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

Genetically altered trees and plants could help counter global warming

Forests of genetically altered trees and other plants could sequester several billion tons of carbon from the atmosphere each year and so help ameliorate global warming, according to estimates published in the October issue of BioScience.

The study [pdf], by researchers at Lawrence Berkeley National Laboratory and Oak Ridge National Laboratory, outlines a variety of strategies for augmenting the processes that plants use to sequester carbon dioxide from the air and convert it into long-lived forms of carbon, first in vegetation and ultimately in soil. Besides increasing the efficiency of plants' absorption of light, researchers might be able to genetically alter plants so they send more carbon into their roots—where some may be converted into soil carbon and remain out of circulation for centuries. Other possibilities include altering plants so that they can better withstand the stresses of growing on marginal land, and so that they yield improved bioenergy and food crops. Such innovations might in combination boost substantially the amount of carbon that vegetation naturally extracts from air, according to the authors' estimates. The researchers stress that the use of genetically engineered plants for carbon sequestration is only one of many policy initiatives and technical tools that might boost the carbon sequestration already occurring in natural vegetation and crops.

The article, by Christer Jansson, Stan D. Wullschleger, Udaya C. Kalluri, and Gerald A. Tuskan, is the first in a Special Section in the October BioScience that includes several perspectives on the prospects for enhancing biological carbon sequestration. Other articles in the section analyze the substantial ecological and economic constraints that limit such efforts. One article discusses the prospects for sequestering carbon by culturing algae to produce biofuel feedstocks; one proposes a modification of the current regulatory climate for producing genetically engineered trees in the United States; and one discusses societal perceptions of the issues surrounding the use of genetically altered organisms to ameliorate warming attributed to the buildup of greenhouse gases.

Genetically Altered Trees and Plants Could Help Counter Global Warming

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Genome of ancient sponge reveals origins of first animals, cancer

The sponge, which was not recognized as an animal until the 19th century, is now the simplest and most ancient group of animals to have their genome sequenced.

In a paper appearing in the August 5 issue of the journal Nature, a team of researchers led by Daniel Rokhsar of the University of California, Berkeley, and the Department of Energy's Joint Genome Institute (JGI), report the draft genome sequence of the sea sponge Amphimedon queenslandica and several insights the genome gives into the origins of both the first animals and cancer.

All living animals are descended from the common ancestor of sponges and humans, which lived more than 600 million years ago. A sponge-like creature may have been the first organism with more than one cell type and the ability to develop from a fertilized egg produced by the merger of sperm and egg cells – that is, an animal.

"Our hypothesis is that multicellularity and cancer are two sides of the same coin," said Rokhsar, program head for computational genomics at JGI and a professor of molecular and cell biology and of physics at UC Berkeley. "If you are a cell in a multicellular organism, you have to cooperate with other cells in your body, making sure that you divide when you are supposed to as part of the team. The genes that regulate this cooperation are also the ones whose disruption can cause cells to behave selfishly and grow in uncontrolled ways to the detriment of the organism."

As part of the new analysis, the team looked in the sponge genome for more than 100 genes that have been implicated in human cancers and found about 90 percent of them. Future research will show what roles these genes play in endowing sponge cells with team spirit.

Sponges are often described as the "simplest" living animals, while humans are considered relatively "complex," but how this differential complexity is encoded in the genome is still a major question in biology The new study shows that, while the sponge genome contains most of the gene families found in humans, the number of genes in each family has changed significantly over the past 600 million years. By analyzing which gene families were enriched or depleted in different groups of animals, the authors identified groups of gene functions that are associated with morphological complexity.

"The genome raises questions of what it means to be an animal," said first author Mansi Srivastava, a former UC Berkeley graduate student who now is a post-doctoral associate at the Whitehead Institute for Biomedical Research in Cambridge, Mass. …

"This incredibly old ancestor possessed the same core building blocks for multicellular form and function that still sits at the heart of all living animals, including humans," said coauthor Bernie Degnan, a professor of biology at the University of Queensland, Australia, who collected the sponge whose genome was sequenced from the Great Barrier Reef. "It now appears that the evolution of these genes not only allowed the first animals to colonize the ancient oceans, but underpinned the evolution of the full biodiversity of animals we see today." …

Genome of ancient sponge reveals origins of first animals, cancer

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Wallabies and bats harbor ‘fossil’ genes from the most deadly family of human viruses

Research reveals potential reservoir species, new mechanism for how mammals acquire genes 

(University at Buffalo)

BUFFALO, N.Y. -- Modern marsupials may be popular animals at the zoo and in children's books, but new findings by University at Buffalo biologists reveal that they harbor a "fossil" copy of a gene that codes for filoviruses, which cause Ebola and Marburg hemorrhagic fevers and are the most lethal viruses known to humans.

Published this week in the online journal BMC Evolutionary Biology, the paper ("Filoviruses are ancient and integrated into mammalian genomes") demonstrates for the first time that mammals have harbored filoviruses for at least tens of millions of years, in contrast to the existing estimate of a few thousand.

It suggests that these species, which maintain a filovirus infection without negative health consequences, could have selectively maintained these so-called "fossil" genes as a genetic defense.

The work has important implications for the development of potential human vaccines, as well as for the modeling of disease outbreaks and the discovery of emerging diseases, including new filoviruses.

"This paper identifies the first captured 'fossil' copies of filovirus-like genes in mammalian genomes," says Derek J. Taylor, PhD, associate professor of biological sciences in the UB College of Arts and Sciences and co-author. "Our results confirm for the first time that several groups of mammals, including groups such as marsupials that never colonized Africa, have had an association with filoviruses."

The UB co-authors say that if the rarely captured genes represent antiviral defenses or genomic scars from persistent infections, then the work opens up new possibilities for identifying reservoir species for filoviruses, which harbor the virus but remain asymptomatic. …

The research also demonstrates a new mechanism by which different species of mammals can acquire genes, through non-retroviral integrated RNA viruses, which the UB scientists had previously identified in eukaryotes but was unknown in mammals.

The UB scientists note that it is well-known that RNA retroviruses, like HIV-AIDS, can be integrated into mammal genomes.

"But because filoviruses infect only the cytoplasm of cells and not the nucleus and because they have no means of making DNA copies that might be integrated into the genome -- as retroviruses do -- it was never thought gene transfer could occur between non-retroviral RNA viruses and hosts," says Bruenn. "This paper shows that it does and it may prove to be a far more general phenomenon than is currently known." …

Wallabies and bats harbor 'fossil' genes from the most deadly family of human viruses

Technorati Tags: genetic engineering,evolutionary biology

Giant salmon will be first GM animal available for eating

By Louise Gray, Environment Correspondent
Published: 1:06PM BST 27 Jun 2010

A salmon that grows at twice the normal rate is set to be the first genetically modified (GM) animal available for human consumption.

Usually Atlantic salmon do not grow during the winter and take three years to fully mature.

But by implanting genetic material from an eel-like species called ocean pout that grows all year round, US scientists have managed to make the fish grow to full size in 18 months.

They hope that the sterile GM salmon can offer an efficient and safe way to breed salmon in fish farms, so that the wild fish can be left in the oceans.

US watchdog the Food and Drug Administration is currently considering whether the GM Atlantic salmon, called AquAdvantage, is safe to eat. The fish could be on supermarket shelves within a year.

But environmental campaigners question whether the GM material is safe for humans to consume and fear the sterile salmon will mutate in the wild and be able to breed.

At the moment only GM crops like corn or soy are available for human consumption. Also the Daily Telegraph revealed recently that most animal products available in supermarkets, like meat, eggs or dairy, are from livestock fed GM. …

Giant salmon will be first GM animal available for eating

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Canada approves Enviropig™ -- piglets inherit genetic modifications for cleaner manure

 Image: Scott Bauer, ARS.USDA

Piglets Inherit Genetic Modification Canada has approved limited production of animals dubbed "enviropigs™," a genetically modified breed of pigs producing up to 65% less phosphorous in pig poo and urine. The pigs pass the genetic modification along to their young, as well. The very idea that a genetically modified animal rates the moniker "enviro-" points to the severity of the issue addressed by the science behind these pigs. Phosphorous is a fertilizer. Phosphorous in animal and human wastes runs off or discharges to surface waters, where it spurs large algal blooms. The algae use up the oxygen in the water, leaving behind a "dead zone," an area of lake, river, or ocean where nothing can live due to the hypoxic conditions. …

Canada Approves Enviropig™, Piglets Inherit Genetic Modifications for Clean Manure

Technorati Tags: biotechnology,genetic engineering,anoxia,eutrophication

Catalyst discovered that reduces CO2 by using light energy

Mar. 5, 2010

ANN ARBOR, Mich. – A recent discovery in understanding how to chemically break down the greenhouse gas carbon dioxide into a useful form opens the doors for scientists to wonder what organism is out there – or could be created – to accomplish the task.

University of Michigan biological chemist Steve Ragsdale, along with research assistant Elizabeth Pierce and scientists led by Fraser Armstrong from the University of Oxford in the U.K., have figured out a way to efficiently turn carbon dioxide into carbon monoxide using visible light, like sunlight.

The results are reported in the recent online edition of the Journal of the American Chemical Society.

Not only is it a demonstration that an abundant compound can be converted into a commercially useful compound with considerably less energy input than current methods, it also is a method not so different from what organisms regularly do.

“This is a first step in showing it’s possible, and imagine microbes doing something similar,” Ragsdale said. “I don’t know of any organism that uses light energy to activate carbon dioxide and reduce it to carbon monoxide, but I can imagine either finding an organism that can do it, or genetically engineering one to channel light energy to coax it to do that.”

In this collaboration between Ann Arbor and Oxford, Ragsdale’s laboratory at the U-M Medical School does the biochemistry and microbiology experiments and Armstrong’s lab performs the physical- and photochemical applications. 

Ragsdale and his associates succeeded in using an enzyme-modified titanium oxide to get carbon dioxide’s electrons excited and willing to jump to the enzyme, which then catalyzes the reduction of carbon dioxide to carbon monoxide. A photosensitizer that binds to the titanium allows the use of visible light for the process. The enzyme is more robust than other catalysts, willing to facilitate the conversion again and again. The trick: It can’t come near oxygen.

“By using this enzyme, you put it into a solution that contains titanium dioxide in the presence of a photosensitizer,” he said. “We looked for a way that seems like nature’s way of doing it, which is more efficient.” Armstrong notes that “essentially it shows what is possible were we to be able to mass-produce a catalyst with such properties”. …

Asking “what would nature do?” leads to a way to break down a greenhouse gas

Technorati Tags: nanotechnology,carbon dioxide,genetic engineering

Genetically modified forest planned for U.S. Southeast

Maybe they can relocate Australia’s endangered koalas to these forests.

International Paper Co. and MeadWestvaco Corp. are planning to transform plantation forests of the southeastern United States by replacing native pine with genetically engineered eucalyptus

By Paul Voosen

Genetic engineering is coming to the forests.

While the practice of splicing foreign DNA into food crops has become common in corn and soy, few companies or researchers have dared to apply genetic engineering to plants that provide an essential strut of the U.S. economy, trees.

But that will soon change. Two industry giants, International Paper Co. and MeadWestvaco Corp., are planning to transform plantation forests of the southeastern United States by replacing native pine with genetically engineered eucalyptus, a rapidly growing Australian tree that in its conventional strains now dominates the tropical timber industry.

The companies' push into genetically modified trees, led by their joint biotech venture, ArborGen LLC, looks to overcome several hurdles for the first time. Most prominently, they are banking on a controversial gene splice that restricts trees' ability to reproduce, meant to allay fears of bioengineered eucalyptus turning invasive and overtaking native forests.

If such a fertility control technology -- which has come under fire in farming for fear seed firms will exploit it -- is proven effective, it could open the door to many varieties of wild plants, including weedy grasses, to be genetically engineered for use in energy applications like biomass and next-generation biofuels without fear of invasiveness.

The use of such perennial plants -- so named because, unlike annual farm crops, they live and grow for many years -- has long interested business and government, including the Energy Department, which has collaborated with ArborGen. The plants, which include many grasses targeted for cellulosic ethanol, can be harvested when needed and, given their hardiness, grow on marginal land.

Yet many questions remain about the effectiveness of the fertility system used by ArborGen, which, according to leading scientists, has never been rigorously studied in multiyear trials to prove that it can effectively control plants' spread. More research must be conducted before such systems are relied upon to restrict pollen and seed spread, they say.

Despite these calls, ArborGen has been seeking government deregulation of its eucalyptus, which is primarily engineered to resist freezing temperatures, since 2008. If successful, ArborGen would likely revolutionize the timber industry and the Southern landscape by becoming the first company to roll out bioengineered trees on a massive scale, observers say. …

Genetically Modified Forest Planned for U.S. Southeast

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Toyota engineers new flower species to absorb emissions at Prius factories

By Brian Merchant, Brooklyn, New York  on 10.28.09

Toyota has long faced the criticism that the process of manufacturing Priuses has a larger environmental impact than most cars. So the giant automaker came up with what's probably the most bizarre solution imaginable--Toyota genetically engineered two brand new species of flowers to absorb greenhouse gases at Prius manufacturing plants. While, you know, still making the place look pretty. …

Toyota Engineers New Flower Species to Absorb Emissions at Prius Factories

Technorati Tags: genetic engineering

Scientists to unlock Great Barrier Reef genome

SYDNEY (AFP) — Australian scientists on Thursday announced a ground-breaking genome-mapping project that could help the Great Barrier Reef fight off the twin threats of climate change and toxic farm chemicals.

Geneticists said they would unlock the secrets of the colourful acropora millepora coral, one of the main components of the northeastern tourist attraction, the growth of which has slowed markedly in recent years.

"This gene-mapping project has both practical and scientific significance," said professor David Miller of Australia's Centre of Excellence for Coral Reef Studies and James Cook University.

"It will help us to understand how corals build reefs -- and why they fail to do so when they are under stress." … the reef has come under growing threat from climate change and chemical run-off with Australia announcing a crackdown in January on farmers who let pesticides and fertilisers leak into the sea. …

Scientists to unlock Great Barrier Reef genome

Technorati Tags: coral,climate change,pollution,Australia,genetic engineering

Amateurs are trying genetic engineering at home

By MARCUS WOHLSEN, Associated Press Writer

SAN FRANCISCO – The Apple computer was invented in a garage. Same with the Google search engine. Now, tinkerers are working at home with the basic building blocks of life itself.

Using homemade lab equipment and the wealth of scientific knowledge available online, these hobbyists are trying to create new life forms through genetic engineering — a field long dominated by Ph.D.s toiling in university and corporate laboratories.

In her San Francisco dining room lab, for example, 31-year-old computer programmer Meredith L. Patterson is trying to develop genetically altered yogurt bacteria that will glow green to signal the presence of melamine, the chemical that turned Chinese-made baby formula and pet food deadly.

"People can really work on projects for the good of humanity while learning about something they want to learn about in the process," she said.

So far, no major gene-splicing discoveries have come out anybody's kitchen or garage.

Amateurs are trying genetic engineering at home

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