DNA replication... without life

• 27 May 2010 by Kate McAlpine
• Magazine issue 2762. Subscribe and save

THE precursor of life may have learned how to copy itself thanks to simple convection at the bottom of the ocean. Lab experiments reveal how DNA replication could have occurred in tiny pores around undersea vents.

One of the initial steps towards life was the first molecule capable of copying itself. In the open ocean of early Earth, strands of DNA and loose nucleotides would have been too diluted for replication to occur. So how did they do it?

Inside many undersea hydrothermal vents, magnesium-rich rocks react with sea water. Such reactions create a heat source that could drive miniature convection currents in nearby pores in the rock, claim Christof Mast and Dieter Braun of Ludwig Maximilian University of Munich, Germany. They propose that such convection could concentrate nucleotides, strands of DNA, and polymerase, providing a setting that would promote replication.

Sea water inside pores on or near a vent's chimney may undergo thermal convection because the water at the wall of the pore closest to the vent's heat source would be warmer than the water near the furthermost wall, say Mast and Braun. If the pore contained strands of DNA, nucleotides, and polymerase they would ride upward in the warm current. The DNA strands would also be "unzipped" in the heat, splitting into two strands that each serve as templates for eventual replication.

All these components would then tend to shift away from the rising warmer region. In air, particles typically shift into a colder current because they are more likely to be pushed away by warmer, more energetic molecules than those on the cooler, calmer side. The researchers reckon a similar process would occur in the fluid in the vents.

Over time, the DNA templates, polymerase and nucleotides would collect at the bottom of a pore. Once there, they could become concentrated enough for the polymerase to bind new nucleotides to the single-strand DNA templates, replicating the original DNA (see diagram).

To test this theory, Mast and Braun put these ingredients into tubes 1.5 millimetres long. They used a laser to heat one side of the water and create thermal convection. Sure enough, they found that the DNA doubled every 50 seconds (Physical Review Letters, vol 104, p 188102).

But how would any replicated DNA have then moved between pores to recombine with new templates, producing a variety of configurations? Fatty acids in the water may have provided a shuttle service, says Braun. Last year, a team at Harvard University found that fatty acids driven by convection will form membranes. Such membranes could trap the concentrated genetic material and transport it, he says (Journal of the American Chemical Society, DOI: 10.1021/ja9029818).

"The work shows that DNA can be both concentrated and replicated under a very simple set of conditions," says Nick Lane at University College London.

http://www.newscientist.com/article/mg20627623.000-dna-replication-without-life.html

Unlocking the Chemistry of Exercise: How Metabolites Separate the Physically Fit from Unfit

A screening of hundreds of metabolites in the blood plasma of people at rest and after exercise paints a newly detailed picture of changes within the body--and reinforces links with metabolic and cardiovascular diseases

By Katherine Harmon   

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EXERCISE'S LASTING EFFECTS: Although many metabolites have been profiled in muscles, the impact of exercise on the levels of these compounds in blood plasma has remained less clear. A new large-scale study begins to describe some of the correlations they seem to have with physical fitness level.
ISTOCKPHOTO/SOUPSTOCK

The virtues of exercise are myriad: better cardiovascular health, decreased risk for diabetes, boosted mood, and even perhaps a leaner physique. But aside from such macro links and knowledge about the heart rates, blood–oxygen levels and hormonal responses related to exercise, scientists have a relatively cursory understanding of the chemical mechanisms at work in the body during and after physical activity.

A new study, published online May 26 in Science Translational Medicine, presents a thorough profile of exercise's impact on the human body's metabolites in plasma—and reveals vast biological differences among more- and less-fit individuals. The findings also reinforce links between exercise and insulin sensitivity as well as point to new ways to enhance exercise for both healthy individuals and those suffering from cardiovascular or metabolic diseases.

suite : http://www.scientificamerican.com/article.cfm?id=chemistry-of-exercise

Créer de toutes pièces une cellule vivante ? L’objectif, encore lointain, se rapproche : Craig Venter vient d'obtenir les premières bactéries au génome synthétisé in vitro.

Craig Venter a encore frappé. Dans la revue Science (1), le célèbre biologiste américain annonce aujourd’hui avoir obtenu la première bactérie contrôlée par un génome « synthétique », c’est-à-dire synthétisé in vitro. « Pour qui ambitionne de créer des bactéries n’existant pas dans la nature, c’est une avancée aussi importante que l’invention de l’imprimerie par rapport à l’écriture ! », s’enthousiasme Philippe Marlière, spécialiste de biologie synthétique au Genopole d’Evry. Certes, depuis les travaux de Miroslav Radman dans les années 1990, on savait déjà que le génome d’une bactérie donnée (en l’occurrence Salmonella) pouvait fonctionner dans une autre bactérie (Escherichia coli). Mais Venter, lui, a mis au point tout une chaîne d’assemblage permettant à terme de travailler avec des génomes conçus « à façon ».

L’histoire commence il y a quinze ans. En 1995, Venter et deux collègues cherchent à déterminer quel pourrait être le « génome minimal » permettant à une bactérie de survivre. Ils travaillent alors avec la bactérie Mycoplasma genitalium dont le génome, long de 600 000 paires de bases seulement, est l’un des plus petits connus. À l’aube des années 2000, ils ont fait le tour des 485 gènes de la bactérie, dont un peu plus d’une centaine, pris individuellement, semblent ne pas être indispensables à l’organisme.

La taille restreinte du génome de Mycoplasma genitalium en fait aussi un bon candidat pour qui ambitionne de synthétiser un génome de toutes pièces. C’est le cas de Venter. Encore faut-il mettre au point les outils nécessaires. Car les 600 000 paires de bases de ce génome dépassent largement les quelques milliers que les techniques alors disponibles permettent de synthétiser sans erreur. Venter franchit ce cap en 2008. La démarche adoptée consiste à synthétiser d’abord de courts fragments d’ADN, qui sont ensuite assemblés grâce à des enzymes permettent de les lier les uns aux autres. Et cela, jusqu’à obtention de fragments de la taille du quart du génome de Mycoplasma genitalium. Puis ces fragments sont introduits dans des levures servant d’usines, qui les assemblent bout à bout. Et l’on récupère le génome complet.

Dès lors, rien de plus simple que de l’introduire dans une bactérie réceptrice ? Erreur ! La tâche s’avère au contraire compliquée, en partie parce que Mycoplasma genitalium croît très lentement. L’équipe décide alors de travailler avec d’autres bactéries se multipliant beaucoup plus vite : le génome synthétisé est celui de Mycoplasma mycoides (nettement plus long que celui de Mycoplasma genitalium puisqu’il comprend un million de paires de bases), et il est transféré dans la bactérie Mycoplasma capricolum. Là encore, les obstacles ne manquent pas. Par exemple, la levure servant d’usine ne fixe pas à l’ADN de Mycoplasma mycoides certains groupements chimiques (des groupements méthyle) comme le ferait la bactérie. Et du coup, une fois transféré dans Mycoplasma capricolum, cet ADN y est détruit. Un problème (parmi d’autres), que les chercheurs résolvent finalement en modifiant in vitro l’ADN produit par la levure, avant de le transférer dans la bactérie hôte.

Et maintenant ? Venter ne s’en cache pas, son objectif est de créer une bactérie synthétique capable de produire des composés chimiques sur mesure. « Cela nécessitera de savoir manipuler des génomes encore plus gros, anticipe Philippe Marlière. Des génomes d’au moins 2 millions de paires de bases, dans lesquels on aura introduit des voies métaboliques artificielles. » Sans compter qu’un jour, il sera peut-être possible de produire des bactéries ayant un génome réellement nouveau. Ce jour-là, les autorités de régulation auront du pain sur la planche !

Cécile Klingler

(1) Daniel G. Gibson et al., Sciences, doi: 10.1126, 1190719, 2010

http://www.larecherche.fr/content/actualite-vie/article?id=27770

Mineral Isotopes Could Reveal Whether Dinosaurs Were Cold- or Warm-Blooded

A new method allows researchers to find the internal body temperature of long-dead animals by examining chemical bonds in their teeth or bones. Will dinosaurs be next?

By Katherine Harmon   

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A COLD-BLOODED KILLER?: Although dinosaurs are often thought of as ectothermic, researchers have yet to prove whether or not they could regulate their own body temperature like most modern birds.
WIKIPEDIA COMMONS/CHARLES R. KNIGHT

The great spine-chilling Tyrannosaurus rex has a reputation for having killed its prey in cold blood. But was this ancient dinosaur really a cold-blooded ectotherm?

Strong evolutionary links among reptiles (ectotherms), birds (mostly endothermic, or warm-blooded) and dinosaurs make it hard to conclude whether nonavian dinosaurs were also unable to regulate their own internal body temperatures.

A new method of studying the chemical bonds in a mineral found in the teeth and bones of animals might finally offer a way to settle the debate.

Researchers found that heavy isotopes of carbon and oxygen bond differently in the biological version of the mineral apatite (which is a main component of bones and teeth of animals, both living and long extinct). These rare isotopes are more prone to bond in big clumps at low temperatures, "therefore, if you can measure the clumping accurately enough, you can work out the temperature at which a mineral precipitated," explains Robert Eagle, a postdoctoral researcher in geochemistry at the California Institute of Technology's Division of Geological and Planetary Sciences, and lead author of the new study, which was published online May 24 in Proceedings of the National Academy of Sciences. "In the case of teeth and bone, this will be the body temperature of the organism."

From ancient seas
A similar way of examining ancient limestone and shells has helped researchers estimate ambient rock temperatures by looking at the bonding structures in calcium carbonate.

"Most people were focused on using this to look at climate change in the past and various geological problems like the heating and cooling of the Earth's crust," Eagle says. But that approach gave John Eiler, a professor of geology and geochemistry at Caltech and co-author of the study, the idea that the same analysis might be applied to the bio-apatite lingering in fossilized teeth or bones. And if it worked, the method "would then measure body temperatures of extinct vertebrates," Eagle says.

Eagle and his colleagues tested the method on a variety of living and extinct endothermic animals, including a tooth from a modern Indian elephant (Elephas maximus indicus), a tooth from a modern white rhinoceros (Ceratotherium simum), teeth from extinct late Pleistocene woolly mammoths (Mammuthus primigenius), and enamel from extinct Miocene rhinocerotid species. Their analysis proved to be accurate to 1 to 2 degrees Celsius for the modern animals, thereby lending a highly precise approximation for animals that died some 12 million years ago, such as the Miocene rhinocerotid.

Unknown origin
Finding out whether or not T. rex were ectotherms would not only sate curiosity, it would also shed light on the whole emergence of internal temperature regulation in animals, which, as the authors of the new study noted, is "among the most fundamental aspects of their biology." And currently, the emergence of warm-bloodedness "is a major physiological change that occurred at an unknown stage during the evolutionary transition to mammals and birds."

As part of the study, the group also tested teeth from modern Nile crocodiles (Crocodylus niloticus), teeth from modern American alligators (Alligator mississippienis), and enamel from extinct Miocene alligator species. Comparing the extinct Miocene endotherms with ectotherms from the same site in Florida found a difference of 6 degrees C, revealing "a measurable difference between mammals and ectotherms," Eagle notes—a difference that might be used to compare even older species found together.

The team has not yet figured out just how far back they can use bio-apatite assessment to determine body temperature. The new study examines materials as old as 12 million years, but parsing out dinosaur temperature regulation patterns will require going back tens and hundreds of millions of years, "so that will be a new frontier," Eagle says.

Ancient climes uncovered
Like the calcium carbonate environmental temperature testing method that inspired Elier to turn to vertebrate measurements, bio-apatite can also help researchers get a sense of ambient temperature. Ectotherms, because their internal temperatures mirror those around them, can be a living gauge and record of past temperatures.

Other estimates for ancient climates have been based on plant fossils, core samples and complex reconstruction models but, as Eagle notes, "all are to some extent uncertain as they are influenced by factors other than temperature that can be difficult to control for, particularly in the distant past." Their measurement of bio-apatite "seems only to be a function of temperature," he says, which is "a big advantage."

The method, however, is not infallible: In modern ectothermic species, it is known that the body temperature can change 8 to 12 degrees C each day and some 20 degrees C throughout the year. So the measurements derived from these animals "seemed to be recording more or less an average temperature," Eagle says. And he also posits that larger ectotherms, the size of big dinosaurs, might be able to sustain warmer body temperatures simply by retaining heat in their larger bodies, so future research might have to take that variable into account.

In the meantime, the group is hoping to uncover more ground-shaking news about how cold-hearted the dinosaurs really were.

http://www.scientificamerican.com/article.cfm?id=body-temperature-extinct-animals