Planning for committee meeting 5-11-13

2015-01-13

azim58 - Planning for committee meeting 5-11-13

I'll basically
-remind them what my goals are
-recap what I've done over the last 5 years
-review what I've done over the last semester
--final experiment for age associated stem cell autoimmunity project
--random hexamer library
--random pentadecamer library
--data reanalyzed and paper submitted to human vaccines and
immunotherapeutics
--PCR Screening Library
-ask them what I should be doing next and if I am close to start focusing
on just writing dissertation and finishing

What was concluded from the last committee meeting?
From the last committee meeting they wanted me to focus on my tumor cDNA
library expression project (They wanted me to make a random hexamer
library)
They also wanted me to complete analysis of the SMC1fs control

Outline of paper for Spring 2013 Committee Meeting
started making word document
"F:\kurt\storage\CIM Research Folder\DR\2013\5-11-13\Outline of Paper for
Spring 2013 Committee Meeting.docx"
but actually I think I would like to make my outline as a plain txt file
and edit it with Notepad++ so that I can have collapsible content.
"F:\kurt\storage\CIM Research Folder\DR\2013\5-11-13\Outline of Paper for
Spring 2013 Committee Meeting.txt"

Summary document
"F:\kurt\storage\CIM Research Folder\kwhittem\Presentations\2013\Spring
2013 Committee Meeting\Spring 2013 Summary Kurt.docx"

Spring 2013 Committee Meeting Presentation
"F:\kurt\storage\CIM Research Folder\kwhittem\Presentations\2013\Spring
2013 Committee Meeting\Spring 2013 Committee Meeting Presentation
5-20-13.pptx"

Issues I could look into
-metric to decide how prevalent is prevalent enough for a cancer vaccine
and how immunogenic is immunogenic enough (look at HER2 and herceptin
example)
-(c) calculations for prevalence of transcripts and expected positive
pools (see issue 5-17-13d0907)
-when I made the dilution did I dilute to 1,000 clones per pool based on
total colonies or total unique colonies?
-(c)keep in mind how I might determine the orientation and frame of
SMC1fs transcript binding clones
--add SMC1fs sera to clones from pool or just design primers that go from
frameshift to vector part to determine orientation (if there are few
enough transcripts)
-(c) could add more gels to presentation to show gradient pcrs as well
-(c)determine the stage at which the tumor tissue was taken from the
mouse, and the stage at which the sera was taken from the mouse
the sera and tumor were taken about 25 days after injection with tumor
cells
-(c) if I were to screen pool 1 and pool 16 from the 4-26-13 and 4-28-13
experiments would they have any spots that even bind high?
smc1fs screen issue 5-18-13d1930

-----------
some slides

Preparing Tumor cDNA and anti-SMC1fs Ab slide 5-19-13

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Supervisory Committee Meeting Record Spring 2013
"F:\kurt\storage\CIM Research Folder\DR\2013\5-21-13\Supervisory
Committee Meeting Record Spring 2013.pdf"

Audio recording of spring 2013 committee meeting
"F:\kurt\storage\DR\Audio 2013\5-20-13\Spring 2013 committee meeting
05-20-13-09-46-31-audio_recording.3gp"

After this committee meeting they concluded that they wanted me to focus
on validating that my antigen screening method works by determining if
certain frameshifts and chimeric transcripts are in my library and if
sera binds to the proteins from these transcripts if they were inserted
into the correct orientation in the library. I may also want to screen
for or validate new antigen candidates. I could also write a paper on the
entropy and age associated stem cell autoimmunity projects.

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