Nuova Sintesi

New synthesis method 

imitates the way molecules were formed 

at the dawn of life on Earth 

Breakingnews, Evolution, Genetics, Origin of Life 

Researchers from the Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), with support from the Nuclear Magnetic Resonance Service of the Universitat Autònoma de Barcelona (UAB) have developed a method for synthesising organic molecules very selectively, by assembling simple molecules and using an enzyme from E. coli (FSA: D-

fructose-6-phosphate aldolase), which acts as a biocatalyst. E-coli enzyme 

[Credit: CSIC]

 This is a significant step forward since it replicates the formation of carbohydrates in conditions resembling those that presumably initiated life on Earth (prebiotic conditions) and because it allows relatively large organic molecules to be obtained very selectively and efficiently. 
Furthermore, it is a process with few steps, that does not use organic solvents and generates no waste, and it has great potential in chemistry, especially for obtaining molecules and active ingredients of interest (drugs, supplements, etc.). 
Pere Clapés, a research professor with the CSIC who led this project, explains that in the synthesis of organic molecules . "it is not only important for them to have the correct structure, but also the right angle and position in space, because this affects their function." 

In fact, this is one of the main problems that can limit the effectiveness of compounds like drugs. 
In the case of pentoses and hexoses, these are simple sugars (monosaccharides) with five and six carbon atoms, respectively: crucial for life thanks to their function in energy production, structuring, communication and cell-cell recognition. 
The results presented in the journal Nature Chemistry show that the scientists obtained pentoses and hexoses by assembling formaldehyde and glycolaldehyde, with a minimal modification to the FSA enzyme sequence. 

A very malleable enzyme 

The enzyme FSA was discovered in 2001 and its physiological function in E. coli is still unknown.
 It is thought to be an ancestral enzyme, and that it is active before a broad range of compounds. 
What surprised the researchers is that it is a very malleable enzyme, much more so than others. 
As a result, with only a small number of genetic mutations in the enzyme, its catalytic capacity can be modulated and increased significantly. 
This is what allows the enzyme to be carefully adapted in order to synthesise several molecules at will. 
The metabolism of carbohydrates in living organisms is a complex process, forged over millions of years of evolution. 
It is no easy task to carry out these processes in a flask, whether by assembling the enzymes involved in the process or by manipulating the metabolic pathways of living organisms. 
Nor is it simple to obtain carbohydrates with conventional chemical methods, which require several stages and the use of organic solvents. The procedure was developed by scientists in the Biotransformation and Active Molecules Group of the Spanish National Research Council (CSIC), with support from the Nuclear Magnetic Resonance Service of the UAB. 
Pere Clapés explains: "we want to prove that the tools of biocatalysis allow complex molecules to be obtained from simpler ones, which are in fact the same ones used in nature." 
He goes on: "Over millions of years, living organisms have forged these metabolic strategies to obtain the carbohydrates they need to survive." "The process is a simple one, mimicking the prebiotic formation of carbohydrates from compounds that were probably around in the world before life began," adds Teodor Parella, of the UAB. 
For these researchers, the engineering of proteins, in particular of biocatalysts, has enormous potential for the sustainable synthesis of natural molecules and their derived products. 

Source: Universitat Autònoma de Barcelona [September 23, 2015]

DNA: grandi capacità di sopravvivenza

DNA survives critical entry into Earth's atmosphere 



 The genetic material DNA can survive a flight through space and re-entry into Earth's atmosphere -- and still pass on genetic information. A team of scientists from UZH obtained these astonishing results during an experiment on the TEXUS-49 research rocket mission. 

DNA can survive a flight through space and re-entry into the earth’s atmosphere and still pass on genetic information [Credit: Ciro Villa] 

Applied to the outer shell of the payload section of a rocket using pipettes, small, double-stranded DNA molecules flew into space from Earth and back again. After the launch, space flight, re-entry into Earth's atmosphere and landing, the so-called plasmid DNA molecules were still found on all the application points on the rocket from the TEXUS-49 mission. And this was not the only surprise: For the most part, the DNA salvaged was even still able to transfer genetic information to bacterial and connective tissue cells. 

"This study provides experimental evidence that the DNA's genetic information is essentially capable of surviving the extreme conditions of space and the re-entry into Earth's dense atmosphere," says study head Professor Oliver Ullrich from the University of Zurich's Institute of Anatomy.

Spontaneous second mission 
The experiment called DARE (DNA atmospheric re-entry experiment) resulted from a spontaneous idea: UZH scientists Dr. Cora Thiel and Professor Ullrich were conducting experiments on the TEXUS-49 mission to study the role of gravity in the regulation of gene expression in human cells using remote-controlled hardware inside the rocket's payload. 

Launch of the rocket TEXUS-49 from the Esrange Space Center in Kiruna,  North Sweden [Credit: Adrian Mettauer] 

During the mission preparations, they began to wonder whether the outer structure of the rocket might also be suitable for stability tests on so-called biosignatures. 
"Biosignatures are molecules that can prove the existence of past or present extraterrestrial life," explains Dr. Thiel. 
And so the two UZH researchers launched a small second mission at the European rocket station Esrange in Kiruna, north of the Arctic Circle.

DNA survives the most extreme conditions 
The quickly conceived additional experiment was originally supposed to be a pretest to check the stability of biomarkers during spaceflight and re-entry into the atmosphere. Dr. Thiel did not expect the results it produced: "We were completely surprised to find so much intact and functionally active DNA." The study reveals that genetic information from the DNA can essentially withstand the most extreme conditions. 

Dr. Cora Thiel and Professor Oliver Ullrich salvage DNA molecules from the outer  shell of the payload section of the TEXUS rocket [Credit: Adrian Mettauer] 

Various scientists believe that DNA could certainly reach us from outer space as Earth is not insulated: in extraterrestrial material made of dust and meteorites, for instance, around 100 tons of which hits our planet every day. 
This extraordinary stability of DNA under space conditions also needs to be factored into the interpretion of results in the search for extraterrestrial life: "The results show that it is by no means unlikely that, despite all the safety precautions, space ships could also carry terrestrial DNA to their landing site. We need to have this under control in the search for extraterrestrial life," points out Ullrich. 
The study is published in the journal PLoS One. 


Source: University of Zurich [November 26, 2014]

Evoluzione ed Ossigeno

La vita sulla Terra è rimasta, obbligatoriamente, 'dormiente' per  un lungo periodo (tra 1,8 e 0,8 miliardi di anni fa). Poi, c'è stata un'improvvisa fioritura della Vita Marina negli oceani ed infine eccoci qua. L'articolo scientifico, autore il prof Ross Large insieme ad una Equipe internazionale, sarà pubblicato nel numero di Marzo di Earth and Planetary Science Letters e tende a dimostrare che il principale responsabile di tutto ciò è l'ossigeno, più o meno abbondante nell'ambiente.

Evolution stuck in slime for a billion years .



Tasmanian researchers have revealed ancient conditions that almost ended life on Earth, using a new technique they developed to hunt for mineral deposits. 

Professor Large and Professor Maslennikov on the hunt for suitable black shales in Siberia [Credit: University of Tasmania] 

The first life developed in the ancient oceans around 3.6 billion years ago, but then nothing much happened. 
Life remained as little more than a layer of slime for a billion years. 

Suddenly, 550 million years ago, evolution burst back into action -- and here we are today. 
So what was the hold-up during those 'boring billion' years? 
According to University of Tasmania geologist Professor Ross Large and his international team, the key was a lack of oxygen and nutrient elements, which placed evolution in a precarious position. "During that billion years, oxygen levels declined and the oceans were losing the ingredients needed for life to develop into more complex organisms." 
By analysing ancient seafloor rocks, Ross and his Australian, Russian, US and Canadian colleagues were able to show that the slowdown in evolution was tightly linked to low levels of oxygen and biologically-important elements in the oceans. "We've looked at thousands of samples of the mineral pyrite in rocks that formed in the ancient oceans. And by measuring the levels of certain trace elements in the pyrite, using a technique developed in our labs, we've found that we can tell an accurate story about how much oxygen and nutrients were around billions of years ago." The red line represents the estimated oxygenation curve based on the abundance of the trace element selenium (Se) in pyrite samples. 

Oxygen levels are presented as %PAL (Present Atmospheric Levels), where 100% PAL represents the Earth's atmospheric oxygen at the present day [Credit: University of Tasmania] 

Their research will be published in the March issue of the journal Earth and Planetary Science Letters. "We were initially looking at oxygen levels in the ancient oceans and atmosphere to understand how mineral deposits form, and where to look for them today. That's a focus of the Centre for Ore Deposit and Exploration Science (CODES), which we established with ARC and industry funding at UTAS in 1989," Ross explains. "But the technology we have developed to find minerals can also tell us much about the evolution of life." After an initial burst of oxygen, the study plots a long decline in oxygen levels during the 'boring billion' years before leaping up about 750-550 million years ago. "We think this recovery of oxygen levels led to a significant increase in trace metals in the ocean and triggered the 'Cambrian explosion of life'. 
"We will be doing much more with this technology, but it's already becoming clear that there have been many fluctuations in trace metal levels over the millennia and these may help us understand a host of events including the emergence of life, fish, plants and dinosaurs, mass extinctions, and the development of seafloor gold and other ore deposits," says Ross. 


Source: Science in Public [February 18, 2014] 

Read more at: http://archaeologynewsnetwork.blogspot.it/2014/02/evolution-stuck-in-slime-for-billion.html?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed:+TheArchaeologyNewsNetwork+(The+Archaeology+News+Network)#.UwYf2Yt0vB-
Follow us: @ArchaeoNewsNet on Twitter | groups/thearchaeologynewsnetwork/ on Facebook

Archeobatteri metanogeni, prima che ci fosse ossigeno.

Discovery opens up new areas of microbiology, evolutionary biology

  An international team of researchers led by scientists at Virginia Tech and the University of California, Berkeley has discovered that a process that turns on photosynthesis in plants likely developed on Earth in ancient microbes 2.5 billion years ago, long before oxygen became available. 

Scientists studying methane-producing microbes, like the ones found in deep-sea hydrothermal vents, discovered that a protein critical to photosynthesis likely developed on Earth long before oxygen became available [Credit: Virginia Tech] 

The research offers new perspective on evolutionary biology, microbiology, and the production of natural gas, and may shed light on climate change, agriculture, and human health. "By looking at this one mechanism that was not previously studied, we will be able to develop new basic information that potentially has broad impact on contemporary issues ranging from climate change to obesity," said Biswarup Mukhopadhyay, an associate professor of biochemistry at the Virginia Tech College of Agriculture and Life Sciences, and the senior author of the study. 
He is also a faculty member at the Virginia Bioinformatics Institute. Plant and microbial biology professor emeritus Bob B. Buchanan co-led the research and co-authored the paper. The findings were described this week in the Proceedings of the National Academy of Sciences. This research concerns methane-forming archaea, a group of microbes known as methanogens, which live in areas where oxygen is absent. 
Methane is the main component of natural gas and a potent greenhouse gas. "This innovative work demonstrates the importance of a new global regulatory system in methanogens," said William Whitman, a professor of microbiology at the University of Georgia who is familiar with the study, but not connected to it. "Understanding this system will provide the tools to use these economically important microorganisms better." Methanogens play a key role in carbon cycling. 
When plants die, some of their biomass is trapped in areas that are devoid of oxygen, such as the bottom of lakes. Methanogens help convert the residual biological material to methane, which other organisms convert to carbon dioxide -- a product that can be used by plants. 
This natural process for producing methane forms the basis for treating municipal and industrial wastes, helps reduce pollution, and provides methane for fuel. The same process allows natural gas production from agricultural residues, a renewable resource. 
Methanogens also play an important role in agriculture and human health. 
They live in the digestive systems of cattle and sheep where they facilitate the digestion of feed consumed in the diet. Efforts to control methanogens in specific ways may improve feed utilization and enhance the production of meat and milk, researchers say. Methanogens are additionally a factor in human nutrition. The organisms live in the large intestine, where they enhance the breakdown of food. Some have proposed that restricting this activity of methanogens could help alleviate obesity. The team investigated an ancient type of methanogen, Methanocaldococcus jannaschii, which lives in deep-sea hydrothermal vents or volcanoes where environmental conditions mimic those that existed on the early Earth. 
They found that the protein thioredoxin, which plays a major role in contemporary photosynthesis, could repair many of the organism's proteins damaged by oxygen. Since methanogens developed before oxygen appeared on earth, the evidence raises the possibility that thioredoxin-based metabolic regulation could have come into play for managing anaerobic life long before the advent of oxygen. "It is rewarding to see that our decades of research on thioredoxin and photosynthesis are contributing to understanding the ancient process of methane formation," Buchanan said. "It is an excellent illustration of how a process that proved successful early in evolution has been retained in the development of highly complex forms of life."


 Source:  Virginia Tech (Virginia Polytechnic Institute and State University) [February 07, 2014]

Read more at: http://archaeologynewsnetwork.blogspot.it/2014/02/discovery-opens-up-new-areas-of.html?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed:+TheArchaeologyNewsNetwork+(The+Archaeology+News+Network)#.Uvkh5WJ5OSo
Follow us: @ArchaeoNewsNet on Twitter | groups/thearchaeologynewsnetwork/ on Facebook

Teoria sull'origine della vita

Paleontologist presents origin of life theory

It has baffled humans for millennia: how did life begin on planet Earth? Now, new research from a Texas Tech University paleontologist suggests it may have rained from the skies and started in the bowels of hell.

Meteorite bombardment left large craters that contained water and chemical building blocks
for life, which ultimately led to the first organisms [Credit: Texas Tech University]

Sankar Chatterjee, Horn Professor of Geosciences and curator of paleontology at The Museum of Texas Tech University believes he has found the answer by connecting theories on chemical evolution with evidence related to our planet’s early geology.

“This is bigger than finding any dinosaur,” Chatterjee said. “This is what we’ve all searched for – the Holy Grail of science.”

Thanks to regular and heavy comet and meteorite bombardment of Earth’s surface during its formative years 4 billion years ago, the large craters left behind not only contained water and the basic chemical building blocks for life, but also became the perfect crucible to concentrate and cook these chemicals to create the first simple organisms.

Crater basins may have been the crucible of life
[Credit: Texas Tech University]

He will present his findings Oct. 30 during the 125th Anniversary Annual Meeting of the Geological Society of America in Denver.

As well as discovering how ancient animals flew, Chatterjee discovered the Shiva Meteorite Crater, which was created by a 25-mile-wide meteorite that struck off the coast of India. This research concluded this giant meteorite wreaked havoc simultaneously with the Chicxulub meteorite strike near Mexico, finishing the dinosaurs 65 million years ago.

Ironically, Chatterjee’s latest research suggests meteorites can be givers of life as well as takers. He said that meteor and comet strikes likely brought the ingredients and created the right conditions for life on our planet. By studying three sites containing the world’s oldest fossils, he believes he knows how the first single-celled organisms formed in hydrothermal crater basins.

As the basins filled, volcanically driven geothermal vents heated the water and
created convection. The result was constant water movement, creating
a thick primordial soup [Credit: Texas Tech University]

“When the Earth formed some 4.5 billion years ago, it was a sterile planet inhospitable to living organisms,” Chatterjee said. “It was a seething cauldron of erupting volcanoes, raining meteors and hot, noxious gasses. One billion years later, it was a placid, watery planet teeming with microbial life – the ancestors to all living things.”
Recipe for Living

“For may years, the debate on the origins of life centered on the chemical evolution of living cells from organic molecules by natural processes. Chatterjee said life began in four steps of increasing complexity – cosmic, geological, chemical and biological.

Hierarchical Origin of Life: Historical Contingency Parsimony principle chooses
the simplest explanation for the origin of life [Credit: Texas Tech University]

In the cosmic stage, a still-forming Earth and our solar system took a daily pounding from rocky asteroids and icy comets between 4.1 to 3.8 billion years ago. Plate tectonics, wind and water have hidden evidence of this early onslaught on our planet, but ancient craters on the surfaces of Mars, Venus, Mercury and our moon show just how heavy the meteorite showers once were.

Larger meteorites that created impact basins of about 350 miles in diameter inadvertently became the perfect crucibles, he said. These meteorites also punched through the Earth’s crust, creating volcanically driven geothermal vents. Also, they brought the basic building blocks of life that could be concentrated and polymerized in the crater basins.

After studying the environments of the oldest fossil-containing rocks on Earth in Greenland, Australia and South Africa, Chatterjee said these could be remnants of ancient craters and may be the very spots where life began in deep, dark and hot environments.

Crater Basin with Hydrothermal Vent System Meteorites brought biomolecules
of cell membrane [Credit: Texas Tech University]

Because of Earth’s perfect proximity to the sun, the comets that crashed here melted into water and filled these basins with water and more ingredients. This gave rise to the geological stage. As these basins filled, geothermal venting heated the water and created convection, causing the water to move constantly and create a thick primordial soup.

“The geological stage provides special dark, hot, and isolated environments of the crater basins with the hydrothermal vent systems that served as incubators for life,” he said. “Segregation and concentration of organic molecules by convective currents took place here, something like the kinds we find on the ocean floor, but still very different. It was a bizarre and isolated world that would seem like a vision of hell with the foul smells of hydrogen sulfide, methane, nitric oxide and steam that provided life-sustaining energy.”

Then began the chemical stage, Chatterjee said. The heat churning the water inside the craters mixed chemicals together and caused simple compounds to grow into larger, more complex ones.
Protecting Important Information

Most likely, pores and crevices on the crater basins acted as scaffolds for concentrations of simple RNA and protein molecules, he said. Unlike a popular theory that believes RNA came first and proteins followed, Chatterjee believes RNA and proteins emerged simultaneously and were encapsulated and protected from the environment.

Endosymbiotic origin of Eukoryote cells
[Credit: Texas Tech University]

“The dual origin of the ‘RNA/protein’ world is more plausible in the vent environments than the popular ‘RNA world,’” he said. “RNA molecules are very unstable. In vent environments, they would decompose quickly. Some catalysts, such as simple proteins, were necessary for primitive RNA to replicate and metabolize. On the other hand, amino acids, from which proteins are made, are easier to make than RNA components.”

The question remains how loose RNA and protein material floating in this soup protected itself in a membrane. Chatterjee believes University of California professor David Deamer’s hypothesis that membranous material existed in the primordial soup. Deamer isolated fatty acid vesicles from the Murchison meteorite that fell in 1969 in Australia. The cosmic fatty bubbles extracted from the meteorite mimic cell membranes.

“Meteorites brought this fatty lipid material to early Earth,” Chatterjee said. “This fatty lipid material floated on top of the water surface of crater basins but moved to the bottom by convection currents. At some point in this process during the course of millions of years, this fatty membrane could have encapsulated simple RNA and proteins together like a soap bubble. The RNA and protein molecules begin interacting and communicating. Eventually RNA gave way to DNA – a much more stable compound – and with the development of the genetic code, the first cells divided.”

Fossilized early life [Credit: Texas Tech University]

The final stage – the biological stage – represents the origin of replicating cells as they began to store, process and transmit genetic information to their daughter cells, Chatterjee said. Infinite combinations took place, and countless numbers must have failed to function before the secret of replication was broken and the proper selection occurred.

“These self-sustaining first cells were capable of Darwinian evolution,” he said. “The emergence of the first cells on the early Earth was the culmination of a long history of prior chemical, geological and cosmic processes.”

Chatterjee also believes that modern RNA-viruses and protein-rich prions that cause deadly diseases probably represent the evolutionary legacy of primitive RNA and protein molecules. They may be the oldest cellular particles that predated the first cellular life. Once cellular life evolved, RNA-viruses and prions became redundant, but survived as parasites on the living cells.

The problem with theories on the origins of life is that they don’t propose any experiments that lead to the emergence of cells, Chatterjee said. However, he suggested an experiment to recreate the ancient prebiotic world and support or refute his theory.

“If future experiments with membrane-bound RNA viruses and prions result in the creation of a synthetic protocell, it may reflect the plausible pathways for the emergence of life on early Earth,” he said.
Author: John Davis | Source: Texas Tech University [October 29, 2013]