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Template:Team:Uppsala/JS/notebook
From 2013.igem.org
(Difference between revisions)
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} | } | ||
} | } | ||
| + | } | ||
| + | |||
| + | function diry(y, m, d) | ||
| + | { | ||
| + | var ds = ''; //diryString | ||
| + | var id = 'd'+y+m+d; | ||
| + | //var ds = y+'-'+m+'-'+d; | ||
| + | if(id == 'd2013630') | ||
| + | { | ||
| + | ds = '<h2>Sunday 2013-06-30</h2><p><strong>Name of participants:</strong> Magnus B, Alexander W, Nils A, Mikael Strandgren (MS), Anders Edlund (AE)<br><br>'+ | ||
| + | '<h3>Ongoing constructs:</h3>75. pEL3A15 - CrtB<br>25. pSB1C3-CrtY<br>27. pEL3K16-red<br>'+ | ||
| + | '51.pEL3C18-red<br>19. pSB4C5-CrtE~I /w RBS, Linker & ZF<br>20. pSB4C5-CrtE~Z /w RBS, Linker & ZF<br>'+ | ||
| + | '21. pSB4C5-CrtE~O-Z /w RBS, Linker & ZF<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><br>'+ | ||
| + | '<b>L. reuteri:</b><br>Lb1. CF48-pLR581<br>Lb2. 1063-pLUL631<br>Lb3. DSM 20016-pVs2<br>'+ | ||
| + | 'Lb4. 100-23-noplasmid<br>Lb6. DSM 20016-pLUL63TsA8<br>Lb7. DSM 20016-pGFP<br>Lb8. 100-23-pGT232<br>'+ | ||
| + | 'Lb12. DSM 20016-noplasmid<br>Lb14. DSM 20016-pLUL631<br><br><strong>L. plantarum:</strong><br>Lb5. 256-rifR-pAMβ1<br><br>'+ | ||
| + | '<b>L. lactis:</b><br>Lb13. MG1363-pJP059<br>Lb15. unknown-pGus<br>Lb16. MG1363-noplasmid<br><br>'+ | ||
| + | 'Lb10. 256-noplasmid<br>Lb11. 36E-noplasmid<br>Lb9. JH2-2 pAMβ1<br><br><h3>Todays work</h3><br><h3>Transformation</h3>'+ | ||
| + | '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>'+ | ||
| + | '75. pEL3A15 - CrtB<br><br><h3>Digest</h3>27. pEL3K16-red<br>51.pEL3C18-red<br><br>'+ | ||
| + | '<h3>Ligation</h3>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 from today, and one from yesterday to try to see if the problem yesterday laid with the transformation or the assembly.<br><br><h3>O/N Screening</h3>'+ | ||
| + | '25. pSB1C3-CrtY<br>19. pSB4C5-CrtE~I /w RBS, Linker & ZF<br>20. pSB4C5-CrtE~Z /w RBS, Linker & ZF<br>'+ | ||
| + | '21. pSB4C5-CrtE~O-Z /w RBS, Linker & ZF<br><br><h3>Results</h3><br><b>Re-streak</b><br>'+ | ||
| + | '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 == 'd201371') | ||
| + | { | ||
| + | ds ='<p>på dig</p>'; | ||
| + | } | ||
| + | else if(id == 'd2013721') | ||
| + | { | ||
| + | ds = '<div id="dairy-text"><h1>Sunday 2013-07-21</h1><p><strong>Name of participants:</strong>Hampus.E, Theodor L, Karl H, Ken B, Kristoffer L, Viktor @, Marcus H. Nils, Christoffer, Anders Edlund (AE)<br><br>'+ | ||
| + | '<h2>Ongoing constructs:</h2>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>'+ | ||
| + | '99. pSB1C3-CrtO<br>108. pSB4A15-J23106-B0034-IspA<br>109. pSB4A15-K206000-B0034-IspA<br>110. pSB4A15-K206001-B0034-IspA<br>123. pSB1C3-ZCD<br>125. pSB1C3-ZCD-His<br>126. pSB1C3-UGTCs2<br>127. pSB1A3-B0034-UGTCs2-His<br>129. pSB1C3-Idi (mut)<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>7.pSB3k3-red<br>22. B0032-BFP<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>81. pSB4S15-CP41-B0032-BFP<br>82. pSB4S15-CP29-B0032-BFP<br>83. pSB4S15-CP30-B0032-BFP<br>84. pSB4S15-CP6<br>85. pSB4S15-CP25<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>90. BBa_J61002-J23101<br>97. pSB4S15-CP8-B0032-BFP<br>98. pSB4S15-CP11-B0032-BFP<br>100. pJP059<br>111. pSBLb4C15<br>112. pSBLbEc4C15<br>136.1 pSB1C3-usp45<br>'+ | ||
| + | '<strong>L. reuteri:</strong><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>14. DSM 20016-pLUL631(B?)<br><br><strong>L. plantarum:</strong><br>5. 256-rifR-pAMβ1<br><br><b>Lb. delbrueckii bulgaricus:</b><br>18. Lb. delbrueckii bulgaricus<br><br><b>Lc. thermophilus:</b><br>19. Lc.thermophilus<br><br>'+ | ||
| + | '<h2>Todays work:</h2><b>Plasmid Prep on:</b><br>117.2 pSB3T5-CP1-B0034-His-TAL<br>119.2 pSB1C3-B0034-4CL<br>120.1 pSB1C3-B0034-HIS-4CL<br>104.2 and 104.5 pSB1C3-B0034-4CL-B0034-STS<br>106.5 and 106.6 pSB3T5-J23110-B0034-TAL<br>122.2 pSB1C3-B0034-His-STS;<br><br><b>Re-streak:</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>134.1 pSB1C3-CBP<br>134.2 pSB1C3-CBP<br>134.3 pSB1C3-CBP<br>134.4 pSB1C3-CBP<br>136.1 pSB1C3-usp45<br>136.2 pSB1C3-usp45<br>136.3 pSB1C3-usp45<br>136.4 pSB1C3-usp45<br><br><b>Gel:</b><br>21. CrtE~I/w RBS,ZF<br><br><b>Overnight & screening:</b><br>99. pSB1C3-CrtO<br>128.pSIM5-tet (E.Coli Nissle) Endast O/N<br>108. pSB4A15-J23106-B0034-IspA<br>109. pSB4A15-K206000-B0034-IspA<br>110. pSB4A15-K206001-B0034-IspA<br><br>'+ | ||
| + | '<b>Overnight:</b><br>84.1 pSB4S15-CP6<br>84.2 pSB4S15-CP6<br>86.1 pSB4S15-CP6-B0032-BFP<br>86.2 pSB4S15-CP6-B0032-BFP<br>87(1.1) pSB4S15-CP25-B0032-BFP<br>87(1.2) 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>97.1 pSB4S15-CP8-B0032-BFP<br>97.2 pSB4S15-CP8-B0032-BFP<br>98.1 pSB4S15-CP11-B0032-BFP<br>98.2 pSB4S15-CP11-B0032-BFP<br><br>'+ | ||
| + | '<h2>Results:</h2><br><b>Re-streak:</b><br>131. pSB4A15-BBa-J61002-J23106-CrtE~I /w RBS, Zinc finger - Unable, no clones<br>132. pSB4A15-BBa-J61002-J23110-CrtE~I /w RBS, Zinc finger - 3 clones restreaked<br>133. pSB4A15-BBa-J61002-J23101-CrtE~I /w RBS, Zinc finger - 3 clones restreaked<br><br><b>Gel</b><br>21. CrtE~I/w RBS,ZF - fail<br><br><b>Overnight & screening:</b><br>99. pSB1C3-CrtO<br>108. pSB4A15-J23106-B0034-IspA - Fail of all clones<br>109. pSB4A15-K206000-B0034-IspA - Fail of all clones<br>110. pSB4A15-K206001-B0034-IspA - Fail of all clones<br><br></div>'; | ||
| + | } | ||
| + | else if(id == 'd2013720') | ||
| + | { | ||
| + | ds = '<div id="dairy-text"><h1>Saturday 2013-07-20</h1><b>Name of participants:</b> Hampus.E, Kristoffer.L, Malin .B, Magnus, Nils, Pontus, Anders Edlund (AE), Stephanie Herman (SH)<br><br><h2>Ongoing constructs:</h2>99. pSB1C3-CrtO<br>108. pSB4A15-J23106-B0034-IspA<br>109. pSB4A15-K206000-B0034-IspA<br>110. pSB4A15-K206001-B0034-IspA<br>123. pSB1C3-ZCD<br>125. pSB1C3-ZCD-His<br>126. pSB1C3-UGTCs2<br>127. pSB1A3-B0034-UGTCs2-His<br>129. pSB1C3-Idi (mut)<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>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>7.pSB3k3-red<br>22. B0032-BFP<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>81. pSB4S15-CP41-B0032-BFP<br>82. pSB4S15-CP29-B0032-BFP<br>83. pSB4S15-CP30-B0032-BFP<br>84. pSB4S15-CP6<br>85. pSB4S15-CP25<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>90. BBa_J61002-J23101<br>97. pSB4S15-CP8-B0032-BFP<br>98. pSB4S15-CP11-B0032-BFP<br>100. pJP059<br>111. pSBLb4C15<br>112. pSBLbEc4C15<br>136.1 pSB1C3-usp45<br><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>14. DSM 20016-pLUL631(B?)<br><br><b>L. plantarum:</b><br>5. 256-rifR-pAMβ1<br><br><b>Lb. delbrueckii bulgaricus:</b><br>18. Lb. delbrueckii bulgaricus<br><br><b>Lc. thermophilus:</b><br>19. Lc.thermophilus<br><br><h2>Todays work</h2><b>Re-streak:</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>99. pSB1C3-CrtO<br><br><b>Overnigth:</b><br>136.1 pSB1C3-usp45<br>136.2 pSB1C3-usp45<br>111.6 pSBLb4C15-red<br>111.7 pSBLb4C15-red<br><br><b>Transformation: </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>134. pSB1C3-CBP<br>135. pSB1C3-CSP<br>136. pSB1C3-USP45<br><br><b>Plasmidprep:</b><br>109. pSB4A15-K206000-B0034-IspA<br>123. pSB1C3-ZCD<br>125. pSB1C3-ZCD-His<br>126. pSB1C3-UGTCs2<br>127. pSB1A3-B0034-UGTCs2-His<br>1.1? 90.3 j23101<br>1.2?<br>2.1?90.4 j23101<br>2.2?<br><br><b>Gel:</b><br>108. pSB4A15-J23106-B0034-IspA<br>109. pSB4A15-K206000-B0034-IspA<br>110. pSB4A15-K206001-B0034-IspA<br><br><b>Screening pcr of constructs:</b><br>119.pSB1C3-B0034-4CL<br>120 pSB1C3-B0034-HIS-4CL<br>106 pSB3T5-J23110-B0034-TAL<br>117 pSB3T5-CP1-B0034-His-TAL<br>107 pSB3T5-CP1-B0034-TAL<br><br><b>PCR:</b><br>21. pSB4C5-pBAD/AraC-CrtE~I/w RBS, ZF (to remove promotor)<br>108. pSB4A15-J23106-B0034-IspA<br>109. pSB4A15-K206000-B0034-IspA<br>110. pSB4A15-K206001-B0034-IspA<br><br><h2>Results</h2><b>Overnight & screening:</b><br>99. pSB1C3-CrtO<br>108. pSB4A15-J23106-B0034-IspA<br>109. pSB4A15-K206000-B0034-IspA<br>110. pSB4A15-K206001-B0034-IspA<br><br><b>Screening of: </b><br>108. pSB4A15-J23106-B0034-IspA<br>109. pSB4A15-K206000-B0034-IspA<br>110. pSB4A15-K206001-B0034-IspA<br><i>showed negative results on all clones but 109.2. A new screening PCR of previously un-screened clones was prepared to run overnight.</i><b>Gel<br><br>Gel succes on: </b><br>106.5 pSB3T5-J23110-B0034-TAL<br>106.6 pSB3T5-J23110-B0034-TAL<br>117.1 pSB3T5-CP1-B0034-His-TAL<br>117.2 pSB3T5-CP1-B0034-His-TAL<br>119.2 pSB1C3-B0034-4CL<br><b>No band on:</b><br>107 pSB3T5-CP1-B0034-TAL<br>116 pSB3T5-J23110-B0034-His-TAL<br>120 pSB1C3-B0034-HIS-4CL<br></div>'; | ||
| + | } | ||
| + | else if(id == 'd2013719') | ||
| + | { | ||
| + | ds = '<div id="dairy-text"><h1>Friday 2013-07-19</h1><br>Name of participants: Ken B-A, Kristoffer L, Malin, Magnus, Sabri, Nils, Pontus, <br>Christoffer Ahlström (CA), Stephanie Herman (SH) <br><br><h2>Ongoing constructs:</h2><b>E.coli (strain D5α): </b><br>108. pSB4A15-J23106-B0034-IspA<br>109. pSB4A15-K206000-B0034-IspA<br>110. pSB4A15-K206001-B0034-IspA<br>123. pSB1C3-ZCD<br>125. pSB1C3-ZCD-His<br>126. pSB1C3-UGTCs2<br>127. pSB1A3-B0034-UGTCs2-His<br>129. pSB1C3-Idi (mut)<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>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>7.pSB3k3-red<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>81. pSB4S15-CP41-B0032-BFP<br>82. pSB4S15-CP29-B0032-BFP<br>83. pSB4S15-CP30-B0032-BFP<br>84. pSB4S15-CP6<br>85. pSB4S15-CP25<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>90. BBa_J61002-J23101<br>97. pSB4S15-CP8-B0032-BFP<br>98. pSB4S15-CP11-B0032-BFP<br>100. pJP059<br>111. pSBLb4C15<br>112. pSBLbEc4C15<br>136.1 pSB1C3-usp45<br><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>14. DSM 20016-pLUL631(B?)<br><br><b>L. plantarum:</b><br>5. 256-rifR-pAMβ1<br><h2>Todays work</h2><b>Screening pcr of constructs:</b><br>106. pSB3T5-J23110-B0034-TAL<br>107. pSB3T5-CP1-B0034-TAL<br>117. pSB3T5-CP1-B0034-His-Tal<br>119. pSB1C3-B0034-4CL (from 15)<br>120. pSB1C3-B0034-His-4CL (from 15)<br><br><b>Overnight & screening:</b><br>108. pSB4A15-J23106-B0034-IspA<br>109. pSB4A15-K206000-B0034-IspA<br>110. pSB4A15-K206001-B0034-IspA<br>123. pSB1C3-ZCD<br>125. pSB1C3-ZCD-His<br>126. pSB1C3-UGTCs2<br>127. pSB1A3-B0034-UGTCs2-His<br><br><b>Plasmid preparation:</b><br>122.2. pSB1C3-B0034-His-STS (from 15)<br>90.3. BBa_J61002 (amp)-J23101<br>90.4. BBa_J61002 (amp)-J23101<br>104.2. pSB1C3-B0034-4CL-B0034-STS <br>104.5. pSB1C3-B0034-4CL-B0034-STS<br>111.2. pSBLb4C15-E.coli ori replaced with ori from lactobacillus (pJP059) in pEL4C15<br>111.3. pSBLb4C15-E.coli ori replaced with ori from lactobacillus (pJP059) in pEL4C15<br>111.4. pSBLb4C15-E.coli ori replaced with ori from lactobacillus (pJP059) in pEL4C15<br>121.1. pSB1C3-B0034-STS (from 15)<br>121.2. pSB1C3-B0034-STS (from 15)<br><br><b>Cloning:</b><br>21. CrtE~I /w RBS, Zinc finger → 1. pSB1C3-red<br><br><b>Assembly:</b><br>21. CrtE~I /w RBS, Zinc finger, 91. BBa-J61002-J23106 → 11. pSB4A15-red <br>21. CrtE~I /w RBS, Zinc finger, 92. BBa-J61002-J23110 → 11. pSB4A15-red <br>21. CrtE~I /w RBS, Zinc finger, 103. BBa-J61002-J23101 → 11. pSB4A15-red <br><br><<b>Gel electrophoresis:</b><br>129. pSB1C3-Idi (mut)<br><br><b>Restreak</b><br>128. pSIM5-tet(Nissle)<br><br><h2>Results:</h2><b>Screening: </b><br> 108. pSB4A15-J23106-B0034-IspA<br>109. pSB4A15-K206000-B0034-IspA<br>110. pSB4A15-K206001-B0034-IspA<br>123. pSB1C3-ZCD<br>125. pSB1C3-ZCD-His<br>126. pSB1C3-UGTCs2<br>127. pSB1A3-B0034-UGTCs2-His<br><i>showed negative results on all clones but 109.2, which proceeded to overnight. A new screening PCR was prepared to run overnight.</i><br><br><i>showed positive results in all cases but 125.4 and 127.3. All other clones proceeded to overnight.</i><br><br><i>The overnight showed no contamination of negative controls, and growth in all clones but 127.1 and 127.2.</i><br><br><b>Transformation:</b><br>Only visual red colonies on CBP & CSP and possible 2 white colonies on usp45.<br>→ Re-do the transformation with the saved ligation solution from (18/07-13)<br>→ Re-streak the possible white colonies. <br><br></div>'; | ||
| + | } | ||
| + | else if(id == 'd2013718') | ||
| + | { | ||
| + | ds = '<div id="dairy-text"><br><h1>Thursday 2013-07-18</h1><br><br><b>Name of participants:</b> Karl H, Ken B-A, Kristoffer L, Christoffer, Alexander, Magnus, Pontus,Sabri,StephanieHerman (SH), Alona Nyberg (AN), Christoffer Ahlström (CA), Viktor Blomkvist (VB)<br><br><br><h2>Ongoing constructs:</h2><b>E.coli (strain D5α):</b><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>7.pSB3k3-red<br>22. B0032-BFP<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>81. pSB4S15-CP41-B0032-BFP<br>82. pSB4S15-CP29-B0032-BFP<br>83. pSB4S15-CP30-B0032-BFP<br>84. pSB4S15-CP6<br>85. pSB4S15-CP25<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>90. BBa_J61002-J23101<br>97. pSB4S15-CP8-B0032-BFP<br>98. pSB4S15-CP11-B0032-BFP<br>100. pJP059<br>111. pSBLb4C15<br>112. pSBLbEc4C15<br>108. pSB4A15-J23106-B0034-IspA<br>109. pSB4A15-K206000-B0034-IspA<br>110. pSB4A15-K206001-B0034-IspA<br>123. pSB1C3-ZCD<br>125. pSB1C3-ZCD-His<br>126. pSB1C3-UGTCs2<br>127. pSB1A3-B0034-UGTCs2-His<br>129. pSB1C3-Idi (mut)<br>113. E.coli Nissle-pSIM5-tet<br><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>14. DSM 20016-pLUL631(B?)<br><br><b>L. plantarum:</b><br>5. 256-rifR-pAMβ1<br><br><b>Lb. delbrueckii bulgaricus:</b><br>18. Lb. delbrueckii bulgaricus<br><br><b>Lc. thermophilus:</b><br>19. Lc.thermophilus<br><br><h2>Todays work</h2><b>Assembly</b><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><br><br>Ligation<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><br><b>Gel-electrophoresis of screening PCR products</b><br>42. pSB4S15-red<br><br><b>Digestion:</b><br>42. pSB4S15-red<br><br><b>Transformation:</b><br>81. pSB4S15-CP41-B0032-BFP<br>82. pSB4S15-CP29-B0032-BFP<br>83. pSB4S15-CP30-B0032-BFP<br>84. pSB4S15-CP6<br>85. pSB4S15-CP25<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>Overnight:</b> <br>90. BBa_J61002-J23101<br><br><b>Spreading of strains:</b> <br>81. pSB4S15-CP41-B0032-BFP<br>82. pSB4S15-CP29-B0032-BFP<br>83. pSB4S15-CP30-B0032-BFP<br>84. pSB4S15-CP6<br>85. pSB4S15-CP25<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>Re-circulization:</b><br>129. pSB1C3-Idi (mut)<br><br><b>Plasmid Prep (Glycerol stock):</b><br>75. pEL3A15 - CrtB (75.1, 75.2, 75.4)<br><br><b>Transformation:</b><br>99. pSB1C3 - Crto <br>129. pSB1C3-Idi (mut)<br>113. E.coli Nissle-pSIM5-tet<br>111. pSBLb4C15<br>112. pSBLbEc4C15<br><br><b>Re-streak:</b><br>108. pSB4A15-J23106-B0034-IspA<br>109. pSB4A15-K206000-B0034-IspA<br>110. pSB4A15-K206001-B0034-IspA<br>123. pSB1C3-ZCD<br>125. pSB1C3-ZCD-His<br>126. pSB1C3-UGTCs2<br>127. pSB1A3-B0034-UGTCs2-His<br><br><br><b>Ligation of strains from yesterdays digest:</b><br>Collagen binding protein → cloned from strain 14.4<br>Cell surface protein → cloned from strain 3.1<br>usp45 → cloned from strain 13.1<br><br>*Ligated to 1.1 pSB1C3-red (From strain database 2013)<br><br><b>Transformation:</b>*<br>Collagen binding protein<br>Cell surface protein <br>usp45 <br><br>*Performed with D5(alpha) competent cells. <br><br><b>Screening:</b><br>111. pSBLb4C15<br><br><b>Spreading of strains:</b><br>Collagen binding protein [D5(alpha)] *<br>Cell surface protein [D5(alpha)] *<br>usp45 [D5(alpha)] *<br>111. pSBLb4C15 **<br>112. pSBLbEc4C15 **<br><br>*With a 10x and 1x dilution. <br><br>** 2 plates of each with 1x dilution.<br><br><h2>Results</h2><b>Re-streaks:</b><br>108. pSB4A15-J23106-B0034-IspA<br>109. pSB4A15-K206000-B0034-IspA<br>110. pSB4A15-K206001-B0034-IspA<br>123. pSB1C3-ZCD<br>125. pSB1C3-ZCD-His<br>126. pSB1C3-UGTCs2<br>127. pSB1A3-B0034-UGTCs2-His<br>were successful on all clones but 108.7.<br><br>Transformation of 129. pSB1C3-Idi (mut) did not grow.<br><br><b>Electrophoresis on digests:</b> <br>*The gel showed that the components (signal peptides and destination plasmid) had been cut and therefore have the digest succeeded. <br><br></div>'; | ||
| + | } | ||
| + | else if(id == 'd2013717') | ||
| + | { | ||
| + | ds = '<div id="dairy-text"><br><h1>Thursday 2013-07-18</h1><br><br><b>Name of participants:</b> Karl H, Ken B-A, Kristoffer L, Christoffer, Sabri, Alexander, Nils, Thorsteinn, Magnus, Malin, Pontus, Niclas<br><br><br><h2>Ongoing constructs:</h2><b>E.coli (strain D5α):</b><br>75. pEL3A15 - CrtB<br>99. pSB1C3 - CrtO<br>79. pEL3K16 - CrtE <br>102. pSB1C3 - CrtE<br>101. pSB1C3 - DNA program123456<br>96. Cs42s-Promoter-ZCD-PsbA2-UGTCs2-PsbA2-Beta-carotene hydroxylase-B1002<br>57.Psb1C3-B0034-Idi<br>108. pSB4A15-J23106-B0034-IspA<br>109. pSB4A15-K206000-B0034-IspA<br>110. pSB4A15-K206001-B0034-IspA<br>123. pSB1C3-ZCD<br>125. pSB1C3-ZCD-His<br>126. pSB1C3-UGTCs2<br>127. pSB1A3-B0034-UGTCs2-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>7.pSB3k3-red<br>22. B0032-BFP<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>81. pSB4S15-CP41-B0032-BFP<br>83. pSB4S15-CP30-B0032-BFP<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>82. pSB4S15-CP29-B0032-BFP<br>98. pSB4S15-CP11-B0032-BFP<br>100. pJP059<br>111. pSBLb4C15<br>112. pSBLbEc4C15<br><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>14. DSM 20016-pLUL631(B?)<br><br><b>L. plantarum:</b><br>5. 256-rifR-pAMβ1<br><br><b>Lb. delbrueckii bulgaricus:</b><br>18. Lb. delbrueckii bulgaricus<br><br><b>Lc. thermophilus:</b><br>19. Lc.thermophilus<br><br><br><h2>Todays work</h2><b>Assembly</b><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><br><br><b>Ligation</b><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><br><b>Digest & Ligation:</b><br>ZCD + 1. pSB1C3-Red -> 123. pSB1C3-ZCD<br>ZCD-His + 1. pSB1C3-Red -> 125. pSB1C3-ZCD-His<br>UGTCs2 + 1. pSB1C3-Red -> 126. pSB1C3-UGTCs2<br>B0034-UGTCs2-His + 4. pSB1A3-Red -> 127. pSB1A3-B0034-UGTCs2-His<br><br><b>Digest</b><br>Collagen binding protein → cloned from strain 14.4<br>Cell surface protein → cloned from strain 3.1<br>usp45 → cloned from strain 13.1<br>1.1 pSB1C3-red (From strain database 2013)<br><br><b>Transformation:</b><br>108. pSB4A15-J23106-B0034-IspA<br>109. pSB4A15-K206000-B0034-IspA<br>110. pSB4A15-K206001-B0034-IspA<br>123. pSB1C3-ZCD<br>125. pSB1C3-ZCD-His<br>126. pSB1C3-UGTCs2<br>127. pSB1A3-B0034-UGTCs2-His<br><br><b>O/N & Screening:</b><br>75. pEL3A15 - CrtB<br>102. pSB1C3 - CrtE<br><br><b>Plasmid Prep(Glycerol stock)</b><br>79. pEL3K16 - CrtE <br>101. pSB1C3 - DNA program123456<br><br><b>PCR</b><br>21. pSB4C5 - pBAD/AraC-CrtE~I /w RBS, ZF (E,P)(To remove promotor)<br>57.pSB1C3-B0034-Idi mutagenesis (Phusion) to remove restriction site. <br><br><b>Gel-electrophoresis of screening PCR products:</b><br>111. pSBLb4C15<br>112. pSBLbEc4C15<br>81. pSB4S15-CP41-B0032-BFP<br>83. pSB4S15-CP30-B0032-BFP<br>86. pSB4S15-CP6-B0032-BFP<br>88. pSB4S15-CP1-B0032-BFP<br>89. pSB4S15-CP44-B0032-BFP<br><br><b>Sequencing preparation:</b><br>62. pSB1C3-CP8<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>71. pSB3K3-CP29-B0032-BFP<br>72. pSB3K3-CP30-B0032-BFP<br>73. pSB3K3-CP41-B0032-BFP<br>74. pSB3K3-CP44-B0032-BFP<br><br><b>Plasmid preparation: </b><br>74. pSB3K3-CP44-B0032-BFP <br><br>Gel-electrophoresis of overnight PCR products:<br>Collagen binding protein → cloned from strain 14.4<br>Cell surface protein → cloned from strain 3.1<br>usp45 → cloned from strain 13.1<br><br><b>Re-streak: </b><br>Lb18. Lb. delbrueckii bulgaricus no plasmid<br><br><b>Spreading of strains: </b><br>Lb19. Lc.thermophilus no plasmid*<br><br>*With 1x, 10x & 50x dilution<br><br><br><h2>Results</h2>57.pSB1C3-B0034-Idi worked, gel run showed a band at suspected size , but also some smudge, probably primer dimers.<br>101. pSB1C3 - DNA program123456 worked and sent for sequence<br><br><b>Transformations:</b><br>108. pSB4A15-J23106-B0034-IspA<br>109. pSB4A15-K206000-B0034-IspA<br>110. pSB4A15-K206001-B0034-IspA<br>123. pSB1C3-ZCD<br>125. pSB1C3-ZCD-His<br>126. pSB1C3-UGTCs2<br>127. pSB1A3-B0034-UGTCs2-His<br>all grew red and white colonies, indicating successful ligation and transformation.<br><br><b>Gel-electrophoresis of overnight PCR products:</b><br>Collagen binding protein → cloned from strain 14.4: NC checks good and lines are equal to ~200bp.<br>Cell surface protein → cloned from strain 3.1: NC checks good and lines are equal to ~150bp.<br>usp45 → cloned from strain 13.1: NC checks good and lines are equal to ~140bp.<br><br></div>'; | ||
| + | } | ||
| + | else if(id == 'd2013716') | ||
| + | { | ||
| + | ds = '<div id="dairy-text"><br><h1>Tuesday 2013-07-16</h1><br><br><b>Name of participants:</b> Karl H, Lovisa P, Theodor L, Ken B-A, Victor S, Hampus.E, Kristoffer L, Christoffer .F, Sabri. J, Alexander, Nils, Thorsteinn, Magnus, Malin, Pontus, Niclas, Viktor Blomkvist(VB), Alona Nyberg (AN), Christoffer Ahlström (CA)<br><br><h2>Ongoing constructs:</h2><br><br><b>E.coli (strain D5α):</b><br>7.pSB3k3-red<br>22. B0032-BFP<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>81. pSB4S15-CP41-B0032-BFP<br>83. pSB4S15-CP30-B0032-BFP<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>82. pSB4S15-CP29-B0032-BFP<br>98. pSB4S15-CP11-B0032-BFP<br>100. pJP059<br>111. pSBLb4C15<br>112. pSBLbEc4C15<br>15. pSB4K5-RBS-TAL-Linker-Zif268-RBS-4cl-Linker-PBSII-STS-OMT<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>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>75. pEL3A15 - CrtB<br>99. pSB1C3 - CrtO<br>79. pEL3K16 - CrtE <br>102. pSB1C3 - CrtE<br>101. pSB1C3 - DNA program123456<br>96. Cs42s-Promoter-ZCD-PsbA2-UGTCs2-PsbA2-Beta-carotene hydroxylase-B1002<br>91. BBa_J61002 (amp)-J23106<br>94. pSB1C3-K206000<br>95. pSB1C3-K206001<br>11. pSB4A15-blue(?)<br>58. pSB1C3-IspA<br>108. pSB4A15-J23106-B0034-IspA<br>109. pSB4A15-K206000-B0034-IspA<br>110. pSB4A15-K206001-B0034-IspA<br>21. pSB4C5 - pBAD/AraC-CrtE~I /w RBS, ZF<br>57. PSB1C3-B0034-Idi <br><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>14. DSM 20016-pLUL631(B?)<br><br><b>L. plantarum:</b><br>5. 256-rifR-pAMβ1<br><br><h2>Todays work</h2><b>Assembly</b><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><br><b>Ligation:</b><br>48. pSB1C3-B0034-His-STS<br><br><b>Gel on Digest:</b><br>45. pSB1C3-B0034-4CL<br>46. pSB1C3-B0034-His-4CL<br>47. pSB1C3-B0034-STS<br>104. pSB1C3-B0034-4CL-B0034-STS<br><br><b>Restreak:</b><br>47. pSB1C3-B0034-STS<br>75. pEL3A15 - CrtB<br><br><b>Screening:</b> <br>111. pSBLb4C15<br>112. pSBLbEc4C15<br>81. pSB4S15-CP41-B0032-BFP<br>83. pSB4S15-CP30-B0032-BFP<br>86. pSB4S15-CP6-B0032-BFP<br>88. pSB4S15-CP1-B0032-BFP<br>89. pSB4S15-CP44-B0032-BFP<br><br><b>Plasmid preparation: </b><br>74. pSB3K3-CP44-B0032-BFP<br>27. pEL3K16-red<br><br><b>Overnight: </b><br>74. pSB3K3-CP44-B0032-BFP<br><br><i>Touchdown PCR with Phusion polymerase (signal peptides): CA<br>Collagen binding protein → cloned from strain 14.4<br>Cell surface protein → cloned from strain 3.1<br>usp45 → cloned from strain 13.1</i><br><br><b>Transformation:</b><br>99. pSB1C3 - CrtO<br><br><b>O/N & Screening</b><br>79. pEL3K16 - CrtE <br>102. pSB1C3 - CrtE<br>101. pSB1C3 - DNA program123456<br><br><b>Gelelectrophoresis</b><br>21. pSB4C5 - pBAD/AraC-CrtE~I /w RBS, ZF<br>57. PSB1C3-B0034-Idi (on pcr product from overnight pcr with new protocol) <br><br><b>PCR </b><br>57.PSB1C3-B0034-IDI (overnight Tuesday-Wednesday new protocol) <br><br><h2>Results</h2><b>Plasmid preparation: </b><br>74. pSB3K3-CP44-B0032-BFP: Failed! → Re-do!<br><br><b>Screening:</b> <br>111. pSBLb4C15: Failed<br>112. pSBLbEc4C15: Failed<br><br><h2>Other experiments</h2>Primer stock preparation: CA *<br>CSP_RF<br>CBP_RF<br>usp45_RF<br>CBP F<br>*Obtained a concentration of 5µM at a volume of 200µl.<br><br></div>'; | ||
| + | } | ||
| + | else if(id == 'd2013715') | ||
| + | { | ||
| + | ds = '<div id="dairy-text"><br><h1>Monday 2013-07-15</h1><br><br><b>Name of participants:</b> Karl H, Lovisa P, Theodor L, Ken B-A, Victor S, Hampus.E, Christoffer, Sabri, Alexander, Nils, Thorsteinn, Magnus, Malin, Pontus, Niclas<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>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>105. pSB3T5-J23101-B0034-TAL<br>104. pSB1C3-B0034-4CL-B0034-STS<br>106. pSB3T5-J23110-B0034-TAL<br>107. pSB3T5-CP1-B0034-TAL<br>79. pEL3K16 - CrtE <br>102. pSB1C3 - CrtE<br>75. pEL3A15 - CrtB<br>101. pSB1C3 - DNA program123456<br>76. pEL3K16-CrtI<br>78. pEL3C18-CrtY<br>99. pSB1C3 - CrtO<br>57.Psb1C3-B0034-Idi<br>91. BBa_J61002 (amp)-J23106<br>94. pSB1C3-K206000<br>95. pSB1C3-K206001<br>11. pSB4A15-blue(?)<br>58. pSB1C3-IspA<br>108. pSB4A15-J23106-B0034-IspA<br>109. pSB4A15-K206000-B0034-IspA<br>110. pSB4A15-K206001-B0034-IspA<br>7.pSB3k3-red<br>22. B0032-BFP<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>81. pSB4S15-CP41-B0032-BFP<br>83. pSB4S15-CP30-B0032-BFP<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>82. pSB4S15-CP29-B0032-BFP<br>98. pSB4S15-CP11-B0032-BFP<br>100. pJP059<br>111. pSBLb4C15<br>112. pSBLbEc4C15<br><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>14. DSM 20016-pLUL631(B?)<br>22. Betacarotene-various plasmids<br><br><b>L. plantarum:</b><br>5. 256-rifR-pAMβ1<br>10. 256-p256<br><br><h2>Todays work</h2><b>PCR Purification:</b><br>111. pSBLb4C15, digest<br>112. pSBLbEc4C15, digest<br><br><b>Ligation: </b><br>111. pSBLb4C15 (MluI+NheI) + Ori from pJP059 (MluI+NheI) <br>112. pSBLbEc4C15: (MluI+ClaI) + Ori from pJP059 (MluI+ClaI)<br><br><b>Transformation: </b><br>111. pSBLb4C15<br>112. pSBLbEc4C15<br>75. pEL3A15 - CrtB<br>99. pSB1c3 - CrtO<br>108. pSB4A15-J23106-B0034-IspA<br>109. pSB4A15-K206000-B0034-IspA<br>110. pSB4A15-K206001-B0034-IspA<br>45. pSB1C3-B0034-4CL<br>46. pSB1C3-B0034-His-4CL<br>47. pSB1C3-B0034-STS<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><br><b>Overnight: </b><br>74. pSB3K3-CP44-B0032-BFP<br>101. pSB1C3 - DNA program123456 <br><br><b>Fluorescence(BFP) experiment with UV: </b><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>81. pSB4S15-CP41-B0032-BFP<br>83. pSB4S15-CP30-B0032-BFP<br>86. pSB4S15-CP6-B0032-BFP<br>88. pSB4S15-CP1-B0032-BFP<br>89. pSB4S15-CP44-B0032-BFP<br><br><b>Plasmid preparation: </b><br>Lb10.1 plantarum 256 p256<br>Lb10.2 plantarum 256 p256<br>Lb10.3 plantarum 256 p256<br>Lb22.1 reuteri betacarotene (strain name?) various plasmids<br>44.5 pSB1C3-b0034-His-Tal<br>74. pSB3K3-CP44-B0032-BFP<br><br><b>PCR:</b><br>48. pSB1C3-B0034-His-STS<br><br><b>Gel electhrophoresis</b><br>48. pSB1C3-B0034-His-STS<br><br><b>Assembly:</b><br>105. pSB3T5-J23101-B0034-TAL<br>106. pSB3T5-J23110-B0034-TAL<br>107. pSB3T5-CP1-B0034-TAL<br><br><b>Re-streak:</b><br>79. pEL3K16 - CrtE <br>102. pSB1C3 - CrtE<br>75. pEL3A15 - CrtB<br><br><br><b>PCR cloning of:</b><br>CrtE~I /w RBS, Zinc finger (PCR is done to remove promoter). Template should be the following construct, digested (E,P) 21. pBAD/AraC-CrtE~I /w RBS, Zinc finger <br><br>CrtE~Z /w RBS, Zinc finger (PCR is done to remove promoter). Template should be the following construct, digested (E,P) 20. pBAD/AraC-CrtE~I /w RBS, Zinc finger <br><br>CrtE~(O)-Z /w RBS, Zinc finger (PCR is done to remove promoter). Template should be the following construct, digested (E,P) 19. pBAD/AraC-CrtE~I /w RBS, Zinc finger <br><br>CrtZ (PCR is done to clone and biobrick CrtZ from the following template, 20. pBAD/AraC-CrtE~CrtZ /w RBS, Zinc Finger<br><br><b>Mutagenesis</b> <br>57. pSB1C3-B0034-Idi <br><br><b>Sequence preperation</b><br>78.1 pEL3C18-CrtY (VF and VR)<br>78.3 pEL3C18-CrtY (VF and VR)<br><br><b>Screening:</b><br>111. pSBLb4C15<br>112. pSBLbEc4C15<br>81. pSB4S15-CP41-B0032-BFP<br>83. pSB4S15-CP30-B0032-BFP<br>86. pSB4S15-CP6-B0032-BFP<br>88. pSB4S15-CP1-B0032-BFP<br>89. pSB4S15-CP44-B0032-BFP<br>101. pSB1C3 - DNA program123456 <br><br><i>Touchdown PCR with Phusion polymerase (signal peptides): CA<br>Collagen binding protein → cloned from strain 14.4<br>Cell surface protein → cloned from strain 3.1<br>usp45 → cloned from strain 13.1</i><br><br><h2>Results</h2><b>PCR, Succes on:</b><br>48. pSB1C3-B0034-His-STS<br><br><b>Transformation </b><br>45. pSB1C3-B0034-4CL, failed<br>46. pSB1C3-B0034-His-4CL, failed<br>104. pSB1C3-B0034-4CL-B0034-STS, failed<br>106. pSB3T5-J23110-B0034-TAL, failed<br>108. pSB4A15-J23106-B0034-IspA, failed<br>109. pSB4A15-K206000-B0034-IspA, failed<br>110. pSB4A15-K206001-B0034-IspA, failed<br>111. pSBLb4C15<br>112. pSBLbEc4C15<br><br><i>-(45,46,104,106) Probably due to weak competent cells<br>-(111-112) No growth. Possible problems: Too short time for proper ligation, no purification before ligation. Another attempt will be madwith the ligation from yesterday and a new one with purified digests.<br><br>Nanodrop measurement of 57.Psb1C3-B0034-Idi was 80 ng/microliter.</i><br><br><b>Gel:</b><br>21 pSB4C5-pBAD/AraC-B0034-Jazz-Linker-CrtE-B0034-Blues-Linker-CrtB-B0034-CrtI-Linker-Zif268, fail<br><br><b>Fluorescence(BFP) experiment with UV:</b><br>68. pSB3K3-CP1-B0032-BFP : Glowing (68.2 68.4)<br>69. pSB3K3-CP8-B0032-BFP : Glowing (69.3 69.4)<br>70. pSB3K3-CP11-B0032-BFP : Glowing (70.3)<br>71. pSB3K3-CP29-B0032-BFP : Glowing (71.1 71.2)<br>72. pSB3K3-CP30-B0032-BFP : Glowing (72.1 72.2)<br>73. pSB3K3-CP41-B0032-BFP : Glowing (73.4)<br>74. pSB3K3-CP44-B0032-BFP : Glowing (74.1.1 74.1.2)<br>81. pSB4S15-CP41-B0032-BFP : Not glowing<br>83. pSB4S15-CP30-B0032-BFP : Not glowing<br>86. pSB4S15-CP6-B0032-BFP : Not glowing<br>88. pSB4S15-CP1-B0032-BFP : Not glowing<br>89. pSB4S15-CP44-B0032-BFP : Not glowing<br><br><b>Plasmid preparation:</b><br>Lb10.1 plantarum 256 p256: 124.7 ng/µl<br>Lb10.2 plantarum 256 p256: 23.5 ng/µl<br>Lb10.3 plantarum 256 p256: 270.9 ng/µl <br>Lb22.1 reuteri betacarotene (strain name?) various plasmids: 51.4 ng/µl<br><br></div>'; | ||
| + | } | ||
| + | else if(id == 'd2013714') | ||
| + | { | ||
| + | ds = '<div id="dairy-text"><h1>Sunday 2013-07-14</h1><b>Name of participants:</b> Anders Edlund (AE), Viktor Blomkvist (VB), Lovisa P, Christoffer F, Sabri J<br><br><h2>Ongoing constructs:</h2><b>E.coli (strain D5α): </b><br>7.pSB3k3-red<br>22. B0032-BFP<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>81. pSB4S15-CP41-B0032-BFP<br>83. pSB4S15-CP30-B0032-BFP<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>82. pSB4S15-CP29-B0032-BFP<br>98. pSB4S15-CP11-B0032-BFP<br>100. pJP059<br>111. pSBLb4C15<br>112. pSBLbEc4C15<br>15. pSB4K5-RBS-TAL-Linker-Zif268-RBS-4cl-Linker-PBSII-STS-OMT<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>91. BBa_J61002-J23106<br>92. BBa_J61002-J23110<br>93. BBa_J61002-J23116<br>103. pSB1k3-J23101<br>79. pEL3K16 - CrtE <br>102. pSB1C3 - CrtE<br>75. pEL3A15 - CrtB<br>101. pSB1C3 - DNA program123456<br>76. pEL3K16-CrtI<br>78. pEL3C18-CrtY<br><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>14. DSM 20016-pLUL631(B?)<br>22. Betacarotene-various plasmids<br><br><b>L. plantarum:</b><br>5. 256-rifR-pAMβ1<br>10. 256-p256<br><br><h2>Todays work</h2><b>Ligation: </b><br>111. pSBLb4C15 (MluI+NheI) + Ori from pJP059 (MluI+NheI) <br>112. pSBLbEc4C15: (MluI+ClaI) + Ori from pJP059 (MluI+ClaI)<br><br><b>Transformation:</b><br>111. pSBLb4C15<br>112. pSBLbEc4C15<br>79. pEL3K16 - CrtE <br>102. pSB1C3 - CrtE<br>75. pEL3A15 - CrtB<br><br><b>Plasmid prep. and glycerol stock:</b><br>103. pSB1k3-J23101<br>91. BBa_J61002-J23106<br>92. BBa_J61002-J23110<br>93. BBa_J61002-J23116<br>44.4 pSB1C3-b0034-His-Tal<br>76.(1-4)-pEL3K16-CrtI<br>78.(1-3)-pEL3C18-CrtY<br><br><b>Overnight:</b><br>44.5 pSB1C3-b0034-His-Tal<br>BBa_J61002-J23101 (amp)<br><br><b>Restreak:</b><br>101. pSB1C3 - DNA program123456 (Picked 4 clones)<br><br><b>Subcloning:</b><br>CrtE (PCR prod) should be digested with X,P (Can be found in digest box)<br>27. pEL3K16 - red should be digested with X,P → CrtE (PCR prod)<br>1. pSB1C3 - red should be digested with X,P → CrtE (PCR prod)<br>38. pEL3A15 - red → 23. pSB1C3-CrtB<br><br><b>PCR cloning:</b><br>CrtE~I /w RBS, Zinc finger (PCR is done to remove promoter). Template should be the following construct, digested (E,P) 21. pBAD/AraC-CrtE~I /w RBS, Zinc finger <br><br>CrtZ (PCR is done to clone and biobrick CrtZ from the following template, 20. pBAD/AraC-CrtE~CrtZ /w RBS, Zinc Finger<br><br>CrtO PCR is done to clone CrtO from the following template, digested (E,P) 19. pBAD/AraC-CrtE~Crt(O)-Crt(Z) /w RBS, Zinc finger<br><br><h2>Results</h2>Problems with the yesterday ligation, the experiment was redone<br>Transformation of 101. DNA program123456 was a sucess although 102. pSB1C3-CrtE failed<br>The PCR failed for CrtE~I, unspecific binding<br>The PCR failed for CrtZ, unspecific binding. <br></div>'; | ||
| + | } | ||
| + | else if(id == 'd2013713') | ||
| + | { | ||
| + | ds = '<div id="dairy-text"><br><h1>Saturday 2013-07-13</h1><b>Name of participants:</b> Sabri J, Nils, Kristoffer L, Theodor Löwe, Viktor Blomkvist (VB), Stephanie Herman (SH), Alona Nyberg (AN)<br><br><h2>Ongoing constructs:</h2><b>E.coli (strain D5α):</b><br>101. pSB1C3 - DNA Program123456<br>79. pEL3K16 - CrtE <br>102. pSB1C3 - CrtE<br>76. pEL3K16 - CrtI <br>78. pEL3C18 - CrtY<br>90 pSB1k3-J23101<br>91 BBa_J61002-J23106<br>92 BBa_J61002-J23110<br>93 BBa_J61002-J23116<br>44.4 pSB1C3-b0034-His-Tal<br>44.5 pSB1C3-b0034-His-Tal<br>111. pSBLb4C15: MluI+NheI<br>112. pSBLbEc4C15: MluI+ClaI<br>68. pSB3K3-CP1-B0032-BFP<br>73. pSB3K3-CP41-B0032-BFP<br><br><h2>Todays work</h2><b>Ligation:</b><br>1. pSB1C3 - red → DNA program123456 (PCR prod)<br>1. pSB1C3 - red → CrtE (PCR prod)<br>27. pEL3K16 - red → CrtE (PCR prod)<br><br><b>PCR and Gelelectrophoresis:</b><br>CrtO<br><br><b>Transformation:</b><br>101. pSB1C3 - DNA program123456<br>102. pSB1C3 - CrtE<br><br><b>Overnight, Screening:</b><br>76.(1-4) pEL3K16 - CrtI <br>78.(1-3) pEL3C18 - CrtY<br><br><b>PCR purification: </b><br>111. pSBLb4C15<br>112. pSBLbEc4C15<br><br><b>Digestion:</b><br>1. pSB1C3 - red → DNA program123456 (PCR prod)<br>111. pSBLb4C15: MluI+NheI<br>112. pSBLbEc4C15: MluI+ClaI<br>Lb13. Lc. lactis MG1363-pJP059, <i>Ori: Two experiments, Mlu1+NheI & MLuI+ClaI<br>* Parts of what will become the first shuttle-vector.</i><br><br><b>Plasmid preparation:</b><br>68. pSB3K3-CP1-B0032-BFP<br>73. pSB3K3-CP41-B0032-BFP<br><br><h2>Results</h2><b>Gel:</b><br>47. pSB1C3-B0034-STS PCR product with and without DMSO (7%)<br>Good results on GEL, both PCR with and without DMSO looks good.<br><br><img class="result-pic" src="https://static.igem.org/mediawiki/igem.org/4/43/Uppsala_gelPic_2013-07-13.jpg"><table class="table-pic-desc-table"><tr><td>1</td><td>2</td><td>3</td><td>4</td><td>5</td><td>6</td><td>7</td><td>8</td><td>9</td><td>10</td></tr><tr><td>N/C</td><td>76.1 (Sucess)</td><td>76.2 (Sucess)</td><td>76.3 (Sucess)</td><td>76.4 (Sucess)</td><td>Ladder</td><td>N/C</td><td>78.1 (Sucess)</td><td>78.2 (Sucess)</td><td>78.3 (Sucess)</td></tr><tr><td>11</td><td>12</td><td>13</td><td>14</td><td>15</td><td>16</td><td>17</td><td>18</td><td>19</td><td>20</td></tr><tr><td>Ladder</td><td>CrtE (digested with E,P)</td><td>CrtE~I (digested with X, P) (Failed)</td><td>CrtE~I (digested with E, P) (Failed)</td><td>N/C</td><td>CrtO (Failed)</td><td>ORI I (Geneticals)</td><td>ORI II (Geneticals)</td><td>Ladder</td></tr></table><br><i>CrtE PCR prod should have been digested with X,P therefore construct 79 and 102 needs to be redone </i><br><br></div>'; | ||
| + | } | ||
| + | else if(id == 'd2013712') | ||
| + | { | ||
| + | ds = '<div id="dairy-text"><br><h1>Friday 2013-07-12</h1><b>Name of participants:</b> Kristoffer L, Emil M, Karl H, Peter C, Lovisa P, Theodor L, Ken B-A, Christoffer F, Sabri J, Niclas<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>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>82. pSB4S15-CP29-B0032-BFP<br>84. pSB4S15-CP6<br>85. pSB4S15-CP25<br>87. pSB4S15-CP25-B0032-BFP<br>89. pSB4S15-CP44-B0032-BFP<br>97. pSB4S15-CP8-B0032-BFP<br>98. pSB4S15-CP11-B0032-BFP<br>100. pJP059<br><br><b>Lb. delbrueckii bulgaricus:</b><br>18. Lb. delbrueckii bulgaricus<br><br><b>Lc. thermophilus:</b><br>19. L.thermophilus<br><br><b>L. plantarum:</b><br>5. 256-rifR-pAMβ1<br>10. 256-p256<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><h2>Todays work</h2>Digestion:<br>22. B0032-BFP - E,P<br>11. psB4A15<br><br><b>Ligation:</b> <br>CrtE~I /w RBS + Zincfinger -> 11. pSB4A15-ed<br>CrtE(PCR-prod.) -> 27. pEL3K16-red <br>CrtE -> 1. pSB1C3 (to registry)<br><br><i>-all AMP plates from yesterday failed 90-93. (J23 series promotors)<br>Digest of construct 14 and 15 from plasmid prep with Pst1, followed by gel analysis.</i><br><br><b>Transformation:</b><br>CrtE~I /w RBS + Zincfinger -> 11. pSB4A15-ed<br>CrtE(PCR-prod.) -> 27. pEL3K16-red <br>82. pSB4S15-CP29-B0032-BFP<br>84. pSB4S15-CP6<br>85. pSB4S15-CP25<br>87. pSB4S15-CP25-B0032-BFP<br>89. pSB4S15-CP44-B0032-BFP<br>97. pSB4S15-CP8-B0032-BFP<br>98. pSB4S15-CP11-B0032-BFP<br>100. pJP059<br>J23101<br><br>PCR on DNA program 123456<br><br>Plasmid prepp on 96.Cs42s clone nr 1 and 2. <br>Glycerol stock on 96.Cs42s clone 1 and 2.<br>Gel run on digest from plasmid preparation of 96.cs42s clone 1 and 2.<br><br><b>Re-streak:</b><br>76 pEL3K16 - CrtI (4 clones)<br>78. pEL3C18 - CrtY (3 clones)<br>74. pSB3K3-CP44-B0032-BFP<br>81. pSB4S15-CP41-B0032-BFP<br>83. pSB4S15-CP30-B0032-BFP<br>86. pSB4S15-CP6-B0032-BFP<br>88. pSB4S15-CP1-B0032-BFP<br>73. pSB3K3-CP41-B0032-BFP<br><br><b>Gel electrophoresis:</b><br>45. pSB1C3-B0034-4CL<br>46. pSB1C3-B0034-His-4CL<br>47. pSB1C3-B0034-STS<br>46. pSB1C3-B0034-His-4CL<br>48. pSB1C3-B0034-His-STS<br>pSB4C15 PCR-product with intact ori<br>pSB4C15 PCR-product without ori<br><br><b>Overnight culture:</b><br>68. pSB3K3-CP1-B0032-BFP<br>73. pSB3K3-CP41-B0032-BFP<br>74. pSB3K3-CP44-B0032-BFP<br>Lb10.3 plantarum 256 p256<br>Lb10.4 plantarum 256 p256<br><br><b>Spreading:</b><br>87. pSB4S15-CP25-B0032-BFP<br>89. pSB4S15-CP44-B0032-BFP<br>97. pSB4S15-CP8-B0032-BFP<br>82. pSB4S15-CP29-B0032-BFP<br>98. pSB4S15-CP11-B0032-BFP<br>Lb10.3 plantarum 256 p256<br>Lb10.4 plantarum 256 p256<br><br><h2>Results</h2><b>Transformation:</b><br>Successful:<br>76 pEL3K16-CrtI<br>78 pEL3C18-CrtY<br> <br>failed:<br>75 pEL3A15-CrtB<br><br>The result from nanodrop measurement of 96.Cs42s clone 1 was 408.3 nanogram/microliter and clone 2 was 332. Also both had a god a260/a280 ratio.<br>The result from the gel run of the two 96.Cs42s clones indicates an construct with a size of ~4000 bp. <br><br><b>Gel on PCRs:</b><br>Successful:<br>45. pSB1C3-B0034-4CL<br>46. pSB1C3-B0034-His-4CL<br><br>failed<br>47. pSB1C3-B0034-STS<br>46. pSB1C3-B0034-His-4CL<br>48. pSB1C3-B0034-His-STS<br><br><i>-PCR-amplification: 47. pSB1C3-B0034-STS, change temperature -2 degrees<br><br>Construct 14 had two bands on the gel, indicating illegal restriction sites. Construct 15 only had one band and no indication of illegal restriction sites.</i><br><br><h2>Other experiments</h2>Casting LB-agar plates: AB<br>27 plates containing spectinomycin.<br><br><b>Preparation for sequencing:</b><br>69.1 pSB3K3-CP8-B0032-BFP<br>71.3 pSB3K3-CP29-B0032-BFP<br>72.3 pSB3K3-CP30-B0032-BFP<br><br><b>Dilution of primers: </b><br>200 µl VF2 (5 µM)<br>200 µl VR (5 µM)<br></div>'; | ||
| + | } | ||
| + | else if(id == 'd2013711') | ||
| + | { | ||
| + | ds = '<div id="dairy-text"><br><h1>Thursday 2013-07-11</h1><br><b>Name of participants:</b> Kristoffer L, Emil M, Karl H, Peter C, Lovisa P, Theodor L, Ken B-A, Christoffer Ahlström (CA), Anton Berglund (AB), Stephanie Herman (SH), Alona Nyberg (AN), Viktor Törnblom (VT), Viktor Blomkvist (VB), Mikael Strandgren (MS), Niclas, Sabri , Nils, Christoffer<br><br><h2>Ongoing constructs:</h2><br><b>E.coli (strain D5α): </b><br>15. pSB4K5-RBS-TAL-Linker-Zif268-RBS-4cl-Linker-PBSII-STS-OMT<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>81. pSB4S15-CP41-B0032-BFP<br>83. pSB4S15-CP30-B0032-BFP<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>82. pSB4S15-CP29-B0032-BFP<br>97. pSB4S15-CP8-B0032-BFP<br>98. pSB4S15-CP11-B0032-BFP<br>74. pSB3K3-CP44-B0032-BFP<br>68. pSB3K3-CP1-B0032-BFP<br>73. pSB3K3-CP41-B0032-BFP<br>84. pSB4S15-CP6<br>85. pSB4S15-CP25<br>96. Cs42s <br><br><b>L. plantarum:</b><br>10. 256-p256<br><br><h2>Todays work</h2><br><b>Transformation:</b> <br>81. pSB4S15-CP41-B0032-BFP<br>83. pSB4S15-CP30-B0032-BFP<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>82. pSB4S15-CP29-B0032-BFP<br>97. pSB4S15-CP8-B0032-BFP<br>98. pSB4S15-CP11-B0032-BFP<br>74. pSB3K3-CP44-B0032-BFP<br>68. pSB3K3-CP1-B0032-BFP<br>73. pSB3K3-CP41-B0032-BFP<br>77. pSB4C15-red*<br>75. pEL3A15 - CrtB<br>76 pEL3K16 - CrtI<br>78. pEL3C18 - CrtY<br><br><b>Restreaks:</b> <br>68. pSB3K3-CP1-B0032-BFP<br>73. pSB3K3-CP41-B0032-BFP<br>Lb10.3 plantarum 256 p256 *<br>Lb10.4 plantarum 256 p256<br>Lb10.5 plantarum 256 p256 *<br>Lb10.6 plantarum 256 p256<br><br><b>PCR:</b><br>77.(1-4) pSB4C15-red*<br><i>*Two different amplifications of plasmid adding restriction-sites with different primers.<br> One product with no removals and one without ori.</i><br><br><b>PCR-amplification:</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>Digest:</b><br>14 pET13b(amp)-zifz:4cl-PBSII:STS<br>15. pSB4K5-RBS-TAL-Linker-Zif268-RBS-4cl-Linker-PBSII-STS-OMT<br><i>-from plasmid prep with Pst1.</i><br><br><b>PCR screening & gel extraction:</b><br>44. pSB1C3-B0034-His-TAL<br>45. pSB1C3-B0034-4CL<br><br><b>Ligation: </b><br>84. pSB4S15-CP6<br>85. pSB4S15-CP25<br><br><b>Plasmid preparation:</b><br>77. pSB4C15-red<br><br>PCR screening of cs42s with RedTaq. Overnight culture on transfrormed 96.Cs42s.<br>Prepare of Vf2 and VR primer solution, 20x. 5 tubes each with 200 microliter/tube.<br><br><b>Subcloning of the following CrtB, CrtI, CrtY</b><br><br>23. pSB1C3-CrtB → pEL3A15 - red<br>24. pSB1C3-CrtI → pEL3K16 - red<br>25. CrtY(PCR prod.) → pEL3C18 - red<br><br><h2>Results</h2><br><b>Plasmid preparation: </b><br>77.1 pSB4C15-red: 47.2 ng/µl<br>77.2 pSB4C15-red: 50.2 ng/µl<br>77.3 pSB4C15-red: 44.0 ng/µl<br>77.4 pSB4C15-red: 54.4 ng/µl<br><br><b>Screening:</b><br>didn’t look good, the pcr product was approximatley 1000 bp on the gel.<br> Should have been around 4000.<br><br><h2>Other experiments</h2><br><b>Sequence verification:</b><br>61.1 pSB1C3-CP1<br>63.1 pSB1C3-CP11<br>67.1 pSB1C3-Cp44<br><br><b>Casting LB-agar plates: </b><br>26 plates containing spectinomycin.<br><br><b>Preparation of LB-agar solution: </b><br><b>transformation from kit:</b><br>90. BBa_J61002 (amp)-J23101<br>91. BBa_J61002 (amp)-J23106<br>92. BBa_J61002 (amp)-J23110<br>93. BBa_J61002 (amp)-J23116<br><br><b>Restreek from stock:</b><br>2012 SD(Strain Database) 13 and 61(promotors).<br>Aliquoting VF2- and VR-primers.<br><br></div>'; | ||
| + | } | ||
| + | else if(id == 'd2013710') | ||
| + | { | ||
| + | ds = '<div id="dairy-text"><br><h1>Wednesday 2013-07-10</h1><br><b>Name of participants:</b> Kristoffer L, Emil M, Karl H, Peter C., Lovisa P, Ken B-A, Alexander, Niclas, Magnus, Nils, Thorsteinn, Christoffer Ahlström (CA), Anton Berglund (AB), Stephanie Herman (SH), Viktor Törnblom (VT)<br><br><h2>Ongoing constructs:</h2><br><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>96. p?A?-Cs42s<br>68. pSB3K3-CP1-B0032-BFP<br>73. pSB3K3-CP41-B0032-BFP<br>74. pSB3K3-Cp44-B0032-BFP<br>81. pSB4S15-CP41-B0032-BFP<br>83. pSB4S15-CP30-B0032-BFP<br>86. pSB3K3-CP44-B0032-BFP<br>87. pSB3K3-CP1-B0032-BFP<br>88. pSB3K3-CP41-B0032-BFP<br>89. pSB4S15-CP44-B0032-BFP<br><br><h2>Todays work</h2><br><b>Digestion:</b> <br>22. pSB1C3-RBS-B0032-BFP<br><br><b>Ligation:</b><br>44. pSB1C3-B0034-His-TAL<br>68. pSB3K3-CP1-B0032-BFP<br>73. pSB3K3-CP41-B0032-BFP<br>74. pSB3K3-Cp44-B0032-BFP<br>81. pSB4S15-CP41-B0032-BFP<br>83. pSB4S15-CP30-B0032-BFP<br>86. pSB3K3-CP44-B0032-BFP<br>87. pSB3K3-CP1-B0032-BFP<br>88. pSB3K3-CP41-B0032-BFP<br>89. pSB4S15-CP44-B0032-BFP<br><br><b>transformation:</b><br>44. pSB1C3-B0034-His-TAL<br>68. pSB3K3-CP1-B0032-BFP<br>73. pSB3K3-CP41-B0032-BFP<br>74. pSB3K3-Cp44-B0032-BFP<br>81. pSB4S15-CP41-B0032-BFP<br>83. pSB4S15-CP30-B0032-BFP<br>86. pSB3K3-CP44-B0032-BFP<br>87. pSB3K3-CP1-B0032-BFP<br>88. pSB3K3-CP41-B0032-BFP<br>89. pSB4S15-CP44-B0032-BFP<br><br><b>Re-streak</b> <br>96. p?A?-cs42s<br><i>-Streak of transformations of ligated 20 and positive controll (AV,NA)<br>PCR of 19(digested EP), 20(digested EP), 21(digested EP) and CrtO(from 21digestEP) (AV,NA)</i><br><br><b>Spreading of strains: </b><br>Lb4. reuteri 100-23 no plasmid<br>Lb12. reuteri DSM 20016 no plasmid<br>Lb10. plantarum 256 p256<br>Lb11. plantarum 36E no plasmid<br>Lb10. plantarum 256 noplasmid: Growth<br>Lb11. plantarum 36E noplasmid: Growth<br>→ Spread out (1x) on erythromycin plates, to examine whether they are naturally resistant.<br><br><h2>Results</h2><br><b>Transformation: </b> <br>Lb4. reuteri 100-23 noplasmid: Growth <br>Lb12. reuteri DSM 20016 noplasmid: Growth<br><br><b>Re-streak:</b> <br>96. p?A?-cs42s worked well. <br><br><b>O/N culture:</b><br>69.1 pSB3K3-CP8-B0032-BFP <br>69.2 pSB3K3-CP8-B0032-BFP <br>69.3 pSB3K3-CP8-B0032-BFP <br>69.4 pSB3K3-CP8-B0032-BFP <br>70.1 pSB3K3-CP11-B0032-BFP <br>70.2 pSB3K3-CP11-B0032-BFP <br>70.3 pSB3K3-CP11-B0032-BFP <br>70.4 pSB3K3-CP11-B0032-BFP <br>71.1 pSB3K3-CP29-B0032-BFP<br>71.2 pSB3K3-CP29-B0032-BFP<br>71.3 pSB3K3-CP29-B0032-BFP<br>71.4 pSB3K3-CP29-B0032-BFP<br>72.1 pSB3K3-CP30-B0032-BFP<br>72.2 pSB3K3-CP30-B0032-BFP<br>72.3 pSB3K3-CP30-B0032-BFP<br>72.4 pSB3K3-CP30-B0032-BFP<br>*Growth<br><br><b>Plasmid preparation: </b><br>69.1 pSB3K3-CP8-B0032-BFP: 80.5 ng/µl<br>69.2 pSB3K3-CP8-B0032-BFP: 75.7 ng/µl<br>69.3 pSB3K3-CP8-B0032-BFP: 60.5 ng/µl<br>69.4 pSB3K3-CP8-B0032-BFP: 50.8 ng/µl<br>70.1 pSB3K3-CP11-B0032-BFP: 71.7 ng/µl<br>70.2 pSB3K3-CP11-B0032-BFP: 56.3 ng/µl<br>70.3 pSB3K3-CP11-B0032-BFP: 56.0 ng/µl<br>70.4 pSB3K3-CP11-B0032-BFP: 45.3 ng/µl<br>71.1 pSB3K3-CP29-B0032-BFP: 54.0 ng/µl<br>71.2 pSB3K3-CP29-B0032-BFP: 49.1 ng/µl<br>71.3 pSB3K3-CP29-B0032-BFP: 83.0 ng/µl<br>71.4 pSB3K3-CP29-B0032-BFP 67.8 ng/µl<br>72.1 pSB3K3-CP30-B0032-BFP 53.8 ng/µl<br>72.2 pSB3K3-CP30-B0032-BFP 71.8 ng/µl<br>72.3 pSB3K3-CP30-B0032-BFP 109.6 ng/µl<br>72.4 pSB3K3-CP30-B0032-BFP 106.8 ng/µl<br></div>'; | ||
| + | } | ||
| + | else if(id == 'd201379') | ||
| + | { | ||
| + | ds = '<div id="dairy-text"><br><h1>Tuesday 2013-07-09</h1><br><b>Name of participants:</b> Kristoffer L, Emil M, Marcus H, Karl H, Peter C, Ken B.-A., Lovisa P, Theodor L, Nils, Alexander, Christoffer, Niclas, Magnus, Thorsteinn, Christoffer Ahlström (CA), Stephanie Herman (SH), Nafisa Bashir (NB), Anton Berglund (AB), Mikael Strandgren (MS), Viktor Blomkvist (VB), Viktor Törnblom (VT)<br><br><h2>Ongoing constructs:</h2><br><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>96. p?-Cs42s<br>81. pSB4S15-CP41<br>83. pSB4S15-CP30<br>84. pSB4S15-CP6<br>85. pSB4S15-CP25<br>86. pSB3K3-CP44<br>87. pSB3K3-CP1<br>88. pSB3K3-CP41<br>89. pSB4S15-CP44<br>90. pSB4S15-CP1<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><br><b>L. reuteri:</b><br>Lb4. 100-23-no plasmid<br>Lb12. DSM 20016-no plasmid<br>Lb10. 256-noplasmid<br>LB11. 36E-noplasmid<br><br><h2>Todays work</h2><br><b>Gel analysis:</b><br>43. pSB1C3-B0034-TAL<br>44. pSB1C3-B0034-His-TAL<br>45. pSB1C3-B0034-4CL<br>46. pSB1C3-B0034-His-4CL<br><br><b>Ligation:</b><br>44. pSB1C3-B0034-His-TAL<br>45. pSB1C3-B0034-4CL<br><br><b>OD600 measurement: </b><br>Lb4. reuteri 100-23 no plasmid<br>Lb12. reuteri DSM 20016 no plasmid<br>Lb10. plantarum 256 no plasmid<br>Lb11. plantarum 36E no plasmid<br><br><b>Competent cells preparation:</b><br>Lb4. reuteri 100-23 no plasmid<br>Lb12. reuteri DSM 20016 no plasmid<br>Lb10. plantarum 256 no plasmid<br>Lb11. plantarum 36E no plasmid<br><br><b>Transfromation:</b><br>Lb4. reuteri 100-23 no plasmid<br>Lb12. reuteri DSM 20016 no plasmid<br>Lb10. plantarum 256 no plasmid<br>Lb11. plantarum 36E no plasmid<br><br><b>Re-streaks:</b><br>77. pSB4C15-red<br><br><b>Transformation:</b><br>81. pSB4S15-CP41<br>83. pSB4S15-CP30<br>84. pSB4S15-CP6<br>85. pSB4S15-CP25<br>86. pSB3K3-CP44<br>87. pSB3K3-CP1<br>88. pSB3K3-CP41<br>89. pSB4S15-CP44<br>90. pSB4S15-CP1<br>44. pSB1C3-B0034-His-TAL<br>45. pSB1C3-B0034-4CL<br><br><b>O/N culture:</b><br>69.1 pSB3K3-CP8-B0032-BFP <br>69.2 pSB3K3-CP8-B0032-BFP <br>69.3 pSB3K3-CP8-B0032-BFP <br>69.4 pSB3K3-CP8-B0032-BFP <br>70.1 pSB3K3-CP11-B0032-BFP <br>70.2 pSB3K3-CP11-B0032-BFP <br>70.3 pSB3K3-CP11-B0032-BFP <br>70.4 pSB3K3-CP11-B0032-BFP <br>71.1 pSB3K3-CP29-B0032-BFP<br>71.2 pSB3K3-CP29-B0032-BFP<br>71.3 pSB3K3-CP29-B0032-BFP<br>71.4 pSB3K3-CP29-B0032-BFP<br>72.1 pSB3K3-CP30-B0032-BFP<br>72.2 pSB3K3-CP30-B0032-BFP<br>72.3 pSB3K3-CP30-B0032-BFP<br>72.4 pSB3K3-CP30-B0032-BFP<br><br>Elution and transformation of 96. The transfrormed samples were plated (80μl of 1x and 200μl of 10x dilution) on all available resistances, as the backbone was unknown.<br>Ligation of 20 with all diffrent combinations of ligase buffer and ligase. (AV, CF, NA)<br>Transformation of ligation mentioned above, and a positive controll of 20 plasmidprepp. Although plates for streaking were missing so we couldn’t streak (CF, AV, NA)<br><br><h2>Results</h2><br><b>O/N:</b><br>Lb4. reuteri 100-23 no plasmid (clone 1): NC ok! → follow protocol for transformation<br>Lb12. reuteri DSM 20016 no plasmid (clone 1): NC ok! → follow protocol for transformation, watch in microscope for contamination<br>Lb10. plantarum 256 no plasmid (clone 1): NC ok! → follow protocol for transformation<br>Lb11. plantarum 36E no plasmid (clone 1): NC ok! → follow protocol for transformation<br><br><b>Transformation:</b><br>77. pSB4C15-red: Growth on Cm, some red colonies, some blue, many white (?!)<br><br><b>OD600 measurement:</b><br>Lb4. reuteri 100-23 no plasmid: 0.195 (Measure) & 0.668 (Cultivate) → proceed<br>Lb12. reuteri DSM 20016 no plasmid: 0.179 (Measure) & 0.680 (Cultivate) --”--<br>Lb10. plantarum 256 no plasmid: 0.115 (Measure) & 0.724 (Cultivate) --”--<br>Lb11. plantarum 36E no plasmid: 0.148 (Measure) & 0.624 (Cultivate) --”--<br><br><b>Microscopy: </b><br>Lb12. reuteri DSM 20016 no plasmid: No contamination was sighted! → proceed!<br><br><b>transformation:</b><br>Successful:<br>45. pSB1C3-B0034-4CL<br>96. p?-Cs42s<br><br><b>failed:</b><br>44. pSB1C3-B0034-His-TAL<br><h2>Other experiments</h2>Cold buffer preparation (1 l) <br><br>50% glycerol stock preparation (100 ml)<br><br>Microscopy: Lb12. reuteri DSM 20016 no plasmid<br></div>'; | ||
| + | } | ||
| + | else if(id == 'd201378') | ||
| + | { | ||
| + | ds = '<div id="dairy-text"><h1>Monday 2013-07-08</h1><br><b>Name of participants:</b> Alexander, Nils, Christofffferz , Magnus, Niclas, Thorsteinn, Kristoffer L, Emil M, Marcus H, Karl H, Peter C, Ken B.-A., Lovisa P<br><br><h2>Ongoing constructs</h2><br><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-B0044-IspA<br>81. pSB4S15-CP41<br>83. pSB4S15-CP30<br>84. pSB4S15-CP6<br>85. pSB4S15-CP25<br>86. pSB3K3-CP44<br>87. pSB3K3-CP1<br>88. pSB3K3-CP41<br>89. pSB4S15-CP44<br>90. pSB4S15-CP1<br><br><b>L. reuteri:</b><br>Lb4. 100-23-no plasmid<br>Lb12. DSM 20016-no plasmid<br><br><b>L. plantarum:</b><br>Lb10. 256-noplasmid<br>LB11. 36E-noplasmid<br><br><h2>Todays work</h2><br><b>PCR amplification and gel analysis:</b><br>43. pSB1C3-B0034-TAL<br>44. pSB1C3-B0034-His-TAL<br>45. pSB1C3-B0034-4CL<br>46. pSB1C3-B0034-His-4CL<br><br><b>Plasmid prep.:</b> <br>47. pSB1C3-B0034-STS<br>Clone: 47.9 and 47.20<br>15. pSB4K5-RBS-TAL-Linker-Zif268-RBS-4cl-Linker-PBSII-STS-OMT<br><br><b>Sequencing prep.:</b><br>47. pSB1C3-B0034-STS <br>Clone: 47.9 and 47.20<br>48. pSB1C3-B0034-His-STS<br>Clone: 48.1<br><br><b>Gel extraction:</b><br>43. pSB1C3-B0034-TAL<br>44. pSB1C3-B0034-His-TAL<br>45. pSB1C3-B0034-4CL<br>46. pSB1C3-B0034-His-4CL<br><br><b>Restreak: </b><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><br><b>Digest</b><br>PCR products from succefull gel extraction.<br><br><b>Ligation: </b><br>81. pSB4S15-CP41<br>83. pSB4S15-CP30<br>84. pSB4S15-CP6<br>85. pSB4S15-CP25<br>86. pSB3K3-CP44<br>87. pSB3K3-CP1<br>88. pSB3K3-CP41<br>89. pSB4S15-CP44<br>90. pSB4S15-CP1<br><br><br><b>Frozen stock: </b><br>Lb4. reuteri 100-23 no plasmid (clone 1 & 2)<br>Lb12. reuteri DSM 20016 no plasmid (clone 1 & 2)<br>Lb10. plantarum 256 noplasmid (clone 1 & 2)<br>Lb11. plantarum 36E no plasmid (clone 1 & 2)<br><br><b>O/N:</b> <br>Lb4. reuteri 100-23 no plasmid (clone 1)<br>Lb12. reuteri DSM 20016 no plasmid (clone 1)<br>Lb10. plantarum 256 no plasmid (clone 1)<br>Lb11. plantarum 36E no plasmid (clone 1)<br><br><b>Screening:</b><br>43. pSB1C3-B0034-TAL<br><br><b>O/N culture:</b><br>43.7. pSB1C3-B0034-TAL<br><br><b>Subcloning:</b><br>23->4, 24->4, 25->4(kontroll), 23->38, 24->27, 25->51 (CF, AV)<br>Transformation of 23->4, 24->4, 25->4(kontroll), 23->38, 24->27, 25->51 (CF, AV)<br>Primer design and order of lambda red (NA)<br>Sequencing preparation of 57.3 and 57.5 (pSB1C3-B0034-Idi), 58.1 and 58.4 (pSB1C3-B0034-IspA)<br><br><h2>Results</h2><br><b>Microscopy:</b> *<br><i>*No contamination was seen, save plates for later. → Proceed with O/N of two clones from the no-plasmid strains.</i> <br><br>Primers for lambda red and Cs42s were ordered today :D.<br>Transformation of 23->4(blank), 24->4(blank), 25->4(blank), 23->38(blank), 24->27(a few clones, both red and white on x1), 25->51(blank)<br><br><b>PCR amplification:</b><br>43-46 failed, most likely primer dimers - retry with different concentrations of template DNA, higher concentration of DMSO and a colony PCR of each construct.<br><br><b>gel extraction: </b><br><b>Successfull </b><br>44. pSB1C3-B0034-His-TAL<br>45. pSB1C3-B0034-4CL<br><br><b>failed</b><br>43. pSB1C3-B0034-STS<br>46. pSB1C3-B0034-His-4CL<br><br><b>Screening:</b><br>one succefull clone - 43.7 pSB1C3-B0034-STS<br><br><h2>Other experiments</h2><br><b>Microscopy:</b> CA*<br>*Of plates from 04/07 and O/N from 07/07 to see if contaminated. </div>'; | ||
| + | } | ||
| + | else if(id == 'd201377') | ||
| + | { | ||
| + | ds = '<div id="dairy-text"><h1>Sunday 2013-07-07</h1><br><b>Name of participants:</b>Anders Edlund (AE)<br><br><h2>Ongoing constructs</h2><br>68. pSB3K3-CP1-B0034-BFP<br>69. pSB3K3-CP8-B0034-BFP<br>70. pSB3K3-CP11-B0034-BFP<br>71. pSB3K3-CP29-B0034-BFP<br>72. pSB3K3-CP30-B0034-BFP<br>73. pSB3K3-CP41-B0034-BFP<br>74. pSB3K3-CP44-B0034-BFP<br>77. pSB4S15-C-resistance<br><br><h2>Todays work</h2><br><b>Transformation (AE)</b><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. pSB4S15-C-resistance<br></div>'; | ||
| + | } | ||
| + | else if(id == 'd201376') | ||
| + | { | ||
| + | ds = '<div id="dairy-text"><h1>Saturday 2013-07-06</h1><br><b>Name of participants:</b> Stephanie Herman (SH), Anders Edlund (AE), Nafisa Bashir (NB)<br><br><h2>Ongoing constructs:</h2><br><b>E.coli (strain D5α):</b><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>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><br><h2>Todays work</h2><br><b>Plasmid Preparation:</b> <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><br><b>Transformation: </b><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><br><h2>Results</h2><br><b>Previous day:</b><br>The O/N on the nonplasmids 4, 10, 11, 12 from the previous day had grown at a previously unexperienced rate. A contamination of the original plates from Stefan Roos was suspected as the NC was clear. The O/N was put in the cold room awaiting examination by microscope.<br><br><b>Today:</b><br><b>Plasmid Preparation:</b><br>42. pSB4S15-red<br>61. pSB1C3-CP1: (1) 203.2, (2) 202.9<br>62. pSB1C3-CP8: (1) 254.5, (2) 229.2<br>63. pSB1C3-CP11: (1) 165.0, (2) 260.1<br>64. pSB1C3-CP29: (1) 315.4, (2) 221.9<br>65. pSB1C3-CP30: (1) 243.1, (2) 101.5<br>66. pSB1C3-CP41: (1) 190.7, (2) 68.4<br>67. pSB1C3-Cp44: (1) 169.1, (2) 188.7<br></div>'; | ||
| + | } | ||
| + | else if(id == 'd201375') | ||
| + | { | ||
| + | ds = '<div id="dairy-text"><h1>Friday 2013-07-05</h1><br><b>Name of participants:</b> Kristoffer L, Emil M, Marcus H, Karl H, Peter C, Ken B.-A., Christoffer Ahlström (CA), Anton Berglund (AB), Stephanie Herman (SH), Mikael Strandgren (MS), Viktor Blomkvist (VB), Nafisa Bashir (NB), Magnus, Thorsteinn, Alexander, Nils, Christoffer<br><br><h2>Ongoing constructs:</h2><br>15. pSB4K5-RBS-TAL-Linker-Zif268-RBS-4cl-Linker-PBSII-STS-OMT<br>43. pSB1C3-B0034-TAL<br>44. pSB1C3-B0034-His-TAL<br>45. pSB1C3-B0034-4CL<br>46. pSB1C3-B0034-His-4CL<br>47. pSB1C3-B0034-STS<br>61. pSB1C3-CP1<br>62. pSB1C3-CP8<br>63. pSB1C3-CP11<br>64. pSB1C3-CP29<br>65. pSB1C3-CP30<br>66. pSB1C3-CP41<br>67. pSB1C3-CP44<br>57. pSB1C3-B0034-Idi<br>58. pSB1C3-B0034-ispA<br><br><b>L. reuteri</b><br>Lb4. 100-23 no plasmid<br>Lb12. DSM 20016 no plasmid<br><br><b>L. plantarum:</b><br>Lb10. 256 no plasmid<br>Lb11. 36E no plasmid<br><br><b>L. thermophilus:</b><br>Lb19. L.thermophilus<br><br><b>Todays work</b><br>Screening PCR & gel analysis of constructs:<br>43. pSB1C3-B0034-TAL<br>44. pSB1C3-B0034-His-TAL<br>45. pSB1C3-B0034-4CL<br>46. pSB1C3-B0034-His-4CL<br>47. pSB1C3-B0034-STS<br>61.1 pSB1C3-CP1<br>61.2 pSB1C3-CP1<br>62.1 pSB1C3-CP8<br>62.2 pSB1C3-CP8<br>62.3 pSB1C3-CP8<br>62.4 pSB1C3-CP8<br>63.1 pSB1C3-CP11<br>63.2 pSB1C3-CP11<br>63.3 pSB1C3-CP11<br>63.4 pSB1C3-CP11<br>64.1.1 pSB1C3-CP29<br>64.1.2 pSB1C3-CP29<br>64.1.3 pSB1C3-CP29<br>64.1.4 pSB1C3-CP29<br>65.1.1 pSB1C3-CP30<br>65.1.2 pSB1C3-CP30<br>65.2.1 pSB1C3-CP30<br>65.2.2 pSB1C3-CP30<br>66.5 pSB1C3-CP41<br>66.6 pSB1C3-CP41<br>66.7 pSB1C3-CP41<br>66.8 pSB1C3-CP41<br>67.1.1 pSB1C3-CP44<br>67.1.2 pSB1C3-CP44<br>67.2.1 pSB1C3-CP44<br>67.2.2 pSB1C3-CP44<br><br><b>Plasmid prep & glycerol stock:</b><br>48. pSB1C3-B0034-His-STS<br><br><b>O/N:</b> <br>57. pSB1C3-B0034-Idi<br>58. pSB1C3-B0034-ispA<br>61. pSB1C3-CP1<br>62. pSB1C3-CP8<br>63. pSB1C3-CP11<br>64. pSB1C3-CP29<br>65. pSB1C3-CP30<br>66. pSB1C3-CP41<br>67. pSB1C3-Cp44<br>47.(9, 20) pSB1C3-B0034-STS<br>Lb4. reuteri 100-23 no plasmid<br>Lb10. plantarum 256 no plasmid<br>Lb11. plantarum 36E no plasmid<br>Lb12. reuteri DSM 20016 no plasmid<br><br><b>Re-streaks:</b><br>Lb19. L.thermophilus<br><br><h2>Results</h2><br>The O/N on 42. pSB4S15-red was done improperly in 15 ml falcon tubes and the lids were screwed on too tightly. A new O/N was done on 42. pSB4S15-red by NB.<br><br><b>PCR screen and gel electrophoresis:</b><br>61.1 pSB1C3-CP1<br>61.2 pSB1C3-CP1<br>62.1 pSB1C3-CP8<br>62.2 pSB1C3-CP8<br>62.3 pSB1C3-CP8<br>62.4 pSB1C3-CP8<br>63.1 pSB1C3-CP11<br>63.2 pSB1C3-CP11<br>63.3 pSB1C3-CP11<br>63.4 pSB1C3-CP11<br>64.1.1 pSB1C3-CP29<br>64.1.2 pSB1C3-CP29<br>64.1.3 pSB1C3-CP29<br>64.1.4 pSB1C3-CP29<br>65.1.1 pSB1C3-CP30<br>65.1.2 pSB1C3-CP30<br>65.2.1 pSB1C3-CP30<br>65.2.2 pSB1C3-CP30<br>66.5 pSB1C3-CP41<br>66.6 pSB1C3-CP41<br>66.7 pSB1C3-CP41<br>66.8 pSB1C3-CP41<br>67.1.1 pSB1C3-CP44<br>67.1.2 pSB1C3-CP44<br>67.2.1 pSB1C3-CP44<br>67.2.2 pSB1C3-CP44<br><br>*The gel only showed smudgy bands.<br><br><b>succesful</b><br>47.9 pSB1C3-B0034-STS<br>47.20 pSB1C3-B0034-STS<br><br><b>failed</b><br>43. pSB1C3-B0034-TAL<br>46. pSB1C3-B0034-His-4CL<br><br>No contamination in negative control -_-<br>Religation from yesterday failed. No colonies, only a few at 76, both red and white. <br><br><h2>ther experiments</h2><br><b>Contamination control:</b> CA *<br><br><i>*Contamination control of growth medium for Lc.lactis and Lb.reuteri.<br> Two test from both bottles. </i><br><br><b>E.coli growth test:</b> CA *<br><br><i>*To see if strain 1 of e.coli in strain database 13 grow on M17 and MRS plates as well. </i></div>'; | ||
| + | } | ||
| + | else if(id == 'd201372') | ||
| + | { | ||
| + | ds = '<div id="dairy-text"></div>'; | ||
| + | } | ||
| + | |||
| + | else if(id == 'd201381') | ||
| + | { | ||
| + | ds = '<div id="dairy-text"><h1>Thursday 2013-08-01</h1><p>Name of participants: Marcus H, Karl H, Lovisa P, Emil M, Victor S, Hampus.E<br><br><h2>Ongoing constructs:</h2>' + | ||
| + | '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>'+ | ||
| + | |||
| + | '<h2>Todays work</h2><b>PCR screening and gel electrophorersis of construct:</b><br>185.(5-10) pEL3S17-J23110-B0034-TAL-B0034-4CL-B0034-STS<br>'+ | ||
| + | |||
| + | '<h2>sequencing prep. of constructs:</h2><br>185.9-185.10<br>'+ | ||
| + | |||
| + | '<h2>Transformation of constructs:</h2><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>'+ | ||
| + | |||
| + | '<h2>Results</h2>Construct 185, clone 9 and 10, bonds around 3000/4000 bp.<br><br>'+ | ||
| + | |||
| + | '<h2>Follow up</h2><br>- <br><br>'+ | ||
| + | |||
| + | '<h2>Other experiments</h2><br>-<br></p></div>'; | ||
| + | } | ||
| + | else if(id == 'd2013919') | ||
| + | { | ||
| + | ds ='<h1>Uppsala iGEMs Synbioday, 12.15 to 17.00</h1>'; | ||
| + | } | ||
| + | else | ||
| + | { | ||
| + | ds = 'Nothing happend during this day!'; | ||
| + | } | ||
| + | document.getElementById(id).setAttribute('onclick','closeNote('+y+', '+m+', '+d+');'); | ||
| + | document.getElementById(id).innerHTML = ds; | ||
} | } | ||
Revision as of 22:41, 18 September 2013
