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Travis Desell
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Message 3167 - Posted: 23 Aug 2014, 20:38:38 UTC
Last modified: 16 Nov 2014, 1:32:43 UTC

Hi Everyone,

I've gotten some more details about what we'll be doing with DNA@Home from Sergei and Archana, who study epigenetics in UND's medical school. Please let us know if you have any questions!




Epigenetic Triad:

The term ‘epigenetics’ means ‘above the gene’, and refers to changes in gene expression that are independent of DNA sequence. What this means is that the way we interact with our environment, the food we eat, the chemicals we are exposed to, etc. can all have the ability to change which genes are on and which are off, without mutating the DNA. These changes, collectively referred to as the “epigenome”, can affect not just our genes, but can be stably inherited and affect our children’s and our grandchildren’s genes too!

Epigenetic regulation of gene expression is accomplished through the actions of DNA methylation, histone code, and noncoding RNAs (e.g., miRNAs) that can function independently or in concert. The precise contribution of each may vary depending on the particular gene of interest and its context, e.g., species, cell type, developmental stage, and age of the organism. Although not all alterations to the epigenome are expected to be problematic, some might have adverse consequences (e.g., abnormal development, increased susceptibility to disease).




Snail and Slug proteins:

We study how proteins known as transcription factors locate and bind to select regions of our genome. Our focus is on two very interesting factors called Snail and Slug (not related to the garden animals!), which have been shown to play critical roles in disease. Expression of Snail and Slug causes loss of cell-adhesion proteins making the cells less "sticky" and more "mobile", causing metastasis. Thus, as you can imagine, understanding how these proteins know which specific DNA sequences to bind to is crucial in developing therapeutic targets for diseases like cancer.

The Snail family of proteins has been shown to play important roles in both development and in disease. The two proteins Snail and Slug are highly similar, as seen in this cartoon. The repressive region in the first half of the proteins are 89% similar, while the end regions (the DNA-binding regions) are 84% identical. There are some differences too, especially in the middle of the proteins.




Snail and EMT:
This image shows what happens to the E-cadherin protein (stained in red) before and after Snail expression. The cells are usually in an “epithelial” state, which means that the cells are sticking together. You can see a nicely defined pattern of E-cadherin, which shows a cobblestone or chicken-wire pattern (red). Upon Snail induction, E-cadherin expression is lost, so the cells lose their “stickiness”, and start to move. The nucleus of each cell is stained in blue.

Tullus
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Message 4638 - Posted: 2 Oct 2014, 5:05:45 UTC - in response to Message 3167.

Hi! Sounds interesting, but what does the application "DNA@Home Gibbs Sampler (gibbs)" actually do?

Travis Desell
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Message 4644 - Posted: 2 Oct 2014, 15:48:24 UTC - in response to Message 4638.
Last modified: 2 Oct 2014, 15:49:14 UTC

Hi! Sounds interesting, but what does the application "DNA@Home Gibbs Sampler (gibbs)" actually do?


Hi Tullus,

It uses a process called "Gibbs Sampling" which performs guided semi-random walks from areas of the genome that we're looking at. Basically, it's trying to find regions of nucleotides (of a similar length) that are similar but not exactly the same, and are common across the areas of the genome that we're looking at. These regions are potential transcription factors, which proteins attach to to either inhibit or exhibit the activation of nearby genes.

If you want some more in depth information, there are some slides and a publication we've made on the project on our publications page which you can get to here:

http://volunteer.cs.und.edu/csg/publications.php

They're right up at the top. Let me know if you have any questions!

Tullus
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Message 4677 - Posted: 11 Oct 2014, 21:37:01 UTC

Thank you, slightly more informed now. By the way, broken links on the publication page:
http://people.aero.und.edu/~tdesell/talks/2011_nov_15_cacs.key
http://people.aero.und.edu/~tdesell/talks/2011_nov_15_cacs.ppt

In layman terms, you look at a sequence of "acgt...", pick random segments and do some form of correlation with the rest of the genom string? In essence, the program only works on "acgt" strings?

yo2013
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Message 4816 - Posted: 10 Nov 2014, 8:32:01 UTC - in response to Message 4644.
Last modified: 10 Nov 2014, 9:08:22 UTC

Thanks for the info! Just started crunching yesterday (I joined the project when it was in the old server, but never received a WU). So, we are still computing for Mycobacterium tuberculosis and Yersinia pestis? Or we switched to other organisms?

Travis Desell
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Message 4824 - Posted: 15 Nov 2014, 4:15:56 UTC - in response to Message 4816.
Last modified: 15 Nov 2014, 4:16:04 UTC

We've currently swapped to different organisms -- humans! I also need to fix the broken links here...

yo2013
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Message 4829 - Posted: 15 Nov 2014, 10:02:02 UTC - in response to Message 4824.

Nice!

[VENETO] boboviz
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Message 4830 - Posted: 15 Nov 2014, 21:22:15 UTC
Last modified: 15 Nov 2014, 21:22:36 UTC

Where are images on first post??

Travis Desell
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Message 4831 - Posted: 16 Nov 2014, 1:33:04 UTC - in response to Message 4830.

Fixed now!

[VENETO] boboviz
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Message 5106 - Posted: 6 Apr 2015, 14:01:17 UTC

There are scientific news? Results? Are you planned scientific articles??

nanoprobe
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Message 5117 - Posted: 9 Apr 2015, 12:49:36 UTC

Any new tasks coming?



41336 Citizen Science Grid 4/9/2015 8:41:01 AM Requesting new tasks for CPU
41337 Citizen Science Grid 4/9/2015 8:41:02 AM Scheduler request completed: got 0 new tasks
41338 Citizen Science Grid 4/9/2015 8:41:02 AM No tasks sent
41339 Citizen Science Grid 4/9/2015 8:41:02 AM No tasks are available for DNA@Home Gibbs Sampler

Travis Desell
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Message 5119 - Posted: 10 Apr 2015, 19:43:15 UTC - in response to Message 5117.

Any new tasks coming?



41336 Citizen Science Grid 4/9/2015 8:41:01 AM Requesting new tasks for CPU
41337 Citizen Science Grid 4/9/2015 8:41:02 AM Scheduler request completed: got 0 new tasks
41338 Citizen Science Grid 4/9/2015 8:41:02 AM No tasks sent
41339 Citizen Science Grid 4/9/2015 8:41:02 AM No tasks are available for DNA@Home Gibbs Sampler


Yes, but I'm currently at a conference in Copenhagen so it won't be until after I get back. I need to talk to our biologists about what runs they want to perform next.

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Message 5164 - Posted: 26 Apr 2015, 22:32:29 UTC

DNA@Home Gibbs Sampler tasks seem to have run out again. Any more in the works?

Travis Desell
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Message 5166 - Posted: 27 Apr 2015, 19:12:07 UTC - in response to Message 5164.

DNA@Home Gibbs Sampler tasks seem to have run out again. Any more in the works?


Definitely, sorry for being slow on this. Our biologists have been moving their lab so we've been a bit slow getting the required data sets and making sure we're sending out the work we want to. Hopefully by the end of the week!

[VENETO] boboviz
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Message 5762 - Posted: 28 Jul 2015, 9:41:37 UTC - in response to Message 4644.

If you want some more in depth information, there are some slides and a publication we've made on the project on our publications page which you can get to here:
http://volunteer.cs.und.edu/csg/publications.php


Latest news of DNA@home was 2012 :-(

Travis Desell
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Message 5911 - Posted: 25 Sep 2015, 0:20:37 UTC - in response to Message 5762.

If you want some more in depth information, there are some slides and a publication we've made on the project on our publications page which you can get to here:
http://volunteer.cs.und.edu/csg/publications.php


Latest news of DNA@home was 2012 :-(


We just published and presented a paper at this yeares e-Science. I need to get the paper and presentation up there.

[VENETO] boboviz
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Message 6115 - Posted: 28 Jan 2016, 19:22:49 UTC - in response to Message 5911.

We just published and presented a paper at this yeares e-Science. I need to get the paper and presentation up there.


Is this, i suppose....


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