Team:BU Wellesley Software/Notebook/ShannonNotebook

From 2011.igem.org

(Difference between revisions)
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* included a boot camp.  
+
* Included a boot camp.  
-
* different topics were discussed (i.e. biobricks, gene regulation, differences between eukaryotes and prokaryotes).  
+
* Different topics were discussed (i.e. biobricks, gene regulation, differences between eukaryotes and prokaryotes).  
-
* boot camp also included a computer science component (focused on Clotho).  
+
* Boot camp also included a computer science component (focused on Clotho).  
-
* miniprepes were done on previously transformed BFP2. After minipreps, the Nanodrop was used to quantify the DNA. Minipreps did not have high DNA concentration, but were run on a gel (to show presence of DNA). Most lanes appeared empty (bands of DNA were not visible).  
+
* Miniprepes were done on previously transformed BFP2. After minipreps, the Nanodrop was used to quantify the DNA. Minipreps did not have high DNA concentration, but were run on a gel (to show presence of DNA). Most lanes appeared empty (bands of DNA were not visible).  
-
* transformations of Pbad was conducted.  
+
* Transformations of Pbad were conducted.  
-
** The following day, transformations appeared to be contaminated. They looked significantly different than usual, but were still were used to produce plasmid preps.  
+
** The following day, transformations appeared to be contaminated. They looked significantly different than usual, but were still were used to produce overnight cultures.  
-
** To ensure that E.coli was present gram staining was performed. Staining showed that no E.coli was present in the cultures. Minipreps and Nanodrop were  used to quantify the DNA from the plasmid preps.  
+
** To ensure that E.coli was present gram staining was performed. Staining showed that no E.coli was present in the cultures. Nanodrop was used to quantify the DNA from the overnight cultures.  
-
*** The results from the Miniprep/Nanodrop varied (some plasmid preps had a decent DNA concentration, others didn’t). Even though yields were not great the samples were run on a gel. However no bands were visible.
+
*** The results from the Miniprep/Nanodrop varied (some overnight cultures had a decent DNA concentration, others didn’t). Even though yields were not great the samples were run on a gel. However no bands were visible.
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|}
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== 6/13/2011-6/17/2011 ==
+
{| style="width:800px;background:#87CEEB;text-align:justify;font-family: helvetica, arial, sans-serif;color:#000000;margin-top:5px;" cellspacing="18"
 +
|style="font-family: helvetica, arial, sans-serif;font-size:1em;color:#ea8828;"|<h5>WEEK 2: 6/13-6/17/2011</h5>
 +
|-
 +
|
-
* plasmid preps were made from the previous week’s transformations.  
+
* Overnight cultures were made from the previous week’s transformations.  
-
** this was done to improve the Nanodrop quantification values.
+
** cultures didn’t grow properly (only UV plasmid).  
-
** plasmid preps didn’t grow properly (only UV plasmid).  
+
* An issue with the plates was discovered. All previous cultures were done on Ampicillian plates, and most were not growing well. We switched to a different antibiotic (Kanamycin) and all proceeding cultures grew well.  
-
* an issue with the plates was discovered. All previous cultures were done on Ampicillian plates, and most were not growing well. We switched to a different antibiotic (Kanamycin) and all proceeding cultures grew well.  
+
* New Ampicillian plates were made.  
-
* new Ampicillian plates were made.  
+
* A side project involved ligating GFP (Bba_J52625) and terminator (Bba_B0015) together for future use.  
-
* a side project involved ligating GFP (Bba_J52625) and terminator (Bba_B0015) together for future use.  
+
* Transformations were completed (involved transforming several different biobrick parts).  
-
* transformations were completed (involved transforming seven different biobrick parts).  
+
** Two seemed to look pinkish, especially towards the center of each colony.  
-
** two seemed to look pinkish, especially towards the center of each colony.  
+
** Successful transformations were then used to produce more overnight cultures.
-
** successful transformations were then used to produce more plasmid preps.
+
|}
 +
{| style="width:800px;background:#87CEEB;text-align:justify;font-family: helvetica, arial, sans-serif;color:#000000;margin-top:5px;" cellspacing="18"
 +
|style="font-family: helvetica, arial, sans-serif;font-size:1em;color:#ea8828;"|<h5>WEEK 3: 6/20-6/24/2011</h5>
 +
|-
 +
|
-
== 6/20/2011-6/24/2011  ==
+
* Overnight cultures were made for the following: Bba_B0015.1, Bba_B0015.2, Bba_B0015.3, Bba_B0015.4, Bba_R0040.1, Bba_R0040.2, Bba_J52028.1, Bba_J52028.2, Bba_J52028.3,and Bba_J52028.4.  
-
* this week plasmid preps were done on the following: Bba_B0015.1, Bba_B0015.2, Bba_B0015.3, Bba_B0015.4, Bba_R0040.1, Bba_R0040.2, Bba_J52028.1, Bba_J52028.2, Bba_J52028.3,and Bba_J52028.4.  
+
* Nanodrop was also conducted. Chart below shows values from 6/23/2011.
* Nanodrop was also conducted. Chart below shows values from 6/23/2011.
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* Ligation was also performed. I tried ligating BFP (Bba_K156010) with terminator (Bba_B0015.2.2). Transformation was done of this ligation later that night. The following morning the transformation plates did not have any colonies on them.
+
* Ligation was also performed. I tried ligating BFP (Bba_K156010) with terminator (Bba_B0015.2.2). Transformation was done of this ligation later that day. The following morning the transformation plates did not have any colonies on them.
-
* Minipreps were conducted on 6/23/2011’s plasmid preps and Nanodrop quantification was then performed. Results are shown below in the following chart:  
+
* Minipreps were conducted on 6/23/2011’s overnight cultures and Nanodrop quantification was then performed. Results are shown below in the following chart:  
{| class="wikitable"
{| class="wikitable"
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| 1.91
| 1.91
| 2.03
| 2.03
 +
|}
|}
|}
 +
{| style="width:800px;background:#87CEEB;text-align:justify;font-family: helvetica, arial, sans-serif;color:#000000;margin-top:5px;" cellspacing="18"
 +
|style="font-family: helvetica, arial, sans-serif;font-size:1em;color:#ea8828;"|<h5>WEEK 4: 6/27-7/01/2011</h5>
 +
|-
 +
|
-
== 6/27/2011-7/01/2011 ==
+
* Overnight cultures made using the following parts: Bba_J23100, Bba_J23101, Bba_E0240, Bba_E0430, Bba_R2000, Bba_I13453, Bba_R4000, and Bba_I14033.
-
 
+
* Restriction digest was done on the following: Bba_R2000.1, Bba_R2000.2, Bba_R0040.1, Bba_E0240.1, Bba_E0240.2, and Bba_J52028.3.  
-
* plasmid preps were done on the following: Bba_J23100, Bba_J23101, Bba_E0240, Bba_E0430, Bba_R2000, Bba_I13453, Bba_R4000, and Bba_I14033.
+
* transformations were done using the following ligations:  
-
* restriction digest was done on the following: Bba_R2000.1, Bba_R2000.2, Bba_R0040.1, Bba_E0240.1, Bba_E0240.2, and Bba_J52028.3.  
+
-
* transformation was also performed on the following ligations:  
+
** Bba_E0240.1 + Bba_R2000.1
** Bba_E0240.1 + Bba_R2000.1
** Bba_E0240.1 + Bba_R2000.2
** Bba_E0240.1 + Bba_R2000.2
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** Bba_E0240.1 + Bba_R0040.1
** Bba_E0240.1 + Bba_R0040.1
** Bba_E0240.2 + Bba_R0040.1
** Bba_E0240.2 + Bba_R0040.1
-
* Minipreps and Nanodrop were done on the previous day’s plasmid preps. Results are shown below.  
+
* Minipreps and Nanodrop were done on the previous day’s overnight cultures. Results are shown below.  
{| class="wikitable"
{| class="wikitable"
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|}
|}
-
* Minipreps and Nanodrop were done on the ligations that were transformed earlier in the week. Results of Nanodrop are shown in the following chart.  
+
* Minipreps and Nanodrop were done on the overnight cultures that were done the previous day. Results of Nanodrop are shown in the following chart.  
{| class="wikitable"
{| class="wikitable"
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* The 2.5A, B, and C all refer to various samples that were ligated with 2.5 uL of ligase. For example, sample 1A was ligated with 1 uL of ligase.   
* The 2.5A, B, and C all refer to various samples that were ligated with 2.5 uL of ligase. For example, sample 1A was ligated with 1 uL of ligase.   
-
* Glycerol stocks were also made from the following plasmid preps(two tubes were made for each, one went in the -90C and another in the -20 C):
+
* Glycerol stocks were also made from the following overnight cultures(two tubes were made for each, one went in the -90C and another in the -20 C):
-
 
+
-
{| class="wikitable"
+
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|-
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! Sample #
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! uL of ligase
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! Sample letter (A,B, or C)
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! Location in box
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|-
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| row 1
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| row 1, cell 2
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| row 1, cell 3
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|-
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| row 2, cell 1
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| row 2, cell 2
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| row 2, cell 3
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|-
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| row 3, cell 1
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| row 3, cell 2
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| row 3, cell 3
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|}
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Revision as of 02:10, 25 August 2011

Contents


WEEK 1: 6/06-6/10/2011
  • Included a boot camp.
  • Different topics were discussed (i.e. biobricks, gene regulation, differences between eukaryotes and prokaryotes).
  • Boot camp also included a computer science component (focused on Clotho).
  • Miniprepes were done on previously transformed BFP2. After minipreps, the Nanodrop was used to quantify the DNA. Minipreps did not have high DNA concentration, but were run on a gel (to show presence of DNA). Most lanes appeared empty (bands of DNA were not visible).
  • Transformations of Pbad were conducted.
    • The following day, transformations appeared to be contaminated. They looked significantly different than usual, but were still were used to produce overnight cultures.
    • To ensure that E.coli was present gram staining was performed. Staining showed that no E.coli was present in the cultures. Nanodrop was used to quantify the DNA from the overnight cultures.
      • The results from the Miniprep/Nanodrop varied (some overnight cultures had a decent DNA concentration, others didn’t). Even though yields were not great the samples were run on a gel. However no bands were visible.
WEEK 2: 6/13-6/17/2011
  • Overnight cultures were made from the previous week’s transformations.
    • cultures didn’t grow properly (only UV plasmid).
  • An issue with the plates was discovered. All previous cultures were done on Ampicillian plates, and most were not growing well. We switched to a different antibiotic (Kanamycin) and all proceeding cultures grew well.
  • New Ampicillian plates were made.
  • A side project involved ligating GFP (Bba_J52625) and terminator (Bba_B0015) together for future use.
  • Transformations were completed (involved transforming several different biobrick parts).
    • Two seemed to look pinkish, especially towards the center of each colony.
    • Successful transformations were then used to produce more overnight cultures.
WEEK 3: 6/20-6/24/2011
  • Overnight cultures were made for the following: Bba_B0015.1, Bba_B0015.2, Bba_B0015.3, Bba_B0015.4, Bba_R0040.1, Bba_R0040.2, Bba_J52028.1, Bba_J52028.2, Bba_J52028.3,and Bba_J52028.4.
  • Nanodrop was also conducted. Chart below shows values from 6/23/2011.
Sample # ng/uL 260/280 260/230
Bba_E0240 2.70 3.54 0.01
Bba_E0430 1.5 -32.2 0.01
Bba_B0015 4.5 2.69 0.03
Bba_I14033.1 3.7 4.41 0.02
Bba_I14033.2 6.3 1.81 0.04
Bba_I13453.1 2.3 3.71 0.01
Bba_I13453.2 1.8 29.53 0.02
Bba_I13453.3 1.9 1.93 0.01
  • Ligation was also performed. I tried ligating BFP (Bba_K156010) with terminator (Bba_B0015.2.2). Transformation was done of this ligation later that day. The following morning the transformation plates did not have any colonies on them.
  • Minipreps were conducted on 6/23/2011’s overnight cultures and Nanodrop quantification was then performed. Results are shown below in the following chart:
Sample # ng/uL 260/280 260/230
Bba_B0015.1, 24.5 1.80 1.78
Bba_B0015.2 20.8 1.72 1.74
Bba_B0015.3 25.0 1.74 1.60
Bba_B0015.4 23.2 1.86 1.95
Bba_R0040.1 20.4 1.75 1.46
Bba_R0040.2 14.5 1.62 0.80
Bba_J52028.1 42.0 1.89 1.98
Bba_J52028.2 54.1 1.77 1.35
Bba_J52028.3 42.5 1.80 2.12
Bba_J52028.4 41.5 1.91 2.03
WEEK 4: 6/27-7/01/2011
  • Overnight cultures made using the following parts: Bba_J23100, Bba_J23101, Bba_E0240, Bba_E0430, Bba_R2000, Bba_I13453, Bba_R4000, and Bba_I14033.
  • Restriction digest was done on the following: Bba_R2000.1, Bba_R2000.2, Bba_R0040.1, Bba_E0240.1, Bba_E0240.2, and Bba_J52028.3.
  • transformations were done using the following ligations:
    • Bba_E0240.1 + Bba_R2000.1
    • Bba_E0240.1 + Bba_R2000.2
    • Bba_E0240.2 + Bba_R2000.1
    • Bba_R0240.2 + Bba_R2000.2
    • Bba_E0240.1 + Bba_R0040.1
    • Bba_E0240.2 + Bba_R0040.1
  • Minipreps and Nanodrop were done on the previous day’s overnight cultures. Results are shown below.
Sample # ng/uL 260/280 260/230
Bba_I13453.1 16.8 1.9 1.98
Bba_I13453.2 17.8 2.19 1.10
Bba_R0040.1 15.4 Missing value Missing value
Bba_R0040.2 20.1 1.58 1.61
Bba_E0240.1 27.9 1.89 1.69
Bba_E0240.2 36.2 2.07 1.85
Bba_J23100.1 49.7 Missing Value Missing Value
Bba_J23100.2 47.8 1.95 1.86
Bba_E0430.1 22.9 1.98 1.76
Bba_E0430.2 39.4 1.90 1.80
  • Minipreps and Nanodrop were done on the overnight cultures that were done the previous day. Results of Nanodrop are shown in the following chart.
Sample # ng/uL 260/280 260/230
Bba_J23100 + Bba_I14033 2.5A 27.3 1.80 1.60
Bba_J23100 + Bba_I14033 2.5B 18.1 1.82 1.55
Bba_J23100 + Bba_I14033 2.5C 26.5 1.91 1.78
Bba_J23100 + Bba_I14033 1A 327.7 1.89 2.31
Bba_J23100 + Bba_I14033 1A (2nd try) 323.9 1.90 2.34
Bba_J23100 + Bba_I14033 1B 32.0 1.76 1.86
Bba_J23100 + Bba_I14033 5A 22.6 1.97 1.65
  • The 2.5A, B, and C all refer to various samples that were ligated with 2.5 uL of ligase. For example, sample 1A was ligated with 1 uL of ligase.
  • Glycerol stocks were also made from the following overnight cultures(two tubes were made for each, one went in the -90C and another in the -20 C):
Retrieved from "http://2011.igem.org/Team:BU_Wellesley_Software/Notebook/ShannonNotebook"