Chris,
Hi. It is kind of an interesting job in that I can keep up with the
latest stuff and I do find the idea of organizing scientific information
very interesting. But, it can be a little boring sometimes, too. But, I
guess most people would say that about their jobs, though.
Epigenetics is pretty neat. When the histones are
methylated/demethylated and acetylated/deacetylated by various enzymes,
this can cause the DNA wrapped around them to become less or more compact,
which affects how the genes in that area are expressed.
You're sure right about their finding more levels of operation than
ever before. Since they developed what they call "next generation
sequencing" about 2005 or so, they've been able to find out a lot more
levels in all areas. One thing that's kind of neat is that the supposedly
junk DNA between genes can encode small RNAs that regulate the expression
of the genes. These "microRNAs" are really a hot area of research now.
Another big breakthrough was the combination of various techniques to make
very large scale analysis of proteins (proteomics) possible. So, they're
combining gene expression, protein studies, epigenetics, etc. to see how it
all fits together in the body. They call that systems biology, and it's
bringing more progress. But, there are so many interacting molecules
inside a single cel, they've got a long way to go.
I'll check out the link you provided on bacterial heredity right after
this post. These microbiome (microbes in intestinal tract, mouth, skin,
etc.) studies are pretty neat, too. One neat thing the next-gen.
sequencing has allowed is that they can now get a big glob of all different
kinds of microbes from a site (intestine, environment), sequence it all and
map the resulting reads to known genomes to find out what microbes are
present at that site.
Sorry to write so much. Biochemistry is one area I know a little about
(real little!) as opposed to metaphysics.
I wish tomorrow weren't Monday. Have a good week!
Roger
On Sunday, April 5, 2015 at 1:11:14 PM UTC-4, cdemorsella wrote:
>
>
>
>
>
> *From:* everyth...@googlegroups.com <javascript:> [mailto:
> everyth...@googlegroups.com <javascript:>]
>
>
>
>
>
> Chris,
>
> Roger – what an interesting job, if you like reading this kind of stuff
> that is J
>
>
>
> I knew about DNA being wound around a supporting matrix – e.g. the
> histones – but I never knew that this non-DNA structural protein had any
> interactions with the DNA Wrapped around it) that could control expressing
> sections of encoding DNA. Of course this implies that the histone does more
> than just provide a structural matrix for the DNA to become tightly packed
> in, and that was news to me.
>
> I have been following epigenetic stuff for a while, especially well
> documented for the methylation pathway, but this appears to be yet a
> separate pathway for genomic expression and hereditary transmission of
> information.
>
> The story of heredity is getting more and more interesting. For example,
> check out the link to the story below; life (and living systems) seem like
> they have more levels of operation than previously believed.
>
>
>
> *Mothers can pass traits to offspring through bacteria's DNA, mouse study
> shows <http://www.sciencedaily.com/releases/2015/02/150216125425.htm> *
> http://www.sciencedaily.com/releases/2015/02/150216125425.htm
>
>
>
> Cheers,
>
> Chris
>
>
>
> Hi. It's good that they have new studies confirming this stuff, but
> the looping of DNA into 3D structures inside the nucleus has been known
> for awhile. I think they're even starting to map these interactions just
> like the human genome project. One of the methods they use is to crosslink
> the DNA in the nucleus so that the shape it's currently in is saved, and
> then sequence the crosslinked areas to identify the crosslinked segments of
> DNA. But, I admit calling this a wormhole is kind of just good marketing.
> I guess the everything list is kind of like a wormhole that brings
> together distant people so they can talk about "everything"! :-)
>
>
>
> Also, on the epigenetic inheritance thing via histones, it's also good
> that new studies are proving this stuff, but epigenetic changes (changes in
> gene expression caused by things other than changes to the DNA sequence)
> that can be inherited have also been known for 10 years or so. So far,
> what they know are that these changes are caused by adding or removing
> methyl groups to the DNA bases or methyl and acetyl groups to the histones.
> That affects how the genes are expressed. These changes can be affected
> by the environment and your own activities (like exercise). So, your
> descendants may thank you for exercising and eating right!
>
>
>
> The only reason I know some stuff about this is that I have kind of a
> weird job where I read biochem. articles all day and put the new stuff into
> a database.
>
>
>
> See you!
>
>
>
> Roger
>
>
>
>
>
>
>
>
> On Saturday, April 4, 2015 at 3:08:19 PM UTC-4, cdemorsella wrote:
>
>
>
> -----Original Message-----
> From: everyth...@googlegroups.com [mailto:everyth...@googlegroups.com] On
> Behalf Of Russell Standish
> Sent: Thursday, February 26, 2015 1:44 PM
> To: 'Chris de Morsella' via Everything List
> Subject: Re: DNA Wormholes can cause cancer (what!?)
>
> Of course, this is what Australia's John Mattick has been saying for
> decades (I heard him talk on this nearly 15 years ago, for instance, and
> he'd been railing at the establishment sometime before that).
>
> >> But "wormholes"? Really? Someone in marketing has been given far too
> liberal a rein.
>
> They're always on the hunt for that catchy title aren't they; I find them
> amusing :)
> Still, in seriousness, it's an interesting idea: that previously
> overlooked, non-local effects, naturally operating within an organisms DNA
> may be playing a more fundamental role in life than previously believed (or
> even considered to be occurring at all)
> Chris
>
> Cheers
>
>
> On Thu, Feb 26, 2015 at 05:26:16PM +0000, 'Chris de Morsella' via
> Everything List wrote:
> > [Have been very busy on a new software project and have not had time
> > to follow and participate on this list... such an active list :). ]
> > Came across this article and found it interesting also from an
> > information science point of view -- taking the perspective of DNA
> > being a fairly dynamic information repository. It seems like the
> > butterfly effect is operating in DNA... a small difference one place
> > can result in effects being triggered in very distant DNA locations...
> > or as the researchers said... kind of like a wormhole.-Chris
> >
> > Cancer risk linked to DNA ‘wormholes’
> >
> > February 25, 2015
> > Single-letter genetic variations within parts of the genome once
> dismissed as “junk DNA” can increase cancer risk through remote effects on
> far-off genes, new research by scientists at The Institute of Cancer
> Research, London shows.The researchers found that DNA sequences within
> “gene deserts” — so called because they are completely devoid of genes —
> can regulate gene activity elsewhere by forming DNA loops across relatively
> large distances.The study helps solve a mystery about how genetic
> variations in parts of the genome that don’t appear to be doing very much
> can increase cancer risk.Their study, published in Nature Communications,
> also has implications for the study of other complex genetic diseases.The
> researchers developed a technique called Capture Hi-C to investigate
> long-range physical interactions between stretches of DNA – allowing them
> to look at how specific areas of chromosomes interact physically in more
> detail.The researchers assessed 14 regions of DNA that contain
> single-letter variations previously linked to bowel cancer risk. They
> detected significant long-range interactions for all 14 regions, confirming
> their role in gene regulation.“Our new technique shows that genetic
> variations are able to increase cancer risk through long-range looping
> interactions with cancer-causing genes elsewhere in the genome,” study
> leader Professor Richard Houlston, Professor of Molecular and Population
> Genetics at The Institute of Cancer Research, London said.“It is sometimes
> described as analogous to a wormhole, where distortions in space and time
> could in theory bring together distant parts of the universe.”The research
> was funded by the EU, Cancer Research UK, Leukaemia & Lymphoma Research,
> and The Institute of Cancer Research (ICR).
> >
> > --
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> --
>
> ----------------------------------------------------------------------------
>
> Prof Russell Standish Phone 0425 253119 (mobile)
> Principal, High Performance Coders
> Visiting Professor of Mathematics hpc...@hpcoders.com.au
> University of New South Wales http://www.hpcoders.com.au
>
> Latest project: The Amoeba's Secret
> (http://www.hpcoders.com.au/AmoebasSecret.html)
> ----------------------------------------------------------------------------
>
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