--- Log opened Thu Feb 28 00:00:02 2019
00:31 -!- Nocturn3Hack [~Anderson@2601:201:c000:633d::b758] has joined ##hplusroadmap
00:31 -!- Nocturn3Hack [~Anderson@2601:201:c000:633d::b758] has left ##hplusroadmap ["Leaving"]
02:01 < fltrz> I realized while sleeping that I forgot 2 possibilities regarding my question number 3 (TAD domains): apart from answer A (2d isolation membranes), answer B (linear concentrations along DNA), answers C and D are also possible: C: "the soapbubble" a planar concentration constrained to a single circular surface contained by the loop, like a soap bubble blower; or answer D: there is no spatial isolation at all, but instead a temporal isolation: something
02:01 < fltrz> sequences the opening and closing of TAD domains and only 1 TAD domain is active at a time? in this way perhaps there can be no unintended interaction
02:59 -!- Cory [Cory@unaffiliated/cory] has quit []
03:01 < fltrz> perhaps "nucleoplasmic veil" is the 2D surface if A or C is correct
03:01 < fltrz> but appears to only be observed during interphase...
03:08 -!- Cory [Cory@unaffiliated/cory] has joined ##hplusroadmap
05:53 < fenn> i think the "isolation" is just a difference in relative rates due to diffusion being faster within a small unconstrained region
05:53 < fenn> and the "boundaries" are just anchor points for the ends of the loop
05:54 < fenn> i've only just now read about it, but i suspected something like TAD existed already
05:55 < fenn> ot
05:56 < fenn> it's easier to travel between, say, germany and belgium, than it is to travel between turkey and belgium, despite there being no hard boundaries
06:04 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has quit [Ping timeout: 246 seconds]
06:40 < TMA> nope. there is still "hard" border between turkey and the EU
07:19 -!- Gurkenglas [~Gurkengla@unaffiliated/gurkenglas] has joined ##hplusroadmap
07:54 -!- yashgaroth [~yashgarot@2606:6000:c308:f700:ad9c:c784:88a9:dd8b] has joined ##hplusroadmap
08:02 -!- mnemon [~null@unaffiliated/mnemon] has joined ##hplusroadmap
08:15 < fltrz> lol TMA
08:17 < fltrz> what if 2 loops get physically close together? i.e. the diameter within the loop could be larger than the distannce between loops?
08:18 < fltrz> fenn, thanks for trying to make sense of the TAD domain boundaries, I really have a hard time findy any discussion about the nature of the isolation
08:20 < fltrz> fenn, also, it would seem the anchor points would be unnecessary, if this was the mechanism
08:21 < fltrz> not only unnecessary, but the anchor points would have nothing to do with genetic interaction isolation
08:32 < fltrz> https://en.wikipedia.org/wiki/File:Structural_organization_of_chromatin.png ok I didnt know nuclear lamina delineate the "chromosomal territories" or am I reading the picture wrong?
08:49 < yashgaroth> yeah in fig. 1A the lines around each 'territory' are kind of misleading; they are delineating discrete regulatory compartments, but don't represent laminar membrane like the circle does
08:49 < fltrz> "In this model, the supercoiling also stimulates enhancer promoter contacts and it is proposed that transcription of eRNA sends the first wave of supercoiling that can activate mRNA transcription in a given TAD." that sounds like option D, sequencing of TAD domains
08:51 < fltrz> yashgaroth, exactly, so now I'm confused if the conventional picture or this picture is correct
08:53 < fltrz> yashgaroth, upon reading your comment more closely is there any known membrane that delineates the "discrete regulatory compartments" ?
08:53 < yashgaroth> there's still spatial isolation, assume the nuclear lamina is a sphere and chromosomes associate with the inner surface; inactive regions of chromatin are stuck to it, anchoring the more active regions (including TADs) near the membrane
08:53 < yashgaroth> there's not really a membrane delineation, they're mostly associated by being from the same chromosome but there is some cross-talk between chromosomes
08:54 < fltrz> would chromosomal homologues be positioned close to each other?
08:55 < yashgaroth> I don't know for sure, but I would assume so yes
08:55 < yashgaroth> this is still a very active area of research btw
08:56 < fltrz> yeah, tbh I'm not really satisfied with the collection of partial explanations that point in different directions
08:57 < fltrz> but the upshot is that it's very clear there is much to learn about the TADs
08:58 < yashgaroth> haha "collection of partial explanations that point in different directions" is a very accurate description of biology research
09:03 < fltrz> ok what if all the ctcf anchor points all attach to the same inner nuclear lamina surface, ... but that this single surface has multiple "bulbs" with a relatively thin neck? so that they form separate "rooms" but essentially still connected?
09:07 < kanzure> cluelessperson: if you ask nicely then fenn will show you his tech tree diagrams
09:08 < fltrz> hey kanzure !
09:14 < kanzure> https://blog.mozilla.org/blog/2019/02/28/sharing-our-common-voices-mozilla-releases-the-largest-to-date-public-domain-transcribed-voice-dataset/
10:03 -!- spaceangel [~spaceange@ip-86-49-16-65.net.upcbroadband.cz] has joined ##hplusroadmap
10:03 -!- spaceangel [~spaceange@ip-86-49-16-65.net.upcbroadband.cz] has quit [Remote host closed the connection]
10:10 -!- spaceangel [~spaceange@ip-86-49-16-65.net.upcbroadband.cz] has joined ##hplusroadmap
10:21 -!- Gurkenglas [~Gurkengla@unaffiliated/gurkenglas] has quit [Ping timeout: 255 seconds]
11:23 < fenn> cluelessperson: no, i won't. sorry.
11:24 < fenn> primarily on account of them not existing
11:25 < kanzure> you what
11:25 < kanzure> what am i paying you for?
11:32 < nsh> pumpkin futures
11:47 -!- TheLive1 [~TheLive1@2001:16a2:893:7900:e936:cef2:cef2:9b56] has joined ##hplusroadmap
12:09 -!- CryptoDavid [uid14990@gateway/web/irccloud.com/x-zknsmgeyadolntyy] has quit [Quit: Connection closed for inactivity]
12:32 -!- TheLive1 [~TheLive1@2001:16a2:893:7900:e936:cef2:cef2:9b56] has quit [Remote host closed the connection]
12:57 < cluelessperson> fenn: I ask very nicely to see your tech tree if it exists.
12:58 < kanzure> tech-tree.yaml or something, surely
13:00 -!- spaceangel [~spaceange@ip-86-49-16-65.net.upcbroadband.cz] has quit [Remote host closed the connection]
13:44 < cluelessperson> I'd like to create one, but I'm a bit ignorant. :)
14:04 < fltrz> I don't think I understand the concept of a tech tree? is it a DAG instead of a tree? what is the parent child relationship?
14:18 -!- sivoais_ [~zaki@199.19.225.239] has quit [Ping timeout: 245 seconds]
14:19 -!- sivoais [~zaki@unaffiliated/sivoais] has joined ##hplusroadmap
14:22 -!- jb55 [~jb55@S010660e327dca171.vc.shawcable.net] has quit [Ping timeout: 245 seconds]
14:49 -!- jb55 [~jb55@S010660e327dca171.vc.shawcable.net] has joined ##hplusroadmap
15:31 -!- justanotheruser [~justanoth@unaffiliated/justanotheruser] has joined ##hplusroadmap
17:37 -!- decal__ is now known as decal
17:47 < kanzure> .title http://www.nhfpc.gov.cn/yzygj/s7659/201902/0f24ddc242c24212abc42aa8b539584d.shtml
17:47 < yoleaux> kanzure: Sorry, that doesn't appear to be an HTML page.
17:48 < kanzure> .title https://www.sciencemag.org/news/2019/02/china-tightens-its-regulation-some-human-gene-editing-labeling-it-high-risk
17:48 < yoleaux> China tightens its regulation of some human gene editing, labeling it ‘high-risk’ | Science | AAAS
17:51 -!- decal [decal@ma.sdf.org] has quit [Quit: leaving]
20:41 -!- hehelleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has joined ##hplusroadmap
20:45 -!- helleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has quit [Ping timeout: 258 seconds]
21:43 -!- yashgaroth [~yashgarot@2606:6000:c308:f700:ad9c:c784:88a9:dd8b] has quit [Quit: Leaving]
22:08 -!- hehelleshin [~talinck@cpe-174-97-113-184.cinci.res.rr.com] has quit [Read error: Connection reset by peer]
--- Log closed Fri Mar 01 00:00:03 2019