T5-J23110-B0034-TAL-B0034-4CL-B0034-STS<br>171. pSB3T5-J23110-B0034-4CL-B0034-STS<br>Failed. Retry assembly<br>110.pSBA15-K206001-B0034-IspA did not grow<br><br><b>Gel electrophoresis: </b><br>147. pSB1C3-B0034-Thioredoxin<br>165.pSB1C3-tsPurple<br>166.pSB1C3-scOrange<br>167.pSB1C3-fwYellow<br>didn’t show on gel<br><br><b>Plasmid Preperation:</b><br>148.1 pSB1C3-gfas purple: 311.6 ng/µl<br>148.2 pSB1C3-gfas purple: 338.0 ng/µl<br>149.1 pSB1C3-meffred: 202.4 ng/µl<br>149.4 pSB1C3-meffred: 310.4 ng/µl<br>150.1 pSB1C3-spispink: 305.4 ng/µl<br>150.2 pSB1C3-spispink: 323.8 ng/µl<br>151.2 pSB1C3-meffblue: 179.2 ng/µl<br><br></div>';
 +
}
 +
else if(id == 'd2013728')
 +
{
 +
  ds = '<div id="dairy-text"><h1>Sunday 2013-07-28</h1><br><b>Name of participants:</b> Mikael Strandgren (MS), Alona Nyberg(AN), Kristoffer L, Marcus H, Karl H.,Malin, Magnus, Nils, Pontus<br><br><h2>Ongoing constructs</h2><br><b>E. coli:</b><br>168. pSBLbC2<br>169. pSBLbEcC2<br>104. pSB1C3-B0034-4CL-B0034-STS<br>105. pSB3T5-J23101-B0034-TAL<br>106. pSB3T5-J23110-B0034-TAL<br>107. pSB3T5-CP1-B0034-TAL<br>115. pSB3T5-J23101-B0034-His-TAL<br>116. pSB3T5-J23110-B0034-His-TAL<br>117. pSB3T5-CP1-B0034-His-TAL<br>119.pSB1C3-B0034-4CL<br>120.pSB1C3-B0034-HIS-4CL<br>121.pSB1C3-B0034-STS<br>121.pSB1C3-B0034-His-STS<br>137. pSB3K3-CP8-B0034-TAL<br>138. pSB3K3-CP8-B0034-His-TAL<br>139. pSB3K3-J23101-B0034-BFP<br>170. pSB3T5-J23110-B0034-TAL-B0034-4CL-B0034-STS<br>171. pSB3T5-J23110-B0034-4CL-B0034-STS<br>172. pSB3T5-CP1-B0034-TAL<br>173. pSB3T5-CP1-B0034-4CL-B0034-STS<br>174. pSB3T5-CP8-B0034-4CL-B0034-STS<br>175. pSB3T5-J23101-B0034-4CL-B0034-STS<br> <br><h2>Todays work</h2><br><b>PCR:</b><br>19. CrtE~(O)-Z/w RBS, ZF<br>20.CrtE~Z/w RBS, ZF<br>21. CrtE~I/wRBS,ZF<br><br><b>Restreak:</b><br>140.pSB3T5-J23110-B0034-UGTCs2-His<br>141.pSB3T5-J23101-B0034-UGTCs2-6xHis<br>142.pSB3T5-CP1-B0034-UGTCs2-His.<br><br><b>Spreading of transformed E. coli (from 20130726):</b><br>90.1 BBa_J61002-J23101<br>153. pSB1C3-j23110-meffBlue <br>155. pSB1C3-j23110-meffRed<br>156. pSB1C3-j23106-meffRed<br>157. pSB1C3-j23110-spisPink<br>159. pSB1C3-j23110-gfasPurple<br>160. pSB1C3-j23106-gfasPurple<br>162. pSB1C3-J23101<br>168. pSBLbC2<br>169. pSBLbEcC2<br><br><b>Frozen stock & plasmid preparation:</b><br>90.1 BBa_J61002-J23101<br>90.2 BBa_J61002-J23101<br>153.1 pSB1C3-j23110-meffBlue <br>153.2 pSB1C3-j23110-meffBlue<br>155.1 pSB1C3-j23110-meffRed<br>156.1 pSB1C3-j23106-meffRed<br>157.1 pSB1C3-j23110-spisPink<br>157.2 pSB1C3-j23110-spisPink<br>159.4 pSB1C3-j23110-gfasPurple<br>160.3 pSB1C3-j23106-gfasPurple<br>160.4 pSB1C3-j23106-gfasPurple<br>162.1 pSB1C3-J23101<br>162.2 pSB1C3-J23101<br><br><b>Overnight:</b><br>106.5 pSB3K3-B0034-J23110-TAL<br>106.6 pSB3K3-B0034-J23110-TAL<br>43.7 pSB1C3-B0034-TAL<br>143.1.pSB3T5-CP8-B0034-UGTCs2-6xHis<br>167.1.pSB1C3-fwYellow<br>167.2.pSB1C3-fwYellow <br><br><b>Digest:</b><br>5.pSB4K15-red digested with E,P<br>111.6.pSBLb4C15-red digested with E,P<br>152.1.pUC57(amp)-B0034-ExpTag-Linker-Miraculin-HisTag digested with E,P<br>152.1.pUC57(amp)-B0034-ExpTag-Linker-Miraculin-HisTag digested with X,P<br><br><b>Assembly:</b><br>105. pSB3T5-J23101-B0034-TAL<br>170. pSB3T5-J23110-B0034-TAL-B0034-4CL-B0034-STS<br>171. pSB3T5-J23110-B0034-4CL-B0034-STS<br>172. pSB3T5-CP1-B0034-TAL<br>173. pSB3T5-CP1-B0034-4CL-B0034-STS<br>174. pSB3T5-CP8-B0034-4CL-B0034-STS<br>175. pSB3T5-J23101-B0034-4CL-B0034-STS<br><br><b>Ligation:</b><br>58.pSB1C3-B0034-IspA, 5.pSB4K15-red, 91.BBa_J61002-J23106 --> 108.pSBA15-J23106-B0034-IspA<br>58.pSB1C3-B0034-IspA, 11.pSB4A15-red, 94.pSB1C3-K206000--> 109.pSBA15-K206000-B0034-IspA<br>58.pSB1C3-B0034-IspA, 11.pSB4A15-red, 95.pSB1C3-K206001 --> 110.pSBA15-K206001-B0034-IspA<br>3.pSB3T5-red, 125.1.pSB1C3-ZCD-His, 127.4.pSB1A3- B0034-UGTCs2-His -> 163.pSB3T5-ZCD-His-B0034-UGTCs2-His<br>152.pUC57-B0034-Exp-Linker-Miraculin-His(E,P), 1.pSB1C3-red->  176.B1C3-B0034-Exp-Linker-Miraculin-His<br>152.pUC57-B0034-Exp-Linker-Miraculin-His(X,P), 3.pSB3T5-red, 103.pSB1K3-J23101 -> 177.pSB3T5-J23101-B0034-Exp-Linker-Miraculin-His<br>152.pUC57-B0034-Exp-Linker-Miraculin-His(X,P), 3.pSB3T5-red, 92.BBa_J61002(amp)_J23110 -> 178.pSB3T5-J23110-B0034-Exp-Linker-Miraculin-His<br>152.pUC57-B0034-Exp-Linker-Miraculin-His(X,P), 3.pSB3T5-red, CP1 -> 179.pSB3T5-CP1-B0034-Exp-Linker-Miraculin-His<br>152.pUC57-B0034-Exp-Linker-Miraculin-His(X,P), 3.pSB3T5-red, CP8 -> 180.pSB3T5-CP8-B0034-Exp-Linker-Miraculin-His<br>152.pUC57-B0034-Exp-Linker-Miraculin-His(X,P), 111.pSBLb4C15-red(E,P), CP1 -> 181.pSBLb4C15-CP1-B0034-Exp-Linker-Miraculin-His<br>152.pUC57-B0034-Exp-Linker-Miraculin-His(X,P), 111.pSBLb4C15-red(E,P), CP8 -> 182.pSBLb4C15-CP8-B0034-Exp-Linker-Miraculin-His<br><br><b>Transformation:</b><br>105. pSB3T5-J23101-B0034-TAL<br>170. pSB3T5-J23110-B0034-TAL-B0034-4CL-B0034-STS<br>171. pSB3T5-J23110-B0034-4CL-B0034-STS<br>172. pSB3T5-CP1-B0034-TAL<br>173. pSB3T5-CP1-B0034-4CL-B0034-STS<br>174. pSB3T5-CP8-B0034-4CL-B0034-STS<br>175. pSB3T5-J23101-B0034-4CL-B0034-STS<br><br><b>Gel electrophoresis: </b><br>76. pEL3K16-CrtI<br>20. CrtZ<br>19.CrtE~(O)-Z<br>20.CrtE~Z<br>21. CrtE~I<br>143.pSB3T5-CP8-B0034-UGTCs2-6xHis<br>163.pSB3T5-ZCD-His-B0034-UGTCs2-His<br>147.pSB1C3-B0034-Thioredoxin<br>165.pSB1C3-tsPurple<br>166.pSB1C3-scOrange<br>167.pSB1C3-fwYellow<br><br><b>Sequence prep:</b><br>144. pSB1C3-B0034-UGTCs2-His<br><br><h2>Results</h2><br><b>Frozen stock & plasmid preparation:</b><br>90.1 BBa_J61002-J23101: 215.4 ng/µl <br>90.3 BBa_J61002-J23101: 210.1 ng/µl<br>153.1 pSB1C3-j23110-meffBlue: 112.6 ng/µl<br>153.2 pSB1C3-j23110-meffBlue: 119 ng/µl<br>155.1 pSB1C3-j23110-meffRed: 169.5 ng/µl<br>156.1 pSB1C3-j23106-meffRed: 200.3 ng/µl<br>157.1 pSB1C3-j23110-spisPink: 73.7 ng/µl<br>157.2 pSB1C3-j23110-spisPink: 222.1 ng/µl<br>159.4 pSB1C3-j23110-gfasPurple: 279.7 ng/µl<br>160.3 pSB1C3-j23106-gfasPurple: 116.1 ng/µl<br>160.4 pSB1C3-j23106-gfasPurple: 122.8 ng/µl<br>162.1 pSB1C3-J23101: 79.9 ng/µl<br>162.2 pSB1C3-J23101: 80.1 ng/µl<br><br><b>Gel electrophoresis: </b><br>76. pEL3K16-CrtI - Correct at 50 degrese tube<br>20. CrtZ - Correct for low temps<br>19.CrtE~(O)-Z - weak incorrect bands<br>20.CrtE~Z - weak incorrect bands<br>21. CrtE~I - 3 bands, one correct 2 wrong<br>143. pSB3T5-CP8-B0034-UGTCs2-6xHis - 143.1 success, other clones failed<br>163.pSB3T5-ZCD-His-B0034-UGTCs2-His - Failed<br>167.1.pSB1C3-fwYellow - Success<br>167.2.pSB1C3-fwYellow - Success<br></div>';
 +
}
 +
else if(id == 'd2013729')
 +
{
 +
  ds = '<div id="dairy-text"><h1>Monday 2013-07-29</h1><br><b>Name of participants:</b> Malin, Magnus, Pontus, Nils, Christoffer, Kristoffer L, Marcus H, Karl H, Theodor L, Emil M, Victor S, Alona Nyberg(AN), Nafisa Bashir (NB), Mikael Strandgren (MS), Jens Isaksson (JI)<br><br><h2>Ongoing constructs</h2><br>108.pSB4K15-J23106-B0034-IspA<br>109.pSB4A15-K206000-B0034-IspA<br>110.pSB4A15-K206001-B0034-IspA<br>163.pSB3T5-ZCD-His-B0034-UGTCs2-His<br>176.B1C3-B0034-Exp-Linker-Miraculin-His<br>177.pSB3T5-J23101-B0034-Exp-Linker-Miraculin-His<br>178.pSB3T5-J23110-B0034-Exp-Linker-Miraculin-His<br>179.pSB3T5-CP1-B0034-Exp-Linker-Miraculin-His<br>180.pSB3T5-CP8-B0034-Exp-Linker-Miraculin-His<br>181.pSBLb4C15-CP1-B0034-Exp-Linker-Miraculin-His<br>182.pSBLb4C15-CP8-B0034-Exp-Linker-Miraculin-His<br>104. pSB1C3-B0034-4CL-B0034-STS<br>105. pSB3T5-J23101-B0034-TAL<br>106. pSB3T5-J23110-B0034-TAL<br>107. pSB3T5-CP1-B0034-TAL<br>115. pSB3T5-J23101-B0034-His-TAL<br>116. pSB3T5-J23110-B0034-His-TAL<br>117. pSB3T5-CP1-B0034-His-TAL<br>119.pSB1C3-B0034-4CL<br>120.pSB1C3-B0034-HIS-4CL<br>121.pSB1C3-B0034-STS<br>121.pSB1C3-B0034-His-STS<br>137. pSB3K3-CP8-B0034-TAL<br>138. pSB3K3-CP8-B0034-His-TAL<br>139. pSB3K3-J23101-B0034-BFP<br>170. pSB3T5-J23110-B0034-TAL-B0034-4CL-B0034-STS<br>171. pSB3T5-J23110-B0034-4CL-B0034-STS<br>172. pSB3T5-CP1-B0034-TAL<br>173. pSB3T5-CP1-B0034-4CL-B0034-STS<br>174. pSB3T5-CP8-B0034-4CL-B0034-STS<br>175. pSB3T5-J23101-B0034-4CL-B0034-STS<br>185. pEL3S17-J23110-B0034-TAL-B0034-4CL-B0034-STS<br>186. pEL3S17-CP1-B0034-4CL-B0034-STS<br>187. pEL3S17-CP8-B0034-4CL-B0034-STS<br>188. pEL3S17-J23101-B0034-4CL-B0034-STS<br>189. pSB3K3-J23101-B0034-TAL<br>Lb10. plantarum 256-p256<br><br><h2>Todays work</h2><br><b>O/N, Frozen Stock:</b><br>76.pEL3K16-CrtI<br><br><b>Screening & Overnight:</b><br>140.pSB3T5-J23110-B0034-UGTCs2-His<br>141.pSB3T5-J23101-B0034-UGTCs2-6xHis<br>142.pSB3T5-CP1-B0034-UGTCs2-His.<br><br><b>Digestion: </b><br>3.    pSB3K3-red<br>36.  pEL3S17-red<br>106. pSB3T5-J23110-B0034-TAL<br><br><b>Assembly:</b><br>170. pSB3T5-J23110-B0034-TAL-B0034-4CL-B0034-STS<br>173. pSB3T5-CP1-B0034-4CL-B0034-STS<br>174. pSB3T5-CP8-B0034-4CL-B0034-STS<br>175. pSB3T5-J23101-B0034-4CL-B0034-STS<br>185. pEL3S17-J23110-B0034-TAL-B0034-4CL-B0034-STS<br>186. pEL3S17-CP1-B0034-4CL-B0034-STS<br>187. pEL3S17-CP8-B0034-4CL-B0034-STS<br>188. pEL3S17-J23101-B0034-4CL-B0034-STS<br>189. pSB3K3-J23101-B0034-TAL<br><br><b>Transformation:</b><br>108.pSBA15-J23106-B0034-IspA<br>109.pSBA15-K206000-B0034-IspA<br>110.pSBA15-K206001-B0034-IspA<br>163.pSB3T5-ZCD-His-B0034-UGTCs2-His<br>176.B1C3-B0034-Exp-Linker-Miraculin-His<br>177.pSB3T5-J23101-B0034-Exp-Linker-Miraculin-His<br>178.pSB3T5-J23110-B0034-Exp-Linker-Miraculin-His<br>179.pSB3T5-CP1-B0034-Exp-Linker-Miraculin-His<br>180.pSB3T5-CP8-B0034-Exp-Linker-Miraculin-His<br>181.pSBLb4C15-CP1-B0034-Exp-Linker-Miraculin-His<br>182.pSBLb4C15-CP8-B0034-Exp-Linker-Miraculin-His<br>183.pEL3A15-B0034-CrtZ<br>184.pSB1C3-B0034-CrtZ<br>170. pSB3T5-J23110-B0034-TAL-B0034-4CL-B0034-STS<br>173. pSB3T5-CP1-B0034-4CL-B0034-STS<br>174. pSB3T5-CP8-B0034-4CL-B0034-STS<br>175. pSB3T5-J23101-B0034-4CL-B0034-STS<br>185. pEL3S17-J23110-B0034-TAL-B0034-4CL-B0034-STS<br>186. pEL3S17-CP1-B0034-4CL-B0034-STS<br>187. pEL3S17-CP8-B0034-4CL-B0034-STS<br>188. pEL3S17-J23101-B0034-4CL-B0034-STS<br>189. pSB3K3-J23101-B0034-TAL<br>Lb10. plantarum 256 p256 (as competence test)<br>Lb11. plantarum 256 plasmid free (as positive control)<br>Lb12. reuteri DSM-20016 plasmid free (as positive control)<br>Lb23. reuteri 100-23-pSBLb4C15-red (single-ori (pJP059) shuttle vector)<br>Lb24. reuteri DSM-20016-pSBLb4C15-red (--”--)<br>Lb25. reuteri 100-23-pSBLbC2-red (single-ori (pAMbeta1) shuttle vector)<br>Lb28. reuteri 100-23-pVS2-red (as competence test)<br><br><b>Restreak:</b><br>171. pSB3T5-J23110-B0034-4CL-B0034-STS<br>172. pSB3T5-CP1-B0034-TAL<br>173. pSB3T5-CP1-B0034-4CL-B0034-STS<br>174. pSB3T5-CP8-B0034-4CL-B0034-STS<br>175. pSB3T5-J23101-B0034-4CL-B0034-STS<br>185. pEL3S17-J23110-B0034-TAL-B0034-4CL-B0034-STS<br>186. pEL3S17-CP1-B0034-4CL-B0034-STS<br>187. pEL3S17-CP8-B0034-4CL-B0034-STS<br>188. pEL3S17-J23101-B0034-4CL-B0034-STS<br>189. pSB3K3-J23101-B0034-TAL<br><br><b>Ligation:</b><br>120. pSB1C3-B0034-His-4CL<br>173. pSB3T5-CP1-B0034-4CL-B0034-STS<br><br><b>Gel:</b><br>147.pSB1C3-B0034-Thioredoxin<br>165.pSB1C3-tsPurple<br>166.pSB1C3-scOrange<br>167.pSB1C3-fwYellow<br>19. CrtE~(O)-Z/w RBS, ZF<br>20. CrtE~Z/w RBS, ZF + gelextraction<br>21. CrtE~I/w RBS, ZF<br>Lb10. plantarum 256 p256 <br>169. pSBLbEcC2-red (20 clones)*<br><i>-* With the purpose of trying to find clones transformed with plasmids containing the pAMbeta1-ori as well as the E. coli ori.</i><br><br><b>Digest, ligate and transformation:</b> <br>90.1 BBa_J61002-J23101  to 139. pSB3K3-J23101-B0032-BFP<br><br>Two phase separation with octanol and acetic acid. Spectrophotometry of 106.5 and 106.6. Comparison between the Shimadzu UV160, Shimadzu UV1800, and the nanodrop.<br><br><h2>Results</h2><br><b>Gel:</b><br>147.pSB1C3-B0034-Thioredoxin - success<br>165.pSB1C3-tsPurple - success<br>166.pSB1C3-scOrange - success<br>167.pSB1C3-fwYellow - success<br>19. CrtE~(O)-Z/w RBS, ZF - No right band<br>20. CrtE~Z/w RBS, ZF - Right band slightly above 10000bp, thou weak and others,<br>21. CrtE~I/w RBS, ZF - Right band at around 8000bp<br>All tranformations but 176 failed. Ligatoins will be redone, but with pSB3T5 replaced with pEL3S17, as this backbone has shown better performance.<br><br><b>Transformation succes on construct:</b><br>173. pSB3T5-CP1-B0034-4CL-B0034-STS<br>174. pSB3T5-CP8-B0034-4CL-B0034-STS<br>175. pSB3T5-J23101-B0034-4CL-B0034-STS<br>185. pEL3S17-J23110-B0034-TAL-B0034-4CL-B0034-STS<br>186. pEL3S17-CP1-B0034-4CL-B0034-STS<br>187. pEL3S17-CP8-B0034-4CL-B0034-STS<br>188. pEL3S17-J23101-B0034-4CL-B0034-STS<br>189. pSB3K3-J23101-B0034-TAL<br><br><br></div>';
 +
}
 +
else if(id == 'd2013730')
 +
{
 +
  ds = '<div id="dairy-text"><h1>Tuesday 2013-07-30</h1><br><b>Name of participants:</b> Christoffer Ahlström (CA), Alona Nyberg (AN), Mikael Strandgren (MS), Malin, Magnus, Pontus, Nils, Christoffer, Sabri, Thorsteinn,  Marcus H, Karl H, Theodor L, Emil M, Victor S<br><br><h2>Ongoing constructs:</h2><br><b>E.coli:</b><br>169. pSBLbEcC2-red<br>191. pSB1A2-fusionGFP<br>108.pSBA15-J23106-B0034-IspA<br>109.pSBA15-K206000-B0034-IspA<br>110.pSBA15-K206001-B0034-IspA<br>143.pSB3T5-CP8-B0034-UGTCs2-6xHis<br>147.pSB1C3-B0034-Thioredoxin<br>163.pEL3S17-ZCD-His-B0034-UGTCs2-His<br>176.pSB1C3-B0034-Exp-Linker-Miraculin-His<br>177.pEL3S17-J23101-B0034-Exp-Linker-Miraculin-His<br>178.pEL3S17-J23110-B0034-Exp-Linker-Miraculin-His<br>179.pEL3S17-CP1-B0034-Exp-Linker-Miraculin-His<br>180.pEL3S17-CP8-B0034-Exp-Linker-Miraculin-His<br>181.pSBLb4C15-CP1-B0034-Exp-Linker-Miraculin-His<br>182.pSBLb4C15-CP8-B0034-Exp-Linker-Miraculin-His<br>193.pSB1C3-amilGFP<br>194.pSB1C3-B0034-amilCP<br>195.pSB1C3-cjBlue<br>196.pSB1C3-eforRed<br>197.pSB1C3-aeBlue<br>198.pSB1C3-B0034-amilGFP<br>199.pSb1C3-amajCFP<br>200.pSB1C3-B0034-asCP<br>104. pSB1C3-B0034-4CL-B0034-STS<br>105. pSB3T5-J23101-B0034-TAL<br>106. pSB3T5-J23110-B0034-TAL<br>107. pSB3T5-CP1-B0034-TAL<br>115. pSB3T5-J23101-B0034-His-TAL<br>116. pSB3T5-J23110-B0034-His-TAL<br>117. pSB3T5-CP1-B0034-His-TAL<br>119.pSB1C3-B0034-4CL<br>120.pSB1C3-B0034-HIS-4CL<br>121.pSB1C3-B0034-STS<br>121.pSB1C3-B0034-His-STS<br>137. pSB3K3-CP8-B0034-TAL<br>138. pSB3K3-CP8-B0034-His-TAL<br>139. pSB3K3-J23101-B0034-BFP<br>170. pSB3T5-J23110-B0034-TAL-B0034-4CL-B0034-STS<br>171. pSB3T5-J23110-B0034-4CL-B0034-STS<br>172. pSB3T5-CP1-B0034-TAL<br>173. pSB3T5-CP1-B0034-4CL-B0034-STS<br>174. pSB3T5-CP8-B0034-4CL-B0034-STS<br>175. pSB3T5-J23101-B0034-4CL-B0034-STS<br>185. pEL3S17-J23110-B0034-TAL-B0034-4CL-B0034-STS<br>186. pEL3S17-CP1-B0034-4CL-B0034-STS<br>187. pEL3S17-CP8-B0034-4CL-B0034-STS<br>188. pEL3S17-J23101-B0034-4CL-B0034-STS<br>189. pSB3K3-J23101-B0034-TAL<br><br><h2>Todays work</h2><br><b>Transformation: </b><br>191. pSB1A2-fusionGFP<br>183.pEL3A15-B0034-CrtZ<br>184.pSB1C3-B0034-CrtZ<br>120. pSB1C3-B0034-His-4CL<br>Spectrofotometry (using the nanodrop) of 106.5 and 106.6. Inconclusive results.<br><br><b>Screening:</b><br>140.pSB3T5-J23110-B0034-UGTCs2-His<br>141.pSB3T5-J23101-B0034-UGTCs2-6xHis<br>142.pSB3T5-CP1-B0034-UGTCs2-His.<br>171. pSB3T5-J23110-B0034-4CL-B0034-STS clone: 1,2,3,4<br>172. pSB3T5-CP1-B0034-TAL clone: 1,2,3,4<br><br><b>Plasmid preparation:</b><br>143.pSB3T5-CP8-B0034-UGTCs2-6xHis<br>147.pSB1C3-B0034-Thioredoxin<br>165.pSB1C3-tsPurple<br>166.pSB1C3-scOrange<br>167.pSB1C3-fwYellow<br><br><b>PCR:</b><br>19. CrtE~(O)-Z/w RBS, ZF<br>20. CrtE~Z/w RBS, ZF<br><br><b>Phosphorylation:</b><br>20. CrtE~Z/w RBS, ZF<br>21. CrtE~I/w RBS, ZF<br><br><b>Streaking of strains: </b><br>191. pSB1A2-fusionGFP<br><br><b>Re-streak:  </b><br>139. pSB3K3-J23101-B0032-BFP<br>185. pEL3S17-J23110-B0034-TAL-B0034-4CL-B0034-STS<br>186. pEL3S17-CP1-B0034-4CL-B0034-STS<br>187. pEL3S17-CP8-B0034-4CL-B0034-STS<br>188. pEL3S17-J23101-B0034-4CL-B0034-STS<br>189. pSB3K3-J23101-B0034-TAL<br>176.pSB1C3-B0034-Exp-Linker-Miraculin-His<br><br><b>Ligate and transformation: </b><br>90. BBa_J61002-J23101 to 139. pSB3K3-J23101-B0032-BFP<br><br><b>Digest and ligate: </b><br>162. pSB1C3-J23101 to 192.pSB3K3-J23101-B0032-BFP<br>58.pSB1C3-B0034-IspA, 5.pSB4K15-red, 91.BBa_J61002-J23106 --> 108.pSBA15-J23106-B0034-IspA<br>58.pSB1C3-B0034-IspA, 11.pSB4A15-red, 94.pSB1C3-K206000--> 109.pSBA15-K206000-B0034-IspA<br>58.pSB1C3-B0034-IspA, 11.pSB4A15-red, 95.pSB1C3-K206001 --> 110.pSBA15-K206001-B0034-IspA<br>36. pEL3S17-red, 125.1.pSB1C3-ZCD-His, 127.4.pSB1A3- B0034-UGTCs2-His -> 163. pEL3S17-ZCD-His-B0034-UGTCs2-His<br>152.pUC57-B0034-Exp-Linker-Miraculin-His(X,P), 36.pEL3S17-red, 103.pSB1K3-J23101 -> 177.pEL3S17-J23101-B0034-Exp-Linker-Miraculin-His<br>152.pUC57-B0034-Exp-Linker-Miraculin-His(X,P), 36.pEL3S17-red, 92.BBa_J61002(amp)_J23110 -> 178.pEL3S17-J23110-B0034-Exp-Linker-Miraculin-His<br>152.pUC57-B0034-Exp-Linker-Miraculin-His(X,P), 36.pEL3S17-red, CP1 -> 179.pEL3S17-CP1-B0034-Exp-Linker-Miraculin-His<br>152.pUC57-B0034-Exp-Linker-Miraculin-His(X,P), 36.pEL3S17-red, CP8 -> 180.pEL3S17-CP8-B0034-Exp-Linker-Miraculin-His<br>152.pUC57-B0034-Exp-Linker-Miraculin-His(X,P), 111.pSBLb4C15-red(E,P), CP1 -> 181.pSBLb4C15-CP1-B0034-Exp-Linker-Miraculin-His<br>152.pUC57-B0034-Exp-Linker-Miraculin-His(X,P), 111.pSBLb4C15-red(E,P), CP8 -> 182.pSBLb4C15-CP8-B0034-Exp-Linker-Miraculin-His<br><br><b>O/N, Frozen Stock:</b><br>193.pSB1C3-amilGFP<br>194.pSB1C3-B0034-amilCP<br>195.pSB1C3-cjBlue<br>196.pSB1C3-eforRed<br>197.pSB1C3-aeBlue<br>198.pSB1C3-B0034-amilGFP<br>199.pSb1C3-amajCFP<br>200.pSB1C3-B0034-asCP<br><br><b>Gel electrophoresis on:</b><br>171. pSB3T5-J23110-B0034-4CL-B0034-STS clone: 1,2,3,4<br>172. pSB3T5-CP1-B0034-TAL clone: 1,2,3,4<br><br><h2>Results</h2><br><b>Previous day: </b><br><br><b>Transformation:</b><br>Lb10. plantarum 256 p256 growing, possibly contaminated<br>Lb11. plantarum 256 plasmid free growing, possibly contaminated<br>Lb12. reuteri DSM-20016 plasmid free growing, possibly contaminated<br>Lb23. reuteri 100-23-pSBLb4C15-red: no growth<br>Lb24. reuteri DSM-20016-pSBLb4C15-red no growth<br>Lb25. reuteri 100-23-pSBLbC2-red no growth<br>Lb28. reuteri 100-23-pVS2-red no growth<br><i>→ Do new competent cells and transformation immediately</i><br><br><b>Today:</b><br><b>Screening-pcr/Gel electrophoresis: </b><br>169. pSBLbEcC2-red (20 clones): No correct bands, just smudges.<br><i>→ Screen 20 new colonies for correct plasmid, use phusion polymerase and pEL-primers, giving some kind of (bigger) fragments regardless of whether the clone has the correct plasmid or not. </i><br></div>';
 +
}
 +
else if(id == 'd2013731')
 +
{
 +
  ds = '<div id="dairy-text"><h1>Wednesday 2013-07-31</h1><br><b>Name of participants:</b> Magnus, Pontus, Sabri, Thorsteinn, Nils, Malin, Alona Nyberg (AN), Christoffer Ahlström (CA), Anton Berglund (AB), Mikael Strandgren (MS), Jens Isaksson (JI), Marcus H, Karl H, Theodor L, Emil M, Victor S, Hampus.E<br><br><h2>Ongoing constructs</h2><br><b>E.coli:</b><br>19.pSB4C5-pBAD/AraC-B0034-Jazz-Linker-CrtE-B0034-Blues-Linker-CrtB-B0034-CrtI-Linker-Zif268-B0034-PBSII-Linker-CrtY-B0034-CrtZ-Linker-Gli1<br>20.pSB4C5-pBAD/AraC-B0034-Jazz-Linker-CrtE-B0034-Blues-Linker-CrtB-B0034-CrtI-Linker-Zif268-B0034-PBSII-Linker-CrtY-B0034-CrtZ-Linker-Gli1<br>108.pSBA15-J23106-B0034-IspA<br>109.pSBA15-K206000-B0034-IspA<br>110.pSBA15-K206001-B0034-IspA<br>140.pSB3T5-J23110-B0034-UGTCs2-6xHis<br>141.pSB3T5-J23101-B0034-UGTCs2-6xHis<br>142.pSB3T5-CP1-B0034-UGTCs2-6xHis<br>143.pSB3T5-CP8-B0034-UGTCs2-6xHis<br>147.pSB1C3-B0034-Thioredoxin<br>163.pEL3S17-ZCD-His-B0034-UGTCs2-His<br>177.pEL3S17-J23101-B0034-Exp-Linker-Miraculin-His<br>178.pEL3S17-J23110-B0034-Exp-Linker-Miraculin-His<br>179.pEL3S17-CP1-B0034-Exp-Linker-Miraculin-His<br>180.pEL3S17-CP8-B0034-Exp-Linker-Miraculin-His<br>181.pSBLb4C15-CP1-B0034-Exp-Linker-Miraculin-His<br>182.pSBLb4C15-CP8-B0034-Exp-Linker-Miraculin-His<br>193.pSB1C3-amilGFP<br>194.pSB1C3-B0034-amilCP<br>195.pSB1C3-cjBlue<br>196.pSB1C3-eforRed<br>197.pSB1C3-aeBlue<br>198.pSB1C3-B0034-amilGFP<br>199.pSb1C3-amajCFP<br>200.pSB1C3-B0034-asCP<br>202.pSB4C5-CrtE-B0034-Blues-CrtB-B0034-CrtI-Linker-Zif268<br>203.pSB1C3-CrtE-B0034-Blues-Linker-CrtB-B0034-CrtI-Linker-Zif268-B0034-PBSII-Linker-CrtY-B0034-CrtZ-Linker-Gli1<br>207.pSB4C5-CrtE-B0034-Blues-Linker-CrtB-B0034-CrtI-Linker-Zif268-B0034-PBSII-Linker-CrtY-B0034-HivC-Linker-CrtO-B0034-CrtZ-Linker-Gli1<br>169. pSBLbEcC2-red<br>191. pSB1A2-fusionGFP<br>139. pSB3K3-J23101-B0032-BFP<br>192.pSB3K3-J23101-B0032-BFP<br>114. pSB1C3-B0034-TAL(MUT)<br>105. pSB3T5-J23101-B0034-TAL<br>107. pSB3T5-CP1-B0034-TAL<br>115. pSB3K5-J23101-B0034-His-TAL<br>116. pSB3T5-J23110-B0034-His-TAL<br>119.pSB1C3-B0034-4CL<br>120.pSB1C3-B0034-HIS-4CL<br>137. pSB3K3-CP8-B0034-TAL<br>138. pSB3K3-CP8-B0034-His-TAL<br>139. pSB3K3-J23101-B0034-BFP<br>171. pSB3T5-J23110-B0034-4CL-B0034-STS<br>172. pSB3T5-CP1-B0034-TAL<br>185. pEL3S17-J23110-B0034-TAL-B0034-4CL-B0034-STS<br>186. pEL3S17-CP1-B0034-4CL-B0034-STS<br>187. pEL3S17-CP8-B0034-4CL-B0034-STS<br>188. pEL3S17-J23101-B0034-4CL-B0034-STS<br>189. pSB3K3-J23101-B0034-TAL<br>204. pEL3S17-J23110-HIS-STS<br>205.pSBLB4C15-CP1-B0034-HIS-TAL<br>206.pSB1C3-J23101-B0034-TAL<br><br><b>L. reuteri:</b><br>4.1 100-23 no plasmid<br>12.1 DSM 20016 no plasmid<br><br><h2>Todays work</h2><br><b>Screening:</b><br>140.pSB3T5-J23110-B0034-UGTCs2-6xHis<br>141.pSB3T5-J23101-B0034-UGTCs2-6xHis<br>142.pSB3T5-CP1-B0034-UGTCs2-6xHis<br>176.pSB1C3-B0034-Exp-Linker-Miraculin-His<br>169. pSBLbEcC2-red (20 clones)<br> <br><b>Overnight:</b><br>142.pSB3T5-CP1-B0034-UGTCs2-6xHis<br>176.pSB1C3-B0034-Exp-Linker-Miraculin-His<br>Lb4.1 reuteri 100-23 no plasmid<br>Lb12.1 reuteri DSM 20016 no plasmid<br>172. pSB3T5-CP1-B0034-TAL (clone 3)<br>188. pEL3S17-J23101-B0034-4CL-B0034-STS (clone 3 and 4)<br>189. pSB3K3-J23101-B0034-TAL (clone 2 and 3)<br><br><b>Ligation:</b><br>202.pSB4C5-CrtE-B0034-Blues-CrtB-B0034-CrtI-Linker-Zif268<br>203.pSB1C3-CrtE-B0034-Blues-Linker-CrtB-B0034-CrtI-Linker-Zif268-B0034-PBSII-Linker-CrtY-B0034-CrtZ-Linker-Gli1<br>36.pEL3S17-Red, 127. pSB1A3-B0034-UGTCs2-His, 92.BBa_J61002 (amp)-J23110 -><br>140.pEL3S17-Red-J23110-B0034-UGTCs2-6xHis <br>36.pEL3S17-Red, 127. pSB1A3-B0034-UGTCs2-His, 90.BBa_J61002 (amp)-J23101 -> 141.pEL3S17-Red-J23101-B0034-UGTCs2-6xHis<br><br><b>Transformation:</b><br>99. pCB1C3 - CrtO<br>190. pEL3K16 - CrtO<br>108.pSBA15-J23106-B0034-IspA<br>109.pSBA15-K206000-B0034-IspA<br>110.pSBA15-K206001-B0034-IspA<br>140.pEL3S17-Red-J23110-B0034-UGTCs2-6xHis<br>141.pEL3S17-Red-J23101-B0034-UGTCs2-6xHis<br>143.pSB3T5-CP8-B0034-UGTCs2-6xHis<br>147.pSB1C3-B0034-Thioredoxin<br>163.pEL3S17-ZCD-His-B0034-UGTCs2-His<br>177.pEL3S17-J23101-B0034-Exp-Linker-Miraculin-His<br>178.pEL3S17-J23110-B0034-Exp-Linker-Miraculin-His<br>179.pEL3S17-CP1-B0034-Exp-Linker-Miraculin-His<br>180.pEL3S17-CP8-B0034-Exp-Linker-Miraculin-His<br>181.pSBLb4C15-CP1-B0034-Exp-Linker-Miraculin-His<br>182.pSBLb4C15-CP8-B0034-Exp-Linker-Miraculin-His<br>139. pSB3K3-J23101-B0032-BFP<br>192.pSB3K3-J23101<br><br><b>Re-Streak:</b><br>183.pEL3A15-B0034-CrtZ<br>184.pSB1C3-B0034-CrtZ<br>191.1 pSB1A2-fusionGFP<br>191.2 pSB1A2-fusionGFP<br>191.3 pSB1A2-fusionGFP<br>191.4 pSB1A2-fusionGFP<br>139. pSB3K3-J23101-B0032-BFP<br>192.pSB3K3-J23101-B0032-BFP<br><br><b>Gel:</b><br>207.pSB4C5-CrtE-B0034-Blues-Linker-CrtB-B0034-CrtI-Linker-Zif268-B0034-PBSII-Linker-CrtY-B0034-HivC-Linker-CrtO-B0034-CrtZ-Linker-Gli1  [Linear from PCR mutagenesis of 19] <br>203.pSB1C3-CrtE-B0034-Blues-Linker-CrtB-B0034-CrtI-Linker-Zif268-B0034-PBSII-Linker-CrtY-B0034-CrtZ-Linker-Gli1 [linear from PCR mutagenesis of 20]<br><br><b>Preparation for sequencing: </b><br>153. pSB1C3-j23110-meffBlue <br>155. pSB1C3-j23110-meffRed<br>156. pSB1C3-j23106-meffRed<br>157. pSB1C3-j23110-spisPink<br>159. pSB1C3-j23110-gfasPurple<br>160. pSB1C3-j23106-gfasPurple<br>150. pSB1C3-spispink<br>151. pSB1C3-meffblue<br>149. pSB1C3-meffred<br>148. pSB1C3-gfas purple<br><br><b>Assembly:</b><br>171. pSB3T5-J23110-B0034-4CL-B0034-STS<br>204. pEL3S17-J23110-HIS-STS<br>205.pSBLB4C15-CP1-B0034-HIS-TAL<br>206.pSB1C3-J23101-B0034-TAL<br><br><b>PCR cloning and screening on gel of constructs:</b><br>185. pEL3S17-J23110-B0034-TAL-B0034-4CL-B0034-STS<br>186. pEL3S17-CP1-B0034-4CL-B0034-STS<br>187. pEL3S17-CP8-B0034-4CL-B0034-STS<br>188. pEL3S17-J23101-B0034-4CL-B0034-STS<br>189. pSB3K3-J23101-B0034-TAL<br><br><h2>Results</h2><br><b>Screening:</b><br>140.pSB3T5-J23110-B0034-UGTCs2-6xHis Failed<br>141.pSB3T5-J23101-B0034-UGTCs2-6xHis Failed<br>142.pSB3T5-CP1-B0034-UGTCs2-6xHis One colony succeded<br>Tranformations of 108, 109, 110, 177, 141, 180, and 182 failed.<br>Tranformations of 163, 178 and 179 succeeded.<br>Transformations of 181 and 140 remain inconclusive.<br><br><b>Screening of PCR products:</b><br>188.3 , 188.4, 189.2 and 189.3 have correct bands on the gel<br><br><h2>Other experiments</h2><br>LB-agar plates making: <br>Ampicillin, 28 plates<br>Chloramphenicol, 30 plates<br>Kanamycin, 31 plates<br>Spectinomycin, 26 plates<br>Tetracycline, 29 plates<br></div>';
 +
}
else if(id == 'd201381')
else if(id == 'd201381')
  {
  {

Revision as of 20:12, 25 September 2013

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