Current To Do List Portal 9-3-13
2015-06-07++ Current To Do List Portal 9-3-13
Current To Do List
Some Finished To Do List Items portal 9-3-13
Recent Places portal 9-3-13
Event Based To Do List portal 9-3-13
Hopeful To Do List 2-28-12
Long term to do list 6-12-14
Cleaning and organizing stuff 07-13-2014d1003
- take care of notebook notes 06-07-2015d1223
- -E:\temp\notebook notes (home computer)
- quantitate colonies for colony formation assay 06-07-2015d1111
- -http://azim58.ngrok.io/files/ws-cnio/DR/2015/06%20June/06-07-2015d0910/colony%20formation%20assay
- -cni_keratinocyte colony formation assay 5-30-15
- organize histopathology slide data 06-07-2015d0911
- -http://azim58.ngrok.io/files/ws-cnio/DR/2015/06%20June/06-07-2015d0910/Histopathology%20slide%20receipts
- -photos of histopathology slide boxes and labels
- --http://azim58.ngrok.io/files/ws-cnio/DR/2015/06%20June/06-07-2015d0910/photos%20of%20histopathology%20slide%20boxes%20and%20labels
analyze pathology results; 05-27-2015d2353
from: Juana María Flores <[email protected]>
to: "Whittemore.Kurt" <[email protected]>
date: Wed, May 27, 2015 at 7:30 PM
subject: histopath 5-5-15
- attend to sphider-plus email
- -
from: Dipl.-Ing. Rolf Kellner <[email protected]>
to: Kurt Whittemore <[email protected]>
date: Wed, May 20, 2015 at 12:02 AM
subject: Sphider-plus
- deal with Juan Molina's email
- -
from: Molina.Juan_Ramón <[email protected]>
to: "Whittemore.Kurt" <[email protected]>
date: Tue, May 19, 2015 at 11:43 AM
subject: RE: planning for student visa
- attend to neurodegeneration CBA
- -
from: Secretaria Ceiyba <[email protected]>
to: "Whittemore.Kurt" <[email protected]>
cc: "Ramos.Celia_Maria" <[email protected]>,
"Blanco.Isabel" <[email protected]>
date: Wed, May 13, 2015 at 9:36 AM
subject: Remisión observaciones CBA 23_2015
- -neurodegeneration CBA revision deadline is June 12th
- -need to get translation from Susa 06-07-2015d1653
- analyze HT Q-FISH data 05-22-2015d1430
- -located here (temporarily): C:\temp_sync\HT Q-FISH results 05-22-2015d1152\Nuclei
- -see also cni_Q-FISH for 3rd round of TRF1 blood samples 03-30-2015d1220
measure amyloid beta in brain of tert ko mice; 05-04-2015d1419
request confocal microscope training
- buy tripod for camera; SANYO and the model HD XACTI (7.1 megapixel); 05-04-2015d1830
make a list of software and projects to contribute to regularly
- need to find papers studying neurogenesis in the brain
setup user accounts in Pydio
- look through CNIO scientific report; email "the 2014 Scientific Report is now online" 3-26-15 from [email protected]; 04-03-2015d1127
- look at DNA damage in TRF1 (maybe you can even do it genome-wide?)
- -email 1-30-15 subject "copy of presentation"; https://mail.google.com/mail/u/0/#search/copy+of+presentation/14b364c39749e008
- maybe try some toxic treatments known to induce parkinson or alzheimer and see whether the TERT KO are more susceptible
- -email 1-30-15 subject "copy of presentation"; https://mail.google.com/mail/u/0/#search/copy+of+presentation/14b364c39749e008
- do regular Q-FISH on 1 yo and 2 yo TRF1 mice for skin brain and intestine tissues (Elisa and I already did heart)
- sort eGFP-TRF1 hi and lo cells from intestine and skin and perform gene expression analysis to see whether they are like stem cells
- -need to prepare for this protocol
- induce cancer in some TRF1 mice and controls with DMPA/TPA
- analyze Christian's heart infarct data using the cardiac regeneration specific geneset from the heatmap (or something) in the paper titled "Complete cardiac regeneration in a mouse model of myocardial infarction"
- -cni_heart infarct gene expression experiment 12-04-2014d1931
- longterm: read Ralph Schneider's dissertation
- take a look at papers from Bioinformatics group 11-17-2014d1531
- -"C:\Sync\cnio\2014\2014\11-17-2014d1104\papers from Bioinformatics group 11-17-2014d1529"
- -Emerging methods in protein co-evolution
- look at Overview of Mouse Models of Parkinson's Disease paper; ch 06-07-2015d1658
- take a look at Correction of Pathological Accumulation of Glycosaminoglycans in Central Nervous System and Peripheral Tissues of MPSIIIA Mice Through Systemic AAV9 Gene Transfer paper
- take a look at paper from Diego
- -Gene network reconstruction reveals cell cycle and antiviral genes as major drivers of cervical cancer
- maybe compare human, mouse, and cow telomerase with bowhead whale telomerase (maybe look at shelterin proteins as well)
- possibly gradually go through TRF1 sequence from ocr and make sure that everything is corrected
- review information related to how I can do my postdoc projects
- -continually review all the things to keep track of the different projects
- -make plans for upcoming tasks
- learn Spanish
- learn bioinformatics
- work on complex adaptive system metric project (aka characterizing networks with age project)
See also
Some finished to do list items (some items)
- analyze new pet data; ch 05-26-2015d2311
- -email about this here
from: Cámara.Juan_Antonio <[email protected]>
to: "Whittemore.Kurt" <[email protected]>
date: Mon, May 18, 2015 at 2:59 PM
subject:
- make sure to remove large files from here; 05-11-2015d1128; ch 05-26-2015d2313
- analyze TRF1 immunofluorescence data; ch 05-25-2015d2228
- perform HT Q-FISH on collected mouse TRF1 samples; 05-06-2015d1116; ch 05-25-2015d2229
--see
from: Tory Leech <[email protected]>
to:
cc: Victoria Ruiz <[email protected]>
bcc: [email protected]
date: Tue, Apr 21, 2015 at 9:42 AM
- add something about detecting respiratory symptoms in mice to lung cancer cba.; 05-11-2015d1041; ch 05-21-2015d2048
- -e.g. resistance of lung or elasticity of lung. Juanma said he knew someone that knew the name of the machine that can quantitate these things
- do Spain taxes; ch 05-19-2015d2315
- -note from Juan Molina about people or organizations that might be able to help me with Spain taxes
- --email "help with taxes" 4-6-15 from " Molina.Juan_Ramón <[email protected]> "
- order materials for colony formation assay; ch 05-19-2015d2316
from: Martinez.Paula <[email protected]>
to: Kurt Whittemore <[email protected]>,
"Tejera.Agueda" <[email protected]>
date: Fri, May 15, 2015 at 10:50 AM
subject: Re: materials for colony formation assay
- a few notes
Cian has mitomycin C
Noelia has the media I need
I need to order: plates, fibronectin, calcium chloride (CaCl2) 1 M solution
- look into plan to get visa and Fulbright issue; ch 05-14-2015d1418
- figure out how to get Fulbright medical records done; ch 05-14-2015d1423 (I'll do it in Utah)
- -reference email "2015-2016 Fulbright U.S. Scholar Grant Selection Status" 2-10-15
- analyze old tail suspension data; ch 05-11-2015d1659
- -I was going to go back and reanalyze the old tail suspension videos with the automatic analysis method, but then I realized that those videos did not have the black background so they can't be analyzed.
- deal with yahoomail bioinformatic emails; ch 05-06-2015d1301
- put text from CBBAs into wiki for better searchability; 04-04-2015d1111; ch 05-06-2015d1137
- finish preparing lung cancer CBBA, and refer to email thread with Rosa "mice for lung cancer project" around the time of 3-24-15; 04-03-2015d1122 ; ch 05-06-2015d1140
- look into amazon cloud drive pydio issue; ch 05-06-2015d1140 (I don't think I'll look into this more)
- -email subject: "Pydio, formerly AjaXplorer Amazon Cloud Drive"
- move the lung cancer aav9-tert; ch 05-06-2015d1141
- -need to make a cbba for this
- CBBA animal approval issue; ch 05-06-2015d1142
- -need CBBA for lung cancer project; 03-01-2015d1533
- straighten out issue with referenced publications in KRAS CBA; ch 05-05-2015d1732
- fix KRAS CBA issues; ch 05-05-2015d1732
- -address comments from Maria Garcia
from: Garcia.Maria <[email protected]>
to: "Whittemore.Kurt" <[email protected]>
date: Tue, Apr 14, 2015 at 9:10 PM
subject: Re: Kras Lung Cancer CBA
- -address comments from Rosa
anesthesia and analgesic info here
{
from: Serrano.Rosa <[email protected]>
to: Kurt Whittemore <[email protected]>
date: Tue, Apr 14, 2015 at 7:17 PM
subject: Re: anesthesia and analgesic questions
}
-record CBBA process ch 05-05-2015d1437
--see
from: Tejera.Agueda <[email protected]>
to: Kurt Whittemore <[email protected]>
date: Tue, Apr 21, 2015 at 5:15 PM
subject: Re: stamped documents
- record notes on Definiens; ch 05-04-2015d1830
- try out pdf note extractor app; ch 05-04-2015d1421
- analyze pathology data; ch 05-04-2015d1421
- analyze rotarod, tightrope, and tail suspension tests; ch 05-04-2015d1421
- figure out how to do automatic analysis of tail suspension videos; ch 05-04-2015d1421
- extract annotations from genes proteins and computers book; ch 05-04-2015d1422
- -E:\kurt\storage\Documents\Books\2015\4 April\04-20-2015d0900
- look into Spain tax issue; ch 05-04-2015d1422
- finish dealing with Genes proteins and computers book annotatons; 4-5-15; ch 05-04-2015d1423
- analyze pathology results from Juana; ch 05-04-2015d1423
- -email "results" 2-16-15 from [email protected] (wrote notes)
- -and email "histopatologia" 3-16-15 from "[email protected]" (wrote notes)
- continue with iodine video; ch 5-3-15
- -https://www.youtube.com/watch?v=ku2lylX13h4
- -figure out dose for neurodegeneration CBA; 04-21-2015d2120
- -anesthesia and analgesic info here
from: Serrano.Rosa <[email protected]>
to: Kurt Whittemore <[email protected]>
date: Tue, Apr 14, 2015 at 7:17 PM
subject: Re: anesthesia and analgesic questions
- order more slides for "1" slides; 04-04-2015d1111
- order more gray boxes; 04-21-2015d1500
- setup goodsync, and bittorrent sync
- I think I will repeat the TRF1 embryo immunofluorescence experiment with just 2 slides with two replicates (4 slides total) with different permeabilization times to test the conditions.
- deal with CBBA issue; 04-03-2015d1105
- -email "IACUC.018-2015" 4-1-15
- deal with TERT probe issue; 04-03-2015d1105; emailed Paula about it 04-04-2015d2004
- -email "question about Terf probes" 4-1-15 (Transnetyx email)
- CBBA animal approval issue
- -CBBA for neurodegeneration project; ch pre 04-04-2015d1954
- -CBBA for TRF1 mice and include DMBA+TPA treatment; ch pre 04-04-2015d1954
- read Maria Garcia's dissertation; finished pre 04-04-2015d1953
- look at ARCS foundation request; I think too much time has passed to look into this issue 04-04-2015d1951
- continue with "Metropolis Algorithms for Representative Subgraph Sampling" paper; 03-30-2015d2311
- look into testing compounds in blood issue
- -https://mail.google.com/mail/u/0/#search/compounds+in+blood/14badca897caa621
- let Gema know she can contact the other guy for the SAMP8 mice; 03-13-2015d1339
- -email "SAMP8 mice" 3(mar)-5-15 1:12pm [email protected]
- Treat TERT KO mice with compound that induces neurodegeneration; 03-13-2015d1340 (well not done, but progress should be made later)
- -look at the "Parkinson's Disease Models.pdf" paper from Maria and order the compounds; pre 03-03-2015d1247
- make sure to make record of approximating search information entropy, and clean up the code; 03-08-2015d2317
- Order SAMP8 mice with help from Rosa Serrano; no longer applicable. . 03-03-2015d1249
- maybe get SMC data for Shen; ch 03-01-2015d2233
- CBBA animal approval issue
- -CBBA for neurodegeneration project; 03-01-2015d1533
- -CBBA for TRF1 mice and include DMBA+TPA treatment; 03-01-2015d1533
- take a look at melatonin article; ch 02-21-2015d2341
- -http://www.lef.org/magazine/2007/6/nu_melatonin/Page-01
- send Gema Luque animal certificate when I get it; 02-09-2015d2254; ch pre 02-13-2015d1220
- do more cognitive tests in tert ko mice; ch 02-13-2015d1220 (I determined that I should do these tests around April 7th)
- do gene expression analysis on embryonic fibroblasts; ch 02-13-2015d1221
- get certificate for working with animals from the animalaria; pre 02-13-2015d1222
- look at tail suspension data in light of new weight data; 02-11-2015d1640
- -weights acquired around 1-8-14 (email subject "Transnetyx results" 1-8-14 https://mail.google.com/mail/u/0/?tab=wm#search/weights/14a77e98b600d96c)
- --"C:\Sync\cnio\2015\01 January\01 January\01-09-2015d1110\weights of some tert ko mice\Weights of some tert ko mice and controls 01-09-2015d1604.pdf"
- --weights in spreadsheet
- ---"C:\Sync\cnio\2015\01 January\01 January\01-09-2015d1110\weights of some tert ko mice\Weights of some tert ko mice and controls in spreadsheet 1-9-15.xlsx"
- do KI67 with Elisa with hearts on eGFP-TRF1 mice; 01-30-2015d1059
- -attend to trf1 embryo gene expression data; 01-30-2015d1059
- -cni_microarray experiment for trf1 embryos 01-08-2015d1947
- -C:\Sync\cnio\lgdata_DR\2015\01 January\01-22-2015d1728\trf1 embryo gene expression data\20150122_KWhittemore_ServiceReport
- look into Life Extension Europe; ch 01-25-2015d1325
- analyze tail suspension test videos 12-4-14; 01-25-2015d1109
- -cni_tail suspension test 12-04-2014d1644; 01-24-2015d1237
- -C:\Sync\cnio\lgdata_DR\2014\December\December\12-12-2014d1213\tail suspension test videos
- analyze confocal data found here; 01-25-2015d1106
- -cni_Q-FISH for 2 backup plates 01-14-2015d2142
- some finished to do list items pre 01-25-2015d1107