Biologi

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Science, May 21, 2010: For 15 years, J. Craig Venter has chased a dream: to build a genome from scratch and use it to make synthetic life. Now, he and his team at the J. Craig Venter Institute (JCVI) in Rockville, Maryland, and San Diego, California, say they have realized that dream. In this week's Science Express they describe the stepwise creation of a bacterial chromosome and the successful transfer of it into a bacterium, where it replaced the native DNA. Powered by the synthetic genome, that microbial cell began replicating and making a new set of proteins. This is "a defining moment in the history of biology and biotechnology," says Mark Bedau, a philosopher at Reed College in Portland, Oregon, and editor of the scientific journal Artificial Life. "It represents an important technical milestone in the new field of synthetic genomics," says yeast biologist Jef Boeke of Johns Hopkins University School of Medicine in Baltimore, Maryland. The synthetic genome created by Venter's team is almost identical to that of a natural bacterium. It was achieved at great expense, an estimated $40 million, and effort, 20 people working for more than a decade. Despite this success, creating heavily customized genomes, such as ones that make fuels or pharmaceuticals, and getting them to "boot" up the same way in a cell is not yet a reality. "There are great challenges ahead before genetic engineers can mix, match, and fully design an organism's genome from scratch," notes Paul Keim, a molecular geneticist at Northern Arizona University in Flagstaff - Synthetic Genome Brings New Life to Bacterium

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Technology Review, September 1, 2010: For years, claims have circulated that red rain which fell in India in 2001, contained cells unlike any found on Earth. Now new evidence that these cells can reproduce is about to set the debate alive. Panspermia is the idea that life exists throughout the universe in comets, asteroids and interstellar dust clouds and that life of Earth was seeded from one or more of these sources. Panspermia holds that we are all extraterrestrials. While this is certainly not a mainstream idea in science, a growing body of evidence suggests that it should be carefully studied rather than casually disregarded - The Extraordinary Tale of Red Rain, Comets and Extraterrestrials

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UPI, September 3, 2010: The start of life on Earth presents a paradox, scientists say: How did amino acids arise before there were biological catalysts needed to build them? It's a chicken-and-the-egg puzzle: How could the basic biochemicals like amino acids and nucleotides have come about when there were no catalysts, like proteins or ribosomes, around to create them? Now scientists propose that a third type of catalyst could have jumpstarted metabolism and life itself, deep in hydrothermal ocean vents, an article in The Biological Bulletin says. The scientists' theory says molecular structures involving transition metal elements -- iron, copper, nickel, etc. -- and ligands -- small organic molecules -- could have catalyzed the synthesis of basic biochemicals, monomers, that acted as building blocks for more complex molecules, leading ultimately to the origin of life - Chemical basis for first life theorized

The first metazoa living in permanently anoxic conditions
Sulfur: Fountainhead of life in the Universe?

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Uniformed Services University of the Health Sciences, September 3, 2010: The discovery of long-sought chemical antioxidants in the world’s toughest microbe is reported in a breakthrough study titled “Small-Molecule Antioxidant Proteome-Shields in Deinococcus radiodurans.” First studied nearly 50 years ago, this bacterium can survive massive exposures to gammaradiation, ultraviolet radiation, desiccation, and other agents which kill cells by generating reactive oxygen species (ROS). The study, headed by Michael J. Daly, Ph.D., professor at the USU Department of Pathology, appears in the September 3 edition of PLoS ONE. Daly’s team previously reported that D. radiodurans accomplishes its astonishing survival feats in an unexpected way - Conan the Bacterium Reveals its Recipe for Survival

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Lawrence Livermore National Laboratory, September 12, 2010: Life on Earth as we know it really could be from out of this world. New research from Lawrence Livermore National Laboratory scientists shows that comets that crashed into Earth millions of years ago could have produced amino acids – the building blocks of life. Amino acids are critical to life and serve as the building blocks of proteins, which are linear chains of amino acids. In the Sept. 12 online edition of the journal Nature Chemistry, LLNL’s Nir Goldman and colleagues found that simple molecules found within comets (such as water, ammonia, methylene and carbon dioxide) just might have been instigators of life on Earth. His team discovered that the sudden compression and heating of cometary ices crashing into Earth can produce complexes resembling the amino acid, glycine. Origins of life research initially focused on the production of amino acids from organic materials already present on the planet. However, further research showed that Earth’s atmospheric conditions consisted mainly of carbon dioxide, nitrogen and water. Shock-heating experiments and calculations eventually proved that synthesis of organic molecules necessary for amino acid production will not occur in this type of environment. “There’s a possibility that the production or delivery of prebiotic molecules came from extraterrestrial sources,” Goldman said - Amino acids could be produced within impacting comets, bringing life to earth


Computer simulations show that long chains containing carbon-nitrogen bonds can form during shock compression of a cometary ice.
Upon expansion, the long chains break apart to form complexes containing the protein building amino acid glycine.

[nico]

Ny interessant viten om vann

http://news.sciencemag.org/sciencenow/2 ... -is-a.html

Water may seem like a dull liquid. But at the molecular scale, there's a party going on. New simulations reveal that water molecules actually form two different types of structures that break apart and recombine at lightning speeds. Such complexity just might be the reason why life as we know it sprang forth in a wet environment.

As simple as an individual water molecule is—two atoms of hydrogen bonded with one of oxygen—it forms weak bonds to its neighbors creating more-complex structures. That's allowed it to serve as the medium for the growth and evolution of the most complex molecules in the universe, including enzymes, proteins, and the mother of all known living creatures, DNA. But why water and not, say, hydrogen peroxide or even ammonia? Scientists have been wrestling with this quandary for over a century. Indeed, 5 years ago, Science called this one of the 125 most important unresolved scientific issues.

A new study might have uncovered an essential clue. Researchers used computer models to probe how water molecules form structures, a phenomenon that has resisted visual examination so far. Working with standard desktop computers, the team applied models originally designed to study complex systems, such as the Internet, the spread of viruses, and the folding of proteins, to investigate the configurations of water at the smallest scales.

What the researchers observed, they reported online in The Journal of Physical Chemistry B, is that water molecules bond with one another in a surprisingly complex and dynamic way. Any given volume of water contains two types of molecular structures—one a blobby, loosely packed agglomeration and the other a tight, regular arrangement resembling a crystal lattice. But both structures tend to break apart and recombine frequently, on the order of extremely tiny fractions of a second. The result is a chaotic mix of water molecules. Within that mix, the hydrogen atoms form connections that function like hooks, onto which carbon or nitrogen atoms can presumably grab to form the beginnings of complex organic molecules. And the process can dramatically influence the motion of even more-complex biological systems, such as proteins, by helping their assembly. As far as anyone knows, no other liquid demonstrates this property.

The finding introduces "a framework to understand how water with its [hidden structure] influences protein function at the fundamental level," says physicist and co-author Francesco Rao of the University of Freiburg in Germany. The models present a "very crude" first look at these structures, adds physical chemist and co-author Peter Hamm of the University of Zürich in Switzerland. "It is becoming clearer and clearer," he says, that "water is more than just a solvent, but actually an integral part of the functional structure of proteins."

It's "a fascinating and provocative paper," says physical chemist James Skinner of the University of Wisconsin, Madison. The study, he says, helps to illuminate subtle but important details about molecular motions in water.

The demonstration by a computer model that water exists in two different microscopic constructions is a "wonderful discovery," adds physicist H. Eugene Stanley of Boston University. Although earlier laboratory experiments have suggested this possibility, he says, the authors are the first to model the process in detail. It's a step toward unraveling why this liquid can produce 15 types of ice, for example. More important, Stanley says, "We will never understand biology until we understand water."

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University of Aberdeen, November 10, 2010: Evidence found in Scottish rocks has revealed that a critical point in evolution took place 1.2 billion years ago — several hundred million years earlier than scientists had previously understood - Scottish rocks reveal key point in evolution occurred 400 million years earlier

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Nature, December 7, 2010: Days after an announcement that a strain of bacteria can apparently use arsenic in place of phosphorous to build its DNA and other biomolecules — an ability unknown in any other organism — some scientists are questioning the finding and taking issue with how it was communicated to non-specialists. Many readily agree that the bacterium, described last week in Science and dubbed GFAJ-1, performs a remarkable feat by surviving high concentrations of arsenic in California's Mono Lake and in the laboratory. But data in the paper, they argue, suggest that it is just as likely that the microbe isn't using the arsenic, but instead is scavenging every possible phosphate molecule while fighting off arsenic toxicity. The claim at a NASA press briefing that the bacterium represents a new chemistry of life is at best premature, they say - Microbe gets toxic response

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The Daily Telegraph, January 13, 2011: Previous efforts in the 1990s to recover nuclei in cells from the skin and muscle tissue from mammoths found in the Siberian permafrost failed because they had been too badly damaged by the extreme cold. But a technique pioneered in 2008 by Dr. Teruhiko Wakayama, of the Riken Centre for Developmental Biology, was successful in cloning a mouse from the cells of another mouse that had been frozen for 16 years. Now that hurdle has been overcome, Akira Iritani, a professor at Kyoto University, is reactivating his campaign to resurrect the species that died out 5,000 years ago. "Now the technical problems have been overcome, all we need is a good sample of soft tissue from a frozen mammoth," he told The Daily Telegraph - Mammoth 'could be reborn in four years'

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The Roslin Institute, University of Edinburgh, January 13, 2011: Chickens genetically modified to prevent them spreading bird flu have been produced by researchers at The Roslin Institute of the University of Edinburgh and the University of Cambridge. The scientists have successfully developed genetically modified (transgenic) chickens that do not transmit avian influenza virus to other chickens with which they are in contact. This genetic modification has the potential to stop bird flu outbreaks spreading within poultry flocks. This would not only protect the health of domestic poultry but could also reduce the risk of bird flu epidemics leading to new flu virus epidemics in the human population. The study, funded by the Biotechnology and Biological Sciences Research Council (BBSRC), is published today in the journal Science - GM chickens that don’t transmit bird flu developed

[Panther]

http://www.newscientist.com/article/dn20265-biologys-dark-matter-hints-at-fourth-domain-of-life.html

The bold statement is the result of an analysis of water samples collected from the world's seas. Jonathan Eisen at the University of California, Davis, Genome Center has identified gene sequences hidden within these samples that are so unusual they seem to have come from organisms that are only distantly related to cellular life as we know it. So distantly related, in fact, that they may belong to an organism that sits in an entirely new domain.

Most species on the planet look like tiny single cells, and to work out where they fit on the tree of life biologists need to be able to grow them in the lab. Colonies like this give them enough DNA to run their genetic analyses. The problem is, the vast majority of these cells species – 99 per cent of them is a reasonable bet – refuse to be cultured in this way. "They really are the dark matter of the biological universe," says Eisen.
Life's dark matter

To probe life's dark matter, Eisen, Craig Venter of the J. Craig Venter Institute in Rockville, Maryland, and their colleagues have resorted to a relatively new technique called metagenomics. This can "sequence the crap out of any DNA samples", whether they are collected from the environment or come from lab cultures, says Eisen.

When Eisen and Venter used the technique on samples collected from the Global Ocean Sampling Expedition, they found that some sequences belonging to two superfamilies of genes – recA and rpoB – were unlike any seen before.

Younger than they look?

But some think any talk of a fourth domain of cellular life is premature. Radhey Gupta at McMaster University in Hamilton, Ontario, Canada, calls the finding "very exciting", but cautions that there are other explanations.

For instance, the sequences could be from cellular organisms living in unique habitats that caused their genes to undergo rapid evolution. That would give the false impression that the "new" life forms diverged from all others a very long time ago.

"There is still debate [over] how to clearly distinguish the three proposed domains of life, and how they are interrelated," Gupta says. "The suggestion [of] a fourth domain will only add to the confusion."

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Massachusetts Institute of Technology, July 15, 2011: MIT and Harvard researchers have developed technologies that could be used to rewrite the genetic code of a living cell, allowing them to make large-scale edits to the cell’s genome. Such technology could enable scientists to design cells that build proteins not found in nature, or engineer bacteria that are resistant to any type of viral infection. The technology, described in the July 15 issue of Science, can overwrite specific DNA sequences throughout the genome, similar to the find-and-replace function in word-processing programs. Using this approach, the researchers can make hundreds of targeted edits to the genome of E. coli, apparently without disrupting the cells’ function - Scientists unveil tools for rewriting the code of life

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Science Fair, July 18, 2011: A stunning movie of the never-before-seen bioelectrical signals that storm across an embryo's surface as it develops has been released by researchers at Tufts University. The footage of frog embryos is like watching weather chasing across a planet, followed by bright fireworks of light signaling the emergence of the brain, spinal cord and eyes. It's an amazing view of something that's always been invisible -- the bioelectric currents that help shape development. It's published online this week in the journal Developmental Dynamics. The time-lapse video shows two frog embryos side by side in a dish. At the two second mark in the video, a bright white dot appears at the top of the embryo on the left, which lengthens out into a line going about halfway down the rounded ball of cells. "The brain is forming," says Dany Adams, a biology professor and member of the Tufts Center for Regenerative and Developmental Biology, and senior author on the paper. "It's coming up on the horizon and as it rolls forward you're seeing the very bright stripe down the middle, which is the nervous system forming." That line then disappears as both dive deep down into the body and are covered up again - VIDEO: Footage of embryo bioelectric currents

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RIKEN Research, July 22, 2011: Researchers at the SPring-8 Photon Science Research Division are developing a range of imaging tools to reveal the remarkable mechanism of bacterial locomotion. Supramolecules comprising many kinds of proteins and nucleic acids are present in all living organisms. Often with precise structures and a variety of parts, these supramolecules exhibit complex movements and exhaustive functions, essentially behaving like nanomachines - New imaging techniques reveal the workings of supramolecular nanomachines

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European Molecular Biology Laboratory, August 7, 2011: Researchers can now watch molecules move in living cells, literally millisecond by millisecond, thanks to a new microscope developed by scientists at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany. Published online today in Nature Biotechnology, the new technique provides insights into processes that were so far invisible - New microscope follows single molecules by the millisecond