Monday, August 29, 2011

Our ancestors evolved from "Jurassic Mother"

Jurassic Mammal Fossil Hints At Earlier Split Between Placental Mammals and Marsupials

By Rebecca Boyle

Jurassic Shrew Juramia sinensis, a shrew-like mammal, is the earliest placental mammal found to date.Mark A. Klingler/Carnegie Museum of Natural History

This pointy-nosed shrew, a new fossil find from China, may be the earliest grandmother of all placental mammals, scientists report in a new study. Or perhaps she is the oldest great-aunt. Either way, it’s another big find this week in paleontology.

The new shrew, Juramia sinensis, is the earliest known example of a placental mammal, which (unlike egg-laying monotremes and pouch-carrying marsupials) gives live birth. All placental mammals — from you to dolphins to bats — diverged from an animal like this one. Its discovery pushes back the marsupial-placental mammal evolutionary divergence by about 35 million years, to 160 million years ago, according to researchers in China and the U.S. This corresponds with DNA research that predicted an earlier divergence than the oldest previously known sample, Eomaia, which was 125 million years old.

The new fossil serves as “a corroboration of the newest fossil record with the molecular clock of evolution,” according to the researchers, led by Zhe-Xi Luo of the Carnegie Museum of Natural History in Pittsburgh.

The shrew lived alongside the Jurassic-era dinosaurs, likely living in fern forests and feeding on insects. It was unearthed in a fossil field in China’s Liaoning Province, where paleontologists found most of its skeleton, all of its teeth, part of its skull and, as Scientific American points out, even some hairs.

Understanding the evolution of placental mammals, also called eutherians, is key to understanding general mammalian evolution, the researchers said.

Luo and colleagues from the Chinese Academy of Geological Sciences and Beijing Museum of Natural History embarked on a detailed study of the shrew’s teeth, which they say represent an ancestral version of modern mammal molar arrangement. Some characteristics of its arms and wrists also represent early eutherian characteristics, the researchers report. Its hands were able to grip objects, which suggests the mammals climbed trees. This ability may have helped the animals exploit new territory, further driving their evolution as distinct from monotremes and marsupials.

The naming of the shrew reflects its importance to mammalian heritage, the researchers explain: Jura means Jurassic; maia means mother, in reference to the placenta; sinensis means "of China." The name means “Jurassic mother from China.”

The shrew is described in this week's issue of the journal Nature.

Jurassic Mother: The earliest-known eutherian mammal is shown hunting on a tree fern. Mark A. Klingler/Carnegie Museum of Natural History

GPS Data Could Help Track and Monitor Secret Nuclear Tests From Rogue Nations

By Dan Nosowitz

Smoke on the Water

The Bulletin of Atomic Scientists may have found a new way to track secret nuclear tests from those rogue nations (cough cough North Korea cough cough) who are trying to keep those tests under wraps. Surprisingly enough, that new solution may be possible with analysis of regular old GPS data, along with some clever mathematics.

In May 2009, North Korea detonated a clandestine nuclear test, a kilometer underground. That's worrisome for obvious reasons, and more worrisome because performing the test underground severely limits our ability to measure the size and specifics of the blast--no radioactive gas or dust was let into the air, as it usually would. But that doesn't mean there are no signs of radioactive explosions.

When a nuclear blast that large goes off underground, it sends a shockwave of disturbed air into the ionosphere. That shockwave is typically hard to measure, but these scientists may have found a way, using regular GPS. GPS, see, relies on timing more than anything else to determine location: it measures the time the signal takes to rebound from a device to the satellite, and vice versa. But disturbances in the air can change those measurements, so GPS units have sophisticated algorithms to sense and adjust to that kind of disturbance--so why not the nuclear shockwave?

The scientists performed some tests after the 2009 blast, and found that they were able to nail down the location and timing of the blast using eleven different satellites. They're optimistic that this tech could be used to supplement other ways of confirming that an illicit blast took place. They even hope that this technology might compel the U.S. to reconsider its refusal to sign the Nuclear Test Ban Treaty, which I personally am skeptical about but would certainly be great if it was true. For more info on nuclear power, check out our explainer.

Filmmaker Rob Spence's Implanted Bionic Camera Eyeball Is Up and Running

By Dan Nosowitz

Rob Spence's Bionic Eye Eyeborg

Rob Spence, a self-proclaimed "Eyeborg," had his eye, which was damaged in a shotgun accident, replaced with a camera about two years ago. It's not too much of a stretch for Spence, who otherwise works as a filmmaker--and now he's been sponsored by video game maker Square Enix, which commissioned Spence to create a video about prostheses to promote their new game, Deux Ex: Human Revolution.

On his blog, which is endearingly named Eyeborg, Spence has posted a new twelve-minute video. He travels around the world, talking to those endowed with the cutting edge of cyborg-dom. Matter of fact, it's not too different from our recent feature, State of the Bionic Art, except Spence investigates the specific real-life counterparts to the crazy-futuristic prostheses and cyborg parts featured in the new Deux Ex game. It's a pretty cool video, game plugs notwithstanding--any video that features a man saying "I am now filming your bionic hand...with my bionic eye" has a way of getting in our good graces. Check out the video below, though a warning that there are a few images that might not be kind to those with weak stomachs.

We'll keep you up to date on Eyeborg--his site teases that there will be more to come on the making of his prosthetic camera-eye in the coming days.

New genome sequence could improve important agricultural crops

Posted by Biomechanism

An international team of scientists, funded in the UK by the Biotechnology and Biological Sciences Research Council (BBSRC), has sequenced the genome of a Chinese cabbage variety of a plant called Brassica rapa, a close relative of oilseed rape. The research, which is published today (28 August) in the journal Nature Genetics, could help improve the efficiency of oilseed rape breeding, as well as that of a host of other important food and oil crops.

The project was conducted by an international consortium involving researchers working across four continents, with the majority of the data generated in China. The UK’s contribution came from scientists at the John Innes Centre in Norwich and Rothamsted Research in Hertfordshire, both of which receive strategic funding from BBSRC.

Oilseed rape is an important source of vegetable oils for cooking and industrial applications and its production has doubled in the last 15 years. It is an unusual hybrid which contains the entire genomes of two other plants:Brassica rapa and another closely related species called Brassica oleracea. By sequencing Brassica rapa, researchers are able to access half of oilseed rape’s genes without having to wrestle with its large and complicated genome.

Professor Ian Bancroft led the research at the John Innes Centre. He explains “Oilseed rape is the second most important oil crop in the world and the most important in Europe. Sequencing its genes will provide breeders with the tools to improve the efficiency of developing new varieties, but this is difficult because it has a really complicated genome. Thankfully, because it is a hybrid, nature has already divided up the oilseed rape genome into two more manageable chunks, one of which we have now sequenced.”

Brassica rapa and oilseed rape are both brassicas, a group which also includes broccoli, turnip, sprouts and cabbages. Together, this important group of plants accounts for more than 10 percent of the world’s vegetable and vegetable oil production and, despite their apparent diversity, they are all closely related. This enables scientists to apply the insights they gain by sequencing one species, such as Brassica rapa to improving the breeding efficiency of a range of crops essential to ensuring global food security.

Professor Bancroft continues “Few people would confuse a turnip with a cauliflower and yet, despite coming in a range of shapes and sizes, brassicas are all very closely related. This means that the many of the 41,000 genes which we found in Brassica rapa will also be found in other brassicas and the insights we gain from having this sequence could be useful for improving everything from plants grown to produce chainsaw oils to the sprouts on your Christmas dinner.”

The Brassica rapa sequence was produced using a technology which breaks the DNA into small segments before reassembling the complete genome. Throughout its evolution Brassica rapa has triplicated its genome meaning that the task of assembling the final picture posed a particular challenge to the scientists and the technology.

Professor Douglas Kell, Chief Executive of the Biotechnology and Biological Sciences Research Council, said “Plants have a tendency to multiply their genomes as they evolve. This means that many important agricultural crops like wheat, potato and oilseed rape have much larger and more complex genomes than most animals, including humans.

“Helping breeders produce new varieties of these staple crops will be essential to ensuring our future food security, so scientists must use their ingenuity to find ways to overcome the challenges posed by these massive genomes. This research shows what can be achieved by applying the latest technology and by combining the expertise of scientists across the world.”

In cell culture, like real estate, the neighborhood matters

Posted by Biomechanism

Ever since scientists first began growing human cells in lab dishes in 1952, they have focused on improving the chemical soup that feeds the cells and helps regulate their growth. But surfaces also matter, says Laura Kiessling, a professor of chemistry at the University of Wisconsin-Madison, who observes that living cells are normally in contact with each other and with a structure called the extracellular matrix, not just with the dissolved chemicals in their surroundings.

“Soluble factors are important, but cells normally interact with the extracellular matrix and with neighboring cells, and these have not been considered in most efforts to refine growth conditions,” says Kiessling. “We wanted to know, can we replace the neighboring cells and extracellular matrix with synthetics?”

Creating a more precise system for growing cells offers both theoretical and practical advantages, Kiessling says. First, it would reduce uncertainty in experiments by simplifying conditions. Second, it would remove the risk of biological contamination like viruses, so the cultured cells could be used in medicine. Third, new surfaces that improve the control over cell growth and development could facilitate the formation of artificial tissues, which are complex assemblies of different cell types.

In a talk on Aug. 28 to the annual meeting of the American Chemical Society in Denver, Kiessling outlined two areas of progress from her lab at UW-Madison. One series of experiments used a lab dish decorated with molecules called peptides to amplify the response of cells to a growth factor called transforming growth factor beta (TGF-beta). TGF-beta can affect healing, cell division and transformation into a more specialized cell or into a tumor cell, Kiessling notes, so TGF-beta can be helpful or harmful in different situations.

After screening thousands of potential anchors, Kiessling, graduate student Joe Klim, former graduate student Lingyin Li and colleagues found a peptide that would safely hold the cells in place and simultaneously make them extremely sensitive to TGF-beta made by the cells themselves. “TGF-beta receptors have to assemble into a complex before TGF-beta sends its signal to the cell,” says Kiessling. “We made surfaces that organized the receptors so they were especially sensitive to this growth factor when the cells were bound to the surface, and so the growth factor affects the cell at incredibly low levels, levels we cannot detect.”

The secret, she says, lies in the preparation: The manufactured surface primes the cells to respond to tiny amounts of growth factor. “It’s like the surface acts as an amplifier to allow the cells to sense the presence of the growth factor.”

When they are grown on surfaces without the peptides, the cells used in the experiment are like skin cells, but when they are on the peptide surface, they detect the growth factor and transform into muscle-like cells. “That shows the power of this approach,” says Kiessling. “We have a way to make cells do one thing if they are attached to this surface and another thing if they are not.”

A second series of experiments concerned human embryonic stem cells — the versatile cells have the potential to form any cell type in the body. Since these cells were first identified in 1998 by James Thomson of UW-Madison, their therapeutic potential has remained tantalizingly difficult to reach, partly because they have been grown with substances derived from mice that could contain viruses or other pathogens.

While scientists have refined the liquid portion of the environment needed to grow and transform embryonic stem cells, the solid portion has received less attention. “Human embryonic stem cells need not only a defined medium, but also a defined substrate,” Kiessling says. “Historically, the field has relied on mouse embryonic feeder cells and various mixtures of proteins isolated from mice, which contain who knows what in the way of viruses or other infectious particles.”

Others have experimented with growing human embryonic stem cells on artificial surfaces, she says, “but there are some advantages to the surface we have found.” She now has to move the defined peptides from the gold backing that she presently use to the polystyrene Petri dishes that are common in cell culture.

There are even hints that surfaces can also control the differentiation of stem cells, Kiessling adds.

“Our work highlights the fact that we can use a patterned surface itself to instruct the cells, which could be really useful for growing cells on a larger scale and differentiating them under defined conditions,” Kiessling says. “Patterned surfaces are found throughout our tissues. Hair, eyes, brain, everywhere we have organized tissues, so if we want to grow different types of cells in ordered arrays to build up a tissue, we need the cells to be organized. We are not close to building a complicated tissue, but the first step is to localize specific types of cells where we want them. We’ve only scratched the surface of our ability to regulate and instruct cell growth and transformation using elaborately structured surfaces.”

New roles emerge for non-coding RNAs in directing embryonic development

Posted by Biomechanism

Scientists at the Broad Institute of MIT and Harvard have discovered that a mysterious class of large RNAs plays a central role in embryonic development, contrary to the dogma that proteins alone are the master regulators of this process. The research, published online August 28 in the journal Nature, reveals that these RNAs orchestrate the fate of embryonic stem (ES) cells by keeping them in their fledgling state or directing them along the path to cell specialization.

Broad scientists discovered several years ago that the human and mouse genomes encode thousands of unusual RNAs — termed large, intergenic non-coding RNAs (lincRNAs) —but their role was almost entirely unknown. By studying more than 100 lincRNAs in ES cells, the researchers now show that these RNAs help regulate development by physically interacting with proteins to coordinate gene expression and suggest that lincRNAs may play similar roles in most cells.

“There’s been a lot of debate about what lincRNAs are doing,” said Eric Lander, director of the Broad Institute and the senior author of the paper. “It’s now clear that they play critical roles in regulating developmental decisions — that is, cell fate. This was a big surprise, because specific types of proteins have been thought to be the master controls of development.”

“This is the first global study of lincRNAs,” said Mitchell Guttman, first author of the paper and a graduate student at MIT and the Broad Institute. “We picked embryonic stem cells in particular because they are so important to development and so well understood. This allowed us to dissect the role of lincRNAs within the circuitry of a cell.”

The researchers used genetic tools to inhibit more than 100 lincRNAs and found that the vast majority — more than 90 percent — had a significant impact on embryonic stem cells, indicating that the RNAs play a key role in the cells’ circuitry.

Embryonic stem cells can follow one of two main routes. They can either differentiate, becoming cells of a specific lineage such as blood cells or neurons, or they can stay in a pluripotent state, duplicating themselves without losing the ability to become any cell in the body. When the researchers turned off each lincRNA in turn, they found dozens that suppress genes that are important only in specific kinds of cells. They also found dozens of lincRNAs that cause the stem cells to exit the pluripotent state.

“It’s a balancing act,” said Guttman. “To maintain the pluripotent state, you need to repress differentiation genes.”

The researchers also uncovered a critical clue about how lincRNAs carry out their important job. Through biochemical analysis, they found that lincRNAs physically interact with key proteins involved in influencing cell fate to coordinate their responses.

“The lincRNAs appear to play an organizing role, acting as a scaffold to assemble a diverse group of proteins into functional units,” said John Rinn, an author on the paper, an assistant professor at Harvard University and Medical School, and a senior associate member of the Broad Institute. “lincRNAs are like team captains, bringing together the right players to get a job done.”

“By understanding how these interactions form, we may be able to engineer these RNAs to do what we want them to do,” said Guttman. “This could make it possible to target key genes that are improperly regulated in disease.”

Aviv Regev, an author on the paper, a core member of the Broad Institute, and associate professor at MIT, sees the team’s approach to studying the lincRNAs as important for the field. “Many people are interested in lincRNAs, but they need a comprehensive view of the whole collection of lincRNAs,” said Regev. “The large-scale data and technology from this study will be useful for scientists worldwide in studying both lincRNAs as well as many other RNAs in the cell.”

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This project marks a collaborative effort involving experts in embryonic stem cells and lincRNAs as well as computational biologists and researchers in the Broad’s RNAi Platform, which developed the tools needed to systematically silence lincRNAs. Other researchers who contributed to this work include Julie Donaghey, Bryce W. Carey, Manuel Garber, Jennifer K. Grenier, Glen Munson, Geneva Young, Anne Bergstrom Lucas, Robert Ach, Xiaoping Yang, Ido Amit, Alexander Meissner, and David E. Root. This work was funded by the National Human Genome Research Institute, the Richard Merkin Foundation for Stem Cell Research at the Broad Institute, and funds from the Broad Institute of MIT and Harvard.

-Written by Haley Bridger, Broad Institute