Unselfish Molecules May Have Helped Give Birth to the Genetic Material of Life

ScienceDaily (Mar. 8, 2010) — One of the biggest questions facing scientists today is how life began. How did non-living molecules come together in that primordial ooze to form the polymers of life? Scientists at the Georgia Institute of Technology have discovered that small molecules could have acted as "molecular midwives" in helping the building blocks of life's genetic material form long chains and may have assisted in selecting the base pairs of the DNA double helix.New research suggests that small molecules could have acted as "molecular midwives" in helping the building blocks of life's genetic material form long chains and may have assisted in selecting the base pairs of the DNA double helix. (Credit: iStockphoto)

The research appears in the online early edition of the Proceedings of the National Academy of Sciences beginning March 8, 2010.

"Our hypothesis is that before there were protein enzymes to make DNA and RNA, there were small molecules present on the pre-biotic Earth that helped make these polymers by promoting molecular self-assembly," said Nicholas V. Hud, professor in the School of Chemistry and Biochemistry at the Georgia Institute of Technology. "We've found that the molecule ethidium can assist short oligonucleotides in forming long polymers and can also select the structure of the base pairs that hold together two strands of DNA."

One of the biggest problems in getting a polymer to form is that, as it grows, its two ends often react with each other instead of forming longer chains. The problem is known as strand cyclization, but Hud and his team discovered that using a molecule that binds between neighboring base pairs of DNA, known as an intercalator, can bring short pieces of DNA and RNA together in a manner that helps them create much longer molecules.

"If you have the intercalator present, you can get polymers. With no intercalator, it doesn't work, it's that simple," said Hud.

Hud and his team also tested how much influence a midwife molecule might have had on creating DNA's Watson-Crick base pairs (A pairs with T, and G pairs with C). They found that the midwife used could determine the base pairing structure of the polymers that formed. Ethidium was most helpful for forming polymers with Watson-Crick base pairs. Another molecule that they call aza3 made polymers in which each A base is paired with another A.

"In our experiment, we found that the midwife molecules present had a direct effect on the kind of base pairs that formed. We're not saying that ethidium was the original midwife, but we've shown that the principle of a small molecule working as a midwife is sound. In our lab, we're now searching for the identity of a molecule that could have helped make the first genetic polymers, a sort of 'unselfish' molecule that was not part of the first genetic polymers, but was critical to their formation," said Hud.

The work was supported by the National Aeronautics and Space Administration and the National Science Foundation.

Read More Here

Why birds are NOT descended from dinosaurs

By Daily Mail Reporter
Last updated at 12:02 PM on 10th June 2009

Birds did not descend from dinosaurs, scientists claim after studying how our feathered friends move and breathe.

It has been known for decades that the femur, or thigh bone in birds is largely fixed making birds 'knee runners.'

But researchers from Oregon State University found the bone also stops their lung collapsing, allowing the breathing capacity for flight.

The thigh bone stops a bird's lungs from collapsing, allowing them the breathing capacity to fly unlike dinosaurs like sauropods

Every other animal that has walked on land, including humans, elephants, lizards and theropod dinosaurs - a family that includes the T Rex, had a moveable thigh bone.

The find may force paleontologists to reconsider their long-held belief that modern birds are direct descendants of ancient, meat-eating dinosaurs.

'It's amazing we didn't understand a basic aspect of bird biology,' said US researcher Professor John Ruben.

'A velociraptor did not just spout feathers at some point and fly off into the sunset.

Running and walking is generated mostly at knee and ankle joints in birds

'Birds probably evolved on a parallel path alongside dinosaurs, starting that process before most dinosaur species even existed.'

Characteristics such as feathers, wings and a bird's unique way of moving therefore developed separately.

Dinosaurs and birds both thrived in the Cretaceous period between 145 and 65 million years ago.

The Archaeopteryx, long considered the oldest bird, lived 150million years ago, while dinosaurs emerged earlier around 200million years ago.

However, Professor Ruben said he didn't discount birds and dinosaurs sharing an ancient ancestor such as the small, reptilian 'thecodonts' that roamed Earth 250million years ago.

'It just seems pretty clear now that birds were evolving all along on their own and did not descend directly from the theropod dinosaurs,' he concluded.

There study has been published in The Journal of Morphology.

Read more: http://www.dailymail.co.uk/sciencetech/article-1192019/Why-birds-NOT-descended-dinosaurs.html#ixzz0hnJtScr9

Bird-from-Dinosaur Theory of Evolution Challenged: Was It the Other Way Around?

ScienceDaily (Feb. 10, 2010) — A new study just published in the Proceedings of the National Academy of Sciences provides yet more evidence that birds did not descend from ground-dwelling theropod dinosaurs, experts say, and continues to challenge decades of accepted theories about the evolution of flight.

An image drawn in 1915 by naturalist William Beebe suggests a hypothetical view of what early birds may have looked like, gliding down from trees - and it bears a striking similarity to a fossil discovered in 2003 that is raising new doubts about whether birds descended from ground-dwelling theropod dinosaurs.

A new analysis was done of an unusual fossil specimen discovered in 2003 called "microraptor," in which three-dimensional models were used to study its possible flight potential, and it concluded this small, feathered species must have been a "glider" that came down from trees. The research is well done and consistent with a string of studies in recent years that pose increasing challenge to the birds-from-dinosaurs theory, said John Ruben, a professor of zoology at Oregon State University who authored a commentary in PNAS on the new research.

The weight of the evidence is now suggesting that not only did birds not descend from dinosaurs, Ruben said, but that some species now believed to be dinosaurs may have descended from birds.

"We're finally breaking out of the conventional wisdom of the last 20 years, which insisted that birds evolved from dinosaurs and that the debate is all over and done with," Ruben said. "This issue isn't resolved at all. There are just too many inconsistencies with the idea that birds had dinosaur ancestors, and this newest study adds to that."

Almost 20 years of research at OSU on the morphology of birds and dinosaurs, along with other studies and the newest PNAS research, Ruben said, are actually much more consistent with a different premise -- that birds may have had an ancient common ancestor with dinosaurs, but they evolved separately on their own path, and after millions of years of separate evolution birds also gave rise to the raptors. Small animals such as velociraptor that have generally been thought to be dinosaurs are more likely flightless birds, he said.

"Raptors look quite a bit like dinosaurs but they have much more in common with birds than they do with other theropod dinosaurs such as Tyrannosaurus," Ruben said. "We think the evidence is finally showing that these animals which are usually considered dinosaurs were actually descended from birds, not the other way around."

Another study last year from Florida State University raised similar doubts, Ruben said.

In the newest PNAS study, scientists examined a remarkable fossil specimen that had feathers on all four limbs, somewhat resembling a bi-plane. Glide tests based on its structure concluded it would not have been practical for it to have flown from the ground up, but it could have glided from the trees down, somewhat like a modern-day flying squirrel. Many researchers have long believed that gliders such as this were the ancestors of modern birds.

"This model was not consistent with successful flight from the ground up, and that makes it pretty difficult to make a case for a ground-dwelling theropod dinosaur to have developed wings and flown away," Ruben said. "On the other hand, it would have been quite possible for birds to have evolved and then, at some point, have various species lose their flight capabilities and become ground-dwelling, flightless animals -- the raptors. This may be hugely upsetting to a lot of people, but it makes perfect sense."

In their own research, including one study just last year in the Journal of Morphology, OSU scientists found that the position of the thigh bone and muscles in birds is critical to their ability to have adequate lung capacity for sustained long-distance flight, a fundamental aspect of bird biology. Theropod dinosaurs did not share this feature. Other morphological features have also been identified that are inconsistent with a bird-from-dinosaur theory. And perhaps most significant, birds were already found in the fossil record before the elaboration of the dinosaurs they supposedly descended from. That would be consistent with raptors descending from birds, Ruben said, but not the reverse.

OSU research on avian biology and physiology has been raising questions on this issue since the 1990s, often in isolation. More scientists and other studies are now challenging the same premise, Ruben said. The old theories were popular, had public appeal and "many people saw what they wanted to see" instead of carefully interpreting the data, he said.

"Pesky new fossils...sharply at odds with conventional wisdom never seem to cease popping up," Ruben wrote in his PNAS commentary. "Given the vagaries of the fossil record, current notions of near resolution of many of the most basic questions about long-extinct forms should probably be regarded with caution."

Read More Here!

Did Bacteria Develop Into More Complex Cells Much Earlier in Evolution Than Thought?

ScienceDaily (Feb. 8, 2010) — Monash University biochemists have found a critical piece in the evolutionary puzzle that explains how life on Earth evolved millions of centuries ago.

The team, from the School of Biomedical Sciences, has described the process by which bacteria developed into more complex cells and found this crucial step happened much earlier in the evolutionary timeline than previously thought.

Team leader and ARC Federation Fellow Trevor Lithgow said the research explained how mitochondria -- the power house of human and other cells, which provide complex eukaryotic cells with energy and ability to produce, divide and move -- were thought to have evolved about 2000 million years ago from primitive bacteria.

"We have now come to understand the processes that drove cell evolution. For some time now the crux of this problem has been to understand how eukaryotes first came to be. The critical step was to transform small bacteria, passengers that rode within the earliest ancestors of these cells, into mitochondria, thereby beginning the evolution of more complex life-forms," Professor Lithgow said.

The team found that the cellular machinery needed to create mitochondria was constructed from parts pre-existing in the bacterium. These parts did other jobs for the bacterium, and were cobbled together by evolution to do something new and more exciting.

"Our research has crystallised with work from other researchers around the world to show how this transformation happened very early on -- that the eukaryotes were spawned by integrating the bacterium as a part of themselves. This process jump-started the evolution of complex life much more rapidly than was previously thought."

The research consisted of two components, the first used computers to read, compare and understand DNA sequences. From this, experiments were designed to do actual laboratory testing using a bacterium that is the closest living relative to the original ancestor of the mitochondria.

The research was published in the journal Science.

Professor Lithgow said the latest findings were only made possible due to a gradual gathering of evidence within the scientific community and recent developments in genome sequencing. "We can now "read" with great care and insight genome sequences -- the complete DNA sequence of any organism. From these sequences we find tell-tale clues to the past. Our findings are relevant to all species, including the evolution of humans," Professor Lithgow said.

"It continues to amaze that this theory, proposed in the century before the advent of molecular investigations, is so accurate on a molecular scale. This improved understanding is directly relevant to the big picture timeline for the evolution of life."

Professor Lithgow said the findings will be regarded by some scientists as controversial as many have long-held views on the process of evolution as a tinkerer. "This will surprise and may even spark debate. However our research compliments the basic rules of life. Even at the molecular level, the rules of the game are the same. Evolution drives biology to more and more complex forms," Professor Lithgow said.

Read here!

Evolutionary Surprise: Eight Percent of Human Genetic Material Comes from a Virus

ScienceDaily (Jan. 8, 2010) — About eight percent of human genetic material comes from a virus and not from our ancestors, according to researchers in Japan and the U.S.

The study, and an accompanying News & Views article by University of Texas at Arlington biology professor Cédric Feschotte, is published in the journal Nature.

The research showed that the genomes of humans and other mammals contain DNA derived from the insertion of bornaviruses, RNA viruses whose replication and transcription takes place in the nucleus. Feschotte wrote on recent research led by Professor Keizo Tomonaga at Osaka University in Japan. Feschotte said this virally transmitted DNA may be a cause of mutation and psychiatric disorders such as schizophrenia and mood disorders.

In his article, Feschotte speculates about the role of such viral insertions in causing mutations with evolutionary and medical consequences.

The assimilation of viral sequences into the host genome is a process referred to as endogenization. This occurs when viral DNA integrates into a chromosome of reproductive cells and is subsequently passed from parent to offspring. Until now, retroviruses were the only viruses known to generate such endogenous copies in vertebrates. But Feschotte said that scientists have found that non-retroviral viruses called bornaviruses have been endogenized repeatedly in mammals throughout evolution.

Bornavirus (BDV) owes its name to the town of Borna, Germany, where a virus epidemic in 1885 wiped out a regiment of cavalry horses. BDV infects a range of birds and mammals, including humans. It is unique because it infects only neurons, establishing a persistent infection in its host's brain, and its entire life cycle takes place in the nucleus of the infected cells. Feschotte said this intimate association of BDV with the cell nucleus prompted researchers to investigate whether bornaviruses may have left behind a record of past infection in the form of endogenous elements. They searched the 234 known eukaryotic genomes (those genomes that have been fully sequenced) for sequences that are similar to that of BDV. "The researchers unearthed a plethora of endogenous Borna-like N (EBLN) elements in many diverse mammals, " Feschotte said.

The scientists also were able to recover spontaneous BDV insertions in the chromosomes of human cultured cells persistently infected by BVD.Based on these data, Feschotte proposes that BDV insertions could be a source of mutations in the brain cells of infected individuals.

"These data yield a testable hypothesis for the alleged, but still controversial, causative association of BDV infection with schizophrenia and mood disorders," Feschotte said. The research in Feschotte 's laboratory, which largely focuses on transposable elements, the genetic elements that are able to move and replicate within the genomes of virtually all living organisms, is representative of the research under way at UT Arlington, an institution of 28,000 students on its way to becoming a nationally recognized, top-tier research university.

http://www.sciencedaily.com/releases/2010/01/100107103621.htm

New Theory on the Origin of Primates

ScienceDaily (Jan. 20, 2010) — A new model for primate origins is presented in Zoologica Scripta, published by the Norwegian Academy of Science and Letters and The Royal Swedish Academy of Sciences. The paper argues that the distributions of the major primate groups are correlated with Mesozoic tectonic features and that their respective ranges are congruent with each evolving locally from a widespread ancestor on the supercontinent of Pangea about 185 million years ago.

Michael Heads, a Research Associate of the Buffalo Museum of Science, arrived at these conclusions by incorporating, for the first time, spatial patterns of primate diversity and distribution as historical evidence for primate evolution. Models had previously been limited to interpretations of the fossil record and molecular clocks.

"According to prevailing theories, primates are supposed to have originated in a geographically small area (center of origin) from where they dispersed to other regions and continents" said Heads, who also noted that widespread misrepresentation of fossil molecular clocks estimates as maximum or actual dates of origin has led to a popular theory that primates somehow crossed the globe and even rafted across oceans to reach America and Madagascar.

In this new approach to molecular phylogenetics, vicariance, and plate tectonics, Heads shows that the distribution ranges of primates and their nearest relatives, the tree shrews and the flying lemurs, conforms to a pattern that would be expected from their having evolved from a widespread ancestor. This ancestor could have evolved into the extinct Plesiadapiformes in north America and Eurasia, the primates in central-South America, Africa, India and south East Asia, and the tree shrews and flying lemurs in South East Asia.

Divergence between strepsirrhines (lemurs and lorises) and haplorhines (tarsiers and anthropoids) is correlated with intense volcanic activity on the Lebombo Monocline in Africa about 180 million years ago. The lemurs of Madagascar diverged from their African relatives with the opening of the Mozambique Channel (160 million years ago), while New and Old World monkeys diverged with the opening of the Atlantic about 120 million years ago.

"This model avoids the confusion created by the center of origin theories and the assumption of a recent origin for major primate groups due to a misrepresentation of the fossil record and molecular clock divergence estimates" said Michael from his New Zealand office. "These models have resulted in all sorts of contradictory centers of origin and imaginary migrations for primates that are biogeographically unnecessary and incompatible with ecological evidence."

The tectonic model also addresses the otherwise insoluble problem of dispersal theories that enable primates to cross the Atlantic to America, and the Mozambique Channel to Madagascar although they have not been able to cross 25 km from Sulawesi to Moluccan islands and from there travel to New Guinea and Australia.

Heads acknowledged that the phylogenetic relationships of some groups such as tarsiers, are controversial, but the various alternatives do not obscure the patterns of diversity and distribution identified in this study.

Biogeographic evidence for the Jurassic origin for primates, and the pre-Cretaceous origin of major primate groups considerably extends their divergence before the fossil record, but Heads notes that fossils only provide minimal dates for the existence of particular groups, and there are many examples of the fossil record being extended for tens of millions of years through new fossil discoveries.

The article notes that increasing numbers of primatologists and paleontologists recognize that the fossil record cannot be used to impose strict limits on primate origins, and that some molecular clock estimates also predict divergence dates pre-dating the earliest fossils. These considerations indicate that there is no necessary objection to the biogeographic evidence for divergence of primates beginning in the Jurassic with the origin of all major groups being correlated with plate tectonics.

Chimp and Human Y Chromosomes Evolving Faster Than Expected

ScienceDaily (Jan. 15, 2010) — Contrary to a widely held scientific theory that the mammalian Y chromosome is slowly decaying or stagnating, new evidence suggests that in fact the Y is actually evolving quite rapidly through continuous, wholesale renovation.

By conducting the first comprehensive interspecies comparison of Y chromosomes, Whitehead Institute researchers have found considerable differences in the genetic sequences of the human and chimpanzee Ys -- an indication that these chromosomes have evolved more quickly than the rest of their respective genomes over the 6 million years since they emerged from a common ancestor. The findings are published online this week in the journal Nature.

"The region of the Y that is evolving the fastest is the part that plays a role in sperm production," say Jennifer Hughes, first author on the Nature paper and a postdoctoral researcher in Whitehead Institute Director David Page's lab. "The rest of the Y is evolving more like the rest of the genome, only a little bit faster."

The chimp Y chromosome is only the second Y chromosome to be comprehensively sequenced. The original chimp genome sequencing completed in 2005 largely excluded the Y chromosome because its hundreds of repetitive sections typically confound standard sequencing techniques. Working closely with the Genome Center at Washington University, the Page lab managed to painstakingly sequence the chimp Y chromosome, allowing for comparison with the human Y, which the Page lab and the Genome Center at Washington University had sequenced successfully back in 2003.

The results overturned the expectation that the chimp and human Y chromosomes would be highly similar. Instead, they differ remarkably in their structure and gene content. The chimp Y, for example, has lost one third to one half of the human Y chromosome genes--a significant change in a relatively short period of time. Page points out that this is not all about gene decay or loss. He likens the Y chromosome changes to a home undergoing continual renovation.

"People are living in the house, but there's always some room that's being demolished and reconstructed," says Page, who is also a Howard Hughes Medical Institute investigator. "And this is not the norm for the genome as a whole."

Wes Warren, Assistant Director of the Washington University Genome Center, agrees. "This work clearly shows that the Y is pretty ingenious at using different tools than the rest of the genome to maintain diversity of genes," he says. "These findings demonstrate that our knowledge of the Y chromosome is still advancing."

Hughes and Page theorize that the divergent evolution of the chimp and human Y chromosomes may be due to several factors, including traits specific to Y chromosomes and differences in mating behaviors.

Because multiple male chimpanzees may mate with a single female in rapid succession, the males' sperm wind up in heated reproductive competition. If a given male produces more sperm, that male would theoretically be more likely to impregnate the female, thereby passing on his superior sperm production genes, some of which may be residing on the Y chromosome, to the next generation.

Because selective pressure to pass on advantageous sperm production genes is so high, those genes may also drag along detrimental genetic traits to the next generation. Such transmission is allowed to occur because, unlike other chromosomes, the Y has no partner with which to swap genes during cell division. Swapping genes between chromosomal partners can eventually associate positive gene versions with each other and eliminate detrimental gene versions. Without this ability, the Y chromosome is treated by evolution as one large entity. Either the entire chromosome is advantageous, or it is not.

In chimps, this potent combination of intense selective pressure on sperm production genes and the inability to swap genes may have fueled the Y chromosome's rapid evolution. Disadvantages from a less-than-ideal gene version or even the deletion of a section of the chromosome may have been outweighed by the advantage of improved sperm production, resulting in a Y chromosome with far fewer genes than its human counterpart.

To determine whether this rapid rate of evolution affects Y chromosomes beyond those of chimps and humans, the Page lab and the Washington University Genome Center are now sequencing and examining the Y chromosomes of several other mammals.

This research was funded by the National Institutes of Health (NIH) and the Howard Hughes Medical Institute (HHMI).

http://www.sciencedaily.com/releases/2010/01/100113131505.htm