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| | <font size="4"> '''3/22/13''' </font> | | <font size="4"> '''3/22/13''' </font> |
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| - | - Discussed results from tittering experiment (preliminary experiment 1)
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| - | : Contamination mostly likely resulted from the step involving suspending phage in LB – obvious contamination in the LB bottle
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| - | : One of the stock phage solution had contamination as well
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| - | - Discussed step of attack with Dr. Grose
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| - | : Decided to go with T7, if necessary Qbeta
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| - | | + | |
| - | : Need to learn to make top agar at various concentrations
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| - | : 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
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| - | :: Need to correspond with the isolation team
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| - | - Sequencing will be for individual genes to cut down cost
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| - | : Need to design primers and get to know the genome of the phage
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| - | | + | |
| - | - Learnt about Mega5 to compare genome and protein sequence
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| | <font size="4"> '''3/25/13''' </font> | | <font size="4"> '''3/25/13''' </font> |
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| - | - Reported on past week and plans for this week
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| - | : From last week: titering experiment
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| - | : This week
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| - | :: Learn to make top agar at various concentrations
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| - | :: Background research to determine in vitro assembly vs altering genome – look into specific techniques
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| - | :: Comparing genome of phage and decide on possible site-directed mutagenesis options
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| - | | + | |
| - | - Start working on designing our site directed mutagenesis
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| - | : Qbeta vs MS2
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| - | :: Look for places where sequences are significantly different
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| - | :: Might be worthwhile to look at capsid structure to identify the regions where interactions between subunits take place
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| - | | + | |
| - | : Qbeta vs T7 major
| + | |
| - | :: No real consensus – more worthwhile to compare capsid protein sequence of T7 with those that have similar size to it
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| - | | + | |
| - | : T7 major vs minor
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| - | :: Minor is longer, but not necessary – the tail overhang is due to ribosome moving two codons downstream instead of three
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| - | :: Suggest we can direct mutation to the poly-U site and prevent ribosome slippage
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| - | | + | |
| - | : Qbeta major vs minor
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| - | :: Just continue transcribing after it reaches the stop codon. What does the stop codon code for?
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| - | | + | |
| - | - Research into in-vitro assembly vs direct mutation of phage genome
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| - | : It seems that we’ll need to clone the genome of the phage into a plasmid and let it assemble in an E coli
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| - | : Using chemicals we can induce random mutations in phage – might be worthwhile if selection in agar is not working as well.
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| | <font size="4"> '''3/27/13''' </font> | | <font size="4"> '''3/27/13''' </font> |
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| - | - More research on genome of enterobacteria phage
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| - | : Generation of the major and minor capsid in Q beta
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| - | : Capsid protein information research
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| - | : Capsid protein sequence comparison
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| - | | + | |
| - | - Outlined protocol for producing stock top agar
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| - | : [[Team:BYU_Provo/Notebook/SmallPhage/Winterexp/Period1/Exp/4.3 Top Agar Stock Preparation|4.3 Top Agar Stock Preparation]]
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| | <font size="4"> '''3/29/13''' </font> | | <font size="4"> '''3/29/13''' </font> |
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| - | - Worked on our first team presentation.
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| | <br> | | <br> |
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