Template:Team:Uppsala/JS/notebook

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Revision as of 23:36, 24 September 2013 (view source)

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'Lb13. Lc. lactis MG1363 pJP059: Good growth Lb16. Lc. lactis MG1363 noplasmid: Good growth Lb15. Lc. lactis MG1363-pGUS: Good growth 19. pSB4C5-CrtE~I /w RBS, Linker & ZF failed '+

'20. pSB4C5-CrtE~Z /w RBS, Linker & ZF failed 21. pSB4C5-CrtE~O-Z /w RBS, Linker & ZF failed 75. pEL3A15 - CrtB failed ';

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ds = '<div id="dairy-text"><h1>Wednesday 2013-07-03</h1> Name of participants: Lovisa P, Kristoffer L, Emil M, Marcus H, Karl H, Peter C, Ken B.-A, Nils A, Alexander W, Christoffer, Thorsteinn, Magnus, Christoffer Ahlström (CA), Mikael Strandgren (MS), Viktor Blomkvist (VB), Stephanie Herman (SH), Anton Berglund (AB) <h2>Ongoing constructs:</h2> E.coli (strain D5α): 1. pSB1C3-red 7. pSB3K3-red 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 61. pSB1C3-CP1 62. pSB1C3-CP8 63. pSB1C3-CP11 64. pSB1C3-CP29 65. pSB1C3-CP30 66. pSB1C3-CP41 67. pSB1C3-Cp44 77. pSB4C15-red L. plantarum: Lb10. 256-noplasmid Lb11. 36E-noplasmid L. reuteri: Lb12. DSM 20016-noplasmid L. lactis: Lb13. MG1363-pJP059 <h2>Todays work</h2> PCR: Lb13.2.3 Lc. lactis MG1363-pJP059 (plasmid)* Lb13.3 Lc. lactis MG1363-pJP059 (colony)* Lb13.4 Lc. lactis MG1363-pJP059 (colony)* *Two PCR tubes of 13.2.3 were prepared along with one of 13.3 and one of 13.4. Lb13.2.2 lactis MG1363 pJP059 (plasmid)** Lb13.2.3 lactis MG1363 pJP059 (plasmid)** Lb13.3 lactis MG1363 pJP059 (colony)** Lb13.4 Lc. lactis MG1363 pJP059 (colony)** **Gel will be done tomorrow. Followed the PCR protocol with DMSO. 78. pEL3C18-CrtY* -*PCR of CrtZ with lower ™-temp(62 insted of 63.6 which was used last time) Digest: 43. pSB1C3-B0034-TAL 44. pSB1C3-B0034-His-TAL 25. pSB1C3-CrtY 27. pEL3K16-red 51. pEL3C18-red Ligation: 43. pSB1C3-B0034-TAL 44. pSB1C3-B0034-His-TAL 75. pEL3A15-CrtB 76. pEL3K16-CrtI 78. pEL3C18-CrtY 1. pSB1C3-red -as N/C, one that we use plus a digest that has worked for other groups 7. pSB3K3-red -as N/C, one that we use plus a digest that has worked for other groups 42. pSB4S15-red 61. pSB1C3-CP1 62. pSB1C3-CP8 63. pSB1C3-CP11 64. pSB1C3-CP29 65. pSB1C3-CP30 66. pSB1C3-CP41 67. pSB1C3-Cp44 77. pSB4C15-red -*We increased the incubation time from 30 min. to 90 min. We also added T4 DNA ligase to the already ligated plasmids we used for transformation yesterday and left them to incubate over night, since we suspect incomplete ligation may be the explanation for the bad results (digests have appeared ok on gel). Thus if transformations fail again, we can use the definitely ligated plasmids to do another immediately in the morning. Transformation: 43. pSB1C3-B0034-TAL 44. pSB1C3-B0034-His-TAL 75. pEL3A15-CrtB 76. pEL3K16-CrtI 78. pEL3C18-CrtY 42. pSB4S15-red 61. pSB1C3-CP1 62. pSB1C3-CP8 63. pSB1C3-CP11 64. pSB1C3-CP29 65. pSB1C3-CP30 66. pSB1C3-CP41 67. pSB1C3-Cp44 77 pSB4C15-red O/N: Lb10.1. plantarum 256 no plasmid Lb11.1. plantarum 36E no plasmid Lb12.1 reuteri DSM 20016 no plasmid Restreak: 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 62. pSB1C3-CP8 63. pSB1C3-CP11 64. pSB1C3-CP29 65. pSB1C3-CP30 67. pSB1C3-Cp44 Plasmid preparation: 7.pSB3K3 22.pSB1C3-B0032-BFP 42. pSB4S15-red Gelelectrophoresis: 19. pSB4C5-pBAD/AraC-B0034-Jazz-Linker-CrtE-B0034-Blues-Linker-CrtB-B0034-CrtI-Linker-Zif268-B0034-PBSII-Linker-CrtY-B0034-HivC-Linker-CrtO-B0034-CrtZ-Linker-Gli1 20. pSB4C5-pBAD/AraC-B0034-Jazz-Linker-CrtE-B0034-Blues-Linker-CrtB-B0034-CrtI-Linker-Zif268-B0034-PBSII-Linker-CrtY-B0034-CrtZ-Linker-Gli1 21. pSB4C5-pBAD/AraC-B0034-Jazz-Linker-CrtE-B0034-Blues-Linker-CrtB-B0034-CrtI-Linker-Zif268 78. pEL3C18-CrtY 25. pSB1C3-CrtY 27. pEL3K16-red 51. pEL3C18-red Lb13.2.3 Lc. lactis MG1363-pJP059* Lb13.3 Lc. lactis MG1363-pJP059* Lb13.4 Lc. lactis MG1363-pJP059* *Of first PCR. Two PCR tubes of 13.2.3 were prepared along with one of 13.3 and one of 13.4. Results Gelelectrophoresis: successful: 25. pSB1C3-CrtY 27. pEL3K16-red 51. pEL3C18-red -Digestion Worked failed: 19. pSB4C5-pBAD/AraC-B0034-Jazz-Linker-CrtE-B0034-Blues-Linker-CrtB-B0034-CrtI-Linker-Zif268-B0034-PBSII-Linker-CrtY-B0034-HivC-Linker-CrtO-B0034-CrtZ-Linker-Gli1 20. pSB4C5-pBAD/AraC-B0034-Jazz-Linker-CrtE-B0034-Blues-Linker-CrtB-B0034-CrtI-Linker-Zif268-B0034-PBSII-Linker-CrtY-B0034-CrtZ-Linker-Gli1 21. pSB4C5-pBAD/AraC-B0034-Jazz-Linker-CrtE-B0034-Blues-Linker-CrtB-B0034-CrtI-Linker-Zif268 78. pEL3C18-CrtY Lb13.2.3 Lc. lactis MG1363-pJP059(plasmid)* Lb13.3 Lc. lactis MG1363-pJP059 (colony)* Lb13.4 Lc. lactis MG1363-pJP059 (colony)* -*The gel showed nothing but primer dimer. Digest: successful: 25. pSB1C3-CrtY 27. pEL3K16-red 51. pEL3C18-red Yesterdays transformation: successful: 61. pSB1C3-CP1: Growth 61. pSB1C3-CP1 10x: Some growth 62. pSB1C3-CP8: Some growth 62. pSB1C3-CP8 10x: No growth 63. pSB1C3-CP11: Some growth 63. pSB1C3-CP11 10x: No growth 64. pSB1C3-CP29: Some growth 64. pSB1C3-CP29 10x: No growth 65. pSB1C3-CP30: Some growth 65. pSB1C3-CP30 10x: No growth 66. pSB1C3-CP41: Growth 66. pSB1C3-CP41 10x: Some growth 67. pSB1C3-Cp44: No growth 67. pSB1C3-Cp44 10x: No growth 68. pSB3K3-CP1-B0032-BFP: No growth 68. pSB3K3-CP1-B0032-BFP 10x: Growth 69. pSB3K3-CP8-B0032-BFP: Growth, possibly contaminated 69. pSB3K3-CP8-B0032-BFP 10x: No growth 70. pSB3K3-CP11-B0032-BFP: Growth 70. pSB3K3-CP11-B0032-BFP 10x: Growth 71. pSB3K3-CP29-B0032-BFP: Growth, olly red colonies 71. pSB3K3-CP29-B0032-BFP 10x: ----- 72. pSB3K3-CP30-B0032-BFP: Growth 72. pSB3K3-CP30-B0032-BFP 10x: No growth 73. pSB3K3-CP41-B0032-BFP: Some growth, only red colonies 73. pSB3K3-CP41-B0032-BFP 10x: No growth 77.1 pSB4C15, clone 1: No growth 77.1 pSB4C15, clone 1 10x: No growth 77.2 pSB4C15, clone 2: Some growth 77.2 pSB4C15, clone 2 10x: No growth 23. pSB1C3-CrtB 24. pSB1C3-CrtI 27. pEL3K16-red 38. pEL3A15-red 51. pEL3C18-red failed: 81. pSB4S15-CP41: No growth 82. pSB4S15-CP29: No growth 83. pSB4S15-CP30: No growth → Redo ligation and transformation. Plasmid preparation: 7.3 pSB3K3 clone 3: 50.1 ng/µl 7. 4 pSB3K3 clone 4: 43.4 ng/µl 7. 5 pSB3K3 clone 5: 48.1 ng/µl 22.1.1 pSB1C3-B0032-BFP clone 1.1: 196.2 ng/µl 22.2.1 pSB1C3-B0032-BFP clone 2.1: 174.3 ng/µ 22.2.2 pSB1C3-B0032-BFP clone 2.2: 189.9 ng/µ 42.1 pSB4S15-red clone 1: 43.6 ng/µl 42.2 pSB4S15-red clone 2: 46.1 ng/µl <h2>Other experiments</h2> Made agarplates with chloramphenicol resistance MRS-broth preparation MRS-broth-agar preparation MRS-broth-agar plates preparation </div>';

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ds = '<div id="dairy-text"><h1>Tuesday 2013-07-02</h1> Name of participants: Christoffer Ahlström (CA), Nafisa Bashir (NB), Viktor Törnblom (VT), Anton Berglund (AB), Mikael Strandgren (MS), Viktor Blomkvist (VB), Thorsteinn O, Magnus B, Nils A, Alexander W, Christoffer F, Lovisa P, Kristoffer L, Emil M, Marcus H, Karl H, Peter C, Ken B.-A. <h2>Ongoing constructs:</h2> L. reuteri: 1. CF48-pLR581 2. 1063-pLUL631 3. DSM 20016-pVs2 4. 100-23-noplasmid 6. DSM 20016-pLUL63TsA8 7. DSM 20016-pGFP 8. 100-23-pGT232 12. DSM 20016-noplasmid 14. DSM 20016-pLUL631(B?) L. plantarum: 5. 256-rifR-pAMβ1 10. 256-noplasmid 11. 36E-noplasmid E. faecalis: 9. JH2-2 pAMβ1 L. lactis: 13. MG1363-pJP059 15. unknown-pGus 16. MG1363-noplasmid E.coli (strain D5α): 42. pSB4S15-red 60. PK401 dam 61. pSB1C3-CP1 62. pSB1C3-CP8 63. pSB1C3-CP11 64. pSB1C3-CP29 65. pSB1C3-CP30 66. pSB1C3-CP41 67. pSB1C3-Cp44 68. pSB3K3-CP1-B0032-BFP 69.pSB3K3-CP8-B0032-BFP 70. pSB3K3-CP11-B0032-BFP 71. pSB3K3-CP29-B0032-BFP 72. pSB3K3-CP30-B0032-BFP 73. pSB3K3-CP41-B0032-BFP 74. pSB3K3-Cp44-B0032-BFP 77. pSB4C15 81. pSB4S15-CP41 82. pSB4S15-CP29 83. pSB4S15-CP30 57. pSB1C3-B0034-Idi 58. pSB1C3-B0034-ispA 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 Lb. delbrueckii bulgaricus: 18. Lb. delbrueckii bulgaricus L. thermophilus: 19. Lc.thermophilus <h2>Todays work</h2> O/N: 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) Lb10.1. plantarum 256 no plasmid Lb11.1. plantarum 36E no plasmid Lb12.1 reuteri DSM 20016 Lb19.5 L. thermophilus Lb19.6 L. thermophilus 7.3. pSB3K3-red 7.4. pSB3K3-red 7.5. pSB3K3-red 22.1.1. pSB1C3 22.2.1. pSB1C3 22.2.2. pSB1C3 42.1.1. pSB4S15-red 42.1.2. pSB4S15-red 42.1.3. pSB4S15-red Digest: Lb9.4 faecalis JH2-2 pAMβ1 45. pSB1C3-B0034-4CL 46. pSB1C3-B0034-His-4CL 47. pSB1C3-B0034-STS 48. pSB1C3-B0034-His-STS Gel electrophoresis: Lb9.4 faecalis JH2-2 pAMβ1 Frozen stock: Lb13.3. Lc. lactis MG1363 pJP059 clone 3 Lb13.4. Lc. lactis MG1363 pJP059 clone 4 Lb15.3. Lc. lactis MG1363 pGus clone 3 Lb15.4. Lc. lactis MG1363 pGus clone 4 Lb16.3. Lc. lactis MG1363 noplasmid clone 3 Lb16.4. Lc. lactis MG1363 noplasmid clone 4 Plasmid preparation: Lb13.3. Lc. lactis MG1363 pJP059 clone 3 Lb13.4. Lc. lactis MG1363 pJP059 clone 4 Lb15.3. Lc. lactis MG1363 pGus clone 3 Lb15.4. Lc. lactis MG1363 pGus clone 4 PCR: Lb13.1 Lc. lactis MG1363 pJP059 Lb13.2 Lc. lactis MG1363 pJP059 Lb13.3 Lc. lactis MG1363 pJP059 Lb13.4 Lc. lactis MG1363 pJP059 The primers for usp45 were used in order to amplify the usp45 signal peptide from the L. lactis chromosome. A gel was run to confirm fragment size. 43. pSB1C3-B0034-TAL 44. pSB1C3-B0034-His-TAL Gel electrophoresis: Lb13.1 Lc. lactis MG1363 pJP059 Lb13.2 Lc. lactis MG1363 pJP059 Lb13.3 Lc. lactis MG1363 pJP059 Lb13.4 Lc. lactis MG1363 pJP059 1. pSB1C3-red (cut with EcoRI and SpeI today) 1. pSB1C3-red (cut with EcoRI and SpeI saturday) 7. pSB3K3-red (cut with EcoRI and PstI today) 22. pSB1C3-B0032-BFP (cut with XbaI and PstI saturday) 42. pSB4S15-red (EcoRI and SpeI today) 42. pSB4S15-red (cut with SalI and SacI saturday) 43. pSB1C3-B0034-TAL 44. pSB1C3-B0034-His-TAL Re-streak from frozen stock: Lb12.1 reuteri DSM 20016 no plasmid Lb12.2 reuteri DSM 20016 no plasmid Two re-streaks of each clone were made on two antibiotics free plates. Re-streak: Lb19.1 L. thermophilus Lb19.2 L. thermophilus Lb19.3 L. thermophilus Lb19.4 L. thermophilus Lb19.7 L. thermophilus Lb19.8 L. thermophilus Lb19.9 L. thermophilus Lb19.10 L. thermophilus Streaking of yogurt culture: Lb18. Lb. delbrueckii bulgaricus Lb19. Lactococcus Thermophilus Assembly and subcloning: 61. pSB1C3-CP1 62. pSB1C3-CP8 63. pSB1C3-CP11 64. pSB1C3-CP29 65. pSB1C3-CP30 66. pSB1C3-CP41 67. pSB1C3-Cp44 68. pSB3K3-CP1-B0032-BFP 69.pSB3K3-CP8-B0032-BFP 70. pSB3K3-CP11-B0032-BFP 71. pSB3K3-CP29-B0032-BFP 72. pSB3K3-CP30-B0032-BFP 73. pSB3K3-CP41-B0032-BFP 74. pSB3K3-Cp44-B0032-BFP 77.1 pSB4C15, clone 1 77.2 pSB4C15, clone 2 had less of plasmid 42 because it ran out. 81. pSB4S15-CP41 82. pSB4S15-CP29 83. pSB4S15-CP30 45. pSB1C3-B0034-4CL 46. pSB1C3-B0034-His-4CL 47. pSB1C3-B0034-STS 48. pSB1C3-B0034-His-STS Transformation: 61. pSB1C3-CP1 * 62. pSB1C3-CP8 63. pSB1C3-CP11 * 64. pSB1C3-CP29 65. pSB1C3-CP30 66. pSB1C3-CP41 67. pSB1C3-Cp44 68. pSB3K3-CP1-B0032-BFP 69.pSB3K3-CP8-B0032-BFP * 70. pSB3K3-CP11-B0032-BFP 71. pSB3K3-CP29-B0032-BFP * 72. pSB3K3-CP30-B0032-BFP * 73. pSB3K3-CP41-B0032-BFP * 74. pSB3K3-Cp44-B0032-BFP 77. pSB4C15, clone 1 77.2 pSB4C15, clone 2 * 81. pSB4S15-CP41 * 82. pSB4S15-CP29 83. pSB4S15-CP30 45. pSB1C3-B0034-4CL 46. pSB1C3-B0034-His-4CL 47. pSB1C3-B0034-STS 48. pSB1C3-B0034-His-STS * Those marked were incubated for maybe 25 minutes longer. Subcloning of 57 and 58 into pSB1C3 (from 1. pSB1C3-Red). PCR of Crt Z(with 7% DMSO), 19, 20, 21(now with VF2, VR and culture) Gelelectroforesis of CrtE, CrtZ, 19, 20, 21 Transformation of 23, 24, 27, 38, 51. <h2>Results</h2> Previous day: O/N: Lb13.3 Lc. lactis MG1363 pJP059 clone 3: Good growth, NC ok! Lb13.4 Lc. lactis MG1363 pJP059 clone 4: Good growth, NC ok! Lb15.3 Lc. lactis MG1363 pGus clone 3: Good growth, NC ok! Lb15.4 Lc. lactis MG1363 pGus clone 4: Good growth, NC ok! → Continue with frozen stock and plasmid preparation. Assembly and transformation: 61. pSB1C3-CP1: Nothing 61. pSB1C3-CP1 10x: Nothing 62. pSB1C3-CP8: Growth 62. pSB1C3-CP8 10x: Nothing 63. pSB1C3-CP11: Growth 63. pSB1C3-CP11 10x: Nothing 64. pSB1C3-CP29: Growth 64. pSB1C3-CP29 10x: Nothing 65. pSB1C3-CP30: Growth 65. pSB1C3-CP30 10x: Nothing 66. pSB1C3-CP41: Nothing 66. pSB1C3-CP41 10x: Nothing 67. pSB1C3-Cp44: Growth 67. pSB1C3-Cp44 10x: Nothing 77. pSB4C15-red: Nothing 77. pSB4C15-red 10x: Nothing 45. pSB1C3-B0034-4CL Growth 46. pSB1C3-B0034-His-4CL Growth 47. pSB1C3-B0034-STS Growth 48. pSB1C3-B0034-His-STS Growth → Redo with extra care, look over the protocols, use new ligase and ligation buffer. Today: Gel electrophoresis: 43. pSB1C3-B0034-TAL Good bands 44. pSB1C3-B0034-His-TAL Good bands Lb13.1 Lc. lactis MG1363-pJP059 13.2 Lc. lactis MG1363-pJP059 13.3 Lc. lactis MG1363-pJP059 13.4 Lc. lactis MG1363-pJP059 Lb9.4 faecalis JH2-2 pAMβ1 Faint blurry bands* 1. pSB1C3-red (cut with EcoRI and SpeI today) Good bands 1. pSB1C3-red (cut with EcoRI and SpeI saturday) Good bands 7. pSB3K3-red (cut with EcoRI and PstI today) Good bands 22. pSB1C3-B0032-BFP (cut with XbaI and PstI saturday) Nothing** 42. pSB4S15-red (EcoRI and SpeI today) Nothing** 42. pSB4S15-red (cut with SalI and SacI saturday) Nothing** → 1 and 7 were ok, they could be reused. *The results were consistent with yesterdays Gel electrophoresis: Very faint smudged bands that lets us think there is only chromosomal DNA in this plasmid preparation. **The results indicate that something may be wrong with the digests of 42. and 22., this may be one of the explanations of why we got no colonies of 77. but many of 61-67. Plasmid preparation: Lb13.3. Lc. lactis MG1363 pJP059 clone 3: 13.4 ng/µl Lb13.4. Lc. lactis MG1363 pJP059 clone 4: 10.3 ng/µl Lb15.3. Lc. lactis MG1363 pGus clone 3: 11.9 ng/µl Lb15.4. Lc. lactis MG1363 pGus clone 4: 12.0 ng/µl → Dispose, to low concentration. Re-do a plasmid preparation from O/N with optimized conditions. Gel showed fail of PCR for 19,20, 21 Gel showed succes of CrtE, but fail of CrtZ(no primer dimers tho) Plates from yesterday showed fail of subclone/transformation <h2>Other experiments</h2> Made agarplates with chloramphenicol resistance Microscopy: Confirming Lc.thermophilus colonies on the yoghurt-plate from the previous day. Confirming contamination on some plates with competent cells. Primer design of lambda red, Crt Y, I and B both F and R </div>';

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ds ='~~på dig~~';

+

ds = '<div id="dairy-text"><h1>Monday 2013-07-01</h1> Name of participants: Lovisa P, Kristoffer L, Emil M, Marcus H, Karl H, Peter C, Christoffer, Nils, Magnus, Alexander, Anders Edlund (AE), Mikael Strandgren (MS), Christoffer Ahlström (CA), Viktor Blomkvist (VB), Viktor Törnblom(VT), Nafisa Bashir (NB), Anton Berglund (AB) <h2>Ongoing constructs:</h2> E.coli (strain D5α): 7. pSB3K3-red 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 61. pSB1C3-CP1 62. pSB1C3-CP8 63. pSB1C3-CP11 64. pSB1C3-CP29 65. pSB1C3-CP30 66. pSB1C3-CP41 67. pSB1C3-Cp44 77. pSB4C15-red 1. pSB1C3-red 60.PK401 dam- L. plantarum: Lb5. 256-rifR-pAMβ1 E. faecalis: Lb9. JH2-2 pAMβ1 L. reuteri: Lb12. DSM 20016-noplasmid L. lactis: Lb15 unknown-pGus Lb. delbrueckii bulgaricus: 18. Lb. delbrueckii bulgaricus L. thermophilus: 19. L.thermophilus <h2>Todays work</h2> Gel electrophoresis: 45. pSB1C3-B0034-4CL 46. pSB1C3-B0034-His-4CL 47. pSB1C3-B0034-STS 48. pSB1C3-B0034-His-STS Lb9.4 faecalis JH2-2 pAMβ1 CBP amplicon from reuteri DSM 20016 usp45 amplicon from lactis strain MG1363 PCR: 45. pSB1C3-B0034-4CL 46. pSB1C3-B0034-His-4CL 47. pSB1C3-B0034-STS 48. pSB1C3-B0034-His-STS 6 colonies of DSM 20016 strain reuteri 4 colonies of MG1363 strain lactis The PCR was carried out with the CBP primers for reuteri and the usp45 primers for lactis. This in order to isolate the signal peptides from each species. O/N: Lb13. Lc. lactis MG1363 pJP059 clone 3 Lb13. Lc. lactis MG1363 pJP059 clone 4 Lb15. Lc. lactis MG1363 pGus clone 3 Lb15. Lc. lactis MG1363 pGus clone 4 7. pSB3K3-red Frozen stock: Lb5.2 plantarum 256 pAMβ1 Lb9. faecalis JH2-2 pAMβ1 clone 4 1. pSB1C3-red 60.PK401 dam Re-streak: Lb9. faecalis JH2-2 pAMβ1 Lb12. reuteri DSM20016 no plasmid Plasmid preparation: Lb5.2 plantarum 256 pAMβ1 Lb9. faecalis JH2-2 pAMβ1 clone 4 1. pSB1C3-red Digest: Lb9.4 faecalis JH2-2 pAMβ1 (To rule out chromosomal contamination in prep) Assembly: 61. pSB1C3-CP1 62. pSB1C3-CP8 63. pSB1C3-CP11 64. pSB1C3-CP29 65. pSB1C3-CP30 66. pSB1C3-CP41 67. pSB1C3-Cp44 77. pSB4C15-red Transformation: 61. pSB1C3-CP1 62. pSB1C3-CP8 63. pSB1C3-CP11 64. pSB1C3-CP29 65. pSB1C3-CP30 66. pSB1C3-CP41 67. pSB1C3-Cp44 77. pSB4C15-red* *We made a transformation with one sample of 77-digest from today, and one from yesterday to try to see if the problem yesterday laid with the assembly or with the transformation Streaking of yogurt culture: 18. Lb. delbrueckii bulgaricus 19. Lactococcus Thermophilus PCR of Crt E, Crt Z, 19, 20, 21, Idi Gelelectroforisis of Crt E, Crt Z, Idi Transformation of 75, 76, 78, 58 Subcloning of IspA ->58 Digest of Idi Ligation of 76, 78 <h2>Results</h2> Previous day: Assembly and transformation: 61. pSB1C3-CP1: No growth 62. pSB1C3-CP8: No growth 63. pSB1C3-CP11: No growth 64. pSB1C3-CP29: No growth 65. pSB1C3-CP30: No growth 66. pSB1C3-CP41: No growth 67. pSB1C3-Cp44: No growth 77. pSB4C15-red: No growth → Re-do all steps, but do one transformation with ligations from yesterday Today: Plasmid preparation: Lb5.2 plantarum 256 pAMβ1 clone 2: 50.7 ng/µl Lb9.4 faecalis JH2-2 pAMβ1 clone 4: 403.7 ng/µl 1.1 pSB1C3-red clone 1: 144.0 ng/µl 1.2 pSB1C3-red clone 2: 96.8 ng/µl Gel electrophoresis: Lb9.4 faecalis JH2-2 pAMβ1* *Very faint smudges that could be a shadow from the dye. Will follow up tomorrow with another gel electrophoresis of a new digest. CBP amplicon from reuteri DSM 20016** usp45 amplicon from lactis strain MG1363** **None of the PCRs showed the desired bands on the gel. PCR with good results: 45. pSB1C3-B0034-4CL 46. pSB1C3-B0034-His-4CL (Note: weak band) 47. pSB1C3-B0034-STS 48. pSB1C3-B0034-His-STS - Very good results on the pcr Gel of Crt E and Crt Z was failed at Ethylium Bromide bath. Redo gel Gel of Idi showed succes, proceed to subclone. Subclone of IspA showed only red colonies. IspA was incorrectly digested with E instead of X. -dunno what this is! :S <h2>Other experiments</h2> M17-broth agar preparation M17-broth medium preparation SET-buffer preparation Preparation of M17 plates</div>';

}

else if(id == 'd2013721')

@@ Line 233: / Line 233: @@
 'Lb13. Lc. lactis MG1363 pJP059: Good growth<br>Lb16. Lc. lactis MG1363 noplasmid: Good growth<br>Lb15. Lc. lactis MG1363-pGUS: Good growth<br><br>19. pSB4C5-CrtE~I /w RBS, Linker & ZF failed<br>'+
   '20. pSB4C5-CrtE~Z /w RBS, Linker & ZF failed<br>21. pSB4C5-CrtE~O-Z /w RBS, Linker & ZF failed<br>75. pEL3A15 - CrtB failed<br><br>';
+ }
+  else if(id == 'd201373')
+ {
+  ds = '<div id="dairy-text"><h1>Wednesday 2013-07-03</h1><br><b>Name of participants:</b> Lovisa P, Kristoffer L, Emil M, Marcus H, Karl H, Peter C, Ken B.-A,  Nils A, Alexander W, Christoffer, Thorsteinn, Magnus, Christoffer Ahlström (CA), Mikael Strandgren (MS), Viktor Blomkvist (VB), Stephanie Herman (SH), Anton Berglund (AB)<br><br><h2>Ongoing constructs:</h2><br><b>E.coli (strain D5α):</b><br>1. pSB1C3-red<br>7. pSB3K3-red<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>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>77. pSB4C15-red<br><br><b>L. plantarum:</b><br>Lb10. 256-noplasmid<br>Lb11. 36E-noplasmid<br><br><br><b>L. reuteri:</b><br>Lb12. DSM 20016-noplasmid<br><br><b>L. lactis:</b><br>Lb13. MG1363-pJP059<br><br><h2>Todays work</h2><br><b>PCR:</b><br>Lb13.2.3 Lc. lactis MG1363-pJP059 (plasmid)*<br>Lb13.3 Lc. lactis MG1363-pJP059	  (colony)*<br>Lb13.4 Lc. lactis MG1363-pJP059	  (colony)*<br><i>*Two PCR tubes of 13.2.3 were prepared along with one of 13.3 and one of 13.4.</i><br>Lb13.2.2 lactis MG1363 pJP059	(plasmid)**<br>Lb13.2.3 lactis MG1363 pJP059	(plasmid)**<br>Lb13.3 lactis MG1363 pJP059		(colony)**<br>Lb13.4 Lc. lactis MG1363 pJP059	(colony)**<br><i>**Gel will be done tomorrow. Followed the PCR protocol with DMSO.</i><br>78. pEL3C18-CrtY*<br><i>-*PCR of CrtZ with lower ™-temp(62 insted of 63.6 which was used last time)</i><br><br>Digest:<br>43. pSB1C3-B0034-TAL<br>44. pSB1C3-B0034-His-TAL<br>25. pSB1C3-CrtY<br>27. pEL3K16-red<br>51. pEL3C18-red<br><br><b>Ligation:</b><br>43. pSB1C3-B0034-TAL<br>44. pSB1C3-B0034-His-TAL<br>75. pEL3A15-CrtB<br>76. pEL3K16-CrtI<br>78. pEL3C18-CrtY<br>1. pSB1C3-red <i>-as N/C, one that we use plus a digest that has worked for other groups<i><br>7. pSB3K3-red <i>-as N/C, one that we use plus a digest that has worked for other groups<i><br>42. pSB4S15-red<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>77. pSB4C15-red<br><i>-*We increased the incubation time from 30 min. to 90 min. We also added T4 DNA ligase to the already ligated plasmids we used for transformation yesterday and left them to incubate over night, since we suspect incomplete ligation may be the explanation for the bad results (digests have appeared ok on gel). Thus if transformations fail again, we can use the definitely ligated plasmids to do another immediately in the morning.</i><br><br><b>Transformation:</b><br>43. pSB1C3-B0034-TAL<br>44. pSB1C3-B0034-His-TAL<br>75. pEL3A15-CrtB<br>76. pEL3K16-CrtI<br>78. pEL3C18-CrtY<br>42. pSB4S15-red<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>77 pSB4C15-red<br><br><b>O/N:</b><br>Lb10.1. plantarum 256 no plasmid<br>Lb11.1. plantarum 36E no plasmid <br>Lb12.1 reuteri DSM 20016 no plasmid<br><br><b>Restreak:</b><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>62. pSB1C3-CP8<br>63. pSB1C3-CP11<br>64. pSB1C3-CP29<br>65. pSB1C3-CP30<br>67. pSB1C3-Cp44<br><br><b>Plasmid preparation:</b><br>7.pSB3K3<br>22.pSB1C3-B0032-BFP<br>42. pSB4S15-red<br><br><b>Gelelectrophoresis:</b><br>19. pSB4C5-pBAD/AraC-B0034-Jazz-Linker-CrtE-B0034-Blues-Linker-CrtB-B0034-CrtI-Linker-Zif268-B0034-PBSII-Linker-CrtY-B0034-HivC-Linker-CrtO-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>21. pSB4C5-pBAD/AraC-B0034-Jazz-Linker-CrtE-B0034-Blues-Linker-CrtB-B0034-CrtI-Linker-Zif268<br>78. pEL3C18-CrtY<br>25. pSB1C3-CrtY<br>27. pEL3K16-red<br>51. pEL3C18-red<br>Lb13.2.3 Lc. lactis MG1363-pJP059*<br>Lb13.3 Lc. lactis MG1363-pJP059*<br>Lb13.4 Lc. lactis MG1363-pJP059*<br><i>*Of first PCR. Two PCR tubes of 13.2.3 were prepared along with one of 13.3 and one of 13.4.</i><br><br><b>Results</b><br><b>Gelelectrophoresis:</b><br><b>successful:</b><br>25. pSB1C3-CrtY<br>27. pEL3K16-red<br>51. pEL3C18-red<br><i>-Digestion Worked</i><br><br><b>failed:</b><br>19. pSB4C5-pBAD/AraC-B0034-Jazz-Linker-CrtE-B0034-Blues-Linker-CrtB-B0034-CrtI-Linker-Zif268-B0034-PBSII-Linker-CrtY-B0034-HivC-Linker-CrtO-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>21. pSB4C5-pBAD/AraC-B0034-Jazz-Linker-CrtE-B0034-Blues-Linker-CrtB-B0034-CrtI-Linker-Zif268<br>78. pEL3C18-CrtY<br>Lb13.2.3 Lc. lactis MG1363-pJP059(plasmid)*<br>Lb13.3 Lc. lactis MG1363-pJP059	(colony)*<br>Lb13.4 Lc. lactis MG1363-pJP059	(colony)*<br><i>-*The gel showed nothing but primer dimer.</i><br><br><b>Digest:</b><br><b>successful:</b><br>25. pSB1C3-CrtY<br>27. pEL3K16-red<br>51. pEL3C18-red<br><br><b>Yesterdays transformation:</b><br><b>successful:</b><br>61. pSB1C3-CP1: Growth<br>61. pSB1C3-CP1 10x: Some growth<br>62. pSB1C3-CP8: Some growth<br>62. pSB1C3-CP8 10x: No growth<br>63. pSB1C3-CP11: Some growth<br>63. pSB1C3-CP11 10x: No growth<br>64. pSB1C3-CP29: Some growth<br>64. pSB1C3-CP29 10x: No growth<br>65. pSB1C3-CP30: Some growth<br>65. pSB1C3-CP30 10x: No growth<br>66. pSB1C3-CP41: Growth<br>66. pSB1C3-CP41 10x: Some growth<br>67. pSB1C3-Cp44: No growth<br>67. pSB1C3-Cp44 10x: No growth<br>68. pSB3K3-CP1-B0032-BFP: No growth<br>68. pSB3K3-CP1-B0032-BFP 10x: Growth<br>69. pSB3K3-CP8-B0032-BFP: Growth, possibly contaminated<br>69. pSB3K3-CP8-B0032-BFP 10x: No growth<br>70. pSB3K3-CP11-B0032-BFP: Growth<br>70. pSB3K3-CP11-B0032-BFP 10x:  Growth<br>71. pSB3K3-CP29-B0032-BFP: Growth, olly red colonies<br>71. pSB3K3-CP29-B0032-BFP 10x: -----<br>72. pSB3K3-CP30-B0032-BFP: Growth<br>72. pSB3K3-CP30-B0032-BFP 10x: No growth<br>73. pSB3K3-CP41-B0032-BFP: Some growth, only red colonies<br>73. pSB3K3-CP41-B0032-BFP 10x: No growth<br>77.1 pSB4C15, clone 1: No growth<br>77.1 pSB4C15, clone 1 10x: No growth<br>77.2 pSB4C15, clone 2: Some  growth<br>77.2 pSB4C15, clone 2 10x: No growth<br>23. pSB1C3-CrtB<br>24. pSB1C3-CrtI<br>27. pEL3K16-red<br>38. pEL3A15-red<br>51. pEL3C18-red<br><br><b>failed:</b><br>81. pSB4S15-CP41: No growth<br>82. pSB4S15-CP29: No growth<br>83. pSB4S15-CP30: No growth<br><i>→ Redo ligation and transformation.</i><br><br><b>Plasmid preparation:</b><br>7.3  pSB3K3 clone 3: 50.1 ng/µl<br>7. 4 pSB3K3 clone 4: 43.4 ng/µl<br>7. 5 pSB3K3 clone 5: 48.1 ng/µl<br>22.1.1 pSB1C3-B0032-BFP clone 1.1: 196.2 ng/µl<br>22.2.1 pSB1C3-B0032-BFP clone 2.1: 174.3 ng/µ<br>22.2.2 pSB1C3-B0032-BFP clone 2.2: 189.9 ng/µ<br>42.1 pSB4S15-red clone 1: 43.6 ng/µl<br>42.2 pSB4S15-red clone 2: 46.1 ng/µl<br><br><h2>Other experiments</h2><br>Made agarplates with chloramphenicol resistance<br>MRS-broth preparation<br>MRS-broth-agar preparation <br>MRS-broth-agar plates preparation </div>';
+ }
+ else if(id == 'd201372')
+ {
+  ds = '<div id="dairy-text"><h1>Tuesday 2013-07-02</h1><br><b>Name of participants:</b> Christoffer Ahlström (CA), Nafisa Bashir (NB),  Viktor Törnblom (VT), Anton Berglund (AB), Mikael Strandgren (MS), Viktor Blomkvist (VB),  Thorsteinn O, Magnus B, Nils A, Alexander W, Christoffer F, Lovisa P, Kristoffer L, Emil M, Marcus H, Karl H, Peter C, Ken B.-A.<br><br><h2>Ongoing constructs:</h2><br><b>L. reuteri:</b><br>1. CF48-pLR581<br>2. 1063-pLUL631<br>3. DSM 20016-pVs2<br>4. 100-23-noplasmid<br>6. DSM 20016-pLUL63TsA8<br>7. DSM 20016-pGFP<br>8. 100-23-pGT232<br>12. DSM 20016-noplasmid<br>14. DSM 20016-pLUL631(B?)<br><br><b>L. plantarum:</b><br>5. 256-rifR-pAMβ1<br>10. 256-noplasmid<br>11. 36E-noplasmid<br><br><b>E. faecalis:</b><br>9. JH2-2 pAMβ1<br><br><b>L. lactis:</b><br>13. MG1363-pJP059<br>15. unknown-pGus<br>16. MG1363-noplasmid<br><br><b>E.coli (strain D5α):</b>  <br>42. pSB4S15-red<br>60. PK401 dam<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>68. pSB3K3-CP1-B0032-BFP<br>69.pSB3K3-CP8-B0032-BFP<br>70. pSB3K3-CP11-B0032-BFP<br>71. pSB3K3-CP29-B0032-BFP<br>72. pSB3K3-CP30-B0032-BFP<br>73. pSB3K3-CP41-B0032-BFP<br>74. pSB3K3-Cp44-B0032-BFP<br>77. pSB4C15<br>81. pSB4S15-CP41<br>82. pSB4S15-CP29<br>83. pSB4S15-CP30<br>57. pSB1C3-B0034-Idi<br>58. pSB1C3-B0034-ispA<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><br><br><b>Lb. delbrueckii bulgaricus:</b><br>18. Lb. delbrueckii bulgaricus<br><br><b>L. thermophilus:</b><br>19. Lc.thermophilus<br><br><h2>Todays work</h2><br><b>O/N:</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>Lb10.1. plantarum 256 no plasmid<br>Lb11.1. plantarum 36E no plasmid<br>Lb12.1 reuteri DSM 20016<br>Lb19.5 L. thermophilus<br>Lb19.6 L. thermophilus<br>7.3. pSB3K3-red<br>7.4. pSB3K3-red<br>7.5. pSB3K3-red<br>22.1.1. pSB1C3<br>22.2.1. pSB1C3<br>22.2.2. pSB1C3<br>42.1.1. pSB4S15-red<br>42.1.2. pSB4S15-red<br>42.1.3. pSB4S15-red<br><br><b>Digest: </b><br>Lb9.4 faecalis JH2-2 pAMβ1<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>Gel electrophoresis: </b><br>Lb9.4 faecalis JH2-2 pAMβ1<br><br><b>Frozen stock: </b><br>Lb13.3. Lc. lactis MG1363 pJP059 clone 3<br>Lb13.4. Lc. lactis MG1363 pJP059 clone 4<br>Lb15.3. Lc. lactis MG1363 pGus clone 3<br>Lb15.4. Lc. lactis MG1363 pGus clone 4<br>Lb16.3. Lc. lactis MG1363 noplasmid clone 3<br>Lb16.4. Lc. lactis MG1363 noplasmid clone 4<br><br><b>Plasmid preparation: </b><br>Lb13.3. Lc. lactis MG1363 pJP059 clone 3<br>Lb13.4. Lc. lactis MG1363 pJP059 clone 4<br>Lb15.3. Lc. lactis MG1363 pGus clone 3<br>Lb15.4. Lc. lactis MG1363 pGus clone 4<br><br><b>PCR: </b><br>Lb13.1 Lc. lactis MG1363 pJP059<br>Lb13.2 Lc. lactis MG1363 pJP059<br>Lb13.3 Lc. lactis MG1363 pJP059<br>Lb13.4 Lc. lactis MG1363 pJP059<br>The primers for usp45 were used in order to amplify the usp45 signal peptide from the L. lactis chromosome. A gel was run to confirm fragment size.<br>43. pSB1C3-B0034-TAL<br>44. pSB1C3-B0034-His-TAL<br><br><b>Gel electrophoresis: </b><br>Lb13.1 Lc. lactis MG1363 pJP059<br>Lb13.2 Lc. lactis MG1363 pJP059<br>Lb13.3 Lc. lactis MG1363 pJP059<br>Lb13.4 Lc. lactis MG1363 pJP059<br>1. pSB1C3-red		 		(cut with EcoRI and SpeI today)<br>1. pSB1C3-red 				(cut with EcoRI and SpeI saturday)<br>7. pSB3K3-red 				(cut with EcoRI and PstI today)<br>22. pSB1C3-B0032-BFP 			(cut with XbaI and PstI saturday)<br>42. pSB4S15-red 				(EcoRI and SpeI today)<br>42. pSB4S15-red 				(cut with SalI and SacI saturday)<br>43. pSB1C3-B0034-TAL<br>44. pSB1C3-B0034-His-TAL<br><br><b>Re-streak from frozen stock: </b><br>Lb12.1 reuteri DSM 20016 no plasmid<br>Lb12.2 reuteri DSM 20016 no plasmid<br>Two re-streaks of each clone were made on two antibiotics free plates.<br><br><b>Re-streak: </b><br>Lb19.1 L. thermophilus<br>Lb19.2 L. thermophilus<br>Lb19.3 L. thermophilus<br>Lb19.4 L. thermophilus<br>Lb19.7 L. thermophilus<br>Lb19.8 L. thermophilus<br>Lb19.9 L. thermophilus<br>Lb19.10 L. thermophilus<br><br><b>Streaking of yogurt culture: </b><br>Lb18. Lb. delbrueckii bulgaricus  <br>Lb19. Lactococcus Thermophilus<br><br><b>Assembly and subcloning: </b><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>68. pSB3K3-CP1-B0032-BFP<br>69.pSB3K3-CP8-B0032-BFP<br>70. pSB3K3-CP11-B0032-BFP<br>71. pSB3K3-CP29-B0032-BFP<br>72. pSB3K3-CP30-B0032-BFP<br>73. pSB3K3-CP41-B0032-BFP<br>74. pSB3K3-Cp44-B0032-BFP<br>77.1 pSB4C15, clone 1<br>77.2 pSB4C15, clone 2 had less of plasmid 42 because it ran out.<br>81. pSB4S15-CP41<br>82. pSB4S15-CP29<br>83. pSB4S15-CP30<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>Transformation: </b><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>68. pSB3K3-CP1-B0032-BFP<br>69.pSB3K3-CP8-B0032-BFP *<br>70. pSB3K3-CP11-B0032-BFP<br>71. pSB3K3-CP29-B0032-BFP *<br>72. pSB3K3-CP30-B0032-BFP *<br>73. pSB3K3-CP41-B0032-BFP *<br>74. pSB3K3-Cp44-B0032-BFP<br>77. pSB4C15, clone 1<br>77.2 pSB4C15, clone 2 *<br>81. pSB4S15-CP41 *<br>82. pSB4S15-CP29<br>83. pSB4S15-CP30<br>45. pSB1C3-B0034-4CL<br>46. pSB1C3-B0034-His-4CL<br>47. pSB1C3-B0034-STS<br>48. pSB1C3-B0034-His-STS<br><i>* Those marked were incubated for maybe 25 minutes longer.</i><br><br><b>Subcloning</b> of 57 and 58 into pSB1C3 (from 1. pSB1C3-Red).<br>PCR of Crt Z(with 7% DMSO), 19, 20, 21(now with VF2, VR and culture)<br><b>Gelelectroforesis</b> of CrtE, CrtZ, 19, 20, 21<br><b>Transformation</b> of 23, 24, 27, 38, 51.<br><br><h2>Results</h2><br><b>Previous day:</b><br><b>O/N: </b><br>Lb13.3 Lc. lactis MG1363 pJP059 clone 3: Good growth, NC ok!<br>Lb13.4 Lc. lactis MG1363 pJP059 clone 4: Good growth, NC ok!<br>Lb15.3 Lc. lactis MG1363 pGus clone 3:   Good growth, NC ok!<br>Lb15.4 Lc. lactis MG1363 pGus clone 4:   Good growth, NC ok!<br><i>→ Continue with frozen stock and plasmid preparation.</i><br><br><b>Assembly and transformation: </b><br>61. pSB1C3-CP1:           Nothing<br>61. pSB1C3-CP1 10x:       Nothing<br>62. pSB1C3-CP8:           Growth<br>62. pSB1C3-CP8 10x:       Nothing<br>63. pSB1C3-CP11:          Growth<br>63. pSB1C3-CP11 10x:      Nothing<br>64. pSB1C3-CP29:          Growth<br>64. pSB1C3-CP29 10x:      Nothing<br>65. pSB1C3-CP30:          Growth<br>65. pSB1C3-CP30 10x:      Nothing<br>66. pSB1C3-CP41:          Nothing<br>66. pSB1C3-CP41 10x:      Nothing<br>67. pSB1C3-Cp44:          Growth<br>67. pSB1C3-Cp44 10x:      Nothing<br>77. pSB4C15-red:          Nothing <br>77. pSB4C15-red 10x:      Nothing<br>45. pSB1C3-B0034-4CL      Growth<br>46. pSB1C3-B0034-His-4CL  Growth<br>47. pSB1C3-B0034-STS      Growth<br>48. pSB1C3-B0034-His-STS  Growth<br><i>→ Redo with extra care, look over the protocols, use new ligase and ligation buffer.</i><br><br><b>Today:</b><br><b>Gel electrophoresis: </b><br>43. pSB1C3-B0034-TAL                                    Good bands<br>44. pSB1C3-B0034-His-TAL                                Good bands<br>Lb13.1 Lc. lactis MG1363-pJP059				<br>13.2 Lc. lactis MG1363-pJP059					<br>13.3 Lc. lactis MG1363-pJP059<br>13.4 Lc. lactis MG1363-pJP059<br>Lb9.4 faecalis JH2-2 pAMβ1                              Faint blurry bands*<br>1. pSB1C3-red (cut with EcoRI and SpeI today)           Good bands<br>1. pSB1C3-red (cut with EcoRI and SpeI saturday)        Good bands<br>7. pSB3K3-red (cut with EcoRI and PstI today)           Good bands<br>22. pSB1C3-B0032-BFP (cut with XbaI and PstI saturday)  Nothing**<br>42. pSB4S15-red (EcoRI and SpeI today)                  Nothing**<br>42. pSB4S15-red (cut with SalI and SacI saturday)       Nothing**<br><i>→ 1 and 7 were ok, they could be reused.</i><br><br><i>*The results were consistent with yesterdays Gel electrophoresis: Very faint smudged bands that lets us think there is only chromosomal DNA in this plasmid preparation.<br>**The results indicate that something may be wrong with the digests of 42. and 22., this may be one of the explanations of why we got no colonies of 77. but many of 61-67.</i><br><br><b>Plasmid preparation: </b><br>Lb13.3. Lc. lactis MG1363 pJP059 clone 3: 13.4 ng/µl<br>Lb13.4. Lc. lactis MG1363 pJP059 clone 4: 10.3 ng/µl<br>Lb15.3. Lc. lactis MG1363 pGus clone 3: 11.9 ng/µl<br>Lb15.4. Lc. lactis MG1363 pGus clone 4: 12.0 ng/µl<br><i>→ Dispose, to low concentration. Re-do a plasmid preparation from O/N with optimized conditions. </i><br><br>Gel showed fail of PCR for 19,20, 21<br>Gel showed succes of CrtE, but fail of CrtZ(no primer dimers tho)<br>Plates from yesterday showed fail of subclone/transformation<br><br><h2>Other experiments</h2><br>Made agarplates with chloramphenicol resistance<br><b>Microscopy:</b><br>Confirming Lc.thermophilus colonies on the yoghurt-plate from the previous day.<br>Confirming contamination on some plates with  competent cells.<br><br>Primer design of lambda red, Crt Y, I and B both F and R<br></div>';
   }
   else if(id == 'd201371')
   {
-   ds ='<p>på dig</p>';
+   ds = '<div id="dairy-text"><h1>Monday 2013-07-01</h1><br><b>Name of participants:</b> Lovisa P, Kristoffer L, Emil M, Marcus H, Karl H, Peter C, Christoffer, Nils, Magnus, Alexander,  Anders Edlund (AE), Mikael Strandgren (MS), Christoffer Ahlström (CA), Viktor Blomkvist (VB), Viktor Törnblom(VT), Nafisa Bashir (NB), Anton Berglund (AB)<br><br><h2>Ongoing constructs:</h2><br><b>E.coli (strain D5α):</b><br>7. pSB3K3-red<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>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>77. pSB4C15-red<br>1. pSB1C3-red<br>60.PK401 dam-<br><br><b>L. plantarum:</b><br>Lb5.  256-rifR-pAMβ1<br><br><b>E. faecalis:</b><br>Lb9. JH2-2 pAMβ1<br><br><b>L. reuteri:</b><br>Lb12. DSM 20016-noplasmid<br><br><b>L. lactis:</b><br>Lb15 unknown-pGus<br><br><b>Lb. delbrueckii bulgaricus:</b><br>18. Lb. delbrueckii bulgaricus<br><br><b>L. thermophilus:</b><br>19. L.thermophilus<br><br><h2>Todays work</h2><br><b>Gel electrophoresis:</b><br>45. pSB1C3-B0034-4CL<br>46. pSB1C3-B0034-His-4CL<br>47. pSB1C3-B0034-STS<br>48. pSB1C3-B0034-His-STS<br>Lb9.4 faecalis JH2-2 pAMβ1<br>CBP amplicon from reuteri DSM 20016<br>usp45 amplicon from lactis strain MG1363<br><br><b>PCR:</b><br>45. pSB1C3-B0034-4CL<br>46. pSB1C3-B0034-His-4CL<br>47. pSB1C3-B0034-STS<br>48. pSB1C3-B0034-His-STS <br>6 colonies of DSM 20016 strain reuteri<br>4 colonies of MG1363 strain lactis<br>The PCR was carried out with the CBP primers for reuteri and the usp45 primers for lactis. This in order to isolate the signal peptides from each species.<br><br><b>O/N: </b><br>Lb13. Lc. lactis MG1363 pJP059 clone 3<br>Lb13. Lc. lactis MG1363 pJP059 clone 4<br>Lb15. Lc. lactis MG1363 pGus clone 3<br>Lb15. Lc. lactis MG1363 pGus clone 4<br>7. pSB3K3-red<br><br><b>Frozen stock:</b><br>Lb5.2 plantarum 256 pAMβ1<br>Lb9. faecalis JH2-2 pAMβ1 clone 4<br>1. pSB1C3-red<br>60.PK401 dam<br><br><b>Re-streak: </b><br>Lb9. faecalis JH2-2 pAMβ1<br>Lb12. reuteri DSM20016 no plasmid<br><br><b>Plasmid preparation:</b><br>Lb5.2 plantarum 256 pAMβ1<br>Lb9. faecalis JH2-2 pAMβ1 clone 4<br>1. pSB1C3-red<br><br><b>Digest: </b><br>Lb9.4 faecalis JH2-2 pAMβ1 (To rule out chromosomal contamination in prep)<br><br><b>Assembly: </b><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>77. pSB4C15-red<br><br><b>Transformation: </b><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>77. pSB4C15-red*<br>*We made a transformation with one sample of 77-digest from today, and one from yesterday to try to see if the problem yesterday laid with the assembly or with the transformation<br><br><b>Streaking of yogurt culture: </b><br>18. Lb. delbrueckii bulgaricus  <br>19. Lactococcus Thermophilus<br><br><b>PCR</b> of Crt E, Crt Z, 19, 20, 21, Idi<br><b>Gelelectroforisis</b> of Crt E, Crt Z, Idi <br><b>Transformation</b> of 75, 76, 78, 58<br><b>Subcloning</b> of IspA ->58<br><b>Digest</b> of Idi<br><b>Ligation</b> of 76, 78<br><br><h2>Results</h2><br><b>Previous day:</b><br><b>Assembly and transformation: </b><br>61. pSB1C3-CP1:  No growth<br>62. pSB1C3-CP8:  No growth<br>63. pSB1C3-CP11: No growth<br>64. pSB1C3-CP29: No growth<br>65. pSB1C3-CP30: No growth <br>66. pSB1C3-CP41: No growth<br>67. pSB1C3-Cp44: No growth<br>77. pSB4C15-red: No growth<br><i>→ Re-do all steps, but do one transformation with ligations from yesterday</i><br><br><b>Today:</b><br><b>Plasmid preparation: </b><br>Lb5.2 plantarum 256 pAMβ1 clone 2: 50.7 ng/µl<br>Lb9.4 faecalis JH2-2 pAMβ1 clone 4: 403.7 ng/µl<br>1.1 pSB1C3-red clone 1: 144.0 ng/µl<br>1.2 pSB1C3-red clone 2: 96.8 ng/µl<br><br><b>Gel electrophoresis: </b><br>Lb9.4 faecalis JH2-2 pAMβ1*<br><i>*Very faint smudges that could be a shadow from the dye. Will follow up tomorrow with another gel electrophoresis of a new digest.</i><br>CBP amplicon from reuteri DSM 20016**<br>usp45 amplicon from lactis strain MG1363**<br><i>**None of the PCRs showed the desired bands on the gel.</i><br><br><b>PCR with good results:</b><br>45. pSB1C3-B0034-4CL<br>46. pSB1C3-B0034-His-4CL (Note: weak band)<br>47. pSB1C3-B0034-STS<br>48. pSB1C3-B0034-His-STS  <br><i>- Very good results on the pcr</i><br><br>Gel of Crt E and Crt Z was failed at Ethylium Bromide bath. Redo gel<br>Gel of Idi showed succes, proceed to subclone. <br>Subclone of IspA showed only red colonies. IspA was incorrectly digested with E instead of X.<br><i>-dunno what this is! :S</i><br><br><h2>Other experiments</h2><br>M17-broth agar preparation<br>M17-broth medium preparation<br>SET-buffer preparation<br>Preparation of M17 plates</div>';
   }
   else if(id == 'd2013721')

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