Scientists decipher 3 billion-year-old genomic fossils

Analysis of modern-day genomes finds evidence for ancient environmental change and a massive expansion in genetic diversity

Contact: Denise Brehm, brehm@mit.edu
Massachusetts Institute of Technology, Department of Civil and Environmental Engineering

About 580 million years ago, life on Earth began a rapid period of change called the Cambrian Explosion, a period defined by the birth of new life forms over many millions of years that ultimately helped bring about the modern diversity of animals. Fossils help palaeontologists chronicle the evolution of life since then, but drawing a picture of life during the 3 billion years that preceded the Cambrian Period is challenging, because the soft-bodied Precambrian cells rarely left fossil imprints. However, those early life forms did leave behind one abundant microscopic fossil: DNA.

Because all living organisms inherit their genomes from ancestral genomes, computational biologists at MIT reasoned that they could use modern-day genomes to reconstruct the evolution of ancient microbes. They combined information from the ever-growing genome library with their own mathematical model that takes into account the ways that genes evolve: new gene families can be born and inherited; genes can be swapped or horizontally transferred between organisms; genes can be duplicated in the same genome; and genes can be lost.

The scientists traced thousands of genes from 100 modern genomes back to those genes' first appearance on Earth to create a genomic fossil telling not only when genes came into being but also which ancient microbes possessed those genes. The work suggests that the collective genome of all life underwent an expansion between 3.3 and 2.8 billion years ago, during which time 27 percent of all presently existing gene families came into being.

Eric Alm, a professor in the Department of Civil and Environmental Engineering and the Department of Biological Engineering, and Lawrence David, who recently received his Ph.D. from MIT and is now a Junior Fellow in the Harvard Society of Fellows, have named this period the Archean Expansion.

Because so many of the new genes they identified are related to oxygen, Alm and David first thought that the emergence of oxygen might be responsible for the Archean Expansion. Oxygen did not exist in the Earth's atmosphere until about 2.5 billion years ago when it began to accumulate, likely killing off vast numbers of anerobic life forms in the Great Oxidation Event.

"The Great Oxidation Event was probably the most catastrophic event in the history of cellular life, but we don't have any biological record of it," says Alm.

Closer inspection, however, showed that oxygen-utilizing genes didn't appear until the tail end of the Archean Expansion 2.8 billion years ago, which is more consistent with the date geochemists assign to the Great Oxidation Event. …

Scientists decipher 3 billion-year-old genomic fossils

Technorati Tags: genetic engineering,evolutionary biology,MIT

MIT researchers harness viruses to split water

Crucial step toward turning water into hydrogen fuel

CAMBRIDGE, Mass. -- A team of MIT researchers has found a novel way to mimic the process by which plants use the power of sunlight to split water and make chemical fuel to power their growth. In this case, the team used a modified virus as a kind of biological scaffold that can assemble the nanoscale components needed to split a water molecule into hydrogen and oxygen atoms.

Splitting water is one way to solve the basic problem of solar energy: It's only available when the sun shines. By using sunlight to make hydrogen from water, the hydrogen can then be stored and used at any time to generate electricity using a fuel cell, or to make liquid fuels (or be used directly) for cars and trucks.

Other researchers have made systems that use electricity, which can be provided by solar panels, to split water molecules, but the new biologically based system skips the intermediate steps and uses sunlight to power the reaction directly. The advance is described in a paper published on April 11 in Nature Nanotechnology.

The team, led by Angela Belcher, the Germeshausen Professor of Materials Science and Engineering and Biological Engineering, engineered a common, harmless bacterial virus called M13 so that it would attract and bind with molecules of a catalyst (the team used iridium oxide) and a biological pigment (zinc porphyrins). The viruses became wire-like devices that could very efficiently split the oxygen from water molecules.

Over time, however, the virus-wires would clump together and lose their effectiveness, so the researchers added an extra step: encapsulating them in a microgel matrix, so they maintained their uniform arrangement and kept their stability and efficiency.

While hydrogen obtained from water is the gas that would be used as a fuel, the splitting of oxygen from water is the more technically challenging "half-reaction" in the process, Belcher explains, so her team focused on this part. Plants and cyanobacteria (also called blue-green algae), she says, "have evolved highly organized photosynthetic systems for the efficient oxidation of water." Other researchers have tried to use the photosynthetic parts of plants directly for harnessing sunlight, but these materials can have structural stability issues.

Belcher decided that instead of borrowing plants' components, she would borrow their methods. In plant cells, natural pigments are used to absorb sunlight, while catalysts then promote the water-splitting reaction. That's the process Belcher and her team, including doctoral student Yoon Sung Nam, the lead author of the new paper, decided to imitate.

In the team's system, the viruses simply act as a kind of scaffolding, causing the pigments and catalysts to line up with the right kind of spacing to trigger the water-splitting reaction. The role of the pigments is "to act as an antenna to capture the light," Belcher explains, "and then transfer the energy down the length of the virus, like a wire. The virus is a very efficient harvester of light, with these porphyrins attached.

"We use components people have used before," she adds, "but we use biology to organize them for us, so you get better efficiency." …

MIT researchers harness viruses to split water

Technorati Tags: nanotechnology,hydrogen economy,solar power,MIT

Urgency of climate change, new research emerges at MIT forum

By Noah Spies

A sense of urgency pervaded Monday’s clean energy forum, which was sponsored by the MIT Energy Initiative and featured a who’s who of energy and climate change policy. The forum was moderated by Rep. Edward Markey (D-Mass.), who is co-authoring legislation designed to tackle technologically and politically difficult global warming and clean energy issues.

The forum featured a presentation by John Holdren ’65, director of the White House Office of Science and Technology Policy. Holdren noted that the rate of global warming continues to outpace predictions, including those made within a 2007 report by the Intergovernmental Panel on Climate Change.

As a student at MIT in the 1960s, Holdren was inspired by the race to put a human on the moon. However, he said that the U.S. and the world face a far greater task in reducing human greenhouse gas emissions to levels that would avoid catastrophic climate changes.

In his presentation, Holdren outlined a number of cost-effective measures that could reduce carbon-dioxide emissions.

Markey noted that his bill would support the realization of many of these measures by spurring energy-efficient retrofits of existing buildings and increasing efficiency in energy utilities.

Markey also emphasized the role research would play in further achieving these goals and highlighted the MIT spinoff company A123 Systems, which aims to dramatically improve the efficiency of existing batteries.

The forum also featured Daniel Yergin, Chairman of Cambridge Energy Research Associates and a Pulitzer Prize-winning author, as well as Prof. Ernest Moniz, Director of the MIT Energy Initiative. …

Urgency of Climate Change, New Research Emerges at MIT Forum

Technorati Tags: climate change,MIT