Monday, October 19, 2009

CHINESE AND AMERICAN PALEONTOLOGISTS DISCOVER A NEW MESOZOIC MAMMAL

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An international team of paleontologists has discovered a new species of mammal that lived 123 million years ago in what is now the Liaoning Province in northeastern China.

The newly discovered animal, Maotherium asiaticus, comes from famous fossil-rich beds of the Yixian Formation. This new remarkably well preserved fossil, as reported in the October 9 issue of the prestigious journal Science, offers an important insight into how the mammalian middle ear evolved. The discoveries of such exquisite dinosaur-age mammals from China provide developmental biologists and paleontologists with evidence of how developmental mechanisms have impacted the morphological (body-structure) evolution of the earliest mammals and sheds light on how complex structures can arise in evolution because of changes in developmental pathways.

"What is most surprising, and thus scientifically interesting, is this animal's ear," says Dr. Zhe-Xi Luo, curator of vertebrate paleontology and associate director of science and research at Carnegie Museum of Natural History. "Mammals have highly sensitive hearing, far better than the hearing capacity of all other vertebrates, and hearing is fundamental to the mammalian way of life. The mammalian ear evolution is important for understanding the origins of key mammalian adaptations."

Thanks to their intricate middle ear structure, mammals (including humans) have more sensitive hearing, discerning a wider range of sounds than other vertebrates. This sensitive hearing was a crucial adaptation, allowing mammals to be active in the darkness of the night and to survive in the dinosaur-dominated Mesozoic.

Mammalian hearing adaptation is made possible by a sophisticated middle ear of three tiny bones, known as the hammer (malleus), the anvil (incus), and the stirrup (stapes), plus a bony ring for the eardrum (tympanic membrane). These mammal middle ear bones evolved from the bones of the jaw hinge in their reptilian relatives. Paleontologists have long attempted to understand the evolutionary pathway via which these precursor jawbones became separated from the jaw and moved into the middle ear of modern mammals.

To evolutionary biologists, an understanding of how the sophisticated and highly sensitive mammalian ear evolved may illuminate how a new and complex structure transforms through evolution. According to the Chinese and American scientists who studied this new mammal, the middle ear bones of Maotherium are partly similar to those of modern mammals; but Maotherium's middle ear has an unusual connection to the lower jaw that is unlike that of adult modern mammals. This middle ear connection, also known as the ossified Meckel's cartilage, resembles the embryonic condition of living mammals and the primitive middle ear of pre-mammalian ancestors.

Because Maotherium asiaticus is preserved three-dimensionally, paleontologists were able to reconstruct how the middle ear attached to the jaw. This can be a new evolutionary feature. Or, it can be interpreted as having a "secondarily reversal to the ancestral condition," meaning that the adaptation is the caused by changes in development.

Modern developmental biology has shown that developmental genes and their gene network can trigger the development of unusual middle ear structures, such as "re-appearance" of the Meckel's cartilage in modern mice. The middle ear morphology in fossil mammal Maotherium of the Cretaceous (145-65 million years ago) is very similar to the mutant morphology in the middle ear of the mice with mutant genes. The scientific team studying the fossil suggests that the unusual middle ear structure, such as the ossified Meckel's cartilage, is actually the manifestation of developmental gene mutations in the deep times of Mesozoic mammal evolution.

Maotherium asiaticus is a symmetrodont, meaning that it has teeth with symmetrically arranged cusps specialized for feeding on insects and worms. It lived on the ground and had a body 15 cm (5 inches) long and weighing approximately 70 to 80 grams (.15 to .17 lbs). By studying all features in this exquisitely preserved fossil, researchers believe Maotherium to be more closely related to marsupials and placentals than to monotremes—primitive egg-laying mammals of Australia and New Guinea such as the platypus.

(Photo: Mark A. Klingler/Carnegie Museum of Natural History)

Carnegie Museum of Natural History

SCIENTISTS DECIPHER THE 3-D STRUCTURE OF THE HUMAN GENOME

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Scientists have deciphered the three-dimensional structure of the human genome, paving the way for new insights into genomic function and expanding our understanding of how cellular DNA folds at scales that dwarf the double helix.

In a paper featured this week on the cover of the journal Science, they describe a new technology called Hi-C and apply it to answer the thorny question of how each of our cells stows some three billion base pairs of DNA while maintaining access to functionally crucial segments. The paper comes from a team led by scientists at Harvard University, the Broad Institute of Harvard and MIT, University of Massachusetts Medical School, and the Massachusetts Institute of Technology.

"We've long known that on a small scale, DNA is a double helix," says co-first author Erez Lieberman-Aiden, a graduate student in the Harvard-MIT Division of Health Science and Technology and a researcher at Harvard's School of Engineering and Applied Sciences and in the laboratory of Eric Lander at the Broad Institute. "But if the double helix didn't fold further, the genome in each cell would be two meters long. Scientists have not really understood how the double helix folds to fit into the nucleus of a human cell, which is only about a hundredth of a millimeter in diameter. This new approach enabled us to probe exactly that question."

The researchers report two striking findings. First, the human genome is organized into two separate compartments, keeping active genes separate and accessible while sequestering unused DNA in a denser storage compartment. Chromosomes snake in and out of the two compartments repeatedly as their DNA alternates between active, gene-rich and inactive, gene-poor stretches.

"Cells cleverly separate the most active genes into their own special neighborhood, to make it easier for proteins and other regulators to reach them," says Job Dekker, associate professor of biochemistry and molecular pharmacology at UMass Medical School and a senior author of the Science paper.

Second, at a finer scale, the genome adopts an unusual organization known in mathematics as a "fractal." The specific architecture the scientists found, called a "fractal globule," enables the cell to pack DNA incredibly tightly -- the information density in the nucleus is trillions of times higher than on a computer chip -- while avoiding the knots and tangles that might interfere with the cell's ability to read its own genome. Moreover, the DNA can easily unfold and refold during gene activation, gene repression, and cell replication.

"Nature's devised a stunningly elegant solution to storing information -- a super-dense, knot-free structure," says senior author Eric Lander, director of the Broad Institute, who is also professor of biology at MIT, and professor of systems biology at Harvard Medical School.

In the past, many scientists had thought that DNA was compressed into a different architecture called an "equilibrium globule," a configuration that is problematic because it can become densely knotted. The fractal globule architecture, while proposed as a theoretical possibility more than 20 years ago, has never previously been observed.

Key to the current work was the development of the new Hi-C technique, which permits genome-wide analysis of the proximity of individual genes. The scientists first used formaldehyde to link together DNA strands that are nearby in the cell's nucleus. They then determined the identity of the neighboring segments by shredding the DNA into many tiny pieces, attaching the linked DNA into small loops, and performing massively parallel DNA sequencing.

"By breaking the genome into millions of pieces, we created a spatial map showing how close different parts are to one another," says co-first author Nynke van Berkum, a postdoctoral researcher at UMass Medical School in Dekker's laboratory. "We made a fantastic three-dimensional jigsaw puzzle and then, with a computer, solved the puzzle."

University of Harvard

SCIENTISTS MEASURE THE RATE OF ASCENT OF VOLCANIC MAGMA

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Plinian volcanic eruptions are notoriously destructive. These very powerful eruptions often occur after long periods of quiescence and are preceded by relatively short periods of seismic restiveness. Volcanoes that tend to show this kind of behaviour include Mount Vesuvius in Italy, Mt. Pinatubo in the Philippines and Mt. St. Helens in the USA. Professor Donald Dingwell of Ludwig-Maximilians-Universität (LMU) in Munich, together with Professor Jonathan Castro of the University of Orléans in France, has now been able experimentally to measure the speed with which molten rock rises during a Plinian eruption.

The two scientists studied rocks that erupted from the volcano Chaitén in Southern Chile in May 2008. Their experimental analyses revealed that the magma must have ascended from the interior of the volcano to the surface within a period of only four hours. These results raise the disturbing prospect that it may not be practically possible to give adequate warning and carry out orderly evacuation procedures prior to this type of eruption.

The first description of a highly explosive volcanic eruption dates from the year 79 AD. In that year, the Roman author Pliny the Younger observed the famous eruption of Mount Vesuvius, which buried the city of Pompeii under enormous amounts of ash and pumice. Pliny's description led later students of volcanology to name eruptions of this type after him. Plinian volcanoes are characterized by long periods of quiescence, during which they show very little activity. Moreover, the rare eruptions are preceded by quite short bursts of tectonic activity, signalled only by minor earth tremors and increased emission of gas. During the build-up that precedes the eruption itself, magma rises to the surface within a very brief interval, and is expelled from the volcano at high pressure in a huge explosion.

More than a dozen Plinian volcanoes are found in the Andes of South America, yet scientists observed a typical Plinian eruption there only last year. On May 2nd 2008, the volcano Chaitén in Southern Chile suddenly began to spew large quantities of ash and rock fragments into the air. The erupted material eventually gave rise to an ash plume some 20 km high. The town of Chaitén, 10 km away, was covered by a layer of ash several centimeters thick and had to be evacuated. "This eruption was particularly noteworthy, because the volcano had been quiescent for over 9000 years", says Professor Donald Dingwell, Director of the Department of Earth and Environmental Sciences at LMU Munich. "The best estimates suggest that the last eruption took place in the year 7240 BC."

Together with the Jonathan Castro from the University of Orléans in France, Dingwell has now been able to calculate the velocity with which the volcanic material must have risen within the magma chamber. The researchers collected samples of pumice from the eruption debris, and these were then subjected to a series of laboratory analyses in Munich, while being heated to a temperature of 825 degrees centigrade at high pressure. After a certain time under these conditions, characteristic crystalline margins begin to develop around the feldspar crystals in the pumice. Dingwell and Castro systematically varied the temperature and pressure, and measured the time it took for these crystalline margins to grow. "The interesting thing is that we found none of these crystalline margins in the natural samples themselves", reports Dingwell. "From that we can conclude that the material must have risen so quickly that there was no time for them to form."

The researchers were surprised by the results of their analyses. Their calculations suggested that the rock fragments they had collected had ascended from the earth's interior to the crater floor in less than four hours. To accomplish this, the material must have risen at a rate of about one meter per second. "This figure is very disturbing, because it implies that a Plinian eruption can develop with astonishing speed", Dingwell points out. "In such a case, it would be well nigh impossible to give adequate warning of an impending eruption, in particular if the period of activity preceding it also happened to be very short." This was precisely what happened at Chaitén. The inhabitants of the town felt the first perceptible earthquakes on the evening of April 30th. The first ashfall arrived on the next day, and on May 2nd there was a violent eruption, followed by the appearance of a huge cloud of ash over the mountain.

"The problem with such short periods of heightened activity is that they may, but do not necessarily, forecast an eruption", explains Dingwell. "In the case of Chaitén we knew that we were dealing with a highly explosive volcano. What we did not know was what kind of activity would give notice of an impending eruption." Normally, patterns of volcanic activity are observed only locally, for instance by geophysicists who measure seismic waves, or by geochemists who analyse the gases emitted in the vicinity of a volcano. "Our study is something entirely new and complements the local observations by using a well-founded experimental and theoretical approach", says Dingwell. "In our view, this will become an important option in future investigations of the behaviour of volcanoes."

Ludwig-Maximilians-Universität

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