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

From 2013.igem.org

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Revision as of 21:45, 5 June 2013

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

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

@@ Line 57: / Line 57: @@
 <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>
-<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>
-<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>
-<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>
-<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>