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Tim Bates Discussion Questions

(wow so good!)

  • Maureen 19:30, 11 October 2017 (PDT) Way to make us look :)

Week 1: Replicative Errors in Cancer

Please see presentation 1 for this week.

Week 2: Persistent Data Identifiers

1) What is the best way to ensure links will continue to work if the hosting service closes?

  A: Always use services with clear data archiving policies discussing the fate of existing data in the case of closure.

2) Who should be responsible for paying the cost of data cataloging and retention?

  A:  This is a very complex issue that has no real answer, but instead depends on the situation and the parties involved.  In the context of publicly funded research, it is important that the data be made available to all taxpayers.  However this entails significant extra costs due to management and distribution that would also be the responsibility of the taxpayer to fund.  The case of private data is more simple, requiring only that data be preserved and made available to those who payed for the research that generated the data.  However, many privately funded studies intermingle with public studies, sharing data and resources.

3) Is the use of alphanumeric characters and symbols to reduce the length of unique identifiers warranted compared to simply using longer strings of numerals only?

  A:  The increase in data storage capacity increases dramatically with the number of increased characters available, however the additional complexity in terms of assigning and processing these more complex identifiers requires some cost benefit analysis.  For example, if a service uses 6 character identifiers of only numbers, then the possible number of identifiers is 10^6 = 1,000,000.  If that same service now allows lower case letters than the possible identifiers becomes 36^6 = 2,176,782,336; however, adding letters will require additional processing to watch for real words, functional code, and combinations which appear to be real words.  If the more complex identifiers require only twice as much code to handle, then processing of the same number of requests could take twice as long.

Week 3: Telomere Length Limiters

1) What is tamoxifen and why did they use it in their assays?

  A:  Tamoxifen is a telomerase activator and acts to lengthen telomeres which have been excessively shortened.  They seem to have been using it in order to test how exactly tamoxifen causes this change.

2) Is their use of a polyclonal antibody here warranted?

  A:  I think their assay did a good job of demonstrating specificity, but I was not able to find any other tests where they actually used this antibody.

3) Do you agree with the conclusion of this article: TZAP is preferentially recruited to and causes trimming of telomeres?

  A:  While it does look like TZAP and TRF1/2 are negatively correlated I am not completely convinced by their evidence that TZAP somehow prevents TRF1/2 from binding.  They looked at binding in western style gel shift assays, but it is unclear how relevant this is outside of the physiological context.  I would have liked to see more colocalization in cell assays.

Many have asked, so here are some pictures of my new kitten!