Team:BYU Provo/Notebook/SmallPhage/Winterexp/Period3/Dailylog

From 2013.igem.org

(Difference between revisions)
 
(2 intermediate revisions not shown)
Line 14: Line 14:
<font color="#333399" size="3" font face="Calibri">
<font color="#333399" size="3" font face="Calibri">
-
: [[Team:BYU_Provo/Small_Phage|Overview]]
+
<font size = "4">
 +
 
 +
: <u> '''Small Phage''' </u> </font>
: [[Team:BYU Provo/Notebook/SmallPhage/Winterexp|March-April]]
: [[Team:BYU Provo/Notebook/SmallPhage/Winterexp|March-April]]
Line 43: Line 45:
- Made fresh LB and concentrated top agar stock
- Made fresh LB and concentrated top agar stock
-
: [[Team:BYU_Provo/Notebook/SmallPhage/Winterexp/Period1/Exp/4.3 Top Agar Stock Preparation|4.3 Top Agar Stock Preparation]]
+
: [[Team:BYU_Provo/Notebook/SmallPhage/Winterexp/Period3/Exp/4.3 Top Agar Stock Preparation|4.3 Top Agar Stock Preparation]]
<br>
<br>
Line 57: Line 59:
<font size="4"> '''4/5/13''' </font>
<font size="4"> '''4/5/13''' </font>
-
- Background research on phiX174: the only phage we have in stock
+
- Performed spot test with E coli BL21 overnight liquid culture and WT T7 phage
-
- Performed [[Team:BYU_Provo/Notebook/SmallPhage/Winterexp/Period1/Exp/3.20 Phage Viability Test|3.20 Phage Viability Test]]
+
: [[Team:BYU_Provo/Notebook/SmallPhage/Winterexp/Period2/Exp/4.5 T7 phage viability assay|4.5 T7 phage viability assay]]
 +
 
 +
- Created bacterial glycerol stock
 +
 
 +
: 0.5mL of bacteria overnight liquid culture + 0.5mL of glycerol
<br>
<br>
-
<font size="4"> '''3/21/13''' </font>
+
<font size="4"> '''4/6/13''' </font>
-
- Checked up on results for [[Team:BYU_Provo/Notebook/SmallPhage/Winterexp/Period1/Exp/3.20 Phage Viability Test|3.20 Phage Viability Test]]
+
- Checked up on [[Team:BYU_Provo/Notebook/SmallPhage/Winterexp/Period2/Exp/4.5 T7 phage viability assay|4.5 T7 phage viability assay]]
-
<br>
+
- 6:00pm overnight E coli liquid culture
-
<font size="4"> '''3/22/13''' </font>
+
: W3110 one colony in 25mL Erlenmeyer flask
-
- Discussed results from tittering experiment (preliminary experiment 1)
+
: BL21 one stab in 25mL Erlenmeyer flask
-
: Contamination mostly likely resulted from the step involving suspending phage in LB – obvious contamination in the LB bottle
+
- 9:00pm Streak bacteria culture to check for contamination and for storage
-
: One of the stock phage solution had contamination as well
+
: performed for both W3110 and BL21
-
- Discussed step of attack with Dr. Grose
+
<br>
-
: Decided to go with T7, if necessary Qbeta
+
<font size="4"> '''4/8/13''' </font>
-
: Need to learn to make top agar at various concentrations
+
- Performed [[Team:BYU_Provo/Notebook/SmallPhage/Winterexp/Period2/Exp/4.8 T7 phage viability assay 2|4.8 T7 phage viability assay 2]]
-
: Need to do more background research and decide whether to assemble phage capsid in vitro (plasmid + E coli) or do direct mutagenesis of phage genome
+
- Outlined final presentation content and divided up assignments
-
:: Need to correspond with the isolation team
+
<br>
-
- Sequencing will be for individual genes to cut down cost
+
<font size="4"> '''4/9/13''' </font>
-
: Need to design primers and get to know the genome of the phage
+
- Checked up on [[Team:BYU_Provo/Notebook/SmallPhage/Winterexp/Period2/Exp/4.8 T7 phage viability assay 2|4.8 T7 phage viability assay 2]]
-
- Learnt about Mega5 to compare genome and protein sequence
+
- Start overnight for E coli BL21
<br>
<br>
-
<font size="4"> '''3/25/13''' </font>
+
<font size="4"> '''4/10/13''' </font>
-
- Reported on past week and plans for this week
+
- Performed [[Team:BYU_Provo/Notebook/SmallPhage/Winterexp/Period2/Exp/4.10 T7 phage viability assay 3|4.10 T7 phage viability assay 3]]
-
: From last week: titering experiment
+
-
: This week
+
-
:: Learn to make top agar at various concentrations
+
-
:: Background research to determine in vitro assembly vs altering genome – look into specific techniques
+
-
:: Comparing genome of phage and decide on possible site-directed mutagenesis options
+
-
- Start working on designing our site directed mutagenesis
+
- Looked into T7-family phage
-
: Qbeta vs MS2
+
-
:: Look for places where sequences are significantly different
+
-
:: Might be worthwhile to look at capsid structure to identify the regions where interactions between subunits take place
+
-
: Qbeta vs T7 major
+
<br>
-
:: No real consensus – more worthwhile to compare capsid protein sequence of T7 with those that have similar size to it
+
-
: T7 major vs minor
+
<font size="4"> '''4/11/13''' </font>
-
:: Minor is longer, but not necessary – the tail overhang is due to ribosome moving two codons downstream instead of three
+
-
:: Suggest we can direct mutation to the poly-U site and prevent ribosome slippage
+
-
: Qbeta major vs minor
+
- Check up on [[Team:BYU_Provo/Notebook/SmallPhage/Winterexp/Period2/Exp/4.10 T7 phage viability assay 3|4.10 T7 phage viability assay 3]]
-
:: Just continue transcribing after it reaches the stop codon. What does the stop codon code for?
+
-
- Research into in-vitro assembly vs direct mutation of phage genome
+
- Worked on [[Team:BYU_Provo/Notebook/SmallPhage/Winterexp/Period3/PR| Presentation]]
-
: It seems that we’ll need to clone the genome of the phage into a plasmid and let it assemble in an E coli
+
-
: Using chemicals we can induce random mutations in phage – might be worthwhile if selection in agar is not working as well.
+
<br>
<br>
-
<font size="4"> '''3/27/13''' </font>
+
<font size="4"> '''4/12/13''' </font>
-
 
+
-
- More research on genome of enterobacteria phage
+
-
: Generation of the major and minor capsid in Q beta
+
- Cholera Presentation
-
: Capsid protein information research
+
-
: Capsid protein sequence comparison
+
-
- Outlined protocol for producing stock top agar
+
- Worked on [[Team:BYU_Provo/Notebook/SmallPhage/Winterexp/Period3/PR| Presentation]]
-
: [[Team:BYU_Provo/Notebook/SmallPhage/Winterexp/Period1/Exp/4.3 Top Agar Stock Preparation|4.3 Top Agar Stock Preparation]]
+
<br>
<br>
-
<font size="4"> '''3/29/13''' </font>
+
<font size="4"> '''4/13/13''' </font>
-
- Worked on our first team presentation.
+
- Continued working on [[Team:BYU_Provo/Notebook/SmallPhage/Winterexp/Period3/PR| Presentation]]
<br>
<br>

Latest revision as of 13:26, 9 September 2013


Small Phage March - April Notebook: April 1 - April 14 Daily Log



Small Phage
March-April
May-June
July-August
September-October

4/1/13

- Presentation day!

Presentation


4/3/13

- Learned about how to start an overnight liquid culture for host bacteria

- Learned about how to create bacterial glycerol stock

- Made fresh LB and concentrated top agar stock

4.3 Top Agar Stock Preparation


4/4/13

- T7 arrived

- Overnight liquid culture for bacterial host started by Dr. Grose


4/5/13

- Performed spot test with E coli BL21 overnight liquid culture and WT T7 phage

4.5 T7 phage viability assay

- Created bacterial glycerol stock

0.5mL of bacteria overnight liquid culture + 0.5mL of glycerol


4/6/13

- Checked up on 4.5 T7 phage viability assay

- 6:00pm overnight E coli liquid culture

W3110 one colony in 25mL Erlenmeyer flask
BL21 one stab in 25mL Erlenmeyer flask

- 9:00pm Streak bacteria culture to check for contamination and for storage

performed for both W3110 and BL21


4/8/13

- Performed 4.8 T7 phage viability assay 2

- Outlined final presentation content and divided up assignments


4/9/13

- Checked up on 4.8 T7 phage viability assay 2

- Start overnight for E coli BL21


4/10/13

- Performed 4.10 T7 phage viability assay 3

- Looked into T7-family phage


4/11/13

- Check up on 4.10 T7 phage viability assay 3

- Worked on Presentation


4/12/13

- Cholera Presentation

- Worked on Presentation


4/13/13

- Continued working on Presentation


Retrieved from "http://2013.igem.org/Team:BYU_Provo/Notebook/SmallPhage/Winterexp/Period3/Dailylog"