суббота, 15 декабря 2018 г.

Dancing Genes Our genes – the snippets of DNA that make us who…


Dancing Genes


Our genes – the snippets of DNA that make us who we are – are wrapped up in spools of chromatin floating in the nucleus of our cells. A bit like a conga line, loops and bends in the chromatin bring distant genes closer together. Here a technique called displacement correlation spectroscopy picks out regions of chromatin moving in the same direction in rainbow colours. Looking at ‘slow’ movements over 2.5 seconds (top middle) or 10 seconds (top right) reveals that DNA is often ‘dancing’ in the same direction, shown as similarly-coloured areas in the nucleus. These patterns disappear when looking for faster movements (top left) suggesting a graceful sway rather than a frantic mosh. Depriving the dancing genes of cellular energy ATP, disrupts the party (bottom row) – giving further clues about these new ways in which genes may come together in health and disease.


Written by John Ankers



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2018 December 15 Geminids and Friends Image Credit &…


2018 December 15


Geminids and Friends
Image Credit & Copyright: Daniel López (El Cielo de Canarias)


Explanation: From a radiant in the constellation of the Twins, the annual Geminid meteor shower rained down on our fair planet this week. This beautiful skyscape collects about 70 of Gemini’s lovely shooting stars in a digital composition made from multiple exposures. The exposures were taken over a six hour period near the shower’s peak. The camera was tracking the dark predawn sky on December 14 from Teide National Park on the Canary Island Tenerife. Though Gemini lies off the top left of the frame, the Milky Way sweeps through the starry background. Sharing the sky below and left of center are recognizable stars and nebulosities of Orion. A yellowish Aldebaran and the Hyades are toward the right along with the Pleiades star cluster. Also a welcome visitor to this night sky, the faint green coma of Comet 46P Wirtanen, closest to Earth this weekend, lies below the Pleiades stars. Dust swept up from the orbit of active asteroid 3200 Phaethon, Gemini’s meteors enter Earth’s atmosphere traveling at about 35 kilometers per second.


∞ Source: apod.nasa.gov/apod/ap181215.html


Fluorite | #Geology #GeologyPage #Mineral Locality: Grimsel,…


Fluorite | #Geology #GeologyPage #Mineral


Locality: Grimsel, Berner Oberland, Switzerland


Size: 6 x 5.1 x 3.2


Photo Copyright © Saphira Minerals


Geology Page

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https://www.instagram.com/p/BrZgbiJFyvR/?utm_source=ig_tumblr_share&igshid=1o0kp59z5guk1


Azurite | #Geology #GeologyPage #Mineral Locality: La Sal, San…


Azurite | #Geology #GeologyPage #Mineral


Locality: La Sal, San Juan Co., Utah, USA


Size: 5.1 x 4.4 x 2.3


Photo Copyright © Saphira Minerals


Geology Page

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https://www.instagram.com/p/BrZg03Tlq-q/?utm_source=ig_tumblr_share&igshid=1o2mxsv2a1i9k


Niagara Falls | #Geology #GeologyPage #NiagaraFalls…


Niagara Falls | #Geology #GeologyPage #NiagaraFalls #USA


Niagara Falls is the collective name for three waterfalls that straddle the international border between Canada and the United States; more specifically, between the province of Ontario and the state of New York. They form the southern end of the Niagara Gorge.


Niagara Falls were formed when glaciers receded at the end of the Wisconsin glaciation (the last ice age), and water from the newly formed Great Lakes carved a path through the Niagara Escarpment en route to the Atlantic Ocean.


Geology Page

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Some German guy once said…

If you repeat a lie often enough, people will believe it, and you will even come to believe it yourself.
On a totally unrelated note, the Max-Planck-Institut für Menschheitsgeschichte (aka MPI-SHH) is apparently still claiming that its southern Proto-Indo-European (PIE) homeland theory has been corroborated by archaeogenetic data. For instance, check out the Youtube clip here.
Below is a screen cap from the clip showing a map that summarizes what the folks at the MPI-SHH are thinking in regards to the PIE question and the early spread of Indo-European languages.



Unfortunately, this map doesn’t make any sense. Why? Here it is, in point form, as simply as I can put it:



1) There’s no evidence in any archaeogenetic data of migrations during the Neolithic from what is now Armenia and surrounds to Western Europe, the Pontic-Casian steppe, or, indeed, South Asia, that may have brought Indo-European languages to these regions. In fact, the currently available ancient DNA data outright contradict this scenario, because:



A) the Corded Ware and Yamnaya archeological cultures, which are generally considered to have been the main vectors for the spread of Indo-European languages from the Pontic-Caspian steppe into Northern and Central Europe, weren’t founded by migrants from south of the Caucasus (see here)
B) the Neolithic farmer populations that migrated deep into Europe and eventually colonized the western third of the continent were especially poor in Caucasus-related ancestry, and, realistically, could only have come from well to the west of the Caucasus
C) conversely, the Neolithic farmer populations that moved deep into South Asia are inferred to have been especially poor in Anatolian-related ancestry, and, realistically, could only have come from well to the east of the Caucasus (see here)
D) Caucasus-related ancestry, of basically the same type that is being associated by the MPI-SHH with the PIE expansion, did move into Western Europe across the Mediterranean, but this happened during the Bronze Age and it impacted the island of Sardinia, which is generally regarded to have been inhabited by non-Indo-European speakers until the Romans got there (see here). Oops.



2) There’s now overwhelming evidence both in ancient and modern DNA data that Eastern Europeans and Indians, especially Indo-European-speaking Indians, share significant ancestry, in particular paternal ancestry, from essentially the same Bronze Age populations living on the Pontic-Caspian steppe (not south of it!), and this is the only obvious, important genetic link between these two linguistically closely related but geographically far flung groups within the last…tens of thousands of years?
3) Ancient samples from Mycenaean, and thus Indo-European-speaking, Greece and parts of Iron Age Iberia where Indo-European languages were attested at the time also show steppe-derived ancestry, and, in fact, of a very similar character to that shared by Eastern Europeans and Indo-European-speaking Indians (see here and here, respectively).
4) However, Pre-Mycenaean and likely non-Indo-European-speaking Minoan samples, also from the Aegean region, don’t show any steppe ancestry, but they do show Caucasus-related ancestry, of basically the same type that is being associated by the MPI-SHH with the PIE expansion. Oops again.


Thus, at the very least, these undeniable and, surely, easy to grasp facts that I’ve just set out should give pause to anyone who still claims that the Near East, rather than the Pontic-Caspian steppe, was the main staging point for the expansions of the early Indo-Europeans. Indeed, methinks it’s now time to admit by all those concerned that the most likely homeland of all surviving branches of the Indo-European language family, and thus of late PIE, was the Pontic-Caspian steppe.
Honestly, I’m shocked, and even disturbed, that none of this seems to have filtered down to the linguists at the MPI-SHH, especially since the MPI-SHH is also heavily populated by scientists who apparently know a thing or two about archaeogenetics.
Now, it’s true that archaeogenetic data are yet to reveal an unambiguous signal of steppe ancestry in samples from Hittite era Anatolia (five have been published to date), which may perhaps suggest that the people who brought Hittite and the other Anatolian languages to Anatolia didn’t come from the steppe. Of course, Anatolian languages represent the earliest, most basal split in the Indo-European phylogeny, and thus aren’t part of the late PIE node. So if the Indo-European-speaking ancestors of the Hittites didn’t come from the steppe, then it stands to reason that early PIE didn’t either.
But this isn’t relevant to my criticism of the MPI-SHH, because even if early PIE didn’t come from the steppe, then like I said, there’s very solid evidence now that late PIE did, and the problem is that the linguists and geneticists at the MPI-SHH appear to be missing this fact, or they’re unwilling to accept it.
Moreover, please note that I’m not arguing that the linguists at the MPI-SHH are getting things wrong when it comes to actual linguistics. For all I know, their approach in this area might well be perfect, and perhaps it has indeed revealed insights that have been missed by others using more traditional methods?
For instance, it’s possible that the phylogenetic relationships of Indo-European languages as shown in the screen cap below (from the video linked to above) reflects the truth better than anything else offered to date. I don’t know, so I’m keeping an open mind about that. But admittedly, I’m skeptical, considering how lousy the MPI-SHH’s interpretation of the archaeogenetic data has been to date in this context, even at the most basic level.



See also…
Late PIE ground zero now obvious; location of PIE homeland still uncertain, but…

Source


NASA Seeks US Partners to Develop Reusable Systems to Land Astronauts on Moon


NASA logo.


Dec. 14, 2018


As the next major step to return astronauts to the Moon under Space Policy Directive-1, NASA announced plans on Dec. 13 to work with American companies to design and develop new reusable systems for astronauts to land on the lunar surface. The agency is planning to test new human-class landers on the Moon beginning in 2024, with the goal of sending crew to the surface in 2028.



Image above: Artist’s concept of undocking Human Landing System from Lunar Orbital Outpost. Image Credit: NASA.


Through upcoming multi-phased lunar exploration partnerships, NASA will ask American companies to study the best approach to landing astronauts on the Moon and start the development as quickly as possible with current and future anticipated technologies.


“Building on our model in low-Earth orbit, we’ll expand our partnerships with industry and other nations to explore the Moon and advance our missions to farther destinations such as Mars, with America leading the way,” said NASA Administrator Jim Bridenstine. “When we send astronauts to the surface of the Moon in the next decade, it will be in a sustainable fashion.”


The agency’s leading approach to sending humans to the Moon is using a system of three separate elements that will provide transfer, landing, and safe return. A key aspect of this proposed approach is to use the Gateway for roundtrip journeys to and from the surface of the Moon.


Using the Gateway to land astronauts on the Moon allows the first building blocks for fully reusable lunar landers. Initially NASA expects two of the lander elements to be reusable and refueled by cargo ships carrying fuel from Earth to the Gateway. The agency is also working on technologies to make rocket propellants using water ice and regolith from the Moon.  Once the ability to harness resources from the Moon for propellant becomes viable, NASA plans to refuel these elements with the Moon’s own resources. This process, known as in-situ resource utilization or ISRU, will make the third element also refuelable and reusable.


NASA expects to publish a formal request for proposals to an appendix of the second Next Space Technologies for Exploration Partnerships (NextSTEP-2) Broad Agency Announcement (BAA) in early January.


According to the synopsis, NASA will fund industry-led development and flight demonstrations of lunar landers built for astronauts by supporting critical studies and risk reduction activities to advance technology requirements, tailor applicable standards, develop technology, and perform initial demonstrations by landing on the Moon.



Image above: Artist’s concept of Human Landing System on the lunar surface with astronaut nearby. Image Credit: NASA.


When NASA again sends humans to the Moon, the surface will be buzzing with new research and robotic activity, and there will be more opportunities for discovery than ever before. Private sector innovation is key to these NASA missions, and the NextSTEP public-private partnership model is advancing capabilities for human spaceflight while stimulating commercial activities in space.


The President’s direction from Space Policy Directive-1 galvanizes NASA’s return to the Moon and builds on progress on the Space Launch System rocket and Orion spacecraft, efforts with commercial and international partners, and knowledge gained from current robotic presence at the Moon and Mars.


For more information about NASA’s Moon to Mars exploration plans, visit:


https://www.nasa.gov/moontomars


Related links:


Space Policy Directive-1: https://www.nasa.gov/press-release/new-space-policy-directive-calls-for-human-expansion-across-solar-system


Landing astronauts on the Moon: https://www.fbo.gov/notices/49ada55b3e532f7cb2cfe04b126f0ee0


ISRU: https://www.nasa.gov/isru


Gateway: https://www.nasa.gov/feature/questions-nasas-new-spaceship


Cargo ships carrying fuel: https://www.nasa.gov/feature/nasa-seeks-information-for-gateway-cargo-delivery-services


Formal request for proposals: https://www.nasa.gov/nextstep/humanlander


Next Space Technologies for Exploration Partnerships (NextSTEP-2): http://www.nasa.gov/nextstep


Images (mentioned), Text, Credits: NASA/Shanessa Jackson.


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Chang’e-4 Probe Enters Lunar Orbit


CLEP – China Lunar Exploration Program logo.


14 December 2018


China’s Chang’e-4 probe decelerated and entered the lunar orbit Wednesday, completing a vital step on its way to make the first-ever soft landing on the far side of the moon, the China National Space Administration (CNSA) announced.



Chang’e-4 probe reach the Moon

After flying about 110 hours from earth, an engine on the probe was ignited when it was 129 km above the surface of the moon, in line with instructions sent from a control center in Beijing at 4:39 p.m., and then the probe slowed and entered an elliptical lunar orbit with the perilune at about 100 km at 4:45 p.m., said CNSA.


The probe, including a lander and a rover, was launched by a Long March-3B carrier rocket last Saturday from the Xichang Satellite Launch Center in southwest China’s Sichuan Province, opening a new chapter in lunar exploration.


As the rocket was able to send the probe into orbit precisely as planned, the control center only adjusted the probe’s orbit once on Sunday and also canceled two pre-planned orbit trimmings before the near-moon deceleration, CNSA said.



Chang’e-4 Mission to the Moon

Next, the control center will adjust the probe’s orbit around the moon and test the communication link between the probe and the relay satellite “Queqiao,” which is operating in the halo orbit around the second Lagrangian (L2) point of the earth-moon system.


Afterward, the control center will choose a proper time to land the probe on the far side of the moon, according to CNSA.


CASC Press Release: http://english.spacechina.com/n16421/n17212/c2002838/content.html


For more information about China Aerospace Science and Technology Corporation (CASC), visit: http://english.spacechina.com/n16421/index.html


For more information about China National Sapce Administration (CNSA): http://www.cnsa.gov.cn/


Images, Text, Credits: CASC/CNSA/China Space News.


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Cosmic Fountain Powered by Giant Black Hole


NASA – Chandra X-ray Observatory patch.


Dec. 14, 2018



Image Credits: X-ray: NASA/CXC/SAO/G. Tremblay et al; Radio:ALMA: ESO/NAOJ/NRAO/G.Tremblay et al, NRAO/AUI/NSF/B.Saxton; Optical: ESO/VLT.


Before electrical power became available, water fountains worked by relying on gravity to channel water from a higher elevation to a lower one. This water could then be redirected to shoot out of the fountain and create a centerpiece for people to admire.


In space, awesome gaseous fountains have been discovered in the centers of galaxy clusters. One such fountain is in the cluster Abell 2597. There, vast amounts of gas fall toward a supermassive black hole, where a combination of gravitational and electromagnetic forces sprays most of the gas away from the black hole in an ongoing cycle lasting tens of millions of years.


Scientists used data from the Atacama Large Millimeter/submillimeter Array (ALMA), the Multi-Unit Spectroscopic Explorer (MUSE) on ESO’s Very Large Telescope (VLT) and NASA’s Chandra X-ray Observatory to find the first clear evidence for the simultaneous inward and outward flow of gas being driven by a supermassive black hole.


Cold gas falls toward the central black hole, like water entering the pump of a fountain. Some of this infalling gas (seen in the image as ALMA data in yellow) eventually reaches the vicinity of the black hole, where the black hole’s gravity causes the gas to swirl around with ever-increasing speeds, and the gas is heated to temperatures of millions of degrees. This swirling motion also creates strong electromagnetic forces that launch high-velocity jets of particles that shoot out of the galaxy.


These jets push away huge amounts of hot gas detected by Chandra (purple) surrounding the black hole, creating enormous cavities that expand away from the center of the cluster. The expanding cavities also lift up clumps of warm and cold gas and carry them away from the black hole, as observed in the MUSE/VLT data (red).



Chandra X-ray Observatory. Animation Credit: NASA/CXC

Eventually this gas slows down and the gravitational pull of material in the center of the galaxy causes the gas to rain back in on the black hole, repeating the entire process.


A substantial fraction of the three billion solar masses of gas are pumped out by this fountain and form a filamentary nebula — or cosmic “spray” — that spans the innermost 100,000 light years of the galaxy.


These observations agree with predictions of models describing how matter falling towards black holes can generate powerful jets. Galaxy clusters like Abell 2597, containing thousands of galaxies, hot gas, and dark matter, are some of the largest structures in the entire Universe. Abell 2597 is located about 1.1 billion light years from Earth.


A paper by Grant Tremblay (Harvard-Smithsonian Center for Astrophysics) et al. describing these results appeared in the September 18, 2018 issue of The Astrophysical Journal (https://arxiv.org/abs/1808.00473). NASA’s Marshall Space Flight Center in Huntsville, Alabama, manages the Chandra program for NASA’s Science Mission Directorate in Washington. The Smithsonian Astrophysical Observatory in Cambridge, Massachusetts, controls Chandra’s science and flight operations.


Read more from NASA’s Chandra X-ray Observatory: http://chandra.cfa.harvard.edu/photo/2018/a2597/


For more Chandra images, multimedia and related materials, visit: http://www.nasa.gov/chandra


Image (mentioned), Animation (mentioned), Text, Credits: NASA/Lee Mohon.


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See a Passing Comet This Sunday


Asteroid Watch logo.


Dec. 14, 2018



Image above: This 120 second image of the comet was taken Dec. 2 by an iTelescope 50 mm refractor located at an observatory near Mayhill, New Mexico. The streak below the comet was produced by a rocket body (upper stage) passing through the telescope’s field of view during the exposure. Image Credit: NASA.


On Sunday, Dec. 16, the comet known as 46P/Wirtanen will make one of the 10 closest comet flybys of Earth in 70 years, and you may even be able to see it without a telescope.


Although the approach will be a distant 7.1 million miles (11.4 million kilometers, or 30 lunar distances) from Earth, it’s still a fairly rare opportunity. “This will be the closest comet Wirtanen has come to Earth for centuries and the closest it will come to Earth for centuries,” said Paul Chodas, manager of the Center for Near-Earth Object Studies at NASA’s Jet Propulsion Laboratory in Pasadena, California. What’s more, Chodas said, “This could be one of the brightest comets in years, offering astronomers an important opportunity to study a comet up close with ground-based telescopes, both optical and radar.”


Comet Wirtanen has already been visible in larger amateur telescopes, and while the brightness of comets is notoriously difficult to predict, there is the possibility that during its close approach comet Wirtanen could be visible with binoculars or to the naked eye.



Comet. Animation Credit: NASA

Astronomer Carl Wirtanen discovered the comet in 1948 at Lick Observatory on Mt. Hamilton in Santa Clara County, California. With a width of 0.7 miles (1.1 kilometers), 46P/Wirtanen orbits the Sun fairly quickly for a comet — once every 5.4 years — making it a short-period comet. (Long-period comets, on the other hand, have orbital periods greater than 200 years.) At the time of closest approach, the comet will appear to be located in the constellation Taurus close to the Pleiades.


An observation campaign is underway to take advantage of the close approach for detailed scientific study of the properties of this “hyperactive” comet, which emits more water than expected, given its relatively small nucleus. The campaign, led by the University of Maryland, has worldwide participation across the professional and amateur astronomical communities. NASA-sponsored ground, air and space-based observatories getting in on the action include NASA’s Goldstone Solar System Radar in California; the NASA Infrared Telescope Facility on Maunakea, Hawaii; the Hubble, Chandra, Swift and Spitzer space telescopes; and an airborne observatory known as the Stratospheric Observatory for Infrared Astronomy (SOFIA). The comet will even pass through the observing field of the Transiting Exoplanet Survey Satellite (TESS).


The Comet Wirtanen Observing Campaign website is: http://wirtanen.astro.umd.edu


Amateur imagery is available on multiple websites, including:


http://aop.astro.umd.edu/gallery/Wirtanen/46P_ccd.shtml


http://spaceweathergallery.com/comet_gallery.html


https://earthsky.org/space/46p-wirtanen-possibly-visible-to-eye-dec-2018


A NASA ScienceCast on Comet Wirtanen is available at:


https://science.nasa.gov/science-news/news-articles/you-light-up-our-night


JPL hosts the Center for Near-Earth Object Studies (CNEOS) for NASA’s Near-Earth Object Observations Program, an element of the Planetary Defense Coordination Office within the agency’s Science Mission Directorate. Along with the resources NASA puts into understanding asteroids and comets, the Planetary Defense Coordination Office partners with other U.S. government agencies, university-based astronomers and space science institutes across the country. It also collaborates with international space agencies and institutions that are working to track and better understand these smaller objects of the solar system. In addition, NASA values the work of numerous highly skilled amateur astronomers, whose accurate observational data help improve comet and asteroid orbits after discovery.


More information about CNEOS, asteroids and near-Earth objects can be found at:


https://cneos.jpl.nasa.gov


https://www.jpl.nasa.gov/asteroidwatch


For more information about NASA’s Planetary Defense Coordination Office, visit:


https://www.nasa.gov/planetarydefense


NASA Infrared Telescope Facility: http://irtfweb.ifa.hawaii.edu/


Image (mentioned), Animation (mentioned), Text, Credits: NASA/Dwayne Brown/JoAnna Wendel/Tony Greicius/JPL/DC Agle​.


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The epoch of planet formation, times twenty

Astronomers have cataloged nearly 4,000 exoplanets in orbit around distant stars. Though the discovery of these newfound worlds has taught us much, there is still a great deal we do not know about the birth of planets and the precise cosmic recipes that spawn the wide array of planetary bodies we have already uncovered, including so-called hot Jupiters, massive rocky worlds, icy dwarf planets, and — hopefully someday soon — distant analogs of Earth.











The epoch of planet formation, times twenty
An international team of astronomers used the powerful ALMA telescope to discover that in other parts of the Milky
Way Galaxy (seen here) there is potentially a large population of young planets — similar in mass to Neptune
or Jupiter — at wide-orbit that are not detectable by other current planet searching techniques
[Credit: NRAO/AUI/NSF, Jeff Hellerman]

To help answer these and other intriguing questions, a team of astronomers has conducted ALMA’s first large-scale, high-resolution survey of protoplanetary disks, the belts of dust and gas around young stars.


Known as the Disk Substructures at High Angular Resolution Project (DSHARP), this “Large Program” of the Atacama Large Millimeter/submillimeter Array (ALMA) has yielded stunning, high-resolution images of 20 nearby protoplanetary disks and given astronomers new insights into the variety of features they contain and the speed with which planets can emerge.


The results of this survey will appear in a special focus issue of the Astrophysical Journal Letters.


According to the researchers, the most compelling interpretation of these observations is that large planets, likely similar in size and composition to Neptune or Saturn, form quickly, much faster than current theory would allow. Such planets also tend to form in the outer reaches of their solar systems at tremendous distances from their host stars.











The epoch of planet formation, times twenty
ALMA’s high-resolution images of nearby protoplanetary disks, which are results of the Disk Substructures
 at High Angular Resolution Project (DSHARP) [Credit: ALMA (ESO/NAOJ/NRAO),
S. Andrews et al.; NRAO/AUI/NSF, S. Dagnello]

Such precocious formation could also help explain how rocky, Earth-size worlds are able to evolve and grow, surviving their presumed self-destructive adolescence.


“The goal of this months-long observing campaign was to search for structural commonalities and differences in protoplanetary disks. ALMA’s remarkably sharp vision has revealed previously unseen structures and unexpectedly complex patterns,” said Sean Andrews, an astronomer at the Harvard-Smithsonian Center for Astrophysics (CfA) and a leader of the ALMA observing campaign, along with Andrea Isella of Rice University, Laura Pérez of the University of Chile, and Cornelis Dullemond of Heidelberg University. “We are seeing distinct details around a wide assortment of young stars of various masses. The most compelling interpretation of these highly diverse, small-scale features is that there are unseen planets interacting with the disk material.”


The leading models for planet formation hold that planets are born by the gradual accumulation of dust and gas inside a protoplanetary disk, beginning with grains of icy dust that coalesce to form larger and larger rocks, until asteroids, planetesimals, and planets emerge. This hierarchical process should take many millions of years to unfold, suggesting that its impact on protoplanetary disks would be most prevalent in older, more mature systems. Mounting evidence, however, indicates that is not always the case.


ALMA’s early observations of young protoplanetary disks, some only about one million years old, reveal surprisingly well-defined structures, including prominent rings and gaps, which appear to be the hallmarks of planets. Astronomers were initially cautious to ascribe these features to the actions of planets since other natural process could be at play.











The epoch of planet formation, times twenty
Four of the twenty disks that comprise ALMA’s highest resolution survey of nearby protoplanetary disks. – AS 209 is a star
hosting a disk that is 1 million years old and located about 400 light-years from Earth. The ALMA image shows a tightly
packed series of dusty rings in its inner disk and two additional thin bands of dust very far from the central star. – HD
143006 is about 5 million years old and resides 540 light-years from Earth. This star hosts a disk that shows wide gaps
between dusty lanes that demarcate the inner and outer portions of the disk. A dense arc-shaped region, possibly heralding
a concentration of material where comets or other icy bodies are forming, can be seen on the lower left portion of the outer
ring. – ALMA reveals sweeping spiral arms in the dust disk orbiting IM Lup, a young star located about 515 light-years from
 Earth. These patterns may be the result of an unseen planetary companion perturbing the disk, or a global instability in the
disk structure similar to those seen in spiral galaxies like the Milky Way. – AS 205 is a multiple star system, with each
 star sporting its own dusty disk. Since most stars in the Milky Way are multiples, this observation provides clues
to the potential for planets in such systems. This system is located about 420 light-years from Earth
[Credit: ALMA (ESO/NAOJ/NRAO) S. Andrews et al.; NRAO/AUI/NSF, S. Dagnello]

“It was surprising to see possible signatures of planet formation in the very first high-resolution images of young disks. It was important to find out whether these were anomalies or if those signatures were common in disks,” said Jane Huang, a graduate student at CfA and a member of the research team.


Since the initial sample of disks that astronomers could study was so small, however, it was impossible to draw any overarching conclusions. It could have been that astronomers were observing atypical systems. More observations on a variety of protoplanetary disks were needed to determine the most likely causes of the features they were seeing.


The DSHARP campaign was designed to do precisely that by studying the relatively small-scale distribution of dust particles around 20 nearby protoplanetary disks. These dust particles naturally glow in millimeter-wavelength light, enabling ALMA to precisely map the density distribution of small, solid particles around young stars.


Depending on the star’s distance from Earth, ALMA was able to distinguish features as small as a few Astronomical Units. (An Astronomical Unit is the average distance of the Earth to the Sun — about 150 million kilometers, which is a useful scale for measuring distances on the scale of star systems). Using these observations, the researchers were able to image an entire population of nearby protoplanetary disks and study their AU-scale features.



The planet excites spiral waves in the disk and later opens gaps. The leftmost panel is the gas distribution in the simulation.


 The middle two panels show the spatial distribution of dust particles in the simulation (small dust at the top panel 


and big dust at the bottom panel). The right panel shows the final synthetic observation that is generated based 


on numerical simulations. The synthetic images are compared with real observations directly 


[Credit: University of Nevada, Las Vegas]


The researchers found that many substructures — concentric gaps, narrow rings — are common to nearly all the disks, while large-scale spiral patterns and arc-like features are also present in some of the cases. Also, the disks and gaps are present at a wide range of distances from their host stars, from a few AU to more than 100 AU, which is more than three times the distance of Neptune from our Sun.


These features, which could be the imprint of large planets, may explain how rocky Earth-size planets are able to form and grow. For decades, astronomers have puzzled over a major hurdle in planet-formation theory: Once dusty bodies grow to a certain size — about one centimeter in diameter — the dynamics of a smooth protoplanetary disk would induce them to fall in on their host star, never acquiring the mass necessary to form planets like Mars, Venus, and Earth.


The dense rings of dust we now see with ALMA would produce a safe haven for rocky worlds to fully mature. Their higher densities and the concentration of dust particles would create perturbations in the disk, forming zones where planetesimals would have more time to grow into fully fledged planets.


“When ALMA truly revealed its capabilities with its iconic image of HL Tau, we had to wonder if that was an outlier since the disk was comparatively massive and young,” noted Pérez. “These latest observations show that, though striking, HL Tau is far from unusual and may actually represent the normal evolution of planets around young stars.”


Author: Charles Blue | Source: National Radio Astronomy Observatory [December 12, 2018]




TANN



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Record levels of mercury released by thawing permafrost in Canadian Arctic

Permafrost thaw slumps in the western Canadian Arctic are releasing record amounts of mercury into waterways, according to new research by University of Alberta ecologists.











Record levels of mercury released by thawing permafrost in Canadian Arctic
Methyl mercury is being released into environments such as this one, on the Peel Plateau
in the Northwest Territories, Canada [Credit: Scott Zolkos]

Mercury is a naturally occuring contaminant that is toxic to humans and other animals in large quantities as it accumulates in organisms and food webs. Sediments in permafrost are estimated to store more mercury than Earth’s oceans, atmosphere, and soil combined. And, as climate change causes permafrost to thaw, the mercury stored in permafrost becomes available for release into the surrounding environment.


“Concentrations of mercury were elevated for at least 2.8 kilometres downstream of thaw slumps,” says Kyra St. Pierre, Vanier Scholar PhD student, who co-led the study with fellow graduate students Scott Zolkos and Sarah Shakil in the Department of Biological Sciences. “This suggests that some mercury from thaw slumps may be transported for many kilometres through downstream ecosystems, and into larger waterways.”


The issue is exacerbated by rising temperatures and increasing precipitation in the Canadian Arctic due to climate change.


“Climate change is inducing widespread permafrost thaw,” explained St. Pierre, who conducted the study under the supervision of Assistant Professor Suzanne Tank, and Professor Vincent St. Louis . “In regions where this results in thaw slumping, this may release a substantial amount of mercury into freshwater ecosystems across the Arctic.”


However, because the mercury is locked within sediments, the scientists are unsure as to whether this mercury could be consumed by organisms in the area and whether this mercury poses any threat to the security of northern food webs.


These results highlight the need for further research on mercury cycling in regions experiencing active permafrost thaw, as well as studies examining if and how this mercury might enter food webs in surrounding ecosystems.


The research was conducted in partnership between the University of Alberta and the Government of the Northwest Territories in response to Northwest Territories’ community interests in the downstream effects of permafrost thaw.


The paper was published in Environmental Science & Technology.


Source: University of Alberta [December 12, 2018]



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Chickens to be marker of Anthropocene

Modern meat chickens are a defining feature of the Anthropocene according to new research by Dr Carys Bennett and colleagues from the University of Leicester in conjunction with Nottingham Trent University, the University of Nottingham and North West University, South Africa.











Chickens to be marker of Anthropocene
Consumption of chickens signals new geological epoch according to new research
[Credit: University of Leicester]

The Anthropocene is the proposed new geological epoch that marks when human impacts on many of the Earth’s geological processes became overwhelmingly evident.


This new research suggests that the Anthropocene will be defined by the breeding and consumption of modern broiler chickens and associated future archaeological and geological deposits.


Dr Bennett, Honorary Fellow at the University of Leicester said: “As the most numerous terrestrial vertebrate species on the planet, with a biology shaped by humans, modern chickens are a symbol of our changed biosphere.”


Modern broiler chickens are identifiable from their ancestors because of their changed biology, and are the kind of data palaeontologists recognise when looking for evidence of biological changes in the environment.


Co-author Professor Mark Williams, Professor of Palaeobiology, University of Leicester said: “These chickens are an artificially evolved new ‘morphospecies’, the kind of thing palaeontologists recognise, that reflect a biosphere unrecognisable from its pre-human state and now dominated by human consumption and resource use.”


The research involved comparing standard supermarket chickens, of which there are now approximately 23 billion in the world at any one time, with the bones of their ancestors dating back to Roman times.


The skeleton, bone chemistry and genetics of broiler chickens, which only survive their six-week lifespan due to the highly technologically-controlled conditions of modern farms, are radically different to their ancestors.


Co-author Dr Alison Foster, former Post-doctoral Research Assistant, University of Leicester, said: “Since domestication there have been many strange and beautiful chicken breeds, but the broiler is perhaps the most extreme form of all.


“The body shape, bone chemistry and genetics of the modern meat chicken is unrecognisable from wild ancestors and anything we see in the archaeological record.”


The body shape of these chickens has changed significantly as a result of their selective breeding over the last 70 years during which time there has been a dramatic growth in the demand for low-fat protein.


The reason why the bone chemistry of these chickens has changed so much is largely a result of the globalisation of food distribution and their associated diet.


Co-author Dr Ben Coles, Lecturer in Human Geography, University of Leicester, who researches the social and economic drivers behind this phenomenon, said: “The food they eat includes soya, maize, wheat, and fish, which likely travelled from the other side of the globe and is embedded in a globalised food system both associated with agri-business and implicated in its effects.”


This diet is very different to the traditional backyard hen that would have been fed on local kitchen scraps. In evolutionary terms, changes in the biology of these modern broiler chickens has happened extremely quickly.


Professor Jan Zalasiewicz, Professor of Palaeobiology, University of Leicester, added: “It usually takes millions of years for evolution to occur, but here it has taken just decades to produce a new form of animal that has the potential to become a marker species of the Anthropocene — and the enormous numbers of these chicken bones discarded worldwide means that we are producing a new kind of fossil for the future geological record.”


The research is published in Royal Society Open Science.


Source: University of Leicester [December 12, 2018]



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Got lots of greetings cards and button badges on sale on our stall this week.Come and...


Got lots of greetings cards and button badges on sale on our stall this week.


Come and find us at The Winter Maker’s Market at The Derby High School, Bury, North Manchester from 5.30pm on Thursday 20th December 2018.


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Gut to Brain Nerve cells in our brain and spinal cord are…


Gut to Brain


Nerve cells in our brain and spinal cord are protected by a layer of protein and fatty substances called myelin. It’s thought that in multiple sclerosis (MS) our own immune T cells are tricked into attacking this protective coating, the result shown in this brain section from an MS patient brain – myelin in blue (top) is absent from the underlying nerves. Scientists have recently shown that perhaps we should be looking to our gut to understand why and how this happens. The team found that T cells respond to an enzyme formed in bacteria often found in the gastrointestinal flora of MS patients. They hypothesise that the presence of this enzyme in the gut activates T cells before they travel up to the brain and ravage through myelin. Not only does this finding tell us more about the processes underlying MS, but it may be used to create new treatments for the disease.


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Biologists shed new light on an old question

For nearly 100 years biologists have argued about how exactly natural selection can possibly work. If nature selects the individuals with the best genes then why aren’t all organisms the same? What maintains the genetic variation that natural selection acts upon, the genetic variation that has ultimately led to the spectacular diversity of life on Earth today? Recent findings made at Uppsala University suggest that the answer could be sex.











Biologists shed new light on an old question
The study is based on a seed beetle population [Credit: Ivain Martinossi-Allibert]

Evolutionary genetic theory shows that genetic variation can be maintained when selection favors different versions of the same genes in males and females — an inevitable outcome of having separate sexes. That is, for many genes there may not be a universally ‘best’ version, but rather one is best for males and one is best for females. This is known as sexually antagonistic genetic variation, but it might only be maintained under a narrow set of conditions, limiting its prevalence in nature. However, Dr. Karl Grieshop and Professor Göran Arnqvist’s study, published in PLoS Biology, may change this view.
“One of the simplest ways for sexually antagonistic selection to maintain genetic variation in fitness is via sex-specific dominance reversal, where neither version of a gene is always dominant or recessive, but rather the version that benefits a given sex is also dominant in that sex. So, whether a given version of a gene is dominant or recessive to the other will depend upon which sex it is in,” says Dr. Karl Grieshop.


This mechanism was met with early skepticism, but has seen recent theoretical and empirical support.


Grieshop and Arnqvist have now provided the first evidence of sex-specific dominance reversal for fitness. Using a panel of genetic strains of a seed beetle population that Grieshop studied throughout his PhD, and analyzing crosses among these strains, they could determine which strains harbored genetic variation that was dominant to the others’. Further, they could do this with regard to male fitness and female fitness separately.


When they ranked the strains according to their relative dominance over one another they found that strains tending to be dominant over other strains with regard to male fitness also tended to be recessive to other strains with regard to female fitness, and vice versa. Thus, whether the genetic variation for fitness in each of their strains was dominant or recessive to that of other strains depended, oppositely, on whether it was in a male or a female.


The pattern suggests that sex-specific dominance reversal for fitness is a strong and common phenomenon throughout the genome in their study population.


Source: Uppsala University [December 12, 2018]



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You are what you eat: High dietary versatility characteristic for early hominins

Studying fossil tooth enamel, German researchers from the Senckenberg research institutes and Goethe University Frankfurt discovered that the early hominins Homo rudolfensis and the so-called Nutcracker Man, Paranthropus boisei, who both lived around 2.4 million years ago in Malawi, were surprisingly adaptable and changed their diet according to the availability of regional resources. Being this versatile contributed to their ability to thrive in different environments. The new findings from southeastern Africa close a significant gap in our knowledge, according to the researchers’ paper just published in Proceedings of the National Academy of Sciences.











You are what you eat: High dietary versatility characteristic for early hominins
Lower jaw of a 2.4-million-year-old Homo rudolfensis, found at Uraha near Lake Malawi
[Credit: (c) Hessisches Landesmuseum Darmstadt]

Those who wonder what our ancestors ate around 4 to 1.4 million years ago may find answers in the data from fossil sites in the East African Rift Valley in modern-day Kenya and Ethiopia, as well as in the cave sites of South Africa. These two regions are separated by around 3,000 kilometers. Until recently, the diet of early hominins inhabiting this gap in the “Cradle of Humankind” remained an enigma to science.


Scientists from Senckenberg and Goethe University Frankfurt examined fossilized tooth enamel of three Homo rudolfensis and Paranthropus boisei individuals. They lived around 2.4 million years ago in the southern part of the East African Rift Valley around Lake Malawi and thus in the center of the blind spot regarding prehistoric human diet.


Tooth enamel is the most durable substance found in vertebrates. Even after millions of years, the carbon and oxygen isotopic compositions in the enamel allow to reconstruct an individual’s diet. Geochemical analyses enable the distinction between proportions of ingested plants which use different photosynthesis.


“The diet of studied Homo rudolfensis and Paranthropus boisei consisted to 60 or 70% of plants using C3 photosynthesis which grew in the Rift Valley. We assume these were primarily parts of trees such as fruits, leaves, and tubers. Parts of C4 plants, which dominate the open savannas of Africa today, made up a significantly lower portion of their diet. One of the Homo rudolfensis individuals even fed almost exclusively on C3 plant material,” the study’s lead author, Dr. Tina Lüdecke of the German Senckenberg Biodiversity and Climate Research Centre, explains.











You are what you eat: High dietary versatility characteristic for early hominins
Tooth remnants of Paranthropus bosei, who lived around the same time. Found at Malema near Lake Malawi
[Credit: (c) Hessisches Landesmuseum Darmstadt]

As reconstructed by the team, the area around Lake Malawi in the early Pleistocene was teeming with a multitude of trees and other C3 plants. Compared to more open habitats in eastern Africa, a cooler and wetter climate favored the spread of wooded savannas here. Additional analyses of fossil teeth from migrating prehistoric horses and antelopes reveal that a sufficient supply of C4 plant material must have been available further away from Lake Malawi. Yet, Homo rudolfensis and Paranthropus boisei preferred to stay close to the lake not only for water but also to benefit from locally available resources.


Paranthropus aethiopicus, a contemporary of the study’s subjects Homo rudolfensis and Paranthropus boisei, lived farther north in the East African Rift Valley. Contrary to the inhabitants of the region around Lake Malawi, his diet involved a significantly higher fraction of C4 plants. Such C4 plants were more easily available in the dry grasslands of the East African Rift Valley that Paranthropus aethiopicus called home. “Surprisingly this shows that already 2.4 million years ago some early hominins were able to adjust their diet to their environment,” says Lüdecke.


This finding is complemented by previous analyses of Paranthropus and Homo representatives living less than 2 million years ago, who continued this type of behavior. Those who dwelt in the South African forests continued to primarily eat C3 plants, while their relatives in the drier north increasingly fed on C4 plants found in their habitat, which continue to constitute the primary food source for many humans on earth today.


“To the best of our current knowledge, there were no other primates that handled their dietary needs in such a flexible manner. The fact that early hominins were able to adapt their diet specifically to different environmental conditions undoubtedly was one of the keys to the success of Homo sapiens,” summarizes PD Dr. Ottmar Kullmer, one of the study’s co-authors, from the Senckenberg Research Institute Frankfurt and Goethe University in Frankfurt.


Source: Senckenberg Research Institute [December 12, 2018]



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Scientists overhaul corn domestication story with multidisciplinary analysis

Smithsonian scientists and collaborators are revising the history of one of the world’s most important crops. Drawing on genetic and archaeological evidence, researchers have found that a predecessor of today’s corn plants still bearing many features of its wild ancestor was likely brought to South America from Mexico more than 6,500 years ago. Farmers in Mexico and the southwestern Amazon continued to improve the crop over thousands of years until it was fully domesticated in each region.











Scientists overhaul corn domestication story with multidisciplinary analysis
Varieties of maize found near Cuscu and Machu Pichu at Salineras de Maras on the Inca Sacred Valley in Peru, June 2007.
The history of maize begins with its wild ancestor, teosinte. Teosinte bears little resemblance to the corn eaten today: Its
cobs are tiny and its few kernels are protected by a nearly impenetrable outer casing. In fact, Kistler said, it is not clear why
 people bothered with it all. Over time, however, as early farmers selected for desirable traits, the descendants of the wild
plant developed larger cobs and more tender, plentiful kernels, eventually becoming the staple crop that maize is today. The
newly published study in shows that the final stages of maize’s domestication happened more than once in more than one
 place, revising the history of one of the world’s most important crops [Credit: Fabio de Oliveira Freitas]

The findings, reported in the journal Science, come from a multidisciplinary, international collaboration between scientists at 14 institutions. Their account deepens researchers’ understanding of the long, shared history between humans and maize, which is critical for managing our fragile relationships with the plants that feed us, said Logan Kistler, curator of archaeogenomics and archaeobotany at the Smithsonian’s National Museum of Natural History and lead author of the study.


“It’s the long-term evolutionary history of domesticated plants that makes them fit for the human environment today,” he said. “Understanding that history gives us tools for assessing the future of corn as we continue to drastically reshape our global environment and increase our agricultural demands on land around the globe.”


The history of maize begins with its wild ancestor, teosinte. Teosinte bears little resemblance to the corn eaten today: Its cobs are tiny and its few kernels are protected by a nearly impenetrable outer casing. In fact, Kistler said, it’s not clear why people bothered with it all. Over time, however, as early farmers selected for desirable traits, the descendants of the wild plant developed larger cobs and more tender, plentiful kernels, eventually becoming the staple crop that maize is today.


For years, geneticists and archaeologists have deduced that teosinte’s transformation into maize began in the tropical lowlands of what is now southern Mexico about 9,000 years ago. The teosinte that grows wild in this region today is more genetically similar to maize than teosinte elsewhere in Mexico and Central America—though all remain separated from the domesticated crop by hundreds of genes.


In the southwest Amazon and coastal Peru, microscopic pollen and other resilient plant remains found in ancient sediments indicate a history of fully domesticated maize use by around 6,500 years ago, and researchers initially reasoned that the fully domesticated plant must have been carried there from the north as people migrated south and across the Americas.











Scientists overhaul corn domestication story with multidisciplinary analysis
Varieties of the Avati ete’i, the sacred Guaranis’ maize, April 2017 during the seed exchange fair, in La Paloma, State of
Rocha, Uruguay. Although the team used maize curated in gene banks for this study, Fabio Freitas, an ethnobotanist and
farm conservationist at Embrapa, said that his work conserving traditional cultivated plants with indigenous groups from
the South border of the Amazon forest helped guide the discussion of how maize diffusion may have played out in the past.
The team mapped out the genetic relationships between the plants and discovered several distinct lineages, each with
its own degree of similarity to their shared ancestor, teosinte. In other words, Kistler explained, the final stages of
maize’s domestication happened more than once in more than one place [Credit: Fabio de Oliveira Freitas]

“As far as we could tell before conducting our study, it looked like there was a single domestication event in Mexico and that people then spread it further south after domestication had taken place,” Kistler said.


But a few years ago, when geneticists sequenced the DNA of 5,000-year-old maize found in Mexico, the story got more complicated. The genetic results showed that what they had found was a proto-corn—its genes were a mixture of those found in teosinte and those of the domesticated plant. According to the ancient DNA, that plant lacked teosinte’s tough kernel casings, but this proto-corn had not yet acquired other traits that eventually made maize into a practical food crop.


“But you’ve got continuous cultivation of maize in the southwest Amazon from 6,500 years ago all the way up through European colonization,” Kistler said. “How can you have this flourishing, fully domesticated maize complex in the southwest Amazon, and meanwhile, near the domestication center in Mexico the domestication process is still ongoing?”


In an effort to try to solve this mystery, Kistler’s team reconstructed the plant’s evolutionary history by undertaking a genetic comparison of more than 100 varieties of modern maize that grow throughout the Americas, including 40 newly sequenced varieties—many from the eastern lowlands of South America, which had been underrepresented in previous studies. Many of these varieties were collected in collaboration with indigenous and traditional farmers over the past 60 years and are curated in the genebank at Embrapa, the Brazilian government’s agriculture enterprise.


Fabio Freitas, an ethnobotanist and farm conservationist at Embrapa, said that his work conserving traditional cultivated plants with indigenous groups from the South border of the Amazon forest helped guide the discussion of how maize diffusion may have played out in the past. The genomes of 11 ancient plants, including nine newly sequenced archaeological samples, were also part of the analysis.


The team mapped out the genetic relationships between the plants and discovered several distinct lineages, each with its own degree of similarity to their shared ancestor, teosinte. In other words, Kistler explained, the final stages of maize’s domestication happened more than once in more than one place.


“This work fundamentally changes our understanding of maize origins,” said study co-author Robin Allaby from the School of Life Sciences at the University of Warwick. “It shows that maize did not have a simple origin story, that it did not really form the crop as we know it until it left its homeland.”











Scientists overhaul corn domestication story with multidisciplinary analysis
Logan Kistler preparing ancient DNA samples for analysis at the University of Warwick in 2016. As curator of
archaeogenomics and archaeobotany at the Smithsonian’s National Museum of Natural History, Kistler uses cutting-edge
genomic and genetic research techniques to understand the evolutionary relationship between people and plants. ‘It’s the
long-term evolutionary history of domesticated plants that makes them fit for the human environment today,’ Kistler said.
 ‘Understanding that history gives us tools for assessing the future of corn as we continue to drastically reshape
 our global environment and increase our agricultural demands on land around the globe’
[Credit: Shahidul Alam, Drik Picture Library]

At first, Kistler said, the genetic evidence was puzzling. But as he and his collaborators began to integrate what each had learned about the history of South America, a picture of how maize may have spread across the continent emerged.


A proto-corn in the midst of becoming domesticated appears to have reached South America at least twice, Kistler said. By 6,500 years ago, the partially domesticated plant had arrived in a region of the southwest Amazon that was already a domestication hotspot, where people were growing rice, cassava and other crops.


The plant was likely adopted as part of the local agriculture and continued to evolve under human influence until, thousands of years later, it became a fully domesticated crop. From there, domesticated maize moved eastward as part of an overall expansion and intensification of agriculture that archaeologists have noted in the region.


By around 4,000 years ago, Kistler said, maize had spread widely through the South American lowlands. Genetic and archaeological evidence also align to suggest that maize cultivation expanded eastward a second time, from the foothills of the Andes toward the Atlantic, about 1,000 years ago. Today, traces of that history exist in the Macro-Jê languages spoken near the Atlantic coast, which use an Amazonian word for maize.


Source: Smithsonian [December 13, 2018]



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New techniques better determine how ancient viral DNA influences human genes

New laboratory techniques can identify which of our genes are influenced by DNA snippets that are left behind in our genetic code by viruses, a new study finds.











New techniques better determine how ancient viral DNA influences human genes
Credit: KTSimage/iStockphoto

Viruses have long been known to reproduce by using the genetic machinery of the cells they invade. As part of that process over time, these microorganisms have left behind thousands of DNA sequences, called transposons, throughout the genetic material (genomes) in many lifeforms, including mice and humans, say the study authors. Studies established decades ago the idea that a few of these viral insertions have come to play a role in the action of genes.


Determining which transposons regulate which genes, however, has proven to be a challenge, as transposons may influence a nearby gene or one that is located far away in the DNA molecular chain.


Published online in Genome Biology, the new study describes methods that capture more information on the location and influence of viral insertions in genomes, identifying genes potentially controlled by active transposons (most are silenced by our cells’ defense mechanisms).


“One of the interesting findings from our study is that a single transposon may control more than one gene and that one gene can be regulated by more than one transposon, increasing the complexity of the potential impact of transposons on health and disease,” says senior study author Jane Skok, PhD, the Sandra and Edward H. Meyer Professor of Radiation Oncology at NYU Langone Health’s Perlmutter Cancer Center. “Furthermore, viral insertions from the same family preferentially interact with each other, possibly reinforcing their impact on genetic activity.”


View of Genetic Reality


For decades after the discovery of DNA, researchers mostly thought of genetics in terms of genes, the pieces or sequences of DNA that encode instructions for building proteins in cells. Then scientists discovered that genes make up just 2 percent of our DNA and that most genetic complexity stems from the vast non-gene code, which influences when genes are turned on or off. Further, half of that non-gene code was found to come from insertions of viral DNA. Consequently, say the authors, genetic variation, and the potential for disease-causing mistakes, occurs in transposons as well as in genes.


The current results are based on the discovery that pieces of DNA, called enhancers, control gene activity. These enhancers may be separated from their target genes by a long distance on a linear DNA chain but can curl around in 3D space to interact with another section of the chain by forming loops. Evidence then emerged that some of these looping enhancers may be parts of viral transposon sequences. But those trying to understand the role of these enhancers faced a problem.


Transposon insertions occur at many sites and are therefore repeats of the same DNA code (not unique). However, popular genome-wide association studies rely on finding a link between a single, unique piece of DNA and risk for a disease. Thus, repeat sequences are typically ignored because it is not clear which of these multiple insertion sites is interacting with a particular disease-related gene.


Experimental evidence supports the idea that to exert influence, enhancers must make physical contact with their target genes through loop formation. Identifying such interactions between different pieces of DNA became possible in 2002 with the development of a technique called chromosome conformation capture.


The current study describes two variations on this technology, collectively called 4TRAN, which take advantage of the repetitive nature of transposons to capture their interactions. The techniques provide direct evidence that some transposons exert long-range control of genes by looping.


One of the new techniques, 4TRAN-PCR, proved to be capable of finding all interactions involving members of a transposon family that contain a particular DNA sequence, enabling the researchers to count the hundreds or thousands of places where such transposons occur. The method demonstrated that transposons are more likely to interact with DNA within local neighborhoods (topologically associating domains), but also that they take part in long-range interactions determined by the activation status of the compartments they are in.


The second technique, Capture 4TRAN, attached probes to each member of a viral family that, in combination with other tricks, enabled the team to determine the influence of any single transposon copy on a specific gene or genes. For example, the study showed that a few of the 7,200 copies of repetitive DNA left behind by the viral MER41 family, which infected our primate ancestors 60 million years ago, now serve as enhancers that turn on immune system genes via long-range DNA contacts by looping. Ironically the target genes in this case act to combat, of all things, viruses.


Moving forward, the team has already begun experiments seeking to identify networks of interactions between transposons and genes that are different in cancer cells than in healthy cells.


Source: NYU Langone Health [December 13, 2018]



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Neanderthal genes influence brain development of modern humans

A characteristic feature of modern humans is the unusually round skull and brain, in contrast to the elongated shape seen in other human species. By studying Neanderthal DNA fragments found in the genomes of living Europeans, scientists have now discovered genes that influence this globular shape. An interdisciplinary research team, led by the Max Planck Institutes for Psycholinguistics and Evolutionary Anthropology, brought together fossil skull data, brain imaging and genomics, as reported in Current Biology.











Neanderthal genes influence brain development of modern humans
Computed tomographic scan of a Neanderthal fossil (La Ferrassie 1; left) and of a modern human (right). One of the
features that distinguishes modern humans from Neanderthals is a globular shape of the braincase. ​The cranium
was cut open virtually to reveal the inside of the braincase [Credit: © Philipp Gunz]

Modern human skulls have a unique ‘globular’ (round) shape. Our closest cousins, the long extinct Neanderthals, had the elongated skulls that are typical of most primates. This striking shape difference is suspected to reflect evolutionary changes in the relative sizes of structures of the human brain, perhaps even in the ways that key brain areas are connected to each other. However, brain tissue doesn’t itself fossilize, so the underlying biological explanation has remained elusive.
An international research team, led by paleoanthropologist Philipp Gunz (MPI, Leipzig) and geneticists Simon Fisher and Amanda Tilot (MPI, Nijmegen), developed a new strategy to investigate this question. The team combined analysis of fossil skulls, ancient genome sequence data and brain imaging.


“Our aim was to identify potential candidate genes and biological pathways that are related to brain globularity,” says Tilot. To focus their search, they took advantage of the fact that living humans with European ancestry carry rare fragments of Neanderthal DNA buried in their genomes, as a result of interbreeding between Neanderthals and the ancestors of modern Europeans. Different people carry different fragments, which are scattered through the genome.











Neanderthal genes influence brain development of modern humans
The authors combine paleoanthropology, archaic genomics, neuroimaging and gene expression to study biological
foundations of the characteristic modern human endocranial shape. Shown here are the coordinate measurements
used to capture endocranial shape from magnetic resonance images of several thousand modern humans
[Credit: © Philipp Gunz]

The researchers first used computed tomographic scans of fossil Neanderthal skulls and skulls of modern humans to make endocasts—virtual imprints of the interior of the braincase. They then developed a single measure of globularity, based on the differences in skull shape between humans and Neanderthals. Next, the scientists teamed up with colleagues at the Radboud University, the University of Greifswald and UC Irvine, to determine the degree of globularity of thousands of healthy present-day humans, using data from magnetic resonance imaging.
Although modern human brain and skull shapes are all clearly distinct from those of Neanderthals, the scientists still found considerable differences in globularity among the participants. Finally, the researchers studied the genomes of around 4,500 of the participants to identify the fragments of Neanderthal DNA that each person carried. Would any of these Neanderthal DNA fragments influence brain globularity in their living human sample?


The team found Neanderthal DNA fragments on chromosomes 1 and 18 that were associated with less globular (more elongated) brains. These fragments were associated with altered activity of two genes, UBR4 and PHLPP1, which are already known to play roles in important aspects of brain development (neurogenesis and myelination respectively). The strongest evidence for effects of these Neanderthal DNA fragments on gene activity were in the putamen (in the basal ganglia) and the cerebellum.











Neanderthal genes influence brain development of modern humans
Computed tomographicscan of the Neanderthal fossil from La Chapelle-aux-Saints (left) with a typical elongated
endocranial imprint (red) and of a modern human (right) showing the characteristic globular endocranial shape (blue).
 Arrows highlight the enlarged posterior cranial fossa (housing the cerebellum) as well as bulging of parietal bones
in modern humans compared to Neanderthals [Credit: © Philipp Gunz]

“The potential for links between evolutionary changes in brain globularity and mechanisms affecting the basal ganglia and cerebellum is intriguing,” says Gunz. Both structures receive direct input from the motor cortex and are involved in the preparation, learning, and coordination of movements. The basal ganglia also contribute to cognitive functions such as memory, attention, planning, skill learning, and potentially speech and language evolution.
The authors stress that recent archaeological evidence has documented sophisticated symbolic behaviours in Neanderthals that had previously been attributed exclusively to modern humans, such as the enigmatic structure built deep inside Bruniquel cave, and Neanderthal cave-art from Iberia. As Gunz notes, “The focus of our study is on understanding the unusual brain shape of modern humans. These results cannot be used to make inferences about what Neanderthals could or could not do.”


“The effects of carrying these rare Neanderthal DNA fragments are really subtle, but detectable due to the large sample size,” explains Fisher, adding “This is only our first glimpse of the molecular underpinnings of globularity. Like other aspects of brain structure, globularity is a trait that is likely to be influenced by the combined effects of many different genetic variants.”


This animation shows computed tomographic (CT) scans of a Neandertal cranium (left) 


and a recent modern human (right) [Credit: Philipp Gunz]


According to the research team, this discovery generates hypotheses that can be tested with new experiments, for example using human neuronal tissue that can be grown in the laboratory. Gunz and Fisher are now scaling-up the approach for investigations in larger samples such as the UK Biobank. They anticipate that future genome-wide screening studies will reveal additional genes associated with globularity, as well as indicate how this fascinating trait is linked to other aspects of human biology.


Source: Max Planck Society [December 13, 2018]



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