Tuesday, March 24, 2015

[tt] arstechnica: gene editing method that changes both alleles present, and both their descendents', for all descendents

(
http://www.sciencemag.org/content/early/2015/03/18/science.aaa5945
and
http://arstechnica.com/science/2015/03/new-dna-construct-can-set-off-a-mutagenic-chain-reaction/
)

The mutagenic chain reaction: A method for converting heterozygous to
homozygous mutations
Valentino M. Gantz*, Ethan Bier*
+ Author Affiliations

Section of Cell and Developmental Biology, University of California, San
Diego, La Jolla, CA 92095, USA.
↵*Corresponding author. E-mail: vgantz@ucsd.edu (V.M.G.); ebier@ucsd.edu
(E.B.)
ABSTRACT
An organism with a single recessive loss-of-function allele will
typically have a wild-type phenotype while individuals homozygous for
two copies of the allele will display a mutant phenotype. Here, we
develop a method that we refer to as the mutagenic chain reaction (MCR),
which is based on the CRISPR/Cas9 genome editing system for generating
autocatalytic mutations to generate homozygous loss-of-function
mutations. We demonstrate in Drosophila that MCR mutations efficiently
spread from their chromosome of origin to the homologous chromosome
thereby converting heterozygous mutations to homozygosity in the vast
majority of somatic and germline cells. MCR technology should have broad
applications in diverse organisms.

---


New DNA construct can set off a "mutagenic chain reaction"
Can sweep through an entire population, changing a gene.
by John Timmer - Mar 24, 2015 7:00am AEDT
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94

Flickr user: St3f4n
A technique for editing genes while they reside in intact chromosomes
has been a real breakthrough. Literally. In 2013, Science magazine named
it the runner-up for breakthrough-of-the-year, and its developers won
the 2015 Breakthrough Prize.

The system being honored is called CRISPR/Cas9, and it evolved as a way
for bacteria to destroy viruses using RNA that matched the virus' DNA
sequence. But it's turned out to be remarkably flexible, and the
technique can be retargeted to any gene simply by modifying the RNA.
Researchers are still figuring out new uses for the system, which means
there are papers coming out nearly every week, many of them difficult to
distinguish.

FURTHER READING


BACTERIAL "IMMUNE SYSTEM" USED TO ENGINEER HUMAN DNA IN HUMAN CELLS
System lets researchers target changes to specific sites in the genome.
That may be precisely why the significance of a paper published last
week wasn't immediately obvious. In it, the authors described a way of
ensuring that if one copy of a gene was modified by CRISPR/Cas9, the
second copy would be—useful, but not revolutionary. What may have been
missed was that this process doesn't stop once those two copies are
modified. Instead, it happens in the next generation as well, and then
the generation after that. In fact, the modified genes could spread
throughout an entire species in a chain reaction, a fact that has raised
ethical and safety concerns about the work.

New developments

The CRISPR/Cas9 system is remarkably simple. It relies on RNA molecules
that have a specific format and are able to base pair with a site in the
genome. Cas9 then cuts the DNA at the site where this base pairing
occurs, creating a break in the chromosome. Cells have systems that
attempt to repair these breaks, and these systems attempt to identify
similar-looking sequences to use as a template for repair. So if you
provide the cells with some similar DNA, it will end up being placed at
the site that the RNA first targeted.

This makes it easy to modify the genome. By providing slightly different
DNA to be used in the repair process, you can substitute altered bases,
short deletions, or even entire additional genes, any of which can take
their place within the chromosome. In short, CRISPR/Cas9 lets you put
any DNA you want anywhere in a genome.

It's possible to use this to eliminate genes you're interested in, so
you can study animals that lack that gene. You simply target the gene
with an RNA, and then provide DNA with a deletion of a key part of the
gene. The repair system will use the deletion as part of its template
and copy it into place on the chromosome. It's also possible to mutate a
gene by replacing key parts of it with something else. For example, you
could swap in a copy of the Green Fluorescent protein and ensure that
all of the resulting mutants glow green.

But you still have to breed these mutations the old-fashioned way: you
need to get two organisms that have a copy of the mutant gene, then
breed them together. Mendel then tells us that one-quarter of the
offspring will have mutant copies in both of their chromosomes.

The authors of the new paper found that frustratingly slow. Working in
flies, they designed a system where CRISPR/Cas9 would do all the work
for them. Their DNA repair template was a bit more complicated than a
simple deletion. Instead, it contained the genes needed to get the
CRISPR/Cas9 system to work, along with a guide RNA that targeted a
specific fly gene (in this case, yellow). They surrounded all these
genes with DNA from the yellow gene itself.

Once injected in the fly, the normal yellow gene was disrupted by the
genes for the CRISPR/Cas9 system. Once that happened on one chromosome,
the system could easily perform the same modification on the other
chromosome, making the animal a homozygous yellow mutant.

But the key thing is what happens in the next generation. In these
animals, a normal copy of the yellow gene comes in from the next parent.
But the CRISPR/Cas9 cassette immediately converts that, too, resulting
in offspring that are all yellow. Well, not all; but the authors found
that the construct was 97 percent effective at converting the next
generation. In fact, there's nothing to stop this system from invading
an entire population, continuing to convert generation after generation
until everything carries the modification.

It's a bit like the futurists' fears of a self-perpetuating "grey goo,"
just played out with yellow-colored flies. (For those of you with a
biology background, this will also sound a lot like an engineered homing
intron.)

Precautions

Fortunately, the researchers were conscious of the issues: "we are also
keenly aware of the substantial risks associated with this highly
invasive method since the failure to take stringent precautions could
lead to the unintentional release of [modified] organisms into the
environment." The flies were bred behind three layers of containment in
a locked facility. The containers were put straight into the freezer to
kill the flies if they were no longer needed. Any manipulations of the
flies were performed while they were anesthetized in a Biosafety Level 2
facility.

Still, there are further precautions that could be taken. The report
cites a draft manuscript, hosted on the bioRxiv, that describes a
similar system in yeast. In this case, however, only the targeting RNA
is inserted into the targeted gene—the rest of the CRISPR/Cas9 system
has to be provided separately for anything to happen. One of the authors
of this manuscript, the synthetic biologist George Church, told a
Science reporter that he felt the fly work should never have been
published because the technology was too dangerous.

Why do the work at all if it's so risky? Because, properly controlled,
there could be some amazing benefits. Imagine using it to quickly breed
traits from non-agricultural plants (drought or pest resistance, for
example) into important food crops. Or converting the entire population
of a dangerous pathogen into one lacking virulence genes. Or releasing a
few mosquitos, allowing them to breed, and creating a population that's
incapable of supporting malarial parasite growth. All of these are very
real possibilities enabled by the technology.

But there's also a very real risk of a giant, uncontrolled experiment if
any of these DNA constructs made it into a wild population. And the
developments come at a time where several researchers (including Church)
have suggested it's time to lay out some formal guidelines for future
research in this area, both for synthetic biology and for human genome
modifications. The authors of the fly paper cite two of these
editorials, while Science and Nature have run editorials urging that we
avoid editing the human germline.

The authors of the fly paper suggest looking to the Asilomar agreement,
which was forged by leading biologists who were leaders in the
development of recombinant DNA. That created a voluntary yet successful
moratorium on the work until safety issues could be examined. We may be
forced to see whether this sort of voluntary agreement would hold in an
era of intense competition. Similar concerns were voiced about work
involving flu viruses, but research continued until the federal
government announced a halt to funding for this research.

Science, 2014. DOI: 10.1126/science.aaa5945 (About DOIs).
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Wednesday, March 18, 2015

[tt] (lem-l) RE: Terry Pratchett R.I.P (fwd)

(Slightly reformatted - TR)

----- Forwarded message from Birger Johansson <arthur99dent@hotmail.com> -----

Date: Fri, 13 Mar 2015 09:26:12 +0000
From: Birger Johansson <arthur99dent@hotmail.com>
To: John Everett Branch Jr <ohmicron271@me.com>, S-Lem listan
<lem-l@lists.rpi.edu>, "lem@lists.rpi.edu" <lem@lists.rpi.edu>
Subject: RE: Terry Pratchett R.I.P

Alas I do not have that power of words. i was quoting a fellow
Pratchett fan from the Pharyngula blog.

Here is another quote, from when the character Susan talks with Death.

.

"All right," said Susan, "I'm not stupid. You're saying humans need …
fantasies to make life bearable"

NO. HUMANS NEED FANTASY TO BE HUMAN. TO BE THE PLACE WHERE THE FALLING
ANGEL MEETS THE RISING APE.

"Tooth Fairies? Hogfathers?"

YES. AS PRACTICE. YOU HAVE TO START OUT LEARNING TO BELIEVE THE LITTLE
LIES.

"So we can believe the big ones?"

YES. JUSTICE, DUTY. MERCY. THAT SORT OF THING.

"They're not the same at all!"

REALLY? THEN TAKE THE UNIVERSE AND GRIND IT DOWN TO THE FINEST POWDER
AND SIEVE IT THROUGH THE FINEST SIEVE AND THEN SHOW ME ONE ATOM OF
JUSTICE, ONE MOLECULE OF MERCY. AND YET YOU ACT LIKE THERE WAS SOME
SORT OF RIGHTNESS IN THE UNIVERSE BY WHICH IT MAY BE JUDGED"

"Yes. But people have to believe that or what's the point?"

MY POINT EXACTLY

From: ohmicron271@me.com
Subject: Re: Terry Pratchett R.I.P
Date: Thu, 12 Mar 2015 19:40:40 -0400
To: lem@lists.rpi.edu

Thanks for that, Birger. My only question is whether, since you used
quotation marks, you were quoting yourself or somebody else.


--John E. Branch Jr.
Vanity Fair: 212-286-6187
cell: 646-789-3103
Twitter: @JEB54
HuffPost: http://www.huffingtonpost.com/john-branch/blog: http://ifitbenotnow.wordpress.com/


On Mar 12, 2015, at 2:14 PM, Birger Johansson <arthur99dent@hotmail.com> wrote:


"I have many friends who I've never met. Terry Pratchett was, I have
to say, the greatest of them. He gave me company, comfort, joy,
laughter tears and sadness tears and new ideas. He constantly
questioned my old ideas, sometimes adding to them, sometimes gently
correcting them or, at times, forcing me to realise that I'd been
flat-out wrong. And all with a wry, twinkly-eyed humour which never
berated nor belittled. I am sad that my friend who I never met has
met his own most sympathetic and memorable character, Death. I am glad
that my friend is no longer suffering. I will miss my friend, though I
never met him, terribly terribly much."


----- End forwarded message -----
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Tuesday, March 17, 2015

[tt] (Rensselaer Poly.Inst.) The Corrugated Galaxy—Milky Way May Be Much Larger Than Previously Estimated

(On ARXIV: "Rings and Radial Waves in the Disk of the Milky Way",
http://arxiv.org/abs/1503.00257
- TR)

[

http://news.rpi.edu:8080/content/2015/03/09/rippling-milky-way-may-be-much-larger-previously-estimated

]

(... links deleted ...)

The Corrugated Galaxy—Milky Way May Be Much Larger Than Previously Estimated

Wed, 2015-03-11 11:12 -- [21]martim12

Findings Led by Rensselaer Polytechnic Institute Researchers Published in the Astrophysical Journal

March 11, 2015
By Mary L. Martialay

The Milky Way galaxy is at least 50 percent larger than is commonly
estimated, according to new findings that reveal that the galactic disk
is contoured into several concentric ripples. The research, conducted
by an international team led by [22]Rensselaer Polytechnic Institute
Professor [23]Heidi Jo Newberg, revisits astronomical data from the
[24]Sloan Digital Sky Survey which, in 2002, established the presence
of a bulging ring of stars beyond the known plane of the Milky Way.

"In essence, what we found is that the disk of the Milky Way isn't just
a disk of stars in a flat plane—it's corrugated," said Heidi Newberg,
professor of physics, applied physics, and astronomy in the Rensselaer
[25]School of Science. "As it radiates outward from the sun, we see at
least four ripples in the disk of the Milky Way. While we can only look
at part of the galaxy with this data, we assume that this pattern is
going to be found throughout the disk."

Importantly, the findings show that the features previously identified
as rings are actually part of the galactic disk, extending the known
width of the Milky Way from 100,000 light years across to 150,000 light
years, said Yan Xu, a scientist at the [26]National Astronomical
Observatories of China (which is part of the Chinese Academy of Science
in Beijing), former visiting scientist at Rensselaer, and lead author
of the paper.

"Going into the research, astronomers had observed that the number of
Milky Way stars diminishes rapidly about 50,000 light years from the
center of the galaxy, and then a ring of stars appears at about 60,000
light years from the center," said Xu. "What we see now is that this
apparent ring is actually a ripple in the disk. And it may well be that
there are more ripples further out which we have not yet seen."

The research, funded in part by the National Science Foundation and
titled "Rings and Radial Waves in the Disk of the Milky Way," was
published today in the Astrophysical Journal. Newberg, Xu, and their
collaborators used data from the Sloan Digital Sky Survey (SDSS) to
show an oscillating asymmetry in the main sequence star counts on
either side of the galactic plane, starting from the sun and looking
outward from the galactic center. In other words, when we look outward
from the sun, the mid-plane of the disk is perturbed up, then down,
then up, and then down again.

"Extending our knowledge of our galaxy's structure is fundamentally
important," said Glen Langston, NSF program manager. "The NSF is proud
to support their effort to map the shape of our galaxy beyond
previously unknown limits."

The new research builds upon a 2002 finding in which Newberg
established the existence of the "Monoceros Ring," an "over-density" of
stars at the outer edges of the galaxy that bulges above the galactic
plane. At the time, Newberg noticed evidence of another over-density of
stars, between the Monoceros Ring and the sun, but was unable to
investigate further. With more data available from the SDSS,
researchers recently returned to the mystery.

"I wanted to figure out what that other over-density was," Newberg
said. "These stars had previously been considered disk stars, but the
stars don't match the density distribution you would expect for disk
stars, so I thought 'well, maybe this could be another ring, or a
highly disrupted dwarf galaxy."

When they revisited the data, they found four anomalies: one north of
the galactic plane at 2 kilo-parsecs (kpc) from the sun, one south of
the plane at 4-6 kpc, a third to the north at 8-10 kpc, and evidence of
a fourth to the south 12-16 kpc from the sun. The Monoceros Ring is
associated with the third ripple. The researchers further found that
the oscillations appear to line up with the locations of the galaxy's
spiral arms. Newberg said the findings support other recent research,
including a theoretical finding that a dwarf galaxy or dark matter lump
passing through the Milky Way would produce a similar rippling effect.
In fact, the ripples might ultimately be used to measure the lumpiness
of dark matter in our galaxy.

"It's very similar to what would happen if you throw a pebble into
still water – the waves will radiate out from the point of impact,"
said Newberg. "If a dwarf galaxy goes through the disk, it would
gravitationally pull the disk up as it comes in, and pull the disk down
as it goes through, and this will set up a wave pattern that propagates
outward. If you view this in the context of other research that's
emerged in the past two to three years, you start to see a picture is
forming."

The research was funded by the NSF, as well as the Chinese National
Science Foundation and the National Basic Research Program of China.

Newberg currently researches the structure and evolution of our own
galaxy, using stars as tracers of the galactic halo and disks. These
stars in turn are used to trace the density distribution of dark matter
in the Milky Way. She has been a participant of the Sloan Digital Sky
Survey and is currently head of participants in LAMOST U.S., a
partnership allowing U.S. astronomers to take part in a survey of more
than 7 million stars by the [27]Large Sky Area Multi-Object Fiber
Spectroscopic Telescope in China (LAMOST).

For more information:

[28]Read a publicly available version of the research article

Watch a [29]20-minute video explaining the findings for the general
public

Watch a [30]50-minute video explaining the findings in greater detail

High-resolution illustrations of the research are [31]available on
Newberg's homepage

Contact: Mary L. Martialay
Phone: (518) 276-2146
E-mail: [32]martim12@rpi.edu
A "rippled" Milky Way may be 50 percent larger than previously
estimated
The density of light detected in the Milky Way reveals a rippling
contour

(... links deleted ...)

Rensselaer is America's oldest technological research university,
offering bachelor's, master's, and doctoral degrees in engineering,
the sciences, information technology and web science, architecture,
management, and the humanities, arts, and social sciences.

Copyright ©2013 Rensselaer Polytechnic Institute (RPI) 110 Eighth
Street, Troy, NY USA 12180 (518) 276-6000 All rights reserved.

Why not change the world?^® is a registered trademark of Rensselaer
Polytechnic Institute. Site design and production by the Rensselaer
Division of Strategic Communications & External Relations and Division
of the Chief Information Officer

References

21. http://news.rpi.edu:8080/users/martim12
22. http://rpi.edu/
23. http://faculty.rpi.edu/node/932
24. http://www.sdss.org/
25. http://science.rpi.edu/
26. http://english.nao.cas.cn/
27. http://www.lamost.org/public/?locale=en
28. http://arxiv.org/abs/1503.00257
29. http://www.youtube.com/watch?v=MO01qDl1np8
30. https://www.youtube.com/watch?v=9nELHo751Y4
31. http://homepages.rpi.edu/~newbeh/
32. mailto:martim12@rpi.edu
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[tt] (IfA) Fastest Star in Our Galaxy Propelled by a Thermonuclear Supernova

[

http://www.ifa.hawaii.edu/info/press-releases/fastest_star/

]

(... links deleted ...)

Fastest Star in Our Galaxy Propelled by a Thermonuclear Supernova

(...)
Maintained by LG

Embargoed until
March 5, 2 p.m. ET
(9 a.m. HST)

Contacts:

Dr. Eugene Magnier
+1 808-956-6317
[90]magnier@ifa.hawaii.edu

Dr. Roy Gal
+1 808-956-6235
cell: +1 301-728-8637
[91]rgal@ifa.hawaii.edu

Ms. Louise Good
Media Contact
+1 808-381-2939
[92]good@ifa.hawaii.edu

High-Resolution Image:

thumbnail

[93]4.5 MbJPEG

See caption above right.

fastest star leaves the Milky Way

Artist's conception of a star (left) being ejected from a galaxy by a
supernova explosion. In reality the supernova would have been faded
away long before the star reached that position. Credit: ESA/Hubble,
NASA.

A team of astronomers, including University of Hawaii at Manoa
astronomer Eugene Magnier, used the 10-meter Keck II and Pan-STARRS1
telescopes in Hawaii to find a star that breaks the galactic speed
record. It travels at about 1,200 kilometers per second (about 2.7
million mph), a speed that will enable the star to escape from our
Milky Way galaxy.

"At that speed, you could travel from Earth to the moon in 5 minutes,"
Magnier commented.

The team showed that unlike the half-dozen other known escaping stars,
this compact star was ejected from an extremely tight binary by a
thermonuclear supernova explosion. These results will be published in
the March 6 issue of the journal Science.

Stars like the sun are bound to our galaxy by its gravity and orbit its
center at relatively moderate velocities, tens to a few hundreds of
kilometers per second. Only a few so-called hypervelocity stars are
known that travel so fast that they are unbound. A close encounter with
the supermassive black hole at the center of the Milky Way is usually
considered the most plausible mechanism for enabling these stars to
escape from the galaxy.

Stephan Geier (European Southern Observatory, Garching, Germany) led
the team that observed the known high-velocity star, US 708, with the
Echellette Spectrograph and Imager on the Keck II telescope to measure
its distance and radial velocity component, that is, how fast it is
moving away from us. By carefully combining position measurements from
digital archives with newer positions measured from images taken during
the Pan-STARRS1 survey, they were also able to derive the tangential
component of the star's velocity, or how fast it is moving
perpendicular to us.

"By observing the sky repeatedly over several years, the Pan-STARRS1
survey, let us make a movie of the motions of the stars in the sky.
That enables us to study the behaviors of extremely rare and weird
stars like US708," Magnier explained.

By putting all the measurements together, they determined the total
velocity of the star is 1,200 kilometers per second, much higher than
the velocities of the other known stars in our galaxy. More
importantly, the trajectory of US 708 allows them to rule out the
Galactic Center, and therefore, its supermassive black hole, as the
possible cause of US 708's extreme velocity.


IFRAME: [94]https://www.youtube.com/embed/kJrHLSld3u4

Animation of the mass-transfer phase to a white dwarf followed by a
double-detonation supernova that leads to the ejection of US 708 from
the galaxy.
Credit: NASA, ESA and P. Ruiz-Lapuente, cut and colored by S. Geier


US 708 has additional peculiar properties that are in marked contrast
to other hypervelocity stars: it is a rapidly rotating, compact helium
star that probably formed as a result of interaction with a close
companion. Helium stars are the remnant of a formerly massive star that
has lost its hydrogen envelope.

Thus, US 708 could have originally been part of an ultracompact binary
system in which it transferred helium to a massive white dwarf
companion, ultimately triggering a thermonuclear explosion known as a
type Ia supernova. As a result of this explosion, the surviving
companion, US 708, was violently ejected from the disrupted binary, and
is now traveling at an extremely high velocity.

These results provide observational evidence that there is a link
between helium stars and thermonuclear supernovae, and are a step
toward understanding the progenitor systems of these mysterious
explosions.

__________________________________________________________________

Founded in 1967, the Institute for Astronomy at the University of
Hawaii at Manoa conducts research into galaxies, cosmology, stars,
planets, and the sun. Its faculty and staff are also involved in
astronomy education, deep space missions, and in the development and
management of the observatories on Haleakala and Maunakea. The
Institute operates facilities on the islands of Oahu, Maui, and Hawaii.

The W. M. Keck Observatory operates the largest, most scientifically
productive telescopes on Earth. The two, 10-meter optical/infrared
telescopes near the summit of Maunakea on the island of Hawaii feature
a suite of advanced instruments including imagers, multi-object
spectrographs, high-resolution spectrographs, integral-field
spectrographs and world-leading laser guide star adaptive optics
systems.

The Pan-STARRS1 Surveys (PS1) have been made possible through
contributions by the Institute for Astronomy, the University of Hawaii,
the Pan-STARRS Project Office, the Max-Planck Society and its
participating institutes, the Max Planck Institute for Astronomy,
Heidelberg and the Max Planck Institute for Extraterrestrial Physics,
Garching, The Johns Hopkins University, Durham University, the
University of Edinburgh, the Queen's University Belfast, the
Harvard-Smithsonian Center for Astrophysics, the Las Cumbres
Observatory Global Telescope Network Incorporated, the National Central
University of Taiwan, the Space Telescope Science Institute, and the
National Aeronautics and Space Administration under Grant No.
NNX08AR22G issued through the Planetary Science Division of the NASA
Science Mission Directorate, the National Science Foundation Grant No.
AST-1238877, the University of Maryland, Eotvos Lorand University
(ELTE), and the Los Alamos National Laboratory.


Copyright 2015 Institute for Astronomy

References

90. mailto:magnier@ifa.hawaii.edu
91. mailto:rgal@ifa.hawaii.edu
92. mailto:good@ifa.hawaii.edu
93. http://www.ifa.hawaii.edu/info/press-releases/fastest_star/us708_sn.jpg
94. https://www.youtube.com/embed/kJrHLSld3u4
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[tt] (Arizona St.Uni.) Researchers discover wealth, power may have played stronger role than 'survival of the fittest'

(A discovery can be observed in everyday life, but genetic bottleneck?
That's not so obvious - TR)

[

https://asunews.asu.edu/20150316-y-chromosome-bottleneck

]

(... links deleted ...)

March 16, 2015
(...)
Researchers discover wealth, power may have played stronger role than 'survival of the fittest'

Posted: March 16, 2015
[56]<
* [57]ancient rock drawings
* [58]genetics infographic

[59]>
ancient rock drawings
Ancient rock drawings (petroglyphs), including one showing a farmer
using oxen. Researchers have discovered that a decrease in genetic
diversity occurred during a time period when when humans in different
parts of the world had become sedentary farmers.
Photo by: Olof Ekström, 2003, Wikimedia Commons
[60]Download image
genetics infographic
The decline in genetic diversity in male lineages is likely the result
of the accumulation of material wealth, while in contrast, female
genetic diversity was on the rise.
Photo by: Sabine Deviche
[61]Download image

Read More

* [62]School of Life Sciences
* [63]College of Liberal Arts & Sciences
* [64]Biodesign Institute
* [65]College of Letters & Sciences

* [66]Office of Knowledge Enterprise Development
* [67]Research Matters

In a study led by scientists from Arizona State University, the
University of Cambridge, University of Tartu and Estonian Biocentre,
researchers discovered a dramatic decline in genetic diversity in male
lineages 4,000 to 8,000 years ago – likely the result of the
accumulation of material wealth, while in contrast, female genetic
diversity was on the rise. This male-specific decline occurred during
the mid- to late-Neolithic period.

"Instead of 'survival of the fittest' in a biological sense, the
accumulation of wealth and power may have increased the reproductive
success of a limited number of 'socially fit' males and their sons,"
said Melissa Wilson Sayres, a leading author and assistant professor
with ASU's School of Life Sciences.

The study was published March 13 in an online issue of the journal
[68]Genome Research.

It is widely recognized among scientists that a major bottleneck, or
decrease in genetic diversity, occurred approximately 50,000 years ago,
when a subset of humans left Africa and migrated across the rest of the
world. Signatures of this bottleneck appear in most genes of
non-African populations, whether they are inherited from both parents
or, as confirmed in this study, only along the father's or mother's
genetic lines.

"Most surprisingly to us, we detected another, male-specific,
bottleneck during a period of global growth. The signal for this
bottleneck dates to a time period 4,000 to 8,000 years ago, when humans
in different parts of the world had become sedentary farmers," said
senior author Toomas Kivisild from the Division of Biological
Anthropology, University of Cambridge.

Researchers studied DNA samples taken from the saliva or blood of 456
males living in seven regions of five continents including Africa, the
Andes, South Asia, near East and Central Asia, Europe and Oceania.
Scientists specifically studied the Y chromosome, which is passed down
through the male lineage, and the mitochondria, which is passed to
offspring by the genetic mother.

After using computer and statistical modeling, they found the two
extreme "bottlenecks" in human genetic history, specifically the second
found only in the male lineage.

The researchers said studying genetic history is important for
understanding underlying levels of genetic variation. Having a high
level of genetic diversity is beneficial to humans for several reasons.
First, when the genes of individuals in a population vary greatly, the
group has a greater chance of thriving and surviving – particularly
against disease. It may also reduce the likelihood of passing along
unfavorable genetic traits, which can weaken a species over time.

According to Monika Karmin, a leading author from University of Tartu,
Estonia, their findings may have implications related to human health.

"We know that some populations are predisposed to certain types of
genetic disorders," said Karmin. "Global population evolution is
important to consider, especially as it relates to medicine."

"When a doctor tries to provide a diagnosis when you are sick, you'll
be asked about your environment, what's going on in your life and your
genetic history based on your family's health," added Wilson Sayres,
who is also with ASU's Biodesign Institute. "If we want to understand
human health on a global scale, we need to know our global genetic
history; that is what we are studying here."

The researchers believe this will be relevant for informing patterns of
genetic diversity across whole human populations, as well as informing
their susceptibility to diseases.

Wilson Sayres said the next step is to continue the research by
gathering a greater number of DNA samples, increasing the diversity of
the samples, and working with anthropologists and sociologists to gain
a broader perspective on the findings.

The research was funded jointly by several sources, with primary
support from the University of Tartu and Estonian Biocentre.
Researchers from 66 institutions around the world participated in this
study.
Sandy Leander, [69]sandra.leander@asu.edu
480-965-9865
School of Life Sciences
*

(... links deleted ...)

Tempe, AZ 85281
Campus mail: 5011 ASU News

References

56. https://asunews.asu.edu/20150316-y-chromosome-bottleneck
57. https://asunews.asu.edu/20150316-y-chromosome-bottleneck
58. https://asunews.asu.edu/20150316-y-chromosome-bottleneck
59. https://asunews.asu.edu/20150316-y-chromosome-bottleneck
60. https://asunews.asu.edu/files/cavedrawings_2.jpg
61. https://asunews.asu.edu/files/ychromosomeinfographic_copy.jpg
62. http://sols.asu.edu/index.php
63. http://clas.asu.edu/
64. http://www.biodesign.asu.edu/
65. https://cls.asu.edu/
66. https://asuresearch.asu.edu/
67. http://researchmatters.asu.edu/
68. http://genome.cshlp.org/content/early/2015/03/13/gr.186684.114.abstract
69. mailto:sandra.leander@asu.edu
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[tt] (NRAO 2015-02) Pockets of Calm Protect Molecules around a Supermassive Black Hole

[

https://public.nrao.edu/news/pressreleases/alma-m77?tmpl=component&print=1

]

[1]Print this page

For Release: February 26, 2015

Pockets of Calm Protect Molecules around a Supermassive Black Hole

Researchers using the Atacama Large Millimeter/submillimeter Array
(ALMA) have discovered regions where certain organic molecules somehow
endure the intense radiation near the supermassive black hole at the
center of galaxy NGC 1068, also known to amateur stargazers as M77.

Such complex carbon-based molecules are thought to be easily
obliterated by the strong X-rays and ultraviolet (UV) photons that
permeate the environment surrounding supermassive black holes. The new
ALMA data indicate, however, that pockets of calm exist even in this
tumultuous region, most likely due to dense areas of dust and gas that
shield molecules from otherwise lethal radiation.

Molecules Reveal Clues to Galactic Environments

Interstellar gas contains a wide variety of molecules, which differ
wildly depending on the environment. For example, high-temperature,
active star forming regions produce different molecules than would be
found in colder interstellar regions. This enables scientists to probe
the temperature and density of certain regions by studying their
chemical composition.

Astronomers have long been studying the molecular signatures around
supermassive black holes: both nearby starburst regions and surrounding
rings of dust and gas known as a circumnuclear disks (CND) that
spiral-in to feed an active black hole. These regions are important for
understanding the evolution of galaxies. However, weak radio emission
from the molecules there often makes observations difficult.

ALMA Observations Trace Molecules

To better understand the complex and energetic environs around a
supermassive black hole, the research team -- led by Shuro Takano at
the National Astronomical Observatory of Japan (NAOJ) and Taku Nakajima
at Nagoya University -- observed the spiral galaxy M77, which is
located about 47 million light-years from Earth in the direction of the
constellation Cetus (the Whale).

This galaxy is known to have an actively feeding central black hole,
which indicates it has a substantial circumnuclear disk. That disk, in
turn, is surrounded by a 3,500 light-year wide starburst ring. To probe
these areas, the research team added ALMA's extreme sensitivity and
high-fidelity imaging capabilities to earlier observations conducted by
the 45-meter radio telescope at the Nobeyama Radio Observatory of the
National Astronomical Observatory of Japan (NAOJ).

The new ALMA observations clearly reveal the distributions of nine
types of molecules in the surrounding disk and starburst ring.

"In this observation, we used only 16 antennas, which are about
one-fourth of the complete number of ALMA antennas, but it was really
surprising that we could get so many molecular distribution maps in
less than two hours. We have never obtained such a quantity of maps in
one observation," said Takano, the leader of the research team.

The results clearly show that the molecular distribution varies
according to the type of molecule. While carbon monoxide (CO) is
distributed mainly in the starburst ring, five types of molecules,
including complex organic molecules such as cyanoacetylene (HC[3]N) and
acetonitrile (CH[3]CN), are concentrated primarily in the CND. In
addition, carbon monosulfide (CS) and methanol (CH[3]OH) are
distributed both in the starburst ring and the CND.

Shielding Complex Organics around a Black Hole

As the supermassive black hole devours the surrounding material, this
disk is heated to such extreme temperatures that it emits intense
X-rays and UV photons. When complex organic molecules are exposed to
these photons, their atomic bonds are broken and the molecules are
destroyed. Astronomers assumed that such regions would therefore be
devoid of such complex organics. The ALMA observations, however, proved
the contrary: Complex organic molecules are abundant in the CND, though
not so in the broader starburst region.

"It was quite unexpected that complex molecules with a large number of
atoms like acetonitrile and cyanoacetylene are concentrated around the
black hole's disk," said Nakajima.

The research team speculates that organic molecules remain intact in
the CND due to the large amount of gas there, which acts as a barrier
for the X-rays and UV photons, while organic molecules cannot survive
the exposure to the strong UV photons in the starburst region where the
gas density is comparatively lower.

The researchers point out that these results are a significant first
step in understanding the structure, temperature, and density of gas
surrounding the active black hole in M77. "We expect that future
observations with wider bandwidth and higher resolution will show us
the whole picture of this region," said Takano.

"ALMA has launched an entirely new era in astrochemistry," said Eric
Herbst of the University of Virginia in Charlottesville and a member of
the research team. "Detecting and tracing molecules throughout the
cosmos enables us to learn so much more about otherwise hidden areas,
like the regions surrounding the black hole in M77."

These results were published by Takano et al. as "Distributions of
molecules in the circumnuclear disk and surrounding starburst ring in
the Seyfert galaxy NGC 1068 observed with ALMA" (in the astronomical
journal Publications of the Astronomical Society of Japan (PASJ),
issued in August 2014) and by Nakajima et al. "A Multi-Transition Study
of Molecules toward NGC 1068 based on High-Resolution Imaging
Observations with ALMA" (in PASJ issued in February 2015).

# # #

Contacts:
Charles Blue, NRAO Public Information Officer
(434) 296-0314; [2]cblue@nrao.edu
Masaaki Hiramatsu, PhD, Public Outreach Officer at NAOJ
+81-422-34-3630; [3]hiramatsu.masaaki@nao.ac.jp

This research was conducted by:
• Shuro TAKANO (NAOJ Nobeyama Radio Observatory/SOKENDAI)
• Taku NAKAJIMA (Solar-Terrestrial Environment Laboratory, Nagoya
University)
• Kotaro KOHNO (Institute of Astronomy/Research Center for the Early
Universe, The University of Tokyo)
• Nanase HARADA (Academia Sinica Institute of Astronomy and
Astrophysics [At the time of writing: Max Planck Institute for Radio
Astronomy])
• Eric HERBST (University of Virginia)
• Yoichi TAMURA (Institute of Astronomy, The University of Tokyo)
• Takuma IZUMI (Institute of Astronomy, The University of Tokyo)
• Akio TANIGUCHI (Institute of Astronomy, The University of Tokyo)
• Tomoka TOSAKI (Joetsu University of Education)

Eric Herbst gratefully acknowledges the support of the National Science
Foundation for his astrochemistry program. He also acknowledges support
from the NASA Exo-biology and Evolutionary Biology program through a
subcontract from Rensselaer Polytechnic Institute.
The Atacama Large Millimeter/submillimeter Array (ALMA), an
international astronomy facility, is a partnership of the European
Organisation for Astronomical Research in the Southern Hemisphere
(ESO), the U.S. National Science Foundation (NSF) and the National
Institutes of Natural Sciences (NINS) of Japan in cooperation with the
Republic of Chile. ALMA is funded by ESO on behalf of its Member
States, by NSF in cooperation with the National Research Council of
Canada (NRC) and the National Science Council of Taiwan (NSC) and by
NINS in cooperation with the Academia Sinica (AS) in Taiwan and the
Korea Astronomy and Space Science Institute (KASI). ALMA construction
and operations are led by ESO on behalf of its Member States; by the
National Radio Astronomy Observatory (NRAO), managed by Associated
Universities, Inc. (AUI), on behalf of North America; and by the
National Astronomical Observatory of Japan (NAOJ) on behalf of East
Asia. The Joint ALMA Observatory (JAO) provides the unified leadership
and management of the construction, commissioning and operation of
ALMA.

NGC1068composite The central part of the galaxy M77, also known as NGC
1068, observed by ALMA and the NASA/ESA Hubble Space Telescope. Yellow:
cyanoacetylene (HC[3]N), Red: carbon monosulfide (CS), Blue: carbon
monoxide (CO), which are observed with ALMA. While HC[3]N is abundant
in the central part of the galaxy (CND), CO is mainly distributed in
the starburst ring. CS is distributed both in the CND and the starburst
ring.

Credit: ALMA(ESO/NAOJ/NRAO), S. Takano et al., NASA/ESA Hubble Space
Telescope and A. van der Hoeven
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References

1. https://public.nrao.edu/news/pressreleases/alma-m77?tmpl=component&print=1
2. mailto:cblue@nrao.edu
3. mailto:hiramatsu.masaaki@nao.ac.jp
4. https://twitter.com/share
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Sunday, March 15, 2015

[tt] (lem-list) Two books on Lem (fwd) (concat)

(Redundant parts edited out - TR)

----- Forwarded message from John Everett Branch Jr <ohmicron271@me.com> -----

Date: Sun, 08 Mar 2015 18:35:12 -0400
From: John Everett Branch Jr <ohmicron271@me.com>
To: LEM List <lem@lists.rpi.edu>
Subject: Two books on Lem

Liverpool University Press has a series called "Liverpool Science
Fiction Texts and Studies," which includes one recently published
collection of essays on Lem and one single-author book planned for
later this year. The web page for the entire series is at

http://www.liverpooluniversitypress.co.uk/index.php?option=com_wrapper&view=wrapper&Itemid=33
<http://www.liverpooluniversitypress.co.uk/index.php?option=com_wrapper&view=wrapper&Itemid=33>

You can find the two titles there. (Oddities of the website kept me
from finding separate URLs for the books.) Peter Swirski is a
co-editor of the collection and the author of the upcoming book.

They're pretty pricey, meaning a library may be the best place to look
if you want to read one.

--John E. Branch Jr.
Vanity Fair: 212-286-6187
cell: 646-789-3103
Twitter: @JEB54
HuffPost: http://www.huffingtonpost.com/john-branch/
blog: http://ifitbenotnow.wordpress.com/


----- End forwarded message -----
----- Forwarded message from Dan Ust <dan_ust@yahoo.com> -----

Date: Mon, 9 Mar 2015 09:06:27 -0700
From: Dan Ust <dan_ust@yahoo.com>
To: S-Lem <lem-l@lists.rpi.edu>
Subject: Re: Two books on Lem

So tempting though!

The links for the two books are:

http://www.liverpooluniversitypress.co.uk/index.php?option=com_wrapper&view=wrapper&Itemid=11&AS1=Lemography

and

http://www.liverpooluniversitypress.co.uk/index.php?option=com_wrapper&view=wrapper&Itemid=11&AS1=Stanislaw+Lem%3A+Philosopher+of+the+Future

Regards,

Dan

(...)
----- End forwarded message -----
----- Forwarded message from Ricardo Tovar <ricardo2001@gmail.com> -----

Date: Mon, 9 Mar 2015 11:18:13 -0600
From: Ricardo Tovar <ricardo2001@gmail.com>
To: lem-l@lists.rpi.edu
Subject: Re: Two books on Lem

Peter Swirski's books in Amazon:
http://www.amazon.com/Peter-Swirski/e/B001HPPK8O/ref=sr_ntt_srch_lnk_1?qid=1425921429&sr=8-1

(...)
----- End forwarded message -----
----- Forwarded message from Ricardo Tovar <ricardo2001@gmail.com> -----

Date: Mon, 9 Mar 2015 11:28:35 -0600
From: Ricardo Tovar <ricardo2001@gmail.com>
To: lem-l@lists.rpi.edu
Subject: Re: Two books on Lem

The links to the books on Lem:

http://www.amazon.com/Stanislaw-Lem-Selected-Letters-Liverpool/dp/1781380171/ref=la_B001HPPK8O_1_2?s=books&ie=UTF8&qid=1425921437&sr=1-2


http://www.amazon.com/Lemography-Stanislaw-Liverpool-Science-Fiction/dp/1781381208/ref=la_B001HPPK8O_1_3?s=books&ie=UTF8&qid=1425921437&sr=1-3

Also from Oxford University Press:

https://global.oup.com/academic/product/stanislaw-lem-philosopher-of-the-future-9781781381861?cc=mx&lang=en&


Also available for awhile:

http://www.amazon.com/Art-Science-Stanislaw-Lem/dp/0773530479/ref=la_B001HPPK8O_1_9?s=books&ie=UTF8&qid=1425921437&sr=1-9

http://www.amazon.com/Stanislaw-Lem-Reader-Rethinking-Theory/dp/081011495X/ref=la_B001HPPK8O_1_5?s=books&ie=UTF8&qid=1425921437&sr=1-5

http://www.amazon.com/Between-Literature-Science-Explorations-Aesthetics/dp/0853239061/ref=la_B001HPPK8O_1_8?s=books&ie=UTF8&qid=1425921437&sr=1-8


(Sorry for the extra message)

(...)
----- End forwarded message -----
----- Forwarded message from Wiktor Jazniewicz <lemolog@gmail.com> -----

Date: Mon, 9 Mar 2015 21:48:37 +0300
From: Wiktor Jazniewicz <lemolog@gmail.com>
Cc: lem-l <lem-l@lists.rpi.edu>
Subject: Re: Two books on Lem

New book on Stanislaw Lem in Russian:
http://urss.ru/cgi-bin/db.pl?lang=en&blang=ru&page=Book&id=191598

(...)
----- End forwarded message -----
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