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TWiV 82 letters

TWiV 82 letters

Erik writes:

Yesterday I sent my Skype audio question again, and I think it worked this time. In my question I mentioned a particular youtube video. Here's the link if you want to see what I was referring to. It's only 5 minutes long. I'm not sure if what I was saying even made sense, so I guess if you see the video then you'll understand at least what I was trying to say.

http://www.youtube.com/watch?v=wJttdkKo4nM

Regards,
~Erik

Joseph writes:

Dear TWIV,

I am a graduate student in the computer science department of the University of New Orleans studying Bioinformatics. I only recently discovered that Biology is nothing like what was presented to me in high school and have found this an excellent service to fill those knowledge gaps I have naively created. I am emailing both a response and a request.

At some point you requested your listeners provide what other webcasts they listen to, so I created a list of them in three orders: favorite, density, and discovered; all from least to greatest. Hopefully this helps. I'm not much of a list person but I figured it would be more useful than just a list of what I listen to. For your reference, I generally listen while doing non-critical tasks at work, driving commutes to work and campus, and walking/biking commutes to campus.

FAVORITE:
1.Software Engineering Radio
2.Machine Structures (Berkeley)
3.This Week in Virology
4.omega tau
5.This Week in Parasitism
6.Structure and Interpretation of Computer Programs (Berkeley)
7.Futures in Biotech
8.NPR: Science Friday
9.Molecular and Cell Biology (Berkeley)
10.Dave's Psych Classes (Berkeley?)
11.Berkeley Speakers
12.Security Now!
13.This Week In Google

DENSITY:
1.omega tau
2.Software Engineering Radio
3.This Week in Virology
4.Machine Structures (Berkeley)
5.This Week in Parasitism
6.Structure and Interpretation of Computer Programs (Berkeley)
7.Futures in Biotech
8.NPR: Science Friday
9.Molecular and Cell Biology (Berkeley)
10.Berkeley Speakers
11.Dave's Psych Classes (Berkeley?)
12.Security Now!
13.This Week In Google

DISCOVERED:
1.Security Now!
2.Futures in Biotech
3.Software Engineering Radio
4.Dave's Psych Classes (Berkeley?)
5.NPR: Science Friday
6.Structure and Interpretation of Computer Programs (Berkeley)
7.omega tau
8.Machine Structures (Berkeley)
9.Molecular and Cell Biology (Berkeley)
10.This Week in Virology
11.This Week In Google
12.This Week in Parasitism
13.Berkeley Speakers

With that aside, I have a question/request. I'm new to the biology field and am working with a bioinformaticist this summer. Specifically, we are corrolaborating with some biologists who have some information (which they published as Human T-Cell Leukemia Virus Type 1 Integration Target Sites in the Human Genome: Comparison with Those of Other Retroviruses published in Journal of Virology June 2007) on preferred integration sites of HTLV-1 in a HeLa cell line. This is contrasted with other virus families' preferred integration sites. Specifically, our goal is to create a model from the HTLV-1 preferred integration sites, hopefully find other studies using HTLV-1 with different cell lines, and incorporate that information into a model which will predict integration sites of HTLV-1 in a T-cell line. Natuarlly, the ultimate goal is to have a general enough model so that, given a virus's phylogeny, we can predict its preferred integration sites. Do you know of any similar studies with HTLV-1 integration sites and, as a complete amateur, what material/tools would you recommend I review? I am currently familiarizing myself with the UCSC Genome Browser and tackling any vocabulary issues I have in the aforementioned paper.

Thanks, I love the show. Maybe shoot for more metaphors when explaining processes or comparing/contrasting things.
~Joseph

P.S. I encourage TWIP on a bi-weekly basis, but I have a lot of TWIV to catch up on, so no rush from me.

José writes:

Hi Dr. Vince, Dick, Alan and Rich

My name is José, Im a PhD student in Mexico City and i´m
working with innate immunity against dengue virus infection.
First of all, thanks for the great job with the cast, before i became a
fan of TWIV, i knew your work with RNA detection and innate immunity and i
never thought that doctors of your level were so enthusiastic with the
academic part of science, making it so fun and interesting.

i have some comments and questions.

1. there´s any viruses that we know that are transmitted in sea water
(seaborn), since there are so many of them in the sea my guess is that
some of them are capable to infect human, do you think that some of these
viruses actually uses the sea water for spread. Might be very interesting
evaluates the stability of the particles since they are resistant to high
concentrations of salt.

2. There are many reports of exclusive detection of viral PAMPs by TLRs
and RLHs, appears to me like the mechanism of detection depends of the
cell type, the genotype of the virus and the genetic aport of the host,
not just by the PRR involved. Since almost all of these kind of receptors
activates the IRF´s and NFkB families of transcript factors, these
differences in the specific combination of elements in the detection part
can give to the activation of a specific kind of dimer in the case of NFkB
(c-Rel, Rel-b, p50, etc) and for IRF´s (IRF3,7,1, etc) given to an
activation of different sets of genes in each case, given by the
differences in the affinity for the promoter sequences and the quantity of
the transcription factor. So the response it´s more complicated that just
"activated the IRF family and NFkB pathway".

3. About the T cell specific retroviral therapy question in TWIV 71 one of
the obstacles is that the region were the specific epitope it´s loaded in
the MHC, is not lineal in sequence it´s formed by the spatial structure of
the MHC. So if a virus have to integrates the sequence that codifies to
the specific CTL or Th must do it in fragments that have to fit exactly in
the gaps of the MHC and have to leave the sequence in open reading frame…i
think that's very difficult.

[the original question in twiv 71: Is possible to use gene therapy to insert genes into the major histocompatibility complex that could encode protien expressed on T-cells for a certain virus? ]

take a look at these microscopy technique that allows visualize in the
range of 40nm!!!!! so cool.

Thank you for the great show and sorry my english it's very precarious.

 

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