Difference between revisions of "Team:CityU HK/Notebook/Lysis plasmid (phage 21)"

Revision as of 04:09, 20 August 2015

Notebook - City University of Hong Kong 2015

Notebook

Lysis plasmid (phage 21)

Keys to the table:
ori: original gene sequence, without codon optimization
co: codon optimized
21Lysis(o_o_o): S21WT(ori)-Rλ(ori)-Rzλ(ori)
21Lysis(c_c_c): S21WT(co)-Rλ(co)-Rzλ(co)
21Lysis_Sm(o_c_c): S21mut(ori)-Rλ(co)-Rzλ(co)
21Lysis_Sm(c_c_c): S21mut(co)-Rλ(co)-Rzλ(co)
[x/y]: restriction sites digested: E, EcoRI; X, XbaI; S, SpeI; P, PstI
Gene name or plasmid name [x/y]: the gene fragment or plasmid flanked with the restriction sites x and y at the ends
-A ribosome binding site (RBS) is linked upstream of each gene
-Coloring refers to sub-tasks in that particular group
-The cells used for transformation were competent JM109 E. coli cells

Week 4 : June 8 – 12
Date	Group 1	Group 2	Group 3	Group 4
Monday 8
Tuesday 9
Wednesday 10				Extraction of the plasmid pGOv4-Rz21(co) by mini-prep Restriction digestion with [E/P]
Thursday 11				Gel purification of the June 10 [E/P] digested Rz21(co) Ligation of the [E/P] digested Rz21(co) insert into [E/P] digested pSB1C3 Transformation
Friday 12				Colony PCR on Rz21(co) clones showed bands of the expected size

Week 5 : June 15 – 19
Date	Group 1	Group 2	Group 3	Group 4
Monday 15
Tuesday 16	Plasmid extraction of the pGOv4-R21(co) Restriction digestion with [E/P]
Wednesday 17	Gel purification of the [E/P] digested R21(co) Ligation of the [E/P] digested R21(co) insert into the [E/P] digested pSB1C3 Transformation
Thursday 18	Colony PCR confirmed the presence of the R21(co) insert
Friday 19

Week 6 : June 22 – 26
Date	Group 1	Group 2	Group 3	Group 4
Monday 22	Extraction of June 17 plasmid pSB1C3-R21(co)
Tuesday 23				Extraction of June 11 plasmid pSB1C3-Rz21(co) Restriction analysis with [E/P]
Wednesday 24
Thursday 25
Friday 26			PCR amplification on phage 21 wild type lysis cassette

Week 7 : June 29 – July 3
Date	Group 1	Group 2	Group 3	Group 4
Monday 29	Restriction digestion of June 22 R21(co) with [S/P] & Gel purification			Extraction of June 11 plasmid pSB1C3-Rz21(co) Restriction digestion with [X/P]
Tuesday 30			Redo the PCR amplification on phage 21 wild type lysis cassette	Redo June 29’s restriction digestion of Rz21(co) with [X/P]
Wednesday 1
Thursday 2				Gel purification of [X/P] digested Rz21(co) Ligation of the [X/P] digested Rz21(co) insert into Gp1 June 29 [S/P] digested pSB1C3-R21(co) in [S/P]
Friday 3				Transformation of July 2 ligation product pSB1C3-R21(co)-Rz21(co)

Week 8 : July 6 – July 10
Date	Group 1	Group 2	Group 3	Group 4
Monday 6				Colony PCR on July 3 R21(co)-Rz21(co) clones. No bands were observed
Tuesday 7			Extraction of June 30 plasmid pSB1C3-S21WT(ori)-R21(ori)-Rz21(ori) (21Lysis(o_o_o)) Restriction digestion with [X/P]	Redo July 6's colony PCR with other colonies. No bands were observed
Wednesday 8			Redo the restriction digestion of 21Lysis(o_o_o) with [X/P]
Thursday 9			Gel purification of July 8 [X/P] digested 21Lysis(o_o_o)
Friday 10			Ligation of the [X/P] digested 21Lysis(o_o_o) insert into [X/P] digested pSB1C3 vector Transformation	Restriction analysis on July 3 R21(co)-Rz21(co) clones. The analysis confirmed the presence of the R21(co)-Rz21(co) insert

Week 9 : July 13 – July 18
Date	Group 1	Group 2	Group 3	Group 4
Monday 13			Colony PCR on July 10 21Lysis(o_o_o) clones. No bands were observed
Tuesday 14			Restriction analysis on the 21Lysis(o_o_o) clones. The analysis confirmed the presence of the 21Lysis(o_o_o) insert	Extraction of the plasmid pSB1C3-R21(co)-Rz21(co) Restriction digestion with [X/P]
Wednesday 15				Gel purification of July 14 [X/P] digested R21(co)-Rz21(co)
Thursday 16
Friday 17
Saturday 18				Extraction of the plasmids pSB1C3-S21mut(ori) and pSB1C3-S21mut(co) Restriction digestion wth [S/P]

Week 10 : July 20 – July 25
Date	Group 1	Group 2	Group 3	Group 4
Monday 20				Gel purification of July 18 [S/P] digested pSB1C3-S21mut(ori) and pSB1C3-S21mut(co) Ligation of July 15 [X/P] digested R21(co)-Rz21(co) insert into [S/P] digested pSB1C3-S21mut(ori) Ligation of July 15 [X/P] digested R21(co)-Rz21(co) insert into [S/P] digested pSB1C3-S21mut(co)
Tuesday 21		Transformation of pGOv4-Ribo_S21WT(co), pGOv4-Ribo_R21(co) and pGOv4-Ribo_Rz21(co)		Transformation of July 20 ligation product pSB1C3-S21mut(ori)-R21(co)-Rz21(co) (21Lysis_Sm(o_c_c)) Transformation of July 20 ligation product pSB1C3-S21mut(co)-R21(co)-Rz21(co) (21Lysis_Sm(c_c_c))
Wednesday 22			Redo the transformation of pGOv4-Ribo_R21(co)	Colony PCR on the 21Lysis_Sm(o_c_c) clones revealed that the colonies contained inserts of the wrong sizes Colony PCR on the 21Lysis_Sm(c_c_c) clones showed bands of the expected size Redo the restriction digestion of R21(co)-Rz21(co) with [S/P] Gel purification
Thursday 23			Extraction of the plasmids pGOv4-Ribo_S21WT(co), pGOv4-Ribo_R21(co) and pGOv4-Ribo_Rz21(co) Restriction digestion of Ribo_S21WT(co) with [E/P] & [E/S], Ribo_R21(co) with [E/P] & [X/P] and Ribo_Rz21(co) with [E/P] & [X/P]	Redo the ligation of the [X/P] digested R21(co)-Rz21(co) insert into [S/P] digested pSB1C3-S21mut(ori) Transformation Ligation of [X/P] digested BBa_I13504 (GFP) insert into [S/P] digested 21Lysis(o_o_o)
Friday 24				Colony PCR on 21Lysis_Sm(o_c_c) clones showed bands of the expected size
Saturday 25

Week 11 : July 27 – August 1
Date	Group 1	Group 2	Group 3	Group 4
Monday 27
Tuesday 28			Extraction of the plasmid pGOv4-Ribo_Rz21(co) Redo the restriction digestion of Ribo_S21WT(co) and Ribo_R21(co) with [E/P]
Wednesday 29			Ligation of the [E/P] digested Ribo_S21WT(co) insert into the [E/P] digested pSB1C3 vector [E/P] & transformation Ligation of the [E/P] digested Ribo_R21(co) insert into [E/P] digested pSB1C3 Extraction of the plasmids pGOv4-Ribo_S21WT(co), pGOv4-Ribo_R21(co) and pGOv4-Ribo_Rz21(co) Restriction digestion of Ribo_S21WT(co) with [E/S], Ribo_R21(co) with [X/P] and Ribo_Rz21(co) with [E/P] Gel purification	Redo the ligation of the [X/P] digested GFP insert into the [S/P] digested pSB1C3-21Lysis(o_o_o) Transformation
Thursday 30			Restriction digestion of Ribo_R21(co) with [X/P]	Colony PCR on 21Lysis(o_o_o)-GFP clones showed bands of the expected size
Friday 31				Restriction digestion of 21Lysis_Sm(o_c_c) with [X/P] Gel purification Redo the extraction of the plasmid pSB1C3-21Lysis_Sm(c_c_c) Restriction digestion of 21Lysis_Sm(c_c_c) with [X/P] Gel purification
Saturday 1

Week 12 : August 3 – 8
Date	Group 1	Group 2	Group 3	Group 4
Monday 3				Extraction of plasmid pGOV4-S21WT(co)/li> Restriction digestion with [E/S] Gel purification Ligation of the [E/S] digested S21WT(co) and July 22 [X/P] digested R21(co)-Rz21(co) into July 22 [E/P] digested pSB1C3 Extraction of the plasmid pGOv4-lacIq (pLacIQ_LacI_L8-UV5 lac) Restriction digestion with [E/S] Gel purification Ligation of the [E/S] digested lacIq and [X/P] digested 21Lysis_Sm(o_c_c) into [E/P] digested pSB1C3 Ligation of the [E/S] digested lacIq promoter cassette and [X/P] digested 21Lysis_Sm(c_c_c) into [E/P] digested pSB1C3
Tuesday 4				Transformation of Aug 3 ligation product
Wednesday 5				Colony PCR on Aug 4 transformed pSB1C3-21Lysis(c_c_c). The clones contained inserts of the expected size Colony PCR on Aug 4 transformed pSB1C3-lacIq-21Lysis_Sm(o_c_c). The clones contained the wrong inserts Colony PCR on Aug 4 transformed pSB1C3-lacIq-21Lysis_Sm(c_c_c). The clones contained the wrong inserts
Thursday 6				Restriction digestion of 21Lysis(c_c_c) with [E/X] Gel purification Ligation of the [E/S] digested lacIq into the [E/X] digested pSB1C3-21Lysis(c_c_c) Restriction digestion of 21Lysis_Sm(o_c_c) and 21Lysis_Sm(c_c_c) with [E/X] Gel purification Redo the ligation of the [E/S] digested lacIq into the [E/X] digested pSB1C3-21Lysis_Sm(o_c_c) and pSB1C3-21Lysis_Sm(c_c_c) respectively
Friday 7				Transformation of Aug 6 ligation product Redo the restriction digestion with [E/S] on the plasmid pGOv4-S21WT(co) Gel purification
Saturday 8				* Colony PCR on Aug 7 transformed cells. The clones lacIq-21Lysis(c_c_c), lacIq-21Lysis_Sm(o_c_c) and lacIq-21Lysis_Sm(c_c_c) all contained inserts of the expected sizes Ligation of the [E/S] digested S21WT(co) into the [E/S] digested pSB1C3 Transformation

Week 13 : August 10 – 16
Date	Group 1	Group 2	Group 3	Group 4
Monday 10				Colony PCR on Aug 8 transformed cells. The S21WT(co) clones contained inset of the expected size

@@ Line 346: / Line 346: @@
 <b>co</b>: codon optimized <br>
-<b>21Lysis(o_o_o):</b> S21WT(ori)-Rλ(ori)-Rzλ(ori)<br>
+<b>21Lysis(o_o_o):</b> <i>S21WT(ori)-Rλ(ori)-Rzλ(ori)</i><br>
-<b>21Lysis(c_c_c):</b> S21WT(co)-Rλ(co)-Rzλ(co)<br>
+<b>21Lysis(c_c_c):</b> <i>S21WT(co)-Rλ(co)-Rzλ(co)</i><br>
-<b>21Lysis_Sm(o_c_c):</b> S21mut(ori)-Rλ(co)-Rzλ(co)<br>
+<b>21Lysis_Sm(o_c_c):</b> <i>S21mut(ori)-Rλ(co)-Rzλ(co)</i><br>
-<b>21Lysis_Sm(c_c_c):</b> S21mut(co)-Rλ(co)-Rzλ(co)<br>
+<b>21Lysis_Sm(c_c_c):</b> <i>S21mut(co)-Rλ(co)-Rzλ(co)</i><br>
 [x/y]: restriction sites digested: E, EcoRI; X, XbaI; S, SpeI; P, PstI <br>
@@ Line 416: / Line 416: @@
      <td></td>
      <td></td>
-     <td><li>Extraction of the plasmid pGOv4-Rz21(co) by mini-prep</li><li>Restriction digestion with [E/P]</li></td>
+     <td><li>Extraction of the plasmid pGOv4-<i>Rz21(co)</i> by mini-prep</li><li>Restriction digestion with [E/P]</li></td>
    </tr>
    <tr>
@@ Line 423: / Line 423: @@
      <td></td>
      <td></td>
-     <td><li>Gel purification of the June 10 [E/P] digested Rz21(co)</li><li>Ligation of the [E/P] digested Rz21(co) insert into [E/P] digested pSB1C3</li><li>Transformation</li></td>
+     <td><li>Gel purification of the June 10 [E/P] digested <i>Rz21(co)</i></li><li>Ligation of the [E/P] digested <i>Rz21(co)</i> insert into [E/P] digested pSB1C3</li><li>Transformation</li></td>
    </tr>
    <tr>
@@ Line 430: / Line 430: @@
      <td></td>
      <td></td>
-     <td><li>Colony PCR on Rz21(co) clones showed bands of the expected size</li></td>
+     <td><li>Colony PCR on <i>Rz21(co)</i> clones showed bands of the expected size</li></td>
    </tr>
 </table>
@@ Line 451: / Line 451: @@
    <tr>
      <td>Tuesday 16</td>
-     <td><li>Plasmid extraction of the pGOv4-R21(co)</li><li>Restriction digestion with [E/P]</li></td>
+     <td><li>Plasmid extraction of the pGOv4-<i>R21(co)</i></li><li>Restriction digestion with [E/P]</li></td>
      <td></td>
      <td></td>
@@ Line 459: / Line 459: @@
    <tr>
      <td>Wednesday 17</td>
-     <td><li>Gel purification of the [E/P] digested R21(co)</li><li>Ligation of the [E/P] digested R21(co) insert into the [E/P] digested pSB1C3</li><li>Transformation</li></td>
+     <td><li>Gel purification of the [E/P] digested <i>R21(co)</i></li><li>Ligation of the [E/P] digested <i>R21(co)</i> insert into the [E/P] digested pSB1C3</li><li>Transformation</li></td>
      <td></td>
      <td></td>
@@ Line 466: / Line 466: @@
    <tr>
      <td>Thursday 18</td>
-     <td><li>Colony PCR confirmed the presence of the R21(co) insert</li></td>
+     <td><li>Colony PCR confirmed the presence of the <i>R21(co)</i> insert</li></td>
      <td></td>
      <td></td>
@@ Line 493: / Line 493: @@
    <tr>
      <td>Monday 22</td>
-     <td><li>Extraction of June 17 plasmid pSB1C3-R21(co)</li></td>
+     <td><li>Extraction of June 17 plasmid pSB1C3-<i>R21(co)</i></li></td>
      <td></td>
      <td></td>
@@ Line 503: / Line 503: @@
      <td></td>
      <td></td>
-     <td><li>Extraction of June 11 plasmid pSB1C3-Rz21(co)</li><li>Restriction analysis with [E/P]</li></td>
+     <td><li>Extraction of June 11 plasmid pSB1C3-<i>Rz21(co)</i></li><li>Restriction analysis with [E/P]</li></td>
    </tr>
@@ Line 542: / Line 542: @@
    <tr>
      <td>Monday 29</td>
-     <td><li>Restriction digestion of June 22 R21(co) with [S/P] & Gel purification</li></td>
+     <td><li>Restriction digestion of June 22 <i>R21(co)</i> with [S/P] & Gel purification</li></td>
      <td></td>
      <td></td>
-     <td><li>Extraction of June 11 plasmid pSB1C3-Rz21(co)</li> <li>Restriction digestion with [X/P]</li></td>
+     <td><li>Extraction of June 11 plasmid pSB1C3-<i>Rz21(co)</i></li> <li>Restriction digestion with [X/P]</li></td>
    </tr>
    <tr>
@@ Line 552: / Line 552: @@
      <td></td>
      <td><li>Redo the PCR amplification on phage 21 wild type lysis cassette</li></td>
-     <td><li>Redo June 29’s restriction digestion of Rz21(co) with [X/P]</li></td>
+     <td><li>Redo June 29’s restriction digestion of <i>Rz21(co)</i> with [X/P]</li></td>
    </tr>
@@ Line 564: / Line 564: @@
      <td></td>
      <td></td>
-     <td><li>Gel purification of [X/P] digested Rz21(co)</li> <li>Ligation of the [X/P] digested Rz21(co) insert into Gp1 June 29 [S/P] digested pSB1C3-R21(co) in [S/P]</li></td>
+     <td><li>Gel purification of [X/P] digested <i>Rz21(co)</i></li> <li>Ligation of the [X/P] digested <i>Rz21(co)</i> insert into Gp1 June 29 [S/P] digested pSB1C3-<i>R21(co)</i> in [S/P]</li></td>
    </tr>
    <tr>
@@ Line 571: / Line 571: @@
      <td></td>
      <td></td>
-     <td><li>Transformation of July 2 ligation product pSB1C3-R21(co)-Rz21(co)</li></td>
+     <td><li>Transformation of July 2 ligation product pSB1C3-<i>R21(co)-Rz21(co)</i></li></td>
    </tr>
 </table>
@@ Line 591: / Line 591: @@
      <td></td>
      <td></td>
-     <td><li>Colony PCR on July 3 R21(co)-Rz21(co) clones. No bands were observed</li></td>
+     <td><li>Colony PCR on July 3 <i>R21(co)-Rz21(co)</i> clones. No bands were observed</li></td>
    </tr>
    <tr>
@@ Line 597: / Line 597: @@
      <td></td>
      <td></td>
-     <td><li>Extraction of June 30 plasmid pSB1C3-S21WT(ori)-R21(ori)-Rz21(ori) (21Lysis(o_o_o))</li> <li>Restriction digestion with [X/P]</li></td>
+     <td><li>Extraction of June 30 plasmid pSB1C3-<i>S21WT(ori)-R21(ori)-Rz21(ori)</i> (21Lysis(o_o_o))</li> <li>Restriction digestion with [X/P]</li></td>
      <td><li>Redo July 6's colony PCR with other colonies. No bands were observed</li></td>
    </tr>
@@ Line 620: / Line 620: @@
      <td></td>
      <td><li>Ligation of the [X/P] digested 21Lysis(o_o_o) insert into [X/P] digested pSB1C3 vector</li> <li>Transformation</li></td>
-     <td><li>Restriction analysis on July 3 R21(co)-Rz21(co) clones. The analysis confirmed the presence of the R21(co)-Rz21(co) insert</li></td>
+     <td><li>Restriction analysis on July 3 <i>R21(co)-Rz21(co)</i> clones. The analysis confirmed the presence of the <i>R21(co)-Rz21(co)</i> insert</li></td>
    </tr>
 </table>
@@ Line 647: / Line 647: @@
      <td></td>
      <td><li>Restriction analysis on the 21Lysis(o_o_o) clones. The analysis confirmed the presence of the 21Lysis(o_o_o) insert</li></td>
-     <td><li>Extraction of the plasmid pSB1C3-R21(co)-Rz21(co)</li> <li>Restriction digestion with [X/P]</li></td>
+     <td><li>Extraction of the plasmid pSB1C3-<i>R21(co)-Rz21(co)</i></li> <li>Restriction digestion with [X/P]</li></td>
    </tr>
@@ Line 655: / Line 655: @@
      <td></td>
      <td></td>
-     <td><li>Gel purification of July 14 [X/P] digested R21(co)-Rz21(co)</li></td>
+     <td><li>Gel purification of July 14 [X/P] digested <i>R21(co)-Rz21(co)</i></li></td>
      </tr>
    <tr>
@@ Line 676: / Line 676: @@
      <td></td>
      <td></td>
-     <td><li><font color="#D633FF">Extraction of the plasmids pSB1C3-S21mut(ori) and pSB1C3-S21mut(co)</li> <li>Restriction digestion wth [S/P]</font></li></td>
+     <td><li><font color="#D633FF">Extraction of the plasmids pSB1C3-<i>S21mut(ori)</i> and pSB1C3-<i>S21mut(co)</i></li> <li>Restriction digestion wth [S/P]</font></li></td>
 </table>
@@ Line 695: / Line 695: @@
      <td></td>
      <td></td>
-     <td><li><font color="#D633FF">Gel purification of July 18 [S/P] digested pSB1C3-S21mut(ori) and pSB1C3-S21mut(co)</font></li> <br> <li><font color="#0099FF">Ligation of July 15 [X/P] digested R21(co)-Rz21(co) insert into [S/P] digested pSB1C3-S21mut(ori)</font></li> <br> <li><font color="#FF9900">Ligation of July 15 [X/P] digested R21(co)-Rz21(co) insert into [S/P] digested pSB1C3-S21mut(co)</font></li></td>
+     <td><li><font color="#D633FF">Gel purification of July 18 [S/P] digested pSB1C3-<i>S21mut(ori)</i> and pSB1C3-<i>S21mut(co)</i></font></li> <br> <li><font color="#0099FF">Ligation of July 15 [X/P] digested <i>R21(co)-Rz21(co)</i> insert into [S/P] digested pSB1C3-<i>S21mut(ori)</i></font></li> <br> <li><font color="#FF9900">Ligation of July 15 [X/P] digested <i>R21(co)-Rz21(co)</i> insert into [S/P] digested pSB1C3-<i>S21mut(co)</i></font></li></td>
    </tr>
    <tr>
      <td>Tuesday 21</td>
      <td></td>
-     <td><li>Transformation of pGOv4-ribo_S21WT(co), pGOv4-Ribo_R21(co) and pGOv4-Ribo_Rz21(co)</li></td>
+     <td><li>Transformation of pGOv4-Ribo_<i>S21WT(co)</i>, pGOv4-Ribo_<i>R21(co)</i> and pGOv4-Ribo_<i>Rz21(co)</i></li></td>
      <td></td>
-     <td><li><font color="#0099FF"> Transformation of July 20 ligation product pSB1C3-S21mut(ori)-R21(co)-Rz21(co) (21Lysis_Sm(o_c_c))</font></li> <li><font color="#FF9900">Transformation of July 20 ligation product pSB1C3-S21mut(co)-R21(co)-Rz21(co) (21Lysis_Sm(c_c_c))</font></li></td>
+     <td><li><font color="#0099FF"> Transformation of July 20 ligation product pSB1C3-<i>S21mut(ori)-R21(co)-Rz21(co)</i> (21Lysis_Sm(o_c_c))</font></li> <li><font color="#FF9900">Transformation of July 20 ligation product pSB1C3-<i>S21mut(co)-R21(co)-Rz21(co)</i> (21Lysis_Sm(c_c_c))</font></li></td>
    </tr>
@@ Line 709: / Line 709: @@
      <td></td>
      <td></td>
-     <td><li>Redo the transformation of pGOv4-Ribo_R21(co)</li></td>
+     <td><li>Redo the transformation of pGOv4-Ribo_<i>R21(co)</i></li></td>
-     <td><li><font color="#0099FF"> Colony PCR on the 21Lysis_Sm(o_c_c) clones revealed that the colonies contained inserts of the wrong sizes</font></li><br><li><font color="#FF9900">Colony PCR on the 21Lysis_Sm(c_c_c) clones showed bands of the expected size</font></li><br><li><font color="#0099FF"> Redo the restriction digestion of R21(co)-Rz21(co) with [S/P]</li><li>Gel purification</font></li></td>
+     <td><li><font color="#0099FF"> Colony PCR on the 21Lysis_Sm(o_c_c) clones revealed that the colonies contained inserts of the wrong sizes</font></li><br><li><font color="#FF9900">Colony PCR on the 21Lysis_Sm(c_c_c) clones showed bands of the expected size</font></li><br><li><font color="#0099FF"> Redo the restriction digestion of <i>R21(co)-Rz21(co)</i> with [S/P]</li><li>Gel purification</font></li></td>
      </tr>
    <tr>
@@ Line 716: / Line 716: @@
      <td></td>
      <td></td>
-     <td><li>Extraction of the plasmids pGOv4-Ribo_S21WT(co), pGOv4-Ribo_R21(co) and pGOv4-Ribo_Rz21(co)</li><li>Restriction digestion of Ribo_S21WT(co) with [E/P] & [E/S], Ribo_R21(co) with [E/P] & [X/P] and Ribo_Rz21(co) with [E/P] & [X/P]</li></td>
+     <td><li>Extraction of the plasmids pGOv4-Ribo_<i>S21WT(co)</i>, pGOv4-Ribo_<i>R21(co)</i> and pGOv4-Ribo_<i>Rz21(co)</i></li><li>Restriction digestion of Ribo_<i>S21WT(co)</i> with [E/P] & [E/S], Ribo_<i>R21(co)</i> with [E/P] & [X/P] and Ribo_<i>Rz21(co)</i> with [E/P] & [X/P]</li></td>
-     <td><li><font color="#0099FF">Redo the ligation of the [X/P] digested R21(co)-Rz21(co) insert into [S/P] digested pSB1C3-S21mut(ori)</li><li>Transformation</font></li><li>Ligation of [X/P] digested BBa_I13504 (GFP) insert into [S/P] digested 21Lysis(o_o_o)</li></td>
+     <td><li><font color="#0099FF">Redo the ligation of the [X/P] digested <i>R21(co)-Rz21(co)</i> insert into [S/P] digested pSB1C3-<i>S21mut(ori)</i></li><li>Transformation</font></li><li>Ligation of [X/P] digested BBa_I13504 (GFP) insert into [S/P] digested 21Lysis(o_o_o)</li></td>
    </tr>
    <tr>
@@ Line 753: / Line 753: @@
      <td></td>
      <td></td>
-     <td><li>Extraction of the plasmid pGOv4-Ribo_Rz21(co)</li><li>Redo the restriction digestion of Ribo_S21WT(co) and Ribo_R21(co) with [E/P]</li></td>
+     <td><li>Extraction of the plasmid pGOv4-Ribo_<i>Rz21(co)</i></li><li>Redo the restriction digestion of Ribo_<i>S21WT(co)</i> and Ribo_<i>R21(co)</i> with [E/P]</li></td>
      <td></td>
    </tr>
@@ Line 761: / Line 761: @@
      <td></td>
      <td></td>
-     <td><li>Ligation of the [E/P] digested Ribo_S21WT(co) insert into the [E/P] digested pSB1C3 vector [E/P] & transformation</li> <li>Ligation of the [E/P] digested Ribo_R21(co) insert into [E/P] digested pSB1C3</li><li>Extraction of the plasmids pGOv4-Ribo_S21WT(co), pGOv4-Ribo_R21(co) and pGOv4-Ribo_Rz21(co)</li><li>Restriction digestion of Ribo_S21WT(co) with [E/S], Ribo_R21(co) with [X/P] and Ribo_Rz21(co) with [E/P]</li> <li>Gel purification</li></td>
+     <td><li>Ligation of the [E/P] digested Ribo_<i>S21WT(co)</i> insert into the [E/P] digested pSB1C3 vector [E/P] & transformation</li> <li>Ligation of the [E/P] digested Ribo_<i>R21(co)</i> insert into [E/P] digested pSB1C3</li><li>Extraction of the plasmids pGOv4-Ribo_<i>S21WT(co)</i>, pGOv4-Ribo_<i>R21(co)</i> and pGOv4-Ribo_<i>Rz21(co)</i></li><li>Restriction digestion of Ribo_<i>S21WT(co)</i> with [E/S], Ribo_<i>R21(co)</i> with [X/P] and Ribo_<i>Rz21(co)</i> with [E/P]</li> <li>Gel purification</li></td>
      <td><li>Redo the ligation of the [X/P] digested GFP insert into the [S/P] digested pSB1C3-21Lysis(o_o_o)</li><li>Transformation</li></td>
      </tr>
@@ Line 768: / Line 768: @@
      <td></td>
      <td></td>
-     <td><li>Restriction digestion of Ribo_R21(co) with [X/P]</li></td>
+     <td><li>Restriction digestion of Ribo_<i>R21(co)</i> with [X/P]</li></td>
      <td><li>Colony PCR on 21Lysis(o_o_o)-GFP clones showed bands of the expected size</li></td>
    </tr>
@@ Line 803: / Line 803: @@
      <td></td>
      <td></td>
-     <td><li><font color="#127633">Extraction of plasmid pGOV4-S21WT(co)</li>
+     <td><li><font color="#127633">Extraction of plasmid pGOV4-<i>S21WT(co)</i>/li>
      <li>Restriction digestion with [E/S]</li>
      <li>Gel purification</li>
-     <li>Ligation of the [E/S] digested S21WT(co) and July 22 [X/P] digested R21(co)-Rz21(co) into July 22 [E/P] digested pSB1C3</font></li> <br>
+     <li>Ligation of the [E/S] digested <i>S21WT(co)</i> and July 22 [X/P] digested <i>R21(co)-Rz21(co)</i> into July 22 [E/P] digested pSB1C3</font></li> <br>
-     <li><font color="#00CC00">Extraction of the plasmid pGOv4-lacIq (pLacIQ_LacI_L8-UV5 lac)</li>
+     <li><font color="#00CC00">Extraction of the plasmid pGOv4-<i>lacIq</i> (pLacIQ_LacI_L8-UV5 lac)</li>
      <li>Restriction digestion with [E/S]</li>
      <li>Gel purification</font></li> <br>
-     <li><font color="#0099FF">Ligation of the [E/S] digested lacIq and [X/P] digested 21Lysis_Sm(o_c_c) into [E/P] digested pSB1C3</font></li>
+     <li><font color="#0099FF">Ligation of the [E/S] digested <i>lacIq</i> and [X/P] digested 21Lysis_Sm(o_c_c) into [E/P] digested pSB1C3</font></li>
-     <li><font color="#FF9900">Ligation of the [E/S] digested lacIQ promoter cassette and [X/P] digested 21Lysis_Sm(c_c_c) into [E/P] digested pSB1C3</font></li></td>
+     <li><font color="#FF9900">Ligation of the [E/S] digested <i>lacIq</i> promoter cassette and [X/P] digested 21Lysis_Sm(c_c_c) into [E/P] digested pSB1C3</font></li></td>
    </tr>
    <tr>
@@ Line 845: / Line 845: @@
      <td></td>
      <td></td>
-     <td><li>Transformation of Aug 6 ligation product</li> <br> <li><font color="#127633">Redo the restriction digestion with [E/S] on the plasmid pGOv4-S21WT(co)</li><li>Gel purification</font></li></td>
+     <td><li>Transformation of Aug 6 ligation product</li> <br> <li><font color="#127633">Redo the restriction digestion with [E/S] on the plasmid pGOv4-<i>S21WT(co)</i></li><li>Gel purification</font></li></td>
    </tr>
    <tr>
@@ Line 852: / Line 852: @@
      <td></td>
      <td></td>
-     <td><li>* Colony PCR on Aug 7 transformed cells. The clones <font color="#127633">lacIq-21Lysis(c_c_c)</font>, <font color="#0099FF">lacIq-21Lysis_Sm(o_c_c)</font> and <font color="#FF9900">lacIq-21Lysis_Sm(c_c_c)</font> all contained inserts of the expected sizes</li><br><li><font color="#127633">Ligation of the [E/S] digested S21WT(co) into the [E/S] digested pSB1C3</li><li>Transformation</font></li></td>
+     <td><li>* Colony PCR on Aug 7 transformed cells. The clones <font color="#127633">lacIq-21Lysis(c_c_c)</font>, <font color="#0099FF">lacIq-21Lysis_Sm(o_c_c)</font> and <font color="#FF9900">lacIq-21Lysis_Sm(c_c_c)</font> all contained inserts of the expected sizes</li><br><li><font color="#127633">Ligation of the [E/S] digested <i>S21WT(co)</i> into the [E/S] digested pSB1C3</li><li>Transformation</font></li></td>
    </tr>
 </table>
@@ Line 872: / Line 872: @@
      <td></td>
      <td></td>
-     <td><li><font color="#127633">Colony PCR on Aug 8 transformed cells. The S21WT(co) clones contained inset of the expected size</li></td>
+     <td><li><font color="#127633">Colony PCR on Aug 8 transformed cells. The <i>S21WT(co)</i> clones contained inset of the expected size</li></td>
    </tr>
 </table>