Methylation of the DNA to inhibit high transposons

In an article published online in Genome Biology , researchers from the University of California at Los Angeles (UCLA) and Parma in Italy were interested in the epigenetic processes that could control these transposons. Thus, methylation of DNA is an epigenetic modification in which a methyl group is added to the nucleotide cytosine . Involved in many process control genetic , it can inactivate transposons. The DNA methylation exist in animals, plants and fungi, but was lost in some invertebrates , which can lead to phenotypes as abnormal developmental problems or cancers .

Methylation of the DNA to inhibit high transposons

Scientists measured the proportion of methylated cytosine in the genome of the black truffle at different stages of development: ascocarp (at which point the truffle is harvested), the mycelium (the fungus grows in the soil after germination of a spore) and ectomycorrhizae (stage symbiosis between the fungus and the roots).

The methylation patterns were very similar in all three stages. The rate of cytosine methylation was especially high (44%), with a preference for GC sites and transposons large (over 1500 bp).

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This work may explain the relationship between DNA methylation and intraspecific variability, but also the properties organoleptic fungus: aromas and color . Matteo Pellegrini, one of the authors of the article, the black truffle would use epigenetic processes to control its genes and adapt to changes in its environment. "This methylation reversible may increase the plasticity of the genome of the nose, which would allow it to adapt to its environment. Because truffles lives below ground and has no active system spore dispersal, it may require plasticity to adapt to sudden changes in their environment, " Has he commented.

Périgord truffles and its genetic secrets

Périgord truffles and its genetic secrets

The genome of the nose contains many "jumping genes" and repeated sequences. Epigenetic processes such as DNA methylation, could control the genes of this famous mushroom, so some characters as its aromas and color characteristics.

On 08/07/2014 at 09:40 - By Marie-Céline Jacquier, Futura-Sciences

No comment  TALK
This black Perigord truffle is a luxury in the kitchen.  © Wikimedia Commons, DP

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Especially prized by gourmets, black truffles, also known by their name Perigord truffles are second species most expensive. The fungi that produce them are from the species Tuber melanosporum . They grow on the roots of oak and hazel, with a symbiotic relationship that forms a ectomycorrhizae.

Its genome has 125 million base pairs (Mbp), that is to say, it is comparable to the size of Arabidopsis  Arabidopsis thaliana , a plant commonly used in laboratories. It contains a particularly high or transposable "elements number  gene jumping "that can move: it would have 6-20 times more than most fungi filamentous sequenced to date and 4 times more than Arabidopsis . Over 58% of the genome of the black truffle is composed of repetitions and jumping genes.

DNA methylation is the addition of a methyl group to a nucleotide. © Christoph Bock ( Max Planck Institute for Informatics ), Wikimedia Commons, cc by sa 3.0

Our Milky Way is old

Even if we accept that technology can never afford to use the Alcubierre drive or traversable wormholes , traveling from star to star comparable to those that can reach speeds today and in multiplying, such probes could colonize the galaxy full in less than 300 million years according to his calculations. Our Milky Way is old and containing a large number of exoplanets , we can not escape the conclusion that the Earth should have been part of a galactic empire for a long time, even before the appearance of man, unless, for one reason or another, the birth and development of technological civilizations are very rare phenomena.

Do you agree with Tipler?
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Max Tegmark: Yes, and I'm going even further than he did. In the last chapter of my book that I dedicated to the future of our universe, of life and our civilization I gave arguments that make me think that not only are we alone in our galaxy but probably throughout the observable universe. As a cosmologist, I am naturally led to reflect on time scales and very large space and not to focus me on the short term as we still do far too often. I believe that humanity has a huge development potential and a bright future ahead. But if we are truly unique in the observable universe, it would be a shame and a tragedy if we did not do anything to avoid disappearing.

I'm not the only one in the scientific community to be concerned about the future of humanity and the various risks facing it, environmental or technological. That's why we decided to create the FLI  ( Future of Life Institute ) in a similar spirit of Foundational Questions Institute . He has a website and a Facebook where you can join us page.

a pioneer in genomics and synthetic biology

Max Tegmark: There is no question of belief ... As scientists we seek only to assess the risks and benefits of visiting an AI beyond the capabilities of the human brain. What will happen from here, for example, a few decades? Frankly, in my opinion, we do not know, really. But it is important that we thought about carefully now to limit the risks we take in creating an artificial intelligence that could turn against us as possible. On the other hand, all the positive aspects of our civilization are related to our intelligence and it is likely that the creation of a smarter AI that humans resulting in huge benefits for humanity as disease control and of poverty. I am among those who are optimistic about technology.

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FLI is composed of prestigious members such as Nobel Prize in Physics Saul Perlmutter and Frank Wilczek, the inventor of Skype Jaan Tallinn, or geneticist George Church, a pioneer in genomics and synthetic biology. © 2014 The Future of Life Institute

Futura-Sciences:  There are more than 30 years the mathematician and cosmologist Frank Tipler said that humanity was probably alone in the Milky Way . He had reached this conclusion by developing an original way the reasoning leading to the Fermi paradox. For him, an advanced technological civilization eventually be able to build what he called a Von Neumann probe. This is an AI capable of making copies of itself in traveling between the stars.

The Machine Intelligence Research Institute

Wheeler was the mentor of Richard Feynman , Hugh Everret, Kip Thorne and Jacob Benkenstein . What role did he have for you?

Max Tegmark: It has been a great source of inspiration and above all encouraged me to pursue my own ideas even if they might seem foolish in the eyes of my colleagues. This is very important when you are a young researcher to have the support of such a giant of physics. I actually agree with him that the information theory should be the key to the most basic physics. Thus, there would be no need to assume the existence of a yet unknown ingredient to explain the nature of consciousness.

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Futura-Sciences:  The Machine Intelligence Research Institute (formerly Singularity Institute for Artificial Intelligence ) organizes conferences around the theme of technological singularity which is one of the gurus Ray Kurzweil . You gave one of them at the Singularity Summit 2011 . More recently, Steven Hawking, Nobel laureate and professor of physics at MIT and Frank Wilczek Stuart Russell, professor of computer science at Berkeley known for his contributions to the AI , you wrote an article in the Huffington Post on the occasion of the release of the film Transcendence that incorporates many of the technological singularity associated with ideas.

According to you, we do not take seriously enough the risks posed the development of artificial intelligence. Does this mean that you, Hawking Russel Wilczek believe in progress by Ray Kurzweil and Eliezer S. Yudkowsky theses?

the first theory of nuclear fission

Co-author of the first theory of nuclear fission and pioneer of the theory of black holes and neutron stars, John Wheeler was also an outstanding teacher and mentor to a generation of physicists. He was the supervisor of Feynman, whom he inspired the idea of considering positrons as electrons going back in time. There will also be student Hugh Everret, the theorist who brought the deterministic interpretation of quantum mechanics that Wheeler baptize a name that will fortune: the theory of multiple worlds. From left to right next to him, Einstein and Bohr busts, thought leaders John Wheeler. © Texas A & M University

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Futura-Sciences:  Recently, you have posted on arxiv an article entitled Consciousness as a State of Matter ( Consciousness as a state of matter ). Your thesis is that consciousness emerges from some simply process information when they are sufficiently complex. In the same way that the solid state differs from the liquid or gaseous state from the point of view of the organization of atoms, it would also be true for the relationship between what we call matter and spirit. With math, you play a central role to the notion of information explaining the ultimate nature of reality.

In 2001, you published an article on the centenary of quantum physics with the great physicist John Wheeler. We owe him a famous statement that goes in the same direction as the idea that you stand for: "every physical quantity derived icts ultimate significance from bits, binary yes-or-no indications, has concluded All which we epitomize in the sentence it from bit " (each physical quantity derives its ultimate significance of information bits that can be reduced to binary yes-no quantities, a conclusion that summarizes the expression it (that exists) from the information (bit)).

the development of consciousness

Futura-Sciences:  In 1999 you wrote an article, with supporting calculations, you put serious doubt on the hypothesis put forward by Roger Penrose and Stuart Hameroff on the role of quantum coherence in the functioning of the brain and especially human the emergence of consciousness. In recent years, however, it seems that we are beginning to find evidence of the existence of coherent quantum states in biology, for example with photosynthesis . This tends to give more weight to as advanced by other researchers ideas as Paul Davies who wonder if the development would not have found a way to still use quantum coherence in biology.

Do you still think, disagree with Penrose and Hameroff, that quantum mechanics is not directly involved in the development of consciousness?

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Max Tegmark: I think that quantum phenomena can actually play a role in biology. It would of course be wonderful to say that the brain is a kind of quantum computer but I still think this is not the case. In our laboratories, we must really extreme conditions, cooled to very low temperatures and high vacuum systems, in order to make quantum calculations and prevent environmental disturbances destroy the quantum coherence necessary to carry out . Conditions in our brain does not really look like that. Our neurons are too hot. It seems that some people are still convinced that there is a link between quantum mechanics and consciousness only because they also seem to us mysterious.

The Nobel Prize for physics

What was your reaction when the results of experiments conducted by David Wineland, Serge Haroche and their collaborators were published in 1996?

Max Tegmark: I found these absolutely spectacular and not just because experiences they have verified the theory of decoherence. The Nobel Prize for physics was awarded to Serge Haroche and David Wineland reward equally achieving these experiments that the techniques of manipulation of individual quantum systems they had developed to achieve this. It's pretty incredible to see the way that was done in less than a century. We have gone from a time when the existence of atoms and quanta of light had begun to doubt the individual mastery of these objects. The implications of the work of Haroche and Wineland are important not only from a theoretical point of view but also because they have great potential in nanotechnology.

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Futura-Sciences:  Many physicists seem to think that the obstacle of decoherence is probably insurmountable and we're never going to build quantum computers powerful enough to compete with computers classics and exceed.

What is your opinion about this?

Max Tegmark: I recently discussed these issues with colleagues. Many of us think that such computers are not likely to see the day before the 2050s.

the theory of decoherence

Max Tegmark: Yes, I absolutely agree with that.

Futura-Sciences:  But you're going even further than Plato affirming that everything in our universe is actually a mathematical structure. This hypothesis is also falsifiable for you because it is possible that future scientific developments lead us to discover that some phenomena can not be completely reduced to pure mathematical structures.

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Max Tegmark: Right. One of the great puzzles that has not yet found a scientific solution of the phenomenon of consciousness. The philosopher David Chalmers called hard problem of consciousness ( Hard problem of consciousness ), the problem of explaining the fact that we have qualitative phenomenal experiences. It might finally be amenable to any explanation that would only consider mathematical structures. This is an example of one of insurmountable obstacles we might encounter that would disprove my hypothesis of a mathematical universe.

Born in 1951, the Polish-born physicist Wojciech Zurzek is the author of major works on the theory of quantum information. He was responsible for the theory of decoherence and a demonstration of the famous impossibility theorem of quantum cloning. © University of Waterloo

Futura-Sciences:  You were still a masters student at the University of Berkeley in 1991 when you rediscovered independently of Wojciech Zurek and Hans Dieter Zeh, the theory of decoherence, which solves the riddle of the paradox of the cat Schrödinger \.

a good understanding of the gravitational quantum

Do you think that in the coming years, as happened with MWI, there will be more and more people are convinced that the distinction between multiverse Level I and Level III does not occur to be?

Max Tegmark: I think this will probably be the case. However, although there are indications of a possible unification as I explain in my book, we still have many issues to resolve before we really know if this is really one and the same multiverse. The controversy of the firewall with the physics of black holes , for example, is an illustration of the fact that we do not yet have a good understanding of the gravitational quantum. It is necessary for us to hope to really decide.

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Futura-Sciences:  The theory of general relativity and the prediction of the existence of antimatter are deeply rooted in pure mathematics, namely the Riemann geometry of curved spaces and n-dimensional spinors that Paul Dirac was led introducing to build his quantum theory of electrons in the space-time . Not regularities in the physical world that the brains of living creatures were able to experiment and to learn to master to survive during evolution. These findings seem to show that we can not have invented these mathematical structures, or have inherited from our predecessors in the history of the biosphere . Indeed, our ordinary intuition after our confrontation with the objects of everyday life fails in the quantum and relativistic world, but not our mathematical theories, on the contrary.

So it seems difficult to escape the conclusion that theoretical physics in the twentieth th century proved that Pythagoras and Plato were right. Or at least that their theories about the nature of human knowledge have falsifiable predictions that, for the moment, were corroborated in the sense of Popper, unlike other explanations offered.

The first satellite mission to measure CO2 in orbit

The first satellite mission to measure CO2 in orbit
The Point.fr - Published 07/02/2014 at 17:43
OCO-2 will provide a more complete picture of emissions of carbon dioxide, the level in the atmosphere is the highest for at least 800,000 years.

The satellite will measure samples of CO2 sources and sinks across the globe.
The satellite will measure samples of CO2 sources and sinks across the globe. © AFP

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The NASA successfully launched Wednesday its first satellite to measure the levels of carbon dioxide (CO2) in the atmosphere, the main greenhouse gas contributing to global warming. The satellite, called OCO-2 (Orbiting Carbon Observatory-2), is very similar to the OCO-1, which was destroyed when it was launched in February 2009 carrying the satellite launcher, a Delta 2 rocket at United Launch Alliance , was torn from its launch pad from Vandenberg Air Force Base, California, as provided in 11 h 56 (time of Paris , 2 h 56). NASA has confirmed about an hour after launching the satellite separates from the second stage of the rocket, which marks the successful implementation orbit.

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OCO-2 will evolve on an almost polar orbit at 705 km altitude, for a mission of at least two years. It will provide a more complete and comprehensive picture of human and natural CO2 emissions and carbon sinks such as oceans and forests, which absorb and capture this gas, the level in the atmosphere is the highest since the least 800 000 years. "Carbon dioxide in the atmosphere plays an essential role in the energy balance of our planet and is key to understanding how our climate is changing," said Michael Freilich, director of the Earth Sciences Division of the agency American space. "Climate change is the challenge of our generation," said Wednesday after the launch of NASA's boss, Charles Bolden . "With OCO-2 and the existing fleet of satellites, NASA can meet the challenge of measuring and understanding these changes, predict their ramifications, and share this information for the good of society," he added in a statement.

Mars habitable day

Curiosity, a six-wheeled robot a ton, landed on Mars in August 2012 Since then he has traveled 700 meters are the first Earth year, and 7 km in the second, ten times more, depending Sylvain Maurice. "We said: We must roll! Simply, we had a problem with wheels and we know we must still mount our household for Curiosity arrives shaped mountain he has to climb At the. look where he's going, it was calculated that there would be at Christmas, once past the sand dunes, "said the French astrophysicist, enthusiastic. Attached to the front of the robot, ChemCam built in Toulouse, operates daily, conducting fire laser beam to determine the chemical composition of rocks.

Mars habitable day
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End of 2013, the mission announced its biggest result show that Mars was a habitable day. "Since then, we have learned about the nature of rocks, water. Was good progress, including the measurement of the ages old rocks billions of years, lists Sylvain Maurice. Was also beautiful discoveries on volcanism of Mars, with lava that comes from a greater depth than on Earth. "

In Toulouse, the Space City - scientific theme park geared towards the conquest of space - for two months presents an exhibition "Extreme Explorations" that puts next two ongoing missions: the Curiosity on Mars and probe Rosetta to comet.

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Mars Curiosity takes confidence after his first "Martian year"

Mars Curiosity takes confidence after his first "Martian year"
The Point.fr - Published 28/06/2014 at 18:16 - Amended 29/06/2014 at 16:29
The robot has already spent one Martian year, or 687 Earth days on Mars. On Friday, he broke his record by traveling 147 meters in a day.

Selfie of the Curiosity rover to its first Martian year.
Selfie of the Curiosity rover to its first Martian year. © Nasa / NASA / JPL-Caltech / MSSS
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The American robot Curiosity - operating on Mars for one Martian year, or 687 Earth days - accelerates its race to try to reach Christmas exciting area of Mount Sharp , said Friday at the Agence France-Presse the French astrophysicist Sylvain Maurice in Toulouse . "There's one week, Curiosity set a record by traveling in one day is 147 meters away," said Sylvain Maurice, co-head of the Franco-American chemical ChemCam camera mounted on Curiosity, reached by telephone in the City of space Toulouse.

"The rover speeds - carefully - because we are trying to cover the ground to reach in the winter, a place that fascinates us, Mount Sharp, with its beautiful landscapes," said Sylvain Maurice, a member of the Institute Research in Astrophysics and Planetology (IRAP, Toulouse III University, CNRS).

the robot Curiosity has opened the door

Since his arrival on Mars, Curiosity seeks to detect whether the Red Planet harbors conditions potentially or historically favorable to life. Since one Martian year, analysis of samples of Martian soil collected using various instruments, including a French named ChemCam, and until then, NASA welcomes its results.

Significant discoveries
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If still no indication that there was life on Mars, the rover explorer was able to determine that it "could have been possible." By analyzing the rock, and there found the essential elements for the emergence of life on a planet. Similarly, its records show that Mars had at least one river. A historic discovery, according to Nasa.

Finally, if one is not yet at the stage of human exploration of Mars, the robot Curiosity has opened the door. Since his arrival on Mars, it was determined that the radiation suffered both during interstellar journey to the Red Planet are tolerable to humans. Significant discoveries in 687 Earth days.

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The robot Curiosity Mars celebrates its first year

The robot Curiosity Mars celebrates its first year
The Point.fr - Published 24/06/2014 to 10:07 p.m. - Amended 06/25/2014 at 7:07
That's 687 days that NASA rover surveyed the soil of Mars, a full year after the Martians standards.

Selfie of the Curiosity rover to its first Martian year.
Selfie of the Curiosity rover to its first Martian year. © Nasa / NASA / JPL-Caltech / MSSS
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Selfie as a birthday gift. If it is not - yet - managed to discover if there was life on Mars, the robot Curiosity on Tuesday celebrated its first anniversary on Mars. A Martian year for the rover, 687 Earth days.

At that time, the Nasa published on Twitter selfie a robot that travels Martian soil since his "landing" on August 6 2012 A self-portrait by a collage of several images made ​​by the machine itself from different angles.

© NASA DR / Screenshot of Twitter

Russia: paleontologists discovered two skeletons of dinosaurs

Russia: paleontologists discovered two skeletons of dinosaurs
The Point.fr - Published 23/06/2014 18:11
After three weeks of excavation, paleontologists have unearthed specimens "intact and in good condition" old 100 to 120 million years.

A specimen of Psittacosaurus exhibited in New York, June 16, 2004.
A specimen of Psittacosaurus exhibited in New York, June 16, 2004. © Mario Tama / Getty Images north America / AFP

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Russian paleontologists unearthed in Siberia two dinosaur skeletons well preserved old about 100 to 120 million years, the museum said Monday that conducted the excavations. "The skeletons are intact and in good condition," said Olga Feofanova, the director of the local museum who directed the excavations. "It is very rare to find whole skeletons dinosaurs in such a state. These findings are of great importance", she added. The two skeletons were found buried at a depth of 2.5 meters after the excavation of more than three weeks on a renamed near the village of Chestakovo site, in the Kemerovo region of Siberia.

According to Olga Feofanova, these two Psittacosaurus sibiricus , herbivorous bipeds whose skeleton is nearly 2 meters long. Excavations began in late May under the guidance of museum Olga Feofanova and with the help of a team of paleontologists Moscow. The discovery will be exhibited at the local museum, local authorities said in a statement.

Seismic waves and wet rocks

Why is this intuition? Because ringwoodite is nothing other than olivine - the main mineral of the mantle - subject to conditions of high temperature and pressure such as those exerted between about 520 and 660 km depth in toward the center of the Earth, in a kind of transition zone between the upper mantle and the lower mantle of the planet. However, the remarkable feature of this ringwoodite is that it tends naturally to trap water in it, not as a liquid, gas or ice, but in the form of hydroxide ions. Moreover, after analysis of their precious sample, the researchers confirmed that it contained well about 1.5% water. In other words, although this percentage may in no circumstances be generalized, firstly it showed that there was indeed somewhere in the ringwoodite in the Earth's mantle and, second, that it could contain a significant amount of water. The hypothesis of a huge water reservoir in the Earth's mantle so out considerably strengthened ...

Seismic waves and wet rocks
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With this result, another team of American researchers led by Steven Jacobsen, Northwestern University in Illinois and Brandon Schmandt of the University of New Mexico, tried to turn light on the question by studying the behavior of seismic waves that ring the Earth like a bell for several days after an earthquake. For when these waves encounter wet rocks, they slow, and this is something that scientists know how to measure. But what with the trapped water in ringwoodite since it is not in liquid form? Is that, through experiments conducted in the laboratory, Steven Jacobsen previously managed to show that under conditions of pressure and temperature comparable to those exerted on the boundary between the transition zone and the lower mantle Earth, the famous rock is forced to return all of its water.

So that's about 700 kilometers deep, which would lie what could be the largest water reservoir in the world. And, after a careful analysis of the data collected by EarthScope USArray - a network of 2,000 seismographs spread on the floor of the United States - when 500 earthquakes, researchers believe. The records seem to corroborate this idea ( article published in the journal Science ). Through this research, scientists now hope to gain a better understanding of the water cycle on our planet, but also how the oceans were formed. All the water on Earth, so necessary for life might not only come from comets 

The existence of an ocean in the bowels of the Earth is confirmed

The existence of an ocean in the bowels of the Earth is confirmed ...
The Point.fr - Published 06/18/2014 at 16:02
Greater than all the oceans and seas combined water storage would be hidden in the transition zone of the Earth's mantle.

The discovery of this including a diamond inclusion of ringwoodite, announced last March, had raised the hypothesis of a gigantic ocean hidden beneath our feet.
The discovery of this including a diamond inclusion of ringwoodite, announced last March, had raised the hypothesis of a gigantic ocean hidden beneath our feet. © Richard Siemens / University of Alberta
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The theory is not new, but in recent months, evidence accumulates. The mantle could house a huge water tank, up to three times larger than all the oceans of our beautiful blue planet. It all started in March with the announcement of the discovery of a brown with little market value but special enough to deserve diamond published in the journal Nature . Indeed, after studying every angle the stone depths brought to the surface by a Brazilian volcano, a scientific team led by Graham Pearson of the University of Alberta in Canada , it was detected first natural inclusion of ringwoodite from land. A mineral that had been found so far in meteorites and produced in the laboratory, but it was only suspect the presence in the depths of the earth very quickly.

Francophone final will be held on 24 and 25 September in Montreal, Quebec.

The great French winner is called Marie-Charlotte Morin and his talents for a PhD student in the Institute of Genetics and Molecular and Cellular Biology at the University of Strasbourg . 26 years old, she was able to convince, and the public, and the jury, with a thesis entitled "The role of lin-15A and retinoblastoma protein in direct cellular reprogramming in vivo in C. elegans." Not very sexy as a subject? And if you were told that it was the story of an epithelial cell of the rectum of a worm naturally able to turn into motor neurons. A mechanism that could open many opportunities to medicine. Now listen to the humorous Marie-Charlotte Morin presentation.

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Came second, Noemie Mermet is, meanwhile, a doctoral student at the University of Auvergne in the Neuro-Dol laboratory. His thesis topic? "The involvement of 5-HT2A receptors in the modulation of interneurons PKCγ amid allodynia" or how to relieve people whose skin can not bear the slightest touch. Watch popularize skillfully his thesis.

Third elected Chrystelle Armata is a lawyer specializing in private law. She defended her thesis on "probationary loyalty to test new technologies," a highly topical subject insofar as it addresses the issue of video surveillance. Smile, you're on camera!

Francophone final will be held on 24 and 25 September in Montreal, Quebec.

Thesis, it can be understandable, exciting and funny. Proof in pictures!

Thesis, it can be understandable, exciting and funny. Proof in pictures!
The Point.fr - Published 06/12/2014 at 14:47
VIDEO. Three researchers, two biologists and a lawyer will defend the colors of France during the grand finale "My thesis in 180 seconds."

The contest my thesis in 180 seconds was organized for the first time in France by the CNRS and the Conference of University Presidents.  The international final will be held in Montreal, Quebec in September.
The contest my thesis in 180 seconds was organized for the first time in France by the CNRS and the Conference of University Presidents. The international final will be held in Montreal, Quebec in September. © © CPU / CNRS

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By CHLOE DURAND-PARENTI
Highlights of Point.fr

These are three young women, three student researchers - two biologists and a lawyer - who will represent France at the international finale of "My thesis in 180 seconds." The principle of the competition organized for the first time in France by the CNRS and the Conference of University Presidents is simple. This is achieved to present a thesis on very sharp in just three minutes, the clearest and most exciting possible for an uninformed public. The concept invented in the United States was imported in Quebec in 2012 and the country has wanted to extend the Francophonie.