What Kind of Life Could Evolve on Titan?

Could there be life on Saturn’s large moon Titan? Asking the question forces astrobiologists and chemists to think carefully and creatively about the chemistry of life, and how it might be different on other worlds than it is on Earth. In February, a team of researchers from Cornell University, including chemical engineering graduate student James Stevenson, planetary scientist Jonathan Lunine, and chemical engineer Paulette Clancy, published a pioneering study arguing that cell membranes could form under the exotic chemical conditions present on this remarkable moon.

link.

Alternate Biochemistries Panel at AAAS in San Jose Tomorrow @ 3 PM

Ideas about directing evolution of life forms on Earth and finding life on other planets are rapidly morphing from science-fiction fantasy into mainstream science, says David Lynn, a chemist at Emory University.

"These areas of science are rapidly coming of age because of our increasing knowledge and advancing technology. It's an exciting time. We're on the threshold of answering fundamental questions including: What is life? Are there forms of life that we haven't even yet imagined? Are we alone in the universe?"

A panel discussion, "Searching for Alternative Chemistries of Life on Earth and Throughout the Universe," is set for Friday, February 13, at 3 pm, during the annual meeting of the American Association for the Advancement of Science (AAAS) in San Jose. Lynn co-organized the panel with Jay Goodwin, a senior Emory research fellow and an AAAS Science and Technology Policy Fellow.

link.

An Intriguing Brain Protein Unique to Humans

A protein that may partly explain why human brains are larger than those of other animals has been identified by scientists from two stem-cell labs at UC San Francisco, in research published in the November 13, 2014 issue of Nature.

Key experiments by the UCSF researchers revealed that the protein, called PDGFD, is made in growing brains of humans, but not in mice, and appears necessary for normal proliferation of human brain stem cells growing in a lab dish.

The scientists made their discovery as part of research in which they identified genes that are activated to make specific proteins in crucial stem cells in the brain known as radial glial cells. The discovery stems from a collaboration between the laboratories of leading radial glial cell scientist Arnold Kriegstein MD, PhD, director of the Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research at UCSF, and Michael Oldham, PhD, who recently made a rapid career leap from graduate student to principal investigator and Sandler Fellow at UCSF.

Radial glial cells make the neurons in the growing brain, including the neurons in the cerebral cortex, the seat of higher brain functions. The cerebral cortex varies in size 10,000-fold among mammals. Changes in the timing, location and degree of cell division and nerve cell generation by radial glial cells can dramatically alter the shape and function of the cortex.

The UCSF team discovered that PDGFD is secreted by human radial glial cells and acts on radial glial cells as well as other progenitor cells in the developing brain.

link.

Studying Precambrian Proteins

Modern proteins exhibit an impressive degree of structural diversity, which has been well characterized, but very little is known about how and when over the course of evolution 3D protein structures arose.

In a study published by Cell Press August 8 in Structure, researchers resurrected 4-billion-year-old Precambrian proteins in the laboratory and gained novel insights into protein evolution by analyzing their X-ray crystal structures. This method has revealed a remarkable degree of structural similarity among proteins since life first evolved on this planet, and it represents a powerful and novel approach to explore the evolution of protein structures.

"So far, attempts to understand protein structure evolution have been based on the comparison between structures of modern proteins. This is equivalent to trying to understand the evolution of birds by comparing several living birds," says senior study author Jose Sanchez-Ruiz of the University of Granada. "But it is most useful to study fossils so that changes over evolutionary time are apparent. Our approach comes as close as possible to 'digging up' fossil protein structures."

In a recent study, Sanchez-Ruiz and his collaborators constructed a phylogenetic tree of protein sequences by analyzing the amino acid sequences of thioredoxins—proteins found in organisms from the three domains of life, including bacteria, archaea and eukaryotes. Using this phylogenetic tree, they were able to resurrect Precambrian proteins in the laboratory and characterize their features.

What a World with Ammonia in Place of Water Would Look Like

Hat tip to Randy.

Biology of an Early Earth: RNA Capable of Catalyzing Electron Transfer With Iron Before Great Oxidation Event

A new study shows how complex biochemical transformations may have been possible under conditions that existed when life began on the early Earth.

The study shows that RNA is capable of catalyzing electron transfer under conditions similar to those of the early Earth. Because electron transfer, the moving of an electron from one chemical species to another, is involved in many biological processes – including photosynthesis, respiration and the reduction of RNA to DNA – the study's findings suggest that complex biochemical transformations may have been possible when life began.

There is considerable evidence that the evolution of life passed through an early stage when RNA played a more central role, before DNA and coded proteins appeared. During that time, more than 3 billion years ago, the environment lacked oxygen but had an abundance of soluble iron.

"Our study shows that when RNA teams up with iron in an oxygen-free environment, RNA displays the powerful ability to catalyze single electron transfer, a process involved in the most sophisticated biochemistry, yet previously uncharacterized for RNA," said Loren Williams, a professor in the School of Chemistry and Biochemistry at the Georgia Institute of Technology.

The results of the study were scheduled to be published online on May 19, 2013, in the journal Nature Chemistry. The study was sponsored by the NASA Astrobiology Institute, which established the Center for Ribosomal Origins and Evolution (Ribo Evo) at Georgia Tech.

Free oxygen gas was almost nonexistent in the Earth's atmosphere more than 3 billion years ago. When free oxygen began entering the environment as a product of photosynthesis, it turned the earth's iron to rust, forming massive banded iron formations that are still mined today. The free oxygen produced by advanced organisms caused iron to be toxic, even though it was – and still is – a requirement for life. Williams believes the environmental transition caused a slow shift from the use of iron to magnesium for RNA binding, folding and catalysis.

Williams and Georgia Tech School of Chemistry and Biochemistry postdoctoral fellow Chiaolong Hsiao used a standard peroxidase assay to detect electron transfer in solutions of RNA and either the iron ion, Fe2+, or magnesium ion, Mg2+. For 10 different types of RNA, the researchers observed catalysis of single electron transfer in the presence of iron and absence of oxygen. They found that two of the most abundant and ancient types of RNA, the 23S ribosomal RNA and transfer RNA, catalyzed electron transfer more efficiently than other types of RNA. However, none of the RNA and magnesium solutions catalyzed single electron transfer in the oxygen-free environment.

"Our findings suggest that the catalytic competence of RNA may have been greater in early Earth conditions than in present conditions, and our experiments may have revived a latent function of RNA," added Williams, who is also director of the RiboEvo Center.

Did Life Originate in a Hapophile (High Salt) Environment?

A structural biologist at the Florida State University College of Medicine has made discoveries that could lead scientists a step closer to understanding how life first emerged on Earth billions of years ago.

Professor Michael Blaber and his team produced data supporting the idea that 10 amino acids believed to exist on Earth around 4 billion years ago were capable of forming foldable proteins in a high-salt (halophile) environment. Such proteins would have been capable of providing metabolic activity for the first living organisms to emerge on the planet between 3.5 and 3.9 billion years ago.

The results of Blaber's three-year study, which was built around investigative techniques that took more than 17 years to develop, are published in the journal Proceedings of the National Academy of Sciences.

The first living organisms would have been microscopic, cell-like organizations capable of replicating and adapting to environmental conditions — a humble beginning to life on Earth.

"The current paradigm on the emergence of life is that RNA came first and in a high-temperature environment," Blaber said. "The data we are generating are much more in favor of a protein-first view in a halophile environment."

The widely accepted view among scientists is that RNA, found in all living cells, would have likely represented the first molecules of life, hypothesizing an "RNA-first" view of the origin of living systems from non-living molecules. Blaber's results indicate that the set of amino acids produced by simple chemical processes contains the requisite information to produce complex folded proteins, which supports an opposing "protein-first" view.

Another prevailing view holds that a high-temperature (thermophile) environment, such as deep-ocean thermal vents, may have been the breeding ground for the origin of life.

"The halophile, or salt-loving, environment has typically been considered one that life adapted into, not started in," Blaber said. "Our study of the prebiotic amino acids and protein design and folding suggests the opposite."

Without the ability to fold, proteins would not be able to form the precise structures essential for functions that sustain life as we know it. Folding allows proteins to take on a globular shape through which they can interact with other proteins, perform specific chemical reactions, and adapt to enable organisms to exploit a given environment.

"There are numerous niches that life can evolve into," Blaber said. "For example, extremophiles are organisms that exist in high temperatures, high acidity, extreme cold, extreme pressure and extreme salt and so on. For life to exist in such environments it is essential that proteins are able to adapt in those conditions. In other words, they have to be able to fold."

Comet and meteorite fragments, like those that recently struck in the Urals region of Russia, have provided evidence regarding the arrival of amino acids on Earth. Such fragments predate the earth and would have been responsible for delivering a set of 10 prebiotic (before life) amino acids, whose origins are in the formation of our solar system.

Today the human body uses 20 common amino acids to make all its proteins. Ten of those emerged through biosynthetic pathways — the way living systems evolve. Ten — the prebiotic set — can be made by chemical reactions without requiring any living system or biosynthetic pathway.

Scientific evidence exists to support many elements in theories of abiogenesis (the emergence of life), including the time frame (around 3.5 to 3.9 billion years ago) and the conditions on Earth and in its atmosphere at that time. Earth would have been made up of volcanic land masses (the beginning of the formation of continents), salty oceans and fresh-water ponds, along with a hot (around 80 degrees Celsius) and steamy atmosphere comprising carbon dioxide and nitrogen. Oxygen would have come later as a by-product of green plant life and bacteria that emerged.

Using a technique called top-down symmetric deconstruction, Blaber's lab has been able to identify small peptide building blocks capable of spontaneous assembly into specific and complex protein architectures. His recent work explored whether such building blocks can be comprised of only the 10 prebiotic amino acids and still fold.

His team has achieved foldability in proteins down to 12 amino acids — about 80 percent of the way to proving his hypothesis.

If Blaber's theory holds, scientists may refocus where they look for evidence in the quest to understand where, and how, life began.

hmm.

Biohydrogen Breakthrough? Using Xytose to Produce Hydrogen

A team of Virginia Tech researchers has discovered a way to extract large quantities of hydrogen from any plant, a breakthrough that has the potential to bring a low-cost, environmentally friendly fuel source to the world.

“Our new process could help end our dependence on fossil fuels,” said Y.H. Percival Zhang, an associate professor of biological systems engineering in the College of Agriculture and Life Sciences and the College of Engineering “Hydrogen is one of the most important biofuels of the future.”

Zhang and his team have succeeded in using xylose, the most abundant simple plant sugar, to produce a large quantity of hydrogen that previously was attainable only in theory. Zhang’s method can be performed using any source of biomass.

The discovery is a featured editor’s choice in an online version of the chemistry journal Angewandte Chemie, International Edition.

[...]

Obstacles to commercial production of hydrogen gas from biomass previously included the high cost of the processes used and the relatively low quantity of the end product.

But Zhang thinks he has found the answers to those problems.

For seven years, Zhang’s team has been focused on finding non-traditional ways to produce high-yield hydrogen at low cost, specifically researching enzyme combinations, discovering novel enzymes, and engineering enzymes with desirable properties.

The team liberates the high-purity hydrogen under mild reaction conditions at 122 degree Fahrenheit and normal atmospheric pressure. The biocatalysts used to release the hydrogen are a group of enzymes artificially isolated from different microorganisms that thrive at extreme temperatures, some of which could grow at around the boiling point of water.

The researchers chose to use xylose, which comprises as much as 30 percent of plant cell walls. Despite its abundance, the use of xylose for releasing hydrogen has been limited. The natural or engineered microorganisms that most scientists use in their experiments cannot produce hydrogen in high yield because these microorganisms grow and reproduce instead of splitting water molecules to yield pure hydrogen.

To liberate the hydrogen, Virginia Tech scientists separated a number of enzymes from their native microorganisms to create a customized enzyme cocktail that does not occur in nature. The enzymes, when combined with xylose and a polyphosphate, liberate the unprecedentedly high volume of hydrogen from xylose, resulting in the production of about three times as much hydrogen as other hydrogen-producing microorganisms.

The energy stored in xylose splits water molecules, yielding high-purity hydrogen that can be directly utilized by proton-exchange membrane fuel cells. Even more appealing, this reaction occurs at low temperatures, generating hydrogen energy that is greater than the chemical energy stored in xylose and the polyphosphate. This results in an energy efficiency of more than 100 percent — a net energy gain. That means that low-temperature waste heat can be used to produce high-quality chemical energy hydrogen for the first time. Other processes that convert sugar into biofuels such as ethanol and butanol always have energy efficiencies of less than 100 percent, resulting in an energy penalty.

I haven't found the paper in the journal...help?

Quadruplex DNA Observed in Cells

There is no more iconic image in biology than that of DNA's double-stranded helix, which coils and supercoils on itself to form dense chromosomes.

But a quite different, square-shaped type of DNA structure can easily be created in the laboratory by the folding of synthetic DNA strands rich in guanine, one of the building blocks of DNA. Scientists have long believed that these so-called 'G-quadruplex structures' may occasionally form in the DNA of living cells. A G-quadruplex comprises four guanines from different places along a G-rich strand held together by a special type of hydrogen bonding to form a compact square structure that interrupts the DNA helix.

In a paper published online today in Nature Chemistry, researchers led by Shankar Balasubramanian at the University of Cambridge, UK, provide strong evidence that G-quadruplexes do occur in cells — and that these unusual structures may have important biological functions.

Multi stranded DNA molecules can no longer be called alien.

Do Aphids Photosynethesize?

The biology of aphids is bizarre: they can be born pregnant and males sometimes lack mouths, causing them to die not long after mating. In an addition to their list of anomalies, work published this week indicates that they may also capture sunlight and use the energy for metabolic purposes.

Aphids are unique among animals in their ability to synthesize pigments called carotenoids. Many creatures rely on these pigments for a variety of functions, such as maintaining a healthy immune system and making certain vitamins, but all other animals must obtain them through their diet. Entomologist Alain Robichon at the Sophia Agrobiotech Institute in Sophia Antipolis, France, and his colleagues suggest that, in aphids, these pigments can absorb energy from the Sun and transfer it to the cellular machinery involved in energy production.

Pop sci write up.

Paper:

Light- induced electron transfer and ATP synthesis in a carotene synthesizing insect

Authors:

1. Jean Christophe Valmalette (a)
2. Aviv Dombrovsky (b,d)
3. Pierre Brat (c)
4. Christian Mertz (c)
5. Maria Capovilla (d)
6. Alain Robichon (d)

Affiliations:

a. IM2NP UMR 7334 CNRS, Université du Sud Toulon Var, P.O. Box 20132, 83957 La Garde CEDEX, France

b. Volcani Center, Institute of Plant Protection, P.O. Box 6, 50250 Bet Dagan, Israel

c. CIRAD UMR QualiSud, 73 rue J.F. Breton, TA B-95/16, 34398 Montpellier CEDEX 5, France

d. UMR7254 INRA/CNRS/UNS, Institut Sophia Agrobiotech, 400 route des Chappes, P. O. Box 167, 06903 Sophia Antipolis, France

Abstract:

A singular adaptive phenotype of a parthenogenetic insect species (Acyrthosiphon pisum) was selected in cold conditions and is characterized by a remarkable apparition of a greenish colour. The aphid pigments involve carotenoid genes well defined in chloroplasts and cyanobacteria and amazingly present in the aphid genome, likely by lateral transfer during evolution. The abundant carotenoid synthesis in aphids suggests strongly that a major and unknown physiological role is related to these compounds beyond their canonical anti-oxidant properties. We report here that the capture of light energy in living aphids results in the photo induced electron transfer from excited chromophores to acceptor molecules. The redox potentials of molecules involved in this process would be compatible with the reduction of the NAD+ coenzyme. This appears as an archaic photosynthetic system consisting of photo-emitted electrons that are in fine funnelled into the mitochondrial reducing power in order to synthesize ATP molecules.

hmmmm.

Why Animals Don't Have IR Vision

On rare occasion, the light-sensing photoreceptor cells in the eye misfire and signal to the brain as if they have captured photons, when in reality they haven't. For years this phenomenon remained a mystery. Reporting in the June 10 issue of Science, neuroscientists at the Johns Hopkins University School of Medicine have discovered that a light-capturing pigment molecule in photoreceptors can be triggered by heat, as well, giving rise to these false alarms.

"A photon, the unit of light, is just energy, which, when captured by the pigment rhodopsin, most of the time causes the molecule to change shape, then triggering the cell to send an electrical signal to the brain to inform about light absorption," explains King-Wai Yau, Ph.D., professor of neuroscience at Johns Hopkins and member of its Center for Sensory Biology. "If rhodopsin can be triggered by light energy," says Yau, "it may also be occasionally triggered by other types of energy, such as heat, producing false alarms. These fake signals compromise our ability to see objects on a moonless night. So we tried to figure it out; namely, how the pigment is tripped by accident."

"Thermal energy is everywhere, as long as the temperature is above absolute zero," says neuroscience research associate Dong-Gen Luo, Ph.D. "The question is: How much heat energy would it take to trigger rhodopsin and enable it to fire off a signal, even without capturing light?" says Johns Hopkins Biochemistry, Cellular and Molecular Biology graduate student Wendy Yue.

For 30 years, the assumption was that heat could trigger a pigment molecule to send a false signal, but through a mechanism different from that of light, says Yau, because it seemed, based on theoretical calculations: that very little thermal energy was required compared to light energy.

But the theory, according to Yau, was based mainly on the pigment rhodopsin. However, rhodopsin is mainly responsible for seeing in dim light and is not the only pigment in the eye; other pigments are present in red-, green- and blue-sensitive cone photoreceptors that are used for color and bright-light vision. Although researchers are able to measure the false events of rhodopsin from a single rhodopsin-containing cell, a long-standing challenge has been to take measurements of the other pigments. "The electrical signal from a single cone pigment molecule is so small in a cone cell that it is simply not measurable," says Luo. "So we had to figure out a new way to measure these false signals from cone pigments."

By engineering a rod cell to make human red cone pigment, which is usually only found in cone cells, Yau's team was able to measure the electrical output from an individual cell and calculate this pigment's false signals by taking advantage of the large and detectable signals sent out from the cell.

As for blue cone pigment, "Nature did the experiment for us," says Yau. "In many amphibians, one type of rod cells called green rods naturally express a blue cone pigment, as do blue cones." So to determine whether heat can cause pigment cells to misfire, the team, working in the dark, first cooled the cells, and then slowly returned the cells to room temperature, measuring the electrical activity of the cells as they warmed up. They found that red-sensing pigment triggers false alarms most frequently, rhodopsin (bluish-green-sensing pigment) triggers falsely less frequently, and blue-sensing pigment does so even less.

"This validates the 60-year-old Barlow's hypothesis that suggested the longer wavelength the pigment senses—meaning the closer to the red end of the spectrum—the noisier it is," says Yau. And this finding led the team to develop and test a new theory: that heat can trigger pigments to misfire, by the same mechanism as light.

Pivotal to this theory is that visual pigment molecules are large, complex molecules containing many chemical bonds. And since each chemical bond has the potential to contain some small amount of thermal energy, the total amount of energy a pigment molecule could contain can, in theory, be enough to trigger the false alarm.

"For a long time, people assumed that light and heat had to trigger via different mechanisms, but now we think that both types of energy, in fact, trigger identical changes in the pigment molecules," says Yau. Moreover, since longer wavelength pigments have higher rates of false alarms, Yau says this may explain why animals never evolved to have infrared-sensing pigments.

"Apart from putting to rest a long-standing debate, it's a wake-up call for researchers to realize that biomolecules in general have more potential thermal energy than previously thought," says Luo.

Link in title.

Reconstructed Enzymes Suggest Hot, Acidic Conditions for Early Life

A new study reveals that a group of ancient enzymes adapted to substantial changes in ocean temperature and acidity during the last four billion years, providing evidence that life on Early Earth evolved from a much hotter, more acidic environment to the cooler, less acidic global environment that exists today.

The study found that a group of ancient enzymes known as thioredoxin were chemically stable at temperatures up to 32 degrees Celsius (58 degrees Fahrenheit) higher than their modern counterparts. The enzymes, which were several billion years old, also showed increased activity at lower pH levels -- which correspond to greater acidity.

"This study shows that a group of ubiquitous proteins operated in a hot, acidic environment during early life, which supports the view that the environment progressively cooled and became more alkaline between four billion and 500 million years ago," said Eric Gaucher, an associate professor in the School of Biology at the Georgia Institute of Technology.

The study, which was published April 3 in the advance online edition of the journal Nature Structural & Molecular Biology, was conducted by an international team of researchers from Georgia Tech, Columbia University and the Universidad de Granada in Spain.

Major funding for this study was provided by two grants from the National Aeronautics and Space Administration to Georgia Tech, a grant from the National Institutes of Health to Columbia University, and a grant from the Spanish Ministry of Science and Innovation to the Universidad de Granada.

Using a technique called ancestral sequence reconstruction, Gaucher and Georgia Tech biology graduate student Zi-Ming Zhao reconstructed seven ancient thioredoxin enzymes from the three domains of life -- archaea, bacteria and eukaryote -- that date back between one and four billion years.

To resurrect these enzymes, which are found in nearly all known modern organisms and are essential for life in mammals, the researchers first constructed a family tree of the more than 200 thioredoxin sequences available from the three domains of life. Then they reconstructed the sequences of the ancestral thioredoxin enzymes using statistical methods based on maximum likelihood. Finally, they synthesized the genes that encoded these sequences, expressed the ancient proteins in the cells of modern Escherichia coli bacteria and then purified the proteins.

"By resurrecting proteins, we are able to gather valuable information about the adaptation of extinct forms of life to climatic, ecological and physiological alterations that cannot be uncovered through fossil record examinations," said Gaucher.

The reconstructed enzymes from the Precambrian period -- which ended about 542 million years ago -- were used to examine how environmental conditions, including pH and temperature, affected the evolution of the enzymes and their chemical mechanisms.

"Given the ancient origin of the reconstructed thioredoxin enzymes, with some of them predating the buildup of atmospheric oxygen, we thought their catalytic chemistry would be simple, but we found that thioredoxin enzymes use a complex mixture of chemical mechanisms that increases their efficiency over the simpler compounds that were available in early geochemistry," said Julio Fernández, a professor in the Department of Biological Sciences professor at Columbia University.

no time.

Are There Alternate Biochemistries Lurking On Earth?

Mono Lake has a bizarre, extraterrestrial beauty. Just east of Yosemite National Park in California, the ancient lake covers about 65 square miles. Above its surface rise the twisted shapes of tufa, formed when freshwater springs bubble up through the alkaline waters.

Felisa Wolfe-Simon, a geobiologist, is interested in the lake not for its scenery but because it may be harbouring alien life forms, or “weird life”. Mono Lake, a basin with no outlet, has built up over many millennia one of the highest natural concentrations of arsenic on Earth. Dr Wolfe-Simon is investigating whether, in the mud around the lake or in the water, there exist microbes whose biological make-up is so fundamentally different from that of any known life on Earth that it may provide proof of a shadow biosphere, a second genesis for life on this planet.

Arsenic is chemically close to phosphorus. While phosphorus is a primary building block of life on Earth — an essential component of DNA and ATP, the energy molecule — arsenic is a deadly poison. In Mono Lake there are micro-organisms that live with arsenic. But they don’t incorporate it into their biology.

Dr Wolfe-Simon has theorised that there may be life that chose an “evolutionary pathway” to utilise arsenic. If such microbes existed, it could suggest that life started on our planet not once but at least twice. In turn this would help to support the idea that life is much more likely to have started elsewhere in the galaxy.

“There is life ‘as we know it’ and there is life ‘as we don’t know it’. What would that look like? I am trying to give us a framework to work with to help us look for what ‘we don’t know’, the particular framework of arsenic,” she says.

Dr Wolfe-Simon has taken samples from the mud and the waters of the lake and is performing a series of multiple dilutions — hugely increasing the levels of arsenic and reducing residual phosphorous to zero. She adds sugar, vitamins and other nutrients to encourage organisms to grow and tests the results.

Her experiments are not yet over but she is quietly pleased with the progress she is making. “We have some very exciting data,” she says. The results should be published by the end of this year.

hmmmm. What do you guys think?

Exciting data can be interpreted in many ways.

Hadrosaur Proteins, Blood Cells, Blood Vessels Recovered

Ancient protein dating back 80 million years to the Cretaceous geologic period has been preserved in bone fragments and soft tissues of a hadrosaur, or duck-billed dinosaur, according to a study in the May 1 issue of Science. Led by scientists at Beth Israel Deaconess Medical Center (BIDMC) and North Carolina State University (NCSU), the new findings support earlier results from analyses suggesting that collagen protein survived in the bones of a well preserved Tyrannosaurus rex, and offer robust new evidence supporting previous conclusions that birds and dinosaurs are evolutionarily related.

In April 2007 John Asara, PhD, Director of the Mass Spectrometry Core at BIDMC, together with NCSU paleontologist Mary Schweitzer, PhD, published two papers in Science describing their discovery that collagen extracted from bone fragments of a 68-million-year-old T. rex closely matched the amino acid sequences of modern day chickens. Not surprisingly, the widely publicized findings created a great deal of controversy.

"With this new paper, we hoped to show that our T. rex discovery was not a unique occurrence," notes Asara, who is also an Instructor in Pathology at Harvard Medical School. "This is the second dinosaur species we've examined and helps verify that our first discovery was not just a one-hit wonder. Our current study was the collaborative effort of a number of independent laboratories, whose findings collectively add up to a robust conclusion."

At the heart of the controversy is the idea that ancient protein can exist at all. When an animal dies, protein immediately begins to degrade and, in the case of fossils, is slowly replaced by mineral, a substitution process assumed to be complete by 1 million years. But with this latest evidence, it appears that some proteins do indeed have real staying power.

"We wound up identifying nearly double the number of amino acids we recovered in the T. rex study," says Asara. "The sequences displayed high spectral quality and the interpretations were of high confidence."

The two scientists had decided to collaborate again after Schweitzer and paleontologist Jack Horner of Montana State University's Museum of the Rockies recovered the 80-million-year-old Brachylophosaurus canadensis femur bone in the summer of 2007 and observed that it appeared to be even better preserved than the original T. rex fossil.

Schweitzer's initial laboratory analyses confirmed this observation: After being subjected to demineralization, the B. canadensis bone fragments showed marked preservation of original tissues and molecules, with microstructures resembling soft, transparent vessels, cells and fibrous matrix – even though the fossil was much older than the T. rex sample.

"Deep burial in sandstone seems to favor exceptional preservation," notes Schweitzer, explaining that this fossil was found under approximately seven meters of sandstone in the Judith River Formation, in parts of what is now Eastern Montana.

Chemical extractions of bone and vessel were subsequently sent to the laboratories of BIDMC scientists Lewis Cantley, PhD, and Raghu Kalluri, PhD, where immunoblots and immunochemistry analyses were conducted to determine the presence of collagen protein in the samples.

"Having been a part of the T. rex study, I was curious to be part of this investigation as well," explains Cantley, Chief of the Division of Signal Transduction at BIDMC. "In view of the skepticism about the original findings, it was important to demonstrate that our findings in T. rex could be verified in another dinosaur and in other laboratories."

The results confirmed the existence of protein. "Because I am a collagen biochemist, our lab was contacted to perform an independent analysis of this new bone find," explains Kalluri, who is Chief of the Division of Matrix Biology at BIDMC. "We isolated the proteins – collagen, laminin and elastin – from the bone, and also extracted bone cells and blood vessels from this sample. Our findings demonstrated that it did contain basement membrane matrix."

Dude. More comments later. Doing major maintenance at work.

Algae Lignin Discovery May Be Evolutionary Significant

Land plants' ability to sprout upward through the air, unsupported except by their own woody tissues, has long been considered one of the characteristics separating them from aquatic plants, which rely on water to support them.

Now lignin, one of the chemical underpinnings vital to the self-supporting nature of land plants – and thought unique to them – has been found in marine algae by a team of researchers including scientists at UBC and Stanford University.

Lignin, a principal component of wood, is a glue-like substance that helps fortify cell walls and is instrumental in the transport of water in many plants.

In a study published in today's issue of the journal Current Biology, lead author Patrick Martone and colleagues describe using powerful chemical and microscopic anatomy techniques to identify and localize lignin within cell walls of a red alga that thrives along the wave-swept California coast. Martone conducted the work described in the paper while a graduate student and postdoctoral researcher in the laboratory of co-author Mark Denny, Professor of Biology at Stanford's Hopkins Marine Station.

"All land plants evolved from aquatic green algae and scientists have long believed that lignin evolved after plants took to land as a mechanical adaptation for stabilizing upright growth and transporting water from the root," says Martone, an assistant professor in the UBC Dept. of Botany, where he is continuing his work on lignin.

"Because red and green algae likely diverged more than a billion years ago, the discovery of lignin in red algae suggests that the basic machinery for producing lignin may have existed long before algae moved to land."

Alternatively, algae and land plants may have evolved the identical compound independently, after they diverged.

"The pathways, enzymes and genes that go into making this stuff are pretty complicated, so to come up with all those separately would be really, really amazing," says Denny. "Anything is possible, but that would be one hell of a coincidence."

The team's finding provides a new perspective on the early evolution of lignified support tissues – such as wood – on land, since the seaweed tissues that are most stressed by waves crashing on shore appear to contain the most lignin, possibly contributing to mechanical support, says Martone.

Were the algae of the Lower Paleozoic preadapted for life on land because of teh crashing of the waves? That's a fascinating thought!

First Synthetic Self Reproducing RNA Created

Findings could inform biochemical questions about how life began

Now, a pair of Scripps Research Institute scientists has taken a significant step toward answering that question. The scientists have synthesized for the first time RNA enzymes that can replicate themselves without the help of any proteins or other cellular components, and the process proceeds indefinitely.

The work was published on Thursday, January 8, 2008, in Science Express, the advanced, online edition of the journal Science.

In the modern world, DNA carries the genetic sequence for advanced organisms, while RNA is dependent on DNA for performing its roles such as building proteins. But one prominent theory about the origins of life, called the RNA World model, postulates that because RNA can function as both a gene and an enzyme, RNA might have come before DNA and protein and acted as the ancestral molecule of life. However, the process of copying a genetic molecule, which is considered a basic qualification for life, appears to be exceedingly complex, involving many proteins and other cellular components.

For years, researchers have wondered whether there might be some simpler way to copy RNA, brought about by the RNA itself. Some tentative steps along this road had previously been taken by the Joyce lab and others, but no one could demonstrate that RNA replication could be self-propagating, that is, result in new copies of RNA that also could copy themselves.

wow.